feat(measurements): add CircleROI Tool (#3211)

* [refactor] measurement service mapping files - rename to .ts files

* [fix] RectangleROI - measurement service mapping _getReport() function - tool name fix

* [feat] added CircleROI tool from updated cornerstone3D

* [refactor] fix for typescript strong typing warnings

* [feat] cornerstone-dicom-sr extension - added CircleROI tool

* [feat] added toolbar button for CircleROI tool

* [doc] doc updates for CircleROI tool

* [update] library - dcmjs to 0.29.5

* [fix] roundNumber() function when given strings

* [fix] refactor after upgrading conerstonejs library 0.49.0

* yarn.lock file change

extensions/cornerstone/package.json

@@ -30,7 +30,7 @@
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
     "cornerstone-wado-image-loader": "^4.13.0",
-    "dcmjs": "^0.29.4",
+    "dcmjs": "^0.29.5",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/cornerstone/src/initCornerstoneTools.js

@@ -9,6 +9,7 @@ import {
   LengthTool,
   RectangleROITool,
   EllipticalROITool,
+  CircleROITool,
   BidirectionalTool,
   ArrowAnnotateTool,
   DragProbeTool,
@@ -41,6 +42,7 @@ export default function initCornerstoneTools(configuration = {}) {
   addTool(LengthTool);
   addTool(RectangleROITool);
   addTool(EllipticalROITool);
+  addTool(CircleROITool);
   addTool(BidirectionalTool);
   addTool(ArrowAnnotateTool);
   addTool(DragProbeTool);
@@ -83,6 +85,7 @@ const toolNames = {
   Probe: ProbeTool.toolName,
   RectangleROI: RectangleROITool.toolName,
   EllipticalROI: EllipticalROITool.toolName,
+  CircleROI: CircleROITool.toolName,
   Bidirectional: BidirectionalTool.toolName,
   Angle: AngleTool.toolName,
   CobbAngle: CobbAngleTool.toolName,

extensions/cornerstone/src/initMeasurementService.js

@@ -24,6 +24,7 @@ const initMeasurementService = (
     Length,
     Bidirectional,
     EllipticalROI,
+    CircleROI,
     ArrowAnnotate,
     Angle,
     CobbAngle,
@@ -78,6 +79,14 @@ const initMeasurementService = (
     EllipticalROI.toMeasurement
   );
 
+  measurementService.addMapping(
+    csTools3DVer1MeasurementSource,
+    'CircleROI',
+    CircleROI.matchingCriteria,
+    CircleROI.toAnnotation,
+    CircleROI.toMeasurement
+  );
+
   measurementService.addMapping(
     csTools3DVer1MeasurementSource,
     'ArrowAnnotate',

extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts

@@ -0,0 +1,228 @@
+import SUPPORTED_TOOLS from './constants/supportedTools';
+import getSOPInstanceAttributes from './utils/getSOPInstanceAttributes';
+import getModalityUnit from './utils/getModalityUnit';
+import { utils } from '@ohif/core';
+
+const CircleROI = {
+  toAnnotation: measurement => {},
+  toMeasurement: (
+    csToolsEventDetail,
+    DisplaySetService,
+    CornerstoneViewportService,
+    getValueTypeFromToolType
+  ) => {
+    const { annotation, viewportId } = csToolsEventDetail;
+    const { metadata, data, annotationUID } = annotation;
+
+    if (!metadata || !data) {
+      console.warn('Length tool: Missing metadata or data');
+      return null;
+    }
+
+    const { toolName, referencedImageId, FrameOfReferenceUID } = metadata;
+    const validToolType = SUPPORTED_TOOLS.includes(toolName);
+
+    if (!validToolType) {
+      throw new Error('Tool not supported');
+    }
+
+    const {
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      StudyInstanceUID,
+    } = getSOPInstanceAttributes(
+      referencedImageId,
+      CornerstoneViewportService,
+      viewportId
+    );
+
+    let displaySet;
+
+    if (SOPInstanceUID) {
+      displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
+        SOPInstanceUID,
+        SeriesInstanceUID
+      );
+    } else {
+      displaySet = DisplaySetService.getDisplaySetsForSeries(SeriesInstanceUID);
+    }
+
+    const { points } = data.handles;
+
+    const mappedAnnotations = getMappedAnnotations(
+      annotation,
+      DisplaySetService
+    );
+
+    const displayText = getDisplayText(mappedAnnotations, displaySet);
+    const getReport = () =>
+      _getReport(mappedAnnotations, points, FrameOfReferenceUID);
+
+    return {
+      uid: annotationUID,
+      SOPInstanceUID,
+      FrameOfReferenceUID,
+      points,
+      metadata,
+      referenceSeriesUID: SeriesInstanceUID,
+      referenceStudyUID: StudyInstanceUID,
+      frameNumber: mappedAnnotations[0]?.frameNumber || 1,
+      toolName: metadata.toolName,
+      displaySetInstanceUID: displaySet.displaySetInstanceUID,
+      label: data.label,
+      displayText: displayText,
+      data: data.cachedStats,
+      type: getValueTypeFromToolType(toolName),
+      getReport,
+    };
+  },
+};
+
+function getMappedAnnotations(annotation, DisplaySetService) {
+  const { metadata, data } = annotation;
+  const { cachedStats } = data;
+  const { referencedImageId } = metadata;
+  const targets = Object.keys(cachedStats);
+
+  if (!targets.length) {
+    return [];
+  }
+
+  const annotations = [];
+  Object.keys(cachedStats).forEach(targetId => {
+    const targetStats = cachedStats[targetId];
+
+    if (!referencedImageId) {
+      // Todo: Non-acquisition plane measurement mapping not supported yet
+      throw new Error(
+        'Non-acquisition plane measurement mapping not supported'
+      );
+    }
+
+    const {
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      frameNumber,
+    } = getSOPInstanceAttributes(referencedImageId);
+
+    const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      frameNumber
+    );
+
+    const { SeriesNumber } = displaySet;
+    const { mean, stdDev, max, area, Modality } = targetStats;
+    const unit = getModalityUnit(Modality);
+
+    annotations.push({
+      SeriesInstanceUID,
+      SOPInstanceUID,
+      SeriesNumber,
+      frameNumber,
+      Modality,
+      unit,
+      mean,
+      stdDev,
+      max,
+      area,
+    });
+  });
+
+  return annotations;
+}
+
+/*
+This function is used to convert the measurement data to a format that is
+suitable for the report generation (e.g. for the csv report). The report
+returns a list of columns and corresponding values.
+*/
+function _getReport(mappedAnnotations, points, FrameOfReferenceUID) {
+  const columns = [];
+  const values = [];
+
+  // Add Type
+  columns.push('AnnotationType');
+  values.push('Cornerstone:CircleROI');
+
+  mappedAnnotations.forEach(annotation => {
+    const { mean, stdDev, max, area, unit } = annotation;
+
+    if (!mean || !unit || !max || !area) {
+      return;
+    }
+
+    columns.push(
+      `max (${unit})`,
+      `mean (${unit})`,
+      `std (${unit})`,
+      `area (mm2)`
+    );
+    values.push(max, mean, stdDev, area);
+  });
+
+  if (FrameOfReferenceUID) {
+    columns.push('FrameOfReferenceUID');
+    values.push(FrameOfReferenceUID);
+  }
+
+  if (points) {
+    columns.push('points');
+    // points has the form of [[x1, y1, z1], [x2, y2, z2], ...]
+    // convert it to string of [[x1 y1 z1];[x2 y2 z2];...]
+    // so that it can be used in the csv report
+    values.push(points.map(p => p.join(' ')).join(';'));
+  }
+
+  return {
+    columns,
+    values,
+  };
+}
+
+function getDisplayText(mappedAnnotations, displaySet) {
+  if (!mappedAnnotations || !mappedAnnotations.length) {
+    return '';
+  }
+
+  const displayText = [];
+
+  // Area is the same for all series
+  const { area, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
+
+  const instance = displaySet.images.find(
+    image => image.SOPInstanceUID === SOPInstanceUID
+  );
+
+  let InstanceNumber;
+  if (instance) {
+    InstanceNumber = instance.InstanceNumber;
+  }
+
+  const instanceText = InstanceNumber ? ` I: ${InstanceNumber}` : '';
+  const frameText = displaySet.isMultiFrame ? ` F: ${frameNumber}` : '';
+
+  // Area sometimes becomes undefined if `preventHandleOutsideImage` is off.
+  const roundedArea = utils.roundNumber(area || 0, 2);
+  displayText.push(`${roundedArea} mm<sup>2</sup>`);
+
+  // Todo: we need a better UI for displaying all these information
+  mappedAnnotations.forEach(mappedAnnotation => {
+    const { unit, max, SeriesNumber } = mappedAnnotation;
+
+    let maxStr = '';
+    if (max) {
+      const roundedMax = utils.roundNumber(max, 2);
+      maxStr = `Max: ${roundedMax} <small>${unit}</small> `;
+    }
+
+    const str = `${maxStr}(S:${SeriesNumber}${instanceText}${frameText})`;
+    if (!displayText.includes(str)) {
+      displayText.push(str);
+    }
+  });
+
+  return displayText;
+}
+
+export default CircleROI;

extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts

@@ -1,6 +1,6 @@
 import SUPPORTED_TOOLS from './constants/supportedTools';
 import getSOPInstanceAttributes from './utils/getSOPInstanceAttributes';
-import { displaySetService, utils } from '@ohif/core';
+import { utils } from '@ohif/core';
 
 const Length = {
   toAnnotation: measurement => {},
@@ -32,15 +32,12 @@ const Length = {
       throw new Error('Tool not supported');
     }
 
-    const {
-      SOPInstanceUID,
-      SeriesInstanceUID,
-      StudyInstanceUID,
-    } = getSOPInstanceAttributes(
-      referencedImageId,
-      cornerstoneViewportService,
-      viewportId
-    );
+    const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } =
+      getSOPInstanceAttributes(
+        referencedImageId,
+        cornerstoneViewportService,
+        viewportId
+      );
 
     let displaySet;
 
@@ -104,11 +101,8 @@ function getMappedAnnotations(annotation, displaySetService) {
       );
     }
 
-    const {
-      SOPInstanceUID,
-      SeriesInstanceUID,
-      frameNumber,
-    } = getSOPInstanceAttributes(referencedImageId);
+    const { SOPInstanceUID, SeriesInstanceUID, frameNumber } =
+      getSOPInstanceAttributes(referencedImageId);
 
     const displaySet = displaySetService.getDisplaySetForSOPInstanceUID(
       SOPInstanceUID,
@@ -179,12 +173,8 @@ function getDisplayText(mappedAnnotations, displaySet) {
   const displayText = [];
 
   // Area is the same for all series
-  const {
-    length,
-    SeriesNumber,
-    SOPInstanceUID,
-    frameNumber,
-  } = mappedAnnotations[0];
+  const { length, SeriesNumber, SOPInstanceUID, frameNumber } =
+    mappedAnnotations[0];
 
   const instance = displaySet.images.find(
     image => image.SOPInstanceUID === SOPInstanceUID

extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts

@@ -4,7 +4,7 @@ import getModalityUnit from './utils/getModalityUnit';
 import { utils } from '@ohif/core';
 
 const RectangleROI = {
-  toAnnotation: measurement => { },
+  toAnnotation: measurement => {},
   toMeasurement: (
     csToolsEventDetail,
     DisplaySetService,
@@ -26,15 +26,12 @@ const RectangleROI = {
       throw new Error('Tool not supported');
     }
 
-    const {
-      SOPInstanceUID,
-      SeriesInstanceUID,
-      StudyInstanceUID,
-    } = getSOPInstanceAttributes(
-      referencedImageId,
-      CornerstoneViewportService,
-      viewportId
-    );
+    const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } =
+      getSOPInstanceAttributes(
+        referencedImageId,
+        CornerstoneViewportService,
+        viewportId
+      );
 
     let displaySet;
 
@@ -99,11 +96,8 @@ function getMappedAnnotations(annotation, DisplaySetService) {
       );
     }
 
-    const {
-      SOPInstanceUID,
-      SeriesInstanceUID,
-      frameNumber,
-    } = getSOPInstanceAttributes(referencedImageId);
+    const { SOPInstanceUID, SeriesInstanceUID, frameNumber } =
+      getSOPInstanceAttributes(referencedImageId);
 
     const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
       SOPInstanceUID,
@@ -143,7 +137,7 @@ function _getReport(mappedAnnotations, points, FrameOfReferenceUID) {
 
   // Add Type
   columns.push('AnnotationType');
-  values.push('Cornerstone:EllipticalROI');
+  values.push('Cornerstone:RectangleROI');
 
   mappedAnnotations.forEach(annotation => {
     const { mean, stdDev, max, area, unit } = annotation;

extensions/cornerstone/src/utils/measurementServiceMappings/constants/supportedTools.js

@@ -1,6 +1,7 @@
 export default [
   'Length',
   'EllipticalROI',
+  'CircleROI',
   'Bidirectional',
   'ArrowAnnotate',
   'Angle',

extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.ts

@@ -2,6 +2,7 @@ import { MeasurementService } from '@ohif/core';
 import Length from './Length';
 import Bidirectional from './Bidirectional';
 import EllipticalROI from './EllipticalROI';
+import CircleROI from './CircleROI';
 import ArrowAnnotate from './ArrowAnnotate';
 import CobbAngle from './CobbAngle';
 import Angle from './Angle';
@@ -25,6 +26,7 @@ const measurementServiceMappingsFactory = (
     const {
       POLYLINE,
       ELLIPSE,
+      CIRCLE,
       RECTANGLE,
       BIDIRECTIONAL,
       POINT,
@@ -37,6 +39,7 @@ const measurementServiceMappingsFactory = (
     const TOOL_TYPE_TO_VALUE_TYPE = {
       Length: POLYLINE,
       EllipticalROI: ELLIPSE,
+      CircleROI: CIRCLE,
       RectangleROI: RECTANGLE,
       PlanarFreehandROI: POLYLINE,
       Bidirectional: BIDIRECTIONAL,
@@ -104,6 +107,22 @@ const measurementServiceMappingsFactory = (
       ],
     },
 
+    CircleROI: {
+      toAnnotation: CircleROI.toAnnotation,
+      toMeasurement: csToolsAnnotation =>
+        CircleROI.toMeasurement(
+          csToolsAnnotation,
+          displaySetService,
+          cornerstoneViewportService,
+          _getValueTypeFromToolType
+        ),
+      matchingCriteria: [
+        {
+          valueType: MeasurementService.VALUE_TYPES.CIRCLE,
+        },
+      ],
+    },
+
     RectangleROI: {
       toAnnotation: RectangleROI.toAnnotation,
       toMeasurement: csToolsAnnotation =>

extensions/cornerstone/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js

@@ -13,8 +13,8 @@ import * as cornerstone from '@cornerstonejs/core';
  */
 export default function getSOPInstanceAttributes(
   imageId,
-  cornerstoneViewportService,
-  viewportId
+  cornerstoneViewportService = undefined,
+  viewportId = undefined
 ) {
   if (imageId) {
     return _getUIDFromImageID(imageId);