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