init

extensions/cornerstone-dicom-sr/src/utils/SRSCOOR3DProbeMapper.ts

@@ -0,0 +1,62 @@
+const SRSCOOR3DProbe = {
+  toAnnotation: measurement => {},
+
+  /**
+   * Maps cornerstone annotation event data to measurement service format.
+   *
+   * @param {Object} cornerstone Cornerstone event data
+   * @return {Measurement} Measurement instance
+   */
+  toMeasurement: (
+    csToolsEventDetail,
+    displaySetService,
+    CornerstoneViewportService,
+    getValueTypeFromToolType,
+    customizationService
+  ) => {
+    const { annotation } = csToolsEventDetail;
+    const { metadata, data, annotationUID } = annotation;
+
+    if (!metadata || !data) {
+      console.warn('Probe tool: Missing metadata or data');
+      return null;
+    }
+
+    const { toolName } = metadata;
+    const { points } = data.handles;
+
+    const displayText = getDisplayText(annotation);
+    return {
+      uid: annotationUID,
+      points,
+      metadata,
+      toolName: metadata.toolName,
+      label: data.label,
+      displayText: displayText,
+      data: data.cachedStats,
+      type: getValueTypeFromToolType?.(toolName) ?? null,
+    };
+  },
+};
+
+function getDisplayText(annotation) {
+  const { data } = annotation;
+
+  if (!data) {
+    return [''];
+  }
+  const { labels } = data;
+
+  const displayText = [];
+
+  for (const label of labels) {
+    // make this generic
+    if (label.label === '33636980076') {
+      displayText.push(`Finding Site: ${label.value}`);
+    }
+  }
+
+  return displayText;
+}
+
+export default SRSCOOR3DProbe;

extensions/cornerstone-dicom-sr/src/utils/addSRAnnotation.ts

@@ -0,0 +1,67 @@
+import { Types, annotation } from '@cornerstonejs/tools';
+import { metaData } from '@cornerstonejs/core';
+
+import getRenderableData from './getRenderableData';
+import toolNames from '../tools/toolNames';
+
+export default function addSRAnnotation(measurement, imageId, frameNumber) {
+  let toolName = toolNames.DICOMSRDisplay;
+  const renderableData = measurement.coords.reduce((acc, coordProps) => {
+    acc[coordProps.GraphicType] = acc[coordProps.GraphicType] || [];
+    acc[coordProps.GraphicType].push(getRenderableData({ ...coordProps, imageId }));
+    return acc;
+  }, {});
+
+  const { TrackingUniqueIdentifier } = measurement;
+  const { ValueType: valueType, GraphicType: graphicType } = measurement.coords[0];
+  const graphicTypePoints = renderableData[graphicType];
+
+  /** TODO: Read the tool name from the DICOM SR identification type in the future. */
+  let frameOfReferenceUID = null;
+
+  if (imageId) {
+    const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
+    frameOfReferenceUID = imagePlaneModule?.frameOfReferenceUID;
+  }
+
+  if (valueType === 'SCOORD3D') {
+    toolName = toolNames.SRSCOORD3DPoint;
+
+    // get the ReferencedFrameOfReferenceUID from the measurement
+    frameOfReferenceUID = measurement.coords[0].ReferencedFrameOfReferenceSequence;
+  }
+
+  const SRAnnotation: Types.Annotation = {
+    annotationUID: TrackingUniqueIdentifier,
+    highlighted: false,
+    isLocked: false,
+    invalidated: false,
+    metadata: {
+      toolName,
+      valueType,
+      graphicType,
+      FrameOfReferenceUID: frameOfReferenceUID,
+      referencedImageId: imageId,
+    },
+    data: {
+      label: measurement.labels?.[0]?.value || undefined,
+      displayText: measurement.displayText || undefined,
+      handles: {
+        textBox: measurement.textBox ?? {},
+        points: graphicTypePoints[0],
+      },
+      cachedStats: {},
+      frameNumber,
+      renderableData,
+      TrackingUniqueIdentifier,
+      labels: measurement.labels,
+    },
+  };
+
+  /**
+   * const annotationManager = annotation.annotationState.getAnnotationManager();
+   * was not triggering annotation_added events.
+   */
+  annotation.state.addAnnotation(SRAnnotation);
+  console.debug('Adding SR annotation:', SRAnnotation);
+}

extensions/cornerstone-dicom-sr/src/utils/addToolInstance.ts

@@ -0,0 +1,14 @@
+import { addTool } from '@cornerstonejs/tools';
+
+export default function addToolInstance(name: string, toolClass, configuration = {}): void {
+  class InstanceClass extends toolClass {
+    static toolName = name;
+    constructor(toolProps, defaultToolProps) {
+      toolProps.configuration = toolProps.configuration
+        ? { ...toolProps.configuration, ...configuration }
+        : configuration;
+      super(toolProps, defaultToolProps);
+    }
+  }
+  addTool(InstanceClass);
+}

extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts

@@ -0,0 +1,95 @@
+import { DisplaySetService, classes } from '@ohif/core';
+
+const ImageSet = classes.ImageSet;
+
+const findInstance = (measurement, displaySetService: DisplaySetService) => {
+  const { displaySetInstanceUID, ReferencedSOPInstanceUID: sopUid } = measurement;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+  if (!referencedDisplaySet.images) {
+    return;
+  }
+  return referencedDisplaySet.images.find(it => it.SOPInstanceUID === sopUid);
+};
+
+/** Finds references to display sets inside the measurements
+ * contained within the provided display set.
+ * @return an array of instances referenced.
+ */
+const findReferencedInstances = (displaySetService: DisplaySetService, displaySet) => {
+  const instances = [];
+  const instanceById = {};
+  for (const measurement of displaySet.measurements) {
+    const { imageId } = measurement;
+    if (!imageId) {
+      continue;
+    }
+    if (instanceById[imageId]) {
+      continue;
+    }
+
+    const instance = findInstance(measurement, displaySetService);
+    if (!instance) {
+      console.log('Measurement', measurement, 'had no instances found');
+      continue;
+    }
+
+    instanceById[imageId] = instance;
+    instances.push(instance);
+  }
+  return instances;
+};
+
+/**
+ * Creates a new display set containing a single image instance for each
+ * referenced image.
+ *
+ * @param displaySetService
+ * @param displaySet - containing measurements referencing images.
+ * @returns A new (registered/active) display set containing the referenced images
+ */
+const createReferencedImageDisplaySet = (displaySetService, displaySet) => {
+  const instances = findReferencedInstances(displaySetService, displaySet);
+  // This will be a  member function of the created image set
+  const updateInstances = function () {
+    this.images.splice(
+      0,
+      this.images.length,
+      ...findReferencedInstances(displaySetService, displaySet)
+    );
+    this.numImageFrames = this.images.length;
+  };
+
+  const imageSet = new ImageSet(instances);
+  const instance = instances[0];
+
+  if (!instance) {
+    return;
+  }
+
+  imageSet.setAttributes({
+    displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID
+    SeriesDate: instance.SeriesDate,
+    SeriesTime: instance.SeriesTime,
+    SeriesInstanceUID: imageSet.uid,
+    StudyInstanceUID: instance.StudyInstanceUID,
+    SeriesNumber: instance.SeriesNumber || 0,
+    SOPClassUID: instance.SOPClassUID,
+    SeriesDescription: `${displaySet.SeriesDescription} KO ${displaySet.instance.SeriesNumber}`,
+    Modality: 'KO',
+    isMultiFrame: false,
+    numImageFrames: instances.length,
+    SOPClassHandlerId: `@ohif/extension-default.sopClassHandlerModule.stack`,
+    isReconstructable: false,
+    // This object is made of multiple instances from other series
+    isCompositeStack: true,
+    madeInClient: true,
+    excludeFromThumbnailBrowser: true,
+    updateInstances,
+  });
+
+  displaySetService.addDisplaySets(imageSet);
+
+  return imageSet;
+};
+
+export default createReferencedImageDisplaySet;

extensions/cornerstone-dicom-sr/src/utils/findInstanceMetadataBySopInstanceUid.js

@@ -0,0 +1,26 @@
+/**
+ *  Should Find the requested instance metadata into the displaySets and return
+ *
+ * @param {Array} displaySets - List of displaySets
+ * @param {string} SOPInstanceUID - sopInstanceUID to look for
+ * @returns {Object} - instance metadata found
+ */
+const findInstanceMetadataBySopInstanceUID = (displaySets, SOPInstanceUID) => {
+  let instanceFound;
+
+  displaySets.find(displaySet => {
+    if (!displaySet.images) {
+      return false;
+    }
+
+    instanceFound = displaySet.images.find(
+      instanceMetadata => instanceMetadata.getSOPInstanceUID() === SOPInstanceUID
+    );
+
+    return !!instanceFound;
+  });
+
+  return instanceFound;
+};
+
+export default findInstanceMetadataBySopInstanceUID;

extensions/cornerstone-dicom-sr/src/utils/findMostRecentStructuredReport.js

@@ -0,0 +1,61 @@
+/**
+ * Should find the most recent Structured Report metadata
+ *
+ * @param {Array} studies
+ * @returns {Object} Series
+ */
+const findMostRecentStructuredReport = studies => {
+  let mostRecentStructuredReport;
+
+  studies.forEach(study => {
+    const allSeries = study.getSeries ? study.getSeries() : [];
+    allSeries.forEach(series => {
+      // Skip series that may not have instances yet
+      // This can happen if we have retrieved just the initial
+      // details about the series via QIDO-RS, but not the full metadata
+      if (!series.instances.length) {
+        return;
+      }
+
+      if (isStructuredReportSeries(series)) {
+        if (!mostRecentStructuredReport || compareSeriesDate(series, mostRecentStructuredReport)) {
+          mostRecentStructuredReport = series;
+        }
+      }
+    });
+  });
+
+  return mostRecentStructuredReport;
+};
+
+/**
+ *  Checks if series sopClassUID matches with the supported Structured Reports sopClassUID
+ *
+ * @param {Object} series - Series metadata
+ * @returns {boolean}
+ */
+const isStructuredReportSeries = series => {
+  const supportedSopClassUIDs = ['1.2.840.10008.5.1.4.1.1.88.22', '1.2.840.10008.5.1.4.1.1.11.1'];
+
+  const firstInstance = series.getFirstInstance();
+  const SOPClassUID = firstInstance.getData().metadata.SOPClassUID;
+
+  return supportedSopClassUIDs.includes(SOPClassUID);
+};
+
+/**
+ *  Checks if series1 is newer than series2
+ *
+ * @param {Object} series1 - Series Metadata 1
+ * @param {Object} series2 - Series Metadata 2
+ * @returns {boolean} true/false if series1 is newer than series2
+ */
+const compareSeriesDate = (series1, series2) => {
+  return (
+    series1._data.SeriesDate > series2._data.SeriesDate ||
+    (series1._data.SeriesDate === series2._data.SeriesDate &&
+      series1._data.SeriesTime > series2._data.SeriesTime)
+  );
+};
+
+export default findMostRecentStructuredReport;

extensions/cornerstone-dicom-sr/src/utils/formatContentItem.ts

@@ -0,0 +1,67 @@
+import { utils } from '@ohif/core';
+
+/**
+ * Formatters used to format each of the content items (SR "nodes") which can be
+ * text, code, UID ref, number, person name, date, time and date time. Each
+ * formatter must be a function with the following signature:
+ *
+ *    [VALUE_TYPE]: (contentItem) => string
+ *
+ */
+const contentItemFormatters = {
+  TEXT: contentItem => contentItem.TextValue,
+  CODE: contentItem => contentItem.ConceptCodeSequence?.[0]?.CodeMeaning,
+  UIDREF: contentItem => contentItem.UID,
+  NUM: contentItem => {
+    const measuredValue = contentItem.MeasuredValueSequence?.[0];
+
+    if (!measuredValue) {
+      return;
+    }
+
+    const { NumericValue, MeasurementUnitsCodeSequence } = measuredValue;
+    const { CodeValue } = MeasurementUnitsCodeSequence;
+
+    return `${NumericValue} ${CodeValue}`;
+  },
+  PNAME: contentItem => {
+    const personName = contentItem.PersonName?.[0]?.Alphabetic;
+    return personName ? utils.formatPN(personName) : undefined;
+  },
+  DATE: contentItem => {
+    const { Date } = contentItem;
+    return Date ? utils.formatDate(Date) : undefined;
+  },
+  TIME: contentItem => {
+    const { Time } = contentItem;
+    return Time ? utils.formatTime(Time) : undefined;
+  },
+  DATETIME: contentItem => {
+    const { DateTime } = contentItem;
+
+    if (typeof DateTime !== 'string') {
+      return;
+    }
+
+    // 14 characters because it should be something like 20180614113714
+    if (DateTime.length < 14) {
+      return DateTime;
+    }
+
+    const dicomDate = DateTime.substring(0, 8);
+    const dicomTime = DateTime.substring(8, 14);
+    const formattedDate = utils.formatDate(dicomDate);
+    const formattedTime = utils.formatTime(dicomTime);
+
+    return `${formattedDate} ${formattedTime}`;
+  },
+};
+
+function formatContentItemValue(contentItem) {
+  const { ValueType } = contentItem;
+  const fnFormat = contentItemFormatters[ValueType];
+
+  return fnFormat ? fnFormat(contentItem) : `[${ValueType} is not supported]`;
+}
+
+export { formatContentItemValue as default, formatContentItemValue };

extensions/cornerstone-dicom-sr/src/utils/getAllDisplaySets.js

@@ -0,0 +1,19 @@
+/**
+ * Retrieve a list of all displaySets of all studies
+ *
+ * @param {Object} studies - List of studies loaded into the viewer
+ * @returns {Object} List of DisplaySets
+ */
+const getAllDisplaySets = studies => {
+  let allDisplaySets = [];
+
+  studies.forEach(study => {
+    if (study.getDisplaySets) {
+      allDisplaySets = allDisplaySets.concat(study.getDisplaySets());
+    }
+  });
+
+  return allDisplaySets;
+};
+
+export default getAllDisplaySets;

extensions/cornerstone-dicom-sr/src/utils/getFilteredCornerstoneToolState.ts

@@ -0,0 +1,103 @@
+import OHIF from '@ohif/core';
+import { annotation } from '@cornerstonejs/tools';
+const { log } = OHIF;
+
+function getFilteredCornerstoneToolState(measurementData, additionalFindingTypes) {
+  const filteredToolState = {};
+
+  function addToFilteredToolState(annotation, toolType) {
+    if (!annotation.metadata?.referencedImageId) {
+      log.warn(`[DICOMSR] No referencedImageId found for ${toolType} ${annotation.id}`);
+      return;
+    }
+
+    const imageId = annotation.metadata.referencedImageId;
+
+    if (!filteredToolState[imageId]) {
+      filteredToolState[imageId] = {};
+    }
+
+    const imageIdSpecificToolState = filteredToolState[imageId];
+
+    if (!imageIdSpecificToolState[toolType]) {
+      imageIdSpecificToolState[toolType] = {
+        data: [],
+      };
+    }
+
+    const measurementDataI = measurementData.find(md => md.uid === annotation.annotationUID);
+    const toolData = imageIdSpecificToolState[toolType].data;
+
+    let { finding } = measurementDataI;
+    const findingSites = [];
+
+    // NOTE -> We use the CORNERSTONEJS coding schemeDesignator which we have
+    // defined in the @cornerstonejs/adapters
+    if (measurementDataI.label) {
+      if (additionalFindingTypes.includes(toolType)) {
+        finding = {
+          CodeValue: 'CORNERSTONEFREETEXT',
+          CodingSchemeDesignator: 'CORNERSTONEJS',
+          CodeMeaning: measurementDataI.label,
+        };
+      } else {
+        findingSites.push({
+          CodeValue: 'CORNERSTONEFREETEXT',
+          CodingSchemeDesignator: 'CORNERSTONEJS',
+          CodeMeaning: measurementDataI.label,
+        });
+      }
+    }
+
+    if (measurementDataI.findingSites) {
+      findingSites.push(...measurementDataI.findingSites);
+    }
+
+    const measurement = Object.assign({}, annotation, {
+      finding,
+      findingSites,
+    });
+
+    toolData.push(measurement);
+  }
+
+  const uidFilter = measurementData.map(md => md.uid);
+  const uids = uidFilter.slice();
+
+  const annotationManager = annotation.state.getAnnotationManager();
+  const framesOfReference = annotationManager.getFramesOfReference();
+
+  for (let i = 0; i < framesOfReference.length; i++) {
+    const frameOfReference = framesOfReference[i];
+
+    const frameOfReferenceAnnotations = annotationManager.getAnnotations(frameOfReference);
+
+    const toolTypes = Object.keys(frameOfReferenceAnnotations);
+
+    for (let j = 0; j < toolTypes.length; j++) {
+      const toolType = toolTypes[j];
+
+      const annotations = frameOfReferenceAnnotations[toolType];
+
+      if (annotations) {
+        for (let k = 0; k < annotations.length; k++) {
+          const annotation = annotations[k];
+          const uidIndex = uids.findIndex(uid => uid === annotation.annotationUID);
+
+          if (uidIndex !== -1) {
+            addToFilteredToolState(annotation, toolType);
+            uids.splice(uidIndex, 1);
+
+            if (!uids.length) {
+              return filteredToolState;
+            }
+          }
+        }
+      }
+    }
+  }
+
+  return filteredToolState;
+}
+
+export default getFilteredCornerstoneToolState;

extensions/cornerstone-dicom-sr/src/utils/getLabelFromDCMJSImportedToolData.js

@@ -0,0 +1,27 @@
+import { adaptersSR } from '@cornerstonejs/adapters';
+
+const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
+
+/**
+ * Extracts the label from the toolData imported from dcmjs. We need to do this
+ * as dcmjs does not depeend on OHIF/the measurementService, it just produces data for cornestoneTools.
+ * This optional data is available for the consumer to process if they wish to.
+ * @param {object} toolData The tooldata relating to the
+ *
+ * @returns {string} The extracted label.
+ */
+export default function getLabelFromDCMJSImportedToolData(toolData) {
+  const { findingSites = [], finding } = toolData;
+
+  let freeTextLabel = findingSites.find(
+    fs => fs.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT
+  );
+
+  if (freeTextLabel) {
+    return freeTextLabel.CodeMeaning;
+  }
+
+  if (finding && finding.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT) {
+    return finding.CodeMeaning;
+  }
+}

extensions/cornerstone-dicom-sr/src/utils/getRenderableData.ts

@@ -0,0 +1,142 @@
+import { vec3 } from 'gl-matrix';
+import { metaData, utilities, Types as csTypes } from '@cornerstonejs/core';
+
+import { SCOORDTypes } from '../enums';
+
+const EPSILON = 1e-4;
+
+const getRenderableCoords = ({ GraphicData, ValueType, imageId }) => {
+  const renderableData = [];
+  if (ValueType === 'SCOORD3D') {
+    for (let i = 0; i < GraphicData.length; i += 3) {
+      renderableData.push([GraphicData[i], GraphicData[i + 1], GraphicData[i + 2]]);
+    }
+  } else {
+    for (let i = 0; i < GraphicData.length; i += 2) {
+      const worldPos = utilities.imageToWorldCoords(imageId, [GraphicData[i], GraphicData[i + 1]]);
+      renderableData.push(worldPos);
+    }
+  }
+  return renderableData;
+};
+
+function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
+  let renderableData = [];
+
+  switch (GraphicType) {
+    case SCOORDTypes.POINT:
+    case SCOORDTypes.MULTIPOINT:
+    case SCOORDTypes.POLYLINE: {
+      renderableData = getRenderableCoords({ GraphicData, ValueType, imageId });
+      break;
+    }
+    case SCOORDTypes.CIRCLE: {
+      const pointsWorld: csTypes.Point3[] = getRenderableCoords({
+        GraphicData,
+        ValueType,
+        imageId,
+      });
+      // We do not have an explicit draw circle svg helper in Cornerstone3D at
+      // this time, but we can use the ellipse svg helper to draw a circle, so
+      // here we reshape the data for that purpose.
+      const center = pointsWorld[0];
+      const onPerimeter = pointsWorld[1];
+      const radius = vec3.distance(center, onPerimeter);
+
+      const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
+      if (!imagePlaneModule) {
+        throw new Error('No imagePlaneModule found');
+      }
+
+      const {
+        columnCosines,
+        rowCosines,
+      }: {
+        columnCosines: csTypes.Point3;
+        rowCosines: csTypes.Point3;
+      } = imagePlaneModule;
+
+      // we need to get major/minor axis (which are both the same size major = minor)
+
+      const firstAxisStart = vec3.create();
+      vec3.scaleAndAdd(firstAxisStart, center, columnCosines, radius);
+
+      const firstAxisEnd = vec3.create();
+      vec3.scaleAndAdd(firstAxisEnd, center, columnCosines, -radius);
+
+      const secondAxisStart = vec3.create();
+      vec3.scaleAndAdd(secondAxisStart, center, rowCosines, radius);
+
+      const secondAxisEnd = vec3.create();
+      vec3.scaleAndAdd(secondAxisEnd, center, rowCosines, -radius);
+
+      renderableData = [
+        firstAxisStart as csTypes.Point3,
+        firstAxisEnd as csTypes.Point3,
+        secondAxisStart as csTypes.Point3,
+        secondAxisEnd as csTypes.Point3,
+      ];
+
+      break;
+    }
+    case SCOORDTypes.ELLIPSE: {
+      // GraphicData is ordered as [majorAxisStartX, majorAxisStartY, majorAxisEndX, majorAxisEndY, minorAxisStartX, minorAxisStartY, minorAxisEndX, minorAxisEndY]
+      // But Cornerstone3D points are ordered as top, bottom, left, right for the
+      // ellipse so we need to identify if the majorAxis is horizontal or vertical
+      // and then choose the correct points to use for the ellipse.
+      const pointsWorld: csTypes.Point3[] = getRenderableCoords({
+        GraphicData,
+        ValueType,
+        imageId,
+      });
+
+      const majorAxisStart = vec3.fromValues(...pointsWorld[0]);
+      const majorAxisEnd = vec3.fromValues(...pointsWorld[1]);
+      const minorAxisStart = vec3.fromValues(...pointsWorld[2]);
+      const minorAxisEnd = vec3.fromValues(...pointsWorld[3]);
+
+      const majorAxisVec = vec3.create();
+      vec3.sub(majorAxisVec, majorAxisEnd, majorAxisStart);
+
+      // normalize majorAxisVec to avoid scaling issues
+      vec3.normalize(majorAxisVec, majorAxisVec);
+
+      const minorAxisVec = vec3.create();
+      vec3.sub(minorAxisVec, minorAxisEnd, minorAxisStart);
+      vec3.normalize(minorAxisVec, minorAxisVec);
+
+      const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
+
+      if (!imagePlaneModule) {
+        throw new Error('imageId does not have imagePlaneModule metadata');
+      }
+
+      const { columnCosines }: { columnCosines: csTypes.Point3 } = imagePlaneModule;
+
+      // find which axis is parallel to the columnCosines
+      const columnCosinesVec = vec3.fromValues(...columnCosines);
+
+      const projectedMajorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, majorAxisVec));
+      const projectedMinorAxisOnColVec = Math.abs(vec3.dot(columnCosinesVec, minorAxisVec));
+
+      const absoluteOfMajorDotProduct = Math.abs(projectedMajorAxisOnColVec);
+      const absoluteOfMinorDotProduct = Math.abs(projectedMinorAxisOnColVec);
+
+      renderableData = [];
+      if (Math.abs(absoluteOfMajorDotProduct - 1) < EPSILON) {
+        renderableData = [pointsWorld[0], pointsWorld[1], pointsWorld[2], pointsWorld[3]];
+      } else if (Math.abs(absoluteOfMinorDotProduct - 1) < EPSILON) {
+        renderableData = [pointsWorld[2], pointsWorld[3], pointsWorld[0], pointsWorld[1]];
+      } else {
+        console.warn('OBLIQUE ELLIPSE NOT YET SUPPORTED');
+      }
+      break;
+    }
+    default:
+      console.warn('Unsupported GraphicType:', GraphicType);
+  }
+
+  return renderableData;
+}
+
+export default getRenderableData;

extensions/cornerstone-dicom-sr/src/utils/hydrateStructuredReport.ts

@@ -0,0 +1,299 @@
+import { utilities, metaData } from '@cornerstonejs/core';
+import OHIF, { DicomMetadataStore } from '@ohif/core';
+import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
+import { adaptersSR } from '@cornerstonejs/adapters';
+import { annotation as CsAnnotation } from '@cornerstonejs/tools';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
+
+const { locking } = CsAnnotation;
+const { guid } = OHIF.utils;
+const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
+
+const convertCode = (codingValues, code) => {
+  if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') {
+    return;
+  }
+  const ref = `${code.CodingSchemeDesignator}:${code.CodeValue}`;
+  const ret = { ...codingValues[ref], ref, ...code, text: code.CodeMeaning };
+  return ret;
+};
+
+const convertSites = (codingValues, sites) => {
+  if (!sites || !sites.length) {
+    return;
+  }
+  const ret = [];
+  // Do as a loop to convert away from Proxy instances
+  for (let i = 0; i < sites.length; i++) {
+    // Deal with irregular conversion from dcmjs
+    const site = convertCode(codingValues, sites[i][0] || sites[i]);
+    if (site) {
+      ret.push(site);
+    }
+  }
+  return (ret.length && ret) || undefined;
+};
+
+/**
+ * Hydrates a structured report, for default viewports.
+ *
+ */
+export default function hydrateStructuredReport(
+  { servicesManager, extensionManager, appConfig }: withAppTypes,
+  displaySetInstanceUID
+) {
+  const annotationManager = CsAnnotation.state.getAnnotationManager();
+  const dataSource = extensionManager.getActiveDataSource()[0];
+  const { measurementService, displaySetService, customizationService } = servicesManager.services;
+
+  const codingValues = customizationService.getCustomization('codingValues', {});
+
+  const { disableEditing } = customizationService.getCustomization(
+    'PanelMeasurement.disableEditing',
+    {
+      id: 'default.disableEditing',
+      disableEditing: false,
+    }
+  );
+
+  const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+
+  // TODO -> We should define a strict versioning somewhere.
+  const mappings = measurementService.getSourceMappings(
+    CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+    CORNERSTONE_3D_TOOLS_SOURCE_VERSION
+  );
+
+  if (!mappings || !mappings.length) {
+    throw new Error(
+      `Attempting to hydrate measurements service when no mappings present. This shouldn't be reached.`
+    );
+  }
+
+  const instance = DicomMetadataStore.getInstance(
+    displaySet.StudyInstanceUID,
+    displaySet.SeriesInstanceUID,
+    displaySet.SOPInstanceUID
+  );
+
+  const sopInstanceUIDToImageId = {};
+  const imageIdsForToolState = {};
+
+  displaySet.measurements.forEach(measurement => {
+    const { ReferencedSOPInstanceUID, imageId, frameNumber } = measurement;
+
+    if (!sopInstanceUIDToImageId[ReferencedSOPInstanceUID]) {
+      sopInstanceUIDToImageId[ReferencedSOPInstanceUID] = imageId;
+      imageIdsForToolState[ReferencedSOPInstanceUID] = [];
+    }
+    if (!imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber]) {
+      imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber] = imageId;
+    }
+  });
+
+  const datasetToUse = _mapLegacyDataSet(instance);
+
+  // Use dcmjs to generate toolState.
+  let storedMeasurementByAnnotationType = MeasurementReport.generateToolState(
+    datasetToUse,
+    // NOTE: we need to pass in the imageIds to dcmjs since the we use them
+    // for the imageToWorld transformation. The following assumes that the order
+    // that measurements were added to the display set are the same order as
+    // the measurementGroups in the instance.
+    sopInstanceUIDToImageId,
+    utilities.imageToWorldCoords,
+    metaData
+  );
+
+  const onBeforeSRHydration =
+    customizationService.getModeCustomization('onBeforeSRHydration')?.value;
+
+  if (typeof onBeforeSRHydration === 'function') {
+    storedMeasurementByAnnotationType = onBeforeSRHydration({
+      storedMeasurementByAnnotationType,
+      displaySet,
+    });
+  }
+
+  // Filter what is found by DICOM SR to measurements we support.
+  const mappingDefinitions = mappings.map(m => m.annotationType);
+  const hydratableMeasurementsInSR = {};
+
+  Object.keys(storedMeasurementByAnnotationType).forEach(key => {
+    if (mappingDefinitions.includes(key)) {
+      hydratableMeasurementsInSR[key] = storedMeasurementByAnnotationType[key];
+    }
+  });
+
+  // Set the series touched as tracked.
+  const imageIds = [];
+
+  // TODO: notification if no hydratable?
+  Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
+    const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
+
+    toolDataForAnnotationType.forEach(toolData => {
+      // Add the measurement to toolState
+      // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
+      // files, and looking up the imageId from sopInstanceUIDToImageId results
+      // in the wrong value.
+      const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
+      const imageId =
+        imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
+        sopInstanceUIDToImageId[toolData.sopInstanceUid];
+
+      if (!imageIds.includes(imageId)) {
+        imageIds.push(imageId);
+      }
+    });
+  });
+
+  let targetStudyInstanceUID;
+  const SeriesInstanceUIDs = [];
+
+  for (let i = 0; i < imageIds.length; i++) {
+    const imageId = imageIds[i];
+    const { SeriesInstanceUID, StudyInstanceUID } = metaData.get('instance', imageId);
+
+    if (!SeriesInstanceUIDs.includes(SeriesInstanceUID)) {
+      SeriesInstanceUIDs.push(SeriesInstanceUID);
+    }
+
+    if (!targetStudyInstanceUID) {
+      targetStudyInstanceUID = StudyInstanceUID;
+    } else if (targetStudyInstanceUID !== StudyInstanceUID) {
+      console.warn('NO SUPPORT FOR SRs THAT HAVE MEASUREMENTS FROM MULTIPLE STUDIES.');
+    }
+  }
+
+  Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
+    const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
+
+    toolDataForAnnotationType.forEach(toolData => {
+      // Add the measurement to toolState
+      // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
+      // files, and looking up the imageId from sopInstanceUIDToImageId results
+      // in the wrong value.
+      const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
+      const imageId =
+        imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
+        sopInstanceUIDToImageId[toolData.sopInstanceUid];
+
+      toolData.uid = guid();
+
+      const instance = metaData.get('instance', imageId);
+      const {
+        FrameOfReferenceUID,
+        // SOPInstanceUID,
+        // SeriesInstanceUID,
+        // StudyInstanceUID,
+      } = instance;
+
+      const annotation = {
+        annotationUID: toolData.annotation.annotationUID,
+        data: toolData.annotation.data,
+        metadata: {
+          toolName: annotationType,
+          referencedImageId: imageId,
+          FrameOfReferenceUID,
+        },
+      };
+
+      const source = measurementService.getSource(
+        CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+        CORNERSTONE_3D_TOOLS_SOURCE_VERSION
+      );
+      annotation.data.label = getLabelFromDCMJSImportedToolData(toolData);
+      annotation.data.finding = convertCode(codingValues, toolData.finding?.[0]);
+      annotation.data.findingSites = convertSites(codingValues, toolData.findingSites);
+      annotation.data.site = annotation.data.findingSites?.[0];
+
+      const matchingMapping = mappings.find(m => m.annotationType === annotationType);
+
+      const newAnnotationUID = measurementService.addRawMeasurement(
+        source,
+        annotationType,
+        { annotation },
+        matchingMapping.toMeasurementSchema,
+        dataSource
+      );
+
+      if (disableEditing) {
+        const addedAnnotation = annotationManager.getAnnotation(newAnnotationUID);
+        locking.setAnnotationLocked(addedAnnotation, true);
+      }
+
+      if (!imageIds.includes(imageId)) {
+        imageIds.push(imageId);
+      }
+    });
+  });
+
+  displaySet.isHydrated = true;
+
+  return {
+    StudyInstanceUID: targetStudyInstanceUID,
+    SeriesInstanceUIDs,
+  };
+}
+
+function _mapLegacyDataSet(dataset) {
+  const REPORT = 'Imaging Measurements';
+  const GROUP = 'Measurement Group';
+  const TRACKING_IDENTIFIER = 'Tracking Identifier';
+
+  // Identify the Imaging Measurements
+  const imagingMeasurementContent = toArray(dataset.ContentSequence).find(
+    codeMeaningEquals(REPORT)
+  );
+
+  // Retrieve the Measurements themselves
+  const measurementGroups = toArray(imagingMeasurementContent.ContentSequence).filter(
+    codeMeaningEquals(GROUP)
+  );
+
+  // For each of the supported measurement types, compute the measurement data
+  const measurementData = {};
+
+  const cornerstoneToolClasses = MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
+
+  const registeredToolClasses = [];
+
+  Object.keys(cornerstoneToolClasses).forEach(key => {
+    registeredToolClasses.push(cornerstoneToolClasses[key]);
+    measurementData[key] = [];
+  });
+
+  measurementGroups.forEach((measurementGroup, index) => {
+    const measurementGroupContentSequence = toArray(measurementGroup.ContentSequence);
+
+    const TrackingIdentifierGroup = measurementGroupContentSequence.find(
+      contentItem => contentItem.ConceptNameCodeSequence.CodeMeaning === TRACKING_IDENTIFIER
+    );
+
+    const TrackingIdentifier = TrackingIdentifierGroup.TextValue;
+
+    let [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
+    if (supportedLegacyCornerstoneTags.includes(cornerstoneTag)) {
+      cornerstoneTag = CORNERSTONE_3D_TAG;
+    }
+
+    const mappedTrackingIdentifier = `${cornerstoneTag}:${toolName}`;
+
+    TrackingIdentifierGroup.TextValue = mappedTrackingIdentifier;
+  });
+
+  return dataset;
+}
+
+const toArray = function (x) {
+  return Array.isArray(x) ? x : [x];
+};
+
+const codeMeaningEquals = codeMeaningName => {
+  return contentItem => {
+    return contentItem.ConceptNameCodeSequence.CodeMeaning === codeMeaningName;
+  };
+};

extensions/cornerstone-dicom-sr/src/utils/isRehydratable.js

@@ -0,0 +1,60 @@
+import { adaptersSR } from '@cornerstonejs/adapters';
+
+const cornerstoneAdapters =
+  adaptersSR.Cornerstone3D.MeasurementReport.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
+
+const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
+const CORNERSTONE_3D_TAG = adaptersSR.Cornerstone3D.CORNERSTONE_3D_TAG;
+
+/**
+ * Checks if the given `displaySet`can be rehydrated into the `measurementService`.
+ *
+ * @param {object} displaySet The SR `displaySet` to check.
+ * @param {object[]} mappings The CornerstoneTools 4 mappings to the `measurementService`.
+ * @returns {boolean} True if the SR can be rehydrated into the `measurementService`.
+ */
+export default function isRehydratable(displaySet, mappings) {
+  if (!mappings || !mappings.length) {
+    return false;
+  }
+
+  const mappingDefinitions = mappings.map(m => m.annotationType);
+  const { measurements } = displaySet;
+
+  const adapterKeys = Object.keys(cornerstoneAdapters).filter(
+    adapterKey =>
+      typeof cornerstoneAdapters[adapterKey].isValidCornerstoneTrackingIdentifier === 'function'
+  );
+
+  const adapters = [];
+
+  adapterKeys.forEach(key => {
+    if (mappingDefinitions.includes(key)) {
+      // Must have both a dcmjs adapter and a measurementService
+      // Definition in order to be a candidate for import.
+      adapters.push(cornerstoneAdapters[key]);
+    }
+  });
+
+  for (let i = 0; i < measurements.length; i++) {
+    const { TrackingIdentifier } = measurements[i] || {};
+    const hydratable = adapters.some(adapter => {
+      let [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
+      if (supportedLegacyCornerstoneTags.includes(cornerstoneTag)) {
+        cornerstoneTag = CORNERSTONE_3D_TAG;
+      }
+
+      const mappedTrackingIdentifier = `${cornerstoneTag}:${toolName}`;
+
+      return adapter.isValidCornerstoneTrackingIdentifier(mappedTrackingIdentifier);
+    });
+
+    if (hydratable) {
+      return true;
+    }
+    console.log('Measurement is not rehydratable', TrackingIdentifier, measurements[i]);
+  }
+
+  console.log('No measurements found which were rehydratable');
+  return false;
+}

extensions/cornerstone-dicom-sr/src/utils/isToolSupported.js

@@ -0,0 +1,14 @@
+import { adaptersSR } from '@cornerstonejs/adapters';
+
+/**
+ *  Checks if dcmjs has support to determined tool
+ *
+ * @param {string} toolName
+ * @returns {boolean}
+ */
+const isToolSupported = toolName => {
+  const adapter = adaptersSR.Cornerstone3D;
+  return !!adapter[toolName];
+};
+
+export default isToolSupported;