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See the CONTRIBUTING guide. Specifically:

Start ITK commit messages with a standard prefix (and a space):

  • BUG: fix for runtime crash or incorrect result
  • COMP: compiler error or warning fix
  • DOC: documentation change
  • ENH: new functionality
  • PERF: performance improvement
  • STYLE: no logic impact (indentation, comments)
  • WIP: Work In Progress not ready for merge

Provide a short, meaningful message that describes the change you made.

When the PR is based on a single commit, the commit message is usually left as the PR message.

A reference to a related issue or pull request in your repository. You can automatically close a related issues using keywords

@mentions of the person or team responsible for reviewing proposed changes.

Thanks for contributing to ITK!

kwrobot pushed a commit that referenced this pull request Sep 6, 2018
@hjmjohnson
COMP: Consistently set use of CMake 3.9.5 and options
6774ad5 
cmake_minimum_required(VERSION 3.9.5 FATAL_ERROR)
foreach(p
    ## Only policies introduced after the cmake_minimum_required
    ## version need to explicitly be set to NEW.
    CMP0070 #3.10.0 Define ``file(GENERATE)`` behavior for relative paths.
    CMP0071 #3.10.0 Let ``AUTOMOC`` and ``AUTOUIC`` process ``GENERATED`` files.
    )
  if(POLICY ${p})
    cmake_policy(SET ${p} NEW)
  endif()
endforeach()

Change-Id: I30c9a4f2401bf83bcdb56ba89d44b24ca8342853
kwrobot pushed a commit that referenced this pull request Mar 4, 2021
@jhlegarreta
BUG: Fix uninitialized variable use in ANTS neighborhood correlatio…
72ea1f2 
…n metric

Fix uninitialized variable use in `ANTS` neighborhood correlation metric:
ensure that `fixedImageGradient` and `movingImageGradient` have valid
values before assigning them to the `scanMem` struct that scans over
images.

Fixes:
```
Run-Time Check Failure #3 - The variable 'fixedImageGradient' is being
used without being initialized.
```

The bug was affecting a number of tests in the
`ITKRegistrationMethodsv4Test` module.

Signaled at
https://open.cdash.org/viewTest.php?onlyfailed&buildid=7067466
and
https://open.cdash.org/viewTest.php?onlyfailed&buildid=7069241
kwrobot pushed a commit that referenced this pull request Apr 29, 2024
@seanm
BUG: fixed race condition setting m_ANTSAssociate
46eed47 
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.

There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).

Partial backtrace from TSan:

```
WARNING: ThreadSanitizer: data race (pid=79176)
  Write of size 8 at 0x000108f02240 by thread T2:
    #0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
    #1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
    #2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
    #3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
    #4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)

  Previous write of size 8 at 0x000108f02240 by thread T14:
    #0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
    #1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
    #2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
    #3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
    #4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
kwrobot pushed a commit that referenced this pull request May 30, 2024
@seanm
BUG: fixed race condition setting m_ANTSAssociate
c48500b 
Found with thread sanitizer (TSan) running the `itkANTSNeighborhoodCorrelationImageToImageRegistrationTest` unit test.

There was already a `m_ANTSAssociateOnceFlag` flag for use with `std::call_once`, so I just used that in this place too (it's already used elsewhere).

Partial backtrace from TSan:

```
WARNING: ThreadSanitizer: data race (pid=79176)
  Write of size 8 at 0x000108f02240 by thread T2:
    #0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
    #1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
    #2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
    #3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
    #4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)

  Previous write of size 8 at 0x000108f02240 by thread T14:
    #0 void itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution_impl<itk::ThreadedIndexedContainerPartitioner>(itk::IdentityHelper<itk::ThreadedIndexedContainerPartitioner>, itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:118 (ITKMetricsv4TestDriver:arm64+0x1004bfe50)
    #1 itk::ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>, itk::ANTSNeighborhoodCorrelationImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreadedExecution(itk::Index<2u> const&, unsigned int) itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h:235 (ITKMetricsv4TestDriver:arm64+0x1004bf9c0)
    #2 itk::DomainThreader<itk::ThreadedIndexedContainerPartitioner, itk::ImageToImageMetricv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<double, 2u>, itk::Image<double, 2u>, itk::Image<double, 2u>, double>>>::ThreaderCallback(void*) itkDomainThreader.hxx:123 (ITKMetricsv4TestDriver:arm64+0x100259b6c)
    #3 std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()::operator()() const itkThreadPool.h:92 (ITKMetricsv4TestDriver:arm64+0x1007d3228)
    #4 decltype(std::declval<void* (*&)(void*)>()(std::declval<itk::PoolMultiThreader::ThreadPoolInfoStruct*>())) std::__1::__invoke[abi:v160006]<std::__1::future<std::__1::invoke_result<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>::type> itk::ThreadPool::AddWork<void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&)::'lambda'()&>(void* (*&)(void*), itk::PoolMultiThreader::ThreadPoolInfoStruct*&&) invoke.h:394 (ITKMetricsv4TestDriver:arm64+0x1007d31a4)
```
blowekamp and others added 26 commits December 6, 2024 20:33
@blowekamp
BUG: openjpeg add missing CMake compile test file
e57b082 
It appears that GDCM's vendored OpenJPEG set the same cache variable,
and the file was not used before.
@blowekamp
Merge branch 'upstream-openjpeg' into gdcm_use_itkopenjpeg
6cb4ee3 
# By OpenJPEG Upstream
* upstream-openjpeg:
  openjpeg 2024-02-28 (39e8c50a)
@kwrobot @blowekamp
openjpeg 2024-02-28 (39e8c50a)
fcd4009 
Code extracted from:

    https://github.com/uclouvain/openjpeg.git

at commit 39e8c50a2f9bdcf36810ee3d41bcbf1cc78968ae (v2.5.2).
@blowekamp
ENH: Configure GDCM to use itkOpenJPEG
ca64d39
@hjmjohnson
Merge pull request #5022 from blowekamp/gdcm_use_itkopenjpeg
95fdd25 
GDCM use itkopenjpeg
@kwrobot @bradking
KWSys 2024-11-30 (dfbcd769)
464940d 
Code extracted from:

    https://gitlab.kitware.com/utils/kwsys.git

at commit dfbcd769aea25157ee65a92f941d0e233fe79826 (master).

Upstream Shortlog
-----------------

Brad King (9):
      beaf1ca1 ConsoleBuf: Fix test case when running under Windows Terminal
      4feb470a SystemTools: Remove GetActualCaseForPath from CollapseFullPath
      6e847d08 SystemInformation: Add missing EOF check when reading /proc/cpuinfo
      741c9c96 SystemTools: Expose GetActualCaseForPathCached publicly
      fdf4f2f8 SystemTools: Fix ReadSymlink for links to absolute paths on Windows
      20b2c992 SystemTools: Remove unused global object
      47dce1a3 SystemTools: Remove path translation map
      30e9db2d SystemTools: Drop GetActualCaseForPathCached
      5995fd7d SystemInformation: Ignore stderr from OS query tools

Daniel Pfeifer (1):
      68e1f35d SystemInformation: fix use of using

Jochem van Boxtel (1):
      510b13b4 SystemTools: Add FileId class and GetFileId function

Juan Ramos (2):
      ff14b4f5 SystemInformation: Fix find logic
      a347a66b SystemInformation: Implement HasFPU on Apple processors

Mike Lundy (1):
      ee3223d7 SystemTools: fix clonefile optimization on macOS

Peter Kokot (1):
      967b2120 Remove legacy unused IMMEDIATE CMake keyword

scivision (4):
      5f4012c6 Don't compare to nullptr
      3f14fce6 Process: Replace 0 with NULL in pointer arguments to GetFullPathNameW
      210cea0a SystemTools: Replace unused argument to GetFullPathNameW with nullptr
      f5e82d63 SystemTools: Replace malloc() with std::string
@bradking
Merge branch 'upstream-KWSys' into update-kwsys
c188c7f 
# By KWSys Upstream
* upstream-KWSys:
  KWSys 2024-11-30 (dfbcd769)
@hjmjohnson
ENH: Changes for preferring initialization to assignment.
db46bb2 
This involved moving variable initialization to
the smallest possible scope.

The more locally scoped variables allow for future
automated code refactorings.
@dzenanz
Merge pull request #5028 from bradking/update-kwsys
c7cdc54
@blowekamp @dzenanz
COMP: libjpeg-turbo: Add object libraries as source files
261b505
@hjmjohnson
STYLE: Replace Fill(0) with {} initializer for local variables in tests
1087045 
Another run to replaced code of the form

    T var;
    var.Fill(0);

with `T var{};`

Using Notepad++, Replace in Files, doing:

    Find what: ^( [ ]+[^ ].* )(\w+);[\r\n]+ [ ]+\2\.Fill\(0\);
    Replace with: $1$2{};
    Filters: itk*Test*.cxx
    [v] Match case
    (*) Regular expression

The empty initializer list `{}` effectively zero-fills those variables.
@hjmjohnson
STYLE: Prefer Filled over MakeFilled
a2a3504 
Prefer Filled over MakeFilled for initializing Size<T> and Index<T> types

Replace in Files, doing:
Find what: ^( [ ]+)(SizeType)[ ]+(\w+);[\r\n]+\1\3\.Fill\(
Replace with: $1auto $3 = $2::Filled\(
@hjmjohnson
ENH: Changes for preferring initialization to assignment.
f7508c0 
This involved moving variable initialization to
the smallest possible scope.

The more locally scoped variables allow for future
automated code refactorings.
@hjmjohnson
STYLE: Manual review of .Fill([0-9]*) patterns
9bc3ea0 
Identified code style improvements based on manually
reviewing use of .Fill for assignment of values
when initialization could have been used.
@thewtex @hjmjohnson
COMP: Update Azure Windows Python version to 3.11
74e226c 
We now require 3.11 -- 3.8 is end-of-life.
@thewtex @hjmjohnson
ENH: Use pixi to install pre-commit, python for pre-commit
6f25d91 
On Windows, Python is not available by default. The
SetupForDevelopment.sh script does not complete successfully in a
default build on Windows.

This uses pixi to install pre-commit, python for pre-commit, so the
contribution experience works out-of-the-box for experienced and new
contributors to ITK.

This also improves the isolation and maintainability of pre-commit
tooling. Everything needed for a commit is local to the ITK repository.
We also get more reproducible versions of Python and pre-commit via
pixi's configuration in pyproject.toml and pixi.lock.

pixi is a self-contained, single-file, cross-platform Rust binary. A local version is
installed to .git/hooks/pixi/bin/pixi. Pixi's python and pre-commit is
installed to .pixi/.

The installation of tools is:

  SetupForDevelopment.sh -> curl -> pixi -> python, pre-commit -> pre-commit's hook dependencies

This also makes it easy to run the pre-commit hooks on demand on all
files via:

```
pixi run pre-commit-run
```
@thewtex @hjmjohnson
STYLE: Add clang-format updates to C++ files
b19aa1f 
Generated via:

  pixi run pre-commit-run
@hjmjohnson
STYLE: Prefer explicit const designation
375ee8c 
Implements detection of local variables which could be declared as const but
are not. Declaring variables as const is recommended by many coding
guidelines, such as: ES.25 from the C++ Core Guidelines.

cd ${BLDDIR}
run-clang-tidy.py -extra-arg=-D__clang__ -checks=-*,misc-const-correctness -header-filter=.* -fix
@hjmjohnson
COMP: Fix unused-lambda-capture statement
38132cb 
lambda capture 'n' is not required to be captured for this use [-Wunused-lambda-capture]
@hjmjohnson
COMP: Fix windows function ambiguity error
81f50c9 
Modules\IO\Meta\test\testMetaImage.cxx(154): error C2666: 'MetaImage::SequenceID': 2 overloads have similar conversions
Modules\ThirdParty\MetaIO\src\MetaIO\src\metaImage.h(182): note: could be 'void MetaImage::SequenceID(const float *)'
Modules\ThirdParty\MetaIO\src\MetaIO\src\metaImage.h(180): note: or       'float MetaImage::SequenceID(int) const'
Modules\IO\Meta\test\testMetaImage.cxx(154): note: while trying to match the argument list '(const int)'
Modules\IO\Meta\test\testMetaImage.cxx(154): note: note: qualification adjustment (const/volatile) may be causing the ambiguity

Modules\IO\Meta\test\testMetaImage.cxx(165): error C2666: 'MetaImage::ElementSize': 3 overloads have similar conversions
Modules\ThirdParty\MetaIO\src\MetaIO\src\metaImage.h(201): note: could be 'void MetaImage::ElementSize(const float *)'
Modules\ThirdParty\MetaIO\src\MetaIO\src\metaImage.h(199): note: or       'void MetaImage::ElementSize(const double *)'
Modules\ThirdParty\MetaIO\src\MetaIO\src\metaImage.h(197): note: or       'double MetaImage::ElementSize(int) const'
Modules\IO\Meta\test\testMetaImage.cxx(165): note: while trying to match the argument list '(const int)'
Modules\IO\Meta\test\testMetaImage.cxx(165): note: note: qualification adjustment (const/volatile) may be causing the ambiguity
@hjmjohnson
COMP: Fix windows compilation warning
557b442 
Modules\Filtering\LabelMap\include\itkShapeKeepNObjectsLabelMapFilter.h(156):

warning C4269: 'comparator': 'const' automatic data initialized with compiler generated default constructor produces unreliable results
@hjmjohnson
COMP: Fix linux compilation warning
9683b52 
Modules/Core/Common/test/itkImageBufferRangeGTest.cxx: In lambda function:
Modules/Core/Common/test/itkImageBufferRangeGTest.cxx:670:61:
      warning: declaration of 'n' shadows a previous local [-Wshadow]
  670 |     const auto expectedResult = [&r](const difference_type n) {
      |                                                             ^
Modules/Core/Common/test/itkImageBufferRangeGTest.cxx:667:31:
      note: shadowed declaration is here
  667 |     constexpr difference_type n = 3;
      |                               ^
Modules/Core/Common/test/itkImageBufferRangeGTest.cxx: In lambda function:
@hjmjohnson
STYLE: Local variables do not start with m_
c88de4a 
The m_ prefix is used for instance (member) variables.
@thewtex
Merge pull request #5035 from hjmjohnson/variable-name-style
ddc8c11 
STYLE: Local variables do not start with m_
@hjmjohnson
BUG: GHA: Cancel-in-progress event if not the same head SHA
e27f2cf 
Grouping based on github.event.pull_request.head.sha, i.e. "the commit
ID for the last commit to the head branch of the pull request" only
cancels commits with the same SHA. With this PR, on-going workflows of
the same PR would be cancelled.
@hjmjohnson
STYLE: Make prototype match definition names
6a5f942 
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
thewtex and others added 30 commits January 17, 2025 16:18
@thewtex
Merge pull request #5138 from thewtex/doxygen-archives-link
8d325a1 
DOC: Update Doxygen footer link to tarballs
@thewtex
DOC: Point to RTD Doxygen documentation, ITKDoxygen Docker build
8ba1cfc 
In the documentation contributing documentation.
@thewtex
DOC: Update Doxygen class links to use ReadTheDocs
d3189c2 
Point to the stable release on the ReadTheDocs CDN host.
@thewtex
DOC: Update versioned Doxygen links to point to ReadTheDocs
