vv/vvImageReader.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ======================================================================-====*/
  18
  19 #ifndef VVIMAGEREADER_TXX
  20 #define VVIMAGEREADER_TXX
  21
  22 #include <string>
  23 #include <itkImageFileReader.h>
  24 #include <itkImageSeriesReader.h>
  25 #include <itkImageToVTKImageFilter.h>
  26
  27 #include <vtkTransform.h>
  28
  29 #include "clitkCommon.h"
  30 #include "vvFromITK.h"
  31 #include "vvConstants.h"
  32
  33 //----------------------------------------------------------------------------
  34 template<unsigned int VImageDimension>
  35 void vvImageReader::UpdateWithDim(std::string InputPixelType) {
  36   if (mType == VECTORFIELD)
  37     UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
  38   else if (InputPixelType == "short")
  39     UpdateWithDimAndInputPixelType<short,VImageDimension>();
  40   else if (InputPixelType == "unsigned_short")
  41     UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
  42   else if (InputPixelType == "char")
  43     UpdateWithDimAndInputPixelType<char,VImageDimension>();
  44   else if (InputPixelType == "unsigned_char")
  45     UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
  46   else if (InputPixelType == "int")
  47     UpdateWithDimAndInputPixelType<int,VImageDimension>();
  48   else if (InputPixelType == "double")
  49     UpdateWithDimAndInputPixelType<double,VImageDimension>();
  50   else if (InputPixelType == "float")
  51     UpdateWithDimAndInputPixelType<float,VImageDimension>();
  52   else
  53     std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
  54
  55   if (CLITK_EXPERIMENTAL)
  56     if (mLastError.size()==0)
  57       ReadNkiImageTransform();
  58 }
  59 //----------------------------------------------------------------------------
  60
  61
  62 //----------------------------------------------------------------------------
  63 template<class InputPixelType, unsigned int VImageDimension>
  64 void vvImageReader::UpdateWithDimAndInputPixelType() {
  65
  66   //  DD(mType);
  67
  68   if (mType == MERGEDWITHTIME)   // In this case we can load the images
  69     // one at the time to avoid excessive
  70     // memory use
  71     {
  72       typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  73       typedef itk::ImageFileReader<InputImageType> ReaderType;
  74       typename ReaderType::Pointer reader = ReaderType::New();
  75       typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
  76       typename ConnectorType::Pointer connector = ConnectorType::New();
  77       connector->SetInput(reader->GetOutput());
  78       mImage=vvImage::New();
  79       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
  80         {
  81           std::cout << (*i) << std::endl;
  82           reader->SetFileName(*i);
  83           try {
  84             reader->Update();
  85           }
  86           catch ( itk::ExceptionObject & err ) {
  87             std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  88                       << " " << err << std::endl;
  89             std::stringstream error;
  90             error << err;
  91             mLastError = error.str();
  92             return;
  93           }
  94           try {
  95             connector->Update();
  96           }
  97           catch ( itk::ExceptionObject & err ) {
  98             std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
  99                       << " " << err << std::endl;
 100           }
 101           vtkImageData *image = vtkImageData::New();
 102           image->DeepCopy(connector->GetOutput());
 103           mImage->AddImage(image);
 104         }
 105     }
 106   else
 107     {
 108       if (mInputFilenames.size() > 1)
 109         {
 110           typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 111           typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 112           typename ReaderType::Pointer reader = ReaderType::New();
 113           for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
 114             std::cout << (*i) << std::endl;
 115           reader->SetFileNames(mInputFilenames);
 116           //if (mUseAnObserver) {
 117           //reader->AddObserver(itk::ProgressEvent(), mObserver);
 118           //}
 119           try {
 120             reader->Update();
 121           }
 122           catch ( itk::ExceptionObject & err ) {
 123             std::cerr << "Error while reading image series:" << err << std::endl;
 124             std::stringstream error;
 125             error << err;
 126             mLastError = error.str();
 127             return;
 128           }
 129
 130           // DD(reader->GetOutput()->GetImageDimension());
 131           //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 132           //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 133           //             DD(reader->GetOutput()->GetSpacing()[i]);
 134           //           }
 135
 136           if (mType == IMAGEWITHTIME)
 137             mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 138           else
 139             mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 140         }
 141       else
 142         {
 143           typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 144           typedef itk::ImageFileReader<InputImageType> ReaderType;
 145           typename ReaderType::Pointer reader = ReaderType::New();
 146           reader->SetFileName(mInputFilenames[0]);
 147           //if (mUseAnObserver) {
 148           //reader->AddObserver(itk::ProgressEvent(), mObserver);
 149           //}
 150           try {
 151             reader->Update();
 152           }
 153           catch ( itk::ExceptionObject & err ) {
 154             std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 155                       << " " << err << std::endl;
 156             std::stringstream error;
 157             error << err;
 158             mLastError = error.str();
 159             return;
 160           }
 161
 162           // DD(reader->GetOutput()->GetImageDimension());
 163           //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 164           //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 165           //             DD(reader->GetOutput()->GetSpacing()[i]);
 166           //             DD(reader->GetOutput()->GetOrigin()[i]);
 167           //           }
 168
 169
 170           if (mType == IMAGEWITHTIME)
 171             mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 172           else
 173             mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 174         }
 175     }
 176 }
 177 //----------------------------------------------------------------------------
 178
 179
 180 #endif /* end #define vvImageReader_TXX */
 181