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5 Commits
siddonTril
...
ScoutRT_Qt
| Author | SHA1 | Date | |
|---|---|---|---|
| 1e26350281 | |||
| 74736603c6 | |||
| ed75b0920d | |||
| 632303efcc | |||
| 14f4aca6d1 |
@@ -1,4 +1,4 @@
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cmake_minimum_required(VERSION 2.8.12)
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cmake_minimum_required(VERSION 3.16)
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SET(LIB_NAME itkDTRrecon)
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@@ -6,12 +6,6 @@
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#include <cstring>
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#include <iterator>
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#ifdef __GNUC__
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#define VARIABLE_IS_NOT_USED __attribute__ ((unused))
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#else
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#define VARIABLE_IS_NOT_USED
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#endif
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//Function to get method and class name for logging purposes.
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template <size_t FL, size_t PFL>
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const char* computeMethodName(const char (&function)[FL], const char (&prettyFunction)[PFL])
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@@ -30,7 +24,7 @@ const char* computeMethodName(const char (&function)[FL], const char (&prettyFun
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namespace itk {
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/* reference string required for comparison with tag values */
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static const char VARIABLE_IS_NOT_USED *ImageOrientationStrings[] = {
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static const char* ImageOrientationStrings[] = {
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"NotDefined",
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"HFS",
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"FFS",
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@@ -46,49 +40,49 @@ static const bool verbose = false;
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/* this is in the end a IEC to HFS...
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* but we keep this for ourselves...
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*/
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static double VARIABLE_IS_NOT_USED Standard_DRT2LPS[9] = {
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static double Standard_DRT2LPS[9] = {
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1, 0, 0,
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0, 0, -1,
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0, 1, 0
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};
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static double VARIABLE_IS_NOT_USED PAElementsIEC[9] = {
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static double PAElementsIEC[9] = {
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1, 0, 0,
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0, -1, 0,
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0, 0, -1
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};
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static double VARIABLE_IS_NOT_USED LATElementsIEC[9] = {
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static double LATElementsIEC[9] = {
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0, 0, -1,
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0, -1, 0,
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-1, 0, 0
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};
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static double VARIABLE_IS_NOT_USED HFS2IEC[9] = {
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static double HFS2IEC[9] = {
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1, 0, 0,
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0, 0, 1,
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0, -1, 0
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};
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static double VARIABLE_IS_NOT_USED FFS2IEC[9] = {
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static double FFS2IEC[9] = {
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-1, 0, 0,
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0, 0, -1,
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0, -1, 0
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};
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static double VARIABLE_IS_NOT_USED HFP2IEC[9] = {
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static double HFP2IEC[9] = {
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-1, 0, 0,
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0, 0, 1,
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0, 1, 0
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};
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static double VARIABLE_IS_NOT_USED FFP2IEC[9] = {
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static double FFP2IEC[9] = {
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1, 0, 0,
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0, 0, -1,
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0, 1, 0
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};
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static double VARIABLE_IS_NOT_USED PAT2IEC[9] = {
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static double PAT2IEC[9] = {
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1, 0, 0,
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0, 0, 1,
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0, -1, 0
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@@ -143,7 +143,7 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
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//std::cout<< "-----> Mutual :: fixedImageRegion1: "<< metric1->GetFixedImageRegion() << std::endl;
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auto movingImageRegion = this->m_Filter1->GetOutput()->GetBufferedRegion();
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//unsigned int numberOfPixels = movingImageRegion.GetNumberOfPixels();
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unsigned int numberOfPixels = movingImageRegion.GetNumberOfPixels();
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//auto numberOfSamples = static_cast<unsigned int>(numberOfPixels * 0.50); //100%
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// since we have a ROI, then we should not set allPixels to TRUE.
