//! populate this InputType with data from in stream
int
TreeInput::
Read(std::istream& in, const std::vector<FactorType>& factorOrder,
AllOptions const& opts)
{
const StaticData &staticData = StaticData::Instance();
string line;
if (getline(in, line, '\n').eof())
return 0;
// remove extra spaces
//line = Trim(line);
m_labelledSpans.clear();
ProcessAndStripXMLTags(line, m_labelledSpans, m_xmlOptions);
// do words 1st - hack
stringstream strme;
strme << line << endl;
Sentence::Read(strme, factorOrder, opts);
// size input chart
size_t sourceSize = GetSize();
m_sourceChart.resize(sourceSize);
for (size_t pos = 0; pos < sourceSize; ++pos) {
m_sourceChart[pos].resize(sourceSize - pos);
}
// do source labels
vector<XMLParseOutput>::const_iterator iterLabel;
for (iterLabel = m_labelledSpans.begin(); iterLabel != m_labelledSpans.end(); ++iterLabel) {
const XMLParseOutput &labelItem = *iterLabel;
const Range &range = labelItem.m_range;
const string &label = labelItem.m_label;
AddChartLabel(range.GetStartPos() + 1, range.GetEndPos() + 1, label, factorOrder);
}
// default label
for (size_t startPos = 0; startPos < sourceSize; ++startPos) {
for (size_t endPos = startPos; endPos < sourceSize; ++endPos) {
NonTerminalSet &list = GetLabelSet(startPos, endPos);
if (list.size() == 0 || !staticData.GetDefaultNonTermOnlyForEmptyRange()) {
AddChartLabel(startPos, endPos, staticData.GetInputDefaultNonTerminal(), factorOrder);
}
}
}
return 1;
}
void TreeInput::AddChartLabel(size_t startPos, size_t endPos, const Word &label
, const std::vector<FactorType>& /* factorOrder */)
{
CHECK(label.IsNonTerminal());
SourceLabelOverlap overlapType = StaticData::Instance().GetSourceLabelOverlap();
NonTerminalSet &list = GetLabelSet(startPos, endPos);
switch (overlapType) {
case SourceLabelOverlapAdd:
list.insert(label);
break;
case SourceLabelOverlapReplace:
if (list.size() > 0) // replace existing label
list.clear();
list.insert(label);
break;
case SourceLabelOverlapDiscard:
if (list.size() == 0)
list.insert(label);
break;
}
}
void DICOMSegmentationIO::Write()
{
ValidateOutputLocation();
mitk::LocaleSwitch localeSwitch("C");
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
auto input = dynamic_cast<const LabelSetImage *>(this->GetInput());
if (input == nullptr)
mitkThrow() << "Cannot write non-image data";
// Get DICOM information from referenced image
vector<DcmDataset *> dcmDatasets;
DcmFileFormat *readFileFormat = new DcmFileFormat();
try
{
// TODO: Generate dcmdataset witk DICOM tags from property list; ATM the source are the filepaths from the
// property list
mitk::StringLookupTableProperty::Pointer filesProp =
dynamic_cast<mitk::StringLookupTableProperty *>(input->GetProperty("files").GetPointer());
if (filesProp.IsNull())
{
mitkThrow() << "No property with dicom file path.";
return;
}
StringLookupTable filesLut = filesProp->GetValue();
const StringLookupTable::LookupTableType &lookUpTableMap = filesLut.GetLookupTable();
for (auto it : lookUpTableMap)
{
const char *fileName = (it.second).c_str();
if (readFileFormat->loadFile(fileName, EXS_Unknown).good())
dcmDatasets.push_back(readFileFormat->getAndRemoveDataset());
}
}
catch (const std::exception &e)
{
MITK_ERROR << "An error occurred while getting the dicom informations: " << e.what() << endl;
return;
}
// Iterate over all layers. For each a dcm file will be generated
for (unsigned int layer = 0; layer < input->GetNumberOfLayers(); ++layer)
{
vector<itkInternalImageType::Pointer> segmentations;
try
{
// Cast mitk layer image to itk
ImageToItk<itkInputImageType>::Pointer imageToItkFilter = ImageToItk<itkInputImageType>::New();
// BUG: It must be the layer image, but there are some errors with it (dcmqi: generate the dcmSeg "No frame data
// available") --> input->GetLayerImage(layer)
imageToItkFilter->SetInput(input);
imageToItkFilter->Update();
// Cast from original itk type to dcmqi input itk image type
typedef itk::CastImageFilter<itkInputImageType, itkInternalImageType> castItkImageFilterType;
castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New();
castFilter->SetInput(imageToItkFilter->GetOutput());
castFilter->Update();
itkInternalImageType::Pointer itkLabelImage = castFilter->GetOutput();
itkLabelImage->DisconnectPipeline();
// Iterate over all labels. For each a segmentation image will be created
const LabelSet *labelSet = input->GetLabelSet(layer);
for (auto itLabel = labelSet->IteratorConstBegin(); itLabel != labelSet->IteratorConstEnd(); ++itLabel)
{
// Thresold over the image with the given label value
itk::ThresholdImageFilter<itkInternalImageType>::Pointer thresholdFilter =
itk::ThresholdImageFilter<itkInternalImageType>::New();
thresholdFilter->SetInput(itkLabelImage);
thresholdFilter->ThresholdOutside(itLabel->first, itLabel->first);
thresholdFilter->SetOutsideValue(0);
thresholdFilter->Update();
itkInternalImageType::Pointer segmentImage = thresholdFilter->GetOutput();
segmentImage->DisconnectPipeline();
segmentations.push_back(segmentImage);
}
}
catch (const itk::ExceptionObject &e)
{
MITK_ERROR << e.GetDescription() << endl;
return;
}
// Create segmentation meta information
const std::string &tmpMetaInfoFile = this->CreateMetaDataJsonFile(layer);
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Convert itk segmentation images to dicom image
dcmqi::ImageSEGConverter *converter = new dcmqi::ImageSEGConverter();
DcmDataset *result = converter->itkimage2dcmSegmentation(dcmDatasets, segmentations, tmpMetaInfoFile);
// Write dicom file
DcmFileFormat dcmFileFormat(result);
std::string filePath = path.substr(0, path.find_last_of("."));
// If there is more than one layer, we have to write more than 1 dicom file
if (input->GetNumberOfLayers() != 1)
filePath = filePath + std::to_string(layer) + ".dcm";
else
filePath = filePath + ".dcm";
dcmFileFormat.saveFile(filePath.c_str(), EXS_LittleEndianExplicit);
// Clean up
if (converter != nullptr)
delete converter;
if (result != nullptr)
delete result;
}
catch (const std::exception &e)
{
MITK_ERROR << "An error occurred during writing the DICOM Seg: " << e.what() << endl;
return;
}
} // Write a dcm file for the next layer
// End of image writing; clean up
if (readFileFormat)
delete readFileFormat;
for (auto obj : dcmDatasets)
delete obj;
dcmDatasets.clear();
}
