From cd34d75d207c09feb5cb48c14a24d8dac1439667 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 29 Dec 2013 22:14:30 -0500
Subject: [PATCH 01/73] ENH: First commit

---
 Modules/IO/IOMeshSTL/CMakeLists.txt           |   3 +
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   | 152 ++++++++++
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  76 +++++
 Modules/IO/IOMeshSTL/itk-module.cmake         |  16 ++
 Modules/IO/IOMeshSTL/src/CMakeLists.txt       |  18 ++
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 270 ++++++++++++++++++
 .../IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx  |  47 +++
 ...lData_MD5_2327dbe1884cbf2b58071501567400f6 |  56 ++++
 ...lData_MD5_545c2293b16e250f25395dabbaa53cbb | 226 +++++++++++++++
 .../IO/IOMeshSTL/test/Baseline/sphere.stl.md5 |   1 +
 .../IO/IOMeshSTL/test/Baseline/sphere.vtk.md5 |   1 +
 Modules/IO/IOMeshSTL/test/CMakeLists.txt      |  14 +
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  64 +++++
 13 files changed, 944 insertions(+)
 create mode 100644 Modules/IO/IOMeshSTL/CMakeLists.txt
 create mode 100644 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
 create mode 100644 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
 create mode 100644 Modules/IO/IOMeshSTL/itk-module.cmake
 create mode 100644 Modules/IO/IOMeshSTL/src/CMakeLists.txt
 create mode 100644 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
 create mode 100644 Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/CMakeLists.txt
 create mode 100644 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
new file mode 100644
index 00000000000..da161c7c69d
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -0,0 +1,3 @@
+project(ITKIOSTLMesh)
+set(ITKIOSTLMesh_LIBRARIES ITKIOSTLMesh)
+itk_module_impl()
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
new file mode 100644
index 00000000000..78f60a237a6
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -0,0 +1,152 @@
+/*=========================================================================
+ *
+ *  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 __itkSTLMeshIO_h
+#define __itkSTLMeshIO_h
+
+#include "itkMeshIOBase.h"
+
+#include <fstream>
+
+namespace itk
+{
+/** \class STLMeshIO
+ * \brief This class defines how to read and write STL file format.
+ *
+ * \author Luis Ibanez, Kitware Inc.
+ * \ingroup IOFilters
+ * \ingroup ITKIOMesh
+ */
+class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
+{
+public:
+  /** Standard "Self" typedef. */
+  typedef STLMeshIO                Self;
+  typedef MeshIOBase               Superclass;
+  typedef SmartPointer<Self>       Pointer;
+  typedef SmartPointer<const Self> ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(STLMeshIO, MeshIOBase);
+
+  /**-------- This part of the interfaces deals with reading data. ----- */
+
+  /** Determine if the file can be read with this MeshIO implementation.
+   * \param FileNameToRead The name of the file to test for reading.
+   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \return Returns true if this MeshIO can read the file specified.
+   */
+  virtual bool
+  CanReadFile(const char * FileNameToRead);
+
+  /** Read the content of the file into a Mesh. */
+  virtual void
+  Read();
+
+  /** Set the spacing and dimension information for the set filename. */
+  virtual void
+  ReadMeshInformation();
+
+  /** Reads the data from disk into the memory buffer provided. */
+  virtual void
+  ReadPoints(void * buffer);
+
+  virtual void
+  ReadCells(void * buffer);
+
+  /** STL files do not carry information in points or cells.
+   * Therefore the following two methods are implemented as null
+   * operations. */
+  virtual void
+  ReadPointData(void * itkNotUsed(buffer)) {};
+  virtual void
+  ReadCellData(void * itkNotUsed(buffer)) {};
+
+  /*-------- This part of the interfaces deals with writing data. ----- */
+  /** Determine if the file can be written with this MeshIO implementation.
+   * \param FileNameToWrite The name of the file to test for writing.
+   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \return Returns true if this MeshIO can write the file specified.
+   */
+  virtual bool
+  CanWriteFile(const char * FileNameToWrite);
+
+  /** Write header of the STL file */
+  virtual void
+  WriteMeshInformation();
+
+  /** Write the content of the Mesh into an STL file. */
+  virtual void
+  Write();
+
+  /** The STL format stores point coordinates repeatedly as part of every
+   * triangle. Therefore point coordinates are writen as part of the
+   * WriteCells() method, and not as an independent operation.
+   * Consequently, this method is implemented as a null operation.
+   */
+  virtual void
+  WritePoints(void * itkNotUsed(buffer)) {};
+
+  /** The WriteCells() method does most of the work. It writes
+   * out every triangle in the mesh. For every triangle, it
+   * writes out its normal, followed by the coordinates of its
+   * three vertices.
+   *
+   * A typical cell looks as follows in an ASCII STL file
+   *
+   *        facet normal 0.357406 0.862856 0.357406
+   *         outer loop
+   *          vertex 0 1 0
+   *          vertex 0 0.707107 0.707107
+   *          vertex 0.707107 0.707107 0
+   *         endloop
+   *        endfacet
+   *
+   */
+  virtual void
+  WriteCells(void * buffer);
+
+  /** STL files do not carry information in points or cells.
+   * Therefore the following two methods are implemented as null
+   * operations. */
+  virtual void
+  WritePointData(void * itkNotUsed(buffer)) {};
+  virtual void
+  WriteCellData(void * itkNotUsed(buffer)) {};
+
+
+protected:
+  STLMeshIO();
+  virtual ~STLMeshIO() {}
+
+  void
+  PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+  STLMeshIO(const Self &); // purposely not implemented
+  void
+  operator=(const Self &); // purposely not implemented
+
+  std::ofstream m_OutputStream; // output file
+  std::ifstream m_InputStream;  // input file
+};
+} // end namespace itk
+
+#endif // __itkSTLMeshIO_h
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
new file mode 100644
index 00000000000..0e675d3c99a
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -0,0 +1,76 @@
+/*=========================================================================
+ *
+ *  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 __itkSTLMeshIOFactory_h
+#define __itkSTLMeshIOFactory_h
+#include "ITKIOMeshExport.h"
+
+#include "itkObjectFactoryBase.h"
+#include "itkMeshIOBase.h"
+
+namespace itk
+{
+/** \class STLMeshIOFactory
+ * \brief Create instances of STLMeshIO objects using an object factory.
+ * \ingroup ITKIOMesh
+ */
+class ITKIOMesh_EXPORT STLMeshIOFactory : public ObjectFactoryBase
+{
+public:
+  /** Standard class typedefs. */
+  typedef STLMeshIOFactory         Self;
+  typedef ObjectFactoryBase        Superclass;
+  typedef SmartPointer<Self>       Pointer;
+  typedef SmartPointer<const Self> ConstPointer;
+
+  /** Class methods used to interface with the registered factories. */
+  virtual const char *
+  GetITKSourceVersion(void) const;
+
+  virtual const char *
+  GetDescription(void) const;
+
+  /** Method for class instantiation. */
+  itkFactorylessNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(STLMeshIOFactory, ObjectFactoryBase);
+
+  /** Register one factory of this type  */
+  static void
+  RegisterOneFactory(void)
+  {
+    STLMeshIOFactory::Pointer vtkFactory = STLMeshIOFactory::New();
+
+    ObjectFactoryBase::RegisterFactory(vtkFactory);
+  }
+
+protected:
+  STLMeshIOFactory();
+  ~STLMeshIOFactory();
+
+  virtual void
+  PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+  STLMeshIOFactory(const Self &); // purposely not implemented
+  void
+  operator=(const Self &); // purposely not implemented
+};
+} // end namespace itk
+
+#endif
diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
new file mode 100644
index 00000000000..71b7119180c
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -0,0 +1,16 @@
+set(
+  DOCUMENTATION
+  "This module contains classes for reading and writing
+QuadEdgeMeshes using the STL file format."
+)
+itk_module(
+  ITKIOSTLMesh
+  ENABLE_SHARED
+  DEPENDS
+    ITKCommon
+    ITKIOMesh
+  TEST_DEPENDS
+    ITKTestKernel
+    ITKQuadEdgeMesh
+  DESCRIPTION "${DOCUMENTATION}"
+)
diff --git a/Modules/IO/IOMeshSTL/src/CMakeLists.txt b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
new file mode 100644
index 00000000000..f96ff34d4c9
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
@@ -0,0 +1,18 @@
+set(
+  ITKIOSTLMesh_SRC
+  itkSTLMeshIO.cxx
+  itkSTLMeshIOFactory.cxx
+)
+
+add_library(
+  ITKIOSTLMesh
+  ${ITK_LIBRARY_BUILD_TYPE}
+  ${ITKIOSTLMesh_SRC}
+)
+target_link_libraries(
+  ITKIOSTLMesh
+  ${ITKCommon_LIBRARIES}
+  ${ITKIOMesh_LIBRARIES}
+)
+
+itk_module_target(ITKIOSTLMesh)
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
new file mode 100644
index 00000000000..03a79cf7872
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -0,0 +1,270 @@
+/*=========================================================================
+ *
+ *  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 "itkSTLMeshIO.h"
+#include "itkMetaDataObject.h"
+
+#include <itksys/SystemTools.hxx>
+#include <fstream>
+
+namespace itk
+{
+// Constructor
+STLMeshIO ::STLMeshIO() { this->AddSupportedWriteExtension(".stl"); }
+
+bool
+STLMeshIO ::CanReadFile(const char * fileName)
+{
+  if (!itksys::SystemTools::FileExists(fileName, true))
+  {
+    return false;
+  }
+
+  if (itksys::SystemTools::GetFilenameLastExtension(fileName) != ".stl")
+  {
+    return false;
+  }
+
+  return true;
+}
+
+bool
+STLMeshIO ::CanWriteFile(const char * fileName)
+{
+  if (itksys::SystemTools::GetFilenameLastExtension(fileName) != ".stl")
+  {
+    return false;
+  }
+
+  return true;
+}
+
+void
+STLMeshIO ::Read()
+{}
+
+void
+STLMeshIO ::ReadMeshInformation()
+{
+
+  // Use default filetype
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
+  }
+  else if (GetFileType() == BINARY)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
+  }
+
+  if (!this->m_InputStream.is_open())
+  {
+    itkExceptionMacro("Unable to open file\n"
+                      "inputFilename= "
+                      << this->m_FileName);
+    return;
+  }
+
+
+  std::string inputLine;
+
+  // Read STL header file(the first line)
+  std::getline(this->m_InputStream, inputLine, '\n');
+
+  // Determine file type
+  if (inputLine.find("solid") != std::string::npos)
+  {
+    if (this->GetFileType() != ASCII)
+    {
+      this->SetFileType(ASCII);
+#ifdef _WIN32
+      this->m_InputStream.close();
+      this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
+      if (!this->m_InputStream.is_open())
+      {
+        itkExceptionMacro("Unable to open file\n"
+                          "inputFilename= "
+                          << this->m_FileName);
+        return;
+      }
+#endif
+    }
+  }
+  else if (inputLine.find("BINARY") != std::string::npos)
+  {
+    if (this->GetFileType() != BINARY)
+    {
+      this->SetFileType(BINARY);
+#ifdef _WIN32
+      this->m_InputStream.close();
+      this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
+      if (!this->m_InputStream.is_open())
+      {
+        itkExceptionMacro("Unable to open file\n"
+                          "inputFilename= "
+                          << this->m_FileName);
+        return;
+      }
+#endif
+    }
+  }
+
+
+  this->m_InputStream.close();
+}
+
+void
+STLMeshIO ::ReadPoints(void * itkNotUsed(buffer))
+{
+  // Read input file
+
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
+  }
+  else if (GetFileType() == BINARY)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
+  }
+
+  // Test whether the file has been opened
+  if (!this->m_InputStream.is_open())
+  {
+    itkExceptionMacro("Unable to open file\n"
+                      "inputFilename= "
+                      << this->m_FileName);
+    return;
+  }
+
+  this->m_InputStream.close();
+}
+
+void
+STLMeshIO ::ReadCells(void * itkNotUsed(buffer))
+{
+  // Read input file
+  std::ifstream inputFile;
+
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
+  }
+  else if (GetFileType() == BINARY)
+  {
+    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
+  }
+
+  // Test whether the file has been opened
+  if (!this->m_InputStream.is_open())
+  {
+    itkExceptionMacro(<< "Unable to open file\n"
+                         "inputFilename= "
+                      << this->m_FileName);
+    return;
+  }
+
+  this->m_InputStream.close();
+}
+
+
+void
+STLMeshIO ::WriteMeshInformation()
+{
+
+  // Use default filetype
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_OutputStream.open(this->m_FileName.c_str(), std::ios::out);
+  }
+  else if (this->GetFileType() == BINARY)
+  {
+    this->m_OutputStream.open(this->m_FileName.c_str(), std::ios::out | std::ios::binary);
+  }
+
+  if (!this->m_OutputStream.is_open())
+  {
+    itkExceptionMacro("Unable to open file\n"
+                      "inputFilename= "
+                      << this->m_FileName);
+    return;
+  }
+
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_OutputStream << "solid ascii" << std::endl;
+  }
+}
+
+
+void
+STLMeshIO ::Write()
+{}
+
+void
+STLMeshIO ::WriteCells(void * buffer)
+{
+
+  IdentifierType numberOfPolygons = this->GetNumberOfCells();
+
+  IdentifierType * cellsBuffer = reinterpret_cast<IdentifierType *>(buffer);
+
+  SizeValueType index = 0;
+
+  typedef MeshIOBase::CellGeometryType CellGeometryType;
+
+  std::cout << "numberOfPolygons " << numberOfPolygons << std::endl;
+
+  for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
+  {
+    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
+    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
+
+    const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+
+    if (isTriangle)
+    {
+      std::cout << "POLYGON_CELL with " << numberOfVerticesInCell << " vertices " << std::endl;
+      this->m_OutputStream << "  facet normal" << std::endl;
+      this->m_OutputStream << "    outer loop" << std::endl;
+      for (unsigned int jj = 0; jj < numberOfVerticesInCell; jj++)
+      {
+        this->m_OutputStream << "      vertex " << cellsBuffer[index++] << std::endl;
+      }
+      this->m_OutputStream << "    endloop" << std::endl;
+      this->m_OutputStream << "  endfacet" << std::endl;
+    }
+    else
+    {
+      index += numberOfVerticesInCell;
+    }
+  }
+
+  if (this->GetFileType() == ASCII)
+  {
+    this->m_OutputStream << "endsolid" << std::endl;
+  }
+}
+
+
+void
+STLMeshIO ::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+}
+
+} // end of namespace itk
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
new file mode 100644
index 00000000000..fcc8c647d99
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
@@ -0,0 +1,47 @@
+/*=========================================================================
+ *
+ *  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 "itkSTLMeshIO.h"
+#include "itkSTLMeshIOFactory.h"
+#include "itkVersion.h"
+
+namespace itk
+{
+void
+STLMeshIOFactory ::PrintSelf(std::ostream &, Indent) const
+{}
+
+STLMeshIOFactory ::STLMeshIOFactory()
+{
+  this->RegisterOverride("itkMeshIOBase", "itkSTLMeshIO", "STL IO", 1, CreateObjectFunction<STLMeshIO>::New());
+}
+
+STLMeshIOFactory ::~STLMeshIOFactory() {}
+
+const char *
+STLMeshIOFactory ::GetITKSourceVersion(void) const
+{
+  return ITK_SOURCE_VERSION;
+}
+
+const char *
+STLMeshIOFactory ::GetDescription() const
+{
+  return "STL MeshIO Factory, allows the loading of STL QuadEdgeMesh data into ITK";
+}
+} // end namespace itk
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6 b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
new file mode 100644
index 00000000000..38a77c65d0e
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
@@ -0,0 +1,56 @@
+# vtk DataFile Version 2.0
+File written by itkVTKPolyDataWriter
+ASCII
+DATASET POLYDATA
+POINTS 18 float
+1 0 0
+-1 0 0
+0 1 0
+0 -1 0
+0 0 1
+0 0 -1
+0 0.707107 0.707107
+0.707107 0 0.707107
+0.707107 0.707107 0
+-0.707107 0.707107 0
+-0.707107 0 0.707107
+-0.707107 -0.707107 0
+0 -0.707107 0.707107
+0.707107 -0.707107 0
+0 0.707107 -0.707107
+0.707107 0 -0.707107
+-0.707107 0 -0.707107
+0 -0.707107 -0.707107
+POLYGONS 32 128
+3 2 6 8
+3 6 4 7
+3 7 0 8
+3 6 7 8
+3 2 9 6
+3 9 1 10
+3 10 4 6
+3 9 10 6
+3 1 11 10
+3 11 3 12
+3 12 4 10
+3 11 12 10
+3 4 12 7
+3 12 3 13
+3 13 0 7
+3 12 13 7
+3 5 14 15
+3 14 2 8
+3 8 0 15
+3 14 8 15
+3 2 14 9
+3 14 5 16
+3 16 1 9
+3 14 16 9
+3 5 17 16
+3 17 3 11
+3 11 1 16
+3 17 11 16
+3 5 15 17
+3 15 0 13
+3 13 3 17
+3 15 13 17
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
new file mode 100644
index 00000000000..7af8c1d6e28
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
@@ -0,0 +1,226 @@
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diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5 b/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
new file mode 100644
index 00000000000..3e9f76652ae
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
@@ -0,0 +1 @@
+545c2293b16e250f25395dabbaa53cbb
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5 b/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
new file mode 100644
index 00000000000..44f4f16d7bd
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
@@ -0,0 +1 @@
+2327dbe1884cbf2b58071501567400f6
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
new file mode 100644
index 00000000000..a05deb71c1a
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -0,0 +1,14 @@
+itk_module_test()
+
+set(ITKIOSTLMeshTests itkSTLMeshIOTest.cxx)
+
+createtestdriver(ITKIOSTLMesh "${ITKIOSTLMesh-Test_LIBRARIES}" "${ITKIOSTLMeshTests}")
+
+itk_add_test(
+  NAME itkSTLMeshIOTest00
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/sphere.vtk}
+    ${ITK_TEST_OUTPUT_DIR}/sphere00.stl
+)
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
new file mode 100644
index 00000000000..1618f95e0c8
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -0,0 +1,64 @@
+/*=========================================================================
+ *
+ *  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 "itkQuadEdgeMesh.h"
+#include "itkSTLMeshIOFactory.h"
+#include "itkMeshFileReader.h"
+#include "itkMeshFileWriter.h"
+
+int
+itkSTLMeshIOTest(int argc, char * argv[])
+{
+  if (argc < 3)
+  {
+    std::cerr << "Invalid commands, You need input and output mesh file name " << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  const unsigned int Dimension = 3;
+  typedef float      PixelType;
+
+  typedef itk::QuadEdgeMesh<PixelType, Dimension> QEMeshType;
+
+  itk::STLMeshIOFactory::RegisterOneFactory();
+
+  typedef itk::MeshFileReader<QEMeshType> ReaderType;
+  typedef itk::MeshFileWriter<QEMeshType> WriterType;
+
+  ReaderType::Pointer reader = ReaderType::New();
+  WriterType::Pointer writer = WriterType::New();
+
+  reader->SetFileName(argv[1]);
+  writer->SetFileName(argv[2]);
+
+  writer->SetInput(reader->GetOutput());
+
+  int result = EXIT_SUCCESS;
+
+  try
+  {
+    writer->Update();
+  }
+  catch (itk::ExceptionObject & excp)
+  {
+    std::cerr << excp << std::endl;
+    result = EXIT_FAILURE;
+  }
+
+  return result;
+}

From 6ba7e6d9e6dac17c7a806bdfa906d5d71fa42281 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Mon, 30 Dec 2013 12:24:15 -0500
Subject: [PATCH 02/73] DOC: Added the Apache 2.0 License file.

---
 Modules/IO/IOMeshSTL/LICENSE | 202 +++++++++++++++++++++++++++++++++++
 1 file changed, 202 insertions(+)
 create mode 100644 Modules/IO/IOMeshSTL/LICENSE

diff --git a/Modules/IO/IOMeshSTL/LICENSE b/Modules/IO/IOMeshSTL/LICENSE
new file mode 100644
index 00000000000..d6456956733
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/LICENSE
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
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+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
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+   6. Trademarks. This License does not grant permission to use the trade
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+
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+
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+
+       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,
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From 3f1e6dfa312cc3c06a7ecfd03c380a3a978e705b Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Mon, 30 Dec 2013 13:47:38 -0500
Subject: [PATCH 03/73] ENH: First working version.

Added internal copy of points in WritePoints(). Added computation
of normal and print out of point coordinates in WriteCells().

Produced first successful write out of the sphere.stl file, and
was able to open it with meshlab.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 15 +++++-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 55 +++++++++++++++++----
 2 files changed, 59 insertions(+), 11 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 78f60a237a6..99477e3d589 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -99,10 +99,11 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   /** The STL format stores point coordinates repeatedly as part of every
    * triangle. Therefore point coordinates are writen as part of the
    * WriteCells() method, and not as an independent operation.
-   * Consequently, this method is implemented as a null operation.
+   * Consequently, this method only performs an internal copy of the Point
+   * coordinates data, than then is used in the WriteCells() method.
    */
   virtual void
-  WritePoints(void * itkNotUsed(buffer)) {};
+  WritePoints(void * buffer);
 
   /** The WriteCells() method does most of the work. It writes
    * out every triangle in the mesh. For every triangle, it
@@ -146,6 +147,16 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 
   std::ofstream m_OutputStream; // output file
   std::ifstream m_InputStream;  // input file
+
+  typedef float PointValueType; // type to represent point coordinates
+
+  typedef Point<PointValueType, 3>           PointType;
+  typedef Vector<PointValueType, 3>          VectorType;
+  typedef CovariantVector<PointValueType, 3> NormalType;
+
+  typedef std::vector<PointType> PointContainerType;
+
+  PointContainerType m_Points;
 };
 } // end namespace itk
 
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 03a79cf7872..7c404652d39 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -215,19 +215,45 @@ void
 STLMeshIO ::Write()
 {}
 
+void
+STLMeshIO ::WritePoints(void * buffer)
+{
+  const IdentifierType numberOfPoints = this->GetNumberOfPoints();
+
+  // Revisit this choice. Although.. STL will only manage 3D.
+  // This probably should throw and exception if the input Mesh is not in 3D space.
+  const unsigned int PointDimension = 3;
+
+  typedef float PointValueType; // FIXME Revisit this choice. It should be read from the MetaData.
+
+  const PointValueType * pointCoordinates = reinterpret_cast<const PointValueType *>(buffer);
+
+  this->m_Points.clear();
+
+  this->m_Points.resize(numberOfPoints);
+
+  for (IdentifierType pi = 0; pi < numberOfPoints; ++pi)
+  {
+    for (unsigned int i = 0; i < PointDimension; ++i)
+    {
+      m_Points[pi][i] = *pointCoordinates++;
+    }
+  }
+}
+
 void
 STLMeshIO ::WriteCells(void * buffer)
 {
 
-  IdentifierType numberOfPolygons = this->GetNumberOfCells();
+  const IdentifierType numberOfPolygons = this->GetNumberOfCells();
 
-  IdentifierType * cellsBuffer = reinterpret_cast<IdentifierType *>(buffer);
+  const IdentifierType * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
 
   SizeValueType index = 0;
 
   typedef MeshIOBase::CellGeometryType CellGeometryType;
 
-  std::cout << "numberOfPolygons " << numberOfPolygons << std::endl;
+  NormalType normal;
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
@@ -238,13 +264,24 @@ STLMeshIO ::WriteCells(void * buffer)
 
     if (isTriangle)
     {
-      std::cout << "POLYGON_CELL with " << numberOfVerticesInCell << " vertices " << std::endl;
-      this->m_OutputStream << "  facet normal" << std::endl;
+      const PointType & p0 = m_Points[cellsBuffer[index++]];
+      const PointType & p1 = m_Points[cellsBuffer[index++]];
+      const PointType & p2 = m_Points[cellsBuffer[index++]];
+
+      const VectorType v10(p0 - p1);
+      const VectorType v12(p2 - p1);
+
+      CrossProduct(normal, v10, v12);
+
+      this->m_OutputStream << "  facet normal ";
+      this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;
+
       this->m_OutputStream << "    outer loop" << std::endl;
-      for (unsigned int jj = 0; jj < numberOfVerticesInCell; jj++)
-      {
-        this->m_OutputStream << "      vertex " << cellsBuffer[index++] << std::endl;
-      }
+
+      this->m_OutputStream << "      vertex " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
+      this->m_OutputStream << "      vertex " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
+      this->m_OutputStream << "      vertex " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
+
       this->m_OutputStream << "    endloop" << std::endl;
       this->m_OutputStream << "  endfacet" << std::endl;
     }

From de9dea291d012c7dc86a6fed386d7ef6c1f10a68 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 11:04:26 -0500
Subject: [PATCH 04/73] ENH: WritePoints now templated on coordinate type.

Introduced a templated function to manage the multiple cases of
point coordinate types.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 32 +++++++++
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 78 +++++++++++++++------
 2 files changed, 90 insertions(+), 20 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 99477e3d589..69e34abcf23 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -140,6 +140,38 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   void
   PrintSelf(std::ostream & os, Indent indent) const;
 
+  /** Templated version of write points method, that is aware of the specific
+   * type used to represent the point coordinates. */
+  template <typename PointValueType>
+  void
+  WritePointsTyped(const PointValueType * buffer)
+  {
+
+    const unsigned int pointDimension = this->GetPointDimension();
+
+    if (pointDimension != 3)
+    {
+      itkExceptionMacro("STL only supports 3D points");
+    }
+
+    const PointValueType * pointCoordinates = buffer;
+
+    this->m_Points.clear();
+
+    const IdentifierType numberOfPoints = this->GetNumberOfPoints();
+
+    this->m_Points.resize(numberOfPoints);
+
+    for (IdentifierType pi = 0; pi < numberOfPoints; ++pi)
+    {
+      for (unsigned int i = 0; i < pointDimension; ++i)
+      {
+        m_Points[pi][i] = *pointCoordinates++;
+      }
+    }
+  }
+
+
 private:
   STLMeshIO(const Self &); // purposely not implemented
   void
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 7c404652d39..b2a290aa45c 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -25,7 +25,11 @@
 namespace itk
 {
 // Constructor
-STLMeshIO ::STLMeshIO() { this->AddSupportedWriteExtension(".stl"); }
+STLMeshIO ::STLMeshIO()
+{
+  this->AddSupportedWriteExtension(".stl");
+  this->AddSupportedWriteExtension(".STL");
+}
 
 bool
 STLMeshIO ::CanReadFile(const char * fileName)
@@ -35,7 +39,9 @@ STLMeshIO ::CanReadFile(const char * fileName)
     return false;
   }
 
-  if (itksys::SystemTools::GetFilenameLastExtension(fileName) != ".stl")
+  const std::string extension = itksys::SystemTools::GetFilenameLastExtension(fileName);
+
+  if (extension != ".stl" && extension != ".STL")
   {
     return false;
   }
@@ -213,34 +219,66 @@ STLMeshIO ::WriteMeshInformation()
 
 void
 STLMeshIO ::Write()
-{}
+{
+  // All has been done in the WriteCells() method.
+
+  // Here we only need to close the output stream.
+  m_OutputStream.close();
+}
 
 void
 STLMeshIO ::WritePoints(void * buffer)
 {
-  const IdentifierType numberOfPoints = this->GetNumberOfPoints();
 
-  // Revisit this choice. Although.. STL will only manage 3D.
-  // This probably should throw and exception if the input Mesh is not in 3D space.
-  const unsigned int PointDimension = 3;
+  const IOComponentType pointValueType = this->GetPointComponentType();
 
-  typedef float PointValueType; // FIXME Revisit this choice. It should be read from the MetaData.
-
-  const PointValueType * pointCoordinates = reinterpret_cast<const PointValueType *>(buffer);
-
-  this->m_Points.clear();
-
-  this->m_Points.resize(numberOfPoints);
-
-  for (IdentifierType pi = 0; pi < numberOfPoints; ++pi)
+  switch (pointValueType)
   {
-    for (unsigned int i = 0; i < PointDimension; ++i)
-    {
-      m_Points[pi][i] = *pointCoordinates++;
-    }
+    case UCHAR:
+      this->WritePointsTyped(reinterpret_cast<unsigned char *>(buffer));
+      break;
+    case CHAR:
+      this->WritePointsTyped(reinterpret_cast<const char *>(buffer));
+      break;
+    case USHORT:
+      this->WritePointsTyped(reinterpret_cast<const unsigned short *>(buffer));
+      break;
+    case SHORT:
+      this->WritePointsTyped(reinterpret_cast<const short *>(buffer));
+      break;
+    case UINT:
+      this->WritePointsTyped(reinterpret_cast<const unsigned int *>(buffer));
+      break;
+    case INT:
+      this->WritePointsTyped(reinterpret_cast<const int *>(buffer));
+      break;
+    case ULONG:
+      this->WritePointsTyped(reinterpret_cast<const unsigned long *>(buffer));
+      break;
+    case LONG:
+      this->WritePointsTyped(reinterpret_cast<const long *>(buffer));
+      break;
+    case ULONGLONG:
+      this->WritePointsTyped(reinterpret_cast<const unsigned long long *>(buffer));
+      break;
+    case LONGLONG:
+      this->WritePointsTyped(reinterpret_cast<const long long *>(buffer));
+      break;
+    case FLOAT:
+      this->WritePointsTyped(reinterpret_cast<const float *>(buffer));
+      break;
+    case DOUBLE:
+      this->WritePointsTyped(reinterpret_cast<const double *>(buffer));
+      break;
+    case LDOUBLE:
+      this->WritePointsTyped(reinterpret_cast<const long double *>(buffer));
+      break;
+    default:
+      itkExceptionMacro(<< "Unknonwn point component type");
   }
 }
 
+
 void
 STLMeshIO ::WriteCells(void * buffer)
 {

From 1541c87f6ca390d77820dcbd02d875ddbaa45696 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 11:06:28 -0500
Subject: [PATCH 05/73] BUG: Fixed direction of normals.

Still assuming that points are provided in a right handed order.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index b2a290aa45c..1b557875640 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -309,7 +309,7 @@ STLMeshIO ::WriteCells(void * buffer)
       const VectorType v10(p0 - p1);
       const VectorType v12(p2 - p1);
 
-      CrossProduct(normal, v10, v12);
+      CrossProduct(normal, v12, v10);
 
       this->m_OutputStream << "  facet normal ";
       this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;

From 16fee790e9c0d4bc19f924340ca7b4f26afb09d0 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 11:14:07 -0500
Subject: [PATCH 06/73] ENH: Now supporting .STL extension too.

The .STL (in capitals) extension is now supported too in the filename.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 1b557875640..1e241c7c13c 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -52,7 +52,9 @@ STLMeshIO ::CanReadFile(const char * fileName)
 bool
 STLMeshIO ::CanWriteFile(const char * fileName)
 {
-  if (itksys::SystemTools::GetFilenameLastExtension(fileName) != ".stl")
+  const std::string extension = itksys::SystemTools::GetFilenameLastExtension(fileName);
+
+  if (extension != ".stl" && extension != ".STL")
   {
     return false;
   }

From a36cca87e2f7047ea248069d5bac259f744f0e44 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 14:00:25 -0500
Subject: [PATCH 07/73] ENH: Added support for BINARY writing.

And corresponding test.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  10 ++
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 121 ++++++++++++++++--
 Modules/IO/IOMeshSTL/test/CMakeLists.txt      |  11 ++
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  17 ++-
 4 files changed, 146 insertions(+), 13 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 69e34abcf23..999688c53ad 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -188,6 +188,16 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 
   typedef std::vector<PointType> PointContainerType;
 
+  /** Helper functions to write elements to binary file */
+  void
+  WriteInt32AsBinary(int32_t value);
+  void
+  WriteInt16AsBinary(int16_t value);
+  void
+  WriteNormalAsBinary(const NormalType & normal);
+  void
+  WritePointAsBinary(const PointType & point);
+
   PointContainerType m_Points;
 };
 } // end namespace itk
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 1e241c7c13c..59762013843 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -21,6 +21,7 @@
 
 #include <itksys/SystemTools.hxx>
 #include <fstream>
+#include <iomanip>
 
 namespace itk
 {
@@ -75,7 +76,7 @@ STLMeshIO ::ReadMeshInformation()
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
   }
-  else if (GetFileType() == BINARY)
+  else if (this->GetFileType() == BINARY)
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
   }
@@ -145,7 +146,7 @@ STLMeshIO ::ReadPoints(void * itkNotUsed(buffer))
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
   }
-  else if (GetFileType() == BINARY)
+  else if (this->GetFileType() == BINARY)
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
   }
@@ -172,7 +173,7 @@ STLMeshIO ::ReadCells(void * itkNotUsed(buffer))
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
   }
-  else if (GetFileType() == BINARY)
+  else if (this->GetFileType() == BINARY)
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
   }
@@ -216,6 +217,15 @@ STLMeshIO ::WriteMeshInformation()
   {
     this->m_OutputStream << "solid ascii" << std::endl;
   }
+  else if (this->GetFileType() == BINARY)
+  {
+    //
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    // UINT8[80] header
+    //
+    this->m_OutputStream << std::setfill(' ') << std::setw(80) << "binary STL generated from ITK";
+  }
 }
 
 
@@ -295,6 +305,35 @@ STLMeshIO ::WriteCells(void * buffer)
 
   NormalType normal;
 
+  if (this->GetFileType() == BINARY)
+  {
+    //
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    // UINT32 -- Number of Triangles
+    //
+    int32_t numberOfTriangles = 0;
+
+    SizeValueType index2 = 0;
+
+    for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
+    {
+      const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
+      const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
+
+      const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+
+      if (isTriangle)
+      {
+        numberOfTriangles++;
+      }
+
+      index2 += numberOfVerticesInCell;
+    }
+
+    this->WriteInt32AsBinary(numberOfTriangles);
+  }
+
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
     const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
@@ -313,17 +352,38 @@ STLMeshIO ::WriteCells(void * buffer)
 
       CrossProduct(normal, v12, v10);
 
-      this->m_OutputStream << "  facet normal ";
-      this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;
+      if (this->GetFileType() == ASCII)
+      {
+        this->m_OutputStream << "  facet normal ";
+        this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;
 
-      this->m_OutputStream << "    outer loop" << std::endl;
+        this->m_OutputStream << "    outer loop" << std::endl;
 
-      this->m_OutputStream << "      vertex " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
-      this->m_OutputStream << "      vertex " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
-      this->m_OutputStream << "      vertex " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
+        this->m_OutputStream << "      vertex " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
+        this->m_OutputStream << "      vertex " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
+        this->m_OutputStream << "      vertex " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
 
-      this->m_OutputStream << "    endloop" << std::endl;
-      this->m_OutputStream << "  endfacet" << std::endl;
+        this->m_OutputStream << "    endloop" << std::endl;
+        this->m_OutputStream << "  endfacet" << std::endl;
+      }
+      else if (this->GetFileType() == BINARY)
+      {
+        //
+        // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+        //
+        //    foreach triangle
+        //    REAL32[3] – Normal vector
+        //    REAL32[3] – Vertex 1
+        //    REAL32[3] – Vertex 2
+        //    REAL32[3] – Vertex 3
+        //    UINT16 – Attribute byte count
+        //
+        this->WriteNormalAsBinary(normal);
+        this->WritePointAsBinary(p0);
+        this->WritePointAsBinary(p1);
+        this->WritePointAsBinary(p2);
+        this->WriteInt16AsBinary(0);
+      }
     }
     else
     {
@@ -335,6 +395,45 @@ STLMeshIO ::WriteCells(void * buffer)
   {
     this->m_OutputStream << "endsolid" << std::endl;
   }
+  //
+  // There is no ending section when doing BINARY
+  //
+}
+
+
+void
+STLMeshIO ::WriteInt32AsBinary(int32_t value)
+{
+  this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
+}
+
+
+void
+STLMeshIO ::WriteInt16AsBinary(int16_t value)
+{
+  this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
+}
+
+
+void
+STLMeshIO ::WriteNormalAsBinary(const NormalType & normal)
+{
+  for (unsigned int i = 0; i < 3; ++i)
+  {
+    const float value = normal[i];
+    this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
+  }
+}
+
+
+void
+STLMeshIO ::WritePointAsBinary(const PointType & point)
+{
+  for (unsigned int i = 0; i < 3; ++i)
+  {
+    const float value = point[i];
+    this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
+  }
 }
 
 
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
index a05deb71c1a..3255ce93f9c 100644
--- a/Modules/IO/IOMeshSTL/test/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -11,4 +11,15 @@ itk_add_test(
     itkSTLMeshIOTest
     DATA{Baseline/sphere.vtk}
     ${ITK_TEST_OUTPUT_DIR}/sphere00.stl
+    0 # write in ASCII
+)
+
+itk_add_test(
+  NAME itkSTLMeshIOTest01
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/sphere.vtk}
+    ${ITK_TEST_OUTPUT_DIR}/sphere01.stl
+    1 # write in BINARY
 )
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 1618f95e0c8..366bd9a75ae 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -24,9 +24,11 @@
 int
 itkSTLMeshIOTest(int argc, char * argv[])
 {
-  if (argc < 3)
+  if (argc < 4)
   {
-    std::cerr << "Invalid commands, You need input and output mesh file name " << std::endl;
+    std::cerr << "Missing Arguments." << std::endl;
+    std::cerr << "Usage: " << std::endl;
+    std::cerr << "inputMesh outputMesh (0:ASCII/1:BINARY) " << std::endl;
     return EXIT_FAILURE;
   }
 
@@ -46,6 +48,17 @@ itkSTLMeshIOTest(int argc, char * argv[])
   reader->SetFileName(argv[1]);
   writer->SetFileName(argv[2]);
 
+  int fileMode = atoi(argv[3]);
+
+  if (fileMode == 0)
+  {
+    writer->SetFileTypeAsASCII();
+  }
+  else if (fileMode == 1)
+  {
+    writer->SetFileTypeAsBINARY();
+  }
+
   writer->SetInput(reader->GetOutput());
 
   int result = EXIT_SUCCESS;

From 083f42d7b0f6e9bb14f73d908141bf80b46ee0d9 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 18:41:37 -0500
Subject: [PATCH 08/73] ENH: Improved code coverage.

---
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 366bd9a75ae..83b0d8a5d7a 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -18,6 +18,7 @@
 
 #include "itkQuadEdgeMesh.h"
 #include "itkSTLMeshIOFactory.h"
+#include "itkSTLMeshIO.h"
 #include "itkMeshFileReader.h"
 #include "itkMeshFileWriter.h"
 
@@ -73,5 +74,12 @@ itkSTLMeshIOTest(int argc, char * argv[])
     result = EXIT_FAILURE;
   }
 
+  //
+  //  Exercising additional methods
+  //
+  itk::STLMeshIO::Pointer meshIO = itk::STLMeshIO::New();
+
+  meshIO->Print(std::cout);
+
   return result;
 }

From 3d51c322a7089d788a6f43925dc626821c7ce4e6 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 21:37:05 -0500
Subject: [PATCH 09/73] ENH: Started to do parsing on Read.

Parsed input file both in ASCII and BINARY,
stored points into an std::set.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h |  59 ++++++
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 212 +++++++++++++++++++-
 Modules/IO/IOMeshSTL/test/CMakeLists.txt    |  20 ++
 3 files changed, 290 insertions(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 999688c53ad..4810c0d2a78 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -21,6 +21,7 @@
 #include "itkMeshIOBase.h"
 
 #include <fstream>
+#include <set>
 
 namespace itk
 {
@@ -180,6 +181,8 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   std::ofstream m_OutputStream; // output file
   std::ifstream m_InputStream;  // input file
 
+  std::string m_InputLine; // helper during reading
+
   typedef float PointValueType; // type to represent point coordinates
 
   typedef Point<PointValueType, 3>           PointType;
@@ -198,7 +201,63 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   void
   WritePointAsBinary(const PointType & point);
 
+  /** Helper functions to read elements from ASCII and BINARY files. */
+  void
+  ReadMeshInternalFromAscii();
+  void
+  ReadMeshInternalFromBinary();
+
+  /** Helper functions to read elements from binary file */
+  void
+  ReadInt32AsBinary(int32_t & value);
+  void
+  ReadInt16AsBinary(int16_t & value);
+  void
+  ReadNormalAsBinary(NormalType & normal);
+  void
+  ReadPointAsBinary(PointType & point);
+
+  /** Helper functions to read elements from ASCII files. */
+  void
+  ReadStringFromAscii(const std::string & keyword);
+  void
+  ReadPointAsAscii(PointType & point);
+  bool
+  CheckStringFromAscii(const std::string & expected);
+
+  /** Functions to create set of points and disambiguate them. */
+  void
+  InsertPointIntoSet(const PointType & point);
+
   PointContainerType m_Points;
+
+  unsigned int m_InputLineNumber;
+
+  static double
+  PointHash(const PointType & point)
+  {
+    double hash = 0;
+    double factor = 1e10;
+    hash = static_cast<double>(point[0]);
+    hash *= factor;
+    hash += static_cast<double>(point[1]);
+    hash *= factor;
+    hash += static_cast<double>(point[2]);
+    return hash;
+  }
+
+  struct PointCompare
+  {
+    bool
+    operator()(const PointType & p1, const PointType & p2) const
+    {
+      return PointHash(p1) < PointHash(p2);
+    }
+  };
+
+  typedef std::set<PointType, PointCompare> PointSetType;
+
+  PointSetType m_PointsSet;
 };
 } // end namespace itk
 
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 59762013843..d5b55f4ecb9 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -113,8 +113,10 @@ STLMeshIO ::ReadMeshInformation()
       }
 #endif
     }
+
+    this->ReadMeshInternalFromAscii();
   }
-  else if (inputLine.find("BINARY") != std::string::npos)
+  else
   {
     if (this->GetFileType() != BINARY)
     {
@@ -131,12 +133,131 @@ STLMeshIO ::ReadMeshInformation()
       }
 #endif
     }
+
+    this->ReadMeshInternalFromBinary();
   }
 
 
   this->m_InputStream.close();
 }
 
+
+void
+STLMeshIO ::ReadMeshInternalFromAscii()
+{
+  // Read all the points, and reduce them to unique ones
+  std::string inputLine;
+  PointType   p0;
+  PointType   p1;
+  PointType   p2;
+
+  this->m_InputLineNumber = 2;
+
+  while (!this->CheckStringFromAscii("endsolid"))
+  {
+    //
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    //  facet normal ni nj nk
+    //      outer loop
+    //          vertex v1x v1y v1z
+    //          vertex v2x v2y v2z
+    //          vertex v3x v3y v3z
+    //      endloop
+    //  endfacet
+    //
+    this->ReadStringFromAscii("facet normal");
+    this->ReadStringFromAscii("outer loop");
+    this->ReadPointAsAscii(p0);
+    this->ReadPointAsAscii(p1);
+    this->ReadPointAsAscii(p2);
+    this->ReadStringFromAscii("endloop");
+    this->ReadStringFromAscii("endfacet");
+  }
+}
+
+
+void
+STLMeshIO ::ReadStringFromAscii(const std::string & expected)
+{
+  if (this->m_InputLine.empty())
+  {
+    std::getline(this->m_InputStream, this->m_InputLine, '\n');
+  }
+
+  if (this->m_InputLine.find(expected) == std::string::npos)
+  {
+    itkExceptionMacro("Parsing error: missed " << expected << " in line " << this->m_InputLineNumber
+                                               << " found: " << this->m_InputLine);
+  }
+
+  this->m_InputLine.clear();
+
+  this->m_InputLineNumber++;
+}
+
+
+bool
+STLMeshIO ::CheckStringFromAscii(const std::string & expected)
+{
+  std::getline(this->m_InputStream, this->m_InputLine, '\n');
+
+  if (this->m_InputLine.find(expected) != std::string::npos)
+  {
+    this->m_InputLineNumber++;
+    return true;
+  }
+
+  return false;
+}
+
+
+void
+STLMeshIO ::ReadMeshInternalFromBinary()
+{
+  //
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  // UINT8[80] header
+  //
+  char header[80];
+  this->m_InputStream.read(header, 80);
+
+  //
+  // UINT32 -- Number of Triangles
+  //
+  int32_t numberOfTriangles;
+  this->m_InputStream.read(reinterpret_cast<char *>(&numberOfTriangles), sizeof(numberOfTriangles));
+
+  this->SetNumberOfCells(numberOfTriangles);
+
+  //
+  // foreach triangle
+  //
+  NormalType normal;
+  PointType  p0;
+  PointType  p1;
+  PointType  p2;
+  int16_t    bytecount;
+
+  while (numberOfTriangles--)
+  {
+    //
+    //    REAL32[3] – Normal vector
+    //    REAL32[3] – Vertex 1
+    //    REAL32[3] – Vertex 2
+    //    REAL32[3] – Vertex 3
+    //    UINT16 – Attribute byte count
+    //
+    this->ReadNormalAsBinary(normal);
+    this->ReadPointAsBinary(p0);
+    this->ReadPointAsBinary(p1);
+    this->ReadPointAsBinary(p2);
+    this->ReadInt16AsBinary(bytecount);
+  }
+}
+
+
 void
 STLMeshIO ::ReadPoints(void * itkNotUsed(buffer))
 {
@@ -437,6 +558,95 @@ STLMeshIO ::WritePointAsBinary(const PointType & point)
 }
 
 
+void
+STLMeshIO ::ReadNormalAsBinary(NormalType & normal)
+{
+  float value;
+  for (unsigned int i = 0; i < 3; ++i)
+  {
+    this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+    normal[i] = value;
+  }
+}
+
+
+void
+STLMeshIO ::ReadInt32AsBinary(int32_t & value)
+{
+  this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+}
+
+
+void
+STLMeshIO ::ReadInt16AsBinary(int16_t & value)
+{
+  this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+}
+
+
+void
+STLMeshIO ::ReadPointAsBinary(PointType & point)
+{
+  float value;
+  for (unsigned int i = 0; i < 3; ++i)
+  {
+    this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+    point[i] = value;
+  }
+}
+
+
+void
+STLMeshIO ::ReadPointAsAscii(PointType & point)
+{
+  std::string keywword;
+  this->m_InputStream >> keywword;
+
+  if (keywword.find("vertex") == std::string::npos)
+  {
+    itkExceptionMacro("Parsing error: missed 'vertex' in line " << this->m_InputLineNumber);
+  }
+
+  this->m_InputStream >> point;
+
+  this->InsertPointIntoSet(point);
+
+  // read remaining of the line, most often just the end of line.
+  std::string restOfLine;
+  std::getline(this->m_InputStream, restOfLine, '\n');
+
+  this->m_InputLineNumber++;
+}
+
+
+void
+STLMeshIO ::InsertPointIntoSet(const PointType & point)
+{
+  //
+  // combines the FLOAT32 bits components of points into a hash
+  //
+  const unsigned int size = sizeof(float);
+
+  char pointHash[3 * size];
+
+  float valueX = point[0];
+  float valueY = point[1];
+  float valueZ = point[2];
+
+  char * destination = pointHash;
+
+  strncpy(destination, reinterpret_cast<char *>(&valueX), size);
+  destination += size;
+
+  strncpy(destination, reinterpret_cast<char *>(&valueY), size);
+  destination += size;
+
+  strncpy(destination, reinterpret_cast<char *>(&valueZ), size);
+
+  this->m_PointsSet.insert(point);
+}
+
+
 void
 STLMeshIO ::PrintSelf(std::ostream & os, Indent indent) const
 {
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
index 3255ce93f9c..5af678e7718 100644
--- a/Modules/IO/IOMeshSTL/test/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -23,3 +23,23 @@ itk_add_test(
     ${ITK_TEST_OUTPUT_DIR}/sphere01.stl
     1 # write in BINARY
 )
+
+itk_add_test(
+  NAME itkSTLMeshIOTest02
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/sphere.stl}
+    ${ITK_TEST_OUTPUT_DIR}/sphere02.stl
+    0 # write in ASCII
+)
+
+itk_add_test(
+  NAME itkSTLMeshIOTest03
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/sphere.stl}
+    ${ITK_TEST_OUTPUT_DIR}/sphere03.stl
+    1 # write in BINARY
+)

From 3931da9bbf3e72ea6ee4c6962f34886a317bdf64 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Tue, 31 Dec 2013 22:18:36 -0500
Subject: [PATCH 10/73] ENH: Added structure for list of Cells and point Ids.

