/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
#include <QApplication>
#include <itkWarpImageFilter.h>
+#if ( ITK_VERSION_MAJOR < 5 )
#include <itkVectorResampleImageFilter.h>
+#else
+#include <itkResampleImageFilter.h>
+#endif
#include "vvMidPosition.h"
#include "clitkCommon.h"
#include "clitkInvertVFFilter.h"
vvMidPosition::vvMidPosition() :
- slicer_manager(0), error(false),
- reference_image_index(0),
- p_bar("Computing mid-position...","Cancel", 0,6),
- progress(0)
+ slicer_manager(0), error(false),
+ reference_image_index(0),
+ p_bar("Computing mid-position...","Cancel", 0,6),
+ progress(0)
{
}
void vvMidPosition::Update()
{
- this->start();
- while (this->isRunning())
- {
- this->wait(50);
- this->update_progress();
- qApp->processEvents();
- }
+ this->start();
+ while (this->isRunning()) {
+ this->wait(50);
+ this->update_progress();
+ qApp->processEvents();
+ }
}
//Common typedefs
void vvMidPosition::run()
{
- error=true;
- if(slicer_manager->GetImage()->GetNumberOfDimensions() != 4)
- error_message="Computation of midposition is only supported for 4D image sequences.";
- else if (!slicer_manager->GetVF())
- error_message="A VF is required for midposition computation";
- else if (slicer_manager->GetVF()->GetScalarTypeAsString() != "float")
- error_message="Please use a vector field of type float.";
- else
- {
- VFType::ConstPointer vf = vvImageToITK<VFType>(slicer_manager->GetVF());
- OutputVFType::Pointer avg_vf=AverageField(vf,this->progress);
- clitk::InvertVFFilter<OutputVFType,OutputVFType>::Pointer inv_filter=
- clitk::InvertVFFilter<OutputVFType,OutputVFType>::New();
- inv_filter->SetInput(avg_vf);
- inv_filter->Update();
- progress++;
- if (slicer_manager->GetImage()->GetScalarTypeAsString() == "short")
- this->output=WarpRefImage<short>(inv_filter->GetOutput(),slicer_manager->GetImage(),reference_image_index);
- else
- {
- error_message="Unsupported image pixel type.";
- return;
- }
- progress++;
- error=false;
+ error=true;
+ if(slicer_manager->GetImage()->GetNumberOfDimensions() != 4)
+ error_message="Computation of midposition is only supported for 4D image sequences.";
+ else if (!slicer_manager->GetVF())
+ error_message="A VF is required for midposition computation";
+ else if (slicer_manager->GetVF()->GetScalarTypeAsITKString() != "float")
+ error_message="Please use a vector field of type float.";
+ else {
+ VFType::ConstPointer vf = vvImageToITK<VFType>(slicer_manager->GetVF());
+ OutputVFType::Pointer avg_vf=AverageField(vf,this->progress);
+ clitk::InvertVFFilter<OutputVFType,OutputVFType>::Pointer inv_filter=
+ clitk::InvertVFFilter<OutputVFType,OutputVFType>::New();
+ inv_filter->SetInput(avg_vf);
+ inv_filter->Update();
+ progress++;
+ if (slicer_manager->GetImage()->GetScalarTypeAsITKString() == "short")
+ this->output=WarpRefImage<short>(inv_filter->GetOutput(),slicer_manager->GetImage(),reference_image_index);
+ else {
+ error_message="Unsupported image pixel type.";
+ return;
}
+ progress++;
+ error=false;
+ }
}
template<class ImagePixelType>
vvImage::Pointer WarpRefImage(OutputVFType::Pointer vf,vvImage::Pointer image,int reference_image_index)
{
- typedef itk::Image<ImagePixelType,3> ImageType;
- typedef itk::WarpImageFilter<ImageType,ImageType,itk::Image<VFPixelType,3> > FilterType;
-
- typename ImageType::ConstPointer input = vvSingleFrameToITK<3,ImagePixelType>(image,reference_image_index);
