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RTKConsortium · Feb 12, 2025 · 27dbf24 · 27dbf24
1 parent 46046e2
commit 27dbf24
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Showing 8 changed files with 72 additions and 61 deletions.
diff --git a/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.cxx b/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.cxx
@@ -67,7 +67,8 @@ main(int argc, char * argv[])
   materialAttenuationsReader->Update();
 
   // Get parameters from the images
-  const unsigned int MaximumEnergy = incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
+  const unsigned int MaximumEnergy =
+    incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
 
   // If the detector response is given by the user, use it. Otherwise, assume it is included in the
   // incident spectrum, and fill the response with ones

diff --git a/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.cxx b/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.cxx
@@ -72,7 +72,8 @@ main(int argc, char * argv[])
   materialAttenuationsReader->Update();
 
   // Get parameters from the images
-  const unsigned int MaximumEnergy = incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
+  const unsigned int MaximumEnergy =
+    incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
 
   // If the detector response is given by the user, use it. Otherwise, assume it is included in the
   // incident spectrum, and fill the response with ones

diff --git a/applications/rtkspectralsimplexdecomposition/rtkspectralsimplexdecomposition.cxx b/applications/rtkspectralsimplexdecomposition/rtkspectralsimplexdecomposition.cxx
@@ -65,7 +65,7 @@ main(int argc, char * argv[])
   const unsigned int NumberOfSpectralBins = spectralProjection->GetVectorLength();
   const unsigned int MaximumEnergy = incidentSpectrum->GetLargestPossibleRegion().GetSize()[0];
 
-         // Read the thresholds on command line and check their number
+  // Read the thresholds on command line and check their number
   itk::VariableLengthVector<unsigned int> thresholds;
   thresholds.SetSize(NumberOfSpectralBins + 1);
   if (args_info.thresholds_given == NumberOfSpectralBins)

diff --git a/include/rtkMechlemOneStepSpectralReconstructionFilter.h b/include/rtkMechlemOneStepSpectralReconstructionFilter.h
@@ -320,30 +320,30 @@ class ITK_TEMPLATE_EXPORT MechlemOneStepSpectralReconstructionFilter
 
