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| /*========================================================================= | ||
| * Copyright NumFOCUS | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * https://www.apache.org/licenses/LICENSE-2.0.txt | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * | ||
| *=========================================================================*/ | ||
|
|
||
| // DCMQI includes | ||
| #include "dcmqi/Itk2DicomConverter.h" | ||
| #undef HAVE_SSTREAM // Avoid redefinition warning | ||
| #include "dcmqi/internal/VersionConfigure.h" | ||
|
|
||
| // DCMTK includes | ||
| #include "dcmtk/oflog/configrt.h" | ||
|
|
||
| #include "itkPipeline.h" | ||
| #include "itkInputImage.h" | ||
| #include "itkOutputBinaryStream.h" | ||
| #include "itkSupportInputImageTypes.h" | ||
| #include "itkSmartPointer.h" | ||
| #include "itkInputTextStream.h" | ||
|
|
||
| typedef dcmqi::Helper helper; | ||
| constexpr unsigned int Dimension = 3; | ||
| using PixelType = short; | ||
| using ScalarImageType = itk::Image<PixelType, Dimension>; | ||
|
|
||
| int runPipeline( | ||
| itk::wasm::InputTextStream& metaInfoStream, | ||
| const std::vector<std::string> & dicomImageFiles, | ||
| const std::vector<std::string> & segImageFiles, | ||
| const std::string & outputDicomFile, | ||
| const bool skipEmptySlices, | ||
| const bool useLabelIDAsSegmentNumber) | ||
| { | ||
| const std::string metaInfo((std::istreambuf_iterator<char>(metaInfoStream.Get())), | ||
| std::istreambuf_iterator<char>()); | ||
|
|
||
| // Pipeline code goes here | ||
| if(dicomImageFiles.empty()){ | ||
| cerr << "Error: No input DICOM files specified!" << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| std::vector<ScalarImageType::Pointer> segmentations; | ||
| for(size_t segFileNumber = 0; segFileNumber < segImageFiles.size(); ++segFileNumber) | ||
| { | ||
| ShortReaderType::Pointer reader = ShortReaderType::New(); | ||
| reader->SetFileName(segImageFiles[segFileNumber]); | ||
| reader->Update(); | ||
| cout << "Loaded segmentation from " << segImageFiles[segFileNumber] << endl; | ||
|
|
||
| ShortImageType::Pointer labelImage = reader->GetOutput(); | ||
| segmentations.push_back(labelImage); | ||
|
|
||
| ShortImageType::SizeType ref_size, cmp_size; | ||
| ref_size = segmentations[0]->GetLargestPossibleRegion().GetSize(); | ||
| cmp_size = labelImage->GetLargestPossibleRegion().GetSize(); | ||
| if(ref_size[0] != cmp_size[0] || ref_size[1] != cmp_size[1]) | ||
| { | ||
| cerr << "Error: In-plane dimensions of segmentations are inconsistent!" << endl; | ||
| cerr << ref_size << " vs " << cmp_size << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } | ||
| // itk::Indent indent; | ||
| // img->Print(std::cout, indent); | ||
|
|
||
| #if !defined(NDEBUG) || defined(_DEBUG) | ||
| // Display DCMTK debug, warning, and error logs in the console | ||
| // For some reason, this code has no effect if it is called too early (e.g., directly after PARSE_ARGS) | ||
| // therefore we call it here. | ||
| dcmtk::log4cplus::BasicConfigurator::doConfigure(); | ||
| #endif | ||
|
|
||
| if(!helper::pathsExist(dicomImageFiles)) | ||
| { | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| std::vector<DcmDataset*> dcmDatasets = helper::loadDatasets(dicomImageFiles); | ||
|
|
||
| if(dcmDatasets.empty()) | ||
| { | ||
| cerr << "Error: no DICOM could be loaded from the specified list/directory" << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| /* | ||
| ifstream metainfoStream(metaInfoFile.c_str(), ios_base::binary); | ||
| std::string metadata( (std::istreambuf_iterator<char>(metainfoStream) ), | ||
| (std::istreambuf_iterator<char>())); | ||
| */ | ||
|
|
||
| Json::Value metaRoot; | ||
| istringstream metainfoisstream(metaInfo); | ||
| metainfoisstream >> metaRoot; | ||
|
|
||
| if(metaRoot.isMember("segmentAttributes")) | ||
| { | ||
| if(metaRoot["segmentAttributes"].size() != segImageFiles.size()) | ||
| { | ||
| cerr << "Error: number of items in the \"segmentAttributes\" metadata array should match the number of input segmentation files!" << endl; | ||
| cerr << "segmentAttributes has: " << metaRoot["segmentAttributes"].size() << " items, the are " << segImageFiles.size() << " input segmentation files!" << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } | ||
|
|
||
| if(metaRoot.isMember("segmentAttributesFileMapping")) | ||
| { | ||
| if(metaRoot["segmentAttributesFileMapping"].size() != metaRoot["segmentAttributes"].size()) | ||
| { | ||
| cerr << "Number of files in segmentAttributesFileMapping should match the number of entries in segmentAttributes!" << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| // otherwise, re-order the entries in the segmentAtrributes list to match the order of files in segmentAttributesFileMapping | ||
| Json::Value reorderedSegmentAttributes; | ||
| vector<int> fileOrder(segImageFiles.size()); | ||
| fill(fileOrder.begin(), fileOrder.end(), -1); | ||
| vector<ShortImageType::Pointer> segmentationsReordered(segImageFiles.size()); | ||
| for(size_t filePosition=0;filePosition<segImageFiles.size();filePosition++) | ||
| { | ||
| for(size_t mappingPosition=0;mappingPosition<segImageFiles.size();mappingPosition++) | ||
| { | ||
| string mappingItem = metaRoot["segmentAttributesFileMapping"][static_cast<int>(mappingPosition)].asCString(); | ||
| size_t foundPos = segImageFiles[filePosition].rfind(mappingItem); | ||
| if(foundPos != std::string::npos) | ||
| { | ||
| fileOrder[filePosition] = mappingPosition; | ||
| break; | ||
| } | ||
| } | ||
| if(fileOrder[filePosition] == -1) | ||
| { | ||
| cerr << "Failed to map " << segImageFiles[filePosition] << " from the segmentAttributesFileMapping attribute to an input file name!" << endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } | ||
| cout << "Order of input ITK images updated as shown below based on the segmentAttributesFileMapping attribute:" << endl; | ||
| for(size_t i=0;i<segImageFiles.size();i++) | ||
| { | ||
| cout << " image " << i << " moved to position " << fileOrder[i] << endl; | ||
| segmentationsReordered[fileOrder[i]] = segmentations[i]; | ||
| } | ||
| segmentations = segmentationsReordered; | ||
| } | ||
|
|
||
| try | ||
| { | ||
| DcmDataset* result = dcmqi::Itk2DicomConverter::itkimage2dcmSegmentation(dcmDatasets, | ||
| segmentations, | ||
| metaInfo, | ||
| skipEmptySlices, | ||
| useLabelIDAsSegmentNumber); | ||
|
|
||
| if (result == NULL) | ||
| { | ||
| std::cerr << "ERROR: Conversion failed." << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| else | ||
| { | ||
| DcmFileFormat segdocFF(result); | ||
| bool compress = false; | ||
| if (compress) | ||
| { | ||
| CHECK_COND(segdocFF.saveFile(outputDicomFile.c_str(), EXS_DeflatedLittleEndianExplicit)); | ||
| } | ||
| else | ||
| { | ||
| CHECK_COND(segdocFF.saveFile(outputDicomFile.c_str(), EXS_LittleEndianExplicit)); | ||
| } | ||
|
|
||
| std::cout << "Saved segmentation as " << outputDicomFile << endl; | ||
| } | ||
|
|
||
| for (size_t i = 0; i < dcmDatasets.size(); i++) | ||
| { | ||
| delete dcmDatasets[i]; | ||
| } | ||
|
|
||
| if (result != NULL) | ||
| { | ||
| delete result; | ||
| } | ||
| return EXIT_SUCCESS; | ||
| } | ||
| catch (int e) | ||
| { | ||
| std::cerr << "Fatal error encountered." << std::endl; | ||
| } | ||
| return EXIT_SUCCESS; | ||
| } | ||
|
|
||
| int main(int argc, char * argv[]) | ||
| { | ||
| itk::wasm::Pipeline pipeline("write-segmentation", "Write DICOM segmentation object", argc, argv); | ||
|
|
||
| //itk::wasm::InputImage<ScalarImageType> inputImage; | ||
| //pipeline.add_option("seg-image", inputImage, "dicom segmentation object as an image")->required()->type_name("INPUT_IMAGE"); | ||
|
|
||
| itk::wasm::InputTextStream metaInfo; | ||
| pipeline.add_option("meta-info", metaInfo, "JSON file containing the meta-information that describes" \ | ||
| "the measurements to be encoded. See DCMQI documentation for details.")->required()->type_name("INPUT_JSON"); | ||
|
|
||
| std::string outputDicomFile; | ||
| pipeline.add_option("output-dicom-file", outputDicomFile, "File name of the DICOM SEG object that will store the" \ | ||
| "result of conversion.")->required()->type_name("OUTPUT_BINARY_FILE"); | ||
|
|
||
| std::vector<std::string> refDicomSeriesFiles; | ||
| pipeline.add_option("-r,--ref-dicom-series", refDicomSeriesFiles, "List of DICOM files that correspond to the original." \ | ||
| "image that was segmented.")->required()->check(CLI::ExistingFile)->expected(1,-1)->type_name("INPUT_BINARY_FILE"); | ||
|
|
||
| std::vector<std::string> segImageFiles; | ||
| pipeline.add_option("-i,--seg-images", segImageFiles, "List of input segmentation images." \ | ||
| "image that was segmented.")->required()->check(CLI::ExistingFile)->expected(1,-1)->type_name("INPUT_BINARY_FILE"); | ||
|
|
||
| bool skipEmptySlices{true}; | ||
| pipeline.add_flag("-s,--skip-empty-slices", skipEmptySlices, "Skip empty slices while encoding segmentation image." \ | ||
| "By default, empty slices will not be encoded, resulting in a smaller output file size."); | ||
|
|
||
| bool useLabelIDAsSegmentNumber{false}; | ||
| pipeline.add_flag("-l,--use-labelid-as-segmentnumber", useLabelIDAsSegmentNumber, "Use label IDs from ITK images as" \ | ||
| "Segment Numbers in DICOM. Only works if label IDs are consecutively numbered starting from 1, otherwise conversion will fail."); | ||
|
|
||
| ITK_WASM_PARSE(pipeline); | ||
|
|
||
| runPipeline( | ||
| metaInfo, | ||
| refDicomSeriesFiles, | ||
| segImageFiles, | ||
| outputDicomFile, | ||
| skipEmptySlices, | ||
| useLabelIDAsSegmentNumber | ||
| ); | ||
| } |
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