Added an std::vector to hold, for each cell, the triplet of point Ids
corresponding to the vertices of that particular triangle. Related the
pointIds to positions in the std::set that de-duplicates points.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 17 +++++++++++++-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 25 +++++++++++++++++----
 2 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 4810c0d2a78..bd19924876a 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -256,8 +256,23 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   };
 
   typedef std::set<PointType, PointCompare> PointSetType;
+  typedef PointSetType::iterator            PointSetIterator;
+  typedef std::pair<PointSetIterator, bool> PointSetResultType;
+  typedef std::vector<PointSetIterator>     PointsVectorType;
 
-  PointSetType m_PointsSet;
+  PointSetType     m_PointsSet;
+  PointsVectorType m_PointsVector;
+
+  // Helper variable to put Ids in points as they are read
+  IdentifierType m_LatestPointId;
+
+  // Triplet to hold the Ids of points in a triagle as they are being read
+  typedef IdentifierType TripletType[3];
+  TripletType            m_TrianglePointIds;
+  unsigned int           m_PointInTriangleCounter;
+
+  typedef std::vector<TripletType> CellsVectorType;
+  CellsVectorType                  m_CellsVector;
 };
 } // end namespace itk
 
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index d5b55f4ecb9..8eb7fa504e3 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -166,6 +166,8 @@ STLMeshIO ::ReadMeshInternalFromAscii()
     //      endloop
     //  endfacet
     //
+    this->m_PointInTriangleCounter = 0;
+
     this->ReadStringFromAscii("facet normal");
     this->ReadStringFromAscii("outer loop");
     this->ReadPointAsAscii(p0);
@@ -173,6 +175,8 @@ STLMeshIO ::ReadMeshInternalFromAscii()
     this->ReadPointAsAscii(p2);
     this->ReadStringFromAscii("endloop");
     this->ReadStringFromAscii("endfacet");
+
+    // this->m_CellsVector.push_back( this->m_TrianglePointIds );
   }
 }
 
@@ -249,11 +253,15 @@ STLMeshIO ::ReadMeshInternalFromBinary()
     //    REAL32[3] – Vertex 3
     //    UINT16 – Attribute byte count
     //
+    this->m_PointInTriangleCounter = 0;
+
     this->ReadNormalAsBinary(normal);
     this->ReadPointAsBinary(p0);
     this->ReadPointAsBinary(p1);
     this->ReadPointAsBinary(p2);
     this->ReadInt16AsBinary(bytecount);
+
+    // this->m_CellsVector.push_back( this->m_TrianglePointIds );
   }
 }
 
@@ -593,16 +601,18 @@ STLMeshIO ::ReadPointAsBinary(PointType & point)
     this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
     point[i] = value;
   }
+
+  this->InsertPointIntoSet(point);
 }
 
 
 void
 STLMeshIO ::ReadPointAsAscii(PointType & point)
 {
-  std::string keywword;
-  this->m_InputStream >> keywword;
+  std::string keyword;
+  this->m_InputStream >> keyword;
 
-  if (keywword.find("vertex") == std::string::npos)
+  if (keyword.find("vertex") == std::string::npos)
   {
     itkExceptionMacro("Parsing error: missed 'vertex' in line " << this->m_InputLineNumber);
   }
@@ -643,7 +653,14 @@ STLMeshIO ::InsertPointIntoSet(const PointType & point)
 
   strncpy(destination, reinterpret_cast<char *>(&valueZ), size);
 
-  this->m_PointsSet.insert(point);
+  PointSetResultType result = this->m_PointsSet.insert(point);
+
+  if (result.second)
+  {
+    this->m_PointsVector.push_back(result.first);
+    this->m_LatestPointId = this->m_PointsVector.size();
+    this->m_TrianglePointIds[this->m_PointInTriangleCounter++] = this->m_LatestPointId;
+  }
 }
 
 

From 07370d20a647b657a3d700f79f9ccf9e76ce9822 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Wed, 1 Jan 2014 11:42:16 -0500
Subject: [PATCH 11/73] ENH: Implemented ReadPoints(buffer).

Now package the information about point coordinates into a buffer
that is passed back to the MeshFileReader.

Adjusted the helper data structures that hold the pointIds and the
iterators to unique points in the a point set.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h |  27 ++++-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 115 +++++++++++++-------
 2 files changed, 95 insertions(+), 47 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index bd19924876a..a33b8fc565f 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -65,13 +65,22 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   virtual void
   ReadMeshInformation();
 
-  /** Reads the data from disk into the memory buffer provided. */
+  /** Stores the point data into the memory buffer provided. */
   virtual void
   ReadPoints(void * buffer);
 
+  /** Stores the cell data into the memory buffer provided. */
   virtual void
   ReadCells(void * buffer);
 
+  /** Indicates whether ReadPoints() should be called. */
+  virtual bool
+  GetUpdatePoints() const;
+
+  /** Indicates whether ReadCells() should be called. */
+  virtual bool
+  GetUpdateCells() const;
+
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
@@ -133,7 +142,6 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   virtual void
   WriteCellData(void * itkNotUsed(buffer)) {};
 
-
 protected:
   STLMeshIO();
   virtual ~STLMeshIO() {}
@@ -237,7 +245,7 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   PointHash(const PointType & point)
   {
     double hash = 0;
-    double factor = 1e10;
+    double factor = 1e5; // one third of the range of the double mantissa
     hash = static_cast<double>(point[0]);
     hash *= factor;
     hash += static_cast<double>(point[1]);
@@ -267,9 +275,16 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   IdentifierType m_LatestPointId;
 
   // Triplet to hold the Ids of points in a triagle as they are being read
-  typedef IdentifierType TripletType[3];
-  TripletType            m_TrianglePointIds;
-  unsigned int           m_PointInTriangleCounter;
+  class TripletType
+  {
+  public:
+    IdentifierType p0;
+    IdentifierType p1;
+    IdentifierType p2;
+  };
+
+  TripletType  m_TrianglePointIds;
+  unsigned int m_PointInTriangleCounter;
 
   typedef std::vector<TripletType> CellsVectorType;
   CellsVectorType                  m_CellsVector;
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 8eb7fa504e3..877eef97643 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -30,6 +30,13 @@ STLMeshIO ::STLMeshIO()
 {
   this->AddSupportedWriteExtension(".stl");
   this->AddSupportedWriteExtension(".STL");
+
+  // STL uses float type by default to store point data
+  this->SetPointComponentType(FLOAT);
+
+  // STL uses UINT32 to store the number of points,
+  // hence the point Ids are of the same UINT32 type.
+  this->SetCellComponentType(UINT);
 }
 
 bool
@@ -176,8 +183,10 @@ STLMeshIO ::ReadMeshInternalFromAscii()
     this->ReadStringFromAscii("endloop");
     this->ReadStringFromAscii("endfacet");
 
-    // this->m_CellsVector.push_back( this->m_TrianglePointIds );
+    this->m_CellsVector.push_back(this->m_TrianglePointIds);
   }
+
+  this->SetNumberOfPoints(this->m_PointsVector.size());
 }
 
 
@@ -261,37 +270,46 @@ STLMeshIO ::ReadMeshInternalFromBinary()
     this->ReadPointAsBinary(p2);
     this->ReadInt16AsBinary(bytecount);
 
-    // this->m_CellsVector.push_back( this->m_TrianglePointIds );
+    this->m_CellsVector.push_back(this->m_TrianglePointIds);
   }
+
+  this->SetNumberOfPoints(this->m_PointsVector.size());
 }
 
 
 void
-STLMeshIO ::ReadPoints(void * itkNotUsed(buffer))
+STLMeshIO ::ReadPoints(void * buffer)
 {
-  // Read input file
+  //
+  // The Point and Cell data were read in the ReadMeshInformation() method.
+  // Here, we can focus on packaging the point data into the return buffer.
+  //
+  std::cout << "Number of Unique Points = " << this->m_PointsVector.size() << std::endl;
+  PointsVectorType::const_iterator pointItr = this->m_PointsVector.begin();
+  PointsVectorType::const_iterator pointEnd = this->m_PointsVector.end();
 
-  if (this->GetFileType() == ASCII)
-  {
-    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
-  }
-  else if (this->GetFileType() == BINARY)
-  {
-    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
-  }
+  float * pointCoordinates = reinterpret_cast<float *>(buffer);
 
-  // Test whether the file has been opened
-  if (!this->m_InputStream.is_open())
+  while (pointItr != pointEnd)
   {
-    itkExceptionMacro("Unable to open file\n"
-                      "inputFilename= "
-                      << this->m_FileName);
-    return;
-  }
+    // get the iterator to the Set, pointing to a unique Point.
+    PointSetIterator uniquePointItr = *pointItr;
 
-  this->m_InputStream.close();
+    // Get the reference to that PointType object.
+    const PointType & point = *uniquePointItr;
+
+    //
+    // Store the Point coordintes in the buffer.
+    //
+    *pointCoordinates++ = point[0];
+    *pointCoordinates++ = point[1];
+    *pointCoordinates++ = point[2];
+
+    ++pointItr;
+  }
 }
 
+
 void
 STLMeshIO ::ReadCells(void * itkNotUsed(buffer))
 {
@@ -632,38 +650,53 @@ STLMeshIO ::ReadPointAsAscii(PointType & point)
 void
 STLMeshIO ::InsertPointIntoSet(const PointType & point)
 {
-  //
-  // combines the FLOAT32 bits components of points into a hash
-  //
-  const unsigned int size = sizeof(float);
-
-  char pointHash[3 * size];
-
-  float valueX = point[0];
-  float valueY = point[1];
-  float valueZ = point[2];
-
-  char * destination = pointHash;
-
-  strncpy(destination, reinterpret_cast<char *>(&valueX), size);
-  destination += size;
-
-  strncpy(destination, reinterpret_cast<char *>(&valueY), size);
-  destination += size;
-
-  strncpy(destination, reinterpret_cast<char *>(&valueZ), size);
 
   PointSetResultType result = this->m_PointsSet.insert(point);
 
   if (result.second)
   {
     this->m_PointsVector.push_back(result.first);
+
     this->m_LatestPointId = this->m_PointsVector.size();
-    this->m_TrianglePointIds[this->m_PointInTriangleCounter++] = this->m_LatestPointId;
+    switch (this->m_PointInTriangleCounter)
+    {
+      case 0:
+        this->m_TrianglePointIds.p0 = this->m_LatestPointId;
+        break;
+      case 1:
+        this->m_TrianglePointIds.p1 = this->m_LatestPointId;
+        break;
+      case 2:
+        this->m_TrianglePointIds.p2 = this->m_LatestPointId;
+        break;
+      default:
+        itkExceptionMacro("Point counter went beyond value 2");
+    }
+    this->m_PointInTriangleCounter++;
   }
 }
 
 
+bool
+STLMeshIO ::GetUpdatePoints() const
+{
+  // Always true, since we are reading the point information
+  // in ReadMeshInformation(), and we need ReadPoints() to be
+  // called in order to store the point data into the buffer.
+  return true;
+}
+
+
+bool
+STLMeshIO ::GetUpdateCells() const
+{
+  // Always true, since we are reading the cell information
+  // in ReadMeshInformation(), and we need ReadCells() to be
+  // called in order to store the cell data into the buffer.
+  return true;
+}
+
+
 void
 STLMeshIO ::PrintSelf(std::ostream & os, Indent indent) const
 {

From 3abcb31b25f2deeb2ee2ff76551f2c82ab7d7eea Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Wed, 1 Jan 2014 20:08:29 -0500
Subject: [PATCH 12/73] ENH: Implemented ReadCells() method.

Now recomposing the cells information in the buffer that goes back
to the MeshFileReader.

Still have debugging issues with reading enough cells, and confounding
the input points.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 70 ++++++++++++++++-------
 1 file changed, 48 insertions(+), 22 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 877eef97643..d4ff372da3a 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -144,7 +144,6 @@ STLMeshIO ::ReadMeshInformation()
     this->ReadMeshInternalFromBinary();
   }
 
-
   this->m_InputStream.close();
 }
 
@@ -187,6 +186,16 @@ STLMeshIO ::ReadMeshInternalFromAscii()
   }
 
   this->SetNumberOfPoints(this->m_PointsVector.size());
+
+  //
+  // The factor 5 accounts for five integers
+  //  1. cell type id
+  //  2. number of points in cell
+  //  3. point id of point 0
+  //  4. point id of point 1
+  //  5. point id of point 2
+  //
+  this->SetCellBufferSize(5 * this->m_CellsVector.size());
 }
 
 
@@ -273,7 +282,19 @@ STLMeshIO ::ReadMeshInternalFromBinary()
     this->m_CellsVector.push_back(this->m_TrianglePointIds);
   }
 
+  std::cout << "Number of Unique Points = " << this->m_PointsVector.size() << std::endl;
+
   this->SetNumberOfPoints(this->m_PointsVector.size());
+
+  //
+  // The factor 5 accounts for five integers
+  //  1. cell type id
+  //  2. number of points in cell
+  //  3. point id of point 0
+  //  4. point id of point 1
+  //  5. point id of point 2
+  //
+  this->SetCellBufferSize(5 * this->m_CellsVector.size());
 }
 
 
@@ -284,7 +305,6 @@ STLMeshIO ::ReadPoints(void * buffer)
   // The Point and Cell data were read in the ReadMeshInformation() method.
   // Here, we can focus on packaging the point data into the return buffer.
   //
-  std::cout << "Number of Unique Points = " << this->m_PointsVector.size() << std::endl;
   PointsVectorType::const_iterator pointItr = this->m_PointsVector.begin();
   PointsVectorType::const_iterator pointEnd = this->m_PointsVector.end();
 
@@ -311,30 +331,36 @@ STLMeshIO ::ReadPoints(void * buffer)
 
 
 void
-STLMeshIO ::ReadCells(void * itkNotUsed(buffer))
+STLMeshIO ::ReadCells(void * buffer)
 {
-  // Read input file
-  std::ifstream inputFile;
+  //
+  // The Point and Cell data were read in the ReadMeshInformation() method.
+  // Here, we can focus on packaging the cell data into the return buffer.
+  //
+  CellsVectorType::const_iterator cellItr = this->m_CellsVector.begin();
+  CellsVectorType::const_iterator cellEnd = this->m_CellsVector.end();
 
-  if (this->GetFileType() == ASCII)
-  {
-    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
-  }
-  else if (this->GetFileType() == BINARY)
-  {
-    this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
-  }
+  unsigned int * cellPointIds = reinterpret_cast<unsigned int *>(buffer);
 
-  // Test whether the file has been opened
-  if (!this->m_InputStream.is_open())
+  const unsigned int numberOfPointsInCell = 3;
+
+  while (cellItr != cellEnd)
   {
-    itkExceptionMacro(<< "Unable to open file\n"
-                         "inputFilename= "
-                      << this->m_FileName);
-    return;
-  }
 
-  this->m_InputStream.close();
+    *cellPointIds++ = MeshIOBase::TRIANGLE_CELL;
+    *cellPointIds++ = numberOfPointsInCell;
+
+    //
+    // Store the Point Ids for this cell, in the buffer.
+    //
+    *cellPointIds++ = cellItr->p0;
+    *cellPointIds++ = cellItr->p1;
+    *cellPointIds++ = cellItr->p2;
+
+    std::cout << "points " << cellItr->p0 << " " << cellItr->p1 << " " << cellItr->p2 << std::endl;
+
+    ++cellItr;
+  }
 }
 
 
@@ -657,7 +683,7 @@ STLMeshIO ::InsertPointIntoSet(const PointType & point)
   {
     this->m_PointsVector.push_back(result.first);
 
-    this->m_LatestPointId = this->m_PointsVector.size();
+    this->m_LatestPointId = this->m_PointsVector.size() - 1;
     switch (this->m_PointInTriangleCounter)
     {
       case 0:

From d7231a2650c8504a634f90d9ad59d5959da85748 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Fri, 3 Jan 2014 22:09:45 -0500
Subject: [PATCH 13/73] BUG: Fixed STL reading. Added tetrahedron test.

After adding a tetrahedron test, debugged the process of reading and
consolidating incoming vertices. Fixed the reading of STL files.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  8 +--
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 68 ++++++++++---------
 ...lData_MD5_4cd09d26436a53a5adedb33d822cabcd | 14 ++++
 ...lData_MD5_70a19e48a4393776cfe02f852f25cbe1 | 30 ++++++++
 .../test/Baseline/tetrahedron.stl.md5         |  1 +
 .../test/Baseline/tetrahedron.vtk.md5         |  1 +
 Modules/IO/IOMeshSTL/test/CMakeLists.txt      | 40 +++++++++++
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  6 ++
 8 files changed, 131 insertions(+), 37 deletions(-)
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index a33b8fc565f..37a69b8cf72 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -263,13 +263,9 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
     }
   };
 
-  typedef std::set<PointType, PointCompare> PointSetType;
-  typedef PointSetType::iterator            PointSetIterator;
-  typedef std::pair<PointSetIterator, bool> PointSetResultType;
-  typedef std::vector<PointSetIterator>     PointsVectorType;
+  typedef std::map<PointType, IdentifierType, PointCompare> PointsMapType;
 
-  PointSetType     m_PointsSet;
-  PointsVectorType m_PointsVector;
+  PointsMapType m_PointsMap;
 
   // Helper variable to put Ids in points as they are read
   IdentifierType m_LatestPointId;
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index d4ff372da3a..9d3ff7dfd5a 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -159,6 +159,8 @@ STLMeshIO ::ReadMeshInternalFromAscii()
 
   this->m_InputLineNumber = 2;
 
+  this->m_LatestPointId = NumericTraits<IdentifierType>::Zero;
+
   while (!this->CheckStringFromAscii("endsolid"))
   {
     //
@@ -185,7 +187,7 @@ STLMeshIO ::ReadMeshInternalFromAscii()
     this->m_CellsVector.push_back(this->m_TrianglePointIds);
   }
 
-  this->SetNumberOfPoints(this->m_PointsVector.size());
+  this->SetNumberOfPoints(this->m_PointsMap.size());
 
   //
   // The factor 5 accounts for five integers
@@ -245,6 +247,8 @@ STLMeshIO ::ReadMeshInternalFromBinary()
   char header[80];
   this->m_InputStream.read(header, 80);
 
+  this->m_LatestPointId = NumericTraits<IdentifierType>::Zero;
+
   //
   // UINT32 -- Number of Triangles
   //
@@ -282,9 +286,7 @@ STLMeshIO ::ReadMeshInternalFromBinary()
     this->m_CellsVector.push_back(this->m_TrianglePointIds);
   }
 
-  std::cout << "Number of Unique Points = " << this->m_PointsVector.size() << std::endl;
-
-  this->SetNumberOfPoints(this->m_PointsVector.size());
+  this->SetNumberOfPoints(this->m_PointsMap.size());
 
   //
   // The factor 5 accounts for five integers
@@ -305,18 +307,15 @@ STLMeshIO ::ReadPoints(void * buffer)
   // The Point and Cell data were read in the ReadMeshInformation() method.
   // Here, we can focus on packaging the point data into the return buffer.
   //
-  PointsVectorType::const_iterator pointItr = this->m_PointsVector.begin();
-  PointsVectorType::const_iterator pointEnd = this->m_PointsVector.end();
+  PointsMapType::const_iterator pointItr = this->m_PointsMap.begin();
+  PointsMapType::const_iterator pointEnd = this->m_PointsMap.end();
 
   float * pointCoordinates = reinterpret_cast<float *>(buffer);
 
   while (pointItr != pointEnd)
   {
-    // get the iterator to the Set, pointing to a unique Point.
-    PointSetIterator uniquePointItr = *pointItr;
-
     // Get the reference to that PointType object.
-    const PointType & point = *uniquePointItr;
+    const PointType & point = pointItr->first;
 
     //
     // Store the Point coordintes in the buffer.
@@ -357,8 +356,6 @@ STLMeshIO ::ReadCells(void * buffer)
     *cellPointIds++ = cellItr->p1;
     *cellPointIds++ = cellItr->p2;
 
-    std::cout << "points " << cellItr->p0 << " " << cellItr->p1 << " " << cellItr->p2 << std::endl;
-
     ++cellItr;
   }
 }
@@ -677,28 +674,37 @@ void
 STLMeshIO ::InsertPointIntoSet(const PointType & point)
 {
 
-  PointSetResultType result = this->m_PointsSet.insert(point);
+  PointsMapType::const_iterator pointMapItr = this->m_PointsMap.find(point);
 
-  if (result.second)
+  IdentifierType pointId = pointMapItr->second;
+
+  if (pointMapItr == this->m_PointsMap.end())
   {
-    this->m_PointsVector.push_back(result.first);
+    this->m_PointsMap[point] = this->m_LatestPointId;
+    pointId = this->m_LatestPointId;
+    this->m_LatestPointId++;
+  }
 
-    this->m_LatestPointId = this->m_PointsVector.size() - 1;
-    switch (this->m_PointInTriangleCounter)
-    {
-      case 0:
-        this->m_TrianglePointIds.p0 = this->m_LatestPointId;
-        break;
-      case 1:
-        this->m_TrianglePointIds.p1 = this->m_LatestPointId;
-        break;
-      case 2:
-        this->m_TrianglePointIds.p2 = this->m_LatestPointId;
-        break;
-      default:
-        itkExceptionMacro("Point counter went beyond value 2");
-    }
-    this->m_PointInTriangleCounter++;
+  switch (this->m_PointInTriangleCounter)
+  {
+    case 0:
+      this->m_TrianglePointIds.p0 = pointId;
+      break;
+    case 1:
+      this->m_TrianglePointIds.p1 = pointId;
+      break;
+    case 2:
+      this->m_TrianglePointIds.p2 = pointId;
+      break;
+    default:
+      itkExceptionMacro("Point counter went beyond value 2");
+  }
+
+  this->m_PointInTriangleCounter++;
+
+  if (this->m_PointInTriangleCounter == 3)
+  {
+    this->m_PointInTriangleCounter = 0;
   }
 }
 
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
new file mode 100644
index 00000000000..9339517655d
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
@@ -0,0 +1,14 @@
+# vtk DataFile Version 2.0
+File written by itkVTKPolyDataWriter
+ASCII
+DATASET POLYDATA
+POINTS 4 float
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+POLYGONS 4 16
+3 0 2 1
+3 0 1 3
+3 0 3 2
+3 1 2 3
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1 b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1
new file mode 100644
index 00000000000..be14d23b637
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1
@@ -0,0 +1,30 @@
+solid ascii
+  facet normal 0 0 -1
+    outer loop
+      vertex 0 0 0
+      vertex 0 1 0
+      vertex 1 0 0
+    endloop
+  endfacet
+  facet normal 0 -1 0
+    outer loop
+      vertex 0 0 0
+      vertex 1 0 0
+      vertex 0 0 1
+    endloop
+  endfacet
+  facet normal -1 0 0
+    outer loop
+      vertex 0 0 0
+      vertex 0 0 1
+      vertex 0 1 0
+    endloop
+  endfacet
+  facet normal 1 1 1
+    outer loop
+      vertex 1 0 0
+      vertex 0 1 0
+      vertex 0 0 1
+    endloop
+  endfacet
+endsolid
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5 b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
new file mode 100644
index 00000000000..78055773cfb
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
@@ -0,0 +1 @@
+70a19e48a4393776cfe02f852f25cbe1
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5 b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5
new file mode 100644
index 00000000000..eea81ea180b
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5
@@ -0,0 +1 @@
+4cd09d26436a53a5adedb33d822cabcd
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
index 5af678e7718..c61d211d72c 100644
--- a/Modules/IO/IOMeshSTL/test/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -43,3 +43,43 @@ itk_add_test(
     ${ITK_TEST_OUTPUT_DIR}/sphere03.stl
     1 # write in BINARY
 )
+
+itk_add_test(
+  NAME itkSTLMeshIOTest04
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/tetrahedron.vtk}
+    ${ITK_TEST_OUTPUT_DIR}/tetrahedron01.stl
+    0 # write in ASCII
+)
+
+itk_add_test(
+  NAME itkSTLMeshIOTest05
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/tetrahedron.vtk}
+    ${ITK_TEST_OUTPUT_DIR}/tetrahedron02.stl
+    1 # write in BINARY
+)
+
+itk_add_test(
+  NAME itkSTLMeshIOTest06
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/tetrahedron.stl}
+    ${ITK_TEST_OUTPUT_DIR}/tetrahedron03.stl
+    0 # write in ASCII
+)
+
+itk_add_test(
+  NAME itkSTLMeshIOTest07
+  COMMAND
+    ITKIOSTLMeshTestDriver
+    itkSTLMeshIOTest
+    DATA{Baseline/tetrahedron.stl}
+    ${ITK_TEST_OUTPUT_DIR}/tetrahedron04.stl
+    1 # write in BINARY
+)
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 83b0d8a5d7a..7f12f84bfb6 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -60,6 +60,12 @@ itkSTLMeshIOTest(int argc, char * argv[])
     writer->SetFileTypeAsBINARY();
   }
 
+  reader->Update();
+  QEMeshType * mesh = reader->GetOutput();
+
+  mesh->Print(std::cout);
+
+
   writer->SetInput(reader->GetOutput());
 
   int result = EXIT_SUCCESS;

From 0ad86235b25aa42f10fb4df55e983eeeaf7b2e0a Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Fri, 3 Jan 2014 23:02:30 -0500
Subject: [PATCH 14/73] ENH: Better Point compare method.

Replaced previous hash, with a more consistent compare method.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 27 ++++++++++-----------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 37a69b8cf72..1a947c00cb1 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -241,25 +241,24 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 
   unsigned int m_InputLineNumber;
 
-  static double
-  PointHash(const PointType & point)
-  {
-    double hash = 0;
-    double factor = 1e5; // one third of the range of the double mantissa
-    hash = static_cast<double>(point[0]);
-    hash *= factor;
-    hash += static_cast<double>(point[1]);
-    hash *= factor;
-    hash += static_cast<double>(point[2]);
-    return hash;
-  }
-
   struct PointCompare
   {
     bool
     operator()(const PointType & p1, const PointType & p2) const
     {
-      return PointHash(p1) < PointHash(p2);
+      if (p1[0] != p2[0])
+      {
+        return p1[0] < p2[0];
+      }
+      else
+      {
+        if (p1[1] != p2[1])
+        {
+          return p1[1] < p2[1];
+        }
+      }
+
+      return p1[2] < p2[2];
     }
   };
 

From 2eb008932416f6f6b42e3a502c8b5f6a133286bc Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Fri, 3 Jan 2014 23:03:36 -0500
Subject: [PATCH 15/73] BUG: Fixed bug. Points must be passed in order.

When transferring points from the Point Map to the points buffer,
the points must be stored in the location indicated by the second
element of the map pairs. Those are the ordered locations of the
points, to which the cell point ids are referring.

Now manage to read and write the sphere.stl file.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 9d3ff7dfd5a..86e26b0c54e 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -310,15 +310,18 @@ STLMeshIO ::ReadPoints(void * buffer)
   PointsMapType::const_iterator pointItr = this->m_PointsMap.begin();
   PointsMapType::const_iterator pointEnd = this->m_PointsMap.end();
 
-  float * pointCoordinates = reinterpret_cast<float *>(buffer);
+  float * pointsBuffer = reinterpret_cast<float *>(buffer);
 
   while (pointItr != pointEnd)
   {
     // Get the reference to that PointType object.
     const PointType & point = pointItr->first;
 
+    // Get the location in the buffer where the point should be stored
+    float * pointCoordinates = pointsBuffer + 3 * pointItr->second;
+
     //
-    // Store the Point coordintes in the buffer.
+    // Store the Point coordinates in the buffer.
     //
     *pointCoordinates++ = point[0];
     *pointCoordinates++ = point[1];

From 4aeac59caefb40c396abcf2dc8c72d3ce3b045eb Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 5 Jan 2014 15:15:07 -0500
Subject: [PATCH 16/73] BUG: Fixed BINARY read.

It was off due to the initial read of the header used to determine
whether the input file is ASCII or BINARY.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 32 +++++++++++++++++------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 86e26b0c54e..a8e9649e953 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -97,13 +97,24 @@ STLMeshIO ::ReadMeshInformation()
   }
 
 
-  std::string inputLine;
-
   // Read STL header file(the first line)
-  std::getline(this->m_InputStream, inputLine, '\n');
+  char headerBuffer[6];
+  this->m_InputStream.read(headerBuffer, 6);
+  this->m_InputStream.seekg(0); // Reset to the beginning of the file.
+
+  headerBuffer[5] = '\0';
+  std::string header(headerBuffer);
+
+  bool inputFileIsASCII = false;
+
+  // Based on the header line define whether the file is ASCII or BINARY
+  if (header.find("solid") != std::string::npos)
+  {
+    inputFileIsASCII = true;
+  }
 
   // Determine file type
-  if (inputLine.find("solid") != std::string::npos)
+  if (inputFileIsASCII)
   {
     if (this->GetFileType() != ASCII)
     {
@@ -152,15 +163,17 @@ void
 STLMeshIO ::ReadMeshInternalFromAscii()
 {
   // Read all the points, and reduce them to unique ones
-  std::string inputLine;
-  PointType   p0;
-  PointType   p1;
-  PointType   p2;
+  PointType p0;
+  PointType p1;
+  PointType p2;
 
   this->m_InputLineNumber = 2;
 
   this->m_LatestPointId = NumericTraits<IdentifierType>::Zero;
 
+  // read header line
+  std::getline(this->m_InputStream, this->m_InputLine, '\n');
+
   while (!this->CheckStringFromAscii("endsolid"))
   {
     //
@@ -247,6 +260,9 @@ STLMeshIO ::ReadMeshInternalFromBinary()
   char header[80];
   this->m_InputStream.read(header, 80);
 
+  header[79] = '\0'; // insert string terminator
+
+
   this->m_LatestPointId = NumericTraits<IdentifierType>::Zero;
 
   //

From 1fe73e6b19185830f603ed410109394a8b6e3ff2 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 12 Jan 2014 09:33:14 -0500
Subject: [PATCH 17/73] DOC: Fixing Doxygen groups.

Added these two classes to the STLMeshIO group.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 1 +
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 1 +
 2 files changed, 2 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 1a947c00cb1..471e4777dbc 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -31,6 +31,7 @@ namespace itk
  * \author Luis Ibanez, Kitware Inc.
  * \ingroup IOFilters
  * \ingroup ITKIOMesh
+ * \ingroup ITKIOSTLMesh
  */
 class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 {
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 0e675d3c99a..bc44447448b 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -27,6 +27,7 @@ namespace itk
 /** \class STLMeshIOFactory
  * \brief Create instances of STLMeshIO objects using an object factory.
  * \ingroup ITKIOMesh
+ * \ingroup ITKIOSTLMesh
  */
 class ITKIOMesh_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {

From 6fd22dbdd9fc1e8e2897a1292c01850fadefeb3f Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 12 Jan 2014 09:34:00 -0500
Subject: [PATCH 18/73] BUG: Now managing Endianness.

The STL format assumes little endianness in the files:

    http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL

Here we introduce conversions between System endianness, and little
endianness when reading and writing in BINARY format.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 51 ++++++++++++++++++++++-
 1 file changed, 49 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index a8e9649e953..3297784b211 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -18,6 +18,7 @@
 
 #include "itkSTLMeshIO.h"
 #include "itkMetaDataObject.h"
+#include "itkByteSwapper.h"
 
 #include <itksys/SystemTools.hxx>
 #include <fstream>
@@ -271,6 +272,12 @@ STLMeshIO ::ReadMeshInternalFromBinary()
   int32_t numberOfTriangles;
   this->m_InputStream.read(reinterpret_cast<char *>(&numberOfTriangles), sizeof(numberOfTriangles));
 
+  //
+  // Binary values in STL files are expected to be in little endian
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&numberOfTriangles);
+
   this->SetNumberOfCells(numberOfTriangles);
 
   //
@@ -593,6 +600,11 @@ STLMeshIO ::WriteCells(void * buffer)
 void
 STLMeshIO ::WriteInt32AsBinary(int32_t value)
 {
+  //
+  // Binary values in STL files are expected to be in little endian
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&value);
   this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
 }
 
@@ -600,6 +612,11 @@ STLMeshIO ::WriteInt32AsBinary(int32_t value)
 void
 STLMeshIO ::WriteInt16AsBinary(int16_t value)
 {
+  //
+  // Binary values in STL files are expected to be in little endian
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  ByteSwapper<int16_t>::SwapFromSystemToLittleEndian(&value);
   this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
 }
 
@@ -609,7 +626,12 @@ STLMeshIO ::WriteNormalAsBinary(const NormalType & normal)
 {
   for (unsigned int i = 0; i < 3; ++i)
   {
-    const float value = normal[i];
+    float value = normal[i];
+    //
+    // Binary values in STL files are expected to be in little endian
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
   }
 }
@@ -620,7 +642,12 @@ STLMeshIO ::WritePointAsBinary(const PointType & point)
 {
   for (unsigned int i = 0; i < 3; ++i)
   {
-    const float value = point[i];
+    float value = point[i];
+    //
+    // Binary values in STL files are expected to be in little endian
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
   }
 }
@@ -633,6 +660,11 @@ STLMeshIO ::ReadNormalAsBinary(NormalType & normal)
   for (unsigned int i = 0; i < 3; ++i)
   {
     this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+    //
+    // Binary values in STL files are expected to be in little endian
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     normal[i] = value;
   }
 }
@@ -642,6 +674,11 @@ void
 STLMeshIO ::ReadInt32AsBinary(int32_t & value)
 {
   this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+  //
+  // Binary values in STL files are expected to be in little endian
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&value);
 }
 
 
@@ -649,6 +686,11 @@ void
 STLMeshIO ::ReadInt16AsBinary(int16_t & value)
 {
   this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+  //
+  // Binary values in STL files are expected to be in little endian
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  ByteSwapper<int16_t>::SwapFromSystemToLittleEndian(&value);
 }
 
 
@@ -659,6 +701,11 @@ STLMeshIO ::ReadPointAsBinary(PointType & point)
   for (unsigned int i = 0; i < 3; ++i)
   {
     this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+    //
+    // Binary values in STL files are expected to be in little endian
+    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    //
+    ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     point[i] = value;
   }
 

From 7bf583057972b51228e01e5eed2cf89c204ce9af Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 12 Jan 2014 09:45:47 -0500
Subject: [PATCH 19/73] ENH: Report the system endianness.

At the end of the test, we now print out the Endianness of the system.
This should be helpful when verifying STL files in BINARY format.
---
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 7f12f84bfb6..76c922be424 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -87,5 +87,18 @@ itkSTLMeshIOTest(int argc, char * argv[])
 
   meshIO->Print(std::cout);
 
+  //
+  //  Report the System Endianness
+  //
+  std::cout << std::endl;
+  if (itk::ByteSwapper<int>::SystemIsLittleEndian())
+  {
+    std::cout << "This system is Little Endian" << std::endl;
+  }
+  else
+  {
+    std::cout << "This system is Big Endian" << std::endl;
+  }
+
   return result;
 }

From 11fcf749c4c2564a6a30de092ed4a79ebf247435 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 12 Jan 2014 10:26:48 -0500
Subject: [PATCH 20/73] ENH: Throwing exception for non-triangle cells.

Suggested in code review by Arnaud Gelas.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 3297784b211..037acbe8d0a 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -523,6 +523,10 @@ STLMeshIO ::WriteCells(void * buffer)
       {
         numberOfTriangles++;
       }
+      else
+      {
+        itkExceptionMacro("Found Non-Triangular Cell.");
+      }
 
       index2 += numberOfVerticesInCell;
     }

From 1cee9a21fdebf9da9a24fbf9a5d664a4a5528c73 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Sun, 12 Jan 2014 10:46:57 -0500
Subject: [PATCH 21/73] ENH: Splitted WriteCells() into BINARY and ASCII.

Splitted the WriteCells() method into BINARY and ASCII cases,
as suggested by Arnaud Gelas in code review.

It makes easier to follow the logic of each individual case.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h |   6 +
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx   | 170 ++++++++++++--------
 2 files changed, 106 insertions(+), 70 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 471e4777dbc..7f76600cdb6 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -234,6 +234,12 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
   bool
   CheckStringFromAscii(const std::string & expected);
 
+  /** Helper function to write cells as ASCII or BINARY. */
+  virtual void
+  WriteCellsAsAscii(void * buffer);
+  virtual void
+  WriteCellsAsBinary(void * buffer);
+
   /** Functions to create set of points and disambiguate them. */
   void
   InsertPointIntoSet(const PointType & point);
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 037acbe8d0a..78c16c7beb9 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -489,6 +489,19 @@ STLMeshIO ::WritePoints(void * buffer)
 
 void
 STLMeshIO ::WriteCells(void * buffer)
+{
+  if (this->GetFileType() == BINARY)
+  {
+    this->WriteCellsAsBinary(buffer);
+  }
+  else
+  {
+    this->WriteCellsAsAscii(buffer);
+  }
+}
+
+void
+STLMeshIO ::WriteCellsAsBinary(void * buffer)
 {
 
   const IdentifierType numberOfPolygons = this->GetNumberOfCells();
@@ -501,38 +514,85 @@ STLMeshIO ::WriteCells(void * buffer)
 
   NormalType normal;
 
-  if (this->GetFileType() == BINARY)
+  //
+  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  //
+  // UINT32 -- Number of Triangles
+  //
+  int32_t numberOfTriangles = 0;
+
+  SizeValueType index2 = 0;
+
+  for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
+  {
+    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
+    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
+
+    const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+
+    if (isTriangle)
+    {
+      numberOfTriangles++;
+    }
+    else
+    {
+      itkExceptionMacro("Found Non-Triangular Cell.");
+    }
+
+    index2 += numberOfVerticesInCell;
+  }
+
+  this->WriteInt32AsBinary(numberOfTriangles);
+
+  for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
+    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
+    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
+
+    const PointType & p0 = m_Points[cellsBuffer[index++]];
+    const PointType & p1 = m_Points[cellsBuffer[index++]];
+    const PointType & p2 = m_Points[cellsBuffer[index++]];
+
+    const VectorType v10(p0 - p1);
+    const VectorType v12(p2 - p1);
+
+    CrossProduct(normal, v12, v10);
+
     //
     // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
-    // UINT32 -- Number of Triangles
+    //    foreach triangle
+    //    REAL32[3] – Normal vector
+    //    REAL32[3] – Vertex 1
+    //    REAL32[3] – Vertex 2
+    //    REAL32[3] – Vertex 3
+    //    UINT16 – Attribute byte count
     //
-    int32_t numberOfTriangles = 0;
+    this->WriteNormalAsBinary(normal);
+    this->WritePointAsBinary(p0);
+    this->WritePointAsBinary(p1);
+    this->WritePointAsBinary(p2);
+    this->WriteInt16AsBinary(0);
+  }
 
-    SizeValueType index2 = 0;
+  //
+  // There is no ending section when doing BINARY
+  //
+}
 
-    for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
-    {
-      const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
-      const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
+void
+STLMeshIO ::WriteCellsAsAscii(void * buffer)
+{
 
-      const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+  const IdentifierType numberOfPolygons = this->GetNumberOfCells();
 
-      if (isTriangle)
-      {
-        numberOfTriangles++;
-      }
-      else
-      {
-        itkExceptionMacro("Found Non-Triangular Cell.");
-      }
+  const IdentifierType * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
 
-      index2 += numberOfVerticesInCell;
-    }
+  SizeValueType index = 0;
 
-    this->WriteInt32AsBinary(numberOfTriangles);
-  }
+  typedef MeshIOBase::CellGeometryType CellGeometryType;
+
+  NormalType normal;
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
@@ -541,65 +601,35 @@ STLMeshIO ::WriteCells(void * buffer)
 
     const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
 
-    if (isTriangle)
+    if (!isTriangle)
     {
-      const PointType & p0 = m_Points[cellsBuffer[index++]];
-      const PointType & p1 = m_Points[cellsBuffer[index++]];
-      const PointType & p2 = m_Points[cellsBuffer[index++]];
+      itkExceptionMacro("Found Non-Triangular Cell.");
+    }
 
-      const VectorType v10(p0 - p1);
-      const VectorType v12(p2 - p1);
+    const PointType & p0 = m_Points[cellsBuffer[index++]];
+    const PointType & p1 = m_Points[cellsBuffer[index++]];
+    const PointType & p2 = m_Points[cellsBuffer[index++]];
 
-      CrossProduct(normal, v12, v10);
+    const VectorType v10(p0 - p1);
+    const VectorType v12(p2 - p1);
 
-      if (this->GetFileType() == ASCII)
-      {
-        this->m_OutputStream << "  facet normal ";
-        this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;
+    CrossProduct(normal, v12, v10);
 
-        this->m_OutputStream << "    outer loop" << std::endl;
+    this->m_OutputStream << "  facet normal ";
+    this->m_OutputStream << normal[0] << " " << normal[1] << " " << normal[2] << std::endl;
 
-        this->m_OutputStream << "      vertex " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
-        this->m_OutputStream << "      vertex " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
-        this->m_OutputStream << "      vertex " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
+    this->m_OutputStream << "    outer loop" << std::endl;
 
-        this->m_OutputStream << "    endloop" << std::endl;
-        this->m_OutputStream << "  endfacet" << std::endl;
-      }
-      else if (this->GetFileType() == BINARY)
-      {
-        //
-        // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
-        //
-        //    foreach triangle
-        //    REAL32[3] – Normal vector
-        //    REAL32[3] – Vertex 1
-        //    REAL32[3] – Vertex 2
-        //    REAL32[3] – Vertex 3
-        //    UINT16 – Attribute byte count
-        //
-        this->WriteNormalAsBinary(normal);
-        this->WritePointAsBinary(p0);
-        this->WritePointAsBinary(p1);
-        this->WritePointAsBinary(p2);
-        this->WriteInt16AsBinary(0);
-      }
-    }
-    else
-    {
-      index += numberOfVerticesInCell;
-    }
-  }
+    this->m_OutputStream << "      vertex " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
+    this->m_OutputStream << "      vertex " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
+    this->m_OutputStream << "      vertex " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
 
-  if (this->GetFileType() == ASCII)
-  {
-    this->m_OutputStream << "endsolid" << std::endl;
+    this->m_OutputStream << "    endloop" << std::endl;
+    this->m_OutputStream << "  endfacet" << std::endl;
   }
-  //
-  // There is no ending section when doing BINARY
-  //
-}
 
+  this->m_OutputStream << "endsolid" << std::endl;
+}
 
 void
 STLMeshIO ::WriteInt32AsBinary(int32_t value)

From 4ab31f249d5cc67b209b8bb6caf5dec3c17d0109 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Thu, 16 Jan 2014 17:14:47 -0500
Subject: [PATCH 22/73] STYLE: Rename module to match ITK standards.

---
 Modules/IO/IOMeshSTL/itk-module.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 71b7119180c..4010b6ecafa 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -4,7 +4,7 @@ set(
 QuadEdgeMeshes using the STL file format."
 )
 itk_module(
-  ITKIOSTLMesh
+  IOSTL
   ENABLE_SHARED
   DEPENDS
     ITKCommon

From 3e42b36c4c44998c75e749c2ef77ec2298027085 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Thu, 16 Jan 2014 17:48:44 -0500
Subject: [PATCH 23/73] ENH: Propagated Module name changes.

To make it consistent in all the CMake infrastructure.
---
 Modules/IO/IOMeshSTL/CMakeLists.txt           |  4 ++--
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  2 +-
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  2 +-
 Modules/IO/IOMeshSTL/src/CMakeLists.txt       | 10 +++++-----
 Modules/IO/IOMeshSTL/test/CMakeLists.txt      | 20 +++++++++----------
 5 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index da161c7c69d..031563575c4 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,3 +1,3 @@
-project(ITKIOSTLMesh)
-set(ITKIOSTLMesh_LIBRARIES ITKIOSTLMesh)
+project(IOSTL)
+set(IOSTL_LIBRARIES IOSTL)
 itk_module_impl()
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 7f76600cdb6..085735640df 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -31,7 +31,7 @@ namespace itk
  * \author Luis Ibanez, Kitware Inc.
  * \ingroup IOFilters
  * \ingroup ITKIOMesh
- * \ingroup ITKIOSTLMesh
+ * \ingroup IOSTL
  */
 class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 {
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index bc44447448b..e55cad44334 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -27,7 +27,7 @@ namespace itk
 /** \class STLMeshIOFactory
  * \brief Create instances of STLMeshIO objects using an object factory.
  * \ingroup ITKIOMesh
- * \ingroup ITKIOSTLMesh
+ * \ingroup IOSTL
  */
 class ITKIOMesh_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
diff --git a/Modules/IO/IOMeshSTL/src/CMakeLists.txt b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
index f96ff34d4c9..685a7312de8 100644
--- a/Modules/IO/IOMeshSTL/src/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
@@ -1,18 +1,18 @@
 set(
-  ITKIOSTLMesh_SRC
+  IOSTL_SRC
   itkSTLMeshIO.cxx
   itkSTLMeshIOFactory.cxx
 )
 
 add_library(
-  ITKIOSTLMesh
+  IOSTL
   ${ITK_LIBRARY_BUILD_TYPE}
-  ${ITKIOSTLMesh_SRC}
+  ${IOSTL_SRC}
 )
 target_link_libraries(
-  ITKIOSTLMesh
+  IOSTL
   ${ITKCommon_LIBRARIES}
   ${ITKIOMesh_LIBRARIES}
 )
 
-itk_module_target(ITKIOSTLMesh)
+itk_module_target(IOSTL)
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
index c61d211d72c..fc19533b77c 100644
--- a/Modules/IO/IOMeshSTL/test/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -1,13 +1,13 @@
 itk_module_test()
 
-set(ITKIOSTLMeshTests itkSTLMeshIOTest.cxx)
+set(IOSTLTests itkSTLMeshIOTest.cxx)
 
-createtestdriver(ITKIOSTLMesh "${ITKIOSTLMesh-Test_LIBRARIES}" "${ITKIOSTLMeshTests}")
+createtestdriver(IOSTL "${IOSTL-Test_LIBRARIES}" "${IOSTLTests}" )
 
 itk_add_test(
   NAME itkSTLMeshIOTest00
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.vtk}
     ${ITK_TEST_OUTPUT_DIR}/sphere00.stl
@@ -17,7 +17,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest01
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.vtk}
     ${ITK_TEST_OUTPUT_DIR}/sphere01.stl
@@ -27,7 +27,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest02
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.stl}
     ${ITK_TEST_OUTPUT_DIR}/sphere02.stl
@@ -37,7 +37,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest03
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.stl}
     ${ITK_TEST_OUTPUT_DIR}/sphere03.stl
@@ -47,7 +47,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest04
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.vtk}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron01.stl
@@ -57,7 +57,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest05
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.vtk}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron02.stl
@@ -67,7 +67,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest06
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.stl}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron03.stl
@@ -77,7 +77,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest07
   COMMAND
-    ITKIOSTLMeshTestDriver
+    IOSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.stl}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron04.stl

From ec2853609884c07ba152639dc4d0c8de2368ff5c Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Thu, 16 Jan 2014 17:53:17 -0500
Subject: [PATCH 24/73] ENH: Removing unused variables.

That before were used to verify that all cells were triangles.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 78c16c7beb9..4a44dc0031b 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -546,9 +546,6 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
-    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
-    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
-
     const PointType & p0 = m_Points[cellsBuffer[index++]];
     const PointType & p1 = m_Points[cellsBuffer[index++]];
     const PointType & p2 = m_Points[cellsBuffer[index++]];

From b9b41ef70965f14c01224ec76aace21245e9cda2 Mon Sep 17 00:00:00 2001
From: Luis Ibanez <luis.ibanez@kitware.com>
Date: Fri, 17 Jan 2014 22:30:16 -0500
Subject: [PATCH 25/73] COMP: Fixing instantiation of templated functions.

To address compilation errors from MacOSX-gcc4.2-Release-IOSTL.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 69 +++++++++++++++++------
 1 file changed, 52 insertions(+), 17 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 4a44dc0031b..3d1f3300b8c 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -443,44 +443,83 @@ STLMeshIO ::WritePoints(void * buffer)
   switch (pointValueType)
   {
     case UCHAR:
-      this->WritePointsTyped(reinterpret_cast<unsigned char *>(buffer));
+    {
+      typedef unsigned char CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case CHAR:
-      this->WritePointsTyped(reinterpret_cast<const char *>(buffer));
+    {
+      typedef char CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case USHORT:
-      this->WritePointsTyped(reinterpret_cast<const unsigned short *>(buffer));
+    {
+      typedef unsigned short CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case SHORT:
-      this->WritePointsTyped(reinterpret_cast<const short *>(buffer));
+    {
+      typedef short CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case UINT:
-      this->WritePointsTyped(reinterpret_cast<const unsigned int *>(buffer));
+    {
+      typedef unsigned int CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case INT:
-      this->WritePointsTyped(reinterpret_cast<const int *>(buffer));
+    {
+      typedef int CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case ULONG:
-      this->WritePointsTyped(reinterpret_cast<const unsigned long *>(buffer));
+    {
+      typedef unsigned long CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case LONG:
-      this->WritePointsTyped(reinterpret_cast<const long *>(buffer));
+    {
+      typedef long CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case ULONGLONG:
-      this->WritePointsTyped(reinterpret_cast<const unsigned long long *>(buffer));
+    {
+      typedef unsigned long long CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case LONGLONG:
-      this->WritePointsTyped(reinterpret_cast<const long long *>(buffer));
+    {
+      typedef long long CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case FLOAT:
-      this->WritePointsTyped(reinterpret_cast<const float *>(buffer));
+    {
+      typedef float CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case DOUBLE:
-      this->WritePointsTyped(reinterpret_cast<const double *>(buffer));
+    {
+      typedef double CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     case LDOUBLE:
-      this->WritePointsTyped(reinterpret_cast<const long double *>(buffer));
+    {
+      typedef long double CoordType;
+      this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
+    }
     default:
       itkExceptionMacro(<< "Unknonwn point component type");
   }
@@ -510,8 +549,6 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   SizeValueType index = 0;
 
-  typedef MeshIOBase::CellGeometryType CellGeometryType;
-
   NormalType normal;
 
   //
@@ -587,8 +624,6 @@ STLMeshIO ::WriteCellsAsAscii(void * buffer)
 
   SizeValueType index = 0;
 
-  typedef MeshIOBase::CellGeometryType CellGeometryType;
-
   NormalType normal;
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)

From 038aafb56fc01219c5bccfea141e609a833ab1e5 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sat, 1 Feb 2014 13:16:07 -0500
Subject: [PATCH 26/73] BUG: Add EXCLUDE_FROM_DEFAULT.

As a Remote Module, EXCLUDE_FROM_DEFAULT needs to be added from the module
being inadvertently turned on in a fresh build after it was downloaded in a
previous build.
---
 Modules/IO/IOMeshSTL/itk-module.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 4010b6ecafa..1c08828db85 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -13,4 +13,5 @@ itk_module(
     ITKTestKernel
     ITKQuadEdgeMesh
   DESCRIPTION "${DOCUMENTATION}"
+  EXCLUDE_FROM_DEFAULT
 )

From c34e0436dc7188885e167513a8ef4c68e0163c71 Mon Sep 17 00:00:00 2001
From: Brian Helba <brian.helba@kitware.com>
Date: Sat, 1 Feb 2014 17:36:03 -0500
Subject: [PATCH 27/73] BUG: Fix WritePointsTyped() to no longer use
 conflicting typenames

"PointValueType" was both the template parmeter of WritePointsTyped() and
a typedef of the enclosing class. This was generating errors with GCC on
OSX. Renamed the template parameter to "TPointsBuffer" to fix this error.

Also added a static_cast to make the conversion to the internal value type
explicit.