 #if !defined(ITK_WRAPPING_PARSER)
   /** Member pointers to the filters used internally (for convenience)*/
-  typename CastMaterialVolumesFilterType::Pointer                  m_CastMaterialVolumesFilter;
-  typename CastMeasuredProjectionsFilterType::Pointer              m_CastMeasuredProjectionsFilter;
-  typename ExtractMeasuredProjectionsFilterType::Pointer           m_ExtractMeasuredProjectionsFilter;
-  typename AddFilterType::Pointer                                  m_AddGradients;
-  typename SingleComponentForwardProjectionFilterType::Pointer     m_SingleComponentForwardProjectionFilter;
-  typename MaterialProjectionsSourceType::Pointer                  m_ProjectionsSource;
-  typename SingleComponentImageSourceType::Pointer                 m_SingleComponentProjectionsSource;
-  typename SingleComponentImageSourceType::Pointer                 m_SingleComponentVolumeSource;
-  typename GradientsSourceType::Pointer                            m_GradientsSource;
-  typename HessiansSourceType::Pointer                             m_HessiansSource;
-  typename WeidingerForwardModelType::Pointer                      m_WeidingerForward;
-  typename SQSRegularizationType::Pointer                          m_SQSRegul;
-  typename AddMatrixAndDiagonalFilterType::Pointer                 m_AddHessians;
-  typename NewtonFilterType::Pointer                               m_NewtonFilter;
-  typename NesterovFilterType::Pointer                             m_NesterovFilter;
-  typename ForwardProjectionFilterType::Pointer                    m_ForwardProjectionFilter;
-  typename GradientsBackProjectionFilterType::Pointer              m_GradientsBackProjectionFilter;
-  typename HessiansBackProjectionFilterType::Pointer               m_HessiansBackProjectionFilter;
-  typename MultiplyFilterType::Pointer                             m_MultiplySupportFilter;
-  typename MultiplyGradientFilterType::Pointer                     m_MultiplyRegulGradientsFilter;
-  typename MultiplyGradientFilterType::Pointer                     m_MultiplyRegulHessiansFilter;
-  typename MultiplyGradientFilterType::Pointer                     m_MultiplyGradientToBeBackprojectedFilter;
-  typename ReorderMeasuredProjectionsFilterType::Pointer           m_ReorderMeasuredProjectionsFilter;
-  typename ReorderProjectionsWeightsFilterType::Pointer            m_ReorderProjectionsWeightsFilter;
+  typename CastMaterialVolumesFilterType::Pointer              m_CastMaterialVolumesFilter;
+  typename CastMeasuredProjectionsFilterType::Pointer          m_CastMeasuredProjectionsFilter;
+  typename ExtractMeasuredProjectionsFilterType::Pointer       m_ExtractMeasuredProjectionsFilter;
+  typename AddFilterType::Pointer                              m_AddGradients;
+  typename SingleComponentForwardProjectionFilterType::Pointer m_SingleComponentForwardProjectionFilter;
+  typename MaterialProjectionsSourceType::Pointer              m_ProjectionsSource;
+  typename SingleComponentImageSourceType::Pointer             m_SingleComponentProjectionsSource;
+  typename SingleComponentImageSourceType::Pointer             m_SingleComponentVolumeSource;
+  typename GradientsSourceType::Pointer                        m_GradientsSource;
+  typename HessiansSourceType::Pointer                         m_HessiansSource;
+  typename WeidingerForwardModelType::Pointer                  m_WeidingerForward;
+  typename SQSRegularizationType::Pointer                      m_SQSRegul;
+  typename AddMatrixAndDiagonalFilterType::Pointer             m_AddHessians;
+  typename NewtonFilterType::Pointer                           m_NewtonFilter;
+  typename NesterovFilterType::Pointer                         m_NesterovFilter;
+  typename ForwardProjectionFilterType::Pointer                m_ForwardProjectionFilter;
+  typename GradientsBackProjectionFilterType::Pointer          m_GradientsBackProjectionFilter;
+  typename HessiansBackProjectionFilterType::Pointer           m_HessiansBackProjectionFilter;
+  typename MultiplyFilterType::Pointer                         m_MultiplySupportFilter;
+  typename MultiplyGradientFilterType::Pointer                 m_MultiplyRegulGradientsFilter;
+  typename MultiplyGradientFilterType::Pointer                 m_MultiplyRegulHessiansFilter;
+  typename MultiplyGradientFilterType::Pointer                 m_MultiplyGradientToBeBackprojectedFilter;
+  typename ReorderMeasuredProjectionsFilterType::Pointer       m_ReorderMeasuredProjectionsFilter;
+  typename ReorderProjectionsWeightsFilterType::Pointer        m_ReorderProjectionsWeightsFilter;
 #endif
 
   /** The inputs of this filter have the same type but not the same meaning

diff --git a/include/rtkMechlemOneStepSpectralReconstructionFilter.hxx b/include/rtkMechlemOneStepSpectralReconstructionFilter.hxx
@@ -87,8 +87,8 @@ MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, T
 
 template <class TOutputImage, class TMeasuredProjections, class TIncidentSpectrum>
 void
-MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>::SetInputMaterialVolumes(
-  const VectorImageType * variableLengthVectorMaterialVolumes)
+MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>::
+  SetInputMaterialVolumes(const VectorImageType * variableLengthVectorMaterialVolumes)
 {
   m_CastMaterialVolumesFilter->SetInput(variableLengthVectorMaterialVolumes);
   this->SetNthInput(0, const_cast<TOutputImage *>(m_CastMaterialVolumesFilter->GetOutput()));
@@ -104,8 +104,8 @@ MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, T
 
 template <class TOutputImage, class TMeasuredProjections, class TIncidentSpectrum>
 void
-MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>::SetInputMeasuredProjections(
-  const VectorImageType * variableLengthVectorMeasuredProjections)
+MechlemOneStepSpectralReconstructionFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>::
+  SetInputMeasuredProjections(const VectorImageType * variableLengthVectorMeasuredProjections)
 {
   m_CastMeasuredProjectionsFilter->SetInput(variableLengthVectorMeasuredProjections);
   this->SetNthInput(1, const_cast<TMeasuredProjections *>(m_CastMeasuredProjectionsFilter->GetOutput()));

