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         reader->Update();
  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       mImage->AddItkImage<InputImageType>(reader->GetOutput());
  96     }
  97   } else if (mType == SLICED) {
  98     mImage=vvImage::New();
  99     typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 100     typedef itk::ImageFileReader<InputImageType> ReaderType;
 101     typename ReaderType::Pointer reader = ReaderType::New();
 102     reader->SetFileName(mInputFilenames[0]);
 103     reader->UpdateOutputInformation();
 104
 105     typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
 106     typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
 107
 108     typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
 109     typename InputImageType::SizeType inputSize = inputRegion.GetSize();
 110     typename InputImageType::IndexType start = inputRegion.GetIndex();
 111     typename InputImageType::SizeType extractedRegionSize = inputSize;
 112     typename InputImageType::RegionType extractedRegion;
 113     extractedRegionSize[VImageDimension - 1] = 0;
 114     extractedRegion.SetSize(extractedRegionSize);
 115     start[VImageDimension - 1] = mSlice;
 116     extractedRegion.SetIndex(start);
 117
 118     typename FilterType::Pointer filter = FilterType::New();
 119     filter->SetExtractionRegion(extractedRegion);
 120     filter->SetInput(reader->GetOutput());
 121     filter->ReleaseDataFlagOn();
 122     try {
 123       filter->Update();
 124     }
 125     catch ( itk::ExceptionObject & err ) {
 126       std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
 127                 << "(slice #" << mSlice << ") " << err << std::endl;
 128       return;
 129     }
 130     mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
 131   } else {
 132     if (mInputFilenames.size() > 1) {
 133       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 134       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 135       typename ReaderType::Pointer reader = ReaderType::New();
 136       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++)
 137         std::cout << (*i) << std::endl;
 138       reader->SetFileNames(mInputFilenames);
 139       //if (mUseAnObserver) {
 140       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 141       //}
 142       try {
 143         reader->Update();
 144       } catch ( itk::ExceptionObject & err ) {
 145         std::cerr << "Error while reading image series:" << err << std::endl;
 146         std::stringstream error;
 147         error << err;
 148         mLastError = error.str();
 149         return;
 150       }
 151
 152       // DD(reader->GetOutput()->GetImageDimension());
 153       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 154       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 155       //             DD(reader->GetOutput()->GetSpacing()[i]);
 156       //           }
 157
 158       if (mType == IMAGEWITHTIME)
 159         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 160       else
 161         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 162     } else {
 163       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 164       typedef itk::ImageFileReader<InputImageType> ReaderType;
 165       typename ReaderType::Pointer reader = ReaderType::New();
 166       reader->SetFileName(mInputFilenames[0]);
 167       //if (mUseAnObserver) {
 168       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 169       //}
 170       try {
 171         reader->Update();
 172       } catch ( itk::ExceptionObject & err ) {
 173         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 174                   << " " << err << std::endl;
 175         std::stringstream error;
 176         error << err;
 177         mLastError = error.str();
 178         return;
 179       }
 180
 181       // DD(reader->GetOutput()->GetImageDimension());
 182       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 183       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 184       //             DD(reader->GetOutput()->GetSpacing()[i]);
 185       //             DD(reader->GetOutput()->GetOrigin()[i]);
 186       //           }
 187
 188
 189       if (mType == IMAGEWITHTIME)
 190         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 191       else
 192         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 193     }
 194   }
 195 }
 196 //----------------------------------------------------------------------------
 197
 198
 199 #endif /* end #define vvImageReader_TXX */
 200