Also made the parameter for WritePointsTyped() a const pointer to const
values, to clarify its intended use as an input buffer.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 085735640df..9dd7779d65e 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -152,9 +152,9 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
 
   /** Templated version of write points method, that is aware of the specific
    * type used to represent the point coordinates. */
-  template <typename PointValueType>
+  template <typename TPointsBuffer>
   void
-  WritePointsTyped(const PointValueType * buffer)
+  WritePointsTyped(const TPointsBuffer * const buffer)
   {
 
     const unsigned int pointDimension = this->GetPointDimension();
@@ -164,7 +164,7 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
       itkExceptionMacro("STL only supports 3D points");
     }
 
-    const PointValueType * pointCoordinates = buffer;
+    const TPointsBuffer * pointCoordinates = buffer;
 
     this->m_Points.clear();
 
@@ -176,7 +176,7 @@ class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
     {
       for (unsigned int i = 0; i < pointDimension; ++i)
       {
-        m_Points[pi][i] = *pointCoordinates++;
+        m_Points[pi][i] = static_cast<PointValueType>(*pointCoordinates++);
       }
     }
   }

From 1e52de56536a4e70d0cd1a269231d51568e2a161 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 29 Jun 2014 14:42:36 -0400
Subject: [PATCH 28/73] COMP: Remove duplicate group entry in ITKIOMesh.

---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 2 +-
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 9dd7779d65e..3a5f25e8716 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -29,8 +29,8 @@ namespace itk
  * \brief This class defines how to read and write STL file format.
  *
  * \author Luis Ibanez, Kitware Inc.
+ *
  * \ingroup IOFilters
- * \ingroup ITKIOMesh
  * \ingroup IOSTL
  */
 class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index e55cad44334..984d2bf2a77 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -26,7 +26,7 @@ namespace itk
 {
 /** \class STLMeshIOFactory
  * \brief Create instances of STLMeshIO objects using an object factory.
- * \ingroup ITKIOMesh
+ *
  * \ingroup IOSTL
  */
 class ITKIOMesh_EXPORT STLMeshIOFactory : public ObjectFactoryBase

From 5bac1afd314e3ef14cf291e8f45a4c31e02ce497 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 29 Jun 2014 17:42:28 -0400
Subject: [PATCH 29/73] COMP: Add export definitions to build on Windows with
 shared libs.

---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 4 +++-
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 5 +++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 9dd7779d65e..5afa7829c62 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -18,6 +18,8 @@
 #ifndef __itkSTLMeshIO_h
 #define __itkSTLMeshIO_h
 
+#include "IOSTLExport.h"
+
 #include "itkMeshIOBase.h"
 
 #include <fstream>
@@ -33,7 +35,7 @@ namespace itk
  * \ingroup ITKIOMesh
  * \ingroup IOSTL
  */
-class ITKIOMesh_EXPORT STLMeshIO : public MeshIOBase
+class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 {
 public:
   /** Standard "Self" typedef. */
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index e55cad44334..2bca963f2c6 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -17,7 +17,8 @@
  *=========================================================================*/
 #ifndef __itkSTLMeshIOFactory_h
 #define __itkSTLMeshIOFactory_h
-#include "ITKIOMeshExport.h"
+
+#include "IOSTLExport.h"
 
 #include "itkObjectFactoryBase.h"
 #include "itkMeshIOBase.h"
@@ -29,7 +30,7 @@ namespace itk
  * \ingroup ITKIOMesh
  * \ingroup IOSTL
  */
-class ITKIOMesh_EXPORT STLMeshIOFactory : public ObjectFactoryBase
+class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
 public:
   /** Standard class typedefs. */

From 8468275e8205d165abd274c7799ca2ab9cf0404d Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Fri, 3 Apr 2015 10:53:32 -0400
Subject: [PATCH 30/73] STYLE: Remove __ in header inclusion guards.

These are reserved for compilers.  This addresses the KWStyle failing test.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 6 +++---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 5fa373c0a38..eefb8b08eb6 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -15,8 +15,8 @@
  *  limitations under the License.
  *
  *=========================================================================*/
-#ifndef __itkSTLMeshIO_h
-#define __itkSTLMeshIO_h
+#ifndef itkSTLMeshIO_h
+#define itkSTLMeshIO_h
 
 #include "IOSTLExport.h"
 
@@ -295,4 +295,4 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 };
 } // end namespace itk
 
-#endif // __itkSTLMeshIO_h
+#endif // itkSTLMeshIO_h
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index e90adaa9df5..a0786d7c8f0 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -15,8 +15,8 @@
  *  limitations under the License.
  *
  *=========================================================================*/
-#ifndef __itkSTLMeshIOFactory_h
-#define __itkSTLMeshIOFactory_h
+#ifndef itkSTLMeshIOFactory_h
+#define itkSTLMeshIOFactory_h
 
 #include "IOSTLExport.h"
 

From 77e5f531dcbb97c39c9665089f6845c2a9f009ae Mon Sep 17 00:00:00 2001
From: Bradley Lowekamp <blowekamp@mail.nih.gov>
Date: Mon, 22 Jun 2015 14:08:00 -0400
Subject: [PATCH 31/73] BUG: Fix incorrect output, and invalid memory access

The m_Points array was incorrectly traversed. It's a mix of cellType,
numberOfVerticiesInCells, followed by index into points. The
first two are not correctly being skipped.

This issue was detected by valgrind defects.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 3d1f3300b8c..842a17232a8 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -583,6 +583,9 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
+    // skip cell type and number of vertices in cell
+    index += 2;
+
     const PointType & p0 = m_Points[cellsBuffer[index++]];
     const PointType & p1 = m_Points[cellsBuffer[index++]];
     const PointType & p2 = m_Points[cellsBuffer[index++]];

From 3c52d2174380d809ce1ccff737d7dacb5d6f91d6 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Wed, 4 Nov 2015 21:44:49 -0500
Subject: [PATCH 32/73] ENH: Add external build support.

---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 031563575c4..13a02c5aed0 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,3 +1,11 @@
+cmake_minimum_required(VERSION 2.9)
 project(IOSTL)
 set(IOSTL_LIBRARIES IOSTL)
-itk_module_impl()
+
+if(NOT ITK_SOURCE_DIR)
+  find_package(ITK REQUIRED)
+  list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
+  include(ITKModuleExternal)
+else()
+  itk_module_impl()
+endif()

From 273e537aaf9ddff8e38bddb1588e0671954877c1 Mon Sep 17 00:00:00 2001
From: Davis Vigneault <davis.vigneault@gmail.com>
Date: Fri, 3 Jun 2016 15:11:11 +0100
Subject: [PATCH 33/73] COMP: Address override warnings.

---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 32 ++++++++++-----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index eefb8b08eb6..93dfdc1385b 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -58,7 +58,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can read the file specified.
    */
   virtual bool
-  CanReadFile(const char * FileNameToRead);
+  CanReadFile(const char * FileNameToRead) ITK_OVERRIDE;
 
   /** Read the content of the file into a Mesh. */
   virtual void
@@ -66,31 +66,31 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 
   /** Set the spacing and dimension information for the set filename. */
   virtual void
-  ReadMeshInformation();
+  ReadMeshInformation() ITK_OVERRIDE;
 
   /** Stores the point data into the memory buffer provided. */
   virtual void
-  ReadPoints(void * buffer);
+  ReadPoints(void * buffer) ITK_OVERRIDE;
 
   /** Stores the cell data into the memory buffer provided. */
   virtual void
-  ReadCells(void * buffer);
+  ReadCells(void * buffer) ITK_OVERRIDE;
 
   /** Indicates whether ReadPoints() should be called. */
   virtual bool
-  GetUpdatePoints() const;
+  GetUpdatePoints() const ITK_OVERRIDE;
 
   /** Indicates whether ReadCells() should be called. */
   virtual bool
-  GetUpdateCells() const;
+  GetUpdateCells() const ITK_OVERRIDE;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
   virtual void
-  ReadPointData(void * itkNotUsed(buffer)) {};
+  ReadPointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
   virtual void
-  ReadCellData(void * itkNotUsed(buffer)) {};
+  ReadCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
 
   /*-------- This part of the interfaces deals with writing data. ----- */
   /** Determine if the file can be written with this MeshIO implementation.
@@ -99,15 +99,15 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can write the file specified.
    */
   virtual bool
-  CanWriteFile(const char * FileNameToWrite);
+  CanWriteFile(const char * FileNameToWrite) ITK_OVERRIDE;
 
   /** Write header of the STL file */
   virtual void
-  WriteMeshInformation();
+  WriteMeshInformation() ITK_OVERRIDE;
 
   /** Write the content of the Mesh into an STL file. */
   virtual void
-  Write();
+  Write() ITK_OVERRIDE;
 
   /** The STL format stores point coordinates repeatedly as part of every
    * triangle. Therefore point coordinates are writen as part of the
@@ -116,7 +116,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * coordinates data, than then is used in the WriteCells() method.
    */
   virtual void
-  WritePoints(void * buffer);
+  WritePoints(void * buffer) ITK_OVERRIDE;
 
   /** The WriteCells() method does most of the work. It writes
    * out every triangle in the mesh. For every triangle, it
@@ -135,22 +135,22 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    *
    */
   virtual void
-  WriteCells(void * buffer);
+  WriteCells(void * buffer) ITK_OVERRIDE;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
   virtual void
-  WritePointData(void * itkNotUsed(buffer)) {};
+  WritePointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
   virtual void
-  WriteCellData(void * itkNotUsed(buffer)) {};
+  WriteCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
 
 protected:
   STLMeshIO();
   virtual ~STLMeshIO() {}
 
   void
-  PrintSelf(std::ostream & os, Indent indent) const;
+  PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
 
   /** Templated version of write points method, that is aware of the specific
    * type used to represent the point coordinates. */

From f5ed3ed7ec70a78567aa3faf4ed4bce2c9296d1e Mon Sep 17 00:00:00 2001
From: Zach Williamson <zachary-williamson@uiowa.edu>
Date: Thu, 23 Jun 2016 11:27:02 -0500
Subject: [PATCH 34/73] COMP: Use override annotations on overridden functions

---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index a0786d7c8f0..6baab46258a 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -41,10 +41,10 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
   /** Class methods used to interface with the registered factories. */
   virtual const char *
-  GetITKSourceVersion(void) const;
+  GetITKSourceVersion(void) const ITK_OVERRIDE;
 
   virtual const char *
-  GetDescription(void) const;
+  GetDescription(void) const ITK_OVERRIDE;
 
   /** Method for class instantiation. */
   itkFactorylessNewMacro(Self);
@@ -66,7 +66,7 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
   ~STLMeshIOFactory();
 
   virtual void
-  PrintSelf(std::ostream & os, Indent indent) const;
+  PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
 
 private:
   STLMeshIOFactory(const Self &); // purposely not implemented

From 24ebcffc15f26c706ebd274ab3a82c1f522c8a33 Mon Sep 17 00:00:00 2001
From: Zach Williamson <zachary-williamson@uiowa.edu>
Date: Wed, 29 Jun 2016 09:59:17 -0500
Subject: [PATCH 35/73] STYLE: Use Macro for Function Deletion

---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 4 +---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 93dfdc1385b..b24a14ec29b 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -185,9 +185,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 
 
 private:
-  STLMeshIO(const Self &); // purposely not implemented
-  void
-  operator=(const Self &); // purposely not implemented
+  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIO);
 
   std::ofstream m_OutputStream; // output file
   std::ifstream m_InputStream;  // input file
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 6baab46258a..f9a3406fab6 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -69,9 +69,7 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
   PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
 
 private:
-  STLMeshIOFactory(const Self &); // purposely not implemented
-  void
-  operator=(const Self &); // purposely not implemented
+  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);
 };
 } // end namespace itk
 

From c58a7ab679f97f7b991d89dc9c4f67c140d57bce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= <dzenan.zukic@kitware.com>
Date: Sun, 5 Nov 2017 10:19:01 -0500
Subject: [PATCH 36/73] BUG: Fixing reading

---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 842a17232a8..8df7672f66b 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -811,7 +811,7 @@ STLMeshIO ::InsertPointIntoSet(const PointType & point)
 
   PointsMapType::const_iterator pointMapItr = this->m_PointsMap.find(point);
 
-  IdentifierType pointId = pointMapItr->second;
+  IdentifierType pointId;
 
   if (pointMapItr == this->m_PointsMap.end())
   {
@@ -819,6 +819,10 @@ STLMeshIO ::InsertPointIntoSet(const PointType & point)
     pointId = this->m_LatestPointId;
     this->m_LatestPointId++;
   }
+  else
+  {
+    pointId = pointMapItr->second;
+  }
 
   switch (this->m_PointInTriangleCounter)
   {

From 0a409b96df58a550d8b98061fd5f72fe47bc45a2 Mon Sep 17 00:00:00 2001
From: Jon Haitz Legarreta <jhlegarreta@vicomtech.org>
Date: Wed, 17 Jan 2018 17:54:44 +0100
Subject: [PATCH 37/73] 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
---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 13a02c5aed0..317be8e06e9 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.9)
+cmake_minimum_required(VERSION 3.9.5)
 project(IOSTL)
 set(IOSTL_LIBRARIES IOSTL)
 

From 6f5c2c6f209f7ecb413e29da0c5b40f64dd4d3f4 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Sat, 16 Dec 2017 19:17:00 -0600
Subject: [PATCH 38/73] 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.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   | 32 +++++++++----------
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  8 ++---
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index b24a14ec29b..cf539d0da25 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -57,7 +57,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
    * \return Returns true if this MeshIO can read the file specified.
    */
-  virtual bool
+  bool
   CanReadFile(const char * FileNameToRead) ITK_OVERRIDE;
 
   /** Read the content of the file into a Mesh. */
@@ -65,31 +65,31 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
   Read();
 
   /** Set the spacing and dimension information for the set filename. */
-  virtual void
+  void
   ReadMeshInformation() ITK_OVERRIDE;
 
   /** Stores the point data into the memory buffer provided. */
-  virtual void
+  void
   ReadPoints(void * buffer) ITK_OVERRIDE;
 
   /** Stores the cell data into the memory buffer provided. */
-  virtual void
+  void
   ReadCells(void * buffer) ITK_OVERRIDE;
 
   /** Indicates whether ReadPoints() should be called. */
-  virtual bool
+  bool
   GetUpdatePoints() const ITK_OVERRIDE;
 
   /** Indicates whether ReadCells() should be called. */
-  virtual bool
+  bool
   GetUpdateCells() const ITK_OVERRIDE;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
-  virtual void
+  void
   ReadPointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
-  virtual void
+  void
   ReadCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
 
   /*-------- This part of the interfaces deals with writing data. ----- */
@@ -98,15 +98,15 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
    * \return Returns true if this MeshIO can write the file specified.
    */
-  virtual bool
+  bool
   CanWriteFile(const char * FileNameToWrite) ITK_OVERRIDE;
 
   /** Write header of the STL file */
-  virtual void
+  void
   WriteMeshInformation() ITK_OVERRIDE;
 
   /** Write the content of the Mesh into an STL file. */
-  virtual void
+  void
   Write() ITK_OVERRIDE;
 
   /** The STL format stores point coordinates repeatedly as part of every
@@ -115,7 +115,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * Consequently, this method only performs an internal copy of the Point
    * coordinates data, than then is used in the WriteCells() method.
    */
-  virtual void
+  void
   WritePoints(void * buffer) ITK_OVERRIDE;
 
   /** The WriteCells() method does most of the work. It writes
@@ -134,20 +134,20 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    *        endfacet
    *
    */
-  virtual void
+  void
   WriteCells(void * buffer) ITK_OVERRIDE;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
-  virtual void
+  void
   WritePointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
-  virtual void
+  void
   WriteCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
 
 protected:
   STLMeshIO();
-  virtual ~STLMeshIO() {}
+  ~STLMeshIO() ITK_OVERRIDE {}
 
   void
   PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index f9a3406fab6..6c757cd0e8e 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -40,10 +40,10 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
   typedef SmartPointer<const Self> ConstPointer;
 
   /** Class methods used to interface with the registered factories. */
-  virtual const char *
+  const char *
   GetITKSourceVersion(void) const ITK_OVERRIDE;
 
-  virtual const char *
+  const char *
   GetDescription(void) const ITK_OVERRIDE;
 
   /** Method for class instantiation. */
@@ -63,9 +63,9 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
 protected:
   STLMeshIOFactory();
-  ~STLMeshIOFactory();
+  ~STLMeshIOFactory() ITK_OVERRIDE;
 
-  virtual void
+  void
   PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
 
 private:

From 86006af4cd00e0825900f22d07e660d82e980e8f Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Sat, 16 Dec 2017 19:36:25 -0600
Subject: [PATCH 39/73] 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"
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   | 34 +++++++++----------
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  8 ++---
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index cf539d0da25..2d5d30ea3a3 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -58,7 +58,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can read the file specified.
    */
   bool
-  CanReadFile(const char * FileNameToRead) ITK_OVERRIDE;
+  CanReadFile(const char * FileNameToRead) override;
 
   /** Read the content of the file into a Mesh. */
   virtual void
@@ -66,31 +66,31 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 
   /** Set the spacing and dimension information for the set filename. */
   void
-  ReadMeshInformation() ITK_OVERRIDE;
+  ReadMeshInformation() override;
 
   /** Stores the point data into the memory buffer provided. */
   void
-  ReadPoints(void * buffer) ITK_OVERRIDE;
+  ReadPoints(void * buffer) override;
 
   /** Stores the cell data into the memory buffer provided. */
   void
-  ReadCells(void * buffer) ITK_OVERRIDE;
+  ReadCells(void * buffer) override;
 
   /** Indicates whether ReadPoints() should be called. */
   bool
-  GetUpdatePoints() const ITK_OVERRIDE;
+  GetUpdatePoints() const override;
 
   /** Indicates whether ReadCells() should be called. */
   bool
-  GetUpdateCells() const ITK_OVERRIDE;
+  GetUpdateCells() const override;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
   void
-  ReadPointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
+  ReadPointData(void * itkNotUsed(buffer)) override {};
   void
-  ReadCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
+  ReadCellData(void * itkNotUsed(buffer)) override {};
 
   /*-------- This part of the interfaces deals with writing data. ----- */
   /** Determine if the file can be written with this MeshIO implementation.
@@ -99,15 +99,15 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can write the file specified.
    */
   bool
-  CanWriteFile(const char * FileNameToWrite) ITK_OVERRIDE;
+  CanWriteFile(const char * FileNameToWrite) override;
 
   /** Write header of the STL file */
   void
-  WriteMeshInformation() ITK_OVERRIDE;
+  WriteMeshInformation() override;
 
   /** Write the content of the Mesh into an STL file. */
   void
-  Write() ITK_OVERRIDE;
+  Write() override;
 
   /** The STL format stores point coordinates repeatedly as part of every
    * triangle. Therefore point coordinates are writen as part of the
@@ -116,7 +116,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    * coordinates data, than then is used in the WriteCells() method.
    */
   void
-  WritePoints(void * buffer) ITK_OVERRIDE;
+  WritePoints(void * buffer) override;
 
   /** The WriteCells() method does most of the work. It writes
    * out every triangle in the mesh. For every triangle, it
@@ -135,22 +135,22 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
    *
    */
   void
-  WriteCells(void * buffer) ITK_OVERRIDE;
+  WriteCells(void * buffer) override;
 
   /** STL files do not carry information in points or cells.
    * Therefore the following two methods are implemented as null
    * operations. */
   void
-  WritePointData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
+  WritePointData(void * itkNotUsed(buffer)) override {};
   void
-  WriteCellData(void * itkNotUsed(buffer)) ITK_OVERRIDE {};
+  WriteCellData(void * itkNotUsed(buffer)) override {};
 
 protected:
   STLMeshIO();
-  ~STLMeshIO() ITK_OVERRIDE {}
+  ~STLMeshIO() override {}
 
   void
-  PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
+  PrintSelf(std::ostream & os, Indent indent) const override;
 
   /** Templated version of write points method, that is aware of the specific
    * type used to represent the point coordinates. */
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 6c757cd0e8e..84ce378c299 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -41,10 +41,10 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
   /** Class methods used to interface with the registered factories. */
   const char *
-  GetITKSourceVersion(void) const ITK_OVERRIDE;
+  GetITKSourceVersion(void) const override;
 
   const char *
-  GetDescription(void) const ITK_OVERRIDE;
+  GetDescription(void) const override;
 
   /** Method for class instantiation. */
   itkFactorylessNewMacro(Self);
@@ -63,10 +63,10 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
 protected:
   STLMeshIOFactory();
-  ~STLMeshIOFactory() ITK_OVERRIDE;
+  ~STLMeshIOFactory() override;
 
   void
-  PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
+  PrintSelf(std::ostream & os, Indent indent) const override;
 
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);

From c765210293889a9045b7ceb6fa3144e2ce1a342f Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Mon, 12 Feb 2018 15:21:08 -0600
Subject: [PATCH 40/73] STYLE: Modernize to C++11 conventions

STYLE: Use auto for variable creation

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

cd /Users/johnsonhj/Dashboard/src/ITK-clangtidy/
run-clang-tidy.py -checks=-*,modernize-use-auto  -header-filter=.* -fix

use auto when declaring iterators
use auto when initializing with a cast to avoid duplicating the type name
use auto when initializing with a template cast to avoid duplicating the type name
use auto when initializing with new to avoid duplicating the type name

SRCDIR=/Users/johnsonhj/Dashboard/src/ITK #My local SRC
BLDDIR=/Users/johnsonhj/Dashboard/src/ITK-clangtidy/ #My local BLD

PERF: Replace explicit return calls of constructor

Replaces explicit calls to the constructor in a return with a braced
initializer list. This way the return type is not needlessly duplicated in the
function definition and the return statement.

SRCDIR=/Users/johnsonhj/Dashboard/src/ITK #My local SRC
BLDDIR=/Users/johnsonhj/Dashboard/src/ITK-clangtidy/ #My local BLD

cd /Users/johnsonhj/Dashboard/src/ITK-clangtidy/
run-clang-tidy.py -checks=-*,modernize-return-braced-init-list  -header-filter=.* -fix

PERF: Allow compiler to choose best way to construct a copy

With move semantics added to the language and the standard library updated with
move constructors added for many types it is now interesting to take an
argument directly by value, instead of by const-reference, and then copy. This
check allows the compiler to take care of choosing the best way to construct
the copy.

The transformation is usually beneficial when the calling code passes an rvalue
and assumes the move construction is a cheap operation. This short example
illustrates how the construction of the value happens:

class Foo {
 public:
-  Foo(const std::string &Copied, const std::string &ReadOnly)
-    : Copied(Copied), ReadOnly(ReadOnly) {}
+  Foo(std::string Moved, const std::string &ReadOnly)
+    : Copied(std::move(Moved)), ReadOnly(ReadOnly) {}
 private:
   private:
   std::string Copied;
   const std::string &ReadOnly;
};

SRCDIR=/Users/johnsonhj/Dashboard/src/ITK #My local SRC
BLDDIR=/Users/johnsonhj/Dashboard/src/ITK-clangtidy/ #My local BLD

cd /Users/johnsonhj/Dashboard/src/ITK-clangtidy/
run-clang-tidy.py -checks=-*,modernize-pass-by-value  -header-filter=.* -fix

STYLE: Use range-based loops from C++11

Used as a more readable equivalent to the traditional for loop operating
over a range of values, such as all elements in a container, in the
forward direction.

