PR Checklist

• [x] No API changes were made (or the changes have been approved)
• [x] No major design changes were made (or the changes have been approved)
• [ ] Added test (or behavior not changed)
• [ ] Updated API documentation (or API not changed)
• [ ] Added license to new files (if any)
• [ ] Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5
• [ ] Added ITK examples for all new major features (if any)

Refer to the ITK Software Guide for further development details if necessary.

Fixes #3333

Co-authored-by: Vladimir S. FONOV [email protected]

PR Checklist

• [x] No API changes were made (or the changes have been approved)

• [x] No major design changes were made (or the changes have been approved)

• [x] Updated API documentation (or API not changed)

• [ ] Added license to new files (if any)

• [X] Added test

• NO Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5

• NO Added ITK examples for all new major features (if any)

ITK/Utilities/Maintenance/clang-format.bash
--clang-format ~/local/llvm/clang+llvm-8.0.0-x86_64-linux-gnu-ubuntu-18.04/bin/clang-format
--tracked

This patch updates the ITK preferred style to one that can be automatically enforced, integrated with many IDE's, and based on externally defined documentation and examples.

See: https://discourse.itk.org/t/update-coding-style-for-itk/2055

Most of the changes make inconsistent coding practices consistent throughout the toolkit.

One large change is changing the {} indentation style from Whitesmiths style https://en.wikipedia.org/wiki/Indentation_style#Whitesmiths_style to an indentation style consistent with many of the other common indentation styles. The primary reason for this change is to overcome the common deficiency of IDE's and formatters to support this uncommon style choice. Completes the work started in #1094

PR Checklist

• :no_entry_sign: Makes breaking changes
• :no_entry_sign: Makes design changes
• :no_entry_sign: Adds the License notice to new files.
• :no_entry_sign: Adds Python wrapping.
• :no_entry_sign: Adds tests and baseline comparison (quantitative).
• :no_entry_sign: Adds test data.
• :no_entry_sign: Adds Examples to ITKExamples
• :no_entry_sign: Adds Documentation.

I would like to build ITK with the module. Setting it in the build system attempts to implicitly download it during install. I would like to avoid this, so as to best ensure that only files explicitly known to be needed by the package manager will be downloaded.

 * Package:    sci-libs/itk-5.0.1
 * Repository: chymeric
 * Maintainer: maintainer-wan[email protected] [email protected]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_single_target_python3_6 python_targets_python2_7 python_targets_python3_6 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking InsightToolkit-5.0.1.tar.gz to /var/tmp/portage/sci-libs/itk-5.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-libs/itk-5.0.1/work
>>> Preparing source in /var/tmp/portage/sci-libs/itk-5.0.1/work/InsightToolkit-5.0.1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/itk-5.0.1/work/InsightToolkit-5.0.1 ...
 * cmake-utils_src_prepare has not been run, please open a bug on https://bugs.gentoo.org/
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/itk-5.0.1/work/itk-5.0.1_build"
cmake -C /var/tmp/portage/sci-libs/itk-5.0.1/work/itk-5.0.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DITK_USE_SYSTEM_DCMTK=ON -DGDCM_USE_SYSTEM_OPENJPEG=ON -DITK_USE_SYSTEM_DOUBLECONVERSION=ON -DITK_USE_SYSTEM_CASTXML=ON -DITK_USE_SYSTEM_HDF5=ON -DITK_USE_SYSTEM_JPEG=ON -DITK_USE_SYSTEM_PNG=ON -DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_TIFF=ON -DITK_USE_SYSTEM_ZLIB=ON -DITK_USE_KWSTYLE=OFF -DITK_BUILD_DEFAULT_MODULES=ON -DITK_COMPUTER_MEMORY_SIZE=1 -DWRAP_ITK_JAVA=OFF -DWRAP_ITK_TCL=OFF -Ddouble-conversion_INCLUDE_DIRS=/usr/include/double-conversion -DExternalData_OBJECT_STORES=/var/tmp/portage/sci-libs/itk-5.0.1/work/InsightToolkit-5.0.1/.ExternalData -DModule_GenericLabelInterpolator:BOOL=ON -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DITK_USE_REVIEW=OFF -DITK_INSTALL_LIBRARY_DIR=lib64 -DITK_WRAP_PYTHON=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/itk-5.0.1/work/itk-5.0.1_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-libs/itk-5.0.1/work/InsightToolkit-5.0.1
loading initial cache file /var/tmp/portage/sci-libs/itk-5.0.1/work/itk-5.0.1_build/gentoo_common_config.cmake
-- The CXX compiler identification is GNU 9.1.0
-- The C compiler identification is GNU 9.1.0
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found Git: /usr/bin/git (found version "2.22.0") 
-- Found PythonInterp: /var/tmp/portage/sci-libs/itk-5.0.1/temp/python3.6/bin/python (found version "3.6.9") 
-- Performing Test C_HAS_WARNING-Wno-uninitialized
-- Performing Test C_HAS_WARNING-Wno-uninitialized - Success
-- Performing Test C_HAS_WARNING-Wno-unused-parameter
-- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success
-- Performing Test C_HAS_WARNING-Wall
-- Performing Test C_HAS_WARNING-Wall - Success
-- Performing Test C_HAS_WARNING-Wno-long-double
-- Performing Test C_HAS_WARNING-Wno-long-double - Failed
-- Performing Test C_HAS_WARNING-Wcast-align
-- Performing Test C_HAS_WARNING-Wcast-align - Success
-- Performing Test C_HAS_WARNING-Wdisabled-optimization
-- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test C_HAS_WARNING-Wextra
-- Performing Test C_HAS_WARNING-Wextra - Success
-- Performing Test C_HAS_WARNING-Wformat_2
-- Performing Test C_HAS_WARNING-Wformat_2 - Success
-- Performing Test C_HAS_WARNING-Winvalid-pch
-- Performing Test C_HAS_WARNING-Winvalid-pch - Success
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral
-- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test C_HAS_WARNING-Wpointer-arith
-- Performing Test C_HAS_WARNING-Wpointer-arith - Success
-- Performing Test C_HAS_WARNING-Wshadow
-- Performing Test C_HAS_WARNING-Wshadow - Success
-- Performing Test C_HAS_WARNING-Wunused
-- Performing Test C_HAS_WARNING-Wunused - Success
-- Performing Test C_HAS_WARNING-Wwrite-strings
-- Performing Test C_HAS_WARNING-Wwrite-strings - Success
-- Performing Test C_HAS_WARNING-funit-at-a-time
-- Performing Test C_HAS_WARNING-funit-at-a-time - Success
-- Performing Test C_HAS_WARNING-Wno-strict-overflow
-- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wall
-- Performing Test CXX_HAS_WARNING-Wall - Success
-- Performing Test CXX_HAS_WARNING-Wno-long-double
-- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
-- Performing Test CXX_HAS_WARNING-Wcast-align
-- Performing Test CXX_HAS_WARNING-Wcast-align - Success
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization
-- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success
-- Performing Test CXX_HAS_WARNING-Wextra
-- Performing Test CXX_HAS_WARNING-Wextra - Success
-- Performing Test CXX_HAS_WARNING-Wformat_2
-- Performing Test CXX_HAS_WARNING-Wformat_2 - Success
-- Performing Test CXX_HAS_WARNING-Winvalid-pch
-- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral
-- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS_WARNING-Wpointer-arith
-- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success
-- Performing Test CXX_HAS_WARNING-Wshadow
-- Performing Test CXX_HAS_WARNING-Wshadow - Success
-- Performing Test CXX_HAS_WARNING-Wunused
-- Performing Test CXX_HAS_WARNING-Wunused - Success
-- Performing Test CXX_HAS_WARNING-Wwrite-strings
-- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success
-- Performing Test CXX_HAS_WARNING-funit-at-a-time
-- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow
-- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success
-- Performing Test CXX_HAS_WARNING-Wno-deprecated
-- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof
-- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template
-- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual
-- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel
-- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Success
-- Performing Test C_HAS_WARNING-mtune_native
-- Performing Test C_HAS_WARNING-mtune_native - Success
-- Performing Test C_HAS_WARNING-march_corei7
-- Performing Test C_HAS_WARNING-march_corei7 - Success
-- Performing Test CXX_HAS_WARNING-mtune_native
-- Performing Test CXX_HAS_WARNING-mtune_native - Success
-- Performing Test CXX_HAS_WARNING-march_corei7
-- Performing Test CXX_HAS_WARNING-march_corei7 - Success
-- Performing Test have_gold
-- Performing Test have_gold - Success
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
CMake Error at CMake/ITKModuleRemote.cmake:12 (message):
  Failed to clone repository:
  'https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git'
Call Stack (most recent call first):
  CMake/ITKModuleRemote.cmake:134 (_git_clone)
  CMake/ITKModuleRemote.cmake:197 (_fetch_with_git)
  Modules/Remote/GenericLabelInterpolator.remote.cmake:1 (itk_fetch_module)
  Modules/Remote/CMakeLists.txt:6 (include)


-- Configuring incomplete, errors occurred!

What would be the best way to go about this? Should I download and unpack some ITKGenericLabelInterpolator tarball explicitly? If so, then to where? If not, perhaps the ITKGenericLabelInterpolator can be built separately and installed into the appropriate path. But I do not see how this can be done, since the module README only lists the ITK CMake flag as an install instruction.

Enlarges the bounding box by half a pixel in each direction, to ensure that a point (in object space) whose nearest pixel has a non-zero value is always treated as being inside the object.

Fixes issue #753 (ImageMaskSpatialObject BoundingBox smaller than before Spatial Object update) and issue #785 (ImageMaskSpatialObject IsInside should not depend on distant pixels). Related to discussion topic "ImageMaskSpatialObject IsInside less than half a pixel away?", https://discourse.itk.org/t/imagemaskspatialobject-isinside-less-than-half-a-pixel-away/1807

Build and test on the new Apple M1 ARM Silicon processor / system.

Description

We will have to work with the newer Xcode / processor / binary system.

Additional Information

This is a tracking issue to discuss issues / progress.

CC: @dzenanz @imikejackson

Description

I want to build insighttoolkit for openSUSE Tumbleweed on s390x and x86. It is failing with the following error message:

[ 1239s] /home/abuild/rpmbuild/BUILD/ITK-5.2.1/build/Wrapping/Typedefs/itkVectorContainer.i:177: Error: Syntax error in input(3).
[ 1239s] ninja: build stopped: subcommand failed.

Steps to Reproduce

%cmake \
  -DITK_INSTALL_LIBRARY_DIR:PATH=%{_lib}/ \
  -DITK_INSTALL_INCLUDE_DIR:PATH=include/%{name}/ \
  -DITK_INSTALL_PACKAGE_DIR:PATH=%{_lib}/cmake/%{name}/ \
  -DITK_INSTALL_RUNTIME_DIR:PATH=%{_bindir} \
  -DITK_INSTALL_DOC_DIR=share/doc/packages/%{name}/ \
  -DBUILD_EXAMPLES:BOOL=ON \
  -DBUILD_SHARED_LIBS:BOOL=ON \
  -DBUILD_TESTING:BOOL=OFF \
  -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \
  -DITK_USE_FFTWD:BOOL=ON \
  -DITK_USE_FFTWF:BOOL=ON \
  -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \
  -DITK_USE_SYSTEM_CASTXML:BOOL=ON \
  -DITK_USE_SYSTEM_GDCM:BOOL=ON \
%if %{without system_eigen}
  -DITK_USE_SYSTEM_EIGEN:BOOL=OFF \
%endif
  -DITK_USE_SYSTEM_SWIG:BOOL=ON \
  -DITK_USE_SYSTEM_VXL:BOOL=OFF \
  -DVXL_BUILD_CORE_NUMERICS:BOOL=OFF \
  -DVCL_INCLUDE_CXX_0X:BOOL=ON \
  -DITK_FORBID_DOWNLOADS=ON \
  -DITK_WRAP_PYTHON:BOOL=ON

Expected behavior

You can build ITK without any syntax error.

