Upgrade to ITK 5.4.4, fixes for GCC 13

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

@@ -73,7 +73,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      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=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$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 ..
 
     - name: Check space6
       run: df -h

.github/workflows/build-linux.yml

@@ -72,7 +72,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      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=$GA_API_SECRET ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$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 ..
 
     - name: Check space5
       run: df -h

.github/workflows/build-windows.yml

@@ -109,7 +109,7 @@ jobs:
       # Note the current convention is to use the -S and -B options here to specify source 
       # and build directories, but this is only available with CMake 3.13 and higher.  
       # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      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
+      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
 
     - name: Build
       working-directory: "C:/build"

Libs/Optimize/Container/GenericContainer.h

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

Libs/Optimize/Container/GenericContainerArray.h

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

Libs/Optimize/Container/MeanCurvatureContainer.h

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

Libs/Optimize/GradientDescentOptimizer.h

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

Support/xlnt.patch

@@ -0,0 +1,12 @@
+diff --git a/include/xlnt/cell/phonetic_run.hpp b/include/xlnt/cell/phonetic_run.hpp
+index cbf62ea7..9f20384e 100644
+--- a/include/xlnt/cell/phonetic_run.hpp
++++ b/include/xlnt/cell/phonetic_run.hpp
+@@ -24,6 +24,7 @@
+ #pragma once
+
+ #include <string>
++#include <cstdint>
+
+ #include <xlnt/xlnt_config.hpp>
+

Testing/CMakeLists.txt

@@ -1,6 +1,9 @@
 # GTest setup
 #find_package(GTest REQUIRED)
 
+set(BUILD_SHARED_LIBS_SAVED ${BUILD_SHARED_LIBS})
+set(BUILD_SHARED_LIBS OFF)
+
 # fetch googletest
 include(FetchContent)
 FetchContent_Declare(
@@ -14,6 +17,10 @@ if(NOT googletest_POPULATED)
   add_subdirectory(${googletest_SOURCE_DIR} ${googletest_BINARY_DIR})
 endif()
 
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+# Restore BUILD_SHARED_LIBS
+set(BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS_SAVED})
 
 # NOTE: must call enable_testing() before this in the top-level CMakeLists.txt
 

build_dependencies.sh

@@ -22,8 +22,8 @@ BUILD_TYPE="Release"
 BUILD_LOG="build_dependencies.log"
 VTK_VER="v9.5.0"
 VTK_VER_STR="9.5"
-ITK_VER="v5.3.0"
-ITK_VER_STR="5.3"
+ITK_VER="v5.4.4"
+ITK_VER_STR="5.4"
 QT_MIN_VER="5.15.4"
 XLNT_VER="538f80794c7d736afc0a452d21313606cc5538fc"
 JKQTPLOTTER_VER="v2022.11.30-refix-rpath"
@@ -201,6 +201,9 @@ build_xlnt()
   # move conflicting file out of the way so it builds on osx
   mv third-party/libstudxml/version third-party/libstudxml/version.bak
 
+  # Fix for GCC 13
+  echo '#include <cstdint>' >> include/xlnt/xlnt_config.hpp
+
   # fix rpath
   sed -i'.original' -e 's/INSTALL_NAME_DIR.*/)/' source/CMakeLists.txt