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ENH: Ingest ITKIOMeshSTL into Modules/IO#6206

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May 5, 2026
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ENH: Ingest ITKIOMeshSTL into Modules/IO#6206
hjmjohnson merged 98 commits intoInsightSoftwareConsortium:mainfrom
hjmjohnson:ingest-iomeshstl

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@hjmjohnson hjmjohnson commented May 4, 2026

Ingests IOMeshSTL from the standalone remote module InsightSoftwareConsortium/ITKIOMeshSTL into ITK at Modules/IO/IOMeshSTL/. Branch is based directly on upstream/main and contains no v4-tooling files in its diff — independently mergeable.

Local validation: pre-commit run --all-files clean; IOMeshSTLTestDriver builds; 10/10 IOMeshSTL tests pass locally (after ExternalData fetches the four .cid content links from the IPFS gateway).

What this provides

IOMeshSTL adds read/write support for the stereolithography (STL) mesh format in both ASCII and binary encodings — 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.

Path: Modules/IO/IOMeshSTL/ (preserving upstream module name IOMeshSTL; renaming to MeshSTL would break the public CMake find_package(IOMeshSTL) API for downstream consumers).

Pipeline metrics
Metric Value
Upstream commits → rewritten 143 → 89
Upstream merges → preserved 44 → 24 (no linearization)
Blobs scanned in sanitize 149 (cxx=106, py=0, cmake=28, text=9, skip=6)
Blobs reformatted 108 (clang-format / gersemi / trailing-ws / EOF)
Commit subjects auto-prefixed 42
Subjects truncated to 78 chars 3
Blank lines inserted after subject 23
README.rst → README.md rewrites in itk-module.cmake 4
Merges visible in git log -- Modules/IO/IOMeshSTL 5
Tooling provenance

This PR was produced via the v4 ingestion pipeline (PR #6204) but the v4 scripts are intentionally not included in this PR's diff — they were invoked from a separate worktree. This makes the PR mergeable independently of #6204.

Phase B (upstream archival) is deferred. After this PR merges:

  1. Wait for PR WIP: Add v4 remote-module ingestion (two-phase, per-commit hooks) #6204 (v4 tooling) to land on main.
  2. Run Utilities/Maintenance/RemoteModuleIngest/archive-remote-module.sh IOMeshSTL --itk-pr-number <THIS-PR> to push the deletion + MIGRATION_README.md → README.md promotion to upstream and flip archived=true.

This PR makes no upstream changes; the upstream ITKIOMeshSTL repository remains live until the operator manually runs Phase B.

Follow-up commits in this PR

After the merge commit (ENH: Ingest ITKIOMeshSTL into Modules/IO), the standard cleanup commits land on top:

  • STYLE: Apply gersemi 0.19.3 to Modules/IO/IOMeshSTL/src/CMakeLists.txt. The v4 sanitize pass uses gersemi 0.24.0; ITK's pre-commit pins 0.19.3. The post-merge pre-commit run --all-files gate caught one CMake file where the two versions disagree.
  • DOC: Add Modules/IO/IOMeshSTL/README.md pointing at the archived upstream.
  • COMP: Remove Modules/Remote/IOMeshSTL.remote.cmake (now in-tree).
  • ENH: Enable Module_IOMeshSTL:BOOL=ON in pyproject.toml configure-ci.

Note: no manual itk-module.cmake patch was needed in this PR — the v4 sanitize pass auto-rewrites file(READ "${...}/README.rst" DOCUMENTATION) to read README.md instead, across every historical commit.

Luis Ibanez and others added 30 commits December 30, 2013 12:00
ENH: First commit
cd34d75
DOC: Added the Apache 2.0 License file.
6ba7e6d
ENH: First working version.
3f1e6df 
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.
ENH: WritePoints now templated on coordinate type.
de9dea2 
Introduced a templated function to manage the multiple cases of
point coordinate types.
BUG: Fixed direction of normals.
1541c87 
Still assuming that points are provided in a right handed order.
ENH: Now supporting .STL extension too.
16fee79 
The .STL (in capitals) extension is now supported too in the filename.
ENH: Added support for BINARY writing.
a36cca8 
And corresponding test.
ENH: Improved code coverage.
083f42d
ENH: Started to do parsing on Read.
3d51c32 
Parsed input file both in ASCII and BINARY,
stored points into an std::set.
ENH: Added structure for list of Cells and point Ids.
3931da9 
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.
ENH: Implemented ReadPoints(buffer).
07370d2 
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.
ENH: Implemented ReadCells() method.
3abcb31 
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.
BUG: Fixed STL reading. Added tetrahedron test.
d7231a2 
After adding a tetrahedron test, debugged the process of reading and
consolidating incoming vertices. Fixed the reading of STL files.
ENH: Better Point compare method.
0ad8623 
Replaced previous hash, with a more consistent compare method.
BUG: Fixed bug. Points must be passed in order.
2eb0089 
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.
BUG: Fixed BINARY read.
4aeac59 
It was off due to the initial read of the header used to determine
whether the input file is ASCII or BINARY.
DOC: Fixing Doxygen groups.
1fe73e6 
Added these two classes to the STLMeshIO group.
BUG: Now managing Endianness.
6fd22db 
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.
ENH: Report the system endianness.
7bf5830 
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.
ENH: Throwing exception for non-triangle cells.
11fcf74 
Suggested in code review by Arnaud Gelas.
ENH: Splitted WriteCells() into BINARY and ASCII.
1cee9a2 
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.
STYLE: Rename module to match ITK standards.
4ab31f2
ENH: Propagated Module name changes.
3e42b36 
To make it consistent in all the CMake infrastructure.
ENH: Removing unused variables.
ec28536 
That before were used to verify that all cells were triangles.
COMP: Fixing instantiation of templated functions.
b9b41ef 
To address compilation errors from MacOSX-gcc4.2-Release-IOSTL.
@thewtex
BUG: Add EXCLUDE_FROM_DEFAULT.
038aafb 
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.
@brianhelba
BUG: Fix WritePointsTyped() to no longer use conflicting typenames
c34e043 
"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.
ENH: Merge pull request #1 from thewtex/exclude
ec9c67d 
BUG: Add EXCLUDE_FROM_DEFAULT.
ENH: Merge pull request #2 from brianhelba/Fix_WritePoints
ee4d1a9 
BUG: Fix WritePointsTyped() to no longer use conflicting typenames
@thewtex
COMP: Remove duplicate group entry in ITKIOMesh.
1e52de5
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dzenanz commented May 4, 2026

in Modules\IO\IOMeshSTL\test\Baseline, there are some weirdly named files (e.g. .ExternalData_MD5_4cd09d26436a53a5adedb33d822cabcd). They should be removed or converted into .cids.

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dzenanz commented May 4, 2026

In Modules\IO\IOMeshSTL\CMakeLists.txt, we don't need if(NOT ITK_SOURCE_DIR) block.

hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 4, 2026
@hjmjohnson
BUG: IOMeshSTL — address Greptile review (uint32 cells, cleanups)
fffd214 
Five concerns from Greptile's draft review of PR InsightSoftwareConsortium#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.
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 5, 2026
@hjmjohnson
DOC: v4 strategy — record ghostflow root-commit + Greptile review pat…
11b1928 
…terns

Add a 'Known artifacts at PR-review time' section to capture two
things future ingest operators need to expect but that v3/v4 do not
fix automatically:

  - The single ghostflow-check-main 'root commit not allowed' error
    that every Mode-A merge produces.  Maintainers override at merge.
    Calling it out keeps operators from chasing a non-fix.

  - A short table of code-level patterns Greptile has flagged
    post-ingest on multiple modules (IOMeshSTL InsightSoftwareConsortium#6206, RLEImage InsightSoftwareConsortium#6208):
    signed-vs-unsigned size types, missing override, dead return after
    itkExceptionMacro, stray test args, external-friend declarations,
    GetBuffer-const correctness, and allocator-init invariants.

The table is the durable channel for cross-ingest review knowledge —
extend it as new recurring patterns surface.
hjmjohnson and others added 8 commits May 5, 2026 05:58
@hjmjohnson @blowekamp
@brianhelba @sudomakeinstall @dzenanz @jhlegarreta @mseng10 @thewtex @tbirdso @zachary-williamson
ENH: Ingest ITKIOMeshSTL into Modules/IO
420a9e2 
Brings IOMeshSTL from a configure-time remote fetch into the ITK
source tree at Modules/IO/IOMeshSTL/ using the v4 ingestion
pipeline (whitelist filter-repo + per-commit clang-format + black +
commit-prefix sanitization).

Upstream repo:  https://github.com/InsightSoftwareConsortium/ITKIOMeshSTL.git
Upstream tip:   fb18e5d83415603d977279e0546bb55c1ece623d
Ingest date:    2026-05-04
Whitelist:      IOMeshSTL.list

Per-commit transforms applied across all 89 commits:
  - filter-repo --paths-from-file (whitelist)
  - filter-repo --to-subdirectory-filter Modules/IO/IOMeshSTL
  - clang-format -style=file (ITK main's .clang-format) for *.cxx/.h/.hxx/...
  - black for *.py
  - heuristic ITK prefix added to commit subjects without one

Merge topology preserved: 44 -> 24 merge(s).

Primary author: Luis Ibanez <luis.ibanez@kitware.com>

Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
Co-authored-by: Brian Helba <brian.helba@kitware.com>
Co-authored-by: Davis Vigneault <davis.vigneault@gmail.com>
Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com>
Co-authored-by: Hans J. Johnson <hans-johnson@uiowa.edu>
Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>
Co-authored-by: Hans Johnson <hans.j.johnson@gmail.com>
Co-authored-by: Jon Haitz Legarreta <jhlegarreta@vicomtech.org>
Co-authored-by: Jon Haitz Legarreta Gorroño <jon.haitz.legarreta@gmail.com>
Co-authored-by: Mathew Seng <mathewseng@gmail.com>
Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>
Co-authored-by: Matt McCormick <matt@mmmccormick.com>
Co-authored-by: Tom Birdsong <tom.birdsong@kitware.com>
Co-authored-by: Zach Williamson <zachary-williamson@uiowa.edu>
@hjmjohnson
STYLE: Apply gersemi 0.19.3 to IOMeshSTL src CMakeLists
58309d3
@hjmjohnson
DOC: Add IOMeshSTL module README pointing at archived upstream
8c09e1d
@hjmjohnson
COMP: Remove IOMeshSTL remote-fetch cmake (now in-tree)
0d5331d
@hjmjohnson
ENH: Enable Module_IOMeshSTL in configure-ci pixi task
fc25610
@hjmjohnson
BUG: IOMeshSTL — address Greptile review (uint32 cells, cleanups)
c1a9bc7 
Five concerns from Greptile's draft review of PR InsightSoftwareConsortium#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.
@hjmjohnson
COMP: Drop standalone-build wrapper from IOMeshSTL CMakeLists
93985ca 
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.
@hjmjohnson
COMP: Remove leftover ExternalData cache from IOMeshSTL Baseline
f100c25 
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.
@hjmjohnson
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hjmjohnson commented May 5, 2026

Both points addressed in the latest push:

  • Standalone-build wrapper: dropped in 93985ca. Modules/IO/IOMeshSTL/CMakeLists.txt is now just itk_module_impl().
  • .ExternalData_MD5_<hash> files: removed in f100c25. They were leftover ExternalData fetch cache from the upstream module — not source. ExternalData regenerates them on demand from the .cid sidecars (sphere.{stl,vtk}, tetrahedron.{stl,vtk}).

Branch was also rebased onto the latest upstream/main (was 127 commits behind) using --rebase-merges to preserve Mode-A merge topology (25 merges, 1 root commit, 95 PR commits — all unchanged from pre-rebase). pre-commit run --all-files clean. Thanks @dzenanz.

@hjmjohnson hjmjohnson requested a review from dzenanz May 5, 2026 11:08
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 5, 2026
@hjmjohnson
COMP: v4 deny-pass — strip ExternalData fetch cache from history
67a965a 
ExternalData stores resolved fetched content as .ExternalData_<algo>_<hash>
files alongside the .cid / .md5 sidecars they correspond to.  These
are local fetch cache, not source — ExternalData regenerates them on
demand at consumer-time.  Upstream remote modules sometimes commit
them inadvertently from a CTest run inside their working tree (e.g.
ITKIOMeshSTL had four such files in test/Baseline/, flagged by
@dzenanz on PR InsightSoftwareConsortium#6206).

Add **/.ExternalData_* to the scaffolding deny-pass so they never
enter ITK history.
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 5, 2026
@hjmjohnson
COMP: v4 sanitize — unwrap standalone-build CMake guard
7f16e2f 
Upstream remote modules wrap their top-level CMakeLists.txt in

    if(NOT ITK_SOURCE_DIR)
      find_package(ITK REQUIRED)
      list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
      include(ITKModuleExternal)
    else()
      itk_module_impl()
    endif()

so the same file works both as a fetched remote module and as a
stand-alone CMake project.  In an in-tree ingested module
ITK_SOURCE_DIR is always defined, so the if-branch is dead code;
@dzenanz flagged it on PR InsightSoftwareConsortium#6206 (IOMeshSTL).

Add patch_standalone_build_guard() that detects the idiom (allowing
2- or 4-space indent variants) and replaces it with a bare
itk_module_impl() before gersemi formatting runs.  Track count via
sanitizer.standalone_guard_patches and print it in the run summary.
This was referenced May 5, 2026
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dzenanz commented May 5, 2026

/azp run ITK.macOS.Python

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Looks good on a glance.

Comment thread Modules/IO/IOMeshSTL/test/Baseline/.ExternalData_MD5_2327dbe1884cbf2b58071501567400f6 Outdated
@hjmjohnson
COMP: Drop redundant cmake_minimum_required from IOMeshSTL/CMakeLists…
1e7dcb4 
….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 InsightSoftwareConsortium#6204
(sanitize-history.py:patch_drop_cmake_minimum_required).
@hjmjohnson hjmjohnson added this to the ITK 6.0 Release Candidate 1 milestone May 5, 2026
@hjmjohnson hjmjohnson mentioned this pull request May 5, 2026
Merged
@hjmjohnson hjmjohnson merged commit 8c008f2 into InsightSoftwareConsortium:main May 5, 2026
14 of 17 checks passed
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 6, 2026
@hjmjohnson
BUG: IOMeshSTL — address Greptile review (uint32 cells, cleanups)
6b3a50b 
Five concerns from Greptile's draft review of PR InsightSoftwareConsortium#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.
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 6, 2026
@hjmjohnson
Merge pull request InsightSoftwareConsortium#6206 from hjmjohnson/ing…
fde53cd 
…est-iomeshstl

ENH: Ingest ITKIOMeshSTL into Modules/IO
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 7, 2026
@hjmjohnson
DOC: v4 strategy — record ghostflow root-commit + Greptile review pat…
f084407 
…terns

Add a 'Known artifacts at PR-review time' section to capture two
things future ingest operators need to expect but that v3/v4 do not
fix automatically:

  - The single ghostflow-check-main 'root commit not allowed' error
    that every Mode-A merge produces.  Maintainers override at merge.
    Calling it out keeps operators from chasing a non-fix.

  - A short table of code-level patterns Greptile has flagged
    post-ingest on multiple modules (IOMeshSTL InsightSoftwareConsortium#6206, RLEImage InsightSoftwareConsortium#6208):
    signed-vs-unsigned size types, missing override, dead return after
    itkExceptionMacro, stray test args, external-friend declarations,
    GetBuffer-const correctness, and allocator-init invariants.

The table is the durable channel for cross-ingest review knowledge —
extend it as new recurring patterns surface.
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 7, 2026
@hjmjohnson
COMP: v4 deny-pass — strip ExternalData fetch cache from history
4e53c93 
ExternalData stores resolved fetched content as .ExternalData_<algo>_<hash>
files alongside the .cid / .md5 sidecars they correspond to.  These
are local fetch cache, not source — ExternalData regenerates them on
demand at consumer-time.  Upstream remote modules sometimes commit
them inadvertently from a CTest run inside their working tree (e.g.
ITKIOMeshSTL had four such files in test/Baseline/, flagged by
@dzenanz on PR InsightSoftwareConsortium#6206).

Add **/.ExternalData_* to the scaffolding deny-pass so they never
enter ITK history.
hjmjohnson added a commit to hjmjohnson/ITK that referenced this pull request May 7, 2026
@hjmjohnson
COMP: v4 sanitize — unwrap standalone-build CMake guard
3eae792 
Upstream remote modules wrap their top-level CMakeLists.txt in

    if(NOT ITK_SOURCE_DIR)
      find_package(ITK REQUIRED)
      list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
      include(ITKModuleExternal)
    else()
      itk_module_impl()
    endif()

so the same file works both as a fetched remote module and as a
stand-alone CMake project.  In an in-tree ingested module
ITK_SOURCE_DIR is always defined, so the if-branch is dead code;
@dzenanz flagged it on PR InsightSoftwareConsortium#6206 (IOMeshSTL).

Add patch_standalone_build_guard() that detects the idiom (allowing
2- or 4-space indent variants) and replaces it with a bare
itk_module_impl() before gersemi formatting runs.  Track count via
sanitizer.standalone_guard_patches and print it in the run summary.
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@hjmjohnson @dzenanz @thewtex @brianhelba @blowekamp @sudomakeinstall @zachary-williamson @jhlegarreta @mseng10 @tbirdso