diff --git a/include/rtkSimplexSpectralProjectionsDecompositionImageFilter.hxx b/include/rtkSimplexSpectralProjectionsDecompositionImageFilter.hxx
@@ -203,12 +203,12 @@ template <typename DecomposedProjectionsType,
           typename DetectorResponseImageType,
           typename MaterialAttenuationsImageType>
 void
-  SimplexSpectralProjectionsDecompositionImageFilter<DecomposedProjectionsType,
-                                                     MeasuredProjectionsType,
-                                                     IncidentSpectrumImageType,
-                                                     DetectorResponseImageType,
-                                                     MaterialAttenuationsImageType>::
-  SetInputSecondIncidentSpectrum(const VectorSpectrumImageType * SecondIncidentSpectrum)
+SimplexSpectralProjectionsDecompositionImageFilter<
+  DecomposedProjectionsType,
+  MeasuredProjectionsType,
+  IncidentSpectrumImageType,
+  DetectorResponseImageType,
+  MaterialAttenuationsImageType>::SetInputSecondIncidentSpectrum(const VectorSpectrumImageType * SecondIncidentSpectrum)
 {
   this->m_FlattenSecondFilter->SetInput(SecondIncidentSpectrum);
   this->m_PermuteSecondFilter->SetInput(this->m_FlattenSecondFilter->GetOutput());
@@ -410,8 +410,8 @@ SimplexSpectralProjectionsDecompositionImageFilter<DecomposedProjectionsType,
   typename IncidentSpectrumImageType::SizeType  sizeRequested = requested.GetSize();
   for (unsigned int i = 0; i < IncidentSpectrumImageType::GetImageDimension() - 1; i++)
   {
-    indexRequested[i+1] = this->GetOutput()->GetRequestedRegion().GetIndex()[i];
-    sizeRequested[i+1] = this->GetOutput()->GetRequestedRegion().GetSize()[i];
+    indexRequested[i + 1] = this->GetOutput()->GetRequestedRegion().GetIndex()[i];
+    sizeRequested[i + 1] = this->GetOutput()->GetRequestedRegion().GetSize()[i];
   }
 
   inputPtr2->SetRequestedRegion(requested);
@@ -560,7 +560,8 @@ SimplexSpectralProjectionsDecompositionImageFilter<DecomposedProjectionsType,
     if (this->GetInputSecondIncidentSpectrum()) // Dual energy CT
     {
       spectra.set_size(2, m_NumberOfEnergies);
-      for (int e = 0; e < m_NumberOfEnergies; e++) {
+      for (int e = 0; e < m_NumberOfEnergies; e++)
+      {
         spectra.put(0, e, spectrumIt.Get());
         spectra.put(1, e, secondSpectrumIt.Get());
         ++spectrumIt;
@@ -570,7 +571,8 @@ SimplexSpectralProjectionsDecompositionImageFilter<DecomposedProjectionsType,
     else
     {
       spectra.set_size(1, m_NumberOfEnergies);
-      for (int e = 0; e < m_NumberOfEnergies; e++) {
+      for (int e = 0; e < m_NumberOfEnergies; e++)
+      {
         spectra.put(0, e, spectrumIt.Get());
         ++spectrumIt;
       }

diff --git a/include/rtkSpectralForwardModelImageFilter.hxx b/include/rtkSpectralForwardModelImageFilter.hxx
@@ -118,12 +118,12 @@ template <typename DecomposedProjectionsType,
           typename DetectorResponseImageType,
           typename MaterialAttenuationsImageType>
 void
-SpectralForwardModelImageFilter<
-  DecomposedProjectionsType,
-  MeasuredProjectionsType,
-  IncidentSpectrumImageType,
-  DetectorResponseImageType,
-  MaterialAttenuationsImageType>::SetInputIncidentSpectrum(const VectorSpectrumImageType * IncidentSpectrum)
+SpectralForwardModelImageFilter<DecomposedProjectionsType,
+                                MeasuredProjectionsType,
+                                IncidentSpectrumImageType,
+                                DetectorResponseImageType,
+                                MaterialAttenuationsImageType>::SetInputIncidentSpectrum(const VectorSpectrumImageType *
+                                                                                           IncidentSpectrum)
 {
   this->m_FlattenFilter->SetInput(IncidentSpectrum);
   this->m_PermuteFilter->SetInput(this->m_FlattenFilter->GetOutput());
@@ -141,12 +141,12 @@ template <typename DecomposedProjectionsType,
           typename DetectorResponseImageType,
           typename MaterialAttenuationsImageType>
 void
-  SpectralForwardModelImageFilter<DecomposedProjectionsType,
-                                  MeasuredProjectionsType,
-                                  IncidentSpectrumImageType,
-                                  DetectorResponseImageType,
-                                  MaterialAttenuationsImageType>::
-  SetInputSecondIncidentSpectrum(const VectorSpectrumImageType * SecondIncidentSpectrum)
+SpectralForwardModelImageFilter<
+  DecomposedProjectionsType,
+  MeasuredProjectionsType,
+  IncidentSpectrumImageType,
+  DetectorResponseImageType,
+  MaterialAttenuationsImageType>::SetInputSecondIncidentSpectrum(const VectorSpectrumImageType * SecondIncidentSpectrum)
 {
   this->m_FlattenSecondFilter->SetInput(SecondIncidentSpectrum);
   this->m_PermuteSecondFilter->SetInput(this->m_FlattenSecondFilter->GetOutput());
@@ -401,8 +401,8 @@ SpectralForwardModelImageFilter<DecomposedProjectionsType,
   typename IncidentSpectrumImageType::SizeType  sizeRequested = requested.GetSize();
   for (unsigned int i = 0; i < IncidentSpectrumImageType::GetImageDimension() - 1; i++)
   {
-    indexRequested[i+1] = this->GetOutput()->GetRequestedRegion().GetIndex()[i];
-    sizeRequested[i+1] = this->GetOutput()->GetRequestedRegion().GetSize()[i];
+    indexRequested[i + 1] = this->GetOutput()->GetRequestedRegion().GetIndex()[i];
+    sizeRequested[i + 1] = this->GetOutput()->GetRequestedRegion().GetSize()[i];
   }
 