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@@ -180,7 +180,7 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
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//std::cout<< "-----> Mutual :: fixedImageRegion2: "<< metric2->GetFixedImageRegion() << std::endl;
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movingImageRegion = this->m_Filter2->GetOutput()->GetBufferedRegion();
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//numberOfPixels = movingImageRegion.GetNumberOfPixels();
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numberOfPixels = movingImageRegion.GetNumberOfPixels();
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//numberOfSamples = static_cast<unsigned int>(numberOfPixels * 0.50); //100%
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//metric2->SetNumberOfSpatialSamples(numberOfSamples);
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@@ -20,7 +20,9 @@
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#include "itkCovariantVector.h"
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#include "itkMacro.h"
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#include "itkNormalizedCorrelationImageToImageMetric.hxx"
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//#include "itkNormalizedCorrelationImageToImageMetric.hxx"
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#include "itkNormalizedCorrelationImageToImageMetric.h"
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#include "itkPoint.h"
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#include "itkgTwoImageToOneImageMetric.h"
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@@ -262,7 +262,7 @@ NormalizedCorrelationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetVal
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}
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// Calculate the measure value between fixed image 1 and the moving image
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//auto oldprecision = std::cout.precision();
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auto oldprecision = std::cout.precision();
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// std::cout<<"Region " <<this->GetFixedImageRegion1() <<std::endl;
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@@ -2127,13 +2127,14 @@ void itkImageProcessor::Write2DImages(){
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vtkImageData* itkImageProcessor::GetLocalizer1VTK()
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{
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// Rescale the intensity of the projection images to 0-32768 for output.
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using RescaleFilterType = itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>;
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RescaleFilterType::Pointer rescaler1 = RescaleFilterType::New();
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rescaler1->SetOutputMinimum(0);
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rescaler1->SetOutputMaximum(IMG_VIS_MAXIMUM_RANGE);
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rescaler1->SetInput( m_PASourceDupli->GetOutput() );
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rescaler1->SetOutputMaximum(32768);
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rescaler1->SetInput(m_PASourceDupli->GetOutput());
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rescaler1->Update();
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toVTKLocalizer1->SetInput(rescaler1->GetOutput());
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@@ -2186,18 +2187,22 @@ vtkImageData* itkImageProcessor::GetLocalizer1VTK()
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vtkImageData* itkImageProcessor::GetLocalizer2VTK()
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{
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// Rescale the intensity of the projection images to 0-32768 for output.
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using RescaleFilterType = itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>;
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RescaleFilterType::Pointer rescaler2 = RescaleFilterType::New();
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rescaler2->SetOutputMinimum(0);
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rescaler2->SetOutputMaximum(IMG_VIS_MAXIMUM_RANGE);
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rescaler2->SetInput( m_LATSourceDupli->GetOutput() );
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rescaler2->SetOutputMaximum(32768);
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rescaler2->SetInput(m_LATSourceDupli ->GetOutput());
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rescaler2->Update();
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toVTKLocalizer2->SetInput(rescaler2->GetOutput());
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toVTKLocalizer2->Update();
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// if(true) {
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// using ImageRegionType3D = ImageType3D::RegionType;
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// using SizeType3D = ImageRegionType3D::SizeType;
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@@ -2241,7 +2246,6 @@ vtkImageData* itkImageProcessor::GetLocalizer2VTK()
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toVTKLocalizer2->GetOutput();
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}
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vtkImageData* itkImageProcessor::GetProjection1VTK()
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{
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@@ -2252,60 +2256,33 @@ vtkImageData* itkImageProcessor::GetProjection1VTK()
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//TODO
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}
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// Rescale the intensity of the projection images to 0-32768 for output.
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using RescaleFilterType = itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>;
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RescaleFilterType::Pointer rescaler1 = RescaleFilterType::New();
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rescaler1->SetOutputMinimum(0);
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rescaler1->SetOutputMaximum(IMG_VIS_MAXIMUM_RANGE);
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rescaler1->SetOutputMaximum(32768);
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rescaler1->SetInput( imageDRT1In );
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rescaler1->Update();
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// using ImageCalculatorFilterType = itk::MinimumMaximumImageCalculator<InternalImageType>;
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// auto imageCalculatorFilter = ImageCalculatorFilterType::New();
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// imageCalculatorFilter->SetImage(imageDRT1In);
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// imageCalculatorFilter->Compute();
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// std::cout<< "itkImageProcessor::imageDRT1In() " <<
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// imageCalculatorFilter <<std::endl;
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// using ImageCalculatorFilterType2 = itk::MinimumMaximumImageCalculator<OutputImageType>;
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// auto imageCalculatorFilter2 = ImageCalculatorFilterType2::New();
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// imageCalculatorFilter2->SetImage(rescaler1->GetOutput());
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// imageCalculatorFilter2->Compute();
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// std::cout<< "itkImageProcessor::imageDRT2In() " <<
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// imageCalculatorFilter2 <<std::endl;
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toVTK2D1->SetInput(rescaler1->GetOutput());
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toVTK2D1->Update();
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return
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toVTK2D1->GetOutput();
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}
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vtkImageData* itkImageProcessor::GetProjection1VTKToWrite()
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{
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if(m_DRTImage1MetaInfo == NULL ||
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m_DRTGeometryMetaInfo == NULL ||
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m_TransformMetaInfo == NULL ){
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return NULL;
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//TODO
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}
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using ImageCalculatorFilterType = itk::MinimumMaximumImageCalculator<InternalImageType>;
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auto imageCalculatorFilter = ImageCalculatorFilterType::New();
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imageCalculatorFilter->SetImage(imageDRT1In);
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imageCalculatorFilter->Compute();
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using IntWindowType = itk::IntensityWindowingImageFilter<InternalImageType, OutputImageType>;
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auto intWindowFilter = IntWindowType::New();
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intWindowFilter->SetWindowMinimum(imageCalculatorFilter->GetMinimum());
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intWindowFilter->SetWindowMaximum(imageCalculatorFilter->GetMaximum());
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intWindowFilter->SetOutputMinimum(0);
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if(imageCalculatorFilter->GetMaximum() > SHRT_MAX){
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intWindowFilter->SetOutputMaximum(SHRT_MAX);
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}else
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intWindowFilter->SetOutputMaximum(imageCalculatorFilter->GetMaximum());
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intWindowFilter->SetInput(imageDRT1In);
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intWindowFilter->Update();
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toVTK2D1->SetInput(intWindowFilter->GetOutput());
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toVTK2D1->Update();
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// using ImageCalculatorFilterType2 = itk::MinimumMaximumImageCalculator<OutputImageType>;
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// auto imageCalculatorFilter2 = ImageCalculatorFilterType2::New();
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// imageCalculatorFilter2->SetImage(intWindowFilter->GetOutput());
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// imageCalculatorFilter2->Compute();
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// std::cout<< "itkImageProcessor::imageCalculatorFilter2() " <<
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// imageCalculatorFilter2->GetMinimum() << " " << imageCalculatorFilter2->GetMaximum() <<std::endl;
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// using ImageRegionType3D = ImageType3D::RegionType;
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// using SizeType3D = ImageRegionType3D::SizeType;
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@@ -2410,63 +2387,19 @@ vtkImageData* itkImageProcessor::GetProjection2VTK()
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//TODO
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}
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// Rescale the intensity of the projection images to 0-32768 for output.
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using RescaleFilterType = itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>;
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RescaleFilterType::Pointer rescaler2 = RescaleFilterType::New();
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rescaler2->SetOutputMinimum(0);
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rescaler2->SetOutputMaximum(IMG_VIS_MAXIMUM_RANGE);
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rescaler2->SetOutputMaximum(32768);
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rescaler2->SetInput( imageDRT2In );
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rescaler2->Update();
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rescaler2->Update();
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toVTK2D2->SetInput(rescaler2->GetOutput());
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toVTK2D2->Update();
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return
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toVTK2D2->GetOutput();
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}
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vtkImageData* itkImageProcessor::GetProjection2VTKToWrite()
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{
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if(m_DRTImage2MetaInfo == NULL ||
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m_DRTGeometryMetaInfo == NULL ||
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m_TransformMetaInfo == NULL ){
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return NULL;
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//TODO
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}
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using ImageCalculatorFilterType = itk::MinimumMaximumImageCalculator<InternalImageType>;
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auto imageCalculatorFilter = ImageCalculatorFilterType::New();
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imageCalculatorFilter->SetImage(imageDRT2In);
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imageCalculatorFilter->Compute();
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using IntWindowType = itk::IntensityWindowingImageFilter<InternalImageType, OutputImageType>;
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auto intWindowFilter = IntWindowType::New();
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intWindowFilter->SetWindowMinimum(imageCalculatorFilter->GetMinimum());
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intWindowFilter->SetWindowMaximum(imageCalculatorFilter->GetMaximum());
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intWindowFilter->SetOutputMinimum(0);
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if(imageCalculatorFilter->GetMaximum() > SHRT_MAX)
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intWindowFilter->SetOutputMaximum(SHRT_MAX);
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else
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intWindowFilter->SetOutputMaximum(imageCalculatorFilter->GetMaximum());
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intWindowFilter->SetInput(imageDRT2In);
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intWindowFilter->Update();
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toVTK2D2->SetInput(intWindowFilter->GetOutput());
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toVTK2D2->Update();
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// using ImageCalculatorFilterType2 = itk::MinimumMaximumImageCalculator<OutputImageType>;
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// auto imageCalculatorFilter2 = ImageCalculatorFilterType2::New();
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// imageCalculatorFilter2->SetImage(intWindowFilter->GetOutput());
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// imageCalculatorFilter2->Compute();
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// std::cout<< "itkImageProcessor::imageCalculatorFilter2() " <<
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// imageCalculatorFilter2->GetMinimum() << " " << imageCalculatorFilter2->GetMaximum() <<std::endl;
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// rescaler2->Print(std::cout);
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// using ImageRegionType3D = ImageType3D::RegionType;
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// using SizeType3D = ImageRegionType3D::SizeType;
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@@ -22,7 +22,6 @@ gfattori 08.11.2021
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#include "itkResampleImageFilter.h"
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#include "itkCastImageFilter.h"
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#include "itkRescaleIntensityImageFilter.h"
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#include "itkIntensityWindowingImageFilter.h"
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#include "itkChangeInformationImageFilter.h"
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#include "itkGDCMImageIO.h"
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#include "itkMetaDataObject.h"
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@@ -50,8 +49,6 @@ gfattori 08.11.2021
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#include "itkReg23.h"
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#include "itkReg23MetaInformation.h"
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#define IMG_VIS_MAXIMUM_RANGE 2048
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namespace itk
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{
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@@ -245,10 +242,6 @@ public:
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vtkImageData* GetProjection1VTK();
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vtkImageData* GetProjection2VTK();
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/** Conveniency methods to get VTK images for rendering */
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vtkImageData* GetProjection1VTKToWrite();
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vtkImageData* GetProjection2VTKToWrite();
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vtkImageData* GetLocalizer1VTK();
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vtkImageData* GetLocalizer2VTK();
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@@ -48,7 +48,6 @@ CIT 6, 89-94 (1998).
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#define itkgSiddonJacobsRayCastInterpolateImageFunction_hxx
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#include "itkgSiddonJacobsRayCastInterpolateImageFunction.h"
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#include "itkContinuousIndex.h"
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#include "itkMath.h"
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#include <cstdlib>
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@@ -129,7 +128,7 @@ gSiddonJacobsRayCastInterpolateImageFunction<TInputImage, TCoordRep>::Evaluate(c
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float alphaX, alphaY, alphaZ, alphaCmin, alphaCminPrev;
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float alphaUx, alphaUy, alphaUz;
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float alphaIntersectionUp[3], alphaIntersectionDown[3];
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float d12, value,valuetril;
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float d12, value;
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float firstIntersectionIndex[3];
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int firstIntersectionIndexUp[3], firstIntersectionIndexDown[3];
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int iU, jU, kU;
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@@ -156,12 +155,9 @@ gSiddonJacobsRayCastInterpolateImageFunction<TInputImage, TCoordRep>::Evaluate(c
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}
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PointType PointReq = point;
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//std::cout<<"PointReq: "<<point[0] <<" "<<point[1] <<" "<<point[2] <<" "<<std::endl;
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PointReq[0] += m_PanelOffset;
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drrPixelWorld = m_InverseTransform->TransformPoint(PointReq);
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//std::cout<<"drrPixelWorld: "<<drrPixelWorld[0] <<" "<<drrPixelWorld[1] <<" "<<drrPixelWorld[2] <<" "<<std::endl;
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// Get ths input pointers
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InputImageConstPointer inputPtr = this->GetInputImage();
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@@ -185,7 +181,6 @@ gSiddonJacobsRayCastInterpolateImageFunction<TInputImage, TCoordRep>::Evaluate(c
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SlidingSourcePoint[2] = 0.;
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PointType SourceWorld = m_InverseTransform->TransformPoint(SlidingSourcePoint);
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//std::cout<<"SourceWorld: "<<SourceWorld[0] <<" "<<SourceWorld[1] <<" "<<SourceWorld[2] <<" "<<std::endl;
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PointType O(3);
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O[0] = -ctPixelSpacing[0]/2.;
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@@ -435,7 +430,6 @@ gSiddonJacobsRayCastInterpolateImageFunction<TInputImage, TCoordRep>::Evaluate(c
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cIndex[1] = firstIntersectionIndexDown[1];
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cIndex[2] = firstIntersectionIndexDown[2];
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while (alphaCmin < alphaMax) /* Check if the ray is still in the CT volume */
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{
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/* Store the current ray position */
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@@ -463,104 +457,17 @@ gSiddonJacobsRayCastInterpolateImageFunction<TInputImage, TCoordRep>::Evaluate(c
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alphaZ = alphaZ + alphaUz;
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}
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if ((cIndex[0] >= 0) && (cIndex[0] < static_cast<IndexValueType>(sizeCT[0])) && (cIndex[1] >= 0) &&
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(cIndex[1] < static_cast<IndexValueType>(sizeCT[1])) && (cIndex[2] >= 0) &&
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(cIndex[2] < static_cast<IndexValueType>(sizeCT[2])))
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(cIndex[1] < static_cast<IndexValueType>(sizeCT[1])) && (cIndex[2] >= 0) &&
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(cIndex[2] < static_cast<IndexValueType>(sizeCT[2])))
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{
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// Calculate entry and exit points using alphaCmin and alphaCminPrev
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/* If it is a valid index, get the voxel intensity. */
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value = static_cast<float>(inputPtr->GetPixel(cIndex));
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// Accumulate the interpolated intensity along the ray path
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if (value > m_Threshold) /* Ignore voxels whose intensities are below the threshold. */
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{
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// Move along the ray by alphaCminPrev to find the entry point of this voxel
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PointType entryPoint;
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entryPoint[0] = SourceWorld[0] + alphaCminPrev * rayVector[0] ;
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entryPoint[1] = SourceWorld[1] + alphaCminPrev * rayVector[1] ;
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entryPoint[2] = SourceWorld[2] + alphaCminPrev * rayVector[2] ;
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// Move along the ray by alphaCmin to find the exit point of this voxel
|
||||
PointType exitPoint;
|
||||
exitPoint[0] = SourceWorld[0] + alphaCmin * rayVector[0] ;
|
||||
exitPoint[1] = SourceWorld[1] + alphaCmin * rayVector[1] ;
|
||||
exitPoint[2] = SourceWorld[2] + alphaCmin * rayVector[2] ;
|
||||
|
||||
// Get the mid-point of the voxel / ray interception
|
||||
PointType midpoint;
|
||||
midpoint[0]= (entryPoint[0] + exitPoint[0]) * 0.5;
|
||||
midpoint[1]= (entryPoint[1] + exitPoint[1]) * 0.5;
|
||||
midpoint[2]= (entryPoint[2] + exitPoint[2]) * 0.5;
|
||||
|
||||
// Ray is computed in 'Siddon' geometry with zero origin,
|
||||
// whereas the continuous index will be computed from the input
|
||||
// image. The origin and shifts to the voxel edge are to be account for
|
||||
midpoint[0] += ctOrigin[0] ;//+ O[0];
|
||||
midpoint[1] += ctOrigin[1] ;//+ O[1];
|
||||
midpoint[2] += ctOrigin[2] ;//+ O[2];
|
||||
|
||||
// Convert mid-point phyisical point into continuous index
|
||||
// We need to use this position to find the neighbouring voxels
|
||||
// for trilinear interpolation - not the cIndex!
|
||||
itk::ContinuousIndex <double,3> continuousIndex;
|
||||
inputPtr->TransformPhysicalPointToContinuousIndex(midpoint,continuousIndex);
|
||||
|
||||
// Get the baseIndex by flooring the continuous index
|
||||
IndexType baseIndex;
|
||||
baseIndex[0]=static_cast<IndexValueType>(std::floor(continuousIndex[0]));
|
||||
baseIndex[1]=static_cast<IndexValueType>(std::floor(continuousIndex[1]));
|
||||
baseIndex[2]=static_cast<IndexValueType>(std::floor(continuousIndex[2]));
|
||||
|
||||
// Calculate fractional parts for interpolation at the midpoint
|
||||
double x_frac = continuousIndex[0] - baseIndex[0];
|
||||
double y_frac = continuousIndex[1] - baseIndex[1];
|
||||
double z_frac = continuousIndex[2] - baseIndex[2];
|
||||
|
||||
// Perform boundary checks for trilinear interpolation
|
||||
bool within_bounds = (baseIndex[0] >= 0 && baseIndex[0] < sizeCT[0] - 1) &&
|
||||
(baseIndex[1] >= 0 && baseIndex[1] < sizeCT[1] - 1) &&
|
||||
(baseIndex[2] >= 0 && baseIndex[2] < sizeCT[2] - 1);
|
||||
if (within_bounds)
|
||||
{
|
||||
// Fetch intensities from neighboring voxels for trilinear interpolation
|
||||
float c000 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[0] += 1;
|
||||
float c100 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[1] += 1;
|
||||
float c110 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[0] -= 1;
|
||||
float c010 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[2] += 1;
|
||||
float c011 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[0] += 1;
|
||||
float c111 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[1] -= 1;
|
||||
float c101 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
baseIndex[0] -= 1;
|
||||
float c001 = static_cast<float>(inputPtr->GetPixel(baseIndex));
|
||||
|
||||
// NOTE: do not use baseIndex anymore after this. It's messed up.
|
||||
|
||||
// Perform trilinear interpolation at the midpoint
|
||||
float c00 = c000 * (1 - x_frac) + c100 * x_frac;
|
||||
float c01 = c001 * (1 - x_frac) + c101 * x_frac;
|
||||
float c10 = c010 * (1 - x_frac) + c110 * x_frac;
|
||||
float c11 = c011 * (1 - x_frac) + c111 * x_frac;
|
||||
|
||||
float c0 = c00 * (1 - y_frac) + c10 * y_frac;
|
||||
float c1 = c01 * (1 - y_frac) + c11 * y_frac;
|
||||
|
||||
valuetril = c0 * (1 - z_frac) + c1 * z_frac;
|
||||
|
||||
d12 += (alphaCmin - alphaCminPrev) * (valuetril - m_Threshold);
|
||||
|
||||
} else {
|
||||
d12 += (alphaCmin - alphaCminPrev) * (value - m_Threshold);
|
||||
}
|
||||
|
||||
d12 += (alphaCmin - alphaCminPrev) * (value - m_Threshold);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if (d12 < minOutputValue)
|
||||
|
||||
Reference in New Issue
Block a user