diff --git a/Modules/DICOMQI/CMakeLists.txt b/Modules/DICOMQI/CMakeLists.txt new file mode 100644 index 0000000000..1ce211e5d1 --- /dev/null +++ b/Modules/DICOMQI/CMakeLists.txt @@ -0,0 +1 @@ +add_subdirectory(autoload/IO) \ No newline at end of file diff --git a/Modules/Multilabel/autoload/DICOMQIIO/CMakeLists.txt b/Modules/DICOMQI/autoload/IO/CMakeLists.txt similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/CMakeLists.txt rename to Modules/DICOMQI/autoload/IO/CMakeLists.txt diff --git a/Modules/Multilabel/autoload/DICOMQIIO/files.cmake b/Modules/DICOMQI/autoload/IO/files.cmake similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/files.cmake rename to Modules/DICOMQI/autoload/IO/files.cmake diff --git a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOActivator.cpp b/Modules/DICOMQI/autoload/IO/mitkDICOMQIIOActivator.cpp similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOActivator.cpp rename to Modules/DICOMQI/autoload/IO/mitkDICOMQIIOActivator.cpp diff --git a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOMimeTypes.cpp b/Modules/DICOMQI/autoload/IO/mitkDICOMQIIOMimeTypes.cpp similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOMimeTypes.cpp rename to Modules/DICOMQI/autoload/IO/mitkDICOMQIIOMimeTypes.cpp diff --git a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOMimeTypes.h b/Modules/DICOMQI/autoload/IO/mitkDICOMQIIOMimeTypes.h similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMQIIOMimeTypes.h rename to Modules/DICOMQI/autoload/IO/mitkDICOMQIIOMimeTypes.h diff --git a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMSegmentationIO.cpp b/Modules/DICOMQI/autoload/IO/mitkDICOMSegmentationIO.cpp similarity index 96% rename from Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMSegmentationIO.cpp rename to Modules/DICOMQI/autoload/IO/mitkDICOMSegmentationIO.cpp index f70783a9d9..b269692655 100644 --- a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMSegmentationIO.cpp +++ b/Modules/DICOMQI/autoload/IO/mitkDICOMSegmentationIO.cpp @@ -1,692 +1,692 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkDICOMSegmentationIO__cpp #define __mitkDICOMSegmentationIO__cpp #include "mitkDICOMSegmentationIO.h" #include "mitkDICOMQIIOMimeTypes.h" #include "mitkDICOMSegmentationConstants.h" #include #include #include #include #include #include #include #include // itk #include // dcmqi #include // us #include #include namespace mitk { DICOMSegmentationIO::DICOMSegmentationIO() : AbstractFileIO(LabelSetImage::GetStaticNameOfClass(), - mitk::MitkDICOMQIIOMimeTypes::DICOMQI_MIMETYPE_NAME(), - "DICOM Segmentation") + mitk::MitkDICOMQIIOMimeTypes::DICOMQI_MIMETYPE_NAME(), + "DICOM Segmentation") { AbstractFileWriter::SetRanking(10); AbstractFileReader::SetRanking(10); this->RegisterService(); this->AddDICOMTagsToService(); } void DICOMSegmentationIO::AddDICOMTagsToService() { IDICOMTagsOfInterest *toiService = GetDicomTagsOfInterestService(); if (toiService != nullptr) { toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_SEQUENCE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::ANATOMIC_REGION_SEQUENCE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENTED_PROPERTY_CATEGORY_SEQUENCE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENTED_PROPERTY_TYPE_SEQUENCE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENTED_PROPERTY_MODIFIER_SEQUENCE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()); toiService->AddTagOfInterest(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()); } } IFileIO::ConfidenceLevel DICOMSegmentationIO::GetWriterConfidenceLevel() const { if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported) return Unsupported; const LabelSetImage *input = static_cast(this->GetInput()); if (input) return Supported; else return Unsupported; } void DICOMSegmentationIO::Write() { ValidateOutputLocation(); mitk::LocaleSwitch localeSwitch("C"); LocalFile localFile(this); const std::string path = localFile.GetFileName(); auto input = dynamic_cast(this->GetInput()); if (input == nullptr) mitkThrow() << "Cannot write non-image data"; // Get DICOM information from referenced image vector> dcmDatasetsSourceImage; std::unique_ptr 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(input->GetProperty("referenceFiles").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()) { std::unique_ptr readDCMDataset(readFileFormat->getAndRemoveDataset()); dcmDatasetsSourceImage.push_back(std::move(readDCMDataset)); } } } 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 segmentations; try { // Hack: Remove the const attribute to switch between the layer images. Normally you could get the different // layer images by input->GetLayerImage(layer) mitk::LabelSetImage *mitkLayerImage = const_cast(input); mitkLayerImage->SetActiveLayer(layer); // Cast mitk layer image to itk ImageToItk::Pointer imageToItkFilter = ImageToItk::New(); imageToItkFilter->SetInput(mitkLayerImage); // Cast from original itk type to dcmqi input itk image type typedef itk::CastImageFilter 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 label a segmentation image will be created const LabelSet *labelSet = input->GetLabelSet(layer); auto labelIter = labelSet->IteratorConstBegin(); // Ignore background label ++labelIter; for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter) { // Thresold over the image with the given label value itk::ThresholdImageFilter::Pointer thresholdFilter = itk::ThresholdImageFilter::New(); thresholdFilter->SetInput(itkLabelImage); thresholdFilter->ThresholdOutside(labelIter->first, labelIter->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 { //TODO is there a better way? Interface expects a vector of raw pointer. vector rawVecDataset; for (const auto& dcmDataSet : dcmDatasetsSourceImage) rawVecDataset.push_back(dcmDataSet.get()); // Convert itk segmentation images to dicom image std::unique_ptr converter = std::make_unique(); std::unique_ptr result(converter->itkimage2dcmSegmentation(rawVecDataset, segmentations, tmpMetaInfoFile)); // Write dicom file DcmFileFormat dcmFileFormat(result.get()); 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); } 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 } IFileIO::ConfidenceLevel DICOMSegmentationIO::GetReaderConfidenceLevel() const { if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported) return Unsupported; const std::string fileName = this->GetLocalFileName(); DcmFileFormat dcmFileFormat; OFCondition status = dcmFileFormat.loadFile(fileName.c_str()); if (status.bad()) return Unsupported; OFString modality; if (dcmFileFormat.getDataset()->findAndGetOFString(DCM_Modality, modality).good()) { if (modality.compare("SEG") == 0) return Supported; else return Unsupported; } return Unsupported; } std::vector DICOMSegmentationIO::Read() { mitk::LocaleSwitch localeSwitch("C"); LabelSetImage::Pointer labelSetImage; std::vector result; const std::string path = this->GetLocalFileName(); MITK_INFO << "loading " << path << std::endl; if (path.empty()) mitkThrow() << "Empty filename in mitk::ItkImageIO "; try { // Get the dcm data set from file path DcmFileFormat dcmFileFormat; OFCondition status = dcmFileFormat.loadFile(path.c_str()); if (status.bad()) mitkThrow() << "Can't read the input file!"; DcmDataset *dataSet = dcmFileFormat.getDataset(); if (dataSet == nullptr) mitkThrow() << "Can't read data from input file!"; //=============================== dcmqi part ==================================== // Read the DICOM SEG images (segItkImages) and DICOM tags (metaInfo) std::unique_ptr converter = std::make_unique(); pair, string> dcmqiOutput = converter->dcmSegmentation2itkimage(dataSet); map segItkImages = dcmqiOutput.first; dcmqi::JSONSegmentationMetaInformationHandler metaInfo(dcmqiOutput.second.c_str()); metaInfo.read(); MITK_INFO << "Input " << metaInfo.getJSONOutputAsString(); //=============================================================================== // Get the label information from segment attributes for each itk image vector>::const_iterator segmentIter = metaInfo.segmentsAttributesMappingList.begin(); // For each itk image add a layer to the LabelSetImage output for (auto &element : segItkImages) { // Get the labeled image and cast it to mitkImage typedef itk::CastImageFilter castItkImageFilterType; castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New(); castFilter->SetInput(element.second); castFilter->Update(); Image::Pointer layerImage; CastToMitkImage(castFilter->GetOutput(), layerImage); // Get pixel value of the label itkInternalImageType::ValueType segValue = 1; typedef itk::ImageRegionIterator IteratorType; // Iterate over the image to find the pixel value of the label IteratorType iter(element.second, element.second->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { itkInputImageType::PixelType value = iter.Get(); if (value != 0) { segValue = value; break; } ++iter; } // Get Segment information map map segmentMap = (*segmentIter); map::const_iterator segmentMapIter = (*segmentIter).begin(); dcmqi::SegmentAttributes *segmentAttribute = (*segmentMapIter).second; OFString labelName; if (segmentAttribute->getSegmentedPropertyTypeCodeSequence() != nullptr) { segmentAttribute->getSegmentedPropertyTypeCodeSequence()->getCodeMeaning(labelName); if (segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence() != nullptr) { OFString modifier; segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence()->getCodeMeaning(modifier); labelName.append(" (").append(modifier).append(")"); } } else { labelName = std::to_string(segmentAttribute->getLabelID()).c_str(); if (labelName.empty()) labelName = "Unnamed"; } float tmp[3] = { 0.0, 0.0, 0.0 }; if (segmentAttribute->getRecommendedDisplayRGBValue() != nullptr) { tmp[0] = segmentAttribute->getRecommendedDisplayRGBValue()[0] / 255.0; tmp[1] = segmentAttribute->getRecommendedDisplayRGBValue()[1] / 255.0; tmp[2] = segmentAttribute->getRecommendedDisplayRGBValue()[2] / 255.0; } Label *newLabel = nullptr; // If labelSetImage do not exists (first image) if (labelSetImage.IsNull()) { // Initialize the labelSetImage with the read image labelSetImage = LabelSetImage::New(); labelSetImage->InitializeByLabeledImage(layerImage); // Already a label was generated, so set the information to this newLabel = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer()); newLabel->SetName(labelName.c_str()); newLabel->SetColor(Color(tmp)); newLabel->SetValue(segValue); } else { // Add a new layer to the labelSetImage. Background label is set automatically labelSetImage->AddLayer(layerImage); // Add new label newLabel = new Label; newLabel->SetName(labelName.c_str()); newLabel->SetColor(Color(tmp)); newLabel->SetValue(segValue); labelSetImage->GetLabelSet(labelSetImage->GetActiveLayer())->AddLabel(newLabel); } // Add some more label properties this->SetLabelProperties(newLabel, segmentAttribute); ++segmentIter; } // Add some general DICOM Segmentation properties mitk::IDICOMTagsOfInterest *toiSrv = GetDicomTagsOfInterestService(); auto tagsOfInterest = toiSrv->GetTagsOfInterest(); DICOMTagPathList tagsOfInterestList; for (const auto &tag : tagsOfInterest) { tagsOfInterestList.push_back(tag.first); } mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New(); scanner->SetInputFiles({ GetInputLocation() }); scanner->AddTagPaths(tagsOfInterestList); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); if (frames.empty()) { MITK_ERROR << "Error reading the DICOM Seg file" << std::endl; return result; } auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames); SetProperties(labelSetImage, findings); // Set active layer to the first layer of the labelset image if (labelSetImage->GetNumberOfLayers() > 1 && labelSetImage->GetActiveLayer() != 0) labelSetImage->SetActiveLayer(0); } catch (const std::exception &e) { MITK_ERROR << "An error occurred while reading the DICOM Seg file: " << e.what(); return result; } catch (...) { MITK_ERROR << "An error occurred in dcmqi while reading the DICOM Seg file"; return result; } result.push_back(labelSetImage.GetPointer()); return result; } const std::string mitk::DICOMSegmentationIO::CreateMetaDataJsonFile(int layer) { const mitk::LabelSetImage *image = dynamic_cast(this->GetInput()); const std::string output; dcmqi::JSONSegmentationMetaInformationHandler handler; // 1. Metadata attributes that will be listed in the resulting DICOM SEG object std::string contentCreatorName; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0070, 0x0084).c_str(), - contentCreatorName)) + contentCreatorName)) contentCreatorName = "MITK"; handler.setContentCreatorName(contentCreatorName); std::string clinicalTrailSeriesId; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0071).c_str(), - clinicalTrailSeriesId)) + clinicalTrailSeriesId)) clinicalTrailSeriesId = "Session 1"; handler.setClinicalTrialSeriesID(clinicalTrailSeriesId); std::string clinicalTrialTimePointID; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0050).c_str(), - clinicalTrialTimePointID)) + clinicalTrialTimePointID)) clinicalTrialTimePointID = "0"; handler.setClinicalTrialTimePointID(clinicalTrialTimePointID); std::string clinicalTrialCoordinatingCenterName = ""; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0060).c_str(), - clinicalTrialCoordinatingCenterName)) + clinicalTrialCoordinatingCenterName)) clinicalTrialCoordinatingCenterName = "Unknown"; handler.setClinicalTrialCoordinatingCenterName(clinicalTrialCoordinatingCenterName); std::string seriesDescription; if (!image->GetPropertyList()->GetStringProperty("name", seriesDescription)) seriesDescription = "MITK Segmentation"; handler.setSeriesDescription(seriesDescription); handler.setSeriesNumber("0" + std::to_string(layer)); handler.setInstanceNumber("1"); handler.setBodyPartExamined(""); const LabelSet *labelSet = image->GetLabelSet(layer); auto labelIter = labelSet->IteratorConstBegin(); // Ignore background label ++labelIter; for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter) { const Label *label = labelIter->second; if (label != nullptr) { TemporoSpatialStringProperty *segmentNumberProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str())); TemporoSpatialStringProperty *segmentLabelProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str())); TemporoSpatialStringProperty *algorithmTypeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str())); dcmqi::SegmentAttributes *segmentAttribute = nullptr; if (segmentNumberProp->GetValue() == "") { MITK_ERROR << "Something went wrong with the label ID."; } else { int labelId = std::stoi(segmentNumberProp->GetValue()); segmentAttribute = handler.createAndGetNewSegment(labelId); } if (segmentAttribute != nullptr) { segmentAttribute->setSegmentDescription(segmentLabelProp->GetValueAsString()); segmentAttribute->setSegmentAlgorithmType(algorithmTypeProp->GetValueAsString()); segmentAttribute->setSegmentAlgorithmName("MITK Segmentation"); if (segmentCategoryCodeValueProp != nullptr && segmentCategoryCodeSchemeProp != nullptr && - segmentCategoryCodeMeaningProp != nullptr) + segmentCategoryCodeMeaningProp != nullptr) segmentAttribute->setSegmentedPropertyCategoryCodeSequence( segmentCategoryCodeValueProp->GetValueAsString(), segmentCategoryCodeSchemeProp->GetValueAsString(), segmentCategoryCodeMeaningProp->GetValueAsString()); else // some default values segmentAttribute->setSegmentedPropertyCategoryCodeSequence( "M-01000", "SRT", "Morphologically Altered Structure"); if (segmentTypeCodeValueProp != nullptr && segmentTypeCodeSchemeProp != nullptr && - segmentTypeCodeMeaningProp != nullptr) + segmentTypeCodeMeaningProp != nullptr) { segmentAttribute->setSegmentedPropertyTypeCodeSequence(segmentTypeCodeValueProp->GetValueAsString(), - segmentTypeCodeSchemeProp->GetValueAsString(), - segmentTypeCodeMeaningProp->GetValueAsString()); + segmentTypeCodeSchemeProp->GetValueAsString(), + segmentTypeCodeMeaningProp->GetValueAsString()); handler.setBodyPartExamined(segmentTypeCodeMeaningProp->GetValueAsString()); } else { // some default values segmentAttribute->setSegmentedPropertyTypeCodeSequence("M-03000", "SRT", "Mass"); handler.setBodyPartExamined("Mass"); } if (segmentModifierCodeValueProp != nullptr && segmentModifierCodeSchemeProp != nullptr && - segmentModifierCodeMeaningProp != nullptr) + segmentModifierCodeMeaningProp != nullptr) segmentAttribute->setSegmentedPropertyTypeModifierCodeSequence( segmentModifierCodeValueProp->GetValueAsString(), segmentModifierCodeSchemeProp->GetValueAsString(), segmentModifierCodeMeaningProp->GetValueAsString()); Color color = label->GetColor(); segmentAttribute->setRecommendedDisplayRGBValue(color[0] * 255, color[1] * 255, color[2] * 255); } } } return handler.getJSONOutputAsString(); } void mitk::DICOMSegmentationIO::SetLabelProperties(mitk::Label *label, dcmqi::SegmentAttributes *segmentAttribute) { // Segment Number:Identification number of the segment.The value of Segment Number(0062, 0004) shall be unique // within the Segmentation instance in which it is created label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str(), - TemporoSpatialStringProperty::New(std::to_string(label->GetValue()))); + TemporoSpatialStringProperty::New(std::to_string(label->GetValue()))); // Segment Label: User-defined label identifying this segment. label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str(), - TemporoSpatialStringProperty::New(label->GetName())); + TemporoSpatialStringProperty::New(label->GetName())); // Segment Algorithm Type: Type of algorithm used to generate the segment. if (!segmentAttribute->getSegmentAlgorithmType().empty()) label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str(), - TemporoSpatialStringProperty::New(segmentAttribute->getSegmentAlgorithmType())); + TemporoSpatialStringProperty::New(segmentAttribute->getSegmentAlgorithmType())); // Add Segmented Property Category Code Sequence tags auto categoryCodeSequence = segmentAttribute->getSegmentedPropertyCategoryCodeSequence(); if (categoryCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value categoryCodeSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator categoryCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning categoryCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Segmented Property Type Code Sequence tags auto typeCodeSequence = segmentAttribute->getSegmentedPropertyTypeCodeSequence(); if (typeCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value typeCodeSequence->getCodeValue(codeValue); label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str(), - TemporoSpatialStringProperty::New(codeValue.c_str())); + TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator typeCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning typeCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Segmented Property Type Modifier Code Sequence tags auto modifierCodeSequence = segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence(); if (modifierCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value modifierCodeSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator modifierCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning modifierCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Atomic RegionSequence tags auto atomicRegionSequence = segmentAttribute->getAnatomicRegionSequence(); if (atomicRegionSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value atomicRegionSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator atomicRegionSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning atomicRegionSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } } DICOMSegmentationIO *DICOMSegmentationIO::IOClone() const { return new DICOMSegmentationIO(*this); } } // namespace #endif //__mitkDICOMSegmentationIO__cpp diff --git a/Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMSegmentationIO.h b/Modules/DICOMQI/autoload/IO/mitkDICOMSegmentationIO.h similarity index 100% rename from Modules/Multilabel/autoload/DICOMQIIO/mitkDICOMSegmentationIO.h rename to Modules/DICOMQI/autoload/IO/mitkDICOMSegmentationIO.h diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake index 00e894d947..7de62d98e6 100644 --- a/Modules/ModuleList.cmake +++ b/Modules/ModuleList.cmake @@ -1,82 +1,83 @@ # The entries in the mitk_modules list must be # ordered according to their dependencies. set(MITK_MODULES Core CommandLine AppUtil RDF LegacyIO DataTypesExt Annotation LegacyGL AlgorithmsExt MapperExt DICOMReader DICOMReaderServices DICOMTesting SceneSerializationBase PlanarFigure ImageDenoising ImageExtraction SceneSerialization Gizmo GraphAlgorithms Multilabel ImageStatistics ContourModel SurfaceInterpolation Segmentation PlanarFigureSegmentation QtWidgets QtWidgetsExt Chart SegmentationUI MatchPointRegistration MatchPointRegistrationUI Classification GPGPU OpenIGTLink IGTBase IGT CameraCalibration OpenCL OpenCVVideoSupport QtOverlays ToFHardware ToFProcessing ToFUI PhotoacousticsHardware PhotoacousticsAlgorithms PhotoacousticsLib US USUI DicomUI Remeshing Python QtPython Persistence OpenIGTLinkUI IGTUI DicomRT RTUI IOExt XNAT TubeGraph BiophotonicsHardware DiffusionImaging TumorInvasionAnalysis BoundingShape RenderWindowManager RenderWindowManagerUI CEST BasicImageProcessing ModelFit ModelFitUI Pharmacokinetics PharmacokineticsUI + DICOMQI ) if(MITK_ENABLE_PIC_READER) list(APPEND MITK_MODULES IpPicSupportIO) endif() diff --git a/Modules/Multilabel/CMakeLists.txt b/Modules/Multilabel/CMakeLists.txt index dfe56177a3..7f696d72eb 100644 --- a/Modules/Multilabel/CMakeLists.txt +++ b/Modules/Multilabel/CMakeLists.txt @@ -1,10 +1,9 @@ MITK_CREATE_MODULE( DEPENDS MitkCore MitkAlgorithmsExt MitkSceneSerializationBase MitkDICOMReader PACKAGE_DEPENDS PRIVATE ITK|ITKQuadEdgeMesh+ITKAntiAlias+ITKIONRRD ) add_subdirectory(autoload/IO) -add_subdirectory(autoload/DICOMQIIO) if(BUILD_TESTING) add_subdirectory(Testing) endif()