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 "clitkConfiguration.h"
  31 #include "vvFromITK.h"
  32 #include "vvConstants.h"
  33
  34 //----------------------------------------------------------------------------
  35 template<unsigned int VImageDimension>
  36 void vvImageReader::UpdateWithDim(std::string InputPixelType)
  37 {
  38   if (mType == VECTORFIELD)
  39     UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
  40   else if (InputPixelType == "short")
  41     UpdateWithDimAndInputPixelType<short,VImageDimension>();
  42   else if (InputPixelType == "unsigned_short")
  43     UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
  44   else if (InputPixelType == "char")
  45     UpdateWithDimAndInputPixelType<char,VImageDimension>();
  46   else if (InputPixelType == "unsigned_char")
  47     UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
  48   else if (InputPixelType == "int")
  49     UpdateWithDimAndInputPixelType<int,VImageDimension>();
  50   else if (InputPixelType == "unsigned_int")
  51     UpdateWithDimAndInputPixelType<unsigned int,VImageDimension>();
  52   else if (InputPixelType == "double")
  53     UpdateWithDimAndInputPixelType<double,VImageDimension>();
  54   else if (InputPixelType == "float")
  55     UpdateWithDimAndInputPixelType<float,VImageDimension>();
  56   else
  57     std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
  58
  59   if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
  60     ReadNkiImageTransform();
  61     ReadMatImageTransform();
  62   }
  63 }
  64 //----------------------------------------------------------------------------
  65
  66
  67 //----------------------------------------------------------------------------
  68 template<class InputPixelType, unsigned int VImageDimension>
  69 void vvImageReader::UpdateWithDimAndInputPixelType()
  70 {
  71
  72   //  DD(mType);
  73
  74   if (mType == MERGEDWITHTIME)   // In this case we can load the images
  75     // one at the time to avoid excessive
  76     // memory use
  77   {
  78       mImage=vvImage::New();
  79       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  80       typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  81       typedef itk::ImageFileReader<InputImageType> ReaderType;
  82       typename ReaderType::Pointer reader = ReaderType::New();
  83       reader->ReleaseDataFlagOn();
  84       std::cout << (*i) << std::endl;
  85       reader->SetFileName(*i);
  86       try {
  87         reader->Update();
  88       } catch ( itk::ExceptionObject & err ) {
  89         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  90                   << " " << err << std::endl;
  91         std::stringstream error;
  92         error << err;
  93         mLastError = error.str();
  94         return;
  95       }
  96       mImage->AddItkImage<InputImageType>(reader->GetOutput());
  97     }
  98   } else {
  99     if (mInputFilenames.size() > 1) {
 100       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 101       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 102       typename ReaderType::Pointer reader = ReaderType::New();
 103       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++)
 104         std::cout << (*i) << std::endl;
 105       reader->SetFileNames(mInputFilenames);
 106       //if (mUseAnObserver) {
 107       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 108       //}
 109       try {
 110         reader->Update();
 111       } catch ( itk::ExceptionObject & err ) {
 112         std::cerr << "Error while reading image series:" << err << std::endl;
 113         std::stringstream error;
 114         error << err;
 115         mLastError = error.str();
 116         return;
 117       }
 118
 119       // DD(reader->GetOutput()->GetImageDimension());
 120       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 121       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 122       //             DD(reader->GetOutput()->GetSpacing()[i]);
 123       //           }
 124
 125       if (mType == IMAGEWITHTIME)
 126         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 127       else
 128         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 129     } else {
 130       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 131       typedef itk::ImageFileReader<InputImageType> ReaderType;
 132       typename ReaderType::Pointer reader = ReaderType::New();
 133       reader->SetFileName(mInputFilenames[0]);
 134       //if (mUseAnObserver) {
 135       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 136       //}
 137       try {
 138         reader->Update();
 139       } catch ( itk::ExceptionObject & err ) {
 140         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 141                   << " " << err << std::endl;
 142         std::stringstream error;
 143         error << err;
 144         mLastError = error.str();
 145         return;
 146       }
 147
 148       // DD(reader->GetOutput()->GetImageDimension());
 149       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 150       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 151       //             DD(reader->GetOutput()->GetSpacing()[i]);
 152       //             DD(reader->GetOutput()->GetOrigin()[i]);
 153       //           }
 154
 155
 156       if (mType == IMAGEWITHTIME)
 157         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 158       else
 159         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 160     }
 161   }
 162 }
 163 //----------------------------------------------------------------------------
 164
 165
 166 #endif /* end #define vvImageReader_TXX */
 167