Sr update aim

src/adapters/Cornerstone/ArrowAnnotate.js

@@ -85,11 +85,12 @@ class ArrowAnnotate {
     static getTID300RepresentationArguments(tool) {
         const points = [tool.handles.start];
 
-        let { finding, findingSites } = tool;
+        let { finding, findingSites, trackingIdentifier } = tool;
 
         const TID300RepresentationArguments = {
             points,
-            trackingIdentifierTextValue: `cornerstoneTools@^4.0.0:ArrowAnnotate`,
+            trackingIdentifierTextValue:
+                trackingIdentifier || `cornerstoneTools@^4.0.0:ArrowAnnotate`,
             findingSites: findingSites || []
         };
 

src/adapters/Cornerstone/Bidirectional.js

@@ -8,6 +8,9 @@ const LONG_AXIS = "Long Axis";
 const SHORT_AXIS = "Short Axis";
 const FINDING = "121071";
 const FINDING_SITE = "G-C0E3";
+const COMMENT = "121106";
+const TRACKING_IDENTIFIER = "112039";
+const TRACKING_UNIQUE_IDENTIFIER = "112040";
 
 class Bidirectional {
     constructor() {}
@@ -24,6 +27,21 @@ class Bidirectional {
             group => group.ConceptNameCodeSequence.CodeValue === FINDING_SITE
         );
 
+        const comment = toArray(ContentSequence).find(
+            group => group.ConceptNameCodeSequence.CodeValue === COMMENT
+        );
+
+        const trackingIdentifier = toArray(ContentSequence).find(
+            group =>
+                group.ConceptNameCodeSequence.CodeValue === TRACKING_IDENTIFIER
+        );
+
+        const trackingUniqueIdentifier = toArray(ContentSequence).find(
+            group =>
+                group.ConceptNameCodeSequence.CodeValue ===
+                TRACKING_UNIQUE_IDENTIFIER
+        );
+
         const longAxisNUMGroup = toArray(ContentSequence).find(
             group => group.ConceptNameCodeSequence.CodeMeaning === LONG_AXIS
         );
@@ -129,15 +147,17 @@ class Bidirectional {
             isCreating: false,
             longestDiameter,
             shortestDiameter,
-            toolType: "Bidirectional",
             toolName: "Bidirectional",
             visible: true,
             finding: findingGroup
                 ? findingGroup.ConceptCodeSequence
                 : undefined,
             findingSites: findingSiteGroups.map(fsg => {
                 return { ...fsg.ConceptCodeSequence };
-            })
+            }),
+            comment: comment ? comment.TextValue : undefined,
+            trackingIdentifier: trackingIdentifier.TextValue,
+            trackingUniqueIdentifier: trackingUniqueIdentifier.UID
         };
 
         return state;
@@ -154,11 +174,14 @@ class Bidirectional {
             shortestDiameter,
             longestDiameter,
             finding,
-            findingSites
+            findingSites,
+            comment,
+            trackingIdentifier,
+            trackingUniqueIdentifier
         } = tool;
 
         const trackingIdentifierTextValue =
-            "cornerstoneTools@^4.0.0:Bidirectional";
+            trackingIdentifier || "cornerstoneTools@^4.0.0:Bidirectional";
 
         return {
             longAxis: {
@@ -172,8 +195,10 @@ class Bidirectional {
             longAxisLength: longestDiameter,
             shortAxisLength: shortestDiameter,
             trackingIdentifierTextValue,
+            trackingUniqueIdentifier,
             finding: finding,
-            findingSites: findingSites || []
+            findingSites: findingSites || [],
+            comment: comment
         };
     }
 }

src/adapters/Cornerstone/EllipticalRoi.js

@@ -115,7 +115,13 @@ class EllipticalRoi {
     }
 
     static getTID300RepresentationArguments(tool) {
-        const { cachedStats, handles, finding, findingSites } = tool;
+        const {
+            cachedStats,
+            handles,
+            finding,
+            findingSites,
+            trackingIdentifier
+        } = tool;
         const { start, end } = handles;
         const { area } = cachedStats;
 
