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     typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  79     typedef itk::ImageFileReader<InputImageType> ReaderType;
  80     typename ReaderType::Pointer reader = ReaderType::New();
  81     typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
  82     typename ConnectorType::Pointer connector = ConnectorType::New();
  83     connector->SetInput(reader->GetOutput());
  84     mImage=vvImage::New();
  85     for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  86       std::cout << (*i) << std::endl;
  87       reader->SetFileName(*i);
  88       try {
  89         reader->Update();
  90       } catch ( itk::ExceptionObject & err ) {
  91         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  92                   << " " << err << std::endl;
  93         std::stringstream error;
  94         error << err;
  95         mLastError = error.str();
  96         return;
  97       }
  98       try {
  99         connector->Update();
 100       } catch ( itk::ExceptionObject & err ) {
 101         std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
 102                   << " " << err << std::endl;
 103       }
 104       vtkImageData *image = vtkImageData::New();
 105       image->ShallowCopy(connector->GetOutput());
 106       mImage->AddImage(image);
 107     }
 108   } else {
 109     if (mInputFilenames.size() > 1) {
 110       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 111       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 112       typename ReaderType::Pointer reader = ReaderType::New();
 113       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++)
 114         std::cout << (*i) << std::endl;
 115       reader->SetFileNames(mInputFilenames);
 116       //if (mUseAnObserver) {
 117       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 118       //}
 119       try {
 120         reader->Update();
 121       } catch ( itk::ExceptionObject & err ) {
 122         std::cerr << "Error while reading image series:" << err << std::endl;
 123         std::stringstream error;
 124         error << err;
 125         mLastError = error.str();
 126         return;
 127       }
 128
 129       // DD(reader->GetOutput()->GetImageDimension());
 130       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 131       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 132       //             DD(reader->GetOutput()->GetSpacing()[i]);
 133       //           }
 134
 135       if (mType == IMAGEWITHTIME)
 136         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 137       else
 138         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 139     } else {
 140       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 141       typedef itk::ImageFileReader<InputImageType> ReaderType;
 142       typename ReaderType::Pointer reader = ReaderType::New();
 143       reader->SetFileName(mInputFilenames[0]);
 144       //if (mUseAnObserver) {
 145       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 146       //}
 147       try {
 148         reader->Update();
 149       } catch ( itk::ExceptionObject & err ) {
 150         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 151                   << " " << err << std::endl;
 152         std::stringstream error;
 153         error << err;
 154         mLastError = error.str();
 155         return;
 156       }
 157
 158       // DD(reader->GetOutput()->GetImageDimension());
 159       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 160       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 161       //             DD(reader->GetOutput()->GetSpacing()[i]);
 162       //             DD(reader->GetOutput()->GetOrigin()[i]);
 163       //           }
 164
 165
 166       if (mType == IMAGEWITHTIME)
 167         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 168       else
 169         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 170     }
 171   }
 172 }
 173 //----------------------------------------------------------------------------
 174
 175
 176 #endif /* end #define vvImageReader_TXX */
 177