From da88996fc94d733930b2c81c64984d1cd2c87233 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Fri, 24 Apr 2015 14:24:27 -0400 Subject: [PATCH 001/176] ENH: Initial commit --- .../MorphologicalContourInterpolation/LICENSE | 201 ++++++++++++++++++ 1 file changed, 201 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/LICENSE diff --git a/Modules/Filtering/MorphologicalContourInterpolation/LICENSE b/Modules/Filtering/MorphologicalContourInterpolation/LICENSE new file mode 100644 index 00000000000..8dada3edaf5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. From 3b13f473adda6077d6beed17f36417fe0682cdce Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Fri, 24 Apr 2015 14:54:12 -0400 Subject: [PATCH 002/176] ENH: Add module skeleton. Issue #1. --- .../CMakeLists.txt | 3 + .../itk-module.cmake | 16 +++++ .../test/CMakeLists.txt | 15 +++++ ...kMorphologicalContourInterpolationTest.cxx | 58 +++++++++++++++++++ 4 files changed, 92 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt new file mode 100644 index 00000000000..29d3da56059 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -0,0 +1,3 @@ +project(MorphologicalContourInterpolation) + +itk_module_impl() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake new file mode 100644 index 00000000000..306a72944a7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -0,0 +1,16 @@ +set( + DOCUMENTATION + "The modules provides filters to do interpolation +of manually segmented anatomical contours." +) + +itk_module( + MorphologicalContourInterpolation + DEPENDS + ITKCommon + ITKBinaryMathematicalMorphology + TEST_DEPENDS + ITKTestKernel + EXCLUDE_FROM_DEFAULT + DESCRIPTION "${DOCUMENTATION}" +) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt new file mode 100644 index 00000000000..d2a2aecfb7e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -0,0 +1,15 @@ +itk_module_test() + +set( + MorphologicalContourInterpolationTests + itkMorphologicalContourInterpolationTest.cxx +) + +createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest +) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx new file mode 100644 index 00000000000..c24a2bdce6f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -0,0 +1,58 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ + +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" + +int +itkMorphologicalContourInterpolationTest(int argc, char * argv[]) +{ + // if( argc < 3 ) + //{ + // std::cerr << "Usage: " << argv[0]; + // std::cerr << " inputImage outputImage"; + // std::cerr << std::endl; + // return EXIT_FAILURE; + // } + // const char * inputImageFileName = argv[1]; + // const char * outputImageFileName = argv[2]; + + // typedef signed short PixelType; + // const unsigned int Dimension = 3; + // typedef itk::Image< PixelType, Dimension > ImageType; + + // typedef itk::ImageFileReader < ImageType > ReaderType; + // ReaderType::Pointer reader = ReaderType::New(); + // reader->SetFileName( inputImageFileName ); + + // typedef itk::ImageFileWriter< ImageType > WriterType; + // WriterType::Pointer writer = WriterType::New(); + // writer->SetFileName( outputImageFileName ); + // writer->SetInput( reader->GetOutput() ); + // try + //{ + // writer->Update(); + // } + // catch( itk::ExceptionObject & error ) + //{ + // std::cerr << "Error: " << error << std::endl; + // return EXIT_FAILURE; + // } + + return EXIT_SUCCESS; +} From 14ee07402b0b0dd7d23a74dc11ef9a808336af5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 24 Apr 2015 15:29:22 -0400 Subject: [PATCH 003/176] ENH: adding test data --- .../MorphologicalContourInterpolation/test/CMakeLists.txt | 1 + .../105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 | 1 + 2 files changed, 2 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index d2a2aecfb7e..870d672226c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -12,4 +12,5 @@ itk_add_test( COMMAND MorphologicalContourInterpolationTestDriver itkMorphologicalContourInterpolationTest + DATA{Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz} ) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 new file mode 100644 index 00000000000..b50a6e6e084 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 @@ -0,0 +1 @@ +176bfd37f8ddbdc197595523693ecc36 \ No newline at end of file From 79dc4ad2bfaf0b56ed3b2f89063688c1ad6d2de2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 24 Apr 2015 15:51:52 -0400 Subject: [PATCH 004/176] ENH: adding the rest of test data from Paul --- .../test/Input/105769fixed.nii.md5 | 1 + .../test/Input/105769fixed_segmentation.nii.gz.md5 | 1 + .../test/Input/105769moving_resliced_to_fixedhz2.nii.md5 | 1 + .../test/Input/64816L_amygdala_fin.nii.gz.md5 | 1 + .../test/Input/64816L_amygdala_int.nii.gz.md5 | 1 + .../test/Input/65239R_amygdala_fin.nii.gz.md5 | 1 + .../test/Input/65239R_amygdala_int.nii.gz.md5 | 1 + .../test/Input/NDRI64816L.nii.md5 | 1 + .../test/Input/NDRI65239R.nii.md5 | 1 + 9 files changed, 9 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI64816L.nii.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI65239R.nii.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.md5 new file mode 100644 index 00000000000..3ff0e942df9 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.md5 @@ -0,0 +1 @@ +ca6b70fd6f50ef9151f9cf02c7ba1ee9 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 new file mode 100644 index 00000000000..d0eb57913c3 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 @@ -0,0 +1 @@ +6e14975a4c0a37dfd3d7d46fe7cf4586 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 new file mode 100644 index 00000000000..1f075d96076 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 @@ -0,0 +1 @@ +8fa331a79cd804ddab8ecb08441029b1 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 new file mode 100644 index 00000000000..4e76e1e7adf --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 @@ -0,0 +1 @@ +dbddb8dfcae92549da37db88de67d093 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 new file mode 100644 index 00000000000..315f54fda70 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 @@ -0,0 +1 @@ +5e9167bee632e1fdde568ea659d512cb \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 new file mode 100644 index 00000000000..36e168a612c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 @@ -0,0 +1 @@ +31eef268b01d90f952bb6d2e1541a12c \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 new file mode 100644 index 00000000000..4ae7d0034f0 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 @@ -0,0 +1 @@ +c3a5b453f40a69d16042a3ca0b36302e \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI64816L.nii.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI64816L.nii.md5 new file mode 100644 index 00000000000..41e2d874d94 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI64816L.nii.md5 @@ -0,0 +1 @@ +e0375552865e1da01999cffc680584d3 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI65239R.nii.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI65239R.nii.md5 new file mode 100644 index 00000000000..63140782759 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NDRI65239R.nii.md5 @@ -0,0 +1 @@ +09d8f41e45de9166b0b7f57ccdd864e2 \ No newline at end of file From 43d594a6bad4f985b816d421a87701bd89a42e8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 May 2015 12:04:15 -0400 Subject: [PATCH 005/176] ENH: creating main filter class --- .../itkMorphologicalContourInterpolator.h | 55 +++++++++++++++ .../itkMorphologicalContourInterpolator.hxx | 32 +++++++++ ...kMorphologicalContourInterpolationTest.cxx | 69 ++++++++++--------- 3 files changed, 125 insertions(+), 31 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h new file mode 100644 index 00000000000..fafc45afbde --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -0,0 +1,55 @@ +#ifndef __itkMorphologicalContourInterpolator_h +#define __itkMorphologicalContourInterpolator_h + +#include "itkImageToImageFilter.h" + +namespace itk +{ +template +class MorphologicalContourInterpolator : public ImageToImageFilter +{ +public: + /** Standard class typedefs. */ + typedef MorphologicalContourInterpolator Self; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Interpolate only this label. Interpolates all labels if set to 0 (default). */ + itkSetMacro(Label, typename TImage::PixelType); + + /** Which label is interpolated. 0 means all labels (default). */ + itkGetMacro(Label, typename TImage::PixelType); + + /** Which label is interpolated. 0 means all labels (default). */ + itkGetConstMacro(Label, typename TImage::PixelType); + + /** Run-time type information (and related methods). */ + itkTypeMacro(MorphologicalContourInterpolator, ImageToImageFilter); + +protected: + MorphologicalContourInterpolator() { this->m_Label = 0; } + ~MorphologicalContourInterpolator() {} + + typename TImage::PixelType m_Label; + + /** Does the real work. */ + virtual void + GenerateData(); + +private: + MorphologicalContourInterpolator(const Self &); // purposely not implemented + void + operator=(const Self &); // purposely not implemented +}; +} // namespace itk + + +#ifndef ITK_MANUAL_INSTANTIATION +# include "itkMorphologicalContourInterpolator.hxx" +#endif + + +#endif // __itkMorphologicalContourInterpolator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx new file mode 100644 index 00000000000..29e9155ad45 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -0,0 +1,32 @@ +#ifndef __itkMorphologicalContourInterpolator_hxx +#define __itkMorphologicalContourInterpolator_hxx + +#include "itkMorphologicalContourInterpolator.h" +#include "itkObjectFactory.h" +#include "itkImageRegionIterator.h" +#include "itkImageRegionConstIterator.h" + +namespace itk +{ + +template +void +MorphologicalContourInterpolator::GenerateData() +{ + typename TImage::ConstPointer input = this->GetInput(); + typename TImage::Pointer output = this->GetOutput(); + this->AllocateOutputs(); + + ImageAlgorithm::Copy( + input.GetPointer(), output.GetPointer(), output->GetRequestedRegion(), output->GetRequestedRegion()); + + itk::Index<3> cornerPixel = input->GetLargestPossibleRegion().GetIndex(); + typename TImage::PixelType newValue = 3; + + output->SetPixel(cornerPixel, newValue); +} + +} // namespace itk + + +#endif //__itkMorphologicalContourInterpolator_hxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index c24a2bdce6f..821645bf942 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -18,41 +18,48 @@ #include "itkImageFileReader.h" #include "itkImageFileWriter.h" +#include "itkMorphologicalContourInterpolator.h" int itkMorphologicalContourInterpolationTest(int argc, char * argv[]) { - // if( argc < 3 ) - //{ - // std::cerr << "Usage: " << argv[0]; - // std::cerr << " inputImage outputImage"; - // std::cerr << std::endl; - // return EXIT_FAILURE; - // } - // const char * inputImageFileName = argv[1]; - // const char * outputImageFileName = argv[2]; - - // typedef signed short PixelType; - // const unsigned int Dimension = 3; - // typedef itk::Image< PixelType, Dimension > ImageType; - - // typedef itk::ImageFileReader < ImageType > ReaderType; - // ReaderType::Pointer reader = ReaderType::New(); - // reader->SetFileName( inputImageFileName ); - - // typedef itk::ImageFileWriter< ImageType > WriterType; - // WriterType::Pointer writer = WriterType::New(); - // writer->SetFileName( outputImageFileName ); - // writer->SetInput( reader->GetOutput() ); - // try - //{ - // writer->Update(); - // } - // catch( itk::ExceptionObject & error ) - //{ - // std::cerr << "Error: " << error << std::endl; - // return EXIT_FAILURE; - // } + if (argc < 3) + { + std::cerr << "Usage: " << argv[0]; + std::cerr << " inputImage outputImage"; + std::cerr << std::endl; + return EXIT_FAILURE; + } + const char * inputImageFileName = argv[1]; + const char * outputImageFileName = argv[2]; + + typedef signed short PixelType; + const unsigned int Dimension = 3; + typedef itk::Image ImageType; + + typedef itk::ImageFileReader ReaderType; + ReaderType::Pointer reader = ReaderType::New(); + reader->SetFileName(inputImageFileName); + + typedef itk::MorphologicalContourInterpolator mciType; + mciType::Pointer mci = mciType::New(); + mci->SetInput(reader->GetOutput()); + mci->SetLabel(0); + + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outputImageFileName); + writer->SetInput(mci->GetOutput()); + + try + { + writer->Update(); + } + catch (itk::ExceptionObject & error) + { + std::cerr << "Error: " << error << std::endl; + return EXIT_FAILURE; + } return EXIT_SUCCESS; } From 6b78b9f8122c85767019b2ff59786a589109dfe9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 May 2015 15:04:29 -0400 Subject: [PATCH 006/176] WIP: created main filter, implementation of orientation determination in progress --- .../itkMorphologicalContourInterpolator.h | 11 +++++ .../itkMorphologicalContourInterpolator.hxx | 43 ++++++++++++++++++- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index fafc45afbde..40acd7906f3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -2,6 +2,8 @@ #define __itkMorphologicalContourInterpolator_h #include "itkImageToImageFilter.h" +#include +#include namespace itk { @@ -39,6 +41,15 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; + // add bounding box + typedef std::map OrientationsType; + OrientationsType m_Orientations; + private: MorphologicalContourInterpolator(const Self &); // purposely not implemented void diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 29e9155ad45..24e9b4cd7ed 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -4,10 +4,48 @@ #include "itkMorphologicalContourInterpolator.h" #include "itkObjectFactory.h" #include "itkImageRegionIterator.h" -#include "itkImageRegionConstIterator.h" +#include "itkImageRegionConstIteratorWithIndex.h" +#include namespace itk { +template +void +MorphologicalContourInterpolator::DetermineSliceOrientations() +{ + typename TImage::ConstPointer input = this->GetInput(); + typename TImage::Pointer output = this->GetOutput(); + m_Orientations.clear(); + typename TImage::RegionType region = output->GetRequestedRegion(); + itk::ImageRegionConstIteratorWithIndex it(input, region); + + OrientationType zeros = OrientationType(); + + while (!it.IsAtEnd()) + { + typename TImage::IndexType indPrev, indNext, ind = it.GetIndex(); + typename TImage::PixelType val = input->GetPixel(ind); + if (val != 0) + { + std::pair res = m_Orientations.insert(make_pair(val, zeros)); + OrientationsType::iterator oRef = res.first; + + for (int a = 0; a < TImage::ImageDimension; a++) + { + indPrev = ind; + indPrev[a]--; + indNext = ind; + indNext[a]++; + if (region.IsInside(indPrev) && region.IsInside(indNext)) + { + if (input->GetPixel(indPrev) == 0 && input->GetPixel(indNext) == 0) + oRef->second[a]++; + } + } + } + ++it; + } +} template void @@ -17,6 +55,8 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer output = this->GetOutput(); this->AllocateOutputs(); + this->DetermineSliceOrientations(); + ImageAlgorithm::Copy( input.GetPointer(), output.GetPointer(), output->GetRequestedRegion(), output->GetRequestedRegion()); @@ -25,7 +65,6 @@ MorphologicalContourInterpolator::GenerateData() output->SetPixel(cornerPixel, newValue); } - } // namespace itk From 6d4931270e7e0d58352ca2664326538ba7996fae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 May 2015 16:31:38 -0400 Subject: [PATCH 007/176] WIP: added bounding boxes --- .../itkMorphologicalContourInterpolator.h | 32 ++++++++++-- .../itkMorphologicalContourInterpolator.hxx | 51 ++++++++++++++----- 2 files changed, 66 insertions(+), 17 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 40acd7906f3..a46bfeb0749 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -28,14 +28,28 @@ class MorphologicalContourInterpolator : public ImageToImageFilterm_Label = 0; } + MorphologicalContourInterpolator() + { + this->m_Label = 0; + this->m_Axis = -1; + } ~MorphologicalContourInterpolator() {} typename TImage::PixelType m_Label; + int m_Axis; /** Does the real work. */ virtual void @@ -43,12 +57,20 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; - // add bounding box + typedef unsigned long long CountType; + typedef std::array OrientationType; typedef std::map OrientationsType; - OrientationsType m_Orientations; + + typedef std::map BoundingBoxesType; + OrientationsType m_Orientations; + BoundingBoxesType m_BoundingBoxes; + + // assumes both valid region and valid index + void + ExpandRegion(typename TImage::RegionType & region, typename TImage::IndexType index); private: MorphologicalContourInterpolator(const Self &); // purposely not implemented diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 24e9b4cd7ed..c1223361973 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -9,6 +9,21 @@ namespace itk { +template +void +MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionType & region, + typename TImage::IndexType index) +{ + for (int a = 0; a < TImage::ImageDimension; a++) + { + if (region.GetIndex(a) > index[a]) + region.SetIndex(a, index[a]); + else if (region.GetIndex(a) + region.GetSize(a) < index[a]) + region.SetSize(a, index[a] - region.GetIndex(a) + 1); + // else it is already within + } +} + template void MorphologicalContourInterpolator::DetermineSliceOrientations() @@ -25,9 +40,17 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { typename TImage::IndexType indPrev, indNext, ind = it.GetIndex(); typename TImage::PixelType val = input->GetPixel(ind); - if (val != 0) + if (val != 0 || (m_Label != 0 && val == m_Label)) { - std::pair res = m_Orientations.insert(make_pair(val, zeros)); + typename TImage::RegionType bb1; + bb1.SetIndex(ind); + for (int a = 0; a < TImage::ImageDimension; a++) + bb1.SetSize(a, 1); + std::pair resBB = m_BoundingBoxes.insert(std::make_pair(val, bb1)); + if (!resBB.second) // include this index in existing BB + ExpandRegion(resBB.first->second, ind); + + std::pair res = m_Orientations.insert(std::make_pair(val, zeros)); OrientationsType::iterator oRef = res.first; for (int a = 0; a < TImage::ImageDimension; a++) @@ -36,7 +59,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() indPrev[a]--; indNext = ind; indNext[a]++; - if (region.IsInside(indPrev) && region.IsInside(indNext)) + if (input->GetLargestPossibleRegion().IsInside(indPrev) && input->GetLargestPossibleRegion().IsInside(indNext)) { if (input->GetPixel(indPrev) == 0 && input->GetPixel(indNext) == 0) oRef->second[a]++; @@ -47,6 +70,11 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } +template +void +MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage::Pointer out) +{} + template void MorphologicalContourInterpolator::GenerateData() @@ -55,15 +83,14 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer output = this->GetOutput(); this->AllocateOutputs(); - this->DetermineSliceOrientations(); - - ImageAlgorithm::Copy( - input.GetPointer(), output.GetPointer(), output->GetRequestedRegion(), output->GetRequestedRegion()); - - itk::Index<3> cornerPixel = input->GetLargestPossibleRegion().GetIndex(); - typename TImage::PixelType newValue = 3; - - output->SetPixel(cornerPixel, newValue); + if (m_Axis == -1) + { + this->DetermineSliceOrientations(); + // do more computation + // invoke interpolation along all axes then do median voting + } + else + InterpolateAlong(m_Axis, output); } } // namespace itk From 343f61ff03d5b7ba2c1955c38f81d4479a6e0c63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 15 May 2015 17:34:27 -0400 Subject: [PATCH 008/176] WIP: slice detection and median voting done, InterpolateAlong needs to be implemented --- .../itkMorphologicalContourInterpolator.h | 3 +- .../itkMorphologicalContourInterpolator.hxx | 113 ++++++++++++++++-- .../test/CMakeLists.txt | 1 + 3 files changed, 105 insertions(+), 12 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index a46bfeb0749..460cbbefec9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -60,8 +60,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; + typedef std::array OrientationType; typedef std::map OrientationsType; typedef std::map BoundingBoxesType; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index c1223361973..788c41108aa 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -6,6 +6,7 @@ #include "itkImageRegionIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" #include +#include namespace itk { @@ -18,7 +19,7 @@ MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionTy { if (region.GetIndex(a) > index[a]) region.SetIndex(a, index[a]); - else if (region.GetIndex(a) + region.GetSize(a) < index[a]) + else if (region.GetIndex(a) + region.GetSize(a) <= index[a]) region.SetSize(a, index[a] - region.GetIndex(a) + 1); // else it is already within } @@ -31,10 +32,19 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() typename TImage::ConstPointer input = this->GetInput(); typename TImage::Pointer output = this->GetOutput(); m_Orientations.clear(); - typename TImage::RegionType region = output->GetRequestedRegion(); - itk::ImageRegionConstIteratorWithIndex it(input, region); - OrientationType zeros = OrientationType(); + typename TImage::RegionType region = output->GetRequestedRegion(); + typename TImage::RegionType lpr = input->GetLargestPossibleRegion(); + for (int a = 0; a < TImage::ImageDimension; a++) + { + if (region.GetIndex(a) < lpr.GetIndex(a) + 1) + region.SetIndex(a, lpr.GetIndex(a) + 1); + if (region.GetIndex(a) + region.GetSize(a) > lpr.GetIndex(a) + lpr.GetSize(a) - 1) + region.SetSize(a, lpr.GetIndex(a) + lpr.GetSize(a) - 1 - region.GetIndex(a)); + } + ImageRegionConstIteratorWithIndex it(input, region); + + OrientationType ors = OrientationType(); while (!it.IsAtEnd()) { @@ -50,24 +60,44 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() if (!resBB.second) // include this index in existing BB ExpandRegion(resBB.first->second, ind); - std::pair res = m_Orientations.insert(std::make_pair(val, zeros)); + std::pair res = m_Orientations.insert(std::make_pair(val, ors)); OrientationsType::iterator oRef = res.first; - + int cTrue = 0; for (int a = 0; a < TImage::ImageDimension; a++) { indPrev = ind; indPrev[a]--; indNext = ind; indNext[a]++; - if (input->GetLargestPossibleRegion().IsInside(indPrev) && input->GetLargestPossibleRegion().IsInside(indNext)) { if (input->GetPixel(indPrev) == 0 && input->GetPixel(indNext) == 0) - oRef->second[a]++; + { + ors[a] = true; + cTrue++; + } } } + if (cTrue == 1) // slice has empty adjacent space only along one axis + { + for (int a = 0; a < TImage::ImageDimension; a++) + oRef->second[a] = oRef->second[a] || ors[a]; // add this dimension for this label + } } ++it; } + + // widen bounding boxes by 1 + region = output->GetRequestedRegion(); + for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) + { + for (int a = 0; a < TImage::ImageDimension; a++) + { + if (it->second.GetIndex(a) - 1 <= region.GetIndex(a)) + it->second.SetIndex(a, it->second.GetIndex(a) - 1); + if (it->second.GetIndex(a) + it->second.GetSize(a) + 1 <= region.GetIndex(a) + region.GetSize(a)) + it->second.SetSize(a, it->second.GetSize(a) + 1); + } + } } template @@ -86,8 +116,71 @@ MorphologicalContourInterpolator::GenerateData() if (m_Axis == -1) { this->DetermineSliceOrientations(); - // do more computation - // invoke interpolation along all axes then do median voting + + OrientationType aggregate = OrientationType(); + if (this->m_Label == 0) + { + for (OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) + for (int a = 0; a < TImage::ImageDimension; a++) + aggregate[a] = aggregate[a] || it->second[a]; // any label needs interpolation along this axis + } + else + aggregate = m_Orientations[m_Label]; // we only care about this label + + std::vector perAxisInterpolates; + for (int a = 0; a < TImage::ImageDimension; a++) + if (aggregate[a]) + { + TImage::Pointer imageA = TImage::New(); + imageA->CopyInformation(output); + imageA->Allocate(); + InterpolateAlong(a, imageA); + perAxisInterpolates.push_back(imageA); + } + + if (perAxisInterpolates.size() == 1) + { + output = perAxisInterpolates[0]; + return; + } + // else + std::vector> iterators; + + for (int i = 0; i < perAxisInterpolates.size(); i++) + { + ImageRegionConstIterator it(perAxisInterpolates[i], output->GetRequestedRegion()); + iterators.push_back(it); + } + + std::vector values; + values.reserve(perAxisInterpolates.size()); + + ImageRegionIterator it(output, output->GetRequestedRegion()); + while (!it.IsAtEnd()) + { + values.clear(); + for (int i = 0; i < perAxisInterpolates.size(); i++) + { + TImage::PixelType val = iterators[i].Value(); + if (val != 0) + values.push_back(val); + } + + if (values.size() == 0) + it.Set(0); // all were zero + else if (values.size() == 1) + it.Set(values[0]); // the only non-zero + else // median, gives preference to higher-numbered axis + { + std::nth_element(values.begin(), values.begin() + values.size() / 2, values.end()); + it.Set(values[values.size() / 2]); + } + + // next pixel + ++it; + for (int i = 0; i < perAxisInterpolates.size(); i++) + ++(iterators[i]); + } } else InterpolateAlong(m_Axis, output); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 870d672226c..56eae9fe5c0 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -13,4 +13,5 @@ itk_add_test( MorphologicalContourInterpolationTestDriver itkMorphologicalContourInterpolationTest DATA{Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/105769moving_resliced_to_fixedhz2_segmentation_interpolated.nii.gz ) From 8aa688e8981448dd7293ff2c58c89c2c036c7169 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 15 May 2015 18:35:36 -0400 Subject: [PATCH 009/176] ENH: using all images in tests --- .../itkMorphologicalContourInterpolator.hxx | 1 + .../test/CMakeLists.txt | 47 ++++++++++++++++++- 2 files changed, 47 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 788c41108aa..5766f54d4aa 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -133,6 +133,7 @@ MorphologicalContourInterpolator::GenerateData() { TImage::Pointer imageA = TImage::New(); imageA->CopyInformation(output); + imageA->SetRegions(output->GetRequestedRegion()); imageA->Allocate(); InterpolateAlong(a, imageA); perAxisInterpolates.push_back(imageA); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 56eae9fe5c0..f008c33f9aa 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -8,10 +8,55 @@ set( createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") itk_add_test( - NAME itkMorphologicalContourInterpolationTest + NAME itkMorphologicalContourInterpolationTest_hippocampus_exvivo COMMAND MorphologicalContourInterpolationTestDriver itkMorphologicalContourInterpolationTest DATA{Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz} ${ITK_TEST_OUTPUT_DIR}/105769moving_resliced_to_fixedhz2_segmentation_interpolated.nii.gz ) + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest_hippocampus_invivo + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/105769fixed_segmentation.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/105769fixed_segmentation_interpolated.nii.gz +) + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoLF + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/64816L_amygdala_fin.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/4816L_amygdala_fin_interpolated.nii.gz +) + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoLI + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/64816L_amygdala_int.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/64816L_amygdala_int_interpolated.nii.gz +) + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoRF + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/65239R_amygdala_fin.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/65239R_amygdala_fin_interpolated.nii.gz +) + +itk_add_test( + NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoRI + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/65239R_amygdala_int.nii.gz} + ${ITK_TEST_OUTPUT_DIR}/65239R_amygdala_int_interpolated.nii.gz +) From 7d5da36f404b83db69fdb1c1d457384130c3b08c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 18 May 2015 16:08:30 -0400 Subject: [PATCH 010/176] WIP: code-review corrections --- .../itkMorphologicalContourInterpolator.h | 51 ++++++++--- .../itkMorphologicalContourInterpolator.hxx | 91 ++++++++++++------- 2 files changed, 98 insertions(+), 44 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 460cbbefec9..45b53b30e78 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -1,9 +1,25 @@ -#ifndef __itkMorphologicalContourInterpolator_h -#define __itkMorphologicalContourInterpolator_h +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#ifndef itkMorphologicalContourInterpolator_h +#define itkMorphologicalContourInterpolator_h #include "itkImageToImageFilter.h" -#include -#include +#include "itksys/hash_map.hxx" namespace itk { @@ -42,10 +58,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilterm_Label = 0; - this->m_Axis = -1; - } + : m_Label(0) + , m_Axis(-1) + {} ~MorphologicalContourInterpolator() {} typename TImage::PixelType m_Label; @@ -53,15 +68,25 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; - typedef std::map OrientationsType; + typedef itk::FixedArray OrientationType; + typedef itksys::hash_map OrientationsType; typedef std::map BoundingBoxesType; OrientationsType m_Orientations; @@ -84,4 +109,4 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::ExpandRegion(typename TImage::RegionType & region, typename TImage::IndexType index) { - for (int a = 0; a < TImage::ImageDimension; a++) + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (region.GetIndex(a) > index[a]) + { region.SetIndex(a, index[a]); + } else if (region.GetIndex(a) + region.GetSize(a) <= index[a]) + { region.SetSize(a, index[a] - region.GetIndex(a) + 1); + } // else it is already within } } @@ -29,41 +50,47 @@ template void MorphologicalContourInterpolator::DetermineSliceOrientations() { - typename TImage::ConstPointer input = this->GetInput(); - typename TImage::Pointer output = this->GetOutput(); + typename const TImage * input = this->GetInput(); + typename TImage * output = this->GetOutput(); m_Orientations.clear(); typename TImage::RegionType region = output->GetRequestedRegion(); - typename TImage::RegionType lpr = input->GetLargestPossibleRegion(); - for (int a = 0; a < TImage::ImageDimension; a++) + typename TImage::RegionType largestPossibleRegion = input->GetLargestPossibleRegion(); + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { - if (region.GetIndex(a) < lpr.GetIndex(a) + 1) - region.SetIndex(a, lpr.GetIndex(a) + 1); - if (region.GetIndex(a) + region.GetSize(a) > lpr.GetIndex(a) + lpr.GetSize(a) - 1) - region.SetSize(a, lpr.GetIndex(a) + lpr.GetSize(a) - 1 - region.GetIndex(a)); + if (region.GetIndex(a) < largestPossibleRegion.GetIndex(a) + 1) + { + region.SetIndex(a, largestPossibleRegion.GetIndex(a) + 1); + } + if (region.GetIndex(a) + region.GetSize(a) > + largestPossibleRegion.GetIndex(a) + largestPossibleRegion.GetSize(a) - 1) + { + region.SetSize(a, largestPossibleRegion.GetIndex(a) + largestPossibleRegion.GetSize(a) - 1 - region.GetIndex(a)); + } } ImageRegionConstIteratorWithIndex it(input, region); - OrientationType ors = OrientationType(); + OrientationType orientations = OrientationType(); while (!it.IsAtEnd()) { - typename TImage::IndexType indPrev, indNext, ind = it.GetIndex(); - typename TImage::PixelType val = input->GetPixel(ind); + typename TImage::IndexType indPrev, indNext; + typename const TImage::IndexType ind = it.GetIndex(); + typename const TImage::PixelType val = input->GetPixel(ind); if (val != 0 || (m_Label != 0 && val == m_Label)) { - typename TImage::RegionType bb1; - bb1.SetIndex(ind); - for (int a = 0; a < TImage::ImageDimension; a++) - bb1.SetSize(a, 1); - std::pair resBB = m_BoundingBoxes.insert(std::make_pair(val, bb1)); + typename TImage::RegionType boundingBox1; + boundingBox1.SetIndex(ind); + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + boundingBox1.SetSize(a, 1); + std::pair resBB = m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); if (!resBB.second) // include this index in existing BB ExpandRegion(resBB.first->second, ind); - std::pair res = m_Orientations.insert(std::make_pair(val, ors)); + std::pair res = m_Orientations.insert(std::make_pair(val, orientations)); OrientationsType::iterator oRef = res.first; int cTrue = 0; - for (int a = 0; a < TImage::ImageDimension; a++) + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { indPrev = ind; indPrev[a]--; @@ -72,15 +99,15 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { if (input->GetPixel(indPrev) == 0 && input->GetPixel(indNext) == 0) { - ors[a] = true; + orientations[a] = true; cTrue++; } } } if (cTrue == 1) // slice has empty adjacent space only along one axis { - for (int a = 0; a < TImage::ImageDimension; a++) - oRef->second[a] = oRef->second[a] || ors[a]; // add this dimension for this label + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + oRef->second[a] = oRef->second[a] || orientations[a]; // add this dimension for this label } } ++it; @@ -90,7 +117,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() region = output->GetRequestedRegion(); for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) { - for (int a = 0; a < TImage::ImageDimension; a++) + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (it->second.GetIndex(a) - 1 <= region.GetIndex(a)) it->second.SetIndex(a, it->second.GetIndex(a) - 1); @@ -102,8 +129,10 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() template void -MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage::Pointer out) -{} +MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage * out) +{ + throw "todo"; +} template void @@ -121,14 +150,14 @@ MorphologicalContourInterpolator::GenerateData() if (this->m_Label == 0) { for (OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) - for (int a = 0; a < TImage::ImageDimension; a++) + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) aggregate[a] = aggregate[a] || it->second[a]; // any label needs interpolation along this axis } else aggregate = m_Orientations[m_Label]; // we only care about this label std::vector perAxisInterpolates; - for (int a = 0; a < TImage::ImageDimension; a++) + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) if (aggregate[a]) { TImage::Pointer imageA = TImage::New(); @@ -171,7 +200,7 @@ MorphologicalContourInterpolator::GenerateData() it.Set(0); // all were zero else if (values.size() == 1) it.Set(values[0]); // the only non-zero - else // median, gives preference to higher-numbered axis + else // median { std::nth_element(values.begin(), values.begin() + values.size() / 2, values.end()); it.Set(values[values.size() / 2]); @@ -189,4 +218,4 @@ MorphologicalContourInterpolator::GenerateData() } // namespace itk -#endif //__itkMorphologicalContourInterpolator_hxx +#endif // itkMorphologicalContourInterpolator_hxx From bd090832aeb074d751781fa89fe089d22c4b1ca4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 19 May 2015 15:58:57 -0400 Subject: [PATCH 011/176] ENH: itk::FixedArray needs to be explicitly set to false --- .../include/itkMorphologicalContourInterpolator.hxx | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 640edc75ccd..866869a7e43 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -71,6 +71,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() ImageRegionConstIteratorWithIndex it(input, region); OrientationType orientations = OrientationType(); + orientations.Fill(false); while (!it.IsAtEnd()) { @@ -147,6 +148,8 @@ MorphologicalContourInterpolator::GenerateData() this->DetermineSliceOrientations(); OrientationType aggregate = OrientationType(); + aggregate.Fill(false); + if (this->m_Label == 0) { for (OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) From ab277d41686c9e7b969effda185dc87a19abdb7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 19 May 2015 16:33:29 -0400 Subject: [PATCH 012/176] WIP: fixing a bug in slice orientation detection --- .../itkMorphologicalContourInterpolator.hxx | 21 +++++++++++-------- ...kMorphologicalContourInterpolationTest.cxx | 1 + 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 866869a7e43..3fcf7f8fb95 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -90,25 +90,28 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() std::pair res = m_Orientations.insert(std::make_pair(val, orientations)); OrientationsType::iterator oRef = res.first; - int cTrue = 0; + unsigned int cTrue = 0, cAdjacent = 0, axis; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { indPrev = ind; indPrev[a]--; indNext = ind; indNext[a]++; + const typename TImage::PixelType prev = input->GetPixel(indPrev); + const typename TImage::PixelType next = input->GetPixel(indNext); + if (prev == 0 && next == 0) { - if (input->GetPixel(indPrev) == 0 && input->GetPixel(indNext) == 0) - { - orientations[a] = true; - cTrue++; - } + axis = a; + cTrue++; + } + else if (prev == val && next == val) + { + cAdjacent++; } } - if (cTrue == 1) // slice has empty adjacent space only along one axis + if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - oRef->second[a] = oRef->second[a] || orientations[a]; // add this dimension for this label + oRef->second[axis] = true; // add this dimension for this label } } ++it; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 821645bf942..b6977f666c1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -50,6 +50,7 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outputImageFileName); writer->SetInput(mci->GetOutput()); + writer->SetUseCompression(true); try { From 96c5eb2471e234fca0c5efbce123094d372efcd7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 22 May 2015 14:14:11 -0400 Subject: [PATCH 013/176] WIP: progress made, TODO: InterpolateBetweenTwo --- .../itkMorphologicalContourInterpolator.h | 18 +++++- .../itkMorphologicalContourInterpolator.hxx | 60 +++++++++++++++++-- 2 files changed, 69 insertions(+), 9 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 45b53b30e78..f1771755536 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -77,6 +77,12 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; typedef itksys::hash_map OrientationsType; + OrientationsType m_Orientations; + + typedef itksys::hash_map BoundingBoxesType; + BoundingBoxesType m_BoundingBoxes; + + // each label gets a set of slices in which it is present + typedef std::set SliceSetType; + typedef itksys::hash_map LabeledSlicesType; + std::vector m_LabeledSlices; // one for each axis - typedef std::map BoundingBoxesType; - OrientationsType m_Orientations; - BoundingBoxesType m_BoundingBoxes; // assumes both valid region and valid index void diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 3fcf7f8fb95..a9accb94664 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -52,7 +52,11 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { typename const TImage * input = this->GetInput(); typename TImage * output = this->GetOutput(); - m_Orientations.clear(); + m_LabeledSlices.resize(TImage::ImageDimension); + // for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + //{ + // m_LabeledSlices[a] = LabeledSlicesType(); + // } typename TImage::RegionType region = output->GetRequestedRegion(); typename TImage::RegionType largestPossibleRegion = input->GetLargestPossibleRegion(); @@ -112,6 +116,10 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis { oRef->second[axis] = true; // add this dimension for this label + if (m_Axis == -1 || m_Axis == axis) + { + m_LabeledSlices[axis][val].insert(ind[axis]); + } } } ++it; @@ -131,11 +139,45 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } +template +void +MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, + typename TImage * out, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j) +{ + // determine inter-slice region correspondences + // then do one of the three cases + // throw "todo"; +} + template void MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage * out) { - throw "todo"; + SliceSetType aggregate; + for (unsigned int i = 0; i < m_LabeledSlices[axis].size(); i++) + { + aggregate.insert(m_LabeledSlices[axis][i].begin(), m_LabeledSlices[axis][i].end()); + } + typename SliceSetType::iterator prev = aggregate.begin(); + if (prev == aggregate.end()) + { + return; // nothing to do + } + +#pragma omp parallel + { + typename SliceSetType::iterator it = aggregate.begin(); + for (++it; it != aggregate.end(); ++it) + { +#pragma omp single nowait + { + InterpolateBetweenTwo(axis, out, *prev, *it); + } + prev = it; + } + } } template @@ -145,11 +187,12 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::ConstPointer input = this->GetInput(); typename TImage::Pointer output = this->GetOutput(); this->AllocateOutputs(); + output->FillBuffer(0); // clear the image now, because interpolation is optimized using bounding boxes + + this->DetermineSliceOrientations(); if (m_Axis == -1) { - this->DetermineSliceOrientations(); - OrientationType aggregate = OrientationType(); aggregate.Fill(false); @@ -163,16 +206,19 @@ MorphologicalContourInterpolator::GenerateData() aggregate = m_Orientations[m_Label]; // we only care about this label std::vector perAxisInterpolates; +#pragma omp parallel for for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + { if (aggregate[a]) { TImage::Pointer imageA = TImage::New(); imageA->CopyInformation(output); imageA->SetRegions(output->GetRequestedRegion()); imageA->Allocate(); - InterpolateAlong(a, imageA); + this->InterpolateAlong(a, imageA); perAxisInterpolates.push_back(imageA); } + } if (perAxisInterpolates.size() == 1) { @@ -219,7 +265,9 @@ MorphologicalContourInterpolator::GenerateData() } } else - InterpolateAlong(m_Axis, output); + { + this->InterpolateAlong(m_Axis, output); + } } } // namespace itk From 2249ef89ff521abd22b15bc4d2580256041d3679 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 22 May 2015 16:54:53 -0400 Subject: [PATCH 014/176] ENH: Getter and Setters for LabeledSlices --- .../itkMorphologicalContourInterpolator.h | 10 ++++- .../itkMorphologicalContourInterpolator.hxx | 44 ++++++++++++++++--- 2 files changed, 46 insertions(+), 8 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index f1771755536..53017ce3788 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -60,7 +60,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter LabeledSlicesType; std::vector m_LabeledSlices; // one for each axis + void + SetLabeledSliceIndices(unsigned int axis, std::vector indices); + void + SetLabeledSliceIndices(unsigned int axis, SliceSetType indices); + SliceSetType + GetLabeledSliceIndices(unsigned int axis); // assumes both valid region and valid index void diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index a9accb94664..b6c949715d8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -27,6 +27,28 @@ namespace itk { +template +typename MorphologicalContourInterpolator::SliceSetType +MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) +{ + return m_LabeledSlices[axis]; +} + +template +void +MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) +{ + m_LabeledSlices[axis] = indices; +} + +template +void +MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, + std::vector indices) +{ + m_LabeledSlices[axis] = SliceSetType().insert(indices.begin(), indices.end()); +} + template void MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionType & region, @@ -52,11 +74,10 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { typename const TImage * input = this->GetInput(); typename TImage * output = this->GetOutput(); - m_LabeledSlices.resize(TImage::ImageDimension); - // for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - //{ - // m_LabeledSlices[a] = LabeledSlicesType(); - // } + m_LabeledSlices.clear(); + m_LabeledSlices.resize(TImage::ImageDimension); // initialize with empty sets + m_BoundingBoxes.clear(); + m_Orientations.clear(); typename TImage::RegionType region = output->GetRequestedRegion(); typename TImage::RegionType largestPossibleRegion = input->GetLargestPossibleRegion(); @@ -148,6 +169,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { // determine inter-slice region correspondences // then do one of the three cases + ; // for breakpoint // throw "todo"; } @@ -156,9 +178,17 @@ void MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage * out) { SliceSetType aggregate; - for (unsigned int i = 0; i < m_LabeledSlices[axis].size(); i++) + if (m_Label == 0) // all labels + { + for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); + ++it) + { + aggregate.insert(it->second.begin(), it->second.end()); + } + } + else // we only care about m_Label { - aggregate.insert(m_LabeledSlices[axis][i].begin(), m_LabeledSlices[axis][i].end()); + aggregate = m_LabeledSlices[axis][m_Label]; } typename SliceSetType::iterator prev = aggregate.begin(); if (prev == aggregate.end()) From 003a7f84f490efde26489afc68b43f06a8440e05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 May 2015 14:00:09 -0400 Subject: [PATCH 015/176] WIP: detecting correspondences --- .../itkMorphologicalContourInterpolator.h | 9 +- .../itkMorphologicalContourInterpolator.hxx | 140 +++++++++++++++--- 2 files changed, 130 insertions(+), 19 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 53017ce3788..f1557db9283 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -114,7 +114,14 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; + typename TImage::Pointer + RegionedConnectedComponents(typename TImage::RegionType region, + typename TImage::PixelType label, + itk::IdentifierType & objectCount); private: MorphologicalContourInterpolator(const Self &); // purposely not implemented diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index b6c949715d8..55dc674e84a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -22,6 +22,8 @@ #include "itkObjectFactory.h" #include "itkImageRegionIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" +#include "itkConnectedComponentImageFilter.h" +#include "itkBinaryThresholdImageFilter.h" #include #include @@ -160,6 +162,26 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } +template +typename TImage::Pointer +MorphologicalContourInterpolator::RegionedConnectedComponents(typename TImage::RegionType region, + typename TImage::PixelType label, + itk::IdentifierType & objectCount) +{ + typedef BinaryThresholdImageFilter BinarizerType; + BinarizerType::Pointer bin = BinarizerType::New(); + bin->SetLowerThreshold(label); + bin->SetUpperThreshold(label); + bin->SetInput(this->GetInput()); + bin->GetOutput()->SetRequestedRegion(region); + typedef ConnectedComponentImageFilter ConnComponentsType; + ConnComponentsType::Pointer conn = ConnComponentsType::New(); + conn->SetInput(bin->GetOutput()); + conn->SetFullyConnected(true); + conn->Update(); + return conn->GetOutput(); +} + template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, @@ -167,10 +189,84 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexValueType i, typename TImage::IndexValueType j) { - // determine inter-slice region correspondences - // then do one of the three cases - ; // for breakpoint - // throw "todo"; + if (i > j) + std::swap(i, j); + if (i == j || i + 1 == j) + return; // nothing to do + + // compare slices i and j + typename TImage::ConstPointer input = this->GetInput(); + typename TImage::RegionType ri = m_TotalBoundingBox; // smaller than or equal to requested region + ri.SetIndex(axis, i); + ri.SetSize(axis, 1); // 1 slice + typename TImage::RegionType rj = ri; + rj.SetIndex(axis, j); + + BoolImageType::Pointer eqResult = BoolImageType::New(); + typename TImage::RegionType rr = rj; + rr.SetIndex(axis, 0); + eqResult->CopyInformation(input); + eqResult->SetRegions(rr); + eqResult->Allocate(); + + typedef std::set LabelSetType; + LabelSetType overlaps; // which labels have overlaps from slice i to slice j + + ImageRegionConstIterator iti(input, ri); + ImageRegionConstIterator itj(input, rj); + ImageRegionIterator itr(eqResult, rr); + while (!itr.IsAtEnd()) + { + bool eq = (iti.Value() == itj.Value()); // are the pixels equal? + itr.Set(eq); + if (eq) + overlaps.insert(iti.Value()); + ++iti; + ++itj; + ++itr; // next pixel + } + + // for each label with overlaps determine inter-slice region correspondences + for (LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) + { + if (m_Label != 0 && *it != m_Label) + continue; // label was specified, and it was not this one, so skip + + // first determine disjoint regions + ri = m_BoundingBoxes[*it]; // even smaller than m_TotalBoundingBox + ri.SetSize(axis, 1); + ri.SetIndex(axis, i); + rj = ri; + rj.SetIndex(axis, j); + rr = rj; + rr.SetIndex(axis, 0); + + // execute connected components + itk::IdentifierType iCount, jCount; + typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, *it, iCount); + typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, *it, jCount); + + // go through comparison image and create correspondence pairs + std::set> pairs; + itr.GoToBegin(); + ImageRegionConstIterator iti(iconn, ri); + ImageRegionConstIterator itj(jconn, rj); + while (!itr.IsAtEnd()) + { + if (itr.Value()) + { + pairs.insert(std::make_pair(iti.Value(), itj.Value())); + } + ++iti; + ++itj; + ++itr; // next pixel + } + + // for labeled regions without overlaps, do extrapolation + + // now do one of the three cases + throw "todo"; + } } template @@ -196,17 +292,11 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TI return; // nothing to do } -#pragma omp parallel + typename SliceSetType::iterator it = aggregate.begin(); + for (++it; it != aggregate.end(); ++it) { - typename SliceSetType::iterator it = aggregate.begin(); - for (++it; it != aggregate.end(); ++it) - { -#pragma omp single nowait - { - InterpolateBetweenTwo(axis, out, *prev, *it); - } - prev = it; - } + InterpolateBetweenTwo(axis, out, *prev, *it); + prev = it; } } @@ -221,7 +311,22 @@ MorphologicalContourInterpolator::GenerateData() this->DetermineSliceOrientations(); - if (m_Axis == -1) + // merge all bounding boxes + if (m_BoundingBoxes.size() == 0) + { + return; // nothing to process + } + else + { + m_TotalBoundingBox = m_BoundingBoxes.begin()->second; + } + for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) + { + ExpandRegion(m_TotalBoundingBox, it->second.GetIndex()); + ExpandRegion(m_TotalBoundingBox, it->second.GetIndex() + it->second.GetSize()); + } + + if (m_Axis == -1) // interpolate along all axes { OrientationType aggregate = OrientationType(); aggregate.Fill(false); @@ -236,7 +341,6 @@ MorphologicalContourInterpolator::GenerateData() aggregate = m_Orientations[m_Label]; // we only care about this label std::vector perAxisInterpolates; -#pragma omp parallel for for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (aggregate[a]) @@ -293,8 +397,8 @@ MorphologicalContourInterpolator::GenerateData() for (int i = 0; i < perAxisInterpolates.size(); i++) ++(iterators[i]); } - } - else + } // interpolate along all axes + else // interpolate along the specified axis { this->InterpolateAlong(m_Axis, output); } From 875626b4310da5cb1ab535bdd603ebaaaeb29b10 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 May 2015 15:44:19 -0400 Subject: [PATCH 016/176] WIP: detected correspondences, TODO: pass correct parameters and implement the 3 cases, implement alignment --- .../itkMorphologicalContourInterpolator.hxx | 135 +++++++++++++++++- 1 file changed, 128 insertions(+), 7 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 55dc674e84a..6fdbc257ca7 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -242,12 +242,13 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int rr.SetIndex(axis, 0); // execute connected components - itk::IdentifierType iCount, jCount; + IdentifierType iCount, jCount; typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, *it, iCount); typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, *it, jCount); // go through comparison image and create correspondence pairs - std::set> pairs; + typedef std::set> PairSet; + PairSet pairs; itr.GoToBegin(); ImageRegionConstIterator iti(iconn, ri); ImageRegionConstIterator itj(jconn, rj); @@ -262,12 +263,132 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++itr; // next pixel } - // for labeled regions without overlaps, do extrapolation + typedef std::map CountMap; + CountMap iCounts, jCounts; + for (PairSet::iterator p = pairs.begin(); p != pairs.end(); ++p) + { + iCounts[p->first]++; + jCounts[p->second]++; + } - // now do one of the three cases - throw "todo"; - } -} + // first do extrapolation for components without overlaps + CountMap::iterator iMapIt = iCounts.begin(); + for (IdentifierType ic = 1; ic <= iCount; ++ic) // component labels + { + if (iMapIt == iCounts.end() || ic < iMapIt->first) + { + extrapolate(); // TODO: pass correct parameters and implement + } + else // ic==iMapIt->first + { + ++iMapIt; + } + } + CountMap::iterator jMapIt = jCounts.begin(); + for (IdentifierType jc = 1; jc <= jCount; ++jc) // component labels + { + if (jMapIt == jCounts.end() || jc < jMapIt->first) + { + extrapolate(); // TODO: pass correct parameters and implement + } + else // jc==jMapIt->first + { + ++jMapIt; + } + } + + // now handle 1 to 1 correspondences + PairSet::iterator p = pairs.begin(); + while (p != pairs.end()) + { + if (iCounts[p->first] == 1 && jCounts[p->second] == 1) + { + interpolate1to1(); // TODO: pass correct parameters and implement + iCounts.erase(p->first); + jCounts.erase(p->second); + pairs.erase(p++); + } + else + { + ++p; + } + } + + // now do 1-to-N and M-to-1 cases + p = pairs.begin(); + while (p != pairs.end()) + { + if (iCounts[p->first] == 1) // 1-to-N + { + interpolate1toN(); // TODO: pass correct parameters and implement + PairSet::iterator rest = p; + ++rest; + while (rest != pairs.end()) + { + if (rest->second == p->second) + { + pairs.erase(rest++); + } + else + { + ++rest; + } + } + iCounts.erase(p->first); + jCounts.erase(p->second); + pairs.erase(p++); + } + else if (jCounts[p->second] == 1) // M-to-1 + { + interpolate1toN(); // TODO: pass correct parameters and implement + PairSet::iterator rest = p; + ++rest; + while (rest != pairs.end()) + { + if (rest->first == p->first) + { + pairs.erase(rest++); + } + else + { + ++rest; + } + } + iCounts.erase(p->first); + jCounts.erase(p->second); + pairs.erase(p++); + } + else + { + ++p; + } + } + + // only M-to-N correspondences remain + // we turn each M-to-N case into m 1-to-N cases + p = pairs.begin(); + while (p != pairs.end()) + { + // TODO: enumerate the labels which correspond to p->first and make it 1-to-N + interpolate1toN(); // TODO: pass correct parameters and implement + PairSet::iterator rest = p; + ++rest; + while (rest != pairs.end()) + { + if (rest->first == p->first) + { + pairs.erase(rest++); + } + else + { + ++rest; + } + } + // counts no longer matter, do not waste time deleting them + pairs.erase(p++); + } // M-to-N + } // for each label with overlaps +} // void MorphologicalContourInterpolator::InterpolateBetweenTwo() template void From b82b034c43104382e3b57a44c261ed317b7242b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 May 2015 16:13:41 -0400 Subject: [PATCH 017/176] WIP: style compliance and other minor changes --- .../itkMorphologicalContourInterpolator.h | 25 ++-- .../itkMorphologicalContourInterpolator.hxx | 118 +++++++++++------- 2 files changed, 88 insertions(+), 55 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index f1557db9283..0b84c7e3749 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -19,6 +19,8 @@ #define itkMorphologicalContourInterpolator_h #include "itkImageToImageFilter.h" +#include "itkConnectedComponentImageFilter.h" +#include "itkBinaryThresholdImageFilter.h" #include "itksys/hash_map.hxx" namespace itk @@ -57,17 +59,16 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; typename TImage::Pointer - RegionedConnectedComponents(typename TImage::RegionType region, - typename TImage::PixelType label, - itk::IdentifierType & objectCount); + RegionedConnectedComponents(const typename TImage::RegionType region, + typename TImage::PixelType label, + IdentifierType & objectCount); + + typedef BinaryThresholdImageFilter BinarizerType; + typename BinarizerType::Pointer m_Binarizer; + + typedef ConnectedComponentImageFilter ConnectedComponentsType; + typename ConnectedComponentsType::Pointer m_ConnectedComponents; private: MorphologicalContourInterpolator(const Self &); // purposely not implemented diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 6fdbc257ca7..d0a5ecbd495 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -22,13 +22,22 @@ #include "itkObjectFactory.h" #include "itkImageRegionIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" -#include "itkConnectedComponentImageFilter.h" -#include "itkBinaryThresholdImageFilter.h" #include #include namespace itk { +template +MorphologicalContourInterpolator::MorphologicalContourInterpolator() + : m_Label(0) + , m_Axis(-1) + , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets +{ + m_Binarizer = BinarizerType::New(); + m_ConnectedComponents = ConnectedComponentsType::New(); + m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); +} + template typename MorphologicalContourInterpolator::SliceSetType MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) @@ -41,6 +50,7 @@ void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) { m_LabeledSlices[axis] = indices; + this->Modified(); } template @@ -49,6 +59,7 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int std::vector indices) { m_LabeledSlices[axis] = SliceSetType().insert(indices.begin(), indices.end()); + this->Modified(); } template @@ -74,15 +85,13 @@ template void MorphologicalContourInterpolator::DetermineSliceOrientations() { - typename const TImage * input = this->GetInput(); - typename TImage * output = this->GetOutput(); m_LabeledSlices.clear(); m_LabeledSlices.resize(TImage::ImageDimension); // initialize with empty sets m_BoundingBoxes.clear(); m_Orientations.clear(); - typename TImage::RegionType region = output->GetRequestedRegion(); - typename TImage::RegionType largestPossibleRegion = input->GetLargestPossibleRegion(); + typename TImage::RegionType region = m_Output->GetRequestedRegion(); + typename TImage::RegionType largestPossibleRegion = m_Input->GetLargestPossibleRegion(); for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (region.GetIndex(a) < largestPossibleRegion.GetIndex(a) + 1) @@ -95,7 +104,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() region.SetSize(a, largestPossibleRegion.GetIndex(a) + largestPossibleRegion.GetSize(a) - 1 - region.GetIndex(a)); } } - ImageRegionConstIteratorWithIndex it(input, region); + ImageRegionConstIteratorWithIndex it(m_Input, region); OrientationType orientations = OrientationType(); orientations.Fill(false); @@ -104,16 +113,20 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { typename TImage::IndexType indPrev, indNext; typename const TImage::IndexType ind = it.GetIndex(); - typename const TImage::PixelType val = input->GetPixel(ind); + typename const TImage::PixelType val = m_Input->GetPixel(ind); if (val != 0 || (m_Label != 0 && val == m_Label)) { typename TImage::RegionType boundingBox1; boundingBox1.SetIndex(ind); for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + { boundingBox1.SetSize(a, 1); + } std::pair resBB = m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); if (!resBB.second) // include this index in existing BB + { ExpandRegion(resBB.first->second, ind); + } std::pair res = m_Orientations.insert(std::make_pair(val, orientations)); OrientationsType::iterator oRef = res.first; @@ -124,16 +137,16 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() indPrev[a]--; indNext = ind; indNext[a]++; - const typename TImage::PixelType prev = input->GetPixel(indPrev); - const typename TImage::PixelType next = input->GetPixel(indNext); + const typename TImage::PixelType prev = m_Input->GetPixel(indPrev); + const typename TImage::PixelType next = m_Input->GetPixel(indNext); if (prev == 0 && next == 0) { axis = a; - cTrue++; + ++cTrue; } else if (prev == val && next == val) { - cAdjacent++; + ++cAdjacent; } } if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis @@ -149,7 +162,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } // widen bounding boxes by 1 - region = output->GetRequestedRegion(); + region = m_Output->GetRequestedRegion(); for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) { for (unsigned int a = 0; a < TImage::ImageDimension; ++a) @@ -164,22 +177,18 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() template typename TImage::Pointer -MorphologicalContourInterpolator::RegionedConnectedComponents(typename TImage::RegionType region, - typename TImage::PixelType label, - itk::IdentifierType & objectCount) +MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, + typename TImage::PixelType label, + IdentifierType & objectCount) { - typedef BinaryThresholdImageFilter BinarizerType; - BinarizerType::Pointer bin = BinarizerType::New(); - bin->SetLowerThreshold(label); - bin->SetUpperThreshold(label); - bin->SetInput(this->GetInput()); - bin->GetOutput()->SetRequestedRegion(region); - typedef ConnectedComponentImageFilter ConnComponentsType; - ConnComponentsType::Pointer conn = ConnComponentsType::New(); - conn->SetInput(bin->GetOutput()); - conn->SetFullyConnected(true); - conn->Update(); - return conn->GetOutput(); + m_Binarizer->SetLowerThreshold(label); + m_Binarizer->SetUpperThreshold(label); + m_Binarizer->SetInput(m_Input); + m_Binarizer->GetOutput()->SetRequestedRegion(region); + m_ConnectedComponents->SetInput(bin->GetOutput()); + m_ConnectedComponents->SetFullyConnected(true); + m_ConnectedComponents->Update(); + return m_ConnectedComponents->GetOutput(); } template @@ -190,13 +199,16 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexValueType j) { if (i > j) + { std::swap(i, j); + } if (i == j || i + 1 == j) + { return; // nothing to do + } // compare slices i and j - typename TImage::ConstPointer input = this->GetInput(); - typename TImage::RegionType ri = m_TotalBoundingBox; // smaller than or equal to requested region + typename TImage::RegionType ri = m_TotalBoundingBox; // smaller than or equal to requested region ri.SetIndex(axis, i); ri.SetSize(axis, 1); // 1 slice typename TImage::RegionType rj = ri; @@ -205,25 +217,28 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int BoolImageType::Pointer eqResult = BoolImageType::New(); typename TImage::RegionType rr = rj; rr.SetIndex(axis, 0); - eqResult->CopyInformation(input); + eqResult->CopyInformation(m_Input); eqResult->SetRegions(rr); eqResult->Allocate(); typedef std::set LabelSetType; LabelSetType overlaps; // which labels have overlaps from slice i to slice j - ImageRegionConstIterator iti(input, ri); - ImageRegionConstIterator itj(input, rj); + ImageRegionConstIterator iti(m_Input, ri); + ImageRegionConstIterator itj(m_Input, rj); ImageRegionIterator itr(eqResult, rr); while (!itr.IsAtEnd()) { bool eq = (iti.Value() == itj.Value()); // are the pixels equal? itr.Set(eq); if (eq) + { overlaps.insert(iti.Value()); + } + // next pixel ++iti; ++itj; - ++itr; // next pixel + ++itr; } // for each label with overlaps determine inter-slice region correspondences @@ -425,16 +440,21 @@ template void MorphologicalContourInterpolator::GenerateData() { - typename TImage::ConstPointer input = this->GetInput(); - typename TImage::Pointer output = this->GetOutput(); + m_Input = TImage::New(); + m_Input->Graft(const_cast(this->GetInput())); this->AllocateOutputs(); - output->FillBuffer(0); // clear the image now, because interpolation is optimized using bounding boxes + m_Output = TImage::New(); + m_Output->Graft(this->GetOutput()); + m_Output->FillBuffer(0); // clear the image now, because interpolation is optimized using bounding boxes + // alternatively, we could have copied the input image into output this->DetermineSliceOrientations(); // merge all bounding boxes if (m_BoundingBoxes.size() == 0) { + this->GraftOutput(m_Output); + this->m_Output = ITK_NULLPTR; return; // nothing to process } else @@ -467,8 +487,8 @@ MorphologicalContourInterpolator::GenerateData() if (aggregate[a]) { TImage::Pointer imageA = TImage::New(); - imageA->CopyInformation(output); - imageA->SetRegions(output->GetRequestedRegion()); + imageA->CopyInformation(m_Output); + imageA->SetRegions(m_Output->GetRequestedRegion()); imageA->Allocate(); this->InterpolateAlong(a, imageA); perAxisInterpolates.push_back(imageA); @@ -477,26 +497,28 @@ MorphologicalContourInterpolator::GenerateData() if (perAxisInterpolates.size() == 1) { - output = perAxisInterpolates[0]; + m_Output = perAxisInterpolates[0]; + this->GraftOutput(m_Output); + this->m_Output = ITK_NULLPTR; return; } // else std::vector> iterators; - for (int i = 0; i < perAxisInterpolates.size(); i++) + for (int i = 0; i < perAxisInterpolates.size(); ++i) { - ImageRegionConstIterator it(perAxisInterpolates[i], output->GetRequestedRegion()); + ImageRegionConstIterator it(perAxisInterpolates[i], m_Output->GetRequestedRegion()); iterators.push_back(it); } std::vector values; values.reserve(perAxisInterpolates.size()); - ImageRegionIterator it(output, output->GetRequestedRegion()); + ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); while (!it.IsAtEnd()) { values.clear(); - for (int i = 0; i < perAxisInterpolates.size(); i++) + for (int i = 0; i < perAxisInterpolates.size(); ++i) { TImage::PixelType val = iterators[i].Value(); if (val != 0) @@ -515,14 +537,18 @@ MorphologicalContourInterpolator::GenerateData() // next pixel ++it; - for (int i = 0; i < perAxisInterpolates.size(); i++) + for (int i = 0; i < perAxisInterpolates.size(); ++i) ++(iterators[i]); } } // interpolate along all axes else // interpolate along the specified axis { - this->InterpolateAlong(m_Axis, output); + this->InterpolateAlong(m_Axis, m_Output); } + + // put the output data back into the regular pipeline + this->GraftOutput(m_Output); + this->m_Output = ITK_NULLPTR; } } // namespace itk From 97cf3db1cebaed26c5c433cc81650d013e03ee35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 1 Jun 2015 17:25:41 -0400 Subject: [PATCH 018/176] WIP: adding handcrafted tests, parameters passed to Interpolate1toN family --- .../itkMorphologicalContourInterpolator.h | 32 ++++++ .../itkMorphologicalContourInterpolator.hxx | 104 +++++++++++++++--- .../test/CMakeLists.txt | 82 +++++--------- .../test/Input/16-5-16.nrrd.md5 | 1 + ...AccidentalMiddleSliceSegmentation.nrrd.md5 | 1 + .../Input/DoubleTwoLabelBranching.nrrd.md5 | 1 + .../test/Input/FullEndSevenLabels.nrrd.md5 | 1 + .../test/Input/ManyToMany.nrrd.md5 | 1 + .../test/Input/OneToOne.nrrd.md5 | 1 + .../test/Input/OneToThree.nrrd.md5 | 1 + .../test/Input/SimplestOneToOne.nrrd.md5 | 1 + .../Input/ThreeAxisFourLabelConflict.nrrd.md5 | 1 + ...isDoubleTwoLabelBranchingConflict.nrrd.md5 | 1 + 13 files changed, 158 insertions(+), 70 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/16-5-16.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 0b84c7e3749..b8e4098ab45 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -94,6 +94,38 @@ class MorphologicalContourInterpolator : public ImageToImageFilter jRegions); + typedef itk::FixedArray OrientationType; typedef itksys::hash_map OrientationsType; OrientationsType m_Orientations; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index d0a5ecbd495..568f16da683 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -175,6 +175,43 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } +template +void +MorphologicalContourInterpolator::Extrapolate(int axis, + typename TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegion) +{} + +template +void +MorphologicalContourInterpolator::Interpolate1to1(int axis, + typename TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegion, + typename TImage::Pointer jConn, + typename TImage::PixelType jRegion) +{} + +template +void +MorphologicalContourInterpolator::Interpolate1toN(int axis, + typename TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegion, + typename TImage::Pointer jConn, + std::vector jRegions) +{} + template typename TImage::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, @@ -185,7 +222,7 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type m_Binarizer->SetUpperThreshold(label); m_Binarizer->SetInput(m_Input); m_Binarizer->GetOutput()->SetRequestedRegion(region); - m_ConnectedComponents->SetInput(bin->GetOutput()); + m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); m_ConnectedComponents->SetFullyConnected(true); m_ConnectedComponents->Update(); return m_ConnectedComponents->GetOutput(); @@ -280,7 +317,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typedef std::map CountMap; CountMap iCounts, jCounts; - for (PairSet::iterator p = pairs.begin(); p != pairs.end(); ++p) + PairSet::iterator p; + for (p = pairs.begin(); p != pairs.end(); ++p) { iCounts[p->first]++; jCounts[p->second]++; @@ -292,7 +330,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (iMapIt == iCounts.end() || ic < iMapIt->first) { - extrapolate(); // TODO: pass correct parameters and implement + Extrapolate(axis, out, *it, i, j, iconn, ic); } else // ic==iMapIt->first { @@ -304,7 +342,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (jMapIt == jCounts.end() || jc < jMapIt->first) { - extrapolate(); // TODO: pass correct parameters and implement + Extrapolate(axis, out, *it, j, i, jconn, jc); } else // jc==jMapIt->first { @@ -313,12 +351,12 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // now handle 1 to 1 correspondences - PairSet::iterator p = pairs.begin(); + p = pairs.begin(); while (p != pairs.end()) { if (iCounts[p->first] == 1 && jCounts[p->second] == 1) { - interpolate1to1(); // TODO: pass correct parameters and implement + Interpolate1to1(axis, out, *it, i, j, iconn, p->first, jconn, p->second); iCounts.erase(p->first); jCounts.erase(p->second); pairs.erase(p++); @@ -329,19 +367,32 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } + std::vector regionIDs(pairs.size()); // preallocate // now do 1-to-N and M-to-1 cases p = pairs.begin(); while (p != pairs.end()) { + regionIDs.clear(); + if (iCounts[p->first] == 1) // 1-to-N { - interpolate1toN(); // TODO: pass correct parameters and implement + for (PairSet::iterator rest = p; p != pairs.end(); ++p) + { + if (rest->first == p->first) + { + regionIDs.push_back(rest->second); + } + } + + Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); + PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { - if (rest->second == p->second) + if (rest->first == p->first) { + --jCounts[rest->second]; pairs.erase(rest++); } else @@ -349,19 +400,29 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } + --jCounts[p->second]; iCounts.erase(p->first); - jCounts.erase(p->second); pairs.erase(p++); - } + } // 1-to-N else if (jCounts[p->second] == 1) // M-to-1 { - interpolate1toN(); // TODO: pass correct parameters and implement + for (PairSet::iterator rest = p; p != pairs.end(); ++p) + { + if (rest->second == p->second) + { + regionIDs.push_back(rest->first); + } + } + + Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs); + PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { - if (rest->first == p->first) + if (rest->second == p->second) { + --iCounts[rest->first]; pairs.erase(rest++); } else @@ -369,23 +430,32 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } - iCounts.erase(p->first); + --iCounts[rest->first]; jCounts.erase(p->second); pairs.erase(p++); - } + } // M-to-1 else { ++p; } - } + } // 1-to-N and M-to-1 // only M-to-N correspondences remain // we turn each M-to-N case into m 1-to-N cases p = pairs.begin(); while (p != pairs.end()) { - // TODO: enumerate the labels which correspond to p->first and make it 1-to-N - interpolate1toN(); // TODO: pass correct parameters and implement + regionIDs.clear(); + for (PairSet::iterator rest = p; p != pairs.end(); ++p) + { + if (rest->first == p->first) + { + regionIDs.push_back(rest->second); + } + } + + Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); + PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index f008c33f9aa..555826e504b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -7,56 +7,32 @@ set( createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_hippocampus_exvivo - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/105769moving_resliced_to_fixedhz2_segmentation_interpolated.nii.gz -) - -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_hippocampus_invivo - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/105769fixed_segmentation.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/105769fixed_segmentation_interpolated.nii.gz -) - -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoLF - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/64816L_amygdala_fin.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/4816L_amygdala_fin_interpolated.nii.gz -) - -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoLI - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/64816L_amygdala_int.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/64816L_amygdala_int_interpolated.nii.gz -) - -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoRF - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/65239R_amygdala_fin.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/65239R_amygdala_fin_interpolated.nii.gz -) - -itk_add_test( - NAME itkMorphologicalContourInterpolationTest_amygdala_exvivoRI - COMMAND - MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest - DATA{Input/65239R_amygdala_int.nii.gz} - ${ITK_TEST_OUTPUT_DIR}/65239R_amygdala_int_interpolated.nii.gz -) +function(JustInputTest ImageName Ext) + itk_add_test( + NAME itkMorphologicalContourInterpolationTest_${ImageName} + COMMAND + MorphologicalContourInterpolationTestDriver + itkMorphologicalContourInterpolationTest + DATA{Input/${ImageName}.${Ext}} + ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + ) +endfunction() + +# Handcrafted tests +justinputtest(SimplestOneToOne nrrd) +justinputtest(OneToOne nrrd) +justinputtest(OneToThree nrrd) +justinputtest(DoubleTwoLabelBranching nrrd) +justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) +justinputtest(ThreeAxisFourLabelConflict nrrd) +justinputtest(AccidentalMiddleSliceSegmentation nrrd) +justinputtest(FullEndSevenLabels nrrd) +justinputtest(ManyToMany nrrd) + +# Paul's tests +justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) +justinputtest(105769fixed_segmentation nii.gz) +justinputtest(64816L_amygdala_fin nii.gz) +justinputtest(64816L_amygdala_int nii.gz) +justinputtest(65239R_amygdala_fin nii.gz) +justinputtest(65239R_amygdala_int nii.gz) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/16-5-16.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/16-5-16.nrrd.md5 new file mode 100644 index 00000000000..8ea1db07098 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/16-5-16.nrrd.md5 @@ -0,0 +1 @@ +92c1a1dc78c2ebb174d481923f449b01 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 new file mode 100644 index 00000000000..4b5db425c69 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 @@ -0,0 +1 @@ +3e882071b670d2bc03d63e4d4df93c77 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 new file mode 100644 index 00000000000..b96b40d8141 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 @@ -0,0 +1 @@ +629b00e719241a15319dca2d5004031e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 new file mode 100644 index 00000000000..2023162395e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 @@ -0,0 +1 @@ +f01238f9cdd1ffab31c8cee126d744b1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 new file mode 100644 index 00000000000..7f212de66bf --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 @@ -0,0 +1 @@ +691b157a661d88396db1823cc3a9c246 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 new file mode 100644 index 00000000000..b9e427d0579 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 @@ -0,0 +1 @@ +53f8156569a78a40f022dda525f31f1d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 new file mode 100644 index 00000000000..8841d9cf868 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 @@ -0,0 +1 @@ +ec6f4f8e620dc7ad681c6c39443b28d4 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 new file mode 100644 index 00000000000..cea2a905518 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 @@ -0,0 +1 @@ +d1dddb01e4c8e018321a657ee8534ee4 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 new file mode 100644 index 00000000000..46676f79f53 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 @@ -0,0 +1 @@ +3328494192eeb9ea192d2100fe9bde45 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 new file mode 100644 index 00000000000..49259a8a2ed --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 @@ -0,0 +1 @@ +84436d25bca2e41381e09a7eda31c731 From 68ed65aa49a376182f0108d1cb745e86cf759efb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 2 Jun 2015 14:49:58 -0400 Subject: [PATCH 019/176] WIP: does not crash, but wrong region ID pairs --- .../itkMorphologicalContourInterpolator.hxx | 92 ++++++++++--------- 1 file changed, 51 insertions(+), 41 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 568f16da683..e110940cbc4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -25,6 +25,10 @@ #include #include +// DEBUG +#include +#include "itkImageFileWriter.h" + namespace itk { template @@ -90,26 +94,13 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() m_BoundingBoxes.clear(); m_Orientations.clear(); - typename TImage::RegionType region = m_Output->GetRequestedRegion(); - typename TImage::RegionType largestPossibleRegion = m_Input->GetLargestPossibleRegion(); - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - { - if (region.GetIndex(a) < largestPossibleRegion.GetIndex(a) + 1) - { - region.SetIndex(a, largestPossibleRegion.GetIndex(a) + 1); - } - if (region.GetIndex(a) + region.GetSize(a) > - largestPossibleRegion.GetIndex(a) + largestPossibleRegion.GetSize(a) - 1) - { - region.SetSize(a, largestPossibleRegion.GetIndex(a) + largestPossibleRegion.GetSize(a) - 1 - region.GetIndex(a)); - } - } + typename TImage::RegionType region = m_Output->GetRequestedRegion(); ImageRegionConstIteratorWithIndex it(m_Input, region); OrientationType orientations = OrientationType(); orientations.Fill(false); - while (!it.IsAtEnd()) + for (; !it.IsAtEnd(); ++it) { typename TImage::IndexType indPrev, indNext; typename const TImage::IndexType ind = it.GetIndex(); @@ -137,8 +128,16 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() indPrev[a]--; indNext = ind; indNext[a]++; - const typename TImage::PixelType prev = m_Input->GetPixel(indPrev); - const typename TImage::PixelType next = m_Input->GetPixel(indNext); + typename TImage::PixelType prev = 0; + if (region.IsInside(indPrev)) + { + prev = m_Input->GetPixel(indPrev); + } + typename TImage::PixelType next = 0; + if (region.IsInside(indNext)) + { + next = m_Input->GetPixel(indNext); + } if (prev == 0 && next == 0) { axis = a; @@ -158,20 +157,6 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } } - ++it; - } - - // widen bounding boxes by 1 - region = m_Output->GetRequestedRegion(); - for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) - { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - { - if (it->second.GetIndex(a) - 1 <= region.GetIndex(a)) - it->second.SetIndex(a, it->second.GetIndex(a) - 1); - if (it->second.GetIndex(a) + it->second.GetSize(a) + 1 <= region.GetIndex(a) + region.GetSize(a)) - it->second.SetSize(a, it->second.GetSize(a) + 1); - } } } @@ -221,13 +206,34 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type m_Binarizer->SetLowerThreshold(label); m_Binarizer->SetUpperThreshold(label); m_Binarizer->SetInput(m_Input); - m_Binarizer->GetOutput()->SetRequestedRegion(region); + // m_Binarizer->GetOutput()->SetRequestedRegion(region); + // m_Binarizer->GetOutput()->Modified(); m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); m_ConnectedComponents->SetFullyConnected(true); + m_ConnectedComponents->GetOutput()->SetRequestedRegion(region); m_ConnectedComponents->Update(); + objectCount = m_ConnectedComponents->GetObjectCount(); return m_ConnectedComponents->GetOutput(); } +template +void +WriteDebug(typename TImage::Pointer out, const char * filename) +{ + typedef ImageFileWriter WriterType; + WriterType::Pointer w = WriterType::New(); + w->SetInput(out); + w->SetFileName(filename); + try + { + w->Update(); + } + catch (itk::ExceptionObject & error) + { + std::cerr << "Error: " << error << std::endl; + } +} + template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, @@ -266,9 +272,9 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ImageRegionIterator itr(eqResult, rr); while (!itr.IsAtEnd()) { - bool eq = (iti.Value() == itj.Value()); // are the pixels equal? + bool eq = (iti.Value() == itj.Value() && iti.Value() != 0); // are the pixels equal and non-zero? itr.Set(eq); - if (eq) + if (eq) // exclude background label { overlaps.insert(iti.Value()); } @@ -277,7 +283,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++itj; ++itr; } - + WriteDebug(eqResult, "C:\\Temp\\eqResult.mha"); // for each label with overlaps determine inter-slice region correspondences for (LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) { @@ -297,7 +303,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int IdentifierType iCount, jCount; typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, *it, iCount); typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, *it, jCount); - + WriteDebug(iconn, "C:\\Temp\\iconn.nrrd"); + WriteDebug(jconn, "C:\\Temp\\jconn.nrrd"); // go through comparison image and create correspondence pairs typedef std::set> PairSet; PairSet pairs; @@ -309,6 +316,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int if (itr.Value()) { pairs.insert(std::make_pair(iti.Value(), itj.Value())); + std::cout << itr.GetIndex() << std::endl; } ++iti; ++itj; @@ -376,7 +384,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int if (iCounts[p->first] == 1) // 1-to-N { - for (PairSet::iterator rest = p; p != pairs.end(); ++p) + for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -406,7 +414,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // 1-to-N else if (jCounts[p->second] == 1) // M-to-1 { - for (PairSet::iterator rest = p; p != pairs.end(); ++p) + for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->second == p->second) { @@ -430,7 +438,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } - --iCounts[rest->first]; + --iCounts[p->first]; jCounts.erase(p->second); pairs.erase(p++); } // M-to-1 @@ -446,7 +454,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int while (p != pairs.end()) { regionIDs.clear(); - for (PairSet::iterator rest = p; p != pairs.end(); ++p) + for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -531,10 +539,12 @@ MorphologicalContourInterpolator::GenerateData() { m_TotalBoundingBox = m_BoundingBoxes.begin()->second; } + typename TImage::SizeType minusOne; + minusOne.Fill(-1); for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) { ExpandRegion(m_TotalBoundingBox, it->second.GetIndex()); - ExpandRegion(m_TotalBoundingBox, it->second.GetIndex() + it->second.GetSize()); + ExpandRegion(m_TotalBoundingBox, it->second.GetIndex() + it->second.GetSize() + minusOne); } if (m_Axis == -1) // interpolate along all axes From 4b58c40f5d2f8d40d1e81363e078263a2d11fdf4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 2 Jun 2015 19:19:49 -0400 Subject: [PATCH 020/176] WIP: region correspondence between slice pairs debugged --- .../itkMorphologicalContourInterpolator.h | 4 ++ .../itkMorphologicalContourInterpolator.hxx | 68 +++++++++++-------- 2 files changed, 43 insertions(+), 29 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index b8e4098ab45..f74fda98fb5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -21,6 +21,7 @@ #include "itkImageToImageFilter.h" #include "itkConnectedComponentImageFilter.h" #include "itkBinaryThresholdImageFilter.h" +#include "itkExtractImageFilter.h" #include "itksys/hash_map.hxx" namespace itk @@ -156,6 +157,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter RoiType; + typename RoiType::Pointer m_RoI; + typedef BinaryThresholdImageFilter BinarizerType; typename BinarizerType::Pointer m_Binarizer; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index e110940cbc4..acaaeef24d4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -22,6 +22,7 @@ #include "itkObjectFactory.h" #include "itkImageRegionIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" +#include "itkImageAlgorithm.h" #include #include @@ -37,9 +38,12 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_Axis(-1) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { + m_RoI = RoiType::New(); m_Binarizer = BinarizerType::New(); + m_Binarizer->SetInput(m_RoI->GetOutput()); m_ConnectedComponents = ConnectedComponentsType::New(); m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); + m_ConnectedComponents->SetFullyConnected(true); } template @@ -75,6 +79,7 @@ MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionTy { if (region.GetIndex(a) > index[a]) { + region.SetSize(a, region.GetSize(a) + region.GetIndex(a) - index[a]); region.SetIndex(a, index[a]); } else if (region.GetIndex(a) + region.GetSize(a) <= index[a]) @@ -203,14 +208,10 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type typename TImage::PixelType label, IdentifierType & objectCount) { + m_RoI->SetExtractionRegion(region); + m_RoI->SetInput(m_Input); m_Binarizer->SetLowerThreshold(label); m_Binarizer->SetUpperThreshold(label); - m_Binarizer->SetInput(m_Input); - // m_Binarizer->GetOutput()->SetRequestedRegion(region); - // m_Binarizer->GetOutput()->Modified(); - m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); - m_ConnectedComponents->SetFullyConnected(true); - m_ConnectedComponents->GetOutput()->SetRequestedRegion(region); m_ConnectedComponents->Update(); objectCount = m_ConnectedComponents->GetObjectCount(); return m_ConnectedComponents->GetOutput(); @@ -283,7 +284,9 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++itj; ++itr; } - WriteDebug(eqResult, "C:\\Temp\\eqResult.mha"); + // typedef unsigned char instead of bool to write it as nrrd + // WriteDebug(eqResult,"C:\\Temp\\eqResult.nrrd"); + // for each label with overlaps determine inter-slice region correspondences for (LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) { @@ -302,21 +305,27 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int // execute connected components IdentifierType iCount, jCount; typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, *it, iCount); + iconn->DisconnectPipeline(); typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, *it, jCount); - WriteDebug(iconn, "C:\\Temp\\iconn.nrrd"); - WriteDebug(jconn, "C:\\Temp\\jconn.nrrd"); + jconn->DisconnectPipeline(); + // WriteDebug(iconn, "C:\\Temp\\iconn.nrrd"); + // WriteDebug(jconn, "C:\\Temp\\jconn.nrrd"); + // go through comparison image and create correspondence pairs typedef std::set> PairSet; PairSet pairs; + itr.SetRegion(rr); itr.GoToBegin(); ImageRegionConstIterator iti(iconn, ri); ImageRegionConstIterator itj(jconn, rj); while (!itr.IsAtEnd()) { - if (itr.Value()) + if (itr.Value() && iti.Value() != 0 && itj.Value() != 0) { pairs.insert(std::make_pair(iti.Value(), itj.Value())); - std::cout << itr.GetIndex() << std::endl; + // std::cout << "itr:" << itr.GetIndex() << + // " iti:" << iti.GetIndex() << iti.Value() << + // " itj:" << itj.GetIndex() << itj.Value() << std::endl; } ++iti; ++itj; @@ -382,24 +391,25 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { regionIDs.clear(); - if (iCounts[p->first] == 1) // 1-to-N + if (iCounts[p->first] == 1) // M-to-1 { for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) { - if (rest->first == p->first) + if (rest->second == p->second) { - regionIDs.push_back(rest->second); + regionIDs.push_back(rest->first); } } - Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); + Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs); PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { - if (rest->first == p->first) + if (rest->second == p->second) { + --iCounts[rest->first]; --jCounts[rest->second]; pairs.erase(rest++); } @@ -408,29 +418,28 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } - --jCounts[p->second]; - iCounts.erase(p->first); pairs.erase(p++); - } // 1-to-N - else if (jCounts[p->second] == 1) // M-to-1 + } // M-to-1 + else if (jCounts[p->second] == 1) // 1-to-N { for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) { - if (rest->second == p->second) + if (rest->first == p->first) { - regionIDs.push_back(rest->first); + regionIDs.push_back(rest->second); } } - Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs); + Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { - if (rest->second == p->second) + if (rest->first == p->first) { --iCounts[rest->first]; + --jCounts[rest->second]; pairs.erase(rest++); } else @@ -438,10 +447,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } - --iCounts[p->first]; - jCounts.erase(p->second); pairs.erase(p++); - } // M-to-1 + } // 1-to-N else { ++p; @@ -523,8 +530,11 @@ MorphologicalContourInterpolator::GenerateData() this->AllocateOutputs(); m_Output = TImage::New(); m_Output->Graft(this->GetOutput()); - m_Output->FillBuffer(0); // clear the image now, because interpolation is optimized using bounding boxes - // alternatively, we could have copied the input image into output + // m_Output->FillBuffer(0); //clear the image now, because interpolation is optimized using bounding boxes + ImageAlgorithm::Copy(m_Input.GetPointer(), + m_Output.GetPointer(), + this->GetOutput()->GetRequestedRegion(), + this->GetOutput()->GetRequestedRegion()); this->DetermineSliceOrientations(); From bb7aa65b98c10dc8daf17a58285737e64077b36e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 3 Jun 2015 18:07:00 -0400 Subject: [PATCH 021/176] WIP: started implementing alignment --- .../itkMorphologicalContourInterpolator.h | 59 +++++++--- .../itkMorphologicalContourInterpolator.hxx | 109 ++++++++++++++---- 2 files changed, 134 insertions(+), 34 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index f74fda98fb5..42cc036642c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -56,6 +56,19 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; void - Interpolate1toN(int axis, - typename TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename TImage::Pointer iConn, - typename TImage::PixelType iRegion, - typename TImage::Pointer jConn, - std::vector jRegions); + Interpolate1toN(int axis, + typename TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds); + + /** How much j needs to be translated to best align with i */ + typename TImage::IndexType + Align(int axis, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds); typedef itk::FixedArray OrientationType; typedef itksys::hash_map OrientationsType; OrientationsType m_Orientations; typedef itksys::hash_map BoundingBoxesType; - BoundingBoxesType m_BoundingBoxes; + BoundingBoxesType m_BoundingBoxes; // bounding box for each label + + // calculate bounding box for each region (connected component) + BoundingBoxesType & + CalculateBoundingBoxes(typename TImage::Pointer image, const PixelList & regions); + + typename TImage::RegionType + MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes); // each label gets a set of slices in which it is present typedef std::set SliceSetType; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index acaaeef24d4..25c48ffb36e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -36,6 +36,7 @@ template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) , m_Axis(-1) + , m_HeuristicAlignment(true) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { m_RoI = RoiType::New(); @@ -173,7 +174,7 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename TImage::Pointer iConn, - typename TImage::PixelType iRegion) + typename TImage::PixelType iRegionId) {} template @@ -184,24 +185,97 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename TImage::Pointer iConn, - typename TImage::PixelType iRegion, + typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, - typename TImage::PixelType jRegion) + typename TImage::PixelType jRegionId) {} template void -MorphologicalContourInterpolator::Interpolate1toN(int axis, - typename TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename TImage::Pointer iConn, - typename TImage::PixelType iRegion, - typename TImage::Pointer jConn, - std::vector jRegions) +MorphologicalContourInterpolator::Interpolate1toN(int axis, + typename TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds) {} +template +typename MorphologicalContourInterpolator::BoundingBoxesType & +MorphologicalContourInterpolator::CalculateBoundingBoxes(typename TImage::Pointer image, + const PixelList & regions) +{ + BoundingBoxesType bb; // result + typename TImage::RegionType zeroRegion; + zeroRegion.GetIndex().Fill(0); + zeroRegion.GetSize().Fill(0); + for (int i = 0; i < regions.size(); i++) + { + bb[regions[i]] = zeroRegion; + } + + ImageRegionConstIteratorWithIndex it(image, image->GetLargestPossibleRegion()); + for (; !it.IsAtEnd(); ++it) + { + typename const TImage::IndexType ind = it.GetIndex(); + typename const TImage::PixelType val = it.Value(); + if (val == 0) + { + continue; // next pixel + } + BoundingBoxesType::iterator bbi = bb.find(val); + if (bbi == bb.end() || bbi->second == zeroRegion) + { + continue; // next pixel + } + ExpandRegion(bbi->second, ind); + } + return bb; +} + +template +typename TImage::RegionType +MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) +{ + BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); + typename TImage::RegionType result = it->second; + typename TImage::SizeType minusOne; + minusOne.Fill(-1); + for (++it; it != m_BoundingBoxes.end(); ++it) + { + ExpandRegion(result, it->second.GetIndex()); + ExpandRegion(result, it->second.GetIndex() + it->second.GetSize() + minusOne); + } + return result; +} + +template +typename TImage::IndexType +MorphologicalContourInterpolator::Align(int axis, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds) +{ + PixelList iId(1); + iId[0] = iRegionId; + BoundingBoxesType iBB = CalculateBoundingBoxes(iConn, iId).begin()->second; + BoundingBoxesType jBB = MergeBoundingBoxes(CalculateBoundingBoxes(iConn, jRegionIds)); + if (m_HeuristicAlignment) + { + // TODO: implement + } + else // optimal alignment + { + // maximum bounding box intersection + } +} + template typename TImage::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, @@ -384,7 +458,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - std::vector regionIDs(pairs.size()); // preallocate + PixelList regionIDs(pairs.size()); // preallocate // now do 1-to-N and M-to-1 cases p = pairs.begin(); while (p != pairs.end()) @@ -547,14 +621,7 @@ MorphologicalContourInterpolator::GenerateData() } else { - m_TotalBoundingBox = m_BoundingBoxes.begin()->second; - } - typename TImage::SizeType minusOne; - minusOne.Fill(-1); - for (BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); it != m_BoundingBoxes.end(); ++it) - { - ExpandRegion(m_TotalBoundingBox, it->second.GetIndex()); - ExpandRegion(m_TotalBoundingBox, it->second.GetIndex() + it->second.GetSize() + minusOne); + m_TotalBoundingBox = MergeBoundingBoxes(m_BoundingBoxes); } if (m_Axis == -1) // interpolate along all axes From 5ef7db5494243279ded1bd6da40847b5827ccdda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 4 Jan 2016 10:13:09 -0500 Subject: [PATCH 022/176] ENH: Uncompressed versions of input test images --- .../MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 | 1 + .../test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 | 2 +- .../test/Input/DoubleTwoLabelBranching.nrrd.md5 | 2 +- .../test/Input/FullEndSevenLabels.nrrd.md5 | 2 +- .../test/Input/ManyToMany.nrrd.md5 | 2 +- .../test/Input/Micro1.nrrd.md5 | 1 + .../test/Input/OneToOne.nrrd.md5 | 2 +- .../test/Input/OneToThree.nrrd.md5 | 2 +- .../test/Input/SimplestOneToOne.nrrd.md5 | 2 +- .../test/Input/ThreeAxisFourLabelConflict.nrrd.md5 | 2 +- .../test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 | 2 +- 11 files changed, 11 insertions(+), 9 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 new file mode 100644 index 00000000000..8fb6c8717be --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 @@ -0,0 +1 @@ +a80c447f5f21bf1e6cb0e8dabbddc920 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 index 4b5db425c69..bb9c43220e6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 @@ -1 +1 @@ -3e882071b670d2bc03d63e4d4df93c77 +d5fb09ab2a91f333668412f16eeade4f diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 index b96b40d8141..de8c21c4ba5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/DoubleTwoLabelBranching.nrrd.md5 @@ -1 +1 @@ -629b00e719241a15319dca2d5004031e +d9735eb87035d8fb268fa3020f81f49d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 index 2023162395e..836713e411f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 @@ -1 +1 @@ -f01238f9cdd1ffab31c8cee126d744b1 +33e77f5b50b971c37ba824546728cea6 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 index 7f212de66bf..a2523936c5b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany.nrrd.md5 @@ -1 +1 @@ -691b157a661d88396db1823cc3a9c246 +d02dfbfcb2926db25c998e65d6fdecf8 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 new file mode 100644 index 00000000000..dfd1be85dac --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 @@ -0,0 +1 @@ +9e0077c2d5a59c9e6aa289f608ad2d92 \ No newline at end of file diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 index b9e427d0579..21bdf8622ae 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToOne.nrrd.md5 @@ -1 +1 @@ -53f8156569a78a40f022dda525f31f1d +3920751d680c921b52cbc56384ef7350 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 index 8841d9cf868..99a7576a0b3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/OneToThree.nrrd.md5 @@ -1 +1 @@ -ec6f4f8e620dc7ad681c6c39443b28d4 +ea6f8e998124c89a0f0b3be77e31378d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 index cea2a905518..9e2a91c4275 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SimplestOneToOne.nrrd.md5 @@ -1 +1 @@ -d1dddb01e4c8e018321a657ee8534ee4 +911c75e989f9a8d05e564969b3835991 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 index 46676f79f53..adec0f7f0b5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ThreeAxisFourLabelConflict.nrrd.md5 @@ -1 +1 @@ -3328494192eeb9ea192d2100fe9bde45 +0a7148f795171af3153ef09ad400e0cd diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 index 49259a8a2ed..e4441030531 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 @@ -1 +1 @@ -84436d25bca2e41381e09a7eda31c731 +8190190d9740735126d7e4320928a24e From bd916a8732574cca051f2918c6bc9ee86d088621 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 8 Jan 2016 18:01:55 -0500 Subject: [PATCH 023/176] ENH: Implemented alignment --- .../itkMorphologicalContourInterpolator.h | 30 ++- .../itkMorphologicalContourInterpolator.hxx | 200 ++++++++++++++++-- 2 files changed, 203 insertions(+), 27 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 42cc036642c..2584b3a3f3a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -143,15 +143,29 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; typedef itksys::hash_map OrientationsType; @@ -160,7 +174,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label - // calculate bounding box for each region (connected component) + // calculate bounding box for each region (connected component) //not used?! BoundingBoxesType & CalculateBoundingBoxes(typename TImage::Pointer image, const PixelList & regions); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 25c48ffb36e..129a39cc2f8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -25,10 +25,10 @@ #include "itkImageAlgorithm.h" #include #include +#include // DEBUG #include -#include "itkImageFileWriter.h" namespace itk { @@ -188,7 +188,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, typename TImage::PixelType jRegionId) -{} +{ + PixelList jRegionIds; + jRegionIds.push_back(jRegionId); + Align(axis, iConn, iRegionId, jConn, jRegionIds); +} template void @@ -201,8 +205,12 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, PixelList jRegionIds) -{} +{ + Align(axis, iConn, iRegionId, jConn, jRegionIds); +} + +// not used? delete template typename MorphologicalContourInterpolator::BoundingBoxesType & MorphologicalContourInterpolator::CalculateBoundingBoxes(typename TImage::Pointer image, @@ -252,28 +260,182 @@ MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxes return result; } +template +IdentifierType +MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds, + typename TImage::IndexType translation) +{ + typename TImage::RegionType iRegion, jRegion; + typename TImage::IndexType iBegin = iConn->GetLargestPossibleRegion().GetIndex(); + typename TImage::IndexType jBegin = jConn->GetLargestPossibleRegion().GetIndex(); + for (IdentifierType d = 0; d < TImage::ImageDimension; d++) + { + IdentifierType iSize = iConn->GetLargestPossibleRegion().GetSize(d); + IdentifierType jSize = jConn->GetLargestPossibleRegion().GetSize(d); + IndexValueType t = translation[d]; + if (t >= 0) + { + iRegion.SetSize(d, std::min(iSize - t, jSize)); + iRegion.SetIndex(d, iBegin[d] + t); + jRegion.SetIndex(d, jBegin[d]); + } + else + { + iRegion.SetSize(d, std::min(iSize, jSize + t)); + iRegion.SetIndex(d, iBegin[d]); + jRegion.SetIndex(d, jBegin[d] - t); + } + } + jRegion.SetSize(iRegion.GetSize()); // size is the same + + IdentifierType count = 0; + ImageRegionConstIterator iIt(iConn, iRegion); + ImageRegionConstIterator jIt(jConn, jRegion); + while (!iIt.IsAtEnd()) + { + if (iIt.Get() == iRegionId) + { + typename TImage::PixelType jVal = jIt.Get(); + PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + if (res != jRegionIds.end()) + { + count++; + } + } + ++iIt; + ++jIt; + } + return count; +} + +// unused +template +IdentifierType +MorphologicalContourInterpolator::Distance2(typename TImage::IndexType t1, typename TImage::IndexType t2) +{ + IdentifierType dist = 0; + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + dist += (t1[d] - t2[d]) * (t1[d] - t2[d]); + } + return dist; +} + template typename TImage::IndexType -MorphologicalContourInterpolator::Align(int axis, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename TImage::Pointer iConn, - typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, - PixelList jRegionIds) +MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn, PixelList regionIds) { - PixelList iId(1); - iId[0] = iRegionId; - BoundingBoxesType iBB = CalculateBoundingBoxes(iConn, iId).begin()->second; - BoundingBoxesType jBB = MergeBoundingBoxes(CalculateBoundingBoxes(iConn, jRegionIds)); - if (m_HeuristicAlignment) + ImageRegionConstIteratorWithIndex it(conn, conn->GetLargestPossibleRegion()); + IndexValueType ind[TImage::ImageDimension] = { 0 }; // all components are initialized to zero + IdentifierType pixelCount = 0; + while (!it.IsAtEnd()) { - // TODO: implement + typename TImage::PixelType val = it.Get(); + PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); + if (res != regionIds.end()) + { + ++pixelCount; + typename TImage::IndexType pInd = it.GetIndex(); + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + ind[d] += pInd[d]; + } + } + ++it; } - else // optimal alignment + typename TImage::IndexType retVal; + for (unsigned d = 0; d < TImage::ImageDimension; d++) { - // maximum bounding box intersection + retVal[d] = ind[d] / pixelCount; + } + return retVal; +} + +template +typename TImage::IndexType +MorphologicalContourInterpolator::Align(int axis, + typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds) +{ + // calculate centroids + PixelList iRegionIds; + iRegionIds.push_back(iRegionId); + typename TImage::IndexType iCentroid = Centroid(iConn, iRegionIds); + typename TImage::IndexType jCentroid = Centroid(jConn, jRegionIds); + + typename TImage::IndexType ind, centroidInd; + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + ind[d] = iCentroid[d] - jCentroid[d]; + } + ind[axis] = 0; // i and j have different coordinate along this axis + centroidInd = ind; + + // construct an image with all possible translations + typename TImage::RegionType searchRegion; + typename TImage::RegionType iLPR = iConn->GetLargestPossibleRegion(); + typename TImage::RegionType jLPR = jConn->GetLargestPossibleRegion(); + for (IdentifierType d = 0; d < TImage::ImageDimension; d++) + { + searchRegion.SetIndex(d, iLPR.GetIndex()[d] - jLPR.GetIndex()[d] - jLPR.GetSize(d) + 1); + searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 2); + } + searchRegion.SetSize(axis, 1); + searchRegion.SetIndex(axis, 0); + typedef Image BitmapType; + BitmapType::Pointer searched = BitmapType::New(); + searched->SetRegions(searchRegion); + searched->Allocate(true); // initialize to zero (false) + + // breadth first search starting from centroid + std::queue uncomputed; + uncomputed.push(ind); + searched->SetPixel(ind, true); + IdentifierType score, maxScore = 0; + typename TImage::IndexType bestIndex; + + while (!uncomputed.empty()) + { + ind = uncomputed.front(); + uncomputed.pop(); + score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); + if (score > maxScore) + { + maxScore = score; + bestIndex = ind; + } + + // we breadth this search + if (!m_HeuristicAlignment || maxScore == 0 || score > maxScore / 2) + { + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + if (d == axis) + { + continue; // do not waste time on additional checks + } + ind[d] -= 1; //"left" + if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) + { + uncomputed.push(ind); + searched->SetPixel(ind, true); + } + ind[d] += 2; //"right" + if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) + { + uncomputed.push(ind); + searched->SetPixel(ind, true); + } + ind[d] -= 1; // return to initial + } + } } + return bestIndex; } template @@ -604,7 +766,7 @@ MorphologicalContourInterpolator::GenerateData() this->AllocateOutputs(); m_Output = TImage::New(); m_Output->Graft(this->GetOutput()); - // m_Output->FillBuffer(0); //clear the image now, because interpolation is optimized using bounding boxes + // copy the input now, because interpolation is optimized using bounding boxes ImageAlgorithm::Copy(m_Input.GetPointer(), m_Output.GetPointer(), this->GetOutput()->GetRequestedRegion(), From 6e9f5e5a1d5e69f23c6996a0fdf04123026777e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 11 Jan 2016 15:26:49 -0500 Subject: [PATCH 024/176] ENH: Deferred extrapolation to 1to1, added a test for it --- .../itkMorphologicalContourInterpolator.h | 6 +- .../itkMorphologicalContourInterpolator.hxx | 119 ++++++++++++------ .../test/CMakeLists.txt | 1 + .../Input/ExtrapolationAppearing.nrrd.md5 | 1 + .../test/Input/Midas3folder.url | 5 + 5 files changed, 95 insertions(+), 37 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/ExtrapolationAppearing.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 2584b3a3f3a..f29a4f7a134 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -128,7 +128,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; @@ -141,7 +142,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter + namespace itk { +template +void +WriteDebug(typename TImage::Pointer out, const char * filename) +{ + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer w = WriterType::New(); + w->SetInput(out); + w->SetFileName(filename); + try + { + w->Update(); + } + catch (itk::ExceptionObject & error) + { + std::cerr << "Error: " << error << std::endl; + } +} + template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) @@ -175,7 +194,44 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::IndexValueType j, typename TImage::Pointer iConn, typename TImage::PixelType iRegionId) -{} +{ + ; + // create a phantom small slice + typename TImage::Pointer phSlice = TImage::New(); + typename TImage::RegionType reg3; + typename TImage::SizeType size; + size.Fill(3); + size[axis] = 1; + reg3.SetSize(size); + reg3.SetIndex(iConn->GetLargestPossibleRegion().GetIndex()); + phSlice->CopyInformation(iConn); + phSlice->SetRegions(reg3); + phSlice->Allocate(true); + + // add a phantom point to a newly constructed slice + typename TImage::IndexType phIndex; + phIndex.Fill(1); + phIndex[axis] = 0; + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + phIndex[d] += reg3.GetIndex(d); + } + phSlice->SetPixel(phIndex, 1); + + // move the constructed image to centroid and interpolate that 1-to-1 + PixelList jRegionIds; + jRegionIds.push_back(1); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(phSlice, "C:\\phSlice.nrrd"); + typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + reg3.SetIndex(d, reg3.GetIndex(d) + translation[d]); + translation[d] = 0; + } + phSlice->SetRegions(reg3); + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, translation); +} template void @@ -187,11 +243,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::Pointer iConn, typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, - typename TImage::PixelType jRegionId) + typename TImage::PixelType jRegionId, + typename TImage::IndexType translation) { - PixelList jRegionIds; - jRegionIds.push_back(jRegionId); - Align(axis, iConn, iRegionId, jConn, jRegionIds); + ; + // build transition sequence and pick the median } template @@ -204,9 +260,11 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::Pointer iConn, typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, - PixelList jRegionIds) + PixelList jRegionIds, + typename TImage::IndexType translation) { - Align(axis, iConn, iRegionId, jConn, jRegionIds); + ; + // split the bigger region and do N 1-to-1 interpolations } @@ -334,14 +392,17 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn while (!it.IsAtEnd()) { typename TImage::PixelType val = it.Get(); - PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); - if (res != regionIds.end()) + if (val) { - ++pixelCount; - typename TImage::IndexType pInd = it.GetIndex(); - for (unsigned d = 0; d < TImage::ImageDimension; d++) + PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); + if (res != regionIds.end()) { - ind[d] += pInd[d]; + ++pixelCount; + typename TImage::IndexType pInd = it.GetIndex(); + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + ind[d] += pInd[d]; + } } } ++it; @@ -453,24 +514,6 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type return m_ConnectedComponents->GetOutput(); } -template -void -WriteDebug(typename TImage::Pointer out, const char * filename) -{ - typedef ImageFileWriter WriterType; - WriterType::Pointer w = WriterType::New(); - w->SetInput(out); - w->SetFileName(filename); - try - { - w->Update(); - } - catch (itk::ExceptionObject & error) - { - std::cerr << "Error: " << error << std::endl; - } -} - template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, @@ -609,7 +652,10 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (iCounts[p->first] == 1 && jCounts[p->second] == 1) { - Interpolate1to1(axis, out, *it, i, j, iconn, p->first, jconn, p->second); + PixelList regionIDs; + regionIDs.push_back(p->second); + typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + Interpolate1to1(axis, out, *it, i, j, iconn, p->first, jconn, p->second, translation); iCounts.erase(p->first); jCounts.erase(p->second); pairs.erase(p++); @@ -637,7 +683,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs); + typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); + Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs, translation); PairSet::iterator rest = p; ++rest; @@ -666,7 +713,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); + typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); PairSet::iterator rest = p; ++rest; @@ -705,7 +753,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs); + typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); PairSet::iterator rest = p; ++rest; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 555826e504b..ddaa30f924b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -22,6 +22,7 @@ endfunction() justinputtest(SimplestOneToOne nrrd) justinputtest(OneToOne nrrd) justinputtest(OneToThree nrrd) +justinputtest(ExtrapolationAppearing nrrd) justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) justinputtest(ThreeAxisFourLabelConflict nrrd) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ExtrapolationAppearing.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ExtrapolationAppearing.nrrd.md5 new file mode 100644 index 00000000000..4a1c80e8080 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ExtrapolationAppearing.nrrd.md5 @@ -0,0 +1 @@ +a6113ece75690fb35fa3d6cf8a2b4399 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url new file mode 100644 index 00000000000..d83372bdd2c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url @@ -0,0 +1,5 @@ +[{000214A0-0000-0000-C000-000000000046}] +Prop3=19,2 +[InternetShortcut] +URL=http://midas3.kitware.com/midas/folder/12980 +IDList= From 6e80e4ce2b1a9e54dca7c7b389044e8e6b24683b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 11 Jan 2016 16:31:16 -0500 Subject: [PATCH 025/176] STYLE: Cleanup: removing unused methods --- .../itkMorphologicalContourInterpolator.h | 8 ---- .../itkMorphologicalContourInterpolator.hxx | 48 ------------------- 2 files changed, 56 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index f29a4f7a134..8520db3a69a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -145,10 +145,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label - // calculate bounding box for each region (connected component) //not used?! - BoundingBoxesType & - CalculateBoundingBoxes(typename TImage::Pointer image, const PixelList & regions); - typename TImage::RegionType MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index a141e9b9ebe..71f88c57239 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -267,41 +267,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int // split the bigger region and do N 1-to-1 interpolations } - -// not used? delete -template -typename MorphologicalContourInterpolator::BoundingBoxesType & -MorphologicalContourInterpolator::CalculateBoundingBoxes(typename TImage::Pointer image, - const PixelList & regions) -{ - BoundingBoxesType bb; // result - typename TImage::RegionType zeroRegion; - zeroRegion.GetIndex().Fill(0); - zeroRegion.GetSize().Fill(0); - for (int i = 0; i < regions.size(); i++) - { - bb[regions[i]] = zeroRegion; - } - - ImageRegionConstIteratorWithIndex it(image, image->GetLargestPossibleRegion()); - for (; !it.IsAtEnd(); ++it) - { - typename const TImage::IndexType ind = it.GetIndex(); - typename const TImage::PixelType val = it.Value(); - if (val == 0) - { - continue; // next pixel - } - BoundingBoxesType::iterator bbi = bb.find(val); - if (bbi == bb.end() || bbi->second == zeroRegion) - { - continue; // next pixel - } - ExpandRegion(bbi->second, ind); - } - return bb; -} - template typename TImage::RegionType MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) @@ -369,19 +334,6 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer return count; } -// unused -template -IdentifierType -MorphologicalContourInterpolator::Distance2(typename TImage::IndexType t1, typename TImage::IndexType t2) -{ - IdentifierType dist = 0; - for (unsigned d = 0; d < TImage::ImageDimension; d++) - { - dist += (t1[d] - t2[d]) * (t1[d] - t2[d]); - } - return dist; -} - template typename TImage::IndexType MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn, PixelList regionIds) From 2579e236b961c7719e222c336ac5615b18864afa Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 12 Jan 2016 21:51:40 -0500 Subject: [PATCH 026/176] ENH: Add support for building the module externally. --- .../MorphologicalContourInterpolation/CMakeLists.txt | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 29d3da56059..38d0e712b48 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,3 +1,10 @@ +cmake_minimum_required(VERSION 2.8.9) project(MorphologicalContourInterpolation) -itk_module_impl() +if(NOT ITK_SOURCE_DIR) + find_package(ITK 4.9 REQUIRED) + list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) + include(ITKModuleExternal) +else() + itk_module_impl() +endif() From 7ee4c2b58d9ea186cd43167dc41e3e265c469fff Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 12 Jan 2016 22:27:41 -0500 Subject: [PATCH 027/176] COMP: Remove unneeded typename. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Addresses: /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h:83:44: error: expected nested-name-specifier before ‘TImage’ void InterpolateAlong(int axis, typename TImage *out); --- .../include/itkMorphologicalContourInterpolator.h | 2 +- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 8520db3a69a..6e1d6f125cc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -107,7 +107,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::DetermineSliceOrientations() for (; !it.IsAtEnd(); ++it) { typename TImage::IndexType indPrev, indNext; - typename const TImage::IndexType ind = it.GetIndex(); - typename const TImage::PixelType val = m_Input->GetPixel(ind); + const typename TImage::IndexType ind = it.GetIndex(); + const typename TImage::PixelType val = m_Input->GetPixel(ind); if (val != 0 || (m_Label != 0 && val == m_Label)) { typename TImage::RegionType boundingBox1; From a40051814350203b035d33947876332efbc405b5 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 12 Jan 2016 22:33:59 -0500 Subject: [PATCH 028/176] COMP: Add missing typename keyword. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Addresses: /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx: In member function ‘void itk::MorphologicalContourInterpolator::DetermineSliceOrientations()’: /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:83:50: error: type/value mismatch at argument 1 in template parameter list for ‘template struct std::pair’ std::pair resBB ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:83:50: error: expected a type, got ‘itk::MorphologicalContourInterpolator::BoundingBoxesType:: iterator’ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:84:9: error: invalid type in declaration before ‘=’ token = m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); Also address bracket style issues. --- .../itkMorphologicalContourInterpolator.h | 23 ++--- .../itkMorphologicalContourInterpolator.hxx | 92 +++++++++++-------- .../itk-module.cmake | 1 + 3 files changed, 67 insertions(+), 49 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 6e1d6f125cc..92f2eadd1ab 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -96,10 +96,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter RoiType; - typename RoiType::Pointer m_RoI; + typedef ExtractImageFilter RoiType; + typename RoiType::Pointer m_RoI; - typedef BinaryThresholdImageFilter BinarizerType; - typename BinarizerType::Pointer m_Binarizer; + typedef BinaryThresholdImageFilter BinarizerType; + typename BinarizerType::Pointer m_Binarizer; - typedef ConnectedComponentImageFilter ConnectedComponentsType; - typename ConnectedComponentsType::Pointer m_ConnectedComponents; + typedef ConnectedComponentImageFilter ConnectedComponentsType; + typename ConnectedComponentsType::Pointer m_ConnectedComponents; private: MorphologicalContourInterpolator(const Self &); // purposely not implemented diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 6abd2de2b06..d2d4bd52279 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -29,6 +29,7 @@ // DEBUG #include +#include "itkImageFileWriter.h" namespace itk @@ -37,8 +38,8 @@ template void WriteDebug(typename TImage::Pointer out, const char * filename) { - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer w = WriterType::New(); + typedef ImageFileWriter WriterType; + typename WriterType::Pointer w = WriterType::New(); w->SetInput(out); w->SetFileName(filename); try @@ -138,15 +139,19 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { boundingBox1.SetSize(a, 1); } - std::pair resBB = m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); + std::pair resBB = + m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); if (!resBB.second) // include this index in existing BB { ExpandRegion(resBB.first->second, ind); } - std::pair res = m_Orientations.insert(std::make_pair(val, orientations)); - OrientationsType::iterator oRef = res.first; - unsigned int cTrue = 0, cAdjacent = 0, axis; + std::pair res = + m_Orientations.insert(std::make_pair(val, orientations)); + typename OrientationsType::iterator oRef = res.first; + unsigned int cTrue = 0; + unsigned int cAdjacent = 0; + unsigned int axis = 0; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { indPrev = ind; @@ -188,7 +193,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() template void MorphologicalContourInterpolator::Extrapolate(int axis, - typename TImage * out, + TImage * out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, @@ -236,7 +241,7 @@ MorphologicalContourInterpolator::Extrapolate(int template void MorphologicalContourInterpolator::Interpolate1to1(int axis, - typename TImage * out, + TImage * out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, @@ -253,7 +258,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int template void MorphologicalContourInterpolator::Interpolate1toN(int axis, - typename TImage * out, + TImage * out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, @@ -271,9 +276,9 @@ template typename TImage::RegionType MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) { - BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); - typename TImage::RegionType result = it->second; - typename TImage::SizeType minusOne; + typename BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); + typename TImage::RegionType result = it->second; + typename TImage::SizeType minusOne; minusOne.Fill(-1); for (++it; it != m_BoundingBoxes.end(); ++it) { @@ -321,8 +326,8 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer { if (iIt.Get() == iRegionId) { - typename TImage::PixelType jVal = jIt.Get(); - PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { count++; @@ -346,7 +351,7 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn typename TImage::PixelType val = it.Get(); if (val) { - PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); + typename PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); if (res != regionIds.end()) { ++pixelCount; @@ -401,7 +406,7 @@ MorphologicalContourInterpolator::Align(int axis, searchRegion.SetSize(axis, 1); searchRegion.SetIndex(axis, 0); typedef Image BitmapType; - BitmapType::Pointer searched = BitmapType::New(); + typename BitmapType::Pointer searched = BitmapType::New(); searched->SetRegions(searchRegion); searched->Allocate(true); // initialize to zero (false) @@ -469,7 +474,7 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, - typename TImage * out, + TImage * out, typename TImage::IndexValueType i, typename TImage::IndexValueType j) { @@ -489,8 +494,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::RegionType rj = ri; rj.SetIndex(axis, j); - BoolImageType::Pointer eqResult = BoolImageType::New(); - typename TImage::RegionType rr = rj; + typename BoolImageType::Pointer eqResult = BoolImageType::New(); + typename TImage::RegionType rr = rj; rr.SetIndex(axis, 0); eqResult->CopyInformation(m_Input); eqResult->SetRegions(rr); @@ -519,7 +524,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int // WriteDebug(eqResult,"C:\\Temp\\eqResult.nrrd"); // for each label with overlaps determine inter-slice region correspondences - for (LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) + for (typename LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) { if (m_Label != 0 && *it != m_Label) continue; // label was specified, and it was not this one, so skip @@ -565,7 +570,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typedef std::map CountMap; CountMap iCounts, jCounts; - PairSet::iterator p; + typename PairSet::iterator p; for (p = pairs.begin(); p != pairs.end(); ++p) { iCounts[p->first]++; @@ -573,7 +578,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // first do extrapolation for components without overlaps - CountMap::iterator iMapIt = iCounts.begin(); + typename CountMap::iterator iMapIt = iCounts.begin(); for (IdentifierType ic = 1; ic <= iCount; ++ic) // component labels { if (iMapIt == iCounts.end() || ic < iMapIt->first) @@ -585,7 +590,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++iMapIt; } } - CountMap::iterator jMapIt = jCounts.begin(); + typename CountMap::iterator jMapIt = jCounts.begin(); for (IdentifierType jc = 1; jc <= jCount; ++jc) // component labels { if (jMapIt == jCounts.end() || jc < jMapIt->first) @@ -627,7 +632,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int if (iCounts[p->first] == 1) // M-to-1 { - for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->second == p->second) { @@ -638,7 +643,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs, translation); - PairSet::iterator rest = p; + typename PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { @@ -657,7 +662,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // M-to-1 else if (jCounts[p->second] == 1) // 1-to-N { - for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -668,7 +673,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); - PairSet::iterator rest = p; + typename PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { @@ -697,7 +702,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int while (p != pairs.end()) { regionIDs.clear(); - for (PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -708,7 +713,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); - PairSet::iterator rest = p; + typename PairSet::iterator rest = p; ++rest; while (rest != pairs.end()) { @@ -729,7 +734,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int template void -MorphologicalContourInterpolator::InterpolateAlong(int axis, typename TImage * out) +MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { SliceSetType aggregate; if (m_Label == 0) // all labels @@ -794,19 +799,25 @@ MorphologicalContourInterpolator::GenerateData() if (this->m_Label == 0) { - for (OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) + for (typename OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) + { for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + { aggregate[a] = aggregate[a] || it->second[a]; // any label needs interpolation along this axis + } + } } else + { aggregate = m_Orientations[m_Label]; // we only care about this label + } - std::vector perAxisInterpolates; + std::vector perAxisInterpolates; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (aggregate[a]) { - TImage::Pointer imageA = TImage::New(); + typename TImage::Pointer imageA = TImage::New(); imageA->CopyInformation(m_Output); imageA->SetRegions(m_Output->GetRequestedRegion()); imageA->Allocate(); @@ -831,7 +842,7 @@ MorphologicalContourInterpolator::GenerateData() iterators.push_back(it); } - std::vector values; + std::vector values; values.reserve(perAxisInterpolates.size()); ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); @@ -840,16 +851,22 @@ MorphologicalContourInterpolator::GenerateData() values.clear(); for (int i = 0; i < perAxisInterpolates.size(); ++i) { - TImage::PixelType val = iterators[i].Value(); + typename TImage::PixelType val = iterators[i].Value(); if (val != 0) + { values.push_back(val); + } } if (values.size() == 0) + { it.Set(0); // all were zero + } else if (values.size() == 1) + { it.Set(values[0]); // the only non-zero - else // median + } + else // median { std::nth_element(values.begin(), values.begin() + values.size() / 2, values.end()); it.Set(values[values.size() / 2]); @@ -858,7 +875,9 @@ MorphologicalContourInterpolator::GenerateData() // next pixel ++it; for (int i = 0; i < perAxisInterpolates.size(); ++i) + { ++(iterators[i]); + } } } // interpolate along all axes else // interpolate along the specified axis @@ -870,6 +889,7 @@ MorphologicalContourInterpolator::GenerateData() this->GraftOutput(m_Output); this->m_Output = ITK_NULLPTR; } + } // namespace itk diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index 306a72944a7..6b62d15ca11 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -9,6 +9,7 @@ itk_module( DEPENDS ITKCommon ITKBinaryMathematicalMorphology + ITKIOImageBase # typename TEST_DEPENDS ITKTestKernel EXCLUDE_FROM_DEFAULT From 1ee0be397a44f00d40dcbed01452669287ff4bb9 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 12 Jan 2016 23:32:21 -0500 Subject: [PATCH 029/176] STYLE: Use 'typename' instead of 'class' in template declarations. Per ITK Style guidelines. --- .../itkMorphologicalContourInterpolator.h | 4 +- .../itkMorphologicalContourInterpolator.hxx | 39 +++++++++---------- 2 files changed, 21 insertions(+), 22 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 92f2eadd1ab..5a07a828987 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -26,7 +26,8 @@ namespace itk { -template + +template class MorphologicalContourInterpolator : public ImageToImageFilter { public: @@ -216,5 +217,4 @@ class MorphologicalContourInterpolator : public ImageToImageFilter +template void WriteDebug(typename TImage::Pointer out, const char * filename) { @@ -52,7 +52,7 @@ WriteDebug(typename TImage::Pointer out, const char * filename) } } -template +template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) , m_Axis(-1) @@ -67,14 +67,14 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_ConnectedComponents->SetFullyConnected(true); } -template +template typename MorphologicalContourInterpolator::SliceSetType MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) { return m_LabeledSlices[axis]; } -template +template void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) { @@ -82,7 +82,7 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int ax this->Modified(); } -template +template void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, std::vector indices) @@ -91,7 +91,7 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int this->Modified(); } -template +template void MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionType & region, typename TImage::IndexType index) @@ -111,7 +111,7 @@ MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionTy } } -template +template void MorphologicalContourInterpolator::DetermineSliceOrientations() { @@ -190,7 +190,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } -template +template void MorphologicalContourInterpolator::Extrapolate(int axis, TImage * out, @@ -238,7 +238,7 @@ MorphologicalContourInterpolator::Extrapolate(int Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, translation); } -template +template void MorphologicalContourInterpolator::Interpolate1to1(int axis, TImage * out, @@ -255,7 +255,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int // build transition sequence and pick the median } -template +template void MorphologicalContourInterpolator::Interpolate1toN(int axis, TImage * out, @@ -272,7 +272,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // split the bigger region and do N 1-to-1 interpolations } -template +template typename TImage::RegionType MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) { @@ -288,7 +288,7 @@ MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxes return result; } -template +template IdentifierType MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, typename TImage::PixelType iRegionId, @@ -339,7 +339,7 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer return count; } -template +template typename TImage::IndexType MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn, PixelList regionIds) { @@ -372,7 +372,7 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn return retVal; } -template +template typename TImage::IndexType MorphologicalContourInterpolator::Align(int axis, typename TImage::Pointer iConn, @@ -456,7 +456,7 @@ MorphologicalContourInterpolator::Align(int axis, return bestIndex; } -template +template typename TImage::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, typename TImage::PixelType label, @@ -471,7 +471,7 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type return m_ConnectedComponents->GetOutput(); } -template +template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, TImage * out, @@ -732,7 +732,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // for each label with overlaps } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() -template +template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { @@ -763,7 +763,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } -template +template void MorphologicalContourInterpolator::GenerateData() { @@ -890,7 +890,6 @@ MorphologicalContourInterpolator::GenerateData() this->m_Output = ITK_NULLPTR; } -} // namespace itk - +} // end namespace itk #endif // itkMorphologicalContourInterpolator_hxx From d4d0e2954989d9586cad2784e70024d24abf2ca1 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 12 Jan 2016 23:35:04 -0500 Subject: [PATCH 030/176] STYLE: Use ITK style in method definitions. --- .../itkMorphologicalContourInterpolator.hxx | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index d16b691ee72..2a5a957d1e9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -52,6 +52,7 @@ WriteDebug(typename TImage::Pointer out, const char * filename) } } + template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) @@ -67,6 +68,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_ConnectedComponents->SetFullyConnected(true); } + template typename MorphologicalContourInterpolator::SliceSetType MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) @@ -74,6 +76,7 @@ MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int ax return m_LabeledSlices[axis]; } + template void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) @@ -82,6 +85,7 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int ax this->Modified(); } + template void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, @@ -91,6 +95,7 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int this->Modified(); } + template void MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionType & region, @@ -111,6 +116,7 @@ MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionTy } } + template void MorphologicalContourInterpolator::DetermineSliceOrientations() @@ -190,6 +196,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } + template void MorphologicalContourInterpolator::Extrapolate(int axis, @@ -200,7 +207,6 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::Pointer iConn, typename TImage::PixelType iRegionId) { - ; // create a phantom small slice typename TImage::Pointer phSlice = TImage::New(); typename TImage::RegionType reg3; @@ -238,6 +244,7 @@ MorphologicalContourInterpolator::Extrapolate(int Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, translation); } + template void MorphologicalContourInterpolator::Interpolate1to1(int axis, @@ -255,6 +262,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int // build transition sequence and pick the median } + template void MorphologicalContourInterpolator::Interpolate1toN(int axis, @@ -272,6 +280,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // split the bigger region and do N 1-to-1 interpolations } + template typename TImage::RegionType MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) @@ -288,6 +297,7 @@ MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxes return result; } + template IdentifierType MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, @@ -339,6 +349,7 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer return count; } + template typename TImage::IndexType MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn, PixelList regionIds) @@ -372,6 +383,7 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn return retVal; } + template typename TImage::IndexType MorphologicalContourInterpolator::Align(int axis, @@ -456,6 +468,7 @@ MorphologicalContourInterpolator::Align(int axis, return bestIndex; } + template typename TImage::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, @@ -471,6 +484,7 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type return m_ConnectedComponents->GetOutput(); } + template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, @@ -732,6 +746,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // for each label with overlaps } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() + template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) @@ -763,6 +778,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } + template void MorphologicalContourInterpolator::GenerateData() From 846f75a5e33f3c3849a761d6530c842495de15ef Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 13 Jan 2016 15:52:40 -0500 Subject: [PATCH 031/176] STYLE: Use ITK_DELETE_FUNCTION. --- .../include/itkMorphologicalContourInterpolator.