@@ -145,7 +151,7 @@ class EllipticalRoi {
         }
 
         const trackingIdentifierTextValue =
-            "cornerstoneTools@^4.0.0:EllipticalRoi";
+            trackingIdentifier || "cornerstoneTools@^4.0.0:EllipticalRoi";
 
         return {
             area,

src/adapters/Cornerstone/Freehand.js

@@ -1,38 +1,158 @@
 import MeasurementReport from "./MeasurementReport";
 import TID300Polyline from "../../utilities/TID300/Polyline";
 import CORNERSTONE_4_TAG from "./cornerstone4Tag";
+import { toArray } from "../helpers.js";
+
+const FREEHAND = "Freehand";
+const FINDING = "121071";
+const FINDING_SITE = "G-C0E3";
+const COMMENT = "121106";
+const TRACKING_IDENTIFIER = "112039";
+const TRACKING_UNIQUE_IDENTIFIER = "112040";
+
+const statNameMap = {
+    Minimum: "min",
+    Maximum: "max",
+    Mean: "mean",
+    "Standard Deviation": "stdDev"
+};
 
 class Freehand {
     constructor() {}
 
-    static measurementContentToLengthState(groupItemContent) {
-        const content = groupItemContent.ContentSequence;
-        const { ReferencedSOPSequence } = content.ContentSequence;
-        const {
-            ReferencedSOPInstanceUID,
-            ReferencedFrameNumber
-        } = ReferencedSOPSequence;
-        const state = {
-            sopInstanceUid: ReferencedSOPInstanceUID,
-            frameIndex: ReferencedFrameNumber || 0,
-            toolType: Freehand.toolType
+    static parseNumComponent(num) {
+        const SCOORDGroup = toArray(num.ContentSequence).find(
+            group => group.ValueType === "SCOORD"
+        );
+        const { ReferencedSOPSequence } = SCOORDGroup.ContentSequence;
+        return {
+            type: num.ConceptNameCodeSequence.CodeMeaning,
+            value: num.MeasuredValueSequence.NumericValue,
+            points: Freehand.extractPoints(SCOORDGroup.GraphicData),
+            ReferencedSOPSequence: ReferencedSOPSequence
         };
+    }
+
+    static parseNumGroup(numGroup) {
+        const stats = {};
+        const scoords = [];
+        const refs = [];
+
+        numGroup.forEach(num => {
+            const {
+                type,
+                value,
+                points,
+                ReferencedSOPSequence
+            } = Freehand.parseNumComponent(num);
+            scoords.push(points);
+            refs.push(ReferencedSOPSequence);
+            stats[statNameMap[type]] = value;
+        });
+        return { scoords, refs, stats };
+    }
+
+    static extractPoints(points) {
+        const allPoints = [];
+
+        for (let i = 0; i < points.length; i += 2) {
+            // TODO z
+            allPoints.push({ x: points[i], y: points[i + 1] });
+        }
+
+        return allPoints;
+    }
 
-        // TODO: To be implemented!
-        // Needs to add points, lengths
+    static measurementContentToLengthState(MeasurementGroup) {
+        const { ContentSequence } = MeasurementGroup;
+
+        const findingGroup = toArray(ContentSequence).find(
+            group => group.ConceptNameCodeSequence.CodeValue === FINDING
+        );
+
+        const findingSiteGroups = toArray(ContentSequence).filter(
+            group => group.ConceptNameCodeSequence.CodeValue === FINDING_SITE
+        );
+
+        const comment = toArray(ContentSequence).find(
+            group => group.ConceptNameCodeSequence.CodeValue === COMMENT
+        );
+
+        const trackingIdentifier = toArray(ContentSequence).find(
+            group =>
+                group.ConceptNameCodeSequence.CodeValue === TRACKING_IDENTIFIER
+        );
+
+        const trackingUniqueIdentifier = toArray(ContentSequence).find(
+            group =>
+                group.ConceptNameCodeSequence.CodeValue ===
+                TRACKING_UNIQUE_IDENTIFIER
+        );
+        const NUMGroup = toArray(ContentSequence).filter(
+            group => group.ValueType === "NUM"
+        );
+        const { scoords, refs, stats } = Freehand.parseNumGroup(NUMGroup);
+        // TODO get/handle distinct shapes. using the first shape for now
+        const state = {
+            sopInstanceUid: refs[0].ReferencedSOPInstanceUID,
+            frameIndex: refs[0].ReferencedFrameNumber || 0,
+            toolType: Freehand.toolType,
+            handles: {
+                points: scoords[0],
+                textBox: {},
+                invalidHandlePlacement: false
+            },
+            active: false,
+            visible: true,
+            toolName: "Freehand",
+            invalidated: false,
+            finding: findingGroup
+                ? findingGroup.ConceptCodeSequence
+                : undefined,
+            findingSites: findingSiteGroups.map(fsg => {
+                return { ...fsg.ConceptCodeSequence };
+            }),
+            comment: comment ? comment.TextValue : undefined,
+            trackingIdentifier: trackingIdentifier.TextValue,
+            trackingUniqueIdentifier: trackingUniqueIdentifier.UID,
+            meanStdDev: stats // TODO check if SUV/Pet
+        };
 
         return state;
     }
 
     // TODO: this function is required for all Cornerstone Tool Adapters, since it is called by MeasurementReport.
     static getMeasurementData(measurementContent) {
-        return measurementContent.map(Freehand.measurementContentToLengthState);
+        return Freehand.measurementContentToLengthState(measurementContent);
     }
 