-
- //We resample the VF because itk's warp filter doesn't like it when the vf and the image have
- //different spacings
- typename itk::VectorResampleImageFilter<OutputVFType, OutputVFType >::Pointer
- resampler =itk::VectorResampleImageFilter<OutputVFType, OutputVFType >::New();
- resampler->SetInput(vf);
- resampler->SetOutputSpacing(input->GetSpacing());
- resampler->SetOutputOrigin(vf->GetOrigin());
- //Calculate the new size so that it contains the vf
- typename ImageType::SizeType newSize;
- for (unsigned int i=0 ; i <3; i++)
- newSize[i]=(unsigned int) (vf->GetLargestPossibleRegion().GetSize()[i]*vf->GetSpacing()[i]/input->GetSpacing()[i]);
- resampler->SetSize( newSize);
-
- typename FilterType::Pointer warp_filter = FilterType::New();
- warp_filter->SetInput(input);
- warp_filter->SetDeformationField(resampler->GetOutput());
- warp_filter->SetOutputSpacing(input->GetSpacing());
- warp_filter->SetOutputOrigin(input->GetOrigin());
- warp_filter->SetOutputSize(input->GetLargestPossibleRegion().GetSize());
- warp_filter->SetEdgePaddingValue(-1000);
- warp_filter->Update();
- return vvImageFromITK<3,ImagePixelType>(warp_filter->GetOutput());
+ typedef itk::Image<ImagePixelType,3> ImageType;
+ typedef itk::WarpImageFilter<ImageType,ImageType,itk::Image<VFPixelType,3> > FilterType;
+
+ typename ImageType::ConstPointer input = vvSingleFrameToITK<3,ImagePixelType>(image,reference_image_index);
+
+ //We resample the VF because itk's warp filter doesn't like it when the vf and the image have
+ //different spacings
+#if ( ITK_VERSION_MAJOR < 5 )
+ typename itk::VectorResampleImageFilter<OutputVFType, OutputVFType >::Pointer
+ resampler =itk::VectorResampleImageFilter<OutputVFType, OutputVFType >::New();
+#else
+ typename itk::ResampleImageFilter<OutputVFType, OutputVFType >::Pointer
+ resampler =itk::ResampleImageFilter<OutputVFType, OutputVFType >::New();
+#endif
+ resampler->SetInput(vf);
+ resampler->SetOutputSpacing(input->GetSpacing());
+ resampler->SetOutputOrigin(vf->GetOrigin());
+ //Calculate the new size so that it contains the vf
+ typename ImageType::SizeType newSize;
+ for (unsigned int i=0 ; i <3; i++)
+ newSize[i]=(unsigned int) (vf->GetLargestPossibleRegion().GetSize()[i]*vf->GetSpacing()[i]/input->GetSpacing()[i]);
+ resampler->SetSize( newSize);
+
+ typename FilterType::Pointer warp_filter = FilterType::New();
+ warp_filter->SetInput(input);
+ warp_filter->SetDisplacementField(resampler->GetOutput());
+ warp_filter->SetOutputSpacing(input->GetSpacing());
+ warp_filter->SetOutputOrigin(input->GetOrigin());
+ warp_filter->SetOutputSize(input->GetLargestPossibleRegion().GetSize());
+ warp_filter->SetEdgePaddingValue(-1000);
+ warp_filter->Update();
+ return vvImageFromITK<3,ImagePixelType>(warp_filter->GetOutput());
}
itk::Image<itk::Vector<float,3>,3>::Pointer AverageField(itk::Image<itk::Vector<float,3>,4>::ConstPointer vf, int& progress)
{
- progress++;
-
- VFType::RegionType region4D=vf->GetLargestPossibleRegion();
- VFType::RegionType::SizeType size4D=region4D.GetSize();
- VFType::IndexType index4D=region4D.GetIndex();
- VFType::SpacingType spacing4D=vf->GetSpacing();
- VFType::PointType origin4D=vf->GetOrigin();
-
- OutputVFType::RegionType region;
- OutputVFType::RegionType::SizeType size;
- OutputVFType::IndexType index;
- OutputVFType::SpacingType spacing;
- OutputVFType::PointType origin;