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 5a07a828987..b0eab145df4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -206,9 +206,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Tue, 12 Jan 2016 16:07:07 -0500 Subject: [PATCH 032/176] ENH: Implemented region splitting (converts 1toN into 1to1) --- .../itkMorphologicalContourInterpolator.h | 7 + .../itkMorphologicalContourInterpolator.hxx | 196 ++++++++++++++++-- 2 files changed, 189 insertions(+), 14 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index b0eab145df4..582a3d346c3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -147,6 +147,13 @@ class MorphologicalContourInterpolator : public ImageToImageFilter #include #include @@ -276,8 +280,161 @@ MorphologicalContourInterpolator::Interpolate1toN(int PixelList jRegionIds, typename TImage::IndexType translation) { - ; // split the bigger region and do N 1-to-1 interpolations + typedef itk::Image BoolImageType; + typedef itk::CastImageFilter CastType; + CastType::Pointer caster = CastType::New(); + caster->SetInput(iConn); + caster->Update(); + BoolImageType::Pointer mask = caster->GetOutput(); + + // construct n empty images + std::vector blobs; + for (unsigned i = 0; i < jRegionIds.size(); i++) + { + BoolImageType::Pointer temp = BoolImageType::New(); + temp->CopyInformation(jConn); + temp->SetRegions(jConn->GetLargestPossibleRegion()); + temp->Allocate(true); + blobs.push_back(temp); + } + + + // fill the n images with intersections - these are seeds + typename TImage::RegionType iRegion, jRegion; + iRegion = iConn->GetLargestPossibleRegion(); + jRegion = jConn->GetLargestPossibleRegion(); + IntersectionRegions(translation, iRegion, jRegion); + ImageRegionConstIterator maskIt(mask, iRegion); + ImageRegionConstIteratorWithIndex jIt(jConn, jRegion); + while (!maskIt.IsAtEnd()) + { + if (maskIt.Get()) + { + typename TImage::PixelType jVal = jIt.Get(); + PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + if (res != jRegionIds.end()) + { + blobs[res - jRegionIds.begin()]->SetPixel(jIt.GetIndex(), true); + } + } + ++maskIt; + ++jIt; + } + + // prepare belonging image and dilation filter + typedef itk::Size SizeType; + SizeType size; + size.Fill(1); + size[axis] = 0; + typedef itk::BinaryCrossStructuringElement StructuringElementType; + StructuringElementType structuringElement; + structuringElement.SetRadius(size); + structuringElement.CreateStructuringElement(); + typedef itk::BinaryDilateImageFilter DilateType; + DilateType::Pointer dilate = DilateType::New(); + dilate->SetKernel(structuringElement); + TImage::Pointer belongs = TImage::New(); + belongs->CopyInformation(mask); + belongs->SetRegions(iRegion); + belongs->Allocate(true); // initialize to zero (false) + ImageRegionIterator belongIt(belongs, iRegion); + + bool hollowedMaskEmpty; + do // while hollowed mask is not empty + { + for (unsigned i = 0; i < jRegionIds.size(); i++) + { + dilate->SetInput(blobs[i]); + dilate->Update(); + blobs[i] = dilate->GetOutput(); + blobs[i]->DisconnectPipeline(); + } + + hollowedMaskEmpty = true; + maskIt.GoToBegin(); + jIt.GoToBegin(); + belongIt.GoToBegin(); + while (!maskIt.IsAtEnd()) + { + if (maskIt.Get()) + { + if (!belongIt.Get()) + { + unsigned i = 0; + for (; i < jRegionIds.size(); i++) + { + if (blobs[i]->GetPixel(jIt.GetIndex())) + { + break; + } + } + if (i < jRegionIds.size()) // covered by a blob, hollow it out + { + belongIt.Value() = i + 1; + for (i++; i < jRegionIds.size(); i++) + { + // pixel does not belong to this blob + blobs[i]->SetPixel(jIt.GetIndex(), false); + } + } + else // keep it + { + hollowedMaskEmpty = false; + } + } + else // the pixel already belongs to some blob + { + for (unsigned i = 0; i < jRegionIds.size(); i++) + { + if (belongIt.Get() != i + 1) + { + // pixel does not belong to this blob + blobs[i]->SetPixel(jIt.GetIndex(), false); + } + } + } + } + else // clip blobs by the original mask + { + for (unsigned i = 0; i < jRegionIds.size(); i++) + { + blobs[i]->SetPixel(jIt.GetIndex(), false); + } + } + ++maskIt; + ++jIt; + ++belongIt; + } + } while (!hollowedMaskEmpty); + blobs.clear(); // deallocates the images + + // convert the belongs into n Conn-style images + std::vector conns; + for (unsigned i = 0; i < jRegionIds.size(); i++) + { + TImage::Pointer temp2 = TImage::New(); + temp2->CopyInformation(iConn); + temp2->SetRegions(iConn->GetLargestPossibleRegion()); + temp2->Allocate(true); + conns.push_back(temp2); + } + ImageRegionConstIteratorWithIndex belongIt2(belongs, iRegion); + while (!belongIt2.IsAtEnd()) + { + typename const TImage::PixelType & belong = belongIt2.Value(); + if (belong > 0) + { + conns[belong - 1]->SetPixel(belongIt2.GetIndex(), iRegionId); + } + ++belongIt2; + } + + // make n 1-to-1 interpolations + for (unsigned x = 0; x < jRegionIds.size(); x++) + { + Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation); + } } @@ -299,20 +456,17 @@ MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxes template -IdentifierType -MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, - typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, - PixelList jRegionIds, - typename TImage::IndexType translation) +void +MorphologicalContourInterpolator::IntersectionRegions(typename TImage::IndexType translation, + typename TImage::RegionType & iRegion, + typename TImage::RegionType & jRegion) { - typename TImage::RegionType iRegion, jRegion; - typename TImage::IndexType iBegin = iConn->GetLargestPossibleRegion().GetIndex(); - typename TImage::IndexType jBegin = jConn->GetLargestPossibleRegion().GetIndex(); + typename TImage::IndexType iBegin = iRegion.GetIndex(); + typename TImage::IndexType jBegin = jRegion.GetIndex(); for (IdentifierType d = 0; d < TImage::ImageDimension; d++) { - IdentifierType iSize = iConn->GetLargestPossibleRegion().GetSize(d); - IdentifierType jSize = jConn->GetLargestPossibleRegion().GetSize(d); + IdentifierType iSize = iRegion.GetSize(d); + IdentifierType jSize = jRegion.GetSize(d); IndexValueType t = translation[d]; if (t >= 0) { @@ -328,6 +482,20 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer } } jRegion.SetSize(iRegion.GetSize()); // size is the same +} + +template +IdentifierType +MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, + typename TImage::PixelType iRegionId, + typename TImage::Pointer jConn, + PixelList jRegionIds, + typename TImage::IndexType translation) +{ + typename TImage::RegionType iRegion, jRegion; + iRegion = iConn->GetLargestPossibleRegion(); + jRegion = jConn->GetLargestPossibleRegion(); + IntersectionRegions(translation, iRegion, jRegion); IdentifierType count = 0; ImageRegionConstIterator iIt(iConn, iRegion); @@ -336,8 +504,8 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer { if (iIt.Get() == iRegionId) { - typename TImage::PixelType jVal = jIt.Get(); - typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { count++; From 32fb6a6e4ad06dd9b44147922299a91c1fdde78e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 12 Jan 2016 17:27:36 -0500 Subject: [PATCH 033/176] ENH: 1toN splits regions properly --- .../itkMorphologicalContourInterpolator.hxx | 107 ++++++++++++------ .../test/CMakeLists.txt | 1 + 2 files changed, 71 insertions(+), 37 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 38984a51d13..542fecf3d86 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -56,6 +56,15 @@ WriteDebug(typename TImage::Pointer out, const char * filename) } } +// void WriteDebug(itk::Image::Pointer out, const char *filename) +//{ +// typedef itk::Image BoolImageType; +// typedef itk::Image ucharImageType; +// typedef itk::CastImageFilter CastType; +// CastType::Pointer caster = CastType::New(); +// caster->SetInput(out); +// WriteDebug(caster->GetOutput(), filename); +// } template MorphologicalContourInterpolator::MorphologicalContourInterpolator() @@ -288,25 +297,35 @@ MorphologicalContourInterpolator::Interpolate1toN(int caster->Update(); BoolImageType::Pointer mask = caster->GetOutput(); + typename TImage::RegionType iRegion, jRegion, newjRegion; + iRegion = iConn->GetLargestPossibleRegion(); + jRegion = jConn->GetLargestPossibleRegion(); + newjRegion = jRegion; + newjRegion.SetSize(iRegion.GetSize()); + // construct n empty images std::vector blobs; - for (unsigned i = 0; i < jRegionIds.size(); i++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { BoolImageType::Pointer temp = BoolImageType::New(); temp->CopyInformation(jConn); - temp->SetRegions(jConn->GetLargestPossibleRegion()); + temp->SetRegions(iRegion); temp->Allocate(true); blobs.push_back(temp); } - // fill the n images with intersections - these are seeds - typename TImage::RegionType iRegion, jRegion; - iRegion = iConn->GetLargestPossibleRegion(); - jRegion = jConn->GetLargestPossibleRegion(); + TImage::Pointer belongs = TImage::New(); + belongs->CopyInformation(mask); + belongs->SetRegions(iRegion); + belongs->Allocate(true); // initialize to zero (false) + ImageRegionIterator belongIt(belongs, iRegion); IntersectionRegions(translation, iRegion, jRegion); ImageRegionConstIterator maskIt(mask, iRegion); ImageRegionConstIteratorWithIndex jIt(jConn, jRegion); + ImageRegionIterator belongInit(belongs, iRegion); + + // convert jConn into n blobs, translating them into the index space of iConn while (!maskIt.IsAtEnd()) { if (maskIt.Get()) @@ -315,16 +334,27 @@ MorphologicalContourInterpolator::Interpolate1toN(int PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { - blobs[res - jRegionIds.begin()]->SetPixel(jIt.GetIndex(), true); + blobs[res - jRegionIds.begin()]->SetPixel(maskIt.GetIndex(), true); + belongInit.Value() = res - jRegionIds.begin() + 1; } } ++maskIt; ++jIt; + ++belongInit; } + // WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare belonging image and dilation filter - typedef itk::Size SizeType; - SizeType size; + iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image + for (unsigned x = 0; x < jRegionIds.size(); x++) + { + blobs[x]->SetRegions(iRegion); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + } + ImageRegionConstIterator maskIt2(mask, iRegion); + ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); + typedef itk::Size SizeType; + SizeType size; size.Fill(1); size[axis] = 0; typedef itk::BinaryCrossStructuringElement StructuringElementType; @@ -334,48 +364,50 @@ MorphologicalContourInterpolator::Interpolate1toN(int typedef itk::BinaryDilateImageFilter DilateType; DilateType::Pointer dilate = DilateType::New(); dilate->SetKernel(structuringElement); - TImage::Pointer belongs = TImage::New(); - belongs->CopyInformation(mask); - belongs->SetRegions(iRegion); - belongs->Allocate(true); // initialize to zero (false) - ImageRegionIterator belongIt(belongs, iRegion); + typedef itk::AndImageFilter AndType; + AndType::Pointer and = AndType::New(); + and->SetInput(0, mask); bool hollowedMaskEmpty; do // while hollowed mask is not empty { - for (unsigned i = 0; i < jRegionIds.size(); i++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { - dilate->SetInput(blobs[i]); + dilate->SetInput(blobs[x]); + and->SetInput(1, dilate->GetOutput()); + // and->Update(); + // blobs[x] = and->GetOutput(); dilate->Update(); - blobs[i] = dilate->GetOutput(); - blobs[i]->DisconnectPipeline(); + blobs[x] = dilate->GetOutput(); + blobs[x]->DisconnectPipeline(); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } hollowedMaskEmpty = true; - maskIt.GoToBegin(); - jIt.GoToBegin(); + maskIt2.GoToBegin(); + jIt2.GoToBegin(); belongIt.GoToBegin(); - while (!maskIt.IsAtEnd()) + while (!maskIt2.IsAtEnd()) { - if (maskIt.Get()) + if (maskIt2.Get()) { if (!belongIt.Get()) { - unsigned i = 0; - for (; i < jRegionIds.size(); i++) + unsigned x = 0; + for (; x < jRegionIds.size(); x++) { - if (blobs[i]->GetPixel(jIt.GetIndex())) + if (blobs[x]->GetPixel(jIt2.GetIndex())) { break; } } - if (i < jRegionIds.size()) // covered by a blob, hollow it out + if (x < jRegionIds.size()) // covered by a blob, hollow it out { - belongIt.Value() = i + 1; - for (i++; i < jRegionIds.size(); i++) + belongIt.Value() = x + 1; + for (x++; x < jRegionIds.size(); x++) { // pixel does not belong to this blob - blobs[i]->SetPixel(jIt.GetIndex(), false); + blobs[x]->SetPixel(jIt2.GetIndex(), false); } } else // keep it @@ -385,33 +417,34 @@ MorphologicalContourInterpolator::Interpolate1toN(int } else // the pixel already belongs to some blob { - for (unsigned i = 0; i < jRegionIds.size(); i++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { - if (belongIt.Get() != i + 1) + if (belongIt.Get() != x + 1) { // pixel does not belong to this blob - blobs[i]->SetPixel(jIt.GetIndex(), false); + blobs[x]->SetPixel(jIt2.GetIndex(), false); } } } } else // clip blobs by the original mask { - for (unsigned i = 0; i < jRegionIds.size(); i++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[i]->SetPixel(jIt.GetIndex(), false); + blobs[x]->SetPixel(jIt2.GetIndex(), false); } } - ++maskIt; - ++jIt; + ++maskIt2; + ++jIt2; ++belongIt; } + // WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images // convert the belongs into n Conn-style images std::vector conns; - for (unsigned i = 0; i < jRegionIds.size(); i++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { TImage::Pointer temp2 = TImage::New(); temp2->CopyInformation(iConn); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index ddaa30f924b..04987fcf8f9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -29,6 +29,7 @@ justinputtest(ThreeAxisFourLabelConflict nrrd) justinputtest(AccidentalMiddleSliceSegmentation nrrd) justinputtest(FullEndSevenLabels nrrd) justinputtest(ManyToMany nrrd) +justinputtest(Micro1 nrrd) # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) From d1935bdb04a7ab0214fba0f1327b275feddcf1c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 13 Jan 2016 18:16:39 -0500 Subject: [PATCH 034/176] BUG: Fixing MtoN infinite loop --- .../itkMorphologicalContourInterpolator.h | 1 + .../itkMorphologicalContourInterpolator.hxx | 60 +++++++++++++------ .../test/Input/Micro1.nrrd.md5 | 2 +- 3 files changed, 44 insertions(+), 19 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 582a3d346c3..cdd6d54c6cb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -131,6 +131,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; + /** Splits the bigger region and does N 1-to-1 interpolations */ void Interpolate1toN(int axis, TImage * out, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 542fecf3d86..d681fca30e3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -26,6 +26,8 @@ #include "itkBinaryDilateImageFilter.h" #include "itkBinaryCrossStructuringElement.h" // #include "itkBinaryBallStructuringElement.h" +#include "itkUnaryFunctorImageFilter.h" +#include "itkAndImageFilter.h" #include "itkCastImageFilter.h" #include #include @@ -289,13 +291,42 @@ MorphologicalContourInterpolator::Interpolate1toN(int PixelList jRegionIds, typename TImage::IndexType translation) { - // split the bigger region and do N 1-to-1 interpolations - typedef itk::Image BoolImageType; - typedef itk::CastImageFilter CastType; - CastType::Pointer caster = CastType::New(); + // first convert iConn into binary mask + class MatchesID + { + typename TImage::PixelType _id; + + public: + MatchesID() {} + MatchesID(typename TImage::PixelType id) + : _id(id) + {} + bool + operator!=(const MatchesID & other) + { + return _id != other._id; + } + bool + operator==(const MatchesID & other) + { + return _id == other._id; + } + inline bool + operator()(const typename TImage::PixelType & val) const + { + return val == _id; + } + } matchesID(iRegionId); + typedef itk::Image BoolImageType; + typedef itk::UnaryFunctorImageFilter CastType; + CastType::Pointer caster = CastType::New(); + caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); BoolImageType::Pointer mask = caster->GetOutput(); + // WriteDebug(mask, "C:\\mask.nrrd"); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -342,9 +373,9 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); - // prepare belonging image and dilation filter + // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image for (unsigned x = 0; x < jRegionIds.size(); x++) { @@ -375,10 +406,10 @@ MorphologicalContourInterpolator::Interpolate1toN(int { dilate->SetInput(blobs[x]); and->SetInput(1, dilate->GetOutput()); - // and->Update(); - // blobs[x] = and->GetOutput(); - dilate->Update(); - blobs[x] = dilate->GetOutput(); + and->Update(); + blobs[x] = and->GetOutput(); + // dilate->Update(); + // blobs[x] = dilate->GetOutput(); blobs[x]->DisconnectPipeline(); // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } @@ -387,7 +418,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int maskIt2.GoToBegin(); jIt2.GoToBegin(); belongIt.GoToBegin(); - while (!maskIt2.IsAtEnd()) + while (!maskIt2.IsAtEnd()) // hollow out the big mask with dilated seeds while avoiding conflicts { if (maskIt2.Get()) { @@ -427,13 +458,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int } } } - else // clip blobs by the original mask - { - for (unsigned x = 0; x < jRegionIds.size(); x++) - { - blobs[x]->SetPixel(jIt2.GetIndex(), false); - } - } ++maskIt2; ++jIt2; ++belongIt; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 index dfd1be85dac..cb30e7742af 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Micro1.nrrd.md5 @@ -1 +1 @@ -9e0077c2d5a59c9e6aa289f608ad2d92 \ No newline at end of file +9e0077c2d5a59c9e6aa289f608ad2d92 From eb32bdc949488d95fffd91f64791237506ec13b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 15 Jan 2016 14:00:44 -0500 Subject: [PATCH 035/176] ENH: Implementing 1to1 --- .../itkMorphologicalContourInterpolator.h | 72 ++- .../itkMorphologicalContourInterpolator.hxx | 529 +++++++++++++----- 2 files changed, 461 insertions(+), 140 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index cdd6d54c6cb..58b8330fbc1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -23,6 +23,12 @@ #include "itkBinaryThresholdImageFilter.h" #include "itkExtractImageFilter.h" #include "itksys/hash_map.hxx" +#include "itkBinaryDilateImageFilter.h" +#include "itkBinaryCrossStructuringElement.h" +// #include "itkBinaryBallStructuringElement.h" +#include "itkAndImageFilter.h" +#include "itkOrImageFilter.h" + namespace itk { @@ -117,6 +123,14 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; + + /** A sequence of conditional dilations starting with begin and reaching end. + begin and end must cover the same region (size and index the same) */ + std::vector + GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end); + + /** Build transition sequence and pick the median */ void Interpolate1to1(int axis, TImage * out, @@ -144,6 +158,21 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; typename TImage::Pointer RegionedConnectedComponents(const typename TImage::RegionType region, typename TImage::PixelType label, IdentifierType & objectCount); + /** seed and mask must cover the same region (size and index the same) */ + typename BoolImageType::Pointer + Dilate1(typename BoolImageType::Pointer seed, typename BoolImageType::Pointer mask); + typedef ExtractImageFilter RoiType; typename RoiType::Pointer m_RoI; @@ -213,6 +245,44 @@ class MorphologicalContourInterpolator : public ImageToImageFilter ConnectedComponentsType; typename ConnectedComponentsType::Pointer m_ConnectedComponents; + typedef itk::BinaryCrossStructuringElement StructuringElementType; + StructuringElementType m_StructuringElement; + + typedef itk::BinaryDilateImageFilter DilateType; + typename DilateType::Pointer m_Dilator; + + typedef itk::AndImageFilter AndFilterType; + typename AndFilterType::Pointer m_And; + + typedef itk::OrImageFilter OrType; + typename OrType::Pointer m_Or; + + class MatchesID + { + typename TImage::PixelType _id; + + public: + MatchesID() {} + MatchesID(typename TImage::PixelType id) + : _id(id) + {} + bool + operator!=(const MatchesID & other) + { + return _id != other._id; + } + bool + operator==(const MatchesID & other) + { + return _id == other._id; + } + inline bool + operator()(const typename TImage::PixelType & val) const + { + return val == _id; + } + }; + private: MorphologicalContourInterpolator(const Self &) ITK_DELETE_FUNCTION; void diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index d681fca30e3..f4e12c8f056 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -23,11 +23,7 @@ #include "itkImageRegionIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" #include "itkImageAlgorithm.h" -#include "itkBinaryDilateImageFilter.h" -#include "itkBinaryCrossStructuringElement.h" -// #include "itkBinaryBallStructuringElement.h" #include "itkUnaryFunctorImageFilter.h" -#include "itkAndImageFilter.h" #include "itkCastImageFilter.h" #include #include @@ -58,15 +54,44 @@ WriteDebug(typename TImage::Pointer out, const char * filename) } } -// void WriteDebug(itk::Image::Pointer out, const char *filename) -//{ -// typedef itk::Image BoolImageType; -// typedef itk::Image ucharImageType; -// typedef itk::CastImageFilter CastType; -// CastType::Pointer caster = CastType::New(); -// caster->SetInput(out); -// WriteDebug(caster->GetOutput(), filename); -// } +void +WriteDebug(itk::Image::Pointer out, const char * filename) +{ + typedef itk::Image BoolImageType; + typedef itk::Image ucharImageType; + typedef itk::CastImageFilter CastType; + CastType::Pointer caster = CastType::New(); + caster->SetInput(out); + WriteDebug(caster->GetOutput(), filename); +} + +template +bool +ImagesEqual(typename TImage::Pointer a, typename TImage::Pointer b) +{ + ImageRegionConstIterator ita(a, a->GetLargestPossibleRegion()); + ImageRegionConstIterator itb(b, b->GetLargestPossibleRegion()); + + while (!ita.IsAtEnd()) + { + if (ita.Get() != itb.Get()) + { + break; + } + ++ita; + ++itb; + } + + if (ita.IsAtEnd()) + { + return true; + } + else + { + return false; + } +} + template MorphologicalContourInterpolator::MorphologicalContourInterpolator() @@ -75,6 +100,11 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_HeuristicAlignment(true) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { + m_Or = OrType::New(); + m_Dilator = DilateType::New(); // structuring element in InterpolateAlong + m_And = AndFilterType::New(); + + // set up pipeline for regioned connected components m_RoI = RoiType::New(); m_Binarizer = BinarizerType::New(); m_Binarizer->SetInput(m_RoI->GetOutput()); @@ -222,44 +252,82 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::Pointer iConn, typename TImage::PixelType iRegionId) { - // create a phantom small slice - typename TImage::Pointer phSlice = TImage::New(); + PixelList jRegionIds; + jRegionIds.push_back(iRegionId); + typename TImage::IndexType centroid = Centroid(iConn, jRegionIds); + centroid[axis] = j; + typename TImage::RegionType reg3; typename TImage::SizeType size; size.Fill(3); size[axis] = 1; reg3.SetSize(size); - reg3.SetIndex(iConn->GetLargestPossibleRegion().GetIndex()); - phSlice->CopyInformation(iConn); - phSlice->SetRegions(reg3); - phSlice->Allocate(true); - // add a phantom point to a newly constructed slice typename TImage::IndexType phIndex; - phIndex.Fill(1); - phIndex[axis] = 0; for (unsigned d = 0; d < TImage::ImageDimension; d++) { - phIndex[d] += reg3.GetIndex(d); + phIndex[d] = centroid.GetIndex()[d] - 1; } - phSlice->SetPixel(phIndex, 1); + phIndex[axis] = j; + reg3.SetIndex(phIndex); - // move the constructed image to centroid and interpolate that 1-to-1 - PixelList jRegionIds; - jRegionIds.push_back(1); + // create a phantom small slice centered around centroid + typename TImage::Pointer phSlice = TImage::New(); + phSlice->CopyInformation(iConn); + phSlice->SetRegions(reg3); + phSlice->Allocate(true); + + // add a phantom point to the center of a newly constructed slice + phSlice->SetPixel(centroid, 1); // WriteDebug(iConn, "C:\\iConn.nrrd"); // WriteDebug(phSlice, "C:\\phSlice.nrrd"); typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); - for (unsigned d = 0; d < TImage::ImageDimension; d++) - { - reg3.SetIndex(d, reg3.GetIndex(d) + translation[d]); - translation[d] = 0; - } - phSlice->SetRegions(reg3); Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, translation); } +template +typename MorphologicalContourInterpolator::BoolImageType::Pointer +MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointer seed, + typename BoolImageType::Pointer mask) +{ + m_Dilator->SetInput(seed); + m_Dilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_Dilator->Update(); + typename BoolImageType::Pointer temp = m_Dilator->GetOutput(); + temp->DisconnectPipeline(); + // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions + m_And->SetInput(0, mask); + m_And->SetInput(1, temp); + m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_And->Update(); + typename BoolImageType::Pointer result = m_And->GetOutput(); + result->DisconnectPipeline(); + WriteDebug(seed, "C:\\seed.nrrd"); + WriteDebug(mask, "C:\\mask.nrrd"); + WriteDebug(temp, "C:\\temp.nrrd"); + WriteDebug(result, "C:\\result.nrrd"); + return result; +} + + +template +std::vector::BoolImageType::Pointer> +MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolImageType::Pointer begin, + typename BoolImageType::Pointer end) +{ + std::vector seq; + seq.push_back(Dilate1(begin, end)); + do + { + seq.back()->DisconnectPipeline(); + seq.push_back(Dilate1(seq.back(), end)); + } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); + seq.pop_back(); // remove duplicate image + return seq; +} + + template void MorphologicalContourInterpolator::Interpolate1to1(int axis, @@ -273,8 +341,154 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::PixelType jRegionId, typename TImage::IndexType translation) { - ; - // build transition sequence and pick the median + // translate iConn by t/2 and jConn by -t/2 + typename TImage::IndexType iTrans; + typename TImage::IndexType jTrans; + typename TImage::RegionType iRegion = iConn->GetLargestPossibleRegion(); + typename TImage::RegionType jRegion = jConn->GetLargestPossibleRegion(); + typename TImage::RegionType newRegion; + // translation[axis] = j - i; + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + iTrans[d] = translation[d] / 2; + jTrans[d] = iTrans[d] - translation[d]; + newRegion.SetIndex(d, (iRegion.GetIndex()[d] + jRegion.GetIndex()[d]) / 2); + newRegion.SetSize(d, std::max(iRegion.GetSize(d), jRegion.GetSize(d))); + } + // newRegion.SetIndex(axis, (i + j) / 2); //redundant + typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); + typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); + WriteDebug(iConnT, "C:\\iConnT.nrrd"); + WriteDebug(jConnT, "C:\\jConnT.nrrd"); + + // convert to binary masks + MatchesID matchesIDi(iRegionId); + MatchesID matchesIDj(jRegionId); + typedef itk::UnaryFunctorImageFilter CastType; + typename CastType::Pointer caster = CastType::New(); + caster->SetFunctor(matchesIDi); + caster->SetInput(iConnT); + caster->Update(); + typename BoolImageType::Pointer iMask = caster->GetOutput(); + iMask->DisconnectPipeline(); + caster->SetFunctor(matchesIDj); + caster->SetInput(jConnT); + caster->Update(); + typename BoolImageType::Pointer jMask = caster->GetOutput(); + jMask->DisconnectPipeline(); + + // generate sequence + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(iMask, "C:\\iMask.nrrd"); + WriteDebug(jMask, "C:\\jMask.nrrd"); + m_And->SetInput(0, iMask); + m_And->SetInput(1, jMask); + m_And->GetOutput()->SetRegions(newRegion); + m_And->Update(); + typename BoolImageType::Pointer intersection = m_And->GetOutput(); + intersection->DisconnectPipeline(); + WriteDebug(intersection, "C:\\intersection.nrrd"); + std::vector iSeq = GenerateDilationSequence(intersection, iMask); + std::vector jSeq = GenerateDilationSequence(intersection, jMask); + unsigned minSeq = std::min(iSeq.size(), jSeq.size()); + unsigned maxSeq = std::max(iSeq.size(), jSeq.size()); + std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection + std::vector seq; + for (unsigned x = 0; x < minSeq; x++) + { + m_Or->SetInput(0, iSeq[x]); + m_Or->SetInput(1, jSeq[x]); + m_Or->GetOutput()->SetRegions(newRegion); + m_Or->Update(); + seq.push_back(m_Or->GetOutput()); + seq.back()->DisconnectPipeline(); + } + if (iSeq.size() < jSeq.size()) + { + for (unsigned x = minSeq; x < maxSeq; x++) + { + seq.push_back(jSeq[x]); + } + } + else + { + for (unsigned x = minSeq; x < maxSeq; x++) + { + seq.push_back(iSeq[x]); + } + } + + // find median + unsigned minIndex; + IdentifierType min = newRegion.GetNumberOfPixels(); + for (unsigned x = 0; x < maxSeq; x++) + { + WriteDebug(seq[x], (std::string("C:\\seq") + char('A' + x) + ".nrrd").c_str()); + IdentifierType iS = CardSymDifference(seq[x], iMask); + IdentifierType jS = CardSymDifference(seq[x], jMask); + IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) + if (xScore < min) + { + min = xScore; + minIndex = x; + } + } + + // finally write it out into the output image pointer + typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); + typename TImage::IndexType t0 = { 0 }; + IntersectionRegions(t0, outRegion, newRegion); + ImageRegionConstIterator seqIt(seq[minIndex], newRegion); + ImageRegionIterator outIt(out, newRegion); + while (!outIt.IsAtEnd()) + { + if (seqIt.Get()) + { + outIt.Set(label); + } + ++outIt; + ++seqIt; + } + + // recurse if needed + typename TImage::IndexValueType mid = (i + j) / 2; + if (abs(i - j) > 2) + { + typename TImage::Pointer midConn = TImage::New(); + midConn->CopyInformation(seq[minIndex]); + midConn->SetRegions(newRegion); + midConn->Allocate(true); + ImageAlgorithm::Copy(out, midConn.GetPointer(), newRegion, newRegion); + WriteDebug(out, "C:\\midConnSource.nrrd"); + WriteDebug(midConn, "C:\\midConn.nrrd"); + // seqIt.GoToBegin(); + // ImageRegionIterator outIt(midConn, newRegion); + // while (!outIt.IsAtEnd()) + // { + // if (seqIt.Get()) + // { + // outIt.Set(label); + // } + // ++outIt; + // ++seqIt; + // } + PixelList regionIDs; + regionIDs.push_back(label); + + if (abs(i - mid) > 1) + { + typename TImage::IndexType tRecurse = Align(axis, iConn, iRegionId, midConn, regionIDs); + // optimization tRecurse=iTrans + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, label, tRecurse); + } + if (abs(j - mid) > 1) + { + typename TImage::IndexType tRecurse = Align(axis, jConn, jRegionId, midConn, regionIDs); + // optimization tRecurse=jTrans + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, label, tRecurse); + } + } } @@ -292,38 +506,14 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::IndexType translation) { // first convert iConn into binary mask - class MatchesID - { - typename TImage::PixelType _id; - - public: - MatchesID() {} - MatchesID(typename TImage::PixelType id) - : _id(id) - {} - bool - operator!=(const MatchesID & other) - { - return _id != other._id; - } - bool - operator==(const MatchesID & other) - { - return _id == other._id; - } - inline bool - operator()(const typename TImage::PixelType & val) const - { - return val == _id; - } - } matchesID(iRegionId); - typedef itk::Image BoolImageType; + MatchesID matchesID(iRegionId); + typedef itk::UnaryFunctorImageFilter CastType; - CastType::Pointer caster = CastType::New(); + typename CastType::Pointer caster = CastType::New(); caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); - BoolImageType::Pointer mask = caster->GetOutput(); + typename BoolImageType::Pointer mask = caster->GetOutput(); // WriteDebug(mask, "C:\\mask.nrrd"); // WriteDebug(iConn, "C:\\iConn.nrrd"); // WriteDebug(jConn, "C:\\jConn.nrrd"); @@ -335,10 +525,10 @@ MorphologicalContourInterpolator::Interpolate1toN(int newjRegion.SetSize(iRegion.GetSize()); // construct n empty images - std::vector blobs; + std::vector blobs; for (unsigned x = 0; x < jRegionIds.size(); x++) { - BoolImageType::Pointer temp = BoolImageType::New(); + typename BoolImageType::Pointer temp = BoolImageType::New(); temp->CopyInformation(jConn); temp->SetRegions(iRegion); temp->Allocate(true); @@ -346,7 +536,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int } // fill the n images with intersections - these are seeds - TImage::Pointer belongs = TImage::New(); + typename TImage::Pointer belongs = TImage::New(); belongs->CopyInformation(mask); belongs->SetRegions(iRegion); belongs->Allocate(true); // initialize to zero (false) @@ -361,12 +551,12 @@ MorphologicalContourInterpolator::Interpolate1toN(int { if (maskIt.Get()) { - typename TImage::PixelType jVal = jIt.Get(); - PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { blobs[res - jRegionIds.begin()]->SetPixel(maskIt.GetIndex(), true); - belongInit.Value() = res - jRegionIds.begin() + 1; + belongInit.Set(res - jRegionIds.begin() + 1); } } ++maskIt; @@ -380,38 +570,20 @@ MorphologicalContourInterpolator::Interpolate1toN(int for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x]->SetRegions(iRegion); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } ImageRegionConstIterator maskIt2(mask, iRegion); ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); - typedef itk::Size SizeType; - SizeType size; - size.Fill(1); - size[axis] = 0; - typedef itk::BinaryCrossStructuringElement StructuringElementType; - StructuringElementType structuringElement; - structuringElement.SetRadius(size); - structuringElement.CreateStructuringElement(); - typedef itk::BinaryDilateImageFilter DilateType; - DilateType::Pointer dilate = DilateType::New(); - dilate->SetKernel(structuringElement); - typedef itk::AndImageFilter AndType; - AndType::Pointer and = AndType::New(); - and->SetInput(0, mask); bool hollowedMaskEmpty; do // while hollowed mask is not empty { for (unsigned x = 0; x < jRegionIds.size(); x++) { - dilate->SetInput(blobs[x]); - and->SetInput(1, dilate->GetOutput()); - and->Update(); - blobs[x] = and->GetOutput(); - // dilate->Update(); - // blobs[x] = dilate->GetOutput(); + blobs[x] = Dilate1(blobs[x], mask); + WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + // TODO: save these in a sequence so we don't have to recalculate it! } hollowedMaskEmpty = true; @@ -434,7 +606,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int } if (x < jRegionIds.size()) // covered by a blob, hollow it out { - belongIt.Value() = x + 1; + belongIt.Set(x + 1); for (x++; x < jRegionIds.size(); x++) { // pixel does not belong to this blob @@ -462,15 +634,15 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images // convert the belongs into n Conn-style images - std::vector conns; + std::vector conns; for (unsigned x = 0; x < jRegionIds.size(); x++) { - TImage::Pointer temp2 = TImage::New(); + typename TImage::Pointer temp2 = TImage::New(); temp2->CopyInformation(iConn); temp2->SetRegions(iConn->GetLargestPossibleRegion()); temp2->Allocate(true); @@ -479,7 +651,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ImageRegionConstIteratorWithIndex belongIt2(belongs, iRegion); while (!belongIt2.IsAtEnd()) { - typename const TImage::PixelType & belong = belongIt2.Value(); + const typename TImage::PixelType belong = belongIt2.Get(); if (belong > 0) { conns[belong - 1]->SetPixel(belongIt2.GetIndex(), iRegionId); @@ -490,7 +662,10 @@ MorphologicalContourInterpolator::Interpolate1toN(int // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { - Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation); + typename TImage::IndexType t0 = { 0 }; + typename TImage::Pointer temp = TranslateImage(conns[x], t0, iRegion); + Interpolate1to1(axis, out, label, i, j, temp, iRegionId, jConn, jRegionIds[x], translation); + // TODO: call sequence construction directly from here! } } @@ -512,6 +687,33 @@ MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxes } +template +typename TImage::Pointer +MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointer image, + typename TImage::IndexType translation, + typename TImage::RegionType newRegion) +{ + // needed? + typename TImage::Pointer result = TImage::New(); + result->CopyInformation(image); + result->SetRegions(newRegion); + result->Allocate(true); // initialize to zero (false) + typename TImage::RegionType inRegion = image->GetLargestPossibleRegion(); + typename TImage::RegionType rRegion = image->GetLargestPossibleRegion(); + IntersectionRegions(translation, inRegion, newRegion); + ImageRegionIterator resultIt(result, newRegion); + ImageRegionConstIterator inIt(image, inRegion); + + while (!resultIt.IsAtEnd()) + { + resultIt.Set(inIt.Get()); + ++resultIt; + ++inIt; + } + return result; +} + + template void MorphologicalContourInterpolator::IntersectionRegions(typename TImage::IndexType translation, @@ -524,23 +726,16 @@ MorphologicalContourInterpolator::IntersectionRegions(typename TImage::I { IdentifierType iSize = iRegion.GetSize(d); IdentifierType jSize = jRegion.GetSize(d); - IndexValueType t = translation[d]; - if (t >= 0) - { - iRegion.SetSize(d, std::min(iSize - t, jSize)); - iRegion.SetIndex(d, iBegin[d] + t); - jRegion.SetIndex(d, jBegin[d]); - } - else - { - iRegion.SetSize(d, std::min(iSize, jSize + t)); - iRegion.SetIndex(d, iBegin[d]); - jRegion.SetIndex(d, jBegin[d] - t); - } + jBegin[d] -= translation[d]; + IndexValueType t = std::max(iBegin[d], jBegin[d]); + iRegion.SetSize(d, std::min(iSize - (t - iBegin[d]), jSize - (t - jBegin[d]))); + iRegion.SetIndex(d, t); + jRegion.SetIndex(d, t + translation[d]); } jRegion.SetSize(iRegion.GetSize()); // size is the same } + template IdentifierType MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, @@ -561,8 +756,8 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer { if (iIt.Get() == iRegionId) { - typename TImage::PixelType jVal = jIt.Get(); - PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { count++; @@ -574,6 +769,27 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer return count; } +template +IdentifierType +MorphologicalContourInterpolator::CardSymDifference( + typename MorphologicalContourInterpolator::BoolImageType::Pointer iShape, + typename MorphologicalContourInterpolator::BoolImageType::Pointer jShape) +{ + typename TImage::RegionType region = iShape->GetLargestPossibleRegion(); + IdentifierType count = 0; + ImageRegionConstIterator iIt(iShape, region); + ImageRegionConstIterator jIt(jShape, region); + while (!iIt.IsAtEnd()) + { + if (iIt.Get() != jIt.Get()) + { + count++; + } + ++iIt; + ++jIt; + } + return count; +} template typename TImage::IndexType @@ -626,9 +842,9 @@ MorphologicalContourInterpolator::Align(int axis, typename TImage::IndexType ind, centroidInd; for (unsigned d = 0; d < TImage::ImageDimension; d++) { - ind[d] = iCentroid[d] - jCentroid[d]; + ind[d] = jCentroid[d] - iCentroid[d]; } - ind[axis] = 0; // i and j have different coordinate along this axis + // ind[axis] = 0; //i and j have different coordinate along this axis centroidInd = ind; // construct an image with all possible translations @@ -637,11 +853,11 @@ MorphologicalContourInterpolator::Align(int axis, typename TImage::RegionType jLPR = jConn->GetLargestPossibleRegion(); for (IdentifierType d = 0; d < TImage::ImageDimension; d++) { - searchRegion.SetIndex(d, iLPR.GetIndex()[d] - jLPR.GetIndex()[d] - jLPR.GetSize(d) + 1); - searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 2); + searchRegion.SetIndex(d, /*jLPR.GetIndex()[d]*/ -iLPR.GetIndex()[d] - jLPR.GetSize(d) + 1); + searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 1); } - searchRegion.SetSize(axis, 1); - searchRegion.SetIndex(axis, 0); + // searchRegion.SetSize(axis, 1); + // searchRegion.SetIndex(axis, 0); typedef Image BitmapType; typename BitmapType::Pointer searched = BitmapType::New(); searched->SetRegions(searchRegion); @@ -690,6 +906,7 @@ MorphologicalContourInterpolator::Align(int axis, } } } + WriteDebug(searched, "C:\\searched.nrrd"); return bestIndex; } @@ -748,11 +965,11 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ImageRegionIterator itr(eqResult, rr); while (!itr.IsAtEnd()) { - bool eq = (iti.Value() == itj.Value() && iti.Value() != 0); // are the pixels equal and non-zero? + bool eq = (iti.Get() == itj.Get() && iti.Get() != 0); // are the pixels equal and non-zero? itr.Set(eq); if (eq) // exclude background label { - overlaps.insert(iti.Value()); + overlaps.insert(iti.Get()); } // next pixel ++iti; @@ -795,12 +1012,12 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ImageRegionConstIterator itj(jconn, rj); while (!itr.IsAtEnd()) { - if (itr.Value() && iti.Value() != 0 && itj.Value() != 0) + if (itr.Get() && iti.Get() != 0 && itj.Get() != 0) { - pairs.insert(std::make_pair(iti.Value(), itj.Value())); + pairs.insert(std::make_pair(iti.Get(), itj.Get())); // std::cout << "itr:" << itr.GetIndex() << - // " iti:" << iti.GetIndex() << iti.Value() << - // " itj:" << itj.GetIndex() << itj.Value() << std::endl; + // " iti:" << iti.GetIndex() << iti.Get() << + // " itj:" << itj.GetIndex() << itj.Get() << std::endl; } ++iti; ++itj; @@ -995,6 +1212,15 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou return; // nothing to do } + // set up structuring element for dilation + typedef itk::Size SizeType; + SizeType size; + size.Fill(1); + size[axis] = 0; + m_StructuringElement.SetRadius(size); + m_StructuringElement.CreateStructuringElement(); + m_Dilator->SetKernel(m_StructuringElement); + typename SliceSetType::iterator it = aggregate.begin(); for (++it; it != aggregate.end(); ++it) { @@ -1004,6 +1230,36 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } +template +void +MorphologicalContourInterpolator::CombineInputAndInterpolate(typename TImage::Pointer interpolate) +{ + ImageRegionIterator itO(m_Output, m_Output->GetBufferedRegion()); + ImageRegionConstIterator itI(m_Input, m_Output->GetBufferedRegion()); + ImageRegionConstIterator it(interpolate, m_Output->GetBufferedRegion()); + while (!it.IsAtEnd()) + { + typename TImage::PixelType val = itI.Get(); + if (val != 0) + { + itO.Set(val); + } + else + { + itO.Set(it.Get()); + } + + ++it; + ++itI; + ++itO; + } + + // put the output data back into the regular pipeline + this->GraftOutput(m_Output); + this->m_Output = ITK_NULLPTR; +} + + template void MorphologicalContourInterpolator::GenerateData() @@ -1013,11 +1269,9 @@ MorphologicalContourInterpolator::GenerateData() this->AllocateOutputs(); m_Output = TImage::New(); m_Output->Graft(this->GetOutput()); - // copy the input now, because interpolation is optimized using bounding boxes - ImageAlgorithm::Copy(m_Input.GetPointer(), - m_Output.GetPointer(), - this->GetOutput()->GetRequestedRegion(), - this->GetOutput()->GetRequestedRegion()); + typename TImage::Pointer tempOut = TImage::New(); + tempOut->CopyInformation(m_Output); + tempOut->SetRegions(m_Output->GetLargestPossibleRegion()); this->DetermineSliceOrientations(); @@ -1069,9 +1323,7 @@ MorphologicalContourInterpolator::GenerateData() if (perAxisInterpolates.size() == 1) { - m_Output = perAxisInterpolates[0]; - this->GraftOutput(m_Output); - this->m_Output = ITK_NULLPTR; + CombineInputAndInterpolate(perAxisInterpolates[0]); return; } // else @@ -1086,13 +1338,14 @@ MorphologicalContourInterpolator::GenerateData() std::vector values; values.reserve(perAxisInterpolates.size()); - ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); + tempOut->Allocate(); + ImageRegionIterator it(tempOut, m_Output->GetRequestedRegion()); while (!it.IsAtEnd()) { values.clear(); for (int i = 0; i < perAxisInterpolates.size(); ++i) { - typename TImage::PixelType val = iterators[i].Value(); + typename TImage::PixelType val = iterators[i].Get(); if (val != 0) { values.push_back(val); @@ -1123,12 +1376,10 @@ MorphologicalContourInterpolator::GenerateData() } // interpolate along all axes else // interpolate along the specified axis { - this->InterpolateAlong(m_Axis, m_Output); + tempOut->Allocate(); + this->InterpolateAlong(m_Axis, tempOut); } - - // put the output data back into the regular pipeline - this->GraftOutput(m_Output); - this->m_Output = ITK_NULLPTR; + CombineInputAndInterpolate(tempOut); } } // end namespace itk From e3cae78b26c31ce7e6e625f68a5104771bb2fa7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 19 Jan 2016 10:56:59 -0500 Subject: [PATCH 036/176] BUG: ironing out the bugs --- .../itkMorphologicalContourInterpolator.hxx | 107 ++++++++++-------- .../test/CMakeLists.txt | 2 +- .../Input/105769fixed_segmentation.nii.gz.md5 | 2 +- ...sliced_to_fixedhz2_segmentation.nii.gz.md5 | 2 +- .../test/Input/64816L_amygdala_fin.nii.gz.md5 | 2 +- .../test/Input/64816L_amygdala_int.nii.gz.md5 | 2 +- .../test/Input/65239R_amygdala_fin.nii.gz.md5 | 2 +- .../test/Input/65239R_amygdala_int.nii.gz.md5 | 2 +- 8 files changed, 66 insertions(+), 55 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index f4e12c8f056..3c7d63783bb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -282,7 +282,18 @@ MorphologicalContourInterpolator::Extrapolate(int // WriteDebug(iConn, "C:\\iConn.nrrd"); // WriteDebug(phSlice, "C:\\phSlice.nrrd"); typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); - Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, translation); + + // now translate the phantom slice for best alignment + for (unsigned d = 0; d < TImage::ImageDimension; d++) + { + phIndex[d] -= translation[d]; + } + phIndex[axis] = j; + reg3.SetIndex(phIndex); + phSlice->SetRegions(reg3); + typename TImage::IndexType t0 = { 0 }; + t0[axis] = j - i; + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, t0); } @@ -303,10 +314,10 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe m_And->Update(); typename BoolImageType::Pointer result = m_And->GetOutput(); result->DisconnectPipeline(); - WriteDebug(seed, "C:\\seed.nrrd"); - WriteDebug(mask, "C:\\mask.nrrd"); - WriteDebug(temp, "C:\\temp.nrrd"); - WriteDebug(result, "C:\\result.nrrd"); + // WriteDebug(seed, "C:\\seed.nrrd"); + // WriteDebug(mask, "C:\\mask.nrrd"); + // WriteDebug(temp, "C:\\temp.nrrd"); + // WriteDebug(result, "C:\\result.nrrd"); return result; } @@ -346,16 +357,21 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::IndexType jTrans; typename TImage::RegionType iRegion = iConn->GetLargestPossibleRegion(); typename TImage::RegionType jRegion = jConn->GetLargestPossibleRegion(); - typename TImage::RegionType newRegion; - // translation[axis] = j - i; + typename TImage::RegionType newRegion = iRegion; + ExpandRegion(newRegion, jRegion.GetIndex()); + typename TImage::IndexType jBottom = jRegion.GetIndex(); + for (unsigned d = 0; d < TImage::ImageDimension; d++) { iTrans[d] = translation[d] / 2; jTrans[d] = iTrans[d] - translation[d]; - newRegion.SetIndex(d, (iRegion.GetIndex()[d] + jRegion.GetIndex()[d]) / 2); - newRegion.SetSize(d, std::max(iRegion.GetSize(d), jRegion.GetSize(d))); + // newRegion.SetIndex(d, (iRegion.GetIndex()[d] + jRegion.GetIndex()[d]) / 2); + // newRegion.SetSize(d, std::max(iRegion.GetSize(d), jRegion.GetSize(d))); + jBottom[d] += jRegion.GetSize(d) - 1; } - // newRegion.SetIndex(axis, (i + j) / 2); //redundant + ExpandRegion(newRegion, jBottom); + newRegion.SetIndex(axis, (i + j) / 2); + newRegion.SetSize(axis, 1); typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); WriteDebug(iConnT, "C:\\iConnT.nrrd"); @@ -378,10 +394,10 @@ MorphologicalContourInterpolator::Interpolate1to1(int jMask->DisconnectPipeline(); // generate sequence - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); - WriteDebug(iMask, "C:\\iMask.nrrd"); - WriteDebug(jMask, "C:\\jMask.nrrd"); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(jConn, "C:\\jConn.nrrd"); + // WriteDebug(iMask, "C:\\iMask.nrrd"); + // WriteDebug(jMask, "C:\\jMask.nrrd"); m_And->SetInput(0, iMask); m_And->SetInput(1, jMask); m_And->GetOutput()->SetRegions(newRegion); @@ -399,6 +415,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int { m_Or->SetInput(0, iSeq[x]); m_Or->SetInput(1, jSeq[x]); + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('A' + x) + ".nrrd").c_str()); + WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('A' + x) + ".nrrd").c_str()); m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); @@ -409,6 +427,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int for (unsigned x = minSeq; x < maxSeq; x++) { seq.push_back(jSeq[x]); + WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('A' + x) + ".nrrd").c_str()); } } else @@ -416,6 +435,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int for (unsigned x = minSeq; x < maxSeq; x++) { seq.push_back(iSeq[x]); + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('A' + x) + ".nrrd").c_str()); } } @@ -462,31 +482,18 @@ MorphologicalContourInterpolator::Interpolate1to1(int ImageAlgorithm::Copy(out, midConn.GetPointer(), newRegion, newRegion); WriteDebug(out, "C:\\midConnSource.nrrd"); WriteDebug(midConn, "C:\\midConn.nrrd"); - // seqIt.GoToBegin(); - // ImageRegionIterator outIt(midConn, newRegion); - // while (!outIt.IsAtEnd()) - // { - // if (seqIt.Get()) - // { - // outIt.Set(label); - // } - // ++outIt; - // ++seqIt; - // } PixelList regionIDs; regionIDs.push_back(label); if (abs(i - mid) > 1) { - typename TImage::IndexType tRecurse = Align(axis, iConn, iRegionId, midConn, regionIDs); - // optimization tRecurse=iTrans - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, label, tRecurse); + // typename TImage::IndexType tRecurse = Align(axis, iConn, iRegionId, midConn, regionIDs); + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, label, iTrans); } if (abs(j - mid) > 1) { - typename TImage::IndexType tRecurse = Align(axis, jConn, jRegionId, midConn, regionIDs); - // optimization tRecurse=jTrans - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, label, tRecurse); + // typename TImage::IndexType tRecurse = Align(axis, jConn, jRegionId, midConn, regionIDs); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, label, jTrans); } } } @@ -662,9 +669,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { - typename TImage::IndexType t0 = { 0 }; - typename TImage::Pointer temp = TranslateImage(conns[x], t0, iRegion); - Interpolate1to1(axis, out, label, i, j, temp, iRegionId, jConn, jRegionIds[x], translation); + Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation); // TODO: call sequence construction directly from here! } } @@ -693,7 +698,6 @@ MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointe typename TImage::IndexType translation, typename TImage::RegionType newRegion) { - // needed? typename TImage::Pointer result = TImage::New(); result->CopyInformation(image); result->SetRegions(newRegion); @@ -724,13 +728,13 @@ MorphologicalContourInterpolator::IntersectionRegions(typename TImage::I typename TImage::IndexType jBegin = jRegion.GetIndex(); for (IdentifierType d = 0; d < TImage::ImageDimension; d++) { - IdentifierType iSize = iRegion.GetSize(d); - IdentifierType jSize = jRegion.GetSize(d); - jBegin[d] -= translation[d]; + IndexValueType iSize = iRegion.GetSize(d); + IndexValueType jSize = jRegion.GetSize(d); + iBegin[d] += translation[d]; IndexValueType t = std::max(iBegin[d], jBegin[d]); - iRegion.SetSize(d, std::min(iSize - (t - iBegin[d]), jSize - (t - jBegin[d]))); - iRegion.SetIndex(d, t); - jRegion.SetIndex(d, t + translation[d]); + iRegion.SetSize(d, std::min(IndexValueType(iSize) - (t - iBegin[d]), IndexValueType(jSize) - (t - jBegin[d]))); + iRegion.SetIndex(d, t - translation[d]); + jRegion.SetIndex(d, t); } jRegion.SetSize(iRegion.GetSize()); // size is the same } @@ -839,13 +843,12 @@ MorphologicalContourInterpolator::Align(int axis, typename TImage::IndexType iCentroid = Centroid(iConn, iRegionIds); typename TImage::IndexType jCentroid = Centroid(jConn, jRegionIds); - typename TImage::IndexType ind, centroidInd; + typename TImage::IndexType ind; for (unsigned d = 0; d < TImage::ImageDimension; d++) { ind[d] = jCentroid[d] - iCentroid[d]; } // ind[axis] = 0; //i and j have different coordinate along this axis - centroidInd = ind; // construct an image with all possible translations typename TImage::RegionType searchRegion; @@ -853,28 +856,35 @@ MorphologicalContourInterpolator::Align(int axis, typename TImage::RegionType jLPR = jConn->GetLargestPossibleRegion(); for (IdentifierType d = 0; d < TImage::ImageDimension; d++) { - searchRegion.SetIndex(d, /*jLPR.GetIndex()[d]*/ -iLPR.GetIndex()[d] - jLPR.GetSize(d) + 1); + searchRegion.SetIndex(d, jLPR.GetIndex()[d] - iLPR.GetIndex()[d] - iLPR.GetSize(d) + 1); searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 1); } // searchRegion.SetSize(axis, 1); // searchRegion.SetIndex(axis, 0); - typedef Image BitmapType; - typename BitmapType::Pointer searched = BitmapType::New(); + + typename BoolImageType::Pointer searched = BoolImageType::New(); searched->SetRegions(searchRegion); searched->Allocate(true); // initialize to zero (false) - // breadth first search starting from centroid + // breadth first search starting from centroid, implicitly: + // when intersection scores are equal, chooses the one closer to centroid std::queue uncomputed; uncomputed.push(ind); searched->SetPixel(ind, true); IdentifierType score, maxScore = 0; typename TImage::IndexType bestIndex; + // debug: construct and later fill the image with intersection scores + typename TImage::Pointer scoreImage = TImage::New(); + scoreImage->SetRegions(searchRegion); + scoreImage->Allocate(true); + while (!uncomputed.empty()) { ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); + scoreImage->SetPixel(ind, score); // debug if (score > maxScore) { maxScore = score; @@ -906,7 +916,8 @@ MorphologicalContourInterpolator::Align(int axis, } } } - WriteDebug(searched, "C:\\searched.nrrd"); + // WriteDebug(searched, "C:\\searched.nrrd"); + WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); return bestIndex; } diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 04987fcf8f9..9c1cdcf9e19 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -19,6 +19,7 @@ function(JustInputTest ImageName Ext) endfunction() # Handcrafted tests +justinputtest(Micro1 nrrd) justinputtest(SimplestOneToOne nrrd) justinputtest(OneToOne nrrd) justinputtest(OneToThree nrrd) @@ -29,7 +30,6 @@ justinputtest(ThreeAxisFourLabelConflict nrrd) justinputtest(AccidentalMiddleSliceSegmentation nrrd) justinputtest(FullEndSevenLabels nrrd) justinputtest(ManyToMany nrrd) -justinputtest(Micro1 nrrd) # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 index d0eb57913c3..55b59bc9e7b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 @@ -1 +1 @@ -6e14975a4c0a37dfd3d7d46fe7cf4586 \ No newline at end of file +6e14975a4c0a37dfd3d7d46fe7cf4586 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 index b50a6e6e084..30f088428cf 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 @@ -1 +1 @@ -176bfd37f8ddbdc197595523693ecc36 \ No newline at end of file +176bfd37f8ddbdc197595523693ecc36 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 index 4e76e1e7adf..30ef48753b3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_fin.nii.gz.md5 @@ -1 +1 @@ -dbddb8dfcae92549da37db88de67d093 \ No newline at end of file +dbddb8dfcae92549da37db88de67d093 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 index 315f54fda70..57b4ad14031 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/64816L_amygdala_int.nii.gz.md5 @@ -1 +1 @@ -5e9167bee632e1fdde568ea659d512cb \ No newline at end of file +5e9167bee632e1fdde568ea659d512cb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 index 36e168a612c..338f3431666 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_fin.nii.gz.md5 @@ -1 +1 @@ -31eef268b01d90f952bb6d2e1541a12c \ No newline at end of file +31eef268b01d90f952bb6d2e1541a12c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 index 4ae7d0034f0..54734c25813 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/65239R_amygdala_int.nii.gz.md5 @@ -1 +1 @@ -c3a5b453f40a69d16042a3ca0b36302e \ No newline at end of file +c3a5b453f40a69d16042a3ca0b36302e From d2b50f1b70542a5f2480cde1b86e42c1f004dcbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 19 Jan 2016 16:17:47 -0500 Subject: [PATCH 037/176] BUG: Doesn't crash any more --- .../itkMorphologicalContourInterpolator.hxx | 66 ++++++++++--------- .../test/Input/ManyToMany16.nrrd.md5 | 1 + 2 files changed, 35 insertions(+), 32 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany16.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 3c7d63783bb..86eb2e5f7c7 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -153,7 +153,7 @@ MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionTy region.SetSize(a, region.GetSize(a) + region.GetIndex(a) - index[a]); region.SetIndex(a, index[a]); } - else if (region.GetIndex(a) + region.GetSize(a) <= index[a]) + else if (region.GetIndex(a) + (typename TImage::IndexValueType)region.GetSize(a) <= index[a]) { region.SetSize(a, index[a] - region.GetIndex(a) + 1); } @@ -279,6 +279,8 @@ MorphologicalContourInterpolator::Extrapolate(int // add a phantom point to the center of a newly constructed slice phSlice->SetPixel(centroid, 1); + jRegionIds.clear(); + jRegionIds.push_back(1); // WriteDebug(iConn, "C:\\iConn.nrrd"); // WriteDebug(phSlice, "C:\\phSlice.nrrd"); typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); @@ -357,21 +359,22 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::IndexType jTrans; typename TImage::RegionType iRegion = iConn->GetLargestPossibleRegion(); typename TImage::RegionType jRegion = jConn->GetLargestPossibleRegion(); - typename TImage::RegionType newRegion = iRegion; - ExpandRegion(newRegion, jRegion.GetIndex()); - typename TImage::IndexType jBottom = jRegion.GetIndex(); + typename TImage::IndexType jBottom = jRegion.GetIndex(); for (unsigned d = 0; d < TImage::ImageDimension; d++) { iTrans[d] = translation[d] / 2; jTrans[d] = iTrans[d] - translation[d]; - // newRegion.SetIndex(d, (iRegion.GetIndex()[d] + jRegion.GetIndex()[d]) / 2); - // newRegion.SetSize(d, std::max(iRegion.GetSize(d), jRegion.GetSize(d))); - jBottom[d] += jRegion.GetSize(d) - 1; + iRegion.SetIndex(d, iRegion.GetIndex()[d] + iTrans[d]); + jRegion.SetIndex(d, jRegion.GetIndex()[d] + jTrans[d]); + jBottom[d] = jRegion.GetIndex()[d] + jRegion.GetSize(d) - 1; } + typename TImage::RegionType newRegion = iRegion; + ExpandRegion(newRegion, jRegion.GetIndex()); ExpandRegion(newRegion, jBottom); - newRegion.SetIndex(axis, (i + j) / 2); - newRegion.SetSize(axis, 1); + + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); WriteDebug(iConnT, "C:\\iConnT.nrrd"); @@ -394,10 +397,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int jMask->DisconnectPipeline(); // generate sequence - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(jConn, "C:\\jConn.nrrd"); - // WriteDebug(iMask, "C:\\iMask.nrrd"); - // WriteDebug(jMask, "C:\\jMask.nrrd"); + WriteDebug(iMask, "C:\\iMask.nrrd"); + WriteDebug(jMask, "C:\\jMask.nrrd"); m_And->SetInput(0, iMask); m_And->SetInput(1, jMask); m_And->GetOutput()->SetRegions(newRegion); @@ -475,27 +476,29 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::IndexValueType mid = (i + j) / 2; if (abs(i - j) > 2) { - typename TImage::Pointer midConn = TImage::New(); - midConn->CopyInformation(seq[minIndex]); - midConn->SetRegions(newRegion); - midConn->Allocate(true); - ImageAlgorithm::Copy(out, midConn.GetPointer(), newRegion, newRegion); - WriteDebug(out, "C:\\midConnSource.nrrd"); + typedef itk::CastImageFilter InvertCastType; + typename InvertCastType::Pointer invCaster = InvertCastType::New(); + invCaster->SetInput(seq[minIndex]); + invCaster->Update(); + typename TImage::Pointer midConn = invCaster->GetOutput(); + // midConn->DisconnectPipeline(); //not needed? + WriteDebug(midConn, "C:\\midConn.nrrd"); PixelList regionIDs; - regionIDs.push_back(label); + regionIDs.push_back(1); if (abs(i - mid) > 1) { // typename TImage::IndexType tRecurse = Align(axis, iConn, iRegionId, midConn, regionIDs); - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, label, iTrans); + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans); } if (abs(j - mid) > 1) { // typename TImage::IndexType tRecurse = Align(axis, jConn, jRegionId, midConn, regionIDs); - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, label, jTrans); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); } } + WriteDebug(out, "C:\\intermediateResult.nrrd"); } @@ -703,17 +706,16 @@ MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointe result->SetRegions(newRegion); result->Allocate(true); // initialize to zero (false) typename TImage::RegionType inRegion = image->GetLargestPossibleRegion(); - typename TImage::RegionType rRegion = image->GetLargestPossibleRegion(); IntersectionRegions(translation, inRegion, newRegion); - ImageRegionIterator resultIt(result, newRegion); - ImageRegionConstIterator inIt(image, inRegion); - - while (!resultIt.IsAtEnd()) - { - resultIt.Set(inIt.Get()); - ++resultIt; - ++inIt; - } + ImageAlgorithm::Copy(image.GetPointer(), result.GetPointer(), inRegion, newRegion); + // ImageRegionIterator resultIt(result, newRegion); + // ImageRegionConstIterator inIt(image, inRegion); + // while (!resultIt.IsAtEnd()) + // { + // resultIt.Set(inIt.Get()); + // ++resultIt; + // ++inIt; + // } return result; } diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany16.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany16.nrrd.md5 new file mode 100644 index 00000000000..3e2293e017e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/ManyToMany16.nrrd.md5 @@ -0,0 +1 @@ +55c1635a7fce5ade730253259a393d7c From 4715d29dddd231ace71b39febf49ae2424cbcb93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 23 Jan 2016 12:10:12 -0500 Subject: [PATCH 038/176] STYLE: code review suggestions --- .../itkMorphologicalContourInterpolator.h | 30 +++++++------- .../itkMorphologicalContourInterpolator.hxx | 39 +++++++++++-------- 2 files changed, 38 insertions(+), 31 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 58b8330fbc1..927a8ffcff2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -123,7 +123,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; + typedef Image BoolImageType; /** A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same) */ @@ -200,7 +200,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; + typedef FixedArray OrientationType; typedef itksys::hash_map OrientationsType; OrientationsType m_Orientations; @@ -245,41 +245,41 @@ class MorphologicalContourInterpolator : public ImageToImageFilter ConnectedComponentsType; typename ConnectedComponentsType::Pointer m_ConnectedComponents; - typedef itk::BinaryCrossStructuringElement StructuringElementType; - StructuringElementType m_StructuringElement; + typedef BinaryCrossStructuringElement StructuringElementType; + StructuringElementType m_StructuringElement; - typedef itk::BinaryDilateImageFilter DilateType; - typename DilateType::Pointer m_Dilator; + typedef BinaryDilateImageFilter DilateType; + typename DilateType::Pointer m_Dilator; - typedef itk::AndImageFilter AndFilterType; - typename AndFilterType::Pointer m_And; + typedef AndImageFilter AndFilterType; + typename AndFilterType::Pointer m_And; - typedef itk::OrImageFilter OrType; - typename OrType::Pointer m_Or; + typedef OrImageFilter OrType; + typename OrType::Pointer m_Or; class MatchesID { - typename TImage::PixelType _id; + typename TImage::PixelType m_ID; public: MatchesID() {} MatchesID(typename TImage::PixelType id) - : _id(id) + : m_ID(id) {} bool operator!=(const MatchesID & other) { - return _id != other._id; + return m_ID != other.m_ID; } bool operator==(const MatchesID & other) { - return _id == other._id; + return m_ID == other.m_ID; } inline bool operator()(const typename TImage::PixelType & val) const { - return val == _id; + return val == m_ID; } }; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 86eb2e5f7c7..44418ac2c8c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -40,6 +40,7 @@ template void WriteDebug(typename TImage::Pointer out, const char * filename) { + // return; //tests run much faster typedef ImageFileWriter WriterType; typename WriterType::Pointer w = WriterType::New(); w->SetInput(out); @@ -48,19 +49,20 @@ WriteDebug(typename TImage::Pointer out, const char * filename) { w->Update(); } - catch (itk::ExceptionObject & error) + catch (ExceptionObject & error) { std::cerr << "Error: " << error << std::endl; } } void -WriteDebug(itk::Image::Pointer out, const char * filename) +WriteDebug(Image::Pointer out, const char * filename) { - typedef itk::Image BoolImageType; - typedef itk::Image ucharImageType; - typedef itk::CastImageFilter CastType; - CastType::Pointer caster = CastType::New(); + // return; //tests run much faster + typedef Image BoolImageType; + typedef Image ucharImageType; + typedef CastImageFilter CastType; + CastType::Pointer caster = CastType::New(); caster->SetInput(out); WriteDebug(caster->GetOutput(), filename); } @@ -329,6 +331,11 @@ std::vector::BoolImageType::Po MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end) { + // typedef Testing::HashImageFilter HashType; + // HashType::Pointer hasher = HashType::New(); + // hasher->SetInPlace(true); + // std::vector hashes; + // TODO: optimization: replace ImagesEqual call with hash comparison? std::vector seq; seq.push_back(Dilate1(begin, end)); do @@ -381,10 +388,10 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(jConnT, "C:\\jConnT.nrrd"); // convert to binary masks - MatchesID matchesIDi(iRegionId); - MatchesID matchesIDj(jRegionId); - typedef itk::UnaryFunctorImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); + MatchesID matchesIDi(iRegionId); + MatchesID matchesIDj(jRegionId); + typedef UnaryFunctorImageFilter CastType; + typename CastType::Pointer caster = CastType::New(); caster->SetFunctor(matchesIDi); caster->SetInput(iConnT); caster->Update(); @@ -476,8 +483,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::IndexValueType mid = (i + j) / 2; if (abs(i - j) > 2) { - typedef itk::CastImageFilter InvertCastType; - typename InvertCastType::Pointer invCaster = InvertCastType::New(); + typedef CastImageFilter InvertCastType; + typename InvertCastType::Pointer invCaster = InvertCastType::New(); invCaster->SetInput(seq[minIndex]); invCaster->Update(); typename TImage::Pointer midConn = invCaster->GetOutput(); @@ -518,8 +525,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int // first convert iConn into binary mask MatchesID matchesID(iRegionId); - typedef itk::UnaryFunctorImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); + typedef UnaryFunctorImageFilter CastType; + typename CastType::Pointer caster = CastType::New(); caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); @@ -1226,8 +1233,8 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } // set up structuring element for dilation - typedef itk::Size SizeType; - SizeType size; + typedef Size SizeType; + SizeType size; size.Fill(1); size[axis] = 0; m_StructuringElement.SetRadius(size); From 90b83be96c0ccb4d93d2f5e8526a48e1d36f0890 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 23 Jan 2016 12:26:35 -0500 Subject: [PATCH 039/176] ENH: easing testing using IDE --- .../test/CMakeLists.txt | 17 ++++++++++++++--- .../test/manualTest.cxx | 15 +++++++++++++++ 2 files changed, 29 insertions(+), 3 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 9c1cdcf9e19..74f60e66a34 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -7,6 +7,16 @@ set( createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") +add_executable( + runFromIDE + manualTest.cxx + ${MorphologicalContourInterpolationTests} +) +target_link_libraries( + runFromIDE + ${MorphologicalContourInterpolation-Test_LIBRARIES} +) + function(JustInputTest ImageName Ext) itk_add_test( NAME itkMorphologicalContourInterpolationTest_${ImageName} @@ -26,10 +36,11 @@ justinputtest(OneToThree nrrd) justinputtest(ExtrapolationAppearing nrrd) justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) -justinputtest(ThreeAxisFourLabelConflict nrrd) +justinputtest(ThreeAxisFourLabelConflict nrrd) #TODO: debug justinputtest(AccidentalMiddleSliceSegmentation nrrd) -justinputtest(FullEndSevenLabels nrrd) -justinputtest(ManyToMany nrrd) +justinputtest(FullEndSevenLabels nrrd) #TODO: debug +justinputtest(ManyToMany16 nrrd) #TODO: debug +justinputtest(ManyToMany nrrd) #TODO: debug # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx new file mode 100644 index 00000000000..9b0893d2457 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx @@ -0,0 +1,15 @@ +#ifdef _MSC_VER +# pragma warning(disable : 4996) /* deprecation */ +#endif + +#include "itkTestDriverIncludeRequiredIOFactories.h" + +extern int +itkMorphologicalContourInterpolationTest(int argc, char * argv[]); + +int +main(int argc, char * argv[]) +{ + RegisterRequiredFactories(); + itkMorphologicalContourInterpolationTest(argc, argv); +} From 332f0e0dc289d19821e84f42b6c3bc27bd9b5e46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 11:54:05 -0500 Subject: [PATCH 040/176] BUG: Fixing slice skipping --- .../itkMorphologicalContourInterpolator.hxx | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 44418ac2c8c..f1904cc41d2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -40,7 +40,7 @@ template void WriteDebug(typename TImage::Pointer out, const char * filename) { - // return; //tests run much faster + return; // tests run much faster typedef ImageFileWriter WriterType; typename WriterType::Pointer w = WriterType::New(); w->SetInput(out); @@ -58,7 +58,6 @@ WriteDebug(typename TImage::Pointer out, const char * filename) void WriteDebug(Image::Pointer out, const char * filename) { - // return; //tests run much faster typedef Image BoolImageType; typedef Image ucharImageType; typedef CastImageFilter CastType; @@ -423,8 +422,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int { m_Or->SetInput(0, iSeq[x]); m_Or->SetInput(1, jSeq[x]); - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('A' + x) + ".nrrd").c_str()); - WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('A' + x) + ".nrrd").c_str()); + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); + WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); @@ -435,15 +434,15 @@ MorphologicalContourInterpolator::Interpolate1to1(int for (unsigned x = minSeq; x < maxSeq; x++) { seq.push_back(jSeq[x]); - WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('A' + x) + ".nrrd").c_str()); + WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); } } else { for (unsigned x = minSeq; x < maxSeq; x++) { - seq.push_back(iSeq[x]); - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('A' + x) + ".nrrd").c_str()); + seq.push_back(iSeq[x]); // seq.push_back(iSeq[0]); //error in paper? + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); } } @@ -452,7 +451,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int IdentifierType min = newRegion.GetNumberOfPixels(); for (unsigned x = 0; x < maxSeq; x++) { - WriteDebug(seq[x], (std::string("C:\\seq") + char('A' + x) + ".nrrd").c_str()); + WriteDebug(seq[x], (std::string("C:\\seq") + char('a' + x) + ".nrrd").c_str()); IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) @@ -480,7 +479,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // recurse if needed - typename TImage::IndexValueType mid = (i + j) / 2; + typename TImage::IndexValueType mid = newRegion.GetIndex()[axis]; if (abs(i - j) > 2) { typedef CastImageFilter InvertCastType; @@ -490,7 +489,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::Pointer midConn = invCaster->GetOutput(); // midConn->DisconnectPipeline(); //not needed? - WriteDebug(midConn, "C:\\midConn.nrrd"); + // WriteDebug(midConn, "C:\\midConn.nrrd"); PixelList regionIDs; regionIDs.push_back(1); @@ -603,6 +602,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // TODO: save these in a sequence so we don't have to recalculate it! } + // TODO: replace this loop by LabelErodeDilate filters? hollowedMaskEmpty = true; maskIt2.GoToBegin(); jIt2.GoToBegin(); From 98219e0c203c68ab8fd02da40411eb1c984606f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 13:15:20 -0500 Subject: [PATCH 041/176] ENH: more continuous sequence union --- .../itkMorphologicalContourInterpolator.hxx | 32 ++++++------------- 1 file changed, 10 insertions(+), 22 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index f1904cc41d2..6bd8e56f4b6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -414,42 +414,30 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(intersection, "C:\\intersection.nrrd"); std::vector iSeq = GenerateDilationSequence(intersection, iMask); std::vector jSeq = GenerateDilationSequence(intersection, jMask); - unsigned minSeq = std::min(iSeq.size(), jSeq.size()); - unsigned maxSeq = std::max(iSeq.size(), jSeq.size()); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection + if (iSeq.size() < jSeq.size()) + { + iSeq.swap(jSeq); // swap so iSeq.size() >= jSeq.size() + } + float ratio = float(jSeq.size()) / iSeq.size(); std::vector seq; - for (unsigned x = 0; x < minSeq; x++) + for (unsigned x = 0; x < iSeq.size(); x++) { m_Or->SetInput(0, iSeq[x]); - m_Or->SetInput(1, jSeq[x]); + unsigned xj = ratio * x; + m_Or->SetInput(1, jSeq[xj]); WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); - WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); + WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); seq.back()->DisconnectPipeline(); } - if (iSeq.size() < jSeq.size()) - { - for (unsigned x = minSeq; x < maxSeq; x++) - { - seq.push_back(jSeq[x]); - WriteDebug(jSeq[x], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); - } - } - else - { - for (unsigned x = minSeq; x < maxSeq; x++) - { - seq.push_back(iSeq[x]); // seq.push_back(iSeq[0]); //error in paper? - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); - } - } // find median unsigned minIndex; IdentifierType min = newRegion.GetNumberOfPixels(); - for (unsigned x = 0; x < maxSeq; x++) + for (unsigned x = 0; x < iSeq.size(); x++) { WriteDebug(seq[x], (std::string("C:\\seq") + char('a' + x) + ".nrrd").c_str()); IdentifierType iS = CardSymDifference(seq[x], iMask); From f7dd1bd77de414d095819f0bd5c371be19ae5435 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 14:20:51 -0500 Subject: [PATCH 042/176] ENH: clear the output image --- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../MorphologicalContourInterpolation/test/CMakeLists.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 6bd8e56f4b6..53ca8351c9a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1323,7 +1323,7 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer imageA = TImage::New(); imageA->CopyInformation(m_Output); imageA->SetRegions(m_Output->GetRequestedRegion()); - imageA->Allocate(); + imageA->Allocate(true); this->InterpolateAlong(a, imageA); perAxisInterpolates.push_back(imageA); } diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 74f60e66a34..adaa35f3ee2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -45,7 +45,7 @@ justinputtest(ManyToMany nrrd) #TODO: debug # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) justinputtest(105769fixed_segmentation nii.gz) -justinputtest(64816L_amygdala_fin nii.gz) justinputtest(64816L_amygdala_int nii.gz) -justinputtest(65239R_amygdala_fin nii.gz) +justinputtest(64816L_amygdala_fin nii.gz) justinputtest(65239R_amygdala_int nii.gz) +justinputtest(65239R_amygdala_fin nii.gz) From c1c5e68e15689bad7b66b5486ba0e43c46bfe3b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 14:28:51 -0500 Subject: [PATCH 043/176] ENH: combine per axis interpolates using last written rule instead of median --- .../itkMorphologicalContourInterpolator.hxx | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 53ca8351c9a..032cea98c96 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1346,7 +1346,7 @@ MorphologicalContourInterpolator::GenerateData() std::vector values; values.reserve(perAxisInterpolates.size()); - tempOut->Allocate(); + tempOut->Allocate(true); ImageRegionIterator it(tempOut, m_Output->GetRequestedRegion()); while (!it.IsAtEnd()) { @@ -1356,24 +1356,10 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::PixelType val = iterators[i].Get(); if (val != 0) { - values.push_back(val); + it.Set(val); // last written value stays } } - if (values.size() == 0) - { - it.Set(0); // all were zero - } - else if (values.size() == 1) - { - it.Set(values[0]); // the only non-zero - } - else // median - { - std::nth_element(values.begin(), values.begin() + values.size() / 2, values.end()); - it.Set(values[values.size() / 2]); - } - // next pixel ++it; for (int i = 0; i < perAxisInterpolates.size(); ++i) From ed1a60ee947bb103d46277817979e7090f76240e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 15:16:33 -0500 Subject: [PATCH 044/176] ENH: adding additional tests --- .../MorphologicalContourInterpolation/test/CMakeLists.txt | 6 ++++-- .../test/Input/BigImage.nrrd.md5 | 1 + .../test/Input/BigZ.nrrd.md5 | 1 + .../test/Input/FullEnd.nrrd.md5 | 1 + .../{FullEndSevenLabels.nrrd.md5 => SevenLabels.nrrd.md5} | 0 5 files changed, 7 insertions(+), 2 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigImage.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigZ.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEnd.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Input/{FullEndSevenLabels.nrrd.md5 => SevenLabels.nrrd.md5} (100%) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index adaa35f3ee2..21533349afb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -36,11 +36,13 @@ justinputtest(OneToThree nrrd) justinputtest(ExtrapolationAppearing nrrd) justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) -justinputtest(ThreeAxisFourLabelConflict nrrd) #TODO: debug +justinputtest(ThreeAxisFourLabelConflict nrrd) justinputtest(AccidentalMiddleSliceSegmentation nrrd) -justinputtest(FullEndSevenLabels nrrd) #TODO: debug +justinputtest(SevenLabels nrrd) #TODO: debug +justinputtest(FullEnd nrrd) #TODO: debug justinputtest(ManyToMany16 nrrd) #TODO: debug justinputtest(ManyToMany nrrd) #TODO: debug +justinputtest(BigZ nrrd) #TODO: debug # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigImage.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigImage.nrrd.md5 new file mode 100644 index 00000000000..aacd04019a6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigImage.nrrd.md5 @@ -0,0 +1 @@ +17f7ef11aa11ae29df8627f9c63d5921 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigZ.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigZ.nrrd.md5 new file mode 100644 index 00000000000..adb6d6a45bf --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/BigZ.nrrd.md5 @@ -0,0 +1 @@ +abecb4cae97a59de55274a6b3da65482 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEnd.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEnd.nrrd.md5 new file mode 100644 index 00000000000..9ea0ac759f8 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEnd.nrrd.md5 @@ -0,0 +1 @@ +75e012162a93b9e19502915adc4a8a20 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/SevenLabels.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/FullEndSevenLabels.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/SevenLabels.nrrd.md5 From c667fde06ecf2f2f1f2ce987325fdbe3ac0d370a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 16:28:46 -0500 Subject: [PATCH 045/176] ENH: 1toN match must intersect all subregions --- .../itkMorphologicalContourInterpolator.hxx | 29 ++++++++++++++----- 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 032cea98c96..986ce82d241 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -518,9 +518,9 @@ MorphologicalContourInterpolator::Interpolate1toN(int caster->SetInput(iConn); caster->Update(); typename BoolImageType::Pointer mask = caster->GetOutput(); - // WriteDebug(mask, "C:\\mask.nrrd"); - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(mask, "C:\\mask.nrrd"); + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -750,7 +750,11 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer jRegion = jConn->GetLargestPossibleRegion(); IntersectionRegions(translation, iRegion, jRegion); - IdentifierType count = 0; + std::vector counts(jRegionIds.size()); + for (int x = 0; x < jRegionIds.size(); x++) + { + counts[x] = 0; + } ImageRegionConstIterator iIt(iConn, iRegion); ImageRegionConstIterator jIt(jConn, jRegion); while (!iIt.IsAtEnd()) @@ -761,13 +765,22 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { - count++; + ++counts[res - jRegionIds.begin()]; } } ++iIt; ++jIt; } - return count; + IdentifierType sum = 0; + for (int x = 0; x < jRegionIds.size(); x++) + { + if (counts[x] == 0) + { + return 0; // iConn must intersect all subregions of jConn + } + sum += counts[x]; + } + return sum; } template @@ -845,7 +858,6 @@ MorphologicalContourInterpolator::Align(int axis, { ind[d] = jCentroid[d] - iCentroid[d]; } - // ind[axis] = 0; //i and j have different coordinate along this axis // construct an image with all possible translations typename TImage::RegionType searchRegion; @@ -866,6 +878,9 @@ MorphologicalContourInterpolator::Align(int axis, // breadth first search starting from centroid, implicitly: // when intersection scores are equal, chooses the one closer to centroid std::queue uncomputed; + typename TImage::IndexType t0 = { 0 }; + t0[axis] = ind[axis]; + uncomputed.push(t0); // no translation uncomputed.push(ind); searched->SetPixel(ind, true); IdentifierType score, maxScore = 0; From 62e1ec13a690da740d8ba0f740296ba9c2d9763f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 25 Jan 2016 17:04:44 -0500 Subject: [PATCH 046/176] ENH: better splitting of translation (using carry) --- .../itkMorphologicalContourInterpolator.hxx | 23 ++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 986ce82d241..6b3ba86fc23 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -366,10 +366,31 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::RegionType iRegion = iConn->GetLargestPossibleRegion(); typename TImage::RegionType jRegion = jConn->GetLargestPossibleRegion(); typename TImage::IndexType jBottom = jRegion.GetIndex(); + bool carry = false; for (unsigned d = 0; d < TImage::ImageDimension; d++) { - iTrans[d] = translation[d] / 2; + if (!carry) + { + iTrans[d] = translation[d] / 2; + carry = translation[d] % 2; + } + else if (translation[d] % 2 == 0) + { + iTrans[d] = translation[d] / 2; + } + else // use carry + { + if (translation[d] > 0) + { + iTrans[d] = translation[d] / 2 + 1; + } + else + { + iTrans[d] = translation[d] / 2 - 1; + } + carry = false; + } jTrans[d] = iTrans[d] - translation[d]; iRegion.SetIndex(d, iRegion.GetIndex()[d] + iTrans[d]); jRegion.SetIndex(d, jRegion.GetIndex()[d] + jTrans[d]); From 945b2ffa000016240b4a1643884faded6bdd4624 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 26 Jan 2016 15:36:41 -0500 Subject: [PATCH 047/176] ENH: different labels can be segmented on different slices --- .../itkMorphologicalContourInterpolator.h | 12 +- .../itkMorphologicalContourInterpolator.hxx | 396 +++++++----------- 2 files changed, 166 insertions(+), 242 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 927a8ffcff2..d6ab6343ab3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -103,7 +103,11 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label - typename TImage::RegionType - MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes); - // each label gets a set of slices in which it is present typedef std::set SliceSetType; typedef itksys::hash_map LabeledSlicesType; @@ -224,8 +225,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::Interpolate1toN(int } -template -typename TImage::RegionType -MorphologicalContourInterpolator::MergeBoundingBoxes(const BoundingBoxesType & boundingBoxes) -{ - typename BoundingBoxesType::iterator it = m_BoundingBoxes.begin(); - typename TImage::RegionType result = it->second; - typename TImage::SizeType minusOne; - minusOne.Fill(-1); - for (++it; it != m_BoundingBoxes.end(); ++it) - { - ExpandRegion(result, it->second.GetIndex()); - ExpandRegion(result, it->second.GetIndex() + it->second.GetSize() + minusOne); - } - return result; -} - - template typename TImage::Pointer MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointer image, @@ -724,14 +707,6 @@ MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointe typename TImage::RegionType inRegion = image->GetLargestPossibleRegion(); IntersectionRegions(translation, inRegion, newRegion); ImageAlgorithm::Copy(image.GetPointer(), result.GetPointer(), inRegion, newRegion); - // ImageRegionIterator resultIt(result, newRegion); - // ImageRegionConstIterator inIt(image, inRegion); - // while (!resultIt.IsAtEnd()) - // { - // resultIt.Set(inIt.Get()); - // ++resultIt; - // ++inIt; - // } return result; } @@ -975,6 +950,7 @@ template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, TImage * out, + typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j) { @@ -987,221 +963,140 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int return; // nothing to do } - // compare slices i and j - typename TImage::RegionType ri = m_TotalBoundingBox; // smaller than or equal to requested region + // determine inter-slice region correspondences + typename TImage::RegionType ri; + ri = m_BoundingBoxes[label]; + ri.SetSize(axis, 1); ri.SetIndex(axis, i); - ri.SetSize(axis, 1); // 1 slice typename TImage::RegionType rj = ri; rj.SetIndex(axis, j); - typename BoolImageType::Pointer eqResult = BoolImageType::New(); - typename TImage::RegionType rr = rj; - rr.SetIndex(axis, 0); - eqResult->CopyInformation(m_Input); - eqResult->SetRegions(rr); - eqResult->Allocate(); - - typedef std::set LabelSetType; - LabelSetType overlaps; // which labels have overlaps from slice i to slice j - - ImageRegionConstIterator iti(m_Input, ri); - ImageRegionConstIterator itj(m_Input, rj); - ImageRegionIterator itr(eqResult, rr); - while (!itr.IsAtEnd()) + // execute connected components + IdentifierType iCount, jCount; + typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, label, iCount); + iconn->DisconnectPipeline(); + typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, label, jCount); + jconn->DisconnectPipeline(); + WriteDebug(iconn, "C:\\iconn.nrrd"); + WriteDebug(jconn, "C:\\jconn.nrrd"); + + // go through comparison image and create correspondence pairs + typedef std::set> PairSet; + PairSet pairs, unwantedPairs, uncleanPairs; + ImageRegionConstIterator iti(iconn, ri); + ImageRegionConstIterator itj(jconn, rj); + while (!iti.IsAtEnd()) { - bool eq = (iti.Get() == itj.Get() && iti.Get() != 0); // are the pixels equal and non-zero? - itr.Set(eq); - if (eq) // exclude background label + if (iti.Get() != 0 || itj.Get() != 0) { - overlaps.insert(iti.Get()); + uncleanPairs.insert(std::make_pair(iti.Get(), itj.Get())); + // std::cout << " iti:" << iti.GetIndex() << iti.Get() << + // " itj:" << itj.GetIndex() << itj.Get() << std::endl; + if (iti.Get() != 0 && itj.Get() != 0) + { + unwantedPairs.insert(std::make_pair(0, itj.Get())); + unwantedPairs.insert(std::make_pair(iti.Get(), 0)); + } } - // next pixel ++iti; ++itj; - ++itr; } - // typedef unsigned char instead of bool to write it as nrrd - // WriteDebug(eqResult,"C:\\Temp\\eqResult.nrrd"); - - // for each label with overlaps determine inter-slice region correspondences - for (typename LabelSetType::iterator it = overlaps.begin(); it != overlaps.end(); ++it) + std::set_difference(uncleanPairs.begin(), + uncleanPairs.end(), + unwantedPairs.begin(), + unwantedPairs.end(), + std::inserter(pairs, pairs.end())); + + // first do extrapolation for components without overlaps + typename PairSet::iterator p = pairs.begin(); + while (p != pairs.end()) { - if (m_Label != 0 && *it != m_Label) - continue; // label was specified, and it was not this one, so skip - - // first determine disjoint regions - ri = m_BoundingBoxes[*it]; // even smaller than m_TotalBoundingBox - ri.SetSize(axis, 1); - ri.SetIndex(axis, i); - rj = ri; - rj.SetIndex(axis, j); - rr = rj; - rr.SetIndex(axis, 0); - - // execute connected components - IdentifierType iCount, jCount; - typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, *it, iCount); - iconn->DisconnectPipeline(); - typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, *it, jCount); - jconn->DisconnectPipeline(); - // WriteDebug(iconn, "C:\\Temp\\iconn.nrrd"); - // WriteDebug(jconn, "C:\\Temp\\jconn.nrrd"); - - // go through comparison image and create correspondence pairs - typedef std::set> PairSet; - PairSet pairs; - itr.SetRegion(rr); - itr.GoToBegin(); - ImageRegionConstIterator iti(iconn, ri); - ImageRegionConstIterator itj(jconn, rj); - while (!itr.IsAtEnd()) + if (p->second == 0) { - if (itr.Get() && iti.Get() != 0 && itj.Get() != 0) - { - pairs.insert(std::make_pair(iti.Get(), itj.Get())); - // std::cout << "itr:" << itr.GetIndex() << - // " iti:" << iti.GetIndex() << iti.Get() << - // " itj:" << itj.GetIndex() << itj.Get() << std::endl; - } - ++iti; - ++itj; - ++itr; // next pixel + Extrapolate(axis, out, label, i, j, iconn, p->first); + pairs.erase(p++); } - - typedef std::map CountMap; - CountMap iCounts, jCounts; - typename PairSet::iterator p; - for (p = pairs.begin(); p != pairs.end(); ++p) + else if (p->first == 0) { - iCounts[p->first]++; - jCounts[p->second]++; + Extrapolate(axis, out, label, j, i, jconn, p->second); + pairs.erase(p++); } - - // first do extrapolation for components without overlaps - typename CountMap::iterator iMapIt = iCounts.begin(); - for (IdentifierType ic = 1; ic <= iCount; ++ic) // component labels + else { - if (iMapIt == iCounts.end() || ic < iMapIt->first) - { - Extrapolate(axis, out, *it, i, j, iconn, ic); - } - else // ic==iMapIt->first - { - ++iMapIt; - } + ++p; } - typename CountMap::iterator jMapIt = jCounts.begin(); - for (IdentifierType jc = 1; jc <= jCount; ++jc) // component labels + } + + // count ocurrances of each component + typedef std::map CountMap; + CountMap iCounts, jCounts; + for (p = pairs.begin(); p != pairs.end(); ++p) + { + iCounts[p->first]++; + jCounts[p->second]++; + } + + // now handle 1 to 1 correspondences + p = pairs.begin(); + while (p != pairs.end()) + { + if (iCounts[p->first] == 1 && jCounts[p->second] == 1) { - if (jMapIt == jCounts.end() || jc < jMapIt->first) - { - Extrapolate(axis, out, *it, j, i, jconn, jc); - } - else // jc==jMapIt->first - { - ++jMapIt; - } + PixelList regionIDs; + regionIDs.push_back(p->second); + typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation); + iCounts.erase(p->first); + jCounts.erase(p->second); + pairs.erase(p++); } - - // now handle 1 to 1 correspondences - p = pairs.begin(); - while (p != pairs.end()) + else { - if (iCounts[p->first] == 1 && jCounts[p->second] == 1) - { - PixelList regionIDs; - regionIDs.push_back(p->second); - typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); - Interpolate1to1(axis, out, *it, i, j, iconn, p->first, jconn, p->second, translation); - iCounts.erase(p->first); - jCounts.erase(p->second); - pairs.erase(p++); - } - else - { - ++p; - } + ++p; } + } - PixelList regionIDs(pairs.size()); // preallocate - // now do 1-to-N and M-to-1 cases - p = pairs.begin(); - while (p != pairs.end()) - { - regionIDs.clear(); + PixelList regionIDs(pairs.size()); // preallocate + // now do 1-to-N and M-to-1 cases + p = pairs.begin(); + while (p != pairs.end()) + { + regionIDs.clear(); - if (iCounts[p->first] == 1) // M-to-1 + if (iCounts[p->first] == 1) // M-to-1 + { + for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) { - for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + if (rest->second == p->second) { - if (rest->second == p->second) - { - regionIDs.push_back(rest->first); - } + regionIDs.push_back(rest->first); } + } - typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); - Interpolate1toN(axis, out, *it, j, i, jconn, p->second, iconn, regionIDs, translation); + typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); + Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); - typename PairSet::iterator rest = p; - ++rest; - while (rest != pairs.end()) - { - if (rest->second == p->second) - { - --iCounts[rest->first]; - --jCounts[rest->second]; - pairs.erase(rest++); - } - else - { - ++rest; - } - } - pairs.erase(p++); - } // M-to-1 - else if (jCounts[p->second] == 1) // 1-to-N + typename PairSet::iterator rest = p; + ++rest; + while (rest != pairs.end()) { - for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + if (rest->second == p->second) { - if (rest->first == p->first) - { - regionIDs.push_back(rest->second); - } + --iCounts[rest->first]; + --jCounts[rest->second]; + pairs.erase(rest++); } - - typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); - - typename PairSet::iterator rest = p; - ++rest; - while (rest != pairs.end()) + else { - if (rest->first == p->first) - { - --iCounts[rest->first]; - --jCounts[rest->second]; - pairs.erase(rest++); - } - else - { - ++rest; - } + ++rest; } - pairs.erase(p++); - } // 1-to-N - else - { - ++p; } - } // 1-to-N and M-to-1 - - // only M-to-N correspondences remain - // we turn each M-to-N case into m 1-to-N cases - p = pairs.begin(); - while (p != pairs.end()) + --iCounts[p->first]; + --jCounts[p->second]; + pairs.erase(p++); + } // M-to-1 + else if (jCounts[p->second] == 1) // 1-to-N { - regionIDs.clear(); for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) @@ -1211,7 +1106,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, *it, i, j, iconn, p->first, jconn, regionIDs, translation); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); typename PairSet::iterator rest = p; ++rest; @@ -1219,6 +1114,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (rest->first == p->first) { + --iCounts[rest->first]; + --jCounts[rest->second]; pairs.erase(rest++); } else @@ -1226,10 +1123,49 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } - // counts no longer matter, do not waste time deleting them + --iCounts[p->first]; + --jCounts[p->second]; pairs.erase(p++); - } // M-to-N - } // for each label with overlaps + } // 1-to-N + else + { + ++p; + } + } // 1-to-N and M-to-1 + + // only M-to-N correspondences remain + // we turn each M-to-N case into m 1-to-N cases + p = pairs.begin(); + while (p != pairs.end()) + { + regionIDs.clear(); + for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + { + if (rest->first == p->first) + { + regionIDs.push_back(rest->second); + } + } + + typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); + + typename PairSet::iterator rest = p; + ++rest; + while (rest != pairs.end()) + { + if (rest->first == p->first) + { + pairs.erase(rest++); + } + else + { + ++rest; + } + } + // counts no longer matter, do not waste time deleting them + pairs.erase(p++); + } // M-to-N } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() @@ -1237,25 +1173,6 @@ template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { - SliceSetType aggregate; - if (m_Label == 0) // all labels - { - for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); - ++it) - { - aggregate.insert(it->second.begin(), it->second.end()); - } - } - else // we only care about m_Label - { - aggregate = m_LabeledSlices[axis][m_Label]; - } - typename SliceSetType::iterator prev = aggregate.begin(); - if (prev == aggregate.end()) - { - return; // nothing to do - } - // set up structuring element for dilation typedef Size SizeType; SizeType size; @@ -1265,11 +1182,22 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou m_StructuringElement.CreateStructuringElement(); m_Dilator->SetKernel(m_StructuringElement); - typename SliceSetType::iterator it = aggregate.begin(); - for (++it; it != aggregate.end(); ++it) + for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { - InterpolateBetweenTwo(axis, out, *prev, *it); - prev = it; + if (m_Label == 0 || m_Label == it->first) // label needs to be interpolated + { + typename SliceSetType::iterator prev = it->second.begin(); + if (prev == it->second.end()) + { + return; // nothing to do + } + typename SliceSetType::iterator next = it->second.begin(); + for (++next; next != it->second.end(); ++next) + { + InterpolateBetweenTwo(axis, out, it->first, *prev, *next); + prev = next; + } + } } } @@ -1326,10 +1254,6 @@ MorphologicalContourInterpolator::GenerateData() this->m_Output = ITK_NULLPTR; return; // nothing to process } - else - { - m_TotalBoundingBox = MergeBoundingBoxes(m_BoundingBoxes); - } if (m_Axis == -1) // interpolate along all axes { From 15b4f9cf1fb336266087c2bd81e9705e9549729a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 26 Jan 2016 16:55:24 -0500 Subject: [PATCH 048/176] ENH: Adding tests and more aggressive heuristic --- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../test/CMakeLists.txt | 10 ++++++---- .../test/Input/FaceRoI.nrrd.md5 | 1 + .../test/Input/FaceRoIFinished.nrrd.md5 | 1 + .../test/Input/GridSeg.nrrd.md5 | 1 + .../test/Input/GridSegBase.nrrd.md5 | 1 + .../test/Input/Midas3folder.url | 5 +++-- 7 files changed, 14 insertions(+), 7 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoI.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoIFinished.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index cdc57d06b21..7875fbf08fe 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -900,7 +900,7 @@ MorphologicalContourInterpolator::Align(int axis, } // we breadth this search - if (!m_HeuristicAlignment || maxScore == 0 || score > maxScore / 2) + if (!m_HeuristicAlignment || maxScore == 0 || score > maxScore * 0.8) { for (unsigned d = 0; d < TImage::ImageDimension; d++) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 21533349afb..179db09e98f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -38,10 +38,12 @@ justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) justinputtest(ThreeAxisFourLabelConflict nrrd) justinputtest(AccidentalMiddleSliceSegmentation nrrd) -justinputtest(SevenLabels nrrd) #TODO: debug -justinputtest(FullEnd nrrd) #TODO: debug -justinputtest(ManyToMany16 nrrd) #TODO: debug -justinputtest(ManyToMany nrrd) #TODO: debug +justinputtest(SevenLabels nrrd) +justinputtest(FullEnd nrrd) +justinputtest(ManyToMany16 nrrd) +justinputtest(ManyToMany nrrd) +justinputtest(FaceRoI nrrd) #TODO: convert into regression test with FaceRoIFinished.nrrd as expected output +justinputtest(GridSeg nrrd) #TODO: debug justinputtest(BigZ nrrd) #TODO: debug # Paul's tests diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoI.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoI.nrrd.md5 new file mode 100644 index 00000000000..aab89b00769 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoI.nrrd.md5 @@ -0,0 +1 @@ +c6d733010091a6af6ef4c21d02fe206e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoIFinished.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoIFinished.nrrd.md5 new file mode 100644 index 00000000000..f8bb0243645 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FaceRoIFinished.nrrd.md5 @@ -0,0 +1 @@ +8c066ca3cb4500d6bbec32254ba34dc1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 new file mode 100644 index 00000000000..a306561e0ea --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 @@ -0,0 +1 @@ +ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 new file mode 100644 index 00000000000..333c41b3419 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 @@ -0,0 +1 @@ +547a7f7fad211ccb9ce79eae68cbf3ca diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url index d83372bdd2c..36048b09b4c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url @@ -1,5 +1,6 @@ [{000214A0-0000-0000-C000-000000000046}] -Prop3=19,2 +Prop3=19,11 [InternetShortcut] -URL=http://midas3.kitware.com/midas/folder/12980 +URL=https://midas3.kitware.com/midas/folder/12980 IDList= +HotKey=0 From 62547bf421171e83757d2e2090685191ca577a81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 26 Jan 2016 18:00:37 -0500 Subject: [PATCH 049/176] ENH: Connected components is using ball structuring element, so we have to use it for dilation too! --- .../include/itkMorphologicalContourInterpolator.h | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index d6ab6343ab3..60af7f86cee 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -24,8 +24,8 @@ #include "itkExtractImageFilter.h" #include "itksys/hash_map.hxx" #include "itkBinaryDilateImageFilter.h" -#include "itkBinaryCrossStructuringElement.h" -// #include "itkBinaryBallStructuringElement.h" +// #include "itkBinaryCrossStructuringElement.h" +#include "itkBinaryBallStructuringElement.h" #include "itkAndImageFilter.h" #include "itkOrImageFilter.h" @@ -245,8 +245,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter ConnectedComponentsType; typename ConnectedComponentsType::Pointer m_ConnectedComponents; - typedef BinaryCrossStructuringElement StructuringElementType; - StructuringElementType m_StructuringElement; + // typedef BinaryCrossStructuringElement StructuringElementType; + typedef BinaryBallStructuringElement StructuringElementType; + StructuringElementType m_StructuringElement; typedef BinaryDilateImageFilter DilateType; typename DilateType::Pointer m_Dilator; From ab6e27b72728edf9375591baf0ed449f90bbd611 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 26 Jan 2016 18:03:33 -0500 Subject: [PATCH 050/176] STYLE: reordering tests (long at the end) --- .../include/itkMorphologicalContourInterpolator.hxx | 6 +++--- .../MorphologicalContourInterpolation/test/CMakeLists.txt | 8 +++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 7875fbf08fe..42776aeebdf 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -447,8 +447,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int m_Or->SetInput(0, iSeq[x]); unsigned xj = ratio * x; m_Or->SetInput(1, jSeq[xj]); - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); - WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); + // WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); + // WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); @@ -460,7 +460,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int IdentifierType min = newRegion.GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { - WriteDebug(seq[x], (std::string("C:\\seq") + char('a' + x) + ".nrrd").c_str()); + // WriteDebug(seq[x], (std::string("C:\\seq") + char('a' + x) + ".nrrd").c_str()); IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 179db09e98f..8265563c07c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -42,9 +42,7 @@ justinputtest(SevenLabels nrrd) justinputtest(FullEnd nrrd) justinputtest(ManyToMany16 nrrd) justinputtest(ManyToMany nrrd) -justinputtest(FaceRoI nrrd) #TODO: convert into regression test with FaceRoIFinished.nrrd as expected output -justinputtest(GridSeg nrrd) #TODO: debug -justinputtest(BigZ nrrd) #TODO: debug +justinputtest(GridSeg nrrd) # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) @@ -53,3 +51,7 @@ justinputtest(64816L_amygdala_int nii.gz) justinputtest(64816L_amygdala_fin nii.gz) justinputtest(65239R_amygdala_int nii.gz) justinputtest(65239R_amygdala_fin nii.gz) + +# Long-running handcrafted tests +justinputtest(BigZ nrrd) +justinputtest(FaceRoI nrrd) #TODO: convert into regression test with FaceRoIFinished.nrrd as expected output From 5037cdf7c113cffcf15806c01afe204dad85f709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 Jan 2016 11:12:22 -0500 Subject: [PATCH 051/176] BUG: adding some regression test cases --- .../test/Baseline/Empty.nrrd.md5 | 1 + .../Baseline/ExtrapolationAppearing.nrrd.md5 | 1 + .../test/Baseline/ManyToMany.nrrd.md5 | 1 + .../test/Baseline/Micro1.nrrd.md5 | 1 + .../test/Baseline/NoSlices.nrrd.md5 | 1 + .../test/Baseline/OneToOne.nrrd.md5 | 1 + .../test/Baseline/OneToThree.nrrd.md5 | 1 + .../test/Baseline/SimplestOneToOne.nrrd.md5 | 1 + .../test/CMakeLists.txt | 30 ++++++++++++++----- .../test/Input/Empty.nrrd.md5 | 1 + .../test/Input/NoSlices.nrrd.md5 | 1 + 11 files changed, 33 insertions(+), 7 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/Empty.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/NoSlices.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty.nrrd.md5 new file mode 100644 index 00000000000..20c34789bed --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty.nrrd.md5 @@ -0,0 +1 @@ +576499ff818311578946a66d8757e5f5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing.nrrd.md5 new file mode 100644 index 00000000000..f6b3f97ce3e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing.nrrd.md5 @@ -0,0 +1 @@ +f8799ca9078a7c2981f6b90f7be9a8ee diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 new file mode 100644 index 00000000000..1ab7a6706e5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 @@ -0,0 +1 @@ +6e172933dfc613dc59f06d18d1306208 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 new file mode 100644 index 00000000000..32b54ad57f9 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 @@ -0,0 +1 @@ +c0c1490e4f37fded3d69fdd9290e2397 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 new file mode 100644 index 00000000000..ad7e5a0c768 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 @@ -0,0 +1 @@ +6f27bdcb62b1f2fd01f78c28e7b64367 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 new file mode 100644 index 00000000000..cd346cbd91c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 @@ -0,0 +1 @@ +62cd3b894f0100a831ebe38a89388618 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 new file mode 100644 index 00000000000..b282bcb15cf --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 @@ -0,0 +1 @@ +e622becf04aeb19dd270542c51930fa0 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 new file mode 100644 index 00000000000..f18e28c4ecd --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 @@ -0,0 +1 @@ +79f2536d04ef29ebee064f551bca44de diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 8265563c07c..bf0a0a39464 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -19,7 +19,7 @@ target_link_libraries( function(JustInputTest ImageName Ext) itk_add_test( - NAME itkMorphologicalContourInterpolationTest_${ImageName} + NAME itkMorphologicalContourInterpolation_JustInputTest_${ImageName} COMMAND MorphologicalContourInterpolationTestDriver itkMorphologicalContourInterpolationTest @@ -28,12 +28,28 @@ function(JustInputTest ImageName Ext) ) endfunction() +function(RegressionTest ImageName Ext) + itk_add_test( + NAME itkMorphologicalContourInterpolation_RegressionTest_${ImageName} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${ImageName}.${Ext}} + ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + itkMorphologicalContourInterpolationTest + DATA{Input/${ImageName}.${Ext}} + ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + ) +endfunction() + # Handcrafted tests -justinputtest(Micro1 nrrd) -justinputtest(SimplestOneToOne nrrd) -justinputtest(OneToOne nrrd) -justinputtest(OneToThree nrrd) -justinputtest(ExtrapolationAppearing nrrd) +regressiontest(Empty nrrd) +regressiontest(NoSlices nrrd) #interpolation should not be invoked (output==input) +regressiontest(Micro1 nrrd) +regressiontest(SimplestOneToOne nrrd) +regressiontest(OneToOne nrrd) +regressiontest(OneToThree nrrd) +regressiontest(ExtrapolationAppearing nrrd) justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) justinputtest(ThreeAxisFourLabelConflict nrrd) @@ -41,7 +57,7 @@ justinputtest(AccidentalMiddleSliceSegmentation nrrd) justinputtest(SevenLabels nrrd) justinputtest(FullEnd nrrd) justinputtest(ManyToMany16 nrrd) -justinputtest(ManyToMany nrrd) +regressiontest(ManyToMany nrrd) justinputtest(GridSeg nrrd) # Paul's tests diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Empty.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Empty.nrrd.md5 new file mode 100644 index 00000000000..20c34789bed --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Empty.nrrd.md5 @@ -0,0 +1 @@ +576499ff818311578946a66d8757e5f5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NoSlices.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NoSlices.nrrd.md5 new file mode 100644 index 00000000000..ad7e5a0c768 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/NoSlices.nrrd.md5 @@ -0,0 +1 @@ +6f27bdcb62b1f2fd01f78c28e7b64367 From 498c38e6d64312e5c5f62dedd85f1c9c786505ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 Jan 2016 12:07:39 -0500 Subject: [PATCH 052/176] ENH: minor improvements --- .../itkMorphologicalContourInterpolator.hxx | 28 +++++++++++++------ 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 42776aeebdf..431b874b564 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -876,23 +876,28 @@ MorphologicalContourInterpolator::Align(int axis, std::queue uncomputed; typename TImage::IndexType t0 = { 0 }; t0[axis] = ind[axis]; - uncomputed.push(t0); // no translation - uncomputed.push(ind); + uncomputed.push(t0); // no translation - guaranteed to find a non-zero intersection + uncomputed.push(ind); // this introduces movement, and possibly has the same score searched->SetPixel(ind, true); IdentifierType score, maxScore = 0; typename TImage::IndexType bestIndex; // debug: construct and later fill the image with intersection scores +#ifdef _DEBUG typename TImage::Pointer scoreImage = TImage::New(); scoreImage->SetRegions(searchRegion); scoreImage->Allocate(true); +#endif // _DEBUG while (!uncomputed.empty()) { ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); - scoreImage->SetPixel(ind, score); // debug +#ifdef _DEBUG + scoreImage->SetPixel(ind, score + 1); // unexplored=0, noIntersection=1 +#endif // _DEBUG + if (score > maxScore) { maxScore = score; @@ -925,7 +930,9 @@ MorphologicalContourInterpolator::Align(int axis, } } // WriteDebug(searched, "C:\\searched.nrrd"); +#ifdef _DEBUG WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); +#endif // _DEBUG return bestIndex; } @@ -1247,12 +1254,11 @@ MorphologicalContourInterpolator::GenerateData() this->DetermineSliceOrientations(); - // merge all bounding boxes - if (m_BoundingBoxes.size() == 0) + if (m_BoundingBoxes.size() == 0) // empty input image { - this->GraftOutput(m_Output); - this->m_Output = ITK_NULLPTR; - return; // nothing to process + tempOut->Allocate(true); + CombineInputAndInterpolate(tempOut); + return; } if (m_Axis == -1) // interpolate along all axes @@ -1289,6 +1295,12 @@ MorphologicalContourInterpolator::GenerateData() } } + if (perAxisInterpolates.size() == 0) // nothing to process + { + tempOut->Allocate(true); + CombineInputAndInterpolate(tempOut); + return; + } if (perAxisInterpolates.size() == 1) { CombineInputAndInterpolate(perAxisInterpolates[0]); From 33c8b513c324df2cdcaf72821e3768c44e6aa8d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 Jan 2016 13:46:33 -0500 Subject: [PATCH 053/176] ENH: adding per axis tests --- .../itkMorphologicalContourInterpolator.hxx | 14 ++--- .../test/Baseline/GridSeg.nrrd.md5 | 1 + .../test/Baseline/GridSeg2.nrrd.md5 | 1 + .../test/Baseline/GridSeg2_0.nrrd.md5 | 1 + .../test/Baseline/GridSeg2_1.nrrd.md5 | 1 + .../test/Baseline/GridSeg2_2.nrrd.md5 | 1 + .../test/Baseline/GridSeg_0.nrrd.md5 | 1 + .../test/Baseline/GridSeg_1.nrrd.md5 | 1 + .../test/Baseline/GridSeg_2.nrrd.md5 | 1 + .../test/CMakeLists.txt | 53 +++++++++++++++---- .../test/Input/GridSeg.nrrd.md5 | 2 +- .../test/Input/GridSeg2.nrrd.md5 | 1 + .../test/Input/GridSegBase.nrrd.md5 | 2 +- .../test/Input/GridSeg_0.nrrd.md5 | 1 + .../test/Input/GridSeg_1.nrrd.md5 | 1 + .../test/Input/GridSeg_2.nrrd.md5 | 1 + ...kMorphologicalContourInterpolationTest.cxx | 20 ++++++- .../test/manualTest.cxx | 18 +++++++ 18 files changed, 100 insertions(+), 21 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 431b874b564..de906320e6c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -883,20 +883,20 @@ MorphologicalContourInterpolator::Align(int axis, typename TImage::IndexType bestIndex; // debug: construct and later fill the image with intersection scores -#ifdef _DEBUG +#ifndef NDEBUG typename TImage::Pointer scoreImage = TImage::New(); scoreImage->SetRegions(searchRegion); scoreImage->Allocate(true); -#endif // _DEBUG +#endif // NDEBUG while (!uncomputed.empty()) { ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); -#ifdef _DEBUG +#ifndef NDEBUG scoreImage->SetPixel(ind, score + 1); // unexplored=0, noIntersection=1 -#endif // _DEBUG +#endif // NDEBUG if (score > maxScore) { @@ -930,9 +930,9 @@ MorphologicalContourInterpolator::Align(int axis, } } // WriteDebug(searched, "C:\\searched.nrrd"); -#ifdef _DEBUG +#ifndef NDEBUG WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); -#endif // _DEBUG +#endif // NDEBUG return bestIndex; } @@ -1342,7 +1342,7 @@ MorphologicalContourInterpolator::GenerateData() } // interpolate along all axes else // interpolate along the specified axis { - tempOut->Allocate(); + tempOut->Allocate(true); this->InterpolateAlong(m_Axis, tempOut); } CombineInputAndInterpolate(tempOut); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 new file mode 100644 index 00000000000..8ce5b70498d --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 @@ -0,0 +1 @@ +0c8a8da2c50ea5bdff9840e0779eed42 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 new file mode 100644 index 00000000000..e2ba4e41a6c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 @@ -0,0 +1 @@ +ded87cb84cdfa5821115fd3934f12c7c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 new file mode 100644 index 00000000000..d76ef381466 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 @@ -0,0 +1 @@ +455631559bbc0822ad5e25f48a00f5ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 new file mode 100644 index 00000000000..bd6a3b2a334 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 @@ -0,0 +1 @@ +7fc5885f19ce95324fdc9b5acdb012b6 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 new file mode 100644 index 00000000000..830267f5eac --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 @@ -0,0 +1 @@ +2a4b6c0b19e512ce347bbbf3997fd5f0 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 new file mode 100644 index 00000000000..6e14c3ef980 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 @@ -0,0 +1 @@ +b839dc3cf067e005c1583e1d7d3a22c0 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 new file mode 100644 index 00000000000..0f8f0ea1e89 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 @@ -0,0 +1 @@ +e9b2328eedabac555f49965859e079e6 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 new file mode 100644 index 00000000000..161c8f31a80 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 @@ -0,0 +1 @@ +e8537f630b96d901fc4eef288a0937e5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index bf0a0a39464..4ae28616a64 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -17,28 +17,51 @@ target_link_libraries( ${MorphologicalContourInterpolation-Test_LIBRARIES} ) -function(JustInputTest ImageName Ext) +function(JustInputTest ImageName Ext) #optional: Axis Label + foreach(f ${ARGN}) #create unique test name + set(optArgs "${optArgs}_${f}") + endforeach() + set( + outImage + "${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated${optArgs}.${Ext}" + ) + # set(imageNameOpt "${ImageName}${optArgs}") # only used for regression + itk_add_test( - NAME itkMorphologicalContourInterpolation_JustInputTest_${ImageName} + NAME + itkMorphologicalContourInterpolation_RegressionTest_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver + # --compare DATA{Baseline/${imageNameOpt}.${Ext}} ${outImage} # no regression itkMorphologicalContourInterpolationTest DATA{Input/${ImageName}.${Ext}} - ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + ${outImage} + ${ARGN} ) endfunction() -function(RegressionTest ImageName Ext) +function(RegressionTest ImageName Ext) #optional: Axis Label + foreach(f ${ARGN}) #create unique test name + set(optArgs "${optArgs}_${f}") + endforeach() + set( + outImage + "${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated${optArgs}.${Ext}" + ) + set(imageNameOpt "${ImageName}${optArgs}") + itk_add_test( - NAME itkMorphologicalContourInterpolation_RegressionTest_${ImageName} + NAME + itkMorphologicalContourInterpolation_RegressionTest_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver --compare - DATA{Baseline/${ImageName}.${Ext}} - ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} itkMorphologicalContourInterpolationTest DATA{Input/${ImageName}.${Ext}} - ${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated.${Ext} + ${outImage} + ${ARGN} ) endfunction() @@ -58,7 +81,16 @@ justinputtest(SevenLabels nrrd) justinputtest(FullEnd nrrd) justinputtest(ManyToMany16 nrrd) regressiontest(ManyToMany nrrd) -justinputtest(GridSeg nrrd) +regressiontest(GridSeg nrrd) +regressiontest(GridSeg2 nrrd) + +# Per axis/label tests +regressiontest(GridSeg nrrd 0) +regressiontest(GridSeg nrrd 1) +regressiontest(GridSeg nrrd 2) +regressiontest(GridSeg2 nrrd 0) +regressiontest(GridSeg2 nrrd 1) +regressiontest(GridSeg2 nrrd 2) # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) @@ -67,7 +99,8 @@ justinputtest(64816L_amygdala_int nii.gz) justinputtest(64816L_amygdala_fin nii.gz) justinputtest(65239R_amygdala_int nii.gz) justinputtest(65239R_amygdala_fin nii.gz) +#TODO: make different combinations of axis and label parameters # Long-running handcrafted tests justinputtest(BigZ nrrd) -justinputtest(FaceRoI nrrd) #TODO: convert into regression test with FaceRoIFinished.nrrd as expected output +justinputtest(FaceRoI nrrd) #TODO: convert into Per axis/label regression test with FaceRoIFinished.nrrd as expected output diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 index a306561e0ea..e7f1eb43a37 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg.nrrd.md5 @@ -1 +1 @@ -ee926367f773a50ac6ae0299d30a9d57 +adfc3511c840ae271ceb1ac98f47b089 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg2.nrrd.md5 new file mode 100644 index 00000000000..f8dd15400f5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg2.nrrd.md5 @@ -0,0 +1 @@ +f584ce5f31ce672767a50e7b4842f8c3 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 index 333c41b3419..e94d15f4fb5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSegBase.nrrd.md5 @@ -1 +1 @@ -547a7f7fad211ccb9ce79eae68cbf3ca +029b845a192b5000a5987d959218a2bc diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 new file mode 100644 index 00000000000..a306561e0ea --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 @@ -0,0 +1 @@ +ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 new file mode 100644 index 00000000000..a306561e0ea --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 @@ -0,0 +1 @@ +ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 new file mode 100644 index 00000000000..a306561e0ea --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 @@ -0,0 +1 @@ +ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index b6977f666c1..6d81a16cb55 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -19,6 +19,14 @@ #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" +#include + +long int +string2int(char * number) +{ + long res = strtol(number, NULL, 10); + return res; +} int itkMorphologicalContourInterpolationTest(int argc, char * argv[]) @@ -26,7 +34,8 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) if (argc < 3) { std::cerr << "Usage: " << argv[0]; - std::cerr << " inputImage outputImage"; + std::cerr << " inputImage outputImage [axis] [label]\n"; + std::cerr << " defaults: axis == -1 (all axes), label == 0 (all labels)"; std::cerr << std::endl; return EXIT_FAILURE; } @@ -44,7 +53,14 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) typedef itk::MorphologicalContourInterpolator mciType; mciType::Pointer mci = mciType::New(); mci->SetInput(reader->GetOutput()); - mci->SetLabel(0); + if (argc >= 4) + { + mci->SetAxis(strtol(argv[3], NULL, 10)); + } + if (argc >= 5) + { + mci->SetLabel(strtol(argv[4], NULL, 10)); + } typedef itk::ImageFileWriter WriterType; WriterType::Pointer writer = WriterType::New(); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx index 9b0893d2457..ac1403ce39a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx @@ -1,3 +1,21 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ + #ifdef _MSC_VER # pragma warning(disable : 4996) /* deprecation */ #endif From e1dbbaa80636cfc38de00400d0cb9be9dbbb74fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 27 Jan 2016 13:46:33 -0500 Subject: [PATCH 054/176] ENH: adding more per axis tests --- .../itkMorphologicalContourInterpolator.hxx | 2 +- .../test/Baseline/FaceRoI.nrrd.md5 | 1 + .../test/Baseline/FaceRoI_0.nrrd.md5 | 1 + .../test/Baseline/FaceRoI_1.nrrd.md5 | 1 + .../test/Baseline/FaceRoI_2.nrrd.md5 | 1 + .../Baseline/ThreeAxisFourLabelConflict.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_0.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_0_0.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_0_4.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_1.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_1_1.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_1_2.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_2.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_2_2.nrrd.md5 | 1 + .../ThreeAxisFourLabelConflict_2_3.nrrd.md5 | 1 + .../test/CMakeLists.txt | 16 ++++++++++++++-- 16 files changed, 29 insertions(+), 3 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index de906320e6c..00f65e25462 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -220,7 +220,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { next = m_Input->GetPixel(indNext); } - if (prev == 0 && next == 0) + if (prev == 0 && next == 0) //&& - isolated slices only, || - flat edges too { axis = a; ++cTrue; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI.nrrd.md5 new file mode 100644 index 00000000000..98cde0b9d35 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI.nrrd.md5 @@ -0,0 +1 @@ +e523459f019e4b15e5e625273d108521 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_0.nrrd.md5 new file mode 100644 index 00000000000..5fc076bf870 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_0.nrrd.md5 @@ -0,0 +1 @@ +590421f2c48c4057891a056c23c6a271 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_1.nrrd.md5 new file mode 100644 index 00000000000..50b39a4cba7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_1.nrrd.md5 @@ -0,0 +1 @@ +77047fc34df5f8478255ef2143f72101 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_2.nrrd.md5 new file mode 100644 index 00000000000..d0eff6c4839 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_2.nrrd.md5 @@ -0,0 +1 @@ +7dd222a95d0d34cf2bf198252aae96f5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 new file mode 100644 index 00000000000..f96035bd016 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 @@ -0,0 +1 @@ +9b05f929b2d30868091c75fb80042804 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 new file mode 100644 index 00000000000..42a1a775f3e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 @@ -0,0 +1 @@ +9e1269e3eab52b3a77f130a58fc32140 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 new file mode 100644 index 00000000000..0692f08003e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 @@ -0,0 +1 @@ +29cc558bd803b6e9f1f2180add128b89 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 new file mode 100644 index 00000000000..3032a13701f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 @@ -0,0 +1 @@ +43f1c85954cc933758d0743fde5c606f diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 new file mode 100644 index 00000000000..e30c578fbcb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 @@ -0,0 +1 @@ +24f59e3a707ad7ea34f015abf7395d37 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 new file mode 100644 index 00000000000..adec0f7f0b5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 @@ -0,0 +1 @@ +0a7148f795171af3153ef09ad400e0cd diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 new file mode 100644 index 00000000000..e30c578fbcb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 @@ -0,0 +1 @@ +24f59e3a707ad7ea34f015abf7395d37 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 4ae28616a64..ea2ee504b9b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -75,7 +75,6 @@ regressiontest(OneToThree nrrd) regressiontest(ExtrapolationAppearing nrrd) justinputtest(DoubleTwoLabelBranching nrrd) justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) -justinputtest(ThreeAxisFourLabelConflict nrrd) justinputtest(AccidentalMiddleSliceSegmentation nrrd) justinputtest(SevenLabels nrrd) justinputtest(FullEnd nrrd) @@ -91,6 +90,16 @@ regressiontest(GridSeg nrrd 2) regressiontest(GridSeg2 nrrd 0) regressiontest(GridSeg2 nrrd 1) regressiontest(GridSeg2 nrrd 2) +regressiontest(ThreeAxisFourLabelConflict nrrd) +regressiontest(ThreeAxisFourLabelConflict nrrd 0) +regressiontest(ThreeAxisFourLabelConflict nrrd 1) +regressiontest(ThreeAxisFourLabelConflict nrrd 2) +regressiontest(ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd 1 1) +regressiontest(ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 +regressiontest(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd 1 2) +regressiontest(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image # Paul's tests justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) @@ -102,5 +111,8 @@ justinputtest(65239R_amygdala_fin nii.gz) #TODO: make different combinations of axis and label parameters # Long-running handcrafted tests +regressiontest(FaceRoI nrrd) +regressiontest(FaceRoI nrrd 0) +regressiontest(FaceRoI nrrd 1) +regressiontest(FaceRoI nrrd 2) justinputtest(BigZ nrrd) -justinputtest(FaceRoI nrrd) #TODO: convert into Per axis/label regression test with FaceRoIFinished.nrrd as expected output From ab942c77e7b6856f3904ac8089b5e4b470bc7877 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Jan 2016 14:13:49 -0500 Subject: [PATCH 055/176] BUG: 1MN1 bug fixed and more regression tests --- .../itkMorphologicalContourInterpolator.hxx | 21 +++++++++---------- .../test/Baseline/1MN1.nrrd.md5 | 1 + ...AccidentalMiddleSliceSegmentation.nrrd.md5 | 1 + .../Baseline/DoubleTwoLabelBranching.nrrd.md5 | 1 + .../test/Baseline/FullEnd.nrrd.md5 | 1 + .../test/Baseline/ManyToMany16.nrrd.md5 | 1 + .../test/Baseline/SevenLabels.nrrd.md5 | 1 + ...isDoubleTwoLabelBranchingConflict.nrrd.md5 | 1 + .../test/CMakeLists.txt | 17 +++++++++------ .../test/Input/1MN1.nrrd.md5 | 1 + 10 files changed, 29 insertions(+), 17 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/1MN1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSegmentation.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/1MN1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 00f65e25462..6847a6ee3ca 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -40,7 +40,7 @@ template void WriteDebug(typename TImage::Pointer out, const char * filename) { - return; // tests run much faster + // return; //tests run much faster typedef ImageFileWriter WriterType; typename WriterType::Pointer w = WriterType::New(); w->SetInput(out); @@ -447,8 +447,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int m_Or->SetInput(0, iSeq[x]); unsigned xj = ratio * x; m_Or->SetInput(1, jSeq[xj]); - // WriteDebug(iSeq[x], (std::string("C:\\iSeq") + char('a' + x) + ".nrrd").c_str()); - // WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + char('a' + x) + ".nrrd").c_str()); + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); + WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); @@ -460,7 +460,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int IdentifierType min = newRegion.GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { - // WriteDebug(seq[x], (std::string("C:\\seq") + char('a' + x) + ".nrrd").c_str()); + WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) @@ -1072,7 +1072,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int if (iCounts[p->first] == 1) // M-to-1 { - for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (typename PairSet::iterator rest = pairs.begin(); rest != pairs.end(); ++rest) { if (rest->second == p->second) { @@ -1083,11 +1083,10 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); - typename PairSet::iterator rest = p; - ++rest; + typename PairSet::iterator rest = pairs.begin(); while (rest != pairs.end()) { - if (rest->second == p->second) + if (rest != p && rest->second == p->second) { --iCounts[rest->first]; --jCounts[rest->second]; @@ -1104,7 +1103,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // M-to-1 else if (jCounts[p->second] == 1) // 1-to-N { - for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (typename PairSet::iterator rest = pairs.begin(); rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -1115,11 +1114,11 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); - typename PairSet::iterator rest = p; + typename PairSet::iterator rest = pairs.begin(); ++rest; while (rest != pairs.end()) { - if (rest->first == p->first) + if (rest != p && rest->first == p->first) { --iCounts[rest->first]; --jCounts[rest->second]; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/1MN1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/1MN1.nrrd.md5 new file mode 100644 index 00000000000..da3463b8eee --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/1MN1.nrrd.md5 @@ -0,0 +1 @@ +7c9ec8535a0d0a24fb6e2cc6db56c9be diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSegmentation.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSegmentation.nrrd.md5 new file mode 100644 index 00000000000..d4c8624f497 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSegmentation.nrrd.md5 @@ -0,0 +1 @@ +3b2c1633ddbab99fcfe8cbbb2e3fb9d9 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching.nrrd.md5 new file mode 100644 index 00000000000..4fdfc958e42 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching.nrrd.md5 @@ -0,0 +1 @@ +0d8d337ba095b31eecd8f61b381aa086 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 new file mode 100644 index 00000000000..413adcfaacb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 @@ -0,0 +1 @@ +400f6cd0ce68d96c7f2ee79b31e52ae0 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 new file mode 100644 index 00000000000..6931643bb66 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 @@ -0,0 +1 @@ +744bfe4f07858c572ed6dc27b20cfc36 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 new file mode 100644 index 00000000000..982290e3d9e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 @@ -0,0 +1 @@ +33fd62ae32279a2c935000fe244bb563 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 new file mode 100644 index 00000000000..1ed463e8866 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 @@ -0,0 +1 @@ +9ac00d13152d0681c6fe8227245753ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index ea2ee504b9b..ef83af949fb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -18,6 +18,7 @@ target_link_libraries( ) function(JustInputTest ImageName Ext) #optional: Axis Label + # used to produce an output which is then taken as a baseline for a regression test foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -73,12 +74,13 @@ regressiontest(SimplestOneToOne nrrd) regressiontest(OneToOne nrrd) regressiontest(OneToThree nrrd) regressiontest(ExtrapolationAppearing nrrd) -justinputtest(DoubleTwoLabelBranching nrrd) -justinputtest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) -justinputtest(AccidentalMiddleSliceSegmentation nrrd) -justinputtest(SevenLabels nrrd) -justinputtest(FullEnd nrrd) -justinputtest(ManyToMany16 nrrd) +regressiontest(DoubleTwoLabelBranching nrrd) +regressiontest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) +regressiontest(AccidentalMiddleSliceSegmentation nrrd) +regressiontest(SevenLabels nrrd) +regressiontest(FullEnd nrrd) +regressiontest(1MN1 nrrd) # double sided many broken into many + 1 +regressiontest(ManyToMany16 nrrd) regressiontest(ManyToMany nrrd) regressiontest(GridSeg nrrd) regressiontest(GridSeg2 nrrd) @@ -116,3 +118,6 @@ regressiontest(FaceRoI nrrd 0) regressiontest(FaceRoI nrrd 1) regressiontest(FaceRoI nrrd 2) justinputtest(BigZ nrrd) +justinputtest(BigZ nrrd 0) +justinputtest(BigZ nrrd 1) +justinputtest(BigZ nrrd 2) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/1MN1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/1MN1.nrrd.md5 new file mode 100644 index 00000000000..9d538c8ecfc --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/1MN1.nrrd.md5 @@ -0,0 +1 @@ +5e46d7abaa53af1c3206c131a586d129 From 6eb7088b4753fbb5ac9d20e0afea8566bbd69d14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Jan 2016 16:13:29 -0500 Subject: [PATCH 056/176] ENH: limiting iteration count in Align() --- .../include/itkMorphologicalContourInterpolator.h | 2 ++ .../include/itkMorphologicalContourInterpolator.hxx | 13 +++++++++++-- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 60af7f86cee..34783e7bf90 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -86,6 +86,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter void WriteDebug(typename TImage::Pointer out, const char * filename) { - // return; //tests run much faster + return; // tests run much faster typedef ImageFileWriter WriterType; typename WriterType::Pointer w = WriterType::New(); w->SetInput(out); @@ -99,6 +99,9 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) , m_Axis(-1) , m_HeuristicAlignment(true) + , m_MinAlignIters(10) + , // smaller of this and max pixel count of the search image + m_MaxAlignIters(256) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { m_Or = OrType::New(); @@ -447,8 +450,10 @@ MorphologicalContourInterpolator::Interpolate1to1(int m_Or->SetInput(0, iSeq[x]); unsigned xj = ratio * x; m_Or->SetInput(1, jSeq[xj]); +#ifdef _DEBUG WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); +#endif // _DEBUG m_Or->GetOutput()->SetRegions(newRegion); m_Or->Update(); seq.push_back(m_Or->GetOutput()); @@ -460,7 +465,9 @@ MorphologicalContourInterpolator::Interpolate1to1(int IdentifierType min = newRegion.GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { +#ifdef _DEBUG WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); +#endif // _DEBUG IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) @@ -881,6 +888,7 @@ MorphologicalContourInterpolator::Align(int axis, searched->SetPixel(ind, true); IdentifierType score, maxScore = 0; typename TImage::IndexType bestIndex; + IdentifierType iter = 0, minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); // debug: construct and later fill the image with intersection scores #ifndef NDEBUG @@ -891,6 +899,7 @@ MorphologicalContourInterpolator::Align(int axis, while (!uncomputed.empty()) { + ++iter; ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); @@ -905,7 +914,7 @@ MorphologicalContourInterpolator::Align(int axis, } // we breadth this search - if (!m_HeuristicAlignment || maxScore == 0 || score > maxScore * 0.8) + if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || score > maxScore * 0.9 && iter <= m_MaxAlignIters) { for (unsigned d = 0; d < TImage::ImageDimension; d++) { From 31ecd0740ade0506f543e38a79990bf2adbf4e81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Jan 2016 16:20:32 -0500 Subject: [PATCH 057/176] BUG: BigZ regression tests --- .../test/Baseline/BigZ.nrrd.md5 | 1 + .../test/Baseline/BigZ_0.nrrd.md5 | 1 + .../test/Baseline/BigZ_1.nrrd.md5 | 1 + .../test/Baseline/BigZ_2.nrrd.md5 | 1 + .../test/CMakeLists.txt | 10 +++++----- 5 files changed, 9 insertions(+), 5 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ.nrrd.md5 new file mode 100644 index 00000000000..ec07630a31a --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ.nrrd.md5 @@ -0,0 +1 @@ +66df271013a1dfdc4e4a626545f44403 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_0.nrrd.md5 new file mode 100644 index 00000000000..cc134078084 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_0.nrrd.md5 @@ -0,0 +1 @@ +0f1bcdc78d46e8f434504da810c20467 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_1.nrrd.md5 new file mode 100644 index 00000000000..a858f0c0ea3 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_1.nrrd.md5 @@ -0,0 +1 @@ +eec2d3127aab56c7b5e445e982752c91 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_2.nrrd.md5 new file mode 100644 index 00000000000..00612433a09 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_2.nrrd.md5 @@ -0,0 +1 @@ +90b7caa24c6f4f2ae9b892e1fc2e776c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index ef83af949fb..3f699c1b4da 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -17,8 +17,8 @@ target_link_libraries( ${MorphologicalContourInterpolation-Test_LIBRARIES} ) +# used to produce an output which is then taken as a baseline for a regression test function(JustInputTest ImageName Ext) #optional: Axis Label - # used to produce an output which is then taken as a baseline for a regression test foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -117,7 +117,7 @@ regressiontest(FaceRoI nrrd) regressiontest(FaceRoI nrrd 0) regressiontest(FaceRoI nrrd 1) regressiontest(FaceRoI nrrd 2) -justinputtest(BigZ nrrd) -justinputtest(BigZ nrrd 0) -justinputtest(BigZ nrrd 1) -justinputtest(BigZ nrrd 2) +regressiontest(BigZ nrrd) +regressiontest(BigZ nrrd 0) +regressiontest(BigZ nrrd 1) +regressiontest(BigZ nrrd 2) From 4d2810d0c0ef80b74568f8dc896119a7b88b93c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Jan 2016 16:50:44 -0500 Subject: [PATCH 058/176] ENH: baseline for Paul's tests --- .../test/Baseline/105769fixed.nii.gz.md5 | 1 + .../test/Baseline/105769fixed_-1_0.nii.gz.md5 | 1 + .../test/Baseline/105769fixed_-1_1.nii.gz.md5 | 1 + .../test/Baseline/105769fixed_-1_2.nii.gz.md5 | 1 + .../test/Baseline/105769fixed_2.nii.gz.md5 | 1 + 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b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_1.nii.gz.md5 new file mode 100644 index 00000000000..c842bd26cd4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_1.nii.gz.md5 @@ -0,0 +1 @@ +7711dbadd1004da7a4b00b352d8d773b diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_2.nii.gz.md5 new file mode 100644 index 00000000000..f8350c1bd37 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_2.nii.gz.md5 @@ -0,0 +1 @@ +225c31150034b1c9b409ee99c410b2eb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_3.nii.gz.md5 new file mode 100644 index 00000000000..3aeac9e7d9b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_3.nii.gz.md5 @@ -0,0 +1 @@ +11482862aa7a5d46e38847380cfda62a diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_4.nii.gz.md5 new file mode 100644 index 00000000000..b58c315f01b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_2_4.nii.gz.md5 @@ -0,0 +1 @@ +438f3ae84503ab382dc06e54e3b40ace diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin.nii.gz.md5 new file mode 100644 index 00000000000..503b774ede3 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin.nii.gz.md5 @@ -0,0 +1 @@ +4012c7a6e5dae4870f957a545c2a31df diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0.nii.gz.md5 new file mode 100644 index 00000000000..82046b6ae9c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0.nii.gz.md5 @@ -0,0 +1 @@ +d74748a09b060f9cb9852e02f8279361 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_1.nii.gz.md5 new file mode 100644 index 00000000000..7cac01a327b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_1.nii.gz.md5 @@ -0,0 +1 @@ +33505f3856d5b12fce8df06903c16804 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_2.nii.gz.md5 new file mode 100644 index 00000000000..22579a1ad8b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_2.nii.gz.md5 @@ -0,0 +1 @@ +714aedc0d2147b9a7f2668df74d32cf3 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_3.nii.gz.md5 new file mode 100644 index 00000000000..3599a1d83c6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_3.nii.gz.md5 @@ -0,0 +1 @@ +24c301502d9651f81de762066d5b979e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_4.nii.gz.md5 new file mode 100644 index 00000000000..4e4f1d52580 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_0_4.nii.gz.md5 @@ -0,0 +1 @@ +8052f6048677ea27dbc86ed7e5513536 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1.nii.gz.md5 new file mode 100644 index 00000000000..b327bad2407 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1.nii.gz.md5 @@ -0,0 +1 @@ +2c9d7e1d5b2454503717f51d0a2914dc diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_1.nii.gz.md5 new file mode 100644 index 00000000000..63cd2f70fa4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_1.nii.gz.md5 @@ -0,0 +1 @@ +c43e9fff58a542472c88e2b3061a8c96 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_2.nii.gz.md5 new file mode 100644 index 00000000000..004541e3dfa --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_2.nii.gz.md5 @@ -0,0 +1 @@ +04a065af89320489a7e5bc0dcf53a7dd diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_3.nii.gz.md5 new file mode 100644 index 00000000000..698dbeb1d42 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_3.nii.gz.md5 @@ -0,0 +1 @@ +fff08f8dcf715484fcd8a997eeb359e2 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_4.nii.gz.md5 new file mode 100644 index 00000000000..02e068ba69a --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_1_4.nii.gz.md5 @@ -0,0 +1 @@ +b540849ece6420d29ae9bbcf0c74be2a diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2.nii.gz.md5 new file mode 100644 index 00000000000..48eb00a265b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2.nii.gz.md5 @@ -0,0 +1 @@ +71365dd0ec2622539a32e9d626eeb7c6 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_1.nii.gz.md5 new file mode 100644 index 00000000000..2c5ce1270c7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_1.nii.gz.md5 @@ -0,0 +1 @@ +cff99924a01405b878135c555a01c954 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_2.nii.gz.md5 new file mode 100644 index 00000000000..7810f9efba0 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_2.nii.gz.md5 @@ -0,0 +1 @@ +84eb95beeb223dd609865cae08390065 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_3.nii.gz.md5 new file mode 100644 index 00000000000..24bcdafff02 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_3.nii.gz.md5 @@ -0,0 +1 @@ +f73eb2c147e808242d553de9ecf76d2e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_4.nii.gz.md5 new file mode 100644 index 00000000000..756164ec772 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_2_4.nii.gz.md5 @@ -0,0 +1 @@ +987a12eaf917a0b05ff002fb823fd356 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int.nii.gz.md5 new file mode 100644 index 00000000000..e0d2d5d4d4f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int.nii.gz.md5 @@ -0,0 +1 @@ +903b88d9e63e081dad1b63e3c1705ae1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0.nii.gz.md5 new file mode 100644 index 00000000000..0fc418036f0 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0.nii.gz.md5 @@ -0,0 +1 @@ +fb5396bc27673fc15395847ded64ba40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_1.nii.gz.md5 new file mode 100644 index 00000000000..fe42570de00 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_1.nii.gz.md5 @@ -0,0 +1 @@ +8caeeff0974f7c30a586a29ecf37bc25 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_2.nii.gz.md5 new file mode 100644 index 00000000000..9924b509b98 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_2.nii.gz.md5 @@ -0,0 +1 @@ +6aba3b5a9a5b5fada3d217286203af76 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_3.nii.gz.md5 new file mode 100644 index 00000000000..ac3596e7ddc --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_3.nii.gz.md5 @@ -0,0 +1 @@ +2d5e9ccc51ff7f9c62d31a2fa05c16c7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_4.nii.gz.md5 new file mode 100644 index 00000000000..3cc22d5e9ef --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_0_4.nii.gz.md5 @@ -0,0 +1 @@ +3ebc56c6e51c72df12e85c492d3adc8e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1.nii.gz.md5 new file mode 100644 index 00000000000..8043c5db711 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1.nii.gz.md5 @@ -0,0 +1 @@ +b8b36cf75cce02cb9d30da496f2f548b diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_1.nii.gz.md5 new file mode 100644 index 00000000000..6965a8d0162 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_1.nii.gz.md5 @@ -0,0 +1 @@ +b054b276f0997d8242021506450f5ee9 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_2.nii.gz.md5 new file mode 100644 index 00000000000..56e9ee49fa4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_2.nii.gz.md5 @@ -0,0 +1 @@ +a7430c64a8e09fde34a0a986ea0eb4ed diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_3.nii.gz.md5 new file mode 100644 index 00000000000..8a13b24dacc --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_3.nii.gz.md5 @@ -0,0 +1 @@ +dd0a05da690a9a0cc70f45ca0ce8b941 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_4.nii.gz.md5 new file mode 100644 index 00000000000..6627d0539b0 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_1_4.nii.gz.md5 @@ -0,0 +1 @@ +930030fd3eccc73fe3d754ca51508f7b diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2.nii.gz.md5 new file mode 100644 index 00000000000..96413520238 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2.nii.gz.md5 @@ -0,0 +1 @@ +9dca42cebd82e1c7d0ea8255d6bf2161 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_1.nii.gz.md5 new file mode 100644 index 00000000000..366f44c6ce9 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_1.nii.gz.md5 @@ -0,0 +1 @@ +94298df53d49d3d84cc9d014c32a9183 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_2.nii.gz.md5 new file mode 100644 index 00000000000..4989aa6336d --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_2.nii.gz.md5 @@ -0,0 +1 @@ +c00975e58a9657b4e9c820fdcc21745a diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_3.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_3.nii.gz.md5 new file mode 100644 index 00000000000..72b8965517c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_3.nii.gz.md5 @@ -0,0 +1 @@ +1e7a21d409e4e3deabca85e4f6da26fd diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_4.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_4.nii.gz.md5 new file mode 100644 index 00000000000..40ce72eb044 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_2_4.nii.gz.md5 @@ -0,0 +1 @@ +5b628656f7b5a54e400524b556996fd4 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 3f699c1b4da..5392d0c8704 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -22,15 +22,11 @@ function(JustInputTest ImageName Ext) #optional: Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() - set( - outImage - "${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated${optArgs}.${Ext}" - ) + set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}${optArgs}.${Ext}") # set(imageNameOpt "${ImageName}${optArgs}") # only used for regression itk_add_test( - NAME - itkMorphologicalContourInterpolation_RegressionTest_${ImageName}${optArgs} + NAME itkMorphologicalContourInterpolation_JustInOut_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver # --compare DATA{Baseline/${imageNameOpt}.${Ext}} ${outImage} # no regression @@ -45,15 +41,11 @@ function(RegressionTest ImageName Ext) #optional: Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() - set( - outImage - "${ITK_TEST_OUTPUT_DIR}/${ImageName}_interpolated${optArgs}.${Ext}" - ) + set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}${optArgs}.${Ext}") set(imageNameOpt "${ImageName}${optArgs}") itk_add_test( - NAME - itkMorphologicalContourInterpolation_RegressionTest_${ImageName}${optArgs} + NAME itkMorphologicalContourInterpolation_Regression_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver --compare @@ -103,21 +95,100 @@ regressiontest(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 regressiontest(ThreeAxisFourLabelConflict nrrd 1 2) regressiontest(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image -# Paul's tests -justinputtest(105769moving_resliced_to_fixedhz2_segmentation nii.gz) -justinputtest(105769fixed_segmentation nii.gz) -justinputtest(64816L_amygdala_int nii.gz) -justinputtest(64816L_amygdala_fin nii.gz) -justinputtest(65239R_amygdala_int nii.gz) -justinputtest(65239R_amygdala_fin nii.gz) -#TODO: make different combinations of axis and label parameters +# Paul's single axis tests +regressiontest(105769moving nii.gz) #defaults: all axes all labels +regressiontest(105769moving nii.gz 2) #axis 2 +regressiontest(105769moving nii.gz -1 0) #all axes all labels +regressiontest(105769moving nii.gz -1 1) #all axes label 1 +regressiontest(105769moving nii.gz -1 2) #all axes label 2 +regressiontest(105769moving nii.gz 2 1) #axis 2 label 1 +regressiontest(105769moving nii.gz 2 2) #axis 2 label 2 +regressiontest(105769fixed nii.gz) #defaults: all axes all labels +regressiontest(105769fixed nii.gz 2) #axis 2 +regressiontest(105769fixed nii.gz -1 0) #all axes all labels +regressiontest(105769fixed nii.gz -1 1) #all axes label 1 +regressiontest(105769fixed nii.gz -1 2) #all axes label 2 +regressiontest(105769fixed nii.gz 2 1) #axis 2 label 1 +regressiontest(105769fixed nii.gz 2 2) #axis 2 label 2 + +# 64816L_amygdala_int +regressiontest(64816L_amygdala_int nii.gz) +regressiontest(64816L_amygdala_int nii.gz 0) +regressiontest(64816L_amygdala_int nii.gz 1) +regressiontest(64816L_amygdala_int nii.gz 2) +regressiontest(64816L_amygdala_int nii.gz 0 1) +regressiontest(64816L_amygdala_int nii.gz 0 2) +regressiontest(64816L_amygdala_int nii.gz 0 3) +regressiontest(64816L_amygdala_int nii.gz 0 4) +regressiontest(64816L_amygdala_int nii.gz 1 1) +regressiontest(64816L_amygdala_int nii.gz 1 2) +regressiontest(64816L_amygdala_int nii.gz 1 3) +regressiontest(64816L_amygdala_int nii.gz 1 4) +regressiontest(64816L_amygdala_int nii.gz 2 1) +regressiontest(64816L_amygdala_int nii.gz 2 2) +regressiontest(64816L_amygdala_int nii.gz 2 3) +regressiontest(64816L_amygdala_int nii.gz 2 4) + +# 64816L_amygdala_fin +regressiontest(64816L_amygdala_fin nii.gz) +regressiontest(64816L_amygdala_fin nii.gz 0) +regressiontest(64816L_amygdala_fin nii.gz 1) +regressiontest(64816L_amygdala_fin nii.gz 2) +regressiontest(64816L_amygdala_fin nii.gz 0 1) +regressiontest(64816L_amygdala_fin nii.gz 0 2) +regressiontest(64816L_amygdala_fin nii.gz 0 3) +regressiontest(64816L_amygdala_fin nii.gz 0 4) +regressiontest(64816L_amygdala_fin nii.gz 1 1) +regressiontest(64816L_amygdala_fin nii.gz 1 2) +regressiontest(64816L_amygdala_fin nii.gz 1 3) +regressiontest(64816L_amygdala_fin nii.gz 1 4) +regressiontest(64816L_amygdala_fin nii.gz 2 1) +regressiontest(64816L_amygdala_fin nii.gz 2 2) +regressiontest(64816L_amygdala_fin nii.gz 2 3) +regressiontest(64816L_amygdala_fin nii.gz 2 4) + +# 65239R_amygdala_int +regressiontest(65239R_amygdala_int nii.gz) +regressiontest(65239R_amygdala_int nii.gz 0) +regressiontest(65239R_amygdala_int nii.gz 1) +regressiontest(65239R_amygdala_int nii.gz 2) +regressiontest(65239R_amygdala_int nii.gz 0 1) +regressiontest(65239R_amygdala_int nii.gz 0 2) +regressiontest(65239R_amygdala_int nii.gz 0 3) +regressiontest(65239R_amygdala_int nii.gz 0 4) +regressiontest(65239R_amygdala_int nii.gz 1 1) +regressiontest(65239R_amygdala_int nii.gz 1 2) +regressiontest(65239R_amygdala_int nii.gz 1 3) +regressiontest(65239R_amygdala_int nii.gz 1 4) +regressiontest(65239R_amygdala_int nii.gz 2 1) +regressiontest(65239R_amygdala_int nii.gz 2 2) +regressiontest(65239R_amygdala_int nii.gz 2 3) +regressiontest(65239R_amygdala_int nii.gz 2 4) + +# 65239R_amygdala_fin +regressiontest(65239R_amygdala_fin nii.gz) +regressiontest(65239R_amygdala_fin nii.gz 0) +regressiontest(65239R_amygdala_fin nii.gz 1) +regressiontest(65239R_amygdala_fin nii.gz 2) +regressiontest(65239R_amygdala_fin nii.gz 0 1) +regressiontest(65239R_amygdala_fin nii.gz 0 2) +regressiontest(65239R_amygdala_fin nii.gz 0 3) +regressiontest(65239R_amygdala_fin nii.gz 0 4) +regressiontest(65239R_amygdala_fin nii.gz 1 1) +regressiontest(65239R_amygdala_fin nii.gz 1 2) +regressiontest(65239R_amygdala_fin nii.gz 1 3) +regressiontest(65239R_amygdala_fin nii.gz 1 4) +regressiontest(65239R_amygdala_fin nii.gz 2 1) +regressiontest(65239R_amygdala_fin nii.gz 2 2) +regressiontest(65239R_amygdala_fin nii.gz 2 3) +regressiontest(65239R_amygdala_fin nii.gz 2 4) # Long-running handcrafted tests -regressiontest(FaceRoI nrrd) -regressiontest(FaceRoI nrrd 0) -regressiontest(FaceRoI nrrd 1) -regressiontest(FaceRoI nrrd 2) regressiontest(BigZ nrrd) regressiontest(BigZ nrrd 0) regressiontest(BigZ nrrd 1) regressiontest(BigZ nrrd 2) +regressiontest(FaceRoI nrrd) +regressiontest(FaceRoI nrrd 0) +regressiontest(FaceRoI nrrd 1) +regressiontest(FaceRoI nrrd 2) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed_segmentation.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2_segmentation.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving_resliced_to_fixedhz2.nii.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url new file mode 100644 index 00000000000..d8e2b7b318f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url @@ -0,0 +1,5 @@ +[{000214A0-0000-0000-C000-000000000046}] +Prop3=19,11 +[InternetShortcut] +URL=https://midas3.kitware.com/midas/folder/13381 +IDList= diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3folder.url rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url From 2ce610e3eb60afad4967e425936de831b2d13520 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 2 Mar 2016 18:09:25 -0500 Subject: [PATCH 059/176] ENH: avoid duplicate execution of connected components --- .../itkMorphologicalContourInterpolator.h | 4 +- .../itkMorphologicalContourInterpolator.hxx | 57 +++++++++---------- 2 files changed, 31 insertions(+), 30 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 34783e7bf90..26382d7f257 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -109,7 +109,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::InterpolateBetweenTwo(int TImage * out, typename TImage::PixelType label, typename TImage::IndexValueType i, - typename TImage::IndexValueType j) + typename TImage::IndexValueType j, + typename TImage::Pointer iconn, + typename TImage::Pointer jconn) { - if (i > j) - { - std::swap(i, j); - } - if (i == j || i + 1 == j) - { - return; // nothing to do - } - - // determine inter-slice region correspondences - typename TImage::RegionType ri; - ri = m_BoundingBoxes[label]; - ri.SetSize(axis, 1); - ri.SetIndex(axis, i); - typename TImage::RegionType rj = ri; - rj.SetIndex(axis, j); - - // execute connected components - IdentifierType iCount, jCount; - typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, label, iCount); - iconn->DisconnectPipeline(); - typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, label, jCount); - jconn->DisconnectPipeline(); - WriteDebug(iconn, "C:\\iconn.nrrd"); - WriteDebug(jconn, "C:\\jconn.nrrd"); - // go through comparison image and create correspondence pairs typedef std::set> PairSet; PairSet pairs, unwantedPairs, uncleanPairs; + typename TImage::RegionType ri = iconn->GetRequestedRegion(); + typename TImage::RegionType rj = jconn->GetRequestedRegion(); ImageRegionConstIterator iti(iconn, ri); ImageRegionConstIterator itj(jconn, rj); while (!iti.IsAtEnd()) @@ -1204,12 +1182,33 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename SliceSetType::iterator prev = it->second.begin(); if (prev == it->second.end()) { - return; // nothing to do + continue; // nothing to do for this label } + + typename TImage::RegionType ri; + ri = m_BoundingBoxes[it->first]; + ri.SetSize(axis, 1); + ri.SetIndex(axis, *prev); + IdentifierType xCount; + typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); + iconn->DisconnectPipeline(); + typename SliceSetType::iterator next = it->second.begin(); for (++next; next != it->second.end(); ++next) { - InterpolateBetweenTwo(axis, out, it->first, *prev, *next); + typename TImage::RegionType rj = ri; + rj.SetIndex(axis, *next); + typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); + jconn->DisconnectPipeline(); + + WriteDebug(iconn, "C:\\iconn.nrrd"); + WriteDebug(jconn, "C:\\jconn.nrrd"); + + if (*prev + 1 < *next) // only if there are not adjacent slices + { + InterpolateBetweenTwo(axis, out, it->first, *prev, *next, iconn, jconn); + } + iconn = jconn; prev = next; } } From 7047e5a4b627a857e6c4c357a97417cb305b3218 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 3 Mar 2016 19:55:33 -0500 Subject: [PATCH 060/176] ENH: parallelizing InterpolateAlong() using C++11 threads per-thread instantiation of ITK filters and forcing ITK filters to be single threaded --- .../itkMorphologicalContourInterpolator.h | 8 +- .../itkMorphologicalContourInterpolator.hxx | 119 ++++++++++++++---- 2 files changed, 99 insertions(+), 28 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 26382d7f257..504a7fba08d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -136,7 +136,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter - GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end); + GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end, int axis); /** Build transition sequence and pick the median */ void @@ -238,7 +238,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter RoiType; typename RoiType::Pointer m_RoI; @@ -251,16 +251,12 @@ class MorphologicalContourInterpolator : public ImageToImageFilter StructuringElementType; typedef BinaryBallStructuringElement StructuringElementType; - StructuringElementType m_StructuringElement; typedef BinaryDilateImageFilter DilateType; - typename DilateType::Pointer m_Dilator; typedef AndImageFilter AndFilterType; - typename AndFilterType::Pointer m_And; typedef OrImageFilter OrType; - typename OrType::Pointer m_Or; class MatchesID { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 0cbead913f0..00d0624696e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -28,6 +28,9 @@ #include #include #include +#include +#include +#include // DEBUG #include @@ -43,6 +46,7 @@ WriteDebug(typename TImage::Pointer out, const char * filename) return; // tests run much faster typedef ImageFileWriter WriterType; typename WriterType::Pointer w = WriterType::New(); + w->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads w->SetInput(out); w->SetFileName(filename); try @@ -62,6 +66,7 @@ WriteDebug(Image::Pointer out, const char * filename) typedef Image ucharImageType; typedef CastImageFilter CastType; CastType::Pointer caster = CastType::New(); + caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetInput(out); WriteDebug(caster->GetOutput(), filename); } @@ -104,10 +109,6 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_MaxAlignIters(256) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { - m_Or = OrType::New(); - m_Dilator = DilateType::New(); // structuring element in InterpolateAlong - m_And = AndFilterType::New(); - // set up pipeline for regioned connected components m_RoI = RoiType::New(); m_Binarizer = BinarizerType::New(); @@ -306,8 +307,23 @@ MorphologicalContourInterpolator::Extrapolate(int template typename MorphologicalContourInterpolator::BoolImageType::Pointer MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointer seed, - typename BoolImageType::Pointer mask) + typename BoolImageType::Pointer mask, + int axis) { + thread_local typename DilateType::Pointer m_Dilator = DilateType::New(); + m_Dilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + // set up structuring element for dilation + typedef Size SizeType; + SizeType size; + size.Fill(1); + size[axis] = 0; + thread_local StructuringElementType m_StructuringElement; + m_StructuringElement.SetRadius(size); + m_StructuringElement.CreateStructuringElement(); + m_Dilator->SetKernel(m_StructuringElement); + + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads m_Dilator->SetInput(seed); m_Dilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); m_Dilator->Update(); @@ -331,7 +347,8 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe template std::vector::BoolImageType::Pointer> MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolImageType::Pointer begin, - typename BoolImageType::Pointer end) + typename BoolImageType::Pointer end, + int axis) { // typedef Testing::HashImageFilter HashType; // HashType::Pointer hasher = HashType::New(); @@ -339,11 +356,11 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool // std::vector hashes; // TODO: optimization: replace ImagesEqual call with hash comparison? std::vector seq; - seq.push_back(Dilate1(begin, end)); + seq.push_back(Dilate1(begin, end, axis)); do { seq.back()->DisconnectPipeline(); - seq.push_back(Dilate1(seq.back(), end)); + seq.push_back(Dilate1(seq.back(), end, axis)); } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image return seq; @@ -415,6 +432,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int MatchesID matchesIDj(jRegionId); typedef UnaryFunctorImageFilter CastType; typename CastType::Pointer caster = CastType::New(); + caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetFunctor(matchesIDi); caster->SetInput(iConnT); caster->Update(); @@ -427,6 +445,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int jMask->DisconnectPipeline(); // generate sequence + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads WriteDebug(iMask, "C:\\iMask.nrrd"); WriteDebug(jMask, "C:\\jMask.nrrd"); m_And->SetInput(0, iMask); @@ -436,14 +456,16 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename BoolImageType::Pointer intersection = m_And->GetOutput(); intersection->DisconnectPipeline(); WriteDebug(intersection, "C:\\intersection.nrrd"); - std::vector iSeq = GenerateDilationSequence(intersection, iMask); - std::vector jSeq = GenerateDilationSequence(intersection, jMask); + std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); + std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection if (iSeq.size() < jSeq.size()) { iSeq.swap(jSeq); // swap so iSeq.size() >= jSeq.size() } - float ratio = float(jSeq.size()) / iSeq.size(); + float ratio = float(jSeq.size()) / iSeq.size(); + thread_local typename OrType::Pointer m_Or = OrType::New(); + m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) { @@ -500,6 +522,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int { typedef CastImageFilter InvertCastType; typename InvertCastType::Pointer invCaster = InvertCastType::New(); + invCaster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads invCaster->SetInput(seq[minIndex]); invCaster->Update(); typename TImage::Pointer midConn = invCaster->GetOutput(); @@ -542,6 +565,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int typedef UnaryFunctorImageFilter CastType; typename CastType::Pointer caster = CastType::New(); + caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); @@ -612,7 +636,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[x] = Dilate1(blobs[x], mask); + blobs[x] = Dilate1(blobs[x], mask, axis); WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); // TODO: save these in a sequence so we don't have to recalculate it! @@ -1162,18 +1186,54 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() +// a crude way to limit the number of threads to number of cores +void +join1(std::list> & threads, int slack = std::thread::hardware_concurrency()) +{ + auto it = threads.begin(); + int count = 0; + auto zeroDuration = std::chrono::microseconds(0); + auto sleepDuration = std::chrono::microseconds(100); + while (it != threads.end()) + { + if (it->wait_for(zeroDuration) == std::future_status::ready) + { + threads.erase(it); + return; + } + else + { + ++it; // check next + count++; + } + } + + if (count > slack) // we really need to wait + { + do + { + std::this_thread::sleep_for(sleepDuration); + it = threads.begin(); + while (it != threads.end()) + { + if (it->wait_for(zeroDuration) == std::future_status::ready) + { + threads.erase(it); + return; + } + ++it; + } + } while (true); + } +} + template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { - // set up structuring element for dilation - typedef Size SizeType; - SizeType size; - size.Fill(1); - size[axis] = 0; - m_StructuringElement.SetRadius(size); - m_StructuringElement.CreateStructuringElement(); - m_Dilator->SetKernel(m_StructuringElement); + // do multithreading by paralellizing for different labels + // and different inter-slice segments [C++11 threads] + std::list> threadResults; for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { @@ -1204,15 +1264,30 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou WriteDebug(iconn, "C:\\iconn.nrrd"); WriteDebug(jconn, "C:\\jconn.nrrd"); - if (*prev + 1 < *next) // only if there are not adjacent slices + if (*prev + 1 < *next) // only if they are not adjacent slices { - InterpolateBetweenTwo(axis, out, it->first, *prev, *next, iconn, jconn); + threadResults.push_back(std::async(std::launch::async, + &MorphologicalContourInterpolator::InterpolateBetweenTwo, + this, + axis, + out, + it->first, + *prev, + *next, + iconn, + jconn)); + join1(threadResults); // wait for one thread to finish + // in case there is more threads than processing cores + // InterpolateBetweenTwo(axis, out, it->first, *prev, *next, iconn, jconn); //sequential } iconn = jconn; prev = next; } } } + + // wait for leftover threads + join1(threadResults, 0); } From 2abde8bd9789cde6f34711c6c581882f8704d658 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 17 Mar 2016 11:24:18 -0400 Subject: [PATCH 061/176] ENH: Cross structuring element works in conjunction with FullyConnected off in ConnectedComponents --- .../include/itkMorphologicalContourInterpolator.hxx | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 00d0624696e..cca4c5c2ffb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -115,6 +115,8 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_Binarizer->SetInput(m_RoI->GetOutput()); m_ConnectedComponents = ConnectedComponentsType::New(); m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); + // FullyConnected is related to structuring element used + // true for ball, false for cross m_ConnectedComponents->SetFullyConnected(true); } From cef7ad88f572149f7d5ef3daf9d7dd29eee14aec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 17 Mar 2016 12:38:50 -0400 Subject: [PATCH 062/176] ENH: Introducing variable for selection of core interpolation algorithm: repeated dilations vs distance map --- .../itkMorphologicalContourInterpolator.h | 21 ++ .../itkMorphologicalContourInterpolator.hxx | 151 +++++++---- .../itk-module.cmake | 1 + ...d.nii.gz.md5 => 105769fixed_RD.nii.gz.md5} | 0 ....gz.md5 => 105769fixed_RD_-1_0.nii.gz.md5} | 0 ....gz.md5 => 105769fixed_RD_-1_1.nii.gz.md5} | 0 ....gz.md5 => 105769fixed_RD_-1_2.nii.gz.md5} | 0 ...nii.gz.md5 => 105769fixed_RD_2.nii.gz.md5} | 0 ...i.gz.md5 => 105769fixed_RD_2_1.nii.gz.md5} | 0 ...i.gz.md5 => 105769fixed_RD_2_2.nii.gz.md5} | 0 ....nii.gz.md5 => 105769moving_RD.nii.gz.md5} | 0 ...gz.md5 => 105769moving_RD_-1_0.nii.gz.md5} | 0 ...gz.md5 => 105769moving_RD_-1_1.nii.gz.md5} | 0 ...gz.md5 => 105769moving_RD_-1_2.nii.gz.md5} | 0 ...ii.gz.md5 => 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64816L_amygdala_fin_RD_0_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_0_2.nii.gz.md5 => 64816L_amygdala_fin_RD_0_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_0_3.nii.gz.md5 => 64816L_amygdala_fin_RD_0_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_0_4.nii.gz.md5 => 64816L_amygdala_fin_RD_0_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_1.nii.gz.md5 => 64816L_amygdala_fin_RD_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_1_1.nii.gz.md5 => 64816L_amygdala_fin_RD_1_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{64816L_amygdala_fin_1_2.nii.gz.md5 => 64816L_amygdala_fin_RD_1_2.nii.gz.md5} (100%) rename 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Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_0.nii.gz.md5 => 65239R_amygdala_fin_RD_0.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_0_1.nii.gz.md5 => 65239R_amygdala_fin_RD_0_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_0_2.nii.gz.md5 => 65239R_amygdala_fin_RD_0_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_0_3.nii.gz.md5 => 65239R_amygdala_fin_RD_0_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_0_4.nii.gz.md5 => 65239R_amygdala_fin_RD_0_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_1.nii.gz.md5 => 65239R_amygdala_fin_RD_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_1_1.nii.gz.md5 => 65239R_amygdala_fin_RD_1_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_1_2.nii.gz.md5 => 65239R_amygdala_fin_RD_1_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_1_3.nii.gz.md5 => 65239R_amygdala_fin_RD_1_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_1_4.nii.gz.md5 => 65239R_amygdala_fin_RD_1_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_2.nii.gz.md5 => 65239R_amygdala_fin_RD_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_2_1.nii.gz.md5 => 65239R_amygdala_fin_RD_2_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_2_2.nii.gz.md5 => 65239R_amygdala_fin_RD_2_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_2_3.nii.gz.md5 => 65239R_amygdala_fin_RD_2_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_2_4.nii.gz.md5 => 65239R_amygdala_fin_RD_2_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int.nii.gz.md5 => 65239R_amygdala_int_RD.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_0.nii.gz.md5 => 65239R_amygdala_int_RD_0.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_0_1.nii.gz.md5 => 65239R_amygdala_int_RD_0_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_0_2.nii.gz.md5 => 65239R_amygdala_int_RD_0_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_0_3.nii.gz.md5 => 65239R_amygdala_int_RD_0_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_0_4.nii.gz.md5 => 65239R_amygdala_int_RD_0_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_1.nii.gz.md5 => 65239R_amygdala_int_RD_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_1_1.nii.gz.md5 => 65239R_amygdala_int_RD_1_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_1_2.nii.gz.md5 => 65239R_amygdala_int_RD_1_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_1_3.nii.gz.md5 => 65239R_amygdala_int_RD_1_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_1_4.nii.gz.md5 => 65239R_amygdala_int_RD_1_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_2.nii.gz.md5 => 65239R_amygdala_int_RD_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_2_1.nii.gz.md5 => 65239R_amygdala_int_RD_2_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_2_2.nii.gz.md5 => 65239R_amygdala_int_RD_2_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_2_3.nii.gz.md5 => 65239R_amygdala_int_RD_2_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_2_4.nii.gz.md5 => 65239R_amygdala_int_RD_2_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{AccidentalMiddleSliceSegmentation.nrrd.md5 => AccidentalMiddleSliceSeg_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ.nrrd.md5 => BigZ_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_0.nrrd.md5 => BigZ_RD_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_1.nrrd.md5 => BigZ_RD_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_2.nrrd.md5 => BigZ_RD_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{DoubleTwoLabelBranching.nrrd.md5 => DoubleTwoLabelBranching_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{Empty.nrrd.md5 => Empty_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ExtrapolationAppearing.nrrd.md5 => ExtrapolationAppearing_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI.nrrd.md5 => FaceRoI_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_0.nrrd.md5 => FaceRoI_RD_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_1.nrrd.md5 => FaceRoI_RD_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_2.nrrd.md5 => FaceRoI_RD_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FullEnd.nrrd.md5 => FullEnd_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2.nrrd.md5 => GridSeg2_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_0.nrrd.md5 => GridSeg2_RD_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_1.nrrd.md5 => GridSeg2_RD_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_2.nrrd.md5 => GridSeg2_RD_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg.nrrd.md5 => GridSeg_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_0.nrrd.md5 => GridSeg_RD_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_1.nrrd.md5 => GridSeg_RD_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_2.nrrd.md5 => GridSeg_RD_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ManyToMany16.nrrd.md5 => ManyToMany16_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ManyToMany.nrrd.md5 => ManyToMany_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{Micro1.nrrd.md5 => Micro1_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{NoSlices.nrrd.md5 => NoSlices_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{OneToOne.nrrd.md5 => OneToOne_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{OneToThree.nrrd.md5 => OneToThree_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{SevenLabels.nrrd.md5 => SevenLabels_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{SimplestOneToOne.nrrd.md5 => SimplestOneToOne_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict.nrrd.md5 => ThreeAxisFourLabelConflict_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_0.nrrd.md5 => ThreeAxisFourLabelConflict_RD_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_0_0.nrrd.md5 => ThreeAxisFourLabelConflict_RD_0_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_0_4.nrrd.md5 => ThreeAxisFourLabelConflict_RD_0_4.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_1.nrrd.md5 => ThreeAxisFourLabelConflict_RD_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_1_1.nrrd.md5 => ThreeAxisFourLabelConflict_RD_1_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_1_2.nrrd.md5 => ThreeAxisFourLabelConflict_RD_1_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_2.nrrd.md5 => ThreeAxisFourLabelConflict_RD_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_2_2.nrrd.md5 => ThreeAxisFourLabelConflict_RD_2_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_2_3.nrrd.md5 => ThreeAxisFourLabelConflict_RD_2_3.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 => TwoAxisDoubleTwoLabelBC_RD.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Input/{AccidentalMiddleSliceSegmentation.nrrd.md5 => AccidentalMiddleSliceSeg.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Input/{TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 => TwoAxisDoubleTwoLabelBC.nrrd.md5} (100%) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 504a7fba08d..ea65f8bdb69 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -76,6 +76,18 @@ class MorphologicalContourInterpolator : public ImageToImageFilter GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end, int axis); + /** Finds an interpolating mask for these two aligned masks */ + typename BoolImageType::Pointer + FindMedianImageDilations(int axis, typename BoolImageType::Pointer iMask, typename BoolImageType::Pointer jMask); + + /** Finds an interpolating mask for these two aligned masks */ + typename BoolImageType::Pointer + FindMedianImageDistances(int axis, typename BoolImageType::Pointer iMask, typename BoolImageType::Pointer jMask); + /** Build transition sequence and pick the median */ void Interpolate1to1(int axis, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index cca4c5c2ffb..b9f11445928 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -25,6 +25,7 @@ #include "itkImageAlgorithm.h" #include "itkUnaryFunctorImageFilter.h" #include "itkCastImageFilter.h" +#include "itkFastChamferDistanceImageFilter.h" #include #include #include @@ -104,6 +105,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) , m_Axis(-1) , m_HeuristicAlignment(true) + , m_UseDistanceTransform(true) , m_MinAlignIters(10) , // smaller of this and max pixel count of the search image m_MaxAlignIters(256) @@ -323,6 +325,7 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe m_StructuringElement.SetRadius(size); m_StructuringElement.CreateStructuringElement(); m_Dilator->SetKernel(m_StructuringElement); + // TODO: keep structuring element and dilator per axis instead of per thread? thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads @@ -369,6 +372,94 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool } +template +typename MorphologicalContourInterpolator::BoolImageType::Pointer +MorphologicalContourInterpolator::FindMedianImageDilations(int axis, + typename BoolImageType::Pointer iMask, + typename BoolImageType::Pointer jMask) +{ + // generate sequence + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + WriteDebug(iMask, "C:\\iMask.nrrd"); + WriteDebug(jMask, "C:\\jMask.nrrd"); + m_And->SetInput(0, iMask); + m_And->SetInput(1, jMask); + m_And->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + m_And->Update(); + typename BoolImageType::Pointer intersection = m_And->GetOutput(); + intersection->DisconnectPipeline(); + WriteDebug(intersection, "C:\\intersection.nrrd"); + std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); + std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); + std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection + if (iSeq.size() < jSeq.size()) + { + iSeq.swap(jSeq); // swap so iSeq.size() >= jSeq.size() + } + float ratio = float(jSeq.size()) / iSeq.size(); + thread_local typename OrType::Pointer m_Or = OrType::New(); + m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + std::vector seq; + for (unsigned x = 0; x < iSeq.size(); x++) + { + m_Or->SetInput(0, iSeq[x]); + unsigned xj = ratio * x; + m_Or->SetInput(1, jSeq[xj]); +#ifdef _DEBUG + WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); + WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); +#endif // _DEBUG + m_Or->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + m_Or->Update(); + seq.push_back(m_Or->GetOutput()); + seq.back()->DisconnectPipeline(); + } + + // find median + unsigned minIndex; + IdentifierType min = iMask->GetRequestedRegion().GetNumberOfPixels(); + for (unsigned x = 0; x < iSeq.size(); x++) + { +#ifdef _DEBUG + WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); +#endif // _DEBUG + IdentifierType iS = CardSymDifference(seq[x], iMask); + IdentifierType jS = CardSymDifference(seq[x], jMask); + IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) + if (xScore < min) + { + min = xScore; + minIndex = x; + } + } + return seq[minIndex]; +} + + +template +typename MorphologicalContourInterpolator::BoolImageType::Pointer +MorphologicalContourInterpolator::FindMedianImageDistances(int axis, + typename BoolImageType::Pointer iMask, + typename BoolImageType::Pointer jMask) +{ + // generate sequence + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + WriteDebug(iMask, "C:\\iMask.nrrd"); + WriteDebug(jMask, "C:\\jMask.nrrd"); + m_And->SetInput(0, iMask); + m_And->SetInput(1, jMask); + m_And->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + m_And->Update(); + typename BoolImageType::Pointer intersection = m_And->GetOutput(); + intersection->DisconnectPipeline(); + WriteDebug(intersection, "C:\\intersection.nrrd"); + itkExceptionMacro("Not implemented yet."); + return intersection; +} + + template void MorphologicalContourInterpolator::Interpolate1to1(int axis, @@ -446,67 +537,21 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename BoolImageType::Pointer jMask = caster->GetOutput(); jMask->DisconnectPipeline(); - // generate sequence - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - WriteDebug(iMask, "C:\\iMask.nrrd"); - WriteDebug(jMask, "C:\\jMask.nrrd"); - m_And->SetInput(0, iMask); - m_And->SetInput(1, jMask); - m_And->GetOutput()->SetRegions(newRegion); - m_And->Update(); - typename BoolImageType::Pointer intersection = m_And->GetOutput(); - intersection->DisconnectPipeline(); - WriteDebug(intersection, "C:\\intersection.nrrd"); - std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); - std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); - std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection - if (iSeq.size() < jSeq.size()) - { - iSeq.swap(jSeq); // swap so iSeq.size() >= jSeq.size() - } - float ratio = float(jSeq.size()) / iSeq.size(); - thread_local typename OrType::Pointer m_Or = OrType::New(); - m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - std::vector seq; - for (unsigned x = 0; x < iSeq.size(); x++) + typename BoolImageType::Pointer median; + if (m_UseDistanceTransform) { - m_Or->SetInput(0, iSeq[x]); - unsigned xj = ratio * x; - m_Or->SetInput(1, jSeq[xj]); -#ifdef _DEBUG - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); - WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); -#endif // _DEBUG - m_Or->GetOutput()->SetRegions(newRegion); - m_Or->Update(); - seq.push_back(m_Or->GetOutput()); - seq.back()->DisconnectPipeline(); + median = FindMedianImageDistances(axis, iMask, jMask); } - - // find median - unsigned minIndex; - IdentifierType min = newRegion.GetNumberOfPixels(); - for (unsigned x = 0; x < iSeq.size(); x++) + else { -#ifdef _DEBUG - WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); -#endif // _DEBUG - IdentifierType iS = CardSymDifference(seq[x], iMask); - IdentifierType jS = CardSymDifference(seq[x], jMask); - IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) - if (xScore < min) - { - min = xScore; - minIndex = x; - } + median = FindMedianImageDilations(axis, iMask, jMask); } // finally write it out into the output image pointer typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); typename TImage::IndexType t0 = { 0 }; IntersectionRegions(t0, outRegion, newRegion); - ImageRegionConstIterator seqIt(seq[minIndex], newRegion); + ImageRegionConstIterator seqIt(median, newRegion); ImageRegionIterator outIt(out, newRegion); while (!outIt.IsAtEnd()) { @@ -525,7 +570,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int typedef CastImageFilter InvertCastType; typename InvertCastType::Pointer invCaster = InvertCastType::New(); invCaster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - invCaster->SetInput(seq[minIndex]); + invCaster->SetInput(median); invCaster->Update(); typename TImage::Pointer midConn = invCaster->GetOutput(); // midConn->DisconnectPipeline(); //not needed? diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index 6b62d15ca11..0f7e888be90 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -10,6 +10,7 @@ itk_module( ITKCommon ITKBinaryMathematicalMorphology ITKIOImageBase # typename + ITKDistanceMap TEST_DEPENDS ITKTestKernel EXCLUDE_FROM_DEFAULT diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_0.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_0.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_0.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_0.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_1.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_1.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_1.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_1.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_2.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_2.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_-1_2.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_2.nii.gz.md5 diff --git 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--git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_0.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_0.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_0.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_1.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_1.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_2.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_0.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_0.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_0.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_1.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_1.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_2.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_RD_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0_0.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_0.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0_0.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0_4.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_0_4.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_0_4.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1_1.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_1.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1_1.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1_2.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_1_2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_1_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2_2.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_2.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2_3.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_2_3.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_RD_2_3.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_RD.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_RD.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 5392d0c8704..e97ee22eba2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -18,7 +18,7 @@ target_link_libraries( ) # used to produce an output which is then taken as a baseline for a regression test -function(JustInputTest ImageName Ext) #optional: Axis Label +function(JustInputTest ImageName Ext) #optional: Algo Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -26,7 +26,7 @@ function(JustInputTest ImageName Ext) #optional: Axis Label # set(imageNameOpt "${ImageName}${optArgs}") # only used for regression itk_add_test( - NAME itkMorphologicalContourInterpolation_JustInOut_${ImageName}${optArgs} + NAME itkMCI_JustInOut_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver # --compare DATA{Baseline/${imageNameOpt}.${Ext}} ${outImage} # no regression @@ -37,7 +37,7 @@ function(JustInputTest ImageName Ext) #optional: Axis Label ) endfunction() -function(RegressionTest ImageName Ext) #optional: Axis Label +function(RegressionTest ImageName Ext) #optional: Algo Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -45,7 +45,7 @@ function(RegressionTest ImageName Ext) #optional: Axis Label set(imageNameOpt "${ImageName}${optArgs}") itk_add_test( - NAME itkMorphologicalContourInterpolation_Regression_${ImageName}${optArgs} + NAME itkMCI_${ImageName}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver --compare @@ -59,136 +59,136 @@ function(RegressionTest ImageName Ext) #optional: Axis Label endfunction() # Handcrafted tests -regressiontest(Empty nrrd) -regressiontest(NoSlices nrrd) #interpolation should not be invoked (output==input) -regressiontest(Micro1 nrrd) -regressiontest(SimplestOneToOne nrrd) -regressiontest(OneToOne nrrd) -regressiontest(OneToThree nrrd) -regressiontest(ExtrapolationAppearing nrrd) -regressiontest(DoubleTwoLabelBranching nrrd) -regressiontest(TwoAxisDoubleTwoLabelBranchingConflict nrrd) -regressiontest(AccidentalMiddleSliceSegmentation nrrd) -regressiontest(SevenLabels nrrd) -regressiontest(FullEnd nrrd) -regressiontest(1MN1 nrrd) # double sided many broken into many + 1 -regressiontest(ManyToMany16 nrrd) -regressiontest(ManyToMany nrrd) -regressiontest(GridSeg nrrd) -regressiontest(GridSeg2 nrrd) +regressiontest(Empty nrrd RD) +regressiontest(NoSlices nrrd RD) #interpolation should not be invoked (output==input) +regressiontest(Micro1 nrrd RD) +regressiontest(SimplestOneToOne nrrd RD) +regressiontest(OneToOne nrrd RD) +regressiontest(OneToThree nrrd RD) +regressiontest(ExtrapolationAppearing nrrd RD) +regressiontest(DoubleTwoLabelBranching nrrd RD) +regressiontest(TwoAxisDoubleTwoLabelBC nrrd RD) +regressiontest(AccidentalMiddleSliceSeg nrrd RD) +regressiontest(SevenLabels nrrd RD) +regressiontest(FullEnd nrrd RD) +regressiontest(1MN1 nrrd RD) # double sided many broken into many + 1 +regressiontest(ManyToMany16 nrrd RD) +regressiontest(ManyToMany nrrd RD) +regressiontest(GridSeg nrrd RD) +regressiontest(GridSeg2 nrrd RD) # Per axis/label tests -regressiontest(GridSeg nrrd 0) -regressiontest(GridSeg nrrd 1) -regressiontest(GridSeg nrrd 2) -regressiontest(GridSeg2 nrrd 0) -regressiontest(GridSeg2 nrrd 1) -regressiontest(GridSeg2 nrrd 2) -regressiontest(ThreeAxisFourLabelConflict nrrd) -regressiontest(ThreeAxisFourLabelConflict nrrd 0) -regressiontest(ThreeAxisFourLabelConflict nrrd 1) -regressiontest(ThreeAxisFourLabelConflict nrrd 2) -regressiontest(ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd 1 1) -regressiontest(ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 -regressiontest(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd 1 2) -regressiontest(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image +regressiontest(GridSeg nrrd RD 0) +regressiontest(GridSeg nrrd RD 1) +regressiontest(GridSeg nrrd RD 2) +regressiontest(GridSeg2 nrrd RD 0) +regressiontest(GridSeg2 nrrd RD 1) +regressiontest(GridSeg2 nrrd RD 2) +regressiontest(ThreeAxisFourLabelConflict nrrd RD) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 0) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 1) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 2) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 0 0) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd RD 1 1) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 2 3) # equals to _2 +regressiontest(ThreeAxisFourLabelConflict nrrd RD 0 4) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd RD 1 2) +regressiontest(ThreeAxisFourLabelConflict nrrd RD 2 2) # does not modify image # Paul's single axis tests -regressiontest(105769moving nii.gz) #defaults: all axes all labels -regressiontest(105769moving nii.gz 2) #axis 2 -regressiontest(105769moving nii.gz -1 0) #all axes all labels -regressiontest(105769moving nii.gz -1 1) #all axes label 1 -regressiontest(105769moving nii.gz -1 2) #all axes label 2 -regressiontest(105769moving nii.gz 2 1) #axis 2 label 1 -regressiontest(105769moving nii.gz 2 2) #axis 2 label 2 -regressiontest(105769fixed nii.gz) #defaults: all axes all labels -regressiontest(105769fixed nii.gz 2) #axis 2 -regressiontest(105769fixed nii.gz -1 0) #all axes all labels -regressiontest(105769fixed nii.gz -1 1) #all axes label 1 -regressiontest(105769fixed nii.gz -1 2) #all axes label 2 -regressiontest(105769fixed nii.gz 2 1) #axis 2 label 1 -regressiontest(105769fixed nii.gz 2 2) #axis 2 label 2 +regressiontest(105769moving nii.gz RD) #defaults: all axes all labels +regressiontest(105769moving nii.gz RD 2) #axis 2 +regressiontest(105769moving nii.gz RD -1 0) #all axes all labels +regressiontest(105769moving nii.gz RD -1 1) #all axes label 1 +regressiontest(105769moving nii.gz RD -1 2) #all axes label 2 +regressiontest(105769moving nii.gz RD 2 1) #axis 2 label 1 +regressiontest(105769moving nii.gz RD 2 2) #axis 2 label 2 +regressiontest(105769fixed nii.gz RD) #defaults: all axes all labels +regressiontest(105769fixed nii.gz RD 2) #axis 2 +regressiontest(105769fixed nii.gz RD -1 0) #all axes all labels +regressiontest(105769fixed nii.gz RD -1 1) #all axes label 1 +regressiontest(105769fixed nii.gz RD -1 2) #all axes label 2 +regressiontest(105769fixed nii.gz RD 2 1) #axis 2 label 1 +regressiontest(105769fixed nii.gz RD 2 2) #axis 2 label 2 # 64816L_amygdala_int -regressiontest(64816L_amygdala_int nii.gz) -regressiontest(64816L_amygdala_int nii.gz 0) -regressiontest(64816L_amygdala_int nii.gz 1) -regressiontest(64816L_amygdala_int nii.gz 2) -regressiontest(64816L_amygdala_int nii.gz 0 1) -regressiontest(64816L_amygdala_int nii.gz 0 2) -regressiontest(64816L_amygdala_int nii.gz 0 3) -regressiontest(64816L_amygdala_int nii.gz 0 4) -regressiontest(64816L_amygdala_int nii.gz 1 1) -regressiontest(64816L_amygdala_int nii.gz 1 2) -regressiontest(64816L_amygdala_int nii.gz 1 3) -regressiontest(64816L_amygdala_int nii.gz 1 4) -regressiontest(64816L_amygdala_int nii.gz 2 1) -regressiontest(64816L_amygdala_int nii.gz 2 2) -regressiontest(64816L_amygdala_int nii.gz 2 3) -regressiontest(64816L_amygdala_int nii.gz 2 4) +regressiontest(64816L_amygdala_int nii.gz RD) +regressiontest(64816L_amygdala_int nii.gz RD 0) +regressiontest(64816L_amygdala_int nii.gz RD 1) +regressiontest(64816L_amygdala_int nii.gz RD 2) +regressiontest(64816L_amygdala_int nii.gz RD 0 1) +regressiontest(64816L_amygdala_int nii.gz RD 0 2) +regressiontest(64816L_amygdala_int nii.gz RD 0 3) +regressiontest(64816L_amygdala_int nii.gz RD 0 4) +regressiontest(64816L_amygdala_int nii.gz RD 1 1) +regressiontest(64816L_amygdala_int nii.gz RD 1 2) +regressiontest(64816L_amygdala_int nii.gz RD 1 3) +regressiontest(64816L_amygdala_int nii.gz RD 1 4) +regressiontest(64816L_amygdala_int nii.gz RD 2 1) +regressiontest(64816L_amygdala_int nii.gz RD 2 2) +regressiontest(64816L_amygdala_int nii.gz RD 2 3) +regressiontest(64816L_amygdala_int nii.gz RD 2 4) # 64816L_amygdala_fin -regressiontest(64816L_amygdala_fin nii.gz) -regressiontest(64816L_amygdala_fin nii.gz 0) -regressiontest(64816L_amygdala_fin nii.gz 1) -regressiontest(64816L_amygdala_fin nii.gz 2) -regressiontest(64816L_amygdala_fin nii.gz 0 1) -regressiontest(64816L_amygdala_fin nii.gz 0 2) -regressiontest(64816L_amygdala_fin nii.gz 0 3) -regressiontest(64816L_amygdala_fin nii.gz 0 4) -regressiontest(64816L_amygdala_fin nii.gz 1 1) -regressiontest(64816L_amygdala_fin nii.gz 1 2) -regressiontest(64816L_amygdala_fin nii.gz 1 3) -regressiontest(64816L_amygdala_fin nii.gz 1 4) -regressiontest(64816L_amygdala_fin nii.gz 2 1) -regressiontest(64816L_amygdala_fin nii.gz 2 2) -regressiontest(64816L_amygdala_fin nii.gz 2 3) -regressiontest(64816L_amygdala_fin nii.gz 2 4) +regressiontest(64816L_amygdala_fin nii.gz RD) +regressiontest(64816L_amygdala_fin nii.gz RD 0) +regressiontest(64816L_amygdala_fin nii.gz RD 1) +regressiontest(64816L_amygdala_fin nii.gz RD 2) +regressiontest(64816L_amygdala_fin nii.gz RD 0 1) +regressiontest(64816L_amygdala_fin nii.gz RD 0 2) +regressiontest(64816L_amygdala_fin nii.gz RD 0 3) +regressiontest(64816L_amygdala_fin nii.gz RD 0 4) +regressiontest(64816L_amygdala_fin nii.gz RD 1 1) +regressiontest(64816L_amygdala_fin nii.gz RD 1 2) +regressiontest(64816L_amygdala_fin nii.gz RD 1 3) +regressiontest(64816L_amygdala_fin nii.gz RD 1 4) +regressiontest(64816L_amygdala_fin nii.gz RD 2 1) +regressiontest(64816L_amygdala_fin nii.gz RD 2 2) +regressiontest(64816L_amygdala_fin nii.gz RD 2 3) +regressiontest(64816L_amygdala_fin nii.gz RD 2 4) # 65239R_amygdala_int -regressiontest(65239R_amygdala_int nii.gz) -regressiontest(65239R_amygdala_int nii.gz 0) -regressiontest(65239R_amygdala_int nii.gz 1) -regressiontest(65239R_amygdala_int nii.gz 2) -regressiontest(65239R_amygdala_int nii.gz 0 1) -regressiontest(65239R_amygdala_int nii.gz 0 2) -regressiontest(65239R_amygdala_int nii.gz 0 3) -regressiontest(65239R_amygdala_int nii.gz 0 4) -regressiontest(65239R_amygdala_int nii.gz 1 1) -regressiontest(65239R_amygdala_int nii.gz 1 2) -regressiontest(65239R_amygdala_int nii.gz 1 3) -regressiontest(65239R_amygdala_int nii.gz 1 4) -regressiontest(65239R_amygdala_int nii.gz 2 1) -regressiontest(65239R_amygdala_int nii.gz 2 2) -regressiontest(65239R_amygdala_int nii.gz 2 3) -regressiontest(65239R_amygdala_int nii.gz 2 4) +regressiontest(65239R_amygdala_int nii.gz RD) +regressiontest(65239R_amygdala_int nii.gz RD 0) +regressiontest(65239R_amygdala_int nii.gz RD 1) +regressiontest(65239R_amygdala_int nii.gz RD 2) +regressiontest(65239R_amygdala_int nii.gz RD 0 1) +regressiontest(65239R_amygdala_int nii.gz RD 0 2) +regressiontest(65239R_amygdala_int nii.gz RD 0 3) +regressiontest(65239R_amygdala_int nii.gz RD 0 4) +regressiontest(65239R_amygdala_int nii.gz RD 1 1) +regressiontest(65239R_amygdala_int nii.gz RD 1 2) +regressiontest(65239R_amygdala_int nii.gz RD 1 3) +regressiontest(65239R_amygdala_int nii.gz RD 1 4) +regressiontest(65239R_amygdala_int nii.gz RD 2 1) +regressiontest(65239R_amygdala_int nii.gz RD 2 2) +regressiontest(65239R_amygdala_int nii.gz RD 2 3) +regressiontest(65239R_amygdala_int nii.gz RD 2 4) # 65239R_amygdala_fin -regressiontest(65239R_amygdala_fin nii.gz) -regressiontest(65239R_amygdala_fin nii.gz 0) -regressiontest(65239R_amygdala_fin nii.gz 1) -regressiontest(65239R_amygdala_fin nii.gz 2) -regressiontest(65239R_amygdala_fin nii.gz 0 1) -regressiontest(65239R_amygdala_fin nii.gz 0 2) -regressiontest(65239R_amygdala_fin nii.gz 0 3) -regressiontest(65239R_amygdala_fin nii.gz 0 4) -regressiontest(65239R_amygdala_fin nii.gz 1 1) -regressiontest(65239R_amygdala_fin nii.gz 1 2) -regressiontest(65239R_amygdala_fin nii.gz 1 3) -regressiontest(65239R_amygdala_fin nii.gz 1 4) -regressiontest(65239R_amygdala_fin nii.gz 2 1) -regressiontest(65239R_amygdala_fin nii.gz 2 2) -regressiontest(65239R_amygdala_fin nii.gz 2 3) -regressiontest(65239R_amygdala_fin nii.gz 2 4) +regressiontest(65239R_amygdala_fin nii.gz RD) +regressiontest(65239R_amygdala_fin nii.gz RD 0) +regressiontest(65239R_amygdala_fin nii.gz RD 1) +regressiontest(65239R_amygdala_fin nii.gz RD 2) +regressiontest(65239R_amygdala_fin nii.gz RD 0 1) +regressiontest(65239R_amygdala_fin nii.gz RD 0 2) +regressiontest(65239R_amygdala_fin nii.gz RD 0 3) +regressiontest(65239R_amygdala_fin nii.gz RD 0 4) +regressiontest(65239R_amygdala_fin nii.gz RD 1 1) +regressiontest(65239R_amygdala_fin nii.gz RD 1 2) +regressiontest(65239R_amygdala_fin nii.gz RD 1 3) +regressiontest(65239R_amygdala_fin nii.gz RD 1 4) +regressiontest(65239R_amygdala_fin nii.gz RD 2 1) +regressiontest(65239R_amygdala_fin nii.gz RD 2 2) +regressiontest(65239R_amygdala_fin nii.gz RD 2 3) +regressiontest(65239R_amygdala_fin nii.gz RD 2 4) # Long-running handcrafted tests -regressiontest(BigZ nrrd) -regressiontest(BigZ nrrd 0) -regressiontest(BigZ nrrd 1) -regressiontest(BigZ nrrd 2) -regressiontest(FaceRoI nrrd) -regressiontest(FaceRoI nrrd 0) -regressiontest(FaceRoI nrrd 1) -regressiontest(FaceRoI nrrd 2) +regressiontest(BigZ nrrd RD) +regressiontest(BigZ nrrd RD 0) +regressiontest(BigZ nrrd RD 1) +regressiontest(BigZ nrrd RD 2) +regressiontest(FaceRoI nrrd RD) +regressiontest(FaceRoI nrrd RD 0) +regressiontest(FaceRoI nrrd RD 1) +regressiontest(FaceRoI nrrd RD 2) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSeg.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSegmentation.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/AccidentalMiddleSliceSeg.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBC.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBranchingConflict.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoAxisDoubleTwoLabelBC.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 6d81a16cb55..0ff89466040 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -20,6 +20,7 @@ #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" #include +#include long int string2int(char * number) @@ -34,7 +35,8 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) if (argc < 3) { std::cerr << "Usage: " << argv[0]; - std::cerr << " inputImage outputImage [axis] [label]\n"; + std::cerr << " inputImage outputImage [algo] [axis] [label]\n"; + std::cerr << " algo: RD (repeated dilations ) or DT (distance transform [default])"; std::cerr << " defaults: axis == -1 (all axes), label == 0 (all labels)"; std::cerr << std::endl; return EXIT_FAILURE; @@ -55,11 +57,20 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) mci->SetInput(reader->GetOutput()); if (argc >= 4) { - mci->SetAxis(strtol(argv[3], NULL, 10)); + std::string algo = argv[3]; + for (auto & c : algo) + { + c = toupper(c); + } + mci->SetUseDistanceTransform(algo != "RD"); } if (argc >= 5) { - mci->SetLabel(strtol(argv[4], NULL, 10)); + mci->SetAxis(strtol(argv[4], NULL, 10)); + } + if (argc >= 6) + { + mci->SetLabel(strtol(argv[5], NULL, 10)); } typedef itk::ImageFileWriter WriterType; From 92fd0ff87f7c10699abd279583bd5f4b6e029b9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 17 Mar 2016 16:41:59 -0400 Subject: [PATCH 063/176] ENH: Switching to preexisting ThreadPool class --- .../include/ThreadPool.h | 117 ++++++++++++++++++ .../itkMorphologicalContourInterpolator.h | 2 + .../itkMorphologicalContourInterpolator.hxx | 72 +++-------- 3 files changed, 134 insertions(+), 57 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h b/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h new file mode 100644 index 00000000000..e0435b729fc --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h @@ -0,0 +1,117 @@ +#ifndef THREAD_POOL_H +#define THREAD_POOL_H + +/*https://github.com/progschj/ThreadPool +Copyright (c) 2012 Jakob Progsch, Václav Zeman + +This software is provided 'as-is', without any express or implied +warranty. In no event will the authors be held liable for any damages +arising from the use of this software. + +Permission is granted to anyone to use this software for any purpose, +including commercial applications, and to alter it and redistribute it +freely, subject to the following restrictions: + + 1. The origin of this software must not be misrepresented; you must not + claim that you wrote the original software. If you use this software + in a product, an acknowledgment in the product documentation would be + appreciated but is not required. + + 2. Altered source versions must be plainly marked as such, and must not be + misrepresented as being the original software. + + 3. This notice may not be removed or altered from any source + distribution.*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +class ThreadPool +{ +public: + ThreadPool(size_t); + template + auto + enqueue(F && f, Args &&... args) -> std::future::type>; + ~ThreadPool(); + +private: + // need to keep track of threads so we can join them + std::vector workers; + // the task queue + std::queue> tasks; + + // synchronization + std::mutex queue_mutex; + std::condition_variable condition; + bool stop; +}; + +// the constructor just launches some amount of workers +inline ThreadPool::ThreadPool(size_t threads) + : stop(false) +{ + for (size_t i = 0; i < threads; ++i) + workers.emplace_back([this] { + for (;;) + { + std::function task; + + { + std::unique_lock lock(this->queue_mutex); + this->condition.wait(lock, [this] { return this->stop || !this->tasks.empty(); }); + if (this->stop && this->tasks.empty()) + return; + task = std::move(this->tasks.front()); + this->tasks.pop(); + } + + task(); + } + }); +} + +// add new work item to the pool +template +auto +ThreadPool::enqueue(F && f, Args &&... args) -> std::future::type> +{ + using return_type = typename std::result_of::type; + + auto task = + std::make_shared>(std::bind(std::forward(f), std::forward(args)...)); + + std::future res = task->get_future(); + { + std::unique_lock lock(queue_mutex); + + // don't allow enqueueing after stopping the pool + if (stop) + throw std::runtime_error("enqueue on stopped ThreadPool"); + + tasks.emplace([task]() { (*task)(); }); + } + condition.notify_one(); + return res; +} + +// the destructor joins all threads +inline ThreadPool::~ThreadPool() +{ + { + std::unique_lock lock(queue_mutex); + stop = true; + } + condition.notify_all(); + for (std::thread & worker : workers) + worker.join(); +} + +#endif diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index ea65f8bdb69..abbb163a8b4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -28,6 +28,7 @@ #include "itkBinaryBallStructuringElement.h" #include "itkAndImageFilter.h" #include "itkOrImageFilter.h" +#include "ThreadPool.h" namespace itk @@ -101,6 +102,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::MorphologicalContourInterpolator() , m_Axis(-1) , m_HeuristicAlignment(true) , m_UseDistanceTransform(true) + , m_ThreadPool(nullptr) , m_MinAlignIters(10) , // smaller of this and max pixel count of the search image m_MaxAlignIters(256) @@ -1233,54 +1234,13 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() -// a crude way to limit the number of threads to number of cores -void -join1(std::list> & threads, int slack = std::thread::hardware_concurrency()) -{ - auto it = threads.begin(); - int count = 0; - auto zeroDuration = std::chrono::microseconds(0); - auto sleepDuration = std::chrono::microseconds(100); - while (it != threads.end()) - { - if (it->wait_for(zeroDuration) == std::future_status::ready) - { - threads.erase(it); - return; - } - else - { - ++it; // check next - count++; - } - } - - if (count > slack) // we really need to wait - { - do - { - std::this_thread::sleep_for(sleepDuration); - it = threads.begin(); - while (it != threads.end()) - { - if (it->wait_for(zeroDuration) == std::future_status::ready) - { - threads.erase(it); - return; - } - ++it; - } - } while (true); - } -} - template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { // do multithreading by paralellizing for different labels - // and different inter-slice segments [C++11 threads] - std::list> threadResults; + // and different inter-slice segments [thread pool of C++11 threads] + m_ThreadPool = new ::ThreadPool(std::thread::hardware_concurrency()); for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { @@ -1313,18 +1273,15 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou if (*prev + 1 < *next) // only if they are not adjacent slices { - threadResults.push_back(std::async(std::launch::async, - &MorphologicalContourInterpolator::InterpolateBetweenTwo, - this, - axis, - out, - it->first, - *prev, - *next, - iconn, - jconn)); - join1(threadResults); // wait for one thread to finish - // in case there is more threads than processing cores + m_ThreadPool->enqueue(&MorphologicalContourInterpolator::InterpolateBetweenTwo, + this, + axis, + out, + it->first, + *prev, + *next, + iconn, + jconn); // InterpolateBetweenTwo(axis, out, it->first, *prev, *next, iconn, jconn); //sequential } iconn = jconn; @@ -1333,8 +1290,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } - // wait for leftover threads - join1(threadResults, 0); + // wait for leftover threads by invoking destructor + delete m_ThreadPool; + m_ThreadPool = nullptr; } From d22594f04501ba6d84097811e33fb8cf143a8128 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 18 Mar 2016 10:45:36 -0400 Subject: [PATCH 064/176] ENH: more aggressive paralellization --- .../itkMorphologicalContourInterpolator.h | 1 + .../itkMorphologicalContourInterpolator.hxx | 63 ++++++++++++++----- ...kMorphologicalContourInterpolationTest.cxx | 9 +++ 3 files changed, 56 insertions(+), 17 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index abbb163a8b4..3450f0c1cb3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -100,6 +100,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::MorphologicalContourInterpolator() , m_HeuristicAlignment(true) , m_UseDistanceTransform(true) , m_ThreadPool(nullptr) + , m_StopSpawning(false) , m_MinAlignIters(10) , // smaller of this and max pixel count of the search image m_MaxAlignIters(256) @@ -580,15 +581,35 @@ MorphologicalContourInterpolator::Interpolate1to1(int PixelList regionIDs; regionIDs.push_back(1); - if (abs(i - mid) > 1) + bool first = abs(i - mid) > 1; // interpolate i-mid? + bool second = abs(j - mid) > 1; // interpolate j-mid? + + if (first && second && !m_StopSpawning) // then first in new thread { - // typename TImage::IndexType tRecurse = Align(axis, iConn, iRegionId, midConn, regionIDs); - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans); + m_ThreadPool->enqueue(&MorphologicalContourInterpolator::Interpolate1to1, + this, + axis, + out, + label, + i, + mid, + iConn, + iRegionId, + midConn, + 1, + iTrans); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); } - if (abs(j - mid) > 1) + else // sequential { - // typename TImage::IndexType tRecurse = Align(axis, jConn, jRegionId, midConn, regionIDs); - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); + if (first) + { + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans); + } + if (second) + { + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); + } } } WriteDebug(out, "C:\\intermediateResult.nrrd"); @@ -1241,6 +1262,10 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou // do multithreading by paralellizing for different labels // and different inter-slice segments [thread pool of C++11 threads] m_ThreadPool = new ::ThreadPool(std::thread::hardware_concurrency()); + std::vectorenqueue( + &MorphologicalContourInterpolator::InterpolateBetweenTwo, this, axis, out, 0, 0, 0, out, out))> + results; // so we can wait for all the results + m_StopSpawning = false; for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { @@ -1273,16 +1298,15 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou if (*prev + 1 < *next) // only if they are not adjacent slices { - m_ThreadPool->enqueue(&MorphologicalContourInterpolator::InterpolateBetweenTwo, - this, - axis, - out, - it->first, - *prev, - *next, - iconn, - jconn); - // InterpolateBetweenTwo(axis, out, it->first, *prev, *next, iconn, jconn); //sequential + results.push_back(m_ThreadPool->enqueue(&MorphologicalContourInterpolator::InterpolateBetweenTwo, + this, + axis, + out, + it->first, + *prev, + *next, + iconn, + jconn)); } iconn = jconn; prev = next; @@ -1290,7 +1314,12 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } - // wait for leftover threads by invoking destructor + for (int i = 0; i < results.size(); i++) + { + results[i].get(); // wait for thread + } + m_StopSpawning = true; + // invoking destructor waits for any leftover threads created by Interpolate1to1 delete m_ThreadPool; m_ThreadPool = nullptr; } diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 0ff89466040..1e07f0472d6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -51,6 +51,15 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(inputImageFileName); + try + { + reader->Update(); + } + catch (itk::ExceptionObject & error) + { + std::cerr << "Error: " << error << std::endl; + return EXIT_FAILURE; + } typedef itk::MorphologicalContourInterpolator mciType; mciType::Pointer mci = mciType::New(); From 1b8106de7b89fadd2799b170c8b14e4e1acda0ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 18 Mar 2016 14:05:17 -0400 Subject: [PATCH 065/176] ENH: Adding 2D and 4D tests --- .../itkMorphologicalContourInterpolator.hxx | 39 ++++---- .../test/Baseline/FourD_RD.nrrd.md5 | 1 + .../test/Baseline/TwoD_RD.png.md5 | 1 + .../test/Baseline/TwoD_RD_-1_1.png.md5 | 1 + .../test/Baseline/TwoD_RD_-1_255.png.md5 | 1 + .../test/Baseline/TwoD_RD_0.png.md5 | 1 + .../test/Baseline/TwoD_RD_1.png.md5 | 1 + .../test/CMakeLists.txt | 8 ++ .../test/Input/FourD.nrrd.md5 | 1 + .../test/Input/TwoD.png.md5 | 1 + ...kMorphologicalContourInterpolationTest.cxx | 91 ++++++++++++------- 11 files changed, 96 insertions(+), 50 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_RD.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/FourD.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index bd3c9ab09e1..ff68e4ee751 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -42,7 +42,7 @@ namespace itk { template void -WriteDebug(typename TImage::Pointer out, const char * filename) +WriteDebug(itk::SmartPointer out, const char * filename) { return; // tests run much faster typedef ImageFileWriter WriterType; @@ -60,13 +60,14 @@ WriteDebug(typename TImage::Pointer out, const char * filename) } } +template void -WriteDebug(Image::Pointer out, const char * filename) +WriteDebug(itk::SmartPointer> out, const char * filename) { - typedef Image BoolImageType; - typedef Image ucharImageType; + typedef Image BoolImageType; + typedef Image ucharImageType; typedef CastImageFilter CastType; - CastType::Pointer caster = CastType::New(); + typename CastType::Pointer caster = CastType::New(); caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetInput(out); WriteDebug(caster->GetOutput(), filename); @@ -292,8 +293,8 @@ MorphologicalContourInterpolator::Extrapolate(int phSlice->SetPixel(centroid, 1); jRegionIds.clear(); jRegionIds.push_back(1); - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(phSlice, "C:\\phSlice.nrrd"); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(phSlice, "C:\\phSlice.nrrd"); typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); // now translate the phantom slice for best alignment @@ -515,12 +516,12 @@ MorphologicalContourInterpolator::Interpolate1to1(int ExpandRegion(newRegion, jRegion.GetIndex()); ExpandRegion(newRegion, jBottom); - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); - WriteDebug(iConnT, "C:\\iConnT.nrrd"); - WriteDebug(jConnT, "C:\\jConnT.nrrd"); + WriteDebug(iConnT, "C:\\iConnT.nrrd"); + WriteDebug(jConnT, "C:\\jConnT.nrrd"); // convert to binary masks MatchesID matchesIDi(iRegionId); @@ -577,7 +578,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::Pointer midConn = invCaster->GetOutput(); // midConn->DisconnectPipeline(); //not needed? - // WriteDebug(midConn, "C:\\midConn.nrrd"); + // WriteDebug(midConn, "C:\\midConn.nrrd"); PixelList regionIDs; regionIDs.push_back(1); @@ -640,8 +641,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int caster->Update(); typename BoolImageType::Pointer mask = caster->GetOutput(); WriteDebug(mask, "C:\\mask.nrrd"); - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -688,7 +689,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image @@ -760,7 +761,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images @@ -1033,7 +1034,7 @@ MorphologicalContourInterpolator::Align(int axis, } // WriteDebug(searched, "C:\\searched.nrrd"); #ifndef NDEBUG - WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); + WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); #endif // NDEBUG return bestIndex; } @@ -1293,8 +1294,8 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); jconn->DisconnectPipeline(); - WriteDebug(iconn, "C:\\iconn.nrrd"); - WriteDebug(jconn, "C:\\jconn.nrrd"); + WriteDebug(iconn, "C:\\iconn.nrrd"); + WriteDebug(jconn, "C:\\jconn.nrrd"); if (*prev + 1 < *next) // only if they are not adjacent slices { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_RD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_RD.nrrd.md5 new file mode 100644 index 00000000000..88b051b5cd2 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_RD.nrrd.md5 @@ -0,0 +1 @@ +bb39b0cec3f671e231754d8442c88f79 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 new file mode 100644 index 00000000000..95365888068 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 @@ -0,0 +1 @@ +e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 new file mode 100644 index 00000000000..95365888068 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 @@ -0,0 +1 @@ +e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index e97ee22eba2..679f89f1a70 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -192,3 +192,11 @@ regressiontest(FaceRoI nrrd RD) regressiontest(FaceRoI nrrd RD 0) regressiontest(FaceRoI nrrd RD 1) regressiontest(FaceRoI nrrd RD 2) + +# Non-3D tests +regressiontest(TwoD png RD) +regressiontest(TwoD png RD -1 255) # same as regular +regressiontest(TwoD png RD 0) # same as regular +regressiontest(TwoD png RD -1 1) # does not modify image +regressiontest(TwoD png RD 1) # does not modify image +regressiontest(FourD nrrd RD) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FourD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FourD.nrrd.md5 new file mode 100644 index 00000000000..0d3bc8f0730 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/FourD.nrrd.md5 @@ -0,0 +1 @@ +6c37204c7255f3c36fdbca83ea33b018 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 new file mode 100644 index 00000000000..95365888068 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 @@ -0,0 +1 @@ +e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 1e07f0472d6..714d6fec0c2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -29,6 +29,29 @@ string2int(char * number) return res; } +template +void +doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, int axis, int label) +{ + typedef itk::ImageFileReader ReaderType; + typename ReaderType::Pointer reader = ReaderType::New(); + reader->SetFileName(inFilename); + + typedef itk::MorphologicalContourInterpolator mciType; + typename mciType::Pointer mci = mciType::New(); + mci->SetInput(reader->GetOutput()); + mci->SetUseDistanceTransform(UseDistanceTransform); + mci->SetAxis(axis); + mci->SetLabel(label); + + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outFilename); + writer->SetInput(mci->GetOutput()); + writer->SetUseCompression(true); + writer->Update(); +} + int itkMorphologicalContourInterpolationTest(int argc, char * argv[]) { @@ -43,27 +66,8 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) } const char * inputImageFileName = argv[1]; const char * outputImageFileName = argv[2]; - - typedef signed short PixelType; - const unsigned int Dimension = 3; - typedef itk::Image ImageType; - - typedef itk::ImageFileReader ReaderType; - ReaderType::Pointer reader = ReaderType::New(); - reader->SetFileName(inputImageFileName); - try - { - reader->Update(); - } - catch (itk::ExceptionObject & error) - { - std::cerr << "Error: " << error << std::endl; - return EXIT_FAILURE; - } - - typedef itk::MorphologicalContourInterpolator mciType; - mciType::Pointer mci = mciType::New(); - mci->SetInput(reader->GetOutput()); + bool dt = true; // DistanceTransform + int axis = -1, label = 0; if (argc >= 4) { std::string algo = argv[3]; @@ -71,32 +75,57 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) { c = toupper(c); } - mci->SetUseDistanceTransform(algo != "RD"); + dt = (algo != "RD"); } if (argc >= 5) { - mci->SetAxis(strtol(argv[4], NULL, 10)); + axis = strtol(argv[4], NULL, 10); } if (argc >= 6) { - mci->SetLabel(strtol(argv[5], NULL, 10)); + label = strtol(argv[5], NULL, 10); } - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer writer = WriterType::New(); - writer->SetFileName(outputImageFileName); - writer->SetInput(mci->GetOutput()); - writer->SetUseCompression(true); + typedef itk::ImageIOBase::IOComponentType ScalarPixelType; + itk::ImageIOBase::Pointer imageIO = + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); + if (!imageIO) + { + std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; + return EXIT_FAILURE; + } + imageIO->SetFileName(inputImageFileName); + imageIO->ReadImageInformation(); + const ScalarPixelType pixelType = imageIO->GetComponentType(); + const size_t numDimensions = imageIO->GetNumberOfDimensions(); try { - writer->Update(); + // unused cases are not instantiated because they greatly increase compile time + if (numDimensions == 2 && pixelType == ScalarPixelType::UCHAR) + { + doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + return EXIT_SUCCESS; + } + if (numDimensions == 3 && (pixelType == ScalarPixelType::SHORT || pixelType == ScalarPixelType::USHORT)) + { + doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + return EXIT_SUCCESS; + } + if (numDimensions == 4 && pixelType == ScalarPixelType::UCHAR) + { + doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + return EXIT_SUCCESS; + } + + std::cerr << "Unsupported image type:\n Dimensions: " << numDimensions; + std::cerr << "\n Pixel type:" << imageIO->GetComponentTypeAsString(pixelType) << std::endl; + return EXIT_FAILURE; } catch (itk::ExceptionObject & error) { std::cerr << "Error: " << error << std::endl; return EXIT_FAILURE; } - return EXIT_SUCCESS; } From 29d45802eb7ceacfaa451d0615a7ec19ac797ddf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 23 Mar 2016 16:14:50 -0400 Subject: [PATCH 066/176] ENH: minor changes --- .../itkMorphologicalContourInterpolator.hxx | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ff68e4ee751..5f622a590bc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -109,10 +109,11 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_UseDistanceTransform(true) , m_ThreadPool(nullptr) , m_StopSpawning(false) - , m_MinAlignIters(10) - , // smaller of this and max pixel count of the search image - m_MaxAlignIters(256) - , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets + , m_MinAlignIters(pow(2, TImage::ImageDimension)) + , // smaller of this and pixel count of the search image + m_MaxAlignIters(pow(6, TImage::ImageDimension)) + , // bigger of this and root of pixel count of the search image + m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { // set up pipeline for regioned connected components m_RoI = RoiType::New(); @@ -979,10 +980,13 @@ MorphologicalContourInterpolator::Align(int axis, t0[axis] = ind[axis]; uncomputed.push(t0); // no translation - guaranteed to find a non-zero intersection uncomputed.push(ind); // this introduces movement, and possibly has the same score + searched->SetPixel(t0, true); searched->SetPixel(ind, true); IdentifierType score, maxScore = 0; typename TImage::IndexType bestIndex; - IdentifierType iter = 0, minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); + IdentifierType iter = 0; + IdentifierType minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); + IdentifierType maxIter = std::max(m_MaxAlignIters, (IdentifierType)sqrt(searchRegion.GetNumberOfPixels())); // debug: construct and later fill the image with intersection scores #ifndef NDEBUG @@ -993,7 +997,6 @@ MorphologicalContourInterpolator::Align(int axis, while (!uncomputed.empty()) { - ++iter; ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); @@ -1008,7 +1011,7 @@ MorphologicalContourInterpolator::Align(int axis, } // we breadth this search - if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || score > maxScore * 0.9 && iter <= m_MaxAlignIters) + if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || score > maxScore * 0.9 && iter <= maxIter) { for (unsigned d = 0; d < TImage::ImageDimension; d++) { @@ -1021,12 +1024,14 @@ MorphologicalContourInterpolator::Align(int axis, { uncomputed.push(ind); searched->SetPixel(ind, true); + ++iter; } ind[d] += 2; //"right" if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) { uncomputed.push(ind); searched->SetPixel(ind, true); + ++iter; } ind[d] -= 1; // return to initial } From 9287d999b7e5bda482ca609629d55d92e3b8be38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 24 Mar 2016 16:06:56 -0400 Subject: [PATCH 067/176] ENH: Restricting to bounding box in Interpolate1to1 --- .../itkMorphologicalContourInterpolator.h | 3 +- .../itkMorphologicalContourInterpolator.hxx | 75 ++++++++++++++++--- 2 files changed, 68 insertions(+), 10 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 3450f0c1cb3..38b5ba9d722 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -173,7 +173,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 5f622a590bc..39861270318 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -25,7 +25,7 @@ #include "itkImageAlgorithm.h" #include "itkUnaryFunctorImageFilter.h" #include "itkCastImageFilter.h" -#include "itkFastChamferDistanceImageFilter.h" +#include "itkSignedMaurerDistanceMapImageFilter.h" #include #include #include @@ -308,7 +308,7 @@ MorphologicalContourInterpolator::Extrapolate(int phSlice->SetRegions(reg3); typename TImage::IndexType t0 = { 0 }; t0[axis] = j - i; - Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, t0); + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, t0, false); } @@ -441,6 +441,20 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int } +template +itk::SmartPointer +MaurerDM(itk::SmartPointer inImage) +{ + typedef itk::SignedMaurerDistanceMapImageFilter FilterType; + thread_local typename FilterType::Pointer filter = FilterType::New(); + filter->SetInput(inImage); + filter->SetUseImageSpacing(false); + filter->SetSquaredDistance(true); + filter->SetNumberOfThreads(1); + filter->Update(); + return filter->GetOutput(); +} + template typename MorphologicalContourInterpolator::BoolImageType::Pointer MorphologicalContourInterpolator::FindMedianImageDistances(int axis, @@ -475,7 +489,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::PixelType iRegionId, typename TImage::Pointer jConn, typename TImage::PixelType jRegionId, - typename TImage::IndexType translation) + typename TImage::IndexType translation, + bool recursive) { // translate iConn by t/2 and jConn by -t/2 typename TImage::IndexType iTrans; @@ -524,6 +539,47 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(iConnT, "C:\\iConnT.nrrd"); WriteDebug(jConnT, "C:\\jConnT.nrrd"); + if (!recursive) // reduce bounding box so we deal with less pixels + { + typename TImage::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); + typename TImage::IndexType maxInd = newRegion.GetIndex(); + ImageRegionConstIteratorWithIndex iIt(iConnT, newRegion); + ImageRegionConstIterator jIt(jConnT, newRegion); + + while (!iIt.IsAtEnd()) + { + if (iIt.Get() || jIt.Get()) + { + typename TImage::IndexType ind = iIt.GetIndex(); + for (int d = 0; d < TImage::ImageDimension; d++) + { + if (ind[d] < minInd[d]) + { + minInd[d] = ind[d]; + } + if (ind[d] > maxInd[d]) + { + maxInd[d] = ind[d]; + } + } + } + ++iIt; + ++jIt; + } + + newRegion.SetIndex(minInd); + for (int d = 0; d < TImage::ImageDimension; d++) + { + newRegion.SetSize(d, maxInd[d] - minInd[d] + 1); + } + typename TImage::IndexType t0; + t0.Fill(0); + iConnT = TranslateImage(iConnT, t0, newRegion); + jConnT = TranslateImage(jConnT, t0, newRegion); + } + WriteDebug(iConnT, "C:\\iConnTb.nrrd"); + WriteDebug(jConnT, "C:\\jConnTb.nrrd"); + // convert to binary masks MatchesID matchesIDi(iRegionId); MatchesID matchesIDj(jRegionId); @@ -599,18 +655,19 @@ MorphologicalContourInterpolator::Interpolate1to1(int iRegionId, midConn, 1, - iTrans); - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); + iTrans, + true); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); } else // sequential { if (first) { - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans); + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true); } if (second) { - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); } } } @@ -790,7 +847,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { - Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation); + Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false); // TODO: call sequence construction directly from here! } } @@ -1138,7 +1195,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int PixelList regionIDs; regionIDs.push_back(p->second); typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); - Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation); + Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false); iCounts.erase(p->first); jCounts.erase(p->second); pairs.erase(p++); From fa95873c1f0e512f57c86bc2c9337b4d19677509 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sun, 27 Mar 2016 09:17:57 -0400 Subject: [PATCH 068/176] ENH: First implementation of distance map approach --- .../itkMorphologicalContourInterpolator.h | 8 +- .../itkMorphologicalContourInterpolator.hxx | 134 ++++++++++++++++-- 2 files changed, 130 insertions(+), 12 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 38b5ba9d722..ce379ce1d0d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -147,7 +147,13 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; + typedef Image BoolImageType; + typedef Image FloatImageType; + typedef Image SliceType; + typedef Image BoolSliceType; + + typename FloatImageType::Pointer + MaurerDM(typename BoolImageType::Pointer inImage); /** A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same) */ diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 39861270318..f16249cf7ad 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -26,6 +26,7 @@ #include "itkUnaryFunctorImageFilter.h" #include "itkCastImageFilter.h" #include "itkSignedMaurerDistanceMapImageFilter.h" +#include #include #include #include @@ -442,15 +443,15 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int template -itk::SmartPointer -MaurerDM(itk::SmartPointer inImage) +typename MorphologicalContourInterpolator::FloatImageType::Pointer +MorphologicalContourInterpolator::MaurerDM(typename BoolImageType::Pointer mask) { - typedef itk::SignedMaurerDistanceMapImageFilter FilterType; - thread_local typename FilterType::Pointer filter = FilterType::New(); - filter->SetInput(inImage); - filter->SetUseImageSpacing(false); - filter->SetSquaredDistance(true); - filter->SetNumberOfThreads(1); + typedef itk::SignedMaurerDistanceMapImageFilter FilterType; + thread_local typename FilterType::Pointer filter = FilterType::New(); + filter->SetInput(mask); + filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space + filter->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + filter->GetOutput()->SetRequestedRegion(mask->GetRequestedRegion()); filter->Update(); return filter->GetOutput(); } @@ -461,7 +462,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int typename BoolImageType::Pointer iMask, typename BoolImageType::Pointer jMask) { - // generate sequence + // create intersection thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads WriteDebug(iMask, "C:\\iMask.nrrd"); @@ -473,8 +474,114 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int typename BoolImageType::Pointer intersection = m_And->GetOutput(); intersection->DisconnectPipeline(); WriteDebug(intersection, "C:\\intersection.nrrd"); - itkExceptionMacro("Not implemented yet."); - return intersection; + + // calculate distance field + typename FloatImageType::Pointer sdf = MaurerDM(intersection); + WriteDebug(sdf, "C:\\sdf.nrrd"); + + // create histograms of distances and union + typename BoolImageType::Pointer orImage = BoolImageType::New(); + orImage->CopyInformation(intersection); + orImage->SetRegions(iMask->GetRequestedRegion()); + orImage->Allocate(true); + std::vector iHist; + std::vector jHist; + ImageRegionConstIterator iti(iMask, iMask->GetRequestedRegion()); + ImageRegionConstIterator itj(jMask, iMask->GetRequestedRegion()); + ImageRegionIterator ito(orImage, iMask->GetRequestedRegion()); + ImageRegionConstIterator itsdf(sdf, iMask->GetRequestedRegion()); + while (!itsdf.IsAtEnd()) + { + ; + bool iM = iti.Get(); + bool jM = itj.Get(); + typename TImage::PixelType dist = itsdf.Get(); + if (iM && !jM) + { + if (dist >= iHist.size()) + { + iHist.resize(dist + 1, 0); + } + iHist[dist]++; + ito.Set(true); + } + else if (jM && !iM) + { + if (dist >= jHist.size()) + { + jHist.resize(dist + 1, 0); + } + jHist[dist]++; + ito.Set(true); + } + else if (iM && jM) + { + ito.Set(true); + } + + ++iti; + ++itj; + ++ito; + ++itsdf; + } + WriteDebug(orImage, "C:\\orImage.nrrd"); + + // sum of histogram bins for i and j and + auto maxSize = std::max(iHist.size(), jHist.size()); + if (maxSize == 0) + { + return intersection; + } + iHist.resize(maxSize, 0); + jHist.resize(maxSize, 0); + assert(iHist[0] == 0); + assert(jHist[0] == 0); + std::vector iSum(maxSize, 0); + std::vector jSum(maxSize, 0); + iSum[0] = iHist[0]; + jSum[0] = jHist[0]; + for (int b = 1; b < maxSize; b++) + { + iSum[b] = iSum[b - 1] + iHist[b]; + jSum[b] = jSum[b - 1] + jHist[b]; + } + long long iTotal = iSum[maxSize - 1]; + long long jTotal = jSum[maxSize - 1]; + + // find minimum of differences of sums + int bestBin = 0; + long long bestDiff = LLONG_MAX; + for (int b = 0; b < maxSize; b++) + { + long long iS = std::abs(iTotal - iSum[b] + jSum[b]); + long long jS = std::abs(jTotal - jSum[b] + iSum[b]); + // long long jS = std::abs(jTotal - jSum[maxSize - b - 1] + iSum[b]); + long long diff = std::abs(iS - jS); + if (diff < bestDiff) + { + bestDiff = diff; + bestBin = b; + } + } + + // threshold at distance bestBin is the median intersection + typedef BinaryThresholdImageFilter FloatBinarizerType; + thread_local FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); + threshold->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + threshold->SetInput(sdf); + threshold->SetUpperThreshold(bestBin); + threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); + threshold->Update(); + + thread_local AndFilterType::Pointer and = AndFilterType::New(); + and->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + and->SetInput(threshold->GetOutput()); + and->SetInput(1, orImage); + and->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); + and->Update(); + BoolImageType::Pointer median = and->GetOutput(); + WriteDebug(median, "C:\\median.nrrd"); + return median; } @@ -581,6 +688,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(jConnT, "C:\\jConnTb.nrrd"); // convert to binary masks + // TODO: do this by iterators and reduce dimension by one MatchesID matchesIDi(iRegionId); MatchesID matchesIDj(jRegionId); typedef UnaryFunctorImageFilter CastType; @@ -657,6 +765,10 @@ MorphologicalContourInterpolator::Interpolate1to1(int 1, iTrans, true); + ////now give this thread a chance to start by yielding + // auto oneMS = std::chrono::microseconds(1000); + // std::this_thread::sleep_for(oneMS); + ////now continue by recursion in this thread Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); } else // sequential From df889a46dc4ff797b3de269be8c21320b42c2878 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 28 Mar 2016 11:34:40 -0400 Subject: [PATCH 069/176] ENH: Finalized non-geodesic distance transform Adding baselines for distance transform approach Splitting repeated dilations into ball and cross structuring element variants --- .../CMakeLists.txt | 10 + .../itkMorphologicalContourInterpolator.h | 25 +- .../itkMorphologicalContourInterpolator.hxx | 101 ++++--- ...RD.nii.gz.md5 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Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_1_4.nii.gz.md5 => 65239R_amygdala_fin_B_1_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_2.nii.gz.md5 => 65239R_amygdala_fin_B_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_2_1.nii.gz.md5 => 65239R_amygdala_fin_B_2_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_2_2.nii.gz.md5 => 65239R_amygdala_fin_B_2_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_2_3.nii.gz.md5 => 65239R_amygdala_fin_B_2_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_fin_RD_2_4.nii.gz.md5 => 65239R_amygdala_fin_B_2_4.nii.gz.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_0.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_0_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_0_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_0_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_0_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_1_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_1_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_1_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_1_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_2_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_2_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_2_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_C_2_4.nii.gz.md5 create mode 100644 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Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_1_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_1_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_1_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_2_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_2_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_2_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_fin_T_2_4.nii.gz.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD.nii.gz.md5 => 65239R_amygdala_int_B.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_0.nii.gz.md5 => 65239R_amygdala_int_B_0.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_0_1.nii.gz.md5 => 65239R_amygdala_int_B_0_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_0_2.nii.gz.md5 => 65239R_amygdala_int_B_0_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_0_3.nii.gz.md5 => 65239R_amygdala_int_B_0_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_0_4.nii.gz.md5 => 65239R_amygdala_int_B_0_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_1.nii.gz.md5 => 65239R_amygdala_int_B_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_1_1.nii.gz.md5 => 65239R_amygdala_int_B_1_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_1_2.nii.gz.md5 => 65239R_amygdala_int_B_1_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_1_3.nii.gz.md5 => 65239R_amygdala_int_B_1_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_1_4.nii.gz.md5 => 65239R_amygdala_int_B_1_4.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_2.nii.gz.md5 => 65239R_amygdala_int_B_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_2_1.nii.gz.md5 => 65239R_amygdala_int_B_2_1.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_2_2.nii.gz.md5 => 65239R_amygdala_int_B_2_2.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_2_3.nii.gz.md5 => 65239R_amygdala_int_B_2_3.nii.gz.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{65239R_amygdala_int_RD_2_4.nii.gz.md5 => 65239R_amygdala_int_B_2_4.nii.gz.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_0.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_0_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_0_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_0_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_0_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_1_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_1_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_1_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_1_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_2_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_2_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_2_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_C_2_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_0.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_0_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_0_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_0_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_0_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_1_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_1_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_1_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_1_4.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_2_1.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_2_2.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_2_3.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/65239R_amygdala_int_T_2_4.nii.gz.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{AccidentalMiddleSliceSeg_RD.nrrd.md5 => AccidentalMiddleSliceSeg_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSeg_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/AccidentalMiddleSliceSeg_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_RD.nrrd.md5 => BigZ_B.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_RD_0.nrrd.md5 => BigZ_B_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_RD_1.nrrd.md5 => BigZ_B_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{BigZ_RD_2.nrrd.md5 => BigZ_B_2.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_T.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_T_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_T_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_T_2.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{DoubleTwoLabelBranching_RD.nrrd.md5 => DoubleTwoLabelBranching_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/DoubleTwoLabelBranching_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{Empty_RD.nrrd.md5 => Empty_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Empty_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ExtrapolationAppearing_RD.nrrd.md5 => ExtrapolationAppearing_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ExtrapolationAppearing_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_RD.nrrd.md5 => FaceRoI_B.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_RD_0.nrrd.md5 => FaceRoI_B_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_RD_1.nrrd.md5 => FaceRoI_B_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FaceRoI_RD_2.nrrd.md5 => FaceRoI_B_2.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_C_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_C_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_C_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_2.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FourD_RD.nrrd.md5 => FourD_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{FullEnd_RD.nrrd.md5 => FullEnd_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_RD.nrrd.md5 => GridSeg2_B.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_RD_0.nrrd.md5 => GridSeg2_B_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_RD_1.nrrd.md5 => GridSeg2_B_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg2_RD_2.nrrd.md5 => GridSeg2_B_2.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_C_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_C_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_C_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_T.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_T_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_T_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_T_2.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_RD.nrrd.md5 => GridSeg_B.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_RD_0.nrrd.md5 => GridSeg_B_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_RD_1.nrrd.md5 => GridSeg_B_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{GridSeg_RD_2.nrrd.md5 => GridSeg_B_2.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_C_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_C_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_C_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T_2.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ManyToMany16_RD.nrrd.md5 => ManyToMany16_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ManyToMany_RD.nrrd.md5 => ManyToMany_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{Micro1_RD.nrrd.md5 => Micro1_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{NoSlices_RD.nrrd.md5 => NoSlices_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{OneToOne_RD.nrrd.md5 => OneToOne_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{OneToThree_RD.nrrd.md5 => OneToThree_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToThree_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{SevenLabels_RD.nrrd.md5 => SevenLabels_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SevenLabels_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{SimplestOneToOne_RD.nrrd.md5 => SimplestOneToOne_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD.nrrd.md5 => ThreeAxisFourLabelConflict_B.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_0.nrrd.md5 => ThreeAxisFourLabelConflict_B_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_0_0.nrrd.md5 => ThreeAxisFourLabelConflict_B_0_0.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_0_4.nrrd.md5 => ThreeAxisFourLabelConflict_B_0_4.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_1.nrrd.md5 => ThreeAxisFourLabelConflict_B_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_1_1.nrrd.md5 => ThreeAxisFourLabelConflict_B_1_1.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_1_2.nrrd.md5 => ThreeAxisFourLabelConflict_B_1_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_2.nrrd.md5 => ThreeAxisFourLabelConflict_B_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_2_2.nrrd.md5 => ThreeAxisFourLabelConflict_B_2_2.nrrd.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{ThreeAxisFourLabelConflict_RD_2_3.nrrd.md5 => ThreeAxisFourLabelConflict_B_2_3.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoAxisDoubleTwoLabelBC_RD.nrrd.md5 => TwoAxisDoubleTwoLabelBC_B.nrrd.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoD_RD.png.md5 => TwoD_B.png.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoD_RD_-1_1.png.md5 => TwoD_B_-1_1.png.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoD_RD_-1_255.png.md5 => TwoD_B_-1_255.png.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoD_RD_0.png.md5 => TwoD_B_0.png.md5} (100%) rename Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/{TwoD_RD_1.png.md5 => TwoD_B_1.png.md5} (100%) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 38d0e712b48..ddd3304567b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,6 +1,16 @@ cmake_minimum_required(VERSION 2.8.9) project(MorphologicalContourInterpolation) +set( + MCI_Algorithm + "B" + CACHE STRING + "Which algorithm should be used for testing. +B = repeated dilations with ball structuring element +C = repeated dilations with cross structuring element +T = distance transform (not geodesic!)" +) + if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index ce379ce1d0d..1503de4dc1b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -24,7 +24,7 @@ #include "itkExtractImageFilter.h" #include "itksys/hash_map.hxx" #include "itkBinaryDilateImageFilter.h" -// #include "itkBinaryCrossStructuringElement.h" +#include "itkBinaryCrossStructuringElement.h" #include "itkBinaryBallStructuringElement.h" #include "itkAndImageFilter.h" #include "itkOrImageFilter.h" @@ -76,7 +76,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilterSetFullyConnected(useBall); + } + + /** Use ball instead of default cross structuring element for repeated dilations. */ + itkGetMacro(UseBallStructuringElement, bool); + + /** Use ball instead of default cross structuring element for repeated dilations. */ + itkGetConstMacro(UseBallStructuringElement, bool); + /** Run-time type information (and related methods). */ itkTypeMacro(MorphologicalContourInterpolator, ImageToImageFilter); @@ -100,6 +113,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter ConnectedComponentsType; typename ConnectedComponentsType::Pointer m_ConnectedComponents; - // typedef BinaryCrossStructuringElement StructuringElementType; - typedef BinaryBallStructuringElement StructuringElementType; + typedef BinaryCrossStructuringElement CrossStructuringElementType; + typedef BinaryBallStructuringElement BallStructuringElementType; - typedef BinaryDilateImageFilter DilateType; + typedef BinaryDilateImageFilter CrossDilateType; + typedef BinaryDilateImageFilter BallDilateType; typedef AndImageFilter AndFilterType; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index f16249cf7ad..3c30c13ffcd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -108,6 +108,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_Axis(-1) , m_HeuristicAlignment(true) , m_UseDistanceTransform(true) + , m_UseBallStructuringElement(false) , m_ThreadPool(nullptr) , m_StopSpawning(false) , m_MinAlignIters(pow(2, TImage::ImageDimension)) @@ -124,7 +125,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_ConnectedComponents->SetInput(m_Binarizer->GetOutput()); // FullyConnected is related to structuring element used // true for ball, false for cross - m_ConnectedComponents->SetFullyConnected(true); + m_ConnectedComponents->SetFullyConnected(m_UseBallStructuringElement); } @@ -319,27 +320,47 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe typename BoolImageType::Pointer mask, int axis) { - thread_local typename DilateType::Pointer m_Dilator = DilateType::New(); - m_Dilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads // set up structuring element for dilation typedef Size SizeType; SizeType size; size.Fill(1); size[axis] = 0; - thread_local StructuringElementType m_StructuringElement; - m_StructuringElement.SetRadius(size); - m_StructuringElement.CreateStructuringElement(); - m_Dilator->SetKernel(m_StructuringElement); + + thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); + m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + thread_local CrossStructuringElementType m_CrossStructuringElement; + m_CrossStructuringElement.SetRadius(size); + m_CrossStructuringElement.CreateStructuringElement(); + m_CrossDilator->SetKernel(m_CrossStructuringElement); + + thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); + m_BallDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + thread_local BallStructuringElementType m_BallStructuringElement; + m_BallStructuringElement.SetRadius(size); + m_BallStructuringElement.CreateStructuringElement(); + m_BallDilator->SetKernel(m_BallStructuringElement); // TODO: keep structuring element and dilator per axis instead of per thread? - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - m_Dilator->SetInput(seed); - m_Dilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_Dilator->Update(); - typename BoolImageType::Pointer temp = m_Dilator->GetOutput(); + typename BoolImageType::Pointer temp; + if (m_UseBallStructuringElement) + { + m_BallDilator->SetInput(seed); + m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_BallDilator->Update(); + temp = m_BallDilator->GetOutput(); + } + else + { + m_CrossDilator->SetInput(seed); + m_CrossDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_CrossDilator->Update(); + temp = m_CrossDilator->GetOutput(); + } temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions + + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads m_And->SetInput(0, mask); m_And->SetInput(1, temp); m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); @@ -490,12 +511,13 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int ImageRegionConstIterator itj(jMask, iMask->GetRequestedRegion()); ImageRegionIterator ito(orImage, iMask->GetRequestedRegion()); ImageRegionConstIterator itsdf(sdf, iMask->GetRequestedRegion()); + const short fractioning = 10; // how many times more precise distance than rounding to int while (!itsdf.IsAtEnd()) { ; bool iM = iti.Get(); bool jM = itj.Get(); - typename TImage::PixelType dist = itsdf.Get(); + typename TImage::PixelType dist = fractioning * itsdf.Get(); if (iM && !jM) { if (dist >= iHist.size()) @@ -538,8 +560,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int assert(jHist[0] == 0); std::vector iSum(maxSize, 0); std::vector jSum(maxSize, 0); - iSum[0] = iHist[0]; - jSum[0] = jHist[0]; for (int b = 1; b < maxSize; b++) { iSum[b] = iSum[b - 1] + iHist[b]; @@ -555,7 +575,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int { long long iS = std::abs(iTotal - iSum[b] + jSum[b]); long long jS = std::abs(jTotal - jSum[b] + iSum[b]); - // long long jS = std::abs(jTotal - jSum[maxSize - b - 1] + iSum[b]); long long diff = std::abs(iS - jS); if (diff < bestDiff) { @@ -566,20 +585,18 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int // threshold at distance bestBin is the median intersection typedef BinaryThresholdImageFilter FloatBinarizerType; - thread_local FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); + thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); threshold->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads threshold->SetInput(sdf); - threshold->SetUpperThreshold(bestBin); + threshold->SetUpperThreshold(float(bestBin) / fractioning); threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); threshold->Update(); - thread_local AndFilterType::Pointer and = AndFilterType::New(); - and->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - and->SetInput(threshold->GetOutput()); - and->SetInput(1, orImage); - and->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); - and->Update(); - BoolImageType::Pointer median = and->GetOutput(); + m_And->SetInput(threshold->GetOutput()); + m_And->SetInput(1, orImage); + m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); + m_And->Update(); + typename BoolImageType::Pointer median = m_And->GetOutput(); WriteDebug(median, "C:\\median.nrrd"); return median; } @@ -639,12 +656,12 @@ MorphologicalContourInterpolator::Interpolate1to1(int ExpandRegion(newRegion, jRegion.GetIndex()); ExpandRegion(newRegion, jBottom); - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); - WriteDebug(iConnT, "C:\\iConnT.nrrd"); - WriteDebug(jConnT, "C:\\jConnT.nrrd"); + // WriteDebug(iConnT, "C:\\iConnT.nrrd"); + // WriteDebug(jConnT, "C:\\jConnT.nrrd"); if (!recursive) // reduce bounding box so we deal with less pixels { @@ -684,8 +701,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int iConnT = TranslateImage(iConnT, t0, newRegion); jConnT = TranslateImage(jConnT, t0, newRegion); } - WriteDebug(iConnT, "C:\\iConnTb.nrrd"); - WriteDebug(jConnT, "C:\\jConnTb.nrrd"); + // WriteDebug(iConnT, "C:\\iConnTb.nrrd"); + // WriteDebug(jConnT, "C:\\jConnTb.nrrd"); // convert to binary masks // TODO: do this by iterators and reduce dimension by one @@ -810,9 +827,9 @@ MorphologicalContourInterpolator::Interpolate1toN(int caster->SetInput(iConn); caster->Update(); typename BoolImageType::Pointer mask = caster->GetOutput(); - WriteDebug(mask, "C:\\mask.nrrd"); - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); + // WriteDebug(mask, "C:\\mask.nrrd"); + // WriteDebug(iConn, "C:\\iConn.nrrd"); + // WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -859,14 +876,14 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + // WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x]->SetRegions(iRegion); - WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } ImageRegionConstIterator maskIt2(mask, iRegion); ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); @@ -877,9 +894,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x] = Dilate1(blobs[x], mask, axis); - WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); - // TODO: save these in a sequence so we don't have to recalculate it! } // TODO: replace this loop by LabelErodeDilate filters? @@ -931,7 +947,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + // WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images @@ -960,7 +976,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int for (unsigned x = 0; x < jRegionIds.size(); x++) { Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false); - // TODO: call sequence construction directly from here! } } @@ -1468,8 +1483,8 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); jconn->DisconnectPipeline(); - WriteDebug(iconn, "C:\\iconn.nrrd"); - WriteDebug(jconn, "C:\\jconn.nrrd"); + // WriteDebug(iconn, "C:\\iconn.nrrd"); + // WriteDebug(jconn, "C:\\jconn.nrrd"); if (*prev + 1 < *next) // only if they are not adjacent slices { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_B.nii.gz.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD.nii.gz.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_B.nii.gz.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_RD_-1_0.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/105769fixed_B_-1_0.nii.gz.md5 similarity index 100% rename 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rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_B_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C.nrrd.md5 new file mode 100644 index 00000000000..722afbbb2fa --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C.nrrd.md5 @@ -0,0 +1 @@ +95c16aa1649afe1904ff699e1815f2bb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_0.nrrd.md5 new file mode 100644 index 00000000000..0eba1df746a --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_0.nrrd.md5 @@ -0,0 +1 @@ +f86cc696fe83653bca608720ecead597 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/BigZ_C_1.nrrd.md5 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b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T.nrrd.md5 @@ -0,0 +1 @@ +66573c086cd23be5a37a6fce2d577b29 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_0.nrrd.md5 new file mode 100644 index 00000000000..50b39a4cba7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_0.nrrd.md5 @@ -0,0 +1 @@ +77047fc34df5f8478255ef2143f72101 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_1.nrrd.md5 new file mode 100644 index 00000000000..50b39a4cba7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FaceRoI_T_1.nrrd.md5 @@ -0,0 +1 @@ +77047fc34df5f8478255ef2143f72101 diff --git 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00000000000..7c1493488c5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_C.nrrd.md5 @@ -0,0 +1 @@ +e3be9a00e5fe62890178b05ed3ba6015 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_T.nrrd.md5 new file mode 100644 index 00000000000..0d4b33c8614 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FourD_T.nrrd.md5 @@ -0,0 +1 @@ +cd1d3317b74a952a3c1f44e82f639a79 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_RD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_B.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_RD.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_B.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_C.nrrd.md5 new file mode 100644 index 00000000000..efb989fa64f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_C.nrrd.md5 @@ -0,0 +1 @@ +28497c0ce2b4ebb1205f4d70bf1fbb8b diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_T.nrrd.md5 new file mode 100644 index 00000000000..15d429ed65b --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/FullEnd_T.nrrd.md5 @@ -0,0 +1 @@ +da1eb42bb8ddc246318b9df7b2ba93a2 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_RD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg2_B.nrrd.md5 similarity index 100% rename from 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a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_C.nrrd.md5 new file mode 100644 index 00000000000..27fc2a83841 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_C.nrrd.md5 @@ -0,0 +1 @@ +02f32af3e386eb2fd918f071ace9be19 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_T.nrrd.md5 new file mode 100644 index 00000000000..27fc2a83841 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/NoSlices_T.nrrd.md5 @@ -0,0 +1 @@ +02f32af3e386eb2fd918f071ace9be19 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_RD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/OneToOne_B.nrrd.md5 similarity index 100% rename from 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/dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 @@ -0,0 +1 @@ +f40e7197f0d6b41f1fd70d6b3587b72f diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 new file mode 100644 index 00000000000..2627a3d7735 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 @@ -0,0 +1 @@ +ee7c148b33b089af63ca53bc5c22af00 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 new file mode 100644 index 00000000000..02a16b13915 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 @@ -0,0 +1 @@ +e6d6ddb6b56c7513ad7e28073599a85a diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 new file mode 100644 index 00000000000..009b35fb194 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 @@ -0,0 +1 @@ +8dff078b502cd3410c7854282f4bd20d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 new file mode 100644 index 00000000000..d72ec7375b8 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 @@ -0,0 +1 @@ +10105725854b7362695fb3d0e5eced38 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 new file mode 100644 index 00000000000..e30c578fbcb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 @@ -0,0 +1 @@ +24f59e3a707ad7ea34f015abf7395d37 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 new file mode 100644 index 00000000000..ab0b979cb96 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 @@ -0,0 +1 @@ +fc3556bc87c3736840173a88dd37bfcf diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 new file mode 100644 index 00000000000..e30c578fbcb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 @@ -0,0 +1 @@ +24f59e3a707ad7ea34f015abf7395d37 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 new file mode 100644 index 00000000000..40245f04746 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 @@ -0,0 +1 @@ +08e4636f1e5ce27376a888d9402c6fcd diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 new file mode 100644 index 00000000000..e348ed9c8b1 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 @@ -0,0 +1 @@ +2ecaf48e0435322619a43a147d0c03e1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 new file mode 100644 index 00000000000..e348ed9c8b1 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 @@ -0,0 +1 @@ +2ecaf48e0435322619a43a147d0c03e1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 new file mode 100644 index 00000000000..e348ed9c8b1 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 @@ -0,0 +1 @@ +2ecaf48e0435322619a43a147d0c03e1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 new file mode 100644 index 00000000000..bdb746f28f6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 @@ -0,0 +1 @@ +2adb499a6d1a09940bfffca003f55889 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 new file mode 100644 index 00000000000..28ca6694ca7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 @@ -0,0 +1 @@ +a87d3fe609b90864418049bae2c9f4d1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 new file mode 100644 index 00000000000..d231d5e8ac7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 @@ -0,0 +1 @@ +c6b947585026af9b9ad368ece7737cfa diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 new file mode 100644 index 00000000000..6d2af13f70a --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 @@ -0,0 +1 @@ +e0824fd32a73a3f683a7f7b611965846 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 new file mode 100644 index 00000000000..ab0b979cb96 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 @@ -0,0 +1 @@ +fc3556bc87c3736840173a88dd37bfcf diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 new file mode 100644 index 00000000000..6d2af13f70a --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 @@ -0,0 +1 @@ +e0824fd32a73a3f683a7f7b611965846 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_RD.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_RD.nrrd.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 new file mode 100644 index 00000000000..f139ed016ff --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 @@ -0,0 +1 @@ +5f8db3dbb727ef8789361db65109a528 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 new file mode 100644 index 00000000000..cb1a17ad5d6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 @@ -0,0 +1 @@ +34781fd28e033c69e4a7e25b2e9b9b9c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD.png.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_1.png.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_-1_255.png.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_0.png.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 similarity index 100% rename from Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_RD_1.png.md5 rename to Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 new file mode 100644 index 00000000000..49456a80c47 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 @@ -0,0 +1 @@ +adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 new file mode 100644 index 00000000000..d648f308c26 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 @@ -0,0 +1 @@ +2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 new file mode 100644 index 00000000000..49456a80c47 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 @@ -0,0 +1 @@ +adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 new file mode 100644 index 00000000000..0d6c68e7ac4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 @@ -0,0 +1 @@ +382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 new file mode 100644 index 00000000000..49456a80c47 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 @@ -0,0 +1 @@ +adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 new file mode 100644 index 00000000000..0d6c68e7ac4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 @@ -0,0 +1 @@ +382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 new file mode 100644 index 00000000000..0d6c68e7ac4 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 @@ -0,0 +1 @@ +382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 new file mode 100644 index 00000000000..49456a80c47 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 @@ -0,0 +1 @@ +adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 679f89f1a70..427fa865198 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -59,144 +59,144 @@ function(RegressionTest ImageName Ext) #optional: Algo Axis Label endfunction() # Handcrafted tests -regressiontest(Empty nrrd RD) -regressiontest(NoSlices nrrd RD) #interpolation should not be invoked (output==input) -regressiontest(Micro1 nrrd RD) -regressiontest(SimplestOneToOne nrrd RD) -regressiontest(OneToOne nrrd RD) -regressiontest(OneToThree nrrd RD) -regressiontest(ExtrapolationAppearing nrrd RD) -regressiontest(DoubleTwoLabelBranching nrrd RD) -regressiontest(TwoAxisDoubleTwoLabelBC nrrd RD) -regressiontest(AccidentalMiddleSliceSeg nrrd RD) -regressiontest(SevenLabels nrrd RD) -regressiontest(FullEnd nrrd RD) -regressiontest(1MN1 nrrd RD) # double sided many broken into many + 1 -regressiontest(ManyToMany16 nrrd RD) -regressiontest(ManyToMany nrrd RD) -regressiontest(GridSeg nrrd RD) -regressiontest(GridSeg2 nrrd RD) +regressiontest(Empty nrrd ${MCI_Algorithm}) +regressiontest(NoSlices nrrd ${MCI_Algorithm}) #interpolation should not be invoked (output==input) +regressiontest(Micro1 nrrd ${MCI_Algorithm}) +regressiontest(SimplestOneToOne nrrd ${MCI_Algorithm}) +regressiontest(OneToOne nrrd ${MCI_Algorithm}) +regressiontest(OneToThree nrrd ${MCI_Algorithm}) +regressiontest(ExtrapolationAppearing nrrd ${MCI_Algorithm}) +regressiontest(DoubleTwoLabelBranching nrrd ${MCI_Algorithm}) +regressiontest(TwoAxisDoubleTwoLabelBC nrrd ${MCI_Algorithm}) +regressiontest(AccidentalMiddleSliceSeg nrrd ${MCI_Algorithm}) +regressiontest(SevenLabels nrrd ${MCI_Algorithm}) +regressiontest(FullEnd nrrd ${MCI_Algorithm}) +regressiontest(1MN1 nrrd ${MCI_Algorithm}) # double sided many broken into many + 1 +regressiontest(ManyToMany16 nrrd ${MCI_Algorithm}) +regressiontest(ManyToMany nrrd ${MCI_Algorithm}) +regressiontest(GridSeg nrrd ${MCI_Algorithm}) +regressiontest(GridSeg2 nrrd ${MCI_Algorithm}) # Per axis/label tests -regressiontest(GridSeg nrrd RD 0) -regressiontest(GridSeg nrrd RD 1) -regressiontest(GridSeg nrrd RD 2) -regressiontest(GridSeg2 nrrd RD 0) -regressiontest(GridSeg2 nrrd RD 1) -regressiontest(GridSeg2 nrrd RD 2) -regressiontest(ThreeAxisFourLabelConflict nrrd RD) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 0) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 1) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 2) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 0 0) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd RD 1 1) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 2 3) # equals to _2 -regressiontest(ThreeAxisFourLabelConflict nrrd RD 0 4) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd RD 1 2) -regressiontest(ThreeAxisFourLabelConflict nrrd RD 2 2) # does not modify image +regressiontest(GridSeg nrrd ${MCI_Algorithm} 0) +regressiontest(GridSeg nrrd ${MCI_Algorithm} 1) +regressiontest(GridSeg nrrd ${MCI_Algorithm} 2) +regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 0) +regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 1) +regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 2) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm}) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0 0) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1 1) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2 3) # equals to _2 +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0 4) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1 2) +regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2 2) # does not modify image # Paul's single axis tests -regressiontest(105769moving nii.gz RD) #defaults: all axes all labels -regressiontest(105769moving nii.gz RD 2) #axis 2 -regressiontest(105769moving nii.gz RD -1 0) #all axes all labels -regressiontest(105769moving nii.gz RD -1 1) #all axes label 1 -regressiontest(105769moving nii.gz RD -1 2) #all axes label 2 -regressiontest(105769moving nii.gz RD 2 1) #axis 2 label 1 -regressiontest(105769moving nii.gz RD 2 2) #axis 2 label 2 -regressiontest(105769fixed nii.gz RD) #defaults: all axes all labels -regressiontest(105769fixed nii.gz RD 2) #axis 2 -regressiontest(105769fixed nii.gz RD -1 0) #all axes all labels -regressiontest(105769fixed nii.gz RD -1 1) #all axes label 1 -regressiontest(105769fixed nii.gz RD -1 2) #all axes label 2 -regressiontest(105769fixed nii.gz RD 2 1) #axis 2 label 1 -regressiontest(105769fixed nii.gz RD 2 2) #axis 2 label 2 +regressiontest(105769moving nii.gz ${MCI_Algorithm}) #defaults: all axes all labels +regressiontest(105769moving nii.gz ${MCI_Algorithm} 2) #axis 2 +regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 0) #all axes all labels +regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 1) #all axes label 1 +regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 2) #all axes label 2 +regressiontest(105769moving nii.gz ${MCI_Algorithm} 2 1) #axis 2 label 1 +regressiontest(105769moving nii.gz ${MCI_Algorithm} 2 2) #axis 2 label 2 +regressiontest(105769fixed nii.gz ${MCI_Algorithm}) #defaults: all axes all labels +regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2) #axis 2 +regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 0) #all axes all labels +regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 1) #all axes label 1 +regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 2) #all axes label 2 +regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2 1) #axis 2 label 1 +regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2 2) #axis 2 label 2 # 64816L_amygdala_int -regressiontest(64816L_amygdala_int nii.gz RD) -regressiontest(64816L_amygdala_int nii.gz RD 0) -regressiontest(64816L_amygdala_int nii.gz RD 1) -regressiontest(64816L_amygdala_int nii.gz RD 2) -regressiontest(64816L_amygdala_int nii.gz RD 0 1) -regressiontest(64816L_amygdala_int nii.gz RD 0 2) -regressiontest(64816L_amygdala_int nii.gz RD 0 3) -regressiontest(64816L_amygdala_int nii.gz RD 0 4) -regressiontest(64816L_amygdala_int nii.gz RD 1 1) -regressiontest(64816L_amygdala_int nii.gz RD 1 2) -regressiontest(64816L_amygdala_int nii.gz RD 1 3) -regressiontest(64816L_amygdala_int nii.gz RD 1 4) -regressiontest(64816L_amygdala_int nii.gz RD 2 1) -regressiontest(64816L_amygdala_int nii.gz RD 2 2) -regressiontest(64816L_amygdala_int nii.gz RD 2 3) -regressiontest(64816L_amygdala_int nii.gz RD 2 4) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm}) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 1) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 2) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 3) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 4) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 1) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 2) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 3) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 4) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 1) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 2) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 3) +regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 4) # 64816L_amygdala_fin -regressiontest(64816L_amygdala_fin nii.gz RD) -regressiontest(64816L_amygdala_fin nii.gz RD 0) -regressiontest(64816L_amygdala_fin nii.gz RD 1) -regressiontest(64816L_amygdala_fin nii.gz RD 2) -regressiontest(64816L_amygdala_fin nii.gz RD 0 1) -regressiontest(64816L_amygdala_fin nii.gz RD 0 2) -regressiontest(64816L_amygdala_fin nii.gz RD 0 3) -regressiontest(64816L_amygdala_fin nii.gz RD 0 4) -regressiontest(64816L_amygdala_fin nii.gz RD 1 1) -regressiontest(64816L_amygdala_fin nii.gz RD 1 2) -regressiontest(64816L_amygdala_fin nii.gz RD 1 3) -regressiontest(64816L_amygdala_fin nii.gz RD 1 4) -regressiontest(64816L_amygdala_fin nii.gz RD 2 1) -regressiontest(64816L_amygdala_fin nii.gz RD 2 2) -regressiontest(64816L_amygdala_fin nii.gz RD 2 3) -regressiontest(64816L_amygdala_fin nii.gz RD 2 4) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm}) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 1) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 2) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 3) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 4) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 1) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 2) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 3) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 4) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 1) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 2) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 3) +regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 4) # 65239R_amygdala_int -regressiontest(65239R_amygdala_int nii.gz RD) -regressiontest(65239R_amygdala_int nii.gz RD 0) -regressiontest(65239R_amygdala_int nii.gz RD 1) -regressiontest(65239R_amygdala_int nii.gz RD 2) -regressiontest(65239R_amygdala_int nii.gz RD 0 1) -regressiontest(65239R_amygdala_int nii.gz RD 0 2) -regressiontest(65239R_amygdala_int nii.gz RD 0 3) -regressiontest(65239R_amygdala_int nii.gz RD 0 4) -regressiontest(65239R_amygdala_int nii.gz RD 1 1) -regressiontest(65239R_amygdala_int nii.gz RD 1 2) -regressiontest(65239R_amygdala_int nii.gz RD 1 3) -regressiontest(65239R_amygdala_int nii.gz RD 1 4) -regressiontest(65239R_amygdala_int nii.gz RD 2 1) -regressiontest(65239R_amygdala_int nii.gz RD 2 2) -regressiontest(65239R_amygdala_int nii.gz RD 2 3) -regressiontest(65239R_amygdala_int nii.gz RD 2 4) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm}) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 1) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 2) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 3) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 4) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 1) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 2) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 3) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 4) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 1) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 2) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 3) +regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 4) # 65239R_amygdala_fin -regressiontest(65239R_amygdala_fin nii.gz RD) -regressiontest(65239R_amygdala_fin nii.gz RD 0) -regressiontest(65239R_amygdala_fin nii.gz RD 1) -regressiontest(65239R_amygdala_fin nii.gz RD 2) -regressiontest(65239R_amygdala_fin nii.gz RD 0 1) -regressiontest(65239R_amygdala_fin nii.gz RD 0 2) -regressiontest(65239R_amygdala_fin nii.gz RD 0 3) -regressiontest(65239R_amygdala_fin nii.gz RD 0 4) -regressiontest(65239R_amygdala_fin nii.gz RD 1 1) -regressiontest(65239R_amygdala_fin nii.gz RD 1 2) -regressiontest(65239R_amygdala_fin nii.gz RD 1 3) -regressiontest(65239R_amygdala_fin nii.gz RD 1 4) -regressiontest(65239R_amygdala_fin nii.gz RD 2 1) -regressiontest(65239R_amygdala_fin nii.gz RD 2 2) -regressiontest(65239R_amygdala_fin nii.gz RD 2 3) -regressiontest(65239R_amygdala_fin nii.gz RD 2 4) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm}) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 1) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 2) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 3) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 4) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 1) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 2) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 3) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 4) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 1) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 2) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 3) +regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 4) # Long-running handcrafted tests -regressiontest(BigZ nrrd RD) -regressiontest(BigZ nrrd RD 0) -regressiontest(BigZ nrrd RD 1) -regressiontest(BigZ nrrd RD 2) -regressiontest(FaceRoI nrrd RD) -regressiontest(FaceRoI nrrd RD 0) -regressiontest(FaceRoI nrrd RD 1) -regressiontest(FaceRoI nrrd RD 2) +regressiontest(BigZ nrrd ${MCI_Algorithm}) +regressiontest(BigZ nrrd ${MCI_Algorithm} 0) +regressiontest(BigZ nrrd ${MCI_Algorithm} 1) +regressiontest(BigZ nrrd ${MCI_Algorithm} 2) +regressiontest(FaceRoI nrrd ${MCI_Algorithm}) +regressiontest(FaceRoI nrrd ${MCI_Algorithm} 0) +regressiontest(FaceRoI nrrd ${MCI_Algorithm} 1) +regressiontest(FaceRoI nrrd ${MCI_Algorithm} 2) # Non-3D tests -regressiontest(TwoD png RD) -regressiontest(TwoD png RD -1 255) # same as regular -regressiontest(TwoD png RD 0) # same as regular -regressiontest(TwoD png RD -1 1) # does not modify image -regressiontest(TwoD png RD 1) # does not modify image -regressiontest(FourD nrrd RD) +regressiontest(TwoD png ${MCI_Algorithm}) +regressiontest(TwoD png ${MCI_Algorithm} -1 255) # same as regular +regressiontest(TwoD png ${MCI_Algorithm} 0) # same as regular +regressiontest(TwoD png ${MCI_Algorithm} -1 1) # does not modify image +regressiontest(TwoD png ${MCI_Algorithm} 1) # does not modify image +regressiontest(FourD nrrd ${MCI_Algorithm}) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 714d6fec0c2..6c5ad9ffe52 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -31,7 +31,7 @@ string2int(char * number) template void -doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, int axis, int label) +doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, bool ball, int axis, int label) { typedef itk::ImageFileReader ReaderType; typename ReaderType::Pointer reader = ReaderType::New(); @@ -41,6 +41,7 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor typename mciType::Pointer mci = mciType::New(); mci->SetInput(reader->GetOutput()); mci->SetUseDistanceTransform(UseDistanceTransform); + mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); @@ -58,24 +59,32 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) if (argc < 3) { std::cerr << "Usage: " << argv[0]; - std::cerr << " inputImage outputImage [algo] [axis] [label]\n"; - std::cerr << " algo: RD (repeated dilations ) or DT (distance transform [default])"; - std::cerr << " defaults: axis == -1 (all axes), label == 0 (all labels)"; + std::cerr << " inputImage outputImage [algorithm] [axis] [label]\n"; + std::cerr << " algorithms:\n"; + std::cerr << " B = repeated dilations with ball structuring element"; + std::cerr << " C = repeated dilations with cross structuring element"; + std::cerr << " T = distance transform (not geodesic!)"; + std::cerr << " defaults: algo B, axis -1 (all axes), label 0 (all labels)"; std::cerr << std::endl; return EXIT_FAILURE; } const char * inputImageFileName = argv[1]; const char * outputImageFileName = argv[2]; - bool dt = true; // DistanceTransform + bool dt = false; // DistanceTransform + bool ball = true; int axis = -1, label = 0; if (argc >= 4) { - std::string algo = argv[3]; - for (auto & c : algo) + char algo = toupper(argv[3][0]); + if (algo == 'T') { - c = toupper(c); + dt = true; } - dt = (algo != "RD"); + else if (algo == 'C') + { + ball = false; + } + // else B } if (argc >= 5) { @@ -104,17 +113,17 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) // unused cases are not instantiated because they greatly increase compile time if (numDimensions == 2 && pixelType == ScalarPixelType::UCHAR) { - doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } if (numDimensions == 3 && (pixelType == ScalarPixelType::SHORT || pixelType == ScalarPixelType::USHORT)) { - doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } if (numDimensions == 4 && pixelType == ScalarPixelType::UCHAR) { - doTest>(inputImageFileName, outputImageFileName, dt, axis, label); + doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } From a04bf4d81eb9b99fffac99cc381504aad9287dcf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 30 Mar 2016 12:22:33 -0400 Subject: [PATCH 070/176] ENH: Reducing dimension of regions passed to findMedian --- .../itkMorphologicalContourInterpolator.h | 53 ++- .../itkMorphologicalContourInterpolator.hxx | 340 ++++++++++-------- ...kMorphologicalContourInterpolationTest.cxx | 11 +- 3 files changed, 228 insertions(+), 176 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 1503de4dc1b..c5a9694fa47 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -19,15 +19,11 @@ #define itkMorphologicalContourInterpolator_h #include "itkImageToImageFilter.h" +#include "itksys/hash_map.hxx" +#include "itkExtractImageFilter.h" #include "itkConnectedComponentImageFilter.h" #include "itkBinaryThresholdImageFilter.h" -#include "itkExtractImageFilter.h" -#include "itksys/hash_map.hxx" -#include "itkBinaryDilateImageFilter.h" -#include "itkBinaryCrossStructuringElement.h" -#include "itkBinaryBallStructuringElement.h" -#include "itkAndImageFilter.h" -#include "itkOrImageFilter.h" + #include "ThreadPool.h" @@ -162,25 +158,31 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; - typedef Image FloatImageType; + typedef Image FloatSliceType; typedef Image SliceType; typedef Image BoolSliceType; - typename FloatImageType::Pointer - MaurerDM(typename BoolImageType::Pointer inImage); + typename FloatSliceType::Pointer + MaurerDM(typename BoolSliceType::Pointer inImage); /** A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same) */ - std::vector - GenerateDilationSequence(typename BoolImageType::Pointer begin, typename BoolImageType::Pointer end, int axis); + std::vector + GenerateDilationSequence(typename BoolSliceType::Pointer begin, typename BoolSliceType::Pointer end, int axis); /** Finds an interpolating mask for these two aligned masks */ - typename BoolImageType::Pointer - FindMedianImageDilations(int axis, typename BoolImageType::Pointer iMask, typename BoolImageType::Pointer jMask); + typename BoolSliceType::Pointer + FindMedianImageDilations(int axis, + typename BoolSliceType::Pointer intersection, + typename BoolSliceType::Pointer iMask, + typename BoolSliceType::Pointer jMask); /** Finds an interpolating mask for these two aligned masks */ - typename BoolImageType::Pointer - FindMedianImageDistances(int axis, typename BoolImageType::Pointer iMask, typename BoolImageType::Pointer jMask); + typename BoolSliceType::Pointer + FindMedianImageDistances(int axis, + typename BoolSliceType::Pointer intersection, + typename BoolSliceType::Pointer iMask, + typename BoolSliceType::Pointer jMask); /** Build transition sequence and pick the median */ void @@ -219,7 +221,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter image); + // assumes both valid region and valid index void ExpandRegion(typename TImage::RegionType & region, typename TImage::IndexType index); @@ -282,8 +287,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter + SmartPointer + Dilate1(SmartPointer seed, SmartPointer mask, bool useBall, int axis); typedef ExtractImageFilter RoiType; typename RoiType::Pointer m_RoI; @@ -294,15 +300,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter ConnectedComponentsType; typename ConnectedComponentsType::Pointer m_ConnectedComponents; - typedef BinaryCrossStructuringElement CrossStructuringElementType; - typedef BinaryBallStructuringElement BallStructuringElementType; - - typedef BinaryDilateImageFilter CrossDilateType; - typedef BinaryDilateImageFilter BallDilateType; - - typedef AndImageFilter AndFilterType; - - typedef OrImageFilter OrType; class MatchesID { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 3c30c13ffcd..bd754fbc96b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -26,6 +26,11 @@ #include "itkUnaryFunctorImageFilter.h" #include "itkCastImageFilter.h" #include "itkSignedMaurerDistanceMapImageFilter.h" +#include "itkBinaryDilateImageFilter.h" +#include "itkBinaryCrossStructuringElement.h" +#include "itkBinaryBallStructuringElement.h" +#include "itkAndImageFilter.h" +#include "itkOrImageFilter.h" #include #include #include @@ -315,16 +320,23 @@ MorphologicalContourInterpolator::Extrapolate(int template -typename MorphologicalContourInterpolator::BoolImageType::Pointer -MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointer seed, - typename BoolImageType::Pointer mask, - int axis) +template +SmartPointer +MorphologicalContourInterpolator::Dilate1(SmartPointer seed, SmartPointer mask, bool useBall, int axis) { // set up structuring element for dilation - typedef Size SizeType; - SizeType size; + typedef Size SizeType; + SizeType size; size.Fill(1); - size[axis] = 0; + if (axis >= 0) + { + size[axis] = 0; + } + + typedef BinaryCrossStructuringElement CrossStructuringElementType; + typedef BinaryBallStructuringElement BallStructuringElementType; + typedef BinaryDilateImageFilter CrossDilateType; + typedef BinaryDilateImageFilter BallDilateType; thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads @@ -341,8 +353,8 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe m_BallDilator->SetKernel(m_BallStructuringElement); // TODO: keep structuring element and dilator per axis instead of per thread? - typename BoolImageType::Pointer temp; - if (m_UseBallStructuringElement) + typename T2::Pointer temp; + if (useBall) { m_BallDilator->SetInput(seed); m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); @@ -359,13 +371,14 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions + typedef AndImageFilter AndFilterType; thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads m_And->SetInput(0, mask); m_And->SetInput(1, temp); m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); m_And->Update(); - typename BoolImageType::Pointer result = m_And->GetOutput(); + typename T2::Pointer result = m_And->GetOutput(); result->DisconnectPipeline(); // WriteDebug(seed, "C:\\seed.nrrd"); // WriteDebug(mask, "C:\\mask.nrrd"); @@ -376,57 +389,49 @@ MorphologicalContourInterpolator::Dilate1(typename BoolImageType::Pointe template -std::vector::BoolImageType::Pointer> -MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolImageType::Pointer begin, - typename BoolImageType::Pointer end, +std::vector::BoolSliceType::Pointer> +MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer begin, + typename BoolSliceType::Pointer end, int axis) { - // typedef Testing::HashImageFilter HashType; + // typedef Testing::HashImageFilter HashType; // HashType::Pointer hasher = HashType::New(); // hasher->SetInPlace(true); // std::vector hashes; // TODO: optimization: replace ImagesEqual call with hash comparison? - std::vector seq; - seq.push_back(Dilate1(begin, end, axis)); + std::vector seq; + seq.push_back(Dilate1(begin, end, m_UseBallStructuringElement, -1)); do { seq.back()->DisconnectPipeline(); - seq.push_back(Dilate1(seq.back(), end, axis)); - } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); + seq.push_back(Dilate1(seq.back(), end, m_UseBallStructuringElement, -1)); + } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image return seq; } template -typename MorphologicalContourInterpolator::BoolImageType::Pointer +typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDilations(int axis, - typename BoolImageType::Pointer iMask, - typename BoolImageType::Pointer jMask) + typename BoolSliceType::Pointer intersection, + typename BoolSliceType::Pointer iMask, + typename BoolSliceType::Pointer jMask) { - // generate sequence - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - WriteDebug(iMask, "C:\\iMask.nrrd"); - WriteDebug(jMask, "C:\\jMask.nrrd"); - m_And->SetInput(0, iMask); - m_And->SetInput(1, jMask); - m_And->GetOutput()->SetRegions(iMask->GetRequestedRegion()); - m_And->Update(); - typename BoolImageType::Pointer intersection = m_And->GetOutput(); - intersection->DisconnectPipeline(); - WriteDebug(intersection, "C:\\intersection.nrrd"); - std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); - std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); + std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); + std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection if (iSeq.size() < jSeq.size()) { iSeq.swap(jSeq); // swap so iSeq.size() >= jSeq.size() } - float ratio = float(jSeq.size()) / iSeq.size(); + float ratio = float(jSeq.size()) / iSeq.size(); + + // generate union of transition sequences + typedef OrImageFilter OrType; thread_local typename OrType::Pointer m_Or = OrType::New(); m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - std::vector seq; + std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) { m_Or->SetInput(0, iSeq[x]); @@ -464,10 +469,10 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int template -typename MorphologicalContourInterpolator::FloatImageType::Pointer -MorphologicalContourInterpolator::MaurerDM(typename BoolImageType::Pointer mask) +typename MorphologicalContourInterpolator::FloatSliceType::Pointer +MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer mask) { - typedef itk::SignedMaurerDistanceMapImageFilter FilterType; + typedef itk::SignedMaurerDistanceMapImageFilter FilterType; thread_local typename FilterType::Pointer filter = FilterType::New(); filter->SetInput(mask); filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space @@ -478,39 +483,27 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolImageType::Point } template -typename MorphologicalContourInterpolator::BoolImageType::Pointer +typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDistances(int axis, - typename BoolImageType::Pointer iMask, - typename BoolImageType::Pointer jMask) + typename BoolSliceType::Pointer intersection, + typename BoolSliceType::Pointer iMask, + typename BoolSliceType::Pointer jMask) { - // create intersection - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - WriteDebug(iMask, "C:\\iMask.nrrd"); - WriteDebug(jMask, "C:\\jMask.nrrd"); - m_And->SetInput(0, iMask); - m_And->SetInput(1, jMask); - m_And->GetOutput()->SetRegions(iMask->GetRequestedRegion()); - m_And->Update(); - typename BoolImageType::Pointer intersection = m_And->GetOutput(); - intersection->DisconnectPipeline(); - WriteDebug(intersection, "C:\\intersection.nrrd"); - // calculate distance field - typename FloatImageType::Pointer sdf = MaurerDM(intersection); + typename FloatSliceType::Pointer sdf = MaurerDM(intersection); WriteDebug(sdf, "C:\\sdf.nrrd"); // create histograms of distances and union - typename BoolImageType::Pointer orImage = BoolImageType::New(); + typename BoolSliceType::Pointer orImage = BoolSliceType::New(); orImage->CopyInformation(intersection); orImage->SetRegions(iMask->GetRequestedRegion()); orImage->Allocate(true); std::vector iHist; std::vector jHist; - ImageRegionConstIterator iti(iMask, iMask->GetRequestedRegion()); - ImageRegionConstIterator itj(jMask, iMask->GetRequestedRegion()); - ImageRegionIterator ito(orImage, iMask->GetRequestedRegion()); - ImageRegionConstIterator itsdf(sdf, iMask->GetRequestedRegion()); + ImageRegionConstIterator iti(iMask, iMask->GetRequestedRegion()); + ImageRegionConstIterator itj(jMask, iMask->GetRequestedRegion()); + ImageRegionIterator ito(orImage, iMask->GetRequestedRegion()); + ImageRegionConstIterator itsdf(sdf, iMask->GetRequestedRegion()); const short fractioning = 10; // how many times more precise distance than rounding to int while (!itsdf.IsAtEnd()) { @@ -584,7 +577,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int } // threshold at distance bestBin is the median intersection - typedef BinaryThresholdImageFilter FloatBinarizerType; + typedef BinaryThresholdImageFilter FloatBinarizerType; thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); threshold->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads threshold->SetInput(sdf); @@ -592,16 +585,55 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); threshold->Update(); + typedef AndImageFilter AndFilterType; + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetInput(threshold->GetOutput()); m_And->SetInput(1, orImage); m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); m_And->Update(); - typename BoolImageType::Pointer median = m_And->GetOutput(); + typename BoolSliceType::Pointer median = m_And->GetOutput(); WriteDebug(median, "C:\\median.nrrd"); return median; } +template +typename TImage::RegionType +MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) +{ + typename TImage::RegionType newRegion = image->GetLargestPossibleRegion(); + typename TImage::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); + typename TImage::IndexType maxInd = newRegion.GetIndex(); + ImageRegionConstIteratorWithIndex iIt(image, newRegion); + + while (!iIt.IsAtEnd()) + { + if (iIt.Get()) + { + typename TImage::IndexType ind = iIt.GetIndex(); + for (int d = 0; d < TImage::ImageDimension; d++) + { + if (ind[d] < minInd[d]) + { + minInd[d] = ind[d]; + } + if (ind[d] > maxInd[d]) + { + maxInd[d] = ind[d]; + } + } + } + ++iIt; + } + + newRegion.SetIndex(minInd); + for (int d = 0; d < TImage::ImageDimension; d++) + { + newRegion.SetSize(d, maxInd[d] - minInd[d] + 1); + } + return newRegion; +} + template void MorphologicalContourInterpolator::Interpolate1to1(int axis, @@ -656,111 +688,138 @@ MorphologicalContourInterpolator::Interpolate1to1(int ExpandRegion(newRegion, jRegion.GetIndex()); ExpandRegion(newRegion, jBottom); - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); - // WriteDebug(iConnT, "C:\\iConnT.nrrd"); - // WriteDebug(jConnT, "C:\\jConnT.nrrd"); + WriteDebug(iConnT, "C:\\iConnT.nrrd"); + WriteDebug(jConnT, "C:\\jConnT.nrrd"); - if (!recursive) // reduce bounding box so we deal with less pixels + if (!recursive) // reduce newRegion to bounding box so we deal with less pixels { - typename TImage::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); - typename TImage::IndexType maxInd = newRegion.GetIndex(); - ImageRegionConstIteratorWithIndex iIt(iConnT, newRegion); - ImageRegionConstIterator jIt(jConnT, newRegion); - - while (!iIt.IsAtEnd()) + newRegion = BoundingBox(iConnT); + typename TImage::RegionType jBB = BoundingBox(jConnT); + typename TImage::IndexType i2 = jBB.GetIndex(); + ExpandRegion(newRegion, i2); + for (int d = 0; d < TImage::ImageDimension; d++) { - if (iIt.Get() || jIt.Get()) - { - typename TImage::IndexType ind = iIt.GetIndex(); - for (int d = 0; d < TImage::ImageDimension; d++) - { - if (ind[d] < minInd[d]) - { - minInd[d] = ind[d]; - } - if (ind[d] > maxInd[d]) - { - maxInd[d] = ind[d]; - } - } - } - ++iIt; - ++jIt; + i2[d] += jBB.GetSize(d) - 1; } + ExpandRegion(newRegion, i2); + } - newRegion.SetIndex(minInd); - for (int d = 0; d < TImage::ImageDimension; d++) + // reduce dimension and convert to binary masks + // start by calculating the correction region (TODO: avoid actual extraction) + typename TImage::RegionType exRegion = newRegion; + exRegion.SetSize(axis, 0); + typedef ExtractImageFilter ExtractorType; + thread_local typename ExtractorType::Pointer extractor = ExtractorType::New(); + extractor->SetDirectionCollapseToIdentity(); + extractor->SetExtractionRegion(exRegion); + extractor->SetInput(iConnT); + extractor->UpdateLargestPossibleRegion(); + typename SliceType::Pointer slice = extractor->GetOutput(); + + // create and allocate slice images + typename BoolSliceType::Pointer iSlice = BoolSliceType::New(); + typename BoolSliceType::RegionType sliceRegion = slice->GetRequestedRegion(); + iSlice->CopyInformation(slice); + iSlice->SetRegions(sliceRegion); + iSlice->Allocate(true); + typename BoolSliceType::Pointer jSlice = BoolSliceType::New(); + jSlice->CopyInformation(slice); + jSlice->SetRegions(sliceRegion); + jSlice->Allocate(true); + + // convert to binary by iteration + ImageRegionConstIterator iIt(iConnT, newRegion); + ImageRegionConstIterator jIt(jConnT, newRegion); + ImageRegionIterator ibIt(iSlice, sliceRegion); + ImageRegionIterator jbIt(jSlice, sliceRegion); + while (!iIt.IsAtEnd()) + { + if (iIt.Get() == iRegionId) { - newRegion.SetSize(d, maxInd[d] - minInd[d] + 1); + ibIt.Set(true); } - typename TImage::IndexType t0; - t0.Fill(0); - iConnT = TranslateImage(iConnT, t0, newRegion); - jConnT = TranslateImage(jConnT, t0, newRegion); + if (jIt.Get() == jRegionId) + { + jbIt.Set(true); + } + ++iIt; + ++jIt; + ++ibIt; + ++jbIt; } - // WriteDebug(iConnT, "C:\\iConnTb.nrrd"); - // WriteDebug(jConnT, "C:\\jConnTb.nrrd"); + WriteDebug(iSlice, "C:\\iSlice.nrrd"); + WriteDebug(jSlice, "C:\\jSlice.nrrd"); - // convert to binary masks - // TODO: do this by iterators and reduce dimension by one - MatchesID matchesIDi(iRegionId); - MatchesID matchesIDj(jRegionId); - typedef UnaryFunctorImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); - caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - caster->SetFunctor(matchesIDi); - caster->SetInput(iConnT); - caster->Update(); - typename BoolImageType::Pointer iMask = caster->GetOutput(); - iMask->DisconnectPipeline(); - caster->SetFunctor(matchesIDj); - caster->SetInput(jConnT); - caster->Update(); - typename BoolImageType::Pointer jMask = caster->GetOutput(); - jMask->DisconnectPipeline(); + // create intersection + typedef AndImageFilter AndSliceType; + thread_local typename AndSliceType::Pointer sAnd = AndSliceType::New(); + sAnd->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + sAnd->SetInput(0, iSlice); + sAnd->SetInput(1, jSlice); + sAnd->GetOutput()->SetRegions(iSlice->GetRequestedRegion()); + sAnd->Update(); + typename BoolSliceType::Pointer intersection = sAnd->GetOutput(); + intersection->DisconnectPipeline(); + WriteDebug(intersection, "C:\\intersection.nrrd"); - typename BoolImageType::Pointer median; + typename BoolSliceType::Pointer median; if (m_UseDistanceTransform) { - median = FindMedianImageDistances(axis, iMask, jMask); + median = FindMedianImageDistances(axis, intersection, iSlice, jSlice); } else { - median = FindMedianImageDilations(axis, iMask, jMask); + median = FindMedianImageDilations(axis, intersection, iSlice, jSlice); } // finally write it out into the output image pointer typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); typename TImage::IndexType t0 = { 0 }; IntersectionRegions(t0, outRegion, newRegion); - ImageRegionConstIterator seqIt(median, newRegion); + // newRegion possibly shrunk, copy it into sliceRegion + for (int d = 0; d < TImage::ImageDimension - 1; d++) + { + if (d < axis) + { + sliceRegion.SetIndex(d, newRegion.GetIndex(d)); + sliceRegion.SetSize(d, newRegion.GetSize(d)); + } + else + { + sliceRegion.SetIndex(d, newRegion.GetIndex(d + 1)); + sliceRegion.SetSize(d, newRegion.GetSize(d + 1)); + } + } + + typename TImage::Pointer midConn = TImage::New(); + midConn->CopyInformation(iConnT); + midConn->SetRegions(newRegion); + midConn->Allocate(true); + + ImageRegionConstIterator seqIt(median, sliceRegion); ImageRegionIterator outIt(out, newRegion); + ImageRegionIterator midIt(midConn, newRegion); while (!outIt.IsAtEnd()) { if (seqIt.Get()) { outIt.Set(label); + midIt.Set(1); } - ++outIt; ++seqIt; + ++outIt; + ++midIt; } + WriteDebug(midConn, "C:\\midConn.nrrd"); // recurse if needed typename TImage::IndexValueType mid = newRegion.GetIndex()[axis]; if (abs(i - j) > 2) { - typedef CastImageFilter InvertCastType; - typename InvertCastType::Pointer invCaster = InvertCastType::New(); - invCaster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - invCaster->SetInput(median); - invCaster->Update(); - typename TImage::Pointer midConn = invCaster->GetOutput(); - // midConn->DisconnectPipeline(); //not needed? - - // WriteDebug(midConn, "C:\\midConn.nrrd"); PixelList regionIDs; regionIDs.push_back(1); @@ -782,10 +841,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int 1, iTrans, true); - ////now give this thread a chance to start by yielding - // auto oneMS = std::chrono::microseconds(1000); - // std::this_thread::sleep_for(oneMS); - ////now continue by recursion in this thread Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); } else // sequential @@ -893,7 +948,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[x] = Dilate1(blobs[x], mask, axis); + blobs[x] = Dilate1(blobs[x], mask, m_UseBallStructuringElement, axis); // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); } @@ -1067,14 +1122,13 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer template IdentifierType -MorphologicalContourInterpolator::CardSymDifference( - typename MorphologicalContourInterpolator::BoolImageType::Pointer iShape, - typename MorphologicalContourInterpolator::BoolImageType::Pointer jShape) +MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceType::Pointer iShape, + typename BoolSliceType::Pointer jShape) { - typename TImage::RegionType region = iShape->GetLargestPossibleRegion(); + typename BoolSliceType::RegionType region = iShape->GetLargestPossibleRegion(); IdentifierType count = 0; - ImageRegionConstIterator iIt(iShape, region); - ImageRegionConstIterator jIt(jShape, region); + ImageRegionConstIterator iIt(iShape, region); + ImageRegionConstIterator jIt(jShape, region); while (!iIt.IsAtEnd()) { if (iIt.Get() != jIt.Get()) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 6c5ad9ffe52..480494ee0dc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -111,11 +111,12 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) try { // unused cases are not instantiated because they greatly increase compile time - if (numDimensions == 2 && pixelType == ScalarPixelType::UCHAR) - { - doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); - return EXIT_SUCCESS; - } + // 2-dim version causes compile errors with Maurer filter + // if (numDimensions==2 && pixelType == ScalarPixelType::UCHAR) + // { + // doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); + // return EXIT_SUCCESS; + // } if (numDimensions == 3 && (pixelType == ScalarPixelType::SHORT || pixelType == ScalarPixelType::USHORT)) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); From 02bd76ba7d480238653cd06a1165a4d0829f81e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 31 Mar 2016 16:54:08 -0400 Subject: [PATCH 071/176] ENH: Reducing dimension early on to reduce number of conversions --- .../itkMorphologicalContourInterpolator.h | 125 ++--- .../itkMorphologicalContourInterpolator.hxx | 457 +++++++++--------- 2 files changed, 287 insertions(+), 295 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index c5a9694fa47..23318a3ac6d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -39,6 +39,12 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Superclass; typedef SmartPointer Pointer; + /** Derived image typedefs. */ + typedef Image BoolImageType; + typedef Image FloatSliceType; + typedef Image SliceType; + typedef Image BoolSliceType; + /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -136,14 +142,14 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; - typedef Image FloatSliceType; - typedef Image SliceType; - typedef Image BoolSliceType; - typename FloatSliceType::Pointer MaurerDM(typename BoolSliceType::Pointer inImage); /** A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same) */ std::vector - GenerateDilationSequence(typename BoolSliceType::Pointer begin, typename BoolSliceType::Pointer end, int axis); + GenerateDilationSequence(typename BoolSliceType::Pointer begin, typename BoolSliceType::Pointer end); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer @@ -191,11 +192,11 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; @@ -207,16 +208,16 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; typedef itksys::hash_map OrientationsType; @@ -274,58 +274,31 @@ class MorphologicalContourInterpolator : public ImageToImageFilter image); + typename SliceType::RegionType + BoundingBox(itk::SmartPointer image); // assumes both valid region and valid index + template void - ExpandRegion(typename TImage::RegionType & region, typename TImage::IndexType index); + ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index); - typename TImage::Pointer + typename SliceType::Pointer RegionedConnectedComponents(const typename TImage::RegionType region, typename TImage::PixelType label, IdentifierType & objectCount); /** seed and mask must cover the same region (size and index the same) */ - template - SmartPointer - Dilate1(SmartPointer seed, SmartPointer mask, bool useBall, int axis); - - typedef ExtractImageFilter RoiType; - typename RoiType::Pointer m_RoI; - - typedef BinaryThresholdImageFilter BinarizerType; - typename BinarizerType::Pointer m_Binarizer; + typename BoolSliceType::Pointer + Dilate1(typename BoolSliceType::Pointer seed, typename BoolSliceType::Pointer mask); - typedef ConnectedComponentImageFilter ConnectedComponentsType; - typename ConnectedComponentsType::Pointer m_ConnectedComponents; + typedef ExtractImageFilter RoiType; + typename RoiType::Pointer m_RoI; + typedef BinaryThresholdImageFilter BinarizerType; + typename BinarizerType::Pointer m_Binarizer; - class MatchesID - { - typename TImage::PixelType m_ID; - - public: - MatchesID() {} - MatchesID(typename TImage::PixelType id) - : m_ID(id) - {} - bool - operator!=(const MatchesID & other) - { - return m_ID != other.m_ID; - } - bool - operator==(const MatchesID & other) - { - return m_ID == other.m_ID; - } - inline bool - operator()(const typename TImage::PixelType & val) const - { - return val == m_ID; - } - }; + typedef ConnectedComponentImageFilter ConnectedComponentsType; + typename ConnectedComponentsType::Pointer m_ConnectedComponents; private: MorphologicalContourInterpolator(const Self &) ITK_DELETE_FUNCTION; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index bd754fbc96b..bf651fe8193 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -124,6 +124,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() { // set up pipeline for regioned connected components m_RoI = RoiType::New(); + m_RoI->SetDirectionCollapseToIdentity(); m_Binarizer = BinarizerType::New(); m_Binarizer->SetInput(m_RoI->GetOutput()); m_ConnectedComponents = ConnectedComponentsType::New(); @@ -162,18 +163,18 @@ MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int template +template void -MorphologicalContourInterpolator::ExpandRegion(typename TImage::RegionType & region, - typename TImage::IndexType index) +MorphologicalContourInterpolator::ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index) { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + for (unsigned int a = 0; a < T2::ImageDimension; ++a) { if (region.GetIndex(a) > index[a]) { region.SetSize(a, region.GetSize(a) + region.GetIndex(a) - index[a]); region.SetIndex(a, index[a]); } - else if (region.GetIndex(a) + (typename TImage::IndexValueType)region.GetSize(a) <= index[a]) + else if (region.GetIndex(a) + (typename T2::IndexValueType)region.GetSize(a) <= index[a]) { region.SetSize(a, index[a] - region.GetIndex(a) + 1); } @@ -214,7 +215,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() m_BoundingBoxes.insert(std::make_pair(val, boundingBox1)); if (!resBB.second) // include this index in existing BB { - ExpandRegion(resBB.first->second, ind); + ExpandRegion(resBB.first->second, ind); } std::pair res = @@ -269,74 +270,67 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename TImage::Pointer iConn, + typename SliceType::Pointer iConn, typename TImage::PixelType iRegionId) { PixelList jRegionIds; jRegionIds.push_back(iRegionId); - typename TImage::IndexType centroid = Centroid(iConn, jRegionIds); - centroid[axis] = j; + typename SliceType::IndexType centroid = Centroid(iConn, jRegionIds); - typename TImage::RegionType reg3; - typename TImage::SizeType size; + typename SliceType::RegionType reg3; + typename SliceType::SizeType size; size.Fill(3); - size[axis] = 1; reg3.SetSize(size); - typename TImage::IndexType phIndex; - for (unsigned d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType phIndex; + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { phIndex[d] = centroid.GetIndex()[d] - 1; } - phIndex[axis] = j; reg3.SetIndex(phIndex); // create a phantom small slice centered around centroid - typename TImage::Pointer phSlice = TImage::New(); + typename SliceType::Pointer phSlice = SliceType::New(); phSlice->CopyInformation(iConn); phSlice->SetRegions(reg3); phSlice->Allocate(true); // add a phantom point to the center of a newly constructed slice - phSlice->SetPixel(centroid, 1); - jRegionIds.clear(); - jRegionIds.push_back(1); + phSlice->SetPixel(centroid, iRegionId); // WriteDebug(iConn, "C:\\iConn.nrrd"); // WriteDebug(phSlice, "C:\\phSlice.nrrd"); - typename TImage::IndexType translation = Align(axis, iConn, iRegionId, phSlice, jRegionIds); + + // do alignment in case the iShape is concave and centroid is not within the iShape + typename SliceType::IndexType translation = Align(iConn, iRegionId, phSlice, jRegionIds); // now translate the phantom slice for best alignment - for (unsigned d = 0; d < TImage::ImageDimension; d++) + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { phIndex[d] -= translation[d]; } - phIndex[axis] = j; reg3.SetIndex(phIndex); phSlice->SetRegions(reg3); - typename TImage::IndexType t0 = { 0 }; - t0[axis] = j - i; - Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, 1, t0, false); + typename SliceType::IndexType t0 = { 0 }; + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false); } template -template -SmartPointer -MorphologicalContourInterpolator::Dilate1(SmartPointer seed, SmartPointer mask, bool useBall, int axis) +typename MorphologicalContourInterpolator::BoolSliceType::Pointer +MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer seed, + typename BoolSliceType::Pointer mask) { // set up structuring element for dilation - typedef Size SizeType; - SizeType size; + typedef Size SizeType; + SizeType size; size.Fill(1); - if (axis >= 0) - { - size[axis] = 0; - } - typedef BinaryCrossStructuringElement CrossStructuringElementType; - typedef BinaryBallStructuringElement BallStructuringElementType; - typedef BinaryDilateImageFilter CrossDilateType; - typedef BinaryDilateImageFilter BallDilateType; + typedef BinaryCrossStructuringElement + CrossStructuringElementType; + typedef BinaryBallStructuringElement + BallStructuringElementType; + typedef BinaryDilateImageFilter CrossDilateType; + typedef BinaryDilateImageFilter BallDilateType; thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads @@ -353,8 +347,8 @@ MorphologicalContourInterpolator::Dilate1(SmartPointer seed, SmartPo m_BallDilator->SetKernel(m_BallStructuringElement); // TODO: keep structuring element and dilator per axis instead of per thread? - typename T2::Pointer temp; - if (useBall) + typename BoolSliceType::Pointer temp; + if (m_UseBallStructuringElement) { m_BallDilator->SetInput(seed); m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); @@ -371,14 +365,14 @@ MorphologicalContourInterpolator::Dilate1(SmartPointer seed, SmartPo temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions - typedef AndImageFilter AndFilterType; - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + typedef AndImageFilter AndFilterType; + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads m_And->SetInput(0, mask); m_And->SetInput(1, temp); m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); m_And->Update(); - typename T2::Pointer result = m_And->GetOutput(); + typename BoolSliceType::Pointer result = m_And->GetOutput(); result->DisconnectPipeline(); // WriteDebug(seed, "C:\\seed.nrrd"); // WriteDebug(mask, "C:\\mask.nrrd"); @@ -391,8 +385,7 @@ MorphologicalContourInterpolator::Dilate1(SmartPointer seed, SmartPo template std::vector::BoolSliceType::Pointer> MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer begin, - typename BoolSliceType::Pointer end, - int axis) + typename BoolSliceType::Pointer end) { // typedef Testing::HashImageFilter HashType; // HashType::Pointer hasher = HashType::New(); @@ -400,11 +393,11 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool // std::vector hashes; // TODO: optimization: replace ImagesEqual call with hash comparison? std::vector seq; - seq.push_back(Dilate1(begin, end, m_UseBallStructuringElement, -1)); + seq.push_back(Dilate1(begin, end)); do { seq.back()->DisconnectPipeline(); - seq.push_back(Dilate1(seq.back(), end, m_UseBallStructuringElement, -1)); + seq.push_back(Dilate1(seq.back(), end)); } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image return seq; @@ -418,8 +411,8 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int typename BoolSliceType::Pointer iMask, typename BoolSliceType::Pointer jMask) { - std::vector iSeq = GenerateDilationSequence(intersection, iMask, axis); - std::vector jSeq = GenerateDilationSequence(intersection, jMask, axis); + std::vector iSeq = GenerateDilationSequence(intersection, iMask); + std::vector jSeq = GenerateDilationSequence(intersection, jMask); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection if (iSeq.size() < jSeq.size()) { @@ -438,8 +431,8 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int unsigned xj = ratio * x; m_Or->SetInput(1, jSeq[xj]); #ifdef _DEBUG - WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); - WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); + // WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); + // WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); #endif // _DEBUG m_Or->GetOutput()->SetRegions(iMask->GetRequestedRegion()); m_Or->Update(); @@ -453,7 +446,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(int for (unsigned x = 0; x < iSeq.size(); x++) { #ifdef _DEBUG - WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); + // WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); #endif // _DEBUG IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); @@ -598,20 +591,20 @@ MorphologicalContourInterpolator::FindMedianImageDistances(int template -typename TImage::RegionType -MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) +typename MorphologicalContourInterpolator::SliceType::RegionType +MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) { - typename TImage::RegionType newRegion = image->GetLargestPossibleRegion(); - typename TImage::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); - typename TImage::IndexType maxInd = newRegion.GetIndex(); - ImageRegionConstIteratorWithIndex iIt(image, newRegion); + typename SliceType::RegionType newRegion = image->GetLargestPossibleRegion(); + typename SliceType::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); + typename SliceType::IndexType maxInd = newRegion.GetIndex(); + ImageRegionConstIteratorWithIndex iIt(image, newRegion); while (!iIt.IsAtEnd()) { if (iIt.Get()) { - typename TImage::IndexType ind = iIt.GetIndex(); - for (int d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType ind = iIt.GetIndex(); + for (int d = 0; d < SliceType::ImageDimension; d++) { if (ind[d] < minInd[d]) { @@ -627,7 +620,7 @@ MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer } newRegion.SetIndex(minInd); - for (int d = 0; d < TImage::ImageDimension; d++) + for (int d = 0; d < SliceType::ImageDimension; d++) { newRegion.SetSize(d, maxInd[d] - minInd[d] + 1); } @@ -641,22 +634,22 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename TImage::Pointer iConn, + typename SliceType::Pointer iConn, typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, + typename SliceType::Pointer jConn, typename TImage::PixelType jRegionId, - typename TImage::IndexType translation, + typename SliceType::IndexType translation, bool recursive) { // translate iConn by t/2 and jConn by -t/2 - typename TImage::IndexType iTrans; - typename TImage::IndexType jTrans; - typename TImage::RegionType iRegion = iConn->GetLargestPossibleRegion(); - typename TImage::RegionType jRegion = jConn->GetLargestPossibleRegion(); - typename TImage::IndexType jBottom = jRegion.GetIndex(); - bool carry = false; - - for (unsigned d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType iTrans; + typename SliceType::IndexType jTrans; + typename SliceType::RegionType iRegion = iConn->GetLargestPossibleRegion(); + typename SliceType::RegionType jRegion = jConn->GetLargestPossibleRegion(); + typename SliceType::IndexType jBottom = jRegion.GetIndex(); + bool carry = false; + + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { if (!carry) { @@ -684,58 +677,46 @@ MorphologicalContourInterpolator::Interpolate1to1(int jRegion.SetIndex(d, jRegion.GetIndex()[d] + jTrans[d]); jBottom[d] = jRegion.GetIndex()[d] + jRegion.GetSize(d) - 1; } - typename TImage::RegionType newRegion = iRegion; - ExpandRegion(newRegion, jRegion.GetIndex()); - ExpandRegion(newRegion, jBottom); + typename SliceType::RegionType newRegion = iRegion; + ExpandRegion(newRegion, jRegion.GetIndex()); + ExpandRegion(newRegion, jBottom); + typename SliceType::IndexValueType mid = (i + j + (carry ? 1 : 0)) / 2; // index of middle slice WriteDebug(iConn, "C:\\iConn.nrrd"); WriteDebug(jConn, "C:\\jConn.nrrd"); - typename TImage::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); - typename TImage::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); + typename SliceType::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); + typename SliceType::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); WriteDebug(iConnT, "C:\\iConnT.nrrd"); WriteDebug(jConnT, "C:\\jConnT.nrrd"); if (!recursive) // reduce newRegion to bounding box so we deal with less pixels { newRegion = BoundingBox(iConnT); - typename TImage::RegionType jBB = BoundingBox(jConnT); - typename TImage::IndexType i2 = jBB.GetIndex(); - ExpandRegion(newRegion, i2); - for (int d = 0; d < TImage::ImageDimension; d++) + typename SliceType::RegionType jBB = BoundingBox(jConnT); + typename SliceType::IndexType i2 = jBB.GetIndex(); + ExpandRegion(newRegion, i2); + for (int d = 0; d < SliceType::ImageDimension; d++) { i2[d] += jBB.GetSize(d) - 1; } - ExpandRegion(newRegion, i2); + ExpandRegion(newRegion, i2); } - // reduce dimension and convert to binary masks - // start by calculating the correction region (TODO: avoid actual extraction) - typename TImage::RegionType exRegion = newRegion; - exRegion.SetSize(axis, 0); - typedef ExtractImageFilter ExtractorType; - thread_local typename ExtractorType::Pointer extractor = ExtractorType::New(); - extractor->SetDirectionCollapseToIdentity(); - extractor->SetExtractionRegion(exRegion); - extractor->SetInput(iConnT); - extractor->UpdateLargestPossibleRegion(); - typename SliceType::Pointer slice = extractor->GetOutput(); - - // create and allocate slice images - typename BoolSliceType::Pointer iSlice = BoolSliceType::New(); - typename BoolSliceType::RegionType sliceRegion = slice->GetRequestedRegion(); - iSlice->CopyInformation(slice); - iSlice->SetRegions(sliceRegion); + // create and allocate slice binary masks + typename BoolSliceType::Pointer iSlice = BoolSliceType::New(); + iSlice->CopyInformation(iConnT); + iSlice->SetRegions(newRegion); iSlice->Allocate(true); typename BoolSliceType::Pointer jSlice = BoolSliceType::New(); - jSlice->CopyInformation(slice); - jSlice->SetRegions(sliceRegion); + jSlice->CopyInformation(jConnT); + jSlice->SetRegions(newRegion); jSlice->Allocate(true); // convert to binary by iteration - ImageRegionConstIterator iIt(iConnT, newRegion); - ImageRegionConstIterator jIt(jConnT, newRegion); - ImageRegionIterator ibIt(iSlice, sliceRegion); - ImageRegionIterator jbIt(jSlice, sliceRegion); + ImageRegionConstIterator iIt(iConnT, newRegion); + ImageRegionConstIterator jIt(jConnT, newRegion); + ImageRegionIterator ibIt(iSlice, newRegion); + ImageRegionIterator jbIt(jSlice, newRegion); while (!iIt.IsAtEnd()) { if (iIt.Get() == iRegionId) @@ -777,32 +758,48 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // finally write it out into the output image pointer - typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); - typename TImage::IndexType t0 = { 0 }; - IntersectionRegions(t0, outRegion, newRegion); - // newRegion possibly shrunk, copy it into sliceRegion + typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); + typename SliceType::RegionType sliceRegion; + for (int d = 0; d < TImage::ImageDimension - 1; d++) + { + if (d < axis) + { + sliceRegion.SetIndex(d, outRegion.GetIndex(d)); + sliceRegion.SetSize(d, outRegion.GetSize(d)); + } + else + { + sliceRegion.SetIndex(d, outRegion.GetIndex(d + 1)); + sliceRegion.SetSize(d, outRegion.GetSize(d + 1)); + } + } + typename SliceType::IndexType t0 = { 0 }; // no translation + IntersectionRegions(t0, sliceRegion, newRegion); // clips new region to output region + // sliceRegion possibly shrunk, copy it into outRegion for (int d = 0; d < TImage::ImageDimension - 1; d++) { if (d < axis) { - sliceRegion.SetIndex(d, newRegion.GetIndex(d)); - sliceRegion.SetSize(d, newRegion.GetSize(d)); + outRegion.SetIndex(d, sliceRegion.GetIndex(d)); + outRegion.SetSize(d, sliceRegion.GetSize(d)); } else { - sliceRegion.SetIndex(d, newRegion.GetIndex(d + 1)); - sliceRegion.SetSize(d, newRegion.GetSize(d + 1)); + outRegion.SetIndex(d + 1, sliceRegion.GetIndex(d)); + outRegion.SetSize(d + 1, sliceRegion.GetSize(d)); } } + outRegion.SetIndex(axis, mid); + outRegion.SetSize(axis, 1); - typename TImage::Pointer midConn = TImage::New(); + typename SliceType::Pointer midConn = SliceType::New(); midConn->CopyInformation(iConnT); midConn->SetRegions(newRegion); midConn->Allocate(true); - ImageRegionConstIterator seqIt(median, sliceRegion); - ImageRegionIterator outIt(out, newRegion); - ImageRegionIterator midIt(midConn, newRegion); + ImageRegionConstIterator seqIt(median, newRegion); + ImageRegionIterator outIt(out, outRegion); + ImageRegionIterator midIt(midConn, newRegion); while (!outIt.IsAtEnd()) { if (seqIt.Get()) @@ -817,7 +814,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(midConn, "C:\\midConn.nrrd"); // recurse if needed - typename TImage::IndexValueType mid = newRegion.GetIndex()[axis]; if (abs(i - j) > 2) { PixelList regionIDs; @@ -866,37 +862,61 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename TImage::Pointer iConn, + typename SliceType::Pointer iConn, typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, + typename SliceType::Pointer jConn, PixelList jRegionIds, - typename TImage::IndexType translation) + typename SliceType::IndexType translation) { // first convert iConn into binary mask - MatchesID matchesID(iRegionId); + class MatchesID + { + typename TImage::PixelType m_ID; + + public: + MatchesID() {} + MatchesID(typename TImage::PixelType id) + : m_ID(id) + {} + bool + operator!=(const MatchesID & other) + { + return m_ID != other.m_ID; + } + bool + operator==(const MatchesID & other) + { + return m_ID == other.m_ID; + } + inline bool + operator()(const typename TImage::PixelType & val) const + { + return val == m_ID; + } + } matchesID(iRegionId); - typedef UnaryFunctorImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); + typedef UnaryFunctorImageFilter CastType; + typename CastType::Pointer caster = CastType::New(); caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); - typename BoolImageType::Pointer mask = caster->GetOutput(); + typename BoolSliceType::Pointer mask = caster->GetOutput(); // WriteDebug(mask, "C:\\mask.nrrd"); - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(jConn, "C:\\jConn.nrrd"); + WriteDebug(iConn, "C:\\iConn.nrrd"); + WriteDebug(jConn, "C:\\jConn.nrrd"); - typename TImage::RegionType iRegion, jRegion, newjRegion; + typename SliceType::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); jRegion = jConn->GetLargestPossibleRegion(); newjRegion = jRegion; newjRegion.SetSize(iRegion.GetSize()); // construct n empty images - std::vector blobs; + std::vector blobs; for (unsigned x = 0; x < jRegionIds.size(); x++) { - typename BoolImageType::Pointer temp = BoolImageType::New(); + typename BoolSliceType::Pointer temp = BoolSliceType::New(); temp->CopyInformation(jConn); temp->SetRegions(iRegion); temp->Allocate(true); @@ -904,15 +924,15 @@ MorphologicalContourInterpolator::Interpolate1toN(int } // fill the n images with intersections - these are seeds - typename TImage::Pointer belongs = TImage::New(); + typename SliceType::Pointer belongs = SliceType::New(); belongs->CopyInformation(mask); belongs->SetRegions(iRegion); belongs->Allocate(true); // initialize to zero (false) - ImageRegionIterator belongIt(belongs, iRegion); + ImageRegionIterator belongIt(belongs, iRegion); IntersectionRegions(translation, iRegion, jRegion); - ImageRegionConstIterator maskIt(mask, iRegion); - ImageRegionConstIteratorWithIndex jIt(jConn, jRegion); - ImageRegionIterator belongInit(belongs, iRegion); + ImageRegionConstIterator maskIt(mask, iRegion); + ImageRegionConstIteratorWithIndex jIt(jConn, jRegion); + ImageRegionIterator belongInit(belongs, iRegion); // convert jConn into n blobs, translating them into the index space of iConn while (!maskIt.IsAtEnd()) @@ -931,25 +951,25 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x]->SetRegions(iRegion); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } - ImageRegionConstIterator maskIt2(mask, iRegion); - ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); + ImageRegionConstIterator maskIt2(mask, iRegion); + ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); bool hollowedMaskEmpty; do // while hollowed mask is not empty { for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[x] = Dilate1(blobs[x], mask, m_UseBallStructuringElement, axis); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + blobs[x] = Dilate1(blobs[x], mask); + WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); } @@ -1002,24 +1022,24 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); + WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images // convert the belongs into n Conn-style images - std::vector conns; + std::vector conns; for (unsigned x = 0; x < jRegionIds.size(); x++) { - typename TImage::Pointer temp2 = TImage::New(); + typename SliceType::Pointer temp2 = SliceType::New(); temp2->CopyInformation(iConn); temp2->SetRegions(iConn->GetLargestPossibleRegion()); temp2->Allocate(true); conns.push_back(temp2); } - ImageRegionConstIteratorWithIndex belongIt2(belongs, iRegion); + ImageRegionConstIteratorWithIndex belongIt2(belongs, iRegion); while (!belongIt2.IsAtEnd()) { - const typename TImage::PixelType belong = belongIt2.Get(); + const typename SliceType::PixelType belong = belongIt2.Get(); if (belong > 0) { conns[belong - 1]->SetPixel(belongIt2.GetIndex(), iRegionId); @@ -1036,31 +1056,31 @@ MorphologicalContourInterpolator::Interpolate1toN(int template -typename TImage::Pointer -MorphologicalContourInterpolator::TranslateImage(typename TImage::Pointer image, - typename TImage::IndexType translation, - typename TImage::RegionType newRegion) +typename MorphologicalContourInterpolator::SliceType::Pointer +MorphologicalContourInterpolator::TranslateImage(typename SliceType::Pointer image, + typename SliceType::IndexType translation, + typename SliceType::RegionType newRegion) { - typename TImage::Pointer result = TImage::New(); + typename SliceType::Pointer result = SliceType::New(); result->CopyInformation(image); result->SetRegions(newRegion); result->Allocate(true); // initialize to zero (false) - typename TImage::RegionType inRegion = image->GetLargestPossibleRegion(); + typename SliceType::RegionType inRegion = image->GetLargestPossibleRegion(); IntersectionRegions(translation, inRegion, newRegion); - ImageAlgorithm::Copy(image.GetPointer(), result.GetPointer(), inRegion, newRegion); + ImageAlgorithm::Copy(image.GetPointer(), result.GetPointer(), inRegion, newRegion); return result; } template void -MorphologicalContourInterpolator::IntersectionRegions(typename TImage::IndexType translation, - typename TImage::RegionType & iRegion, - typename TImage::RegionType & jRegion) +MorphologicalContourInterpolator::IntersectionRegions(typename SliceType::IndexType translation, + typename SliceType::RegionType & iRegion, + typename SliceType::RegionType & jRegion) { - typename TImage::IndexType iBegin = iRegion.GetIndex(); - typename TImage::IndexType jBegin = jRegion.GetIndex(); - for (IdentifierType d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType iBegin = iRegion.GetIndex(); + typename SliceType::IndexType jBegin = jRegion.GetIndex(); + for (IdentifierType d = 0; d < SliceType::ImageDimension; d++) { IndexValueType iSize = iRegion.GetSize(d); IndexValueType jSize = jRegion.GetSize(d); @@ -1076,13 +1096,13 @@ MorphologicalContourInterpolator::IntersectionRegions(typename TImage::I template IdentifierType -MorphologicalContourInterpolator::Intersection(typename TImage::Pointer iConn, - typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, - PixelList jRegionIds, - typename TImage::IndexType translation) +MorphologicalContourInterpolator::Intersection(typename SliceType::Pointer iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer jConn, + PixelList jRegionIds, + typename SliceType::IndexType translation) { - typename TImage::RegionType iRegion, jRegion; + typename SliceType::RegionType iRegion, jRegion; iRegion = iConn->GetLargestPossibleRegion(); jRegion = jConn->GetLargestPossibleRegion(); IntersectionRegions(translation, iRegion, jRegion); @@ -1092,8 +1112,8 @@ MorphologicalContourInterpolator::Intersection(typename TImage::Pointer { counts[x] = 0; } - ImageRegionConstIterator iIt(iConn, iRegion); - ImageRegionConstIterator jIt(jConn, jRegion); + ImageRegionConstIterator iIt(iConn, iRegion); + ImageRegionConstIterator jIt(jConn, jRegion); while (!iIt.IsAtEnd()) { if (iIt.Get() == iRegionId) @@ -1142,11 +1162,11 @@ MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceTy } template -typename TImage::IndexType -MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn, PixelList regionIds) +typename MorphologicalContourInterpolator::SliceType::IndexType +MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer conn, PixelList regionIds) { - ImageRegionConstIteratorWithIndex it(conn, conn->GetLargestPossibleRegion()); - IndexValueType ind[TImage::ImageDimension] = { 0 }; // all components are initialized to zero + ImageRegionConstIteratorWithIndex it(conn, conn->GetLargestPossibleRegion()); + IndexValueType ind[SliceType::ImageDimension] = { 0 }; // all components are initialized to zero IdentifierType pixelCount = 0; while (!it.IsAtEnd()) { @@ -1157,8 +1177,8 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn if (res != regionIds.end()) { ++pixelCount; - typename TImage::IndexType pInd = it.GetIndex(); - for (unsigned d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType pInd = it.GetIndex(); + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { ind[d] += pInd[d]; } @@ -1166,8 +1186,8 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn } ++it; } - typename TImage::IndexType retVal; - for (unsigned d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType retVal; + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { retVal[d] = ind[d] / pixelCount; } @@ -1176,30 +1196,29 @@ MorphologicalContourInterpolator::Centroid(typename TImage::Pointer conn template -typename TImage::IndexType -MorphologicalContourInterpolator::Align(int axis, - typename TImage::Pointer iConn, - typename TImage::PixelType iRegionId, - typename TImage::Pointer jConn, - PixelList jRegionIds) +typename MorphologicalContourInterpolator::SliceType::IndexType +MorphologicalContourInterpolator::Align(typename SliceType::Pointer iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer jConn, + PixelList jRegionIds) { // calculate centroids PixelList iRegionIds; iRegionIds.push_back(iRegionId); - typename TImage::IndexType iCentroid = Centroid(iConn, iRegionIds); - typename TImage::IndexType jCentroid = Centroid(jConn, jRegionIds); + typename SliceType::IndexType iCentroid = Centroid(iConn, iRegionIds); + typename SliceType::IndexType jCentroid = Centroid(jConn, jRegionIds); - typename TImage::IndexType ind; - for (unsigned d = 0; d < TImage::ImageDimension; d++) + typename SliceType::IndexType ind; + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { ind[d] = jCentroid[d] - iCentroid[d]; } // construct an image with all possible translations - typename TImage::RegionType searchRegion; - typename TImage::RegionType iLPR = iConn->GetLargestPossibleRegion(); - typename TImage::RegionType jLPR = jConn->GetLargestPossibleRegion(); - for (IdentifierType d = 0; d < TImage::ImageDimension; d++) + typename SliceType::RegionType searchRegion; + typename SliceType::RegionType iLPR = iConn->GetLargestPossibleRegion(); + typename SliceType::RegionType jLPR = jConn->GetLargestPossibleRegion(); + for (IdentifierType d = 0; d < SliceType::ImageDimension; d++) { searchRegion.SetIndex(d, jLPR.GetIndex()[d] - iLPR.GetIndex()[d] - iLPR.GetSize(d) + 1); searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 1); @@ -1207,28 +1226,27 @@ MorphologicalContourInterpolator::Align(int axis, // searchRegion.SetSize(axis, 1); // searchRegion.SetIndex(axis, 0); - typename BoolImageType::Pointer searched = BoolImageType::New(); + typename BoolSliceType::Pointer searched = BoolSliceType::New(); searched->SetRegions(searchRegion); searched->Allocate(true); // initialize to zero (false) // breadth first search starting from centroid, implicitly: // when intersection scores are equal, chooses the one closer to centroid - std::queue uncomputed; - typename TImage::IndexType t0 = { 0 }; - t0[axis] = ind[axis]; + std::queue uncomputed; + typename SliceType::IndexType t0 = { 0 }; uncomputed.push(t0); // no translation - guaranteed to find a non-zero intersection uncomputed.push(ind); // this introduces movement, and possibly has the same score searched->SetPixel(t0, true); searched->SetPixel(ind, true); - IdentifierType score, maxScore = 0; - typename TImage::IndexType bestIndex; - IdentifierType iter = 0; - IdentifierType minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); + IdentifierType score, maxScore = 0; + typename SliceType::IndexType bestIndex; + IdentifierType iter = 0; + IdentifierType minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); IdentifierType maxIter = std::max(m_MaxAlignIters, (IdentifierType)sqrt(searchRegion.GetNumberOfPixels())); // debug: construct and later fill the image with intersection scores #ifndef NDEBUG - typename TImage::Pointer scoreImage = TImage::New(); + typename SliceType::Pointer scoreImage = SliceType::New(); scoreImage->SetRegions(searchRegion); scoreImage->Allocate(true); #endif // NDEBUG @@ -1251,12 +1269,8 @@ MorphologicalContourInterpolator::Align(int axis, // we breadth this search if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || score > maxScore * 0.9 && iter <= maxIter) { - for (unsigned d = 0; d < TImage::ImageDimension; d++) + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { - if (d == axis) - { - continue; // do not waste time on additional checks - } ind[d] -= 1; //"left" if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) { @@ -1284,7 +1298,7 @@ MorphologicalContourInterpolator::Align(int axis, template -typename TImage::Pointer +typename MorphologicalContourInterpolator::SliceType::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, typename TImage::PixelType label, IdentifierType & objectCount) @@ -1306,16 +1320,16 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename TImage::Pointer iconn, - typename TImage::Pointer jconn) + typename SliceType::Pointer iconn, + typename SliceType::Pointer jconn) { // go through comparison image and create correspondence pairs typedef std::set> PairSet; - PairSet pairs, unwantedPairs, uncleanPairs; - typename TImage::RegionType ri = iconn->GetRequestedRegion(); - typename TImage::RegionType rj = jconn->GetRequestedRegion(); - ImageRegionConstIterator iti(iconn, ri); - ImageRegionConstIterator itj(jconn, rj); + PairSet pairs, unwantedPairs, uncleanPairs; + typename SliceType::RegionType ri = iconn->GetRequestedRegion(); + typename SliceType::RegionType rj = jconn->GetRequestedRegion(); + ImageRegionConstIterator iti(iconn, ri); + ImageRegionConstIterator itj(jconn, rj); while (!iti.IsAtEnd()) { if (iti.Get() != 0 || itj.Get() != 0) @@ -1375,7 +1389,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { PixelList regionIDs; regionIDs.push_back(p->second); - typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false); iCounts.erase(p->first); jCounts.erase(p->second); @@ -1404,7 +1418,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - typename TImage::IndexType translation = Align(axis, jconn, p->second, iconn, regionIDs); + typename SliceType::IndexType translation = Align(jconn, p->second, iconn, regionIDs); Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); typename PairSet::iterator rest = pairs.begin(); @@ -1435,7 +1449,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); typename PairSet::iterator rest = pairs.begin(); @@ -1477,7 +1491,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } } - typename TImage::IndexType translation = Align(axis, iconn, p->first, jconn, regionIDs); + typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); typename PairSet::iterator rest = p; @@ -1505,9 +1519,14 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { // do multithreading by paralellizing for different labels // and different inter-slice segments [thread pool of C++11 threads] +#ifdef _DEBUG + m_ThreadPool = new ::ThreadPool(1); // single threading makes tracing easier +#else m_ThreadPool = new ::ThreadPool(std::thread::hardware_concurrency()); +#endif + typename SliceType::Pointer sliceVar; std::vectorenqueue( - &MorphologicalContourInterpolator::InterpolateBetweenTwo, this, axis, out, 0, 0, 0, out, out))> + &MorphologicalContourInterpolator::InterpolateBetweenTwo, this, axis, out, 0, 0, 0, sliceVar, sliceVar))> results; // so we can wait for all the results m_StopSpawning = false; @@ -1523,10 +1542,10 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename TImage::RegionType ri; ri = m_BoundingBoxes[it->first]; - ri.SetSize(axis, 1); + ri.SetSize(axis, 0); ri.SetIndex(axis, *prev); - IdentifierType xCount; - typename TImage::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); + IdentifierType xCount; + typename SliceType::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); iconn->DisconnectPipeline(); typename SliceSetType::iterator next = it->second.begin(); @@ -1534,7 +1553,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { typename TImage::RegionType rj = ri; rj.SetIndex(axis, *next); - typename TImage::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); + typename SliceType::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); jconn->DisconnectPipeline(); // WriteDebug(iconn, "C:\\iconn.nrrd"); From afa116ff28d94a381eb993d1081f129b2f6891df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 31 Mar 2016 18:13:07 -0400 Subject: [PATCH 072/176] COMP: Removing 2D test which now does not compile --- .../test/Baseline/TwoD_B.png.md5 | 1 - .../test/Baseline/TwoD_B_-1_1.png.md5 | 1 - .../test/Baseline/TwoD_B_-1_255.png.md5 | 1 - .../test/Baseline/TwoD_B_0.png.md5 | 1 - .../test/Baseline/TwoD_B_1.png.md5 | 1 - .../test/Baseline/TwoD_C.png.md5 | 1 - .../test/Baseline/TwoD_C_-1_1.png.md5 | 1 - .../test/Baseline/TwoD_C_-1_255.png.md5 | 1 - .../test/Baseline/TwoD_C_0.png.md5 | 1 - .../test/Baseline/TwoD_C_1.png.md5 | 1 - .../test/Baseline/TwoD_T.png.md5 | 1 - .../test/Baseline/TwoD_T_-1_1.png.md5 | 1 - .../test/Baseline/TwoD_T_-1_255.png.md5 | 1 - .../test/Baseline/TwoD_T_0.png.md5 | 1 - .../test/Baseline/TwoD_T_1.png.md5 | 1 - .../MorphologicalContourInterpolation/test/CMakeLists.txt | 5 ----- .../test/Input/TwoD.png.md5 | 1 - .../test/itkMorphologicalContourInterpolationTest.cxx | 6 ------ 18 files changed, 27 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 deleted file mode 100644 index 95365888068..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_-1_255.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_0.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 deleted file mode 100644 index 95365888068..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_B_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 deleted file mode 100644 index 49456a80c47..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_-1_255.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 deleted file mode 100644 index d648f308c26..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_0.png.md5 +++ /dev/null @@ -1 +0,0 @@ -2d56dd55796bca913bf8ad9555259c40 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 deleted file mode 100644 index 49456a80c47..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_C_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 deleted file mode 100644 index 0d6c68e7ac4..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T.png.md5 +++ /dev/null @@ -1 +0,0 @@ -382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 deleted file mode 100644 index 49456a80c47..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 deleted file mode 100644 index 0d6c68e7ac4..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_-1_255.png.md5 +++ /dev/null @@ -1 +0,0 @@ -382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 deleted file mode 100644 index 0d6c68e7ac4..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_0.png.md5 +++ /dev/null @@ -1 +0,0 @@ -382d89e5c38bb2f42d90ac06b17d9c02 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 deleted file mode 100644 index 49456a80c47..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoD_T_1.png.md5 +++ /dev/null @@ -1 +0,0 @@ -adbd21ffff229a38e9fed5946234eda7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 427fa865198..5cf9acdfa9c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -194,9 +194,4 @@ regressiontest(FaceRoI nrrd ${MCI_Algorithm} 1) regressiontest(FaceRoI nrrd ${MCI_Algorithm} 2) # Non-3D tests -regressiontest(TwoD png ${MCI_Algorithm}) -regressiontest(TwoD png ${MCI_Algorithm} -1 255) # same as regular -regressiontest(TwoD png ${MCI_Algorithm} 0) # same as regular -regressiontest(TwoD png ${MCI_Algorithm} -1 1) # does not modify image -regressiontest(TwoD png ${MCI_Algorithm} 1) # does not modify image regressiontest(FourD nrrd ${MCI_Algorithm}) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 deleted file mode 100644 index 95365888068..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/TwoD.png.md5 +++ /dev/null @@ -1 +0,0 @@ -e568124ab02e4811160c61901ba352ab diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 480494ee0dc..3832519716c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -111,12 +111,6 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) try { // unused cases are not instantiated because they greatly increase compile time - // 2-dim version causes compile errors with Maurer filter - // if (numDimensions==2 && pixelType == ScalarPixelType::UCHAR) - // { - // doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); - // return EXIT_SUCCESS; - // } if (numDimensions == 3 && (pixelType == ScalarPixelType::SHORT || pixelType == ScalarPixelType::USHORT)) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); From 16a2b1d60850ab9e2593d30860251fae1f43c9ad Mon Sep 17 00:00:00 2001 From: Dzenan Zukic Date: Fri, 1 Apr 2016 14:13:27 -0400 Subject: [PATCH 073/176] ENH: New baselines after thorough 2D refactoring --- .../test/Baseline/105769fixed_B.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_-1_0.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_-1_1.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_-1_2.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_2.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_2_1.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_B_2_2.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C_-1_0.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C_-1_1.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C_-1_2.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C_2.nii.gz.md5 | 2 +- .../test/Baseline/105769fixed_C_2_1.nii.gz.md5 | 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a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/GridSeg_T_2.nrrd.md5 @@ -1 +1 @@ -f0fa4937ce6f7f75397e9627624dd484 +57078cccded0c7642a0c660e441ba93b diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_B.nrrd.md5 index 6931643bb66..d43992fcd20 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_B.nrrd.md5 @@ -1 +1 @@ -744bfe4f07858c572ed6dc27b20cfc36 +d9c0e6d796a439794019f78b6ae23c3e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany16_C.nrrd.md5 index 8b73643efb3..7874d01c533 100644 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--- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_T.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ManyToMany_T.nrrd.md5 @@ -1 +1 @@ -3022ae0fc72f07881dd46ead64b11803 +280216957015620dfebc73627a4357cb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_B.nrrd.md5 index 32b54ad57f9..695e97a3b4c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_B.nrrd.md5 @@ -1 +1 @@ -c0c1490e4f37fded3d69fdd9290e2397 +efdefd9a493158532651fd4e84728ad4 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/Micro1_C.nrrd.md5 index 32b54ad57f9..695e97a3b4c 100644 --- 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100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_B.nrrd.md5 @@ -1 +1 @@ -79f2536d04ef29ebee064f551bca44de +74db7779b7c24ac84bc7cc5d6bdadf36 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_C.nrrd.md5 index 9ec2d635638..87642c386a4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_C.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_C.nrrd.md5 @@ -1 +1 @@ -59caa9d68ba3a013c6085ccb46a73732 +a907f1b7d07a3be5a02fe4bd1fc5cdcc diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_T.nrrd.md5 index 9981afa31a1..b928ec245cd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_T.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/SimplestOneToOne_T.nrrd.md5 @@ -1 +1 @@ -5af824ac59f4d9da79325e1a53132c6a +01dce02f87463fe696b7cbd8a748d6ee diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 index f96035bd016..eda606514d4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 @@ -1 +1 @@ -9b05f929b2d30868091c75fb80042804 +86127ff7b17f26feb58bae4051b056eb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_0.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_0.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_4.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_4.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_0_4.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1.nrrd.md5 index 42a1a775f3e..8f555d8df9e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1.nrrd.md5 @@ -1 +1 @@ -9e1269e3eab52b3a77f130a58fc32140 +6359ebeca1664d3cf06c0b047fef17e4 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_1.nrrd.md5 index 0692f08003e..554ae41ef3a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_1.nrrd.md5 @@ -1 +1 @@ -29cc558bd803b6e9f1f2180add128b89 +84ec6b6ac6ad9dd229995ef09879905d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_2.nrrd.md5 index 3032a13701f..255234b73fc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_1_2.nrrd.md5 @@ -1 +1 @@ -43f1c85954cc933758d0743fde5c606f +a8991995386caae4183021baa7d48eac diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2.nrrd.md5 index e30c578fbcb..4350fdaa505 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2.nrrd.md5 @@ -1 +1 @@ -24f59e3a707ad7ea34f015abf7395d37 +a73baeeead1edebea9d1b9b398e982e7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_2.nrrd.md5 index adec0f7f0b5..f30be3ad965 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_2.nrrd.md5 @@ -1 +1 @@ -0a7148f795171af3153ef09ad400e0cd +67a542bf9049c9df8baed21201bc1e96 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_3.nrrd.md5 index e30c578fbcb..4350fdaa505 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_3.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B_2_3.nrrd.md5 @@ -1 +1 @@ -24f59e3a707ad7ea34f015abf7395d37 +a73baeeead1edebea9d1b9b398e982e7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 index b0020804e07..530a5b21ef1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 @@ -1 +1 @@ -f40e7197f0d6b41f1fd70d6b3587b72f +40175885c5c1ac61ff343ab5ad18335e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_0.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 index 2627a3d7735..e118727bd4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_0_4.nrrd.md5 @@ -1 +1 @@ -ee7c148b33b089af63ca53bc5c22af00 +2aede0868e9f6518e4690116cecd289d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 index 02a16b13915..69a2a737fdc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1.nrrd.md5 @@ -1 +1 @@ -e6d6ddb6b56c7513ad7e28073599a85a +f3cbf00b18d5c0f9417ad2858702fe4d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 index 009b35fb194..4ec52ac6cf3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_1.nrrd.md5 @@ -1 +1 @@ -8dff078b502cd3410c7854282f4bd20d +519af01d278e7367015f2ca1802b6ab3 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 index d72ec7375b8..3640ba7bb65 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_1_2.nrrd.md5 @@ -1 +1 @@ -10105725854b7362695fb3d0e5eced38 +c87843828b72a9d18602dad2a8ff58e5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 index e30c578fbcb..4350fdaa505 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2.nrrd.md5 @@ -1 +1 @@ -24f59e3a707ad7ea34f015abf7395d37 +a73baeeead1edebea9d1b9b398e982e7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 index ab0b979cb96..f30be3ad965 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_2.nrrd.md5 @@ -1 +1 @@ -fc3556bc87c3736840173a88dd37bfcf +67a542bf9049c9df8baed21201bc1e96 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 index e30c578fbcb..4350fdaa505 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C_2_3.nrrd.md5 @@ -1 +1 @@ -24f59e3a707ad7ea34f015abf7395d37 +a73baeeead1edebea9d1b9b398e982e7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 index 40245f04746..b338aed2c7e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 @@ -1 +1 @@ -08e4636f1e5ce27376a888d9402c6fcd +32ff91938ae6b0015760c2c2a8d4d156 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 index e348ed9c8b1..c973f66bb7d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0.nrrd.md5 @@ -1 +1 @@ -2ecaf48e0435322619a43a147d0c03e1 +580a8477d35d8770a682d95016e7ba2c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 index e348ed9c8b1..c973f66bb7d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_0.nrrd.md5 @@ -1 +1 @@ -2ecaf48e0435322619a43a147d0c03e1 +580a8477d35d8770a682d95016e7ba2c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 index e348ed9c8b1..c973f66bb7d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_0_4.nrrd.md5 @@ -1 +1 @@ -2ecaf48e0435322619a43a147d0c03e1 +580a8477d35d8770a682d95016e7ba2c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 index bdb746f28f6..ae89f375d1b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1.nrrd.md5 @@ -1 +1 @@ -2adb499a6d1a09940bfffca003f55889 +aadc9811c16b4e88fbc8ca863f1ec01e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 index 28ca6694ca7..ac0e1741619 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_1.nrrd.md5 @@ -1 +1 @@ -a87d3fe609b90864418049bae2c9f4d1 +ce625dd7a2052ec3588247ddd9070ae8 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 index d231d5e8ac7..037a1fd273a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_1_2.nrrd.md5 @@ -1 +1 @@ -c6b947585026af9b9ad368ece7737cfa +d2e5aebfeb715fb6e7e21c0a8e0a1819 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 index 6d2af13f70a..e979aef983d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2.nrrd.md5 @@ -1 +1 @@ -e0824fd32a73a3f683a7f7b611965846 +ad9185510c387b2bc696846ac8b0d84d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 index ab0b979cb96..f30be3ad965 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.md5 @@ -1 +1 @@ -fc3556bc87c3736840173a88dd37bfcf +67a542bf9049c9df8baed21201bc1e96 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 index 6d2af13f70a..e979aef983d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 @@ -1 +1 @@ -e0824fd32a73a3f683a7f7b611965846 +ad9185510c387b2bc696846ac8b0d84d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 index 1ed463e8866..4a34b999e98 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 @@ -1 +1 @@ -9ac00d13152d0681c6fe8227245753ab +c7fc0c04bf25a032adf3a626d7e11da5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 index f139ed016ff..38d98e359ac 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 @@ -1 +1 @@ -5f8db3dbb727ef8789361db65109a528 +82e90710e28dc831a2b5059664ef3839 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 index cb1a17ad5d6..2977e281d7a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 @@ -1 +1 @@ -34781fd28e033c69e4a7e25b2e9b9b9c +945f23411e77a73e7f5ac16a27778d39 From b480fbb4a7f7ddcd5c15d8dd117782efbaa3ff41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Apr 2016 10:35:53 -0400 Subject: [PATCH 074/176] STYLE: Started cleanup --- .../itkMorphologicalContourInterpolator.h | 1 + .../itkMorphologicalContourInterpolator.hxx | 52 +++++++++---------- 2 files changed, 26 insertions(+), 27 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 23318a3ac6d..d0c05f6c48c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -278,6 +278,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter image); // assumes both valid region and valid index + // it can be invoked with 2D or 3D region, hence additional template parameter template void ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index bf651fe8193..54c5c5f3af2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -321,10 +321,6 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typename BoolSliceType::Pointer mask) { // set up structuring element for dilation - typedef Size SizeType; - SizeType size; - size.Fill(1); - typedef BinaryCrossStructuringElement CrossStructuringElementType; typedef BinaryBallStructuringElement @@ -332,20 +328,28 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typedef BinaryDilateImageFilter CrossDilateType; typedef BinaryDilateImageFilter BallDilateType; + thread_local bool initialized = false; thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); - m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - thread_local CrossStructuringElementType m_CrossStructuringElement; - m_CrossStructuringElement.SetRadius(size); - m_CrossStructuringElement.CreateStructuringElement(); - m_CrossDilator->SetKernel(m_CrossStructuringElement); - - thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); - m_BallDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - thread_local BallStructuringElementType m_BallStructuringElement; - m_BallStructuringElement.SetRadius(size); - m_BallStructuringElement.CreateStructuringElement(); - m_BallDilator->SetKernel(m_BallStructuringElement); - // TODO: keep structuring element and dilator per axis instead of per thread? + thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); + if (!initialized) // make sure these non-trivial operations are executed only once per thread + { + typedef Size SizeType; + SizeType size; + size.Fill(1); + + m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + thread_local CrossStructuringElementType m_CrossStructuringElement; + m_CrossStructuringElement.SetRadius(size); + m_CrossStructuringElement.CreateStructuringElement(); + m_CrossDilator->SetKernel(m_CrossStructuringElement); + + m_BallDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + thread_local BallStructuringElementType m_BallStructuringElement; + m_BallStructuringElement.SetRadius(size); + m_BallStructuringElement.CreateStructuringElement(); + m_BallDilator->SetKernel(m_BallStructuringElement); + } + initialized = true; typename BoolSliceType::Pointer temp; if (m_UseBallStructuringElement) @@ -387,11 +391,6 @@ std::vector::BoolSliceType::Po MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer begin, typename BoolSliceType::Pointer end) { - // typedef Testing::HashImageFilter HashType; - // HashType::Pointer hasher = HashType::New(); - // hasher->SetInPlace(true); - // std::vector hashes; - // TODO: optimization: replace ImagesEqual call with hash comparison? std::vector seq; seq.push_back(Dilate1(begin, end)); do @@ -951,14 +950,14 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + // WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x]->SetRegions(iRegion); - WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } ImageRegionConstIterator maskIt2(mask, iRegion); ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); @@ -969,11 +968,10 @@ MorphologicalContourInterpolator::Interpolate1toN(int for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x] = Dilate1(blobs[x], mask); - WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); + // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); } - // TODO: replace this loop by LabelErodeDilate filters? hollowedMaskEmpty = true; maskIt2.GoToBegin(); jIt2.GoToBegin(); @@ -1022,7 +1020,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - WriteDebug(belongs, "C:\\belongs.nrrd"); + // WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images From 1a982a08aa48c7774ec013c3c5439d8ad732833e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Apr 2016 17:26:39 -0400 Subject: [PATCH 075/176] ENH: Avoiding the temporary output image reduces overall memory requirements to approximately imageSize*(1+numberOfInterpolationAxes). --- .../itkMorphologicalContourInterpolator.h | 9 ++- .../itkMorphologicalContourInterpolator.hxx | 55 +++++++++++-------- 2 files changed, 39 insertions(+), 25 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index d0c05f6c48c..06a34543c87 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -224,10 +224,13 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::InterpolateAlong(int axis, TImage * ou template void -MorphologicalContourInterpolator::CombineInputAndInterpolate(typename TImage::Pointer interpolate) +MorphologicalContourInterpolator::OverlayInput() { ImageRegionIterator itO(m_Output, m_Output->GetBufferedRegion()); ImageRegionConstIterator itI(m_Input, m_Output->GetBufferedRegion()); - ImageRegionConstIterator it(interpolate, m_Output->GetBufferedRegion()); - while (!it.IsAtEnd()) + while (!itI.IsAtEnd()) { typename TImage::PixelType val = itI.Get(); if (val != 0) { itO.Set(val); } - else - { - itO.Set(it.Get()); - } - ++it; ++itI; ++itO; } @@ -1616,6 +1610,24 @@ MorphologicalContourInterpolator::CombineInputAndInterpolate(typename TI } +template +void +MorphologicalContourInterpolator::AllocateOutputs() +{ + typedef ImageBase ImageBaseType; + typename ImageBaseType::Pointer outputPtr; + + for (OutputDataObjectIterator it(this); !it.IsAtEnd(); it++) + { + outputPtr = dynamic_cast(it.GetOutput()); + if (outputPtr) + { + outputPtr->SetBufferedRegion(outputPtr->GetRequestedRegion()); + outputPtr->Allocate(true); + } + } +} + template void MorphologicalContourInterpolator::GenerateData() @@ -1625,16 +1637,13 @@ MorphologicalContourInterpolator::GenerateData() this->AllocateOutputs(); m_Output = TImage::New(); m_Output->Graft(this->GetOutput()); - typename TImage::Pointer tempOut = TImage::New(); - tempOut->CopyInformation(m_Output); - tempOut->SetRegions(m_Output->GetLargestPossibleRegion()); this->DetermineSliceOrientations(); - if (m_BoundingBoxes.size() == 0) // empty input image + if (m_BoundingBoxes.size() == 0) // no contours detected { - tempOut->Allocate(true); - CombineInputAndInterpolate(tempOut); + ImageAlgorithm::Copy( + m_Input.GetPointer(), m_Output.GetPointer(), m_Output->GetRequestedRegion(), m_Output->GetRequestedRegion()); return; } @@ -1674,13 +1683,17 @@ MorphologicalContourInterpolator::GenerateData() if (perAxisInterpolates.size() == 0) // nothing to process { - tempOut->Allocate(true); - CombineInputAndInterpolate(tempOut); + ImageAlgorithm::Copy( + m_Input.GetPointer(), m_Output.GetPointer(), m_Output->GetRequestedRegion(), m_Output->GetRequestedRegion()); return; } if (perAxisInterpolates.size() == 1) { - CombineInputAndInterpolate(perAxisInterpolates[0]); + ImageAlgorithm::Copy(perAxisInterpolates[0].GetPointer(), + m_Output.GetPointer(), + m_Output->GetRequestedRegion(), + m_Output->GetRequestedRegion()); + OverlayInput(); return; } // else @@ -1695,8 +1708,7 @@ MorphologicalContourInterpolator::GenerateData() std::vector values; values.reserve(perAxisInterpolates.size()); - tempOut->Allocate(true); - ImageRegionIterator it(tempOut, m_Output->GetRequestedRegion()); + ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); while (!it.IsAtEnd()) { values.clear(); @@ -1719,10 +1731,9 @@ MorphologicalContourInterpolator::GenerateData() } // interpolate along all axes else // interpolate along the specified axis { - tempOut->Allocate(true); - this->InterpolateAlong(m_Axis, tempOut); + this->InterpolateAlong(m_Axis, m_Output); } - CombineInputAndInterpolate(tempOut); + OverlayInput(); } } // end namespace itk From 9a4e480b83c6085019b4934ab4a89e7fa959a825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Apr 2016 18:22:18 -0400 Subject: [PATCH 076/176] ENH: Improving documentation and avoid passing of axis where not needed. --- .../itkMorphologicalContourInterpolator.h | 88 ++++++++++++++++--- .../itkMorphologicalContourInterpolator.hxx | 23 +++-- 2 files changed, 85 insertions(+), 26 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 06a34543c87..49b573083c4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -29,7 +29,47 @@ namespace itk { - +/** \class MorphologicalContourInterpolator + * + * \brief Interpolates contours between slices. Based on a paper by Albu et al. + * + * \par Inputs and Outputs + * This is an image-to-image filter. The dimensionality is 3D or higher. + * Input contains an image with some slices segmented (manually). + * The output has all in-between slices also segmented. + * + * Memory required by the filter is a bit higher than + * outputImageSize*(1+numberOfInterpolatedAxes). + * If interpolation is done along just one axis, memory used is reduced to + * just outputImageSize*1, since interpolations along multiple axes + * do not need to be calculated separately and then combined. + * + * \par Parameters + * Slices are detected at positions where a pixel exists with same labeled + * neighbors in slice and only 0 neighbors perpendicular to the slice. + * If default behaviour is unwanted, contour indices can be set for each axis. + * + * Filter can be restricted to run along only one axis, and/or to interpolate + * just one label. + * + * Since optimal alignment between slices would require exhaustive search, + * the default is to use heuristic (breadth first search startin from centroid). + * + * There is also an alternative algorithm based on distance transform approach. + * It is slightly faster, but it can jump across a twisty shape (not geodesic). + * + * Reference: + * Albu AB, Beugeling T, Laurendeau D. "A morphology-based approach for + * interslice interpolation of anatomical slices from volumetric images." + * IEEE Trans Biomed Eng. 2008 Aug;55(8):2022-38. DOI:10.1109/TBME.2008.921158 + * + * Acknowledgement: + * This work is supported by NIH grant R01 EB014346, "Continued development + * and maintenance of the ITK-SNAP 3D image segmentation software." + * + * \ingroup Filtering + * \ingroup Segmentation + */ template class MorphologicalContourInterpolator : public ImageToImageFilter { @@ -78,16 +118,19 @@ class MorphologicalContourInterpolator : public ImageToImageFilter LabeledSlicesType; std::vector m_LabeledSlices; // one for each axis + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ void SetLabeledSliceIndices(unsigned int axis, std::vector indices); + + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ void SetLabeledSliceIndices(unsigned int axis, SliceSetType indices); + + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ SliceSetType GetLabeledSliceIndices(unsigned int axis); + /** Calculates a bounding box of non-zero pixels. */ typename SliceType::RegionType BoundingBox(itk::SmartPointer image); - // assumes both valid region and valid index - // it can be invoked with 2D or 3D region, hence additional template parameter + /** Expands a region to incorporate the provided index. + * Assumes both a valid region and a valid index. + * It can be invoked with 2D or 3D region, hence the additional template parameter. */ template void ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index); + /** Connected components of a specified region. */ typename SliceType::Pointer RegionedConnectedComponents(const typename TImage::RegionType region, typename TImage::PixelType label, IdentifierType & objectCount); - /** seed and mask must cover the same region (size and index the same) */ + /** Seed and mask must cover the same region (size and index the same). */ typename BoolSliceType::Pointer Dilate1(typename BoolSliceType::Pointer seed, typename BoolSliceType::Pointer mask); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 9340effc919..87af3b9b524 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -81,10 +81,11 @@ WriteDebug(itk::SmartPointer> out, const char * filename) template bool -ImagesEqual(typename TImage::Pointer a, typename TImage::Pointer b) +MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Pointer a, + typename BoolSliceType::Pointer b) { - ImageRegionConstIterator ita(a, a->GetLargestPossibleRegion()); - ImageRegionConstIterator itb(b, b->GetLargestPossibleRegion()); + ImageRegionConstIterator ita(a, a->GetLargestPossibleRegion()); + ImageRegionConstIterator itb(b, b->GetLargestPossibleRegion()); while (!ita.IsAtEnd()) { @@ -397,7 +398,7 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool { seq.back()->DisconnectPipeline(); seq.push_back(Dilate1(seq.back(), end)); - } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); + } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image return seq; } @@ -405,8 +406,7 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool template typename MorphologicalContourInterpolator::BoolSliceType::Pointer -MorphologicalContourInterpolator::FindMedianImageDilations(int axis, - typename BoolSliceType::Pointer intersection, +MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, typename BoolSliceType::Pointer jMask) { @@ -476,8 +476,7 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point template typename MorphologicalContourInterpolator::BoolSliceType::Pointer -MorphologicalContourInterpolator::FindMedianImageDistances(int axis, - typename BoolSliceType::Pointer intersection, +MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, typename BoolSliceType::Pointer jMask) { @@ -749,11 +748,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename BoolSliceType::Pointer median; if (m_UseDistanceTransform) { - median = FindMedianImageDistances(axis, intersection, iSlice, jSlice); + median = FindMedianImageDistances(intersection, iSlice, jSlice); } else { - median = FindMedianImageDilations(axis, intersection, iSlice, jSlice); + median = FindMedianImageDilations(intersection, iSlice, jSlice); } // finally write it out into the output image pointer @@ -1614,8 +1613,8 @@ template void MorphologicalContourInterpolator::AllocateOutputs() { - typedef ImageBase ImageBaseType; - typename ImageBaseType::Pointer outputPtr; + typedef ImageBase ImageBaseType; + typename ImageBaseType::Pointer outputPtr; for (OutputDataObjectIterator it(this); !it.IsAtEnd(); it++) { From f156de47800244d7e65b51e2a48619489890e542 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 2 Apr 2016 10:51:13 -0400 Subject: [PATCH 077/176] ENH: Reducing memory consumption by using the already allocated output for interpolation along the first axis --- .../itkMorphologicalContourInterpolator.h | 5 +- .../itkMorphologicalContourInterpolator.hxx | 86 +++++++++---------- 2 files changed, 40 insertions(+), 51 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 49b573083c4..c38aad63727 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -39,10 +39,7 @@ namespace itk * The output has all in-between slices also segmented. * * Memory required by the filter is a bit higher than - * outputImageSize*(1+numberOfInterpolatedAxes). - * If interpolation is done along just one axis, memory used is reduced to - * just outputImageSize*1, since interpolations along multiple axes - * do not need to be calculated separately and then combined. + * outputImageSize*(max(1,numberOfInterpolatedAxes)). * * \par Parameters * Slices are detected at positions where a pixel exists with same labeled diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 87af3b9b524..7e214175747 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1516,11 +1516,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { // do multithreading by paralellizing for different labels // and different inter-slice segments [thread pool of C++11 threads] -#ifdef _DEBUG - m_ThreadPool = new ::ThreadPool(1); // single threading makes tracing easier -#else m_ThreadPool = new ::ThreadPool(std::thread::hardware_concurrency()); -#endif typename SliceType::Pointer sliceVar; std::vectorenqueue( &MorphologicalContourInterpolator::InterpolateBetweenTwo, this, axis, out, 0, 0, 0, sliceVar, sliceVar))> @@ -1666,65 +1662,61 @@ MorphologicalContourInterpolator::GenerateData() aggregate = m_Orientations[m_Label]; // we only care about this label } + bool outputUsed = false; std::vector perAxisInterpolates; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (aggregate[a]) { - typename TImage::Pointer imageA = TImage::New(); - imageA->CopyInformation(m_Output); - imageA->SetRegions(m_Output->GetRequestedRegion()); - imageA->Allocate(true); - this->InterpolateAlong(a, imageA); - perAxisInterpolates.push_back(imageA); + if (outputUsed) + { + typename TImage::Pointer imageA = TImage::New(); + imageA->CopyInformation(m_Output); + imageA->SetRegions(m_Output->GetRequestedRegion()); + imageA->Allocate(true); + this->InterpolateAlong(a, imageA); + perAxisInterpolates.push_back(imageA); + } + else // output not yet used + { + this->InterpolateAlong(a, m_Output); + outputUsed = true; + } } } - if (perAxisInterpolates.size() == 0) // nothing to process + if (perAxisInterpolates.size() > 0) // something to combine { - ImageAlgorithm::Copy( - m_Input.GetPointer(), m_Output.GetPointer(), m_Output->GetRequestedRegion(), m_Output->GetRequestedRegion()); - return; - } - if (perAxisInterpolates.size() == 1) - { - ImageAlgorithm::Copy(perAxisInterpolates[0].GetPointer(), - m_Output.GetPointer(), - m_Output->GetRequestedRegion(), - m_Output->GetRequestedRegion()); - OverlayInput(); - return; - } - // else - std::vector> iterators; + std::vector> iterators; - for (int i = 0; i < perAxisInterpolates.size(); ++i) - { - ImageRegionConstIterator it(perAxisInterpolates[i], m_Output->GetRequestedRegion()); - iterators.push_back(it); - } + for (int i = 0; i < perAxisInterpolates.size(); ++i) + { + ImageRegionConstIterator it(perAxisInterpolates[i], m_Output->GetRequestedRegion()); + iterators.push_back(it); + } - std::vector values; - values.reserve(perAxisInterpolates.size()); + std::vector values; + values.reserve(perAxisInterpolates.size()); - ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); - while (!it.IsAtEnd()) - { - values.clear(); - for (int i = 0; i < perAxisInterpolates.size(); ++i) + ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); + while (!it.IsAtEnd()) { - typename TImage::PixelType val = iterators[i].Get(); - if (val != 0) + values.clear(); + for (int i = 0; i < perAxisInterpolates.size(); ++i) { - it.Set(val); // last written value stays + typename TImage::PixelType val = iterators[i].Get(); + if (val != 0) + { + it.Set(val); // last written value stays + } } - } - // next pixel - ++it; - for (int i = 0; i < perAxisInterpolates.size(); ++i) - { - ++(iterators[i]); + // next pixel + ++it; + for (int i = 0; i < perAxisInterpolates.size(); ++i) + { + ++(iterators[i]); + } } } } // interpolate along all axes From c87539589017b4754be482f3770a24dca3f1e944 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 2 Apr 2016 11:44:29 -0400 Subject: [PATCH 078/176] ENH: Enable setting custom slice positions --- .../itkMorphologicalContourInterpolator.h | 20 ++++++++++++++++--- .../itkMorphologicalContourInterpolator.hxx | 17 +++++++++++++++- 2 files changed, 33 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index c38aad63727..2616aa7f73e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -35,7 +35,7 @@ namespace itk * * \par Inputs and Outputs * This is an image-to-image filter. The dimensionality is 3D or higher. - * Input contains an image with some slices segmented (manually). + * Input contains an image with some slices segmented, usually manually. * The output has all in-between slices also segmented. * * Memory required by the filter is a bit higher than @@ -43,8 +43,9 @@ namespace itk * * \par Parameters * Slices are detected at positions where a pixel exists with same labeled - * neighbors in slice and only 0 neighbors perpendicular to the slice. - * If default behaviour is unwanted, contour indices can be set for each axis. + * neighbors in slice and only clear (0) neighbors perpendicular to the slice. + * If default behaviour is unwanted, contour indices can be set for each axis + * by enabling UseCustomSlicePositions and calling SetLabeledSliceIndices. * * Filter can be restricted to run along only one axis, and/or to interpolate * just one label. @@ -130,6 +131,18 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::MorphologicalContourInterpolator() , m_HeuristicAlignment(true) , m_UseDistanceTransform(true) , m_UseBallStructuringElement(false) + , m_UseCustomSlicePositions(false) , m_ThreadPool(nullptr) , m_StopSpawning(false) , m_MinAlignIters(pow(2, TImage::ImageDimension)) @@ -1633,7 +1634,21 @@ MorphologicalContourInterpolator::GenerateData() m_Output = TImage::New(); m_Output->Graft(this->GetOutput()); - this->DetermineSliceOrientations(); + std::vector labeledSlices; + if (m_UseCustomSlicePositions) + { + labeledSlices.swap(m_LabeledSlices); + } + this->DetermineSliceOrientations(); // calculates bounding boxes + if (m_UseCustomSlicePositions) + { + m_LabeledSlices.swap(labeledSlices); + labeledSlices.clear(); + for (int i = 0; i < m_LabeledSlices.size(); i++) + { + m_Orientations[i] = (m_LabeledSlices[i].size() > 0); // non-zero + } + } if (m_BoundingBoxes.size() == 0) // no contours detected { From ba970a413795cf941604622406cb6b5a29510dd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 2 Apr 2016 13:20:32 -0400 Subject: [PATCH 079/176] ENH: Avoid grafting to enable working with RLEImages --- .../itkMorphologicalContourInterpolator.h | 3 --- .../itkMorphologicalContourInterpolator.hxx | 21 ++++++++----------- 2 files changed, 9 insertions(+), 15 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 2616aa7f73e..e1707117c62 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -179,9 +179,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::DetermineSliceOrientations() m_BoundingBoxes.clear(); m_Orientations.clear(); + typename TImage::ConstPointer m_Input = this->GetInput(); + typename TImage::Pointer m_Output = this->GetOutput(); + typename TImage::RegionType region = m_Output->GetRequestedRegion(); ImageRegionConstIteratorWithIndex it(m_Input, region); @@ -757,7 +760,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // finally write it out into the output image pointer - typename TImage::RegionType outRegion = m_Input->GetLargestPossibleRegion(); + typename TImage::RegionType outRegion = this->GetOutput()->GetRequestedRegion(); typename SliceType::RegionType sliceRegion; for (int d = 0; d < TImage::ImageDimension - 1; d++) { @@ -1302,7 +1305,7 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type IdentifierType & objectCount) { m_RoI->SetExtractionRegion(region); - m_RoI->SetInput(m_Input); + m_RoI->SetInput(this->GetInput()); m_Binarizer->SetLowerThreshold(label); m_Binarizer->SetUpperThreshold(label); m_ConnectedComponents->Update(); @@ -1586,8 +1589,8 @@ template void MorphologicalContourInterpolator::OverlayInput() { - ImageRegionIterator itO(m_Output, m_Output->GetBufferedRegion()); - ImageRegionConstIterator itI(m_Input, m_Output->GetBufferedRegion()); + ImageRegionIterator itO(this->GetOutput(), this->GetOutput()->GetBufferedRegion()); + ImageRegionConstIterator itI(this->GetInput(), this->GetOutput()->GetBufferedRegion()); while (!itI.IsAtEnd()) { typename TImage::PixelType val = itI.Get(); @@ -1599,10 +1602,6 @@ MorphologicalContourInterpolator::OverlayInput() ++itI; ++itO; } - - // put the output data back into the regular pipeline - this->GraftOutput(m_Output); - this->m_Output = ITK_NULLPTR; } @@ -1628,11 +1627,9 @@ template void MorphologicalContourInterpolator::GenerateData() { - m_Input = TImage::New(); - m_Input->Graft(const_cast(this->GetInput())); + typename TImage::ConstPointer m_Input = this->GetInput(); + typename TImage::Pointer m_Output = this->GetOutput(); this->AllocateOutputs(); - m_Output = TImage::New(); - m_Output->Graft(this->GetOutput()); std::vector labeledSlices; if (m_UseCustomSlicePositions) From a8ba2566b020148de97bef92a7a138428d4f016f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 2 Apr 2016 15:03:06 -0400 Subject: [PATCH 080/176] BUG: Fixing custom slice indices --- .../itkMorphologicalContourInterpolator.h | 56 +++++----- .../itkMorphologicalContourInterpolator.hxx | 104 ++++++++++++------ 2 files changed, 104 insertions(+), 56 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index e1707117c62..8e873307712 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -77,12 +77,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Superclass; typedef SmartPointer Pointer; - /** Derived image typedefs. */ - typedef Image BoolImageType; - typedef Image FloatSliceType; - typedef Image SliceType; - typedef Image BoolSliceType; - /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -147,8 +141,12 @@ class MorphologicalContourInterpolator : public ImageToImageFilterSetFullyConnected(useBall); + if (useBall != m_UseBallStructuringElement) + { + m_UseBallStructuringElement = useBall; + m_ConnectedComponents->SetFullyConnected(useBall); + this->Modified(); + } } /** Use ball instead of default cross structuring element for repeated dilations. */ @@ -157,6 +155,24 @@ class MorphologicalContourInterpolator : public ImageToImageFilter SliceSetType; + + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ + void + SetLabeledSliceIndices(unsigned int axis, std::vector indices); + + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ + void + SetLabeledSliceIndices(unsigned int axis, SliceSetType indices); + + /** If default slice detection is not wanted, slice indices + * between which interpolation is done can be set using this method. */ + SliceSetType + GetLabeledSliceIndices(unsigned int axis); + /** Run-time type information (and related methods). */ itkTypeMacro(MorphologicalContourInterpolator, ImageToImageFilter); @@ -164,6 +180,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; + typedef Image FloatSliceType; + typedef Image SliceType; + typedef Image BoolSliceType; + /** Are these two slices equal? */ bool ImagesEqual(typename BoolSliceType::Pointer a, typename BoolSliceType::Pointer b); - /** Does the real work. */ virtual void GenerateData() ITK_OVERRIDE; @@ -323,25 +345,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter SliceSetType; typedef itksys::hash_map LabeledSlicesType; std::vector m_LabeledSlices; // one for each axis - /** If default slice detection is not wanted, slice indices - * between which interpolation is done can be set using this method. */ - void - SetLabeledSliceIndices(unsigned int axis, std::vector indices); - - /** If default slice detection is not wanted, slice indices - * between which interpolation is done can be set using this method. */ - void - SetLabeledSliceIndices(unsigned int axis, SliceSetType indices); - - /** If default slice detection is not wanted, slice indices - * between which interpolation is done can be set using this method. */ - SliceSetType - GetLabeledSliceIndices(unsigned int axis); - /** Calculates a bounding box of non-zero pixels. */ typename SliceType::RegionType BoundingBox(itk::SmartPointer image); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 9dc692ac0d7..6808c498405 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -51,19 +51,19 @@ void WriteDebug(itk::SmartPointer out, const char * filename) { return; // tests run much faster - typedef ImageFileWriter WriterType; - typename WriterType::Pointer w = WriterType::New(); - w->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - w->SetInput(out); - w->SetFileName(filename); - try - { - w->Update(); - } - catch (ExceptionObject & error) - { - std::cerr << "Error: " << error << std::endl; - } + // typedef ImageFileWriter WriterType; + // typename WriterType::Pointer w = WriterType::New(); + // w->SetNumberOfThreads(1); //otherwise conflicts with C++11 threads + // w->SetInput(out); + // w->SetFileName(filename); + // try + // { + // w->Update(); + // } + // catch (ExceptionObject & error) + // { + // std::cerr << "Error: " << error << std::endl; + // } } template @@ -121,8 +121,10 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_MinAlignIters(pow(2, TImage::ImageDimension)) , // smaller of this and pixel count of the search image m_MaxAlignIters(pow(6, TImage::ImageDimension)) - , // bigger of this and root of pixel count of the search image - m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets + , // bigger of this and root of pixel count of the search image + m_LabeledSlices(TImage::ImageDimension) + , // initialize with empty sets + m_SliceSets{ {} } // initialize with empty sets { // set up pipeline for regioned connected components m_RoI = RoiType::New(); @@ -141,7 +143,7 @@ template typename MorphologicalContourInterpolator::SliceSetType MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) { - return m_LabeledSlices[axis]; + return m_SliceSets[axis]; } @@ -149,7 +151,7 @@ template void MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) { - m_LabeledSlices[axis] = indices; + m_SliceSets[axis] = indices; this->Modified(); } @@ -193,6 +195,13 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() m_LabeledSlices.resize(TImage::ImageDimension); // initialize with empty sets m_BoundingBoxes.clear(); m_Orientations.clear(); + if (!m_UseCustomSlicePositions) + { + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + { + m_SliceSets[a] = {}; + } + } typename TImage::ConstPointer m_Input = this->GetInput(); typename TImage::Pointer m_Output = this->GetOutput(); @@ -261,6 +270,10 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() if (m_Axis == -1 || m_Axis == axis) { m_LabeledSlices[axis][val].insert(ind[axis]); + if (!m_UseCustomSlicePositions) + { + m_SliceSets[axis].insert(ind[axis]); + } } } } @@ -1531,7 +1544,16 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { if (m_Label == 0 || m_Label == it->first) // label needs to be interpolated { - typename SliceSetType::iterator prev = it->second.begin(); + typename SliceSetType::iterator prev; + if (m_UseCustomSlicePositions && m_Label != 0) + { + prev = m_SliceSets[axis].begin(); + } + else + { + prev = it->second.begin(); + } + if (prev == it->second.end()) { continue; // nothing to do for this label @@ -1545,7 +1567,16 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename SliceType::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); iconn->DisconnectPipeline(); - typename SliceSetType::iterator next = it->second.begin(); + typename SliceSetType::iterator next; + if (m_UseCustomSlicePositions && m_Label != 0) + { + next = m_SliceSets[axis].begin(); + } + else + { + next = it->second.begin(); + } + for (++next; next != it->second.end(); ++next) { typename TImage::RegionType rj = ri; @@ -1631,19 +1662,23 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer m_Output = this->GetOutput(); this->AllocateOutputs(); - std::vector labeledSlices; - if (m_UseCustomSlicePositions) - { - labeledSlices.swap(m_LabeledSlices); - } - this->DetermineSliceOrientations(); // calculates bounding boxes - if (m_UseCustomSlicePositions) + this->DetermineSliceOrientations(); // calculates bounding boxes + if (m_UseCustomSlicePositions && m_Label == 0) // we need to adjust m_LabeledSlices { - m_LabeledSlices.swap(labeledSlices); - labeledSlices.clear(); - for (int i = 0; i < m_LabeledSlices.size(); i++) + for (int i = 0; i < TImage::ImageDimension; i++) { - m_Orientations[i] = (m_LabeledSlices[i].size() > 0); // non-zero + for (typename LabeledSlicesType::iterator lIt = m_LabeledSlices[i].begin(); lIt != m_LabeledSlices[i].end(); + ++lIt) + { + // typename SliceSetType::iterator sIt = lIt->second.begin(); + SliceSetType newIndices; + std::set_intersection(lIt->second.begin(), + lIt->second.end(), + m_SliceSets[i].begin(), + m_SliceSets[i].end(), + std::inserter(newIndices, newIndices.end())); + lIt->second = newIndices; + } } } @@ -1659,7 +1694,14 @@ MorphologicalContourInterpolator::GenerateData() OrientationType aggregate = OrientationType(); aggregate.Fill(false); - if (this->m_Label == 0) + if (m_UseCustomSlicePositions) + { + for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + { + aggregate[a] = m_SliceSets[a].size() > 0; + } + } + else if (this->m_Label == 0) { for (typename OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) { From 5e84f60e63ce3893a7ac2d0167cb542bc78ee9a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 4 Apr 2016 11:29:09 -0400 Subject: [PATCH 081/176] BUG: Fixing Doxygen error --- .../include/itkMorphologicalContourInterpolator.