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
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef VVIMAGEREADER_TXX
#define VVIMAGEREADER_TXX
#include <itkImageFileReader.h>
#include <itkImageSeriesReader.h>
#include <itkImageToVTKImageFilter.h>
+#include <itkFlexibleVectorCastImageFilter.h>
+#include "itkVectorImageToImageAdaptor.h"
#include <vtkTransform.h>
template<unsigned int VImageDimension>
void vvImageReader::UpdateWithDim(std::string InputPixelType)
{
- if (mType == VECTORFIELD)
- UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
+ if (mType == VECTORFIELD || mType == VECTORFIELDWITHTIME)
+ {
+ if (VImageDimension == 4)
+ UpdateWithDimAndInputVectorPixelType<itk::Vector<float,3>,VImageDimension>();
+ else
+ UpdateWithDimAndInputVectorPixelType<itk::Vector<float,VImageDimension>,VImageDimension>();
+ }
else if (InputPixelType == "short")
UpdateWithDimAndInputPixelType<short,VImageDimension>();
else if (InputPixelType == "unsigned_short")
else
std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
- if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
+ if (mLastError.size()==0) {
//ReadNkiImageTransform();
ReadMatImageTransform();
}
reader->SetFileName(*i);
try {
mImage->AddItkImage<InputImageType>(reader->GetOutput());
+ mImage->ComputeScalarRangeBase<InputPixelType, VImageDimension-1>(reader->GetOutput());
} catch ( itk::ExceptionObject & err ) {
std::cerr << "Error while reading " << mInputFilenames[0].c_str()
<< " " << err << std::endl;
filter->SetExtractionRegion(extractedRegion);
filter->SetInput(reader->GetOutput());
filter->ReleaseDataFlagOn();
+ filter->SetDirectionCollapseToSubmatrix();
try {
mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
- }
- catch ( itk::ExceptionObject & err ) {
+ mImage->ComputeScalarRangeBase<InputPixelType, VImageDimension-1>(filter->GetOutput());
+ } catch ( itk::ExceptionObject & err ) {
std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
<< "(slice #" << mSlice << ") " << err << std::endl;
return;
}
+ } else if (mType == VECTORPIXELIMAGE) {
+ mImage=vvImage::New();
+ typedef itk::VectorImage< InputPixelType, VImageDimension-1 > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typedef itk::Image<InputPixelType, VImageDimension> OutputImageType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(mInputFilenames[0]);
+ reader->Update();
+ typename InputImageType::Pointer input= reader->GetOutput();
+
+ typedef itk::VectorImageToImageAdaptor<InputPixelType, VImageDimension-1> ImageAdaptorType;
+ typename ImageAdaptorType::Pointer adaptor = ImageAdaptorType::New();
+ typename OutputImageType::Pointer output = OutputImageType::New();
+
+ adaptor->SetExtractComponentIndex(0);
+ adaptor->SetImage(input);
+
+ //Create the output
+ typename OutputImageType::IndexType index;
+ index.Fill(0);
+ typename OutputImageType::SizeType size;
+ size.Fill(input->GetNumberOfComponentsPerPixel());
+ typename OutputImageType::SpacingType spacing;
+ spacing.Fill(1);
+ typename OutputImageType::PointType origin;
+ origin.Fill(0);
+ typename OutputImageType::DirectionType direction;
+ direction.SetIdentity();
+ for (unsigned int pixelDim=0; pixelDim<VImageDimension-1; ++pixelDim)
+ {
+ size[pixelDim]=adaptor->GetLargestPossibleRegion().GetSize(pixelDim);
+ spacing[pixelDim]=input->GetSpacing()[pixelDim];
+ origin[pixelDim]=input->GetOrigin()[pixelDim];
+ for (unsigned int pixelDim2=0; pixelDim2<VImageDimension-1; ++pixelDim2)
+ {
+ direction[pixelDim][pixelDim2]=input->GetDirection()[pixelDim][pixelDim2];
+ }
+ }
+ typename OutputImageType::RegionType region;
+ region.SetSize(size);
+ region.SetIndex(index);
+ output->SetRegions(region);
+ output->SetOrigin(origin);
+ output->SetSpacing(spacing);
+ output->SetDirection(direction);
+ output->Allocate();
+
+ //Copy each channel