ce4fa18 
These are now available for each release tag.
@thewtex
Merge pull request #5140 from thewtex/doxygen-links-for-release
9fd4b5a 
Doxygen links for release
@thewtex
Merge pull request #5139 from thewtex/release-branches-doc-for-release
807c962 
DOC: Update maintenance branch for 5.4 series
@thewtex
Merge remote-tracking branch 'upstream/release' into release-5.4
8ef0826
@smr99
DOC: Revise class documentation, remove term 'experimental'
9856051 
Removing language suggesting the filter is "experimental".
Dženan Zukić says it "is one of the most used and well tested filters in ITK".
https://discourse.itk.org/t/connectedcomponentimagefilter-vs-hardconnectedcomponentimagefilter/7379/2

Added a note on connectivity.
@thewtex
Merge branch 'release'
5947578
@thewtex
DOC: ITK 5.4.0 release notes
f2852f6 
Also update the download page with the new links. The pre-release
section is removed until the ITK 6 pre-releases are out.

Update the download links and cookiecutter to include .asc signature
files.
@thewtex
Merge branch 'release-5.4' into release
4c8ccfb
@thewtex
Merge branch 'release'
b4ce0a5
@thewtex
Merge pull request #5141 from smr99/doc-connected-component-image-filter
8b816db 
DOC: Revise class documentation, remove term 'experimental'
@thewtex
DOC: Release process updates with ITK 5.4.0
e6eda75 
Archive tarballs on the NumFOCUS GDrive ITKReleases folder.
data.kitware.com throws bad gateway errors and Kitware said that
data.kitware.com is no longer supported and data should migrate off it.

Sign the source tarballs per OSSF Scorecard best practices:

  https://github.com/ossf/scorecard/blob/49c0eed3a423f00c872b5c3c9f1bbca9e8aae799/docs/checks.md#signed-releases

Doxygen is now mostly automated via GitHub Actions and ReadTheDocs.
@thewtex
Merge pull request #5142 from thewtex/itk-5-4-0-release-updates
dfd4a40 
DOC: Release process updates with ITK 5.4.0
@thewtex
ENH: Update ExternalDataVersion in CI to 5.4.0
fa9027a 
Use the updated testing data tarball.

The hash has changed from MD5 to CID.
@thewtex
Merge pull request #5143 from thewtex/ci-testing-data-5.4.0
06484b7 
ENH: Update ExternalDataVersion in CI to 5.4.0
@thewtex
DOC: Clarify MAJOR_VERSION is a variable
47f646e 
In the release process documentation. Follow-up to #5142.
@thewtex
Merge pull request #5145 from thewtex/release-major-var
259ad17 
DOC: Clarify MAJOR_VERSION is a variable
@dzenanz
DOC: Remove duplicate new author name (Matthieu LAURENDEAU)
6d82d2b
@thewtex
Merge pull request #5146 from dzenanz/releaseNotes54
acbba17 
DOC: Remove duplicate new author name (Matthieu LAURENDEAU)
@thewtex
Merge branch 'release-5.4' into release
36478b2
@thewtex
Merge branch 'release'
9597266
@blowekamp @dzenanz
ENH: add test to reproduce SimpleITK issue #2220
ec75692 
Incorrect results are being computed on windows with the Compose
filter (and other filters) and VectorImages of sizes >4GB.

Bug was addressed in PR #5071.
@Leengit @dzenanz
DOC: Update link to dashboard
f56ed1a
@Leengit @hjmjohnson
STYLE: Remove whitespace before scope resolution operator
480559b
@jhlegarreta @dzenanz
DOC: Fix defgroup command in Doxygen Modules file
0db7870 
Fix `defgroup` command in Doxygen `Modules` file: do not allow any
whitespace between the backward slash and `defgroup`.

The affected group, `ImageEnhancement` is not being displayed in the
list of modules/groups and no filter is currently being attributed the
affected group, despite some filters, e.g. `itk::ConvertLabelMapFilter`,
being within that group.

Reported by: albert-github <albert.tests@gmail.com>
@sbelsk @dzenanz
BUG: Fix broken link on the contributing docs
dab08e7
@seanm @hjmjohnson
ENH: fixed issue 4818 with itkMemoryProbesCollecterBaseTest
524df2a 
On macOS, itkMemoryProbesCollecterBaseTest would often fail with messages like:

Freeing memory should result in less memory but it is 262216kB instead of 262164kB

Just increased the amout of memory allocated in this test to make it more likely to pass.
@krupalbhat @dzenanz
STYLE: Modified Optimizer classes to avoid printing non-self member v…
5a6d1e9 
…ariables
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