void transform(string inputFilename, string outputFilename)
{
typedef itk::Image< TPixelType, N > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
typename ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading image " << std::endl;
std::cerr << e << std::endl;
}
typename WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(io);
writer->SetFileName(outputFilename);
writer->SetInput(reader->GetOutput());
try {
writer->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing image " << std::endl;
std::cerr << e << std::endl;
}
}
int changeOrientationMethod(string inputFilename, string outputFilename, OrientationType orientation, bool changeOrientation, bool displayInitialOrientation, bool displayAvailableOrientation)
{
typedef itk::Image< TPixelType, N > ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
typename ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
OrientImage<ImageType> orientationFilter;
orientationFilter.setInputImage(reader->GetOutput());
if (displayInitialOrientation)
{
try {
io->SetFileName(inputFilename);
io->ReadImageInformation();
//reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading input image " << std::endl;
std::cerr << e << std::endl;
}
typename ImageType::DirectionType direction;
vector<double> dir0 = io->GetDirection(0);
for (int i=0; i<dir0.size(); i++)
direction(i,0) = dir0[i];
vector<double> dir1 = io->GetDirection(1);
for (int i=0; i<dir1.size(); i++)
direction(i,1) = dir1[i];
vector<double> dir2 = io->GetDirection(2);
for (int i=0; i<dir2.size(); i++)
direction(i,2) = dir2[i];
cout << direction << endl;
cout << "Input image orientation : " << FlagToString(orientationFilter.getOrientationFromDirection(direction)) << endl;
}
if (changeOrientation)
{
try {
io->SetFileName(inputFilename);
io->ReadImageInformation();
//reader->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading input image " << std::endl;
std::cerr << e << std::endl;
}
orientationFilter.orientation(orientation);
typename WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(io);
writer->SetFileName(outputFilename);
writer->SetInput(orientationFilter.getOutputImage());
try {
writer->Write();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing output image " << std::endl;
std::cerr << e << std::endl;
}
}
return EXIT_SUCCESS;
}
void operator()( const Parameter ¶m )
{
OSLM_DEBUG( "itk::ImageSeriesWriter with PIXELTYPE "<< fwTools::DynamicType::string<PIXELTYPE>() );
::fwData::Image::sptr image = param.m_dataImage;
// VAG attention : ImageFileReader ne notifie AUCUNE progressEvent mais son ImageIO oui!!!! mais ImageFileReader ne permet pas de l'atteindre
// car soit mis a la mano ou alors construit lors de l'Update donc trop tard
// Il faut dont creer une ImageIO a la mano (*1*): affecter l'observation sur IO (*2*) et mettre le IO dans le reader (voir *3*)
// Reader IO (*1*)
typename itk::ImageIOBase::Pointer imageIOWrite = itk::ImageIOFactory::CreateImageIO( "image.jpg", itk::ImageIOFactory::WriteMode);
assert( imageIOWrite.IsNotNull() );
// create writer
typedef itk::Image< PIXELTYPE, 3> itkImageType;
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef typename itk::ImageSeriesWriter< itkImageType, Image2DType > WriterType;
typename WriterType::Pointer writer = WriterType::New();
// set observation (*2*)
itk::LightProcessObject::Pointer castHelper= (itk::LightProcessObject *)(imageIOWrite.GetPointer());
assert( castHelper.IsNotNull() );
Progressor progress(castHelper, param.m_fwWriter, param.m_filename);
// create itk Image
typename itkImageType::Pointer itkImage = ::fwItkIO::itkImageFactory<itkImageType>( image );
typedef ::itk::IntensityWindowingImageFilter< itkImageType, itkImageType > RescaleFilterType;
typename RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
double min, max;
::fwData::Composite::sptr poolTF;
poolTF = image->getField< ::fwData::Composite>( ::fwComEd::Dictionary::m_transferFunctionCompositeId );
if(poolTF)
{
::fwData::Composite::iterator iter = poolTF->find(::fwData::TransferFunction::s_DEFAULT_TF_NAME);
if(iter != poolTF->end())
{
::fwData::TransferFunction::sptr tf;
tf = ::fwData::TransferFunction::dynamicCast(iter->second);
min = tf->getWLMinMax().first;
max = tf->getWLMinMax().second;
}
}
else
{
::fwComEd::fieldHelper::MedicalImageHelpers::getMinMax(image, min, max);
}
rescaleFilter->SetWindowMinimum( min );
rescaleFilter->SetWindowMaximum( max );
rescaleFilter->SetOutputMinimum( 0 );
rescaleFilter->SetOutputMaximum( 255 );
rescaleFilter->InPlaceOff();
rescaleFilter->SetInput( itkImage );
rescaleFilter->Update();
writer->SetInput( rescaleFilter->GetOutput() );
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
std::string format = param.m_filename;
format += "/%04d.jpg";
nameGenerator->SetSeriesFormat( format.c_str() );
nameGenerator->SetStartIndex( 1 );
nameGenerator->SetEndIndex( image->getSize()[2] );
nameGenerator->SetIncrementIndex( 1 );
writer->SetFileNames( nameGenerator->GetFileNames() );
writer->SetImageIO( imageIOWrite );
// save image;
writer->Update();
}
