@cornerstonejs/adapters 4.0.0-beta.2 → 4.0.0-beta.4

package/README.md

@@ -9,17 +9,17 @@
 # History
 
 - 2014
-  - [DCMTK](dcmtk.org) cross compiled to javascript at [CTK Hackfest](http://www.commontk.org/index.php/CTK-Hackfest-May-2014). While this was useful and powerful, it was heavyweight for typical web usage.
+    - [DCMTK](dcmtk.org) cross compiled to javascript at [CTK Hackfest](http://www.commontk.org/index.php/CTK-Hackfest-May-2014). While this was useful and powerful, it was heavyweight for typical web usage.
 - 2016
-  - A [Medical Imaging Web Appliction meeting at Stanford](http://qiicr.org/web/outreach/Medical-Imaging-Web-Apps/) and [follow-on hackfest in Boston](http://qiicr.org/web/outreach/MIWS-hackfest/) helped elaborate the needs for manipulating DICOM in pure Javascript.
-  - Based on [DICOM Part 10 read/write code](https://github.com/OHIF/dicom-dimse) initiated by Weiwei Wu of [OHIF](http://ohif.org), Steve Pieper [developed further features](https://github.com/pieper/sites/tree/gh-pages/dcmio) and [examples of creating multiframe and segmentation objects](https://github.com/pieper/sites/tree/gh-pages/DICOMzero) discussed with the community at RSNA
+    - A [Medical Imaging Web Appliction meeting at Stanford](http://qiicr.org/web/outreach/Medical-Imaging-Web-Apps/) and [follow-on hackfest in Boston](http://qiicr.org/web/outreach/MIWS-hackfest/) helped elaborate the needs for manipulating DICOM in pure Javascript.
+    - Based on [DICOM Part 10 read/write code](https://github.com/OHIF/dicom-dimse) initiated by Weiwei Wu of [OHIF](http://ohif.org), Steve Pieper [developed further features](https://github.com/pieper/sites/tree/gh-pages/dcmio) and [examples of creating multiframe and segmentation objects](https://github.com/pieper/sites/tree/gh-pages/DICOMzero) discussed with the community at RSNA
 - 2017
-  - At [NA-MIC Project Week 25](https://na-mic.org/wiki/Project_Week_25) Erik Ziegler and Steve Pieper [worked](https://na-mic.org/wiki/Project_Week_25/DICOM_Segmentation_Support_for_Cornerstone_and_OHIF_Viewer)
-    with the community to define some example use cases to mix the pure JavaScript DICOM code with Cornerstone and [CornerstoneTools](https://github.com/chafey/cornerstoneTools).
+    - At [NA-MIC Project Week 25](https://na-mic.org/wiki/Project_Week_25) Erik Ziegler and Steve Pieper [worked](https://na-mic.org/wiki/Project_Week_25/DICOM_Segmentation_Support_for_Cornerstone_and_OHIF_Viewer)
+      with the community to define some example use cases to mix the pure JavaScript DICOM code with Cornerstone and [CornerstoneTools](https://github.com/chafey/cornerstoneTools).
 - 2018-2022
-  - Work continues to develop SR and SEG support to [OHIFViewer](http://ohif.org) allow interoperability with [DICOM4QI](https://legacy.gitbook.com/book/qiicr/dicom4qi/details)
+    - Work continues to develop SR and SEG support to [OHIFViewer](http://ohif.org) allow interoperability with [DICOM4QI](https://legacy.gitbook.com/book/qiicr/dicom4qi/details)
 - 2023
-  - Moved the adapters into cornerstone3D from dcmjsj
+    - Moved the adapters into cornerstone3D from dcmjsj
 
 # Support
 

package/dist/esm/adapters/Cornerstone/Bidirectional.js

@@ -3,6 +3,7 @@ import MeasurementReport from './MeasurementReport.js';
 import CORNERSTONE_4_TAG from './cornerstone4Tag.js';
 import { toArray } from '../helpers/toArray.js';
 import 'buffer';
+import '@cornerstonejs/core';
 
 const {
   Bidirectional: TID300Bidirectional

package/dist/esm/adapters/Cornerstone/MeasurementReport.js

@@ -2,6 +2,7 @@ import { utilities, derivations, normalizers, data } from 'dcmjs';
 import { toArray } from '../helpers/toArray.js';
 import { codeMeaningEquals } from '../helpers/codeMeaningEquals.js';
 import 'buffer';
+import '@cornerstonejs/core';
 
 const {
   TID1500,
@@ -48,8 +49,9 @@ const codeValueMatch = (group, code, oldCode) => {
 function getTID300ContentItem(tool, ReferencedSOPSequence, adapterClass) {
   const args = adapterClass.getTID300RepresentationArguments(tool);
   args.ReferencedSOPSequence = ReferencedSOPSequence;
-  const TID300Measurement = new adapterClass.TID300Representation(args);
-  return TID300Measurement;
+  args.ReferencedFrameOfReferenceUID = args.use3DSpatialCoordinates ? tool.metadata.FrameOfReferenceUID : null;
+  const tid300Measurement = new adapterClass.TID300Representation(args);
+  return tid300Measurement;
 }
 function getMeasurementGroup(toolType, toolData, ReferencedSOPSequence) {
   const toolTypeData = toolData[toolType];
@@ -60,10 +62,10 @@ function getMeasurementGroup(toolType, toolData, ReferencedSOPSequence) {
 
   // Loop through the array of tool instances
   // for this tool
-  const Measurements = toolTypeData.data.map(tool => {
+  const measurements = toolTypeData.data.map(tool => {
     return getTID300ContentItem(tool, ReferencedSOPSequence, toolClass);
   });
-  return new TID1501MeasurementGroup(Measurements);
+  return new TID1501MeasurementGroup(measurements);
 }
 class MeasurementReport {
   static getSetupMeasurementData(MeasurementGroup) {
@@ -161,7 +163,7 @@ class MeasurementReport {
       });
       allMeasurementGroups = allMeasurementGroups.concat(measurementGroups);
     });
-    const MeasurementReport = new TID1500MeasurementReport({
+    const tid1500MeasurementReport = new TID1500MeasurementReport({
       TID1501MeasurementGroups: allMeasurementGroups
     }, options);
 
@@ -203,7 +205,7 @@ class MeasurementReport {
     derivationSourceDataset._meta = _meta;
     derivationSourceDataset._vrMap = _vrMap;
     const report = new StructuredReport([derivationSourceDataset]);
-    const contentItem = MeasurementReport.contentItem(derivationSourceDataset);
+    const contentItem = tid1500MeasurementReport.contentItem(derivationSourceDataset);
 
     // Merge the derived dataset with the content from the Measurement Report
     report.dataset = Object.assign(report.dataset, contentItem);

package/dist/esm/adapters/Cornerstone/ParametricMap.js

@@ -1,6 +1,6 @@
 import { log, data, normalizers } from 'dcmjs';
 import checkOrientation from '../helpers/checkOrientation.js';
-import compareArrays from '../helpers/compareArrays.js';
+import { utilities } from '@cornerstonejs/core';
 
 const {
   DicomMessage,
@@ -167,7 +167,7 @@ function getImageIdOfSourceImagebyGeometry(ReferencedSeriesInstanceUID, FrameOfR
     if (sourceImageMetadata === undefined || sourceImageMetadata.ImagePositionPatient === undefined || sourceImageMetadata.FrameOfReferenceUID !== FrameOfReferenceUID || sourceImageMetadata.SeriesInstanceUID !== ReferencedSeriesInstanceUID) {
       continue;
     }
-    if (compareArrays(PerFrameFunctionalGroup.PlanePositionSequence[0].ImagePositionPatient, sourceImageMetadata.ImagePositionPatient, tolerance)) {
+    if (utilities.isEqual(PerFrameFunctionalGroup.PlanePositionSequence[0].ImagePositionPatient, sourceImageMetadata.ImagePositionPatient, tolerance)) {
       return imageIds[imageIdsIndex];
     }
   }

package/dist/esm/adapters/Cornerstone/Segmentation_4X.js

@@ -2,7 +2,7 @@ import { utilities, log, data, normalizers, derivations } from 'dcmjs';
 import ndarray from 'ndarray';
 import getDatasetsFromImages from '../helpers/getDatasetsFromImages.js';
 import checkOrientation from '../helpers/checkOrientation.js';
-import compareArrays from '../helpers/compareArrays.js';
+import { utilities as utilities$1 } from '@cornerstonejs/core';
 import { Events } from '../enums/Events.js';
 
 const {
@@ -913,6 +913,9 @@ function getImageIdOfSourceImageBySourceImageSequence(SourceImageSequence, sopUI
   if (ReferencedFrameNumber !== undefined) {
     if (baseImageId.includes("frames/")) {
       return baseImageId.replace(/frames\/\d+/, `frames/${ReferencedFrameNumber}`);
+    } else if (baseImageId.includes("dicomfile:")) {
+      // dicomfile base 1, despite having frame=
+      return baseImageId.replace(/frame=\d+/, `frame=${ReferencedFrameNumber}`);
     } else if (baseImageId.includes("frame=")) {
       return baseImageId.replace(/frame=\d+/, `frame=${ReferencedFrameNumber - 1}`);
     } else {
@@ -967,10 +970,10 @@ function getImageIdOfSourceImagebyGeometry(ReferencedSeriesInstanceUID, FrameOfR
     // For multiframe images, check each frame's position
     if (isMultiframe) {
       const framePosition = metadataProvider.get("imagePlaneModule", imageId)?.imagePositionPatient;
-      if (framePosition && compareArrays(segFramePosition, framePosition, tolerance)) {
+      if (framePosition && utilities$1.isEqual(segFramePosition, framePosition, tolerance)) {
         return imageId;
       }
-    } else if (compareArrays(segFramePosition, sourceImageMetadata.ImagePositionPatient, tolerance)) {
+    } else if (utilities$1.isEqual(segFramePosition, sourceImageMetadata.ImagePositionPatient, tolerance)) {
       return imageId;
     }
   }
@@ -1012,38 +1015,38 @@ function getValidOrientations(iop) {
  * @return {Ndarray} The aligned pixelData.
  */
 function alignPixelDataWithSourceData(pixelData2D, iop, orientations, tolerance) {
-  if (compareArrays(iop, orientations[0], tolerance)) {
+  if (utilities$1.isEqual(iop, orientations[0], tolerance)) {
     return pixelData2D;
-  } else if (compareArrays(iop, orientations[1], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[1], tolerance)) {
     // Flipped vertically.
 
     // Undo Flip
     return flipMatrix2D.v(pixelData2D);
-  } else if (compareArrays(iop, orientations[2], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[2], tolerance)) {
     // Flipped horizontally.
 
     // Unfo flip
     return flipMatrix2D.h(pixelData2D);
-  } else if (compareArrays(iop, orientations[3], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[3], tolerance)) {
     //Rotated 90 degrees
 
     // Rotate back
     return rotateMatrix902D(pixelData2D);
-  } else if (compareArrays(iop, orientations[4], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[4], tolerance)) {
     //Rotated 90 degrees and fliped horizontally.
 
     // Undo flip and rotate back.
     return rotateMatrix902D(flipMatrix2D.h(pixelData2D));
-  } else if (compareArrays(iop, orientations[5], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[5], tolerance)) {
     // Rotated 90 degrees and fliped vertically
 
     // Unfo flip and rotate back.
     return rotateMatrix902D(flipMatrix2D.v(pixelData2D));
-  } else if (compareArrays(iop, orientations[6], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[6], tolerance)) {
     // Rotated 180 degrees. // TODO -> Do this more effeciently, there is a 1:1 mapping like 90 degree rotation.
 
     return rotateMatrix902D(rotateMatrix902D(pixelData2D));
-  } else if (compareArrays(iop, orientations[7], tolerance)) {
+  } else if (utilities$1.isEqual(iop, orientations[7], tolerance)) {
     // Rotated 270 degrees
 
     // Rotate back.

package/dist/esm/adapters/Cornerstone3D/Angle.d.ts

@@ -1,87 +1,50 @@
 import BaseAdapter3D from "./BaseAdapter3D";
 declare class Angle extends BaseAdapter3D {
-    static getMeasurementData(MeasurementGroup: any, sopInstanceUIDToImageIdMap: any, imageToWorldCoords: any, metadata: any): any;
-    static getMeasurementDataFromScoord({ defaultState, SCOORDGroup, imageToWorldCoords, NUMGroup, ReferencedFrameNumber }: {
-        defaultState: any;
-        SCOORDGroup: any;
-        imageToWorldCoords: any;
-        NUMGroup: any;
-        ReferencedFrameNumber: any;
-    }): any;
-    static getMeasurementDataFromScoord3D({ defaultState, SCOORD3DGroup }: {
-        defaultState: any;
-        SCOORD3DGroup: any;
-    }): any;
-    static getTID300RepresentationArguments(tool: any, worldToImageCoords: any): {
-        point1: {
-            x: any;
-            y: any;
-            z: any;
-        };
-        point2: {
-            x: any;
-            y: any;
-            z: any;
-        };
-        point3: {
-            x: any;
-            y: any;
-            z: any;
-        };
-        point4: {
-            x: any;
-            y: any;
-            z: any;
-        };
-        rAngle: any;
-        trackingIdentifierTextValue: string;
-        finding: any;
-        findingSites: any;
-        ReferencedFrameOfReferenceUID: any;
-        use3DSpatialCoordinates: boolean;
-    } | {
-        point1: {
-            x: any;
-            y: any;
-        };
-        point2: {
-            x: any;
-            y: any;
-        };
-        point3: {
-            x: any;
-            y: any;
-        };
-        point4: {
-            x: any;
-            y: any;
-        };
-        rAngle: any;
-        trackingIdentifierTextValue: string;
-        finding: any;
-        findingSites: any;
-        use3DSpatialCoordinates: boolean;
+    static getMeasurementData(MeasurementGroup: any, sopInstanceUIDToImageIdMap: any, metadata: any): {
+        description?: string;
+        sopInstanceUid?: string;
+        annotation: import("packages/tools/dist/esm/types").Annotation;
+        finding?: unknown;
+        findingSites?: unknown;
+        commentGroup?: any;
+        commentPositionGroup?: any;
     };
-    static getTID300RepresentationArgumentsSCOORD3D(tool: any): {
+    static getTID300RepresentationArguments(tool: any, is3DMeasurement?: boolean): {
         point1: {
             x: any;
             y: any;
             z: any;
+        } | {
+            x: number;
+            y: number;
+            z?: undefined;
         };
         point2: {
             x: any;
             y: any;
             z: any;
+        } | {
+            x: number;
+            y: number;
+            z?: undefined;
         };
         point3: {
             x: any;
             y: any;
             z: any;
+        } | {
+            x: number;
+            y: number;
+            z?: undefined;
         };
         point4: {
             x: any;
             y: any;
             z: any;
+        } | {
+            x: number;
+            y: number;
+            z?: undefined;
         };
         rAngle: any;
         trackingIdentifierTextValue: string;

package/dist/esm/adapters/Cornerstone3D/Angle.js

@@ -1,99 +1,41 @@
 import { utilities } from 'dcmjs';
 import MeasurementReport from './MeasurementReport.js';
 import BaseAdapter3D from './BaseAdapter3D.js';
+import 'buffer';
+import { toScoord } from '../helpers/toScoordType.js';
+import '@cornerstonejs/core';
 
 var _Angle;
 const {
   CobbAngle: TID300CobbAngle
 } = utilities.TID300;
 class Angle extends BaseAdapter3D {
-  static getMeasurementData(MeasurementGroup, sopInstanceUIDToImageIdMap, imageToWorldCoords, metadata) {
+  static getMeasurementData(MeasurementGroup, sopInstanceUIDToImageIdMap, metadata) {
     const {
-      defaultState,
+      state,
       NUMGroup,
-      SCOORDGroup,
-      SCOORD3DGroup,
+      worldCoords,
+      referencedImageId,
       ReferencedFrameNumber
-    } = MeasurementReport.getSetupMeasurementData(MeasurementGroup, sopInstanceUIDToImageIdMap, metadata, Angle.toolType);
-    if (SCOORDGroup) {
-      return this.getMeasurementDataFromScoord({
-        defaultState,
-        SCOORDGroup,
-        imageToWorldCoords,
-        NUMGroup,
-        ReferencedFrameNumber
-      });
-    } else if (SCOORD3DGroup) {
-      return this.getMeasurementDataFromScoord3D({
-        defaultState,
-        SCOORD3DGroup
-      });
-    } else {
-      throw new Error("Can't get measurement data with missing SCOORD and SCOORD3D groups.");
-    }
-  }
-  static getMeasurementDataFromScoord(_ref) {
-    let {
-      defaultState,
-      SCOORDGroup,
-      imageToWorldCoords,
-      NUMGroup,
-      ReferencedFrameNumber
-    } = _ref;
-    const referencedImageId = defaultState.annotation.metadata.referencedImageId;
-    const {
-      GraphicData
-    } = SCOORDGroup;
-    const worldCoords = [];
-    for (let i = 0; i < GraphicData.length; i += 2) {
-      const point = imageToWorldCoords(referencedImageId, [GraphicData[i], GraphicData[i + 1]]);
-      worldCoords.push(point);
-    }
-    const state = defaultState;
+    } = MeasurementReport.getSetupMeasurementData(MeasurementGroup, sopInstanceUIDToImageIdMap, metadata, this.toolType);
+    const cachedStats = referencedImageId ? {
+      [`imageId:${referencedImageId}`]: {
+        angle: NUMGroup ? NUMGroup.MeasuredValueSequence.NumericValue : null
+      }
+    } : {};
     state.annotation.data = {
+      ...state.annotation.data,
       handles: {
-        points: [worldCoords[0], worldCoords[1], worldCoords[3]],
-        activeHandleIndex: 0,
-        textBox: {
-          hasMoved: false
-        }
-      },
-      cachedStats: {
-        [`imageId:${referencedImageId}`]: {
-          angle: NUMGroup ? NUMGroup.MeasuredValueSequence.NumericValue : null
-        }
+        ...state.annotation.data.handles,
+        points: [worldCoords[0], worldCoords[1], worldCoords[3]]
       },
+      cachedStats,
       frameNumber: ReferencedFrameNumber
     };
     return state;
   }
-  static getMeasurementDataFromScoord3D(_ref2) {
-    let {
-      defaultState,
-      SCOORD3DGroup
-    } = _ref2;
-    const {
-      GraphicData
-    } = SCOORD3DGroup;
-    const worldCoords = [];
-    for (let i = 0; i < GraphicData.length; i += 3) {
-      const point = [GraphicData[i], GraphicData[i + 1], GraphicData[i + 2]];
-      worldCoords.push(point);
-    }
-    const state = defaultState;
-    state.annotation.data = {
-      handles: {
-        points: [worldCoords[0], worldCoords[1], worldCoords[3]],
-        activeHandleIndex: 0,
-        textBox: {
-          hasMoved: false
-        }
-      },
-      cachedStats: {}
-    };
-    return state;
-  }
-  static getTID300RepresentationArguments(tool, worldToImageCoords) {
+  static getTID300RepresentationArguments(tool) {
+    let is3DMeasurement = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
     const {
       data,
       finding,
@@ -107,74 +49,15 @@ class Angle extends BaseAdapter3D {
     const {
       referencedImageId
     } = metadata;
-    if (!referencedImageId) {
-      return this.getTID300RepresentationArgumentsSCOORD3D(tool);
-    }
-    const start1 = worldToImageCoords(referencedImageId, handles.points[0]);
-    const middle = worldToImageCoords(referencedImageId, handles.points[1]);
-    const end = worldToImageCoords(referencedImageId, handles.points[2]);
-    const point1 = {
-      x: start1[0],
-      y: start1[1]
-    };
-    const point2 = {
-      x: middle[0],
-      y: middle[1]
-    };
-    const point3 = point2;
-    const point4 = {
-      x: end[0],
-      y: end[1]
-    };
-    const {
-      angle
-    } = cachedStats[`imageId:${referencedImageId}`] || {};
-    return {
-      point1,
-      point2,
-      point3,
-      point4,
-      rAngle: angle,
-      trackingIdentifierTextValue: this.trackingIdentifierTextValue,
-      finding,
-      findingSites: findingSites || [],
-      use3DSpatialCoordinates: false
-    };
-  }
-  static getTID300RepresentationArgumentsSCOORD3D(tool) {
-    const {
-      data,
-      finding,
-      findingSites,
-      metadata
-    } = tool;
-    const {
-      cachedStats = {},
-      handles
-    } = data;
-    const start = handles.points[0];
-    const middle = handles.points[1];
-    const end = handles.points[2];
-    const point1 = {
-      x: start[0],
-      y: start[1],
-      z: start[2]
-    };
-    const point2 = {
-      x: middle[0],
-      y: middle[1],
-      z: middle[2]
-    };
-    const point3 = point2;
-    const point4 = {
-      x: end[0],
-      y: end[1],
-      z: end[2]
+    const scoordProps = {
+      is3DMeasurement,
+      referencedImageId
     };
-    const cachedStatsKeys = Object.keys(cachedStats)[0];
-    const {
-      angle
-    } = cachedStatsKeys ? cachedStats[cachedStatsKeys] : {};
+    const point1 = toScoord(scoordProps, handles.points[0]);
+    const point2 = toScoord(scoordProps, handles.points[1]);
+    const point3 = toScoord(scoordProps, handles.points[1]);
+    const point4 = toScoord(scoordProps, handles.points[2]);
+    const angle = cachedStats[`imageId:${referencedImageId}`]?.angle;
     return {
       point1,
       point2,
@@ -184,8 +67,8 @@ class Angle extends BaseAdapter3D {
       trackingIdentifierTextValue: this.trackingIdentifierTextValue,
       finding,
       findingSites: findingSites || [],
-      ReferencedFrameOfReferenceUID: metadata.FrameOfReferenceUID,
-      use3DSpatialCoordinates: true
+      ReferencedFrameOfReferenceUID: is3DMeasurement ? metadata.FrameOfReferenceUID : null,
+      use3DSpatialCoordinates: is3DMeasurement
     };
   }
 }

package/dist/esm/adapters/Cornerstone3D/ArrowAnnotate.d.ts

@@ -1,36 +1,24 @@
 import BaseAdapter3D from "./BaseAdapter3D";
 declare class ArrowAnnotate extends BaseAdapter3D {
-    static getMeasurementData(MeasurementGroup: any, sopInstanceUIDToImageIdMap: any, imageToWorldCoords: any, metadata: any, _trackingIdentifier: any): any;
-    static getMeasurementDataFromScoord3D({ SCOORD3DGroup, defaultState, text }: {
-        SCOORD3DGroup: any;
-        defaultState: any;
-        text: any;
-    }): any;
-    static getMeasurementDataFromScoord({ SCOORDGroup, referencedImageId, metadata, imageToWorldCoords, defaultState, text, ReferencedFrameNumber }: {
-        SCOORDGroup: any;
-        referencedImageId: any;
-        metadata: any;
-        imageToWorldCoords: any;
-        defaultState: any;
-        text: any;
-        ReferencedFrameNumber: any;
-    }): any;
-    static getTID300RepresentationArguments(tool: any, worldToImageCoords: any): {
-        points: {
-            x: any;
-            y: any;
-        }[];
-        trackingIdentifierTextValue: string;
-        findingSites: any;
-        finding: any;
-        use3DSpatialCoordinates: boolean;
+    static getMeasurementData(MeasurementGroup: any, sopInstanceUIDToImageIdMap: any, metadata: any, _trackingIdentifier: any): {
+        description?: string;
+        sopInstanceUid?: string;
+        annotation: import("packages/tools/dist/esm/types").Annotation;
+        finding?: unknown;
+        findingSites?: unknown;
+        commentGroup?: any;
+        commentPositionGroup?: any;
     };
-    static getTID300RepresentationArgumentsSCOORD3D(tool: any): {
-        points: {
+    static getTID300RepresentationArguments(tool: any, is3DMeasurement?: boolean): {
+        points: ({
             x: any;
             y: any;
             z: any;
-        }[];
+        } | {
+            x: number;
+            y: number;
+            z?: undefined;
+        })[];
         trackingIdentifierTextValue: string;
         findingSites: any;
         finding: any;