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::DICOMITKSeriesGDCMReader::SortingBlockList
mitk::ThreeDnTDICOMSeriesReader
::Condense3DBlocks(SortingBlockList& resultOf3DGrouping)
{
if (!m_Group3DandT)
{
return resultOf3DGrouping; // don't work if nobody asks us to
}
SortingBlockList remainingBlocks = resultOf3DGrouping;
SortingBlockList non3DnTBlocks;
SortingBlockList true3DnTBlocks;
std::vector<unsigned int> true3DnTBlocksTimeStepCount;
// we should describe our need for this tag as needed via a function
// (however, we currently know that the superclass will always need this tag)
const DICOMTag tagImagePositionPatient(0x0020, 0x0032);
while (!remainingBlocks.empty())
{
// new block to fill up
const DICOMDatasetAccessingImageFrameList& firstBlock = remainingBlocks.front();
DICOMDatasetAccessingImageFrameList current3DnTBlock = firstBlock;
int current3DnTBlockNumberOfTimeSteps = 1;
// get block characteristics of first block
const unsigned int currentBlockNumberOfSlices = firstBlock.size();
const std::string currentBlockFirstOrigin = firstBlock.front()->GetTagValueAsString( tagImagePositionPatient ).value;
const std::string currentBlockLastOrigin = firstBlock.back()->GetTagValueAsString( tagImagePositionPatient ).value;
remainingBlocks.erase( remainingBlocks.begin() );
// compare all other blocks against the first one
for (auto otherBlockIter = remainingBlocks.begin();
otherBlockIter != remainingBlocks.cend();
/*++otherBlockIter*/) // <-- inside loop
{
// get block characteristics from first block
const DICOMDatasetAccessingImageFrameList otherBlock = *otherBlockIter;
const unsigned int otherBlockNumberOfSlices = otherBlock.size();
const std::string otherBlockFirstOrigin = otherBlock.front()->GetTagValueAsString( tagImagePositionPatient ).value;
const std::string otherBlockLastOrigin = otherBlock.back()->GetTagValueAsString( tagImagePositionPatient ).value;
// add matching blocks to current3DnTBlock
// keep other blocks for later
if ( otherBlockNumberOfSlices == currentBlockNumberOfSlices
&& otherBlockFirstOrigin == currentBlockFirstOrigin
&& otherBlockLastOrigin == currentBlockLastOrigin
)
{ // matching block
++current3DnTBlockNumberOfTimeSteps;
current3DnTBlock.insert( current3DnTBlock.end(), otherBlock.begin(), otherBlock.end() ); // append
// remove this block from remainingBlocks
otherBlockIter = remainingBlocks.erase(otherBlockIter); // make sure iterator otherBlockIter is valid afterwards
}
else
{
++otherBlockIter;
}
}
// in any case, we now now all about the first block of our list ...
// ... and we wither call it 3D o 3D+t
if (current3DnTBlockNumberOfTimeSteps > 1)
{
true3DnTBlocks.push_back(current3DnTBlock);
true3DnTBlocksTimeStepCount.push_back(current3DnTBlockNumberOfTimeSteps);
}
else
{
non3DnTBlocks.push_back(current3DnTBlock);
}
}
// create output for real 3D+t blocks (other outputs will be created by superclass)
// set 3D+t flag on output block
this->SetNumberOfOutputs( true3DnTBlocks.size() );
unsigned int o = 0;
for (auto blockIter = true3DnTBlocks.cbegin();
blockIter != true3DnTBlocks.cend();
++o, ++blockIter)
{
// bad copy&paste code from DICOMITKSeriesGDCMReader, should be handled in a better way
DICOMDatasetAccessingImageFrameList gdcmFrameInfoList = *blockIter;
assert(!gdcmFrameInfoList.empty());
// reverse frames if necessary
// update tilt information from absolute last sorting
const DICOMDatasetList datasetList = ConvertToDICOMDatasetList( gdcmFrameInfoList );
m_NormalDirectionConsistencySorter->SetInput( datasetList );
m_NormalDirectionConsistencySorter->Sort();
const DICOMDatasetAccessingImageFrameList sortedGdcmInfoFrameList = ConvertToDICOMDatasetAccessingImageFrameList( m_NormalDirectionConsistencySorter->GetOutput(0) );
const GantryTiltInformation& tiltInfo = m_NormalDirectionConsistencySorter->GetTiltInformation();
// set frame list for current block
const DICOMImageFrameList frameList = ConvertToDICOMImageFrameList( sortedGdcmInfoFrameList );
assert(!frameList.empty());
DICOMImageBlockDescriptor block;
block.SetTagCache( this->GetTagCache() ); // important: this must be before SetImageFrameList(), because SetImageFrameList will trigger reading of lots of interesting tags!
block.SetAdditionalTagsOfInterest(GetAdditionalTagsOfInterest());
block.SetTagLookupTableToPropertyFunctor(GetTagLookupTableToPropertyFunctor());
block.SetImageFrameList( frameList );
block.SetTiltInformation( tiltInfo );
block.SetFlag("3D+t", true);
block.SetIntProperty("timesteps", true3DnTBlocksTimeStepCount[o]);
MITK_DEBUG << "Found " << true3DnTBlocksTimeStepCount[o] << " timesteps";
this->SetOutput( o, block );
}
return non3DnTBlocks;
}