Initial commit from prod-batam

extensions/dicom-microscopy/src/utils/loadSR.ts

@@ -0,0 +1,184 @@
+import dcmjs from 'dcmjs';
+
+import DCM_CODE_VALUES from './dcmCodeValues';
+import toArray from './toArray';
+
+const MeasurementReport = dcmjs.adapters.DICOMMicroscopyViewer.MeasurementReport;
+
+// Define as async so that it returns a promise, expected by the ViewportGrid
+export default async function loadSR(
+  microscopyService,
+  microscopySRDisplaySet,
+  referencedDisplaySet
+) {
+  const naturalizedDataset = microscopySRDisplaySet.metadata;
+
+  const { StudyInstanceUID, FrameOfReferenceUID } = referencedDisplaySet;
+
+  const managedViewers = microscopyService.getManagedViewersForStudy(StudyInstanceUID);
+
+  if (!managedViewers || !managedViewers.length) {
+    return;
+  }
+
+  microscopySRDisplaySet.isLoaded = true;
+
+  const { rois, labels } = await _getROIsFromToolState(microscopyService, naturalizedDataset, FrameOfReferenceUID);
+
+  const managedViewer = managedViewers[0];
+
+  for (let i = 0; i < rois.length; i++) {
+    // NOTE: When saving Microscopy SR, we are attaching identifier property
+    // to each ROI, and when read for display, it is coming in as "TEXT"
+    // evaluation.
+    // As the Dicom Microscopy Viewer will override styles for "Text" evaluations
+    // to hide all other geometries, we are going to manually remove that
+    // evaluation item.
+    const roi = rois[i];
+    const roiSymbols = Object.getOwnPropertySymbols(roi);
+    const _properties = roiSymbols.find(s => s.description === 'properties');
+    const properties = roi[_properties];
+    properties['evaluations'] = [];
+
+    managedViewer.addRoiGraphicWithLabel(roi, labels[i]);
+  }
+}
+
+async function _getROIsFromToolState(microscopyService, naturalizedDataset, FrameOfReferenceUID) {
+  const toolState = MeasurementReport.generateToolState(naturalizedDataset);
+  const tools = Object.getOwnPropertyNames(toolState);
+  // Does a dynamic import to prevent webpack from rebuilding the library
+  const DICOMMicroscopyViewer = await microscopyService.importDicomMicroscopyViewer();
+
+  const measurementGroupContentItems = _getMeasurementGroups(naturalizedDataset);
+
+  const rois = [];
+  const labels = [];
+
+  tools.forEach(t => {
+    const toolSpecificToolState = toolState[t];
+    let scoord3d;
+
+    const capsToolType = t.toUpperCase();
+
+    const measurementGroupContentItemsForTool = measurementGroupContentItems.filter(mg => {
+      const imageRegionContentItem = toArray(mg.ContentSequence).find(
+        ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.IMAGE_REGION
+      );
+
+      return imageRegionContentItem.GraphicType === capsToolType;
+    });
+
+    toolSpecificToolState.forEach((coordinates, index) => {
+      const properties = {};
+
+      const options = {
+        coordinates,
+        frameOfReferenceUID: FrameOfReferenceUID,
+      };
+
+      if (t === 'Polygon') {
+        scoord3d = new DICOMMicroscopyViewer.scoord3d.Polygon(options);
+      } else if (t === 'Polyline') {
+        scoord3d = new DICOMMicroscopyViewer.scoord3d.Polyline(options);
+      } else if (t === 'Point') {
+        scoord3d = new DICOMMicroscopyViewer.scoord3d.Point(options);
+      } else if (t === 'Ellipse') {
+        scoord3d = new DICOMMicroscopyViewer.scoord3d.Ellipse(options);
+      } else {
+        throw new Error('Unsupported tool type');
+      }
+
+      const measurementGroup = measurementGroupContentItemsForTool[index];
+      const findingGroup = toArray(measurementGroup.ContentSequence).find(
+        ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.FINDING
+      );
+
+      const trackingGroup = toArray(measurementGroup.ContentSequence).find(
+        ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER
+      );
+
+      /**
+       * Extract presentation state from tracking identifier.
+       * Currently is stored in SR but should be stored in its tags.
+       */
+      if (trackingGroup) {
+        const regExp = /\(([^)]+)\)/;
+        const matches = regExp.exec(trackingGroup.TextValue);
+        if (matches && matches[1]) {
+          properties.presentationState = JSON.parse(matches[1]);
+          properties.marker = properties.presentationState.marker;
+        }
+      }
+
+      let measurements = toArray(measurementGroup.ContentSequence).filter(ci =>
+        [
+          DCM_CODE_VALUES.LENGTH,
+          DCM_CODE_VALUES.AREA,
+          DCM_CODE_VALUES.SHORT_AXIS,
+          DCM_CODE_VALUES.LONG_AXIS,
+          DCM_CODE_VALUES.ELLIPSE_AREA,
+        ].includes(ci.ConceptNameCodeSequence.CodeValue)
+      );
+
+      let evaluations = toArray(measurementGroup.ContentSequence).filter(ci =>
+        [DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER].includes(ci.ConceptNameCodeSequence.CodeValue)
+      );
+
+      /**
+       * TODO: Resolve bug in DCMJS.
+       * ConceptNameCodeSequence should be a sequence with only one item.
+       */
+      evaluations = evaluations.map(evaluation => {
+        const e = { ...evaluation };
+        e.ConceptNameCodeSequence = toArray(e.ConceptNameCodeSequence);
+        return e;
+      });
+
+      /**
+       * TODO: Resolve bug in DCMJS.
+       * ConceptNameCodeSequence should be a sequence with only one item.
+       */
+      measurements = measurements.map(measurement => {
+        const m = { ...measurement };
+        m.ConceptNameCodeSequence = toArray(m.ConceptNameCodeSequence);
+        return m;
+      });
+
+      if (measurements && measurements.length) {
+        properties.measurements = measurements;
+        console.log('[SR] retrieving measurements...', measurements);
+      }
+
+      if (evaluations && evaluations.length) {
+        properties.evaluations = evaluations;
+        console.log('[SR] retrieving evaluations...', evaluations);
+      }
+
+      const roi = new DICOMMicroscopyViewer.roi.ROI({ scoord3d, properties });
+      rois.push(roi);
+
+      if (findingGroup) {
+        labels.push(findingGroup.ConceptCodeSequence.CodeValue);
+      } else {
+        labels.push('');
+      }
+    });
+  });
+
+  return { rois, labels };
+}
+
+function _getMeasurementGroups(naturalizedDataset) {
+  const { ContentSequence } = naturalizedDataset;
+
+  const imagingMeasurementsContentItem = ContentSequence.find(
+    ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.IMAGING_MEASUREMENTS
+  );
+
+  const measurementGroupContentItems = toArray(
+    imagingMeasurementsContentItem.ContentSequence
+  ).filter(ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.MEASUREMENT_GROUP);
+
+  return measurementGroupContentItems;
+}