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 8e873307712..6a4b822d025 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -65,8 +65,7 @@ namespace itk * This work is supported by NIH grant R01 EB014346, "Continued development * and maintenance of the ITK-SNAP 3D image segmentation software." * - * \ingroup Filtering - * \ingroup Segmentation + * \ingroup MorphologicalContourInterpolation */ template class MorphologicalContourInterpolator : public ImageToImageFilter From 7f5b5d0b73c2f8350a1dbf319f5c9ccc73504651 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 4 Apr 2016 11:30:04 -0400 Subject: [PATCH 082/176] ENH: Removing ThreadPool to keep C++98 compatibility *Mutexed writing prevents random crashes when instantiated with RLEImage *Always writing largest label prevents results being dependent on threading data races --- .../include/ThreadPool.h | 117 ------------- .../itkMorphologicalContourInterpolator.h | 20 +-- .../itkMorphologicalContourInterpolator.hxx | 160 +++++++++++------- 3 files changed, 110 insertions(+), 187 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h b/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h deleted file mode 100644 index e0435b729fc..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/ThreadPool.h +++ /dev/null @@ -1,117 +0,0 @@ -#ifndef THREAD_POOL_H -#define THREAD_POOL_H - -/*https://github.com/progschj/ThreadPool -Copyright (c) 2012 Jakob Progsch, Václav Zeman - -This software is provided 'as-is', without any express or implied -warranty. In no event will the authors be held liable for any damages -arising from the use of this software. - -Permission is granted to anyone to use this software for any purpose, -including commercial applications, and to alter it and redistribute it -freely, subject to the following restrictions: - - 1. The origin of this software must not be misrepresented; you must not - claim that you wrote the original software. If you use this software - in a product, an acknowledgment in the product documentation would be - appreciated but is not required. - - 2. Altered source versions must be plainly marked as such, and must not be - misrepresented as being the original software. - - 3. This notice may not be removed or altered from any source - distribution.*/ - -#include -#include -#include -#include -#include -#include -#include -#include -#include - -class ThreadPool -{ -public: - ThreadPool(size_t); - template - auto - enqueue(F && f, Args &&... args) -> std::future::type>; - ~ThreadPool(); - -private: - // need to keep track of threads so we can join them - std::vector workers; - // the task queue - std::queue> tasks; - - // synchronization - std::mutex queue_mutex; - std::condition_variable condition; - bool stop; -}; - -// the constructor just launches some amount of workers -inline ThreadPool::ThreadPool(size_t threads) - : stop(false) -{ - for (size_t i = 0; i < threads; ++i) - workers.emplace_back([this] { - for (;;) - { - std::function task; - - { - std::unique_lock lock(this->queue_mutex); - this->condition.wait(lock, [this] { return this->stop || !this->tasks.empty(); }); - if (this->stop && this->tasks.empty()) - return; - task = std::move(this->tasks.front()); - this->tasks.pop(); - } - - task(); - } - }); -} - -// add new work item to the pool -template -auto -ThreadPool::enqueue(F && f, Args &&... args) -> std::future::type> -{ - using return_type = typename std::result_of::type; - - auto task = - std::make_shared>(std::bind(std::forward(f), std::forward(args)...)); - - std::future res = task->get_future(); - { - std::unique_lock lock(queue_mutex); - - // don't allow enqueueing after stopping the pool - if (stop) - throw std::runtime_error("enqueue on stopped ThreadPool"); - - tasks.emplace([task]() { (*task)(); }); - } - condition.notify_one(); - return res; -} - -// the destructor joins all threads -inline ThreadPool::~ThreadPool() -{ - { - std::unique_lock lock(queue_mutex); - stop = true; - } - condition.notify_all(); - for (std::thread & worker : workers) - worker.join(); -} - -#endif diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 6a4b822d025..e30c58f2148 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -24,8 +24,6 @@ #include "itkConnectedComponentImageFilter.h" #include "itkBinaryThresholdImageFilter.h" -#include "ThreadPool.h" - namespace itk { @@ -70,11 +68,15 @@ namespace itk template class MorphologicalContourInterpolator : public ImageToImageFilter { + template + friend class MorphologicalContourInterpolatorParallelInvoker; + public: /** Standard class typedefs. */ - typedef MorphologicalContourInterpolator Self; - typedef ImageToImageFilter Superclass; - typedef SmartPointer Pointer; + typedef MorphologicalContourInterpolator Self; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + typedef Image SliceType; /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -189,13 +191,11 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; - typedef Image FloatSliceType; - typedef Image SliceType; - typedef Image BoolSliceType; + typedef Image BoolImageType; + typedef Image FloatSliceType; + typedef Image BoolSliceType; /** Are these two slices equal? */ bool diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 6808c498405..8b5517d1e62 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -31,10 +31,14 @@ #include "itkBinaryBallStructuringElement.h" #include "itkAndImageFilter.h" #include "itkOrImageFilter.h" +#include "itkMultiThreader.h" +#include "itkThreadedIndexedContainerPartitioner.h" +#include "itkSimpleFastMutexLock.h" #include #include #include #include +#include #include #include #include @@ -79,6 +83,74 @@ WriteDebug(itk::SmartPointer> out, const char * filename) WriteDebug(caster->GetOutput(), filename); } + +template +struct SegmentBetweenTwo +{ + int axis; + typename TImage * out; + int label, i, j; + typename MorphologicalContourInterpolator::SliceType::Pointer iconn, jconn; +}; + + +template +class MorphologicalContourInterpolatorParallelInvoker + : public itk::DomainThreader> +{ +public: + // Standard ITK typedefs. + typedef MorphologicalContourInterpolatorParallelInvoker Self; + typedef itk::DomainThreader> + Superclass; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + // The domain is an index range. + typedef typename Superclass::DomainType DomainType; + + // This creates the ::New() method for instantiating the class. + itkNewMacro(Self); + + /** Array of segments which need to be interpolated. */ + void + SetWorkArray(std::vector> & workArray) + { + m_WorkArray = workArray; + } + + /** Array of segments which need to be interpolated. */ + void + ClearWorkArray() + { + m_WorkArray.clear(); + } + +protected: + // We need a constructor for the itkNewMacro. + MorphologicalContourInterpolatorParallelInvoker() {} + +private: + virtual void + ThreadedExecution(const DomainType & subDomain, const itk::ThreadIdType threadId) + { + // Look only at the range of cells by the set of indices in the subDomain. + for (itk::IndexValueType ii = subDomain[0]; ii <= subDomain[1] && ii < m_WorkArray.size(); ++ii) + { + this->m_Associate->InterpolateBetweenTwo(m_WorkArray[ii].axis, + m_WorkArray[ii].out, + m_WorkArray[ii].label, + m_WorkArray[ii].i, + m_WorkArray[ii].j, + m_WorkArray[ii].iconn, + m_WorkArray[ii].jconn); + } + } + + std::vector> m_WorkArray; +}; + + template bool MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Pointer a, @@ -116,7 +188,6 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_UseDistanceTransform(true) , m_UseBallStructuringElement(false) , m_UseCustomSlicePositions(false) - , m_ThreadPool(nullptr) , m_StopSpawning(false) , m_MinAlignIters(pow(2, TImage::ImageDimension)) , // smaller of this and pixel count of the search image @@ -815,11 +886,17 @@ MorphologicalContourInterpolator::Interpolate1to1(int ImageRegionConstIterator seqIt(median, newRegion); ImageRegionIterator outIt(out, outRegion); ImageRegionIterator midIt(midConn, newRegion); + static SimpleFastMutexLock mutex; while (!outIt.IsAtEnd()) { if (seqIt.Get()) { - outIt.Set(label); + mutex.Lock(); + if (outIt.Get() < label) + { + outIt.Set(label); + } + mutex.Unlock(); midIt.Set(1); } ++seqIt; @@ -837,24 +914,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int bool first = abs(i - mid) > 1; // interpolate i-mid? bool second = abs(j - mid) > 1; // interpolate j-mid? - if (first && second && !m_StopSpawning) // then first in new thread - { - m_ThreadPool->enqueue(&MorphologicalContourInterpolator::Interpolate1to1, - this, - axis, - out, - label, - i, - mid, - iConn, - iRegionId, - midConn, - 1, - iTrans, - true); - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); - } - else // sequential { if (first) { @@ -1531,14 +1590,8 @@ template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) { - // do multithreading by paralellizing for different labels - // and different inter-slice segments [thread pool of C++11 threads] - m_ThreadPool = new ::ThreadPool(std::thread::hardware_concurrency()); - typename SliceType::Pointer sliceVar; - std::vectorenqueue( - &MorphologicalContourInterpolator::InterpolateBetweenTwo, this, axis, out, 0, 0, 0, sliceVar, sliceVar))> - results; // so we can wait for all the results - m_StopSpawning = false; + // a list of segments which need to be interpolated + std::vector> segments; for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { @@ -1547,13 +1600,10 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename SliceSetType::iterator prev; if (m_UseCustomSlicePositions && m_Label != 0) { - prev = m_SliceSets[axis].begin(); - } - else - { - prev = it->second.begin(); + it->second = m_SliceSets[axis]; } + prev = it->second.begin(); if (prev == it->second.end()) { continue; // nothing to do for this label @@ -1567,16 +1617,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typename SliceType::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); iconn->DisconnectPipeline(); - typename SliceSetType::iterator next; - if (m_UseCustomSlicePositions && m_Label != 0) - { - next = m_SliceSets[axis].begin(); - } - else - { - next = it->second.begin(); - } - + typename SliceSetType::iterator next = it->second.begin(); for (++next; next != it->second.end(); ++next) { typename TImage::RegionType rj = ri; @@ -1589,15 +1630,15 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou if (*prev + 1 < *next) // only if they are not adjacent slices { - results.push_back(m_ThreadPool->enqueue(&MorphologicalContourInterpolator::InterpolateBetweenTwo, - this, - axis, - out, - it->first, - *prev, - *next, - iconn, - jconn)); + SegmentBetweenTwo s; + s.axis = axis; + s.out = out; + s.label = it->first; + s.i = *prev; + s.j = *next; + s.iconn = iconn; + s.jconn = jconn; + segments.push_back(s); } iconn = jconn; prev = next; @@ -1605,14 +1646,13 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } - for (int i = 0; i < results.size(); i++) - { - results[i].get(); // wait for thread - } - m_StopSpawning = true; - // invoking destructor waits for any leftover threads created by Interpolate1to1 - delete m_ThreadPool; - m_ThreadPool = nullptr; + typedef MorphologicalContourInterpolatorParallelInvoker Parallelizer; + typename Parallelizer::Pointer parallizer = Parallelizer::New(); + parallizer->SetWorkArray(segments); + Parallelizer::DomainType completeDomain; + completeDomain[0] = 0; + completeDomain[1] = std::max(0, int(segments.size()) - 1); + parallizer->Execute(this, completeDomain); } From 0c1e9a4c79cd1c2d1f3fd5a804a8f127049bafc0 Mon Sep 17 00:00:00 2001 From: Dzenan Zukic Date: Thu, 30 Jun 2016 15:36:20 -0400 Subject: [PATCH 083/176] COMP: Linux non C++11 compile fixes --- .../itkMorphologicalContourInterpolator.hxx | 100 +++++++++--------- ...kMorphologicalContourInterpolationTest.cxx | 4 +- 2 files changed, 51 insertions(+), 53 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 8b5517d1e62..03599277942 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -39,9 +39,6 @@ #include #include #include -#include -#include -#include // DEBUG #include @@ -88,7 +85,7 @@ template struct SegmentBetweenTwo { int axis; - typename TImage * out; + TImage * out; int label, i, j; typename MorphologicalContourInterpolator::SliceType::Pointer iconn, jconn; }; @@ -192,10 +189,9 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_MinAlignIters(pow(2, TImage::ImageDimension)) , // smaller of this and pixel count of the search image m_MaxAlignIters(pow(6, TImage::ImageDimension)) - , // bigger of this and root of pixel count of the search image - m_LabeledSlices(TImage::ImageDimension) - , // initialize with empty sets - m_SliceSets{ {} } // initialize with empty sets + , // bigger of this and root of pixel count of the search image + m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets +//,m_SliceSets({{}}) //initialize with empty sets { // set up pipeline for regioned connected components m_RoI = RoiType::New(); @@ -270,7 +266,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { - m_SliceSets[a] = {}; + m_SliceSets[a] = SliceSetType(); } } @@ -417,9 +413,9 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typedef BinaryDilateImageFilter CrossDilateType; typedef BinaryDilateImageFilter BallDilateType; - thread_local bool initialized = false; - thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); - thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); + /*thread_local*/ static bool initialized = false; + /*thread_local*/ static typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); + /*thread_local*/ static typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); if (!initialized) // make sure these non-trivial operations are executed only once per thread { typedef Size SizeType; @@ -427,13 +423,13 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe size.Fill(1); m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - thread_local CrossStructuringElementType m_CrossStructuringElement; + /*thread_local*/ static CrossStructuringElementType m_CrossStructuringElement; m_CrossStructuringElement.SetRadius(size); m_CrossStructuringElement.CreateStructuringElement(); m_CrossDilator->SetKernel(m_CrossStructuringElement); m_BallDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - thread_local BallStructuringElementType m_BallStructuringElement; + /*thread_local*/ static BallStructuringElementType m_BallStructuringElement; m_BallStructuringElement.SetRadius(size); m_BallStructuringElement.CreateStructuringElement(); m_BallDilator->SetKernel(m_BallStructuringElement); @@ -459,7 +455,7 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions typedef AndImageFilter AndFilterType; - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + /*thread_local*/ static typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads m_And->SetInput(0, mask); m_And->SetInput(1, temp); @@ -508,8 +504,8 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool float ratio = float(jSeq.size()) / iSeq.size(); // generate union of transition sequences - typedef OrImageFilter OrType; - thread_local typename OrType::Pointer m_Or = OrType::New(); + typedef OrImageFilter OrType; + /*thread_local*/ static typename OrType::Pointer m_Or = OrType::New(); m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) @@ -553,7 +549,7 @@ typename MorphologicalContourInterpolator::FloatSliceType::Pointer MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer mask) { typedef itk::SignedMaurerDistanceMapImageFilter FilterType; - thread_local typename FilterType::Pointer filter = FilterType::New(); + /*thread_local*/ static typename FilterType::Pointer filter = FilterType::New(); filter->SetInput(mask); filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space filter->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads @@ -621,7 +617,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool WriteDebug(orImage, "C:\\orImage.nrrd"); // sum of histogram bins for i and j and - auto maxSize = std::max(iHist.size(), jHist.size()); + std::vector::size_type maxSize = std::max(iHist.size(), jHist.size()); if (maxSize == 0) { return intersection; @@ -657,7 +653,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool // threshold at distance bestBin is the median intersection typedef BinaryThresholdImageFilter FloatBinarizerType; - thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); + /*thread_local*/ static typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); threshold->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads threshold->SetInput(sdf); threshold->SetUpperThreshold(float(bestBin) / fractioning); @@ -665,7 +661,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool threshold->Update(); typedef AndImageFilter AndFilterType; - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + /*thread_local*/ static typename AndFilterType::Pointer m_And = AndFilterType::New(); m_And->SetInput(threshold->GetOutput()); m_And->SetInput(1, orImage); m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); @@ -822,8 +818,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(jSlice, "C:\\jSlice.nrrd"); // create intersection - typedef AndImageFilter AndSliceType; - thread_local typename AndSliceType::Pointer sAnd = AndSliceType::New(); + typedef AndImageFilter AndSliceType; + /*thread_local*/ static typename AndSliceType::Pointer sAnd = AndSliceType::New(); sAnd->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads sAnd->SetInput(0, iSlice); sAnd->SetInput(1, jSlice); @@ -928,6 +924,32 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(out, "C:\\intermediateResult.nrrd"); } +template +class MatchesID +{ + typename TImage::PixelType m_ID; + +public: + MatchesID() {} + MatchesID(typename TImage::PixelType id) + : m_ID(id) + {} + bool + operator!=(const MatchesID & other) + { + return m_ID != other.m_ID; + } + bool + operator==(const MatchesID & other) + { + return m_ID == other.m_ID; + } + inline bool + operator()(const typename TImage::PixelType & val) const + { + return val == m_ID; + } +}; template void @@ -943,34 +965,10 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename SliceType::IndexType translation) { // first convert iConn into binary mask - class MatchesID - { - typename TImage::PixelType m_ID; - - public: - MatchesID() {} - MatchesID(typename TImage::PixelType id) - : m_ID(id) - {} - bool - operator!=(const MatchesID & other) - { - return m_ID != other.m_ID; - } - bool - operator==(const MatchesID & other) - { - return m_ID == other.m_ID; - } - inline bool - operator()(const typename TImage::PixelType & val) const - { - return val == m_ID; - } - } matchesID(iRegionId); + MatchesID matchesID(iRegionId); - typedef UnaryFunctorImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); + typedef UnaryFunctorImageFilter> CastType; + typename CastType::Pointer caster = CastType::New(); caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads caster->SetFunctor(matchesID); caster->SetInput(iConn); @@ -1649,7 +1647,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou typedef MorphologicalContourInterpolatorParallelInvoker Parallelizer; typename Parallelizer::Pointer parallizer = Parallelizer::New(); parallizer->SetWorkArray(segments); - Parallelizer::DomainType completeDomain; + typename Parallelizer::DomainType completeDomain; completeDomain[0] = 0; completeDomain[1] = std::max(0, int(segments.size()) - 1); parallizer->Execute(this, completeDomain); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 3832519716c..8444f6a2762 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -111,12 +111,12 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) try { // unused cases are not instantiated because they greatly increase compile time - if (numDimensions == 3 && (pixelType == ScalarPixelType::SHORT || pixelType == ScalarPixelType::USHORT)) + if (numDimensions == 3 && (pixelType == itk::ImageIOBase::SHORT || pixelType == itk::ImageIOBase::USHORT)) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } - if (numDimensions == 4 && pixelType == ScalarPixelType::UCHAR) + if (numDimensions == 4 && pixelType == itk::ImageIOBase::UCHAR) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; From 0a27fdd0a0658d64072df64b01972947655eaf34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Jul 2016 09:18:41 -0400 Subject: [PATCH 084/176] ENH: Adding threadId parameter to manually create thread-local storage in absence of C++11 --- .../itkMorphologicalContourInterpolator.h | 28 +- .../itkMorphologicalContourInterpolator.hxx | 244 ++++++++++-------- 2 files changed, 161 insertions(+), 111 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index e30c58f2148..d6fb8369a68 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -188,9 +188,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; @@ -220,7 +220,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter - GenerateDilationSequence(typename BoolSliceType::Pointer begin, typename BoolSliceType::Pointer end); + GenerateDilationSequence(typename BoolSliceType::Pointer begin, + typename BoolSliceType::Pointer end, + ThreadIdType threadId); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer FindMedianImageDilations(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask); + typename BoolSliceType::Pointer jMask, + ThreadIdType threadId); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer FindMedianImageDistances(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask); + typename BoolSliceType::Pointer jMask, + ThreadIdType threadId); /** Build transition sequence and pick the median */ void @@ -274,7 +280,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; @@ -289,7 +296,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter RoiType; typename RoiType::Pointer m_RoI; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 03599277942..3526cc66ec5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -129,7 +129,7 @@ protected: private: virtual void - ThreadedExecution(const DomainType & subDomain, const itk::ThreadIdType threadId) + ThreadedExecution(const DomainType & subDomain, const ThreadIdType threadId) { // Look only at the range of cells by the set of indices in the subDomain. for (itk::IndexValueType ii = subDomain[0]; ii <= subDomain[1] && ii < m_WorkArray.size(); ++ii) @@ -140,7 +140,8 @@ private: m_WorkArray[ii].i, m_WorkArray[ii].j, m_WorkArray[ii].iconn, - m_WorkArray[ii].jconn); + m_WorkArray[ii].jconn, + threadId); } } @@ -185,7 +186,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_UseDistanceTransform(true) , m_UseBallStructuringElement(false) , m_UseCustomSlicePositions(false) - , m_StopSpawning(false) + , m_ThreadCount(MultiThreader::GetGlobalDefaultNumberOfThreads()) , m_MinAlignIters(pow(2, TImage::ImageDimension)) , // smaller of this and pixel count of the search image m_MaxAlignIters(pow(6, TImage::ImageDimension)) @@ -356,7 +357,8 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId) + typename TImage::PixelType iRegionId, + ThreadIdType threadId) { PixelList jRegionIds; jRegionIds.push_back(iRegionId); @@ -396,14 +398,15 @@ MorphologicalContourInterpolator::Extrapolate(int reg3.SetIndex(phIndex); phSlice->SetRegions(reg3); typename SliceType::IndexType t0 = { 0 }; - Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false); + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false, threadId); } template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer seed, - typename BoolSliceType::Pointer mask) + typename BoolSliceType::Pointer mask, + ThreadIdType threadId) { // set up structuring element for dilation typedef BinaryCrossStructuringElement @@ -413,55 +416,60 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typedef BinaryDilateImageFilter CrossDilateType; typedef BinaryDilateImageFilter BallDilateType; - /*thread_local*/ static bool initialized = false; - /*thread_local*/ static typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); - /*thread_local*/ static typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); - if (!initialized) // make sure these non-trivial operations are executed only once per thread + static std::vector initialized(m_ThreadCount); // default: false + static std::vector m_CrossDilator(m_ThreadCount); + static std::vector m_BallDilator(m_ThreadCount); + static std::vector m_CrossStructuringElement(m_ThreadCount); + static std::vector m_BallStructuringElement(m_ThreadCount); + typedef AndImageFilter AndFilterType; + static std::vector m_And(m_ThreadCount); + + if (!initialized[threadId]) // make sure these non-trivial operations are executed only once per thread { + m_CrossDilator[threadId] = CrossDilateType::New(); + m_BallDilator[threadId] = BallDilateType::New(); + m_And[threadId] = AndFilterType::New(); + m_And[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads typedef Size SizeType; SizeType size; size.Fill(1); - m_CrossDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - /*thread_local*/ static CrossStructuringElementType m_CrossStructuringElement; - m_CrossStructuringElement.SetRadius(size); - m_CrossStructuringElement.CreateStructuringElement(); - m_CrossDilator->SetKernel(m_CrossStructuringElement); + m_CrossDilator[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_CrossStructuringElement[threadId].SetRadius(size); + m_CrossStructuringElement[threadId].CreateStructuringElement(); + m_CrossDilator[threadId]->SetKernel(m_CrossStructuringElement[threadId]); + + m_BallDilator[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_BallStructuringElement[threadId].SetRadius(size); + m_BallStructuringElement[threadId].CreateStructuringElement(); + m_BallDilator[threadId]->SetKernel(m_BallStructuringElement[threadId]); - m_BallDilator->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - /*thread_local*/ static BallStructuringElementType m_BallStructuringElement; - m_BallStructuringElement.SetRadius(size); - m_BallStructuringElement.CreateStructuringElement(); - m_BallDilator->SetKernel(m_BallStructuringElement); + initialized[threadId] = true; } - initialized = true; typename BoolSliceType::Pointer temp; if (m_UseBallStructuringElement) { - m_BallDilator->SetInput(seed); - m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_BallDilator->Update(); - temp = m_BallDilator->GetOutput(); + m_BallDilator[threadId]->SetInput(seed); + m_BallDilator[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_BallDilator[threadId]->Update(); + temp = m_BallDilator[threadId]->GetOutput(); } else { - m_CrossDilator->SetInput(seed); - m_CrossDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_CrossDilator->Update(); - temp = m_CrossDilator->GetOutput(); + m_CrossDilator[threadId]->SetInput(seed); + m_CrossDilator[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_CrossDilator[threadId]->Update(); + temp = m_CrossDilator[threadId]->GetOutput(); } temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions - typedef AndImageFilter AndFilterType; - /*thread_local*/ static typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - m_And->SetInput(0, mask); - m_And->SetInput(1, temp); - m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_And->Update(); - typename BoolSliceType::Pointer result = m_And->GetOutput(); + m_And[threadId]->SetInput(0, mask); + m_And[threadId]->SetInput(1, temp); + m_And[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_And[threadId]->Update(); + typename BoolSliceType::Pointer result = m_And[threadId]->GetOutput(); result->DisconnectPipeline(); // WriteDebug(seed, "C:\\seed.nrrd"); // WriteDebug(mask, "C:\\mask.nrrd"); @@ -474,14 +482,15 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe template std::vector::BoolSliceType::Pointer> MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer begin, - typename BoolSliceType::Pointer end) + typename BoolSliceType::Pointer end, + ThreadIdType threadId) { std::vector seq; - seq.push_back(Dilate1(begin, end)); + seq.push_back(Dilate1(begin, end, threadId)); do { seq.back()->DisconnectPipeline(); - seq.push_back(Dilate1(seq.back(), end)); + seq.push_back(Dilate1(seq.back(), end, threadId)); } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image return seq; @@ -492,10 +501,11 @@ template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask) + typename BoolSliceType::Pointer jMask, + ThreadIdType threadId) { - std::vector iSeq = GenerateDilationSequence(intersection, iMask); - std::vector jSeq = GenerateDilationSequence(intersection, jMask); + std::vector iSeq = GenerateDilationSequence(intersection, iMask, threadId); + std::vector jSeq = GenerateDilationSequence(intersection, jMask, threadId); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection if (iSeq.size() < jSeq.size()) { @@ -504,22 +514,29 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool float ratio = float(jSeq.size()) / iSeq.size(); // generate union of transition sequences - typedef OrImageFilter OrType; - /*thread_local*/ static typename OrType::Pointer m_Or = OrType::New(); - m_Or->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + typedef OrImageFilter OrType; + static std::vector initialized(m_ThreadCount); // default: false + static std::vector m_Or(m_ThreadCount); + if (!initialized[threadId]) + { + m_Or[threadId] = OrType::New(); + m_Or[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + initialized[threadId] = true; + } + std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) { - m_Or->SetInput(0, iSeq[x]); + m_Or[threadId]->SetInput(0, iSeq[x]); unsigned xj = ratio * x; - m_Or->SetInput(1, jSeq[xj]); + m_Or[threadId]->SetInput(1, jSeq[xj]); #ifdef _DEBUG // WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); // WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); #endif // _DEBUG - m_Or->GetOutput()->SetRegions(iMask->GetRequestedRegion()); - m_Or->Update(); - seq.push_back(m_Or->GetOutput()); + m_Or[threadId]->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + m_Or[threadId]->Update(); + seq.push_back(m_Or[threadId]->GetOutput()); seq.back()->DisconnectPipeline(); } @@ -546,26 +563,33 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool template typename MorphologicalContourInterpolator::FloatSliceType::Pointer -MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer mask) +MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer mask, ThreadIdType threadId) { typedef itk::SignedMaurerDistanceMapImageFilter FilterType; - /*thread_local*/ static typename FilterType::Pointer filter = FilterType::New(); - filter->SetInput(mask); - filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space - filter->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - filter->GetOutput()->SetRequestedRegion(mask->GetRequestedRegion()); - filter->Update(); - return filter->GetOutput(); + static std::vector initialized(m_ThreadCount); // default: false + static std::vector filter(m_ThreadCount); + if (!initialized[threadId]) + { + filter[threadId] = FilterType::New(); + filter[threadId]->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space + filter[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + initialized[threadId] = true; + } + filter[threadId]->SetInput(mask); + filter[threadId]->GetOutput()->SetRequestedRegion(mask->GetRequestedRegion()); + filter[threadId]->Update(); + return filter[threadId]->GetOutput(); } template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer intersection, typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask) + typename BoolSliceType::Pointer jMask, + ThreadIdType threadId) { // calculate distance field - typename FloatSliceType::Pointer sdf = MaurerDM(intersection); + typename FloatSliceType::Pointer sdf = MaurerDM(intersection, threadId); WriteDebug(sdf, "C:\\sdf.nrrd"); // create histograms of distances and union @@ -652,21 +676,29 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool } // threshold at distance bestBin is the median intersection - typedef BinaryThresholdImageFilter FloatBinarizerType; - /*thread_local*/ static typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); - threshold->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - threshold->SetInput(sdf); - threshold->SetUpperThreshold(float(bestBin) / fractioning); - threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); - threshold->Update(); - + typedef BinaryThresholdImageFilter FloatBinarizerType; typedef AndImageFilter AndFilterType; - /*thread_local*/ static typename AndFilterType::Pointer m_And = AndFilterType::New(); - m_And->SetInput(threshold->GetOutput()); - m_And->SetInput(1, orImage); - m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); - m_And->Update(); - typename BoolSliceType::Pointer median = m_And->GetOutput(); + static std::vector initialized(m_ThreadCount); // default: false + static std::vector threshold(m_ThreadCount); + static std::vector m_And(m_ThreadCount); + if (!initialized[threadId]) + { + threshold[threadId] = FloatBinarizerType::New(); + threshold[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_And[threadId] = AndFilterType::New(); + m_And[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + initialized[threadId] = true; + } + threshold[threadId]->SetInput(sdf); + threshold[threadId]->SetUpperThreshold(float(bestBin) / fractioning); + threshold[threadId]->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); + threshold[threadId]->Update(); + + m_And[threadId]->SetInput(threshold[threadId]->GetOutput()); + m_And[threadId]->SetInput(1, orImage); + m_And[threadId]->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); + m_And[threadId]->Update(); + typename BoolSliceType::Pointer median = m_And[threadId]->GetOutput(); WriteDebug(median, "C:\\median.nrrd"); return median; } @@ -721,7 +753,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename SliceType::Pointer jConn, typename TImage::PixelType jRegionId, typename SliceType::IndexType translation, - bool recursive) + bool recursive, + ThreadIdType threadId) { // translate iConn by t/2 and jConn by -t/2 typename SliceType::IndexType iTrans; @@ -818,25 +851,31 @@ MorphologicalContourInterpolator::Interpolate1to1(int WriteDebug(jSlice, "C:\\jSlice.nrrd"); // create intersection - typedef AndImageFilter AndSliceType; - /*thread_local*/ static typename AndSliceType::Pointer sAnd = AndSliceType::New(); - sAnd->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads - sAnd->SetInput(0, iSlice); - sAnd->SetInput(1, jSlice); - sAnd->GetOutput()->SetRegions(iSlice->GetRequestedRegion()); - sAnd->Update(); - typename BoolSliceType::Pointer intersection = sAnd->GetOutput(); + typedef AndImageFilter AndSliceType; + static std::vector initialized(m_ThreadCount); // default: false + static std::vector sAnd(m_ThreadCount); + if (!initialized[threadId]) + { + sAnd[threadId] = AndSliceType::New(); + sAnd[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + initialized[threadId] = true; + } + sAnd[threadId]->SetInput(0, iSlice); + sAnd[threadId]->SetInput(1, jSlice); + sAnd[threadId]->GetOutput()->SetRegions(iSlice->GetRequestedRegion()); + sAnd[threadId]->Update(); + typename BoolSliceType::Pointer intersection = sAnd[threadId]->GetOutput(); intersection->DisconnectPipeline(); WriteDebug(intersection, "C:\\intersection.nrrd"); typename BoolSliceType::Pointer median; if (m_UseDistanceTransform) { - median = FindMedianImageDistances(intersection, iSlice, jSlice); + median = FindMedianImageDistances(intersection, iSlice, jSlice, threadId); } else { - median = FindMedianImageDilations(intersection, iSlice, jSlice); + median = FindMedianImageDilations(intersection, iSlice, jSlice, threadId); } // finally write it out into the output image pointer @@ -913,11 +952,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int { if (first) { - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true); + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true, threadId); } if (second) { - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); } } } @@ -962,7 +1001,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::PixelType iRegionId, typename SliceType::Pointer jConn, PixelList jRegionIds, - typename SliceType::IndexType translation) + typename SliceType::IndexType translation, + ThreadIdType threadId) { // first convert iConn into binary mask MatchesID matchesID(iRegionId); @@ -1040,7 +1080,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[x] = Dilate1(blobs[x], mask); + blobs[x] = Dilate1(blobs[x], mask, threadId); // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); } @@ -1121,7 +1161,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { - Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false); + Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false, threadId); } } @@ -1392,7 +1432,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer iconn, - typename SliceType::Pointer jconn) + typename SliceType::Pointer jconn, + ThreadIdType threadId) { // go through comparison image and create correspondence pairs typedef std::set> PairSet; @@ -1429,12 +1470,12 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (p->second == 0) { - Extrapolate(axis, out, label, i, j, iconn, p->first); + Extrapolate(axis, out, label, i, j, iconn, p->first, threadId); pairs.erase(p++); } else if (p->first == 0) { - Extrapolate(axis, out, label, j, i, jconn, p->second); + Extrapolate(axis, out, label, j, i, jconn, p->second, threadId); pairs.erase(p++); } else @@ -1461,7 +1502,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int PixelList regionIDs; regionIDs.push_back(p->second); typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false); + Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false, threadId); iCounts.erase(p->first); jCounts.erase(p->second); pairs.erase(p++); @@ -1490,7 +1531,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(jconn, p->second, iconn, regionIDs); - Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); + Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation, threadId); typename PairSet::iterator rest = pairs.begin(); while (rest != pairs.end()) @@ -1521,7 +1562,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation, threadId); typename PairSet::iterator rest = pairs.begin(); ++rest; @@ -1563,7 +1604,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation, threadId); typename PairSet::iterator rest = p; ++rest; @@ -1645,12 +1686,13 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } typedef MorphologicalContourInterpolatorParallelInvoker Parallelizer; - typename Parallelizer::Pointer parallizer = Parallelizer::New(); - parallizer->SetWorkArray(segments); + typename Parallelizer::Pointer parallelizer = Parallelizer::New(); + parallelizer->SetWorkArray(segments); typename Parallelizer::DomainType completeDomain; completeDomain[0] = 0; completeDomain[1] = std::max(0, int(segments.size()) - 1); - parallizer->Execute(this, completeDomain); + parallelizer->Execute(this, completeDomain); + parallelizer->ClearWorkArray(); } From 7a637be7c5787fc8470fc7eb72ca62a91f3d8828 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Jul 2016 15:51:20 -0400 Subject: [PATCH 085/176] ENH: Testing RLEImage --- .../test/RLEImage/RLEImage.h | 283 ++++++++++ .../test/RLEImage/RLEImage.txx | 260 +++++++++ .../test/RLEImage/RLEImageConstIterator.h | 440 +++++++++++++++ .../test/RLEImage/RLEImageIterator.h | 161 ++++++ .../RLEImage/RLEImageRegionConstIterator.h | 232 ++++++++ .../test/RLEImage/RLEImageRegionIterator.h | 144 +++++ .../RLEImage/RLEImageScanlineConstIterator.h | 155 +++++ .../test/RLEImage/RLEImageScanlineIterator.h | 86 +++ .../RLEImage/RLERegionOfInterestImageFilter.h | 293 ++++++++++ .../RLERegionOfInterestImageFilter.txx | 531 ++++++++++++++++++ ...kMorphologicalContourInterpolationTest.cxx | 47 +- 11 files changed, 2628 insertions(+), 4 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h new file mode 100644 index 00000000000..32f30db30e6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h @@ -0,0 +1,283 @@ +#ifndef RLEImage_h +#define RLEImage_h + +#include //std::pair +#include +#include +#include + +/** Run-Length Encoded image. + * It saves memory for label images at the expense of processing times. + * Unsuitable for ordinary images (in which case it is counterproductive). + * + * BufferedRegion must include complete run-length lines (along X index axis). + * BufferedRegion can be smaller than LargestPossibleRegion along other axes. + * + * It is best if pixel type and counter type have the same byte size + * (for memory alignment purposes). + * + * Copied and adapted from itk::Image. + */ +template +class RLEImage : public itk::ImageBase +{ + +public: + /** Standard class typedefs */ + typedef RLEImage Self; + typedef itk::ImageBase Superclass; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + typedef itk::WeakPointer ConstWeakPointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(RLEImage, ImageBase); + + /** Pixel typedef support. Used to declare pixel type in filters + * or other operations. */ + typedef TPixel PixelType; + + /** Typedef alias for PixelType */ + typedef TPixel ValueType; + + /** First element is count of repetitions, + * second element is the pixel value. */ + typedef std::pair RLSegment; + + /** A Run-Length encoded line of pixels. */ + typedef std::vector RLLine; + + /** Internal Pixel representation. Used to maintain a uniform API + * with Image Adaptors and allow to keep a particular internal + * representation of data while showing a different external + * representation. */ + typedef RLLine InternalPixelType; + + // typedef PixelType IOPixelType; + + /** Dimension of the image. This constant is used by functions that are + * templated over image type (as opposed to being templated over pixel type + * and dimension) when they need compile time access to the dimension of + * the image. */ + itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); + + /** Index typedef support. An index is used to access pixel values. */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::IndexValueType IndexValueType; + + /** Offset typedef support. An offset is used to access pixel values. */ + typedef typename Superclass::OffsetType OffsetType; + + /** Size typedef support. A size is used to define region bounds. */ + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::SizeValueType SizeValueType; + + /** Direction typedef support. A matrix of direction cosines. */ + typedef typename Superclass::DirectionType DirectionType; + + /** Region typedef support. A region is used to specify a subset of an image. + */ + typedef typename Superclass::RegionType RegionType; + + /** Spacing typedef support. Spacing holds the size of a pixel. The + * spacing is the geometric distance between image samples. */ + typedef typename Superclass::SpacingType SpacingType; + typedef typename Superclass::SpacingValueType SpacingValueType; + + /** Origin typedef support. The origin is the geometric coordinates + * of the index (0,0). */ + typedef typename Superclass::PointType PointType; + + /** Offset typedef (relative position between indices) */ + typedef typename Superclass::OffsetValueType OffsetValueType; + + /** Allocate the image memory. The size of the image must + * already be set, e.g. by calling SetRegions(). + * Pixel values are initialized using default constructor. */ + virtual void + Allocate(bool initialize = false); + + /** Restore the data object to its initial state. This means releasing + * memory. */ + virtual void + Initialize() + { + // Call the superclass which should initialize the BufferedRegion ivar. + Superclass::Initialize(); + m_OnTheFlyCleanup = true; + myBuffer = BufferType::New(); + } + + /** Fill the image buffer with a value. Be sure to call Allocate() + * first. */ + void + FillBuffer(const TPixel & value); + + virtual void + SetLargestPossibleRegion(const RegionType & region) + { + Superclass::SetLargestPossibleRegion(region); + myBuffer->SetLargestPossibleRegion(truncateRegion(region)); + } + + virtual void + SetBufferedRegion(const RegionType & region) + { + Superclass::SetBufferedRegion(region); + myBuffer->SetBufferedRegion(truncateRegion(region)); + } + + virtual void + SetRequestedRegion(const RegionType & region) + { + Superclass::SetRequestedRegion(region); + myBuffer->SetRequestedRegion(truncateRegion(region)); + } + + /** \brief Set a pixel value. + * + * Allocate() needs to have been called first -- for efficiency, + * this function does not check that the image has actually been + * allocated yet. SLOW -> Use iterators instead. */ + void + SetPixel(const IndexType & index, const TPixel & value); + + /** Set a pixel value in the given line and updates segmentRemainder + * and realIndex to refer to the same pixel. + * Returns difference in line length which happens due to merging or splitting segments. + * This method is used by iterators directly. */ + int + SetPixel(RLLine & line, IndexValueType & segmentRemainder, IndexValueType & realIndex, const TPixel & value); + + /** \brief Get a pixel. SLOW! Better use iterators for pixel access. */ + const TPixel & + GetPixel(const IndexType & index) const; + + ///** Get a reference to a pixel. Chaning it changes the whole RLE segment! */ + // TPixel & GetPixel(const IndexType & index); + + ///** \brief Access a pixel. Chaning it changes the whole RLE segment! */ + // TPixel & operator[](const IndexType & index) + //{ + // return this->GetPixel(index); + // } + + /** \brief Access a pixel. This version can only be an rvalue. + * SLOW -> Use iterators instead. */ + const TPixel & + operator[](const IndexType & index) const + { + return this->GetPixel(index); + } + + virtual unsigned int + GetNumberOfComponentsPerPixel() const + { + // use the GetLength() method which works with variable length arrays, + // to make it work with as much pixel types as possible + PixelType p; + return itk::NumericTraits::GetLength(p); + } + + /** Typedef for the internally used buffer. */ + typedef typename itk::Image BufferType; + + /** We need to allow itk-style iterators to be constructed. */ + typename BufferType::Pointer + GetBuffer() + { + return myBuffer; + } + + /** We need to allow itk-style const iterators to be constructed. */ + typename BufferType::Pointer + GetBuffer() const + { + return myBuffer; + } + + /** Returns N-1-dimensional index, the remainder after 0-index is removed. */ + static inline typename BufferType::IndexType + truncateIndex(const IndexType & index); + + /** Returns N-1-dimensional size, the remainder after 0-size is removed. */ + static inline typename BufferType::SizeType + truncateSize(const SizeType & size); + + /** Returns N-1-dimensional region, the remainder after 0-index and size are removed. */ + static typename BufferType::RegionType + truncateRegion(const RegionType & region); + + /** Merges adjacent segments with duplicate values. + * Automatically called when turning on OnTheFlyCleanup. */ + void + CleanUp() const; + + /** Should same-valued segments be merged on the fly? + * On the fly merging usually provides better performance. */ + bool + GetOnTheFlyCleanup() const + { + return m_OnTheFlyCleanup; + } + + /** Should same-valued segments be merged on the fly? + * On the fly merging usually provides better performance. */ + void + SetOnTheFlyCleanup(bool value) + { + if (value == m_OnTheFlyCleanup) + return; + m_OnTheFlyCleanup = value; + if (m_OnTheFlyCleanup) + CleanUp(); // put the image into a clean state + } + + +protected: + RLEImage() + : itk::ImageBase() + { + m_OnTheFlyCleanup = true; + myBuffer = BufferType::New(); + } + void + PrintSelf(std::ostream & os, itk::Indent indent) const; + + virtual ~RLEImage() {} + + /** Compute helper matrices used to transform Index coordinates to + * PhysicalPoint coordinates and back. This method is virtual and will be + * overloaded in derived classes in order to provide backward compatibility + * behavior in classes that did not used to take image orientation into + * account. */ + virtual void + ComputeIndexToPhysicalPointMatrices() + { + this->Superclass::ComputeIndexToPhysicalPointMatrices(); + } + + /** Merges adjacent segments with duplicate values in a single line. */ + void + CleanUpLine(RLLine & line) const; + +private: + bool m_OnTheFlyCleanup; // should same-valued segments be merged on the fly + + RLEImage(const Self &); // purposely not implemented + void + operator=(const Self &); // purposely not implemented + + /** Memory for the current buffer. */ + mutable typename BufferType::Pointer myBuffer; +}; + + +#ifndef ITK_MANUAL_INSTANTIATION +# include "RLEImage.txx" +#endif + +#endif // RLEImage_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx new file mode 100644 index 00000000000..80e1b7f9509 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx @@ -0,0 +1,260 @@ +#ifndef RLEImage_txx +#define RLEImage_txx + +#include "RLEImage.h" +#include "itkImageRegionConstIterator.h" + +template +inline typename RLEImage::BufferType::IndexType +RLEImage::truncateIndex(const IndexType & index) +{ + typename BufferType::IndexType result; + for (IndexValueType i = 0; i < VImageDimension - 1; i++) + result[i] = index[i + 1]; + return result; +} + +template +inline typename RLEImage::BufferType::SizeType +RLEImage::truncateSize(const SizeType & size) +{ + typename BufferType::SizeType result; + for (IndexValueType i = 0; i < VImageDimension - 1; i++) + result[i] = size[i + 1]; + return result; +} + +template +typename RLEImage::BufferType::RegionType +RLEImage::truncateRegion(const RegionType & region) +{ + typename BufferType::RegionType result; + result.SetIndex(truncateIndex(region.GetIndex())); + result.SetSize(truncateSize(region.GetSize())); + return result; +} + +template +void +RLEImage::Allocate(bool initialize) +{ + itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), + "BufferedRegion must contain complete run-length lines!"); + itkAssertOrThrowMacro(this->GetLargestPossibleRegion().GetSize(0) <= std::numeric_limits::max(), + "CounterType is not large enough to support image's X dimension!"); + this->ComputeOffsetTable(); + // SizeValueType num = static_cast(this->GetOffsetTable()[VImageDimension]); + myBuffer->Allocate(false); + // if (initialize) //there is assumption that the image is fully formed after a call to allocate + { + RLSegment segment(CounterType(this->GetBufferedRegion().GetSize(0)), TPixel()); + RLLine line(1); + line[0] = segment; + myBuffer->FillBuffer(line); + } +} + +template +void +RLEImage::FillBuffer(const TPixel & value) +{ + RLSegment segment(CounterType(this->GetBufferedRegion().GetSize(0)), value); + RLLine line(1); + line[0] = segment; + myBuffer->FillBuffer(line); +} + +template +void +RLEImage::CleanUpLine(RLLine & line) const +{ + CounterType x = 0; + RLLine out; + out.reserve(this->GetLargestPossibleRegion().GetSize(0)); + do + { + out.push_back(line[x]); + while (++x < line.size() && line[x].second == line[x - 1].second) + out.back().first += line[x].first; + } while (x < line.size()); + out.swap(line); +} + +template +void +RLEImage::CleanUp() const +{ + assert(!myBuffer.empty()); + if (this->GetLargestPossibleRegion().GetSize(0) == 0) + return; +#pragma omp parallel for + for (CounterType z = 0; z < myBuffer.size(); z++) + for (CounterType y = 0; y < myBuffer[0].size(); y++) + CleanUpLine(myBuffer[z][y]); +} + +template +int +RLEImage::SetPixel(RLLine & line, + IndexValueType & segmentRemainder, + IndexValueType & realIndex, + const TPixel & value) +{ + // complete Run-Length Lines have to be buffered + itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), + "BufferedRegion must contain complete run-length lines!"); + if (line[realIndex].second == value) // already correct value + return 0; + else if (line[realIndex].first == 1) // single pixel segment + { + line[realIndex].second = value; + if (m_OnTheFlyCleanup) // now see if we can merge it into adjacent segments + { + if (realIndex > 0 && realIndex < line.size() - 1 && line[realIndex + 1].second == value && + line[realIndex - 1].second == value) + { + // merge these 3 segments + line[realIndex - 1].first += 1 + line[realIndex + 1].first; + segmentRemainder += line[realIndex + 1].first; + line.erase(line.begin() + realIndex, line.begin() + realIndex + 2); + realIndex--; + return -2; + } + if (realIndex > 0 && line[realIndex - 1].second == value) + { + // merge into previous + line[realIndex - 1].first++; + line.erase(line.begin() + realIndex); + realIndex--; + assert(segmentRemainder == 1); + return -1; + } + else if (realIndex < line.size() - 1 && line[realIndex + 1].second == value) + { + // merge into next + segmentRemainder = ++(line[realIndex + 1].first); + line.erase(line.begin() + realIndex); + return -1; + } + } + return 0; + } + else if (segmentRemainder == 1 && realIndex < line.size() - 1 && line[realIndex + 1].second == value) + { + // shift this pixel to next segment + line[realIndex].first--; + segmentRemainder = ++(line[realIndex + 1].first); + realIndex++; + return 0; + } + else if (realIndex > 0 && segmentRemainder == line[realIndex].first && line[realIndex - 1].second == value) + { + // shift this pixel to previous segment + line[realIndex].first--; + line[realIndex - 1].first++; + realIndex--; + segmentRemainder = 1; + return 0; + } + else if (segmentRemainder == 1) // insert after + { + line[realIndex].first--; + line.insert(line.begin() + realIndex + 1, RLSegment(1, value)); + realIndex++; + return +1; + } + else if (segmentRemainder == line[realIndex].first) // insert before + { + line[realIndex].first--; + line.insert(line.begin() + realIndex, RLSegment(1, value)); + segmentRemainder = 1; + return +1; + } + else // general case: split a segment into 3 segments + { + // first take care of values + line.insert(line.begin() + realIndex + 1, 2, RLSegment(1, value)); + line[realIndex + 2].second = line[realIndex].second; + + // now take care of counts + line[realIndex].first -= segmentRemainder; + line[realIndex + 2].first = segmentRemainder - 1; + realIndex++; + segmentRemainder = 1; + return +2; + } +} + +template +void +RLEImage::SetPixel(const IndexType & index, const TPixel & value) +{ + // complete Run-Length Lines have to be buffered + itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), + "BufferedRegion must contain complete run-length lines!"); + IndexValueType bri0 = this->GetBufferedRegion().GetIndex(0); + typename BufferType::IndexType bi = truncateIndex(index); + RLLine & line = myBuffer->GetPixel(bi); + IndexValueType t = 0; + for (IndexValueType x = 0; x < line.size(); x++) + { + t += line[x].first; + if (t > index[0] - bri0) + { + t -= index[0] - bri0; // we need to supply a reference + SetPixel(line, t, x, value); + return; + } + } + throw itk::ExceptionObject(__FILE__, __LINE__, "Reached past the end of Run-Length line!", __FUNCTION__); +} + +template +const TPixel & +RLEImage::GetPixel(const IndexType & index) const +{ + // complete Run-Length Lines have to be buffered + itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), + "BufferedRegion must contain complete run-length lines!"); + IndexValueType bri0 = this->GetBufferedRegion().GetIndex(0); + typename BufferType::IndexType bi = truncateIndex(index); + RLLine & line = myBuffer->GetPixel(bi); + IndexValueType t = 0; + for (IndexValueType x = 0; x < line.size(); x++) + { + t += line[x].first; + if (t > index[0] - bri0) + return line[x].second; + } + throw itk::ExceptionObject(__FILE__, __LINE__, "Reached past the end of Run-Length line!", __FUNCTION__); +} + +template +void +RLEImage::PrintSelf(std::ostream & os, itk::Indent indent) const +{ + Superclass::PrintSelf(os, indent); + os << indent << "Internal image (for storage of RLLine-s): " << std::endl; + myBuffer->Print(os, indent.GetNextIndent()); + + itk::SizeValueType c = 0; + itk::ImageRegionConstIterator it(myBuffer, myBuffer->GetBufferedRegion()); + while (!it.IsAtEnd()) + { + c += it.Get().capacity(); + ++it; + } + + double cr = + double(c * (sizeof(PixelType) + sizeof(CounterType)) + + sizeof(std::vector) * this->GetOffsetTable()[VImageDimension] / this->GetOffsetTable()[1]) / + (this->GetOffsetTable()[VImageDimension] * sizeof(PixelType)); + + os << indent << "OnTheFlyCleanup: " << (m_OnTheFlyCleanup ? "On" : "Off") << std::endl; + os << indent << "RLEImage compressed pixel count: " << c << std::endl; + int prec = os.precision(3); + os << indent << "Compressed size in relation to original size: " << cr * 100 << "%" << std::endl; + os.precision(prec); +} + +#endif // RLEImage_txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h new file mode 100644 index 00000000000..49ad4d261a1 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h @@ -0,0 +1,440 @@ +#ifndef RLEImageConstIterator_h +#define RLEImageConstIterator_h + +#include "itkImage.h" +#include "itkIndex.h" +#include "itkNumericTraits.h" +#include "RLEImage.h" +#include "itkImageConstIterator.h" +#include "itkImageConstIteratorWithIndex.h" +#include "itkImageConstIteratorWithOnlyIndex.h" +#include "itkImageRegionIterator.h" + +class MultiLabelMeshPipeline; + +namespace itk +{ +/** \class ImageConstIterator + * \brief A multi-dimensional image iterator templated over image type. + */ + +template +class ImageConstIterator> +{ + friend class ::MultiLabelMeshPipeline; + +public: + /** Standard class typedefs. */ + typedef ImageConstIterator Self; + + /** Dimension of the image the iterator walks. This constant is needed so + * functions that are templated over image iterator type (as opposed to + * being templated over pixel type and dimension) can have compile time + * access to the dimension of the image that the iterator walks. */ + itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); + + /** Run-time type information (and related methods). */ + itkTypeMacroNoParent(ImageConstIterator); + + /** Image typedef support. */ + typedef RLEImage ImageType; + + /** Run-Length Line (we iterate along it). */ + typedef typename ImageType::RLLine RLLine; + + /** Buffer Type used. */ + typedef typename ImageType::BufferType BufferType; + + /** Type for the internal buffer iterator. */ + typedef ImageRegionIterator BufferIterator; + + /** Index typedef support. */ + typedef typename ImageType::IndexType IndexType; + + /** Index typedef support. */ + typedef typename ImageType::IndexValueType IndexValueType; + + /** Size typedef support. */ + typedef typename ImageType::SizeType SizeType; + + /** Offset typedef support. */ + typedef typename ImageType::OffsetType OffsetType; + + /** Region typedef support. */ + typedef typename ImageType::RegionType RegionType; + + /** Internal Pixel Type */ + typedef typename ImageType::InternalPixelType InternalPixelType; + + /** External Pixel Type */ + typedef typename ImageType::PixelType PixelType; + + /** Default Constructor. Need to provide a default constructor since we + * provide a copy constructor. */ + ImageConstIterator() + : myBuffer(0) + , rlLine(0) + { + m_Image = ITK_NULLPTR; + m_Index0 = 0; + m_BeginIndex0 = 0; + m_EndIndex0 = 0; + realIndex = 0; + segmentRemainder = 0; + } + + /** Default Destructor. */ + virtual ~ImageConstIterator() {} + + /** Copy Constructor. The copy constructor is provided to make sure the + * handle to the image is properly reference counted. */ + ImageConstIterator(const Self & it) + : myBuffer(const_cast(it.GetImage())->GetBuffer()) + { + rlLine = it.rlLine; + m_Image = it.m_Image; // copy the smart pointer + m_Index0 = it.m_Index0; + this->bi = it.bi; + + realIndex = it.realIndex; + segmentRemainder = it.segmentRemainder; + m_BeginIndex0 = it.m_BeginIndex0; + m_EndIndex0 = it.m_EndIndex0; + } + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageConstIterator(const ImageType * ptr, const RegionType & region) + : myBuffer(const_cast(ptr)->GetBuffer()) + { + m_Image = ptr; + SetRegion(region); + } + + /** operator= is provided to make sure the handle to the image is properly + * reference counted. */ + Self & + operator=(const Self & it) + { + if (this != &it) + { + myBuffer = it.myBuffer; + rlLine = it.rlLine; + m_Image = it.m_Image; // copy the smart pointer + m_Index0 = it.m_Index0; + bi = it.bi; + + realIndex = it.realIndex; + segmentRemainder = it.segmentRemainder; + m_BeginIndex0 = it.m_BeginIndex0; + m_EndIndex0 = it.m_EndIndex0; + } + return *this; + } + + /** Set the region of the image to iterate over. */ + virtual void + SetRegion(const RegionType & region) + { + // m_Region = region; + + if (region.GetNumberOfPixels() > 0) // If region is non-empty + { + const RegionType & bufferedRegion = m_Image->GetBufferedRegion(); + itkAssertOrThrowMacro((bufferedRegion.IsInside(region)), + "Region " << region << " is outside of buffered region " << bufferedRegion); + } + + bi = BufferIterator(myBuffer, ImageType::truncateRegion(region)); + m_Index0 = region.GetIndex(0); + m_BeginIndex0 = m_Index0 - m_Image->GetBufferedRegion().GetIndex(0); + m_EndIndex0 = m_BeginIndex0 + region.GetSize(0); + SetIndexInternal(m_BeginIndex0); // sets realIndex and segmentRemainder + } + + /** Get the dimension (size) of the index. */ + static unsigned int + GetImageIteratorDimension() + { + return VImageDimension; + } + + /** Comparison operator. Two iterators are the same if they "point to" the + * same memory location */ + bool + operator!=(const Self & it) const + { + return bi != it.bi || m_Index0 + m_BeginIndex0 != it.m_Index0 + it.m_BeginIndex0; + } + + /** Comparison operator. Two iterators are the same if they "point to" the + * same memory location */ + bool + operator==(const Self & it) const + { + return bi == it.bi && m_Index0 + m_BeginIndex0 == it.m_Index0 + it.m_BeginIndex0; + } + + /** Comparison operator. An iterator is "less than" another if it "points to" + * a lower memory location. */ + bool + operator<=(const Self & it) const + { + if (bi < it.bi) + return true; + else if (bi > it.bi) + return false; + return m_Index0 + m_BeginIndex0 <= it.m_Index0 + it.m_BeginIndex0; + } + + /** Comparison operator. An iterator is "less than" another if it "points to" + * a lower memory location. */ + bool + operator<(const Self & it) const + { + if (bi < it.bi) + return true; + else if (bi > it.bi) + return false; + return m_Index0 + m_BeginIndex0 < it.m_Index0 + it.m_BeginIndex0; + } + + /** Comparison operator. An iterator is "greater than" another if it + * "points to" a higher location. */ + bool + operator>=(const Self & it) const + { + if (bi > it.bi) + return true; + else if (bi < it.bi) + return false; + return m_Index0 + m_BeginIndex0 >= it.m_Index0 + it.m_BeginIndex0; + } + + /** Comparison operator. An iterator is "greater than" another if it + * "points to" a higher location. */ + bool + operator>(const Self & it) const + { + if (bi > it.bi) + return true; + else if (bi < it.bi) + return false; + return m_Index0 + m_BeginIndex0 > it.m_Index0 + it.m_BeginIndex0; + } + + /** Get the index. This provides a read only copy of the index. */ + const IndexType + GetIndex() const + { + IndexType indR(m_Image->GetBufferedRegion().GetIndex()); + indR[0] += m_Index0; + typename BufferType::IndexType bufInd = bi.GetIndex(); + for (IndexValueType i = 1; i < VImageDimension; i++) + indR[i] = bufInd[i - 1]; + return indR; + } + + /** Sets the image index. No bounds checking is performed. */ + virtual void + SetIndex(const IndexType & ind) + { + typename BufferType::IndexType bufInd; + for (IndexValueType i = 1; i < VImageDimension; i++) + bufInd[i - 1] = ind[i]; + bi.SetIndex(bufInd); + SetIndexInternal(ind[0] - m_Image->GetBufferedRegion().GetIndex(0)); + } + + /** Get the region that this iterator walks. ImageConstIterators know the + * beginning and the end of the region of the image to iterate over. */ + const RegionType + GetRegion() const + { + RegionType r; + r.SetIndex(0, m_BeginIndex0 + m_Image->GetBufferedRegion().GetIndex(0)); + r.SetSize(0, m_EndIndex0 - m_BeginIndex0); + typename BufferType::RegionType ir = bi.GetRegion(); + for (IndexValueType i = 1; i < VImageDimension; i++) + { + r.SetIndex(i, ir.GetIndex(i - 1)); + r.SetSize(i, ir.GetSize(i - 1)); + } + return r; + } + + /** Get the image that this iterator walks. */ + const ImageType * + GetImage() const + { + return m_Image.GetPointer(); + } + + /** Get the pixel value */ + PixelType + Get(void) const + { + return Value(); + } + + /** Return a const reference to the pixel + * This method will provide the fastest access to pixel + * data, but it will NOT support ImageAdaptors. */ + const PixelType & + Value(void) const + { + RLLine & line = const_cast(this)->bi.Value(); + return line[realIndex].second; + } + + /** Move an iterator to the beginning of the region. "Begin" is + * defined as the first pixel in the region. */ + void + GoToBegin() + { + bi.GoToBegin(); + SetIndexInternal(m_BeginIndex0); + } + + /** Move an iterator to the end of the region. "End" is defined as + * one pixel past the last pixel of the region. */ + void + GoToEnd() + { + bi.GoToEnd(); + m_Index0 = m_BeginIndex0; + } + + /** Is the iterator at the beginning of the region? "Begin" is defined + * as the first pixel in the region. */ + bool + IsAtBegin(void) const + { + return m_Index0 == m_BeginIndex0 && bi.IsAtBegin(); + } + + /** Is the iterator at the end of the region? "End" is defined as one + * pixel past the last pixel of the region. */ + bool + IsAtEnd(void) const + { + return m_Index0 == m_BeginIndex0 && bi.IsAtEnd(); + } + +protected: // made protected so other iterators can access + /** Set the internal index, realIndex and segmentRemainder. */ + virtual void + SetIndexInternal(const IndexValueType ind0) + { + m_Index0 = ind0; + rlLine = &bi.Value(); + + CounterType t = 0; + SizeValueType x = 0; + + for (; x < (*rlLine).size(); x++) + { + t += (*rlLine)[x].first; + if (t > m_Index0) + break; + } + realIndex = x; + segmentRemainder = t - m_Index0; + } + + typename ImageType::ConstWeakPointer m_Image; + + IndexValueType m_Index0; // index into the RLLine + + const RLLine * rlLine; + + mutable IndexValueType realIndex; // index into line's segment + mutable IndexValueType segmentRemainder; // how many pixels remain in current segment + + IndexValueType m_BeginIndex0; // index to first pixel in region in relation to buffer start + IndexValueType m_EndIndex0; // index to one pixel past last pixel in region in relation to buffer start + + BufferIterator bi; // iterator over internal buffer image + typename BufferType::Pointer myBuffer; +}; + +template +class ImageConstIteratorWithIndex> + : public ImageConstIterator> +{ + // just inherit constructors +public: + /** Image typedef support. */ + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + void + GoToReverseBegin() + { + this->bi.GoToReverseBegin(); + this->m_Index0 = this->m_EndIndex0 - 1; + SetIndexInternal(this->m_Index0); + } + + bool + IsAtReverseEnd() + { + return this->bi.IsAtReverseEnd(); + } + + /** Default Constructor. Need to provide a default constructor since we + * provide a copy constructor. */ + ImageConstIteratorWithIndex() + : ImageConstIterator() + {} + + /** Copy Constructor. The copy constructor is provided to make sure the + * handle to the image is properly reference counted. */ + ImageConstIteratorWithIndex(const ImageConstIteratorWithIndex & it) + { + this->ImageConstIterator::operator=(it); + } + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageConstIteratorWithIndex(const ImageType * ptr, const RegionType & region) + : ImageConstIterator(ptr, region) + {} +}; // no additional implementation required + +template +class ImageConstIteratorWithOnlyIndex> + : public ImageConstIteratorWithIndex> +{ + // just inherit constructors +public: + /** Image typedef support. */ + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + /** Default Constructor. Need to provide a default constructor since we + * provide a copy constructor. */ + ImageConstIteratorWithOnlyIndex() + : ImageConstIterator() + {} + + + /** Copy Constructor. The copy constructor is provided to make sure the + * handle to the image is properly reference counted. */ + ImageConstIteratorWithOnlyIndex(const ImageConstIteratorWithOnlyIndex & it) + { + this->ImageConstIterator::operator=(it); + } + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageConstIteratorWithOnlyIndex(const ImageType * ptr, const RegionType & region) + : ImageConstIterator(ptr, region) + {} +}; // no additional implementation required + +} // end namespace itk + +#endif // RLEImageConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h new file mode 100644 index 00000000000..d7d60026237 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h @@ -0,0 +1,161 @@ +#ifndef RLEImageIterator_h +#define RLEImageIterator_h + +#include "RLEImageConstIterator.h" +#include "itkImageIteratorWithIndex.h" + +namespace itk +{ +/** + * \class ImageIterator + * \brief A multi-dimensional iterator templated over image type. + * + * This is a base class of ImageConstIterator that adds write-access + * functionality. Please see ImageConstIterator for more information. + * + */ + +template +class ImageIterator> + : public ImageConstIterator> +{ +public: + /** Standard class typedefs. */ + typedef ImageIterator Self; + + /** Dimension of the image the iterator walks. This constant is needed so + * functions that are templated over image iterator type (as opposed to + * being templated over pixel type and dimension) can have compile time + * access to the dimension of the image that the iterator walks. */ + itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); + + /** Define the superclass */ + typedef ImageConstIterator> Superclass; + + /** Inherit types from the superclass */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::RegionType RegionType; + typedef typename Superclass::ImageType ImageType; + typedef typename Superclass::InternalPixelType InternalPixelType; + typedef typename Superclass::PixelType PixelType; + + /** Default Constructor. Need to provide a default constructor since we + * provide a copy constructor. */ + ImageIterator() {} + + /** Default Destructor */ + ~ImageIterator() {} + + /** Copy Constructor. The copy constructor is provided to make sure the + * handle to the image is properly reference counted. */ + ImageIterator(const Self & it) + : ImageConstIterator(it) + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageIterator(ImageType * ptr, const RegionType & region) + : ImageConstIterator(ptr, region) + {} + + /** operator= is provided to make sure the handle to the image is properly + * reference counted. */ + Self & + operator=(const Self & it) + { + this->ImageConstIterator::operator=(it); + return *this; + } + + /** Set the pixel value. + * Changing the RLE structure invalidates all other iterators (except this one). */ + void + Set(const PixelType & value) const + { + const_cast(this->m_Image.GetPointer()) + ->SetPixel( + *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); + } + + ///** Return a reference to the pixel + // * Setting this value would change value of the whole run-length segment. + // * If we wanted to safely enable it, + // * we would isolate this pixel into its own segment. */ + // PixelType & Value(void) + //{ + // return myBuffer[m_Index[2]][m_Index[1]][realIndex].second; + //} + + /** Get the image that this iterator walks. */ + ImageType * + GetImage() const + { + // const_cast is needed here because m_Image is declared as a const pointer + // in the base class which is the ConstIterator. + return const_cast(this->m_Image.GetPointer()); + } + +protected: + /** This constructor is declared protected in order to enforce + const-correctness */ + ImageIterator(const ImageConstIterator & it) + : ImageConstIterator(it) + {} + Self & + operator=(const ImageConstIterator & it) + { + this->ImageConstIterator::operator=(it); + return *this; + } +}; + +template +class ImageIteratorWithIndex> + : public ImageConstIteratorWithIndex> +{ +public: + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + /** Default Constructor. Need to provide a default constructor since we + * provide a copy constructor. */ + ImageIteratorWithIndex() + : ImageConstIteratorWithIndex() + {} + + + /** Copy Constructor. The copy constructor is provided to make sure the + * handle to the image is properly reference counted. */ + ImageIteratorWithIndex(const ImageIteratorWithIndex & it) { this->ImageIterator::operator=(it); } + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageIteratorWithIndex(const ImageType * ptr, const RegionType & region) + : ImageConstIteratorWithIndex(ptr, region) + {} + + /** Set the pixel value. + * Changing the RLE structure invalidates all other iterators (except this one). */ + void + Set(const TPixel & value) const + { + const_cast(this->m_Image.GetPointer()) + ->SetPixel( + *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); + } + + /** Get the image that this iterator walks. */ + ImageType * + GetImage() const + { + // const_cast is needed here because m_Image is declared as a const pointer + // in the base class which is the ConstIterator. + return const_cast(this->m_Image.GetPointer()); + } +}; // no additional implementation required +} // end namespace itk + +#endif // RLEImageIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h new file mode 100644 index 00000000000..88951b7f386 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h @@ -0,0 +1,232 @@ +#ifndef RLEImageRegionConstIterator_h +#define RLEImageRegionConstIterator_h + +#include "RLEImageConstIterator.h" +#include "itkImageRegionConstIterator.h" +#include "itkImageRegionConstIteratorWithIndex.h" +#include "itkImageRegionConstIteratorWithOnlyIndex.h" + +class MultiLabelMeshPipeline; + +namespace itk +{ +/** \class ImageRegionConstIterator + * \brief A multi-dimensional iterator templated over image type that walks a + * region of pixels. + * + * ImageRegionConstIterator provides read-only access to image data. It is the + * base class for the read/write access ImageRegionIterator. + * + */ +template +class ImageRegionConstIterator> + : public ImageConstIterator> +{ + friend class ::MultiLabelMeshPipeline; + +public: + /** Standard class typedef. */ + typedef ImageRegionConstIterator> Self; + typedef ImageConstIterator> Superclass; + + /** Dimension of the image that the iterator walks. This constant is needed so + * functions that are templated over image iterator type (as opposed to + * being templated over pixel type and dimension) can have compile time + * access to the dimension of the image that the iterator walks. */ + itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); + + /** + * Index typedef support. While these were already typdef'ed in the superclass, + * they need to be redone here for this subclass to compile properly with gcc. + */ + /** Types inherited from the Superclass */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::RegionType RegionType; + typedef typename Superclass::ImageType ImageType; + typedef typename Superclass::InternalPixelType InternalPixelType; + typedef typename Superclass::PixelType PixelType; + + /** Run-time type information (and related methods). */ + itkTypeMacro(ImageRegionConstIterator, ImageConstIterator); + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageRegionConstIterator() + : ImageConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageRegionConstIterator(const ImageType * ptr, const RegionType & region) + : ImageConstIterator(ptr, region) + {} + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageRegionConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionConstIterator. */ + ImageRegionConstIterator(const ImageIterator & it) + { + this->ImageConstIterator::operator=(it); + // this->ImageConstIterator< ImageType >::operator=(static_cast >(it)); + } + + /** Constructor that can be used to cast from an ImageConstIterator to an + * ImageRegionConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionConstIterator. */ + ImageRegionConstIterator(const ImageConstIterator & it) + { + this->ImageConstIterator::operator=(it); + } + + /** Increment (prefix) the fastest moving dimension of the iterator's index. + * This operator will constrain the iterator within the region (i.e. the + * iterator will automatically wrap from the end of the row of the region + * to the beginning of the next row of the region) up until the iterator + * tries to moves past the last pixel of the region. Here, the iterator + * will be set to be one pixel past the end of the region. + * \sa operator++(int) */ + Self & + operator++() + { + this->m_Index0++; + + if (this->m_Index0 >= this->m_EndIndex0) + { + ++(this->bi); + if (!this->bi.IsAtEnd()) + this->SetIndexInternal(this->m_BeginIndex0); + else + this->m_Index0 = this->m_BeginIndex0; + return *this; + } + + this->segmentRemainder--; + if (this->segmentRemainder > 0) + return *this; + + this->realIndex++; + this->segmentRemainder = (*this->rlLine)[this->realIndex].first; + return *this; + } + + /** Decrement (prefix) the fastest moving dimension of the iterator's index. + * This operator will constrain the iterator within the region (i.e. the + * iterator will automatically wrap from the beginning of the row of the region + * to the end of the next row of the region) up until the iterator + * tries to moves past the first pixel of the region. Here, the iterator + * will be set to be one pixel past the beginning of the region. + * \sa operator--(int) */ + Self & + operator--() + { + this->m_Index0--; + + if (this->m_Index0 < this->m_BeginIndex0) + { + --(this->bi); + this->SetIndexInternal(this->m_EndIndex0 - 1); + return *this; + } + + this->segmentRemainder++; + if (this->segmentRemainder <= (*this->rlLine)[this->realIndex].first) + return *this; + + this->realIndex--; + this->segmentRemainder = 1; + return *this; + } +}; + +template +class ImageRegionConstIteratorWithIndex> + : public ImageRegionConstIterator> +{ +public: + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageRegionConstIteratorWithIndex() + : ImageRegionConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageRegionConstIteratorWithIndex(const ImageType * ptr, const RegionType & region) + : ImageRegionConstIterator(ptr, region) + {} + + void + GoToReverseBegin() + { + this->bi.GoToEnd(); // after last pixel + --(this->bi); // go to last valid pixel + this->m_Index0 = this->m_EndIndex0 - 1; + this->SetIndexInternal(this->m_Index0); // valid index required + } + + bool + IsAtReverseEnd() + { + return (this->m_Index0 == this->m_BeginIndex0) && this->bi.IsAtBegin(); + } + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageRegionConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionConstIterator. */ + ImageRegionConstIteratorWithIndex(const ImageIterator & it) + { + this->ImageRegionConstIterator::operator=(it); + } + +}; // no additional implementation required + +template +class ImageRegionConstIteratorWithOnlyIndex> + : public ImageRegionConstIteratorWithIndex> +{ + // just inherit constructors +public: + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageRegionConstIteratorWithOnlyIndex() + : ImageRegionConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageRegionConstIteratorWithOnlyIndex(const ImageType * ptr, const RegionType & region) + : ImageRegionConstIteratorWithIndex(ptr, region) + {} + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageRegionConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionConstIterator. */ + ImageRegionConstIteratorWithOnlyIndex(const ImageIterator & it) + { + this->ImageRegionConstIterator::operator=(it); + } + +}; // no additional implementation required + +} // end namespace itk + +#endif // RLEImageRegionConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h new file mode 100644 index 00000000000..4280e5df047 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h @@ -0,0 +1,144 @@ +#ifndef RLEImageRegionIterator_h +#define RLEImageRegionIterator_h + +#include "RLEImageRegionConstIterator.h" +#include "itkImageRegionIterator.h" +#include "itkImageRegionIteratorWithIndex.h" +#include "RLEImageIterator.h" + +namespace itk +{ +/** \class ImageRegionIterator + * \brief A multi-dimensional iterator templated over image type that walks a + * region of pixels. + * + * The itk::ImageRegionIterator is optimized for iteration speed and is the + * first choice for iterative, pixel-wise operations on an image. + * ImageRegionIterator is the least specialized of the ITK image iterator + * classes. ImageRegionIterator is templated over the image type, and is + * constrained to walk only within the specified region and along a line + * parallel to one of the coordinate axes, "wrapping" to the next line as it + * reaches the boundary of the image. To walk the entire image, specify the + * region to be \c image->GetRequestedRegion(). + * + * Most of the functionality is inherited from the ImageRegionConstIterator. + * The current class only adds write access to image pixels. + */ + +template +class ImageRegionIterator> + : public ImageRegionConstIterator> +{ +public: + /** Standard class typedefs. */ + typedef ImageRegionIterator Self; + typedef ImageRegionConstIterator> Superclass; + + /** Types inherited from the Superclass */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::RegionType RegionType; + typedef typename Superclass::ImageType ImageType; + typedef typename Superclass::InternalPixelType InternalPixelType; + typedef typename Superclass::PixelType PixelType; + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageRegionIterator() + : ImageRegionConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageRegionIterator(ImageType * ptr, const RegionType & region) + : ImageRegionConstIterator(ptr, region) + {} + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageRegionIterator. Many routines return an ImageIterator but for a + * particular task, you may want an ImageRegionIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionIterator. */ + ImageRegionIterator(const ImageIterator & it) { this->ImageConstIterator::operator=(it); } + + /** Set the pixel value. + * Changing the RLE structure invalidates all other iterators (except this one). */ + void + Set(const PixelType & value) const + { + const_cast(this->m_Image.GetPointer()) + ->SetPixel( + *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); + } + +protected: + /** the construction from a const iterator is declared protected + in order to enforce const correctness. */ + ImageRegionIterator(const ImageRegionConstIterator & it) + { + this->ImageConstIterator::operator=(it); + } + Self & + operator=(const ImageRegionConstIterator & it) + { + this->ImageConstIterator::operator=(it); + } +}; + +template +class ImageRegionIteratorWithIndex> + : public ImageRegionConstIteratorWithIndex> +{ +public: + typedef RLEImage ImageType; + + typedef typename itk::ImageConstIterator>::RegionType RegionType; + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageRegionIteratorWithIndex() + : ImageRegionConstIteratorWithIndex() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageRegionIteratorWithIndex(ImageType * ptr, const RegionType & region) + : ImageRegionConstIteratorWithIndex(ptr, region) + {} + + /** Set the pixel value. + * Changing the RLE structure invalidates all other iterators (except this one). */ + void + Set(const TPixel & value) const + { + const_cast(this->m_Image.GetPointer()) + ->SetPixel( + *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); + } + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageRegionIteratorWithIndex. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionConstIterator. */ + ImageRegionIteratorWithIndex(const ImageIterator & it) + { + this->ImageRegionConstIteratorWithIndex::operator=(it); + } + + /** Constructor that can be used to cast from an ImageConstIterator to an + * ImageRegionIteratorWithIndex. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageRegionConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageRegionIteratorWithIndex. */ + ImageRegionIteratorWithIndex(const ImageConstIterator & it) + { + this->ImageRegionConstIterator::operator=(it); + } + +}; // no additional implementation required +} // end namespace itk + +#endif // RLEImageRegionIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h new file mode 100644 index 00000000000..7bd59ec774f --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h @@ -0,0 +1,155 @@ +#ifndef RLEImageScanlineConstIterator_h +#define RLEImageScanlineConstIterator_h + +#include "RLEImageRegionConstIterator.h" +#include "itkImageScanlineIterator.h" + +namespace itk +{ +/** \class ImageScanlineConstIterator + * \brief A multi-dimensional iterator templated over image type that walks a + * region of pixels, scanline by scanline or in the direction of the + * fastest axis. + */ +template +class ImageScanlineConstIterator> + : public ImageRegionConstIterator> +{ +public: + /** Standard class typedef. */ + typedef ImageScanlineConstIterator Self; + typedef ImageRegionConstIterator> Superclass; + + /** Dimension of the image that the iterator walks. This constant is needed so + * functions that are templated over image iterator type (as opposed to + * being templated over pixel type and dimension) can have compile time + * access to the dimension of the image that the iterator walks. */ + itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); + + /** + * Index typedef support. While these were already typdef'ed in the superclass, + * they need to be redone here for this subclass to compile properly with gcc. + */ + /** Types inherited from the Superclass */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::RegionType RegionType; + typedef typename Superclass::ImageType ImageType; + typedef typename Superclass::InternalPixelType InternalPixelType; + typedef typename Superclass::PixelType PixelType; + + /** Run-time type information (and related methods). */ + itkTypeMacro(ImageScanlineConstIterator, ImageRegionConstIterator); + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageScanlineConstIterator() + : ImageRegionConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageScanlineConstIterator(const ImageType * ptr, const RegionType & region) + : ImageRegionConstIterator(ptr, region) + {} + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageScanlineConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageScanlineConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageScanlineConstIterator. */ + ImageScanlineConstIterator(const ImageIterator & it) + : ImageRegionConstIterator(it) + {} + + /** Constructor that can be used to cast from an ImageConstIterator to an + * ImageScanlineConstIterator. Many routines return an ImageIterator, but for a + * particular task, you may want an ImageScanlineConstIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageScanlineConstIterator. */ + ImageScanlineConstIterator(const ImageConstIterator & it) + { + this->ImageRegionConstIterator::operator=(it); + } + + + /** Go to the beginning pixel of the current line. */ + void + GoToBeginOfLine(void) + { + this->m_Index0 = this->m_BeginIndex0; + this->realIndex = 0; + this->segmentRemainder = (*this->rlLine)[this->realIndex].first; + } + + /** Go to the past end pixel of the current line. */ + void + GoToEndOfLine(void) + { + this->m_Index0 = this->m_EndIndex0; + this->realIndex = this->rlLine->size() - 1; + this->segmentRemainder = 0; + } + + /** Test if the index is at the end of line. */ + inline bool + IsAtEndOfLine(void) + { + return this->m_Index0 == this->m_EndIndex0; + } + + /** Go to the next line. */ + inline void + NextLine(void) + { + ++(this->bi); + if (!this->bi.IsAtEnd()) + this->SetIndexInternal(this->m_BeginIndex0); + else + this->m_Index0 = this->m_BeginIndex0; // make this iterator at end too + } + + /** Increment (prefix) along the scanline. + * + * If the iterator is at the end of the scanline ( one past the last + * valid element in the row ), then the results are undefined. Which + * means is may assert in debug mode or result in an undefined + * iterator which may have unknown consequences if used. + */ + Self & + operator++() + { + itkAssertInDebugAndIgnoreInReleaseMacro(!this->IsAtEndOfLine()); + this->m_Index0++; + this->segmentRemainder--; + if (this->segmentRemainder > 0) + return *this; + + if (this->IsAtEndOfLine()) + return *this; + this->realIndex++; + this->segmentRemainder = (*this->rlLine)[this->realIndex].first; + return *this; + } + + /** Decrement (prefix) along the scanline. + * + */ + Self & + operator--() + { + this->m_Index0--; + this->segmentRemainder++; + if (this->segmentRemainder <= (*this->rlLine)[this->realIndex].first) + return *this; + + this->realIndex--; + this->segmentRemainder = 1; + return *this; + } +}; +} // end namespace itk + +#endif // RLEImageScanlineConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h new file mode 100644 index 00000000000..d0fabe33d38 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h @@ -0,0 +1,86 @@ +#ifndef RLEImageScanlineIterator_h +#define RLEImageScanlineIterator_h + +#include "RLEImageScanlineConstIterator.h" +#include "RLEImageIterator.h" +#include "itkImageScanlineIterator.h" + +namespace itk +{ +/** \class ImageScanlineIterator + * \brief A multi-dimensional iterator templated over image type that walks a + * region of pixels, scanline by scanline or in the direction of the + * fastest axis. + */ +template +class ImageScanlineIterator> + : public ImageScanlineConstIterator> +{ +public: + /** Standard class typedefs. */ + typedef ImageScanlineIterator Self; + typedef ImageScanlineConstIterator> Superclass; + + /** Types inherited from the Superclass */ + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::SizeType SizeType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::RegionType RegionType; + typedef typename Superclass::ImageType ImageType; + typedef typename Superclass::InternalPixelType InternalPixelType; + typedef typename Superclass::PixelType PixelType; + + /** Default constructor. Needed since we provide a cast constructor. */ + ImageScanlineIterator() + : ImageScanlineConstIterator() + {} + + /** Constructor establishes an iterator to walk a particular image and a + * particular region of that image. */ + ImageScanlineIterator(ImageType * ptr, const RegionType & region) + : ImageScanlineConstIterator(ptr, region) + {} + + /** Constructor that can be used to cast from an ImageIterator to an + * ImageScanlineIterator. Many routines return an ImageIterator but for a + * particular task, you may want an ImageScanlineIterator. Rather than + * provide overloaded APIs that return different types of Iterators, itk + * returns ImageIterators and uses constructors to cast from an + * ImageIterator to a ImageScanlineIterator. */ + ImageScanlineIterator(const ImageIterator & it) + : ImageScanlineConstIterator(it) + {} + + /** Set the pixel value */ + void + Set(const PixelType & value) const + { + const_cast(this->m_Image.GetPointer()) + ->SetPixel( + *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); + } + + ///** Return a reference to the pixel + //* This method will provide the fastest access to pixel + //* data, but it will NOT support ImageAdaptors. */ + // PixelType & Value(void) + //{ + // return myBuffer[m_Index[2]][m_Index[1]][realIndex].second; + //} + +protected: + /** the construction from a const iterator is declared protected + in order to enforce const correctness. */ + ImageScanlineIterator(const ImageScanlineConstIterator & it) + : ImageScanlineConstIterator(it) + {} + Self & + operator=(const ImageScanlineConstIterator & it) + { + this->ImageScanlineConstIterator::operator=(it); + return *this; + } +}; +} // end namespace itk + +#endif // RLEImageScanlineIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h new file mode 100644 index 00000000000..5a4c6d12cf3 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h @@ -0,0 +1,293 @@ +#ifndef RLERegionOfInterestImageFilter_h +#define RLERegionOfInterestImageFilter_h + +#include "itkImageToImageFilter.h" +#include "itkSmartPointer.h" +#include "itkRegionOfInterestImageFilter.h" +#include "RLEImage.h" + +namespace itk +{ +/** \class RegionOfInterestImageFilter + * \brief Extract a region of interest from the input image + * or convert between itk::Image and RLEImage (a custom region can be used). + * + * This filter produces an output image of the same dimension as the input + * image. The user specifies the region of the input image that will be + * contained in the output image. The origin coordinates of the output images + * will be computed in such a way that if mapped to physical space, the output + * image will overlay the input image with perfect registration. In other + * words, a registration process between the output image and the input image + * will return an identity transform. + * + * The region to extract is set using the method SetRegionOfInterest. + */ +template +class RegionOfInterestImageFilter, + RLEImage> + : public ImageToImageFilter, + RLEImage> +{ +public: + /** Standard class typedefs. */ + typedef RegionOfInterestImageFilter Self; + typedef RLEImage RLEImageType; + typedef RLEImageType ImageType; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef typename Superclass::InputImageRegionType InputImageRegionType; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); + + /** Typedef to describe the input image region types. */ + typedef typename RLEImageType::RegionType RegionType; + typedef typename RLEImageType::IndexType IndexType; + typedef typename RLEImageType::SizeType SizeType; + + /** Typedef to describe the type of pixel. */ + typedef typename RLEImageType::PixelType OutputImagePixelType; + typedef typename RLEImageType::PixelType InputImagePixelType; + + /** Set/Get the output image region. */ + itkSetMacro(RegionOfInterest, RegionType); + itkGetConstMacro(RegionOfInterest, RegionType); + + /** ImageDimension enumeration */ + itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); + itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); + +#ifdef ITK_USE_CONCEPT_CHECKING + // Begin concept checking + itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); + itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); + // End concept checking +#endif + +protected: + RegionOfInterestImageFilter() {} + ~RegionOfInterestImageFilter() {} + void + PrintSelf(std::ostream & os, Indent indent) const; + + virtual void + GenerateInputRequestedRegion(); + + virtual void + EnlargeOutputRequestedRegion(DataObject * output); + + /** RegionOfInterestImageFilter can produce an image which is a different + * size than its input image. As such, RegionOfInterestImageFilter + * needs to provide an implementation for + * GenerateOutputInformation() in order to inform the pipeline + * execution model. The original documentation of this method is + * below. + * + * \sa ProcessObject::GenerateOutputInformaton() */ + virtual void + GenerateOutputInformation(); + + /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() */ + void + ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); + +private: + RegionOfInterestImageFilter(const Self &); // purposely not implemented + void + operator=(const Self &); // purposely not implemented + + RegionType m_RegionOfInterest; +}; + +template +class RegionOfInterestImageFilter, RLEImage> + : public ImageToImageFilter, RLEImage> +{ +public: + /** Standard class typedefs. */ + typedef RegionOfInterestImageFilter Self; + typedef RLEImage RLEImageType; + typedef Image ImageType; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef typename Superclass::InputImageRegionType InputImageRegionType; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); + + /** Typedef to describe the input image region types. */ + typedef typename RLEImageType::RegionType RegionType; + typedef typename RLEImageType::IndexType IndexType; + typedef typename RLEImageType::SizeType SizeType; + + /** Typedef to describe the type of pixel. */ + typedef typename RLEImageType::PixelType OutputImagePixelType; + typedef typename RLEImageType::PixelType InputImagePixelType; + + /** Set/Get the output image region. */ + itkSetMacro(RegionOfInterest, RegionType); + itkGetConstMacro(RegionOfInterest, RegionType); + + /** ImageDimension enumeration */ + itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); + itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); + +#ifdef ITK_USE_CONCEPT_CHECKING + // Begin concept checking + itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); + itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); + // End concept checking +#endif + +protected: + RegionOfInterestImageFilter() {} + ~RegionOfInterestImageFilter() {} + void + PrintSelf(std::ostream & os, Indent indent) const; + + virtual void + GenerateInputRequestedRegion(); + + virtual void + EnlargeOutputRequestedRegion(DataObject * output); + + /** RegionOfInterestImageFilter can produce an image which is a different + * size than its input image. As such, RegionOfInterestImageFilter + * needs to provide an implementation for + * GenerateOutputInformation() in order to inform the pipeline + * execution model. The original documentation of this method is + * below. + * + * \sa ProcessObject::GenerateOutputInformaton() */ + virtual void + GenerateOutputInformation(); + + /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() */ + void + ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); + +private: + RegionOfInterestImageFilter(const Self &); // purposely not implemented + void + operator=(const Self &); // purposely not implemented + + RegionType m_RegionOfInterest; +}; + +template +class RegionOfInterestImageFilter, Image> + : public ImageToImageFilter, Image> +{ +public: + /** Standard class typedefs. */ + typedef RegionOfInterestImageFilter Self; + typedef RLEImage RLEImageType; + typedef Image ImageType; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef typename Superclass::InputImageRegionType InputImageRegionType; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); + + /** Typedef to describe the input image region types. */ + typedef typename RLEImageType::RegionType RegionType; + typedef typename RLEImageType::IndexType IndexType; + typedef typename RLEImageType::SizeType SizeType; + + /** Typedef to describe the type of pixel. */ + typedef typename RLEImageType::PixelType OutputImagePixelType; + typedef typename RLEImageType::PixelType InputImagePixelType; + + /** Set/Get the output image region. */ + itkSetMacro(RegionOfInterest, RegionType); + itkGetConstMacro(RegionOfInterest, RegionType); + + /** ImageDimension enumeration */ + itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); + itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); + +#ifdef ITK_USE_CONCEPT_CHECKING + // Begin concept checking + itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); + itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); + // End concept checking +#endif + +protected: + RegionOfInterestImageFilter() {} + ~RegionOfInterestImageFilter() {} + void + PrintSelf(std::ostream & os, Indent indent) const; + + virtual void + GenerateInputRequestedRegion(); + + virtual void + EnlargeOutputRequestedRegion(DataObject * output); + + /** RegionOfInterestImageFilter can produce an image which is a different + * size than its input image. As such, RegionOfInterestImageFilter + * needs to provide an implementation for + * GenerateOutputInformation() in order to inform the pipeline + * execution model. The original documentation of this method is + * below. + * + * \sa ProcessObject::GenerateOutputInformaton() */ + virtual void + GenerateOutputInformation(); + + /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() */ + void + ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); + +private: + RegionOfInterestImageFilter(const Self &); // purposely not implemented + void + operator=(const Self &); // purposely not implemented + + RegionType m_RegionOfInterest; +}; +} // end namespace itk + +#ifndef ITK_MANUAL_INSTANTIATION +# include "RLERegionOfInterestImageFilter.txx" +#endif + +#endif // RLERegionOfInterestImageFilter_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx new file mode 100644 index 00000000000..321f7bbf250 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx @@ -0,0 +1,531 @@ +#ifndef RLERegionOfInterestImageFilter_txx +#define RLERegionOfInterestImageFilter_txx + +#include "itkRegionOfInterestImageFilter.h" +#include "itkImageAlgorithm.h" +#include "itkObjectFactory.h" +#include "itkProgressReporter.h" +#include "itkImage.h" + +namespace itk +{ +template +void +RegionOfInterestImageFilter, + RLEImage>::PrintSelf(std::ostream & os, + Indent indent) const +{ + Superclass::PrintSelf(os, indent); + + os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; +} + +template +void +RegionOfInterestImageFilter, + RLEImage>::GenerateInputRequestedRegion() +{ + // call the superclass' implementation of this method + Superclass::GenerateInputRequestedRegion(); + + // get pointer to the input + typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); + + if (inputPtr) + { + // request the region of interest + inputPtr->SetRequestedRegion(m_RegionOfInterest); + } +} + +template +void +RegionOfInterestImageFilter, + RLEImage>::EnlargeOutputRequestedRegion(DataObject * + output) +{ + // call the superclass' implementation of this method + Superclass::EnlargeOutputRequestedRegion(output); + + // generate everything in the region of interest + output->SetRequestedRegionToLargestPossibleRegion(); +} + +/** + * RegionOfInterestImageFilter can produce an image which is a different size + * than its input image. As such, RegionOfInterestImageFilter needs to provide an + * implementation for GenerateOutputInformation() in order to inform + * the pipeline execution model. The original documentation of this + * method is below. + * + * \sa ProcessObject::GenerateOutputInformaton() + */ +template +void +RegionOfInterestImageFilter, + RLEImage>::GenerateOutputInformation() +{ + // do not call the superclass' implementation of this method since + // this filter allows the input the output to be of different dimensions + + // get pointers to the input and output + typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); + typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); + + if (!outputPtr || !inputPtr) + { + return; + } + + // Set the output image size to the same value as the region of interest. + RegionType region; + IndexType start; + start.Fill(0); + + region.SetSize(m_RegionOfInterest.GetSize()); + region.SetIndex(start); + + // Copy Information without modification. + outputPtr->CopyInformation(inputPtr); + + // Adjust output region + outputPtr->SetLargestPossibleRegion(region); + + // Correct origin of the extracted region. + IndexType roiStart(m_RegionOfInterest.GetIndex()); + typename Superclass::OutputImageType::PointType outputOrigin; + inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); + outputPtr->SetOrigin(outputOrigin); +} + +/** + * RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() + */ +template +void +RegionOfInterestImageFilter< + RLEImage, + RLEImage>::ThreadedGenerateData(const RegionType & outputRegionForThread, + ThreadIdType threadId) +{ + // Get the input and output pointers + const RLEImageType * in = this->GetInput(); + RLEImageType * out = this->GetOutput(); + + // Define the portion of the input to walk for this thread + InputImageRegionType inputRegionForThread; + inputRegionForThread.SetSize(outputRegionForThread.GetSize()); + + IndexType start, end; + IndexType roiStart(m_RegionOfInterest.GetIndex()); + IndexType threadStart(outputRegionForThread.GetIndex()); + for (unsigned int i = 0; i < VImageDimension; i++) + { + start[i] = roiStart[i] + threadStart[i]; + end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); + } + inputRegionForThread.SetIndex(start); + + bool copyLines = (in->GetLargestPossibleRegion().GetSize(0) == outputRegionForThread.GetSize(0)); + typename ImageType::BufferType::RegionType oReg = ImageType::truncateRegion(outputRegionForThread), + iReg = ImageType::truncateRegion(inputRegionForThread); + ImageRegionConstIterator iIt(in->GetBuffer(), iReg); + ImageRegionIterator oIt(out->GetBuffer(), oReg); + + while (!oIt.IsAtEnd()) + { + if (copyLines) + oIt.Set(iIt.Get()); + else // determine begin and end iterator and copy range + { + typename RLEImageType::RLLine & oLine = oIt.Value(); + oLine.clear(); + const typename RLEImageType::RLLine & iLine = iIt.Value(); + CounterType t = 0; + SizeValueType x = 0; + // find start + for (; x < iLine.size(); x++) + { + t += iLine[x].first; + if (t > start[0]) + break; + } + assert(x < iLine.size()); + + SizeValueType begin = x; + if (t >= end[0]) // both begin and end are in this segment + { + oLine.push_back(typename RLEImageType::RLSegment(end[0] - start[0], iLine[x].second)); + ++iIt; + ++oIt; + continue; // next line + } + else if (t - start[0] < iLine[x].first) // not the first pixel in segment + { + oLine.push_back(typename RLEImageType::RLSegment(t - start[0], iLine[x].second)); + begin++; // start copying from next segment + } + + // if (t < end[0]) + for (x++; x < iLine.size(); x++) + { + t += iLine[x].first; + if (t >= end[0]) + break; + } + if (t == end[0]) + oLine.insert(oLine.end(), iLine.begin() + begin, iLine.begin() + x + 1); + else // we need to take special care of the last segment + { + oLine.insert(oLine.end(), iLine.begin() + begin, iLine.begin() + x); + oLine.push_back(typename RLEImageType::RLSegment(end[0] + iLine[x].first - t, iLine[x].second)); + } + } + ++iIt; + ++oIt; + } +} + + +template +void +RegionOfInterestImageFilter, RLEImage>::PrintSelf( + std::ostream & os, + Indent indent) const +{ + Superclass::PrintSelf(os, indent); + + os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; +} + +template +void +RegionOfInterestImageFilter, + RLEImage>::GenerateInputRequestedRegion() +{ + // call the superclass' implementation of this method + Superclass::GenerateInputRequestedRegion(); + + // get pointer to the input + typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); + + if (inputPtr) + { + // request the region of interest + inputPtr->SetRequestedRegion(m_RegionOfInterest); + } +} + +template +void +RegionOfInterestImageFilter, RLEImage>:: + EnlargeOutputRequestedRegion(DataObject * output) +{ + // call the superclass' implementation of this method + Superclass::EnlargeOutputRequestedRegion(output); + + // generate everything in the region of interest + output->SetRequestedRegionToLargestPossibleRegion(); +} + +/** + * RegionOfInterestImageFilter can produce an image which is a different size + * than its input image. As such, RegionOfInterestImageFilter needs to provide an + * implementation for GenerateOutputInformation() in order to inform + * the pipeline execution model. The original documentation of this + * method is below. + * + * \sa ProcessObject::GenerateOutputInformaton() + */ +template +void +RegionOfInterestImageFilter, + RLEImage>::GenerateOutputInformation() +{ + // do not call the superclass' implementation of this method since + // this filter allows the input the output to be of different dimensions + + // get pointers to the input and output + typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); + typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); + + if (!outputPtr || !inputPtr) + { + return; + } + + // Set the output image size to the same value as the region of interest. + RegionType region; + IndexType start; + start.Fill(0); + + region.SetSize(m_RegionOfInterest.GetSize()); + region.SetIndex(start); + + // Copy Information without modification. + outputPtr->CopyInformation(inputPtr); + + // Adjust output region + outputPtr->SetLargestPossibleRegion(region); + + // Correct origin of the extracted region. + IndexType roiStart(m_RegionOfInterest.GetIndex()); + typename Superclass::OutputImageType::PointType outputOrigin; + inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); + outputPtr->SetOrigin(outputOrigin); +} + +/** + * RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() + */ +template +void +RegionOfInterestImageFilter, RLEImage>:: + ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId) +{ + // Get the input and output pointers + const ImageType * in = this->GetInput(); + RLEImageType * out = this->GetOutput(); + + // Define the portion of the input to walk for this thread + InputImageRegionType inputRegionForThread; + inputRegionForThread.SetSize(outputRegionForThread.GetSize()); + + IndexType start, end; + IndexType roiStart(m_RegionOfInterest.GetIndex()); + IndexType threadStart(outputRegionForThread.GetIndex()); + for (unsigned int i = 0; i < VImageDimension; i++) + { + start[i] = roiStart[i] + threadStart[i]; + end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); + } + inputRegionForThread.SetIndex(start); + + typename RLEImageType::BufferType::RegionType oReg = RLEImageType::truncateRegion(outputRegionForThread); + ImageRegionConstIterator iIt(in, inputRegionForThread); + ImageRegionIterator oIt(out->GetBuffer(), oReg); + SizeValueType size0 = outputRegionForThread.GetSize(0); + typename RLEImageType::RLLine temp; + temp.reserve(size0); // pessimistically preallocate buffer, otherwise reallocations can occur + + while (!oIt.IsAtEnd()) + { + SizeValueType x = 0; + temp.clear(); + while (x < size0) + { + typename RLEImageType::RLSegment s(0, iIt.Value()); + while (x < size0 && iIt.Value() == s.second) + { + x++; + s.first++; + ++(iIt); + } + temp.push_back(s); + } + oIt.Value() = temp; + ++oIt; + } +} + + +template +void +RegionOfInterestImageFilter, Image>::PrintSelf( + std::ostream & os, + Indent indent) const +{ + Superclass::PrintSelf(os, indent); + + os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; +} + +template +void +RegionOfInterestImageFilter, + Image>::GenerateInputRequestedRegion() +{ + // call the superclass' implementation of this method + Superclass::GenerateInputRequestedRegion(); + + // get pointer to the input + typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); + + if (inputPtr) + { + // request the region of interest + inputPtr->SetRequestedRegion(m_RegionOfInterest); + } +} + +template +void +RegionOfInterestImageFilter, + Image>::EnlargeOutputRequestedRegion(DataObject * output) +{ + // call the superclass' implementation of this method + Superclass::EnlargeOutputRequestedRegion(output); + + // generate everything in the region of interest + output->SetRequestedRegionToLargestPossibleRegion(); +} + +/** + * RegionOfInterestImageFilter can produce an image which is a different size + * than its input image. As such, RegionOfInterestImageFilter needs to provide an + * implementation for GenerateOutputInformation() in order to inform + * the pipeline execution model. The original documentation of this + * method is below. + * + * \sa ProcessObject::GenerateOutputInformaton() + */ +template +void +RegionOfInterestImageFilter, + Image>::GenerateOutputInformation() +{ + // do not call the superclass' implementation of this method since + // this filter allows the input the output to be of different dimensions + + // get pointers to the input and output + typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); + typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); + + if (!outputPtr || !inputPtr) + { + return; + } + + // Set the output image size to the same value as the region of interest. + RegionType region; + IndexType start; + start.Fill(0); + + region.SetSize(m_RegionOfInterest.GetSize()); + region.SetIndex(start); + + // Copy Information without modification. + outputPtr->CopyInformation(inputPtr); + + // Adjust output region + outputPtr->SetLargestPossibleRegion(region); + + // Correct origin of the extracted region. + IndexType roiStart(m_RegionOfInterest.GetIndex()); + typename Superclass::OutputImageType::PointType outputOrigin; + inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); + outputPtr->SetOrigin(outputOrigin); +} + +/** + * RegionOfInterestImageFilter can be implemented as a multithreaded filter. + * Therefore, this implementation provides a ThreadedGenerateData() + * routine which is called for each processing thread. The output + * image data is allocated automatically by the superclass prior to + * calling ThreadedGenerateData(). ThreadedGenerateData can only + * write to the portion of the output image specified by the + * parameter "outputRegionForThread" + * + * \sa ImageToImageFilter::ThreadedGenerateData(), + * ImageToImageFilter::GenerateData() + */ +template +void +RegionOfInterestImageFilter, Image>:: + ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId) +{ + // Get the input and output pointers + const RLEImageType * in = this->GetInput(); + ImageType * out = this->GetOutput(); + + // Define the portion of the input to walk for this thread + InputImageRegionType inputRegionForThread; + inputRegionForThread.SetSize(outputRegionForThread.GetSize()); + + IndexType start, end; + IndexType roiStart(m_RegionOfInterest.GetIndex()); + IndexType threadStart(outputRegionForThread.GetIndex()); + for (unsigned int i = 0; i < VImageDimension; i++) + { + start[i] = roiStart[i] + threadStart[i]; + end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); + } + inputRegionForThread.SetIndex(start); + + typename RLEImageType::BufferType::RegionType iReg = RLEImageType::truncateRegion(inputRegionForThread); + ImageRegionConstIterator iIt(in->GetBuffer(), iReg); + ImageRegionIterator oIt(out, outputRegionForThread); + + while (!iIt.IsAtEnd()) + { + const typename RLEImageType::RLLine & iLine = iIt.Value(); + CounterType t = 0; + SizeValueType x = 0; + // find start + for (; x < iLine.size(); x++) + { + t += iLine[x].first; + if (t > start[0]) + break; + } + assert(x < iLine.size()); + + SizeValueType begin = x; + if (t >= end[0]) // both begin and end are in this segment + { + for (SizeValueType i = start[0]; i < end[0]; i++) + { + oIt.Set(iLine[x].second); + ++oIt; + } + ++iIt; + continue; // next line + } + // else handle the beginning segment + for (SizeValueType i = start[0]; i < t; i++) + { + oIt.Set(iLine[x].second); + ++oIt; + } + // now handle middle segments + for (x++; x < iLine.size(); x++) + { + t += iLine[x].first; + if (t >= end[0]) + break; + for (SizeValueType i = 0; i < iLine[x].first; i++) + { + oIt.Set(iLine[x].second); + ++oIt; + } + } + // handle the last segment + for (SizeValueType i = 0; i < end[0] + iLine[x].first - t; i++) + { + oIt.Set(iLine[x].second); + ++oIt; + } + ++iIt; + } +} +} // end namespace itk + +#endif // RLERegionOfInterestImageFilter_txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 8444f6a2762..c20a5dde9b1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -16,6 +16,9 @@ * *=========================================================================*/ +#include "RLEImage/RLEImageScanlineIterator.h" +#include "RLEImage/RLEImageRegionIterator.h" +#include "RLEImage/RLERegionOfInterestImageFilter.