+ for (unsigned int pixelDim=0; pixelDim<input->GetNumberOfComponentsPerPixel(); ++pixelDim)
+ {
+ adaptor->SetExtractComponentIndex(pixelDim);
+
+ itk::ImageRegionIterator<InputImageType> imageIterator(input,input->GetLargestPossibleRegion());
+
+ while(!imageIterator.IsAtEnd())
+ {
+ typename OutputImageType::IndexType indexVector;
+ indexVector.Fill(0);
+ for (unsigned int indexDim=0; indexDim<VImageDimension-1; ++indexDim)
+ {
+ indexVector[indexDim]=imageIterator.GetIndex().GetElement(indexDim);
+ }
+ indexVector[VImageDimension-1]=pixelDim;
+
+ output->SetPixel(indexVector, adaptor->GetPixel(imageIterator.GetIndex()));
+ ++imageIterator;
+ }
+ }
+
+/* if (VImageDimension == 4)
+ mType == VECTORPIXELIMAGEWITHTIME;
+ else
+ mType == VECTORPIXELIMAGE;*/
+
+ try {
+ mImage = vvImageFromITK<VImageDimension,InputPixelType>(output, mType == VECTORPIXELIMAGEWITHTIME);
+ mImage->ComputeScalarRangeBase<InputPixelType, VImageDimension>(output);
+ } catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
+ << " " << err << std::endl;
+ return;
+ }
} else {
if (mInputFilenames.size() > 1) {
typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
try {
if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+ {
+ std::cerr << "We should never come here:" << std::endl
+ << " Calling vvImageReader with multiple images and IMAGEWITHTIME is undefined." << std::endl
+ << " You are probably looking for MERGEDWITHTIME Type." << std::endl;
+ return;
+ }
else
mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
} catch ( itk::ExceptionObject & err ) {
reader->ReleaseDataFlagOn();
try {
- if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
- else
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
+ mImage = vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(), mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME);
} catch ( itk::ExceptionObject & err ) {
std::cerr << "Error while reading " << mInputFilenames[0].c_str()
<< " " << err << std::endl;
}
}
}
+
+ if (mType == DICOM && !mPatientCoordinateSystem)
+ mImage->InitializeTransform();
}
//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+template<class InputPixelType, unsigned int VImageDimension>
+void vvImageReader::UpdateWithDimAndInputVectorPixelType()
+{
+ typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+ typename InputImageType::Pointer input;
+
+ if (mInputFilenames.size() > 1) {
+ typedef itk::ImageSeriesReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileNames(mInputFilenames);
+ reader->ReleaseDataFlagOn();
+ try {
+ reader->Update();
+ input = reader->GetOutput();
+ } catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while reading image series:" << err << std::endl;
+ std::stringstream error;
+ error << err;
+ mLastError = error.str();
+ return;
+ }
+ } else {
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(mInputFilenames[0]);
+ reader->ReleaseDataFlagOn();
+ try {
+ reader->Update();
+ input = reader->GetOutput();
+ } catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while reading " << mInputFilenames[0].c_str()
+ << " " << err << std::endl;
+ std::stringstream error;
+ error << err;
+ mLastError = error.str();
+ return;
+ }
+ }
+
+ typedef itk::Image< itk::Vector<float , 3>, VImageDimension > VectorImageType;
+ typedef itk::FlexibleVectorCastImageFilter<InputImageType, VectorImageType> CasterType;
+ typename VectorImageType::Pointer casted_input;
+ typename CasterType::Pointer caster = CasterType::New();
+ caster->SetInput(input);
+ caster->Update();
+ casted_input = caster->GetOutput();
+
+ mImage = vvImageFromITK<VImageDimension, itk::Vector<float, 3> >(casted_input, mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME);
+}
+//----------------------------------------------------------------------------
#endif /* end #define vvImageReader_TXX */
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff