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STYLE: Rename variables and types in spectral applications
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This commit makes variable and type names in spectral applications consistent
with the recent changes in spectral filters
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@cyrilmory @SimonRit
cyrilmory authored and SimonRit committed Feb 11, 2025
1 parent faf4926 commit cd0c841
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Showing 9 changed files with 212 additions and 168 deletions.
21 changes: 11 additions & 10 deletions applications/rtkspectralforwardmodel/rtkspectralforwardmodel.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ main(int argc, char * argv[])
using PixelValueType = float;
constexpr unsigned int Dimension = 3;
using DecomposedProjectionType = itk::VectorImage<PixelValueType, Dimension>;
using SpectralProjectionsType = itk::VectorImage<PixelValueType, Dimension>;
using MeasuredProjectionsType = itk::VectorImage<PixelValueType, Dimension>;
using IncidentSpectrumImageType = itk::VectorImage<PixelValueType, Dimension - 1>;
using DetectorResponseImageType = itk::Image<PixelValueType, Dimension - 1>;
using MaterialAttenuationsImageType = itk::Image<PixelValueType, Dimension - 1>;
Expand All @@ -58,10 +58,10 @@ main(int argc, char * argv[])
const unsigned int MaximumEnergy = incidentSpectrum->GetVectorLength();

// Generate a set of zero-filled photon count projections
SpectralProjectionsType::Pointer photonCounts = SpectralProjectionsType::New();
photonCounts->CopyInformation(decomposedProjection);
photonCounts->SetVectorLength(NumberOfSpectralBins);
photonCounts->Allocate();
MeasuredProjectionsType::Pointer measuredProjections = MeasuredProjectionsType::New();
measuredProjections->CopyInformation(decomposedProjection);
measuredProjections->SetVectorLength(NumberOfSpectralBins);
measuredProjections->Allocate();

// Read the thresholds on command line
itk::VariableLengthVector<unsigned int> thresholds;
Expand All @@ -81,11 +81,12 @@ main(int argc, char * argv[])
<< decomposedProjection->GetPixel(indexDecomp).Size() << ", should be "
<< NumberOfMaterials);

SpectralProjectionsType::IndexType indexSpect;
MeasuredProjectionsType::IndexType indexSpect;
indexSpect.Fill(0);
if (photonCounts->GetPixel(indexSpect).Size() != NumberOfSpectralBins)
if (measuredProjections->GetPixel(indexSpect).Size() != NumberOfSpectralBins)
itkGenericExceptionMacro(<< "Spectral projections (i.e. photon count data) image has vector size "
<< photonCounts->GetPixel(indexSpect).Size() << ", should be " << NumberOfSpectralBins);
<< measuredProjections->GetPixel(indexSpect).Size() << ", should be "
<< NumberOfSpectralBins);

IncidentSpectrumImageType::IndexType indexIncident;
indexIncident.Fill(0);
Expand All @@ -100,10 +101,10 @@ main(int argc, char * argv[])

// Create and set the filter
using ForwardModelFilterType =
rtk::SpectralForwardModelImageFilter<DecomposedProjectionType, SpectralProjectionsType, IncidentSpectrumImageType>;
rtk::SpectralForwardModelImageFilter<DecomposedProjectionType, MeasuredProjectionsType, IncidentSpectrumImageType>;
ForwardModelFilterType::Pointer forward = ForwardModelFilterType::New();
forward->SetInputDecomposedProjections(decomposedProjection);
forward->SetInputMeasuredProjections(photonCounts);
forward->SetInputMeasuredProjections(measuredProjections);
forward->SetInputIncidentSpectrum(incidentSpectrum);
forward->SetDetectorResponse(detectorResponse);
forward->SetMaterialAttenuations(materialAttenuations);
Expand Down
16 changes: 8 additions & 8 deletions applications/rtkspectralonestep/rtkspectralonestep.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -58,21 +58,21 @@ rtkspectralonestep(const args_info_rtkspectralonestep & args_info)
// Define types for the input images
#ifdef RTK_USE_CUDA
using MaterialVolumesType = typename itk::CudaImage<itk::Vector<dataType, VNumberOfMaterials>, Dimension>;
using PhotonCountsType = typename itk::CudaImage<itk::Vector<dataType, VNumberOfBins>, Dimension>;
using MeasuredProjectionsType = typename itk::CudaImage<itk::Vector<dataType, VNumberOfBins>, Dimension>;
using IncidentSpectrumType = itk::CudaImage<dataType, Dimension>;
using DetectorResponseType = itk::CudaImage<dataType, 2>;
using MaterialAttenuationsType = itk::CudaImage<dataType, 2>;
#else
using MaterialVolumesType = typename itk::Image<itk::Vector<dataType, VNumberOfMaterials>, Dimension>;
using PhotonCountsType = typename itk::Image<itk::Vector<dataType, VNumberOfBins>, Dimension>;
using MeasuredProjectionsType = typename itk::Image<itk::Vector<dataType, VNumberOfBins>, Dimension>;
using IncidentSpectrumType = itk::Image<dataType, Dimension>;
using DetectorResponseType = itk::Image<dataType, 2>;
using MaterialAttenuationsType = itk::Image<dataType, 2>;
#endif

// Instantiate and update the readers
typename PhotonCountsType::Pointer photonCounts;
TRY_AND_EXIT_ON_ITK_EXCEPTION(photonCounts = itk::ReadImage<PhotonCountsType>(args_info.spectral_arg))
typename MeasuredProjectionsType::Pointer mea;
TRY_AND_EXIT_ON_ITK_EXCEPTION(mea = itk::ReadImage<MeasuredProjectionsType>(args_info.spectral_arg))

IncidentSpectrumType::Pointer incidentSpectrum;
TRY_AND_EXIT_ON_ITK_EXCEPTION(incidentSpectrum = itk::ReadImage<IncidentSpectrumType>(args_info.incident_arg))
Expand Down Expand Up @@ -183,7 +183,7 @@ rtkspectralonestep(const args_info_rtkspectralonestep & args_info)

// Set the forward and back projection filters to be used
using MechlemFilterType = typename rtk::
MechlemOneStepSpectralReconstructionFilter<MaterialVolumesType, PhotonCountsType, IncidentSpectrumType>;
MechlemOneStepSpectralReconstructionFilter<MaterialVolumesType, MeasuredProjectionsType, IncidentSpectrumType>;
typename MechlemFilterType::Pointer mechlemOneStep = MechlemFilterType::New();
SetForwardProjectionFromGgo(args_info, mechlemOneStep.GetPointer());
SetBackProjectionFromGgo(args_info, mechlemOneStep.GetPointer());
Expand All @@ -201,7 +201,7 @@ rtkspectralonestep(const args_info_rtkspectralonestep & args_info)
mechlemOneStep->SetSupportMask(supportmask);
if (args_info.regul_spatial_weights_given)
mechlemOneStep->SetSpatialRegularizationWeights(spatialRegulWeighs);
mechlemOneStep->SetInputMeasuredProjections(photonCounts);
mechlemOneStep->SetInputMeasuredProjections(mea);
mechlemOneStep->SetGeometry(geometry);
if (args_info.projection_weights_given)
mechlemOneStep->SetProjectionWeights(projectionWeights);
Expand All @@ -221,8 +221,8 @@ main(int argc, char * argv[])
GGO(rtkspectralonestep, args_info);
try
{
itk::ImageIOBase::Pointer headerInputPhotonCounts = GetFileHeader(args_info.spectral_arg);
unsigned int nBins = headerInputPhotonCounts->GetNumberOfComponents();
itk::ImageIOBase::Pointer headerInputMeasuredProjections = GetFileHeader(args_info.spectral_arg);
unsigned int nBins = headerInputMeasuredProjections->GetNumberOfComponents();
itk::ImageIOBase::Pointer headerAttenuations = GetFileHeader(args_info.attenuations_arg);
unsigned int nMaterials = headerAttenuations->GetDimensions(0);

Expand Down
38 changes: 22 additions & 16 deletions include/rtkCudaWeidingerForwardModelImageFilter.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@ CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjection

template <class TDecomposedProjections, class TMeasuredProjections, class TIncidentSpectrum, class TProjections>
void
CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjections, TIncidentSpectrum, TProjections>::GPUGenerateData()
CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjections, TIncidentSpectrum, TProjections>::
GPUGenerateData()
{
this->AllocateOutputs();

Expand Down Expand Up @@ -71,21 +72,26 @@ CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjection
# endif

// Run the forward projection with a slab of SLAB_SIZE or less projections
CUDA_WeidingerForwardModel(
projectionSize,
this->m_MaterialAttenuations.data_block(),
this->m_BinnedDetectorResponse.data_block(),
pMatProj,
pPhoCount,
pSpectrum,
pProjOnes,
pOut1,
pOut2,
CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjections, TIncidentSpectrum, TProjections>::nBins,
nEnergies,
CudaWeidingerForwardModelImageFilter<TDecomposedProjections, TMeasuredProjections, TIncidentSpectrum, TProjections>::nMaterials,
this->m_NumberOfProjectionsInIncidentSpectrum,
this->GetInputMeasuredProjections()->GetBufferedRegion().GetIndex(Dimension - 1));
CUDA_WeidingerForwardModel(projectionSize,
this->m_MaterialAttenuations.data_block(),
this->m_BinnedDetectorResponse.data_block(),
pMatProj,
pPhoCount,
pSpectrum,
pProjOnes,
pOut1,
pOut2,
CudaWeidingerForwardModelImageFilter<TDecomposedProjections,
TMeasuredProjections,
TIncidentSpectrum,
TProjections>::nBins,
nEnergies,
CudaWeidingerForwardModelImageFilter<TDecomposedProjections,
TMeasuredProjections,
TIncidentSpectrum,
TProjections>::nMaterials,
this->m_NumberOfProjectionsInIncidentSpectrum,
this->GetInputMeasuredProjections()->GetBufferedRegion().GetIndex(Dimension - 1));
}

} // end namespace rtk
Expand Down
54 changes: 28 additions & 26 deletions include/rtkMechlemOneStepSpectralReconstructionFilter.h
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Original file line number Diff line number Diff line change
Expand Up @@ -192,9 +192,10 @@ class ITK_TEMPLATE_EXPORT MechlemOneStepSpectralReconstructionFilter

#if !defined(ITK_WRAPPING_PARSER)
# ifdef RTK_USE_CUDA
typedef typename std::conditional<std::is_same<TOutputImage, CPUOutputImageType>::value,
WeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>,
CudaWeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>>::type
typedef typename std::conditional<
std::is_same<TOutputImage, CPUOutputImageType>::value,
WeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>,
CudaWeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>>::type
WeidingerForwardModelType;
typedef
typename std::conditional<std::is_same<TOutputImage, CPUOutputImageType>::value,
Expand All @@ -206,7 +207,8 @@ class ITK_TEMPLATE_EXPORT MechlemOneStepSpectralReconstructionFilter
CudaBackProjectionImageFilter<HessiansImageType>>::type
CudaHessiansBackProjectionImageFilterType;
# else
using WeidingerForwardModelType = WeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>;
using WeidingerForwardModelType =
WeidingerForwardModelImageFilter<TOutputImage, TMeasuredProjections, TIncidentSpectrum>;
using CudaSingleComponentForwardProjectionImageFilterType =
JosephForwardProjectionImageFilter<SingleComponentImageType, SingleComponentImageType>;
using CudaHessiansBackProjectionImageFilterType = BackProjectionImageFilter<HessiansImageType, HessiansImageType>;
Expand Down Expand Up @@ -307,28 +309,28 @@ class ITK_TEMPLATE_EXPORT MechlemOneStepSpectralReconstructionFilter

#if !defined(ITK_WRAPPING_PARSER)
/** Member pointers to the filters used internally (for convenience)*/
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 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
Expand Down
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