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       reader->SetFileName(*i);
  85       try {
  86         mImage->AddItkImage<InputImageType>(reader->GetOutput());
  87       } catch ( itk::ExceptionObject & err ) {
  88         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  89                   << " " << err << std::endl;
  90         std::stringstream error;
  91         error << err;
  92         mLastError = error.str();
  93         return;
  94       }
  95     }
  96   } else if (mType == SLICED) {
  97     mImage=vvImage::New();
  98     typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
  99     typedef itk::ImageFileReader<InputImageType> ReaderType;
 100     typename ReaderType::Pointer reader = ReaderType::New();
 101     reader->SetFileName(mInputFilenames[0]);
 102     reader->UpdateOutputInformation();
 103
 104     typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
 105     typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
 106
 107     typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
 108     typename InputImageType::SizeType inputSize = inputRegion.GetSize();
 109     typename InputImageType::IndexType start = inputRegion.GetIndex();
 110     typename InputImageType::SizeType extractedRegionSize = inputSize;
 111     typename InputImageType::RegionType extractedRegion;
 112     extractedRegionSize[VImageDimension - 1] = 0;
 113     extractedRegion.SetSize(extractedRegionSize);
 114     start[VImageDimension - 1] = mSlice;
 115     extractedRegion.SetIndex(start);
 116
 117     typename FilterType::Pointer filter = FilterType::New();
 118     filter->SetExtractionRegion(extractedRegion);
 119     filter->SetInput(reader->GetOutput());
 120     filter->ReleaseDataFlagOn();
 121     try {
 122       mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
 123     }
 124     catch ( itk::ExceptionObject & err ) {
 125       std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
 126                 << "(slice #" << mSlice << ") " << err << std::endl;
 127       return;
 128     }
 129   } else {
 130     if (mInputFilenames.size() > 1) {
 131       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 132       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 133       typename ReaderType::Pointer reader = ReaderType::New();
 134       reader->SetFileNames(mInputFilenames);
 135       reader->ReleaseDataFlagOn();
 136
 137       try {
 138         if (mType == IMAGEWITHTIME)
 139           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 140         else
 141           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 142       } catch ( itk::ExceptionObject & err ) {
 143         std::cerr << "Error while reading image series:" << err << std::endl;
 144         std::stringstream error;
 145         error << err;
 146         mLastError = error.str();
 147         return;
 148       }
 149     } else {
 150       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 151       typedef itk::ImageFileReader<InputImageType> ReaderType;
 152       typename ReaderType::Pointer reader = ReaderType::New();
 153       reader->SetFileName(mInputFilenames[0]);
 154       reader->ReleaseDataFlagOn();
 155
 156       try {
 157         if (mType == IMAGEWITHTIME)
 158           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 159         else
 160           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 161       } catch ( itk::ExceptionObject & err ) {
 162         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 163                   << " " << err << std::endl;
 164         std::stringstream error;
 165         error << err;
 166         mLastError = error.str();
 167         return;
 168       }
 169     }
 170   }
 171 }
 172 //----------------------------------------------------------------------------
 173
 174
 175 #endif /* end #define vvImageReader_TXX */
 176