WS improved

README.md

@@ -8,9 +8,9 @@
 
 ## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 2.5.6
+### Current version: 2.5.7
 
-### Latest Published Release: 2.5.6
+### Latest Published Release: 2.5.7
 
 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-2.5.6">Current version: 2.5.6</h3>
-<h3 id="latest-published-release%3A-2.5.6">Latest Published Release: 2.5.6</h3>
+<h3 id="current-version%3A-2.5.7">Current version: 2.5.7</h3>
+<h3 id="latest-published-release%3A-2.5.7">Latest Published Release: 2.5.7</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>

docs/examples/watershedSegmentationTool.html

@@ -97,6 +97,7 @@
         </button>
       </div>
       <div id="viewer" class="col-8 h-100" style="background-color: black">
+        <canvas id="outputContainer"></canvas>
         <p id="info " style="position: absolute; color: white">
           <b>ctrl+mouse wheel to change brush radius</b><br /><b
             >click to activate watershed segmentation of features with greyscale
@@ -262,7 +263,7 @@
   </pre>
       </div>
     </div>
-    <script src="../../dist/larvitar.js"></script>
+    <script src="./larvitar.js"></script>
     <script src="../../node_modules/cornerstone-core/dist/cornerstone.js"></script>
     <script src="../../node_modules/cornerstone-wado-image-loader/dist/cornerstoneWADOImageLoader.bundle.min.js"></script>
     <script src="../../node_modules/dicom-parser/dist/dicomParser.js"></script>

imaging/tools/custom/utils/watershedSegmentationToolUtils/WSUtils.ts

@@ -56,7 +56,7 @@ export function calculateThresholds(
   const meanNorm = mapToRange(mean, minThreshold, maxThreshold);
   const stdDevNorm = mapToRange(stddev, minThreshold, maxThreshold);
 
-  let xFactor = 1.7;
+  let xFactor = 1;
   xFactor = xFactor;
   let lowerThreshold = meanNorm - xFactor * stdDevNorm;
   let upperThreshold = meanNorm + xFactor * stdDevNorm;

imaging/tools/custom/watershedSegmentationTool.ts

@@ -70,7 +70,8 @@ export default class WSToggleTool extends BaseBrushTool {
     multiImage: false,
     startIndex: null,
     endIndex: null,
-    masksNumber: 10
+    masksNumber: 10,
+    thresholdFactor: 0
   };
   constructor(props = {}) {
     const defaultProps = {
@@ -80,7 +81,8 @@ export default class WSToggleTool extends BaseBrushTool {
         multiImage: false,
         startIndex: null,
         endIndex: null,
-        masksNumber: 10
+        masksNumber: 10,
+        thresholdFactor: 0
       },
       mixins: ["renderBrushMixin"]
     };
@@ -319,7 +321,12 @@ export default class WSToggleTool extends BaseBrushTool {
           lowerThreshold,
           upperThreshold
         ).then(result => {
-          this.maskArrayCurrentImage = result;
+          this._labelPicker(circleArray, image, result);
+          let filteredMarkersArray = result.map(value =>
+            value === this.pickedLabel ? value : 0
+          );
+
+          this.maskArrayCurrentImage = filteredMarkersArray;
           labelmap2D.pixelData = this.maskArrayCurrentImage as number[];
           external.cornerstone.updateImage(evt.detail.element);
           (DEFAULT_TOOLS["WSToggle"] as WSToolConfig).configuration.onload =
@@ -648,6 +655,9 @@ export default class WSToggleTool extends BaseBrushTool {
         // Combine the binary masks using bitwise_and
         cv.bitwise_and(lowerBinary, upperBinary, gray);
 
+        //const element = document.getElementById("outputContainer");
+        // Display the result using cv.imshow
+        //cv.imshow(element, gray);
         // get background
         let M = cv.Mat.ones(3, 3, cv.CV_8U);
         cv.erode(gray, gray, M);
@@ -656,8 +666,15 @@ export default class WSToggleTool extends BaseBrushTool {
         // distance transform
         cv.distanceTransform(opening, distTrans, cv.DIST_L2, 5);
         cv.normalize(distTrans, distTrans, 1, 0, cv.NORM_INF);
-        // get foreground
-        cv.threshold(distTrans, Fg, 0, 255, cv.THRESH_BINARY);
+        // get foreground-> configurable factor (0 for lungs, 0.4 for mediastinum)
+        cv.threshold(
+          distTrans,
+          Fg,
+          this.configuration.thresholdFactor * 1,
+          255,
+          cv.THRESH_BINARY
+        );
+        //cv.imshow(element, Fg);
         Fg.convertTo(Fg, cv.CV_8U, 1, 0);
         cv.subtract(Bg, Fg, unknown);
         // get connected components markers
@@ -675,6 +692,7 @@ export default class WSToggleTool extends BaseBrushTool {
 
         cv.cvtColor(src, src, cv.COLOR_RGBA2RGB, 0);
         cv.watershed(src, markers);
+
         //postProcess(markers: cv.Mat,gray: cv.Mat,markersArray: number[]) //OPTIONAL
 
         shiftAndZeroOut(markersArray, 100);

imaging/tools/types.d.ts

@@ -67,6 +67,7 @@ export type WSConfig = {
   endIndex: number | null;
   masksNumber: number;
   onload?: boolean;
+  thresholdFactor: number;
 };
 export type WSToolConfig = {
   name: string;

package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "2.5.6",
+  "version": "2.5.7",
   "description": "typescript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",