COMP: Update CI best practices and Python 3.10+

.github/workflows/build-test-package.yml

@@ -12,9 +12,9 @@ on:
 
 jobs:
   cxx-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.0
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.6
 
   python-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.0
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.6
     secrets:
       pypi_password: ${{ secrets.pypi_password }}

.github/workflows/clang-format-linter.yml

@@ -7,6 +7,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
-    - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master
+    - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@main
+      with:
+        itk-branch: main

include/itkContinuousBorderWarpImageFilter.hxx

@@ -72,7 +72,10 @@ ContinuousBorderWarpImageFilter<TInputImage, TOutputImage, TDisplacementField>::
       }
 
       // project point into image region
-      inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex);
+      if (!inputPtr->TransformPhysicalPointToContinuousIndex(point, contIndex))
+      {
+        itkExceptionMacro("Physical point " << point << " is outside the image domain");
+      }
 
       for (unsigned int j = 0; j < ImageDimension; j++)
       {

include/itkVariationalRegistrationElasticRegularizer.h

@@ -189,9 +189,9 @@ class VariationalRegistrationElasticRegularizer : public VariationalRegistration
   typename FFTWProxyType::PlanType m_PlanForward[ImageDimension];  /** FFT forward plan  */
   typename FFTWProxyType::PlanType m_PlanBackward[ImageDimension]; /** FFT backward plan */
   typename FFTWProxyType::ComplexType *
-                                      m_ComplexBuffer[ImageDimension]; /** memory space for output of forward and input of backward FFT*/
-  typename FFTWProxyType::PixelType * m_InputBuffer;                   /** FFT memory space for input data */
-  typename FFTWProxyType::PixelType * m_OutputBuffer;                  /** FFT memory space for output data */
+    m_ComplexBuffer[ImageDimension];                  /** memory space for output of forward and input of backward FFT*/
+  typename FFTWProxyType::PixelType * m_InputBuffer;  /** FFT memory space for input data */
+  typename FFTWProxyType::PixelType * m_OutputBuffer; /** FFT memory space for output data */
 
   struct ElasticFFTThreadStruct
   {

include/itkVariationalRegistrationFunction.h

@@ -19,7 +19,7 @@
 #define itkVariationalRegistrationFunction_h
 
 #include "itkFiniteDifferenceFunction.h"
-//#include "itkWarpImageFilter.h"
+// #include "itkWarpImageFilter.h"
 #include "itkContinuousBorderWarpImageFilter.h"
 #include <mutex>
 

include/itkVariationalRegistrationRegularizer.h

@@ -90,7 +90,7 @@ class VariationalRegistrationRegularizer : public InPlaceImageFilter<TDisplaceme
 
   /** Initialize the filter. */
   virtual void
-  Initialize(){};
+  Initialize() {};
 
 private:
   /** A boolean that indicates, if image spacing is considered. */

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
     "Topic :: Software Development :: Libraries",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
     "itk",
 ]

src/CMakeLists.txt

@@ -1,3 +1,4 @@
+include_directories("${VariationalRegistration_SOURCE_DIR}/include")
 include_directories("${VariationalRegistration_SOURCE_DIR}/src")
 
 # Test if ITK is built with FFTW. FFTWD is recommended and required for the

src/VariationalRegistrationMain.cxx

@@ -640,8 +640,7 @@ main(int argc, char * argv[])
   FunctionType::Pointer function;
   switch (forceType)
   {
-    case 0:
-    {
+    case 0: {
       DemonsFunctionType::Pointer demonsFunction = DemonsFunctionType::New();
       switch (forceDomain)
       {
@@ -659,8 +658,7 @@ main(int argc, char * argv[])
       function = demonsFunction;
     }
     break;
-    case 1:
-    {
+    case 1: {
       SSDFunctionType::Pointer ssdFunction = SSDFunctionType::New();
       switch (forceDomain)
       {
@@ -678,8 +676,7 @@ main(int argc, char * argv[])
       function = ssdFunction;
     }
     break;
-    case 2:
-    {
+    case 2: {
       NCCFunctionType::Pointer    nccFunction = NCCFunctionType::New();
       NCCFunctionType::RadiusType r;
       for (unsigned int dim = 0; dim < NCCFunctionType::ImageDimension; dim++)
@@ -722,22 +719,19 @@ main(int argc, char * argv[])
   RegularizerType::Pointer regularizer;
   switch (regularizerType)
   {
-    case 0:
-    {
+    case 0: {
       GaussianRegularizerType::Pointer gaussRegularizer = GaussianRegularizerType::New();
       gaussRegularizer->SetStandardDeviations(std::sqrt(regulVar));
       regularizer = gaussRegularizer;
     }
     break;
-    case 1:
-    {
+    case 1: {
       DiffusionRegularizerType::Pointer diffRegularizer = DiffusionRegularizerType::New();
       diffRegularizer->SetAlpha(regulAlpha);
       regularizer = diffRegularizer;
     }
     break;
-    case 2:
-    {
+    case 2: {
 #if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
       ElasticRegularizerType::Pointer elasticRegularizer = ElasticRegularizerType::New();
       elasticRegularizer->SetMu(regulMu);
@@ -748,8 +742,7 @@ main(int argc, char * argv[])
 #endif
     }
     break;
-    case 3:
-    {
+    case 3: {
 #if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
       CurvatureRegularizerType::Pointer curvatureRegularizer = CurvatureRegularizerType::New();
       curvatureRegularizer->SetAlpha(regulAlpha);
@@ -775,20 +768,17 @@ main(int argc, char * argv[])
   RegistrationFilterType::Pointer regFilter;
   switch (searchSpace)
   {
-    case 0:
-    {
+    case 0: {
       regFilter = RegistrationFilterType::New();
       break;
     }
-    case 1:
-    {
+    case 1: {
       DiffeomorphicRegistrationFilterType::Pointer diffeoRegFilter = DiffeomorphicRegistrationFilterType::New();
       diffeoRegFilter->SetNumberOfExponentiatorIterations(numberOfExponentiatorIterations);
       regFilter = diffeoRegFilter;
       break;
     }
-    case 2:
-    {
+    case 2: {
       SymmetricDiffeomorphicRegistrationFilterType::Pointer symmDiffeoRegFilter =
         SymmetricDiffeomorphicRegistrationFilterType::New();
       symmDiffeoRegFilter->SetNumberOfExponentiatorIterations(numberOfExponentiatorIterations);

src/itkVariationalRegistrationIncludeRequiredIOFactories.h

@@ -28,7 +28,7 @@
 #include "itkNrrdImageIOFactory.h"
 #include "itkGiplImageIOFactory.h"
 #include "itkNiftiImageIOFactory.h"
-//#include "itkTestDriverInclude.h"
+// #include "itkTestDriverInclude.h"
 #include "itkObjectFactoryBase.h"
 
 void

src/win32_compatibility/getopt.c

@@ -59,7 +59,9 @@ char * optarg;  /* argument associated with option */
  * getopt --
  *	Parse argc/argv argument vector.
  */
-int            getopt(nargc, nargv, ostr) int nargc;
+int
+               getopt(nargc, nargv, ostr)
+int            nargc;
 char * const * nargv;
 const char *   ostr;
 {