fix: 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases (#862)
* fix: 🐛 Local file: failing when retrieving segmentation data Fix segmentation data retrieval issues for local file. Changed from fecthing to use cornerstone loadAndCache method BREAKING CHANGE: DICOM Seg Closes: part of #838 * Switch SEG retrieval to WADO-RS * Forgot a debugger * refactor: 💡 Code refactor. Minor changes into methods * fix: 🐛 Load local files: PDF Items: 1. FileLoaderService: used for serveral operations on local files(load it, get list of studies, group them, accepting dicom and pdf) 2. DicomLoaderService: used for loading dicom based on dataset and studies. Depending on type of dicom loader might change. WIP 3. Refactor PDF and handleSegmentationStorage to use DicomLoaderService * fix: 🐛 Code review * fix: 🐛 Code review. Changed:Folder organization and dicom file Move fileLoaderService and others to a specific folder. When loading dicom file change to only retrieve the file(not use cornerstone to cache or anything else). * fix: 🐛 Code review. Move dicomLoaderService to core Moved dicomLoaderService to ohif/core and localFileLoaders to a specific folder. * fix: 🐛 Code review Simplified method to get study for dicom file. Added error handling on file loading. DicomLoaderService to be exposed on ohif/core/utils instead. * fix: 🐛 Reduce local load to one method only Reduced local file load to one method only * fix: 🐛 HTML to use dicomLoaderService. Prefer wadors than (uri) * fix: 🐛 Code implementation for multiframe files * fix: 🐛 Code review. Default local loader to dicom Closes: 838 * fix: 🐛 Code review. Use relative path to require DICOMWeb Closes: 838 * fix: 🐛 Code review. Fix unit test. Added DicomLoaderService mod Closes: 838 * fix: 🐛 Code review. Add 'Seg' on left thumb When getting/creating dataset get modality for file/image read Closes: 838
This commit is contained in:
ladeirarodolfo authored and Erik Ziegler committed
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@@ -79,6 +79,9 @@ class ViewerLocalFileData extends Component {
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studyMetadata.createDisplaySets(sopClassHandlerModules);
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studyMetadata.setDisplaySets(study.displaySets);
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studyMetadata.forEachDisplaySet(displayset => {
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displayset.localFile = true;
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});
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// Updates WADO-RS metaDataManager
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updateMetaDataManager(study);
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@@ -1,160 +1,26 @@
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import cornerstone from 'cornerstone-core';
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import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
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import * as dcmjs from 'dcmjs';
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import FileLoaderService from './localFileLoaders/fileLoaderService';
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function datasetsToStudies(datasets) {
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const StudyInstanceUIDs = new Set();
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datasets.forEach(ds => {
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StudyInstanceUIDs.add(ds.StudyInstanceUID);
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});
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const processFile = async file => {
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try {
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const fileLoaderService = new FileLoaderService(file);
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const imageId = fileLoaderService.addFile(file);
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const image = await fileLoaderService.loadFile(file, imageId);
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const dataset = await fileLoaderService.getDataset(image, imageId);
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const studies = await fileLoaderService.getStudies(dataset, imageId);
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const studies = [];
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Array.from(StudyInstanceUIDs).forEach(studyInstanceUid => {
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const studyDatasets = datasets.filter(
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ds => ds.StudyInstanceUID === studyInstanceUid
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return studies;
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} catch (error) {
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console.log(
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error.name,
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':Error when trying to load and process local files:',
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error.message
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);
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const firstDataset = studyDatasets[0];
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const study = {
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studyInstanceUid: firstDataset.StudyInstanceUID,
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studyDate: firstDataset.StudyDate,
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studyTime: firstDataset.StudyTime,
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accessionNumber: firstDataset.AccessionNumber,
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referringPhysicianName: firstDataset.ReferringPhysicianName,
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patientName: firstDataset.PatientName,
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patientId: firstDataset.PatientID,
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patientBirthdate: firstDataset.PatientBirthDate,
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patientSex: firstDataset.PatientSex,
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studyId: firstDataset.StudyID,
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studyDescription: firstDataset.StudyDescription,
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//numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
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//numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
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// modality: DICOMWeb.getString(study['00080060']),
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// modalitiesInStudy: DICOMWeb.getString(study['00080061']),
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//modalities:
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seriesList: [],
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};
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const SeriesInstanceUIDs = new Set();
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studyDatasets.forEach(ds => {
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SeriesInstanceUIDs.add(ds.SeriesInstanceUID);
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});
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Array.from(SeriesInstanceUIDs).forEach(seriesInstanceUid => {
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const seriesDatasets = studyDatasets.filter(
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ds => ds.SeriesInstanceUID === seriesInstanceUid
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);
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const SOPInstanceUIDs = new Set();
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seriesDatasets.forEach(ds => {
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SOPInstanceUIDs.add(ds.SOPInstanceUID);
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study.seriesList.push({
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seriesInstanceUid: ds.SeriesInstanceUID,
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seriesDescription: ds.SeriesDescription,
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seriesNumber: ds.SeriesNumber,
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instances: [],
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});
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});
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Array.from(SOPInstanceUIDs).forEach(sopInstanceUid => {
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const instance = seriesDatasets.find(
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a => a.SOPInstanceUID === sopInstanceUid
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);
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const series = study.seriesList.find(
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a => a.seriesInstanceUid === seriesInstanceUid
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);
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series.instances.push({
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sopInstanceUid: instance.SOPInstanceUID,
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sopClassUid: instance.SOPClassUID,
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rows: instance.Rows,
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columns: instance.Columns,
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numberOfFrames: instance.NumberOfFrames,
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instanceNumber: instance.InstanceNumber,
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getImageId: () => instance.imageId, // TODO: Change getImageId to check for instance.imageId property first.
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/*imageType: DICOMWeb.getString(instance['00080008']),
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modality: DICOMWeb.getString(instance['00080060']),
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instanceNumber: DICOMWeb.getNumber(instance['00200013']),
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imagePositionPatient: DICOMWeb.getString(instance['00200032']),
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imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
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frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
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sliceLocation: DICOMWeb.getNumber(instance['00201041']),
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samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
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photometricInterpretation: DICOMWeb.getString(instance['00280004']),
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planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
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pixelSpacing: DICOMWeb.getString(instance['00280030']),
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pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
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bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
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bitsStored: DICOMWeb.getNumber(instance['00280101']),
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highBit: DICOMWeb.getNumber(instance['00280102']),
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pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
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smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
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largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
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windowCenter: DICOMWeb.getString(instance['00281050']),
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windowWidth: DICOMWeb.getString(instance['00281051']),
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rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
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rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
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rescaleType: DICOMWeb.getNumber(instance['00281054']),
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sourceImageInstanceUid: getSourceImageInstanceUid(instance),
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laterality: DICOMWeb.getString(instance['00200062']),
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viewPosition: DICOMWeb.getString(instance['00185101']),
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acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
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frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
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frameTime: DICOMWeb.getNumber(instance['00181063']),
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frameTimeVector: parseFloatArray(
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DICOMWeb.getString(instance['00181065'])
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),
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sliceThickness: DICOMWeb.getNumber(instance['00180050']),
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spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
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lossyImageCompression: DICOMWeb.getString(instance['00282110']),
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derivationDescription: DICOMWeb.getString(instance['00282111']),
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lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
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lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
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echoNumber: DICOMWeb.getString(instance['00180086']),
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contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
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radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
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wadouri: WADOProxy.convertURL(wadouri, server),
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wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
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});
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});
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});
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studies.push(study);
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});
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console.warn(studies);
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return studies;
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}
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}
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};
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export default async function filesToStudies(files) {
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const imagePromises = files.map(file => {
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const imageId = cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
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return cornerstone
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.loadAndCacheImage(imageId)
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.catch(error => console.warn(error));
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});
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const processFilesPromises = files.map(processFile);
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const studies = await Promise.all(processFilesPromises);
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const images = await Promise.all(imagePromises);
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const datasets = [];
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images.forEach(image => {
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if (!image || !image.data) {
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return;
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}
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const arrayBuffer = image.data.byteArray.buffer;
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const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
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const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
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dicomData.dict
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);
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dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
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dicomData.meta
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);
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dataset.imageId = image.imageId;
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datasets.push(dataset);
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});
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return datasetsToStudies(datasets);
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return FileLoaderService.groupSeries(studies.flat());
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}
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@@ -0,0 +1,192 @@
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import * as dcmjs from 'dcmjs';
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import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
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import FileLoader from './fileLoader';
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const DICOMFileLoader = new (class extends FileLoader {
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fileType = 'application/dicom';
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loadFile(file, imageId) {
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return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
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}
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getDataset(image, imageId) {
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let dataset = {};
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try {
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const dicomData = dcmjs.data.DicomMessage.readFile(image);
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dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
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dicomData.dict
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);
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dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
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dicomData.meta
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);
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} catch (e) {
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console.log('Error on getting dicom file dataset. It defaults to empty');
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}
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// Set imageId on dataset to be consumed later on
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dataset.imageId = imageId;
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return dataset;
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}
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getStudies(dataset, imageId) {
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return this.getStudyFromDataset(dataset);
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}
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getStudyFromDataset(dataset = {}) {
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const {
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StudyInstanceUID,
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StudyDate,
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StudyTime,
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AccessionNumber,
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ReferringPhysicianName,
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PatientName,
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PatientID,
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PatientBirthDate,
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PatientSex,
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StudyID,
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StudyDescription,
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/*
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NumberOfStudyRelatedSeries,
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NumberOfStudyRelatedInstances,
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Modality,
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ModalitiesInStudy,
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*/
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SeriesInstanceUID,
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SeriesDescription,
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SeriesNumber,
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SOPInstanceUID,
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SOPClassUID,
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Rows,
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Columns,
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NumberOfFrames,
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InstanceNumber,
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imageId,
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Modality,
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/*ImageType,
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InstanceNumber,
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ImagePositionPatient,
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ImageOrientationPatient,
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FrameOfReferenceUID,
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SliceLocation,
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SamplesPerPixel,
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PhotometricInterpretation,
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PlanarConfiguration,
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PixelSpacing,
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PixelAspectRatio,
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BitsAllocated,
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BitsStored,
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HighBit,
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PixelRepresentation,
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SmallestPixelValue,
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LargestPixelValue,
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WindowCenter,
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WindowWidth,
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RescaleIntercept,
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RescaleSlope,
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RescaleType,
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Laterality,
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ViewPosition,
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AcquisitionDateTime,
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FrameIncrementPointer,
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FrameTime,
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FrameTimeVector,
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SliceThickness,
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SpacingBetweenSlices,
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LossyImageCompression,
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DerivationDescription,
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LossyImageCompressionRatio,
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LossyImageCompressionMethod,
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EchoNumber,
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ContrastBolusAgent,
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*/
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} = dataset;
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const instance = {
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sopInstanceUid: SOPInstanceUID,
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sopClassUid: SOPClassUID,
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rows: Rows,
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columns: Columns,
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numberOfFrames: NumberOfFrames,
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instanceNumber: InstanceNumber,
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url: imageId,
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modality: Modality,
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/*
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TODO: in case necessary to uncoment this block, double check every property
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imageType: ImageType || DICOMWeb.getString(dataset['00080008']),
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instanceNumber: InstanceNumber || DICOMWeb.getNumber(dataset['00200013']),
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imagePositionPatient: ImagePositionPatient || DICOMWeb.getString(dataset['00200032']),
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imageOrientationPatient: ImageOrientationPatient || DICOMWeb.getString(dataset['00200037']),
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frameOfReferenceUID: FrameOfReferenceUID || DICOMWeb.getString(dataset['00200052']),
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sliceLocation: SliceLocation || DICOMWeb.getNumber(dataset['00201041']),
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samplesPerPixel: SamplesPerPixel || DICOMWeb.getNumber(dataset['00280002']),
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photometricInterpretation: PhotometricInterpretation || DICOMWeb.getString(dataset['00280004']),
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planarConfiguration: PlanarConfiguration || DICOMWeb.getNumber(dataset['00280006']),
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pixelSpacing: PixelSpacing || DICOMWeb.getString(dataset['00280030']),
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pixelAspectRatio: PixelAspectRatio || DICOMWeb.getString(dataset['00280034']),
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bitsAllocated: BitsAllocated || DICOMWeb.getNumber(dataset['00280100']),
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bitsStored: BitsStored || DICOMWeb.getNumber(dataset['00280101']),
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highBit: HighBit || DICOMWeb.getNumber(dataset['00280102']),
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pixelRepresentation: PixelRepresentation || DICOMWeb.getNumber(dataset['00280103']),
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smallestPixelValue: SmallestPixelValue || DICOMWeb.getNumber(dataset['00280106']),
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largestPixelValue: LargestPixelValue || DICOMWeb.getNumber(dataset['00280107']),
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windowCenter: WindowCenter || DICOMWeb.getString(dataset['00281050']),
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windowWidth: WindowWidth || DICOMWeb.getString(dataset['00281051']),
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rescaleIntercept: RescaleIntercept || DICOMWeb.getNumber(dataset['00281052']),
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rescaleSlope: RescaleSlope || DICOMWeb.getNumber(dataset['00281053']),
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rescaleType: RescaleType || DICOMWeb.getNumber(dataset['00281054']),
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sourceImageInstanceUid: getSourceImageInstanceUid(dataset),
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laterality: Laterality || DICOMWeb.getString(dataset['00200062']),
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viewPosition: ViewPosition || DICOMWeb.getString(dataset['00185101']),
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acquisitionDateTime: AcquisitionDateTime || DICOMWeb.getString(dataset['0008002A']),
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frameIncrementPointer: FrameIncrementPointer || getFrameIncrementPointer(dataset['00280009']),
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frameTime: FrameTime || DICOMWeb.getNumber(dataset['00181063']),
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frameTimeVector: FrameTimeVector || parseFloatArray(
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DICOMWeb.getString(dataset['00181065'])
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),
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sliceThickness: SliceThickness || DICOMWeb.getNumber(dataset['00180050']),
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spacingBetweenSlices: SpacingBetweenSlices || DICOMWeb.getString(dataset['00180088']),
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lossyImageCompression: LossyImageCompression || DICOMWeb.getString(dataset['00282110']),
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derivationDescription: DerivationDescription || DICOMWeb.getString(dataset['00282111']),
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lossyImageCompressionRatio: LossyImageCompressionRatio || DICOMWeb.getString(dataset['00282112']),
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lossyImageCompressionMethod: LossyImageCompressionMethod || DICOMWeb.getString(dataset['00282114']),
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echoNumber: EchoNumber || DICOMWeb.getString(dataset['00180086']),
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contrastBolusAgent: ContrastBolusAgent || DICOMWeb.getString(dataset['00180010']),
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radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(dataset),
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wadouri: WADOProxy.convertURL(wadouri, server),
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wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
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};
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const series = {
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seriesInstanceUid: SeriesInstanceUID,
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seriesDescription: SeriesDescription,
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seriesNumber: SeriesNumber,
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instances: [instance],
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};
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const study = {
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studyInstanceUid: StudyInstanceUID,
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studyDate: StudyDate,
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studyTime: StudyTime,
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accessionNumber: AccessionNumber,
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referringPhysicianName: ReferringPhysicianName,
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patientName: PatientName,
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patientId: PatientID,
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patientBirthdate: PatientBirthDate,
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patientSex: PatientSex,
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studyId: StudyID,
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studyDescription: StudyDescription,
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/*
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TODO: in case necessary to uncomment this block, double check every property
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numberOfStudyRelatedSeries: NumberOfStudyRelatedSeries || DICOMWeb.getString(dataset['00201206']),
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numberOfStudyRelatedInstances: NumberOfStudyRelatedInstances || DICOMWeb.getString(dataset['00201208']),
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modality: Modality || DICOMWeb.getString(dataset['00080060']),
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modalitiesInStudy: ModalitiesInStudy || DICOMWeb.getString(dataset['00080061']),
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modalities:
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*/
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seriesList: [series],
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};
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return study;
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||||
}
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||||
})();
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export default DICOMFileLoader;
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@@ -0,0 +1,6 @@
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export default class FileLoader {
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fileType;
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loadFile(file, imageId) { }
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getDataset(image, imageId) { }
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getStudies(dataset, imageId) { }
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}
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@@ -0,0 +1,82 @@
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import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
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import FileLoader from './fileLoader';
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import PDFFileLoader from './pdfFileLoader';
|
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import DICOMFileLoader from './dicomFileLoader';
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class FileLoaderService extends FileLoader {
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fileType;
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loader;
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constructor(file) {
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super();
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const fileType = file && file.type;
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this.loader = this.getLoader(fileType);
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this.fileType = this.loader.fileType;
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}
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static groupSeries(studies) {
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const groupBy = (list, groupByKey, listKey) => {
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let nonKeyCounter = 1;
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return list.reduce((acc, obj) => {
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let key = obj[groupByKey];
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const list = obj[listKey];
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||||
|
||||
// in case key not found, group it using counter
|
||||
key = !!key ? key : '' + nonKeyCounter++;
|
||||
|
||||
if (!acc[key]) {
|
||||
acc[key] = { ...obj };
|
||||
acc[key][listKey] = [];
|
||||
}
|
||||
|
||||
acc[key][listKey].push(...list);
|
||||
|
||||
return acc;
|
||||
}, {});
|
||||
};
|
||||
|
||||
const studiesGrouped = Object.values(
|
||||
groupBy(studies, 'studyInstanceUid', 'seriesList')
|
||||
);
|
||||
|
||||
const result = studiesGrouped.map(studyGroup => {
|
||||
const seriesGrouped = groupBy(
|
||||
studyGroup.seriesList,
|
||||
'seriesInstanceUid',
|
||||
'instances'
|
||||
);
|
||||
studyGroup.seriesList = Object.values(seriesGrouped);
|
||||
|
||||
return studyGroup;
|
||||
});
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
addFile(file) {
|
||||
return cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
|
||||
}
|
||||
|
||||
loadFile(file, imageId) {
|
||||
return this.loader.loadFile(file, imageId);
|
||||
}
|
||||
|
||||
getDataset(image, imageId) {
|
||||
return this.loader.getDataset(image, imageId);
|
||||
}
|
||||
|
||||
getStudies(dataset, imageId) {
|
||||
return this.loader.getStudies(dataset, imageId);
|
||||
}
|
||||
|
||||
getLoader(fileType) {
|
||||
if (fileType === 'application/pdf') {
|
||||
return PDFFileLoader;
|
||||
} else {
|
||||
// Default to dicom loader
|
||||
return DICOMFileLoader;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
export default FileLoaderService;
|
||||
@@ -0,0 +1,58 @@
|
||||
import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
|
||||
import FileLoader from './fileLoader';
|
||||
|
||||
const PDFFileLoader = new (class extends FileLoader {
|
||||
fileType = 'application/pdf';
|
||||
loadFile(file, imageId) {
|
||||
return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
|
||||
}
|
||||
|
||||
getDataset(image, imageId) {
|
||||
const dataset = {};
|
||||
dataset.imageId = image.imageId || imageId;
|
||||
return dataset;
|
||||
}
|
||||
|
||||
getStudies(dataset, imageId) {
|
||||
return this.getDefaultStudy(imageId);
|
||||
}
|
||||
|
||||
getDefaultStudy(imageId) {
|
||||
const study = {
|
||||
studyInstanceUid: '',
|
||||
studyDate: '',
|
||||
studyTime: '',
|
||||
accessionNumber: '',
|
||||
referringPhysicianName: '',
|
||||
patientName: '',
|
||||
patientId: '',
|
||||
patientBirthdate: '',
|
||||
patientSex: '',
|
||||
studyId: '',
|
||||
studyDescription: '',
|
||||
seriesList: [
|
||||
{
|
||||
seriesInstanceUid: '',
|
||||
seriesDescription: '',
|
||||
seriesNumber: '',
|
||||
instances: [
|
||||
{
|
||||
sopInstanceUid: '',
|
||||
sopClassUid: '1.2.840.10008.5.1.4.1.1.104.1',
|
||||
rows: '',
|
||||
columns: '',
|
||||
numberOfFrames: 0,
|
||||
instanceNumber: 1,
|
||||
getImageId: () => imageId,
|
||||
isLocalFile: true,
|
||||
},
|
||||
],
|
||||
},
|
||||
],
|
||||
};
|
||||
|
||||
return study;
|
||||
}
|
||||
})();
|
||||
|
||||
export default PDFFileLoader;
|
||||
Reference in new issue
Block a user