-    static getTID300RepresentationArguments(/*tool*/) {
-        // TO BE IMPLEMENTED
+    static getTID300RepresentationArguments(tool) {
+        const {
+            handles,
+            finding,
+            findingSites,
+            trackingIdentifier,
+            perimeter,
+            area,
+            meanStdDev,
+            meanStdDevSUV,
+            pixelUnit
+        } = tool;
+        const points = handles.points;
+        // console.error('tool', handles);
+        const trackingIdentifierTextValue =
+            trackingIdentifier || "cornerstoneTools@^4.0.0:Freehand";
+
         return {
-            /*points, lengths*/
+            points,
+            perimeter,
+            area,
+            meanStdDev,
+            meanStdDevSUV,
+            pixelUnit,
+            trackingIdentifierTextValue,
+            finding,
+            findingSites: findingSites || []
         };
     }
 }
@@ -41,7 +161,17 @@ Freehand.toolType = "Freehand";
 Freehand.utilityToolType = "Freehand";
 Freehand.TID300Representation = TID300Polyline;
 Freehand.isValidCornerstoneTrackingIdentifier = TrackingIdentifier => {
-    return false; // TODO
+    if (!TrackingIdentifier.includes(":")) {
+        return false;
+    }
+
+    const [cornerstone4Tag, toolType] = TrackingIdentifier.split(":");
+
+    if (cornerstone4Tag !== CORNERSTONE_4_TAG) {
+        return false;
+    }
+
+    return toolType === FREEHAND;
 };
 
 MeasurementReport.registerTool(Freehand);

src/adapters/Cornerstone/Length.js

@@ -70,12 +70,13 @@ class Length {
     }
 
     static getTID300RepresentationArguments(tool) {
-        const { handles, finding, findingSites } = tool;
+        const { handles, finding, findingSites, trackingIdentifier } = tool;
         const point1 = handles.start;
         const point2 = handles.end;
         const distance = tool.length;
 
-        const trackingIdentifierTextValue = "cornerstoneTools@^4.0.0:Length";
+        const trackingIdentifierTextValue =
+            trackingIdentifier || "cornerstoneTools@^4.0.0:Length";
 
         return {
             point1,

src/adapters/Cornerstone/MeasurementReport.js

@@ -69,8 +69,18 @@ export default class MeasurementReport {
             "generalSeriesModule",
             firstImageId
         );
+        const patientModule = metadataProvider.get(
+            "patientModule",
+            firstImageId
+        );
         //const sopCommonModule = metadataProvider.get('sopCommonModule', firstImageId);
         const { studyInstanceUID, seriesInstanceUID } = generalSeriesModule;
+        const {
+            patientID,
+            patientName,
+            patientBirthDate,
+            patientSex
+        } = patientModule;
 
         // Loop through each image in the toolData
         Object.keys(toolState).forEach(imageId => {
@@ -125,9 +135,13 @@ export default class MeasurementReport {
 
         const derivationSourceDataset = {
             StudyInstanceUID: studyInstanceUID,
-            SeriesInstanceUID: seriesInstanceUID
+            SeriesInstanceUID: seriesInstanceUID,
             //SOPInstanceUID: sopInstanceUID, // TODO: Necessary?
             //SOPClassUID: sopClassUID,
+            PatientID: patientID,
+            PatientName: patientName,
+            PatientBirthDate: patientBirthDate,
+            PatientSex: patientSex
         };
 
         const _meta = {
@@ -158,9 +172,10 @@ export default class MeasurementReport {
         derivationSourceDataset._meta = _meta;
         derivationSourceDataset._vrMap = _vrMap;
 
-        const report = new StructuredReport([derivationSourceDataset]);
+        const report = new StructuredReport([derivationSourceDataset], options);
         const contentItem = MeasurementReport.contentItem(
-            derivationSourceDataset
+            derivationSourceDataset,
+            options
         );
 
         // Merge the derived dataset with the content from the Measurement Report