bool
mitk::ThreeDnTDICOMSeriesReader
::LoadMitkImageForImageBlockDescriptor(DICOMImageBlockDescriptor& block) const
{
PushLocale();
const DICOMImageFrameList& frames = block.GetImageFrameList();
const GantryTiltInformation tiltInfo = block.GetTiltInformation();
const bool hasTilt = tiltInfo.IsRegularGantryTilt();
const int numberOfTimesteps = block.GetNumberOfTimeSteps();
if (numberOfTimesteps == 1)
{
return DICOMITKSeriesGDCMReader::LoadMitkImageForImageBlockDescriptor(block);
}
const int numberOfFramesPerTimestep = block.GetNumberOfFramesPerTimeStep();
ITKDICOMSeriesReaderHelper::StringContainerList filenamesPerTimestep;
for (int timeStep = 0; timeStep<numberOfTimesteps; ++timeStep)
{
// use numberOfFramesPerTimestep frames for a new item in filenamesPerTimestep
ITKDICOMSeriesReaderHelper::StringContainer filenamesOfThisTimeStep;
auto timeStepStart = frames.cbegin() + timeStep * numberOfFramesPerTimestep;
auto timeStepEnd = frames.cbegin() + (timeStep+1) * numberOfFramesPerTimestep;
for (auto frameIter = timeStepStart;
frameIter != timeStepEnd;
++frameIter)
{
filenamesOfThisTimeStep.push_back( (*frameIter)->Filename );
}
filenamesPerTimestep.push_back( filenamesOfThisTimeStep );
}
mitk::ITKDICOMSeriesReaderHelper helper;
mitk::Image::Pointer mitkImage = helper.Load3DnT( filenamesPerTimestep, m_FixTiltByShearing && hasTilt, tiltInfo );
block.SetMitkImage( mitkImage );
PopLocale();
return true;
}
mitk::Image::Pointer
mitk::TestDICOMLoading
::DecorateVerifyCachedImage( const StringList& files, mitk::DICOMTagCache* tagCache, mitk::Image::Pointer cachedImage )
{
DICOMImageBlockDescriptor block;
DICOMImageFrameList framelist;
for (auto iter = files.begin();
iter != files.end();
++iter)
{
framelist.push_back( DICOMImageFrameInfo::New(*iter) );
}
block.SetImageFrameList( framelist );
block.SetTagCache( tagCache );
block.SetMitkImage( cachedImage ); // this should/will create a propertylist describing the image slices
return block.GetMitkImage();
}
mitk::Image::Pointer
mitk::TestDICOMLoading
::DecorateVerifyCachedImage( const StringList& files, mitk::Image::Pointer cachedImage )
{
ClassicDICOMSeriesReader::Pointer reader = this->BuildDICOMReader();
reader->SetInputFiles( files );
reader->AnalyzeInputFiles(); // This just creates a "tag cache and a nice DICOMImageBlockDescriptor.
// Both of these could also be produced in a different way. The only
// important thing is, that the DICOMImageBlockDescriptor knows a
// tag-cache object when PropertyDecorateCachedMitkImageForImageBlockDescriptor
// is called.
if ( reader->GetNumberOfOutputs() != 1 )
{
MITK_ERROR << "Reader produce " << reader->GetNumberOfOutputs() << " images instead of 1 expected..";
return nullptr;
}
DICOMImageBlockDescriptor block = reader->GetOutput(0); // creates a block copy
block.SetMitkImage( cachedImage ); // this should/will create a propertylist describing the image slices
return block.GetMitkImage();
}
bool mitk::DiffusionDICOMFileReader
::LoadSingleOutputImage( DiffusionHeaderDICOMFileReader::DICOMHeaderListType retrievedHeader,
DICOMImageBlockDescriptor& block, bool is_mosaic)
{
// prepare data reading
DiffusionDICOMFileReaderHelper helper;
DiffusionDICOMFileReaderHelper::VolumeFileNamesContainer filenames;
const DICOMImageFrameList& frames = block.GetImageFrameList();
int numberOfDWImages = block.GetIntProperty("timesteps", 1);
int numberOfFramesPerDWImage = frames.size() / numberOfDWImages;
assert( int( double((double) frames.size() / (double) numberOfDWImages)) == numberOfFramesPerDWImage );
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
std::vector< std::string > FileNamesPerVolume;
auto timeStepStart = frames.begin() + idx * numberOfFramesPerDWImage;
auto timeStepEnd = frames.begin() + (idx+1) * numberOfFramesPerDWImage;
for (auto frameIter = timeStepStart;
frameIter != timeStepEnd;
++frameIter)
{
FileNamesPerVolume.push_back( (*frameIter)->Filename );
}
filenames.push_back( FileNamesPerVolume );
}
// TODO : only prototyping to test loading of diffusion images
// we need some solution for the different types
mitk::Image::Pointer output_image = mitk::Image::New();
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer directions =
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New();
double max_bvalue = 0;
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
if( max_bvalue < header.b_value )
max_bvalue = header.b_value;
}
// normalize the retrieved gradient directions according to the set b-value (maximal one)
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
mitk::DiffusionPropertyHelper::GradientDirectionType grad = header.g_vector;
grad.normalize();
grad *= sqrt( header.b_value / max_bvalue );
directions->push_back( grad );
}
// initialize the output image
output_image->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( directions ) );
output_image->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( max_bvalue ) );
if( is_mosaic && this->m_ResolveMosaic )
{
mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::Pointer mosaic_reader =
mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::New();
// retrieve the remaining meta-information needed for mosaic reconstruction
// it suffices to get it exemplatory from the first file in the file list
mosaic_reader->RetrieveMosaicInformation( filenames.at(0).at(0) );
mitk::MosaicDescriptor mdesc = mosaic_reader->GetMosaicDescriptor();
mitk::CastToMitkImage( helper.LoadMosaicToVector<short, 3>( filenames, mdesc ), output_image );
}
else
{
mitk::CastToMitkImage( helper.LoadToVector<short, 3>( filenames ), output_image );
}
mitk::DiffusionPropertyHelper propertyHelper( output_image );
propertyHelper.InitializeImage();
output_image->SetProperty("diffusion.dicom.importname", mitk::StringProperty::New( helper.GetOutputName(filenames) ) );
block.SetMitkImage( (mitk::Image::Pointer) output_image );
return block.GetMitkImage().IsNotNull();
}