Instance metadata/metadata providers overhaul (#1481)
* Instance metadata plus metadata provider overhaul. Fix consumption of wado-uri urls fallbacks + datatype agnosticism. WIP DICOMify things. fix various issues with naturalized variable naming migration. Remove metadata provider. Fix consumption of multiframe images and addition of CWIL metadata. Fix strange build issues. Fix CWIL style windowWidth to array from naturalized DICOM. Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs. Move color palette fetching down to the natuaralized JSON level. Remove unused StudyMetadataSummary Remove redundant dicom metadata dictionary. Working local + json routes. Fix SR read. Finished first round of testing + cleaned up debugging etc. * data => metadata for instance naturalizedJSON * Update dcmjs version * Correct github isssues. * Fix erroneously replaced files. * Danny's recommended changes. * Instance metadata plus metadata provider overhaul. Fix consumption of wado-uri urls fallbacks + datatype agnosticism. WIP DICOMify things. fix various issues with naturalized variable naming migration. Remove metadata provider. Fix consumption of multiframe images and addition of CWIL metadata. Fix strange build issues. Fix CWIL style windowWidth to array from naturalized DICOM. Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs. Move color palette fetching down to the natuaralized JSON level. Remove unused StudyMetadataSummary Remove redundant dicom metadata dictionary. Working local + json routes. Fix SR read. Finished first round of testing + cleaned up debugging etc. * data => metadata for instance naturalizedJSON * Update dcmjs version * Correct github isssues. * Fix erroneously replaced files. * Danny's recommended changes. * Update JSON CI * Update casing of import. * Fix jump for SR. * Fix unit tests for measurements service * Fix json CI test. * fix: update yarn lock * Fix local non-encapsulated pdf view * CI updated to new sucess message. Co-authored-by: Danny <danny.ri.brown@gmail.com>
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James PettsandDanny authored and GitHub committed
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@@ -1,412 +1,508 @@
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import { parsingUtils } from '../lib/parsingUtils';
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const FUNCTION = 'function';
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import * as dcmjs from 'dcmjs';
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import queryString from 'query-string';
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import dicomParser from 'dicom-parser';
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import { getFallbackTagFromInstance } from '../utils/metadataProvider/metadataProviderFallbackTags';
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import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
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import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
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class MetadataProvider {
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constructor() {
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// Define the main "metadataLookup" private property as an immutable property.
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Object.defineProperty(this, 'metadataLookup', {
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Object.defineProperty(this, 'studies', {
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configurable: false,
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enumerable: false,
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writable: false,
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value: new Map(),
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});
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// Local reference to provider function bound to current instance.
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Object.defineProperty(this, '_provider', {
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Object.defineProperty(this, 'imageIdToUIDs', {
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configurable: false,
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enumerable: false,
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writable: true,
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value: null,
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writable: false,
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value: new Map(),
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});
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}
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/**
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* Cornerstone Metadata provider to store image meta data
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* Data from instances, series, and studies are associated with
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* imageIds to facilitate usage of this information by Cornerstone's Tools
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*
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* e.g. the imagePlane metadata object contains instance information about
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* row/column pixel spacing, patient position, and patient orientation. It
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* is used in CornerstoneTools to position reference lines and orientation markers.
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*
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* @param {String} imageId The Cornerstone ImageId
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* @param {Object} data An object containing instance, series, and study metadata
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*/
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addMetadata(imageId, data) {
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const instanceMetadata = data.instance;
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const seriesMetadata = data.series;
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const studyMetadata = data.study;
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const numImages = data.numImages;
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const metadata = {};
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async addInstance(dicomJSONDatasetOrP10ArrayBuffer, options = {}) {
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let dicomJSONDataset;
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metadata.frameNumber = data.frameNumber;
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// If Arraybuffer, parse to DICOMJSON before naturalizing.
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if (dicomJSONDatasetOrP10ArrayBuffer instanceof ArrayBuffer) {
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const dicomData = DicomMessage.readFile(dicomJSONDatasetOrP10ArrayBuffer);
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metadata.study = {
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accessionNumber: studyMetadata.accessionNumber,
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patientId: studyMetadata.patientId,
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studyInstanceUid: studyMetadata.studyInstanceUid,
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studyDate: studyMetadata.studyDate,
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studyTime: studyMetadata.studyTime,
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studyDescription: studyMetadata.studyDescription,
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institutionName: studyMetadata.institutionName,
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patientHistory: studyMetadata.patientHistory,
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};
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metadata.series = {
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seriesDescription: seriesMetadata.seriesDescription,
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seriesNumber: seriesMetadata.seriesNumber,
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seriesDate: seriesMetadata.seriesDate,
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seriesTime: seriesMetadata.seriesTime,
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modality: seriesMetadata.modality,
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seriesInstanceUid: seriesMetadata.seriesInstanceUid,
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numImages: numImages,
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};
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metadata.instance = instanceMetadata;
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metadata.patient = {
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name: studyMetadata.patientName,
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id: studyMetadata.patientId,
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birthDate: studyMetadata.patientBirthDate,
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sex: studyMetadata.patientSex,
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age: studyMetadata.patientAge,
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};
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// If there is sufficient information, populate
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// the imagePlane object for easier use in the Viewer
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metadata.imagePlane = this.getImagePlane(instanceMetadata);
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// Add the metadata to the imageId lookup object
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this.metadataLookup.set(imageId, metadata);
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}
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/**
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* Return the metadata for the given imageId
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* @param {String} imageId The Cornerstone ImageId
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* @returns image metadata
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*/
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getMetadata(imageId) {
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return this.metadataLookup.get(imageId);
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}
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/**
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* Adds a set of metadata to the Cornerstone metadata provider given a specific
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* imageId, type, and dataset
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*
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* @param imageId
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* @param type (e.g. series, instance, tagDisplay)
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* @param data
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*/
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addSpecificMetadata(imageId, type, data) {
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const metadata = {};
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metadata[type] = data;
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const oldMetadata = this.metadataLookup.get(imageId);
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this.metadataLookup.set(imageId, Object.assign(oldMetadata, metadata));
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}
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getFromImage(image, type, tag, attrName, defaultValue) {
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let value;
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if (image.data) {
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value = this.getFromDataSet(image.data, type, tag);
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dicomJSONDataset = dicomData.dict;
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} else {
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value = image.instance[attrName];
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dicomJSONDataset = dicomJSONDatasetOrP10ArrayBuffer;
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}
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return value === null ? defaultValue : value;
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}
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// Check if dataset is already naturalized.
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getFromDataSet(dataSet, type, tag) {
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if (!dataSet) {
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return;
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}
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let naturalizedDataset;
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const fn = dataSet[type];
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if (!fn) {
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return;
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}
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return fn.call(dataSet, tag);
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}
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getFrameIncrementPointer(image) {
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const dataSet = image.data;
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let frameInstancePointer = '';
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if (parsingUtils.isValidDataSet(dataSet)) {
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const frameInstancePointerNames = {
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x00181063: 'frameTime',
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x00181065: 'frameTimeVector',
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};
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// (0028,0009) = Frame Increment Pointer
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const frameInstancePointerTag = parsingUtils.attributeTag(
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dataSet,
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'x00280009'
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if (dicomJSONDataset['SeriesInstanceUID'] === undefined) {
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naturalizedDataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
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dicomJSONDataset
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);
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frameInstancePointer = frameInstancePointerNames[frameInstancePointerTag];
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} else {
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frameInstancePointer = image.instance.frameIncrementPointer;
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naturalizedDataset = dicomJSONDataset;
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}
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return frameInstancePointer || '';
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}
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const {
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StudyInstanceUID,
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SeriesInstanceUID,
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SOPInstanceUID,
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} = naturalizedDataset;
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getFrameTimeVector(image) {
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const dataSet = image.data;
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const study = this._getAndCacheStudy(StudyInstanceUID);
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const series = this._getAndCacheSeriesFromStudy(study, SeriesInstanceUID);
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const instance = this._getAndCacheInstanceFromStudy(series, SOPInstanceUID);
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if (parsingUtils.isValidDataSet(dataSet)) {
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// Frame Increment Pointer points to Frame Time Vector (0018,1065) field
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return parsingUtils.floatArray(dataSet, 'x00181065');
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Object.assign(instance, naturalizedDataset);
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if (options.server) {
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await this._checkBulkDataAndInlineBinaries(instance, options.server);
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}
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return image.instance.frameTimeVector;
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return instance;
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}
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getFrameTime(image) {
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const dataSet = image.data;
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addImageIdToUIDs(imageId, uids) {
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// This method is a fallback for when you don't have WADO-URI or WADO-RS.
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// You can add instances fetched by any method by calling addInstance, and hook an imageId to point at it here.
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// An example would be dicom hosted at some random site.
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if (parsingUtils.isValidDataSet(dataSet)) {
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// Frame Increment Pointer points to Frame Time (0018,1063) field or is not defined (for addtional flexibility).
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// Yet another value is possible for this field (5200,9230 for Multi-frame Functional Groups)
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// but that case is currently not supported.
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return dataSet.floatString('x00181063', -1);
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this.imageIdToUIDs.set(imageId, uids);
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}
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_getAndCacheStudy(StudyInstanceUID) {
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const studies = this.studies;
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let study = studies.get(StudyInstanceUID);
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if (!study) {
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study = { series: new Map() };
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studies.set(StudyInstanceUID, study);
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}
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return image.instance.frameTime;
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return study;
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}
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_getAndCacheSeriesFromStudy(study, SeriesInstanceUID) {
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let series = study.series.get(SeriesInstanceUID);
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if (!series) {
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series = { instances: new Map() };
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study.series.set(SeriesInstanceUID, series);
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}
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return series;
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}
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/**
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* Updates the related metadata for missing fields given a specified image
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*
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* @param image
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*/
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updateMetadata(image) {
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const imageMetadata = this.metadataLookup.get(image.imageId);
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if (!imageMetadata) {
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_getAndCacheInstanceFromStudy(series, SOPInstanceUID) {
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let instance = series.instances.get(SOPInstanceUID);
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if (!instance) {
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instance = {};
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series.instances.set(SOPInstanceUID, instance);
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}
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return instance;
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}
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async _checkBulkDataAndInlineBinaries(instance, server) {
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await fetchOverlayData(instance, server);
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if (instance.PhotometricInterpretation === 'PALETTE COLOR') {
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await fetchPaletteColorLookupTableData(instance, server);
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}
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}
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_getInstance(imageId) {
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const uids = this._getUIDsFromImageID(imageId);
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if (!uids) {
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return;
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}
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imageMetadata.patient.age =
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imageMetadata.patient.age ||
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this.getFromDataSet(image.data, 'string', 'x00101010');
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const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = uids;
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imageMetadata.instance.rows = imageMetadata.instance.rows || image.rows;
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imageMetadata.instance.columns =
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imageMetadata.instance.columns || image.columns;
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imageMetadata.instance.sopClassUid =
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imageMetadata.instance.sopClassUid ||
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this.getFromDataSet(image.data, 'string', 'x00080016');
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imageMetadata.instance.sopInstanceUid =
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imageMetadata.instance.sopInstanceUid ||
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this.getFromDataSet(image.data, 'string', 'x00080018');
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imageMetadata.instance.pixelSpacing =
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imageMetadata.instance.pixelSpacing ||
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this.getFromDataSet(image.data, 'string', 'x00280030');
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imageMetadata.instance.frameOfReferenceUID =
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imageMetadata.instance.frameOfReferenceUID ||
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this.getFromDataSet(image.data, 'string', 'x00200052');
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imageMetadata.instance.imageOrientationPatient =
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imageMetadata.instance.imageOrientationPatient ||
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this.getFromDataSet(image.data, 'string', 'x00200037');
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imageMetadata.instance.imagePositionPatient =
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imageMetadata.instance.imagePositionPatient ||
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this.getFromDataSet(image.data, 'string', 'x00200032');
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imageMetadata.instance.sliceThickness =
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imageMetadata.instance.sliceThickness ||
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this.getFromDataSet(image.data, 'string', 'x00180050');
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imageMetadata.instance.sliceLocation =
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imageMetadata.instance.sliceLocation ||
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this.getFromDataSet(image.data, 'string', 'x00201041');
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imageMetadata.instance.tablePosition =
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imageMetadata.instance.tablePosition ||
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this.getFromDataSet(image.data, 'string', 'x00189327');
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imageMetadata.instance.spacingBetweenSlices =
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imageMetadata.instance.spacingBetweenSlices ||
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this.getFromDataSet(image.data, 'string', 'x00180088');
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imageMetadata.instance.lossyImageCompression =
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imageMetadata.instance.lossyImageCompression ||
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this.getFromDataSet(image.data, 'string', 'x00282110');
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imageMetadata.instance.lossyImageCompressionRatio =
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imageMetadata.instance.lossyImageCompressionRatio ||
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this.getFromDataSet(image.data, 'string', 'x00282112');
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imageMetadata.instance.frameIncrementPointer =
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imageMetadata.instance.frameIncrementPointer ||
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this.getFromDataSet(image.data, 'string', 'x00280009');
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imageMetadata.instance.frameTime =
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imageMetadata.instance.frameTime ||
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this.getFromDataSet(image.data, 'string', 'x00181063');
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imageMetadata.instance.frameTimeVector =
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imageMetadata.instance.frameTimeVector ||
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this.getFromDataSet(image.data, 'string', 'x00181065');
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if (
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(image.data || image.instance) &&
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!imageMetadata.instance.multiframeMetadata
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) {
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imageMetadata.instance.multiframeMetadata = this.getMultiframeModuleMetadata(
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image
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);
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}
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imageMetadata.imagePlane =
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imageMetadata.imagePlane || this.getImagePlane(imageMetadata.instance);
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}
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/**
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* Constructs and returns the imagePlane given the metadata instance
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*
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* @param metadataInstance The metadata instance (InstanceMetadata class) containing information to construct imagePlane
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* @returns imagePlane The constructed imagePlane to be used in viewer easily
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*/
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getImagePlane(instance) {
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if (
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!instance.rows ||
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!instance.columns ||
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!instance.pixelSpacing ||
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!instance.frameOfReferenceUID ||
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!instance.imageOrientationPatient ||
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!instance.imagePositionPatient
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) {
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return;
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}
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const imageOrientation = instance.imageOrientationPatient.split('\\');
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const imagePosition = instance.imagePositionPatient.split('\\');
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let columnPixelSpacing = 1.0;
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let rowPixelSpacing = 1.0;
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if (instance.pixelSpacing) {
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const split = instance.pixelSpacing.split('\\');
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rowPixelSpacing = parseFloat(split[0]);
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columnPixelSpacing = parseFloat(split[1]);
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}
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return {
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frameOfReferenceUID: instance.frameOfReferenceUID,
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rows: instance.rows,
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columns: instance.columns,
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rowCosines: [
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parseFloat(imageOrientation[0]),
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parseFloat(imageOrientation[1]),
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parseFloat(imageOrientation[2]),
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],
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columnCosines: [
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parseFloat(imageOrientation[3]),
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parseFloat(imageOrientation[4]),
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parseFloat(imageOrientation[5]),
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],
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imagePositionPatient: [
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parseFloat(imagePosition[0]),
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parseFloat(imagePosition[1]),
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parseFloat(imagePosition[2]),
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],
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rowPixelSpacing,
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columnPixelSpacing,
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};
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}
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/**
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* This function extracts miltiframe information from a dicomParser.DataSet object.
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*
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* @param dataSet {Object} An instance of dicomParser.DataSet object where multiframe information can be found.
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* @return {Object} An object containing multiframe image metadata (frameIncrementPointer, frameTime, frameTimeVector, etc).
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*/
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getMultiframeModuleMetadata(image) {
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const imageInfo = {
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isMultiframeImage: false,
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frameIncrementPointer: null,
|
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numberOfFrames: 0,
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||||
frameTime: 0,
|
||||
frameTimeVector: null,
|
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averageFrameRate: 0, // backwards compatibility only... it might be useless in the future
|
||||
};
|
||||
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let frameTime;
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||||
|
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const numberOfFrames = this.getFromImage(
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image,
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||||
'intString',
|
||||
'x00280008',
|
||||
'numberOfFrames',
|
||||
-1
|
||||
return this._getInstanceData(
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StudyInstanceUID,
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SeriesInstanceUID,
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||||
SOPInstanceUID
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||||
);
|
||||
}
|
||||
|
||||
if (numberOfFrames > 0) {
|
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// set multi-frame image indicator
|
||||
imageInfo.isMultiframeImage = true;
|
||||
imageInfo.numberOfFrames = numberOfFrames;
|
||||
get(query, imageId, options = { fallback: false }) {
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const instance = this._getInstance(imageId);
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||||
|
||||
// (0028,0009) = Frame Increment Pointer
|
||||
const frameIncrementPointer = this.getFrameIncrementPointer(image);
|
||||
if (query === INSTANCE) {
|
||||
return instance;
|
||||
}
|
||||
|
||||
if (frameIncrementPointer === 'frameTimeVector') {
|
||||
// Frame Increment Pointer points to Frame Time Vector (0018,1065) field
|
||||
const frameTimeVector = this.getFrameTimeVector(image);
|
||||
return this.getTagFromInstance(query, instance, options);
|
||||
}
|
||||
|
||||
if (frameTimeVector instanceof Array && frameTimeVector.length > 0) {
|
||||
imageInfo.frameIncrementPointer = frameIncrementPointer;
|
||||
imageInfo.frameTimeVector = frameTimeVector;
|
||||
frameTime =
|
||||
frameTimeVector.reduce((a, b) => a + b) / frameTimeVector.length;
|
||||
imageInfo.averageFrameRate = 1000 / frameTime;
|
||||
}
|
||||
} else if (
|
||||
frameIncrementPointer === 'frameTime' ||
|
||||
frameIncrementPointer === ''
|
||||
) {
|
||||
frameTime = this.getFrameTime(image);
|
||||
getTag(query, imageId, options) {
|
||||
return this.get(query, imageId, options);
|
||||
}
|
||||
|
||||
if (frameTime > 0) {
|
||||
imageInfo.frameIncrementPointer = frameIncrementPointer;
|
||||
imageInfo.frameTime = frameTime;
|
||||
imageInfo.averageFrameRate = 1000 / frameTime;
|
||||
}
|
||||
getInstance(imageId) {
|
||||
return this.get(INSTANCE, imageId);
|
||||
}
|
||||
|
||||
getTagFromInstance(
|
||||
naturalizedTagOrWADOImageLoaderTag,
|
||||
instance,
|
||||
options = { fallback: false }
|
||||
) {
|
||||
if (!instance) {
|
||||
return;
|
||||
}
|
||||
|
||||
// If its a naturalized dcmjs tag present on the instance, return.
|
||||
if (instance[naturalizedTagOrWADOImageLoaderTag]) {
|
||||
return instance[naturalizedTagOrWADOImageLoaderTag];
|
||||
}
|
||||
|
||||
if (options.fallback) {
|
||||
// Perhaps the tag has fallbacks?
|
||||
const fallbackTag = getFallbackTagFromInstance(
|
||||
naturalizedTagOrWADOImageLoaderTag,
|
||||
instance
|
||||
);
|
||||
|
||||
if (fallbackTag) {
|
||||
return fallbackTag;
|
||||
}
|
||||
}
|
||||
|
||||
return imageInfo;
|
||||
// Maybe its a legacy CornerstoneWADOImageLoader tag then:
|
||||
return this._getCornerstoneWADOImageLoaderTag(
|
||||
naturalizedTagOrWADOImageLoaderTag,
|
||||
instance
|
||||
);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a bound reference to the provider function.
|
||||
*/
|
||||
getProvider() {
|
||||
let provider = this._provider;
|
||||
if (typeof this._provider !== FUNCTION) {
|
||||
provider = this.provider.bind(this);
|
||||
this._provider = provider;
|
||||
_getCornerstoneWADOImageLoaderTag(wadoImageLoaderTag, instance) {
|
||||
let metadata;
|
||||
|
||||
switch (wadoImageLoaderTag) {
|
||||
case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
|
||||
const { SeriesDate, SeriesTime } = instance;
|
||||
|
||||
let seriesDate;
|
||||
let seriesTime;
|
||||
|
||||
if (SeriesDate) {
|
||||
seriesDate = dicomParser.parseDA(SeriesDate);
|
||||
}
|
||||
|
||||
if (SeriesTime) {
|
||||
seriesTime = dicomParser.parseTM(SeriesTime);
|
||||
}
|
||||
|
||||
metadata = {
|
||||
modality: instance.Modality,
|
||||
seriesInstanceUID: instance.SeriesInstanceUID,
|
||||
seriesNumber: instance.SeriesNumber,
|
||||
studyInstanceUID: instance.StudyInstanceUID,
|
||||
seriesDate,
|
||||
seriesTime,
|
||||
};
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.PATIENT_STUDY_MODULE:
|
||||
metadata = {
|
||||
patientAge: instance.PatientAge,
|
||||
patientSize: instance.PatientSize,
|
||||
patientWeight: instance.PatientWeight,
|
||||
};
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.IMAGE_PLANE_MODULE:
|
||||
const { ImageOrientationPatient } = instance;
|
||||
|
||||
// Fallback for DX images.
|
||||
const PixelSpacing = getFallbackTagFromInstance(
|
||||
'PixelSpacing',
|
||||
instance
|
||||
);
|
||||
|
||||
let rowPixelSpacing;
|
||||
let columnPixelSpacing;
|
||||
|
||||
let rowCosines;
|
||||
let columnCosines;
|
||||
|
||||
if (PixelSpacing) {
|
||||
rowPixelSpacing = PixelSpacing[0];
|
||||
columnPixelSpacing = PixelSpacing[1];
|
||||
}
|
||||
|
||||
if (ImageOrientationPatient) {
|
||||
rowCosines = ImageOrientationPatient.slice(0, 3);
|
||||
columnCosines = ImageOrientationPatient.slice(3, 6);
|
||||
}
|
||||
|
||||
metadata = {
|
||||
frameOfReferenceUID: instance.FrameOfReferenceUID,
|
||||
rows: instance.Rows,
|
||||
columns: instance.Columns,
|
||||
imageOrientationPatient: ImageOrientationPatient,
|
||||
rowCosines,
|
||||
columnCosines,
|
||||
imagePositionPatient: instance.ImagePositionPatient,
|
||||
sliceThickness: instance.SliceThickness,
|
||||
sliceLocation: instance.SliceLocation,
|
||||
pixelSpacing: PixelSpacing,
|
||||
rowPixelSpacing,
|
||||
columnPixelSpacing,
|
||||
};
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.IMAGE_PIXEL_MODULE:
|
||||
metadata = {
|
||||
samplesPerPixel: instance.SamplesPerPixel,
|
||||
photometricInterpretation: instance.PhotometricInterpretation,
|
||||
rows: instance.Rows,
|
||||
columns: instance.Columns,
|
||||
bitsAllocated: instance.BitsAllocated,
|
||||
bitsStored: instance.BitsStored,
|
||||
highBit: instance.HighBit,
|
||||
pixelRepresentation: instance.PixelRepresentation,
|
||||
planarConfiguration: instance.PlanarConfiguration,
|
||||
pixelAspectRatio: instance.PixelAspectRatio,
|
||||
smallestPixelValue: instance.SmallestPixelValue,
|
||||
largestPixelValue: instance.LargestPixelValue,
|
||||
redPaletteColorLookupTableDescriptor:
|
||||
instance.RedPaletteColorLookupTableDescriptor,
|
||||
greenPaletteColorLookupTableDescriptor:
|
||||
instance.GreenPaletteColorLookupTableDescriptor,
|
||||
bluePaletteColorLookupTableDescriptor:
|
||||
instance.BluePaletteColorLookupTableDescriptor,
|
||||
redPaletteColorLookupTableData:
|
||||
instance.RedPaletteColorLookupTableData,
|
||||
greenPaletteColorLookupTableData:
|
||||
instance.GreenPaletteColorLookupTableData,
|
||||
bluePaletteColorLookupTableData:
|
||||
instance.BluePaletteColorLookupTableData,
|
||||
};
|
||||
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.VOI_LUT_MODULE:
|
||||
const { WindowCenter, WindowWidth } = instance;
|
||||
|
||||
const windowCenter = Array.isArray(WindowCenter)
|
||||
? WindowCenter
|
||||
: [WindowCenter];
|
||||
const windowWidth = Array.isArray(WindowWidth)
|
||||
? WindowWidth
|
||||
: [WindowWidth];
|
||||
|
||||
metadata = {
|
||||
windowCenter,
|
||||
windowWidth,
|
||||
};
|
||||
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.MODALITY_LUT_MODULE:
|
||||
metadata = {
|
||||
rescaleIntercept: instance.RescaleIntercept,
|
||||
rescaleSlope: instance.RescaleSlope,
|
||||
rescaleType: instance.RescaleType,
|
||||
};
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.SOP_COMMON_MODULE:
|
||||
metadata = {
|
||||
sopClassUID: instance.SOPClassUID,
|
||||
sopInstanceUID: instance.SOPInstanceUID,
|
||||
};
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.PET_ISOTOPE_MODULE:
|
||||
const { RadiopharmaceuticalInformationSequence } = instance;
|
||||
|
||||
if (RadiopharmaceuticalInformationSequence) {
|
||||
const RadiopharmaceuticalInformation = Array.isArray(
|
||||
RadiopharmaceuticalInformationSequence
|
||||
)
|
||||
? RadiopharmaceuticalInformationSequence[0]
|
||||
: RadiopharmaceuticalInformationSequence;
|
||||
|
||||
const {
|
||||
RadiopharmaceuticalStartTime,
|
||||
RadionuclideTotalDose,
|
||||
RadionuclideHalfLife,
|
||||
} = RadiopharmaceuticalInformation;
|
||||
|
||||
const radiopharmaceuticalInfo = {
|
||||
radiopharmaceuticalStartTime: dicomParser.parseTM(
|
||||
RadiopharmaceuticalStartTime
|
||||
),
|
||||
radionuclideTotalDose: RadionuclideTotalDose,
|
||||
radionuclideHalfLife: RadionuclideHalfLife,
|
||||
};
|
||||
metadata = {
|
||||
radiopharmaceuticalInfo,
|
||||
};
|
||||
}
|
||||
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.OVERLAY_PLANE_MODULE:
|
||||
metadata = [];
|
||||
|
||||
for (
|
||||
let overlayGroup = 0x00;
|
||||
overlayGroup <= 0x1e;
|
||||
overlayGroup += 0x02
|
||||
) {
|
||||
let groupStr = `60${overlayGroup.toString(16)}`;
|
||||
|
||||
if (groupStr.length === 3) {
|
||||
groupStr = `600${overlayGroup.toString(16)}`;
|
||||
}
|
||||
|
||||
const OverlayDataTag = `${groupStr}3000`;
|
||||
const OverlayData = instance[OverlayDataTag];
|
||||
|
||||
if (!OverlayData) {
|
||||
continue;
|
||||
}
|
||||
|
||||
const OverlayRowsTag = `${groupStr}0010`;
|
||||
const OverlayColumnsTag = `${groupStr}0011`;
|
||||
const OverlayType = `${groupStr}0040`;
|
||||
const OverlayOriginTag = `${groupStr}0050`;
|
||||
const OverlayDescriptionTag = `${groupStr}0022`;
|
||||
const OverlayLabelTag = `${groupStr}1500`;
|
||||
const ROIAreaTag = `${groupStr}1301`;
|
||||
const ROIMeanTag = `${groupStr}1302`;
|
||||
const ROIStandardDeviationTag = `${groupStr}1303`;
|
||||
const OverlayOrigin = instance[OverlayOriginTag];
|
||||
|
||||
const overlay = {
|
||||
rows: instance[OverlayRowsTag],
|
||||
columns: instance[OverlayColumnsTag],
|
||||
type: instance[OverlayType],
|
||||
x: OverlayOrigin[0],
|
||||
y: OverlayOrigin[1],
|
||||
pixelData: OverlayData,
|
||||
description: instance[OverlayDescriptionTag],
|
||||
label: instance[OverlayLabelTag],
|
||||
roiArea: instance[ROIAreaTag],
|
||||
roiMean: instance[ROIMeanTag],
|
||||
roiStandardDeviation: instance[ROIStandardDeviationTag],
|
||||
};
|
||||
|
||||
metadata.push(overlay);
|
||||
}
|
||||
|
||||
break;
|
||||
|
||||
case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:
|
||||
const { PatientName } = instance;
|
||||
|
||||
let patientName;
|
||||
if (PatientName) {
|
||||
patientName = PatientName.Alphabetic;
|
||||
}
|
||||
|
||||
metadata = {
|
||||
patientName,
|
||||
patientId: instance.PatientID,
|
||||
};
|
||||
|
||||
break;
|
||||
|
||||
case WADO_IMAGE_LOADER_TAGS.GENERAL_IMAGE_MODULE:
|
||||
metadata = {
|
||||
instanceNumber: instance.InstanceNumber,
|
||||
lossyImageCompression: instance.LossyImageCompression,
|
||||
lossyImageCompressionRatio: instance.LossyImageCompressionRatio,
|
||||
lossyImageCompressionMethod: instance.LossyImageCompressionMethod,
|
||||
};
|
||||
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.GENERAL_STUDY_MODULE:
|
||||
metadata = {
|
||||
studyDescription: instance.StudyDescription,
|
||||
studyDate: instance.StudyDate,
|
||||
studyTime: instance.StudyTime,
|
||||
accessionNumber: instance.AccessionNumber,
|
||||
};
|
||||
|
||||
break;
|
||||
case WADO_IMAGE_LOADER_TAGS.CINE_MODULE:
|
||||
metadata = {
|
||||
frameTime: instance.FrameTime,
|
||||
};
|
||||
|
||||
break;
|
||||
}
|
||||
|
||||
return provider;
|
||||
return metadata;
|
||||
}
|
||||
|
||||
/**
|
||||
* Looks up metadata for Cornerstone Tools given a specified type and imageId
|
||||
* A type may be, e.g. 'study', or 'patient', or 'imagePlaneModule'. These types
|
||||
* are keys in the stored metadata objects.
|
||||
*
|
||||
* @param type
|
||||
* @param imageId
|
||||
* @returns {Object} Relevant metadata of the specified type
|
||||
*/
|
||||
provider(type, imageId) {
|
||||
const imageMetadata = this.metadataLookup.get(imageId);
|
||||
if (!imageMetadata) {
|
||||
_getInstanceData(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) {
|
||||
const study = this.studies.get(StudyInstanceUID);
|
||||
|
||||
if (!study) {
|
||||
return;
|
||||
}
|
||||
|
||||
if (imageMetadata.hasOwnProperty(type)) {
|
||||
return imageMetadata[type];
|
||||
const series = study.series.get(SeriesInstanceUID);
|
||||
|
||||
if (!series) {
|
||||
return;
|
||||
}
|
||||
|
||||
const instance = series.instances.get(SOPInstanceUID);
|
||||
|
||||
return instance;
|
||||
}
|
||||
|
||||
_getUIDsFromImageID(imageId) {
|
||||
if (imageId.includes('wadors:')) {
|
||||
const strippedImageId = imageId.split('studies/')[1];
|
||||
const splitImageId = strippedImageId.split('/');
|
||||
|
||||
return {
|
||||
StudyInstanceUID: splitImageId[0], // Note: splitImageId[1] === 'series'
|
||||
SeriesInstanceUID: splitImageId[2], // Note: splitImageId[3] === 'instances'
|
||||
SOPInstanceUID: splitImageId[4],
|
||||
};
|
||||
}
|
||||
if (imageId.includes('wado?requestType=WADO')) {
|
||||
const qs = queryString.parse(imageId);
|
||||
|
||||
return {
|
||||
StudyInstanceUID: qs.studyUID,
|
||||
SeriesInstanceUID: qs.seriesUID,
|
||||
SOPInstanceUID: qs.objectUID,
|
||||
};
|
||||
} else {
|
||||
// Maybe its a non-standard imageId
|
||||
return this.imageIdToUIDs.get(imageId);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
export default MetadataProvider;
|
||||
const metadataProvider = new MetadataProvider();
|
||||
|
||||
export default metadataProvider;
|
||||
|
||||
const WADO_IMAGE_LOADER_TAGS = {
|
||||
// CornerstoneWADOImageLoader specific
|
||||
GENERAL_SERIES_MODULE: 'generalSeriesModule',
|
||||
PATIENT_STUDY_MODULE: 'patientStudyModule',
|
||||
IMAGE_PLANE_MODULE: 'imagePlaneModule',
|
||||
IMAGE_PIXEL_MODULE: 'imagePixelModule',
|
||||
VOI_LUT_MODULE: 'voiLutModule',
|
||||
MODALITY_LUT_MODULE: 'modalityLutModule',
|
||||
SOP_COMMON_MODULE: 'sopCommonModule',
|
||||
PET_ISOTOPE_MODULE: 'petIsotopeModule',
|
||||
OVERLAY_PLANE_MODULE: 'overlayPlaneModule',
|
||||
|
||||
// react-cornerstone-viewport specifc
|
||||
PATIENT_MODULE: 'patientModule',
|
||||
GENERAL_IMAGE_MODULE: 'generalImageModule',
|
||||
GENERAL_STUDY_MODULE: 'generalStudyModule',
|
||||
CINE_MODULE: 'cineModule',
|
||||
};
|
||||
|
||||
const INSTANCE = 'instance';
|
||||
Reference in new issue
Block a user