   requested.SetIndex(indexRequested);
@@ -539,7 +539,8 @@ SpectralForwardModelImageFilter<DecomposedProjectionsType,
     // Fill in the spectra matrix
     if (this->GetInputSecondIncidentSpectrum()) // Dual energy CT
     {
-      for (int e = 0; e < m_NumberOfEnergies; e++) {
+      for (int e = 0; e < m_NumberOfEnergies; e++)
+      {
         spectra.put(0, e, spectrumIt.Get());
         spectra.put(1, e, secondSpectrumIt.Get());
         ++spectrumIt;
@@ -548,7 +549,8 @@ SpectralForwardModelImageFilter<DecomposedProjectionsType,
     }
     else
     {
-      for (int e = 0; e < m_NumberOfEnergies; e++) {
+      for (int e = 0; e < m_NumberOfEnergies; e++)
+      {
         spectra.put(0, e, spectrumIt.Get());
         ++spectrumIt;
       }

diff --git a/test/rtkspectralonesteptest.cxx b/test/rtkspectralonesteptest.cxx
@@ -254,7 +254,8 @@ main(int argc, char * argv[])
 
   // Convert the itk::VectorImage<> returned by "forward" into
   // an itk::Image<itk::Vector<>>
-  typename CastMeasuredProjectionsFilterType::Pointer castMeasuredProjections = CastMeasuredProjectionsFilterType::New();
+  typename CastMeasuredProjectionsFilterType::Pointer castMeasuredProjections =
+    CastMeasuredProjectionsFilterType::New();
   castMeasuredProjections->SetInput(forward->GetOutput());
 
   // Read the material attenuations image as a matrix
@@ -331,11 +332,15 @@ main(int argc, char * argv[])
 #endif
 
 #ifdef RTK_USE_CUDA
-  std::cout << "\n\n****** Case 5: CUDA voxel-based Backprojector, 4 subsets, with regularization, itkVectorImage inputs ******" << std::endl;
+  std::cout
+    << "\n\n****** Case 5: CUDA voxel-based Backprojector, 4 subsets, with regularization, itkVectorImage inputs ******"
+    << std::endl;
 #else
-  std::cout << "\n\n****** Case 4: Voxel-based Backprojector, 4 subsets, with regularization, itkVectorImage inputs ******" << std::endl;
+  std::cout
+    << "\n\n****** Case 4: Voxel-based Backprojector, 4 subsets, with regularization, itkVectorImage inputs ******"
+    << std::endl;
 #endif
-  //Add a cast to itkVectorImage, to test the overloaded SetInputMaterialVolumes method
+  // Add a cast to itkVectorImage, to test the overloaded SetInputMaterialVolumes method
   typename CastMaterialVolumesFilterType::Pointer castMaterials = CastMaterialVolumesFilterType::New();
   castMaterials->SetInput(materialVolumeSource->GetOutput());
   mechlemOneStep->SetInputMaterialVolumes(castMaterials->GetOutput());