common/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://www.centreleonberard.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 //----------------------------------------------------------------------------
  33 template<unsigned int VImageDimension>
  34 void vvImageReader::UpdateWithDim(std::string InputPixelType)
  35 {
  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 == "unsigned_int")
  49     UpdateWithDimAndInputPixelType<unsigned int,VImageDimension>();
  50   else if (InputPixelType == "double")
  51     UpdateWithDimAndInputPixelType<double,VImageDimension>();
  52   else if (InputPixelType == "float")
  53     UpdateWithDimAndInputPixelType<float,VImageDimension>();
  54   else
  55     std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
  56
  57   if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
  58     //ReadNkiImageTransform();
  59     ReadMatImageTransform();
  60   }
  61 }
  62 //----------------------------------------------------------------------------
  63
  64
  65 //----------------------------------------------------------------------------
  66 template<class InputPixelType, unsigned int VImageDimension>
  67 void vvImageReader::UpdateWithDimAndInputPixelType()
  68 {
  69   if (mType == MERGEDWITHTIME)   // In this case we can load the images
  70     // one at the time to avoid excessive
  71     // memory use
  72   {
  73     mImage=vvImage::New();
  74
  75     for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  76       typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  77       typedef itk::ImageFileReader<InputImageType> ReaderType;
  78       typename ReaderType::Pointer reader = ReaderType::New();
  79       reader->ReleaseDataFlagOn();
  80       reader->SetFileName(*i);
  81       try {
  82         mImage->AddItkImage<InputImageType>(reader->GetOutput());
  83       } catch ( itk::ExceptionObject & err ) {
  84         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  85                   << " " << err << std::endl;
  86         std::stringstream error;
  87         error << err;
  88         mLastError = error.str();
  89         return;
  90       }
  91     }
  92   } else if (mType == SLICED) {
  93     mImage=vvImage::New();
  94     typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
  95     typedef itk::ImageFileReader<InputImageType> ReaderType;
  96     typename ReaderType::Pointer reader = ReaderType::New();
  97     reader->SetFileName(mInputFilenames[0]);
  98     reader->UpdateOutputInformation();
  99
 100     typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
 101     typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
 102
 103     typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
 104     typename InputImageType::SizeType inputSize = inputRegion.GetSize();
 105     typename InputImageType::IndexType start = inputRegion.GetIndex();
 106     typename InputImageType::SizeType extractedRegionSize = inputSize;
 107     typename InputImageType::RegionType extractedRegion;
 108     extractedRegionSize[VImageDimension - 1] = 0;
 109     extractedRegion.SetSize(extractedRegionSize);
 110     start[VImageDimension - 1] = mSlice;
 111     extractedRegion.SetIndex(start);
 112
 113     typename FilterType::Pointer filter = FilterType::New();
 114     filter->SetExtractionRegion(extractedRegion);
 115     filter->SetInput(reader->GetOutput());
 116     filter->ReleaseDataFlagOn();
 117     try {
 118       mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
 119     }
 120     catch ( itk::ExceptionObject & err ) {
 121       std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
 122                 << "(slice #" << mSlice << ") " << err << std::endl;
 123       return;
 124     }
 125   } else {
 126     if (mInputFilenames.size() > 1) {
 127       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 128       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 129       typename ReaderType::Pointer reader = ReaderType::New();
 130       reader->SetFileNames(mInputFilenames);
 131       reader->ReleaseDataFlagOn();
 132
 133       try {
 134         if (mType == IMAGEWITHTIME)
 135           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 136         else
 137           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 138       } catch ( itk::ExceptionObject & err ) {
 139         std::cerr << "Error while reading image series:" << err << std::endl;
 140         std::stringstream error;
 141         error << err;
 142         mLastError = error.str();
 143         return;
 144       }
 145     } else {
 146       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 147       typedef itk::ImageFileReader<InputImageType> ReaderType;
 148       typename ReaderType::Pointer reader = ReaderType::New();
 149       reader->SetFileName(mInputFilenames[0]);
 150       reader->ReleaseDataFlagOn();
 151
 152       try {
 153         if (mType == IMAGEWITHTIME)
 154           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 155         else
 156           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 157       } catch ( itk::ExceptionObject & err ) {
 158         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 159                   << " " << err << std::endl;
 160         std::stringstream error;
 161         error << err;
 162         mLastError = error.str();
 163         return;
 164       }
 165     }
 166   }
 167 }
 168 //----------------------------------------------------------------------------
 169
 170
 171 #endif /* end #define vvImageReader_TXX */
 172