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" @@ -36,19 +39,55 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor typedef itk::ImageFileReader ReaderType; typename ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(inFilename); + reader->Update(); - typedef itk::MorphologicalContourInterpolator mciType; - typename mciType::Pointer mci = mciType::New(); - mci->SetInput(reader->GetOutput()); + typedef RLEImage myRLEImage; + typedef itk::RegionOfInterestImageFilter inConverterType; + inConverterType::Pointer inConv = inConverterType::New(); + inConv->SetInput(reader->GetOutput()); + inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); + inConv->Update(); + myRLEImage::Pointer test = inConv->GetOutput(); + + typedef itk::MorphologicalContourInterpolator mciType; + typename mciType::Pointer mci = mciType::New(); + mci->SetInput(test); mci->SetUseDistanceTransform(UseDistanceTransform); mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); + mci->Update(); + + std::vector indices(ImageType::ImageDimension); + for (int i = 0; i < ImageType::ImageDimension; i++) + { + indices[i] = mci->GetLabeledSliceIndices(i); + } + // reuse the already calculated indices + + typename mciType::Pointer mci2 = mciType::New(); + mci2->SetInput(test); + mci2->SetUseDistanceTransform(UseDistanceTransform); + mci2->SetUseBallStructuringElement(ball); + mci2->SetAxis(axis); + mci2->SetLabel(label); + mci2->SetUseCustomSlicePositions(true); + for (int i = 0; i < ImageType::ImageDimension; i++) + { + mci2->SetLabeledSliceIndices(i, indices[i]); + } + // mci2->Update(); + + typedef itk::RegionOfInterestImageFilter outConverterType; + outConverterType::Pointer outConv = outConverterType::New(); + outConv->SetInput(mci->GetOutput()); + outConv->SetRegionOfInterest(mci->GetOutput()->GetLargestPossibleRegion()); + outConv->Update(); typedef itk::ImageFileWriter WriterType; typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outFilename); - writer->SetInput(mci->GetOutput()); + writer->SetInput(outConv->GetOutput()); writer->SetUseCompression(true); writer->Update(); } From 29a63ef85dcfce5d653e1fd797bc9cbef366c8fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Jul 2016 16:37:24 -0400 Subject: [PATCH 086/176] BUG: Allowing filters to have more than one thread does not cause crashes, but slightly reduces performance --- .../itkMorphologicalContourInterpolator.hxx | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 3526cc66ec5..13567fbe3e4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -54,7 +54,7 @@ WriteDebug(itk::SmartPointer out, const char * filename) return; // tests run much faster // typedef ImageFileWriter WriterType; // typename WriterType::Pointer w = WriterType::New(); - // w->SetNumberOfThreads(1); //otherwise conflicts with C++11 threads + // w->SetNumberOfThreads(1); //excessive threading is counterproductive // w->SetInput(out); // w->SetFileName(filename); // try @@ -75,7 +75,7 @@ WriteDebug(itk::SmartPointer> out, const char * filename) typedef Image ucharImageType; typedef CastImageFilter CastType; typename CastType::Pointer caster = CastType::New(); - caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + caster->SetNumberOfThreads(1); // excessive threading is counterproductive caster->SetInput(out); WriteDebug(caster->GetOutput(), filename); } @@ -429,17 +429,17 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe m_CrossDilator[threadId] = CrossDilateType::New(); m_BallDilator[threadId] = BallDilateType::New(); m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_And[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive typedef Size SizeType; SizeType size; size.Fill(1); - m_CrossDilator[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_CrossDilator[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive m_CrossStructuringElement[threadId].SetRadius(size); m_CrossStructuringElement[threadId].CreateStructuringElement(); m_CrossDilator[threadId]->SetKernel(m_CrossStructuringElement[threadId]); - m_BallDilator[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_BallDilator[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive m_BallStructuringElement[threadId].SetRadius(size); m_BallStructuringElement[threadId].CreateStructuringElement(); m_BallDilator[threadId]->SetKernel(m_BallStructuringElement[threadId]); @@ -520,7 +520,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool if (!initialized[threadId]) { m_Or[threadId] = OrType::New(); - m_Or[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_Or[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive initialized[threadId] = true; } @@ -572,7 +572,7 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point { filter[threadId] = FilterType::New(); filter[threadId]->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space - filter[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + filter[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive initialized[threadId] = true; } filter[threadId]->SetInput(mask); @@ -684,9 +684,9 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool if (!initialized[threadId]) { threshold[threadId] = FloatBinarizerType::New(); - threshold[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + threshold[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + m_And[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive initialized[threadId] = true; } threshold[threadId]->SetInput(sdf); @@ -857,7 +857,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int if (!initialized[threadId]) { sAnd[threadId] = AndSliceType::New(); - sAnd[threadId]->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + sAnd[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive initialized[threadId] = true; } sAnd[threadId]->SetInput(0, iSlice); @@ -1009,7 +1009,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int typedef UnaryFunctorImageFilter> CastType; typename CastType::Pointer caster = CastType::New(); - caster->SetNumberOfThreads(1); // otherwise conflicts with C++11 threads + caster->SetNumberOfThreads(1); // excessive threading is counterproductive caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); From 0e383830cba269a7949e7d211366a7dbdb40fde2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Jul 2016 16:46:58 -0400 Subject: [PATCH 087/176] ENH: Whole writing loop mutexed --- .../include/itkMorphologicalContourInterpolator.hxx | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 13567fbe3e4..9d7d6a352e3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -921,23 +921,26 @@ MorphologicalContourInterpolator::Interpolate1to1(int ImageRegionConstIterator seqIt(median, newRegion); ImageRegionIterator outIt(out, outRegion); ImageRegionIterator midIt(midConn, newRegion); - static SimpleFastMutexLock mutex; + + // writing through one RLEImage iterator invalidates all the others + // so this whole writing loop needs to be serialized + static SimpleFastMutexLock mutex; + mutex.Lock(); while (!outIt.IsAtEnd()) { if (seqIt.Get()) { - mutex.Lock(); if (outIt.Get() < label) { outIt.Set(label); } - mutex.Unlock(); midIt.Set(1); } ++seqIt; ++outIt; ++midIt; } + mutex.Unlock(); WriteDebug(midConn, "C:\\midConn.nrrd"); // recurse if needed From c8fd9f5c786b73dcdbed9e11d7164b94bd1e67dd Mon Sep 17 00:00:00 2001 From: Dzenan Zukic Date: Fri, 1 Jul 2016 17:21:46 -0400 Subject: [PATCH 088/176] ENH: GCC compatibility --- .../test/itkMorphologicalContourInterpolationTest.cxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index c20a5dde9b1..2c46dca5ff0 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -43,11 +43,11 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor typedef RLEImage myRLEImage; typedef itk::RegionOfInterestImageFilter inConverterType; - inConverterType::Pointer inConv = inConverterType::New(); + typename inConverterType::Pointer inConv = inConverterType::New(); inConv->SetInput(reader->GetOutput()); inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); inConv->Update(); - myRLEImage::Pointer test = inConv->GetOutput(); + typename myRLEImage::Pointer test = inConv->GetOutput(); typedef itk::MorphologicalContourInterpolator mciType; typename mciType::Pointer mci = mciType::New(); @@ -79,7 +79,7 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // mci2->Update(); typedef itk::RegionOfInterestImageFilter outConverterType; - outConverterType::Pointer outConv = outConverterType::New(); + typename outConverterType::Pointer outConv = outConverterType::New(); outConv->SetInput(mci->GetOutput()); outConv->SetRegionOfInterest(mci->GetOutput()->GetLargestPossibleRegion()); outConv->Update(); From 0912230094af68e8b9574381d152164dc5eecbe8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 1 Jul 2016 17:33:14 -0400 Subject: [PATCH 089/176] ENH: Mutexing iterator constructor --- .../itkMorphologicalContourInterpolator.hxx | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 9d7d6a352e3..a7c2ce08fa9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -919,26 +919,29 @@ MorphologicalContourInterpolator::Interpolate1to1(int midConn->Allocate(true); ImageRegionConstIterator seqIt(median, newRegion); - ImageRegionIterator outIt(out, outRegion); ImageRegionIterator midIt(midConn, newRegion); // writing through one RLEImage iterator invalidates all the others // so this whole writing loop needs to be serialized static SimpleFastMutexLock mutex; mutex.Lock(); - while (!outIt.IsAtEnd()) { - if (seqIt.Get()) + ImageRegionIterator outIt(out, outRegion); + while (!outIt.IsAtEnd()) { - if (outIt.Get() < label) + if (seqIt.Get()) { - outIt.Set(label); + if (outIt.Get() < label) + { + outIt.Set(label); + } + midIt.Set(1); } - midIt.Set(1); + ++seqIt; + ++outIt; + ++midIt; } - ++seqIt; - ++outIt; - ++midIt; + // iterator destroyed here } mutex.Unlock(); WriteDebug(midConn, "C:\\midConn.nrrd"); From 06cd214de26c7c629ea112c5c5ce253a3729fe93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 12 Jul 2016 16:37:08 -0400 Subject: [PATCH 090/176] ENH: Finalizing custom slice positions --- .../itkMorphologicalContourInterpolator.h | 56 +++++++++---- .../itkMorphologicalContourInterpolator.hxx | 81 +++---------------- ...kMorphologicalContourInterpolationTest.cxx | 17 ++-- 3 files changed, 60 insertions(+), 94 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index d6fb8369a68..3c63ca64f52 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -42,14 +42,14 @@ namespace itk * \par Parameters * Slices are detected at positions where a pixel exists with same labeled * neighbors in slice and only clear (0) neighbors perpendicular to the slice. - * If default behaviour is unwanted, contour indices can be set for each axis + * If default behaviour is unwanted, contour indices can be set * by enabling UseCustomSlicePositions and calling SetLabeledSliceIndices. * * Filter can be restricted to run along only one axis, and/or to interpolate * just one label. * * Since optimal alignment between slices would require exhaustive search, - * the default is to use heuristic (breadth first search startin from centroid). + * the default is to use heuristic (breadth first search starting from centroid). * * There is also an alternative algorithm based on distance transform approach. * It is slightly faster, but it can jump across a twisty shape (not geodesic). @@ -81,6 +81,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter SliceSetType; - /** If default slice detection is not wanted, slice indices - * between which interpolation is done can be set using this method. */ + /** Clears all custom slice positions. */ void - SetLabeledSliceIndices(unsigned int axis, std::vector indices); + ClearLabeledSliceIndices() + { + m_LabeledSlices.clear(); + m_LabeledSlices.resize(TImage::ImageDimension); + this->Modified(); + } /** If default slice detection is not wanted, slice indices * between which interpolation is done can be set using this method. */ void - SetLabeledSliceIndices(unsigned int axis, SliceSetType indices); + SetLabeledSliceIndices(unsigned int axis, + typename TImage::PixelType label, + std::vector indices) + { + m_LabeledSlices[axis][label] = SliceSetType().insert(indices.begin(), indices.end()); + this->Modified(); + } /** If default slice detection is not wanted, slice indices * between which interpolation is done can be set using this method. */ + void + SetLabeledSliceIndices(unsigned int axis, typename TImage::PixelType label, SliceSetType indices) + { + m_LabeledSlices[axis][label] = indices; + this->Modified(); + } + + /** Slice indices between which interpolation is done. */ SliceSetType - GetLabeledSliceIndices(unsigned int axis); + GetLabeledSliceIndices(unsigned int axis, typename TImage::PixelType label) + { + return m_LabeledSlices[axis][label]; + } - /** Run-time type information (and related methods). */ - itkTypeMacro(MorphologicalContourInterpolator, ImageToImageFilter); + // each label gets a set of slices in which it is present + typedef itksys::hash_map LabeledSlicesType; + typedef std::vector SliceIndicesType; + + /** Slice indices between which interpolation is done. */ + SliceIndicesType + GetLabeledSliceIndices() + { + return m_LabeledSlices; + } protected: MorphologicalContourInterpolator(); ~MorphologicalContourInterpolator() {} - SliceSetType m_SliceSets[TImage::ImageDimension]; typename TImage::PixelType m_Label; int m_Axis; bool m_HeuristicAlignment; @@ -191,6 +222,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; @@ -351,10 +383,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label - // each label gets a set of slices in which it is present - typedef itksys::hash_map LabeledSlicesType; - std::vector m_LabeledSlices; // one for each axis - /** Calculates a bounding box of non-zero pixels. */ typename SliceType::RegionType BoundingBox(itk::SmartPointer image); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index a7c2ce08fa9..09c92822fe3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -192,7 +192,6 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_MaxAlignIters(pow(6, TImage::ImageDimension)) , // bigger of this and root of pixel count of the search image m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets -//,m_SliceSets({{}}) //initialize with empty sets { // set up pipeline for regioned connected components m_RoI = RoiType::New(); @@ -207,33 +206,6 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() } -template -typename MorphologicalContourInterpolator::SliceSetType -MorphologicalContourInterpolator::GetLabeledSliceIndices(unsigned int axis) -{ - return m_SliceSets[axis]; -} - - -template -void -MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, SliceSetType indices) -{ - m_SliceSets[axis] = indices; - this->Modified(); -} - - -template -void -MorphologicalContourInterpolator::SetLabeledSliceIndices(unsigned int axis, - std::vector indices) -{ - m_LabeledSlices[axis] = SliceSetType().insert(indices.begin(), indices.end()); - this->Modified(); -} - - template template void @@ -263,13 +235,6 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() m_LabeledSlices.resize(TImage::ImageDimension); // initialize with empty sets m_BoundingBoxes.clear(); m_Orientations.clear(); - if (!m_UseCustomSlicePositions) - { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - { - m_SliceSets[a] = SliceSetType(); - } - } typename TImage::ConstPointer m_Input = this->GetInput(); typename TImage::Pointer m_Output = this->GetOutput(); @@ -338,10 +303,6 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() if (m_Axis == -1 || m_Axis == axis) { m_LabeledSlices[axis][val].insert(ind[axis]); - if (!m_UseCustomSlicePositions) - { - m_SliceSets[axis].insert(ind[axis]); - } } } } @@ -1642,13 +1603,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { if (m_Label == 0 || m_Label == it->first) // label needs to be interpolated { - typename SliceSetType::iterator prev; - if (m_UseCustomSlicePositions && m_Label != 0) - { - it->second = m_SliceSets[axis]; - } - - prev = it->second.begin(); + typename SliceSetType::iterator prev = it->second.begin(); if (prev == it->second.end()) { continue; // nothing to do for this label @@ -1748,24 +1703,15 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer m_Output = this->GetOutput(); this->AllocateOutputs(); - this->DetermineSliceOrientations(); // calculates bounding boxes - if (m_UseCustomSlicePositions && m_Label == 0) // we need to adjust m_LabeledSlices + if (m_UseCustomSlicePositions) // we need to adjust m_LabeledSlices { - for (int i = 0; i < TImage::ImageDimension; i++) - { - for (typename LabeledSlicesType::iterator lIt = m_LabeledSlices[i].begin(); lIt != m_LabeledSlices[i].end(); - ++lIt) - { - // typename SliceSetType::iterator sIt = lIt->second.begin(); - SliceSetType newIndices; - std::set_intersection(lIt->second.begin(), - lIt->second.end(), - m_SliceSets[i].begin(), - m_SliceSets[i].end(), - std::inserter(newIndices, newIndices.end())); - lIt->second = newIndices; - } - } + SliceIndicesType t = m_LabeledSlices; + this->DetermineSliceOrientations(); // calculates bounding boxes + m_LabeledSlices = t; // restore custom positions + } + else + { + this->DetermineSliceOrientations(); } if (m_BoundingBoxes.size() == 0) // no contours detected @@ -1780,14 +1726,7 @@ MorphologicalContourInterpolator::GenerateData() OrientationType aggregate = OrientationType(); aggregate.Fill(false); - if (m_UseCustomSlicePositions) - { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) - { - aggregate[a] = m_SliceSets[a].size() > 0; - } - } - else if (this->m_Label == 0) + if (this->m_Label == 0) { for (typename OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 2c46dca5ff0..51a602d77f5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -58,12 +58,8 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor mci->SetLabel(label); mci->Update(); - std::vector indices(ImageType::ImageDimension); - for (int i = 0; i < ImageType::ImageDimension; i++) - { - indices[i] = mci->GetLabeledSliceIndices(i); - } // reuse the already calculated indices + std::vector indices = mci->GetLabeledSliceIndices(); typename mciType::Pointer mci2 = mciType::New(); mci2->SetInput(test); @@ -74,14 +70,17 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor mci2->SetUseCustomSlicePositions(true); for (int i = 0; i < ImageType::ImageDimension; i++) { - mci2->SetLabeledSliceIndices(i, indices[i]); + for (int l = 0; l < indices[i].size(); l++) + { + mci2->SetLabeledSliceIndices(i, l, indices[i][l]); + } } - // mci2->Update(); + mci2->Update(); typedef itk::RegionOfInterestImageFilter outConverterType; typename outConverterType::Pointer outConv = outConverterType::New(); - outConv->SetInput(mci->GetOutput()); - outConv->SetRegionOfInterest(mci->GetOutput()->GetLargestPossibleRegion()); + outConv->SetInput(mci2->GetOutput()); + outConv->SetRegionOfInterest(mci2->GetOutput()->GetLargestPossibleRegion()); outConv->Update(); typedef itk::ImageFileWriter WriterType; From 6f6d752767f017de3129703e73c0de04b2c4533d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 13 Jul 2016 15:38:01 -0400 Subject: [PATCH 091/176] ENH: Only interpolating in the requested region --- .../itkMorphologicalContourInterpolator.h | 18 +-- .../itkMorphologicalContourInterpolator.hxx | 140 +++++++++++------- ...kMorphologicalContourInterpolationTest.cxx | 35 +++-- 3 files changed, 115 insertions(+), 78 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 3c63ca64f52..295e65df2e8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -159,6 +159,13 @@ class MorphologicalContourInterpolator : public ImageToImageFilter SliceSetType; @@ -237,13 +244,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter OrientationType; - typedef itksys::hash_map OrientationsType; - OrientationsType m_Orientations; - typedef itksys::hash_map BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 09c92822fe3..94c9a411599 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -234,7 +234,6 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() m_LabeledSlices.clear(); m_LabeledSlices.resize(TImage::ImageDimension); // initialize with empty sets m_BoundingBoxes.clear(); - m_Orientations.clear(); typename TImage::ConstPointer m_Input = this->GetInput(); typename TImage::Pointer m_Output = this->GetOutput(); @@ -242,15 +241,12 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() typename TImage::RegionType region = m_Output->GetRequestedRegion(); ImageRegionConstIteratorWithIndex it(m_Input, region); - OrientationType orientations = OrientationType(); - orientations.Fill(false); - for (; !it.IsAtEnd(); ++it) { typename TImage::IndexType indPrev, indNext; const typename TImage::IndexType ind = it.GetIndex(); const typename TImage::PixelType val = m_Input->GetPixel(ind); - if (val != 0 || (m_Label != 0 && val == m_Label)) + if (val != 0) { typename TImage::RegionType boundingBox1; boundingBox1.SetIndex(ind); @@ -265,12 +261,9 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() ExpandRegion(resBB.first->second, ind); } - std::pair res = - m_Orientations.insert(std::make_pair(val, orientations)); - typename OrientationsType::iterator oRef = res.first; - unsigned int cTrue = 0; - unsigned int cAdjacent = 0; - unsigned int axis = 0; + unsigned int cTrue = 0; + unsigned int cAdjacent = 0; + unsigned int axis = 0; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { indPrev = ind; @@ -299,7 +292,6 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis { - oRef->second[axis] = true; // add this dimension for this label if (m_Axis == -1 || m_Axis == axis) { m_LabeledSlices[axis][val].insert(ind[axis]); @@ -881,31 +873,49 @@ MorphologicalContourInterpolator::Interpolate1to1(int ImageRegionConstIterator seqIt(median, newRegion); ImageRegionIterator midIt(midConn, newRegion); + while (!seqIt.IsAtEnd()) + { + if (seqIt.Get()) + { + midIt.Set(1); + } + ++seqIt; + ++midIt; + } + WriteDebug(midConn, "C:\\midConn.nrrd"); + + bool withinReq = true; + typename TImage::RegionType reqRegion = this->GetOutput()->GetRequestedRegion(); + for (int d = 0; d < TImage::ImageDimension; d++) + { + if (outRegion.GetIndex(d) < reqRegion.GetIndex(d) || + outRegion.GetIndex(d) + outRegion.GetSize(d) > reqRegion.GetIndex(d) + reqRegion.GetSize(d)) + { + withinReq = false; + break; + } + } - // writing through one RLEImage iterator invalidates all the others - // so this whole writing loop needs to be serialized static SimpleFastMutexLock mutex; - mutex.Lock(); + if (withinReq) // else we should not write it { + seqIt.GoToBegin(); + // writing through one RLEImage iterator invalidates all the others + // so this whole writing loop needs to be serialized + mutex.Lock(); ImageRegionIterator outIt(out, outRegion); while (!outIt.IsAtEnd()) { - if (seqIt.Get()) + if (seqIt.Get() && outIt.Get() < label) { - if (outIt.Get() < label) - { - outIt.Set(label); - } - midIt.Set(1); + outIt.Set(label); } ++seqIt; ++outIt; - ++midIt; } - // iterator destroyed here - } - mutex.Unlock(); - WriteDebug(midConn, "C:\\midConn.nrrd"); + mutex.Unlock(); + WriteDebug(midConn, "C:\\midConn.nrrd"); + } // iterator destroyed here // recurse if needed if (abs(i - j) > 2) @@ -913,18 +923,20 @@ MorphologicalContourInterpolator::Interpolate1to1(int PixelList regionIDs; regionIDs.push_back(1); - bool first = abs(i - mid) > 1; // interpolate i-mid? - bool second = abs(j - mid) > 1; // interpolate j-mid? + int iReq = i < reqRegion.GetIndex(axis) ? -1 : (i > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + int jReq = j < reqRegion.GetIndex(axis) ? -1 : (j > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + int mReq = + mid < reqRegion.GetIndex(axis) ? -1 : (mid > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + bool first = abs(i - mid) > 1 && abs(iReq + mReq) <= 1; // i-mid? + bool second = abs(j - mid) > 1 && abs(jReq + mReq) <= 1; // j-mid? + if (first) { - if (first) - { - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true, threadId); - } - if (second) - { - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); - } + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true, threadId); + } + if (second) + { + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); } } WriteDebug(out, "C:\\intermediateResult.nrrd"); @@ -1598,6 +1610,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou { // a list of segments which need to be interpolated std::vector> segments; + typename TImage::RegionType reqRegion = this->GetOutput()->GetRequestedRegion(); for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { @@ -1609,13 +1622,26 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou continue; // nothing to do for this label } - typename TImage::RegionType ri; - ri = m_BoundingBoxes[it->first]; + typename TImage::RegionType ri = reqRegion; + if (!m_UseCustomSlicePositions) + { + typename BoundingBoxesType::iterator iBB = m_BoundingBoxes.find(it->first); + if (iBB == m_BoundingBoxes.end()) + { + continue; // this label not present in requested region + } + else + { + ri = iBB->second; + } + } ri.SetSize(axis, 0); ri.SetIndex(axis, *prev); IdentifierType xCount; typename SliceType::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); iconn->DisconnectPipeline(); + int iReq = + *prev < reqRegion.GetIndex(axis) ? -1 : (*prev > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); typename SliceSetType::iterator next = it->second.begin(); for (++next; next != it->second.end(); ++next) @@ -1624,11 +1650,16 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou rj.SetIndex(axis, *next); typename SliceType::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); jconn->DisconnectPipeline(); + int jReq = + *next < reqRegion.GetIndex(axis) ? -1 : (*next > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + // WriteDebug(iconn, "C:\\iconn.nrrd"); // WriteDebug(jconn, "C:\\jconn.nrrd"); - if (*prev + 1 < *next) // only if they are not adjacent slices + if (*prev + 1 < *next // only if they are not adjacent slices + && abs(iReq + jReq) <= 1) // and not out of the requested region + // unless they are on opposite ends { SegmentBetweenTwo s; s.axis = axis; @@ -1641,6 +1672,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou segments.push_back(s); } iconn = jconn; + iReq = jReq; prev = next; } } @@ -1703,7 +1735,7 @@ MorphologicalContourInterpolator::GenerateData() typename TImage::Pointer m_Output = this->GetOutput(); this->AllocateOutputs(); - if (m_UseCustomSlicePositions) // we need to adjust m_LabeledSlices + if (m_UseCustomSlicePositions) { SliceIndicesType t = m_LabeledSlices; this->DetermineSliceOrientations(); // calculates bounding boxes @@ -1714,31 +1746,37 @@ MorphologicalContourInterpolator::GenerateData() this->DetermineSliceOrientations(); } - if (m_BoundingBoxes.size() == 0) // no contours detected + if (m_BoundingBoxes.size() == 0 && !m_UseCustomSlicePositions) { ImageAlgorithm::Copy( m_Input.GetPointer(), m_Output.GetPointer(), m_Output->GetRequestedRegion(), m_Output->GetRequestedRegion()); - return; + return; // no contours detected } if (m_Axis == -1) // interpolate along all axes { - OrientationType aggregate = OrientationType(); + FixedArray aggregate; aggregate.Fill(false); - if (this->m_Label == 0) + for (int i = 0; i < TImage::ImageDimension; i++) { - for (typename OrientationsType::iterator it = m_Orientations.begin(); it != m_Orientations.end(); ++it) + if (this->m_Label == 0) // examine all labels { - for (unsigned int a = 0; a < TImage::ImageDimension; ++a) + for (int l = 0; l < m_LabeledSlices[i].size(); l++) { - aggregate[a] = aggregate[a] || it->second[a]; // any label needs interpolation along this axis + if (m_LabeledSlices[i][l].size() > 1) + { + aggregate[i] = true; + } + } + } + else // we only care about this label + { + if (m_LabeledSlices[i][m_Label].size() > 1) + { + aggregate[i] = true; } } - } - else - { - aggregate = m_Orientations[m_Label]; // we only care about this label } bool outputUsed = false; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 51a602d77f5..380f7c8d298 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -49,6 +49,15 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor inConv->Update(); typename myRLEImage::Pointer test = inConv->GetOutput(); + // region for partial coverage + typename myRLEImage::RegionType reg = test->GetLargestPossibleRegion(); + // skip X due to RLE representation constraints + for (int i = 1; i < ImageType::ImageDimension; i++) + { + reg.GetModifiableIndex()[i] += reg.GetSize(i) / 4; + reg.GetModifiableSize()[i] /= 2; + } + typedef itk::MorphologicalContourInterpolator mciType; typename mciType::Pointer mci = mciType::New(); mci->SetInput(test); @@ -56,31 +65,25 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); - mci->Update(); - - // reuse the already calculated indices - std::vector indices = mci->GetLabeledSliceIndices(); - - typename mciType::Pointer mci2 = mciType::New(); - mci2->SetInput(test); - mci2->SetUseDistanceTransform(UseDistanceTransform); - mci2->SetUseBallStructuringElement(ball); - mci2->SetAxis(axis); - mci2->SetLabel(label); - mci2->SetUseCustomSlicePositions(true); + mci->GetOutput()->SetRequestedRegion(test->GetLargestPossibleRegion()); + mci->DetermineSliceOrientations(); // calculates indices + typename mciType::SliceIndicesType indices = mci->GetLabeledSliceIndices(); + // mci->GetOutput()->SetRequestedRegion(reg); + mci->SetUseCustomSlicePositions(true); for (int i = 0; i < ImageType::ImageDimension; i++) { for (int l = 0; l < indices[i].size(); l++) { - mci2->SetLabeledSliceIndices(i, l, indices[i][l]); + mci->SetLabeledSliceIndices(i, l, indices[i][l]); } } - mci2->Update(); + // mci->Update(); typedef itk::RegionOfInterestImageFilter outConverterType; typename outConverterType::Pointer outConv = outConverterType::New(); - outConv->SetInput(mci2->GetOutput()); - outConv->SetRegionOfInterest(mci2->GetOutput()->GetLargestPossibleRegion()); + outConv->SetInput(mci->GetOutput()); + outConv->SetRegionOfInterest(reg); + // outConv->SetRegionOfInterest(test->GetLargestPossibleRegion()); outConv->Update(); typedef itk::ImageFileWriter WriterType; From fcef88c6c085f873a5964d5ea9aabb1310cfff8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 13 Jul 2016 18:28:26 -0400 Subject: [PATCH 092/176] ENH: reducing memory usage requirements --- .../itkMorphologicalContourInterpolator.h | 3 -- .../itkMorphologicalContourInterpolator.hxx | 52 +------------------ 2 files changed, 1 insertion(+), 54 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 295e65df2e8..8840714ed0b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -36,9 +36,6 @@ namespace itk * Input contains an image with some slices segmented, usually manually. * The output has all in-between slices also segmented. * - * Memory required by the filter is a bit higher than - * outputImageSize*(max(1,numberOfInterpolatedAxes)). - * * \par Parameters * Slices are detected at positions where a pixel exists with same labeled * neighbors in slice and only clear (0) neighbors perpendicular to the slice. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 94c9a411599..ec8dc2d360a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1779,61 +1779,11 @@ MorphologicalContourInterpolator::GenerateData() } } - bool outputUsed = false; - std::vector perAxisInterpolates; for (unsigned int a = 0; a < TImage::ImageDimension; ++a) { if (aggregate[a]) { - if (outputUsed) - { - typename TImage::Pointer imageA = TImage::New(); - imageA->CopyInformation(m_Output); - imageA->SetRegions(m_Output->GetRequestedRegion()); - imageA->Allocate(true); - this->InterpolateAlong(a, imageA); - perAxisInterpolates.push_back(imageA); - } - else // output not yet used - { - this->InterpolateAlong(a, m_Output); - outputUsed = true; - } - } - } - - if (perAxisInterpolates.size() > 0) // something to combine - { - std::vector> iterators; - - for (int i = 0; i < perAxisInterpolates.size(); ++i) - { - ImageRegionConstIterator it(perAxisInterpolates[i], m_Output->GetRequestedRegion()); - iterators.push_back(it); - } - - std::vector values; - values.reserve(perAxisInterpolates.size()); - - ImageRegionIterator it(m_Output, m_Output->GetRequestedRegion()); - while (!it.IsAtEnd()) - { - values.clear(); - for (int i = 0; i < perAxisInterpolates.size(); ++i) - { - typename TImage::PixelType val = iterators[i].Get(); - if (val != 0) - { - it.Set(val); // last written value stays - } - } - - // next pixel - ++it; - for (int i = 0; i < perAxisInterpolates.size(); ++i) - { - ++(iterators[i]); - } + this->InterpolateAlong(a, m_Output); } } } // interpolate along all axes From e90a4f1708d82704c415820c324ecf8daf659a1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 Jul 2016 10:50:10 -0400 Subject: [PATCH 093/176] ENH: RequestedRegion works --- .../include/itkMorphologicalContourInterpolator.hxx | 3 ++- .../test/itkMorphologicalContourInterpolationTest.cxx | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ec8dc2d360a..a6aab44aec0 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -939,7 +939,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); } } - WriteDebug(out, "C:\\intermediateResult.nrrd"); + // does not compile for RLEImage + // WriteDebug(out, "C:\\intermediateResult.nrrd"); } template diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 380f7c8d298..479d5c127bd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -54,8 +54,8 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // skip X due to RLE representation constraints for (int i = 1; i < ImageType::ImageDimension; i++) { - reg.GetModifiableIndex()[i] += reg.GetSize(i) / 4; - reg.GetModifiableSize()[i] /= 2; + reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; + reg.SetSize(i, (reg.GetSize(i) + 1) / 2); } typedef itk::MorphologicalContourInterpolator mciType; From 9193058cfe38ff3e0a1100cf3eaba72e588e0129 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 Jul 2016 12:27:30 -0400 Subject: [PATCH 094/176] STYLE: Started code cleanup with integration of OverlayInput into GenerateData --- .../itkMorphologicalContourInterpolator.h | 4 --- .../itkMorphologicalContourInterpolator.hxx | 36 ++++++++----------- ...kMorphologicalContourInterpolationTest.cxx | 10 +++--- 3 files changed, 20 insertions(+), 30 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 8840714ed0b..47532426ce9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -343,10 +343,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::InterpolateAlong(int axis, TImage * ou } -template -void -MorphologicalContourInterpolator::OverlayInput() -{ - ImageRegionIterator itO(this->GetOutput(), this->GetOutput()->GetBufferedRegion()); - ImageRegionConstIterator itI(this->GetInput(), this->GetOutput()->GetBufferedRegion()); - while (!itI.IsAtEnd()) - { - typename TImage::PixelType val = itI.Get(); - if (val != 0) - { - itO.Set(val); - } - - ++itI; - ++itO; - } -} - - template void MorphologicalContourInterpolator::AllocateOutputs() @@ -1792,7 +1772,21 @@ MorphologicalContourInterpolator::GenerateData() { this->InterpolateAlong(m_Axis, m_Output); } - OverlayInput(); + + // Overwrites m_Output with non non-zeroes from m_Input + ImageRegionIterator itO(this->GetOutput(), this->GetOutput()->GetBufferedRegion()); + ImageRegionConstIterator itI(this->GetInput(), this->GetOutput()->GetBufferedRegion()); + while (!itI.IsAtEnd()) + { + typename TImage::PixelType val = itI.Get(); + if (val != 0) + { + itO.Set(val); + } + + ++itI; + ++itO; + } } } // end namespace itk diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 479d5c127bd..a950233dcef 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -52,11 +52,11 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // region for partial coverage typename myRLEImage::RegionType reg = test->GetLargestPossibleRegion(); // skip X due to RLE representation constraints - for (int i = 1; i < ImageType::ImageDimension; i++) - { - reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; - reg.SetSize(i, (reg.GetSize(i) + 1) / 2); - } + // for (int i = 1; i < ImageType::ImageDimension; i++) + // { + // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; + // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); + // } typedef itk::MorphologicalContourInterpolator mciType; typename mciType::Pointer mci = mciType::New(); From e8252b97d733466e5f96b4ae96edf5b897d4ac79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 Jul 2016 12:53:28 -0400 Subject: [PATCH 095/176] ENH: Updating baseline output after reducing memory usage requirements --- .../test/Baseline/64816L_amygdala_fin_B.nii.gz.md5 | 2 +- .../test/Baseline/64816L_amygdala_int_B.nii.gz.md5 | 2 +- .../test/Baseline/64816L_amygdala_int_C.nii.gz.md5 | 2 +- .../test/Baseline/64816L_amygdala_int_T.nii.gz.md5 | 2 +- .../Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 | 2 +- .../Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 | 2 +- .../Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 | 2 +- .../itkMorphologicalContourInterpolationTest.cxx | 14 -------------- 8 files changed, 7 insertions(+), 21 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_fin_B.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_fin_B.nii.gz.md5 index 28f740d26b1..d79cfcf7e99 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_fin_B.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_fin_B.nii.gz.md5 @@ -1 +1 @@ -3ee4eff89bce1dd084214fccaabc15a2 +2ff042b68ae1f44127776e8e546223b7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_B.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_B.nii.gz.md5 index b3ff7ef3d06..563c4d416b2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_B.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_B.nii.gz.md5 @@ -1 +1 @@ -086a946a79c3b2c07d2a073045f985f2 +863f38492ccfd2fdec93508f0e454e63 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_C.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_C.nii.gz.md5 index d6729d084d2..7197afb9837 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_C.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_C.nii.gz.md5 @@ -1 +1 @@ -6db59bb45887b69b43386ab37d18d17b +62b4cfafda50707575df7dd3eede9cdf diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_T.nii.gz.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_T.nii.gz.md5 index aa5aebb8488..72768815790 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_T.nii.gz.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/64816L_amygdala_int_T.nii.gz.md5 @@ -1 +1 @@ -ff2061ee02c700cd92175a99c8f87a3b +1eefdfe31b567e9fab5f8a3f645991be diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 index eda606514d4..6556e621abd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_B.nrrd.md5 @@ -1 +1 @@ -86127ff7b17f26feb58bae4051b056eb +76726944bf4261b5098ce6d47c695353 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 index 530a5b21ef1..f65275550c5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_C.nrrd.md5 @@ -1 +1 @@ -40175885c5c1ac61ff343ab5ad18335e +e82e53b0feef7c64930d69507e9878e3 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 index b338aed2c7e..b32a93e4e37 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T.nrrd.md5 @@ -1 +1 @@ -32ff91938ae6b0015760c2c2a8d4d156 +09c6e923cf5a75cf648f58cc2c329e3d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index a950233dcef..46349cf81af 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -65,25 +65,11 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); - mci->GetOutput()->SetRequestedRegion(test->GetLargestPossibleRegion()); - mci->DetermineSliceOrientations(); // calculates indices - typename mciType::SliceIndicesType indices = mci->GetLabeledSliceIndices(); - // mci->GetOutput()->SetRequestedRegion(reg); - mci->SetUseCustomSlicePositions(true); - for (int i = 0; i < ImageType::ImageDimension; i++) - { - for (int l = 0; l < indices[i].size(); l++) - { - mci->SetLabeledSliceIndices(i, l, indices[i][l]); - } - } - // mci->Update(); typedef itk::RegionOfInterestImageFilter outConverterType; typename outConverterType::Pointer outConv = outConverterType::New(); outConv->SetInput(mci->GetOutput()); outConv->SetRegionOfInterest(reg); - // outConv->SetRegionOfInterest(test->GetLargestPossibleRegion()); outConv->Update(); typedef itk::ImageFileWriter WriterType; From 00bb2af8fae4a8e0bbb94cf92a8dc7039d605871 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 Jul 2016 16:21:26 -0400 Subject: [PATCH 096/176] ENH: Converting non-POD method parameters into (const) references --- .../itkMorphologicalContourInterpolator.h | 130 ++++++++-------- .../itkMorphologicalContourInterpolator.hxx | 141 +++++++++--------- 2 files changed, 136 insertions(+), 135 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 47532426ce9..1edf357b244 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -178,9 +178,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter indices) + SetLabeledSliceIndices(unsigned int axis, + typename TImage::PixelType label, + const std::vector & indices) { m_LabeledSlices[axis][label] = SliceSetType().insert(indices.begin(), indices.end()); this->Modified(); @@ -189,7 +189,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilterModified(); @@ -235,7 +235,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter - GenerateDilationSequence(typename BoolSliceType::Pointer begin, - typename BoolSliceType::Pointer end, - ThreadIdType threadId); + GenerateDilationSequence(typename BoolSliceType::Pointer & begin, + typename BoolSliceType::Pointer & end, + ThreadIdType threadId); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer - FindMedianImageDilations(typename BoolSliceType::Pointer intersection, - typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask, - ThreadIdType threadId); + FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, + typename BoolSliceType::Pointer & iMask, + typename BoolSliceType::Pointer & jMask, + ThreadIdType threadId); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer - FindMedianImageDistances(typename BoolSliceType::Pointer intersection, - typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask, - ThreadIdType threadId); + FindMedianImageDistances(typename BoolSliceType::Pointer & intersection, + typename BoolSliceType::Pointer & iMask, + typename BoolSliceType::Pointer & jMask, + ThreadIdType threadId); /** Build transition sequence and pick the median */ void - Interpolate1to1(int axis, - TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - typename TImage::PixelType jRegionId, - typename SliceType::IndexType translation, - bool recursive, - ThreadIdType threadId); + Interpolate1to1(int axis, + TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + typename TImage::PixelType jRegionId, + const typename SliceType::IndexType & translation, + bool recursive, + ThreadIdType threadId); typedef std::vector PixelList; /** Splits the bigger region and does N 1-to-1 interpolations */ void - Interpolate1toN(int axis, - TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - PixelList jRegionIds, - typename SliceType::IndexType translation, - ThreadIdType threadId); + Interpolate1toN(int axis, + TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + const PixelList & jRegionIds, + const typename SliceType::IndexType & translation, + ThreadIdType threadId); /** Crates a translated copy of part of the image which fits in the newRegion. */ typename SliceType::Pointer - TranslateImage(typename SliceType::Pointer image, - typename SliceType::IndexType translation, - typename SliceType::RegionType newRegion); + TranslateImage(typename SliceType::Pointer & image, + const typename SliceType::IndexType & translation, + typename SliceType::RegionType newRegion); /** The returns cardingal of the symmetric distance between images. The images must cover the same region */ IdentifierType - CardSymDifference(typename BoolSliceType::Pointer shape1, typename BoolSliceType::Pointer shape2); + CardSymDifference(typename BoolSliceType::Pointer & shape1, typename BoolSliceType::Pointer & shape2); /** Copied from ImageSource and changed to allocate a cleared buffer. */ virtual void @@ -345,29 +345,29 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; BoundingBoxesType m_BoundingBoxes; // bounding box for each label @@ -381,17 +381,17 @@ class MorphologicalContourInterpolator : public ImageToImageFilter void - ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index); + ExpandRegion(typename T2::RegionType & region, const typename T2::IndexType & index); /** Connected components of a specified region. */ typename SliceType::Pointer - RegionedConnectedComponents(const typename TImage::RegionType region, - typename TImage::PixelType label, - IdentifierType & objectCount); + RegionedConnectedComponents(const typename TImage::RegionType & region, + typename TImage::PixelType label, + IdentifierType & objectCount); /** Seed and mask must cover the same region (size and index the same). */ typename BoolSliceType::Pointer - Dilate1(typename BoolSliceType::Pointer seed, typename BoolSliceType::Pointer mask, ThreadIdType threadId); + Dilate1(typename BoolSliceType::Pointer & seed, typename BoolSliceType::Pointer & mask, ThreadIdType threadId); typedef ExtractImageFilter RoiType; typename RoiType::Pointer m_RoI; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 97cd2660121..6f95d9bf56f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -151,8 +151,8 @@ private: template bool -MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Pointer a, - typename BoolSliceType::Pointer b) +MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Pointer & a, + typename BoolSliceType::Pointer & b) { ImageRegionConstIterator ita(a, a->GetLargestPossibleRegion()); ImageRegionConstIterator itb(b, b->GetLargestPossibleRegion()); @@ -209,7 +209,8 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() template template void -MorphologicalContourInterpolator::ExpandRegion(typename T2::RegionType & region, typename T2::IndexType index) +MorphologicalContourInterpolator::ExpandRegion(typename T2::RegionType & region, + const typename T2::IndexType & index) { for (unsigned int a = 0; a < T2::ImageDimension; ++a) { @@ -309,7 +310,7 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename SliceType::Pointer iConn, + typename SliceType::Pointer & iConn, typename TImage::PixelType iRegionId, ThreadIdType threadId) { @@ -357,9 +358,9 @@ MorphologicalContourInterpolator::Extrapolate(int template typename MorphologicalContourInterpolator::BoolSliceType::Pointer -MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer seed, - typename BoolSliceType::Pointer mask, - ThreadIdType threadId) +MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer & seed, + typename BoolSliceType::Pointer & mask, + ThreadIdType threadId) { // set up structuring element for dilation typedef BinaryCrossStructuringElement @@ -434,9 +435,9 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe template std::vector::BoolSliceType::Pointer> -MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer begin, - typename BoolSliceType::Pointer end, - ThreadIdType threadId) +MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer & begin, + typename BoolSliceType::Pointer & end, + ThreadIdType threadId) { std::vector seq; seq.push_back(Dilate1(begin, end, threadId)); @@ -452,10 +453,10 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool template typename MorphologicalContourInterpolator::BoolSliceType::Pointer -MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer intersection, - typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask, - ThreadIdType threadId) +MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, + typename BoolSliceType::Pointer & iMask, + typename BoolSliceType::Pointer & jMask, + ThreadIdType threadId) { std::vector iSeq = GenerateDilationSequence(intersection, iMask, threadId); std::vector jSeq = GenerateDilationSequence(intersection, jMask, threadId); @@ -516,7 +517,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool template typename MorphologicalContourInterpolator::FloatSliceType::Pointer -MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer mask, ThreadIdType threadId) +MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask, ThreadIdType threadId) { typedef itk::SignedMaurerDistanceMapImageFilter FilterType; static std::vector initialized(m_ThreadCount); // default: false @@ -536,10 +537,10 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point template typename MorphologicalContourInterpolator::BoolSliceType::Pointer -MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer intersection, - typename BoolSliceType::Pointer iMask, - typename BoolSliceType::Pointer jMask, - ThreadIdType threadId) +MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer & intersection, + typename BoolSliceType::Pointer & iMask, + typename BoolSliceType::Pointer & jMask, + ThreadIdType threadId) { // calculate distance field typename FloatSliceType::Pointer sdf = MaurerDM(intersection, threadId); @@ -696,18 +697,18 @@ MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer void -MorphologicalContourInterpolator::Interpolate1to1(int axis, - TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - typename TImage::PixelType jRegionId, - typename SliceType::IndexType translation, - bool recursive, - ThreadIdType threadId) +MorphologicalContourInterpolator::Interpolate1to1(int axis, + TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + typename TImage::PixelType jRegionId, + const typename SliceType::IndexType & translation, + bool recursive, + ThreadIdType threadId) { // translate iConn by t/2 and jConn by -t/2 typename SliceType::IndexType iTrans; @@ -972,17 +973,17 @@ public: template void -MorphologicalContourInterpolator::Interpolate1toN(int axis, - TImage * out, - typename TImage::PixelType label, - typename TImage::IndexValueType i, - typename TImage::IndexValueType j, - typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - PixelList jRegionIds, - typename SliceType::IndexType translation, - ThreadIdType threadId) +MorphologicalContourInterpolator::Interpolate1toN(int axis, + TImage * out, + typename TImage::PixelType label, + typename TImage::IndexValueType i, + typename TImage::IndexValueType j, + typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + const PixelList & jRegionIds, + const typename SliceType::IndexType & translation, + ThreadIdType threadId) { // first convert iConn into binary mask MatchesID matchesID(iRegionId); @@ -1031,8 +1032,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int { if (maskIt.Get()) { - typename TImage::PixelType jVal = jIt.Get(); - typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + typename PixelList::const_iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { blobs[res - jRegionIds.begin()]->SetPixel(maskIt.GetIndex(), true); @@ -1148,9 +1149,9 @@ MorphologicalContourInterpolator::Interpolate1toN(int template typename MorphologicalContourInterpolator::SliceType::Pointer -MorphologicalContourInterpolator::TranslateImage(typename SliceType::Pointer image, - typename SliceType::IndexType translation, - typename SliceType::RegionType newRegion) +MorphologicalContourInterpolator::TranslateImage(typename SliceType::Pointer & image, + const typename SliceType::IndexType & translation, + typename SliceType::RegionType newRegion) { typename SliceType::Pointer result = SliceType::New(); result->CopyInformation(image); @@ -1165,9 +1166,9 @@ MorphologicalContourInterpolator::TranslateImage(typename SliceType::Poi template void -MorphologicalContourInterpolator::IntersectionRegions(typename SliceType::IndexType translation, - typename SliceType::RegionType & iRegion, - typename SliceType::RegionType & jRegion) +MorphologicalContourInterpolator::IntersectionRegions(const typename SliceType::IndexType & translation, + typename SliceType::RegionType & iRegion, + typename SliceType::RegionType & jRegion) { typename SliceType::IndexType iBegin = iRegion.GetIndex(); typename SliceType::IndexType jBegin = jRegion.GetIndex(); @@ -1187,11 +1188,11 @@ MorphologicalContourInterpolator::IntersectionRegions(typename SliceType template IdentifierType -MorphologicalContourInterpolator::Intersection(typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - PixelList jRegionIds, - typename SliceType::IndexType translation) +MorphologicalContourInterpolator::Intersection(typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + const PixelList & jRegionIds, + const typename SliceType::IndexType & translation) { typename SliceType::RegionType iRegion, jRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -1209,8 +1210,8 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point { if (iIt.Get() == iRegionId) { - typename TImage::PixelType jVal = jIt.Get(); - typename PixelList::iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + typename PixelList::const_iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { ++counts[res - jRegionIds.begin()]; @@ -1233,8 +1234,8 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point template IdentifierType -MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceType::Pointer iShape, - typename BoolSliceType::Pointer jShape) +MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceType::Pointer & iShape, + typename BoolSliceType::Pointer & jShape) { typename BoolSliceType::RegionType region = iShape->GetLargestPossibleRegion(); IdentifierType count = 0; @@ -1254,7 +1255,7 @@ MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceTy template typename MorphologicalContourInterpolator::SliceType::IndexType -MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer conn, PixelList regionIds) +MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & conn, const PixelList & regionIds) { ImageRegionConstIteratorWithIndex it(conn, conn->GetLargestPossibleRegion()); IndexValueType ind[SliceType::ImageDimension] = { 0 }; // all components are initialized to zero @@ -1264,7 +1265,7 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer c typename TImage::PixelType val = it.Get(); if (val) { - typename PixelList::iterator res = std::find(regionIds.begin(), regionIds.end(), val); + typename PixelList::const_iterator res = std::find(regionIds.begin(), regionIds.end(), val); if (res != regionIds.end()) { ++pixelCount; @@ -1288,10 +1289,10 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer c template typename MorphologicalContourInterpolator::SliceType::IndexType -MorphologicalContourInterpolator::Align(typename SliceType::Pointer iConn, - typename TImage::PixelType iRegionId, - typename SliceType::Pointer jConn, - PixelList jRegionIds) +MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iConn, + typename TImage::PixelType iRegionId, + typename SliceType::Pointer & jConn, + const PixelList & jRegionIds) { // calculate centroids PixelList iRegionIds; @@ -1390,9 +1391,9 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer iCon template typename MorphologicalContourInterpolator::SliceType::Pointer -MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType region, - typename TImage::PixelType label, - IdentifierType & objectCount) +MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType & region, + typename TImage::PixelType label, + IdentifierType & objectCount) { m_RoI->SetExtractionRegion(region); m_RoI->SetInput(this->GetInput()); @@ -1411,8 +1412,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, - typename SliceType::Pointer iconn, - typename SliceType::Pointer jconn, + typename SliceType::Pointer & iconn, + typename SliceType::Pointer & jconn, ThreadIdType threadId) { // go through comparison image and create correspondence pairs From 45de58df22ebef9b27746f40883da56c71f053e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 14 Jul 2016 17:03:38 -0400 Subject: [PATCH 097/176] BUG: Removing WriteDebug and trailing space --- .../itkMorphologicalContourInterpolator.hxx | 94 +------------------ 1 file changed, 1 insertion(+), 93 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 6f95d9bf56f..48fc91e764b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -40,47 +40,9 @@ #include #include -// DEBUG -#include -#include "itkImageFileWriter.h" - namespace itk { -template -void -WriteDebug(itk::SmartPointer out, const char * filename) -{ - return; // tests run much faster - // typedef ImageFileWriter WriterType; - // typename WriterType::Pointer w = WriterType::New(); - // w->SetNumberOfThreads(1); //excessive threading is counterproductive - // w->SetInput(out); - // w->SetFileName(filename); - // try - // { - // w->Update(); - // } - // catch (ExceptionObject & error) - // { - // std::cerr << "Error: " << error << std::endl; - // } -} - -template -void -WriteDebug(itk::SmartPointer> out, const char * filename) -{ - typedef Image BoolImageType; - typedef Image ucharImageType; - typedef CastImageFilter CastType; - typename CastType::Pointer caster = CastType::New(); - caster->SetNumberOfThreads(1); // excessive threading is counterproductive - caster->SetInput(out); - WriteDebug(caster->GetOutput(), filename); -} - - template struct SegmentBetweenTwo { @@ -338,8 +300,6 @@ MorphologicalContourInterpolator::Extrapolate(int // add a phantom point to the center of a newly constructed slice phSlice->SetPixel(centroid, iRegionId); - // WriteDebug(iConn, "C:\\iConn.nrrd"); - // WriteDebug(phSlice, "C:\\phSlice.nrrd"); // do alignment in case the iShape is concave and centroid is not within the iShape typename SliceType::IndexType translation = Align(iConn, iRegionId, phSlice, jRegionIds); @@ -425,10 +385,6 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe m_And[threadId]->Update(); typename BoolSliceType::Pointer result = m_And[threadId]->GetOutput(); result->DisconnectPipeline(); - // WriteDebug(seed, "C:\\seed.nrrd"); - // WriteDebug(mask, "C:\\mask.nrrd"); - // WriteDebug(temp, "C:\\temp.nrrd"); - // WriteDebug(result, "C:\\result.nrrd"); return result; } @@ -484,10 +440,6 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool m_Or[threadId]->SetInput(0, iSeq[x]); unsigned xj = ratio * x; m_Or[threadId]->SetInput(1, jSeq[xj]); -#ifdef _DEBUG - // WriteDebug(iSeq[x], (std::string("C:\\iSeq") + std::to_string(x) + ".nrrd").c_str()); - // WriteDebug(jSeq[xj], (std::string("C:\\jSeq") + std::to_string(x) + ".nrrd").c_str()); -#endif // _DEBUG m_Or[threadId]->GetOutput()->SetRegions(iMask->GetRequestedRegion()); m_Or[threadId]->Update(); seq.push_back(m_Or[threadId]->GetOutput()); @@ -499,9 +451,6 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool IdentifierType min = iMask->GetRequestedRegion().GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { -#ifdef _DEBUG - // WriteDebug(seq[x], (std::string("C:\\seq") + std::to_string(x) + ".nrrd").c_str()); -#endif // _DEBUG IdentifierType iS = CardSymDifference(seq[x], iMask); IdentifierType jS = CardSymDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) @@ -544,7 +493,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool { // calculate distance field typename FloatSliceType::Pointer sdf = MaurerDM(intersection, threadId); - WriteDebug(sdf, "C:\\sdf.nrrd"); // create histograms of distances and union typename BoolSliceType::Pointer orImage = BoolSliceType::New(); @@ -592,7 +540,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool ++ito; ++itsdf; } - WriteDebug(orImage, "C:\\orImage.nrrd"); // sum of histogram bins for i and j and std::vector::size_type maxSize = std::max(iHist.size(), jHist.size()); @@ -653,7 +600,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool m_And[threadId]->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); m_And[threadId]->Update(); typename BoolSliceType::Pointer median = m_And[threadId]->GetOutput(); - WriteDebug(median, "C:\\median.nrrd"); return median; } @@ -751,12 +697,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int ExpandRegion(newRegion, jBottom); typename SliceType::IndexValueType mid = (i + j + (carry ? 1 : 0)) / 2; // index of middle slice - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); typename SliceType::Pointer iConnT = TranslateImage(iConn, iTrans, newRegion); typename SliceType::Pointer jConnT = TranslateImage(jConn, jTrans, newRegion); - WriteDebug(iConnT, "C:\\iConnT.nrrd"); - WriteDebug(jConnT, "C:\\jConnT.nrrd"); if (!recursive) // reduce newRegion to bounding box so we deal with less pixels { @@ -801,8 +743,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int ++ibIt; ++jbIt; } - WriteDebug(iSlice, "C:\\iSlice.nrrd"); - WriteDebug(jSlice, "C:\\jSlice.nrrd"); // create intersection typedef AndImageFilter AndSliceType; @@ -820,7 +760,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int sAnd[threadId]->Update(); typename BoolSliceType::Pointer intersection = sAnd[threadId]->GetOutput(); intersection->DisconnectPipeline(); - WriteDebug(intersection, "C:\\intersection.nrrd"); typename BoolSliceType::Pointer median; if (m_UseDistanceTransform) @@ -883,7 +822,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int ++seqIt; ++midIt; } - WriteDebug(midConn, "C:\\midConn.nrrd"); bool withinReq = true; typename TImage::RegionType reqRegion = this->GetOutput()->GetRequestedRegion(); @@ -915,7 +853,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int ++outIt; } mutex.Unlock(); - WriteDebug(midConn, "C:\\midConn.nrrd"); } // iterator destroyed here // recurse if needed @@ -940,8 +877,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); } } - // does not compile for RLEImage - // WriteDebug(out, "C:\\intermediateResult.nrrd"); } template @@ -995,9 +930,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int caster->SetInput(iConn); caster->Update(); typename BoolSliceType::Pointer mask = caster->GetOutput(); - // WriteDebug(mask, "C:\\mask.nrrd"); - WriteDebug(iConn, "C:\\iConn.nrrd"); - WriteDebug(jConn, "C:\\jConn.nrrd"); typename SliceType::RegionType iRegion, jRegion, newjRegion; iRegion = iConn->GetLargestPossibleRegion(); @@ -1044,14 +976,12 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt; ++belongInit; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); // prepare dilation filter iRegion = iConn->GetLargestPossibleRegion(); // expand to full i image for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x]->SetRegions(iRegion); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); } ImageRegionConstIterator maskIt2(mask, iRegion); ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); @@ -1062,7 +992,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int for (unsigned x = 0; x < jRegionIds.size(); x++) { blobs[x] = Dilate1(blobs[x], mask, threadId); - // WriteDebug(blobs[x], (std::string("C:\\blob") + char('0' + x) + ".nrrd").c_str()); blobs[x]->DisconnectPipeline(); } @@ -1114,7 +1043,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++jIt2; ++belongIt; } - // WriteDebug(belongs, "C:\\belongs.nrrd"); } while (!hollowedMaskEmpty); blobs.clear(); // deallocates the images @@ -1315,8 +1243,6 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC searchRegion.SetIndex(d, jLPR.GetIndex()[d] - iLPR.GetIndex()[d] - iLPR.GetSize(d) + 1); searchRegion.SetSize(d, iLPR.GetSize(d) + jLPR.GetSize(d) - 1); } - // searchRegion.SetSize(axis, 1); - // searchRegion.SetIndex(axis, 0); typename BoolSliceType::Pointer searched = BoolSliceType::New(); searched->SetRegions(searchRegion); @@ -1336,22 +1262,11 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC IdentifierType minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); IdentifierType maxIter = std::max(m_MaxAlignIters, (IdentifierType)sqrt(searchRegion.GetNumberOfPixels())); - // debug: construct and later fill the image with intersection scores -#ifndef NDEBUG - typename SliceType::Pointer scoreImage = SliceType::New(); - scoreImage->SetRegions(searchRegion); - scoreImage->Allocate(true); -#endif // NDEBUG - while (!uncomputed.empty()) { ind = uncomputed.front(); uncomputed.pop(); score = Intersection(iConn, iRegionId, jConn, jRegionIds, ind); -#ifndef NDEBUG - scoreImage->SetPixel(ind, score + 1); // unexplored=0, noIntersection=1 -#endif // NDEBUG - if (score > maxScore) { maxScore = score; @@ -1381,10 +1296,7 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC } } } - // WriteDebug(searched, "C:\\searched.nrrd"); -#ifndef NDEBUG - WriteDebug(scoreImage, "C:\\scoreImage.nrrd"); -#endif // NDEBUG + return bestIndex; } @@ -1655,10 +1567,6 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou int jReq = *next < reqRegion.GetIndex(axis) ? -1 : (*next > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); - - // WriteDebug(iconn, "C:\\iconn.nrrd"); - // WriteDebug(jconn, "C:\\jconn.nrrd"); - if (*prev + 1 < *next // only if they are not adjacent slices && abs(iReq + jReq) <= 1) // and not out of the requested region // unless they are on opposite ends From 8cb431e0ec99deb1f16c282e608f5cb2abf599f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 15 Jul 2016 16:15:29 -0400 Subject: [PATCH 098/176] ENH: simplifying dependency --- .../MorphologicalContourInterpolation/itk-module.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index 0f7e888be90..fedd165367b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -9,9 +9,9 @@ itk_module( DEPENDS ITKCommon ITKBinaryMathematicalMorphology - ITKIOImageBase # typename ITKDistanceMap TEST_DEPENDS + ITKIOImageBase # typename ITKTestKernel EXCLUDE_FROM_DEFAULT DESCRIPTION "${DOCUMENTATION}" From 8305cb7bd6be5d97da20cfbfe4f133e198d0c756 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 19 Jul 2016 13:03:13 -0400 Subject: [PATCH 099/176] ENH: Testing and improvements Removing local copy of RLEImage and relying on RLEImage module Renaming CMake target to avoid conflict with RLEImage Taking care of signed/unsigned warnings Applying code formatting --- .../itkMorphologicalContourInterpolator.h | 9 +- .../itkMorphologicalContourInterpolator.hxx | 87 +-- .../itk-module.cmake | 1 + .../test/CMakeLists.txt | 4 +- .../test/RLEImage/RLEImage.h | 283 ---------- .../test/RLEImage/RLEImage.txx | 260 --------- .../test/RLEImage/RLEImageConstIterator.h | 440 --------------- .../test/RLEImage/RLEImageIterator.h | 161 ------ .../RLEImage/RLEImageRegionConstIterator.h | 232 -------- .../test/RLEImage/RLEImageRegionIterator.h | 144 ----- .../RLEImage/RLEImageScanlineConstIterator.h | 155 ----- .../test/RLEImage/RLEImageScanlineIterator.h | 86 --- .../RLEImage/RLERegionOfInterestImageFilter.h | 293 ---------- .../RLERegionOfInterestImageFilter.txx | 531 ------------------ ...kMorphologicalContourInterpolationTest.cxx | 17 +- 15 files changed, 57 insertions(+), 2646 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 1edf357b244..ceb50f04411 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -18,11 +18,11 @@ #ifndef itkMorphologicalContourInterpolator_h #define itkMorphologicalContourInterpolator_h +#include "itkBinaryThresholdImageFilter.h" +#include "itkConnectedComponentImageFilter.h" +#include "itkExtractImageFilter.h" #include "itkImageToImageFilter.h" #include "itksys/hash_map.hxx" -#include "itkExtractImageFilter.h" -#include "itkConnectedComponentImageFilter.h" -#include "itkBinaryThresholdImageFilter.h" namespace itk @@ -65,7 +65,7 @@ namespace itk template class MorphologicalContourInterpolator : public ImageToImageFilter { - template + template friend class MorphologicalContourInterpolatorParallelInvoker; public: @@ -216,7 +216,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter -#include +#include "itkThreadedIndexedContainerPartitioner.h" +#include "itkUnaryFunctorImageFilter.h" #include +#include #include +#include #include @@ -94,7 +94,7 @@ private: ThreadedExecution(const DomainType & subDomain, const ThreadIdType threadId) { // Look only at the range of cells by the set of indices in the subDomain. - for (itk::IndexValueType ii = subDomain[0]; ii <= subDomain[1] && ii < m_WorkArray.size(); ++ii) + for (itk::IndexValueType ii = subDomain[0]; ii <= subDomain[1] && ii < IndexValueType(m_WorkArray.size()); ++ii) { this->m_Associate->InterpolateBetweenTwo(m_WorkArray[ii].axis, m_WorkArray[ii].out, @@ -105,7 +105,7 @@ private: m_WorkArray[ii].jconn, threadId); } - } + } // ThreadedExecution std::vector> m_WorkArray; }; @@ -137,7 +137,7 @@ MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Po { return false; } -} +} // >::ImagesEqual template @@ -262,7 +262,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } } -} +} // >::DetermineSliceOrientations template @@ -313,7 +313,7 @@ MorphologicalContourInterpolator::Extrapolate(int phSlice->SetRegions(reg3); typename SliceType::IndexType t0 = { 0 }; Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false, threadId); -} +} // >::Extrapolate template @@ -386,7 +386,7 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typename BoolSliceType::Pointer result = m_And[threadId]->GetOutput(); result->DisconnectPipeline(); return result; -} +} // >::Dilate1 template @@ -461,7 +461,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool } } return seq[minIndex]; -} +} // >::FindMedianImageDilations template @@ -508,7 +508,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool const short fractioning = 10; // how many times more precise distance than rounding to int while (!itsdf.IsAtEnd()) { - ; bool iM = iti.Get(); bool jM = itj.Get(); typename TImage::PixelType dist = fractioning * itsdf.Get(); @@ -601,7 +600,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool m_And[threadId]->Update(); typename BoolSliceType::Pointer median = m_And[threadId]->GetOutput(); return median; -} +} // >::FindMedianImageDistances template @@ -639,7 +638,7 @@ MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer::BoundingBox template void @@ -861,10 +860,15 @@ MorphologicalContourInterpolator::Interpolate1to1(int PixelList regionIDs; regionIDs.push_back(1); - int iReq = i < reqRegion.GetIndex(axis) ? -1 : (i > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); - int jReq = j < reqRegion.GetIndex(axis) ? -1 : (j > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); - int mReq = - mid < reqRegion.GetIndex(axis) ? -1 : (mid > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + int iReq = i < reqRegion.GetIndex(axis) + ? -1 + : (i > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); + int jReq = j < reqRegion.GetIndex(axis) + ? -1 + : (j > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); + int mReq = mid < reqRegion.GetIndex(axis) + ? -1 + : (mid > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); bool first = abs(i - mid) > 1 && abs(iReq + mReq) <= 1; // i-mid? bool second = abs(j - mid) > 1 && abs(jReq + mReq) <= 1; // j-mid? @@ -877,7 +881,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); } } -} +} // >::Interpolate1to1 template class MatchesID @@ -1072,7 +1076,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false, threadId); } -} +} // >::Interpolate1toN template @@ -1158,7 +1162,7 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point sum += counts[x]; } return sum; -} +} // >::Intersection template IdentifierType @@ -1212,7 +1216,7 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & retVal[d] = ind[d] / pixelCount; } return retVal; -} +} // >::Centroid template @@ -1298,7 +1302,7 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC } return bestIndex; -} +} // >::Align template @@ -1341,7 +1345,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { uncleanPairs.insert(std::make_pair(iti.Get(), itj.Get())); // std::cout << " iti:" << iti.GetIndex() << iti.Get() << - // " itj:" << itj.GetIndex() << itj.Get() << std::endl; + // " itj:" << itj.GetIndex() << itj.Get() << std::endl; if (iti.Get() != 0 && itj.Get() != 0) { unwantedPairs.insert(std::make_pair(0, itj.Get())); @@ -1554,8 +1558,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou IdentifierType xCount; typename SliceType::Pointer iconn = this->RegionedConnectedComponents(ri, it->first, xCount); iconn->DisconnectPipeline(); - int iReq = - *prev < reqRegion.GetIndex(axis) ? -1 : (*prev > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + int iReq = *prev < reqRegion.GetIndex(axis) + ? -1 + : (*prev > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); typename SliceSetType::iterator next = it->second.begin(); for (++next; next != it->second.end(); ++next) @@ -1564,8 +1569,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou rj.SetIndex(axis, *next); typename SliceType::Pointer jconn = this->RegionedConnectedComponents(rj, it->first, xCount); jconn->DisconnectPipeline(); - int jReq = - *next < reqRegion.GetIndex(axis) ? -1 : (*next > reqRegion.GetIndex(axis) + reqRegion.GetSize(axis) ? +1 : 0); + int jReq = *next < reqRegion.GetIndex(axis) + ? -1 + : (*next > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); if (*prev + 1 < *next // only if they are not adjacent slices && abs(iReq + jReq) <= 1) // and not out of the requested region @@ -1596,7 +1602,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou completeDomain[1] = std::max(0, int(segments.size()) - 1); parallelizer->Execute(this, completeDomain); parallelizer->ClearWorkArray(); -} +} // >::InterpolateAlong template @@ -1696,8 +1702,7 @@ MorphologicalContourInterpolator::GenerateData() ++itI; ++itO; } -} - +} // >::GenerateData } // end namespace itk #endif // itkMorphologicalContourInterpolator_hxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index fedd165367b..6df356092ca 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -13,6 +13,7 @@ itk_module( TEST_DEPENDS ITKIOImageBase # typename ITKTestKernel + RLEImage EXCLUDE_FROM_DEFAULT DESCRIPTION "${DOCUMENTATION}" ) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 5cf9acdfa9c..8dce950903c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -8,12 +8,12 @@ set( createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") add_executable( - runFromIDE + manualTest manualTest.cxx ${MorphologicalContourInterpolationTests} ) target_link_libraries( - runFromIDE + manualTest ${MorphologicalContourInterpolation-Test_LIBRARIES} ) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h deleted file mode 100644 index 32f30db30e6..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.h +++ /dev/null @@ -1,283 +0,0 @@ -#ifndef RLEImage_h -#define RLEImage_h - -#include //std::pair -#include -#include -#include - -/** Run-Length Encoded image. - * It saves memory for label images at the expense of processing times. - * Unsuitable for ordinary images (in which case it is counterproductive). - * - * BufferedRegion must include complete run-length lines (along X index axis). - * BufferedRegion can be smaller than LargestPossibleRegion along other axes. - * - * It is best if pixel type and counter type have the same byte size - * (for memory alignment purposes). - * - * Copied and adapted from itk::Image. - */ -template -class RLEImage : public itk::ImageBase -{ - -public: - /** Standard class typedefs */ - typedef RLEImage Self; - typedef itk::ImageBase Superclass; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - typedef itk::WeakPointer ConstWeakPointer; - - /** Method for creation through the object factory. */ - itkNewMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(RLEImage, ImageBase); - - /** Pixel typedef support. Used to declare pixel type in filters - * or other operations. */ - typedef TPixel PixelType; - - /** Typedef alias for PixelType */ - typedef TPixel ValueType; - - /** First element is count of repetitions, - * second element is the pixel value. */ - typedef std::pair RLSegment; - - /** A Run-Length encoded line of pixels. */ - typedef std::vector RLLine; - - /** Internal Pixel representation. Used to maintain a uniform API - * with Image Adaptors and allow to keep a particular internal - * representation of data while showing a different external - * representation. */ - typedef RLLine InternalPixelType; - - // typedef PixelType IOPixelType; - - /** Dimension of the image. This constant is used by functions that are - * templated over image type (as opposed to being templated over pixel type - * and dimension) when they need compile time access to the dimension of - * the image. */ - itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); - - /** Index typedef support. An index is used to access pixel values. */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::IndexValueType IndexValueType; - - /** Offset typedef support. An offset is used to access pixel values. */ - typedef typename Superclass::OffsetType OffsetType; - - /** Size typedef support. A size is used to define region bounds. */ - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::SizeValueType SizeValueType; - - /** Direction typedef support. A matrix of direction cosines. */ - typedef typename Superclass::DirectionType DirectionType; - - /** Region typedef support. A region is used to specify a subset of an image. - */ - typedef typename Superclass::RegionType RegionType; - - /** Spacing typedef support. Spacing holds the size of a pixel. The - * spacing is the geometric distance between image samples. */ - typedef typename Superclass::SpacingType SpacingType; - typedef typename Superclass::SpacingValueType SpacingValueType; - - /** Origin typedef support. The origin is the geometric coordinates - * of the index (0,0). */ - typedef typename Superclass::PointType PointType; - - /** Offset typedef (relative position between indices) */ - typedef typename Superclass::OffsetValueType OffsetValueType; - - /** Allocate the image memory. The size of the image must - * already be set, e.g. by calling SetRegions(). - * Pixel values are initialized using default constructor. */ - virtual void - Allocate(bool initialize = false); - - /** Restore the data object to its initial state. This means releasing - * memory. */ - virtual void - Initialize() - { - // Call the superclass which should initialize the BufferedRegion ivar. - Superclass::Initialize(); - m_OnTheFlyCleanup = true; - myBuffer = BufferType::New(); - } - - /** Fill the image buffer with a value. Be sure to call Allocate() - * first. */ - void - FillBuffer(const TPixel & value); - - virtual void - SetLargestPossibleRegion(const RegionType & region) - { - Superclass::SetLargestPossibleRegion(region); - myBuffer->SetLargestPossibleRegion(truncateRegion(region)); - } - - virtual void - SetBufferedRegion(const RegionType & region) - { - Superclass::SetBufferedRegion(region); - myBuffer->SetBufferedRegion(truncateRegion(region)); - } - - virtual void - SetRequestedRegion(const RegionType & region) - { - Superclass::SetRequestedRegion(region); - myBuffer->SetRequestedRegion(truncateRegion(region)); - } - - /** \brief Set a pixel value. - * - * Allocate() needs to have been called first -- for efficiency, - * this function does not check that the image has actually been - * allocated yet. SLOW -> Use iterators instead. */ - void - SetPixel(const IndexType & index, const TPixel & value); - - /** Set a pixel value in the given line and updates segmentRemainder - * and realIndex to refer to the same pixel. - * Returns difference in line length which happens due to merging or splitting segments. - * This method is used by iterators directly. */ - int - SetPixel(RLLine & line, IndexValueType & segmentRemainder, IndexValueType & realIndex, const TPixel & value); - - /** \brief Get a pixel. SLOW! Better use iterators for pixel access. */ - const TPixel & - GetPixel(const IndexType & index) const; - - ///** Get a reference to a pixel. Chaning it changes the whole RLE segment! */ - // TPixel & GetPixel(const IndexType & index); - - ///** \brief Access a pixel. Chaning it changes the whole RLE segment! */ - // TPixel & operator[](const IndexType & index) - //{ - // return this->GetPixel(index); - // } - - /** \brief Access a pixel. This version can only be an rvalue. - * SLOW -> Use iterators instead. */ - const TPixel & - operator[](const IndexType & index) const - { - return this->GetPixel(index); - } - - virtual unsigned int - GetNumberOfComponentsPerPixel() const - { - // use the GetLength() method which works with variable length arrays, - // to make it work with as much pixel types as possible - PixelType p; - return itk::NumericTraits::GetLength(p); - } - - /** Typedef for the internally used buffer. */ - typedef typename itk::Image BufferType; - - /** We need to allow itk-style iterators to be constructed. */ - typename BufferType::Pointer - GetBuffer() - { - return myBuffer; - } - - /** We need to allow itk-style const iterators to be constructed. */ - typename BufferType::Pointer - GetBuffer() const - { - return myBuffer; - } - - /** Returns N-1-dimensional index, the remainder after 0-index is removed. */ - static inline typename BufferType::IndexType - truncateIndex(const IndexType & index); - - /** Returns N-1-dimensional size, the remainder after 0-size is removed. */ - static inline typename BufferType::SizeType - truncateSize(const SizeType & size); - - /** Returns N-1-dimensional region, the remainder after 0-index and size are removed. */ - static typename BufferType::RegionType - truncateRegion(const RegionType & region); - - /** Merges adjacent segments with duplicate values. - * Automatically called when turning on OnTheFlyCleanup. */ - void - CleanUp() const; - - /** Should same-valued segments be merged on the fly? - * On the fly merging usually provides better performance. */ - bool - GetOnTheFlyCleanup() const - { - return m_OnTheFlyCleanup; - } - - /** Should same-valued segments be merged on the fly? - * On the fly merging usually provides better performance. */ - void - SetOnTheFlyCleanup(bool value) - { - if (value == m_OnTheFlyCleanup) - return; - m_OnTheFlyCleanup = value; - if (m_OnTheFlyCleanup) - CleanUp(); // put the image into a clean state - } - - -protected: - RLEImage() - : itk::ImageBase() - { - m_OnTheFlyCleanup = true; - myBuffer = BufferType::New(); - } - void - PrintSelf(std::ostream & os, itk::Indent indent) const; - - virtual ~RLEImage() {} - - /** Compute helper matrices used to transform Index coordinates to - * PhysicalPoint coordinates and back. This method is virtual and will be - * overloaded in derived classes in order to provide backward compatibility - * behavior in classes that did not used to take image orientation into - * account. */ - virtual void - ComputeIndexToPhysicalPointMatrices() - { - this->Superclass::ComputeIndexToPhysicalPointMatrices(); - } - - /** Merges adjacent segments with duplicate values in a single line. */ - void - CleanUpLine(RLLine & line) const; - -private: - bool m_OnTheFlyCleanup; // should same-valued segments be merged on the fly - - RLEImage(const Self &); // purposely not implemented - void - operator=(const Self &); // purposely not implemented - - /** Memory for the current buffer. */ - mutable typename BufferType::Pointer myBuffer; -}; - - -#ifndef ITK_MANUAL_INSTANTIATION -# include "RLEImage.txx" -#endif - -#endif // RLEImage_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx deleted file mode 100644 index 80e1b7f9509..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImage.txx +++ /dev/null @@ -1,260 +0,0 @@ -#ifndef RLEImage_txx -#define RLEImage_txx - -#include "RLEImage.h" -#include "itkImageRegionConstIterator.h" - -template -inline typename RLEImage::BufferType::IndexType -RLEImage::truncateIndex(const IndexType & index) -{ - typename BufferType::IndexType result; - for (IndexValueType i = 0; i < VImageDimension - 1; i++) - result[i] = index[i + 1]; - return result; -} - -template -inline typename RLEImage::BufferType::SizeType -RLEImage::truncateSize(const SizeType & size) -{ - typename BufferType::SizeType result; - for (IndexValueType i = 0; i < VImageDimension - 1; i++) - result[i] = size[i + 1]; - return result; -} - -template -typename RLEImage::BufferType::RegionType -RLEImage::truncateRegion(const RegionType & region) -{ - typename BufferType::RegionType result; - result.SetIndex(truncateIndex(region.GetIndex())); - result.SetSize(truncateSize(region.GetSize())); - return result; -} - -template -void -RLEImage::Allocate(bool initialize) -{ - itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), - "BufferedRegion must contain complete run-length lines!"); - itkAssertOrThrowMacro(this->GetLargestPossibleRegion().GetSize(0) <= std::numeric_limits::max(), - "CounterType is not large enough to support image's X dimension!"); - this->ComputeOffsetTable(); - // SizeValueType num = static_cast(this->GetOffsetTable()[VImageDimension]); - myBuffer->Allocate(false); - // if (initialize) //there is assumption that the image is fully formed after a call to allocate - { - RLSegment segment(CounterType(this->GetBufferedRegion().GetSize(0)), TPixel()); - RLLine line(1); - line[0] = segment; - myBuffer->FillBuffer(line); - } -} - -template -void -RLEImage::FillBuffer(const TPixel & value) -{ - RLSegment segment(CounterType(this->GetBufferedRegion().GetSize(0)), value); - RLLine line(1); - line[0] = segment; - myBuffer->FillBuffer(line); -} - -template -void -RLEImage::CleanUpLine(RLLine & line) const -{ - CounterType x = 0; - RLLine out; - out.reserve(this->GetLargestPossibleRegion().GetSize(0)); - do - { - out.push_back(line[x]); - while (++x < line.size() && line[x].second == line[x - 1].second) - out.back().first += line[x].first; - } while (x < line.size()); - out.swap(line); -} - -template -void -RLEImage::CleanUp() const -{ - assert(!myBuffer.empty()); - if (this->GetLargestPossibleRegion().GetSize(0) == 0) - return; -#pragma omp parallel for - for (CounterType z = 0; z < myBuffer.size(); z++) - for (CounterType y = 0; y < myBuffer[0].size(); y++) - CleanUpLine(myBuffer[z][y]); -} - -template -int -RLEImage::SetPixel(RLLine & line, - IndexValueType & segmentRemainder, - IndexValueType & realIndex, - const TPixel & value) -{ - // complete Run-Length Lines have to be buffered - itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), - "BufferedRegion must contain complete run-length lines!"); - if (line[realIndex].second == value) // already correct value - return 0; - else if (line[realIndex].first == 1) // single pixel segment - { - line[realIndex].second = value; - if (m_OnTheFlyCleanup) // now see if we can merge it into adjacent segments - { - if (realIndex > 0 && realIndex < line.size() - 1 && line[realIndex + 1].second == value && - line[realIndex - 1].second == value) - { - // merge these 3 segments - line[realIndex - 1].first += 1 + line[realIndex + 1].first; - segmentRemainder += line[realIndex + 1].first; - line.erase(line.begin() + realIndex, line.begin() + realIndex + 2); - realIndex--; - return -2; - } - if (realIndex > 0 && line[realIndex - 1].second == value) - { - // merge into previous - line[realIndex - 1].first++; - line.erase(line.begin() + realIndex); - realIndex--; - assert(segmentRemainder == 1); - return -1; - } - else if (realIndex < line.size() - 1 && line[realIndex + 1].second == value) - { - // merge into next - segmentRemainder = ++(line[realIndex + 1].first); - line.erase(line.begin() + realIndex); - return -1; - } - } - return 0; - } - else if (segmentRemainder == 1 && realIndex < line.size() - 1 && line[realIndex + 1].second == value) - { - // shift this pixel to next segment - line[realIndex].first--; - segmentRemainder = ++(line[realIndex + 1].first); - realIndex++; - return 0; - } - else if (realIndex > 0 && segmentRemainder == line[realIndex].first && line[realIndex - 1].second == value) - { - // shift this pixel to previous segment - line[realIndex].first--; - line[realIndex - 1].first++; - realIndex--; - segmentRemainder = 1; - return 0; - } - else if (segmentRemainder == 1) // insert after - { - line[realIndex].first--; - line.insert(line.begin() + realIndex + 1, RLSegment(1, value)); - realIndex++; - return +1; - } - else if (segmentRemainder == line[realIndex].first) // insert before - { - line[realIndex].first--; - line.insert(line.begin() + realIndex, RLSegment(1, value)); - segmentRemainder = 1; - return +1; - } - else // general case: split a segment into 3 segments - { - // first take care of values - line.insert(line.begin() + realIndex + 1, 2, RLSegment(1, value)); - line[realIndex + 2].second = line[realIndex].second; - - // now take care of counts - line[realIndex].first -= segmentRemainder; - line[realIndex + 2].first = segmentRemainder - 1; - realIndex++; - segmentRemainder = 1; - return +2; - } -} - -template -void -RLEImage::SetPixel(const IndexType & index, const TPixel & value) -{ - // complete Run-Length Lines have to be buffered - itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), - "BufferedRegion must contain complete run-length lines!"); - IndexValueType bri0 = this->GetBufferedRegion().GetIndex(0); - typename BufferType::IndexType bi = truncateIndex(index); - RLLine & line = myBuffer->GetPixel(bi); - IndexValueType t = 0; - for (IndexValueType x = 0; x < line.size(); x++) - { - t += line[x].first; - if (t > index[0] - bri0) - { - t -= index[0] - bri0; // we need to supply a reference - SetPixel(line, t, x, value); - return; - } - } - throw itk::ExceptionObject(__FILE__, __LINE__, "Reached past the end of Run-Length line!", __FUNCTION__); -} - -template -const TPixel & -RLEImage::GetPixel(const IndexType & index) const -{ - // complete Run-Length Lines have to be buffered - itkAssertOrThrowMacro(this->GetBufferedRegion().GetSize(0) == this->GetLargestPossibleRegion().GetSize(0), - "BufferedRegion must contain complete run-length lines!"); - IndexValueType bri0 = this->GetBufferedRegion().GetIndex(0); - typename BufferType::IndexType bi = truncateIndex(index); - RLLine & line = myBuffer->GetPixel(bi); - IndexValueType t = 0; - for (IndexValueType x = 0; x < line.size(); x++) - { - t += line[x].first; - if (t > index[0] - bri0) - return line[x].second; - } - throw itk::ExceptionObject(__FILE__, __LINE__, "Reached past the end of Run-Length line!", __FUNCTION__); -} - -template -void -RLEImage::PrintSelf(std::ostream & os, itk::Indent indent) const -{ - Superclass::PrintSelf(os, indent); - os << indent << "Internal image (for storage of RLLine-s): " << std::endl; - myBuffer->Print(os, indent.GetNextIndent()); - - itk::SizeValueType c = 0; - itk::ImageRegionConstIterator it(myBuffer, myBuffer->GetBufferedRegion()); - while (!it.IsAtEnd()) - { - c += it.Get().capacity(); - ++it; - } - - double cr = - double(c * (sizeof(PixelType) + sizeof(CounterType)) + - sizeof(std::vector) * this->GetOffsetTable()[VImageDimension] / this->GetOffsetTable()[1]) / - (this->GetOffsetTable()[VImageDimension] * sizeof(PixelType)); - - os << indent << "OnTheFlyCleanup: " << (m_OnTheFlyCleanup ? "On" : "Off") << std::endl; - os << indent << "RLEImage compressed pixel count: " << c << std::endl; - int prec = os.precision(3); - os << indent << "Compressed size in relation to original size: " << cr * 100 << "%" << std::endl; - os.precision(prec); -} - -#endif // RLEImage_txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h deleted file mode 100644 index 49ad4d261a1..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageConstIterator.h +++ /dev/null @@ -1,440 +0,0 @@ -#ifndef RLEImageConstIterator_h -#define RLEImageConstIterator_h - -#include "itkImage.h" -#include "itkIndex.h" -#include "itkNumericTraits.h" -#include "RLEImage.h" -#include "itkImageConstIterator.h" -#include "itkImageConstIteratorWithIndex.h" -#include "itkImageConstIteratorWithOnlyIndex.h" -#include "itkImageRegionIterator.h" - -class MultiLabelMeshPipeline; - -namespace itk -{ -/** \class ImageConstIterator - * \brief A multi-dimensional image iterator templated over image type. - */ - -template -class ImageConstIterator> -{ - friend class ::MultiLabelMeshPipeline; - -public: - /** Standard class typedefs. */ - typedef ImageConstIterator Self; - - /** Dimension of the image the iterator walks. This constant is needed so - * functions that are templated over image iterator type (as opposed to - * being templated over pixel type and dimension) can have compile time - * access to the dimension of the image that the iterator walks. */ - itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); - - /** Run-time type information (and related methods). */ - itkTypeMacroNoParent(ImageConstIterator); - - /** Image typedef support. */ - typedef RLEImage ImageType; - - /** Run-Length Line (we iterate along it). */ - typedef typename ImageType::RLLine RLLine; - - /** Buffer Type used. */ - typedef typename ImageType::BufferType BufferType; - - /** Type for the internal buffer iterator. */ - typedef ImageRegionIterator BufferIterator; - - /** Index typedef support. */ - typedef typename ImageType::IndexType IndexType; - - /** Index typedef support. */ - typedef typename ImageType::IndexValueType IndexValueType; - - /** Size typedef support. */ - typedef typename ImageType::SizeType SizeType; - - /** Offset typedef support. */ - typedef typename ImageType::OffsetType OffsetType; - - /** Region typedef support. */ - typedef typename ImageType::RegionType RegionType; - - /** Internal Pixel Type */ - typedef typename ImageType::InternalPixelType InternalPixelType; - - /** External Pixel Type */ - typedef typename ImageType::PixelType PixelType; - - /** Default Constructor. Need to provide a default constructor since we - * provide a copy constructor. */ - ImageConstIterator() - : myBuffer(0) - , rlLine(0) - { - m_Image = ITK_NULLPTR; - m_Index0 = 0; - m_BeginIndex0 = 0; - m_EndIndex0 = 0; - realIndex = 0; - segmentRemainder = 0; - } - - /** Default Destructor. */ - virtual ~ImageConstIterator() {} - - /** Copy Constructor. The copy constructor is provided to make sure the - * handle to the image is properly reference counted. */ - ImageConstIterator(const Self & it) - : myBuffer(const_cast(it.GetImage())->GetBuffer()) - { - rlLine = it.rlLine; - m_Image = it.m_Image; // copy the smart pointer - m_Index0 = it.m_Index0; - this->bi = it.bi; - - realIndex = it.realIndex; - segmentRemainder = it.segmentRemainder; - m_BeginIndex0 = it.m_BeginIndex0; - m_EndIndex0 = it.m_EndIndex0; - } - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageConstIterator(const ImageType * ptr, const RegionType & region) - : myBuffer(const_cast(ptr)->GetBuffer()) - { - m_Image = ptr; - SetRegion(region); - } - - /** operator= is provided to make sure the handle to the image is properly - * reference counted. */ - Self & - operator=(const Self & it) - { - if (this != &it) - { - myBuffer = it.myBuffer; - rlLine = it.rlLine; - m_Image = it.m_Image; // copy the smart pointer - m_Index0 = it.m_Index0; - bi = it.bi; - - realIndex = it.realIndex; - segmentRemainder = it.segmentRemainder; - m_BeginIndex0 = it.m_BeginIndex0; - m_EndIndex0 = it.m_EndIndex0; - } - return *this; - } - - /** Set the region of the image to iterate over. */ - virtual void - SetRegion(const RegionType & region) - { - // m_Region = region; - - if (region.GetNumberOfPixels() > 0) // If region is non-empty - { - const RegionType & bufferedRegion = m_Image->GetBufferedRegion(); - itkAssertOrThrowMacro((bufferedRegion.IsInside(region)), - "Region " << region << " is outside of buffered region " << bufferedRegion); - } - - bi = BufferIterator(myBuffer, ImageType::truncateRegion(region)); - m_Index0 = region.GetIndex(0); - m_BeginIndex0 = m_Index0 - m_Image->GetBufferedRegion().GetIndex(0); - m_EndIndex0 = m_BeginIndex0 + region.GetSize(0); - SetIndexInternal(m_BeginIndex0); // sets realIndex and segmentRemainder - } - - /** Get the dimension (size) of the index. */ - static unsigned int - GetImageIteratorDimension() - { - return VImageDimension; - } - - /** Comparison operator. Two iterators are the same if they "point to" the - * same memory location */ - bool - operator!=(const Self & it) const - { - return bi != it.bi || m_Index0 + m_BeginIndex0 != it.m_Index0 + it.m_BeginIndex0; - } - - /** Comparison operator. Two iterators are the same if they "point to" the - * same memory location */ - bool - operator==(const Self & it) const - { - return bi == it.bi && m_Index0 + m_BeginIndex0 == it.m_Index0 + it.m_BeginIndex0; - } - - /** Comparison operator. An iterator is "less than" another if it "points to" - * a lower memory location. */ - bool - operator<=(const Self & it) const - { - if (bi < it.bi) - return true; - else if (bi > it.bi) - return false; - return m_Index0 + m_BeginIndex0 <= it.m_Index0 + it.m_BeginIndex0; - } - - /** Comparison operator. An iterator is "less than" another if it "points to" - * a lower memory location. */ - bool - operator<(const Self & it) const - { - if (bi < it.bi) - return true; - else if (bi > it.bi) - return false; - return m_Index0 + m_BeginIndex0 < it.m_Index0 + it.m_BeginIndex0; - } - - /** Comparison operator. An iterator is "greater than" another if it - * "points to" a higher location. */ - bool - operator>=(const Self & it) const - { - if (bi > it.bi) - return true; - else if (bi < it.bi) - return false; - return m_Index0 + m_BeginIndex0 >= it.m_Index0 + it.m_BeginIndex0; - } - - /** Comparison operator. An iterator is "greater than" another if it - * "points to" a higher location. */ - bool - operator>(const Self & it) const - { - if (bi > it.bi) - return true; - else if (bi < it.bi) - return false; - return m_Index0 + m_BeginIndex0 > it.m_Index0 + it.m_BeginIndex0; - } - - /** Get the index. This provides a read only copy of the index. */ - const IndexType - GetIndex() const - { - IndexType indR(m_Image->GetBufferedRegion().GetIndex()); - indR[0] += m_Index0; - typename BufferType::IndexType bufInd = bi.GetIndex(); - for (IndexValueType i = 1; i < VImageDimension; i++) - indR[i] = bufInd[i - 1]; - return indR; - } - - /** Sets the image index. No bounds checking is performed. */ - virtual void - SetIndex(const IndexType & ind) - { - typename BufferType::IndexType bufInd; - for (IndexValueType i = 1; i < VImageDimension; i++) - bufInd[i - 1] = ind[i]; - bi.SetIndex(bufInd); - SetIndexInternal(ind[0] - m_Image->GetBufferedRegion().GetIndex(0)); - } - - /** Get the region that this iterator walks. ImageConstIterators know the - * beginning and the end of the region of the image to iterate over. */ - const RegionType - GetRegion() const - { - RegionType r; - r.SetIndex(0, m_BeginIndex0 + m_Image->GetBufferedRegion().GetIndex(0)); - r.SetSize(0, m_EndIndex0 - m_BeginIndex0); - typename BufferType::RegionType ir = bi.GetRegion(); - for (IndexValueType i = 1; i < VImageDimension; i++) - { - r.SetIndex(i, ir.GetIndex(i - 1)); - r.SetSize(i, ir.GetSize(i - 1)); - } - return r; - } - - /** Get the image that this iterator walks. */ - const ImageType * - GetImage() const - { - return m_Image.GetPointer(); - } - - /** Get the pixel value */ - PixelType - Get(void) const - { - return Value(); - } - - /** Return a const reference to the pixel - * This method will provide the fastest access to pixel - * data, but it will NOT support ImageAdaptors. */ - const PixelType & - Value(void) const - { - RLLine & line = const_cast(this)->bi.Value(); - return line[realIndex].second; - } - - /** Move an iterator to the beginning of the region. "Begin" is - * defined as the first pixel in the region. */ - void - GoToBegin() - { - bi.GoToBegin(); - SetIndexInternal(m_BeginIndex0); - } - - /** Move an iterator to the end of the region. "End" is defined as - * one pixel past the last pixel of the region. */ - void - GoToEnd() - { - bi.GoToEnd(); - m_Index0 = m_BeginIndex0; - } - - /** Is the iterator at the beginning of the region? "Begin" is defined - * as the first pixel in the region. */ - bool - IsAtBegin(void) const - { - return m_Index0 == m_BeginIndex0 && bi.IsAtBegin(); - } - - /** Is the iterator at the end of the region? "End" is defined as one - * pixel past the last pixel of the region. */ - bool - IsAtEnd(void) const - { - return m_Index0 == m_BeginIndex0 && bi.IsAtEnd(); - } - -protected: // made protected so other iterators can access - /** Set the internal index, realIndex and segmentRemainder. */ - virtual void - SetIndexInternal(const IndexValueType ind0) - { - m_Index0 = ind0; - rlLine = &bi.Value(); - - CounterType t = 0; - SizeValueType x = 0; - - for (; x < (*rlLine).size(); x++) - { - t += (*rlLine)[x].first; - if (t > m_Index0) - break; - } - realIndex = x; - segmentRemainder = t - m_Index0; - } - - typename ImageType::ConstWeakPointer m_Image; - - IndexValueType m_Index0; // index into the RLLine - - const RLLine * rlLine; - - mutable IndexValueType realIndex; // index into line's segment - mutable IndexValueType segmentRemainder; // how many pixels remain in current segment - - IndexValueType m_BeginIndex0; // index to first pixel in region in relation to buffer start - IndexValueType m_EndIndex0; // index to one pixel past last pixel in region in relation to buffer start - - BufferIterator bi; // iterator over internal buffer image - typename BufferType::Pointer myBuffer; -}; - -template -class ImageConstIteratorWithIndex> - : public ImageConstIterator> -{ - // just inherit constructors -public: - /** Image typedef support. */ - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - void - GoToReverseBegin() - { - this->bi.GoToReverseBegin(); - this->m_Index0 = this->m_EndIndex0 - 1; - SetIndexInternal(this->m_Index0); - } - - bool - IsAtReverseEnd() - { - return this->bi.IsAtReverseEnd(); - } - - /** Default Constructor. Need to provide a default constructor since we - * provide a copy constructor. */ - ImageConstIteratorWithIndex() - : ImageConstIterator() - {} - - /** Copy Constructor. The copy constructor is provided to make sure the - * handle to the image is properly reference counted. */ - ImageConstIteratorWithIndex(const ImageConstIteratorWithIndex & it) - { - this->ImageConstIterator::operator=(it); - } - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageConstIteratorWithIndex(const ImageType * ptr, const RegionType & region) - : ImageConstIterator(ptr, region) - {} -}; // no additional implementation required - -template -class ImageConstIteratorWithOnlyIndex> - : public ImageConstIteratorWithIndex> -{ - // just inherit constructors -public: - /** Image typedef support. */ - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - /** Default Constructor. Need to provide a default constructor since we - * provide a copy constructor. */ - ImageConstIteratorWithOnlyIndex() - : ImageConstIterator() - {} - - - /** Copy Constructor. The copy constructor is provided to make sure the - * handle to the image is properly reference counted. */ - ImageConstIteratorWithOnlyIndex(const ImageConstIteratorWithOnlyIndex & it) - { - this->ImageConstIterator::operator=(it); - } - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageConstIteratorWithOnlyIndex(const ImageType * ptr, const RegionType & region) - : ImageConstIterator(ptr, region) - {} -}; // no additional implementation required - -} // end namespace itk - -#endif // RLEImageConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h deleted file mode 100644 index d7d60026237..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageIterator.h +++ /dev/null @@ -1,161 +0,0 @@ -#ifndef RLEImageIterator_h -#define RLEImageIterator_h - -#include "RLEImageConstIterator.h" -#include "itkImageIteratorWithIndex.h" - -namespace itk -{ -/** - * \class ImageIterator - * \brief A multi-dimensional iterator templated over image type. - * - * This is a base class of ImageConstIterator that adds write-access - * functionality. Please see ImageConstIterator for more information. - * - */ - -template -class ImageIterator> - : public ImageConstIterator> -{ -public: - /** Standard class typedefs. */ - typedef ImageIterator Self; - - /** Dimension of the image the iterator walks. This constant is needed so - * functions that are templated over image iterator type (as opposed to - * being templated over pixel type and dimension) can have compile time - * access to the dimension of the image that the iterator walks. */ - itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); - - /** Define the superclass */ - typedef ImageConstIterator> Superclass; - - /** Inherit types from the superclass */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::OffsetType OffsetType; - typedef typename Superclass::RegionType RegionType; - typedef typename Superclass::ImageType ImageType; - typedef typename Superclass::InternalPixelType InternalPixelType; - typedef typename Superclass::PixelType PixelType; - - /** Default Constructor. Need to provide a default constructor since we - * provide a copy constructor. */ - ImageIterator() {} - - /** Default Destructor */ - ~ImageIterator() {} - - /** Copy Constructor. The copy constructor is provided to make sure the - * handle to the image is properly reference counted. */ - ImageIterator(const Self & it) - : ImageConstIterator(it) - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageIterator(ImageType * ptr, const RegionType & region) - : ImageConstIterator(ptr, region) - {} - - /** operator= is provided to make sure the handle to the image is properly - * reference counted. */ - Self & - operator=(const Self & it) - { - this->ImageConstIterator::operator=(it); - return *this; - } - - /** Set the pixel value. - * Changing the RLE structure invalidates all other iterators (except this one). */ - void - Set(const PixelType & value) const - { - const_cast(this->m_Image.GetPointer()) - ->SetPixel( - *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); - } - - ///** Return a reference to the pixel - // * Setting this value would change value of the whole run-length segment. - // * If we wanted to safely enable it, - // * we would isolate this pixel into its own segment. */ - // PixelType & Value(void) - //{ - // return myBuffer[m_Index[2]][m_Index[1]][realIndex].second; - //} - - /** Get the image that this iterator walks. */ - ImageType * - GetImage() const - { - // const_cast is needed here because m_Image is declared as a const pointer - // in the base class which is the ConstIterator. - return const_cast(this->m_Image.GetPointer()); - } - -protected: - /** This constructor is declared protected in order to enforce - const-correctness */ - ImageIterator(const ImageConstIterator & it) - : ImageConstIterator(it) - {} - Self & - operator=(const ImageConstIterator & it) - { - this->ImageConstIterator::operator=(it); - return *this; - } -}; - -template -class ImageIteratorWithIndex> - : public ImageConstIteratorWithIndex> -{ -public: - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - /** Default Constructor. Need to provide a default constructor since we - * provide a copy constructor. */ - ImageIteratorWithIndex() - : ImageConstIteratorWithIndex() - {} - - - /** Copy Constructor. The copy constructor is provided to make sure the - * handle to the image is properly reference counted. */ - ImageIteratorWithIndex(const ImageIteratorWithIndex & it) { this->ImageIterator::operator=(it); } - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageIteratorWithIndex(const ImageType * ptr, const RegionType & region) - : ImageConstIteratorWithIndex(ptr, region) - {} - - /** Set the pixel value. - * Changing the RLE structure invalidates all other iterators (except this one). */ - void - Set(const TPixel & value) const - { - const_cast(this->m_Image.GetPointer()) - ->SetPixel( - *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); - } - - /** Get the image that this iterator walks. */ - ImageType * - GetImage() const - { - // const_cast is needed here because m_Image is declared as a const pointer - // in the base class which is the ConstIterator. - return const_cast(this->m_Image.GetPointer()); - } -}; // no additional implementation required -} // end namespace itk - -#endif // RLEImageIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h deleted file mode 100644 index 88951b7f386..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionConstIterator.h +++ /dev/null @@ -1,232 +0,0 @@ -#ifndef RLEImageRegionConstIterator_h -#define RLEImageRegionConstIterator_h - -#include "RLEImageConstIterator.h" -#include "itkImageRegionConstIterator.h" -#include "itkImageRegionConstIteratorWithIndex.h" -#include "itkImageRegionConstIteratorWithOnlyIndex.h" - -class MultiLabelMeshPipeline; - -namespace itk -{ -/** \class ImageRegionConstIterator - * \brief A multi-dimensional iterator templated over image type that walks a - * region of pixels. - * - * ImageRegionConstIterator provides read-only access to image data. It is the - * base class for the read/write access ImageRegionIterator. - * - */ -template -class ImageRegionConstIterator> - : public ImageConstIterator> -{ - friend class ::MultiLabelMeshPipeline; - -public: - /** Standard class typedef. */ - typedef ImageRegionConstIterator> Self; - typedef ImageConstIterator> Superclass; - - /** Dimension of the image that the iterator walks. This constant is needed so - * functions that are templated over image iterator type (as opposed to - * being templated over pixel type and dimension) can have compile time - * access to the dimension of the image that the iterator walks. */ - itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); - - /** - * Index typedef support. While these were already typdef'ed in the superclass, - * they need to be redone here for this subclass to compile properly with gcc. - */ - /** Types inherited from the Superclass */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::OffsetType OffsetType; - typedef typename Superclass::RegionType RegionType; - typedef typename Superclass::ImageType ImageType; - typedef typename Superclass::InternalPixelType InternalPixelType; - typedef typename Superclass::PixelType PixelType; - - /** Run-time type information (and related methods). */ - itkTypeMacro(ImageRegionConstIterator, ImageConstIterator); - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageRegionConstIterator() - : ImageConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageRegionConstIterator(const ImageType * ptr, const RegionType & region) - : ImageConstIterator(ptr, region) - {} - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageRegionConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionConstIterator. */ - ImageRegionConstIterator(const ImageIterator & it) - { - this->ImageConstIterator::operator=(it); - // this->ImageConstIterator< ImageType >::operator=(static_cast >(it)); - } - - /** Constructor that can be used to cast from an ImageConstIterator to an - * ImageRegionConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionConstIterator. */ - ImageRegionConstIterator(const ImageConstIterator & it) - { - this->ImageConstIterator::operator=(it); - } - - /** Increment (prefix) the fastest moving dimension of the iterator's index. - * This operator will constrain the iterator within the region (i.e. the - * iterator will automatically wrap from the end of the row of the region - * to the beginning of the next row of the region) up until the iterator - * tries to moves past the last pixel of the region. Here, the iterator - * will be set to be one pixel past the end of the region. - * \sa operator++(int) */ - Self & - operator++() - { - this->m_Index0++; - - if (this->m_Index0 >= this->m_EndIndex0) - { - ++(this->bi); - if (!this->bi.IsAtEnd()) - this->SetIndexInternal(this->m_BeginIndex0); - else - this->m_Index0 = this->m_BeginIndex0; - return *this; - } - - this->segmentRemainder--; - if (this->segmentRemainder > 0) - return *this; - - this->realIndex++; - this->segmentRemainder = (*this->rlLine)[this->realIndex].first; - return *this; - } - - /** Decrement (prefix) the fastest moving dimension of the iterator's index. - * This operator will constrain the iterator within the region (i.e. the - * iterator will automatically wrap from the beginning of the row of the region - * to the end of the next row of the region) up until the iterator - * tries to moves past the first pixel of the region. Here, the iterator - * will be set to be one pixel past the beginning of the region. - * \sa operator--(int) */ - Self & - operator--() - { - this->m_Index0--; - - if (this->m_Index0 < this->m_BeginIndex0) - { - --(this->bi); - this->SetIndexInternal(this->m_EndIndex0 - 1); - return *this; - } - - this->segmentRemainder++; - if (this->segmentRemainder <= (*this->rlLine)[this->realIndex].first) - return *this; - - this->realIndex--; - this->segmentRemainder = 1; - return *this; - } -}; - -template -class ImageRegionConstIteratorWithIndex> - : public ImageRegionConstIterator> -{ -public: - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageRegionConstIteratorWithIndex() - : ImageRegionConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageRegionConstIteratorWithIndex(const ImageType * ptr, const RegionType & region) - : ImageRegionConstIterator(ptr, region) - {} - - void - GoToReverseBegin() - { - this->bi.GoToEnd(); // after last pixel - --(this->bi); // go to last valid pixel - this->m_Index0 = this->m_EndIndex0 - 1; - this->SetIndexInternal(this->m_Index0); // valid index required - } - - bool - IsAtReverseEnd() - { - return (this->m_Index0 == this->m_BeginIndex0) && this->bi.IsAtBegin(); - } - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageRegionConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionConstIterator. */ - ImageRegionConstIteratorWithIndex(const ImageIterator & it) - { - this->ImageRegionConstIterator::operator=(it); - } - -}; // no additional implementation required - -template -class ImageRegionConstIteratorWithOnlyIndex> - : public ImageRegionConstIteratorWithIndex> -{ - // just inherit constructors -public: - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageRegionConstIteratorWithOnlyIndex() - : ImageRegionConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageRegionConstIteratorWithOnlyIndex(const ImageType * ptr, const RegionType & region) - : ImageRegionConstIteratorWithIndex(ptr, region) - {} - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageRegionConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionConstIterator. */ - ImageRegionConstIteratorWithOnlyIndex(const ImageIterator & it) - { - this->ImageRegionConstIterator::operator=(it); - } - -}; // no additional implementation required - -} // end namespace itk - -#endif // RLEImageRegionConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h deleted file mode 100644 index 4280e5df047..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageRegionIterator.h +++ /dev/null @@ -1,144 +0,0 @@ -#ifndef RLEImageRegionIterator_h -#define RLEImageRegionIterator_h - -#include "RLEImageRegionConstIterator.h" -#include "itkImageRegionIterator.h" -#include "itkImageRegionIteratorWithIndex.h" -#include "RLEImageIterator.h" - -namespace itk -{ -/** \class ImageRegionIterator - * \brief A multi-dimensional iterator templated over image type that walks a - * region of pixels. - * - * The itk::ImageRegionIterator is optimized for iteration speed and is the - * first choice for iterative, pixel-wise operations on an image. - * ImageRegionIterator is the least specialized of the ITK image iterator - * classes. ImageRegionIterator is templated over the image type, and is - * constrained to walk only within the specified region and along a line - * parallel to one of the coordinate axes, "wrapping" to the next line as it - * reaches the boundary of the image. To walk the entire image, specify the - * region to be \c image->GetRequestedRegion(). - * - * Most of the functionality is inherited from the ImageRegionConstIterator. - * The current class only adds write access to image pixels. - */ - -template -class ImageRegionIterator> - : public ImageRegionConstIterator> -{ -public: - /** Standard class typedefs. */ - typedef ImageRegionIterator Self; - typedef ImageRegionConstIterator> Superclass; - - /** Types inherited from the Superclass */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::OffsetType OffsetType; - typedef typename Superclass::RegionType RegionType; - typedef typename Superclass::ImageType ImageType; - typedef typename Superclass::InternalPixelType InternalPixelType; - typedef typename Superclass::PixelType PixelType; - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageRegionIterator() - : ImageRegionConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageRegionIterator(ImageType * ptr, const RegionType & region) - : ImageRegionConstIterator(ptr, region) - {} - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageRegionIterator. Many routines return an ImageIterator but for a - * particular task, you may want an ImageRegionIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionIterator. */ - ImageRegionIterator(const ImageIterator & it) { this->ImageConstIterator::operator=(it); } - - /** Set the pixel value. - * Changing the RLE structure invalidates all other iterators (except this one). */ - void - Set(const PixelType & value) const - { - const_cast(this->m_Image.GetPointer()) - ->SetPixel( - *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); - } - -protected: - /** the construction from a const iterator is declared protected - in order to enforce const correctness. */ - ImageRegionIterator(const ImageRegionConstIterator & it) - { - this->ImageConstIterator::operator=(it); - } - Self & - operator=(const ImageRegionConstIterator & it) - { - this->ImageConstIterator::operator=(it); - } -}; - -template -class ImageRegionIteratorWithIndex> - : public ImageRegionConstIteratorWithIndex> -{ -public: - typedef RLEImage ImageType; - - typedef typename itk::ImageConstIterator>::RegionType RegionType; - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageRegionIteratorWithIndex() - : ImageRegionConstIteratorWithIndex() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageRegionIteratorWithIndex(ImageType * ptr, const RegionType & region) - : ImageRegionConstIteratorWithIndex(ptr, region) - {} - - /** Set the pixel value. - * Changing the RLE structure invalidates all other iterators (except this one). */ - void - Set(const TPixel & value) const - { - const_cast(this->m_Image.GetPointer()) - ->SetPixel( - *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); - } - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageRegionIteratorWithIndex. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionConstIterator. */ - ImageRegionIteratorWithIndex(const ImageIterator & it) - { - this->ImageRegionConstIteratorWithIndex::operator=(it); - } - - /** Constructor that can be used to cast from an ImageConstIterator to an - * ImageRegionIteratorWithIndex. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageRegionConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageRegionIteratorWithIndex. */ - ImageRegionIteratorWithIndex(const ImageConstIterator & it) - { - this->ImageRegionConstIterator::operator=(it); - } - -}; // no additional implementation required -} // end namespace itk - -#endif // RLEImageRegionIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h deleted file mode 100644 index 7bd59ec774f..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineConstIterator.h +++ /dev/null @@ -1,155 +0,0 @@ -#ifndef RLEImageScanlineConstIterator_h -#define RLEImageScanlineConstIterator_h - -#include "RLEImageRegionConstIterator.h" -#include "itkImageScanlineIterator.h" - -namespace itk -{ -/** \class ImageScanlineConstIterator - * \brief A multi-dimensional iterator templated over image type that walks a - * region of pixels, scanline by scanline or in the direction of the - * fastest axis. - */ -template -class ImageScanlineConstIterator> - : public ImageRegionConstIterator> -{ -public: - /** Standard class typedef. */ - typedef ImageScanlineConstIterator Self; - typedef ImageRegionConstIterator> Superclass; - - /** Dimension of the image that the iterator walks. This constant is needed so - * functions that are templated over image iterator type (as opposed to - * being templated over pixel type and dimension) can have compile time - * access to the dimension of the image that the iterator walks. */ - itkStaticConstMacro(ImageIteratorDimension, unsigned int, VImageDimension); - - /** - * Index typedef support. While these were already typdef'ed in the superclass, - * they need to be redone here for this subclass to compile properly with gcc. - */ - /** Types inherited from the Superclass */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::OffsetType OffsetType; - typedef typename Superclass::RegionType RegionType; - typedef typename Superclass::ImageType ImageType; - typedef typename Superclass::InternalPixelType InternalPixelType; - typedef typename Superclass::PixelType PixelType; - - /** Run-time type information (and related methods). */ - itkTypeMacro(ImageScanlineConstIterator, ImageRegionConstIterator); - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageScanlineConstIterator() - : ImageRegionConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageScanlineConstIterator(const ImageType * ptr, const RegionType & region) - : ImageRegionConstIterator(ptr, region) - {} - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageScanlineConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageScanlineConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageScanlineConstIterator. */ - ImageScanlineConstIterator(const ImageIterator & it) - : ImageRegionConstIterator(it) - {} - - /** Constructor that can be used to cast from an ImageConstIterator to an - * ImageScanlineConstIterator. Many routines return an ImageIterator, but for a - * particular task, you may want an ImageScanlineConstIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageScanlineConstIterator. */ - ImageScanlineConstIterator(const ImageConstIterator & it) - { - this->ImageRegionConstIterator::operator=(it); - } - - - /** Go to the beginning pixel of the current line. */ - void - GoToBeginOfLine(void) - { - this->m_Index0 = this->m_BeginIndex0; - this->realIndex = 0; - this->segmentRemainder = (*this->rlLine)[this->realIndex].first; - } - - /** Go to the past end pixel of the current line. */ - void - GoToEndOfLine(void) - { - this->m_Index0 = this->m_EndIndex0; - this->realIndex = this->rlLine->size() - 1; - this->segmentRemainder = 0; - } - - /** Test if the index is at the end of line. */ - inline bool - IsAtEndOfLine(void) - { - return this->m_Index0 == this->m_EndIndex0; - } - - /** Go to the next line. */ - inline void - NextLine(void) - { - ++(this->bi); - if (!this->bi.IsAtEnd()) - this->SetIndexInternal(this->m_BeginIndex0); - else - this->m_Index0 = this->m_BeginIndex0; // make this iterator at end too - } - - /** Increment (prefix) along the scanline. - * - * If the iterator is at the end of the scanline ( one past the last - * valid element in the row ), then the results are undefined. Which - * means is may assert in debug mode or result in an undefined - * iterator which may have unknown consequences if used. - */ - Self & - operator++() - { - itkAssertInDebugAndIgnoreInReleaseMacro(!this->IsAtEndOfLine()); - this->m_Index0++; - this->segmentRemainder--; - if (this->segmentRemainder > 0) - return *this; - - if (this->IsAtEndOfLine()) - return *this; - this->realIndex++; - this->segmentRemainder = (*this->rlLine)[this->realIndex].first; - return *this; - } - - /** Decrement (prefix) along the scanline. - * - */ - Self & - operator--() - { - this->m_Index0--; - this->segmentRemainder++; - if (this->segmentRemainder <= (*this->rlLine)[this->realIndex].first) - return *this; - - this->realIndex--; - this->segmentRemainder = 1; - return *this; - } -}; -} // end namespace itk - -#endif // RLEImageScanlineConstIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h deleted file mode 100644 index d0fabe33d38..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLEImageScanlineIterator.h +++ /dev/null @@ -1,86 +0,0 @@ -#ifndef RLEImageScanlineIterator_h -#define RLEImageScanlineIterator_h - -#include "RLEImageScanlineConstIterator.h" -#include "RLEImageIterator.h" -#include "itkImageScanlineIterator.h" - -namespace itk -{ -/** \class ImageScanlineIterator - * \brief A multi-dimensional iterator templated over image type that walks a - * region of pixels, scanline by scanline or in the direction of the - * fastest axis. - */ -template -class ImageScanlineIterator> - : public ImageScanlineConstIterator> -{ -public: - /** Standard class typedefs. */ - typedef ImageScanlineIterator Self; - typedef ImageScanlineConstIterator> Superclass; - - /** Types inherited from the Superclass */ - typedef typename Superclass::IndexType IndexType; - typedef typename Superclass::SizeType SizeType; - typedef typename Superclass::OffsetType OffsetType; - typedef typename Superclass::RegionType RegionType; - typedef typename Superclass::ImageType ImageType; - typedef typename Superclass::InternalPixelType InternalPixelType; - typedef typename Superclass::PixelType PixelType; - - /** Default constructor. Needed since we provide a cast constructor. */ - ImageScanlineIterator() - : ImageScanlineConstIterator() - {} - - /** Constructor establishes an iterator to walk a particular image and a - * particular region of that image. */ - ImageScanlineIterator(ImageType * ptr, const RegionType & region) - : ImageScanlineConstIterator(ptr, region) - {} - - /** Constructor that can be used to cast from an ImageIterator to an - * ImageScanlineIterator. Many routines return an ImageIterator but for a - * particular task, you may want an ImageScanlineIterator. Rather than - * provide overloaded APIs that return different types of Iterators, itk - * returns ImageIterators and uses constructors to cast from an - * ImageIterator to a ImageScanlineIterator. */ - ImageScanlineIterator(const ImageIterator & it) - : ImageScanlineConstIterator(it) - {} - - /** Set the pixel value */ - void - Set(const PixelType & value) const - { - const_cast(this->m_Image.GetPointer()) - ->SetPixel( - *const_cast(this->rlLine), this->segmentRemainder, this->realIndex, value); - } - - ///** Return a reference to the pixel - //* This method will provide the fastest access to pixel - //* data, but it will NOT support ImageAdaptors. */ - // PixelType & Value(void) - //{ - // return myBuffer[m_Index[2]][m_Index[1]][realIndex].second; - //} - -protected: - /** the construction from a const iterator is declared protected - in order to enforce const correctness. */ - ImageScanlineIterator(const ImageScanlineConstIterator & it) - : ImageScanlineConstIterator(it) - {} - Self & - operator=(const ImageScanlineConstIterator & it) - { - this->ImageScanlineConstIterator::operator=(it); - return *this; - } -}; -} // end namespace itk - -#endif // RLEImageScanlineIterator_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h deleted file mode 100644 index 5a4c6d12cf3..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.h +++ /dev/null @@ -1,293 +0,0 @@ -#ifndef RLERegionOfInterestImageFilter_h -#define RLERegionOfInterestImageFilter_h - -#include "itkImageToImageFilter.h" -#include "itkSmartPointer.h" -#include "itkRegionOfInterestImageFilter.h" -#include "RLEImage.h" - -namespace itk -{ -/** \class RegionOfInterestImageFilter - * \brief Extract a region of interest from the input image - * or convert between itk::Image and RLEImage (a custom region can be used). - * - * This filter produces an output image of the same dimension as the input - * image. The user specifies the region of the input image that will be - * contained in the output image. The origin coordinates of the output images - * will be computed in such a way that if mapped to physical space, the output - * image will overlay the input image with perfect registration. In other - * words, a registration process between the output image and the input image - * will return an identity transform. - * - * The region to extract is set using the method SetRegionOfInterest. - */ -template -class RegionOfInterestImageFilter, - RLEImage> - : public ImageToImageFilter, - RLEImage> -{ -public: - /** Standard class typedefs. */ - typedef RegionOfInterestImageFilter Self; - typedef RLEImage RLEImageType; - typedef RLEImageType ImageType; - typedef ImageToImageFilter Superclass; - typedef SmartPointer Pointer; - typedef SmartPointer ConstPointer; - typedef typename Superclass::InputImageRegionType InputImageRegionType; - - /** Method for creation through the object factory. */ - itkNewMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); - - /** Typedef to describe the input image region types. */ - typedef typename RLEImageType::RegionType RegionType; - typedef typename RLEImageType::IndexType IndexType; - typedef typename RLEImageType::SizeType SizeType; - - /** Typedef to describe the type of pixel. */ - typedef typename RLEImageType::PixelType OutputImagePixelType; - typedef typename RLEImageType::PixelType InputImagePixelType; - - /** Set/Get the output image region. */ - itkSetMacro(RegionOfInterest, RegionType); - itkGetConstMacro(RegionOfInterest, RegionType); - - /** ImageDimension enumeration */ - itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); - itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); - -#ifdef ITK_USE_CONCEPT_CHECKING - // Begin concept checking - itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); - itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); - // End concept checking -#endif - -protected: - RegionOfInterestImageFilter() {} - ~RegionOfInterestImageFilter() {} - void - PrintSelf(std::ostream & os, Indent indent) const; - - virtual void - GenerateInputRequestedRegion(); - - virtual void - EnlargeOutputRequestedRegion(DataObject * output); - - /** RegionOfInterestImageFilter can produce an image which is a different - * size than its input image. As such, RegionOfInterestImageFilter - * needs to provide an implementation for - * GenerateOutputInformation() in order to inform the pipeline - * execution model. The original documentation of this method is - * below. - * - * \sa ProcessObject::GenerateOutputInformaton() */ - virtual void - GenerateOutputInformation(); - - /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() */ - void - ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); - -private: - RegionOfInterestImageFilter(const Self &); // purposely not implemented - void - operator=(const Self &); // purposely not implemented - - RegionType m_RegionOfInterest; -}; - -template -class RegionOfInterestImageFilter, RLEImage> - : public ImageToImageFilter, RLEImage> -{ -public: - /** Standard class typedefs. */ - typedef RegionOfInterestImageFilter Self; - typedef RLEImage RLEImageType; - typedef Image ImageType; - typedef ImageToImageFilter Superclass; - typedef SmartPointer Pointer; - typedef SmartPointer ConstPointer; - typedef typename Superclass::InputImageRegionType InputImageRegionType; - - /** Method for creation through the object factory. */ - itkNewMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); - - /** Typedef to describe the input image region types. */ - typedef typename RLEImageType::RegionType RegionType; - typedef typename RLEImageType::IndexType IndexType; - typedef typename RLEImageType::SizeType SizeType; - - /** Typedef to describe the type of pixel. */ - typedef typename RLEImageType::PixelType OutputImagePixelType; - typedef typename RLEImageType::PixelType InputImagePixelType; - - /** Set/Get the output image region. */ - itkSetMacro(RegionOfInterest, RegionType); - itkGetConstMacro(RegionOfInterest, RegionType); - - /** ImageDimension enumeration */ - itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); - itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); - -#ifdef ITK_USE_CONCEPT_CHECKING - // Begin concept checking - itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); - itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); - // End concept checking -#endif - -protected: - RegionOfInterestImageFilter() {} - ~RegionOfInterestImageFilter() {} - void - PrintSelf(std::ostream & os, Indent indent) const; - - virtual void - GenerateInputRequestedRegion(); - - virtual void - EnlargeOutputRequestedRegion(DataObject * output); - - /** RegionOfInterestImageFilter can produce an image which is a different - * size than its input image. As such, RegionOfInterestImageFilter - * needs to provide an implementation for - * GenerateOutputInformation() in order to inform the pipeline - * execution model. The original documentation of this method is - * below. - * - * \sa ProcessObject::GenerateOutputInformaton() */ - virtual void - GenerateOutputInformation(); - - /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() */ - void - ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); - -private: - RegionOfInterestImageFilter(const Self &); // purposely not implemented - void - operator=(const Self &); // purposely not implemented - - RegionType m_RegionOfInterest; -}; - -template -class RegionOfInterestImageFilter, Image> - : public ImageToImageFilter, Image> -{ -public: - /** Standard class typedefs. */ - typedef RegionOfInterestImageFilter Self; - typedef RLEImage RLEImageType; - typedef Image ImageType; - typedef ImageToImageFilter Superclass; - typedef SmartPointer Pointer; - typedef SmartPointer ConstPointer; - typedef typename Superclass::InputImageRegionType InputImageRegionType; - - /** Method for creation through the object factory. */ - itkNewMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(RegionOfInterestImageFilter, ImageToImageFilter); - - /** Typedef to describe the input image region types. */ - typedef typename RLEImageType::RegionType RegionType; - typedef typename RLEImageType::IndexType IndexType; - typedef typename RLEImageType::SizeType SizeType; - - /** Typedef to describe the type of pixel. */ - typedef typename RLEImageType::PixelType OutputImagePixelType; - typedef typename RLEImageType::PixelType InputImagePixelType; - - /** Set/Get the output image region. */ - itkSetMacro(RegionOfInterest, RegionType); - itkGetConstMacro(RegionOfInterest, RegionType); - - /** ImageDimension enumeration */ - itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension); - itkStaticConstMacro(OutputImageDimension, unsigned int, VImageDimension); - -#ifdef ITK_USE_CONCEPT_CHECKING - // Begin concept checking - itkConceptMacro(SameDimensionCheck, (Concept::SameDimension)); - itkConceptMacro(InputConvertibleToOutputCheck, (Concept::Convertible)); - // End concept checking -#endif - -protected: - RegionOfInterestImageFilter() {} - ~RegionOfInterestImageFilter() {} - void - PrintSelf(std::ostream & os, Indent indent) const; - - virtual void - GenerateInputRequestedRegion(); - - virtual void - EnlargeOutputRequestedRegion(DataObject * output); - - /** RegionOfInterestImageFilter can produce an image which is a different - * size than its input image. As such, RegionOfInterestImageFilter - * needs to provide an implementation for - * GenerateOutputInformation() in order to inform the pipeline - * execution model. The original documentation of this method is - * below. - * - * \sa ProcessObject::GenerateOutputInformaton() */ - virtual void - GenerateOutputInformation(); - - /** RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() */ - void - ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId); - -private: - RegionOfInterestImageFilter(const Self &); // purposely not implemented - void - operator=(const Self &); // purposely not implemented - - RegionType m_RegionOfInterest; -}; -} // end namespace itk - -#ifndef ITK_MANUAL_INSTANTIATION -# include "RLERegionOfInterestImageFilter.txx" -#endif - -#endif // RLERegionOfInterestImageFilter_h diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx b/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx deleted file mode 100644 index 321f7bbf250..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/RLEImage/RLERegionOfInterestImageFilter.txx +++ /dev/null @@ -1,531 +0,0 @@ -#ifndef RLERegionOfInterestImageFilter_txx -#define RLERegionOfInterestImageFilter_txx - -#include "itkRegionOfInterestImageFilter.h" -#include "itkImageAlgorithm.h" -#include "itkObjectFactory.h" -#include "itkProgressReporter.h" -#include "itkImage.h" - -namespace itk -{ -template -void -RegionOfInterestImageFilter, - RLEImage>::PrintSelf(std::ostream & os, - Indent indent) const -{ - Superclass::PrintSelf(os, indent); - - os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; -} - -template -void -RegionOfInterestImageFilter, - RLEImage>::GenerateInputRequestedRegion() -{ - // call the superclass' implementation of this method - Superclass::GenerateInputRequestedRegion(); - - // get pointer to the input - typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); - - if (inputPtr) - { - // request the region of interest - inputPtr->SetRequestedRegion(m_RegionOfInterest); - } -} - -template -void -RegionOfInterestImageFilter, - RLEImage>::EnlargeOutputRequestedRegion(DataObject * - output) -{ - // call the superclass' implementation of this method - Superclass::EnlargeOutputRequestedRegion(output); - - // generate everything in the region of interest - output->SetRequestedRegionToLargestPossibleRegion(); -} - -/** - * RegionOfInterestImageFilter can produce an image which is a different size - * than its input image. As such, RegionOfInterestImageFilter needs to provide an - * implementation for GenerateOutputInformation() in order to inform - * the pipeline execution model. The original documentation of this - * method is below. - * - * \sa ProcessObject::GenerateOutputInformaton() - */ -template -void -RegionOfInterestImageFilter, - RLEImage>::GenerateOutputInformation() -{ - // do not call the superclass' implementation of this method since - // this filter allows the input the output to be of different dimensions - - // get pointers to the input and output - typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); - typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); - - if (!outputPtr || !inputPtr) - { - return; - } - - // Set the output image size to the same value as the region of interest. - RegionType region; - IndexType start; - start.Fill(0); - - region.SetSize(m_RegionOfInterest.GetSize()); - region.SetIndex(start); - - // Copy Information without modification. - outputPtr->CopyInformation(inputPtr); - - // Adjust output region - outputPtr->SetLargestPossibleRegion(region); - - // Correct origin of the extracted region. - IndexType roiStart(m_RegionOfInterest.GetIndex()); - typename Superclass::OutputImageType::PointType outputOrigin; - inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); - outputPtr->SetOrigin(outputOrigin); -} - -/** - * RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() - */ -template -void -RegionOfInterestImageFilter< - RLEImage, - RLEImage>::ThreadedGenerateData(const RegionType & outputRegionForThread, - ThreadIdType threadId) -{ - // Get the input and output pointers - const RLEImageType * in = this->GetInput(); - RLEImageType * out = this->GetOutput(); - - // Define the portion of the input to walk for this thread - InputImageRegionType inputRegionForThread; - inputRegionForThread.SetSize(outputRegionForThread.GetSize()); - - IndexType start, end; - IndexType roiStart(m_RegionOfInterest.GetIndex()); - IndexType threadStart(outputRegionForThread.GetIndex()); - for (unsigned int i = 0; i < VImageDimension; i++) - { - start[i] = roiStart[i] + threadStart[i]; - end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); - } - inputRegionForThread.SetIndex(start); - - bool copyLines = (in->GetLargestPossibleRegion().GetSize(0) == outputRegionForThread.GetSize(0)); - typename ImageType::BufferType::RegionType oReg = ImageType::truncateRegion(outputRegionForThread), - iReg = ImageType::truncateRegion(inputRegionForThread); - ImageRegionConstIterator iIt(in->GetBuffer(), iReg); - ImageRegionIterator oIt(out->GetBuffer(), oReg); - - while (!oIt.IsAtEnd()) - { - if (copyLines) - oIt.Set(iIt.Get()); - else // determine begin and end iterator and copy range - { - typename RLEImageType::RLLine & oLine = oIt.Value(); - oLine.clear(); - const typename RLEImageType::RLLine & iLine = iIt.Value(); - CounterType t = 0; - SizeValueType x = 0; - // find start - for (; x < iLine.size(); x++) - { - t += iLine[x].first; - if (t > start[0]) - break; - } - assert(x < iLine.size()); - - SizeValueType begin = x; - if (t >= end[0]) // both begin and end are in this segment - { - oLine.push_back(typename RLEImageType::RLSegment(end[0] - start[0], iLine[x].second)); - ++iIt; - ++oIt; - continue; // next line - } - else if (t - start[0] < iLine[x].first) // not the first pixel in segment - { - oLine.push_back(typename RLEImageType::RLSegment(t - start[0], iLine[x].second)); - begin++; // start copying from next segment - } - - // if (t < end[0]) - for (x++; x < iLine.size(); x++) - { - t += iLine[x].first; - if (t >= end[0]) - break; - } - if (t == end[0]) - oLine.insert(oLine.end(), iLine.begin() + begin, iLine.begin() + x + 1); - else // we need to take special care of the last segment - { - oLine.insert(oLine.end(), iLine.begin() + begin, iLine.begin() + x); - oLine.push_back(typename RLEImageType::RLSegment(end[0] + iLine[x].first - t, iLine[x].second)); - } - } - ++iIt; - ++oIt; - } -} - - -template -void -RegionOfInterestImageFilter, RLEImage>::PrintSelf( - std::ostream & os, - Indent indent) const -{ - Superclass::PrintSelf(os, indent); - - os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; -} - -template -void -RegionOfInterestImageFilter, - RLEImage>::GenerateInputRequestedRegion() -{ - // call the superclass' implementation of this method - Superclass::GenerateInputRequestedRegion(); - - // get pointer to the input - typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); - - if (inputPtr) - { - // request the region of interest - inputPtr->SetRequestedRegion(m_RegionOfInterest); - } -} - -template -void -RegionOfInterestImageFilter, RLEImage>:: - EnlargeOutputRequestedRegion(DataObject * output) -{ - // call the superclass' implementation of this method - Superclass::EnlargeOutputRequestedRegion(output); - - // generate everything in the region of interest - output->SetRequestedRegionToLargestPossibleRegion(); -} - -/** - * RegionOfInterestImageFilter can produce an image which is a different size - * than its input image. As such, RegionOfInterestImageFilter needs to provide an - * implementation for GenerateOutputInformation() in order to inform - * the pipeline execution model. The original documentation of this - * method is below. - * - * \sa ProcessObject::GenerateOutputInformaton() - */ -template -void -RegionOfInterestImageFilter, - RLEImage>::GenerateOutputInformation() -{ - // do not call the superclass' implementation of this method since - // this filter allows the input the output to be of different dimensions - - // get pointers to the input and output - typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); - typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); - - if (!outputPtr || !inputPtr) - { - return; - } - - // Set the output image size to the same value as the region of interest. - RegionType region; - IndexType start; - start.Fill(0); - - region.SetSize(m_RegionOfInterest.GetSize()); - region.SetIndex(start); - - // Copy Information without modification. - outputPtr->CopyInformation(inputPtr); - - // Adjust output region - outputPtr->SetLargestPossibleRegion(region); - - // Correct origin of the extracted region. - IndexType roiStart(m_RegionOfInterest.GetIndex()); - typename Superclass::OutputImageType::PointType outputOrigin; - inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); - outputPtr->SetOrigin(outputOrigin); -} - -/** - * RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() - */ -template -void -RegionOfInterestImageFilter, RLEImage>:: - ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId) -{ - // Get the input and output pointers - const ImageType * in = this->GetInput(); - RLEImageType * out = this->GetOutput(); - - // Define the portion of the input to walk for this thread - InputImageRegionType inputRegionForThread; - inputRegionForThread.SetSize(outputRegionForThread.GetSize()); - - IndexType start, end; - IndexType roiStart(m_RegionOfInterest.GetIndex()); - IndexType threadStart(outputRegionForThread.GetIndex()); - for (unsigned int i = 0; i < VImageDimension; i++) - { - start[i] = roiStart[i] + threadStart[i]; - end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); - } - inputRegionForThread.SetIndex(start); - - typename RLEImageType::BufferType::RegionType oReg = RLEImageType::truncateRegion(outputRegionForThread); - ImageRegionConstIterator iIt(in, inputRegionForThread); - ImageRegionIterator oIt(out->GetBuffer(), oReg); - SizeValueType size0 = outputRegionForThread.GetSize(0); - typename RLEImageType::RLLine temp; - temp.reserve(size0); // pessimistically preallocate buffer, otherwise reallocations can occur - - while (!oIt.IsAtEnd()) - { - SizeValueType x = 0; - temp.clear(); - while (x < size0) - { - typename RLEImageType::RLSegment s(0, iIt.Value()); - while (x < size0 && iIt.Value() == s.second) - { - x++; - s.first++; - ++(iIt); - } - temp.push_back(s); - } - oIt.Value() = temp; - ++oIt; - } -} - - -template -void -RegionOfInterestImageFilter, Image>::PrintSelf( - std::ostream & os, - Indent indent) const -{ - Superclass::PrintSelf(os, indent); - - os << indent << "RegionOfInterest: " << m_RegionOfInterest << std::endl; -} - -template -void -RegionOfInterestImageFilter, - Image>::GenerateInputRequestedRegion() -{ - // call the superclass' implementation of this method - Superclass::GenerateInputRequestedRegion(); - - // get pointer to the input - typename Superclass::InputImagePointer inputPtr = const_cast(this->GetInput()); - - if (inputPtr) - { - // request the region of interest - inputPtr->SetRequestedRegion(m_RegionOfInterest); - } -} - -template -void -RegionOfInterestImageFilter, - Image>::EnlargeOutputRequestedRegion(DataObject * output) -{ - // call the superclass' implementation of this method - Superclass::EnlargeOutputRequestedRegion(output); - - // generate everything in the region of interest - output->SetRequestedRegionToLargestPossibleRegion(); -} - -/** - * RegionOfInterestImageFilter can produce an image which is a different size - * than its input image. As such, RegionOfInterestImageFilter needs to provide an - * implementation for GenerateOutputInformation() in order to inform - * the pipeline execution model. The original documentation of this - * method is below. - * - * \sa ProcessObject::GenerateOutputInformaton() - */ -template -void -RegionOfInterestImageFilter, - Image>::GenerateOutputInformation() -{ - // do not call the superclass' implementation of this method since - // this filter allows the input the output to be of different dimensions - - // get pointers to the input and output - typename Superclass::OutputImagePointer outputPtr = this->GetOutput(); - typename Superclass::InputImageConstPointer inputPtr = this->GetInput(); - - if (!outputPtr || !inputPtr) - { - return; - } - - // Set the output image size to the same value as the region of interest. - RegionType region; - IndexType start; - start.Fill(0); - - region.SetSize(m_RegionOfInterest.GetSize()); - region.SetIndex(start); - - // Copy Information without modification. - outputPtr->CopyInformation(inputPtr); - - // Adjust output region - outputPtr->SetLargestPossibleRegion(region); - - // Correct origin of the extracted region. - IndexType roiStart(m_RegionOfInterest.GetIndex()); - typename Superclass::OutputImageType::PointType outputOrigin; - inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin); - outputPtr->SetOrigin(outputOrigin); -} - -/** - * RegionOfInterestImageFilter can be implemented as a multithreaded filter. - * Therefore, this implementation provides a ThreadedGenerateData() - * routine which is called for each processing thread. The output - * image data is allocated automatically by the superclass prior to - * calling ThreadedGenerateData(). ThreadedGenerateData can only - * write to the portion of the output image specified by the - * parameter "outputRegionForThread" - * - * \sa ImageToImageFilter::ThreadedGenerateData(), - * ImageToImageFilter::GenerateData() - */ -template -void -RegionOfInterestImageFilter, Image>:: - ThreadedGenerateData(const RegionType & outputRegionForThread, ThreadIdType threadId) -{ - // Get the input and output pointers - const RLEImageType * in = this->GetInput(); - ImageType * out = this->GetOutput(); - - // Define the portion of the input to walk for this thread - InputImageRegionType inputRegionForThread; - inputRegionForThread.SetSize(outputRegionForThread.GetSize()); - - IndexType start, end; - IndexType roiStart(m_RegionOfInterest.GetIndex()); - IndexType threadStart(outputRegionForThread.GetIndex()); - for (unsigned int i = 0; i < VImageDimension; i++) - { - start[i] = roiStart[i] + threadStart[i]; - end[i] = roiStart[i] + threadStart[i] + outputRegionForThread.GetSize(i); - } - inputRegionForThread.SetIndex(start); - - typename RLEImageType::BufferType::RegionType iReg = RLEImageType::truncateRegion(inputRegionForThread); - ImageRegionConstIterator iIt(in->GetBuffer(), iReg); - ImageRegionIterator oIt(out, outputRegionForThread); - - while (!iIt.IsAtEnd()) - { - const typename RLEImageType::RLLine & iLine = iIt.Value(); - CounterType t = 0; - SizeValueType x = 0; - // find start - for (; x < iLine.size(); x++) - { - t += iLine[x].first; - if (t > start[0]) - break; - } - assert(x < iLine.size()); - - SizeValueType begin = x; - if (t >= end[0]) // both begin and end are in this segment - { - for (SizeValueType i = start[0]; i < end[0]; i++) - { - oIt.Set(iLine[x].second); - ++oIt; - } - ++iIt; - continue; // next line - } - // else handle the beginning segment - for (SizeValueType i = start[0]; i < t; i++) - { - oIt.Set(iLine[x].second); - ++oIt; - } - // now handle middle segments - for (x++; x < iLine.size(); x++) - { - t += iLine[x].first; - if (t >= end[0]) - break; - for (SizeValueType i = 0; i < iLine[x].first; i++) - { - oIt.Set(iLine[x].second); - ++oIt; - } - } - // handle the last segment - for (SizeValueType i = 0; i < end[0] + iLine[x].first - t; i++) - { - oIt.Set(iLine[x].second); - ++oIt; - } - ++iIt; - } -} -} // end namespace itk - -#endif // RLERegionOfInterestImageFilter_txx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 46349cf81af..8d384128bae 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -16,22 +16,13 @@ * *=========================================================================*/ -#include "RLEImage/RLEImageScanlineIterator.h" -#include "RLEImage/RLEImageRegionIterator.h" -#include "RLEImage/RLERegionOfInterestImageFilter.h" +#include "itkRLEImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" #include #include -long int -string2int(char * number) -{ - long res = strtol(number, NULL, 10); - return res; -} - template void doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, bool ball, int axis, int label) @@ -41,9 +32,9 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor reader->SetFileName(inFilename); reader->Update(); - typedef RLEImage myRLEImage; - typedef itk::RegionOfInterestImageFilter inConverterType; - typename inConverterType::Pointer inConv = inConverterType::New(); + typedef itk::RLEImage myRLEImage; + typedef itk::RegionOfInterestImageFilter inConverterType; + typename inConverterType::Pointer inConv = inConverterType::New(); inConv->SetInput(reader->GetOutput()); inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); inConv->Update(); From 61469b3ea210766cfac96b83b855fd2addfd1983 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 10 Aug 2016 10:26:31 -0400 Subject: [PATCH 100/176] DOC: Module docs say that testing requires RLEImage --- .../MorphologicalContourInterpolation/itk-module.cmake | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index 6df356092ca..e7fb195a262 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -1,7 +1,8 @@ set( DOCUMENTATION "The modules provides filters to do interpolation -of manually segmented anatomical contours." +of manually segmented anatomical contours. +Enabling testing requires RLEImage module to be enabled." ) itk_module( From 538108bf767af7afe758ebceb7691ce3d7eb99f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 15 Aug 2016 12:26:33 -0400 Subject: [PATCH 101/176] STYLE: Complying better with ITK style --- .../itkMorphologicalContourInterpolator.h | 3 -- .../itkMorphologicalContourInterpolator.hxx | 53 ++++++++----------- 2 files changed, 22 insertions(+), 34 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index ceb50f04411..ef85cf8a86e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -24,7 +24,6 @@ #include "itkImageToImageFilter.h" #include "itksys/hash_map.hxx" - namespace itk { /** \class MorphologicalContourInterpolator @@ -270,7 +269,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter #include - namespace itk { template @@ -52,7 +51,6 @@ struct SegmentBetweenTwo typename MorphologicalContourInterpolator::SliceType::Pointer iconn, jconn; }; - template class MorphologicalContourInterpolatorParallelInvoker : public itk::DomainThreader> @@ -110,7 +108,6 @@ private: std::vector> m_WorkArray; }; - template bool MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Pointer & a, @@ -139,7 +136,6 @@ MorphologicalContourInterpolator::ImagesEqual(typename BoolSliceType::Po } } // >::ImagesEqual - template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) @@ -167,7 +163,6 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() m_ConnectedComponents->SetFullyConnected(m_UseBallStructuringElement); } - template template void @@ -189,7 +184,6 @@ MorphologicalContourInterpolator::ExpandRegion(typename T2::RegionType & } } - template void MorphologicalContourInterpolator::DetermineSliceOrientations() @@ -203,8 +197,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() typename TImage::RegionType region = m_Output->GetRequestedRegion(); ImageRegionConstIteratorWithIndex it(m_Input, region); - - for (; !it.IsAtEnd(); ++it) + while (!it.IsAtEnd()) { typename TImage::IndexType indPrev, indNext; const typename TImage::IndexType ind = it.GetIndex(); @@ -243,7 +236,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() { next = m_Input->GetPixel(indNext); } - if (prev == 0 && next == 0) //&& - isolated slices only, || - flat edges too + if (prev == 0 && next == 0) // && - isolated slices only, || - flat edges too { axis = a; ++cTrue; @@ -253,7 +246,8 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() ++cAdjacent; } } - if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis + if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) + // slice has empty adjacent space only along one axis { if (m_Axis == -1 || m_Axis == axis) { @@ -261,10 +255,10 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() } } } + ++it; } } // >::DetermineSliceOrientations - template void MorphologicalContourInterpolator::Extrapolate(int axis, @@ -277,6 +271,7 @@ MorphologicalContourInterpolator::Extrapolate(int ThreadIdType threadId) { PixelList jRegionIds; + jRegionIds.push_back(iRegionId); typename SliceType::IndexType centroid = Centroid(iConn, jRegionIds); @@ -303,7 +298,6 @@ MorphologicalContourInterpolator::Extrapolate(int // do alignment in case the iShape is concave and centroid is not within the iShape typename SliceType::IndexType translation = Align(iConn, iRegionId, phSlice, jRegionIds); - // now translate the phantom slice for best alignment for (unsigned d = 0; d < SliceType::ImageDimension; d++) { @@ -315,7 +309,6 @@ MorphologicalContourInterpolator::Extrapolate(int Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false, threadId); } // >::Extrapolate - template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer & seed, @@ -388,7 +381,6 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe return result; } // >::Dilate1 - template std::vector::BoolSliceType::Pointer> MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer & begin, @@ -406,7 +398,6 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool return seq; } - template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, @@ -463,7 +454,6 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool return seq[minIndex]; } // >::FindMedianImageDilations - template typename MorphologicalContourInterpolator::FloatSliceType::Pointer MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask, ThreadIdType threadId) @@ -602,7 +592,6 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool return median; } // >::FindMedianImageDistances - template typename MorphologicalContourInterpolator::SliceType::RegionType MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) @@ -898,11 +887,13 @@ public: { return m_ID != other.m_ID; } + bool operator==(const MatchesID & other) { return m_ID == other.m_ID; } + inline bool operator()(const typename TImage::PixelType & val) const { @@ -991,6 +982,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ImageRegionConstIteratorWithIndex jIt2(blobs[0], iRegion); bool hollowedMaskEmpty; + do // while hollowed mask is not empty { for (unsigned x = 0; x < jRegionIds.size(); x++) @@ -1010,12 +1002,13 @@ MorphologicalContourInterpolator::Interpolate1toN(int if (!belongIt.Get()) { unsigned x = 0; - for (; x < jRegionIds.size(); x++) + while (x < jRegionIds.size()) { if (blobs[x]->GetPixel(jIt2.GetIndex())) { break; } + ++x; } if (x < jRegionIds.size()) // covered by a blob, hollow it out { @@ -1048,6 +1041,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int ++belongIt; } } while (!hollowedMaskEmpty); + blobs.clear(); // deallocates the images // convert the belongs into n Conn-style images @@ -1070,7 +1064,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int } ++belongIt2; } - // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { @@ -1078,7 +1071,6 @@ MorphologicalContourInterpolator::Interpolate1toN(int } } // >::Interpolate1toN - template typename MorphologicalContourInterpolator::SliceType::Pointer MorphologicalContourInterpolator::TranslateImage(typename SliceType::Pointer & image, @@ -1095,7 +1087,6 @@ MorphologicalContourInterpolator::TranslateImage(typename SliceType::Poi return result; } - template void MorphologicalContourInterpolator::IntersectionRegions(const typename SliceType::IndexType & translation, @@ -1117,7 +1108,6 @@ MorphologicalContourInterpolator::IntersectionRegions(const typename Sli jRegion.SetSize(iRegion.GetSize()); // size is the same } - template IdentifierType MorphologicalContourInterpolator::Intersection(typename SliceType::Pointer & iConn, @@ -1152,6 +1142,7 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point ++iIt; ++jIt; } + IdentifierType sum = 0; for (int x = 0; x < jRegionIds.size(); x++) { @@ -1210,6 +1201,7 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & } ++it; } + typename SliceType::IndexType retVal; for (unsigned d = 0; d < SliceType::ImageDimension; d++) { @@ -1218,7 +1210,6 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & return retVal; } // >::Centroid - template typename MorphologicalContourInterpolator::SliceType::IndexType MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iConn, @@ -1228,6 +1219,7 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC { // calculate centroids PixelList iRegionIds; + iRegionIds.push_back(iRegionId); typename SliceType::IndexType iCentroid = Centroid(iConn, iRegionIds); typename SliceType::IndexType jCentroid = Centroid(jConn, jRegionIds); @@ -1282,14 +1274,14 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC { for (unsigned d = 0; d < SliceType::ImageDimension; d++) { - ind[d] -= 1; //"left" + ind[d] -= 1; // "left" if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) { uncomputed.push(ind); searched->SetPixel(ind, true); ++iter; } - ind[d] += 2; //"right" + ind[d] += 2; // "right" if (searchRegion.IsInside(ind) && !searched->GetPixel(ind)) { uncomputed.push(ind); @@ -1304,7 +1296,6 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC return bestIndex; } // >::Align - template typename MorphologicalContourInterpolator::SliceType::Pointer MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType & region, @@ -1320,7 +1311,6 @@ MorphologicalContourInterpolator::RegionedConnectedComponents(const type return m_ConnectedComponents->GetOutput(); } - template void MorphologicalContourInterpolator::InterpolateBetweenTwo(int axis, @@ -1355,6 +1345,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++iti; ++itj; } + std::set_difference(uncleanPairs.begin(), uncleanPairs.end(), unwantedPairs.begin(), @@ -1444,6 +1435,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } + --iCounts[p->first]; --jCounts[p->second]; pairs.erase(p++); @@ -1476,6 +1468,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } + --iCounts[p->first]; --jCounts[p->second]; pairs.erase(p++); @@ -1516,12 +1509,12 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ++rest; } } + // counts no longer matter, do not waste time deleting them pairs.erase(p++); } // M-to-N } // void MorphologicalContourInterpolator::InterpolateBetweenTwo() - template void MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) @@ -1529,7 +1522,6 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou // a list of segments which need to be interpolated std::vector> segments; typename TImage::RegionType reqRegion = this->GetOutput()->GetRequestedRegion(); - for (typename LabeledSlicesType::iterator it = m_LabeledSlices[axis].begin(); it != m_LabeledSlices[axis].end(); ++it) { if (m_Label == 0 || m_Label == it->first) // label needs to be interpolated @@ -1575,7 +1567,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou if (*prev + 1 < *next // only if they are not adjacent slices && abs(iReq + jReq) <= 1) // and not out of the requested region - // unless they are on opposite ends + // unless they are on opposite ends { SegmentBetweenTwo s; s.axis = axis; @@ -1604,7 +1596,6 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou parallelizer->ClearWorkArray(); } // >::InterpolateAlong - template void MorphologicalContourInterpolator::AllocateOutputs() From 4e371aa38ad337f575b3668dab0a850af985dc25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 18 Aug 2016 09:58:33 -0400 Subject: [PATCH 102/176] ENH: Adding functional test Starting from a fully manually segmented image, leave every n-th slice (to simulate sparse manual segmentation) then use that as input to interpolation filter and compare output with the original image. --- .../test/CMakeLists.txt | 32 +++ .../test/Input/c10.mha.md5 | 1 + .../test/Input/c10b.mha.md5 | 1 + .../test/Input/c10l.mha.md5 | 1 + .../test/Input/c2.mha.md5 | 1 + .../test/Input/c2b.mha.md5 | 1 + .../test/Input/c2l.mha.md5 | 1 + .../test/Input/case_10_binary.mha.md5 | 1 + .../test/Input/case_10_labels.mha.md5 | 1 + .../test/Input/case_2_binary.mha.md5 | 1 + .../test/Input/case_2_labels.mha.md5 | 1 + .../test/dscComparison.cxx | 202 ++++++++++++++++++ 12 files changed, 244 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10b.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10l.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 8dce950903c..b87ef9a78a3 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -17,6 +17,12 @@ target_link_libraries( ${MorphologicalContourInterpolation-Test_LIBRARIES} ) +add_executable(dscComparison dscComparison.cxx) +target_link_libraries( + dscComparison + ${MorphologicalContourInterpolation-Test_LIBRARIES} +) + # used to produce an output which is then taken as a baseline for a regression test function(JustInputTest ImageName Ext) #optional: Algo Axis Label foreach(f ${ARGN}) #create unique test name @@ -58,6 +64,20 @@ function(RegressionTest ImageName Ext) #optional: Algo Axis Label ) endfunction() +# functional comparison using Dice Similarity Coefficient +function(DSCTest ImageName Ext) + set(outFilenameBase "${ITK_TEST_OUTPUT_DIR}/${ImageName}") + + itk_add_test( + NAME itkMCI_DSC_${ImageName} + COMMAND + dscComparison + DATA{Input/${ImageName}.${Ext}} + ${outFilenameBase} + ${ARGN} + ) +endfunction() + # Handcrafted tests regressiontest(Empty nrrd ${MCI_Algorithm}) regressiontest(NoSlices nrrd ${MCI_Algorithm}) #interpolation should not be invoked (output==input) @@ -195,3 +215,15 @@ regressiontest(FaceRoI nrrd ${MCI_Algorithm} 2) # Non-3D tests regressiontest(FourD nrrd ${MCI_Algorithm}) + +# dscComparison (crops) +dsctest(c2l mha saveImages) +dsctest(c2b mha saveImages) +dsctest(c10l mha saveImages) +dsctest(c10b mha saveImages) + +# dscComparison (full resolution) +dsctest(case_2_labels mha saveImages) +dsctest(case_2_binary mha saveImages) +dsctest(case_10_labels mha saveImages) +dsctest(case_10_binary mha saveImages) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10.mha.md5 new file mode 100644 index 00000000000..4f6542bae40 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10.mha.md5 @@ -0,0 +1 @@ +cc415936aa8463b18e44425b31a9a444 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10b.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10b.mha.md5 new file mode 100644 index 00000000000..a2e40f22459 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10b.mha.md5 @@ -0,0 +1 @@ +da0e074d92c3b89508f15d71a9979434 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10l.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10l.mha.md5 new file mode 100644 index 00000000000..1cf72ef298c --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c10l.mha.md5 @@ -0,0 +1 @@ +837379f430c4fe8b0fbee9c2c93c5562 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.md5 new file mode 100644 index 00000000000..2f2357d4f41 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.md5 @@ -0,0 +1 @@ +4601f3a9d4a9ee7f6f3177efdadc8cbb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 new file mode 100644 index 00000000000..d6b27e3fa70 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 @@ -0,0 +1 @@ +45e6886ea895af85026f4afff0cbdf1e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 new file mode 100644 index 00000000000..af1baadf362 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 @@ -0,0 +1 @@ +2d8e4b6dcd2a9499f680388497782c66 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 new file mode 100644 index 00000000000..c7f3f6c0cf5 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 @@ -0,0 +1 @@ +684fb9347d9ba6a6db0237a0cc32306e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 new file mode 100644 index 00000000000..c6bbae2bb8d --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 @@ -0,0 +1 @@ +2b7dc9466c4b72915eddbe1623958b28 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 new file mode 100644 index 00000000000..e452a4ff117 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 @@ -0,0 +1 @@ +b9f29368bacdc279b2aa1e76e1d25704 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 new file mode 100644 index 00000000000..0420d4fb201 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 @@ -0,0 +1 @@ +3b817726a059554cf37dd8202d965249 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx new file mode 100644 index 00000000000..afd2d27880e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -0,0 +1,202 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ + +#include +#include +#include +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" +#include "itkMorphologicalContourInterpolator.h" +#include "itkTestDriverIncludeRequiredIOFactories.h" +#include "itkTimeProbe.h" + +typedef unsigned char PixelType; +const unsigned int dim = 3; +typedef itk::Image ImageType; + +ImageType::Pointer +createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) +{ + const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); + ImageType::Pointer outImage = ImageType::New(); + outImage->CopyInformation(inImage); + outImage->SetRegions(lpr); + outImage->Allocate(true); + + itk::ImageRegionConstIterator iIt(inImage, lpr); + itk::ImageRegionIteratorWithIndex oIt(outImage, lpr); + + while (!oIt.IsAtEnd()) + { + const PixelType & val = iIt.Get(); + if (val) + { + const ImageType::IndexType & ind = oIt.GetIndex(); + bool write = false; + + for (int axis = 0; axis < dim; axis++) + { + if (ind[axis] % nth[axis] == 0) + { + write = true; + break; + } + } + + if (write) + { + oIt.Set(val); + } + } + ++iIt; + ++oIt; + } + + return outImage; +} + +void +calcOverlap(const ImageType::Pointer & autoSeg, + const ImageType::Pointer & groundTruth, + unsigned long long & tpCount, + unsigned long long & fpCount, + unsigned long long & fnCount) +{ + const ImageType::RegionType & lpr = groundTruth->GetLargestPossibleRegion(); + itk::ImageRegionConstIterator itAS(autoSeg, lpr); + itk::ImageRegionConstIterator itGT(groundTruth, lpr); + tpCount = 0; + fpCount = 0; + fnCount = 0; + + while (!itAS.IsAtEnd()) + { + if (itAS.Get() != 0 && itAS.Get() == itGT.Get()) + { + tpCount++; // true positive + } + else if (itAS.Get() != 0) + { + fpCount++; // false positive + } + if (itAS.Get() == 0 && itGT.Get() != 0) + { + fnCount++; // false negative + } + + ++itAS; + ++itGT; + } +} + +int +main(int argc, char * argv[]) +{ + if (argc < 2) + { + std::cerr << "Usage: " << argv[0]; + std::cerr << " inputImage [outFilenameBase] [saveIntermediateImages]\n"; + return 1; + } + bool saveImages = argc > 3; + std::string outFilenameBase; + std::fstream fout; + if (argc > 2) + { + outFilenameBase = argv[2]; + fout.open((outFilenameBase + ".csv").c_str(), std::ios::out); + } + else + { + fout.set_rdbuf(std::cout.rdbuf()); + } + RegisterRequiredFactories(); + + typedef itk::ImageFileReader ReaderType; + typename ReaderType::Pointer reader = ReaderType::New(); + reader->SetFileName(argv[1]); + reader->Update(); + ImageType::Pointer inImage = reader->GetOutput(); + inImage->DisconnectPipeline(); + + typedef itk::MorphologicalContourInterpolator mciType; + typename mciType::Pointer mci = mciType::New(); + mci->SetUseBallStructuringElement(true); // test cross? + + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->SetUseCompression(true); + + const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); + ImageType::IndexType maxInd; + for (int axis = 0; axis < dim; axis++) + { + maxInd[axis] = itk::IndexValueType(lpr.GetSize(axis)); + } + fout << "Image, nth, axis, time, TP, FP, FN, TN\n"; + + // the big for loop which does the work + for (int sparsity = 2; sparsity <= 8; sparsity++) + { + unsigned long long tpCount, fpCount, fnCount; + for (int axis = -1; axis < int(dim); axis++) + { + mci->SetAxis(axis); + ImageType::IndexType axisSparsity = maxInd; + if (axis < 0) // all axes + { + for (int axis = 0; axis < dim; axis++) + { + axisSparsity[axis] = sparsity; + } + } + else // just one axis + { + axisSparsity[axis] = sparsity; + } + + ImageType::Pointer sparseImage = createSparseCopy(inImage, axisSparsity); + mci->SetInput(sparseImage); + itk::TimeProbe timeProbe; + timeProbe.Start(); + mci->Update(); + timeProbe.Stop(); + ImageType::Pointer result = mci->GetOutput(); + result->DisconnectPipeline(); + calcOverlap(result, inImage, tpCount, fpCount, fnCount); + + fout << argv[1] << ", " << sparsity << ", " << axis << ", " << timeProbe.GetMean(); + fout << ", " << tpCount << ", " << fpCount << ", " << fnCount << ", "; + fout << (lpr.GetNumberOfPixels() - tpCount - fpCount - fnCount) << std::endl; + + if (saveImages) + { + std::cout << outFilenameBase + '_' + char(sparsity + '0') + char(axis + 'X') + "\nWriting sparse... "; + writer->SetInput(sparseImage); + writer->SetFileName(outFilenameBase + "_in" + char(sparsity + '0') + char(axis + 'X') + ".mha"); + writer->Update(); + std::cout << "interpolated... "; + writer->SetInput(result); + writer->SetFileName(outFilenameBase + "_out" + char(sparsity + '0') + char(axis + 'X') + ".mha"); + writer->Update(); + std::cout << "finished." << std::endl; + } + } + } + return 0; +} From 01fe4611fa405665f211a006cef5c0e6c08d220f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 19 Aug 2016 17:49:25 -0400 Subject: [PATCH 103/176] ENH: C++98 compliance --- .../MorphologicalContourInterpolation/test/dscComparison.cxx | 4 ---- 1 file changed, 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index afd2d27880e..0a838250deb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -121,10 +121,6 @@ main(int argc, char * argv[]) outFilenameBase = argv[2]; fout.open((outFilenameBase + ".csv").c_str(), std::ios::out); } - else - { - fout.set_rdbuf(std::cout.rdbuf()); - } RegisterRequiredFactories(); typedef itk::ImageFileReader ReaderType; From 049d4c765489cb67bd5fdaddfb6216396b21e385 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 19 Aug 2016 17:55:00 -0400 Subject: [PATCH 104/176] ENH: Uncrustifying --- .../test/dscComparison.cxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index 0a838250deb..d6eacba799d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -33,7 +33,8 @@ ImageType::Pointer createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) { const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); - ImageType::Pointer outImage = ImageType::New(); + + ImageType::Pointer outImage = ImageType::New(); outImage->CopyInformation(inImage); outImage->SetRegions(lpr); outImage->Allocate(true); @@ -48,7 +49,6 @@ createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) { const ImageType::IndexType & ind = oIt.GetIndex(); bool write = false; - for (int axis = 0; axis < dim; axis++) { if (ind[axis] % nth[axis] == 0) @@ -77,7 +77,8 @@ calcOverlap(const ImageType::Pointer & autoSeg, unsigned long long & fpCount, unsigned long long & fnCount) { - const ImageType::RegionType & lpr = groundTruth->GetLargestPossibleRegion(); + const ImageType::RegionType & lpr = groundTruth->GetLargestPossibleRegion(); + itk::ImageRegionConstIterator itAS(autoSeg, lpr); itk::ImageRegionConstIterator itGT(groundTruth, lpr); tpCount = 0; @@ -145,7 +146,6 @@ main(int argc, char * argv[]) maxInd[axis] = itk::IndexValueType(lpr.GetSize(axis)); } fout << "Image, nth, axis, time, TP, FP, FN, TN\n"; - // the big for loop which does the work for (int sparsity = 2; sparsity <= 8; sparsity++) { From 36ca5643e2ce49f07d74d318f1b438642433f4a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 22 Aug 2016 13:39:38 -0400 Subject: [PATCH 105/176] STYLE: Cleanup of module specification --- .../MorphologicalContourInterpolation/CMakeLists.txt | 4 +++- .../MorphologicalContourInterpolation/itk-module.cmake | 2 -- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index ddd3304567b..57f290ae6fe 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -5,7 +5,9 @@ set( MCI_Algorithm "B" CACHE STRING - "Which algorithm should be used for testing. + "Which algorithm should be used for testing +the module MorphologicalContourInterpolation. + B = repeated dilations with ball structuring element C = repeated dilations with cross structuring element T = distance transform (not geodesic!)" diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index e7fb195a262..b943bbb28c1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -8,11 +8,9 @@ Enabling testing requires RLEImage module to be enabled." itk_module( MorphologicalContourInterpolation DEPENDS - ITKCommon ITKBinaryMathematicalMorphology ITKDistanceMap TEST_DEPENDS - ITKIOImageBase # typename ITKTestKernel RLEImage EXCLUDE_FROM_DEFAULT From 9d8fe1067fb8caaf3827fb40a60b3977fe190199 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 23 Aug 2016 16:59:53 -0400 Subject: [PATCH 106/176] COMP: Depend on RLEImage only when building standalone --- .../CMakeLists.txt | 1 + .../test/CMakeLists.txt | 16 +- ...kMorphologicalContourInterpolationTest.cxx | 26 +-- ...alContourInterpolationTestWithRLEImage.cxx | 153 ++++++++++++++++++ 4 files changed, 172 insertions(+), 24 deletions(-) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 57f290ae6fe..8cc5fbd437c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -16,6 +16,7 @@ T = distance transform (not geodesic!)" if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) + set(MCI_TestWithRLEImage 1 CACHE BOOL "Whether to test with RLEImage") include(ITKModuleExternal) else() itk_module_impl() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index b87ef9a78a3..2a4bb2ca9dc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -1,9 +1,17 @@ itk_module_test() -set( - MorphologicalContourInterpolationTests - itkMorphologicalContourInterpolationTest.cxx -) +if(${MCI_TestWithRLEImage}) + set( + MorphologicalContourInterpolationTests + itkMorphologicalContourInterpolationTest.cxx + itkMorphologicalContourInterpolationTestWithRLEImage.cxx + ) +else(${MCI_TestWithRLEImage}) + set( + MorphologicalContourInterpolationTests + itkMorphologicalContourInterpolationTest.cxx + ) +endif(${MCI_TestWithRLEImage}) createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 8d384128bae..b478b3258e9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -16,7 +16,6 @@ * *=========================================================================*/ -#include "itkRLEImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" @@ -32,41 +31,28 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor reader->SetFileName(inFilename); reader->Update(); - typedef itk::RLEImage myRLEImage; - typedef itk::RegionOfInterestImageFilter inConverterType; - typename inConverterType::Pointer inConv = inConverterType::New(); - inConv->SetInput(reader->GetOutput()); - inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); - inConv->Update(); - typename myRLEImage::Pointer test = inConv->GetOutput(); + typename ImageType::Pointer test = reader->GetOutput(); // region for partial coverage - typename myRLEImage::RegionType reg = test->GetLargestPossibleRegion(); - // skip X due to RLE representation constraints - // for (int i = 1; i < ImageType::ImageDimension; i++) + typename ImageType::RegionType reg = test->GetLargestPossibleRegion(); + // for (int i = 0; i < ImageType::ImageDimension; i++) // { // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); // } - typedef itk::MorphologicalContourInterpolator mciType; - typename mciType::Pointer mci = mciType::New(); + typedef itk::MorphologicalContourInterpolator mciType; + typename mciType::Pointer mci = mciType::New(); mci->SetInput(test); mci->SetUseDistanceTransform(UseDistanceTransform); mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); - typedef itk::RegionOfInterestImageFilter outConverterType; - typename outConverterType::Pointer outConv = outConverterType::New(); - outConv->SetInput(mci->GetOutput()); - outConv->SetRegionOfInterest(reg); - outConv->Update(); - typedef itk::ImageFileWriter WriterType; typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outFilename); - writer->SetInput(outConv->GetOutput()); + writer->SetInput(mci->GetOutput()); writer->SetUseCompression(true); writer->Update(); } diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx new file mode 100644 index 00000000000..861a9714181 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -0,0 +1,153 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ + +#include "itkRLEImage.h" +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" +#include "itkMorphologicalContourInterpolator.h" +#include +#include + +template +void +doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, bool ball, int axis, int label) +{ + typedef itk::ImageFileReader ReaderType; + typename ReaderType::Pointer reader = ReaderType::New(); + reader->SetFileName(inFilename); + reader->Update(); + + typedef itk::RLEImage myRLEImage; + typedef itk::RegionOfInterestImageFilter inConverterType; + typename inConverterType::Pointer inConv = inConverterType::New(); + inConv->SetInput(reader->GetOutput()); + inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); + inConv->Update(); + typename myRLEImage::Pointer test = inConv->GetOutput(); + + // region for partial coverage + typename myRLEImage::RegionType reg = test->GetLargestPossibleRegion(); + // skip X due to RLE representation constraints + // for (int i = 1; i < ImageType::ImageDimension; i++) + // { + // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; + // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); + // } + + typedef itk::MorphologicalContourInterpolator mciType; + typename mciType::Pointer mci = mciType::New(); + mci->SetInput(test); + mci->SetUseDistanceTransform(UseDistanceTransform); + mci->SetUseBallStructuringElement(ball); + mci->SetAxis(axis); + mci->SetLabel(label); + + typedef itk::RegionOfInterestImageFilter outConverterType; + typename outConverterType::Pointer outConv = outConverterType::New(); + outConv->SetInput(mci->GetOutput()); + outConv->SetRegionOfInterest(reg); + outConv->Update(); + + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outFilename); + writer->SetInput(outConv->GetOutput()); + writer->SetUseCompression(true); + writer->Update(); +} + +int +itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) +{ + if (argc < 3) + { + std::cerr << "Usage: " << argv[0]; + std::cerr << " inputImage outputImage [algorithm] [axis] [label]\n"; + std::cerr << " algorithms:\n"; + std::cerr << " B = repeated dilations with ball structuring element"; + std::cerr << " C = repeated dilations with cross structuring element"; + std::cerr << " T = distance transform (not geodesic!)"; + std::cerr << " defaults: algo B, axis -1 (all axes), label 0 (all labels)"; + std::cerr << std::endl; + return EXIT_FAILURE; + } + const char * inputImageFileName = argv[1]; + const char * outputImageFileName = argv[2]; + bool dt = false; // DistanceTransform + bool ball = true; + int axis = -1, label = 0; + if (argc >= 4) + { + char algo = toupper(argv[3][0]); + if (algo == 'T') + { + dt = true; + } + else if (algo == 'C') + { + ball = false; + } + // else B + } + if (argc >= 5) + { + axis = strtol(argv[4], NULL, 10); + } + if (argc >= 6) + { + label = strtol(argv[5], NULL, 10); + } + + typedef itk::ImageIOBase::IOComponentType ScalarPixelType; + itk::ImageIOBase::Pointer imageIO = + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); + if (!imageIO) + { + std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; + return EXIT_FAILURE; + } + imageIO->SetFileName(inputImageFileName); + imageIO->ReadImageInformation(); + const ScalarPixelType pixelType = imageIO->GetComponentType(); + const size_t numDimensions = imageIO->GetNumberOfDimensions(); + + try + { + // unused cases are not instantiated because they greatly increase compile time + if (numDimensions == 3 && (pixelType == itk::ImageIOBase::SHORT || pixelType == itk::ImageIOBase::USHORT)) + { + doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); + return EXIT_SUCCESS; + } + if (numDimensions == 4 && pixelType == itk::ImageIOBase::UCHAR) + { + doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); + return EXIT_SUCCESS; + } + + std::cerr << "Unsupported image type:\n Dimensions: " << numDimensions; + std::cerr << "\n Pixel type:" << imageIO->GetComponentTypeAsString(pixelType) << std::endl; + return EXIT_FAILURE; + } + catch (itk::ExceptionObject & error) + { + std::cerr << "Error: " << error << std::endl; + return EXIT_FAILURE; + } + return EXIT_SUCCESS; +} From a843aa06ba4bf62202f063bf2bb20d1856b4b0e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 24 Aug 2016 11:17:48 -0400 Subject: [PATCH 107/176] COMP: Use RLE version when available, more elegant CMake code --- .../test/CMakeLists.txt | 55 ++++++++++++------- 1 file changed, 34 insertions(+), 21 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 2a4bb2ca9dc..d269ca85491 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -1,16 +1,15 @@ itk_module_test() +set( + MorphologicalContourInterpolationTests + itkMorphologicalContourInterpolationTest.cxx +) + if(${MCI_TestWithRLEImage}) - set( - MorphologicalContourInterpolationTests - itkMorphologicalContourInterpolationTest.cxx + list( + APPEND MorphologicalContourInterpolationTests itkMorphologicalContourInterpolationTestWithRLEImage.cxx ) -else(${MCI_TestWithRLEImage}) - set( - MorphologicalContourInterpolationTests - itkMorphologicalContourInterpolationTest.cxx - ) endif(${MCI_TestWithRLEImage}) createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") @@ -57,19 +56,33 @@ function(RegressionTest ImageName Ext) #optional: Algo Axis Label endforeach() set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}${optArgs}.${Ext}") set(imageNameOpt "${ImageName}${optArgs}") - - itk_add_test( - NAME itkMCI_${ImageName}${optArgs} - COMMAND - MorphologicalContourInterpolationTestDriver - --compare - DATA{Baseline/${imageNameOpt}.${Ext}} - ${outImage} - itkMorphologicalContourInterpolationTest - DATA{Input/${ImageName}.${Ext}} - ${outImage} - ${ARGN} - ) + if(${MCI_TestWithRLEImage}) + itk_add_test( + NAME rleMCI_${ImageName}${optArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} + itkMorphologicalContourInterpolationTestWithRLEImage + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${ARGN} + ) + else(${MCI_TestWithRLEImage}) + itk_add_test( + NAME itkMCI_${ImageName}${optArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} + itkMorphologicalContourInterpolationTest + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${ARGN} + ) + endif(${MCI_TestWithRLEImage}) endfunction() # functional comparison using Dice Similarity Coefficient From a2cf13b5817cd6893750b6d40de3749a0aabad97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 24 Aug 2016 13:40:44 -0400 Subject: [PATCH 108/176] ENH: Uncrustify with finalized configuration --- .../include/itkMorphologicalContourInterpolator.hxx | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 13b5bbe408b..b5d589f3073 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -389,11 +389,13 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool { std::vector seq; seq.push_back(Dilate1(begin, end, threadId)); + do { seq.back()->DisconnectPipeline(); seq.push_back(Dilate1(seq.back(), end, threadId)); } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); + seq.pop_back(); // remove duplicate image return seq; } @@ -651,7 +653,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename SliceType::RegionType jRegion = jConn->GetLargestPossibleRegion(); typename SliceType::IndexType jBottom = jRegion.GetIndex(); bool carry = false; - for (unsigned d = 0; d < SliceType::ImageDimension; d++) { if (!carry) @@ -840,6 +841,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int ++seqIt; ++outIt; } + mutex.Unlock(); } // iterator destroyed here @@ -1010,6 +1012,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int } ++x; } + if (x < jRegionIds.size()) // covered by a blob, hollow it out { belongIt.Set(x + 1); @@ -1173,6 +1176,7 @@ MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceTy ++iIt; ++jIt; } + return count; } @@ -1644,7 +1648,6 @@ MorphologicalContourInterpolator::GenerateData() { FixedArray aggregate; aggregate.Fill(false); - for (int i = 0; i < TImage::ImageDimension; i++) { if (this->m_Label == 0) // examine all labels From 49a1dff6d192af860e821f7a75e2bef752937320 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 24 Aug 2016 13:44:54 -0400 Subject: [PATCH 109/176] ENH: RLEImage test OFF by default --- .../Filtering/MorphologicalContourInterpolation/CMakeLists.txt | 2 +- .../MorphologicalContourInterpolation/itk-module.cmake | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 8cc5fbd437c..8ead5fa5741 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -16,7 +16,7 @@ T = distance transform (not geodesic!)" if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) - set(MCI_TestWithRLEImage 1 CACHE BOOL "Whether to test with RLEImage") + set(MCI_TestWithRLEImage 0 CACHE BOOL "Whether to test with RLEImage") include(ITKModuleExternal) else() itk_module_impl() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index b943bbb28c1..126f2942782 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -12,7 +12,6 @@ itk_module( ITKDistanceMap TEST_DEPENDS ITKTestKernel - RLEImage EXCLUDE_FROM_DEFAULT DESCRIPTION "${DOCUMENTATION}" ) From 53512abee9a2729b4361f59fa5978acd29cb320e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 24 Aug 2016 14:03:51 -0400 Subject: [PATCH 110/176] BUG: Fixing warnings --- .../itkMorphologicalContourInterpolator.hxx | 22 ++++++++++--------- .../test/dscComparison.cxx | 14 ++++++------ 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index b5d589f3073..ae2566fca70 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -144,12 +144,12 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_UseDistanceTransform(true) , m_UseBallStructuringElement(false) , m_UseCustomSlicePositions(false) - , m_ThreadCount(MultiThreader::GetGlobalDefaultNumberOfThreads()) , m_MinAlignIters(pow(2, TImage::ImageDimension)) , // smaller of this and pixel count of the search image m_MaxAlignIters(pow(6, TImage::ImageDimension)) - , // bigger of this and root of pixel count of the search image - m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets + , // bigger of this and root of pixel count of the search image + m_ThreadCount(MultiThreader::GetGlobalDefaultNumberOfThreads()) + , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { // set up pipeline for regioned connected components m_RoI = RoiType::New(); @@ -249,7 +249,7 @@ MorphologicalContourInterpolator::DetermineSliceOrientations() if (cTrue == 1 && cAdjacent == TImage::ImageDimension - 1) // slice has empty adjacent space only along one axis { - if (m_Axis == -1 || m_Axis == axis) + if (m_Axis == -1 || m_Axis == int(axis)) { m_LabeledSlices[axis][val].insert(ind[axis]); } @@ -305,7 +305,8 @@ MorphologicalContourInterpolator::Extrapolate(int } reg3.SetIndex(phIndex); phSlice->SetRegions(reg3); - typename SliceType::IndexType t0 = { 0 }; + typename SliceType::IndexType t0; + t0.Fill(0); Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false, threadId); } // >::Extrapolate @@ -814,7 +815,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int bool withinReq = true; typename TImage::RegionType reqRegion = this->GetOutput()->GetRequestedRegion(); - for (int d = 0; d < TImage::ImageDimension; d++) + for (unsigned d = 0; d < TImage::ImageDimension; d++) { if (outRegion.GetIndex(d) < reqRegion.GetIndex(d) || outRegion.GetIndex(d) + outRegion.GetSize(d) > reqRegion.GetIndex(d) + reqRegion.GetSize(d)) @@ -1251,7 +1252,8 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC // breadth first search starting from centroid, implicitly: // when intersection scores are equal, chooses the one closer to centroid std::queue uncomputed; - typename SliceType::IndexType t0 = { 0 }; + typename SliceType::IndexType t0; + t0.Fill(0); uncomputed.push(t0); // no translation - guaranteed to find a non-zero intersection uncomputed.push(ind); // this introduces movement, and possibly has the same score searched->SetPixel(t0, true); @@ -1274,7 +1276,7 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC } // we breadth this search - if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || score > maxScore * 0.9 && iter <= maxIter) + if (!m_HeuristicAlignment || maxScore == 0 || iter <= minIter || (score > maxScore * 0.9 && iter <= maxIter)) { for (unsigned d = 0; d < SliceType::ImageDimension; d++) { @@ -1648,11 +1650,11 @@ MorphologicalContourInterpolator::GenerateData() { FixedArray aggregate; aggregate.Fill(false); - for (int i = 0; i < TImage::ImageDimension; i++) + for (unsigned i = 0; i < TImage::ImageDimension; i++) { if (this->m_Label == 0) // examine all labels { - for (int l = 0; l < m_LabeledSlices[i].size(); l++) + for (unsigned l = 0; l < m_LabeledSlices[i].size(); l++) { if (m_LabeledSlices[i][l].size() > 1) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index d6eacba799d..056c7877949 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -49,7 +49,7 @@ createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) { const ImageType::IndexType & ind = oIt.GetIndex(); bool write = false; - for (int axis = 0; axis < dim; axis++) + for (unsigned axis = 0; axis < dim; axis++) { if (ind[axis] % nth[axis] == 0) { @@ -125,23 +125,23 @@ main(int argc, char * argv[]) RegisterRequiredFactories(); typedef itk::ImageFileReader ReaderType; - typename ReaderType::Pointer reader = ReaderType::New(); + ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(argv[1]); reader->Update(); ImageType::Pointer inImage = reader->GetOutput(); inImage->DisconnectPipeline(); typedef itk::MorphologicalContourInterpolator mciType; - typename mciType::Pointer mci = mciType::New(); + mciType::Pointer mci = mciType::New(); mci->SetUseBallStructuringElement(true); // test cross? typedef itk::ImageFileWriter WriterType; - typename WriterType::Pointer writer = WriterType::New(); + WriterType::Pointer writer = WriterType::New(); writer->SetUseCompression(true); const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); ImageType::IndexType maxInd; - for (int axis = 0; axis < dim; axis++) + for (unsigned axis = 0; axis < dim; axis++) { maxInd[axis] = itk::IndexValueType(lpr.GetSize(axis)); } @@ -156,9 +156,9 @@ main(int argc, char * argv[]) ImageType::IndexType axisSparsity = maxInd; if (axis < 0) // all axes { - for (int axis = 0; axis < dim; axis++) + for (unsigned a = 0; a < dim; a++) { - axisSparsity[axis] = sparsity; + axisSparsity[a] = sparsity; } } else // just one axis From e763e5fd50f95f22b3b477786cd9b2ec9da221c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 24 Aug 2016 17:22:26 -0400 Subject: [PATCH 111/176] BUG: Fixing more warnings --- .../itkMorphologicalContourInterpolator.hxx | 23 +++--- .../test/dscComparison.cxx | 72 +++++++++---------- 2 files changed, 48 insertions(+), 47 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ae2566fca70..d1d4ea46899 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -441,7 +441,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool } // find median - unsigned minIndex; + unsigned minIndex = 0; IdentifierType min = iMask->GetRequestedRegion().GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { @@ -506,7 +506,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool typename TImage::PixelType dist = fractioning * itsdf.Get(); if (iM && !jM) { - if (dist >= iHist.size()) + if (size_t(dist) >= iHist.size()) { iHist.resize(dist + 1, 0); } @@ -545,7 +545,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool assert(jHist[0] == 0); std::vector iSum(maxSize, 0); std::vector jSum(maxSize, 0); - for (int b = 1; b < maxSize; b++) + for (unsigned b = 1; b < maxSize; b++) { iSum[b] = iSum[b - 1] + iHist[b]; jSum[b] = jSum[b - 1] + jHist[b]; @@ -609,7 +609,7 @@ MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer::BoundingBox(itk::SmartPointer::Interpolate1to1(int typename SliceType::RegionType jBB = BoundingBox(jConnT); typename SliceType::IndexType i2 = jBB.GetIndex(); ExpandRegion(newRegion, i2); - for (int d = 0; d < SliceType::ImageDimension; d++) + for (unsigned d = 0; d < SliceType::ImageDimension; d++) { i2[d] += jBB.GetSize(d) - 1; } @@ -764,7 +764,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int // finally write it out into the output image pointer typename TImage::RegionType outRegion = this->GetOutput()->GetRequestedRegion(); typename SliceType::RegionType sliceRegion; - for (int d = 0; d < TImage::ImageDimension - 1; d++) + for (int d = 0; d < int(TImage::ImageDimension) - 1; d++) { if (d < axis) { @@ -777,10 +777,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int sliceRegion.SetSize(d, outRegion.GetSize(d + 1)); } } - typename SliceType::IndexType t0 = { 0 }; // no translation + typename SliceType::IndexType t0; + t0.Fill(0); IntersectionRegions(t0, sliceRegion, newRegion); // clips new region to output region // sliceRegion possibly shrunk, copy it into outRegion - for (int d = 0; d < TImage::ImageDimension - 1; d++) + for (int d = 0; d < int(TImage::ImageDimension) - 1; d++) { if (d < axis) { @@ -1126,7 +1127,7 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point IntersectionRegions(translation, iRegion, jRegion); std::vector counts(jRegionIds.size()); - for (int x = 0; x < jRegionIds.size(); x++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { counts[x] = 0; } @@ -1148,7 +1149,7 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point } IdentifierType sum = 0; - for (int x = 0; x < jRegionIds.size(); x++) + for (unsigned x = 0; x < jRegionIds.size(); x++) { if (counts[x] == 0) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index 056c7877949..675430fa36c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -25,31 +25,31 @@ #include "itkTestDriverIncludeRequiredIOFactories.h" #include "itkTimeProbe.h" -typedef unsigned char PixelType; -const unsigned int dim = 3; -typedef itk::Image ImageType; +typedef unsigned char TestPixelType; +const unsigned int testDim = 3; +typedef itk::Image TestImageType; -ImageType::Pointer -createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) +TestImageType::Pointer +createSparseCopy(const TestImageType::Pointer & inImage, TestImageType::IndexType nth) { - const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); + const TestImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); - ImageType::Pointer outImage = ImageType::New(); + TestImageType::Pointer outImage = TestImageType::New(); outImage->CopyInformation(inImage); outImage->SetRegions(lpr); outImage->Allocate(true); - itk::ImageRegionConstIterator iIt(inImage, lpr); - itk::ImageRegionIteratorWithIndex oIt(outImage, lpr); + itk::ImageRegionConstIterator iIt(inImage, lpr); + itk::ImageRegionIteratorWithIndex oIt(outImage, lpr); while (!oIt.IsAtEnd()) { - const PixelType & val = iIt.Get(); + const TestPixelType & val = iIt.Get(); if (val) { - const ImageType::IndexType & ind = oIt.GetIndex(); - bool write = false; - for (unsigned axis = 0; axis < dim; axis++) + const TestImageType::IndexType & ind = oIt.GetIndex(); + bool write = false; + for (unsigned axis = 0; axis < testDim; axis++) { if (ind[axis] % nth[axis] == 0) { @@ -71,16 +71,16 @@ createSparseCopy(const ImageType::Pointer & inImage, ImageType::IndexType nth) } void -calcOverlap(const ImageType::Pointer & autoSeg, - const ImageType::Pointer & groundTruth, - unsigned long long & tpCount, - unsigned long long & fpCount, - unsigned long long & fnCount) +calcOverlap(const TestImageType::Pointer & autoSeg, + const TestImageType::Pointer & groundTruth, + unsigned long long & tpCount, + unsigned long long & fpCount, + unsigned long long & fnCount) { - const ImageType::RegionType & lpr = groundTruth->GetLargestPossibleRegion(); + const TestImageType::RegionType & lpr = groundTruth->GetLargestPossibleRegion(); - itk::ImageRegionConstIterator itAS(autoSeg, lpr); - itk::ImageRegionConstIterator itGT(groundTruth, lpr); + itk::ImageRegionConstIterator itAS(autoSeg, lpr); + itk::ImageRegionConstIterator itGT(groundTruth, lpr); tpCount = 0; fpCount = 0; fnCount = 0; @@ -124,24 +124,24 @@ main(int argc, char * argv[]) } RegisterRequiredFactories(); - typedef itk::ImageFileReader ReaderType; - ReaderType::Pointer reader = ReaderType::New(); + typedef itk::ImageFileReader ReaderType; + ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(argv[1]); reader->Update(); - ImageType::Pointer inImage = reader->GetOutput(); + TestImageType::Pointer inImage = reader->GetOutput(); inImage->DisconnectPipeline(); - typedef itk::MorphologicalContourInterpolator mciType; - mciType::Pointer mci = mciType::New(); + typedef itk::MorphologicalContourInterpolator mciType; + mciType::Pointer mci = mciType::New(); mci->SetUseBallStructuringElement(true); // test cross? - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer writer = WriterType::New(); + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer writer = WriterType::New(); writer->SetUseCompression(true); - const ImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); - ImageType::IndexType maxInd; - for (unsigned axis = 0; axis < dim; axis++) + const TestImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); + TestImageType::IndexType maxInd; + for (unsigned axis = 0; axis < testDim; axis++) { maxInd[axis] = itk::IndexValueType(lpr.GetSize(axis)); } @@ -150,13 +150,13 @@ main(int argc, char * argv[]) for (int sparsity = 2; sparsity <= 8; sparsity++) { unsigned long long tpCount, fpCount, fnCount; - for (int axis = -1; axis < int(dim); axis++) + for (int axis = -1; axis < int(testDim); axis++) { mci->SetAxis(axis); - ImageType::IndexType axisSparsity = maxInd; + TestImageType::IndexType axisSparsity = maxInd; if (axis < 0) // all axes { - for (unsigned a = 0; a < dim; a++) + for (unsigned a = 0; a < testDim; a++) { axisSparsity[a] = sparsity; } @@ -166,13 +166,13 @@ main(int argc, char * argv[]) axisSparsity[axis] = sparsity; } - ImageType::Pointer sparseImage = createSparseCopy(inImage, axisSparsity); + TestImageType::Pointer sparseImage = createSparseCopy(inImage, axisSparsity); mci->SetInput(sparseImage); itk::TimeProbe timeProbe; timeProbe.Start(); mci->Update(); timeProbe.Stop(); - ImageType::Pointer result = mci->GetOutput(); + TestImageType::Pointer result = mci->GetOutput(); result->DisconnectPipeline(); calcOverlap(result, inImage, tpCount, fpCount, fnCount); From c060c0d109125f8f6dfe5638bb2e866db4827afb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 25 Aug 2016 08:05:15 -0400 Subject: [PATCH 112/176] COMP: 3 signed/unsigned comparison warnings fixed --- .../include/itkMorphologicalContourInterpolator.hxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index d1d4ea46899..5b6e9725fcb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -515,7 +515,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool } else if (jM && !iM) { - if (dist >= jHist.size()) + if (size_t(dist) >= jHist.size()) { jHist.resize(dist + 1, 0); } @@ -556,7 +556,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool // find minimum of differences of sums int bestBin = 0; long long bestDiff = LLONG_MAX; - for (int b = 0; b < maxSize; b++) + for (unsigned b = 0; b < maxSize; b++) { long long iS = std::abs(iTotal - iSum[b] + jSum[b]); long long jS = std::abs(jTotal - jSum[b] + iSum[b]); @@ -1033,7 +1033,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { for (unsigned x = 0; x < jRegionIds.size(); x++) { - if (belongIt.Get() != x + 1) + if (unsigned(belongIt.Get()) != x + 1) { // pixel does not belong to this blob blobs[x]->SetPixel(jIt2.GetIndex(), false); From b7aea138205b058f8c98d0bfa55e52d47b50f248 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 20 Sep 2017 15:25:44 -0400 Subject: [PATCH 113/176] COMP: Expand slice set assignment MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Avoids Wrapping/Modules/MorphologicalContourInterpolation/itkMorphologicalContourInterpolatorPython.cpp:7347:105: required from here ../../include/itkMorphologicalContourInterpolator.h:185:34: error: no match for ‘operator=’ (operand types are ‘std::set, std::allocator >’ and ‘void’) m_LabeledSlices[axis][label] = SliceSetType().insert( indices.begin(), indices.end() ); with Clang and GCC on Linux. --- .../include/itkMorphologicalContourInterpolator.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index ef85cf8a86e..5a220f48b94 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -181,7 +181,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter & indices) { - m_LabeledSlices[axis][label] = SliceSetType().insert(indices.begin(), indices.end()); + SliceSetType sliceSet; + sliceSet.insert(indices.begin(), indices.end()); + m_LabeledSlices[axis][label] = sliceSet; this->Modified(); } From 2bf2b3b84e0fe30cd949003f342c8cbf20845162 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 20 Sep 2017 15:27:58 -0400 Subject: [PATCH 114/176] COMP: Use std::abs Addresses: /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:874:19: note: use function 'std::abs' instead bool second = abs( j - mid ) > 1 && abs( jReq + mReq ) <= 1; // j-mid? ^~~ std::abs /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:862:8: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] if ( abs( i - j ) > 2 ) ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:1415:7: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::Interpolate1to1' requested here Interpolate1to1( axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false, threadId ); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:97:26: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::InterpolateBetweenTwo' requested here this->m_Associate->InterpolateBetweenTwo( ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:88:3: note: in instantiation of member function 'itk::MorphologicalContourInterpolatorParallelInvoker >::ThreadedExecution' requested here MorphologicalContourInterpolatorParallelInvoker() {} ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:70:16: note: in instantiation of member function 'itk::MorphologicalContourInterpolatorParallelInvoker >::MorphologicalContourInterpolatorParallelInvoker' requested here itkNewMacro( Self ); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:1613:63: note: in instantiation of member function 'itk::MorphologicalContourInterpolatorParallelInvoker >::New' requested here typename Parallelizer::Pointer parallelizer = Parallelizer::New(); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:1697:15: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::InterpolateAlong' requested here this->InterpolateAlong( a, m_Output ); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h:220:3: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::GenerateData' requested here MorphologicalContourInterpolator(); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h:79:16: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::MorphologicalContourInterpolator' requested here itkNewMacro( Self ); ^ /home/matt/src/ITKMorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx:45:44: note: in instantiation of member function 'itk::MorphologicalContourInterpolator >::New' requested here typename mciType::Pointer mci = mciType::New(); ^ /home/matt/src/ITKMorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx:125:7: note: in instantiation of function template specialization 'doTest >' requested here doTest >(inputImageFileName, outputImageFileName, dt, ball, axis, label); ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:862:8: note: use function 'std::abs' instead if ( abs( i - j ) > 2 ) ^~~ std::abs /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:873:18: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] bool first = abs( i - mid ) > 1 && abs( iReq + mReq ) <= 1; // i-mid? ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:873:18: note: use function 'std::abs' instead bool first = abs( i - mid ) > 1 && abs( iReq + mReq ) <= 1; // i-mid? ^~~ std::abs /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:874:19: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] bool second = abs( j - mid ) > 1 && abs( jReq + mReq ) <= 1; // j-mid? ^ /home/matt/src/ITKMorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx:874:19: note: use function 'std::abs' instead bool second = abs( j - mid ) > 1 && abs( jReq + mReq ) <= 1; // j-mid? ^~~ std::abs --- .../include/itkMorphologicalContourInterpolator.hxx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 5b6e9725fcb..3348c9b786a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -848,7 +848,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // iterator destroyed here // recurse if needed - if (abs(i - j) > 2) + if (std::abs(i - j) > 2) { PixelList regionIDs; regionIDs.push_back(1); @@ -862,8 +862,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int int mReq = mid < reqRegion.GetIndex(axis) ? -1 : (mid > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - bool first = abs(i - mid) > 1 && abs(iReq + mReq) <= 1; // i-mid? - bool second = abs(j - mid) > 1 && abs(jReq + mReq) <= 1; // j-mid? + bool first = std::abs(i - mid) > 1 && std::abs(iReq + mReq) <= 1; // i-mid? + bool second = std::abs(j - mid) > 1 && std::abs(jReq + mReq) <= 1; // j-mid? if (first) { @@ -1572,9 +1572,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou ? -1 : (*next > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - if (*prev + 1 < *next // only if they are not adjacent slices - && abs(iReq + jReq) <= 1) // and not out of the requested region - // unless they are on opposite ends + if (*prev + 1 < *next // only if they are not adjacent slices + && std::abs(iReq + jReq) <= 1) // and not out of the requested region + // unless they are on opposite ends { SegmentBetweenTwo s; s.axis = axis; From 0e3e7fdb0dea78abe1c71b5442e44a603d1de8f3 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 20 Sep 2017 15:30:24 -0400 Subject: [PATCH 115/176] ENH: Add wrapping configuration --- .../wrapping/CMakeLists.txt | 3 +++ .../wrapping/itkMorphologicalContourInterpolator.wrap | 10 ++++++++++ 2 files changed, 13 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/wrapping/CMakeLists.txt create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/wrapping/itkMorphologicalContourInterpolator.wrap diff --git a/Modules/Filtering/MorphologicalContourInterpolation/wrapping/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/wrapping/CMakeLists.txt new file mode 100644 index 00000000000..3771062ae86 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/wrapping/CMakeLists.txt @@ -0,0 +1,3 @@ +itk_wrap_module(MorphologicalContourInterpolation) +itk_auto_load_submodules() +itk_end_wrap_module() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/wrapping/itkMorphologicalContourInterpolator.wrap b/Modules/Filtering/MorphologicalContourInterpolation/wrapping/itkMorphologicalContourInterpolator.wrap new file mode 100644 index 00000000000..c006d6c9699 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/wrapping/itkMorphologicalContourInterpolator.wrap @@ -0,0 +1,10 @@ +list(FIND ITK_WRAP_IMAGE_DIMS 3 _have_dim_3) +if(NOT ${_have_dim_3} EQUAL -1) + itk_wrap_class("itk::MorphologicalContourInterpolator" POINTER) + # See ITK/Wrapping/WrapBasicTypes.cmake for definition of SMALLER_THAN_SL + # Includes unsigned char, signed char, unsigned short, or short if enabled + foreach(t ${SMALLER_THAN_SL}) + itk_wrap_template("${ITKM_I${t}3}" "${ITKT_I${t}3}") + endforeach() + itk_end_wrap_class() +endif() From ccf0d218dd155db0646053602dc3790580c2414a Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 21 Sep 2017 18:34:18 -0400 Subject: [PATCH 116/176] COMP: Specify std:: prefix for pow To address: /FdWrapping\Modules\MorphologicalContourInterpolation\CMakeFiles\MorphologicalContourInterpolationPython.dir\ -c Wrapping\Modules\MorphologicalContourInterpolation\itkMorphologicalContourInterpolatorPython.cpp c:\projects\itkmorphologicalcontourinterpolation\include\itkMorphologicalContourInterpolator.hxx(149) : error C2668: 'pow' : ambiguous call to overloaded function --- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 3348c9b786a..ad4e29663d4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -144,9 +144,9 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , m_UseDistanceTransform(true) , m_UseBallStructuringElement(false) , m_UseCustomSlicePositions(false) - , m_MinAlignIters(pow(2, TImage::ImageDimension)) + , m_MinAlignIters(std::pow(2., static_cast(TImage::ImageDimension))) , // smaller of this and pixel count of the search image - m_MaxAlignIters(pow(6, TImage::ImageDimension)) + m_MaxAlignIters(std::pow(6., static_cast(TImage::ImageDimension))) , // bigger of this and root of pixel count of the search image m_ThreadCount(MultiThreader::GetGlobalDefaultNumberOfThreads()) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets From 6c95f26aa14611fb3bb4a1cf29dd98d465ddcaf0 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 21 Sep 2017 20:36:45 -0400 Subject: [PATCH 117/176] COMP: Replace std::abs with itk::Math::abs To address: /FoWrapping\Modules\MorphologicalContourInterpolation\CMakeFiles\MorphologicalContourInterpolationPython.dir\itkMorphologicalContourInterpolatorPython.cpp.obj /FdWrapping\Modules\MorphologicalContourInterpolation\CMakeFiles\MorphologicalContourInterpolationPython.dir\ -c Wrapping\Modules\MorphologicalContourInterpolation\itkMorphologicalContourInterpolatorPython.cpp c:\projects\itkmorphologicalcontourinterpolation\include\itkMorphologicalContourInterpolator.hxx(862) : error C2668: 'std::abs' : ambiguous call to overloaded function C:\Users\appveyor\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Include\stdlib.h(380): could be 'int abs(int)' --- .../itkMorphologicalContourInterpolator.hxx | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ad4e29663d4..1f54e795bad 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -558,9 +558,9 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool long long bestDiff = LLONG_MAX; for (unsigned b = 0; b < maxSize; b++) { - long long iS = std::abs(iTotal - iSum[b] + jSum[b]); - long long jS = std::abs(jTotal - jSum[b] + iSum[b]); - long long diff = std::abs(iS - jS); + long long iS = Math::abs(iTotal - iSum[b] + jSum[b]); + long long jS = Math::abs(jTotal - jSum[b] + iSum[b]); + long long diff = Math::abs(iS - jS); if (diff < bestDiff) { bestDiff = diff; @@ -848,7 +848,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // iterator destroyed here // recurse if needed - if (std::abs(i - j) > 2) + if (Math::abs(i - j) > 2) { PixelList regionIDs; regionIDs.push_back(1); @@ -862,8 +862,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int int mReq = mid < reqRegion.GetIndex(axis) ? -1 : (mid > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - bool first = std::abs(i - mid) > 1 && std::abs(iReq + mReq) <= 1; // i-mid? - bool second = std::abs(j - mid) > 1 && std::abs(jReq + mReq) <= 1; // j-mid? + bool first = Math::abs(i - mid) > 1 && Math::abs(iReq + mReq) <= 1; // i-mid? + bool second = Math::abs(j - mid) > 1 && Math::abs(jReq + mReq) <= 1; // j-mid? if (first) { @@ -1572,9 +1572,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou ? -1 : (*next > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - if (*prev + 1 < *next // only if they are not adjacent slices - && std::abs(iReq + jReq) <= 1) // and not out of the requested region - // unless they are on opposite ends + if (*prev + 1 < *next // only if they are not adjacent slices + && Math::abs(iReq + jReq) <= 1) // and not out of the requested region + // unless they are on opposite ends { SegmentBetweenTwo s; s.axis = axis; From 8ec47ef61744ff5d3d34e555c726064417a8aa2c Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 21 Sep 2017 20:44:21 -0400 Subject: [PATCH 118/176] COMP: sqrt disambiguation To address: /FoWrapping\Modules\MorphologicalContourInterpolation\CMakeFiles\MorphologicalContourInterpolationPython.dir\itkMorphologicalContourInterpolatorPython.cpp.obj /FdWrapping\Modules\MorphologicalContourInterpolation\CMakeFiles\MorphologicalContourInterpolationPython.dir\ -c Wrapping\Modules\MorphologicalContourInterpolation\itkMorphologicalContourInterpolatorPython.cpp c:\projects\itkmorphologicalcontourinterpolation\include\itkMorphologicalContourInterpolator.hxx(1282) : error C2668: 'sqrt' : ambiguous call to overloaded function --- .../include/itkMorphologicalContourInterpolator.hxx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 1f54e795bad..b4f91daea0a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1263,7 +1263,8 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC typename SliceType::IndexType bestIndex; IdentifierType iter = 0; IdentifierType minIter = std::min(m_MinAlignIters, searchRegion.GetNumberOfPixels()); - IdentifierType maxIter = std::max(m_MaxAlignIters, (IdentifierType)sqrt(searchRegion.GetNumberOfPixels())); + IdentifierType maxIter = std::max( + m_MaxAlignIters, static_cast(std::sqrt(static_cast(searchRegion.GetNumberOfPixels())))); while (!uncomputed.empty()) { From 9ca124e6052bb28fdab767f4d263330304e95d9c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Sep 2017 11:45:35 -0400 Subject: [PATCH 119/176] ENH: Minor improvements --- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index b4f91daea0a..c1c8ed75be1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -541,10 +541,10 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool } iHist.resize(maxSize, 0); jHist.resize(maxSize, 0); - assert(iHist[0] == 0); - assert(jHist[0] == 0); std::vector iSum(maxSize, 0); std::vector jSum(maxSize, 0); + iSum[0] = iHist[0]; + jSum[0] = jHist[0]; for (unsigned b = 1; b < maxSize; b++) { iSum[b] = iSum[b - 1] + iHist[b]; From c0db3820d2f004441a4a1f949cb6ed3201816462 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Sep 2017 11:56:39 -0400 Subject: [PATCH 120/176] ENH: Running tests on all algorithms --- .../CMakeLists.txt | 12 - .../test/CMakeLists.txt | 329 +++++++++--------- 2 files changed, 169 insertions(+), 172 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 8ead5fa5741..bd13ea7189d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,18 +1,6 @@ cmake_minimum_required(VERSION 2.8.9) project(MorphologicalContourInterpolation) -set( - MCI_Algorithm - "B" - CACHE STRING - "Which algorithm should be used for testing -the module MorphologicalContourInterpolation. - -B = repeated dilations with ball structuring element -C = repeated dilations with cross structuring element -T = distance transform (not geodesic!)" -) - if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index d269ca85491..990fc9d2ab8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -31,58 +31,67 @@ target_link_libraries( ) # used to produce an output which is then taken as a baseline for a regression test -function(JustInputTest ImageName Ext) #optional: Algo Axis Label +function(JustInputTest ImageName Ext) #optional: Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() - set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}${optArgs}.${Ext}") - # set(imageNameOpt "${ImageName}${optArgs}") # only used for regression + foreach(algo B;C;T) + set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}_${algo}${optArgs}.${Ext}") - itk_add_test( - NAME itkMCI_JustInOut_${ImageName}${optArgs} - COMMAND - MorphologicalContourInterpolationTestDriver - # --compare DATA{Baseline/${imageNameOpt}.${Ext}} ${outImage} # no regression - itkMorphologicalContourInterpolationTest - DATA{Input/${ImageName}.${Ext}} - ${outImage} - ${ARGN} - ) -endfunction() - -function(RegressionTest ImageName Ext) #optional: Algo Axis Label - foreach(f ${ARGN}) #create unique test name - set(optArgs "${optArgs}_${f}") - endforeach() - set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}${optArgs}.${Ext}") - set(imageNameOpt "${ImageName}${optArgs}") - if(${MCI_TestWithRLEImage}) itk_add_test( - NAME rleMCI_${ImageName}${optArgs} + NAME itkMCI_JustInOut_${ImageName}_${algo}${optArgs} COMMAND MorphologicalContourInterpolationTestDriver - --compare - DATA{Baseline/${imageNameOpt}.${Ext}} - ${outImage} - itkMorphologicalContourInterpolationTestWithRLEImage - DATA{Input/${ImageName}.${Ext}} - ${outImage} - ${ARGN} - ) - else(${MCI_TestWithRLEImage}) - itk_add_test( - NAME itkMCI_${ImageName}${optArgs} - COMMAND - MorphologicalContourInterpolationTestDriver - --compare - DATA{Baseline/${imageNameOpt}.${Ext}} - ${outImage} itkMorphologicalContourInterpolationTest DATA{Input/${ImageName}.${Ext}} ${outImage} + ${algo} ${ARGN} ) - endif(${MCI_TestWithRLEImage}) + endforeach() +endfunction() + +function(RegressionTest ImageName Ext) #optional: Axis Label + foreach(f ${ARGN}) #create unique test name + set(optArgs "${optArgs}_${f}") + endforeach() + + # B = repeated dilations with ball structuring element + # C = repeated dilations with cross structuring element + # T = distance transform (not geodesic!) + foreach(algo B;C;T) + set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}_${algo}${optArgs}.${Ext}") + set(imageNameOpt "${ImageName}_${algo}${optArgs}") + if(${MCI_TestWithRLEImage}) + itk_add_test( + NAME rleMCI_${ImageName}_${algo}${optArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} + itkMorphologicalContourInterpolationTestWithRLEImage + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${algo} + ${ARGN} + ) + else(${MCI_TestWithRLEImage}) + itk_add_test( + NAME itkMCI_${ImageName}_${algo}${optArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} + itkMorphologicalContourInterpolationTest + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${algo} + ${ARGN} + ) + endif(${MCI_TestWithRLEImage}) + endforeach() endfunction() # functional comparison using Dice Similarity Coefficient @@ -100,142 +109,142 @@ function(DSCTest ImageName Ext) endfunction() # Handcrafted tests -regressiontest(Empty nrrd ${MCI_Algorithm}) -regressiontest(NoSlices nrrd ${MCI_Algorithm}) #interpolation should not be invoked (output==input) -regressiontest(Micro1 nrrd ${MCI_Algorithm}) -regressiontest(SimplestOneToOne nrrd ${MCI_Algorithm}) -regressiontest(OneToOne nrrd ${MCI_Algorithm}) -regressiontest(OneToThree nrrd ${MCI_Algorithm}) -regressiontest(ExtrapolationAppearing nrrd ${MCI_Algorithm}) -regressiontest(DoubleTwoLabelBranching nrrd ${MCI_Algorithm}) -regressiontest(TwoAxisDoubleTwoLabelBC nrrd ${MCI_Algorithm}) -regressiontest(AccidentalMiddleSliceSeg nrrd ${MCI_Algorithm}) -regressiontest(SevenLabels nrrd ${MCI_Algorithm}) -regressiontest(FullEnd nrrd ${MCI_Algorithm}) -regressiontest(1MN1 nrrd ${MCI_Algorithm}) # double sided many broken into many + 1 -regressiontest(ManyToMany16 nrrd ${MCI_Algorithm}) -regressiontest(ManyToMany nrrd ${MCI_Algorithm}) -regressiontest(GridSeg nrrd ${MCI_Algorithm}) -regressiontest(GridSeg2 nrrd ${MCI_Algorithm}) +regressiontest(Empty nrrd) +regressiontest(NoSlices nrrd) #interpolation should not be invoked (output==input) +regressiontest(Micro1 nrrd) +regressiontest(SimplestOneToOne nrrd) +regressiontest(OneToOne nrrd) +regressiontest(OneToThree nrrd) +regressiontest(ExtrapolationAppearing nrrd) +regressiontest(DoubleTwoLabelBranching nrrd) +regressiontest(TwoAxisDoubleTwoLabelBC nrrd) +regressiontest(AccidentalMiddleSliceSeg nrrd) +regressiontest(SevenLabels nrrd) +regressiontest(FullEnd nrrd) +regressiontest(1MN1 nrrd) # double sided many broken into many + 1 +regressiontest(ManyToMany16 nrrd) +regressiontest(ManyToMany nrrd) +regressiontest(GridSeg nrrd) +regressiontest(GridSeg2 nrrd) # Per axis/label tests -regressiontest(GridSeg nrrd ${MCI_Algorithm} 0) -regressiontest(GridSeg nrrd ${MCI_Algorithm} 1) -regressiontest(GridSeg nrrd ${MCI_Algorithm} 2) -regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 0) -regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 1) -regressiontest(GridSeg2 nrrd ${MCI_Algorithm} 2) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm}) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0 0) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1 1) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2 3) # equals to _2 -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 0 4) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 1 2) -regressiontest(ThreeAxisFourLabelConflict nrrd ${MCI_Algorithm} 2 2) # does not modify image +regressiontest(GridSeg nrrd 0) +regressiontest(GridSeg nrrd 1) +regressiontest(GridSeg nrrd 2) +regressiontest(GridSeg2 nrrd 0) +regressiontest(GridSeg2 nrrd 1) +regressiontest(GridSeg2 nrrd 2) +regressiontest(ThreeAxisFourLabelConflict nrrd) +regressiontest(ThreeAxisFourLabelConflict nrrd 0) +regressiontest(ThreeAxisFourLabelConflict nrrd 1) +regressiontest(ThreeAxisFourLabelConflict nrrd 2) +regressiontest(ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd 1 1) +regressiontest(ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 +regressiontest(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 +regressiontest(ThreeAxisFourLabelConflict nrrd 1 2) +regressiontest(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image # Paul's single axis tests -regressiontest(105769moving nii.gz ${MCI_Algorithm}) #defaults: all axes all labels -regressiontest(105769moving nii.gz ${MCI_Algorithm} 2) #axis 2 -regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 0) #all axes all labels -regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 1) #all axes label 1 -regressiontest(105769moving nii.gz ${MCI_Algorithm} -1 2) #all axes label 2 -regressiontest(105769moving nii.gz ${MCI_Algorithm} 2 1) #axis 2 label 1 -regressiontest(105769moving nii.gz ${MCI_Algorithm} 2 2) #axis 2 label 2 -regressiontest(105769fixed nii.gz ${MCI_Algorithm}) #defaults: all axes all labels -regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2) #axis 2 -regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 0) #all axes all labels -regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 1) #all axes label 1 -regressiontest(105769fixed nii.gz ${MCI_Algorithm} -1 2) #all axes label 2 -regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2 1) #axis 2 label 1 -regressiontest(105769fixed nii.gz ${MCI_Algorithm} 2 2) #axis 2 label 2 +regressiontest(105769moving nii.gz) #defaults: all axes all labels +regressiontest(105769moving nii.gz 2) #axis 2 +regressiontest(105769moving nii.gz -1 0) #all axes all labels +regressiontest(105769moving nii.gz -1 1) #all axes label 1 +regressiontest(105769moving nii.gz -1 2) #all axes label 2 +regressiontest(105769moving nii.gz 2 1) #axis 2 label 1 +regressiontest(105769moving nii.gz 2 2) #axis 2 label 2 +regressiontest(105769fixed nii.gz) #defaults: all axes all labels +regressiontest(105769fixed nii.gz 2) #axis 2 +regressiontest(105769fixed nii.gz -1 0) #all axes all labels +regressiontest(105769fixed nii.gz -1 1) #all axes label 1 +regressiontest(105769fixed nii.gz -1 2) #all axes label 2 +regressiontest(105769fixed nii.gz 2 1) #axis 2 label 1 +regressiontest(105769fixed nii.gz 2 2) #axis 2 label 2 # 64816L_amygdala_int -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm}) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 1) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 2) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 3) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 0 4) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 1) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 2) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 3) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 1 4) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 1) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 2) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 3) -regressiontest(64816L_amygdala_int nii.gz ${MCI_Algorithm} 2 4) +regressiontest(64816L_amygdala_int nii.gz) +regressiontest(64816L_amygdala_int nii.gz 0) +regressiontest(64816L_amygdala_int nii.gz 1) +regressiontest(64816L_amygdala_int nii.gz 2) +regressiontest(64816L_amygdala_int nii.gz 0 1) +regressiontest(64816L_amygdala_int nii.gz 0 2) +regressiontest(64816L_amygdala_int nii.gz 0 3) +regressiontest(64816L_amygdala_int nii.gz 0 4) +regressiontest(64816L_amygdala_int nii.gz 1 1) +regressiontest(64816L_amygdala_int nii.gz 1 2) +regressiontest(64816L_amygdala_int nii.gz 1 3) +regressiontest(64816L_amygdala_int nii.gz 1 4) +regressiontest(64816L_amygdala_int nii.gz 2 1) +regressiontest(64816L_amygdala_int nii.gz 2 2) +regressiontest(64816L_amygdala_int nii.gz 2 3) +regressiontest(64816L_amygdala_int nii.gz 2 4) # 64816L_amygdala_fin -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm}) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 1) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 2) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 3) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 0 4) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 1) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 2) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 3) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 1 4) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 1) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 2) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 3) -regressiontest(64816L_amygdala_fin nii.gz ${MCI_Algorithm} 2 4) +regressiontest(64816L_amygdala_fin nii.gz) +regressiontest(64816L_amygdala_fin nii.gz 0) +regressiontest(64816L_amygdala_fin nii.gz 1) +regressiontest(64816L_amygdala_fin nii.gz 2) +regressiontest(64816L_amygdala_fin nii.gz 0 1) +regressiontest(64816L_amygdala_fin nii.gz 0 2) +regressiontest(64816L_amygdala_fin nii.gz 0 3) +regressiontest(64816L_amygdala_fin nii.gz 0 4) +regressiontest(64816L_amygdala_fin nii.gz 1 1) +regressiontest(64816L_amygdala_fin nii.gz 1 2) +regressiontest(64816L_amygdala_fin nii.gz 1 3) +regressiontest(64816L_amygdala_fin nii.gz 1 4) +regressiontest(64816L_amygdala_fin nii.gz 2 1) +regressiontest(64816L_amygdala_fin nii.gz 2 2) +regressiontest(64816L_amygdala_fin nii.gz 2 3) +regressiontest(64816L_amygdala_fin nii.gz 2 4) # 65239R_amygdala_int -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm}) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 1) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 2) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 3) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 0 4) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 1) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 2) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 3) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 1 4) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 1) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 2) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 3) -regressiontest(65239R_amygdala_int nii.gz ${MCI_Algorithm} 2 4) +regressiontest(65239R_amygdala_int nii.gz) +regressiontest(65239R_amygdala_int nii.gz 0) +regressiontest(65239R_amygdala_int nii.gz 1) +regressiontest(65239R_amygdala_int nii.gz 2) +regressiontest(65239R_amygdala_int nii.gz 0 1) +regressiontest(65239R_amygdala_int nii.gz 0 2) +regressiontest(65239R_amygdala_int nii.gz 0 3) +regressiontest(65239R_amygdala_int nii.gz 0 4) +regressiontest(65239R_amygdala_int nii.gz 1 1) +regressiontest(65239R_amygdala_int nii.gz 1 2) +regressiontest(65239R_amygdala_int nii.gz 1 3) +regressiontest(65239R_amygdala_int nii.gz 1 4) +regressiontest(65239R_amygdala_int nii.gz 2 1) +regressiontest(65239R_amygdala_int nii.gz 2 2) +regressiontest(65239R_amygdala_int nii.gz 2 3) +regressiontest(65239R_amygdala_int nii.gz 2 4) # 65239R_amygdala_fin -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm}) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 1) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 2) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 3) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 0 4) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 1) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 2) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 3) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 1 4) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 1) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 2) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 3) -regressiontest(65239R_amygdala_fin nii.gz ${MCI_Algorithm} 2 4) +regressiontest(65239R_amygdala_fin nii.gz) +regressiontest(65239R_amygdala_fin nii.gz 0) +regressiontest(65239R_amygdala_fin nii.gz 1) +regressiontest(65239R_amygdala_fin nii.gz 2) +regressiontest(65239R_amygdala_fin nii.gz 0 1) +regressiontest(65239R_amygdala_fin nii.gz 0 2) +regressiontest(65239R_amygdala_fin nii.gz 0 3) +regressiontest(65239R_amygdala_fin nii.gz 0 4) +regressiontest(65239R_amygdala_fin nii.gz 1 1) +regressiontest(65239R_amygdala_fin nii.gz 1 2) +regressiontest(65239R_amygdala_fin nii.gz 1 3) +regressiontest(65239R_amygdala_fin nii.gz 1 4) +regressiontest(65239R_amygdala_fin nii.gz 2 1) +regressiontest(65239R_amygdala_fin nii.gz 2 2) +regressiontest(65239R_amygdala_fin nii.gz 2 3) +regressiontest(65239R_amygdala_fin nii.gz 2 4) # Long-running handcrafted tests -regressiontest(BigZ nrrd ${MCI_Algorithm}) -regressiontest(BigZ nrrd ${MCI_Algorithm} 0) -regressiontest(BigZ nrrd ${MCI_Algorithm} 1) -regressiontest(BigZ nrrd ${MCI_Algorithm} 2) -regressiontest(FaceRoI nrrd ${MCI_Algorithm}) -regressiontest(FaceRoI nrrd ${MCI_Algorithm} 0) -regressiontest(FaceRoI nrrd ${MCI_Algorithm} 1) -regressiontest(FaceRoI nrrd ${MCI_Algorithm} 2) +regressiontest(BigZ nrrd) +regressiontest(BigZ nrrd 0) +regressiontest(BigZ nrrd 1) +regressiontest(BigZ nrrd 2) +regressiontest(FaceRoI nrrd) +regressiontest(FaceRoI nrrd 0) +regressiontest(FaceRoI nrrd 1) +regressiontest(FaceRoI nrrd 2) # Non-3D tests -regressiontest(FourD nrrd ${MCI_Algorithm}) +regressiontest(FourD nrrd) # dscComparison (crops) dsctest(c2l mha saveImages) From df232a2c3db3979d65c53c865e33a2ccfdf30013 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Sep 2017 12:30:40 -0400 Subject: [PATCH 121/176] ENH: Adding RUNS_LONG label to some tests --- .../test/CMakeLists.txt | 303 +++++++++--------- 1 file changed, 156 insertions(+), 147 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 990fc9d2ab8..c63d8a5eff2 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -51,7 +51,7 @@ function(JustInputTest ImageName Ext) #optional: Axis Label endforeach() endfunction() -function(RegressionTest ImageName Ext) #optional: Axis Label +function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label foreach(f ${ARGN}) #create unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -62,35 +62,36 @@ function(RegressionTest ImageName Ext) #optional: Axis Label foreach(algo B;C;T) set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}_${algo}${optArgs}.${Ext}") set(imageNameOpt "${ImageName}_${algo}${optArgs}") + if(${MCI_TestWithRLEImage}) - itk_add_test( - NAME rleMCI_${ImageName}_${algo}${optArgs} - COMMAND - MorphologicalContourInterpolationTestDriver - --compare - DATA{Baseline/${imageNameOpt}.${Ext}} - ${outImage} - itkMorphologicalContourInterpolationTestWithRLEImage - DATA{Input/${ImageName}.${Ext}} - ${outImage} - ${algo} - ${ARGN} - ) + set(TestExe itkMorphologicalContourInterpolationTestWithRLEImage) else(${MCI_TestWithRLEImage}) - itk_add_test( - NAME itkMCI_${ImageName}_${algo}${optArgs} - COMMAND - MorphologicalContourInterpolationTestDriver - --compare - DATA{Baseline/${imageNameOpt}.${Ext}} - ${outImage} - itkMorphologicalContourInterpolationTest - DATA{Input/${ImageName}.${Ext}} - ${outImage} - ${algo} - ${ARGN} - ) + set(TestExe itkMorphologicalContourInterpolationTest) endif(${MCI_TestWithRLEImage}) + + itk_add_test( + NAME itkMCI_${ImageName}_${algo}${optArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageNameOpt}.${Ext}} + ${outImage} + ${TestExe} + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${algo} + ${ARGN} + ) + if(RunsLong) + set_property( + TEST + itkMCI_${ImageName}_${algo}${optArgs} + APPEND + PROPERTY + LABELS + RUNS_LONG + ) + endif() endforeach() endfunction() @@ -106,145 +107,153 @@ function(DSCTest ImageName Ext) ${outFilenameBase} ${ARGN} ) + set_property( + TEST + itkMCI_DSC_${ImageName} + APPEND + PROPERTY + LABELS + RUNS_LONG + ) endfunction() # Handcrafted tests -regressiontest(Empty nrrd) -regressiontest(NoSlices nrrd) #interpolation should not be invoked (output==input) -regressiontest(Micro1 nrrd) -regressiontest(SimplestOneToOne nrrd) -regressiontest(OneToOne nrrd) -regressiontest(OneToThree nrrd) -regressiontest(ExtrapolationAppearing nrrd) -regressiontest(DoubleTwoLabelBranching nrrd) -regressiontest(TwoAxisDoubleTwoLabelBC nrrd) -regressiontest(AccidentalMiddleSliceSeg nrrd) -regressiontest(SevenLabels nrrd) -regressiontest(FullEnd nrrd) -regressiontest(1MN1 nrrd) # double sided many broken into many + 1 -regressiontest(ManyToMany16 nrrd) -regressiontest(ManyToMany nrrd) -regressiontest(GridSeg nrrd) -regressiontest(GridSeg2 nrrd) +regressiontest(0 Empty nrrd) +regressiontest(0 NoSlices nrrd) #interpolation should not be invoked (output==input) +regressiontest(0 Micro1 nrrd) +regressiontest(0 SimplestOneToOne nrrd) +regressiontest(0 OneToOne nrrd) +regressiontest(0 OneToThree nrrd) +regressiontest(0 ExtrapolationAppearing nrrd) +regressiontest(0 DoubleTwoLabelBranching nrrd) +regressiontest(0 TwoAxisDoubleTwoLabelBC nrrd) +regressiontest(0 AccidentalMiddleSliceSeg nrrd) +regressiontest(0 SevenLabels nrrd) +regressiontest(0 FullEnd nrrd) +regressiontest(0 1MN1 nrrd) # double sided many broken into many + 1 +regressiontest(0 ManyToMany16 nrrd) +regressiontest(0 ManyToMany nrrd) +regressiontest(0 GridSeg nrrd) +regressiontest(0 GridSeg2 nrrd) # Per axis/label tests -regressiontest(GridSeg nrrd 0) -regressiontest(GridSeg nrrd 1) -regressiontest(GridSeg nrrd 2) -regressiontest(GridSeg2 nrrd 0) -regressiontest(GridSeg2 nrrd 1) -regressiontest(GridSeg2 nrrd 2) -regressiontest(ThreeAxisFourLabelConflict nrrd) -regressiontest(ThreeAxisFourLabelConflict nrrd 0) -regressiontest(ThreeAxisFourLabelConflict nrrd 1) -regressiontest(ThreeAxisFourLabelConflict nrrd 2) -regressiontest(ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd 1 1) -regressiontest(ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 -regressiontest(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 -regressiontest(ThreeAxisFourLabelConflict nrrd 1 2) -regressiontest(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image +regressiontest(0 GridSeg nrrd 0) +regressiontest(0 GridSeg nrrd 1) +regressiontest(0 GridSeg nrrd 2) +regressiontest(0 GridSeg2 nrrd 0) +regressiontest(0 GridSeg2 nrrd 1) +regressiontest(0 GridSeg2 nrrd 2) +regressiontest(0 ThreeAxisFourLabelConflict nrrd) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 0) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 1) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 2) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 +regressiontest(0 ThreeAxisFourLabelConflict nrrd 1 1) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 +regressiontest(0 ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 +regressiontest(0 ThreeAxisFourLabelConflict nrrd 1 2) +regressiontest(0 ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image # Paul's single axis tests -regressiontest(105769moving nii.gz) #defaults: all axes all labels -regressiontest(105769moving nii.gz 2) #axis 2 -regressiontest(105769moving nii.gz -1 0) #all axes all labels -regressiontest(105769moving nii.gz -1 1) #all axes label 1 -regressiontest(105769moving nii.gz -1 2) #all axes label 2 -regressiontest(105769moving nii.gz 2 1) #axis 2 label 1 -regressiontest(105769moving nii.gz 2 2) #axis 2 label 2 -regressiontest(105769fixed nii.gz) #defaults: all axes all labels -regressiontest(105769fixed nii.gz 2) #axis 2 -regressiontest(105769fixed nii.gz -1 0) #all axes all labels -regressiontest(105769fixed nii.gz -1 1) #all axes label 1 -regressiontest(105769fixed nii.gz -1 2) #all axes label 2 -regressiontest(105769fixed nii.gz 2 1) #axis 2 label 1 -regressiontest(105769fixed nii.gz 2 2) #axis 2 label 2 +regressiontest(0 105769moving nii.gz) #defaults: all axes all labels +regressiontest(0 105769moving nii.gz 2) #axis 2 +regressiontest(0 105769moving nii.gz -1 0) #all axes all labels +regressiontest(0 105769moving nii.gz -1 1) #all axes label 1 +regressiontest(0 105769moving nii.gz -1 2) #all axes label 2 +regressiontest(0 105769moving nii.gz 2 1) #axis 2 label 1 +regressiontest(0 105769moving nii.gz 2 2) #axis 2 label 2 +regressiontest(0 105769fixed nii.gz) #defaults: all axes all labels +regressiontest(0 105769fixed nii.gz 2) #axis 2 +regressiontest(0 105769fixed nii.gz -1 0) #all axes all labels +regressiontest(0 105769fixed nii.gz -1 1) #all axes label 1 +regressiontest(0 105769fixed nii.gz -1 2) #all axes label 2 +regressiontest(0 105769fixed nii.gz 2 1) #axis 2 label 1 +regressiontest(0 105769fixed nii.gz 2 2) #axis 2 label 2 # 64816L_amygdala_int -regressiontest(64816L_amygdala_int nii.gz) -regressiontest(64816L_amygdala_int nii.gz 0) -regressiontest(64816L_amygdala_int nii.gz 1) -regressiontest(64816L_amygdala_int nii.gz 2) -regressiontest(64816L_amygdala_int nii.gz 0 1) -regressiontest(64816L_amygdala_int nii.gz 0 2) -regressiontest(64816L_amygdala_int nii.gz 0 3) -regressiontest(64816L_amygdala_int nii.gz 0 4) -regressiontest(64816L_amygdala_int nii.gz 1 1) -regressiontest(64816L_amygdala_int nii.gz 1 2) -regressiontest(64816L_amygdala_int nii.gz 1 3) -regressiontest(64816L_amygdala_int nii.gz 1 4) -regressiontest(64816L_amygdala_int nii.gz 2 1) -regressiontest(64816L_amygdala_int nii.gz 2 2) -regressiontest(64816L_amygdala_int nii.gz 2 3) -regressiontest(64816L_amygdala_int nii.gz 2 4) +regressiontest(0 64816L_amygdala_int nii.gz) +regressiontest(0 64816L_amygdala_int nii.gz 0) +regressiontest(0 64816L_amygdala_int nii.gz 1) +regressiontest(0 64816L_amygdala_int nii.gz 2) +regressiontest(0 64816L_amygdala_int nii.gz 0 1) +regressiontest(0 64816L_amygdala_int nii.gz 0 2) +regressiontest(0 64816L_amygdala_int nii.gz 0 3) +regressiontest(0 64816L_amygdala_int nii.gz 0 4) +regressiontest(0 64816L_amygdala_int nii.gz 1 1) +regressiontest(0 64816L_amygdala_int nii.gz 1 2) +regressiontest(0 64816L_amygdala_int nii.gz 1 3) +regressiontest(0 64816L_amygdala_int nii.gz 1 4) +regressiontest(0 64816L_amygdala_int nii.gz 2 1) +regressiontest(0 64816L_amygdala_int nii.gz 2 2) +regressiontest(0 64816L_amygdala_int nii.gz 2 3) +regressiontest(0 64816L_amygdala_int nii.gz 2 4) # 64816L_amygdala_fin -regressiontest(64816L_amygdala_fin nii.gz) -regressiontest(64816L_amygdala_fin nii.gz 0) -regressiontest(64816L_amygdala_fin nii.gz 1) -regressiontest(64816L_amygdala_fin nii.gz 2) -regressiontest(64816L_amygdala_fin nii.gz 0 1) -regressiontest(64816L_amygdala_fin nii.gz 0 2) -regressiontest(64816L_amygdala_fin nii.gz 0 3) -regressiontest(64816L_amygdala_fin nii.gz 0 4) -regressiontest(64816L_amygdala_fin nii.gz 1 1) -regressiontest(64816L_amygdala_fin nii.gz 1 2) -regressiontest(64816L_amygdala_fin nii.gz 1 3) -regressiontest(64816L_amygdala_fin nii.gz 1 4) -regressiontest(64816L_amygdala_fin nii.gz 2 1) -regressiontest(64816L_amygdala_fin nii.gz 2 2) -regressiontest(64816L_amygdala_fin nii.gz 2 3) -regressiontest(64816L_amygdala_fin nii.gz 2 4) +regressiontest(0 64816L_amygdala_fin nii.gz) +regressiontest(0 64816L_amygdala_fin nii.gz 0) +regressiontest(0 64816L_amygdala_fin nii.gz 1) +regressiontest(0 64816L_amygdala_fin nii.gz 2) +regressiontest(0 64816L_amygdala_fin nii.gz 0 1) +regressiontest(0 64816L_amygdala_fin nii.gz 0 2) +regressiontest(0 64816L_amygdala_fin nii.gz 0 3) +regressiontest(0 64816L_amygdala_fin nii.gz 0 4) +regressiontest(0 64816L_amygdala_fin nii.gz 1 1) +regressiontest(0 64816L_amygdala_fin nii.gz 1 2) +regressiontest(0 64816L_amygdala_fin nii.gz 1 3) +regressiontest(0 64816L_amygdala_fin nii.gz 1 4) +regressiontest(0 64816L_amygdala_fin nii.gz 2 1) +regressiontest(0 64816L_amygdala_fin nii.gz 2 2) +regressiontest(0 64816L_amygdala_fin nii.gz 2 3) +regressiontest(0 64816L_amygdala_fin nii.gz 2 4) # 65239R_amygdala_int -regressiontest(65239R_amygdala_int nii.gz) -regressiontest(65239R_amygdala_int nii.gz 0) -regressiontest(65239R_amygdala_int nii.gz 1) -regressiontest(65239R_amygdala_int nii.gz 2) -regressiontest(65239R_amygdala_int nii.gz 0 1) -regressiontest(65239R_amygdala_int nii.gz 0 2) -regressiontest(65239R_amygdala_int nii.gz 0 3) -regressiontest(65239R_amygdala_int nii.gz 0 4) -regressiontest(65239R_amygdala_int nii.gz 1 1) -regressiontest(65239R_amygdala_int nii.gz 1 2) -regressiontest(65239R_amygdala_int nii.gz 1 3) -regressiontest(65239R_amygdala_int nii.gz 1 4) -regressiontest(65239R_amygdala_int nii.gz 2 1) -regressiontest(65239R_amygdala_int nii.gz 2 2) -regressiontest(65239R_amygdala_int nii.gz 2 3) -regressiontest(65239R_amygdala_int nii.gz 2 4) +regressiontest(0 65239R_amygdala_int nii.gz) +regressiontest(0 65239R_amygdala_int nii.gz 0) +regressiontest(0 65239R_amygdala_int nii.gz 1) +regressiontest(0 65239R_amygdala_int nii.gz 2) +regressiontest(0 65239R_amygdala_int nii.gz 0 1) +regressiontest(0 65239R_amygdala_int nii.gz 0 2) +regressiontest(0 65239R_amygdala_int nii.gz 0 3) +regressiontest(0 65239R_amygdala_int nii.gz 0 4) +regressiontest(0 65239R_amygdala_int nii.gz 1 1) +regressiontest(0 65239R_amygdala_int nii.gz 1 2) +regressiontest(0 65239R_amygdala_int nii.gz 1 3) +regressiontest(0 65239R_amygdala_int nii.gz 1 4) +regressiontest(0 65239R_amygdala_int nii.gz 2 1) +regressiontest(0 65239R_amygdala_int nii.gz 2 2) +regressiontest(0 65239R_amygdala_int nii.gz 2 3) +regressiontest(0 65239R_amygdala_int nii.gz 2 4) # 65239R_amygdala_fin -regressiontest(65239R_amygdala_fin nii.gz) -regressiontest(65239R_amygdala_fin nii.gz 0) -regressiontest(65239R_amygdala_fin nii.gz 1) -regressiontest(65239R_amygdala_fin nii.gz 2) -regressiontest(65239R_amygdala_fin nii.gz 0 1) -regressiontest(65239R_amygdala_fin nii.gz 0 2) -regressiontest(65239R_amygdala_fin nii.gz 0 3) -regressiontest(65239R_amygdala_fin nii.gz 0 4) -regressiontest(65239R_amygdala_fin nii.gz 1 1) -regressiontest(65239R_amygdala_fin nii.gz 1 2) -regressiontest(65239R_amygdala_fin nii.gz 1 3) -regressiontest(65239R_amygdala_fin nii.gz 1 4) -regressiontest(65239R_amygdala_fin nii.gz 2 1) -regressiontest(65239R_amygdala_fin nii.gz 2 2) -regressiontest(65239R_amygdala_fin nii.gz 2 3) -regressiontest(65239R_amygdala_fin nii.gz 2 4) +regressiontest(0 65239R_amygdala_fin nii.gz) +regressiontest(0 65239R_amygdala_fin nii.gz 0) +regressiontest(0 65239R_amygdala_fin nii.gz 1) +regressiontest(0 65239R_amygdala_fin nii.gz 2) +regressiontest(0 65239R_amygdala_fin nii.gz 0 1) +regressiontest(0 65239R_amygdala_fin nii.gz 0 2) +regressiontest(0 65239R_amygdala_fin nii.gz 0 3) +regressiontest(0 65239R_amygdala_fin nii.gz 0 4) +regressiontest(0 65239R_amygdala_fin nii.gz 1 1) +regressiontest(0 65239R_amygdala_fin nii.gz 1 2) +regressiontest(0 65239R_amygdala_fin nii.gz 1 3) +regressiontest(0 65239R_amygdala_fin nii.gz 1 4) +regressiontest(0 65239R_amygdala_fin nii.gz 2 1) +regressiontest(0 65239R_amygdala_fin nii.gz 2 2) +regressiontest(0 65239R_amygdala_fin nii.gz 2 3) +regressiontest(0 65239R_amygdala_fin nii.gz 2 4) # Long-running handcrafted tests -regressiontest(BigZ nrrd) -regressiontest(BigZ nrrd 0) -regressiontest(BigZ nrrd 1) -regressiontest(BigZ nrrd 2) -regressiontest(FaceRoI nrrd) -regressiontest(FaceRoI nrrd 0) -regressiontest(FaceRoI nrrd 1) -regressiontest(FaceRoI nrrd 2) +regressiontest(1 BigZ nrrd) +regressiontest(1 BigZ nrrd 0) +regressiontest(1 BigZ nrrd 1) +regressiontest(1 BigZ nrrd 2) +regressiontest(1 FaceRoI nrrd) +regressiontest(1 FaceRoI nrrd 0) +regressiontest(1 FaceRoI nrrd 1) +regressiontest(1 FaceRoI nrrd 2) # Non-3D tests -regressiontest(FourD nrrd) +regressiontest(0 FourD nrrd) # dscComparison (crops) dsctest(c2l mha saveImages) From fd49f327b3a6bf66f5cf4d03ed5fef5bdd7e8caa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Thu, 28 Sep 2017 12:43:57 -0400 Subject: [PATCH 122/176] COMP: Simplifying CMake code --- .../test/CMakeLists.txt | 33 +++++++++---------- 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index c63d8a5eff2..499ad432422 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -4,13 +4,15 @@ set( MorphologicalContourInterpolationTests itkMorphologicalContourInterpolationTest.cxx ) +set(TestExe itkMorphologicalContourInterpolationTest) if(${MCI_TestWithRLEImage}) list( APPEND MorphologicalContourInterpolationTests itkMorphologicalContourInterpolationTestWithRLEImage.cxx ) -endif(${MCI_TestWithRLEImage}) + set(TestExe itkMorphologicalContourInterpolationTestWithRLEImage) +endif() createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") @@ -32,19 +34,19 @@ target_link_libraries( # used to produce an output which is then taken as a baseline for a regression test function(JustInputTest ImageName Ext) #optional: Axis Label - foreach(f ${ARGN}) #create unique test name + foreach(f ${ARGN}) # for creating unique test name set(optArgs "${optArgs}_${f}") endforeach() foreach(algo B;C;T) - set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}_${algo}${optArgs}.${Ext}") + set(imageAlgoArgs "${ImageName}_${algo}${optArgs}") itk_add_test( - NAME itkMCI_JustInOut_${ImageName}_${algo}${optArgs} + NAME itkMCI_JustInOut_${imageAlgoArgs} COMMAND MorphologicalContourInterpolationTestDriver - itkMorphologicalContourInterpolationTest + ${TestExe} DATA{Input/${ImageName}.${Ext}} - ${outImage} + "${ITK_TEST_OUTPUT_DIR}/${imageAlgoArgs}.${Ext}" ${algo} ${ARGN} ) @@ -52,7 +54,7 @@ function(JustInputTest ImageName Ext) #optional: Axis Label endfunction() function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label - foreach(f ${ARGN}) #create unique test name + foreach(f ${ARGN}) # for creating unique test name set(optArgs "${optArgs}_${f}") endforeach() @@ -60,21 +62,15 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label # C = repeated dilations with cross structuring element # T = distance transform (not geodesic!) foreach(algo B;C;T) - set(outImage "${ITK_TEST_OUTPUT_DIR}/${ImageName}_${algo}${optArgs}.${Ext}") - set(imageNameOpt "${ImageName}_${algo}${optArgs}") - - if(${MCI_TestWithRLEImage}) - set(TestExe itkMorphologicalContourInterpolationTestWithRLEImage) - else(${MCI_TestWithRLEImage}) - set(TestExe itkMorphologicalContourInterpolationTest) - endif(${MCI_TestWithRLEImage}) + set(imageAlgoArgs "${ImageName}_${algo}${optArgs}") + set(outImage "${ITK_TEST_OUTPUT_DIR}/${imageAlgoArgs}.${Ext}") itk_add_test( - NAME itkMCI_${ImageName}_${algo}${optArgs} + NAME itkMCI_${imageAlgoArgs} COMMAND MorphologicalContourInterpolationTestDriver --compare - DATA{Baseline/${imageNameOpt}.${Ext}} + DATA{Baseline/${imageAlgoArgs}.${Ext}} ${outImage} ${TestExe} DATA{Input/${ImageName}.${Ext}} @@ -82,10 +78,11 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label ${algo} ${ARGN} ) + if(RunsLong) set_property( TEST - itkMCI_${ImageName}_${algo}${optArgs} + itkMCI_${imageAlgoArgs} APPEND PROPERTY LABELS From 25c87a83202fc0c50e4ca3b90b44be1edecea41f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 29 Sep 2017 16:52:39 -0400 Subject: [PATCH 123/176] ENH: Making RLEImage a testing dependency --- .../CMakeLists.txt | 1 - .../itk-module.cmake | 1 + .../test/CMakeLists.txt | 36 +++++++++++++------ 3 files changed, 26 insertions(+), 12 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index bd13ea7189d..38d0e712b48 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -4,7 +4,6 @@ project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) - set(MCI_TestWithRLEImage 0 CACHE BOOL "Whether to test with RLEImage") include(ITKModuleExternal) else() itk_module_impl() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index 126f2942782..b943bbb28c1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -12,6 +12,7 @@ itk_module( ITKDistanceMap TEST_DEPENDS ITKTestKernel + RLEImage EXCLUDE_FROM_DEFAULT DESCRIPTION "${DOCUMENTATION}" ) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 499ad432422..014fc5f1784 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -3,16 +3,8 @@ itk_module_test() set( MorphologicalContourInterpolationTests itkMorphologicalContourInterpolationTest.cxx + itkMorphologicalContourInterpolationTestWithRLEImage.cxx ) -set(TestExe itkMorphologicalContourInterpolationTest) - -if(${MCI_TestWithRLEImage}) - list( - APPEND MorphologicalContourInterpolationTests - itkMorphologicalContourInterpolationTestWithRLEImage.cxx - ) - set(TestExe itkMorphologicalContourInterpolationTestWithRLEImage) -endif() createtestdriver( MorphologicalContourInterpolation "${MorphologicalContourInterpolation-Test_LIBRARIES}" "${MorphologicalContourInterpolationTests}") @@ -44,7 +36,7 @@ function(JustInputTest ImageName Ext) #optional: Axis Label NAME itkMCI_JustInOut_${imageAlgoArgs} COMMAND MorphologicalContourInterpolationTestDriver - ${TestExe} + itkMorphologicalContourInterpolationTest DATA{Input/${ImageName}.${Ext}} "${ITK_TEST_OUTPUT_DIR}/${imageAlgoArgs}.${Ext}" ${algo} @@ -72,7 +64,21 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label --compare DATA{Baseline/${imageAlgoArgs}.${Ext}} ${outImage} - ${TestExe} + itkMorphologicalContourInterpolationTest + DATA{Input/${ImageName}.${Ext}} + ${outImage} + ${algo} + ${ARGN} + ) + + itk_add_test( + NAME itkMCIRLE_${imageAlgoArgs} + COMMAND + MorphologicalContourInterpolationTestDriver + --compare + DATA{Baseline/${imageAlgoArgs}.${Ext}} + ${outImage} + itkMorphologicalContourInterpolationTestWithRLEImage DATA{Input/${ImageName}.${Ext}} ${outImage} ${algo} @@ -88,6 +94,14 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label LABELS RUNS_LONG ) + set_property( + TEST + itkMCIRLE_${imageAlgoArgs} + APPEND + PROPERTY + LABELS + RUNS_LONG + ) endif() endforeach() endfunction() From 7363fd7f4ec756f1f13766c13f91e35ee4309797 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 29 Sep 2017 17:12:21 -0400 Subject: [PATCH 124/176] ENH: More elegant declaration of short/long tests --- .../test/CMakeLists.txt | 248 +++++++++--------- 1 file changed, 128 insertions(+), 120 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 014fc5f1784..71eafcf44cb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -106,6 +106,14 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label endforeach() endfunction() +function(RegressionTestShort) + regressiontest(No ${ARGN}) +endfunction() + +function(RegressionTestLong) + regressiontest(Yes ${ARGN}) +endfunction() + # functional comparison using Dice Similarity Coefficient function(DSCTest ImageName Ext) set(outFilenameBase "${ITK_TEST_OUTPUT_DIR}/${ImageName}") @@ -129,142 +137,142 @@ function(DSCTest ImageName Ext) endfunction() # Handcrafted tests -regressiontest(0 Empty nrrd) -regressiontest(0 NoSlices nrrd) #interpolation should not be invoked (output==input) -regressiontest(0 Micro1 nrrd) -regressiontest(0 SimplestOneToOne nrrd) -regressiontest(0 OneToOne nrrd) -regressiontest(0 OneToThree nrrd) -regressiontest(0 ExtrapolationAppearing nrrd) -regressiontest(0 DoubleTwoLabelBranching nrrd) -regressiontest(0 TwoAxisDoubleTwoLabelBC nrrd) -regressiontest(0 AccidentalMiddleSliceSeg nrrd) -regressiontest(0 SevenLabels nrrd) -regressiontest(0 FullEnd nrrd) -regressiontest(0 1MN1 nrrd) # double sided many broken into many + 1 -regressiontest(0 ManyToMany16 nrrd) -regressiontest(0 ManyToMany nrrd) -regressiontest(0 GridSeg nrrd) -regressiontest(0 GridSeg2 nrrd) +regressiontestshort(Empty nrrd) +regressiontestshort(NoSlices nrrd) #interpolation should not be invoked (output==input) +regressiontestshort(Micro1 nrrd) +regressiontestshort(SimplestOneToOne nrrd) +regressiontestshort(OneToOne nrrd) +regressiontestshort(OneToThree nrrd) +regressiontestshort(ExtrapolationAppearing nrrd) +regressiontestshort(DoubleTwoLabelBranching nrrd) +regressiontestshort(TwoAxisDoubleTwoLabelBC nrrd) +regressiontestshort(AccidentalMiddleSliceSeg nrrd) +regressiontestshort(SevenLabels nrrd) +regressiontestshort(FullEnd nrrd) +regressiontestshort(1MN1 nrrd) # double sided many broken into many + 1 +regressiontestshort(ManyToMany16 nrrd) +regressiontestshort(ManyToMany nrrd) +regressiontestshort(GridSeg nrrd) +regressiontestshort(GridSeg2 nrrd) # Per axis/label tests -regressiontest(0 GridSeg nrrd 0) -regressiontest(0 GridSeg nrrd 1) -regressiontest(0 GridSeg nrrd 2) -regressiontest(0 GridSeg2 nrrd 0) -regressiontest(0 GridSeg2 nrrd 1) -regressiontest(0 GridSeg2 nrrd 2) -regressiontest(0 ThreeAxisFourLabelConflict nrrd) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 0) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 1) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 2) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 -regressiontest(0 ThreeAxisFourLabelConflict nrrd 1 1) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 -regressiontest(0 ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 -regressiontest(0 ThreeAxisFourLabelConflict nrrd 1 2) -regressiontest(0 ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image +regressiontestshort(GridSeg nrrd 0) +regressiontestshort(GridSeg nrrd 1) +regressiontestshort(GridSeg nrrd 2) +regressiontestshort(GridSeg2 nrrd 0) +regressiontestshort(GridSeg2 nrrd 1) +regressiontestshort(GridSeg2 nrrd 2) +regressiontestshort(ThreeAxisFourLabelConflict nrrd) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 0) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 1) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 2) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 0 0) # equals to _0 +regressiontestshort(ThreeAxisFourLabelConflict nrrd 1 1) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 2 3) # equals to _2 +regressiontestshort(ThreeAxisFourLabelConflict nrrd 0 4) # equals to _0 +regressiontestshort(ThreeAxisFourLabelConflict nrrd 1 2) +regressiontestshort(ThreeAxisFourLabelConflict nrrd 2 2) # does not modify image # Paul's single axis tests -regressiontest(0 105769moving nii.gz) #defaults: all axes all labels -regressiontest(0 105769moving nii.gz 2) #axis 2 -regressiontest(0 105769moving nii.gz -1 0) #all axes all labels -regressiontest(0 105769moving nii.gz -1 1) #all axes label 1 -regressiontest(0 105769moving nii.gz -1 2) #all axes label 2 -regressiontest(0 105769moving nii.gz 2 1) #axis 2 label 1 -regressiontest(0 105769moving nii.gz 2 2) #axis 2 label 2 -regressiontest(0 105769fixed nii.gz) #defaults: all axes all labels -regressiontest(0 105769fixed nii.gz 2) #axis 2 -regressiontest(0 105769fixed nii.gz -1 0) #all axes all labels -regressiontest(0 105769fixed nii.gz -1 1) #all axes label 1 -regressiontest(0 105769fixed nii.gz -1 2) #all axes label 2 -regressiontest(0 105769fixed nii.gz 2 1) #axis 2 label 1 -regressiontest(0 105769fixed nii.gz 2 2) #axis 2 label 2 +regressiontestshort(105769moving nii.gz) #defaults: all axes all labels +regressiontestshort(105769moving nii.gz 2) #axis 2 +regressiontestshort(105769moving nii.gz -1 0) #all axes all labels +regressiontestshort(105769moving nii.gz -1 1) #all axes label 1 +regressiontestshort(105769moving nii.gz -1 2) #all axes label 2 +regressiontestshort(105769moving nii.gz 2 1) #axis 2 label 1 +regressiontestshort(105769moving nii.gz 2 2) #axis 2 label 2 +regressiontestshort(105769fixed nii.gz) #defaults: all axes all labels +regressiontestshort(105769fixed nii.gz 2) #axis 2 +regressiontestshort(105769fixed nii.gz -1 0) #all axes all labels +regressiontestshort(105769fixed nii.gz -1 1) #all axes label 1 +regressiontestshort(105769fixed nii.gz -1 2) #all axes label 2 +regressiontestshort(105769fixed nii.gz 2 1) #axis 2 label 1 +regressiontestshort(105769fixed nii.gz 2 2) #axis 2 label 2 # 64816L_amygdala_int -regressiontest(0 64816L_amygdala_int nii.gz) -regressiontest(0 64816L_amygdala_int nii.gz 0) -regressiontest(0 64816L_amygdala_int nii.gz 1) -regressiontest(0 64816L_amygdala_int nii.gz 2) -regressiontest(0 64816L_amygdala_int nii.gz 0 1) -regressiontest(0 64816L_amygdala_int nii.gz 0 2) -regressiontest(0 64816L_amygdala_int nii.gz 0 3) -regressiontest(0 64816L_amygdala_int nii.gz 0 4) -regressiontest(0 64816L_amygdala_int nii.gz 1 1) -regressiontest(0 64816L_amygdala_int nii.gz 1 2) -regressiontest(0 64816L_amygdala_int nii.gz 1 3) -regressiontest(0 64816L_amygdala_int nii.gz 1 4) -regressiontest(0 64816L_amygdala_int nii.gz 2 1) -regressiontest(0 64816L_amygdala_int nii.gz 2 2) -regressiontest(0 64816L_amygdala_int nii.gz 2 3) -regressiontest(0 64816L_amygdala_int nii.gz 2 4) +regressiontestshort(64816L_amygdala_int nii.gz) +regressiontestshort(64816L_amygdala_int nii.gz 0) +regressiontestshort(64816L_amygdala_int nii.gz 1) +regressiontestshort(64816L_amygdala_int nii.gz 2) +regressiontestshort(64816L_amygdala_int nii.gz 0 1) +regressiontestshort(64816L_amygdala_int nii.gz 0 2) +regressiontestshort(64816L_amygdala_int nii.gz 0 3) +regressiontestshort(64816L_amygdala_int nii.gz 0 4) +regressiontestshort(64816L_amygdala_int nii.gz 1 1) +regressiontestshort(64816L_amygdala_int nii.gz 1 2) +regressiontestshort(64816L_amygdala_int nii.gz 1 3) +regressiontestshort(64816L_amygdala_int nii.gz 1 4) +regressiontestshort(64816L_amygdala_int nii.gz 2 1) +regressiontestshort(64816L_amygdala_int nii.gz 2 2) +regressiontestshort(64816L_amygdala_int nii.gz 2 3) +regressiontestshort(64816L_amygdala_int nii.gz 2 4) # 64816L_amygdala_fin -regressiontest(0 64816L_amygdala_fin nii.gz) -regressiontest(0 64816L_amygdala_fin nii.gz 0) -regressiontest(0 64816L_amygdala_fin nii.gz 1) -regressiontest(0 64816L_amygdala_fin nii.gz 2) -regressiontest(0 64816L_amygdala_fin nii.gz 0 1) -regressiontest(0 64816L_amygdala_fin nii.gz 0 2) -regressiontest(0 64816L_amygdala_fin nii.gz 0 3) -regressiontest(0 64816L_amygdala_fin nii.gz 0 4) -regressiontest(0 64816L_amygdala_fin nii.gz 1 1) -regressiontest(0 64816L_amygdala_fin nii.gz 1 2) -regressiontest(0 64816L_amygdala_fin nii.gz 1 3) -regressiontest(0 64816L_amygdala_fin nii.gz 1 4) -regressiontest(0 64816L_amygdala_fin nii.gz 2 1) -regressiontest(0 64816L_amygdala_fin nii.gz 2 2) -regressiontest(0 64816L_amygdala_fin nii.gz 2 3) -regressiontest(0 64816L_amygdala_fin nii.gz 2 4) +regressiontestshort(64816L_amygdala_fin nii.gz) +regressiontestshort(64816L_amygdala_fin nii.gz 0) +regressiontestshort(64816L_amygdala_fin nii.gz 1) +regressiontestshort(64816L_amygdala_fin nii.gz 2) +regressiontestshort(64816L_amygdala_fin nii.gz 0 1) +regressiontestshort(64816L_amygdala_fin nii.gz 0 2) +regressiontestshort(64816L_amygdala_fin nii.gz 0 3) +regressiontestshort(64816L_amygdala_fin nii.gz 0 4) +regressiontestshort(64816L_amygdala_fin nii.gz 1 1) +regressiontestshort(64816L_amygdala_fin nii.gz 1 2) +regressiontestshort(64816L_amygdala_fin nii.gz 1 3) +regressiontestshort(64816L_amygdala_fin nii.gz 1 4) +regressiontestshort(64816L_amygdala_fin nii.gz 2 1) +regressiontestshort(64816L_amygdala_fin nii.gz 2 2) +regressiontestshort(64816L_amygdala_fin nii.gz 2 3) +regressiontestshort(64816L_amygdala_fin nii.gz 2 4) # 65239R_amygdala_int -regressiontest(0 65239R_amygdala_int nii.gz) -regressiontest(0 65239R_amygdala_int nii.gz 0) -regressiontest(0 65239R_amygdala_int nii.gz 1) -regressiontest(0 65239R_amygdala_int nii.gz 2) -regressiontest(0 65239R_amygdala_int nii.gz 0 1) -regressiontest(0 65239R_amygdala_int nii.gz 0 2) -regressiontest(0 65239R_amygdala_int nii.gz 0 3) -regressiontest(0 65239R_amygdala_int nii.gz 0 4) -regressiontest(0 65239R_amygdala_int nii.gz 1 1) -regressiontest(0 65239R_amygdala_int nii.gz 1 2) -regressiontest(0 65239R_amygdala_int nii.gz 1 3) -regressiontest(0 65239R_amygdala_int nii.gz 1 4) -regressiontest(0 65239R_amygdala_int nii.gz 2 1) -regressiontest(0 65239R_amygdala_int nii.gz 2 2) -regressiontest(0 65239R_amygdala_int nii.gz 2 3) -regressiontest(0 65239R_amygdala_int nii.gz 2 4) +regressiontestshort(65239R_amygdala_int nii.gz) +regressiontestshort(65239R_amygdala_int nii.gz 0) +regressiontestshort(65239R_amygdala_int nii.gz 1) +regressiontestshort(65239R_amygdala_int nii.gz 2) +regressiontestshort(65239R_amygdala_int nii.gz 0 1) +regressiontestshort(65239R_amygdala_int nii.gz 0 2) +regressiontestshort(65239R_amygdala_int nii.gz 0 3) +regressiontestshort(65239R_amygdala_int nii.gz 0 4) +regressiontestshort(65239R_amygdala_int nii.gz 1 1) +regressiontestshort(65239R_amygdala_int nii.gz 1 2) +regressiontestshort(65239R_amygdala_int nii.gz 1 3) +regressiontestshort(65239R_amygdala_int nii.gz 1 4) +regressiontestshort(65239R_amygdala_int nii.gz 2 1) +regressiontestshort(65239R_amygdala_int nii.gz 2 2) +regressiontestshort(65239R_amygdala_int nii.gz 2 3) +regressiontestshort(65239R_amygdala_int nii.gz 2 4) # 65239R_amygdala_fin -regressiontest(0 65239R_amygdala_fin nii.gz) -regressiontest(0 65239R_amygdala_fin nii.gz 0) -regressiontest(0 65239R_amygdala_fin nii.gz 1) -regressiontest(0 65239R_amygdala_fin nii.gz 2) -regressiontest(0 65239R_amygdala_fin nii.gz 0 1) -regressiontest(0 65239R_amygdala_fin nii.gz 0 2) -regressiontest(0 65239R_amygdala_fin nii.gz 0 3) -regressiontest(0 65239R_amygdala_fin nii.gz 0 4) -regressiontest(0 65239R_amygdala_fin nii.gz 1 1) -regressiontest(0 65239R_amygdala_fin nii.gz 1 2) -regressiontest(0 65239R_amygdala_fin nii.gz 1 3) -regressiontest(0 65239R_amygdala_fin nii.gz 1 4) -regressiontest(0 65239R_amygdala_fin nii.gz 2 1) -regressiontest(0 65239R_amygdala_fin nii.gz 2 2) -regressiontest(0 65239R_amygdala_fin nii.gz 2 3) -regressiontest(0 65239R_amygdala_fin nii.gz 2 4) +regressiontestshort(65239R_amygdala_fin nii.gz) +regressiontestshort(65239R_amygdala_fin nii.gz 0) +regressiontestshort(65239R_amygdala_fin nii.gz 1) +regressiontestshort(65239R_amygdala_fin nii.gz 2) +regressiontestshort(65239R_amygdala_fin nii.gz 0 1) +regressiontestshort(65239R_amygdala_fin nii.gz 0 2) +regressiontestshort(65239R_amygdala_fin nii.gz 0 3) +regressiontestshort(65239R_amygdala_fin nii.gz 0 4) +regressiontestshort(65239R_amygdala_fin nii.gz 1 1) +regressiontestshort(65239R_amygdala_fin nii.gz 1 2) +regressiontestshort(65239R_amygdala_fin nii.gz 1 3) +regressiontestshort(65239R_amygdala_fin nii.gz 1 4) +regressiontestshort(65239R_amygdala_fin nii.gz 2 1) +regressiontestshort(65239R_amygdala_fin nii.gz 2 2) +regressiontestshort(65239R_amygdala_fin nii.gz 2 3) +regressiontestshort(65239R_amygdala_fin nii.gz 2 4) # Long-running handcrafted tests -regressiontest(1 BigZ nrrd) -regressiontest(1 BigZ nrrd 0) -regressiontest(1 BigZ nrrd 1) -regressiontest(1 BigZ nrrd 2) -regressiontest(1 FaceRoI nrrd) -regressiontest(1 FaceRoI nrrd 0) -regressiontest(1 FaceRoI nrrd 1) -regressiontest(1 FaceRoI nrrd 2) +regressiontestlong(BigZ nrrd) +regressiontestlong(BigZ nrrd 0) +regressiontestlong(BigZ nrrd 1) +regressiontestlong(BigZ nrrd 2) +regressiontestlong(FaceRoI nrrd) +regressiontestlong(FaceRoI nrrd 0) +regressiontestlong(FaceRoI nrrd 1) +regressiontestlong(FaceRoI nrrd 2) # Non-3D tests -regressiontest(0 FourD nrrd) +regressiontestshort(FourD nrrd) # dscComparison (crops) dsctest(c2l mha saveImages) From 577469e36db2ebeaf3097494e8bd2b329afc80a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Fri, 29 Sep 2017 17:16:53 -0400 Subject: [PATCH 125/176] ENH: Adding labels to distinguish RLE from plain ITK image tests --- .../test/CMakeLists.txt | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 71eafcf44cb..6b88e60b867 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -85,6 +85,23 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label ${ARGN} ) + set_property( + TEST + itkMCI_${imageAlgoArgs} + APPEND + PROPERTY + LABELS + MCI_PLAIN + ) + set_property( + TEST + itkMCIRLE_${imageAlgoArgs} + APPEND + PROPERTY + LABELS + MCI_RLE + ) + if(RunsLong) set_property( TEST From 0e64247ea371ceaa81805cdb05974f53bee3b8c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 20 Nov 2017 11:54:57 -0500 Subject: [PATCH 126/176] BUG: fix random tests failure with parallel invocation --- .../MorphologicalContourInterpolation/test/CMakeLists.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 6b88e60b867..67f811de743 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -56,6 +56,10 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label foreach(algo B;C;T) set(imageAlgoArgs "${ImageName}_${algo}${optArgs}") set(outImage "${ITK_TEST_OUTPUT_DIR}/${imageAlgoArgs}.${Ext}") + # have the RLE version output the results into a different file + # otherwise parallel invocation of tests causes undeterministic failures + # when both tests try to write to the same file at the same time + set(outImageRLE "${ITK_TEST_OUTPUT_DIR}/${imageAlgoArgs}_RLE.${Ext}") itk_add_test( NAME itkMCI_${imageAlgoArgs} @@ -77,10 +81,10 @@ function(RegressionTest RunsLong ImageName Ext) #optional: Axis Label MorphologicalContourInterpolationTestDriver --compare DATA{Baseline/${imageAlgoArgs}.${Ext}} - ${outImage} + ${outImageRLE} itkMorphologicalContourInterpolationTestWithRLEImage DATA{Input/${ImageName}.${Ext}} - ${outImage} + ${outImageRLE} ${algo} ${ARGN} ) From eb892615ebf1831c2e4448f65ae7fc9b80101656 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Sat, 16 Dec 2017 16:27:25 -0600 Subject: [PATCH 127/176] COMP: Remove reliance on deprecated code ITKv5 no longer supports deprecated interfaces. --- .../include/itkMorphologicalContourInterpolator.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 5a220f48b94..29f2e1ab6ba 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -402,9 +402,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Sat, 16 Dec 2017 19:17:07 -0600 Subject: [PATCH 128/176] ENH: ITKv5 override consistency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Provide remove virtual and override Use clang-tidy to add ITK_OVERRIDE, and to remove redundant virtual on functions. cd ../ITK; clang-tidy -p ITK-clangtidy $find Modules/[A-J]* -name *.cxx |fgrep -v ThirdParty) -checks=-*,modernize-use-override -header-filter=.* -fix clang-tidy -p ITK-clangtidy $(find Modules/[K-Z]* -name *.cxx |fgrep -v ThirdParty) -checks=-*,modernize-use-override -header-filter=.* -fix https://stackoverflow.com/questions/39932391/virtual-override-or-both-c When you override a function you don't technically need to write either virtual or override. The original base class declaration needs the keyword virtual to mark it as virtual. In the derived class the function is virtual by way of having the ¹same type as the base class function. However, an override can help avoid bugs by producing a compilation error when the intended override isn't technically an override. E.g. that the function type isn't exactly like the base class function. Or that a maintenance of the base class changes that function's type, e.g. adding a defaulted argument. In the same way, a virtual keyword in the derived class can make such a bug more subtle, by ensuring that the function is still is virtual in further derived classes. So the general advice is, virtual for the base class function declaration. This is technically necessary. Use override (only) for a derived class' override. This helps with maintenance. --- .../include/itkMorphologicalContourInterpolator.h | 6 +++--- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 29f2e1ab6ba..e91ebdb20c5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -216,7 +216,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Mon, 15 Jan 2018 18:42:36 -0500 Subject: [PATCH 129/176] ENH: Invoking itk_module_examples() macro --- .../MorphologicalContourInterpolation/CMakeLists.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 38d0e712b48..36abc0f19dd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 2.8.9) +cmake_minimum_required(VERSION 2.8.12) project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) @@ -8,3 +8,5 @@ if(NOT ITK_SOURCE_DIR) else() itk_module_impl() endif() + +itk_module_examples() From 6fd2d8f4957d2a356e7c87b8dcf5e046bf0046be Mon Sep 17 00:00:00 2001 From: Jon Haitz Legarreta Date: Fri, 19 Jan 2018 08:10:46 +0100 Subject: [PATCH 130/176] ENH: Require cmake minimum version to be 3.9.5. Require CMake minimum version to be 3.9.5 following ITKv5 requiring C++11: https://discourse.itk.org/t/minimum-cmake-version-update/585 --- .../Filtering/MorphologicalContourInterpolation/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 36abc0f19dd..b834ad128fe 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 2.8.12) +cmake_minimum_required(VERSION 3.9.5) project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) From 730a3e5e6bc5f1a5ebd8241cd69c78273a103c75 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Sat, 16 Dec 2017 19:36:26 -0600 Subject: [PATCH 131/176] COMP: Use C++11 override directly git grep -l "ITK_OVERRIDE" | fgrep -v itk_compiler_detection.h | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/ITK_OVERRIDE/override/g" --- .../include/itkMorphologicalContourInterpolator.h | 6 +++--- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index e91ebdb20c5..db284c23607 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -216,7 +216,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Sun, 17 Dec 2017 08:22:48 -0600 Subject: [PATCH 132/176] COMP: Use nullptr instead of 0 or NULL The check converts the usage of null pointer constants (eg. NULL, 0) to use the new C++11 nullptr keyword. SRCDIR= #My local SRC BLDDIR= #My local BLD clang-tidy -p ${BLD} $(find Modules/[A-J]* -name "*.cxx" \|fgrep -v ThirdParty) -checks=-*,modernize-use-nullptr -header-filter=.* -fix clang-tidy -p ${BLD} $(find Modules/[K-Z]* -name "*.cxx" \|fgrep -v ThirdParty) -checks=-*,modernize-use-nullptr -header-filter=.* -fix --- .../test/itkMorphologicalContourInterpolationTest.cxx | 4 ++-- .../itkMorphologicalContourInterpolationTestWithRLEImage.cxx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index b478b3258e9..8f0a989f03a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -92,11 +92,11 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) } if (argc >= 5) { - axis = strtol(argv[4], NULL, 10); + axis = strtol(argv[4], nullptr, 10); } if (argc >= 6) { - label = strtol(argv[5], NULL, 10); + label = strtol(argv[5], nullptr, 10); } typedef itk::ImageIOBase::IOComponentType ScalarPixelType; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 861a9714181..12616411744 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -106,11 +106,11 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) } if (argc >= 5) { - axis = strtol(argv[4], NULL, 10); + axis = strtol(argv[4], nullptr, 10); } if (argc >= 6) { - label = strtol(argv[5], NULL, 10); + label = strtol(argv[5], nullptr, 10); } typedef itk::ImageIOBase::IOComponentType ScalarPixelType; From 72bad8f421cb67a94b51fb53927f09b03b306839 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 12 Feb 2018 23:30:29 -0600 Subject: [PATCH 133/176] STYLE: Prefer C++11 type alias over typedef == http://en.cppreference.com/w/cpp/language/type_alias == Type alias is a name that refers to a previously defined type (similar to typedef). A type alias declaration introduces a name which can be used as a synonym for the type denoted by type-id. It does not introduce a new type and it cannot change the meaning of an existing type name. There is no difference between a type alias declaration and typedef declaration. This declaration may appear in block scope, class scope, or namespace scope. == https://www.quora.com/Is-using-typedef-in-C++-considered-a-bad-practice == While typedef is still available for backward compatibility, the new Type Alias syntax 'using Alias = ExistingLongName;' is more consistent with the flow of C++ than the old typedef syntax 'typedef ExistingLongName Alias;', and it also works for templates (Type alias, alias template (since C++11)), so leftover 'typedef' aliases will differ in style from any alias templates. --- .../itkMorphologicalContourInterpolator.h | 40 +++++----- .../itkMorphologicalContourInterpolator.hxx | 80 +++++++++---------- .../test/dscComparison.cxx | 18 ++--- ...kMorphologicalContourInterpolationTest.cxx | 16 ++-- ...alContourInterpolationTestWithRLEImage.cxx | 26 +++--- 5 files changed, 90 insertions(+), 90 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index db284c23607..5040a234c5f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -68,11 +68,11 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Superclass; - typedef SmartPointer Pointer; - typedef Image SliceType; + /** Standard class type alias. */ + using Self = MorphologicalContourInterpolator; + using Superclass = ImageToImageFilter; + using Pointer = SmartPointer; + using SliceType = Image; /** Method for creation through the object factory. */ itkNewMacro(Self); @@ -163,7 +163,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter SliceSetType; + using SliceSetType = std::set; /** Clears all custom slice positions. */ void @@ -204,8 +204,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter LabeledSlicesType; - typedef std::vector SliceIndicesType; + using LabeledSlicesType = itksys::hash_map; + using SliceIndicesType = std::vector; /** Slice indices between which interpolation is done. */ SliceIndicesType @@ -228,10 +228,10 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoolImageType; - typedef Image FloatSliceType; - typedef Image BoolSliceType; + /** Derived image type alias. */ + using BoolImageType = Image; + using FloatSliceType = Image; + using BoolSliceType = Image; /** Are these two slices equal? */ bool @@ -311,7 +311,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter PixelList; + using PixelList = std::vector; /** Splits the bigger region and does N 1-to-1 interpolations */ void @@ -368,7 +368,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter BoundingBoxesType; + using BoundingBoxesType = itksys::hash_map; BoundingBoxesType m_BoundingBoxes; // bounding box for each label /** Calculates a bounding box of non-zero pixels. */ @@ -392,14 +392,14 @@ class MorphologicalContourInterpolator : public ImageToImageFilter RoiType; - typename RoiType::Pointer m_RoI; + using RoiType = ExtractImageFilter; + typename RoiType::Pointer m_RoI; - typedef BinaryThresholdImageFilter BinarizerType; - typename BinarizerType::Pointer m_Binarizer; + using BinarizerType = BinaryThresholdImageFilter; + typename BinarizerType::Pointer m_Binarizer; - typedef ConnectedComponentImageFilter ConnectedComponentsType; - typename ConnectedComponentsType::Pointer m_ConnectedComponents; + using ConnectedComponentsType = ConnectedComponentImageFilter; + typename ConnectedComponentsType::Pointer m_ConnectedComponents; private: MorphologicalContourInterpolator(const Self &) ITK_DELETED_FUNCTION; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ca94cc1cd35..2675a889eb1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -56,15 +56,15 @@ class MorphologicalContourInterpolatorParallelInvoker : public itk::DomainThreader> { public: - // Standard ITK typedefs. - typedef MorphologicalContourInterpolatorParallelInvoker Self; - typedef itk::DomainThreader> - Superclass; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; + // Standard ITK type alias. + using Self = MorphologicalContourInterpolatorParallelInvoker; + using Superclass = + itk::DomainThreader>; + using Pointer = itk::SmartPointer; + using ConstPointer = itk::SmartPointer; // The domain is an index range. - typedef typename Superclass::DomainType DomainType; + using DomainType = typename Superclass::DomainType; // This creates the ::New() method for instantiating the class. itkNewMacro(Self); @@ -317,20 +317,20 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe ThreadIdType threadId) { // set up structuring element for dilation - typedef BinaryCrossStructuringElement - CrossStructuringElementType; - typedef BinaryBallStructuringElement - BallStructuringElementType; - typedef BinaryDilateImageFilter CrossDilateType; - typedef BinaryDilateImageFilter BallDilateType; - - static std::vector initialized(m_ThreadCount); // default: false - static std::vector m_CrossDilator(m_ThreadCount); - static std::vector m_BallDilator(m_ThreadCount); - static std::vector m_CrossStructuringElement(m_ThreadCount); - static std::vector m_BallStructuringElement(m_ThreadCount); - typedef AndImageFilter AndFilterType; - static std::vector m_And(m_ThreadCount); + using CrossStructuringElementType = + BinaryCrossStructuringElement; + using BallStructuringElementType = + BinaryBallStructuringElement; + using CrossDilateType = BinaryDilateImageFilter; + using BallDilateType = BinaryDilateImageFilter; + + static std::vector initialized(m_ThreadCount); // default: false + static std::vector m_CrossDilator(m_ThreadCount); + static std::vector m_BallDilator(m_ThreadCount); + static std::vector m_CrossStructuringElement(m_ThreadCount); + static std::vector m_BallStructuringElement(m_ThreadCount); + using AndFilterType = AndImageFilter; + static std::vector m_And(m_ThreadCount); if (!initialized[threadId]) // make sure these non-trivial operations are executed only once per thread { @@ -338,8 +338,8 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe m_BallDilator[threadId] = BallDilateType::New(); m_And[threadId] = AndFilterType::New(); m_And[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive - typedef Size SizeType; - SizeType size; + using SizeType = Size; + SizeType size; size.Fill(1); m_CrossDilator[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive @@ -418,7 +418,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool float ratio = float(jSeq.size()) / iSeq.size(); // generate union of transition sequences - typedef OrImageFilter OrType; + using OrType = OrImageFilter; static std::vector initialized(m_ThreadCount); // default: false static std::vector m_Or(m_ThreadCount); if (!initialized[threadId]) @@ -461,7 +461,7 @@ template typename MorphologicalContourInterpolator::FloatSliceType::Pointer MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask, ThreadIdType threadId) { - typedef itk::SignedMaurerDistanceMapImageFilter FilterType; + using FilterType = itk::SignedMaurerDistanceMapImageFilter; static std::vector initialized(m_ThreadCount); // default: false static std::vector filter(m_ThreadCount); if (!initialized[threadId]) @@ -569,11 +569,11 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool } // threshold at distance bestBin is the median intersection - typedef BinaryThresholdImageFilter FloatBinarizerType; - typedef AndImageFilter AndFilterType; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector threshold(m_ThreadCount); - static std::vector m_And(m_ThreadCount); + using FloatBinarizerType = BinaryThresholdImageFilter; + using AndFilterType = AndImageFilter; + static std::vector initialized(m_ThreadCount); // default: false + static std::vector threshold(m_ThreadCount); + static std::vector m_And(m_ThreadCount); if (!initialized[threadId]) { threshold[threadId] = FloatBinarizerType::New(); @@ -735,7 +735,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // create intersection - typedef AndImageFilter AndSliceType; + using AndSliceType = AndImageFilter; static std::vector initialized(m_ThreadCount); // default: false static std::vector sAnd(m_ThreadCount); if (!initialized[threadId]) @@ -922,8 +922,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int // first convert iConn into binary mask MatchesID matchesID(iRegionId); - typedef UnaryFunctorImageFilter> CastType; - typename CastType::Pointer caster = CastType::New(); + using CastType = UnaryFunctorImageFilter>; + typename CastType::Pointer caster = CastType::New(); caster->SetNumberOfThreads(1); // excessive threading is counterproductive caster->SetFunctor(matchesID); caster->SetInput(iConn); @@ -1331,7 +1331,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int ThreadIdType threadId) { // go through comparison image and create correspondence pairs - typedef std::set> PairSet; + using PairSet = std::set>; PairSet pairs, unwantedPairs, uncleanPairs; typename SliceType::RegionType ri = iconn->GetRequestedRegion(); typename SliceType::RegionType rj = jconn->GetRequestedRegion(); @@ -1381,8 +1381,8 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // count ocurrances of each component - typedef std::map CountMap; - CountMap iCounts, jCounts; + using CountMap = std::map; + CountMap iCounts, jCounts; for (p = pairs.begin(); p != pairs.end(); ++p) { iCounts[p->first]++; @@ -1594,8 +1594,8 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } - typedef MorphologicalContourInterpolatorParallelInvoker Parallelizer; - typename Parallelizer::Pointer parallelizer = Parallelizer::New(); + using Parallelizer = MorphologicalContourInterpolatorParallelInvoker; + typename Parallelizer::Pointer parallelizer = Parallelizer::New(); parallelizer->SetWorkArray(segments); typename Parallelizer::DomainType completeDomain; completeDomain[0] = 0; @@ -1608,8 +1608,8 @@ template void MorphologicalContourInterpolator::AllocateOutputs() { - typedef ImageBase ImageBaseType; - typename ImageBaseType::Pointer outputPtr; + using ImageBaseType = ImageBase; + typename ImageBaseType::Pointer outputPtr; for (OutputDataObjectIterator it(this); !it.IsAtEnd(); it++) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index 675430fa36c..e3960df458a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -25,9 +25,9 @@ #include "itkTestDriverIncludeRequiredIOFactories.h" #include "itkTimeProbe.h" -typedef unsigned char TestPixelType; -const unsigned int testDim = 3; -typedef itk::Image TestImageType; +using TestPixelType = unsigned char; +const unsigned int testDim = 3; +using TestImageType = itk::Image; TestImageType::Pointer createSparseCopy(const TestImageType::Pointer & inImage, TestImageType::IndexType nth) @@ -124,19 +124,19 @@ main(int argc, char * argv[]) } RegisterRequiredFactories(); - typedef itk::ImageFileReader ReaderType; - ReaderType::Pointer reader = ReaderType::New(); + using ReaderType = itk::ImageFileReader; + ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(argv[1]); reader->Update(); TestImageType::Pointer inImage = reader->GetOutput(); inImage->DisconnectPipeline(); - typedef itk::MorphologicalContourInterpolator mciType; - mciType::Pointer mci = mciType::New(); + using mciType = itk::MorphologicalContourInterpolator; + mciType::Pointer mci = mciType::New(); mci->SetUseBallStructuringElement(true); // test cross? - typedef itk::ImageFileWriter WriterType; - WriterType::Pointer writer = WriterType::New(); + using WriterType = itk::ImageFileWriter; + WriterType::Pointer writer = WriterType::New(); writer->SetUseCompression(true); const TestImageType::RegionType & lpr = inImage->GetLargestPossibleRegion(); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 8f0a989f03a..163b7ebda24 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -26,8 +26,8 @@ template void doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, bool ball, int axis, int label) { - typedef itk::ImageFileReader ReaderType; - typename ReaderType::Pointer reader = ReaderType::New(); + using ReaderType = itk::ImageFileReader; + typename ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(inFilename); reader->Update(); @@ -41,16 +41,16 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); // } - typedef itk::MorphologicalContourInterpolator mciType; - typename mciType::Pointer mci = mciType::New(); + using mciType = itk::MorphologicalContourInterpolator; + typename mciType::Pointer mci = mciType::New(); mci->SetInput(test); mci->SetUseDistanceTransform(UseDistanceTransform); mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); - typedef itk::ImageFileWriter WriterType; - typename WriterType::Pointer writer = WriterType::New(); + using WriterType = itk::ImageFileWriter; + typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outFilename); writer->SetInput(mci->GetOutput()); writer->SetUseCompression(true); @@ -99,8 +99,8 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) label = strtol(argv[5], nullptr, 10); } - typedef itk::ImageIOBase::IOComponentType ScalarPixelType; - itk::ImageIOBase::Pointer imageIO = + using ScalarPixelType = itk::ImageIOBase::IOComponentType; + itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); if (!imageIO) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 12616411744..533cefc7a89 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -27,14 +27,14 @@ template void doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransform, bool ball, int axis, int label) { - typedef itk::ImageFileReader ReaderType; - typename ReaderType::Pointer reader = ReaderType::New(); + using ReaderType = itk::ImageFileReader; + typename ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(inFilename); reader->Update(); - typedef itk::RLEImage myRLEImage; - typedef itk::RegionOfInterestImageFilter inConverterType; - typename inConverterType::Pointer inConv = inConverterType::New(); + using myRLEImage = itk::RLEImage; + using inConverterType = itk::RegionOfInterestImageFilter; + typename inConverterType::Pointer inConv = inConverterType::New(); inConv->SetInput(reader->GetOutput()); inConv->SetRegionOfInterest(reader->GetOutput()->GetLargestPossibleRegion()); inConv->Update(); @@ -49,22 +49,22 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); // } - typedef itk::MorphologicalContourInterpolator mciType; - typename mciType::Pointer mci = mciType::New(); + using mciType = itk::MorphologicalContourInterpolator; + typename mciType::Pointer mci = mciType::New(); mci->SetInput(test); mci->SetUseDistanceTransform(UseDistanceTransform); mci->SetUseBallStructuringElement(ball); mci->SetAxis(axis); mci->SetLabel(label); - typedef itk::RegionOfInterestImageFilter outConverterType; - typename outConverterType::Pointer outConv = outConverterType::New(); + using outConverterType = itk::RegionOfInterestImageFilter; + typename outConverterType::Pointer outConv = outConverterType::New(); outConv->SetInput(mci->GetOutput()); outConv->SetRegionOfInterest(reg); outConv->Update(); - typedef itk::ImageFileWriter WriterType; - typename WriterType::Pointer writer = WriterType::New(); + using WriterType = itk::ImageFileWriter; + typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outFilename); writer->SetInput(outConv->GetOutput()); writer->SetUseCompression(true); @@ -113,8 +113,8 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) label = strtol(argv[5], nullptr, 10); } - typedef itk::ImageIOBase::IOComponentType ScalarPixelType; - itk::ImageIOBase::Pointer imageIO = + using ScalarPixelType = itk::ImageIOBase::IOComponentType; + itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); if (!imageIO) { From 74bb58e1761e9e6747e4ad215b8978ed1c5015bc Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Tue, 13 Feb 2018 08:15:13 -0600 Subject: [PATCH 134/176] COMP: Use C++11 = delete directly git grep -l \"ITK_DELETED_FUNCTION\" | fgrep -v itk_compiler_detection.h | fgrep -v itkMacro.h | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e \"s/ ITK_DELETED_FUNCTION/ = delete/g\" --- .../include/itkMorphologicalContourInterpolator.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 5040a234c5f..57328e63506 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -402,9 +402,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Tue, 13 Feb 2018 08:24:50 -0600 Subject: [PATCH 135/176] STYLE: Prefer constexpr for const numeric literals Use constexpr for constant numeric literals. --- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../MorphologicalContourInterpolation/test/dscComparison.cxx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 2675a889eb1..f8722290cb8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -498,7 +498,7 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool ImageRegionConstIterator itj(jMask, iMask->GetRequestedRegion()); ImageRegionIterator ito(orImage, iMask->GetRequestedRegion()); ImageRegionConstIterator itsdf(sdf, iMask->GetRequestedRegion()); - const short fractioning = 10; // how many times more precise distance than rounding to int + constexpr short fractioning = 10; // how many times more precise distance than rounding to int while (!itsdf.IsAtEnd()) { bool iM = iti.Get(); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index e3960df458a..da9ffaa83d8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -26,7 +26,7 @@ #include "itkTimeProbe.h" using TestPixelType = unsigned char; -const unsigned int testDim = 3; +constexpr unsigned int testDim = 3; using TestImageType = itk::Image; TestImageType::Pointer From faf0055919f1209729f3a586f1bb4beb74a0d948 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 24 Feb 2018 14:59:55 -0500 Subject: [PATCH 136/176] ENH: Using MultiThreaderBase --- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index f8722290cb8..de73ec652e7 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -27,7 +27,7 @@ #include "itkImageRegionConstIteratorWithIndex.h" #include "itkImageRegionIterator.h" #include "itkMorphologicalContourInterpolator.h" -#include "itkMultiThreader.h" +#include "itkMultiThreaderBase.h" #include "itkObjectFactory.h" #include "itkOrImageFilter.h" #include "itkSignedMaurerDistanceMapImageFilter.h" @@ -148,7 +148,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() , // smaller of this and pixel count of the search image m_MaxAlignIters(std::pow(6., static_cast(TImage::ImageDimension))) , // bigger of this and root of pixel count of the search image - m_ThreadCount(MultiThreader::GetGlobalDefaultNumberOfThreads()) + m_ThreadCount(MultiThreaderBase::GetGlobalDefaultNumberOfThreads()) , m_LabeledSlices(TImage::ImageDimension) // initialize with empty sets { // set up pipeline for regioned connected components From 920c2c37ce963e444308542fcce8379959957ff9 Mon Sep 17 00:00:00 2001 From: Jon Haitz Legarreta Date: Sat, 14 Apr 2018 19:05:02 +0200 Subject: [PATCH 137/176] COMP: Move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section. Move `ITK_DISALLOW_COPY_AND_ASSIGN` calls to public section following the discussion in https://discourse.itk.org/t/noncopyable If legacy (pre-macro) copy and assing methods existed, subsitute them for the `ITK_DISALLOW_COPY_AND_ASSIGN` macro. --- .../include/itkMorphologicalContourInterpolator.h | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 57328e63506..5592c52ff7a 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -68,6 +68,8 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; @@ -400,11 +402,6 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; typename ConnectedComponentsType::Pointer m_ConnectedComponents; - -private: - MorphologicalContourInterpolator(const Self &) = delete; - void - operator=(const Self &) = delete; }; } // namespace itk From 35d8fb1d12d6ff613e816bf1afd4723a9e631bf1 Mon Sep 17 00:00:00 2001 From: Jon Haitz Legarreta Date: Sat, 5 May 2018 12:27:15 +0200 Subject: [PATCH 138/176] COMP: Set the minimum required CMake version to 3.10.2. As agreed in: https://discourse.itk.org/t/cmake-update/870/ Set the `cmake_minimum_required` to version **3.10.2**. --- .../Filtering/MorphologicalContourInterpolation/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index b834ad128fe..447dafca781 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.9.5) +cmake_minimum_required(VERSION 3.10.2) project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) From 56258d4545eb60c93b8bd7f883a1cba9abc290d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 1 Aug 2018 09:49:52 -0400 Subject: [PATCH 139/176] COMP: adjusting to split between threads and work units in ITKv5 --- .../itkMorphologicalContourInterpolator.hxx | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index de73ec652e7..4bd071ebab6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -337,17 +337,17 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe m_CrossDilator[threadId] = CrossDilateType::New(); m_BallDilator[threadId] = BallDilateType::New(); m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + m_And[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive using SizeType = Size; SizeType size; size.Fill(1); - m_CrossDilator[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + m_CrossDilator[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive m_CrossStructuringElement[threadId].SetRadius(size); m_CrossStructuringElement[threadId].CreateStructuringElement(); m_CrossDilator[threadId]->SetKernel(m_CrossStructuringElement[threadId]); - m_BallDilator[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + m_BallDilator[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive m_BallStructuringElement[threadId].SetRadius(size); m_BallStructuringElement[threadId].CreateStructuringElement(); m_BallDilator[threadId]->SetKernel(m_BallStructuringElement[threadId]); @@ -424,7 +424,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool if (!initialized[threadId]) { m_Or[threadId] = OrType::New(); - m_Or[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + m_Or[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive initialized[threadId] = true; } @@ -468,7 +468,7 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point { filter[threadId] = FilterType::New(); filter[threadId]->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space - filter[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + filter[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive initialized[threadId] = true; } filter[threadId]->SetInput(mask); @@ -577,9 +577,9 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool if (!initialized[threadId]) { threshold[threadId] = FloatBinarizerType::New(); - threshold[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + threshold[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + m_And[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive initialized[threadId] = true; } threshold[threadId]->SetInput(sdf); @@ -741,7 +741,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int if (!initialized[threadId]) { sAnd[threadId] = AndSliceType::New(); - sAnd[threadId]->SetNumberOfThreads(1); // excessive threading is counterproductive + sAnd[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive initialized[threadId] = true; } sAnd[threadId]->SetInput(0, iSlice); @@ -924,7 +924,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int using CastType = UnaryFunctorImageFilter>; typename CastType::Pointer caster = CastType::New(); - caster->SetNumberOfThreads(1); // excessive threading is counterproductive + caster->SetNumberOfWorkUnits(1); // excessive threading is counterproductive caster->SetFunctor(matchesID); caster->SetInput(iConn); caster->Update(); From 017a693c5d98c3f3bb59ce41305295f5dca67ad9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 27 Aug 2018 11:55:28 -0400 Subject: [PATCH 140/176] ENH: switching to ITKv5 threading model --- .../itkMorphologicalContourInterpolator.h | 28 +- .../itkMorphologicalContourInterpolator.hxx | 315 +++++++----------- 2 files changed, 128 insertions(+), 215 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 5592c52ff7a..adeb8a683e5 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -251,8 +251,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter - GenerateDilationSequence(typename BoolSliceType::Pointer & begin, - typename BoolSliceType::Pointer & end, - ThreadIdType threadId); + GenerateDilationSequence(typename BoolSliceType::Pointer & begin, typename BoolSliceType::Pointer & end); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask, - ThreadIdType threadId); + typename BoolSliceType::Pointer & jMask); /** Finds an interpolating mask for these two aligned masks */ typename BoolSliceType::Pointer FindMedianImageDistances(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask, - ThreadIdType threadId); + typename BoolSliceType::Pointer & jMask); /** Build transition sequence and pick the median */ void @@ -310,8 +304,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; @@ -326,8 +319,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; typename RoiType::Pointer m_RoI; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 4bd071ebab6..4d53bb72f92 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -32,8 +32,8 @@ #include "itkOrImageFilter.h" #include "itkSignedMaurerDistanceMapImageFilter.h" #include "itkSimpleFastMutexLock.h" -#include "itkThreadedIndexedContainerPartitioner.h" #include "itkUnaryFunctorImageFilter.h" +#include "itkProgressTransformer.h" #include #include #include @@ -51,62 +51,6 @@ struct SegmentBetweenTwo typename MorphologicalContourInterpolator::SliceType::Pointer iconn, jconn; }; -template -class MorphologicalContourInterpolatorParallelInvoker - : public itk::DomainThreader> -{ -public: - // Standard ITK type alias. - using Self = MorphologicalContourInterpolatorParallelInvoker; - using Superclass = - itk::DomainThreader>; - using Pointer = itk::SmartPointer; - using ConstPointer = itk::SmartPointer; - - // The domain is an index range. - using DomainType = typename Superclass::DomainType; - - // This creates the ::New() method for instantiating the class. - itkNewMacro(Self); - - /** Array of segments which need to be interpolated. */ - void - SetWorkArray(std::vector> & workArray) - { - m_WorkArray = workArray; - } - - /** Array of segments which need to be interpolated. */ - void - ClearWorkArray() - { - m_WorkArray.clear(); - } - -protected: - // We need a constructor for the itkNewMacro. - MorphologicalContourInterpolatorParallelInvoker() {} - -private: - void - ThreadedExecution(const DomainType & subDomain, const ThreadIdType threadId) override - { - // Look only at the range of cells by the set of indices in the subDomain. - for (itk::IndexValueType ii = subDomain[0]; ii <= subDomain[1] && ii < IndexValueType(m_WorkArray.size()); ++ii) - { - this->m_Associate->InterpolateBetweenTwo(m_WorkArray[ii].axis, - m_WorkArray[ii].out, - m_WorkArray[ii].label, - m_WorkArray[ii].i, - m_WorkArray[ii].j, - m_WorkArray[ii].iconn, - m_WorkArray[ii].jconn, - threadId); - } - } // ThreadedExecution - - std::vector> m_WorkArray; -}; template bool @@ -267,8 +211,7 @@ MorphologicalContourInterpolator::Extrapolate(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer & iConn, - typename TImage::PixelType iRegionId, - ThreadIdType threadId) + typename TImage::PixelType iRegionId) { PixelList jRegionIds; @@ -307,14 +250,13 @@ MorphologicalContourInterpolator::Extrapolate(int phSlice->SetRegions(reg3); typename SliceType::IndexType t0; t0.Fill(0); - Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false, threadId); + Interpolate1to1(axis, out, label, i, j, iConn, iRegionId, phSlice, iRegionId, t0, false); } // >::Extrapolate template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer & seed, - typename BoolSliceType::Pointer & mask, - ThreadIdType threadId) + typename BoolSliceType::Pointer & mask) { // set up structuring element for dilation using CrossStructuringElementType = @@ -324,60 +266,57 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe using CrossDilateType = BinaryDilateImageFilter; using BallDilateType = BinaryDilateImageFilter; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector m_CrossDilator(m_ThreadCount); - static std::vector m_BallDilator(m_ThreadCount); - static std::vector m_CrossStructuringElement(m_ThreadCount); - static std::vector m_BallStructuringElement(m_ThreadCount); + thread_local bool initialized = false; + thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); + thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); + thread_local CrossStructuringElementType m_CrossStructuringElement; + thread_local BallStructuringElementType m_BallStructuringElement; using AndFilterType = AndImageFilter; - static std::vector m_And(m_ThreadCount); + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); - if (!initialized[threadId]) // make sure these non-trivial operations are executed only once per thread + if (!initialized) // make sure these non-trivial operations are executed only once per thread { - m_CrossDilator[threadId] = CrossDilateType::New(); - m_BallDilator[threadId] = BallDilateType::New(); - m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + m_And->SetNumberOfWorkUnits(1); // excessive threading is counterproductive using SizeType = Size; SizeType size; size.Fill(1); - m_CrossDilator[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - m_CrossStructuringElement[threadId].SetRadius(size); - m_CrossStructuringElement[threadId].CreateStructuringElement(); - m_CrossDilator[threadId]->SetKernel(m_CrossStructuringElement[threadId]); + m_CrossDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + m_CrossStructuringElement.SetRadius(size); + m_CrossStructuringElement.CreateStructuringElement(); + m_CrossDilator->SetKernel(m_CrossStructuringElement); - m_BallDilator[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - m_BallStructuringElement[threadId].SetRadius(size); - m_BallStructuringElement[threadId].CreateStructuringElement(); - m_BallDilator[threadId]->SetKernel(m_BallStructuringElement[threadId]); + m_BallDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + m_BallStructuringElement.SetRadius(size); + m_BallStructuringElement.CreateStructuringElement(); + m_BallDilator->SetKernel(m_BallStructuringElement); - initialized[threadId] = true; + initialized = true; } typename BoolSliceType::Pointer temp; if (m_UseBallStructuringElement) { - m_BallDilator[threadId]->SetInput(seed); - m_BallDilator[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_BallDilator[threadId]->Update(); - temp = m_BallDilator[threadId]->GetOutput(); + m_BallDilator->SetInput(seed); + m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_BallDilator->Update(); + temp = m_BallDilator->GetOutput(); } else { - m_CrossDilator[threadId]->SetInput(seed); - m_CrossDilator[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_CrossDilator[threadId]->Update(); - temp = m_CrossDilator[threadId]->GetOutput(); + m_CrossDilator->SetInput(seed); + m_CrossDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_CrossDilator->Update(); + temp = m_CrossDilator->GetOutput(); } temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions - m_And[threadId]->SetInput(0, mask); - m_And[threadId]->SetInput(1, temp); - m_And[threadId]->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_And[threadId]->Update(); - typename BoolSliceType::Pointer result = m_And[threadId]->GetOutput(); + m_And->SetInput(0, mask); + m_And->SetInput(1, temp); + m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); + m_And->Update(); + typename BoolSliceType::Pointer result = m_And->GetOutput(); result->DisconnectPipeline(); return result; } // >::Dilate1 @@ -385,16 +324,15 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe template std::vector::BoolSliceType::Pointer> MorphologicalContourInterpolator::GenerateDilationSequence(typename BoolSliceType::Pointer & begin, - typename BoolSliceType::Pointer & end, - ThreadIdType threadId) + typename BoolSliceType::Pointer & end) { std::vector seq; - seq.push_back(Dilate1(begin, end, threadId)); + seq.push_back(Dilate1(begin, end)); do { seq.back()->DisconnectPipeline(); - seq.push_back(Dilate1(seq.back(), end, threadId)); + seq.push_back(Dilate1(seq.back(), end)); } while (!ImagesEqual(seq.back(), seq[seq.size() - 2])); seq.pop_back(); // remove duplicate image @@ -405,11 +343,10 @@ template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask, - ThreadIdType threadId) + typename BoolSliceType::Pointer & jMask) { - std::vector iSeq = GenerateDilationSequence(intersection, iMask, threadId); - std::vector jSeq = GenerateDilationSequence(intersection, jMask, threadId); + std::vector iSeq = GenerateDilationSequence(intersection, iMask); + std::vector jSeq = GenerateDilationSequence(intersection, jMask); std::reverse(iSeq.begin(), iSeq.end()); // we want to start from i and end at intersection if (iSeq.size() < jSeq.size()) { @@ -419,24 +356,18 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool // generate union of transition sequences using OrType = OrImageFilter; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector m_Or(m_ThreadCount); - if (!initialized[threadId]) - { - m_Or[threadId] = OrType::New(); - m_Or[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - initialized[threadId] = true; - } + thread_local typename OrType::Pointer m_Or = OrType::New(); + m_Or->SetNumberOfWorkUnits(1); // excessive threading is counterproductive std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) { - m_Or[threadId]->SetInput(0, iSeq[x]); + m_Or->SetInput(0, iSeq[x]); unsigned xj = ratio * x; - m_Or[threadId]->SetInput(1, jSeq[xj]); - m_Or[threadId]->GetOutput()->SetRegions(iMask->GetRequestedRegion()); - m_Or[threadId]->Update(); - seq.push_back(m_Or[threadId]->GetOutput()); + m_Or->SetInput(1, jSeq[xj]); + m_Or->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + m_Or->Update(); + seq.push_back(m_Or->GetOutput()); seq.back()->DisconnectPipeline(); } @@ -459,33 +390,26 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool template typename MorphologicalContourInterpolator::FloatSliceType::Pointer -MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask, ThreadIdType threadId) +MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask) { using FilterType = itk::SignedMaurerDistanceMapImageFilter; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector filter(m_ThreadCount); - if (!initialized[threadId]) - { - filter[threadId] = FilterType::New(); - filter[threadId]->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space - filter[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - initialized[threadId] = true; - } - filter[threadId]->SetInput(mask); - filter[threadId]->GetOutput()->SetRequestedRegion(mask->GetRequestedRegion()); - filter[threadId]->Update(); - return filter[threadId]->GetOutput(); + thread_local typename FilterType::Pointer filter = FilterType::New(); + filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space + filter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + filter->SetInput(mask); + filter->GetOutput()->SetRequestedRegion(mask->GetRequestedRegion()); + filter->Update(); + return filter->GetOutput(); } template typename MorphologicalContourInterpolator::BoolSliceType::Pointer MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask, - ThreadIdType threadId) + typename BoolSliceType::Pointer & jMask) { // calculate distance field - typename FloatSliceType::Pointer sdf = MaurerDM(intersection, threadId); + typename FloatSliceType::Pointer sdf = MaurerDM(intersection); // create histograms of distances and union typename BoolSliceType::Pointer orImage = BoolSliceType::New(); @@ -571,27 +495,22 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool // threshold at distance bestBin is the median intersection using FloatBinarizerType = BinaryThresholdImageFilter; using AndFilterType = AndImageFilter; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector threshold(m_ThreadCount); - static std::vector m_And(m_ThreadCount); - if (!initialized[threadId]) - { - threshold[threadId] = FloatBinarizerType::New(); - threshold[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - m_And[threadId] = AndFilterType::New(); - m_And[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - initialized[threadId] = true; - } - threshold[threadId]->SetInput(sdf); - threshold[threadId]->SetUpperThreshold(float(bestBin) / fractioning); - threshold[threadId]->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); - threshold[threadId]->Update(); - - m_And[threadId]->SetInput(threshold[threadId]->GetOutput()); - m_And[threadId]->SetInput(1, orImage); - m_And[threadId]->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); - m_And[threadId]->Update(); - typename BoolSliceType::Pointer median = m_And[threadId]->GetOutput(); + thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); + thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + // excessive threading is counterproductive + threshold->SetNumberOfWorkUnits(1); + m_And->SetNumberOfWorkUnits(1); + + threshold->SetInput(sdf); + threshold->SetUpperThreshold(float(bestBin) / fractioning); + threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); + threshold->Update(); + + m_And->SetInput(threshold->GetOutput()); + m_And->SetInput(1, orImage); + m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); + m_And->Update(); + typename BoolSliceType::Pointer median = m_And->GetOutput(); return median; } // >::FindMedianImageDistances @@ -644,8 +563,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int typename SliceType::Pointer & jConn, typename TImage::PixelType jRegionId, const typename SliceType::IndexType & translation, - bool recursive, - ThreadIdType threadId) + bool recursive) { // translate iConn by t/2 and jConn by -t/2 typename SliceType::IndexType iTrans; @@ -736,29 +654,23 @@ MorphologicalContourInterpolator::Interpolate1to1(int // create intersection using AndSliceType = AndImageFilter; - static std::vector initialized(m_ThreadCount); // default: false - static std::vector sAnd(m_ThreadCount); - if (!initialized[threadId]) - { - sAnd[threadId] = AndSliceType::New(); - sAnd[threadId]->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - initialized[threadId] = true; - } - sAnd[threadId]->SetInput(0, iSlice); - sAnd[threadId]->SetInput(1, jSlice); - sAnd[threadId]->GetOutput()->SetRegions(iSlice->GetRequestedRegion()); - sAnd[threadId]->Update(); - typename BoolSliceType::Pointer intersection = sAnd[threadId]->GetOutput(); + thread_local typename AndSliceType::Pointer sAnd = AndSliceType::New(); + sAnd->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + sAnd->SetInput(0, iSlice); + sAnd->SetInput(1, jSlice); + sAnd->GetOutput()->SetRegions(iSlice->GetRequestedRegion()); + sAnd->Update(); + typename BoolSliceType::Pointer intersection = sAnd->GetOutput(); intersection->DisconnectPipeline(); typename BoolSliceType::Pointer median; if (m_UseDistanceTransform) { - median = FindMedianImageDistances(intersection, iSlice, jSlice, threadId); + median = FindMedianImageDistances(intersection, iSlice, jSlice); } else { - median = FindMedianImageDilations(intersection, iSlice, jSlice, threadId); + median = FindMedianImageDilations(intersection, iSlice, jSlice); } // finally write it out into the output image pointer @@ -867,11 +779,11 @@ MorphologicalContourInterpolator::Interpolate1to1(int if (first) { - Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true, threadId); + Interpolate1to1(axis, out, label, i, mid, iConn, iRegionId, midConn, 1, iTrans, true); } if (second) { - Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true, threadId); + Interpolate1to1(axis, out, label, j, mid, jConn, jRegionId, midConn, 1, jTrans, true); } } } // >::Interpolate1to1 @@ -916,8 +828,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int typename TImage::PixelType iRegionId, typename SliceType::Pointer & jConn, const PixelList & jRegionIds, - const typename SliceType::IndexType & translation, - ThreadIdType threadId) + const typename SliceType::IndexType & translation) { // first convert iConn into binary mask MatchesID matchesID(iRegionId); @@ -991,7 +902,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int { for (unsigned x = 0; x < jRegionIds.size(); x++) { - blobs[x] = Dilate1(blobs[x], mask, threadId); + blobs[x] = Dilate1(blobs[x], mask); blobs[x]->DisconnectPipeline(); } @@ -1072,7 +983,7 @@ MorphologicalContourInterpolator::Interpolate1toN(int // make n 1-to-1 interpolations for (unsigned x = 0; x < jRegionIds.size(); x++) { - Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false, threadId); + Interpolate1to1(axis, out, label, i, j, conns[x], iRegionId, jConn, jRegionIds[x], translation, false); } } // >::Interpolate1toN @@ -1327,8 +1238,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer & iconn, - typename SliceType::Pointer & jconn, - ThreadIdType threadId) + typename SliceType::Pointer & jconn) { // go through comparison image and create correspondence pairs using PairSet = std::set>; @@ -1366,12 +1276,12 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int { if (p->second == 0) { - Extrapolate(axis, out, label, i, j, iconn, p->first, threadId); + Extrapolate(axis, out, label, i, j, iconn, p->first); pairs.erase(p++); } else if (p->first == 0) { - Extrapolate(axis, out, label, j, i, jconn, p->second, threadId); + Extrapolate(axis, out, label, j, i, jconn, p->second); pairs.erase(p++); } else @@ -1398,7 +1308,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int PixelList regionIDs; regionIDs.push_back(p->second); typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false, threadId); + Interpolate1to1(axis, out, label, i, j, iconn, p->first, jconn, p->second, translation, false); iCounts.erase(p->first); jCounts.erase(p->second); pairs.erase(p++); @@ -1427,7 +1337,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(jconn, p->second, iconn, regionIDs); - Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation, threadId); + Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); typename PairSet::iterator rest = pairs.begin(); while (rest != pairs.end()) @@ -1459,7 +1369,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation, threadId); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); typename PairSet::iterator rest = pairs.begin(); ++rest; @@ -1502,7 +1412,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); - Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation, threadId); + Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); typename PairSet::iterator rest = p; ++rest; @@ -1525,7 +1435,10 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int template void -MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * out) +MorphologicalContourInterpolator::InterpolateAlong(int axis, + TImage * out, + float startProgress, + float endProgress) { // a list of segments which need to be interpolated std::vector> segments; @@ -1594,14 +1507,22 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, TImage * ou } } - using Parallelizer = MorphologicalContourInterpolatorParallelInvoker; - typename Parallelizer::Pointer parallelizer = Parallelizer::New(); - parallelizer->SetWorkArray(segments); - typename Parallelizer::DomainType completeDomain; - completeDomain[0] = 0; - completeDomain[1] = std::max(0, int(segments.size()) - 1); - parallelizer->Execute(this, completeDomain); - parallelizer->ClearWorkArray(); + ProgressTransformer pt(startProgress, endProgress, this); + MultiThreaderBase * mt = this->GetMultiThreader(); + mt->ParallelizeArray( + 0, + segments.size(), + [&](SizeValueType ii) { + this->InterpolateBetweenTwo(segments[ii].axis, + segments[ii].out, + segments[ii].label, + segments[ii].i, + segments[ii].j, + segments[ii].iconn, + segments[ii].jconn); + }, + pt.GetProcessObject()); + } // >::InterpolateAlong template @@ -1677,16 +1598,16 @@ MorphologicalContourInterpolator::GenerateData() { if (aggregate[a]) { - this->InterpolateAlong(a, m_Output); + this->InterpolateAlong(a, m_Output, a / float(TImage::ImageDimension), (a + 1) / float(TImage::ImageDimension)); } } } // interpolate along all axes else // interpolate along the specified axis { - this->InterpolateAlong(m_Axis, m_Output); + this->InterpolateAlong(m_Axis, m_Output, 0.0f, 1.0f); } - // Overwrites m_Output with non non-zeroes from m_Input + // Overwrites m_Output with non-zeroes from m_Input ImageRegionIterator itO(this->GetOutput(), this->GetOutput()->GetBufferedRegion()); ImageRegionConstIterator itI(this->GetInput(), this->GetOutput()->GetBufferedRegion()); while (!itI.IsAtEnd()) From 223d5e472c12735abfe6edfd7c60d942e6a59b51 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 27 Aug 2018 13:32:49 -0400 Subject: [PATCH 141/176] STYLE: method-local variables do not follow member-name pattern --- .../itkMorphologicalContourInterpolator.h | 4 +- .../itkMorphologicalContourInterpolator.hxx | 90 +++++++++---------- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index adeb8a683e5..50a90d0714f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -328,9 +328,9 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::Dilate1(typename BoolSliceType::Pointe using BallDilateType = BinaryDilateImageFilter; thread_local bool initialized = false; - thread_local typename CrossDilateType::Pointer m_CrossDilator = CrossDilateType::New(); - thread_local typename BallDilateType::Pointer m_BallDilator = BallDilateType::New(); - thread_local CrossStructuringElementType m_CrossStructuringElement; - thread_local BallStructuringElementType m_BallStructuringElement; + thread_local typename CrossDilateType::Pointer crossDilator = CrossDilateType::New(); + thread_local typename BallDilateType::Pointer ballDilator = BallDilateType::New(); + thread_local CrossStructuringElementType crossStructuringElement; + thread_local BallStructuringElementType ballStructuringElement; using AndFilterType = AndImageFilter; - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + thread_local typename AndFilterType::Pointer andFilter = AndFilterType::New(); if (!initialized) // make sure these non-trivial operations are executed only once per thread { - m_And->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + andFilter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive using SizeType = Size; SizeType size; size.Fill(1); - m_CrossDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - m_CrossStructuringElement.SetRadius(size); - m_CrossStructuringElement.CreateStructuringElement(); - m_CrossDilator->SetKernel(m_CrossStructuringElement); + crossDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + crossStructuringElement.SetRadius(size); + crossStructuringElement.CreateStructuringElement(); + crossDilator->SetKernel(crossStructuringElement); - m_BallDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - m_BallStructuringElement.SetRadius(size); - m_BallStructuringElement.CreateStructuringElement(); - m_BallDilator->SetKernel(m_BallStructuringElement); + ballDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + ballStructuringElement.SetRadius(size); + ballStructuringElement.CreateStructuringElement(); + ballDilator->SetKernel(ballStructuringElement); initialized = true; } @@ -297,26 +297,26 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe typename BoolSliceType::Pointer temp; if (m_UseBallStructuringElement) { - m_BallDilator->SetInput(seed); - m_BallDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_BallDilator->Update(); - temp = m_BallDilator->GetOutput(); + ballDilator->SetInput(seed); + ballDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + ballDilator->Update(); + temp = ballDilator->GetOutput(); } else { - m_CrossDilator->SetInput(seed); - m_CrossDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_CrossDilator->Update(); - temp = m_CrossDilator->GetOutput(); + crossDilator->SetInput(seed); + crossDilator->GetOutput()->SetRegions(seed->GetRequestedRegion()); + crossDilator->Update(); + temp = crossDilator->GetOutput(); } temp->DisconnectPipeline(); // temp->SetRegions(mask->GetLargestPossibleRegion()); //not needed when seed and mask have same regions - m_And->SetInput(0, mask); - m_And->SetInput(1, temp); - m_And->GetOutput()->SetRegions(seed->GetRequestedRegion()); - m_And->Update(); - typename BoolSliceType::Pointer result = m_And->GetOutput(); + andFilter->SetInput(0, mask); + andFilter->SetInput(1, temp); + andFilter->GetOutput()->SetRegions(seed->GetRequestedRegion()); + andFilter->Update(); + typename BoolSliceType::Pointer result = andFilter->GetOutput(); result->DisconnectPipeline(); return result; } // >::Dilate1 @@ -356,18 +356,18 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool // generate union of transition sequences using OrType = OrImageFilter; - thread_local typename OrType::Pointer m_Or = OrType::New(); - m_Or->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + thread_local typename OrType::Pointer orFilter = OrType::New(); + orFilter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive std::vector seq; for (unsigned x = 0; x < iSeq.size(); x++) { - m_Or->SetInput(0, iSeq[x]); + orFilter->SetInput(0, iSeq[x]); unsigned xj = ratio * x; - m_Or->SetInput(1, jSeq[xj]); - m_Or->GetOutput()->SetRegions(iMask->GetRequestedRegion()); - m_Or->Update(); - seq.push_back(m_Or->GetOutput()); + orFilter->SetInput(1, jSeq[xj]); + orFilter->GetOutput()->SetRegions(iMask->GetRequestedRegion()); + orFilter->Update(); + seq.push_back(orFilter->GetOutput()); seq.back()->DisconnectPipeline(); } @@ -376,8 +376,8 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool IdentifierType min = iMask->GetRequestedRegion().GetNumberOfPixels(); for (unsigned x = 0; x < iSeq.size(); x++) { - IdentifierType iS = CardSymDifference(seq[x], iMask); - IdentifierType jS = CardSymDifference(seq[x], jMask); + IdentifierType iS = CardinalSymmetricDifference(seq[x], iMask); + IdentifierType jS = CardinalSymmetricDifference(seq[x], jMask); IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) if (xScore < min) { @@ -496,21 +496,21 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool using FloatBinarizerType = BinaryThresholdImageFilter; using AndFilterType = AndImageFilter; thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); - thread_local typename AndFilterType::Pointer m_And = AndFilterType::New(); + thread_local typename AndFilterType::Pointer andFilter = AndFilterType::New(); // excessive threading is counterproductive threshold->SetNumberOfWorkUnits(1); - m_And->SetNumberOfWorkUnits(1); + andFilter->SetNumberOfWorkUnits(1); threshold->SetInput(sdf); threshold->SetUpperThreshold(float(bestBin) / fractioning); threshold->GetOutput()->SetRequestedRegion(sdf->GetRequestedRegion()); threshold->Update(); - m_And->SetInput(threshold->GetOutput()); - m_And->SetInput(1, orImage); - m_And->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); - m_And->Update(); - typename BoolSliceType::Pointer median = m_And->GetOutput(); + andFilter->SetInput(threshold->GetOutput()); + andFilter->SetInput(1, orImage); + andFilter->GetOutput()->SetRequestedRegion(orImage->GetRequestedRegion()); + andFilter->Update(); + typename BoolSliceType::Pointer median = andFilter->GetOutput(); return median; } // >::FindMedianImageDistances @@ -1073,8 +1073,8 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point template IdentifierType -MorphologicalContourInterpolator::CardSymDifference(typename BoolSliceType::Pointer & iShape, - typename BoolSliceType::Pointer & jShape) +MorphologicalContourInterpolator::CardinalSymmetricDifference(typename BoolSliceType::Pointer & iShape, + typename BoolSliceType::Pointer & jShape) { typename BoolSliceType::RegionType region = iShape->GetLargestPossibleRegion(); IdentifierType count = 0; From c77c86541e1134aeb689c09eda4477dd2dd25029 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 15 Oct 2018 16:29:05 -0400 Subject: [PATCH 142/176] ENH: Removing outdated links --- .../test/Input/Midas3real.url | 5 ----- .../test/Input/Midas3synthetic.url | 6 ------ 2 files changed, 11 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url deleted file mode 100644 index d8e2b7b318f..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3real.url +++ /dev/null @@ -1,5 +0,0 @@ -[{000214A0-0000-0000-C000-000000000046}] -Prop3=19,11 -[InternetShortcut] -URL=https://midas3.kitware.com/midas/folder/13381 -IDList= diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url deleted file mode 100644 index 36048b09b4c..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/Midas3synthetic.url +++ /dev/null @@ -1,6 +0,0 @@ -[{000214A0-0000-0000-C000-000000000046}] -Prop3=19,11 -[InternetShortcut] -URL=https://midas3.kitware.com/midas/folder/12980 -IDList= -HotKey=0 From c2f3168554b0f09d224f31b8444b7c4e3078e557 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 15 Oct 2018 17:04:31 -0400 Subject: [PATCH 143/176] ENH: remove redundant/unused input files --- .../test/Input/GridSeg_0.nrrd.md5 | 1 - .../test/Input/GridSeg_1.nrrd.md5 | 1 - .../test/Input/GridSeg_2.nrrd.md5 | 1 - 3 files changed, 3 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 deleted file mode 100644 index a306561e0ea..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_0.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 deleted file mode 100644 index a306561e0ea..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_1.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -ee926367f773a50ac6ae0299d30a9d57 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 deleted file mode 100644 index a306561e0ea..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/GridSeg_2.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -ee926367f773a50ac6ae0299d30a9d57 From b6d573f0f8130cc31da874b55eaab35c3e133cc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 15 Oct 2018 16:31:18 -0400 Subject: [PATCH 144/176] ENH: Replacing MD5 hashes by SHA512 hashes in test baseline data --- .../test/Baseline/105769fixed_B.nii.gz.md5 | 1 - .../test/Baseline/105769fixed_B.nii.gz.sha512 | 1 + .../test/Baseline/105769fixed_B_-1_0.nii.gz.md5 | 1 - .../test/Baseline/105769fixed_B_-1_0.nii.gz.sha512 | 1 + .../test/Baseline/105769fixed_B_-1_1.nii.gz.md5 | 1 - .../test/Baseline/105769fixed_B_-1_1.nii.gz.sha512 | 1 + .../test/Baseline/105769fixed_B_-1_2.nii.gz.md5 | 1 - .../test/Baseline/105769fixed_B_-1_2.nii.gz.sha512 | 1 + .../test/Baseline/105769fixed_B_2.nii.gz.md5 | 1 - .../test/Baseline/105769fixed_B_2.nii.gz.sha512 | 1 + .../test/Baseline/105769fixed_B_2_1.nii.gz.md5 | 1 - 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b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_2.nrrd.sha512 @@ -0,0 +1 @@ +b085b41afbe9e07f2a88bd6520d00660abeba51952b8b2065a674a50fbd3e2b71e3bb1c37cadd11c8b54e69c4008ae79e4b4a3e3745c0e82be9cf1b6a4c5a608 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 deleted file mode 100644 index e979aef983d..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -ad9185510c387b2bc696846ac8b0d84d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.sha512 new file mode 100644 index 00000000000..5e76cc12ccd --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/ThreeAxisFourLabelConflict_T_2_3.nrrd.sha512 @@ -0,0 +1 @@ +94a80f3427f5b9f99a2b680c5bd040b1b9b0bcaf99efeebc4017d70b297c4deeaa1a789f98b513d3e8b7fc99327cd4aa4151d987204098dfff275c2e95e97e51 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 deleted file mode 100644 index 4a34b999e98..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -c7fc0c04bf25a032adf3a626d7e11da5 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.sha512 new file mode 100644 index 00000000000..d55cce878d0 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_B.nrrd.sha512 @@ -0,0 +1 @@ +1310fc4e2cdca6bbba95a4ce10bfe3a7219e1d795d5e5ecd757a2d9e68911a13426053a6915309ddc6527b45199809bcb0098114a7ed4c677b448d75b4fd1b44 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 deleted file mode 100644 index 38d98e359ac..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -82e90710e28dc831a2b5059664ef3839 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.sha512 new file mode 100644 index 00000000000..4cce9927efb --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_C.nrrd.sha512 @@ -0,0 +1 @@ +a08282d21bcb3976436b4f612cbdef2e85cebff1961e345620e2370dcbdfbbaff7f01d5062a6a83ed09cb840cd204c78ea9a090b4f097e0cf69b5293f9851d9c diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 deleted file mode 100644 index 2977e281d7a..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.md5 +++ /dev/null @@ -1 +0,0 @@ -945f23411e77a73e7f5ac16a27778d39 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.sha512 new file mode 100644 index 00000000000..f7a24c43709 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Baseline/TwoAxisDoubleTwoLabelBC_T.nrrd.sha512 @@ -0,0 +1 @@ +0a324a0cd6c9cc09bb66f5991859c02ec9abcd8212499a374e78a2e9258fe400b356574f9c2f5946ae6ba332cd6d739f72fcfbb449ee604f90b0f764b9fc0a98 From 2367bca2fda9935564d851a711ab8f5411269822 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 15 Oct 2018 17:17:11 -0400 Subject: [PATCH 145/176] ENH: Replacing MD5 hashes by SHA512 hashes in test input data --- .../test/Input/105769fixed.nii.gz.md5 | 1 - .../test/Input/105769fixed.nii.gz.sha512 | 1 + .../test/Input/105769fixed.nii.md5 | 1 - .../test/Input/105769fixed.nii.sha512 | 1 + .../test/Input/105769moving.nii.gz.md5 | 1 - .../test/Input/105769moving.nii.gz.sha512 | 1 + .../test/Input/105769moving.nii.md5 | 1 - .../test/Input/105769moving.nii.sha512 | 1 + .../test/Input/16-5-16.nrrd.md5 | 1 - .../test/Input/16-5-16.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/1MN1.nrrd.md5 | 1 - .../test/Input/1MN1.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/3x3x3.nrrd.md5 | 1 - .../test/Input/3x3x3.nrrd.sha512 | 1 + .../test/Input/64816L_amygdala_fin.nii.gz.md5 | 1 - .../test/Input/64816L_amygdala_fin.nii.gz.sha512 | 1 + .../test/Input/64816L_amygdala_int.nii.gz.md5 | 1 - .../test/Input/64816L_amygdala_int.nii.gz.sha512 | 1 + .../test/Input/65239R_amygdala_fin.nii.gz.md5 | 1 - .../test/Input/65239R_amygdala_fin.nii.gz.sha512 | 1 + .../test/Input/65239R_amygdala_int.nii.gz.md5 | 1 - .../test/Input/65239R_amygdala_int.nii.gz.sha512 | 1 + .../test/Input/AccidentalMiddleSliceSeg.nrrd.md5 | 1 - .../test/Input/AccidentalMiddleSliceSeg.nrrd.sha512 | 1 + .../test/Input/BigImage.nrrd.md5 | 1 - .../test/Input/BigImage.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/BigZ.nrrd.md5 | 1 - .../test/Input/BigZ.nrrd.sha512 | 1 + .../test/Input/DoubleTwoLabelBranching.nrrd.md5 | 1 - .../test/Input/DoubleTwoLabelBranching.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/Empty.nrrd.md5 | 1 - .../test/Input/Empty.nrrd.sha512 | 1 + .../test/Input/ExtrapolationAppearing.nrrd.md5 | 1 - .../test/Input/ExtrapolationAppearing.nrrd.sha512 | 1 + .../test/Input/FaceRoI.nrrd.md5 | 1 - .../test/Input/FaceRoI.nrrd.sha512 | 1 + .../test/Input/FaceRoIFinished.nrrd.md5 | 1 - .../test/Input/FaceRoIFinished.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/FourD.nrrd.md5 | 1 - .../test/Input/FourD.nrrd.sha512 | 1 + .../test/Input/FullEnd.nrrd.md5 | 1 - .../test/Input/FullEnd.nrrd.sha512 | 1 + .../test/Input/GridSeg.nrrd.md5 | 1 - .../test/Input/GridSeg.nrrd.sha512 | 1 + .../test/Input/GridSeg2.nrrd.md5 | 1 - .../test/Input/GridSeg2.nrrd.sha512 | 1 + .../test/Input/GridSegBase.nrrd.md5 | 1 - .../test/Input/GridSegBase.nrrd.sha512 | 1 + .../test/Input/ManyToMany.nrrd.md5 | 1 - .../test/Input/ManyToMany.nrrd.sha512 | 1 + 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.../test/Input/TwoAxisDoubleTwoLabelBC.nrrd.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c10.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c10.mha.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c10b.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c10b.mha.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c10l.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c10l.mha.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c2.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c2.mha.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c2b.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c2b.mha.sha512 | 1 + .../MorphologicalContourInterpolation/test/Input/c2l.mha.md5 | 1 - .../MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 | 1 + .../test/Input/case_10_binary.mha.md5 | 1 - .../test/Input/case_10_binary.mha.sha512 | 1 + .../test/Input/case_10_labels.mha.md5 | 1 - .../test/Input/case_10_labels.mha.sha512 | 1 + .../test/Input/case_2_binary.mha.md5 | 1 - .../test/Input/case_2_binary.mha.sha512 | 1 + .../test/Input/case_2_labels.mha.md5 | 1 - .../test/Input/case_2_labels.mha.sha512 | 1 + 92 files changed, 46 insertions(+), 46 deletions(-) delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.gz.sha512 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769fixed.nii.sha512 delete mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.gz.md5 create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/test/Input/105769moving.nii.gz.sha512 delete mode 100644 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mode 100644 index 2f2357d4f41..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -4601f3a9d4a9ee7f6f3177efdadc8cbb diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.sha512 new file mode 100644 index 00000000000..38089050881 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2.mha.sha512 @@ -0,0 +1 @@ +bb469e11f3f394ab8df1c024916fabfcb1769040f9f19dd18842e53ada99e5002175ecaf8e037836d8d1d0025806d14496497f87c6ea604b4ca085698ce2d2e3 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 deleted file mode 100644 index d6b27e3fa70..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -45e6886ea895af85026f4afff0cbdf1e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.sha512 new file mode 100644 index 00000000000..9ba8294dc9e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2b.mha.sha512 @@ -0,0 +1 @@ +51627cdd80c05fa8fd875cb09f46d882f962fe841efa7e8d8f5b5699fda5868911c2ea161bdc197fbf63a4c72b25d1c5e0984c615b06c6d08fb68017c6668144 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 deleted file mode 100644 index af1baadf362..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -2d8e4b6dcd2a9499f680388497782c66 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 new file mode 100644 index 00000000000..3c5328f664e --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 @@ -0,0 +1 @@ +0f3dcfd029041fb339353718e062befe5a58812fabe9323840dfea43730d520080c27b2f37f553cac78d602ee36b9148eb2d25383baf3cd4280567bdad34a8f7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 deleted file mode 100644 index c7f3f6c0cf5..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -684fb9347d9ba6a6db0237a0cc32306e diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 new file mode 100644 index 00000000000..e5cf7a5d053 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 @@ -0,0 +1 @@ +e9793f3cb49cdf4357d224b2dbc8932b538cd7ae750a2577404e70b8361acab28a7d70f060025ec85d5d91e50447433f38246efc0ec48c68d8d9677727a693b1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 deleted file mode 100644 index c6bbae2bb8d..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -2b7dc9466c4b72915eddbe1623958b28 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 new file mode 100644 index 00000000000..cc973f75cf7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 @@ -0,0 +1 @@ +e3f372362fb6fa1ef18cfb09f852e3463febff6ed86a6061e065e2b67a98116d40502e806d971ac53b8bd7d56713bda002245cd78f9338c2e86e150036fa2f24 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 deleted file mode 100644 index e452a4ff117..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -b9f29368bacdc279b2aa1e76e1d25704 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 new file mode 100644 index 00000000000..a34dd211203 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 @@ -0,0 +1 @@ +e0c819093d45dd891aaae1f12a91a8c008c5d4028de6851b7bef8498d72f25894f055217e0c4dac2451f0e6815093e6f909b32b47a0d31f2281cd724b679c91d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 deleted file mode 100644 index 0420d4fb201..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.md5 +++ /dev/null @@ -1 +0,0 @@ -3b817726a059554cf37dd8202d965249 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 new file mode 100644 index 00000000000..f496c4c3bd7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 @@ -0,0 +1 @@ +1bd86e2c4906e74c0b0ef7dd5def6d13d61a5bf4a8c044b58498474aa83dacfd1d5bf110a1091445d5672fc58e98932675818317bcf9560315732c6a9855e65e From 0bea9ed55ef57fe182f5b97deab351f9d8cc8a9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 16 Oct 2018 15:13:11 -0400 Subject: [PATCH 146/176] BUG: explicitly request 0 background value Default background value was recently changed from 0 to NonPositiveMin in ITK master branch. We now explicitly set desired background to zero. --- .../include/itkMorphologicalContourInterpolator.hxx | 1 + 1 file changed, 1 insertion(+) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 31315adb2e6..4c969a1bfeb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -105,6 +105,7 @@ MorphologicalContourInterpolator::MorphologicalContourInterpolator() // FullyConnected is related to structuring element used // true for ball, false for cross m_ConnectedComponents->SetFullyConnected(m_UseBallStructuringElement); + m_ConnectedComponents->SetBackgroundValue(NumericTraits::ZeroValue()); } template From 83b3aa162aa10b124dd132daaf5b2d9ad14edc01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Sat, 20 Oct 2018 12:55:48 -0400 Subject: [PATCH 147/176] ENH: switch from ITK's mutex wrapper to std::mutex --- .../include/itkMorphologicalContourInterpolator.hxx | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 4c969a1bfeb..1c78057eb6d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -31,11 +31,11 @@ #include "itkObjectFactory.h" #include "itkOrImageFilter.h" #include "itkSignedMaurerDistanceMapImageFilter.h" -#include "itkSimpleFastMutexLock.h" #include "itkUnaryFunctorImageFilter.h" #include "itkProgressTransformer.h" #include #include +#include #include #include #include @@ -739,13 +739,13 @@ MorphologicalContourInterpolator::Interpolate1to1(int } } - static SimpleFastMutexLock mutex; + static std::mutex mutexLock; if (withinReq) // else we should not write it { seqIt.GoToBegin(); // writing through one RLEImage iterator invalidates all the others // so this whole writing loop needs to be serialized - mutex.Lock(); + std::lock_guard mutexHolder(mutexLock); ImageRegionIterator outIt(out, outRegion); while (!outIt.IsAtEnd()) { @@ -756,8 +756,6 @@ MorphologicalContourInterpolator::Interpolate1to1(int ++seqIt; ++outIt; } - - mutex.Unlock(); } // iterator destroyed here // recurse if needed From ec98a037173b78264e3d338e3017be99bd9ca003 Mon Sep 17 00:00:00 2001 From: "Mathew J. Seng" Date: Fri, 23 Aug 2019 12:24:39 -0500 Subject: [PATCH 148/176] STYLE: Change to enum to new enum class definitions Changed to reference enum class: FileModeType Located in namespace ITK STYLE: Change to enum to new enum class definitions Changed to reference enum class: FileModeType Located in namespace ITK --- .../test/itkMorphologicalContourInterpolationTest.cxx | 2 +- .../itkMorphologicalContourInterpolationTestWithRLEImage.cxx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 163b7ebda24..eb0fa6c9d52 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -101,7 +101,7 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) using ScalarPixelType = itk::ImageIOBase::IOComponentType; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeType::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 533cefc7a89..afd5762bd3c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -115,7 +115,7 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) using ScalarPixelType = itk::ImageIOBase::IOComponentType; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeType::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; From 4c31f1f87d38d6130c5d4e31108bd7b1dfce7592 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 11 Dec 2019 15:42:23 -0500 Subject: [PATCH 149/176] COMP: follow rename of ImageIOFactory FileModeType into FileModeEnum --- .../test/itkMorphologicalContourInterpolationTest.cxx | 2 +- .../itkMorphologicalContourInterpolationTestWithRLEImage.cxx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index eb0fa6c9d52..b7c8c6fd2dd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -101,7 +101,7 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) using ScalarPixelType = itk::ImageIOBase::IOComponentType; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeType::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeEnum::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index afd5762bd3c..35cdaab0d7f 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -115,7 +115,7 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) using ScalarPixelType = itk::ImageIOBase::IOComponentType; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeType::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeEnum::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; From 6a7ff171f813cbd51c1917841cb405e5530ab4c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 17 Feb 2020 17:20:23 -0500 Subject: [PATCH 150/176] COMP: use STL's unordered map instead of KWSYS's hash map --- .../include/itkMorphologicalContourInterpolator.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 50a90d0714f..849c0c5f096 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -22,7 +22,7 @@ #include "itkConnectedComponentImageFilter.h" #include "itkExtractImageFilter.h" #include "itkImageToImageFilter.h" -#include "itksys/hash_map.hxx" +#include namespace itk { @@ -206,7 +206,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; + using LabeledSlicesType = std::unordered_map; using SliceIndicesType = std::vector; /** Slice indices between which interpolation is done. */ @@ -362,7 +362,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter; + using BoundingBoxesType = std::unordered_map; BoundingBoxesType m_BoundingBoxes; // bounding box for each label /** Calculates a bounding box of non-zero pixels. */ From 757260df37dd2d727d115784b2254ec79ff6f830 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Mon, 17 Feb 2020 18:05:25 -0500 Subject: [PATCH 151/176] ENH: update enums to match recent changes in ITK --- .../test/itkMorphologicalContourInterpolationTest.cxx | 9 +++++---- ...MorphologicalContourInterpolationTestWithRLEImage.cxx | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index b7c8c6fd2dd..e53f275e3e6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -99,9 +99,9 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) label = strtol(argv[5], nullptr, 10); } - using ScalarPixelType = itk::ImageIOBase::IOComponentType; + using ScalarPixelType = itk::CommonEnums::IOComponent; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeEnum::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::CommonEnums::IOFileMode::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; @@ -115,12 +115,13 @@ itkMorphologicalContourInterpolationTest(int argc, char * argv[]) try { // unused cases are not instantiated because they greatly increase compile time - if (numDimensions == 3 && (pixelType == itk::ImageIOBase::SHORT || pixelType == itk::ImageIOBase::USHORT)) + if (numDimensions == 3 && + (pixelType == itk::CommonEnums::IOComponent::SHORT || pixelType == itk::CommonEnums::IOComponent::USHORT)) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } - if (numDimensions == 4 && pixelType == itk::ImageIOBase::UCHAR) + if (numDimensions == 4 && pixelType == itk::CommonEnums::IOComponent::UCHAR) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 35cdaab0d7f..06d35fb98ad 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -113,9 +113,9 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) label = strtol(argv[5], nullptr, 10); } - using ScalarPixelType = itk::ImageIOBase::IOComponentType; + using ScalarPixelType = itk::CommonEnums::IOComponent; itk::ImageIOBase::Pointer imageIO = - itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::ImageIOFactory::FileModeEnum::ReadMode); + itk::ImageIOFactory::CreateImageIO(inputImageFileName, itk::CommonEnums::IOFileMode::ReadMode); if (!imageIO) { std::cerr << "Could not CreateImageIO for: " << inputImageFileName << std::endl; @@ -129,12 +129,13 @@ itkMorphologicalContourInterpolationTestWithRLEImage(int argc, char * argv[]) try { // unused cases are not instantiated because they greatly increase compile time - if (numDimensions == 3 && (pixelType == itk::ImageIOBase::SHORT || pixelType == itk::ImageIOBase::USHORT)) + if (numDimensions == 3 && + (pixelType == itk::CommonEnums::IOComponent::SHORT || pixelType == itk::CommonEnums::IOComponent::USHORT)) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; } - if (numDimensions == 4 && pixelType == itk::ImageIOBase::UCHAR) + if (numDimensions == 4 && pixelType == itk::CommonEnums::IOComponent::UCHAR) { doTest>(inputImageFileName, outputImageFileName, dt, ball, axis, label); return EXIT_SUCCESS; From 858f8ef1f4a22ef3f04e90e6a20ef2e87235c063 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Wed, 19 Feb 2020 14:40:53 -0600 Subject: [PATCH 152/176] ENH: Add .gitattributes to allow running ITK clang-formatting scripts ``` git filter-branch -f \ --tree-filter "~/ITK/Utilities/Maintenance/clang-format.bash --clang-format ~/Dashboard/src/ITK-clang11/clang-format-Linux --tracked" \ master.. ``` --- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../test/dscComparison.cxx | 6 +++--- .../test/itkMorphologicalContourInterpolationTest.cxx | 8 ++++---- ...rphologicalContourInterpolationTestWithRLEImage.cxx | 10 +++++----- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 1c78057eb6d..892a53964fc 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -30,9 +30,9 @@ #include "itkMultiThreaderBase.h" #include "itkObjectFactory.h" #include "itkOrImageFilter.h" +#include "itkProgressTransformer.h" #include "itkSignedMaurerDistanceMapImageFilter.h" #include "itkUnaryFunctorImageFilter.h" -#include "itkProgressTransformer.h" #include #include #include diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index da9ffaa83d8..9c219a18a0b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -16,14 +16,14 @@ * *=========================================================================*/ -#include -#include -#include #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" #include "itkTestDriverIncludeRequiredIOFactories.h" #include "itkTimeProbe.h" +#include +#include +#include using TestPixelType = unsigned char; constexpr unsigned int testDim = 3; diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index e53f275e3e6..f888726739c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -36,10 +36,10 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor // region for partial coverage typename ImageType::RegionType reg = test->GetLargestPossibleRegion(); // for (int i = 0; i < ImageType::ImageDimension; i++) - // { - // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; - // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); - // } + // { + // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; + // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); + // } using mciType = itk::MorphologicalContourInterpolator; typename mciType::Pointer mci = mciType::New(); diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 06d35fb98ad..ab21d848c45 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -16,10 +16,10 @@ * *=========================================================================*/ -#include "itkRLEImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkMorphologicalContourInterpolator.h" +#include "itkRLEImage.h" #include #include @@ -44,10 +44,10 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor typename myRLEImage::RegionType reg = test->GetLargestPossibleRegion(); // skip X due to RLE representation constraints // for (int i = 1; i < ImageType::ImageDimension; i++) - // { - // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; - // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); - // } + // { + // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; + // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); + // } using mciType = itk::MorphologicalContourInterpolator; typename mciType::Pointer mci = mciType::New(); From 10440d7e208048cef2b97ece0b5ad7c8738090e2 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 17 Feb 2020 14:30:02 -0600 Subject: [PATCH 153/176] STYLE: Prefer = default to explicitly trivial implementations This check replaces default bodies of special member functions with = default;. The explicitly defaulted function declarations enable more opportunities in optimization, because the compiler might treat explicitly defaulted functions as trivial. Additionally, the C++11 use of = default more clearly expreses the intent for the special member functions. --- .../include/itkMorphologicalContourInterpolator.h | 2 +- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 849c0c5f096..4e81101884d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -218,7 +218,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Mon, 17 Feb 2020 15:50:25 -0600 Subject: [PATCH 154/176] STYLE: Use default member initialization MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Converts a default constructor’s member initializers into the new default member initializers in C++11. Other member initializers that match the default member initializer are removed. This can reduce repeated code or allow use of ‘= default’. --- .../include/itkMorphologicalContourInterpolator.h | 10 +++++----- .../include/itkMorphologicalContourInterpolator.hxx | 9 +++------ 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 4e81101884d..f17dcb8754b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -220,11 +220,11 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::ImagesEqual(typename BoolSliceType::Po template MorphologicalContourInterpolator::MorphologicalContourInterpolator() : m_Label(0) - , m_Axis(-1) - , m_HeuristicAlignment(true) - , m_UseDistanceTransform(true) - , m_UseBallStructuringElement(false) - , m_UseCustomSlicePositions(false) - , m_MinAlignIters(std::pow(2., static_cast(TImage::ImageDimension))) + , + + m_MinAlignIters(std::pow(2., static_cast(TImage::ImageDimension))) , // smaller of this and pixel count of the search image m_MaxAlignIters(std::pow(6., static_cast(TImage::ImageDimension))) , // bigger of this and root of pixel count of the search image From a67cb9313f51ff40627e1467a91150eac3145d2a Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 17 Feb 2020 23:35:00 -0600 Subject: [PATCH 155/176] STYLE: Use auto for variable type matches the type of the initializer expression This check is responsible for using the auto type specifier for variable declarations to improve code readability and maintainability. The auto type specifier will only be introduced in situations where the variable type matches the type of the initializer expression. In other words auto should deduce the same type that was originally spelled in the source --- .../itkMorphologicalContourInterpolator.hxx | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 5ac9a8b87d8..f24c9e24f4e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -870,8 +870,8 @@ MorphologicalContourInterpolator::Interpolate1toN(int { if (maskIt.Get()) { - typename TImage::PixelType jVal = jIt.Get(); - typename PixelList::const_iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + auto res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { blobs[res - jRegionIds.begin()]->SetPixel(maskIt.GetIndex(), true); @@ -1044,8 +1044,8 @@ MorphologicalContourInterpolator::Intersection(typename SliceType::Point { if (iIt.Get() == iRegionId) { - typename TImage::PixelType jVal = jIt.Get(); - typename PixelList::const_iterator res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); + typename TImage::PixelType jVal = jIt.Get(); + auto res = std::find(jRegionIds.begin(), jRegionIds.end(), jVal); if (res != jRegionIds.end()) { ++counts[res - jRegionIds.begin()]; @@ -1101,7 +1101,7 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & typename TImage::PixelType val = it.Get(); if (val) { - typename PixelList::const_iterator res = std::find(regionIds.begin(), regionIds.end(), val); + auto res = std::find(regionIds.begin(), regionIds.end(), val); if (res != regionIds.end()) { ++pixelCount; @@ -1267,7 +1267,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int std::inserter(pairs, pairs.end())); // first do extrapolation for components without overlaps - typename PairSet::iterator p = pairs.begin(); + auto p = pairs.begin(); while (p != pairs.end()) { if (p->second == 0) @@ -1324,7 +1324,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int if (iCounts[p->first] == 1) // M-to-1 { - for (typename PairSet::iterator rest = pairs.begin(); rest != pairs.end(); ++rest) + for (auto rest = pairs.begin(); rest != pairs.end(); ++rest) { if (rest->second == p->second) { @@ -1335,7 +1335,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename SliceType::IndexType translation = Align(jconn, p->second, iconn, regionIDs); Interpolate1toN(axis, out, label, j, i, jconn, p->second, iconn, regionIDs, translation); - typename PairSet::iterator rest = pairs.begin(); + auto rest = pairs.begin(); while (rest != pairs.end()) { if (rest != p && rest->second == p->second) @@ -1356,7 +1356,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int } // M-to-1 else if (jCounts[p->second] == 1) // 1-to-N { - for (typename PairSet::iterator rest = pairs.begin(); rest != pairs.end(); ++rest) + for (auto rest = pairs.begin(); rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -1367,7 +1367,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); - typename PairSet::iterator rest = pairs.begin(); + auto rest = pairs.begin(); ++rest; while (rest != pairs.end()) { @@ -1399,7 +1399,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int while (p != pairs.end()) { regionIDs.clear(); - for (typename PairSet::iterator rest = p; rest != pairs.end(); ++rest) + for (auto rest = p; rest != pairs.end(); ++rest) { if (rest->first == p->first) { @@ -1410,7 +1410,7 @@ MorphologicalContourInterpolator::InterpolateBetweenTwo(int typename SliceType::IndexType translation = Align(iconn, p->first, jconn, regionIDs); Interpolate1toN(axis, out, label, i, j, iconn, p->first, jconn, regionIDs, translation); - typename PairSet::iterator rest = p; + auto rest = p; ++rest; while (rest != pairs.end()) { @@ -1443,7 +1443,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, { if (m_Label == 0 || m_Label == it->first) // label needs to be interpolated { - typename SliceSetType::iterator prev = it->second.begin(); + auto prev = it->second.begin(); if (prev == it->second.end()) { continue; // nothing to do for this label @@ -1471,7 +1471,7 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, ? -1 : (*prev > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - typename SliceSetType::iterator next = it->second.begin(); + auto next = it->second.begin(); for (++next; next != it->second.end(); ++next) { typename TImage::RegionType rj = ri; From 65714ff1f00e06b2e7f7cf475f8c51db70c1d92b Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 17 Feb 2020 23:52:07 -0600 Subject: [PATCH 156/176] PERF: readability container size empty The emptiness of a container should be checked using the empty() method instead of the size() method. It is not guaranteed that size() is a constant-time function, and it is generally more efficient and also shows clearer intent to use empty(). Furthermore some containers may implement the empty() method but not implement the size() method. Using empty() whenever possible makes it easier to switch to another container in the future. SRCDIR= #My local SRC BLDDIR= #My local BLD cd run-clang-tidy.py -extra-arg=-D__clang__ -checks=-*,readability-container-size-empty -header-filter=.* -fix --- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index f24c9e24f4e..58a202de6b1 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1558,7 +1558,7 @@ MorphologicalContourInterpolator::GenerateData() this->DetermineSliceOrientations(); } - if (m_BoundingBoxes.size() == 0 && !m_UseCustomSlicePositions) + if (m_BoundingBoxes.empty() && !m_UseCustomSlicePositions) { ImageAlgorithm::Copy( m_Input.GetPointer(), m_Output.GetPointer(), m_Output->GetRequestedRegion(), m_Output->GetRequestedRegion()); From 3172c8ad4b612df7cc3dd818ef0a53196d6d6545 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Wed, 19 Feb 2020 10:45:26 -0600 Subject: [PATCH 157/176] DOC: Update copyright assignment to NumFOCUS The mission of NumFOCUS is to promote open practices in research, data, and scientific computing. https://numfocus.org --- .../include/itkMorphologicalContourInterpolator.h | 2 +- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../MorphologicalContourInterpolation/test/dscComparison.cxx | 2 +- .../test/itkMorphologicalContourInterpolationTest.cxx | 2 +- .../itkMorphologicalContourInterpolationTestWithRLEImage.cxx | 2 +- .../MorphologicalContourInterpolation/test/manualTest.cxx | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index f17dcb8754b..2691796df85 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 58a202de6b1..715fcc59e5d 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index 9c219a18a0b..5e70d5286b8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index f888726739c..2c11a8add33 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index ab21d848c45..545255bbea4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx index ac1403ce39a..90ee43735c8 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx @@ -1,6 +1,6 @@ /*========================================================================= * - * Copyright Insight Software Consortium + * Copyright NumFOCUS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. From d105991f8bc1ead1dd4e47cff1aa5d45998e3716 Mon Sep 17 00:00:00 2001 From: Mathew Seng Date: Wed, 14 Oct 2020 11:47:49 -0500 Subject: [PATCH 158/176] STYLE: Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. --- .../include/itkMorphologicalContourInterpolator.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 2691796df85..1d97a36c183 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -68,7 +68,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Wed, 27 Jan 2021 14:00:58 -0500 Subject: [PATCH 159/176] ENH: build examples as part of CI testing --- .../CMakeLists.txt | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 447dafca781..a95a1480c9e 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,4 +1,22 @@ cmake_minimum_required(VERSION 3.10.2) + +if(CMAKE_CXX_STANDARD EQUAL "98") + message( + FATAL_ERROR + "CMAKE_CXX_STANDARD:STRING=98 is not supported in ITK version 5 and greater." + ) +endif() + +if(NOT CMAKE_CXX_STANDARD) + set(CMAKE_CXX_STANDARD 11) # Supported values are ``11``, ``14``, and ``17``. +endif() +if(NOT CMAKE_CXX_STANDARD_REQUIRED) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +endif() +if(NOT CMAKE_CXX_EXTENSIONS) + set(CMAKE_CXX_EXTENSIONS OFF) +endif() + project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) @@ -6,6 +24,7 @@ if(NOT ITK_SOURCE_DIR) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) include(ITKModuleExternal) else() + set(ITK_DIR ${CMAKE_BINARY_DIR}) itk_module_impl() endif() From 5697399dc9da9eea9073ce49b1f61fcfe0e335e5 Mon Sep 17 00:00:00 2001 From: Adrien Boucaud Date: Tue, 16 Mar 2021 12:15:57 +0100 Subject: [PATCH 160/176] =?UTF-8?q?ENH:=C2=A0Add=20a=20flag=20to=20enable/?= =?UTF-8?q?disable=20extrapolation?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../include/itkMorphologicalContourInterpolator.h | 8 ++++++++ .../include/itkMorphologicalContourInterpolator.hxx | 10 ++++++++-- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index 1d97a36c183..b28ecf67d62 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -139,6 +139,13 @@ class MorphologicalContourInterpolator : public ImageToImageFilter::InterpolateBetweenTwo(int { if (p->second == 0) { - Extrapolate(axis, out, label, i, j, iconn, p->first); + if (m_UseExtrapolation) + { + Extrapolate(axis, out, label, i, j, iconn, p->first); + } pairs.erase(p++); } else if (p->first == 0) { - Extrapolate(axis, out, label, j, i, jconn, p->second); + if (m_UseExtrapolation) + { + Extrapolate(axis, out, label, j, i, jconn, p->second); + } pairs.erase(p++); } else From af6eba4de9bfa138dd9645274532ed0bdf552a75 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Fri, 17 Dec 2021 09:39:35 -0600 Subject: [PATCH 161/176] COMP: Remove inclusion of .hxx files as headers The ability to include either .h or .hxx files as header files required recursively reading the .h files twice. The added complexity is unnecessary, costly, and can confuse static analysis tools that monitor header guardes (due to reaching the maximum depth of recursion limits for nested #ifdefs in checking). --- .../include/itkMorphologicalContourInterpolator.hxx | 1 - 1 file changed, 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index b3bb563c93f..2271d5ebb20 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -26,7 +26,6 @@ #include "itkImageAlgorithm.h" #include "itkImageRegionConstIteratorWithIndex.h" #include "itkImageRegionIterator.h" -#include "itkMorphologicalContourInterpolator.h" #include "itkMultiThreaderBase.h" #include "itkObjectFactory.h" #include "itkOrImageFilter.h" From d2009e1a33b2a0828b57bcc0c286f028ccb77783 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Fri, 17 Dec 2021 12:23:04 -0600 Subject: [PATCH 162/176] STYLE: Prefer itk::Math::abs for consistency. --- .../itkMorphologicalContourInterpolator.hxx | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 2271d5ebb20..ad1ce145a26 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -375,7 +375,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool { IdentifierType iS = CardinalSymmetricDifference(seq[x], iMask); IdentifierType jS = CardinalSymmetricDifference(seq[x], jMask); - IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // abs(iS-jS) + IdentifierType xScore = iS >= jS ? iS - jS : jS - iS; // itk::Math::abs(iS-jS) if (xScore < min) { min = xScore; @@ -479,9 +479,9 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool long long bestDiff = LLONG_MAX; for (unsigned b = 0; b < maxSize; b++) { - long long iS = Math::abs(iTotal - iSum[b] + jSum[b]); - long long jS = Math::abs(jTotal - jSum[b] + iSum[b]); - long long diff = Math::abs(iS - jS); + long long iS = itk::Math::abs(iTotal - iSum[b] + jSum[b]); + long long jS = itk::Math::abs(jTotal - jSum[b] + iSum[b]); + long long diff = itk::Math::abs(iS - jS); if (diff < bestDiff) { bestDiff = diff; @@ -755,7 +755,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int } // iterator destroyed here // recurse if needed - if (Math::abs(i - j) > 2) + if (itk::Math::abs(i - j) > 2) { PixelList regionIDs; regionIDs.push_back(1); @@ -769,8 +769,8 @@ MorphologicalContourInterpolator::Interpolate1to1(int int mReq = mid < reqRegion.GetIndex(axis) ? -1 : (mid > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - bool first = Math::abs(i - mid) > 1 && Math::abs(iReq + mReq) <= 1; // i-mid? - bool second = Math::abs(j - mid) > 1 && Math::abs(jReq + mReq) <= 1; // j-mid? + bool first = itk::Math::abs(i - mid) > 1 && itk::Math::abs(iReq + mReq) <= 1; // i-mid? + bool second = itk::Math::abs(j - mid) > 1 && itk::Math::abs(jReq + mReq) <= 1; // j-mid? if (first) { @@ -1487,9 +1487,9 @@ MorphologicalContourInterpolator::InterpolateAlong(int axis, ? -1 : (*next > reqRegion.GetIndex(axis) + IndexValueType(reqRegion.GetSize(axis)) ? +1 : 0); - if (*prev + 1 < *next // only if they are not adjacent slices - && Math::abs(iReq + jReq) <= 1) // and not out of the requested region - // unless they are on opposite ends + if (*prev + 1 < *next // only if they are not adjacent slices + && itk::Math::abs(iReq + jReq) <= 1) // and not out of the requested region + // unless they are on opposite ends { SegmentBetweenTwo s; s.axis = axis; From 6fc58413feeb9abe93a039a501a564a72e2c9ec7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Tue, 1 Mar 2022 15:48:35 -0500 Subject: [PATCH 163/176] ENH: Updating MCI for ITK 5.3RC3 Bumping Python version number in the process. --- .../MorphologicalContourInterpolation/CMakeLists.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index a95a1480c9e..39e3ef25ac6 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,14 +1,14 @@ -cmake_minimum_required(VERSION 3.10.2) +cmake_minimum_required(VERSION 3.16.3) -if(CMAKE_CXX_STANDARD EQUAL "98") +if(CMAKE_CXX_STANDARD EQUAL "11") message( FATAL_ERROR - "CMAKE_CXX_STANDARD:STRING=98 is not supported in ITK version 5 and greater." + "CMAKE_CXX_STANDARD:STRING=11 is not supported in ITK version 5.3 and greater." ) endif() if(NOT CMAKE_CXX_STANDARD) - set(CMAKE_CXX_STANDARD 11) # Supported values are ``11``, ``14``, and ``17``. + set(CMAKE_CXX_STANDARD 14) # Supported values are ``14``, ``17``, and ``20``. endif() if(NOT CMAKE_CXX_STANDARD_REQUIRED) set(CMAKE_CXX_STANDARD_REQUIRED ON) From 84970126c7c925a36196164b22d422cf01bc473f Mon Sep 17 00:00:00 2001 From: Tom Birdsong Date: Tue, 31 May 2022 15:14:10 -0400 Subject: [PATCH 164/176] ENH: Bump ITK version and apply http to https reformatting --- Modules/Filtering/MorphologicalContourInterpolation/LICENSE | 4 ++-- .../include/itkMorphologicalContourInterpolator.h | 2 +- .../include/itkMorphologicalContourInterpolator.hxx | 2 +- .../MorphologicalContourInterpolation/test/dscComparison.cxx | 2 +- .../test/itkMorphologicalContourInterpolationTest.cxx | 2 +- .../itkMorphologicalContourInterpolationTestWithRLEImage.cxx | 2 +- .../MorphologicalContourInterpolation/test/manualTest.cxx | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/LICENSE b/Modules/Filtering/MorphologicalContourInterpolation/LICENSE index 8dada3edaf5..9b259bdfcf9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/LICENSE +++ b/Modules/Filtering/MorphologicalContourInterpolation/LICENSE @@ -1,6 +1,6 @@ Apache License Version 2.0, January 2004 - http://www.apache.org/licenses/ + https://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION @@ -192,7 +192,7 @@ you may not use this file except in compliance with the License. You may obtain a copy of the License at - http://www.apache.org/licenses/LICENSE-2.0 + https://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index b28ecf67d62..c39fbd24686 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index ad1ce145a26..20bb63e7322 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx index 5e70d5286b8..e6000bd1a62 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/dscComparison.cxx @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 2c11a8add33..71c352f91eb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx index 545255bbea4..aecea4e1874 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTestWithRLEImage.cxx @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx index 90ee43735c8..5b6d80f2a56 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/manualTest.cxx @@ -6,7 +6,7 @@ * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, From aaae5b73fbf1e8930f6224de1218456eb7ca784f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= Date: Wed, 26 Apr 2023 16:05:02 -0400 Subject: [PATCH 165/176] STYLE: Use trailing return type instead of typename + dependent type --- .../itkMorphologicalContourInterpolator.hxx | 44 +++++++++++-------- 1 file changed, 26 insertions(+), 18 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 20bb63e7322..176b3fbb2a4 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -251,9 +251,10 @@ MorphologicalContourInterpolator::Extrapolate(int } // >::Extrapolate template -typename MorphologicalContourInterpolator::BoolSliceType::Pointer +auto MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointer & seed, - typename BoolSliceType::Pointer & mask) + typename BoolSliceType::Pointer & mask) -> + typename BoolSliceType::Pointer { // set up structuring element for dilation using CrossStructuringElementType = @@ -337,10 +338,11 @@ MorphologicalContourInterpolator::GenerateDilationSequence(typename Bool } template -typename MorphologicalContourInterpolator::BoolSliceType::Pointer +auto MorphologicalContourInterpolator::FindMedianImageDilations(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask) + typename BoolSliceType::Pointer & jMask) -> + typename BoolSliceType::Pointer { std::vector iSeq = GenerateDilationSequence(intersection, iMask); std::vector jSeq = GenerateDilationSequence(intersection, jMask); @@ -386,8 +388,9 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool } // >::FindMedianImageDilations template -typename MorphologicalContourInterpolator::FloatSliceType::Pointer -MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask) +auto +MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Pointer & mask) -> + typename FloatSliceType::Pointer { using FilterType = itk::SignedMaurerDistanceMapImageFilter; thread_local typename FilterType::Pointer filter = FilterType::New(); @@ -400,10 +403,11 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point } template -typename MorphologicalContourInterpolator::BoolSliceType::Pointer +auto MorphologicalContourInterpolator::FindMedianImageDistances(typename BoolSliceType::Pointer & intersection, typename BoolSliceType::Pointer & iMask, - typename BoolSliceType::Pointer & jMask) + typename BoolSliceType::Pointer & jMask) -> + typename BoolSliceType::Pointer { // calculate distance field typename FloatSliceType::Pointer sdf = MaurerDM(intersection); @@ -512,8 +516,9 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool } // >::FindMedianImageDistances template -typename MorphologicalContourInterpolator::SliceType::RegionType -MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) +auto +MorphologicalContourInterpolator::BoundingBox(itk::SmartPointer image) -> + typename SliceType::RegionType { typename SliceType::RegionType newRegion = image->GetLargestPossibleRegion(); typename SliceType::IndexType minInd = newRegion.GetIndex() + newRegion.GetSize(); @@ -983,10 +988,11 @@ MorphologicalContourInterpolator::Interpolate1toN(int } // >::Interpolate1toN template -typename MorphologicalContourInterpolator::SliceType::Pointer +auto MorphologicalContourInterpolator::TranslateImage(typename SliceType::Pointer & image, const typename SliceType::IndexType & translation, - typename SliceType::RegionType newRegion) + typename SliceType::RegionType newRegion) -> + typename SliceType::Pointer { typename SliceType::Pointer result = SliceType::New(); result->CopyInformation(image); @@ -1089,8 +1095,9 @@ MorphologicalContourInterpolator::CardinalSymmetricDifference(typename B } template -typename MorphologicalContourInterpolator::SliceType::IndexType -MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & conn, const PixelList & regionIds) +auto +MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & conn, const PixelList & regionIds) -> + typename SliceType::IndexType { ImageRegionConstIteratorWithIndex it(conn, conn->GetLargestPossibleRegion()); IndexValueType ind[SliceType::ImageDimension] = { 0 }; // all components are initialized to zero @@ -1123,11 +1130,11 @@ MorphologicalContourInterpolator::Centroid(typename SliceType::Pointer & } // >::Centroid template -typename MorphologicalContourInterpolator::SliceType::IndexType +auto MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer & jConn, - const PixelList & jRegionIds) + const PixelList & jRegionIds) -> typename SliceType::IndexType { // calculate centroids PixelList iRegionIds; @@ -1211,10 +1218,11 @@ MorphologicalContourInterpolator::Align(typename SliceType::Pointer & iC } // >::Align template -typename MorphologicalContourInterpolator::SliceType::Pointer +auto MorphologicalContourInterpolator::RegionedConnectedComponents(const typename TImage::RegionType & region, typename TImage::PixelType label, - IdentifierType & objectCount) + IdentifierType & objectCount) -> + typename SliceType::Pointer { m_RoI->SetExtractionRegion(region); m_RoI->SetInput(this->GetInput()); From 806a2143a25e4bb298cfb5c85859256cf9cc3ef0 Mon Sep 17 00:00:00 2001 From: Stephen Aylward Date: Sun, 17 Dec 2023 10:55:12 -0500 Subject: [PATCH 166/176] ENH: Bump setup.py and CI to use ITK v5.4 rc2 This includes enabling shared libraries in itk-module.cmake and addressing CMake policy CMP0135 and its associated warning. --- .../MorphologicalContourInterpolation/CMakeLists.txt | 6 +++++- .../MorphologicalContourInterpolation/itk-module.cmake | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 39e3ef25ac6..935e4fa1f9b 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,5 +1,9 @@ cmake_minimum_required(VERSION 3.16.3) +if(POLICY CMP0135) + cmake_policy(SET CMP0135 NEW) +endif() + if(CMAKE_CXX_STANDARD EQUAL "11") message( FATAL_ERROR @@ -20,7 +24,7 @@ endif() project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) - find_package(ITK 4.9 REQUIRED) + find_package(ITK REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) include(ITKModuleExternal) else() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake index b943bbb28c1..90ad9cda8f9 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake +++ b/Modules/Filtering/MorphologicalContourInterpolation/itk-module.cmake @@ -7,6 +7,7 @@ Enabling testing requires RLEImage module to be enabled." itk_module( MorphologicalContourInterpolation + ENABLE_SHARED DEPENDS ITKBinaryMathematicalMorphology ITKDistanceMap From b7cdc618b4fc1a0b4359d5d3e53df833bf10488c Mon Sep 17 00:00:00 2001 From: Stephen Aylward Date: Sun, 17 Dec 2023 11:55:46 -0500 Subject: [PATCH 167/176] ENH: Eliminate old compiler requirements --- .../CMakeLists.txt | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 935e4fa1f9b..0cb9835cb8c 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -4,23 +4,6 @@ if(POLICY CMP0135) cmake_policy(SET CMP0135 NEW) endif() -if(CMAKE_CXX_STANDARD EQUAL "11") - message( - FATAL_ERROR - "CMAKE_CXX_STANDARD:STRING=11 is not supported in ITK version 5.3 and greater." - ) -endif() - -if(NOT CMAKE_CXX_STANDARD) - set(CMAKE_CXX_STANDARD 14) # Supported values are ``14``, ``17``, and ``20``. -endif() -if(NOT CMAKE_CXX_STANDARD_REQUIRED) - set(CMAKE_CXX_STANDARD_REQUIRED ON) -endif() -if(NOT CMAKE_CXX_EXTENSIONS) - set(CMAKE_CXX_EXTENSIONS OFF) -endif() - project(MorphologicalContourInterpolation) if(NOT ITK_SOURCE_DIR) From 9544e1bbc84b4a561e79addd032b76ed2655e61e Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 14 Feb 2024 22:53:42 -0500 Subject: [PATCH 168/176] ENH: Add wasm configuration Build javascript, typescript, cli, packages, documentation via ITK-Wasm. A few tests added for the CLI, javascript, typescript to ensure they run. Other testing is left to the module. CI for build/test of everything and build / deploy of the documentation to GitHub Pages. --- .../MorphologicalContourInterpolation/CMakeLists.txt | 10 +++++++++- .../include/itkMorphologicalContourInterpolator.hxx | 4 ++++ .../test/CMakeLists.txt | 4 ++++ 3 files changed, 17 insertions(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 39e3ef25ac6..3b2dccb8024 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -8,7 +8,11 @@ if(CMAKE_CXX_STANDARD EQUAL "11") endif() if(NOT CMAKE_CXX_STANDARD) - set(CMAKE_CXX_STANDARD 14) # Supported values are ``14``, ``17``, and ``20``. + if(WASI OR EMSCRIPTEN) + set(CMAKE_CXX_STANDARD 20) # Supported values are ``14``, ``17``, and ``20``. + else() + set(CMAKE_CXX_STANDARD 17) # Supported values are ``14``, ``17``, and ``20``. + endif() endif() if(NOT CMAKE_CXX_STANDARD_REQUIRED) set(CMAKE_CXX_STANDARD_REQUIRED ON) @@ -23,6 +27,10 @@ if(NOT ITK_SOURCE_DIR) find_package(ITK 4.9 REQUIRED) list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) include(ITKModuleExternal) + if(WASI OR EMSCRIPTEN) + set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + add_subdirectory(wasm) + endif() else() set(ITK_DIR ${CMAKE_BINARY_DIR}) itk_module_impl() diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 176b3fbb2a4..216d0752b25 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -740,13 +740,17 @@ MorphologicalContourInterpolator::Interpolate1to1(int } } +#if !defined(__wasi__) && !defined(__EMSCRIPTEN__) static std::mutex mutexLock; +#endif if (withinReq) // else we should not write it { seqIt.GoToBegin(); // writing through one RLEImage iterator invalidates all the others // so this whole writing loop needs to be serialized +#if !defined(__wasi__) && !defined(__EMSCRIPTEN__) std::lock_guard mutexHolder(mutexLock); +#endif ImageRegionIterator outIt(out, outRegion); while (!outIt.IsAtEnd()) { diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt index 67f811de743..937545394dd 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/CMakeLists.txt @@ -1,3 +1,7 @@ +if(WASI OR EMSCRIPTEN) + # Avoid RLEImage dependency for wasm builds + return() +endif() itk_module_test() set( From 7c3986dc5a395309a08670cfb43874f021c8d00a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Thu, 23 Jan 2025 11:06:07 -0500 Subject: [PATCH 169/176] ENH: Remove unused variable and commented code block Remove unused variable and commented code block: getting the largest possible region of the superclass (`ImageToImageFilter`) is most likely being exercised in ITK proper. Fixes: ``` test/itkMorphologicalContourInterpolationTest.cxx:37:34: warning: unused variable 'reg' [-Wunused-variable] 37 | typename ImageType::RegionType reg = test->GetLargestPossibleRegion(); | ^~~ ``` raised for example in: https://open.cdash.org/viewBuildError.php?type=1&buildid=10154304 --- .../test/itkMorphologicalContourInterpolationTest.cxx | 8 -------- 1 file changed, 8 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx index 71c352f91eb..960ee564e01 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/itkMorphologicalContourInterpolationTest.cxx @@ -33,14 +33,6 @@ doTest(std::string inFilename, std::string outFilename, bool UseDistanceTransfor typename ImageType::Pointer test = reader->GetOutput(); - // region for partial coverage - typename ImageType::RegionType reg = test->GetLargestPossibleRegion(); - // for (int i = 0; i < ImageType::ImageDimension; i++) - // { - // reg.GetModifiableIndex()[i] += (reg.GetSize(i) - 1) / 4; - // reg.SetSize(i, (reg.GetSize(i) + 1) / 2); - // } - using mciType = itk::MorphologicalContourInterpolator; typename mciType::Pointer mci = mciType::New(); mci->SetInput(test); From 61f29281eb35d9f6c1820d69c83f26532a06594e Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Sat, 25 Jan 2025 11:07:25 -0600 Subject: [PATCH 170/176] COMP: Use modern macro for name of class MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit When preparing for the future with ITK by setting ITK_FUTURE_LEGACY_REMOVE:BOOL=ON ITK_LEGACY_REMOVEBOOL=ON The future preferred macro should be used │ - itkTypeMacro │ + itkOverrideGetNameOfClassMacro --- .../include/itkMorphologicalContourInterpolator.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h index c39fbd24686..9ba6882d535 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.h @@ -80,7 +80,7 @@ class MorphologicalContourInterpolator : public ImageToImageFilter Date: Wed, 22 Apr 2026 18:54:03 -0500 Subject: [PATCH 171/176] ENH: Convert from md5 to .cid tags. --- .../test/Baseline/105769fixed_B.nii.gz.cid | 1 + .../test/Baseline/105769fixed_B.nii.gz.sha512 | 1 - .../test/Baseline/105769fixed_B_-1_0.nii.gz.cid | 1 + .../test/Baseline/105769fixed_B_-1_0.nii.gz.sha512 | 1 - .../test/Baseline/105769fixed_B_-1_1.nii.gz.cid | 1 + .../test/Baseline/105769fixed_B_-1_1.nii.gz.sha512 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a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 deleted file mode 100644 index 3c5328f664e..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/c2l.mha.sha512 +++ /dev/null @@ -1 +0,0 @@ -0f3dcfd029041fb339353718e062befe5a58812fabe9323840dfea43730d520080c27b2f37f553cac78d602ee36b9148eb2d25383baf3cd4280567bdad34a8f7 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.cid b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.cid new file mode 100644 index 00000000000..f781e222946 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.cid @@ -0,0 +1 @@ +bafkreifpyjzaleo6kssix6pim5smyg5l4le6cao3jq2ibrgzewe337dbmq diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 deleted file mode 100644 index e5cf7a5d053..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_binary.mha.sha512 +++ /dev/null @@ -1 +0,0 @@ -e9793f3cb49cdf4357d224b2dbc8932b538cd7ae750a2577404e70b8361acab28a7d70f060025ec85d5d91e50447433f38246efc0ec48c68d8d9677727a693b1 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.cid b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.cid new file mode 100644 index 00000000000..2af739f8455 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.cid @@ -0,0 +1 @@ +bafkreiapyugfzw2syniuvvbn6os7vaobplrr47clelwcwnbygbwcml5wdq diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 deleted file mode 100644 index cc973f75cf7..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_10_labels.mha.sha512 +++ /dev/null @@ -1 +0,0 @@ -e3f372362fb6fa1ef18cfb09f852e3463febff6ed86a6061e065e2b67a98116d40502e806d971ac53b8bd7d56713bda002245cd78f9338c2e86e150036fa2f24 diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.cid b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.cid new file mode 100644 index 00000000000..a8402b5d3e6 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.cid @@ -0,0 +1 @@ +bafkreiccykh5i54qje2nyk4rasxhsfcpjz7lverkfntpc2ieeip2sr5whi diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 deleted file mode 100644 index a34dd211203..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_binary.mha.sha512 +++ /dev/null @@ -1 +0,0 @@ -e0c819093d45dd891aaae1f12a91a8c008c5d4028de6851b7bef8498d72f25894f055217e0c4dac2451f0e6815093e6f909b32b47a0d31f2281cd724b679c91d diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.cid b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.cid new file mode 100644 index 00000000000..00acba808b7 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.cid @@ -0,0 +1 @@ +bafkreic7tpglu6k3qnpv5omf4lg6yic4xb6hnr64vx3myiobtsbffr2gnm diff --git a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 b/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 deleted file mode 100644 index f496c4c3bd7..00000000000 --- a/Modules/Filtering/MorphologicalContourInterpolation/test/Input/case_2_labels.mha.sha512 +++ /dev/null @@ -1 +0,0 @@ -1bd86e2c4906e74c0b0ef7dd5def6d13d61a5bf4a8c044b58498474aa83dacfd1d5bf110a1091445d5672fc58e98932675818317bcf9560315732c6a9855e65e From c69d8d17de43179df8bf29124c8fbf51c2c9c135 Mon Sep 17 00:00:00 2001 From: "Hans J. Johnson" Date: Mon, 4 May 2026 16:52:02 -0500 Subject: [PATCH 172/176] DOC: Add MorphologicalContourInterpolation README pointing at upstream --- .../README.md | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 Modules/Filtering/MorphologicalContourInterpolation/README.md diff --git a/Modules/Filtering/MorphologicalContourInterpolation/README.md b/Modules/Filtering/MorphologicalContourInterpolation/README.md new file mode 100644 index 00000000000..85a42f69010 --- /dev/null +++ b/Modules/Filtering/MorphologicalContourInterpolation/README.md @@ -0,0 +1,34 @@ +# MorphologicalContourInterpolation + +In-tree ITK module providing filters that interpolate manually +segmented anatomical contours through volumetric label data, using +morphological reconstruction techniques. The result is a 3D label +mask reconstructed from a sparse set of 2D contours drawn on +arbitrary slices. + +The flagship class is `itk::MorphologicalContourInterpolator`. + +## Origin + +Ingested from the standalone remote module +[**KitwareMedical/ITKMorphologicalContourInterpolation**](https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation) +on 2026-05-04 via the v4 ingestion pipeline. The upstream repository +will be archived read-only after this PR merges; it remains +reachable at the URL above for historical reference (including the +`examples/`, `wasm/`, and `doc/` directories which were intentionally +left in the upstream archive). + +## Test dependency on RLEImage + +This module's tests `TEST_DEPENDS` on `RLEImage` (also in-tree at +`Modules/Filtering/RLEImage/`). Setting both +`Module_MorphologicalContourInterpolation:BOOL=ON` and +`Module_RLEImage:BOOL=ON` enables the full test set; with only the +former the module library still builds and is usable, but the +RLEImage-flavored tests are not configured. + +## References + +- Zukić D., Vlašić-Cicvarić I., Beichel R.R., Sonka M., Hodgdon T., + Aylward S. *Interpolation of label maps from morphological contour + data.* The Insight Journal. 2016. From 53cedb6d58d41f58b50d298eb9dae910eeb13237 Mon Sep 17 00:00:00 2001 From: "Hans J. Johnson" Date: Mon, 4 May 2026 16:52:08 -0500 Subject: [PATCH 173/176] COMP: Remove MorphologicalContourInterpolation .remote.cmake (in-tree) --- ...hologicalContourInterpolation.remote.cmake | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 Modules/Remote/MorphologicalContourInterpolation.remote.cmake diff --git a/Modules/Remote/MorphologicalContourInterpolation.remote.cmake b/Modules/Remote/MorphologicalContourInterpolation.remote.cmake deleted file mode 100644 index fc263538f24..00000000000 --- a/Modules/Remote/MorphologicalContourInterpolation.remote.cmake +++ /dev/null @@ -1,62 +0,0 @@ -#-- # Grading Level Criteria Report -#-- EVALUATION DATE: 2020-03-24 -#-- EVALUATORS: [Dženan Zukić] -#-- -#-- ## Compliance level 5 star (AKA ITK main modules, or remote modules that could become core modules) -#-- - [ ] Widespread community dependance -#-- - [ ] Above 90% code coverage -#-- - [X] CI dashboards and testing monitored rigorously -#-- - [X] Key API features are exposed in wrapping interface -#-- - [ ] All requirements of Levels 4,3,2,1 -#-- -#-- ## Compliance Level 4 star (Very high-quality code, perhaps small community dependance) -#-- - [X] Meets all ITK code style standards -#-- - [X] No external requirements beyond those needed by ITK proper -#-- - [X] Builds and passes tests on all supported platforms within 1 month of each core tagged release -#-- - [X] Windows Shared Library Build with Visual Studio -#-- - [X] Mac with clang compiller -#-- - [X] Linux with gcc compiler -#-- - [X] Active developer community dedicated to maintaining code-base -#-- - [ ] 75% code coverage demonstrated for testing suite -#-- - [X] Continuous integration testing performed -#-- - [X] All requirements of Levels 3,2,1 -#-- -#-- ## Compliance Level 3 star (Quality beta code) -#-- - [X] API | executable interface is considered mostly stable and feature complete -#-- - [X] 10% C0-code coverage demonstrated for testing suite -#-- - [X] Some tests exist and pass on at least some platform -#-- - [X] All requirements of Levels 2,1 -#-- -#-- ## Compliance Level 2 star (Alpha code feature API development or niche community/execution environment dependance ) -#-- - [X] Compiles for at least 1 niche set of execution envirionments, and perhaps others -#-- (may depend on specific external tools like a java environment, or specific external libraries to work ) -#-- - [X] All requirements of Levels 1 -#-- -#-- ## Compliance Level 1 star (Pre-alpha features under development and code of unknown quality) -#-- - [X] Code complies on at least 1 platform -#-- -#-- ## Compliance Level 0 star ( Code/Feature of known poor-quality or deprecated status ) -#-- - [ ] Code reviewed and explicitly identified as not recommended for use -#-- -#-- ### Please document here any justification for the criteria above -# Code style enforced by clang-format on 2020-02-19, and clang-tidy modernizations completed - -# Contact: Dženan Zukić -itk_fetch_module( - MorphologicalContourInterpolation - "nD morphological contour interpolation - -Insight Journal article: -https://doi.org/10.54294/achtrg - -An ITK-based implementation of morphological contour interpolation based off the paper: -Albu AB, Beugeling T, Laurendeau D. -'A morphology-based approach for interslice interpolation of anatomical slices from volumetric images.' -IEEE Trans Biomed Eng. 2008 Aug;55(8):2022-38. doi: 10.1109/TBME.2008.921158. - -This work is supported by NIH grant R01 EB014346 -'Continued development and maintenance of the ITK-SNAP 3D image segmentation software'." - MODULE_COMPLIANCE_LEVEL 3 - GIT_REPOSITORY https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation.git - GIT_TAG 75c256e066e92aad42f02792218eacebf2ae13f5 - ) From 31a6904a733fb3d31694217099f0461e273f5451 Mon Sep 17 00:00:00 2001 From: "Hans J. Johnson" Date: Mon, 4 May 2026 16:52:09 -0500 Subject: [PATCH 174/176] ENH: Enable Module_MorphologicalContourInterpolation in configure-ci --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 9f1dd62bf5b..ad9c7f162ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ cmd = '''cmake -DModule_SplitComponents:BOOL=ON -DModule_IOMeshMZ3:BOOL=ON -DModule_IOFDF:BOOL=ON + -DModule_MorphologicalContourInterpolation:BOOL=ON -DModule_RLEImage:BOOL=ON -DITK_COMPUTER_MEMORY_SIZE:STRING=11 -DModule_StructuralSimilarity:BOOL=ON''' From 23bcfbffd399e46a09a2690ea5887420b9896117 Mon Sep 17 00:00:00 2001 From: "Hans J. Johnson" Date: Tue, 5 May 2026 19:49:11 -0500 Subject: [PATCH 175/176] COMP: Drop dead boilerplate from MorphologicalContourInterpolation CMakeLists Removes cmake_minimum_required, CXX_STANDARD policing, and the standalone-build wrapper that the in-tree module never uses. --- .../CMakeLists.txt | 40 +------------------ 1 file changed, 1 insertion(+), 39 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt index 086aea7e99d..effa52b1bde 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt +++ b/Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt @@ -1,43 +1,5 @@ -cmake_minimum_required(VERSION 3.16.3) - -if(POLICY CMP0135) - cmake_policy(SET CMP0135 NEW) -endif() - -if(CMAKE_CXX_STANDARD EQUAL "11") - message( - FATAL_ERROR - "CMAKE_CXX_STANDARD:STRING=11 is not supported in ITK version 5.3 and greater." - ) -endif() - -if(NOT CMAKE_CXX_STANDARD) - if(WASI OR EMSCRIPTEN) - set(CMAKE_CXX_STANDARD 20) # Supported values are ``14``, ``17``, and ``20``. - else() - set(CMAKE_CXX_STANDARD 17) # Supported values are ``14``, ``17``, and ``20``. - endif() -endif() -if(NOT CMAKE_CXX_STANDARD_REQUIRED) - set(CMAKE_CXX_STANDARD_REQUIRED ON) -endif() -if(NOT CMAKE_CXX_EXTENSIONS) - set(CMAKE_CXX_EXTENSIONS OFF) -endif() - project(MorphologicalContourInterpolation) -if(NOT ITK_SOURCE_DIR) - find_package(ITK REQUIRED) - list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR}) - include(ITKModuleExternal) - if(WASI OR EMSCRIPTEN) - set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - add_subdirectory(wasm) - endif() -else() - set(ITK_DIR ${CMAKE_BINARY_DIR}) - itk_module_impl() -endif() +itk_module_impl() itk_module_examples() From fb04c62c3b3e2123ae8f694ad79e28e73b8a9e6c Mon Sep 17 00:00:00 2001 From: "Hans J. Johnson" Date: Wed, 6 May 2026 19:07:41 -0500 Subject: [PATCH 176/176] BUG: Replace thread_local SmartPointers with local variables in MCI thread_local ITK SmartPointers in template functions crash on MSVC at program shutdown: ITK thread-pool workers destroy their thread_local objects after ITK's reference-count infrastructure is partially torn down. The per-thread caching is unnecessary given ITKv5's threading model; local variables are correct and the allocation overhead is negligible relative to the filter computations. --- .../itkMorphologicalContourInterpolator.hxx | 50 ++++++++----------- 1 file changed, 22 insertions(+), 28 deletions(-) diff --git a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx index 216d0752b25..7676f577bbb 100644 --- a/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx +++ b/Modules/Filtering/MorphologicalContourInterpolation/include/itkMorphologicalContourInterpolator.hxx @@ -264,33 +264,27 @@ MorphologicalContourInterpolator::Dilate1(typename BoolSliceType::Pointe using CrossDilateType = BinaryDilateImageFilter; using BallDilateType = BinaryDilateImageFilter; - thread_local bool initialized = false; - thread_local typename CrossDilateType::Pointer crossDilator = CrossDilateType::New(); - thread_local typename BallDilateType::Pointer ballDilator = BallDilateType::New(); - thread_local CrossStructuringElementType crossStructuringElement; - thread_local BallStructuringElementType ballStructuringElement; + typename CrossDilateType::Pointer crossDilator = CrossDilateType::New(); + typename BallDilateType::Pointer ballDilator = BallDilateType::New(); + CrossStructuringElementType crossStructuringElement; + BallStructuringElementType ballStructuringElement; using AndFilterType = AndImageFilter; - thread_local typename AndFilterType::Pointer andFilter = AndFilterType::New(); + typename AndFilterType::Pointer andFilter = AndFilterType::New(); - if (!initialized) // make sure these non-trivial operations are executed only once per thread - { - andFilter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - using SizeType = Size; - SizeType size; - size.Fill(1); - - crossDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - crossStructuringElement.SetRadius(size); - crossStructuringElement.CreateStructuringElement(); - crossDilator->SetKernel(crossStructuringElement); + andFilter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + using SizeType = Size; + SizeType size; + size.Fill(1); - ballDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive - ballStructuringElement.SetRadius(size); - ballStructuringElement.CreateStructuringElement(); - ballDilator->SetKernel(ballStructuringElement); + crossDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + crossStructuringElement.SetRadius(size); + crossStructuringElement.CreateStructuringElement(); + crossDilator->SetKernel(crossStructuringElement); - initialized = true; - } + ballDilator->SetNumberOfWorkUnits(1); // excessive threading is counterproductive + ballStructuringElement.SetRadius(size); + ballStructuringElement.CreateStructuringElement(); + ballDilator->SetKernel(ballStructuringElement); typename BoolSliceType::Pointer temp; if (m_UseBallStructuringElement) @@ -355,7 +349,7 @@ MorphologicalContourInterpolator::FindMedianImageDilations(typename Bool // generate union of transition sequences using OrType = OrImageFilter; - thread_local typename OrType::Pointer orFilter = OrType::New(); + typename OrType::Pointer orFilter = OrType::New(); orFilter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive std::vector seq; @@ -393,7 +387,7 @@ MorphologicalContourInterpolator::MaurerDM(typename BoolSliceType::Point typename FloatSliceType::Pointer { using FilterType = itk::SignedMaurerDistanceMapImageFilter; - thread_local typename FilterType::Pointer filter = FilterType::New(); + typename FilterType::Pointer filter = FilterType::New(); filter->SetUseImageSpacing(false); // interpolation algorithm calls for working in index space filter->SetNumberOfWorkUnits(1); // excessive threading is counterproductive filter->SetInput(mask); @@ -496,8 +490,8 @@ MorphologicalContourInterpolator::FindMedianImageDistances(typename Bool // threshold at distance bestBin is the median intersection using FloatBinarizerType = BinaryThresholdImageFilter; using AndFilterType = AndImageFilter; - thread_local typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); - thread_local typename AndFilterType::Pointer andFilter = AndFilterType::New(); + typename FloatBinarizerType::Pointer threshold = FloatBinarizerType::New(); + typename AndFilterType::Pointer andFilter = AndFilterType::New(); // excessive threading is counterproductive threshold->SetNumberOfWorkUnits(1); andFilter->SetNumberOfWorkUnits(1); @@ -656,7 +650,7 @@ MorphologicalContourInterpolator::Interpolate1to1(int // create intersection using AndSliceType = AndImageFilter; - thread_local typename AndSliceType::Pointer sAnd = AndSliceType::New(); + typename AndSliceType::Pointer sAnd = AndSliceType::New(); sAnd->SetNumberOfWorkUnits(1); // excessive threading is counterproductive sAnd->SetInput(0, iSlice); sAnd->SetInput(1, jSlice);