====
Range based loopes are more explicit for only computing the
end location once for containers.

for ( ImageIORegion::IndexType::const_iterator i = this->GetIndex().begin();
  i != this->GetIndex().end(); //<- NOTE: Compute end every loop iteration
  ++i )

for (long i : this->GetIndex()) //<- NOTE: Implicitly only compute end once

====
Explicitly reduce the amount of index computations: (The compiler
probably does this too)

for(int i = 0; i < 11; i++)
  {
  pos[0] = testPoints[i][0];
  pos[1] = testPoints[i][1];
                    ^^^^

for(auto & testPoint : testPoints)
  {
  pos[0] = testPoint[0];
  pos[1] = testPoint[1];

====

SRCDIR=/Users/johnsonhj/Dashboard/src/ITK #My local SRC
BLDDIR=/Users/johnsonhj/Dashboard/src/ITK-clangtidy/ #My local BLD

cd /Users/johnsonhj/Dashboard/src/ITK-clangtidy/
run-clang-tidy.py -checks=-*,modernize-loop-convert  -header-filter=.* -fix
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 8df7672f66b..70b5f639ca8 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -333,7 +333,7 @@ STLMeshIO ::ReadPoints(void * buffer)
   PointsMapType::const_iterator pointItr = this->m_PointsMap.begin();
   PointsMapType::const_iterator pointEnd = this->m_PointsMap.end();
 
-  float * pointsBuffer = reinterpret_cast<float *>(buffer);
+  auto * pointsBuffer = reinterpret_cast<float *>(buffer);
 
   while (pointItr != pointEnd)
   {
@@ -365,7 +365,7 @@ STLMeshIO ::ReadCells(void * buffer)
   CellsVectorType::const_iterator cellItr = this->m_CellsVector.begin();
   CellsVectorType::const_iterator cellEnd = this->m_CellsVector.end();
 
-  unsigned int * cellPointIds = reinterpret_cast<unsigned int *>(buffer);
+  auto * cellPointIds = reinterpret_cast<unsigned int *>(buffer);
 
   const unsigned int numberOfPointsInCell = 3;
 
@@ -545,7 +545,7 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   const IdentifierType numberOfPolygons = this->GetNumberOfCells();
 
-  const IdentifierType * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
+  const auto * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
 
   SizeValueType index = 0;
 
@@ -562,8 +562,8 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
-    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
-    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
+    const auto cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
+    const auto numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
 
     const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
 
@@ -623,7 +623,7 @@ STLMeshIO ::WriteCellsAsAscii(void * buffer)
 
   const IdentifierType numberOfPolygons = this->GetNumberOfCells();
 
-  const IdentifierType * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
+  const auto * cellsBuffer = reinterpret_cast<const IdentifierType *>(buffer);
 
   SizeValueType index = 0;
 
@@ -631,8 +631,8 @@ STLMeshIO ::WriteCellsAsAscii(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
-    const MeshIOBase::CellGeometryType cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
-    const IdentifierType               numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
+    const auto cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
+    const auto numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
 
     const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
 

From 05a3eb53bd1da38c78b546048f4dc7092963c789 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Mon, 12 Feb 2018 23:29:57 -0600
Subject: [PATCH 41/73] 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.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   | 26 +++++++++----------
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   | 10 +++----
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 26 +++++++++----------
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  8 +++---
 4 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 2d5d30ea3a3..aeb997cde7a 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -38,11 +38,11 @@ namespace itk
 class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 {
 public:
-  /** Standard "Self" typedef. */
-  typedef STLMeshIO                Self;
-  typedef MeshIOBase               Superclass;
-  typedef SmartPointer<Self>       Pointer;
-  typedef SmartPointer<const Self> ConstPointer;
+  /** Standard "Self" type alias. */
+  using Self = STLMeshIO;
+  using Superclass = MeshIOBase;
+  using Pointer = SmartPointer<Self>;
+  using ConstPointer = SmartPointer<const Self>;
 
   /** Method for creation through the object factory. */
   itkNewMacro(Self);
@@ -192,13 +192,13 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 
   std::string m_InputLine; // helper during reading
 
-  typedef float PointValueType; // type to represent point coordinates
+  using PointValueType = float; // type to represent point coordinates
 
-  typedef Point<PointValueType, 3>           PointType;
-  typedef Vector<PointValueType, 3>          VectorType;
-  typedef CovariantVector<PointValueType, 3> NormalType;
+  using PointType = Point<PointValueType, 3>;
+  using VectorType = Vector<PointValueType, 3>;
+  using NormalType = CovariantVector<PointValueType, 3>;
 
-  typedef std::vector<PointType> PointContainerType;
+  using PointContainerType = std::vector<PointType>;
 
   /** Helper functions to write elements to binary file */
   void
@@ -269,7 +269,7 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
     }
   };
 
-  typedef std::map<PointType, IdentifierType, PointCompare> PointsMapType;
+  using PointsMapType = std::map<PointType, IdentifierType, PointCompare>;
 
   PointsMapType m_PointsMap;
 
@@ -288,8 +288,8 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
   TripletType  m_TrianglePointIds;
   unsigned int m_PointInTriangleCounter;
 
-  typedef std::vector<TripletType> CellsVectorType;
-  CellsVectorType                  m_CellsVector;
+  using CellsVectorType = std::vector<TripletType>;
+  CellsVectorType m_CellsVector;
 };
 } // end namespace itk
 
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 84ce378c299..d0939237434 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -33,11 +33,11 @@ namespace itk
 class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
 public:
-  /** Standard class typedefs. */
-  typedef STLMeshIOFactory         Self;
-  typedef ObjectFactoryBase        Superclass;
-  typedef SmartPointer<Self>       Pointer;
-  typedef SmartPointer<const Self> ConstPointer;
+  /** Standard class type alias. */
+  using Self = STLMeshIOFactory;
+  using Superclass = ObjectFactoryBase;
+  using Pointer = SmartPointer<Self>;
+  using ConstPointer = SmartPointer<const Self>;
 
   /** Class methods used to interface with the registered factories. */
   const char *
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 70b5f639ca8..ef08e6d9ec4 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -444,79 +444,79 @@ STLMeshIO ::WritePoints(void * buffer)
   {
     case UCHAR:
     {
-      typedef unsigned char CoordType;
+      using CoordType = unsigned char;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case CHAR:
     {
-      typedef char CoordType;
+      using CoordType = char;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case USHORT:
     {
-      typedef unsigned short CoordType;
+      using CoordType = unsigned short;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case SHORT:
     {
-      typedef short CoordType;
+      using CoordType = short;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case UINT:
     {
-      typedef unsigned int CoordType;
+      using CoordType = unsigned int;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case INT:
     {
-      typedef int CoordType;
+      using CoordType = int;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case ULONG:
     {
-      typedef unsigned long CoordType;
+      using CoordType = unsigned long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case LONG:
     {
-      typedef long CoordType;
+      using CoordType = long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case ULONGLONG:
     {
-      typedef unsigned long long CoordType;
+      using CoordType = unsigned long long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case LONGLONG:
     {
-      typedef long long CoordType;
+      using CoordType = long long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case FLOAT:
     {
-      typedef float CoordType;
+      using CoordType = float;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case DOUBLE:
     {
-      typedef double CoordType;
+      using CoordType = double;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
     case LDOUBLE:
     {
-      typedef long double CoordType;
+      using CoordType = long double;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 76c922be424..ad1da619f69 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -34,14 +34,14 @@ itkSTLMeshIOTest(int argc, char * argv[])
   }
 
   const unsigned int Dimension = 3;
-  typedef float      PixelType;
+  using PixelType = float;
 
-  typedef itk::QuadEdgeMesh<PixelType, Dimension> QEMeshType;
+  using QEMeshType = itk::QuadEdgeMesh<PixelType, Dimension>;
 
   itk::STLMeshIOFactory::RegisterOneFactory();
 
-  typedef itk::MeshFileReader<QEMeshType> ReaderType;
-  typedef itk::MeshFileWriter<QEMeshType> WriterType;
+  using ReaderType = itk::MeshFileReader<QEMeshType>;
+  using WriterType = itk::MeshFileWriter<QEMeshType>;
 
   ReaderType::Pointer reader = ReaderType::New();
   WriterType::Pointer writer = WriterType::New();

From e08b4b4fc500ec450654753307b363bc30736e98 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Tue, 13 Feb 2018 08:24:24 -0600
Subject: [PATCH 42/73] STYLE: Prefer constexpr for const numeric literals

Use constexpr for constant numeric literals.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx      | 2 +-
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index ef08e6d9ec4..753962d7156 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -367,7 +367,7 @@ STLMeshIO ::ReadCells(void * buffer)
 
   auto * cellPointIds = reinterpret_cast<unsigned int *>(buffer);
 
-  const unsigned int numberOfPointsInCell = 3;
+  constexpr unsigned int numberOfPointsInCell = 3;
 
   while (cellItr != cellEnd)
   {
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index ad1da619f69..95f40791e5c 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -33,7 +33,7 @@ itkSTLMeshIOTest(int argc, char * argv[])
     return EXIT_FAILURE;
   }
 
-  const unsigned int Dimension = 3;
+  constexpr unsigned int Dimension = 3;
   using PixelType = float;
 
   using QEMeshType = itk::QuadEdgeMesh<PixelType, Dimension>;

From 76530e4f518dc3ae4c8910e99ee18178e6566fdd Mon Sep 17 00:00:00 2001
From: Jon Haitz Legarreta <jhlegarreta@vicomtech.org>
Date: Sat, 14 Apr 2018 19:13:54 +0200
Subject: [PATCH 43/73] 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.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 4 ++--
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 5 ++---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index aeb997cde7a..1ceb8d0b53f 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -38,6 +38,8 @@ namespace itk
 class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 {
 public:
+  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIO);
+
   /** Standard "Self" type alias. */
   using Self = STLMeshIO;
   using Superclass = MeshIOBase;
@@ -185,8 +187,6 @@ class IOSTL_EXPORT STLMeshIO : public MeshIOBase
 
 
 private:
-  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIO);
-
   std::ofstream m_OutputStream; // output file
   std::ifstream m_InputStream;  // input file
 
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index d0939237434..269358a0175 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -33,6 +33,8 @@ namespace itk
 class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
 public:
+  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);
+
   /** Standard class type alias. */
   using Self = STLMeshIOFactory;
   using Superclass = ObjectFactoryBase;
@@ -67,9 +69,6 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
   void
   PrintSelf(std::ostream & os, Indent indent) const override;
-
-private:
-  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);
 };
 } // end namespace itk
 

From c9fe725efd0658a251fd795298cb46f1b59a29e2 Mon Sep 17 00:00:00 2001
From: Jon Haitz Legarreta <jhlegarreta@vicomtech.org>
Date: Sat, 5 May 2018 12:43:32 +0200
Subject: [PATCH 44/73] 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**.
---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 317be8e06e9..52a47f829d4 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.9.5)
+cmake_minimum_required(VERSION 3.10.2)
 project(IOSTL)
 set(IOSTL_LIBRARIES IOSTL)
 

From 93f817a6faffbbc9191901efcf28ab2ed731f091 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Thu, 20 Dec 2018 23:28:49 -0500
Subject: [PATCH 45/73] ENH: Enable mesh module factory registration

Also address a few minor style issues.
---
 .../IO/IOMeshSTL/include/itkSTLMeshIOFactory.h  | 10 +++++-----
 Modules/IO/IOMeshSTL/itk-module.cmake           |  2 ++
 .../IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx    | 17 ++++++++++++++++-
 3 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 269358a0175..95ad6fec9e6 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -43,10 +43,10 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
   /** Class methods used to interface with the registered factories. */
   const char *
-  GetITKSourceVersion(void) const override;
+  GetITKSourceVersion() const override;
 
   const char *
-  GetDescription(void) const override;
+  GetDescription() const override;
 
   /** Method for class instantiation. */
   itkFactorylessNewMacro(Self);
@@ -56,11 +56,11 @@ class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 
   /** Register one factory of this type  */
   static void
-  RegisterOneFactory(void)
+  RegisterOneFactory()
   {
-    STLMeshIOFactory::Pointer vtkFactory = STLMeshIOFactory::New();
+    STLMeshIOFactory::Pointer meshFactory = STLMeshIOFactory::New();
 
-    ObjectFactoryBase::RegisterFactory(vtkFactory);
+    ObjectFactoryBase::RegisterFactory(meshFactory);
   }
 
 protected:
diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 1c08828db85..440dd6d9f81 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -12,6 +12,8 @@ itk_module(
   TEST_DEPENDS
     ITKTestKernel
     ITKQuadEdgeMesh
+  FACTORY_NAMES
+    MeshIO::STL
   DESCRIPTION "${DOCUMENTATION}"
   EXCLUDE_FROM_DEFAULT
 )
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index fcc8c647d99..e6c880c9f3d 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
@@ -16,6 +16,7 @@
  *
  *=========================================================================*/
 
+#include "IOSTLExport.h"
 #include "itkSTLMeshIO.h"
 #include "itkSTLMeshIOFactory.h"
 #include "itkVersion.h"
@@ -34,7 +35,7 @@ STLMeshIOFactory ::STLMeshIOFactory()
 STLMeshIOFactory ::~STLMeshIOFactory() {}
 
 const char *
-STLMeshIOFactory ::GetITKSourceVersion(void) const
+STLMeshIOFactory ::GetITKSourceVersion() const
 {
   return ITK_SOURCE_VERSION;
 }
@@ -44,4 +45,18 @@ STLMeshIOFactory ::GetDescription() const
 {
   return "STL MeshIO Factory, allows the loading of STL QuadEdgeMesh data into ITK";
 }
+
+// Undocumented API used to register during static initialization.
+// DO NOT CALL DIRECTLY.
+static bool STLMeshIOFactoryHasBeenRegistered;
+
+void IOSTL_EXPORT
+STLMeshIOFactoryRegister__Private()
+{
+  if (!STLMeshIOFactoryHasBeenRegistered)
+  {
+    STLMeshIOFactoryHasBeenRegistered = true;
+    STLMeshIOFactory::RegisterOneFactory();
+  }
+}
 } // end namespace itk

From c08e845b76db5691814d9a97033a9326140784dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Fri, 21 Dec 2018 17:29:01 -0500
Subject: [PATCH 46/73] ENH: Add CI.

Add CI:
- Add `*.yml` configuration files for CI.
- Add the `setup.py` Python setup file.
- Add Python wrapping files.
- Add the `CTestConfig.cmake` file to make the build results be sent to
  the **Insight** project in **open.cdash.org**.
---
 Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt    | 3 +++
 Modules/IO/IOMeshSTL/wrapping/itkSTLMeshIO.wrap | 2 ++
 2 files changed, 5 insertions(+)
 create mode 100644 Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
 create mode 100644 Modules/IO/IOMeshSTL/wrapping/itkSTLMeshIO.wrap

diff --git a/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
new file mode 100644
index 00000000000..5bb5423f673
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
@@ -0,0 +1,3 @@
+itk_wrap_module(SkullStrip)
+itk_auto_load_submodules()
+itk_end_wrap_module()
diff --git a/Modules/IO/IOMeshSTL/wrapping/itkSTLMeshIO.wrap b/Modules/IO/IOMeshSTL/wrapping/itkSTLMeshIO.wrap
new file mode 100644
index 00000000000..96be3782361
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/wrapping/itkSTLMeshIO.wrap
@@ -0,0 +1,2 @@
+itk_wrap_simple_class("itk::STLMeshIO" POINTER)
+itk_wrap_simple_class("itk::STLMeshIOFactory" POINTER)

From 53453d60ca9b0d09d56f236571e401f6fb0ea939 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Fri, 21 Dec 2018 20:44:41 -0500
Subject: [PATCH 47/73] DOC: Re-use `README.rst` info in `itk-module.cmake`.

Re-use `README.rst` info in `itk-module.cmake`.

Helps avoiding duplications/diverging versions of the documentation.
---
 Modules/IO/IOMeshSTL/itk-module.cmake | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 1c08828db85..8af93ebaa05 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -1,8 +1,14 @@
-set(
-  DOCUMENTATION
-  "This module contains classes for reading and writing
-QuadEdgeMeshes using the STL file format."
-)
+# the top-level README is used for describing this module, just
+# re-used it for documentation here
+get_filename_component(MY_CURRENT_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+file(READ "${MY_CURRENT_DIR}/README.md" DOCUMENTATION)
+
+# itk_module() defines the module dependencies in IOSTL
+# The testing module in IOSTL depends on ITKTestKernel
+# By convention those modules outside of ITK are not prefixed with
+# ITK.
+
+# define the dependencies of the include module and the tests
 itk_module(
   IOSTL
   ENABLE_SHARED

From 6183f4a07656af7a12f37d893c39d3b144aa32f7 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sat, 19 Jan 2019 17:45:00 -0500
Subject: [PATCH 48/73] BUG: Set PointDimension to 3

STL meshes are always 3D. The default is 0.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 753962d7156..cd42f4d41c0 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -38,6 +38,8 @@ STLMeshIO ::STLMeshIO()
   // STL uses UINT32 to store the number of points,
   // hence the point Ids are of the same UINT32 type.
   this->SetCellComponentType(UINT);
+
+  this->SetPointDimension(3);
 }
 
 bool

From e216d8f8501f824bdbaf3f9758b902b966272915 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sat, 19 Jan 2019 17:47:39 -0500
Subject: [PATCH 49/73] BUG: Fix wrapping module name

---
 Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
index 5bb5423f673..22ecdf90abd 100644
--- a/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
@@ -1,3 +1,3 @@
-itk_wrap_module(SkullStrip)
+itk_wrap_module(IOSTL)
 itk_auto_load_submodules()
 itk_end_wrap_module()

From a2045b0d093926ef212b837dc01ca1dadd3f1b2b Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 20 Jan 2019 20:52:19 -0500
Subject: [PATCH 50/73] ENH: Make module name consistent with conventions

Since the repository name is ITKIOMeshSTL and it is an external/remote
module, name the module IOMeshSTL according to our naming convention.
---
 Modules/IO/IOMeshSTL/CMakeLists.txt           |  4 ++--
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  6 +++---
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  6 +++---
 Modules/IO/IOMeshSTL/itk-module.cmake         |  6 +++---
 Modules/IO/IOMeshSTL/src/CMakeLists.txt       | 10 +++++-----
 .../IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx  |  4 ++--
 Modules/IO/IOMeshSTL/test/CMakeLists.txt      | 20 +++++++++----------
 Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt  |  2 +-
 8 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 52a47f829d4..90a56f1297b 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.10.2)
-project(IOSTL)
-set(IOSTL_LIBRARIES IOSTL)
+project(IOMeshSTL)
+set(IOMeshSTL_LIBRARIES IOMeshSTL)
 
 if(NOT ITK_SOURCE_DIR)
   find_package(ITK REQUIRED)
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 1ceb8d0b53f..23b6a3f8b30 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -18,7 +18,7 @@
 #ifndef itkSTLMeshIO_h
 #define itkSTLMeshIO_h
 
-#include "IOSTLExport.h"
+#include "IOMeshSTLExport.h"
 
 #include "itkMeshIOBase.h"
 
@@ -33,9 +33,9 @@ namespace itk
  * \author Luis Ibanez, Kitware Inc.
  *
  * \ingroup IOFilters
- * \ingroup IOSTL
+ * \ingroup IOMeshSTL
  */
-class IOSTL_EXPORT STLMeshIO : public MeshIOBase
+class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
 {
 public:
   ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIO);
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 95ad6fec9e6..bc06fffed3f 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -18,7 +18,7 @@
 #ifndef itkSTLMeshIOFactory_h
 #define itkSTLMeshIOFactory_h
 
-#include "IOSTLExport.h"
+#include "IOMeshSTLExport.h"
 
 #include "itkObjectFactoryBase.h"
 #include "itkMeshIOBase.h"
@@ -28,9 +28,9 @@ namespace itk
 /** \class STLMeshIOFactory
  * \brief Create instances of STLMeshIO objects using an object factory.
  *
- * \ingroup IOSTL
+ * \ingroup IOMeshSTL
  */
-class IOSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
+class IOMeshSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
 public:
   ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);
diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 4ca6afe720e..13439b52a2c 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -3,14 +3,14 @@
 get_filename_component(MY_CURRENT_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
 file(READ "${MY_CURRENT_DIR}/README.md" DOCUMENTATION)
 
-# itk_module() defines the module dependencies in IOSTL
-# The testing module in IOSTL depends on ITKTestKernel
+# itk_module() defines the module dependencies in IOMeshSTL
+# The testing module in IOMeshSTL depends on ITKTestKernel
 # By convention those modules outside of ITK are not prefixed with
 # ITK.
 
 # define the dependencies of the include module and the tests
 itk_module(
-  IOSTL
+  IOMeshSTL
   ENABLE_SHARED
   DEPENDS
     ITKCommon
diff --git a/Modules/IO/IOMeshSTL/src/CMakeLists.txt b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
index 685a7312de8..4ed281d28d6 100644
--- a/Modules/IO/IOMeshSTL/src/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
@@ -1,18 +1,18 @@
 set(
-  IOSTL_SRC
+  IOMeshSTL_SRC
   itkSTLMeshIO.cxx
   itkSTLMeshIOFactory.cxx
 )
 
 add_library(
-  IOSTL
+  IOMeshSTL
   ${ITK_LIBRARY_BUILD_TYPE}
-  ${IOSTL_SRC}
+  ${IOMeshSTL_SRC}
 )
 target_link_libraries(
-  IOSTL
+  IOMeshSTL
   ${ITKCommon_LIBRARIES}
   ${ITKIOMesh_LIBRARIES}
 )
 
-itk_module_target(IOSTL)
+itk_module_target(IOMeshSTL)
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index e6c880c9f3d..65ae5f76209 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
@@ -16,7 +16,7 @@
  *
  *=========================================================================*/
 
-#include "IOSTLExport.h"
+#include "IOMeshSTLExport.h"
 #include "itkSTLMeshIO.h"
 #include "itkSTLMeshIOFactory.h"
 #include "itkVersion.h"
@@ -50,7 +50,7 @@ STLMeshIOFactory ::GetDescription() const
 // DO NOT CALL DIRECTLY.
 static bool STLMeshIOFactoryHasBeenRegistered;
 
-void IOSTL_EXPORT
+void IOMeshSTL_EXPORT
 STLMeshIOFactoryRegister__Private()
 {
   if (!STLMeshIOFactoryHasBeenRegistered)
diff --git a/Modules/IO/IOMeshSTL/test/CMakeLists.txt b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
index fc19533b77c..d667e49bfcb 100644
--- a/Modules/IO/IOMeshSTL/test/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/test/CMakeLists.txt
@@ -1,13 +1,13 @@
 itk_module_test()
 
-set(IOSTLTests itkSTLMeshIOTest.cxx)
+set(IOMeshSTLTests itkSTLMeshIOTest.cxx)
 
-createtestdriver(IOSTL "${IOSTL-Test_LIBRARIES}" "${IOSTLTests}" )
+createtestdriver(IOMeshSTL "${IOMeshSTL-Test_LIBRARIES}" "${IOMeshSTLTests}" )
 
 itk_add_test(
   NAME itkSTLMeshIOTest00
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.vtk}
     ${ITK_TEST_OUTPUT_DIR}/sphere00.stl
@@ -17,7 +17,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest01
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.vtk}
     ${ITK_TEST_OUTPUT_DIR}/sphere01.stl
@@ -27,7 +27,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest02
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.stl}
     ${ITK_TEST_OUTPUT_DIR}/sphere02.stl
@@ -37,7 +37,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest03
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/sphere.stl}
     ${ITK_TEST_OUTPUT_DIR}/sphere03.stl
@@ -47,7 +47,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest04
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.vtk}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron01.stl
@@ -57,7 +57,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest05
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.vtk}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron02.stl
@@ -67,7 +67,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest06
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.stl}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron03.stl
@@ -77,7 +77,7 @@ itk_add_test(
 itk_add_test(
   NAME itkSTLMeshIOTest07
   COMMAND
-    IOSTLTestDriver
+    IOMeshSTLTestDriver
     itkSTLMeshIOTest
     DATA{Baseline/tetrahedron.stl}
     ${ITK_TEST_OUTPUT_DIR}/tetrahedron04.stl
diff --git a/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
index 22ecdf90abd..acc04954e53 100644
--- a/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/wrapping/CMakeLists.txt
@@ -1,3 +1,3 @@
-itk_wrap_module(IOSTL)
+itk_wrap_module(IOMeshSTL)
 itk_auto_load_submodules()
 itk_end_wrap_module()

From efcab1b7acae8b4235eadc42f122e8ad4dacafde Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Thu, 24 Jan 2019 16:19:06 -0500
Subject: [PATCH 51/73] BUG: Set NumberOfCells for ASCII files

---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx      | 1 +
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 7 +++----
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index cd42f4d41c0..0d8f6ad8759 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -204,6 +204,7 @@ STLMeshIO ::ReadMeshInternalFromAscii()
   }
 
   this->SetNumberOfPoints(this->m_PointsMap.size());
+  this->SetNumberOfCells(this->m_CellsVector.size());
 
   //
   // The factor 5 accounts for five integers
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 95f40791e5c..508f075262f 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -63,9 +63,6 @@ itkSTLMeshIOTest(int argc, char * argv[])
   reader->Update();
   QEMeshType * mesh = reader->GetOutput();
 
-  mesh->Print(std::cout);
-
-
   writer->SetInput(reader->GetOutput());
 
   int result = EXIT_SUCCESS;
@@ -85,7 +82,9 @@ itkSTLMeshIOTest(int argc, char * argv[])
   //
   itk::STLMeshIO::Pointer meshIO = itk::STLMeshIO::New();
 
-  meshIO->Print(std::cout);
+  mesh->Print(std::cout);
+  reader->GetMeshIO()->Print(std::cout);
+  writer->GetMeshIO()->Print(std::cout);
 
   //
   //  Report the System Endianness

From 30c6d8775ebfbe29325d85e85348ce5cbeb90a04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Sat, 26 Jan 2019 18:20:27 -0500
Subject: [PATCH 52/73] STYLE: Improve test style.

Improve test style:
- Use the `TRY_EXPECT_NO_EXCEPTION` macro to avoid boilerplate code.
- Add a test ending message as recommened by the ITK SW Guide.