- for (unsigned int i=0; i< 3; i++)
- {
- size[i]=size4D[i];
- index[i]=index4D[i];
- spacing[i]=spacing4D[i];
- origin[i]=origin4D[i];
- }
- region.SetSize(size);
- region.SetIndex(index);
- OutputVFType::Pointer output= OutputVFType::New();
- output->SetRegions(region);
- output->SetSpacing(spacing);
- output->SetOrigin(origin);
- output->Allocate();
- progress++;
-
-
- // Region iterators
- typedef itk::ImageRegionConstIterator<VFType> IteratorType;
- std::vector<IteratorType> iterators(size4D[3]);
- for (unsigned int i=0; i< size4D[3]; i++)
- {
- VFType::RegionType regionIt=region4D;
- VFType::RegionType::SizeType sizeIt=regionIt.GetSize();
- sizeIt[3]=1;
- regionIt.SetSize(sizeIt);
- VFType::IndexType indexIt=regionIt.GetIndex();
- indexIt[3]=i;
- regionIt.SetIndex(indexIt);
- iterators[i]=IteratorType(vf, regionIt);
- }
- progress++;
-
- typedef itk::ImageRegionIterator<OutputVFType> OutputIteratorType;
- OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
-
- // Average
- VFPixelType vector;
- VFPixelType zeroVector=itk::NumericTraits<VFPixelType>::Zero;
-
- while (!(iterators[0]).IsAtEnd())
- {
- vector=zeroVector;
- for (unsigned int i=0; i<size4D[3]; i++)
- {
- vector+=iterators[i].Get();
- ++(iterators[i]);
- }
- vector/=size4D[3];
- avIt.Set(vector);
- ++avIt;
+ progress++;
+
+ VFType::RegionType region4D=vf->GetLargestPossibleRegion();
+ VFType::RegionType::SizeType size4D=region4D.GetSize();
+ VFType::IndexType index4D=region4D.GetIndex();
+ VFType::SpacingType spacing4D=vf->GetSpacing();
+ VFType::PointType origin4D=vf->GetOrigin();
+
+ OutputVFType::RegionType region;
+ OutputVFType::RegionType::SizeType size;
+ OutputVFType::IndexType index;
+ OutputVFType::SpacingType spacing;
+ OutputVFType::PointType origin;
+ for (unsigned int i=0; i< 3; i++) {
+ size[i]=size4D[i];
+ index[i]=index4D[i];
+ spacing[i]=spacing4D[i];
+ origin[i]=origin4D[i];
+ }
+ region.SetSize(size);
+ region.SetIndex(index);
+ OutputVFType::Pointer output= OutputVFType::New();
+ output->SetRegions(region);
+ output->SetSpacing(spacing);
+ output->SetOrigin(origin);
+ output->Allocate();
+ progress++;
+
+
+ // Region iterators
+ typedef itk::ImageRegionConstIterator<VFType> IteratorType;
+ std::vector<IteratorType> iterators(size4D[3]);
+ for (unsigned int i=0; i< size4D[3]; i++) {
+ VFType::RegionType regionIt=region4D;
+ VFType::RegionType::SizeType sizeIt=regionIt.GetSize();
+ sizeIt[3]=1;
+ regionIt.SetSize(sizeIt);
+ VFType::IndexType indexIt=regionIt.GetIndex();
+ indexIt[3]=i;
+ regionIt.SetIndex(indexIt);
+ iterators[i]=IteratorType(vf, regionIt);
+ }
+ progress++;
+
+ typedef itk::ImageRegionIterator<OutputVFType> OutputIteratorType;
+ OutputIteratorType avIt(output, output->GetLargestPossibleRegion());
+
+ // Average
+ VFPixelType vector;
+ VFPixelType zeroVector;//=itk::NumericTraits<VFPixelType>::Zero;
+ for(unsigned int i=0;i <VFPixelType::Dimension; i++) zeroVector[i] = 0.0;
+
+ while (!(iterators[0]).IsAtEnd()) {
+ vector=zeroVector;
+ for (unsigned int i=0; i<size4D[3]; i++) {
+ vector+=iterators[i].Get();
+ ++(iterators[i]);
}
- progress++;
- return output;
+ vector/=size4D[3];
+ avIt.Set(vector);
+ ++avIt;
+ }
+ progress++;
+ return output;
}
void vvMidPosition::update_progress()
{
- p_bar.setValue(progress);
- p_bar.show();
+ p_bar.setValue(progress);
+ p_bar.show();
}
-
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff