typename TInputImage::Pointer SegmentationIntensityAndTextureImages<TInputImage>::getIntensityImage()
{
typedef itk::HistogramEqualizationFilter<ImageType,ImageType> EqualizationFilterType;
typename EqualizationFilterType::Pointer equalizationFilter = EqualizationFilterType::New();
equalizationFilter->SetInput(inputImage);
equalizationFilter->Update();
typedef itk::GradientAnisotropicDiffusionImageFilter<ImageType,ImageType> AnisotropicFilterType;
typename AnisotropicFilterType::Pointer anisotropicFilter = AnisotropicFilterType::New();
anisotropicFilter->SetInput(equalizationFilter->GetOutput());
anisotropicFilter->SetNumberOfIterations(25);
anisotropicFilter->SetTimeStep(timeStep);
anisotropicFilter->SetConductanceParameter(3);
anisotropicFilter->Update();
typename RescaleFilterType::Pointer normalizeFilter = RescaleFilterType::New();
normalizeFilter->SetOutputMaximum(255);
normalizeFilter->SetOutputMinimum(0);
normalizeFilter->SetInput(anisotropicFilter->GetOutput());
normalizeFilter->Update();
return normalizeFilter->GetOutput();
}
void SegmentationIntensityAndTextureImages<TInputImage>::setInput(ImageType* image)
{
typename RescaleFilterType::Pointer normalizeFilter = RescaleFilterType::New();
normalizeFilter->SetOutputMaximum(255);
normalizeFilter->SetOutputMinimum(0);
normalizeFilter->SetInput(image);
normalizeFilter->Update();
this->inputImage = normalizeFilter->GetOutput();
this->timeStep = 0.125;
}
typename TInputImage::Pointer SegmentationIntensityAndTextureImages<TInputImage>::getTextureImage()
{
typedef itk::ScalarToTextureRLImageFilter<ImageType,ImageType> FilterType;
typename FilterType::Pointer textureFilter = FilterType::New();
textureFilter->SetInput(inputImage);
textureFilter->SetTextureFeature(8);
typename FilterType::RegionSizeType size;
size.Fill(13);
textureFilter->SetRegionSize(size);
textureFilter->Update();
typename RescaleFilterType::Pointer normalizeFilter = RescaleFilterType::New();
normalizeFilter->SetOutputMaximum(255);
normalizeFilter->SetOutputMinimum(0);
normalizeFilter->SetInput(textureFilter->GetOutput());
normalizeFilter->Update();
return normalizeFilter->GetOutput();
}
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();
}