Actual behavior

Build of the openSUSE package is failing because of a syntax error.

Reproducibility

100% on s390x and x86

Versions

5.2.1

Environment

openSUSE Tumbleweed architecture: s390x or x86 cpp-12-2.2 cmake-3.23.2-2.1 gcc-12-2.2 gtk2-devel-2.24.33-2.5

Additional Information

(see build log: https://build.opensuse.org/public/build/Application:Geo/openSUSE_Factory_zSystems/s390x/insighttoolkit/_log )

Building ITK on Windows (through R)

I'm trying to build ITK on Windows, through R in the ITKR package (https://github.com/muschellij2/ITKR). I'm testing this through appveyor (https://ci.appveyor.com/project/muschellij2/itkr). I'm getting the following error:

[ 73%] Building C object Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/H5Defl.c.obj
In file included from C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5private.h:615:0,
                 from C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c:29:
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c: In function 'H5D__efl_read':
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5win32defs.h:57:66: error: expected expression before ')' token
 #define HDopen(S,F,...)       _open(S, F | _O_BINARY, __VA_ARGS__)
                                                                  ^
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c:291:18: note: in expansion of macro 'HDopen'
         if((fd = HDopen(full_name, O_RDONLY)) < 0)
                  ^
Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\hdf5-static.dir\build.make:770: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/H5Defl.c.obj' failed

This worked using commit 4f89edd8334da198099c686b993ec9f9f12dccdf, but not the latest or anything with respect to v5.0.

Steps to Reproduce

The steps can be seen here: https://ci.appveyor.com/project/muschellij2/itkr

1. The main configure script is https://github.com/muschellij2/ITKR/blob/master/configure.win
2. The make version is mingw32-make, and the Makevars necessary to reproduce are: https://github.com/muschellij2/ITKR/blob/master/src/Makevars.win
3. See the attached 00install.txt file below.

Expected behavior

Successful build such as https://ci.appveyor.com/project/muschellij2/itkr/build/1.0.278

Actual behavior

Build failure such as https://ci.appveyor.com/project/muschellij2/itkr/build/1.0.282

Reproducibility

100% of the builds with

Versions

ITK_VERSION_MAJOR = 5 ITK_VERSION_MINOR = 0 ITK_VERSION_PATCH = 0

Environment

Windows on Appveyor (I believe Windows Server 2012 R2 )

Additional Information

I've uploaded the CMakeLists and the installation output CMakeLists.txt 00install.txt

Load IO and FFT factories at runtime based on the itk-module.cmake FACTORY_NAMES metadata, as is done with C++ static binary initialization.

This enables run-time discovery of all Python IO or FFT implementations. Some may be added with remote module Python packages.

This also addresses Slicer's use case where Slicer is performing initialization of IO factories with static initialization. Only one static binary initialization is intended to be supported per application. Do not perform static binary initialization in the Python modules.

FFTImageFilter consolidation was finalized, and the required corresponding VnlFFTImageFilterFactory and FFTWFFTImageFilterFactory classes created and wrapped.

Add the missing required TransformIO wrapping.

This switch is useless, forced Tag is (0028,0030), so entry is always from dictionary {0x0028,0x0030,VR::DS,VM::VM2,"Pixel Spacing","PixelSpacing",false }, this switch was simply copy/pasted, s. here and dictionary lookup above is useless too, it is loop.

Edit: m_El.SetLength(entry.GetVM().GetLength() * entry.GetVR().GetSizeof()) is from dictionary and always 2 * 8 = 16.