Take advantage to call the `EXERCISE_BASIC_OBJECT_METHODS` macro to
improve coverage.
---
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 508f075262f..c7f669adeb5 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -21,6 +21,7 @@
 #include "itkSTLMeshIO.h"
 #include "itkMeshFileReader.h"
 #include "itkMeshFileWriter.h"
+#include "itkTestingMacros.h"
 
 int
 itkSTLMeshIOTest(int argc, char * argv[])
@@ -65,23 +66,16 @@ itkSTLMeshIOTest(int argc, char * argv[])
 
   writer->SetInput(reader->GetOutput());
 
-  int result = EXIT_SUCCESS;
+  TRY_EXPECT_NO_EXCEPTION(writer->Update());
 
-  try
-  {
-    writer->Update();
-  }
-  catch (itk::ExceptionObject & excp)
-  {
-    std::cerr << excp << std::endl;
-    result = EXIT_FAILURE;
-  }
 
   //
   //  Exercising additional methods
   //
   itk::STLMeshIO::Pointer meshIO = itk::STLMeshIO::New();
 
+  EXERCISE_BASIC_OBJECT_METHODS(meshIO, STLMeshIO, MeshIOBase);
+
   mesh->Print(std::cout);
   reader->GetMeshIO()->Print(std::cout);
   writer->GetMeshIO()->Print(std::cout);
@@ -99,5 +93,7 @@ itkSTLMeshIOTest(int argc, char * argv[])
     std::cout << "This system is Big Endian" << std::endl;
   }
 
-  return result;
+
+  std::cout << "Test finished." << std::endl;
+  return EXIT_SUCCESS;
 }

From cd85e79f3b5d0ad64f98308f6f6e91679bebb13f Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Fri, 15 Feb 2019 14:15:04 -0500
Subject: [PATCH 53/73] BUG: Dependency is on ITKIOMeshBase vs ITKIOMesh

---
 Modules/IO/IOMeshSTL/itk-module.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/itk-module.cmake b/Modules/IO/IOMeshSTL/itk-module.cmake
index 13439b52a2c..7d1208b98d2 100644
--- a/Modules/IO/IOMeshSTL/itk-module.cmake
+++ b/Modules/IO/IOMeshSTL/itk-module.cmake
@@ -14,7 +14,7 @@ itk_module(
   ENABLE_SHARED
   DEPENDS
     ITKCommon
-    ITKIOMesh
+    ITKIOMeshBase
   TEST_DEPENDS
     ITKTestKernel
     ITKQuadEdgeMesh

From 9eff1236e503b3e33cef29c45058f1f0728eddbd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Fri, 14 Jun 2019 20:27:38 -0400
Subject: [PATCH 54/73] STYLE: Add ITK prefix to testing macros

---
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index c7f669adeb5..9ca0b97a9d7 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -66,7 +66,7 @@ itkSTLMeshIOTest(int argc, char * argv[])
 
   writer->SetInput(reader->GetOutput());
 
-  TRY_EXPECT_NO_EXCEPTION(writer->Update());
+  ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
 
 
   //
@@ -74,7 +74,7 @@ itkSTLMeshIOTest(int argc, char * argv[])
   //
   itk::STLMeshIO::Pointer meshIO = itk::STLMeshIO::New();
 
-  EXERCISE_BASIC_OBJECT_METHODS(meshIO, STLMeshIO, MeshIOBase);
+  ITK_EXERCISE_BASIC_OBJECT_METHODS(meshIO, STLMeshIO, MeshIOBase);
 
   mesh->Print(std::cout);
   reader->GetMeshIO()->Print(std::cout);

From 5d9171ceeeec2dffe954a5d3a39139a7020b8ff2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?D=C5=BEenan=20Zuki=C4=87?= <dzenan.zukic@kitware.com>
Date: Fri, 16 Aug 2019 14:18:10 -0400
Subject: [PATCH 55/73] COMP: fix link errors

Creating library C:/Libs/ITK-5.0.1-vs2015/lib/Debug/itkIOMeshSTL-5.0.lib and object C:/Libs/ITK-5.0.1-vs2015/lib/Debug/itkIOMeshSTL-5.0.exp
itkSTLMeshIO.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual void __cdecl itk::MeshIOBase::SetPointComponentType(enum itk::MeshIOBase::IOComponentType)" (__imp_?SetPointComponentType@MeshIOBase@itk@@UEAAXW4IOComponentType@12@@Z) referenced in function "protected: __cdecl itk::STLMeshIO::STLMeshIO(void)" (??0STLMeshIO@itk@@IEAA@XZ)
---
 Modules/IO/IOMeshSTL/src/CMakeLists.txt | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/CMakeLists.txt b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
index 4ed281d28d6..e2e927802e4 100644
--- a/Modules/IO/IOMeshSTL/src/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
@@ -1,18 +1,6 @@
-set(
-  IOMeshSTL_SRC
+set(IOMeshSTL_SRC
   itkSTLMeshIO.cxx
   itkSTLMeshIOFactory.cxx
 )
 
-add_library(
-  IOMeshSTL
-  ${ITK_LIBRARY_BUILD_TYPE}
-  ${IOMeshSTL_SRC}
-)
-target_link_libraries(
-  IOMeshSTL
-  ${ITKCommon_LIBRARIES}
-  ${ITKIOMesh_LIBRARIES}
-)
-
-itk_module_target(IOMeshSTL)
+itk_module_add_library(IOMeshSTL ${ITK_LIBRARY_BUILD_TYPE} ${IOMeshSTL_SRC})

From 9c2f1cee322b11499ba908c8dc7d86868f4cdccc Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Sun, 16 Feb 2020 12:09:47 -0600
Subject: [PATCH 56/73] COMP: Enumeration type to store as unsigned int

Explicit static cast needed to convert enumerations.
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 0d8f6ad8759..6e07d9014ec 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -368,14 +368,15 @@ STLMeshIO ::ReadCells(void * buffer)
   CellsVectorType::const_iterator cellItr = this->m_CellsVector.begin();
   CellsVectorType::const_iterator cellEnd = this->m_CellsVector.end();
 
-  auto * cellPointIds = reinterpret_cast<unsigned int *>(buffer);
+  using CellIDType = unsigned int;
+  auto * cellPointIds = reinterpret_cast<CellIDType *>(buffer);
 
   constexpr unsigned int numberOfPointsInCell = 3;
 
   while (cellItr != cellEnd)
   {
 
-    *cellPointIds++ = MeshIOBase::TRIANGLE_CELL;
+    *cellPointIds++ = static_cast<CellIDType>(MeshIOBase::TRIANGLE_CELL);
     *cellPointIds++ = numberOfPointsInCell;
 
     //

From e85d651b08057f281f72a53a3ca1cb95bd6890ce Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Sun, 16 Feb 2020 19:08:58 -0600
Subject: [PATCH 57/73] STYLE: Make prototype match definition names

Enforce consistency in large projects, where it often happens that a definition
of function is refactored, changing the parameter names, but its declaration in
header file is not updated. With this check, we can easily find and correct
such inconsistencies, keeping declaration and definition always in sync.

Unnamed parameters are allowed and are not taken into account when comparing
function declarations
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 23b6a3f8b30..9f6529bc5c7 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -60,7 +60,7 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can read the file specified.
    */
   bool
-  CanReadFile(const char * FileNameToRead) override;
+  CanReadFile(const char * fileName) override;
 
   /** Read the content of the file into a Mesh. */
   virtual void
@@ -101,7 +101,7 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
    * \return Returns true if this MeshIO can write the file specified.
    */
   bool
-  CanWriteFile(const char * FileNameToWrite) override;
+  CanWriteFile(const char * fileName) override;
 
   /** Write header of the STL file */
   void
@@ -228,7 +228,7 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
 
   /** Helper functions to read elements from ASCII files. */
   void
-  ReadStringFromAscii(const std::string & keyword);
+  ReadStringFromAscii(const std::string & expected);
   void
   ReadPointAsAscii(PointType & point);
   bool

From 8505e7c05324ee28851d37fb9478e8ff58647394 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Sun, 16 Feb 2020 22:07:45 -0600
Subject: [PATCH 58/73] STYLE: Replace integer literals which are cast to bool.

Finds and replaces integer literals which are cast to bool.

SRCDIR= #My local SRC
BLDDIR= #My local BLD

cd
run-clang-tidy.py -extra-arg=-D__clang__ -checks=-*,modernize-use-bool-literals  -header-filter=.* -fix
---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index 65ae5f76209..21951f5cc38 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
@@ -29,7 +29,7 @@ STLMeshIOFactory ::PrintSelf(std::ostream &, Indent) const
 
 STLMeshIOFactory ::STLMeshIOFactory()
 {
-  this->RegisterOverride("itkMeshIOBase", "itkSTLMeshIO", "STL IO", 1, CreateObjectFunction<STLMeshIO>::New());
+  this->RegisterOverride("itkMeshIOBase", "itkSTLMeshIO", "STL IO", true, CreateObjectFunction<STLMeshIO>::New());
 }
 
 STLMeshIOFactory ::~STLMeshIOFactory() {}

From 0c7f3a378e766ab5cc1d0ca769a31f2699777ae7 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Mon, 17 Feb 2020 11:58:48 -0600
Subject: [PATCH 59/73] STYLE: Pefer = 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.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h      | 2 +-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 9f6529bc5c7..26113bb7bf1 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -149,7 +149,7 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
 
 protected:
   STLMeshIO();
-  ~STLMeshIO() override {}
+  ~STLMeshIO() override = default;
 
   void
   PrintSelf(std::ostream & os, Indent indent) const override;
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index 21951f5cc38..13584b23e11 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
@@ -32,7 +32,7 @@ STLMeshIOFactory ::STLMeshIOFactory()
   this->RegisterOverride("itkMeshIOBase", "itkSTLMeshIO", "STL IO", true, CreateObjectFunction<STLMeshIO>::New());
 }
 
-STLMeshIOFactory ::~STLMeshIOFactory() {}
+STLMeshIOFactory ::~STLMeshIOFactory() = default;
 
 const char *
 STLMeshIOFactory ::GetITKSourceVersion() const

From f00a465a17cd3ada3a224f042ff38bcf301af482 Mon Sep 17 00:00:00 2001
From: Mathew Seng <mathewseng@gmail.com>
Date: Tue, 18 Feb 2020 09:02:19 -0600
Subject: [PATCH 60/73] ENH: Update enums from recent enum changes in ITK

---
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx | 66 ++++++++++++-----------
 1 file changed, 34 insertions(+), 32 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 6e07d9014ec..144fd90e32f 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -33,11 +33,11 @@ STLMeshIO ::STLMeshIO()
   this->AddSupportedWriteExtension(".STL");
 
   // STL uses float type by default to store point data
-  this->SetPointComponentType(FLOAT);
+  this->SetPointComponentType(IOComponentEnum::FLOAT);
 
   // STL uses UINT32 to store the number of points,
   // hence the point Ids are of the same UINT32 type.
-  this->SetCellComponentType(UINT);
+  this->SetCellComponentType(IOComponentEnum::UINT);
 
   this->SetPointDimension(3);
 }
@@ -82,11 +82,11 @@ STLMeshIO ::ReadMeshInformation()
 {
 
   // Use default filetype
-  if (this->GetFileType() == ASCII)
+  if (this->GetFileType() == IOFileEnum::ASCII)
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
   }
-  else if (this->GetFileType() == BINARY)
+  else if (this->GetFileType() == IOFileEnum::BINARY)
   {
     this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
   }
@@ -119,9 +119,9 @@ STLMeshIO ::ReadMeshInformation()
   // Determine file type
   if (inputFileIsASCII)
   {
-    if (this->GetFileType() != ASCII)
+    if (this->GetFileType() != IOFileEnum::ASCII)
     {
-      this->SetFileType(ASCII);
+      this->SetFileType(IOFileEnum::ASCII);
 #ifdef _WIN32
       this->m_InputStream.close();
       this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in);
@@ -139,9 +139,9 @@ STLMeshIO ::ReadMeshInformation()
   }
   else
   {
-    if (this->GetFileType() != BINARY)
+    if (this->GetFileType() != IOFileEnum::BINARY)
     {
-      this->SetFileType(BINARY);
+      this->SetFileType(IOFileEnum::BINARY);
 #ifdef _WIN32
       this->m_InputStream.close();
       this->m_InputStream.open(this->m_FileName.c_str(), std::ios::in | std::ios::binary);
@@ -376,7 +376,7 @@ STLMeshIO ::ReadCells(void * buffer)
   while (cellItr != cellEnd)
   {
 
-    *cellPointIds++ = static_cast<CellIDType>(MeshIOBase::TRIANGLE_CELL);
+    *cellPointIds++ = static_cast<CellIDType>(CellGeometryEnum::TRIANGLE_CELL);
     *cellPointIds++ = numberOfPointsInCell;
 
     //
@@ -396,11 +396,11 @@ STLMeshIO ::WriteMeshInformation()
 {
 
   // Use default filetype
-  if (this->GetFileType() == ASCII)
+  if (this->GetFileType() == IOFileEnum::ASCII)
   {
     this->m_OutputStream.open(this->m_FileName.c_str(), std::ios::out);
   }
-  else if (this->GetFileType() == BINARY)
+  else if (this->GetFileType() == IOFileEnum::BINARY)
   {
     this->m_OutputStream.open(this->m_FileName.c_str(), std::ios::out | std::ios::binary);
   }
@@ -413,11 +413,11 @@ STLMeshIO ::WriteMeshInformation()
     return;
   }
 
-  if (this->GetFileType() == ASCII)
+  if (this->GetFileType() == IOFileEnum::ASCII)
   {
     this->m_OutputStream << "solid ascii" << std::endl;
   }
-  else if (this->GetFileType() == BINARY)
+  else if (this->GetFileType() == IOFileEnum::BINARY)
   {
     //
     // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
@@ -442,83 +442,83 @@ void
 STLMeshIO ::WritePoints(void * buffer)
 {
 
-  const IOComponentType pointValueType = this->GetPointComponentType();
+  const IOComponentEnum pointValueType = this->GetPointComponentType();
 
   switch (pointValueType)
   {
-    case UCHAR:
+    case IOComponentEnum::UCHAR:
     {
       using CoordType = unsigned char;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case CHAR:
+    case IOComponentEnum::CHAR:
     {
       using CoordType = char;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case USHORT:
+    case IOComponentEnum::USHORT:
     {
       using CoordType = unsigned short;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case SHORT:
+    case IOComponentEnum::SHORT:
     {
       using CoordType = short;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case UINT:
+    case IOComponentEnum::UINT:
     {
       using CoordType = unsigned int;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case INT:
+    case IOComponentEnum::INT:
     {
       using CoordType = int;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case ULONG:
+    case IOComponentEnum::ULONG:
     {
       using CoordType = unsigned long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case LONG:
+    case IOComponentEnum::LONG:
     {
       using CoordType = long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case ULONGLONG:
+    case IOComponentEnum::ULONGLONG:
     {
       using CoordType = unsigned long long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case LONGLONG:
+    case IOComponentEnum::LONGLONG:
     {
       using CoordType = long long;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case FLOAT:
+    case IOComponentEnum::FLOAT:
     {
       using CoordType = float;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case DOUBLE:
+    case IOComponentEnum::DOUBLE:
     {
       using CoordType = double;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
       break;
     }
-    case LDOUBLE:
+    case IOComponentEnum::LDOUBLE:
     {
       using CoordType = long double;
       this->WritePointsTyped<CoordType>(reinterpret_cast<CoordType *>(buffer));
@@ -533,7 +533,7 @@ STLMeshIO ::WritePoints(void * buffer)
 void
 STLMeshIO ::WriteCells(void * buffer)
 {
-  if (this->GetFileType() == BINARY)
+  if (this->GetFileType() == IOFileEnum::BINARY)
   {
     this->WriteCellsAsBinary(buffer);
   }
@@ -566,10 +566,11 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
-    const auto cellType = static_cast<CellGeometryType>(cellsBuffer[index2++]);
+    const auto cellType = static_cast<CellGeometryEnum>(cellsBuffer[index2++]);
     const auto numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index2++]);
 
-    const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+    const bool isTriangle = (cellType == CellGeometryEnum::TRIANGLE_CELL) ||
+                            (cellType == CellGeometryEnum::POLYGON_CELL && numberOfVerticesInCell == 3);
 
     if (isTriangle)
     {
@@ -635,10 +636,11 @@ STLMeshIO ::WriteCellsAsAscii(void * buffer)
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
-    const auto cellType = static_cast<CellGeometryType>(cellsBuffer[index++]);
+    const auto cellType = static_cast<CellGeometryEnum>(cellsBuffer[index++]);
     const auto numberOfVerticesInCell = static_cast<IdentifierType>(cellsBuffer[index++]);
 
-    const bool isTriangle = (cellType == TRIANGLE_CELL) || (cellType == POLYGON_CELL && numberOfVerticesInCell == 3);
+    const bool isTriangle = (cellType == CellGeometryEnum::TRIANGLE_CELL) ||
+                            (cellType == CellGeometryEnum::POLYGON_CELL && numberOfVerticesInCell == 3);
 
     if (!isTriangle)
     {

From 4f236e04f67ed6ad21c5fd0130b0ad2d9393e598 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans-johnson@uiowa.edu>
Date: Wed, 19 Feb 2020 10:45:25 -0600
Subject: [PATCH 61/73] DOC: Update copyright assignment to NumFOCUS

The mission of NumFOCUS is to promote open
practices in research, data, and scientific
computing.

https://numfocus.org
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 2 +-
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 2 +-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx          | 2 +-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx   | 2 +-
 Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx     | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 26113bb7bf1..099f5cc5b70 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.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/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index bc06fffed3f..5a3b38077ce 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.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/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 144fd90e32f..455ce1d1608 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.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/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index 13584b23e11..e77b333688a 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.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/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 9ca0b97a9d7..1e584f3f0c5 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.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 b09fb2656c63cb768fccd6869f31b0f707fb1191 Mon Sep 17 00:00:00 2001
From: Mathew Seng <mathewseng@gmail.com>
Date: Wed, 14 Oct 2020 11:19:21 -0500
Subject: [PATCH 62/73] 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.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h        | 2 +-
 Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 099f5cc5b70..04d53fff838 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -38,7 +38,7 @@ namespace itk
 class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
 {
 public:
-  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIO);
+  ITK_DISALLOW_COPY_AND_MOVE(STLMeshIO);
 
   /** Standard "Self" type alias. */
   using Self = STLMeshIO;
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 5a3b38077ce..9c3db7a7fb5 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
@@ -33,7 +33,7 @@ namespace itk
 class IOMeshSTL_EXPORT STLMeshIOFactory : public ObjectFactoryBase
 {
 public:
-  ITK_DISALLOW_COPY_AND_ASSIGN(STLMeshIOFactory);
+  ITK_DISALLOW_COPY_AND_MOVE(STLMeshIOFactory);
 
   /** Standard class type alias. */
   using Self = STLMeshIOFactory;

From 1b1bf327ca554bb01ce1ac0982b9b936c2521f1d Mon Sep 17 00:00:00 2001
From: Tom Birdsong <tom.birdsong@kitware.com>
Date: Wed, 1 Jun 2022 08:46:47 -0400
Subject: [PATCH 63/73] ENH: Bump ITK and replace http with https

---
 Modules/IO/IOMeshSTL/LICENSE                  |  4 +--
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  2 +-
 .../IOMeshSTL/include/itkSTLMeshIOFactory.h   |  2 +-
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 30 +++++++++----------
 .../IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx  |  2 +-
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  2 +-
 6 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/LICENSE b/Modules/IO/IOMeshSTL/LICENSE
index d6456956733..62589edd12a 100644
--- a/Modules/IO/IOMeshSTL/LICENSE
+++ b/Modules/IO/IOMeshSTL/LICENSE
@@ -1,7 +1,7 @@
 
                                  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
 
@@ -193,7 +193,7 @@
    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/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 04d53fff838..0e96e184fb2 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.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/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
index 9c3db7a7fb5..4e6cc79235b 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIOFactory.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/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 455ce1d1608..1bae38ac578 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.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,
@@ -180,7 +180,7 @@ STLMeshIO ::ReadMeshInternalFromAscii()
   while (!this->CheckStringFromAscii("endsolid"))
   {
     //
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     //  facet normal ni nj nk
     //      outer loop
@@ -257,7 +257,7 @@ void
 STLMeshIO ::ReadMeshInternalFromBinary()
 {
   //
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   // UINT8[80] header
   //
@@ -277,7 +277,7 @@ STLMeshIO ::ReadMeshInternalFromBinary()
 
   //
   // Binary values in STL files are expected to be in little endian
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&numberOfTriangles);
 
@@ -420,7 +420,7 @@ STLMeshIO ::WriteMeshInformation()
   else if (this->GetFileType() == IOFileEnum::BINARY)
   {
     //
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     // UINT8[80] header
     //
@@ -556,7 +556,7 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
   NormalType normal;
 
   //
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   // UINT32 -- Number of Triangles
   //
@@ -601,7 +601,7 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
     CrossProduct(normal, v12, v10);
 
     //
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     //    foreach triangle
     //    REAL32[3] – Normal vector
@@ -677,7 +677,7 @@ STLMeshIO ::WriteInt32AsBinary(int32_t value)
 {
   //
   // Binary values in STL files are expected to be in little endian
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&value);
   this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
@@ -689,7 +689,7 @@ STLMeshIO ::WriteInt16AsBinary(int16_t value)
 {
   //
   // Binary values in STL files are expected to be in little endian
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   ByteSwapper<int16_t>::SwapFromSystemToLittleEndian(&value);
   this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
@@ -704,7 +704,7 @@ STLMeshIO ::WriteNormalAsBinary(const NormalType & normal)
     float value = normal[i];
     //
     // Binary values in STL files are expected to be in little endian
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
@@ -720,7 +720,7 @@ STLMeshIO ::WritePointAsBinary(const PointType & point)
     float value = point[i];
     //
     // Binary values in STL files are expected to be in little endian
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
@@ -737,7 +737,7 @@ STLMeshIO ::ReadNormalAsBinary(NormalType & normal)
     this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
     //
     // Binary values in STL files are expected to be in little endian
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     normal[i] = value;
@@ -751,7 +751,7 @@ STLMeshIO ::ReadInt32AsBinary(int32_t & value)
   this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
   //
   // Binary values in STL files are expected to be in little endian
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&value);
 }
@@ -763,7 +763,7 @@ STLMeshIO ::ReadInt16AsBinary(int16_t & value)
   this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
   //
   // Binary values in STL files are expected to be in little endian
-  // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
   //
   ByteSwapper<int16_t>::SwapFromSystemToLittleEndian(&value);
 }
@@ -778,7 +778,7 @@ STLMeshIO ::ReadPointAsBinary(PointType & point)
     this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
     //
     // Binary values in STL files are expected to be in little endian
-    // http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
+    // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
     //
     ByteSwapper<float>::SwapFromSystemToLittleEndian(&value);
     point[i] = value;
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
index e77b333688a..8653dfe6de6 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIOFactory.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/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index 1e584f3f0c5..a887c58a95f 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.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 df365ebb1a33158246fa17a1275cc766ef8954e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Wed, 28 Dec 2022 16:42:11 -0500
Subject: [PATCH 64/73] COMP: Match CMake minimum required version to  ITK's

Match CMake minimum required version to  ITK's.

Fixes:
```
CMake Warning at D:/a/ITKIOMeshSTL/ITK/CMake/ITKModuleExternal.cmake:12 (message):
-- cmake_minimum_required of 3.10.2 is not enough.
  cmake_minimum_required must be at least 3.16.3
Call Stack (most recent call first):
  CMakeLists.txt:8 (include)

-- This is needed to allow proper setting of CMAKE_MSVC_RUNTIME_LIBRARY.
-- Do not be surprised if you run into link errors of the style:
  LNK2038: mismatch detected for 'RuntimeLibrary': value 'MTd_Static' doesn't match value 'MDd_Dynamic' in module.obj
```

raised for example at:
https://open.cdash.org/build/8362376/configure
---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 90a56f1297b..45deffbedea 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.10.2)
+cmake_minimum_required(VERSION 3.16.3)
 project(IOMeshSTL)
 set(IOMeshSTL_LIBRARIES IOMeshSTL)
 

From b02d674ed72e243c09851850c781c407c46d49ae Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Wed, 22 Apr 2026 18:52:43 -0500
Subject: [PATCH 65/73] ENH: Convert from md5 to .cid tags.

