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   if (mType == MERGEDWITHTIME)   // In this case we can load the images
  72     // one at the time to avoid excessive
  73     // memory use
  74   {
  75     mImage=vvImage::New();
  76
  77     for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  78       typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  79       typedef itk::ImageFileReader<InputImageType> ReaderType;
  80       typename ReaderType::Pointer reader = ReaderType::New();
  81       reader->ReleaseDataFlagOn();
  82       reader->SetFileName(*i);
  83       try {
  84         mImage->AddItkImage<InputImageType>(reader->GetOutput());
  85       } catch ( itk::ExceptionObject & err ) {
  86         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  87                   << " " << err << std::endl;
  88         std::stringstream error;
  89         error << err;
  90         mLastError = error.str();
  91         return;
  92       }
  93     }
  94   } else if (mType == SLICED) {
  95     mImage=vvImage::New();
  96     typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
  97     typedef itk::ImageFileReader<InputImageType> ReaderType;
  98     typename ReaderType::Pointer reader = ReaderType::New();
  99     reader->SetFileName(mInputFilenames[0]);
 100     reader->UpdateOutputInformation();
 101
 102     typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
 103     typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
 104
 105     typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
 106     typename InputImageType::SizeType inputSize = inputRegion.GetSize();
 107     typename InputImageType::IndexType start = inputRegion.GetIndex();
 108     typename InputImageType::SizeType extractedRegionSize = inputSize;
 109     typename InputImageType::RegionType extractedRegion;
 110     extractedRegionSize[VImageDimension - 1] = 0;
 111     extractedRegion.SetSize(extractedRegionSize);
 112     start[VImageDimension - 1] = mSlice;
 113     extractedRegion.SetIndex(start);
 114
 115     typename FilterType::Pointer filter = FilterType::New();
 116     filter->SetExtractionRegion(extractedRegion);
 117     filter->SetInput(reader->GetOutput());
 118     filter->ReleaseDataFlagOn();
 119     try {
 120       mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
 121     }
 122     catch ( itk::ExceptionObject & err ) {
 123       std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
 124                 << "(slice #" << mSlice << ") " << err << std::endl;
 125       return;
 126     }
 127   } else {
 128     if (mInputFilenames.size() > 1) {
 129       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 130       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 131       typename ReaderType::Pointer reader = ReaderType::New();
 132       reader->SetFileNames(mInputFilenames);
 133       reader->ReleaseDataFlagOn();
 134
 135       try {
 136         if (mType == IMAGEWITHTIME)
 137           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 138         else
 139           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 140       } catch ( itk::ExceptionObject & err ) {
 141         std::cerr << "Error while reading image series:" << err << std::endl;
 142         std::stringstream error;
 143         error << err;
 144         mLastError = error.str();
 145         return;
 146       }
 147     } else {
 148       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 149       typedef itk::ImageFileReader<InputImageType> ReaderType;
 150       typename ReaderType::Pointer reader = ReaderType::New();
 151       reader->SetFileName(mInputFilenames[0]);
 152       reader->ReleaseDataFlagOn();
 153
 154       try {
 155         if (mType == IMAGEWITHTIME)
 156           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 157         else
 158           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 159       } catch ( itk::ExceptionObject & err ) {
 160         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 161                   << " " << err << std::endl;
 162         std::stringstream error;
 163         error << err;
 164         mLastError = error.str();
 165         return;
 166       }
 167     }
 168   }
 169 }
 170 //----------------------------------------------------------------------------
 171
 172
 173 #endif /* end #define vvImageReader_TXX */
 174