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Merge pull request #2418 from SCIInstitute/try_itk-5.4.4
Upgrade to ITK 5.4.4, fixes for GCC 13
2 parents d80558b + 9285806 commit 8a8530e

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‎.github/workflows/build-linux-debug.yml‎

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- name: cmake
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shell: bash -l {0}
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.5 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.4 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.5 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
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- name: Check space6
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run: df -h

‎.github/workflows/build-linux.yml‎

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@@ -72,7 +72,7 @@ jobs:
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- name: cmake
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shell: bash -l {0}
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.5 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
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run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.4 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.5 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
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- name: Check space5
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run: df -h

‎.github/workflows/build-windows.yml‎

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# Note the current convention is to use the -S and -B options here to specify source
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# and build directories, but this is only available with CMake 3.13 and higher.
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# The CMake binaries on the Github Actions machines are (as of this writing) 3.12
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run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.3" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.5" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
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run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.4" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.5" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
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- name: Build
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working-directory: "C:/build"

‎Libs/Optimize/Container/GenericContainer.h‎

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@@ -28,7 +28,7 @@ class GenericContainer : public itk::DataObject {
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itkNewMacro(Self);
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/** Run-time type information (and related methods). */
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itkTypeMacro(ParticleContainer, itk::DataObject);
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itkTypeMacro(GenericContainer, itk::DataObject);
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/** Returns a reference to the object associated with index k. If the index
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k does not already exist, this method inserts a new entry for k. */

‎Libs/Optimize/Container/GenericContainerArray.h‎

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@@ -30,7 +30,7 @@ class GenericContainerArray : public std::vector<typename GenericContainer<T>::P
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itkNewMacro(Self);
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/** Run-time type information (and related methods). */
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itkTypeMacro(ParticleContainer, Observer);
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itkTypeMacro(GenericContainerArray, Observer);
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/** Callbacks that may be defined by a subclass. If a subclass defines one
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of these callback methods, the corresponding flag in m_DefinedCallbacks

‎Libs/Optimize/Container/MeanCurvatureContainer.h‎

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@@ -31,7 +31,7 @@ class MeanCurvatureContainer : public GenericContainerArray<TNumericType> {
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itkNewMacro(Self);
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/** Run-time type information (and related methods). */
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itkTypeMacro(ParticleMeanCurvatureAttribute, GenericContainerArray);
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itkTypeMacro(MeanCurvatureContainer, GenericContainerArray);
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void SetVerbosity(unsigned int val) { m_verbosity = val; }
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‎Libs/Optimize/GradientDescentOptimizer.h‎

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@@ -43,7 +43,7 @@ class GradientDescentOptimizer : public itk::Object {
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typedef shapeworks::ImageDomainWithGradients<TGradientNumericType> DomainType;
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/** Run-time type information (and related methods). */
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itkTypeMacro(ParticleGradientDescentPositionOptimizer, Object);
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itkTypeMacro(GradientDescentOptimizer, Object);
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/** Dimensionality of the domain of the particle system. */
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itkStaticConstMacro(Dimension, unsigned int, VDimension);

‎Support/xlnt.patch‎

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diff --git a/include/xlnt/cell/phonetic_run.hpp b/include/xlnt/cell/phonetic_run.hpp
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index cbf62ea7..9f20384e 100644
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--- a/include/xlnt/cell/phonetic_run.hpp
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+++ b/include/xlnt/cell/phonetic_run.hpp
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@@ -24,6 +24,7 @@
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#pragma once
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#include <string>
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+#include <cstdint>
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#include <xlnt/xlnt_config.hpp>
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‎Testing/CMakeLists.txt‎

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# GTest setup
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#find_package(GTest REQUIRED)
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set(BUILD_SHARED_LIBS_SAVED ${BUILD_SHARED_LIBS})
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set(BUILD_SHARED_LIBS OFF)
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# fetch googletest
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include(FetchContent)
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FetchContent_Declare(
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add_subdirectory(${googletest_SOURCE_DIR} ${googletest_BINARY_DIR})
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endif()
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set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
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# Restore BUILD_SHARED_LIBS
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set(BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS_SAVED})
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# NOTE: must call enable_testing() before this in the top-level CMakeLists.txt
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‎build_dependencies.sh‎

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@@ -22,8 +22,8 @@ BUILD_TYPE="Release"
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BUILD_LOG="build_dependencies.log"
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VTK_VER="v9.5.0"
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VTK_VER_STR="9.5"
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ITK_VER="v5.3.0"
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ITK_VER_STR="5.3"
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ITK_VER="v5.4.4"
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ITK_VER_STR="5.4"
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QT_MIN_VER="5.15.4"
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XLNT_VER="538f80794c7d736afc0a452d21313606cc5538fc"
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JKQTPLOTTER_VER="v2022.11.30-refix-rpath"
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# move conflicting file out of the way so it builds on osx
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mv third-party/libstudxml/version third-party/libstudxml/version.bak
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# Fix for GCC 13
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echo '#include <cstdint>' >> include/xlnt/xlnt_config.hpp
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# fix rpath
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sed -i'.original' -e 's/INSTALL_NAME_DIR.*/)/' source/CMakeLists.txt
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