Hi, I am working on Power9 with ppcle-64 arch. I tried to compile it. It shows error.

Scanning dependencies of target ITKReview-all
[100%] Built target ITKReview-all
[100%] Linking CXX static library ../../../../lib/libITKTestKernel-5.1.a
[100%] Built target ITKTestKernel
Scanning dependencies of target itkTestDriver
[100%] Building CXX object Modules/Core/TestKernel/src/CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o
[100%] Linking CXX executable ../../../../bin/itkTestDriver
../../../../lib/libitkpng-5.1.a(pngrutil.c.o):pngrutil.c:function itk_png_read_filter_row: error: undefined reference to 'png_init_filter_functions_vsx'
collect2: error: ld returned 1 exit status
make[5]: *** [bin/itkTestDriver] Error 1
make[4]: *** [Modules/Core/TestKernel/src/CMakeFiles/itkTestDriver.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [ITKv5-prefix/src/ITKv5-stamp/ITKv5-build] Error 2
make[1]: *** [CMakeFiles/ITKv5.dir/all] Error 2
make: *** [all] Error 2

Fix uninitialized value warning.

Fixes:

UMC ==16463== Conditional jump or move depends on uninitialised value(s)
==16463==    at 0x9BD983: itk::ImageRegistrationMethodv4, itk::Image, itk::DisplacementFieldTransform, itk::Image, itk::PointSet > >::SetNumberOfLevels(unsigned long) (itkImageRegistrationMethodv4.hxx:881)
==16463==    by 0x9C44B6: itk::ImageRegistrationMethodv4, itk::Image, itk::DisplacementFieldTransform, itk::Image, itk::PointSet > >::ImageRegistrationMethodv4() (itkImageRegistrationMethodv4.hxx:103)
==16463==    by 0x9BBFA0: itk::SyNImageRegistrationMethod, itk::Image, itk::DisplacementFieldTransform, itk::Image, itk::PointSet > >::SyNImageRegistrationMethod() (itkSyNImageRegistrationMethod.hxx:41)
==16463==    by 0x9B5974: itk::SyNImageRegistrationMethod, itk::Image, itk::DisplacementFieldTransform, itk::Image, itk::PointSet > >::New() (itkSyNImageRegistrationMethod.h:84)
==16463==    by 0xA15CD4: itkSyNPointSetRegistrationTest(int, char**) (itkSyNPointSetRegistrationTest.cxx:132)
==16463==    by 0x317927: main (ITKRegistrationMethodsv4TestDriver.cxx:222)

and similar warnings triggered by registration testing code.

Visible in: https://open.cdash.org/viewDynamicAnalysis.php?buildid=8374098

Introduced in d1c46d63be7f78d758720e1e0a463b73b30a4055.

PR Checklist

• [X] No API changes were made (or the changes have been approved)
• [X] No major design changes were made (or the changes have been approved)

Originally reported by Astha, March 14, 2022, and further discussed at "ITK build Error in itk::ShapedNeighborhoodIterator", https://discourse.itk.org/t/itk-build-error-in-itk-shapedneighborhooditerator/4861

Fixed Visual Studio 2019 Code Analysis warnings from both MetaDataObject and WindowsMemoryUsageObserver, saying:

warning C26495: Variable is uninitialized. Always initialize a member variable (type.6)

OverrideInformation is just an internal implementation class type of ObjectFactorBase, so it is not meant to be part of the interface of ObjectFactorBase.

Add a test for the itk::BoundedReciprocalImageFilter class.

PR Checklist

• [X] No API changes were made (or the changes have been approved)
• [X] No major design changes were made (or the changes have been approved)

• STYLE: Use canonical naming in itkRecursiveGaussianImageFilter tests
• ENH: Add boolean macro to across-scale normalization ivar
• ENH: Increase coverage for itk::RecursiveGaussianImageFilter

PR Checklist

• [X] No API changes were made (or the changes have been approved)
• [X] No major design changes were made (or the changes have been approved)