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|---|---|---|
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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 | ||
| // #undef HAVE_SSTREAM // Avoid redefinition warning | ||
| #include "dcmqi/Dicom2ItkConverter.h" | ||
| #include "dcmqi/internal/VersionConfigure.h" | ||
|
|
||
| // DCMTK includes | ||
| #include "dcmtk/oflog/configrt.h" | ||
|
|
||
| // ITK includes | ||
| #include "itkComposeImageFilter.h" | ||
| #include "itkVectorImage.h" | ||
|
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||
| // ITK-wasm includes | ||
| #include "itkPipeline.h" | ||
| #include "itkOutputImage.h" | ||
| #include "itkOutputTextStream.h" | ||
|
|
||
| typedef dcmqi::Helper helper; | ||
| constexpr unsigned int Dimension = 3; | ||
| using PixelType = short; | ||
| using ScalarImageType = itk::Image<PixelType, Dimension>; | ||
| using VectorImageType = itk::VectorImage<PixelType, Dimension>; | ||
|
|
||
| int runPipeline( | ||
| itk::wasm::Pipeline & pipeline, | ||
| const std::string & inputSEGFileName, | ||
| itk::wasm::OutputImage<VectorImageType>& outputImage, | ||
| itk::wasm::OutputTextStream& outputMetaInfoJSON, | ||
| const bool mergeSegments) | ||
| { | ||
| #if !defined(NDEBUG) || defined(_DEBUG) | ||
| // Display DCMTK debug, warning, and error logs in the console | ||
| dcmtk::log4cplus::BasicConfigurator::doConfigure(); | ||
| #endif | ||
|
|
||
| if(helper::isUndefinedOrPathDoesNotExist(inputSEGFileName, "Input DICOM file")) | ||
| { | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| DcmRLEDecoderRegistration::registerCodecs(); | ||
|
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| DcmFileFormat sliceFF; | ||
| // std::cout << "Loading DICOM SEG file " << inputSEGFileName << std::endl; | ||
| CHECK_COND(sliceFF.loadFile(inputSEGFileName.c_str())); | ||
| DcmDataset* dataset = sliceFF.getDataset(); | ||
|
|
||
| try | ||
| { | ||
| dcmqi::Dicom2ItkConverter converter; | ||
| std::string metaInfo; | ||
| OFCondition result = converter.dcmSegmentation2itkimage(dataset, metaInfo, mergeSegments); | ||
| if (result.bad()) | ||
| { | ||
| std::cerr << "ERROR: Failed to convert DICOM SEG to ITK image: " << result.text() << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| using ImageToVectorImageFilterType = itk::ComposeImageFilter<ScalarImageType>; | ||
| auto imageToVectorImageFilter = ImageToVectorImageFilterType::New(); | ||
| int inputNumber = 0; | ||
| for (auto itkImage = converter.begin(); itkImage != nullptr; itkImage = converter.next()) | ||
| { | ||
| imageToVectorImageFilter->SetInput(inputNumber++, itkImage); | ||
| } | ||
| imageToVectorImageFilter->Update(); | ||
| VectorImageType::Pointer vectorImage = imageToVectorImageFilter->GetOutput(); | ||
| if (!vectorImage) | ||
| { | ||
| std::cerr << "Failed to create VectorImage." << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
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||
| outputImage.Set(vectorImage); | ||
| outputMetaInfoJSON.Get() << metaInfo.c_str(); | ||
| return EXIT_SUCCESS; | ||
| } | ||
| catch (int e) | ||
| { | ||
| std::cerr << "Fatal error encountered." << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| return EXIT_FAILURE; | ||
| } | ||
|
|
||
| int main(int argc, char * argv[]) | ||
| { | ||
| itk::wasm::Pipeline pipeline("read-overlapping-segmentation", "Read DICOM segmentation objects", argc, argv); | ||
|
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| std::string dicomFileName; | ||
| pipeline.add_option("dicom-file", dicomFileName, "Input DICOM file")->required()->check(CLI::ExistingFile)->type_name("INPUT_BINARY_FILE"); | ||
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| itk::wasm::OutputImage<VectorImageType> outputImage; | ||
| pipeline.add_option("seg-image", outputImage, "dicom segmentation object as an image")->required()->type_name("OUTPUT_IMAGE"); | ||
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| itk::wasm::OutputTextStream outputMetaInfoJSON; | ||
| pipeline.add_option("meta-info", outputMetaInfoJSON, "Output overlay information")->type_name("OUTPUT_JSON"); | ||
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| bool mergeSegments{false}; | ||
| pipeline.add_flag("--merge-segments", mergeSegments, "Merge segments into a single image"); | ||
|
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| ITK_WASM_PARSE(pipeline); | ||
|
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| // Pipeline code goes here | ||
| runPipeline(pipeline, dicomFileName, outputImage, outputMetaInfoJSON, mergeSegments); | ||
|
|
||
| return EXIT_SUCCESS; | ||
| } | ||
|
|
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