/*=========================================================================
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
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
- 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<string>
+ ======================================================================-====*/
+#ifndef VVIMAGEREADER_TXX
+#define VVIMAGEREADER_TXX
+
+#include <string>
#include <itkImageFileReader.h>
#include <itkImageSeriesReader.h>
+#include <itkImageToVTKImageFilter.h>
+
+#include <vtkTransform.h>
#include "clitkCommon.h"
-#include "itkImageToVTKImageFilter.h"
+#include "clitkConfiguration.h"
#include "vvFromITK.h"
#include "vvConstants.h"
+//----------------------------------------------------------------------------
template<unsigned int VImageDimension>
void vvImageReader::UpdateWithDim(std::string InputPixelType)
{
- if (mType == VECTORFIELD)
- UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
- else if (InputPixelType == "short")
- UpdateWithDimAndInputPixelType<short,VImageDimension>();
- else if (InputPixelType == "unsigned_short")
- UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
- else if (InputPixelType == "char")
- UpdateWithDimAndInputPixelType<char,VImageDimension>();
- else if (InputPixelType == "unsigned_char")
- UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
- else if (InputPixelType == "int")
- UpdateWithDimAndInputPixelType<int,VImageDimension>();
- else if (InputPixelType == "double")
- UpdateWithDimAndInputPixelType<double,VImageDimension>();
- else if (InputPixelType == "float")
- UpdateWithDimAndInputPixelType<float,VImageDimension>();
- else
- std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
+ if (mType == VECTORFIELD)
+ UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
+ else if (InputPixelType == "short")
+ UpdateWithDimAndInputPixelType<short,VImageDimension>();
+ else if (InputPixelType == "unsigned_short")
+ UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
+ else if (InputPixelType == "char")
+ UpdateWithDimAndInputPixelType<char,VImageDimension>();
+ else if (InputPixelType == "unsigned_char")
+ UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
+ else if (InputPixelType == "int")
+ UpdateWithDimAndInputPixelType<int,VImageDimension>();
+ else if (InputPixelType == "unsigned_int")
+ UpdateWithDimAndInputPixelType<unsigned int,VImageDimension>();
+ else if (InputPixelType == "double")
+ UpdateWithDimAndInputPixelType<double,VImageDimension>();
+ else if (InputPixelType == "float")
+ UpdateWithDimAndInputPixelType<float,VImageDimension>();
+ else
+ std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
+
+ if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
+ //ReadNkiImageTransform();
+ ReadMatImageTransform();
+ }
}
-//====================================================================
+//----------------------------------------------------------------------------
+
+//----------------------------------------------------------------------------
template<class InputPixelType, unsigned int VImageDimension>
void vvImageReader::UpdateWithDimAndInputPixelType()
{
- if (mType == MERGEDWITHTIME) // In this case we can load the images
- // one at the time to avoid excessive
- // memory use
- {
- typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
- typedef itk::ImageFileReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
- typename ConnectorType::Pointer connector = ConnectorType::New();
- connector->SetInput(reader->GetOutput());
- mImage=vvImage::New();
- for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
- {
- std::cout << (*i) << std::endl;
- reader->SetFileName(*i);
- try {
- reader->Update();
- }
- 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;
- }
- try {
- connector->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
- << " " << err << std::endl;
- }
- vtkImageData *image = vtkImageData::New();
- image->DeepCopy(connector->GetOutput());
- mImage->AddImage(image);
- }
+ if (mType == MERGEDWITHTIME) // In this case we can load the images
+ // one at the time to avoid excessive
+ // memory use
+ {
+ mImage=vvImage::New();
+
+ for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
+ typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->ReleaseDataFlagOn();
+ reader->SetFileName(*i);
+ try {
+ mImage->AddItkImage<InputImageType>(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;
+ }
}
- else
- {
- if (mInputFilenames.size() > 1)
- {
- typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
- typedef itk::ImageSeriesReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
- std::cout << (*i) << std::endl;
- reader->SetFileNames(mInputFilenames);
- //if (mUseAnObserver) {
- //reader->AddObserver(itk::ProgressEvent(), mObserver);
- //}
- try {
- reader->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while reading image series:" << err << std::endl;
- std::stringstream error;
- error << err;
- mLastError = error.str();
- return;
- }
- if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
- else
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
- }
+ } else if (mType == SLICED) {
+ mImage=vvImage::New();
+ typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(mInputFilenames[0]);
+ reader->UpdateOutputInformation();
+
+ typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
+ typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
+
+ typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
+ typename InputImageType::SizeType inputSize = inputRegion.GetSize();
+ typename InputImageType::IndexType start = inputRegion.GetIndex();
+ typename InputImageType::SizeType extractedRegionSize = inputSize;
+ typename InputImageType::RegionType extractedRegion;
+ extractedRegionSize[VImageDimension - 1] = 0;
+ extractedRegion.SetSize(extractedRegionSize);
+ start[VImageDimension - 1] = mSlice;
+ extractedRegion.SetIndex(start);
+
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetExtractionRegion(extractedRegion);
+ filter->SetInput(reader->GetOutput());
+ filter->ReleaseDataFlagOn();
+ try {
+ mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
+ }
+ catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
+ << "(slice #" << mSlice << ") " << err << std::endl;
+ return;
+ }
+ } else {
+ if (mInputFilenames.size() > 1) {
+ typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+ typedef itk::ImageSeriesReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileNames(mInputFilenames);
+ reader->ReleaseDataFlagOn();
+
+ try {
+ if (mType == IMAGEWITHTIME)
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+ else
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(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::Image< InputPixelType, VImageDimension > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(mInputFilenames[0]);
+ reader->ReleaseDataFlagOn();
+
+ try {
+ if (mType == IMAGEWITHTIME)
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
else
- {
- typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
- typedef itk::ImageFileReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- reader->SetFileName(mInputFilenames[0]);
- //if (mUseAnObserver) {
- //reader->AddObserver(itk::ProgressEvent(), mObserver);
- //}
- try {
- reader->Update();
- }
- 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;
- }
- if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
- else
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
- }
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(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;
+ }
}
+ }
}
-//====================================================================
+//----------------------------------------------------------------------------
#endif /* end #define vvImageReader_TXX */
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff