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 && mLastError.size()==0) {
  57     ReadNkiImageTransform();
  58     ReadMatImageTransform();
  59   }
  60 }
  61 //----------------------------------------------------------------------------
  62
  63
  64 //----------------------------------------------------------------------------
  65 template<class InputPixelType, unsigned int VImageDimension>
  66 void vvImageReader::UpdateWithDimAndInputPixelType()
  67 {
  68
  69   //  DD(mType);
  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     typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
  76     typedef itk::ImageFileReader<InputImageType> ReaderType;
  77     typename ReaderType::Pointer reader = ReaderType::New();
  78     typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
  79     typename ConnectorType::Pointer connector = ConnectorType::New();
  80     connector->SetInput(reader->GetOutput());
  81     mImage=vvImage::New();
  82     for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
  83       std::cout << (*i) << std::endl;
  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       try {
  96         connector->Update();
  97       } catch ( itk::ExceptionObject & err ) {
  98         std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
  99                   << " " << err << std::endl;
 100       }
 101       vtkImageData *image = vtkImageData::New();
 102       image->DeepCopy(connector->GetOutput());
 103       mImage->AddImage(image);
 104     }
 105   } else {
 106     if (mInputFilenames.size() > 1) {
 107       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 108       typedef itk::ImageSeriesReader<InputImageType> ReaderType;
 109       typename ReaderType::Pointer reader = ReaderType::New();
 110       for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++)
 111         std::cout << (*i) << std::endl;
 112       reader->SetFileNames(mInputFilenames);
 113       //if (mUseAnObserver) {
 114       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 115       //}
 116       try {
 117         reader->Update();
 118       } catch ( itk::ExceptionObject & err ) {
 119         std::cerr << "Error while reading image series:" << err << std::endl;
 120         std::stringstream error;
 121         error << err;
 122         mLastError = error.str();
 123         return;
 124       }
 125
 126       // DD(reader->GetOutput()->GetImageDimension());
 127       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 128       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 129       //             DD(reader->GetOutput()->GetSpacing()[i]);
 130       //           }
 131
 132       if (mType == IMAGEWITHTIME)
 133         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 134       else
 135         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 136     } else {
 137       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
 138       typedef itk::ImageFileReader<InputImageType> ReaderType;
 139       typename ReaderType::Pointer reader = ReaderType::New();
 140       reader->SetFileName(mInputFilenames[0]);
 141       //if (mUseAnObserver) {
 142       //reader->AddObserver(itk::ProgressEvent(), mObserver);
 143       //}
 144       try {
 145         reader->Update();
 146       } catch ( itk::ExceptionObject & err ) {
 147         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
 148                   << " " << err << std::endl;
 149         std::stringstream error;
 150         error << err;
 151         mLastError = error.str();
 152         return;
 153       }
 154
 155       // DD(reader->GetOutput()->GetImageDimension());
 156       //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
 157       //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
 158       //             DD(reader->GetOutput()->GetSpacing()[i]);
 159       //             DD(reader->GetOutput()->GetOrigin()[i]);
 160       //           }
 161
 162
 163       if (mType == IMAGEWITHTIME)
 164         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
 165       else
 166         mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
 167     }
 168   }
 169 }
 170 //----------------------------------------------------------------------------
 171
 172
 173 #endif /* end #define vvImageReader_TXX */
 174