---
 Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.cid      | 1 +
 Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5      | 1 -
 Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.cid      | 1 +
 Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5      | 1 -
 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.cid | 1 +
 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5 | 1 -
 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.cid | 1 +
 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5 | 1 -
 8 files changed, 4 insertions(+), 4 deletions(-)
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.cid
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.cid
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.cid
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
 create mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.cid
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5

diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.cid b/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.cid
new file mode 100644
index 00000000000..00350e63653
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.cid
@@ -0,0 +1 @@
+bafkreigjpheqapzh2bfdd7prplhccxc4kr452lgkjmmbigqidlos2slrzm
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5 b/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
deleted file mode 100644
index 3e9f76652ae..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/sphere.stl.md5
+++ /dev/null
@@ -1 +0,0 @@
-545c2293b16e250f25395dabbaa53cbb
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.cid b/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.cid
new file mode 100644
index 00000000000..fb4ce908e40
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.cid
@@ -0,0 +1 @@
+bafkreicks2ostzx2se6mfkbcgx3my5rpil4lwguga4gwomcjwo6rr5eyga
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5 b/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
deleted file mode 100644
index 44f4f16d7bd..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/sphere.vtk.md5
+++ /dev/null
@@ -1 +0,0 @@
-2327dbe1884cbf2b58071501567400f6
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.cid b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.cid
new file mode 100644
index 00000000000..ef63e2ea1b1
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.cid
@@ -0,0 +1 @@
+bafkreidm3izfjpw456c5pezwg74xdiaoe7f6xeafo2jsnyyqgxeevrwj54
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5 b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
deleted file mode 100644
index 78055773cfb..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.stl.md5
+++ /dev/null
@@ -1 +0,0 @@
-70a19e48a4393776cfe02f852f25cbe1
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.cid b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.cid
new file mode 100644
index 00000000000..72bffdba630
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.cid
@@ -0,0 +1 @@
+bafkreihljrjpezuelqzwp5qqhhjzfnru4nvwthnjerkkffuha2t2budvpu
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5 b/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5
deleted file mode 100644
index eea81ea180b..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/tetrahedron.vtk.md5
+++ /dev/null
@@ -1 +0,0 @@
-4cd09d26436a53a5adedb33d822cabcd

From 58309d357d19af1de757cb51d1b8719b5a79cf7e Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Mon, 4 May 2026 14:50:52 -0500
Subject: [PATCH 66/73] STYLE: Apply gersemi 0.19.3 to IOMeshSTL src CMakeLists

---
 Modules/IO/IOMeshSTL/src/CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/src/CMakeLists.txt b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
index e2e927802e4..1ab15198734 100644
--- a/Modules/IO/IOMeshSTL/src/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/src/CMakeLists.txt
@@ -1,4 +1,5 @@
-set(IOMeshSTL_SRC
+set(
+  IOMeshSTL_SRC
   itkSTLMeshIO.cxx
   itkSTLMeshIOFactory.cxx
 )

From 8c09e1d45a19e88982a9807d59beaf9dc7e11b0a Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Mon, 4 May 2026 14:50:56 -0500
Subject: [PATCH 67/73] DOC: Add IOMeshSTL module README pointing at archived
 upstream

---
 Modules/IO/IOMeshSTL/README.md | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 Modules/IO/IOMeshSTL/README.md

diff --git a/Modules/IO/IOMeshSTL/README.md b/Modules/IO/IOMeshSTL/README.md
new file mode 100644
index 00000000000..41cf600827d
--- /dev/null
+++ b/Modules/IO/IOMeshSTL/README.md
@@ -0,0 +1,22 @@
+# IOMeshSTL
+
+In-tree ITK module providing read/write support for the
+stereolithography (STL) mesh format, in both ASCII and binary
+encodings. STL is the canonical interchange format for 3D-printing,
+CAD, and surgical-planning workflows.
+
+The flagship classes are `itk::STLMeshIO` and the `STLMeshIOFactory`
+plug-in registration that lets `itk::MeshFileReader` /
+`itk::MeshFileWriter` discover STL automatically.
+
+## Origin
+
+Ingested from the standalone remote module
+[**InsightSoftwareConsortium/ITKIOMeshSTL**](https://github.com/InsightSoftwareConsortium/ITKIOMeshSTL)
+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.
+
+## References
+
+- Mueller D. *STL file format reader and writer for ITK.* The Insight Journal. 2014. <https://doi.org/10.54294/jdvcg7>

From 0d5331daec93c863f8b9f0135f3432df87b22171 Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Mon, 4 May 2026 14:50:59 -0500
Subject: [PATCH 68/73] COMP: Remove IOMeshSTL remote-fetch cmake (now in-tree)

---
 Modules/Remote/IOMeshSTL.remote.cmake | 52 ---------------------------
 1 file changed, 52 deletions(-)
 delete mode 100644 Modules/Remote/IOMeshSTL.remote.cmake

diff --git a/Modules/Remote/IOMeshSTL.remote.cmake b/Modules/Remote/IOMeshSTL.remote.cmake
deleted file mode 100644
index 9c7d3c44612..00000000000
--- a/Modules/Remote/IOMeshSTL.remote.cmake
+++ /dev/null
@@ -1,52 +0,0 @@
-#-- # Grading Level Criteria Report
-#-- EVALUATION DATE: 2020-03-01
-#-- EVALUATORS: [<<NO EVALUATOR>>,<<NO EVALUATOR>>]
-#--
-#-- ## Compliance level 5 star (AKA ITK main modules, or remote modules that could become core modules)
-#--   - [ ] Widespread community dependance
-#--   - [ ] Above 90% code coverage
-#--   - [ ] CI dashboards and testing monitored rigorously
-#--   - [ ] 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)
-#--   - [ ] Meets all ITK code style standards
-#--   - [ ] No external requirements beyond those needed by ITK proper
-#--   - [ ] Builds and passes tests on all supported platforms within 1 month of each core tagged release
-#--            - [ ] Windows Shared Library Build with Visual Studio
-#--            - [ ] Mac with clang compiller
-#--            - [ ] Linux with gcc compiler
-#--   - [ ] Active developer community dedicated to maintaining code-base
-#--   - [ ] 75% code coverage demonstrated for testing suite
-#--   - [ ] Continuous integration testing performed
-#--   - [ ] All requirements of Levels 3,2,1
-#--
-#-- ## Compliance Level 3 star (Quality beta code)
-#--   - [ ] API | executable interface is considered mostly stable and feature complete
-#--   - [ ] 10% C0-code coverage demonstrated for testing suite
-#--   - [ ] 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: Luis Ibanez <luis.ibanez@kitware.com>
-itk_fetch_module(
-  IOMeshSTL
-  "This module contains classes for reading and writing QuadEdgeMeshes using
-  the STL (STereoLithography) file format. https://doi.org/10.54294/7rr2te"
-  MODULE_COMPLIANCE_LEVEL 2
-  GIT_REPOSITORY https://github.com/InsightSoftwareConsortium/ITKIOMeshSTL.git
-  GIT_TAG 8b76de8678c1a4ec2cd177fd32c44099dcd29667
-  )

From fc256109f9d49cd7c53f9ad826500a3832a3f28e Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Mon, 4 May 2026 14:51:00 -0500
Subject: [PATCH 69/73] ENH: Enable Module_IOMeshSTL in configure-ci pixi task

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 52c56027848..79285e9fbab 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,6 +57,7 @@ cmd = '''cmake
   -DModule_Montage:BOOL=ON
   -DModule_FastBilateral:BOOL=ON
   -DModule_GenericLabelInterpolator:BOOL=ON
+  -DModule_IOMeshSTL:BOOL=ON
   -DModule_LabelErodeDilate:BOOL=ON
   -DModule_MeshNoise:BOOL=ON
   -DModule_MGHIO:BOOL=ON

From c1a9bc7df351ca721788a10cfdedc0772c4d6654 Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Mon, 4 May 2026 15:17:49 -0500
Subject: [PATCH 70/73] =?UTF-8?q?BUG:=20IOMeshSTL=20=E2=80=94=20address=20?=
 =?UTF-8?q?Greptile=20review=20(uint32=20cells,=20cleanups)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Five concerns from Greptile's draft review of PR #6206:

P1: STL binary spec is UINT32, but read/write paths declared int32_t.
The high-bit case decremented through negative values (signed-integer
overflow, UB) and SetNumberOfCells silently wrapped to huge unsigned
IdentifierType. Switched both call sites to uint32_t and added
Read/WriteUInt32AsBinary helpers (int32 helpers kept for source compat).

P2: Three unreachable returns after itkExceptionMacro removed.

P2: WriteMeshInformation 'Unable to open file' said 'inputFilename='
while opening the OUTPUT stream. Corrected to 'outputFilename='.

P2: Test reader->Update() now wrapped in ITK_TRY_EXPECT_NO_EXCEPTION
to match writer->Update() and the rest of ITK's tests.

P2 (greptile false positive): STLMeshIO::Read() was suggested for an
override specifier. MeshIOBase has no virtual Read() to override, so
'virtual void Read();' is correct as-is. Reverted.
---
 Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h   |  4 +++
 Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx     | 36 +++++++++++--------
 .../IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx    |  2 +-
 3 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
index 0e96e184fb2..2f04ef52c5f 100644
--- a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
+++ b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -204,6 +204,8 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
   void
   WriteInt32AsBinary(int32_t value);
   void
+  WriteUInt32AsBinary(uint32_t value);
+  void
   WriteInt16AsBinary(int16_t value);
   void
   WriteNormalAsBinary(const NormalType & normal);
@@ -220,6 +222,8 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
   void
   ReadInt32AsBinary(int32_t & value);
   void
+  ReadUInt32AsBinary(uint32_t & value);
+  void
   ReadInt16AsBinary(int16_t & value);
   void
   ReadNormalAsBinary(NormalType & normal);
diff --git a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
index 1bae38ac578..cdb29980442 100644
--- a/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
+++ b/Modules/IO/IOMeshSTL/src/itkSTLMeshIO.cxx
@@ -96,7 +96,6 @@ STLMeshIO ::ReadMeshInformation()
     itkExceptionMacro("Unable to open file\n"
                       "inputFilename= "
                       << this->m_FileName);
-    return;
   }
 
 
@@ -130,7 +129,6 @@ STLMeshIO ::ReadMeshInformation()
         itkExceptionMacro("Unable to open file\n"
                           "inputFilename= "
                           << this->m_FileName);
-        return;
       }
 #endif
     }
@@ -150,7 +148,6 @@ STLMeshIO ::ReadMeshInformation()
         itkExceptionMacro("Unable to open file\n"
                           "inputFilename= "
                           << this->m_FileName);
-        return;
       }
 #endif
     }
@@ -272,14 +269,8 @@ STLMeshIO ::ReadMeshInternalFromBinary()
   //
   // UINT32 -- Number of Triangles
   //
-  int32_t numberOfTriangles;
-  this->m_InputStream.read(reinterpret_cast<char *>(&numberOfTriangles), sizeof(numberOfTriangles));
-
-  //
-  // Binary values in STL files are expected to be in little endian
-  // https://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL
-  //
-  ByteSwapper<int32_t>::SwapFromSystemToLittleEndian(&numberOfTriangles);
+  uint32_t numberOfTriangles;
+  this->ReadUInt32AsBinary(numberOfTriangles);
 
   this->SetNumberOfCells(numberOfTriangles);
 
@@ -408,9 +399,8 @@ STLMeshIO ::WriteMeshInformation()
   if (!this->m_OutputStream.is_open())
   {
     itkExceptionMacro("Unable to open file\n"
-                      "inputFilename= "
+                      "outputFilename= "
                       << this->m_FileName);
-    return;
   }
 
   if (this->GetFileType() == IOFileEnum::ASCII)
@@ -560,7 +550,7 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
   //
   // UINT32 -- Number of Triangles
   //
-  int32_t numberOfTriangles = 0;
+  uint32_t numberOfTriangles = 0;
 
   SizeValueType index2 = 0;
 
@@ -584,7 +574,7 @@ STLMeshIO ::WriteCellsAsBinary(void * buffer)
     index2 += numberOfVerticesInCell;
   }
 
-  this->WriteInt32AsBinary(numberOfTriangles);
+  this->WriteUInt32AsBinary(numberOfTriangles);
 
   for (SizeValueType polygonItr = 0; polygonItr < numberOfPolygons; polygonItr++)
   {
@@ -684,6 +674,14 @@ STLMeshIO ::WriteInt32AsBinary(int32_t value)
 }
 
 
+void
+STLMeshIO ::WriteUInt32AsBinary(uint32_t value)
+{
+  ByteSwapper<uint32_t>::SwapFromSystemToLittleEndian(&value);
+  this->m_OutputStream.write(reinterpret_cast<const char *>(&value), sizeof(value));
+}
+
+
 void
 STLMeshIO ::WriteInt16AsBinary(int16_t value)
 {
@@ -757,6 +755,14 @@ STLMeshIO ::ReadInt32AsBinary(int32_t & value)
 }
 
 
+void
+STLMeshIO ::ReadUInt32AsBinary(uint32_t & value)
+{
+  this->m_InputStream.read(reinterpret_cast<char *>(&value), sizeof(value));
+  ByteSwapper<uint32_t>::SwapFromSystemToLittleEndian(&value);
+}
+
+
 void
 STLMeshIO ::ReadInt16AsBinary(int16_t & value)
 {
diff --git a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
index a887c58a95f..d8c41cc2b6a 100644
--- a/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
+++ b/Modules/IO/IOMeshSTL/test/itkSTLMeshIOTest.cxx
@@ -61,7 +61,7 @@ itkSTLMeshIOTest(int argc, char * argv[])
     writer->SetFileTypeAsBINARY();
   }
 
-  reader->Update();
+  ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());
   QEMeshType * mesh = reader->GetOutput();
 
   writer->SetInput(reader->GetOutput());

From 93985caf8d75edd75222b7ad528b12d8960aef76 Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Tue, 5 May 2026 06:02:42 -0500
Subject: [PATCH 71/73] COMP: Drop standalone-build wrapper from IOMeshSTL
 CMakeLists

In-tree, ITK_SOURCE_DIR is always defined, so the
'if(NOT ITK_SOURCE_DIR) ... find_package(ITK) ... else() itk_module_impl()'
guard is dead code.  Address @dzenanz review comment.
---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 45deffbedea..7aea1b33aa0 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -2,10 +2,4 @@ cmake_minimum_required(VERSION 3.16.3)
 project(IOMeshSTL)
 set(IOMeshSTL_LIBRARIES IOMeshSTL)
 
-if(NOT ITK_SOURCE_DIR)
-  find_package(ITK REQUIRED)
-  list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
-  include(ITKModuleExternal)
-else()
-  itk_module_impl()
-endif()
+itk_module_impl()

From f100c257b6b11180a65158c760efa144e90a0ab1 Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Tue, 5 May 2026 06:02:46 -0500
Subject: [PATCH 72/73] COMP: Remove leftover ExternalData cache from IOMeshSTL
 Baseline
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Four .ExternalData_MD5_<hash> files survived the ingest from the
upstream module's local fetch cache.  They are not source — ExternalData
re-creates them on demand alongside the .cid sidecars they correspond
to (sphere.{stl,vtk}, tetrahedron.{stl,vtk}).  Address @dzenanz review
comment.
---
 ...lData_MD5_2327dbe1884cbf2b58071501567400f6 |  56 -----
 ...lData_MD5_4cd09d26436a53a5adedb33d822cabcd |  14 --
 ...lData_MD5_545c2293b16e250f25395dabbaa53cbb | 226 ------------------
 ...lData_MD5_70a19e48a4393776cfe02f852f25cbe1 |  30 ---
 4 files changed, 326 deletions(-)
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
 delete mode 100644 Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1

diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6 b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
deleted file mode 100644
index 38a77c65d0e..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6
+++ /dev/null
@@ -1,56 +0,0 @@
-# vtk DataFile Version 2.0
-File written by itkVTKPolyDataWriter
-ASCII
-DATASET POLYDATA
-POINTS 18 float
-1 0 0
--1 0 0
-0 1 0
-0 -1 0
-0 0 1
-0 0 -1
-0 0.707107 0.707107
-0.707107 0 0.707107
-0.707107 0.707107 0
--0.707107 0.707107 0
--0.707107 0 0.707107
--0.707107 -0.707107 0
-0 -0.707107 0.707107
-0.707107 -0.707107 0
-0 0.707107 -0.707107
-0.707107 0 -0.707107
--0.707107 0 -0.707107
-0 -0.707107 -0.707107
-POLYGONS 32 128
-3 2 6 8
-3 6 4 7
-3 7 0 8
-3 6 7 8
-3 2 9 6
-3 9 1 10
-3 10 4 6
-3 9 10 6
-3 1 11 10
-3 11 3 12
-3 12 4 10
-3 11 12 10
-3 4 12 7
-3 12 3 13
-3 13 0 7
-3 12 13 7
-3 5 14 15
-3 14 2 8
-3 8 0 15
-3 14 8 15
-3 2 14 9
-3 14 5 16
-3 16 1 9
-3 14 16 9
-3 5 17 16
-3 17 3 11
-3 11 1 16
-3 17 11 16
-3 5 15 17
-3 15 0 13
-3 13 3 17
-3 15 13 17
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
deleted file mode 100644
index 9339517655d..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd
+++ /dev/null
@@ -1,14 +0,0 @@
-# vtk DataFile Version 2.0
-File written by itkVTKPolyDataWriter
-ASCII
-DATASET POLYDATA
-POINTS 4 float
-0 0 0
-1 0 0
-0 1 0
-0 0 1
-POLYGONS 4 16
-3 0 2 1
-3 0 1 3
-3 0 3 2
-3 1 2 3
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
deleted file mode 100644
index 7af8c1d6e28..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_545c2293b16e250f25395dabbaa53cbb
+++ /dev/null
@@ -1,226 +0,0 @@
-solid ascii
- facet normal 0.357406 0.862856 0.357406
-  outer loop
-   vertex 0 1 0
-   vertex 0 0.707107 0.707107
-   vertex 0.707107 0.707107 0
-  endloop
- endfacet
- facet normal 0.357406 0.357406 0.862856
-  outer loop
-   vertex 0 0.707107 0.707107
-   vertex 0 0 1
-   vertex 0.707107 0 0.707107
-  endloop
- endfacet
- facet normal 0.862856 0.357406 0.357406
-  outer loop
-   vertex 0.707107 0 0.707107
-   vertex 1 0 0
-   vertex 0.707107 0.707107 0
-  endloop
- endfacet
- facet normal 0.57735 0.57735 0.57735
-  outer loop
-   vertex 0 0.707107 0.707107
-   vertex 0.707107 0 0.707107
-   vertex 0.707107 0.707107 0
-  endloop
- endfacet
- facet normal -0.357406 0.862856 0.357406
-  outer loop
-   vertex 0 1 0
-   vertex -0.707107 0.707107 0
-   vertex 0 0.707107 0.707107
-  endloop
- endfacet
- facet normal -0.862856 0.357406 0.357406
-  outer loop
-   vertex -0.707107 0.707107 0
-   vertex -1 0 0
-   vertex -0.707107 0 0.707107
-  endloop
- endfacet
- facet normal -0.357406 0.357406 0.862856
-  outer loop
-   vertex -0.707107 0 0.707107
-   vertex 0 0 1
-   vertex 0 0.707107 0.707107
-  endloop
- endfacet
- facet normal -0.57735 0.57735 0.57735
-  outer loop
-   vertex -0.707107 0.707107 0
-   vertex -0.707107 0 0.707107
-   vertex 0 0.707107 0.707107
-  endloop
- endfacet
- facet normal -0.862856 -0.357406 0.357406
-  outer loop
-   vertex -1 0 0
-   vertex -0.707107 -0.707107 0
-   vertex -0.707107 0 0.707107
-  endloop
- endfacet
- facet normal -0.357406 -0.862856 0.357406
-  outer loop
-   vertex -0.707107 -0.707107 0
-   vertex 0 -1 0
-   vertex 0 -0.707107 0.707107
-  endloop
- endfacet
- facet normal -0.357406 -0.357406 0.862856
-  outer loop
-   vertex 0 -0.707107 0.707107
-   vertex 0 0 1
-   vertex -0.707107 0 0.707107
-  endloop
- endfacet
- facet normal -0.57735 -0.57735 0.57735
-  outer loop
-   vertex -0.707107 -0.707107 0
-   vertex 0 -0.707107 0.707107
-   vertex -0.707107 0 0.707107
-  endloop
- endfacet
- facet normal 0.357406 -0.357406 0.862856
-  outer loop
-   vertex 0 0 1
-   vertex 0 -0.707107 0.707107
-   vertex 0.707107 0 0.707107
-  endloop
- endfacet
- facet normal 0.357406 -0.862856 0.357406
-  outer loop
-   vertex 0 -0.707107 0.707107
-   vertex 0 -1 0
-   vertex 0.707107 -0.707107 0
-  endloop
- endfacet
- facet normal 0.862856 -0.357406 0.357406
-  outer loop
-   vertex 0.707107 -0.707107 0
-   vertex 1 0 0
-   vertex 0.707107 0 0.707107
-  endloop
- endfacet
- facet normal 0.57735 -0.57735 0.57735
-  outer loop
-   vertex 0 -0.707107 0.707107
-   vertex 0.707107 -0.707107 0
-   vertex 0.707107 0 0.707107
-  endloop
- endfacet
- facet normal 0.357406 0.357406 -0.862856
-  outer loop
-   vertex 0 0 -1
-   vertex 0 0.707107 -0.707107
-   vertex 0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal 0.357406 0.862856 -0.357406
-  outer loop
-   vertex 0 0.707107 -0.707107
-   vertex 0 1 0
-   vertex 0.707107 0.707107 0
-  endloop
- endfacet
- facet normal 0.862856 0.357406 -0.357406
-  outer loop
-   vertex 0.707107 0.707107 0
-   vertex 1 0 0
-   vertex 0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal 0.57735 0.57735 -0.57735
-  outer loop
-   vertex 0 0.707107 -0.707107
-   vertex 0.707107 0.707107 0
-   vertex 0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal -0.357406 0.862856 -0.357406
-  outer loop
-   vertex 0 1 0
-   vertex 0 0.707107 -0.707107
-   vertex -0.707107 0.707107 0
-  endloop
- endfacet
- facet normal -0.357406 0.357406 -0.862856
-  outer loop
-   vertex 0 0.707107 -0.707107
-   vertex 0 0 -1
-   vertex -0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal -0.862856 0.357406 -0.357406
-  outer loop
-   vertex -0.707107 0 -0.707107
-   vertex -1 0 0
-   vertex -0.707107 0.707107 0
-  endloop
- endfacet
- facet normal -0.57735 0.57735 -0.57735
-  outer loop
-   vertex 0 0.707107 -0.707107
-   vertex -0.707107 0 -0.707107
-   vertex -0.707107 0.707107 0
-  endloop
- endfacet
- facet normal -0.357406 -0.357406 -0.862856
-  outer loop
-   vertex 0 0 -1
-   vertex 0 -0.707107 -0.707107
-   vertex -0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal -0.357406 -0.862856 -0.357406
-  outer loop
-   vertex 0 -0.707107 -0.707107
-   vertex 0 -1 0
-   vertex -0.707107 -0.707107 0
-  endloop
- endfacet
- facet normal -0.862856 -0.357406 -0.357406
-  outer loop
-   vertex -0.707107 -0.707107 0
-   vertex -1 0 0
-   vertex -0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal -0.57735 -0.57735 -0.57735
-  outer loop
-   vertex 0 -0.707107 -0.707107
-   vertex -0.707107 -0.707107 0
-   vertex -0.707107 0 -0.707107
-  endloop
- endfacet
- facet normal 0.357406 -0.357406 -0.862856
-  outer loop
-   vertex 0 0 -1
-   vertex 0.707107 0 -0.707107
-   vertex 0 -0.707107 -0.707107
-  endloop
- endfacet
- facet normal 0.862856 -0.357406 -0.357406
-  outer loop
-   vertex 0.707107 0 -0.707107
-   vertex 1 0 0
-   vertex 0.707107 -0.707107 0
-  endloop
- endfacet
- facet normal 0.357406 -0.862856 -0.357406
-  outer loop
-   vertex 0.707107 -0.707107 0
-   vertex 0 -1 0
-   vertex 0 -0.707107 -0.707107
-  endloop
- endfacet
- facet normal 0.57735 -0.57735 -0.57735
-  outer loop
-   vertex 0.707107 0 -0.707107
-   vertex 0.707107 -0.707107 0
-   vertex 0 -0.707107 -0.707107
-  endloop
- endfacet
-endsolid
diff --git a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1 b/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1
deleted file mode 100644
index be14d23b637..00000000000
--- a/Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_70a19e48a4393776cfe02f852f25cbe1
+++ /dev/null
@@ -1,30 +0,0 @@
-solid ascii
-  facet normal 0 0 -1
-    outer loop
-      vertex 0 0 0
-      vertex 0 1 0
-      vertex 1 0 0
-    endloop
-  endfacet
-  facet normal 0 -1 0
-    outer loop
-      vertex 0 0 0
-      vertex 1 0 0
-      vertex 0 0 1
-    endloop
-  endfacet
-  facet normal -1 0 0
-    outer loop
-      vertex 0 0 0
-      vertex 0 0 1
-      vertex 0 1 0
-    endloop
-  endfacet
-  facet normal 1 1 1
-    outer loop
-      vertex 1 0 0
-      vertex 0 1 0
-      vertex 0 0 1
-    endloop
-  endfacet
-endsolid

From 1e7dcb41af4be50d237a4aa140af63f4c47c3aaf Mon Sep 17 00:00:00 2001
From: "Hans J. Johnson" <hans-johnson@uiowa.edu>
Date: Tue, 5 May 2026 11:26:25 -0500
Subject: [PATCH 73/73] COMP: Drop redundant cmake_minimum_required from
 IOMeshSTL/CMakeLists.txt

In-tree, ITK's top-level CMakeLists pins the CMake minimum, so the
per-module declaration is dead code.  Pre-emptive cleanup matching the
v4 ingest-pipeline rule codified in PR #6204
(sanitize-history.py:patch_drop_cmake_minimum_required).
---
 Modules/IO/IOMeshSTL/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Modules/IO/IOMeshSTL/CMakeLists.txt b/Modules/IO/IOMeshSTL/CMakeLists.txt
index 7aea1b33aa0..9f9ce821e7f 100644
--- a/Modules/IO/IOMeshSTL/CMakeLists.txt
+++ b/Modules/IO/IOMeshSTL/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 3.16.3)
 project(IOMeshSTL)
 set(IOMeshSTL_LIBRARIES IOMeshSTL)