Fix mm/px (#331)

* fixed tools length, rectangleRoi, ellipticalRoi + imageTracker

* build + version + docs

* Update docs

* logs removed + rebuild

* Update docs

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

README.md

@@ -8,9 +8,9 @@
 
 ## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 2.4.11
+### Current version: 2.4.12
 
-### Latest Published Release: 2.4.11
+### Latest Published Release: 2.4.12
 
 This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornerstone-js environment.
 

docs/documentation/index.html

@@ -74,8 +74,8 @@ <h3> </h3>
 <h1 id="larvitar">Larvitar</h1>
 <p><a href="https://github.com/dvisionlab/Larvitar"><img src="https://img.shields.io/badge/dynamic/json.svg?label=type-coverage&amp;prefix=%E2%89%A5&amp;suffix=%25&amp;query=$.typeCoverage.atLeast&amp;uri=https%3A%2F%2Fraw.githubusercontent.com%2Fplantain-00%2Ftype-coverage%2Fmaster%2Fpackage.json" alt="type-coverage"></a></p>
 <h2 id="dicom-image-toolkit-for-cornerstonejs">Dicom Image Toolkit for CornerstoneJS</h2>
-<h3 id="current-version%3A-2.4.11">Current version: 2.4.11</h3>
-<h3 id="latest-published-release%3A-2.4.11">Latest Published Release: 2.4.11</h3>
+<h3 id="current-version%3A-2.4.12">Current version: 2.4.12</h3>
+<h3 id="latest-published-release%3A-2.4.12">Latest Published Release: 2.4.12</h3>
 <p>This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornerstone-js environment.</p>
 <h2 id="features%3A">Features:</h2>
 <ul>

imaging/imageLoading.ts

@@ -20,7 +20,10 @@ import { loadReslicedImage } from "./loaders/resliceLoader";
 import { loadMultiFrameImage } from "./loaders/multiframeLoader";
 import { loadDsaImage } from "./loaders/dsaImageLoader";
 import { ImageObject, Instance, Series, StagedProtocol } from "./types";
-import { getLarvitarManager } from "./loaders/commonLoader";
+import {
+  getLarvitarImageTracker,
+  getLarvitarManager
+} from "./loaders/commonLoader";
 
 /**
  * Global standard configuration
@@ -154,6 +157,7 @@ export const updateLoadedStack = function (
   customId?: string,
   sliceIndex?: number
 ) {
+  let imageTracker = getLarvitarImageTracker();
   let lid = seriesData.metadata.larvitarSeriesInstanceUID;
   let sid = seriesData.metadata.seriesUID;
   let ssid = seriesData.metadata.studyUID;
@@ -250,7 +254,7 @@ export const updateLoadedStack = function (
     let imageId = cornerstoneDICOMImageLoader.wadouri.fileManager.add(
       seriesData.file
     ) as string;
-
+    imageTracker[imageId] = lid as string;
     if (sliceIndex !== undefined) {
       allSeriesStack[id].imageIds[sliceIndex] = imageId;
     } else {

imaging/tools/custom/EllipticalRoiUSTool.ts

@@ -1,5 +1,6 @@
 //external imports
 import cornerstoneTools from "cornerstone-tools";
+import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 const external = cornerstoneTools.external;
 const BaseAnnotationTool = cornerstoneTools.importInternal(
   "base/BaseAnnotationTool"
@@ -49,9 +50,10 @@ import {
   Rectangle,
   Stats
 } from "../types";
-import { StoreViewport } from "../../types";
+import { LarvitarManager, Series, StoreViewport } from "../../types";
 import store from "../../imageStore";
-
+import { getLarvitarImageTracker } from "../../loaders/commonLoader";
+import { getLarvitarManager } from "../../loaders/commonLoader";
 /**
  * @public
  * @class EllipticalRoiTool
@@ -199,6 +201,25 @@ export default class EllipticalRoiTool extends BaseAnnotationTool {
     data: MeasurementData
   ) {
     const pixelSpacing: PixelSpacing = getPixelSpacing(image);
+    if (
+      pixelSpacing.rowPixelSpacing ||
+      pixelSpacing.colPixelSpacing === undefined
+    ) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager() as LarvitarManager;
+      if (manager && seriesId) {
+        let series = manager[seriesId] as Series;
+        pixelSpacing.rowPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing![0];
+        pixelSpacing.colPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing![1];
+      }
+    }
 
     const stats: Stats = _calculateStats(
       image,
@@ -237,6 +258,22 @@ export default class EllipticalRoiTool extends BaseAnnotationTool {
       colPixelSpacing = image.columnPixelSpacing;
       rowPixelSpacing = image.rowPixelSpacing;
     }
+    if (rowPixelSpacing || colPixelSpacing === undefined) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        eventData.image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager() as LarvitarManager;
+      if (manager && seriesId) {
+        let series = manager[seriesId] as Series;
+        rowPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![0];
+        colPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![1];
+      }
+    }
     const hasPixelSpacing: boolean =
       rowPixelSpacing != undefined &&
       rowPixelSpacing != 0 &&

imaging/tools/custom/FreehandRoiUSTool.js

@@ -1,5 +1,6 @@
 //external imports
 import csTools from "cornerstone-tools";
+import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 // cornerstone tools imports
 const external = csTools.external;
 const EVENTS = csTools.EVENTS;
@@ -27,6 +28,7 @@ const throttle = csTools.importInternal("util/throttle");
 const freehandUtils = csTools.importInternal("util/freehandUtils");
 const getModule = csTools.getModule;
 const state = getModule("segmentation").state;
+
 const {
   insertOrDelete,
   freehandArea,
@@ -37,7 +39,8 @@ const {
 
 //internal imports
 import store from "../../imageStore";
-
+import { getLarvitarImageTracker } from "../../loaders/commonLoader";
+import { getLarvitarManager } from "../../loaders/commonLoader";
 /**
  * @public
  * @class FreehandRoiTool
@@ -318,6 +321,23 @@ export default class FreehandRoiTool extends BaseAnnotationTool {
       colPixelSpacing = image.columnPixelSpacing;
       rowPixelSpacing = image.rowPixelSpacing;
     }
+    if (rowPixelSpacing || colPixelSpacing === undefined) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager();
+      if (manager && seriesId) {
+        let series = manager[seriesId];
+        rowPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing[0];
+        colPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing[1];
+      }
+    }
+
     const scaling = (colPixelSpacing || 1) * (rowPixelSpacing || 1);
 
     const area = freehandArea(data.handles.points, scaling);
@@ -546,6 +566,24 @@ export default class FreehandRoiTool extends BaseAnnotationTool {
           colPixelSpacing = image.columnPixelSpacing;
           rowPixelSpacing = image.rowPixelSpacing;
         }
+        if (rowPixelSpacing || colPixelSpacing === undefined) {
+          let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+            eventData.image.imageId
+          );
+          let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+          let imageTracker = getLarvitarImageTracker();
+          let seriesId = imageTracker[rootImageId];
+          let manager = getLarvitarManager();
+          if (manager && seriesId) {
+            let series = manager[seriesId];
+            rowPixelSpacing =
+              series.instances[eventData.image.imageId].metadata
+                .pixelSpacing[0];
+            colPixelSpacing =
+              series.instances[eventData.image.imageId].metadata
+                .pixelSpacing[1];
+          }
+        }
 
         if (
           rowPixelSpacing === undefined ||
@@ -1501,7 +1539,7 @@ export default class FreehandRoiTool extends BaseAnnotationTool {
     this._drawingInteractionType = interactionType;
 
     state.isMultiPartToolActive = true;
-    hideToolCursor(this.element);
+    // hideToolCursor(this.element);
 
     // Polygonal Mode
     element.addEventListener(EVENTS.MOUSE_DOWN, this._drawingMouseDownCallback);
@@ -1548,7 +1586,7 @@ export default class FreehandRoiTool extends BaseAnnotationTool {
     state.isMultiPartToolActive = false;
     this._activeDrawingToolReference = null;
     this._drawingInteractionType = null;
-    setToolCursor(this.element, this.svgCursor);
+    //setToolCursor(this.element, this.svgCursor);
 
     element.removeEventListener(
       EVENTS.MOUSE_DOWN,

imaging/tools/custom/LengthUSTool.ts

@@ -1,5 +1,6 @@
 // external libraries
 import cornerstoneTools from "cornerstone-tools";
+import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 const getToolState = cornerstoneTools.getToolState;
 const toolColors = cornerstoneTools.toolColors;
 const draw = cornerstoneTools.importInternal("drawing/draw");
@@ -29,8 +30,10 @@ import {
   EventData
 } from "../types";
 
-import { StoreViewport } from "../../types";
+import { LarvitarManager, Series, StoreViewport } from "../../types";
 import store from "../../imageStore";
+import { getLarvitarImageTracker } from "../../loaders/commonLoader";
+import { getLarvitarManager } from "../../loaders/commonLoader";
 /*
 /**
  *
@@ -194,6 +197,24 @@ export default class LengthTool extends BaseAnnotationTool {
       colPixelSpacing = image.columnPixelSpacing;
       rowPixelSpacing = image.rowPixelSpacing;
     }
+
+    if (rowPixelSpacing || colPixelSpacing === undefined) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        eventData.image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager() as LarvitarManager;
+      if (manager && seriesId) {
+        let series = manager[seriesId] as Series;
+        rowPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![0];
+        colPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![1];
+      }
+    }
+
     const lineWidth: number = toolStyle.getToolWidth();
     const lineDash: boolean = getModule("globalConfiguration").configuration
       .lineDash;

imaging/tools/custom/RectangleRoiUSTool.ts

@@ -1,5 +1,6 @@
 //external imports
 import cornerstoneTools from "cornerstone-tools";
+import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 const external = cornerstoneTools.external;
 const BaseAnnotationTool = cornerstoneTools.importInternal(
   "base/BaseAnnotationTool"
@@ -43,8 +44,10 @@ import {
   Rectangle,
   Stats
 } from "../types";
-import { StoreViewport } from "../../types";
+import { LarvitarManager, Series, StoreViewport } from "../../types";
 import store from "../../imageStore";
+import { getLarvitarImageTracker } from "../../loaders/commonLoader";
+import { getLarvitarManager } from "../../loaders/commonLoader";
 
 /**
  * @public
@@ -172,6 +175,25 @@ export default class RectangleRoiTool extends BaseAnnotationTool {
   ) {
     const pixelSpacing: { colPixelSpacing: number; rowPixelSpacing: number } =
       getPixelSpacing(image);
+    if (
+      pixelSpacing.rowPixelSpacing ||
+      pixelSpacing.colPixelSpacing === undefined
+    ) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager() as LarvitarManager;
+      if (manager && seriesId) {
+        let series = manager[seriesId] as Series;
+        pixelSpacing.rowPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing![0];
+        pixelSpacing.colPixelSpacing =
+          series.instances[image.imageId].metadata.pixelSpacing![1];
+      }
+    }
 
     const stats: Stats = _calculateStats(
       image,
@@ -205,13 +227,27 @@ export default class RectangleRoiTool extends BaseAnnotationTool {
     const context: CanvasRenderingContext2D = getNewContext(
       eventData.canvasContext.canvas
     );
-    let { rowPixelSpacing, colPixelSpacing }: PixelSpacing =
-      getPixelSpacing(image);
+    let { rowPixelSpacing, colPixelSpacing }: PixelSpacing = getPixelSpacing;
     if (this.modality === "US") {
       colPixelSpacing = image.columnPixelSpacing;
       rowPixelSpacing = image.rowPixelSpacing;
     }
-
+    if (rowPixelSpacing || colPixelSpacing === undefined) {
+      let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(
+        eventData.image.imageId
+      );
+      let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
+      let imageTracker = getLarvitarImageTracker();
+      let seriesId = imageTracker[rootImageId];
+      let manager = getLarvitarManager() as LarvitarManager;
+      if (manager && seriesId) {
+        let series = manager[seriesId] as Series;
+        rowPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![0];
+        colPixelSpacing =
+          series.instances[eventData.image.imageId].metadata.pixelSpacing![1];
+      }
+    }
     const hasPixelSpacing: boolean =
       rowPixelSpacing != undefined &&
       rowPixelSpacing != 0 &&

package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "2.4.11",
+  "version": "2.4.12",
   "description": "typescript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",