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 "vvFromITK.h"
  31 #include "vvConstants.h"
  32
  33 //----------------------------------------------------------------------------
  34 template<unsigned int VImageDimension>
  35 void vvImageReader::UpdateWithDim(std::string InputPixelType)
  36 {
  37   if (mType == VECTORFIELD)
  38     UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
  39   else if (InputPixelType == "short")
  40     UpdateWithDimAndInputPixelType<short,VImageDimension>();
  41   else if (InputPixelType == "unsigned_short")
  42     UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
  43   else if (InputPixelType == "char")
  44     UpdateWithDimAndInputPixelType<char,VImageDimension>();
  45   else if (InputPixelType == "unsigned_char")
  46     UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
  47   else if (InputPixelType == "int")
  48     UpdateWithDimAndInputPixelType<int,VImageDimension>();
  49   else if (InputPixelType == "unsigned_int")
  50     UpdateWithDimAndInputPixelType<unsigned int,VImageDimension>();
  51   else if (InputPixelType == "double")
  52     UpdateWithDimAndInputPixelType<double,VImageDimension>();
  53   else if (InputPixelType == "float")
  54     UpdateWithDimAndInputPixelType<float,VImageDimension>();
  55   else
  56     std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
  57
  58   if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
  59     ReadNkiImageTransform();
  60     ReadMatImageTransform();
  61   }
  62 }
  63 //----------------------------------------------------------------------------
  64
  65
  66 //----------------------------------------------------------------------------
  67 template<class InputPixelType, unsigned int VImageDimension>
  68 void vvImageReader::UpdateWithDimAndInputPixelType()
  69 {
  70
  71   //  DD(mType);
  72
  73   if (mType == MERGEDWITHTIME)   // In this case we can load the images
  74     // one at the time to avoid excessive
  75     // memory use
  76   {
  77     typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  78     typedef itk::ImageFileReader<InputImageType> ReaderType;
  79     typename ReaderType::Pointer reader = ReaderType::New();
  80     typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
  81     typename ConnectorType::Pointer connector = ConnectorType::New();
  82     connector->SetInput(reader->GetOutput());
  83     mImage=vvImage::New();
  84     for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  85       std::cout << (*i) << std::endl;
  86       reader->SetFileName(*i);
  87       try {
  88         reader->Update();
  89       } catch ( itk::ExceptionObject & err ) {
  90         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
  91                   << " " << err << std::endl;
  92         std::stringstream error;
  93         error << err;
  94         mLastError = error.str();
  95         return;
  96       }
  97       try {
  98         connector->Update();
  99       } catch ( itk::ExceptionObject & err ) {
 100         std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
 101                   << " " << err << std::endl;
 102       }
 103       vtkImageData *image = vtkImageData::New();
 104       image->ShallowCopy(connector->GetOutput());
 105       mImage->AddImage(image);
 106     }
 107   } else {
 108     if (mInputFilenames.size() > 1) {
 109       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 110       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 111       typename ReaderType::Pointer reader = ReaderType::New();
 112       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++)
 113         std::cout << (*i) << std::endl;
 114       reader->SetFileNames(mInputFilenames);
 115       //if (mUseAnObserver) {
 116       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 117       //}
 118       try {
 119         reader->Update();
 120       } catch ( itk::ExceptionObject & err ) {
 121         std::cerr << "Error while reading image series:" << err << std::endl;
 122         std::stringstream error;
 123         error << err;
 124         mLastError = error.str();
 125         return;
 126       }
 127
 128       // DD(reader->GetOutput()->GetImageDimension());
 129       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 130       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 131       //             DD(reader->GetOutput()->GetSpacing()[i]);
 132       //           }
 133
 134       if (mType == IMAGEWITHTIME)
 135         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 136       else
 137         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 138     } else {
 139       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 140       typedef itk::ImageFileReader<InputImageType> ReaderType;
 141       typename ReaderType::Pointer reader = ReaderType::New();
 142       reader->SetFileName(mInputFilenames[0]);
 143       //if (mUseAnObserver) {
 144       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 145       //}
 146       try {
 147         reader->Update();
 148       } catch ( itk::ExceptionObject & err ) {
 149         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 150                   << " " << err << std::endl;
 151         std::stringstream error;
 152         error << err;
 153         mLastError = error.str();
 154         return;
 155       }
 156
 157       // DD(reader->GetOutput()->GetImageDimension());
 158       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 159       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 160       //             DD(reader->GetOutput()->GetSpacing()[i]);
 161       //             DD(reader->GetOutput()->GetOrigin()[i]);
 162       //           }
 163
 164
 165       if (mType == IMAGEWITHTIME)
 166         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 167       else
 168         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 169     }
 170   }
 171 }
 172 //----------------------------------------------------------------------------
 173
 174
 175 #endif /* end #define vvImageReader_TXX */
 176