ENH: Ingest ITKIOMeshMZ3 into Modules/IO#6214
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hjmjohnson merged 22 commits intoInsightSoftwareConsortium:mainfrom May 5, 2026
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ENH: Ingest ITKIOMeshMZ3 into Modules/IO#6214hjmjohnson merged 22 commits intoInsightSoftwareConsortium:mainfrom
hjmjohnson merged 22 commits intoInsightSoftwareConsortium:mainfrom
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Read and write, vertex, cells, point data. Compressed or uncompressed.
To address macos-14 CI build warning: src/itkMZ3MeshIO.cxx:484:11: warning: 11 enumeration values not handled in switch: 'UNKNOWNCOMPONENTTYPE', 'UCHAR', 'CHAR'... [-Wswitch]
COMP: Add switch default for point component type
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Two upstream bugs caught by Greptile review on PR InsightSoftwareConsortium#6214: 1. WritePointData() printed to std::cerr and returned silently when m_PointPixelComponentType was UNKNOWNCOMPONENTTYPE, leaving the output file in a partially-written state. Replace with itkExceptionMacro so the failure surfaces to the caller. 2. ~MZ3MeshIO() never closed m_Ofstream — a write that threw between WriteMeshInformation()'s open and Write()'s explicit close leaked the output stream. Close both m_Ifstream and m_Ofstream in the destructor's uncompressed branch (guarded by is_open() so closing twice is safe). Also rewrites the 20 C-style (char *)& casts on gzread / gzwrite / ifstream / ofstream calls to reinterpret_cast<char *>(&...) per ITK style guide (Greptile P2 #6). Also fixes the WriteCells CHAR case that cast the buffer to unsigned char * instead of char *, which would silently corrupt negative vertex indices on signed cell-component types (Greptile P2 #5).
dzenanz
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Brings IOMeshMZ3 from a configure-time remote fetch into the ITK source tree at Modules/IO/IOMeshMZ3/ using the v4 ingestion pipeline (whitelist filter-repo + per-commit clang-format + black + commit-prefix sanitization). Upstream repo: https://github.com/InsightSoftwareConsortium/ITKIOMeshMZ3.git Upstream tip: fbeed91e6800830e84a7ba5e3461addd98a2e772 Ingest date: 2026-05-05 Whitelist: IOMeshMZ3.list Per-commit transforms applied across all 13 commits: - filter-repo --paths-from-file (whitelist) - filter-repo --to-subdirectory-filter Modules/IO/IOMeshMZ3 - 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: 4 -> 1 merge(s). Primary author: Matt McCormick <matt@mmmccormick.com> Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu>
The Phase A sanitizer's text/cmake classifier did not pick this small file up as 'cmake' (its sniff treated it as 'text'), so gersemi's pass was skipped. Apply the formatter now to satisfy ITK's pre-commit gersemi hook. Same one-off observed on PR InsightSoftwareConsortium#6215 (IOFDF).
Two upstream bugs caught by Greptile review on PR InsightSoftwareConsortium#6214: 1. WritePointData() printed to std::cerr and returned silently when m_PointPixelComponentType was UNKNOWNCOMPONENTTYPE, leaving the output file in a partially-written state. Replace with itkExceptionMacro so the failure surfaces to the caller. 2. ~MZ3MeshIO() never closed m_Ofstream — a write that threw between WriteMeshInformation()'s open and Write()'s explicit close leaked the output stream. Close both m_Ifstream and m_Ofstream in the destructor's uncompressed branch (guarded by is_open() so closing twice is safe). Also rewrites the 20 C-style (char *)& casts on gzread / gzwrite / ifstream / ofstream calls to reinterpret_cast<char *>(&...) per ITK style guide (Greptile P2 #6). Also fixes the WriteCells CHAR case that cast the buffer to unsigned char * instead of char *, which would silently corrupt negative vertex indices on signed cell-component types (Greptile P2 #5).
- Drop a duplicate consecutive 'protected:' access specifier in itkMZ3MeshIO.h (harmless, but warned by some compilers). - Correct the Doxygen \ingroup tag on itkMZ3MeshIOFactory.h from the outdated upstream remote-module name 'ITKIOMeshMZ3' to 'IOMeshMZ3' so the factory class shows up under the module's Doxygen group alongside MZ3MeshIO.
…shMZ3
In-tree, ITK_SOURCE_DIR is always defined and ITK's top-level
CMakeLists pins the CMake minimum version. The per-module
cmake_minimum_required line and if(NOT ITK_SOURCE_DIR) ... else()
itk_module_impl() endif() guard are dead code. The 'set(ITK_DIR
${CMAKE_BINARY_DIR})' line that was inside the in-tree else branch
is preserved (now unconditional) since it actually had effect during
the in-tree build path. Matches the v4 ingest-pipeline rules in
PR InsightSoftwareConsortium#6204 (sanitize-history.py:patch_drop_cmake_minimum_required and
:patch_standalone_build_guard).
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Symmetric counterpart to the gzopen() failure check in the gzip branch of the same function: when m_Ofstream.open() fails (target directory absent, filesystem read-only, permissions), the open silently leaves the stream in failbit state. Every subsequent m_Ofstream.write() in WriteCells / WritePoints / WritePointData / Write() then no-ops, and Write() closes the stream without surfacing an error — the caller believes the write succeeded while the output file is empty or absent. Throw itkExceptionMacro if !m_Ofstream.is_open() after the open call, matching the existing gzopen guard. Greptile P1 review on PR InsightSoftwareConsortium#6214 (post-rebase re-review).
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Two upstream bugs caught by Greptile review on PR InsightSoftwareConsortium#6214: 1. WritePointData() printed to std::cerr and returned silently when m_PointPixelComponentType was UNKNOWNCOMPONENTTYPE, leaving the output file in a partially-written state. Replace with itkExceptionMacro so the failure surfaces to the caller. 2. ~MZ3MeshIO() never closed m_Ofstream — a write that threw between WriteMeshInformation()'s open and Write()'s explicit close leaked the output stream. Close both m_Ifstream and m_Ofstream in the destructor's uncompressed branch (guarded by is_open() so closing twice is safe). Also rewrites the 20 C-style (char *)& casts on gzread / gzwrite / ifstream / ofstream calls to reinterpret_cast<char *>(&...) per ITK style guide (Greptile P2 #6). Also fixes the WriteCells CHAR case that cast the buffer to unsigned char * instead of char *, which would silently corrupt negative vertex indices on signed cell-component types (Greptile P2 #5).
hjmjohnson
added a commit
to hjmjohnson/ITK
that referenced
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May 6, 2026
Symmetric counterpart to the gzopen() failure check in the gzip branch of the same function: when m_Ofstream.open() fails (target directory absent, filesystem read-only, permissions), the open silently leaves the stream in failbit state. Every subsequent m_Ofstream.write() in WriteCells / WritePoints / WritePointData / Write() then no-ops, and Write() closes the stream without surfacing an error — the caller believes the write succeeded while the output file is empty or absent. Throw itkExceptionMacro if !m_Ofstream.is_open() after the open call, matching the existing gzopen guard. Greptile P1 review on PR InsightSoftwareConsortium#6214 (post-rebase re-review).
hjmjohnson
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May 6, 2026
…est-iomeshmz3 ENH: Ingest ITKIOMeshMZ3 into Modules/IO
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Ingests ITKIOMeshMZ3 (read/write of Surf Ice's MZ3 surface-mesh format via
itk::MZ3MeshIO+ factory) intoModules/IO/IOMeshMZ3/using the v4 ingestion pipeline. Tier-A Wave-1 candidate from #6160. Upstream: InsightSoftwareConsortium/ITKIOMeshMZ3 atfbeed91e; will be archived after this lands.Sanitizer report (Phase A)
Smaller and more recent upstream than the other v4 ingests so far (PolarTransform, SplitComponents) — fewer style and prefix fixups needed.
Topology and CI expectations
upstream/main@777a69ffab(zero commits behind at push time)Expected CI state: all green except
ghostflow-check-main's single root-commit error — accepted perINGESTION_STRATEGY_v4.md§"Known artifacts at PR-review time".Local verification
pre-commit run --all-files→ exit 0cmake -DModule_IOMeshMZ3:BOOL=ON .configure cleanninja IOMeshMZ3TestDriver8/8 build steps OKninja ITKDatato populate fixtures — all 4 CIDs already published on the ITKTestingData GitHub Pages mirror, HTTP 200:bafkreid6pbxwl6yr76kgqjaim3ibqefco5oxdxwzxpamwlyichrmjkf3cu—11ScalarMesh.mz3bafkreidhhxis77p7idu2oqko5u3tix665he65kn4yssrweivvtjpbg5yv4—3Mesh.mz3bafkreib5l2ftbgzhluru2wssotet4l74te3zmmqaj6cr7sl34q4in6cr6i—BrainMesh_ICBM152.lh.motor.mz3bafkreieag2mwi2fs5p7lka542fxis2o6tonz5h2v545pnlxtaqvbogwlie—cortex_5124.mz3ctest -R MZ3: 6/6 tests pass (itkMZ3MeshIOTest1..4, plusKWStyleandInDoxygenGroup)Phase B (post-merge) plan
Once this PR lands on
main:~/src/ITK-ingest-v4/Utilities/Maintenance/RemoteModuleIngest/archive-remote-module.sh IOMeshMZ3Phase B publishes the upstream-side removal commit (whitelisted files deleted,
MIGRATION_README.mdpromoted toREADME.md) directly toInsightSoftwareConsortium/ITKIOMeshMZ3'smainand flipsarchived=trueon the GitHub repo settings, perfeedback_ingest_archive_readme.md.