feat(Segmentation): download RTSS from Labelmap(#3692)

Co-authored-by: Alireza <[email protected]>
OHIF · Oct 6, 2023 · 40673f6 · 40673f6
1 parent eab42c1
commit 40673f6
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Showing 22 changed files with 177 additions and 429 deletions.
diff --git a/extensions/cornerstone-dicom-seg/package.json b/extensions/cornerstone-dicom-seg/package.json
@@ -44,7 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/tools": "^1.19.4",
+    "@cornerstonejs/tools": "^1.20.1",
+    "@cornerstonejs/adapters": "^1.20.1",
+    "@kitware/vtk.js": "27.3.1",
     "react-color": "^2.19.3"
   }
 }
diff --git a/extensions/cornerstone-dicom-seg/src/commandsModule.ts b/extensions/cornerstone-dicom-seg/src/commandsModule.ts
@@ -2,22 +2,37 @@ import dcmjs from 'dcmjs';
 import { createReportDialogPrompt } from '@ohif/extension-default';
 import { ServicesManager, Types } from '@ohif/core';
 import { cache, metaData } from '@cornerstonejs/core';
-import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
-import { adaptersSEG, helpers } from '@cornerstonejs/adapters';
-import { DicomMetadataStore } from '@ohif/core';
+import {
+  segmentation as cornerstoneToolsSegmentation,
+  Enums as cornerstoneToolsEnums,
+} from '@cornerstonejs/tools';
+import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
+import { classes, DicomMetadataStore } from '@ohif/core';
+
+import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchingSquares';
+import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
+import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
 
 import {
   updateViewportsForSegmentationRendering,
   getUpdatedViewportsForSegmentation,
   getTargetViewport,
 } from './utils/hydrationUtils';
 
+const { datasetToBlob } = dcmjs.data;
+
 const {
   Cornerstone3D: {
     Segmentation: { generateLabelMaps2DFrom3D, generateSegmentation },
   },
 } = adaptersSEG;
 
+const {
+  Cornerstone3D: {
+    RTSS: { generateRTSSFromSegmentations },
+  },
+} = adaptersRT;
+
 const { downloadDICOMData } = helpers;
 
 const commandsModule = ({
@@ -348,6 +363,40 @@ const commandsModule = ({
 
       return naturalizedReport;
     },
+    /**
+     * Converts segmentations into RTSS for download.
+     * This sample function retrieves all segentations and passes to
+     * cornerstone tool adapter to convert to DICOM RTSS format. It then
+     * converts dataset to downloadable blob.
+     *
+     */
+    downloadRTSS: ({ segmentationId }) => {
+      const segmentations = segmentationService.getSegmentation(segmentationId);
+      const vtkUtils = {
+        vtkImageMarchingSquares,
+        vtkDataArray,
+        vtkImageData,
+      };
+
+      const RTSS = generateRTSSFromSegmentations(
+        segmentations,
+        classes.MetadataProvider,
+        DicomMetadataStore,
+        cache,
+        cornerstoneToolsEnums,
+        vtkUtils
+      );
+
+      try {
+        const reportBlob = datasetToBlob(RTSS);
+
+        //Create a URL for the binary.
+        const objectUrl = URL.createObjectURL(reportBlob);
+        window.location.assign(objectUrl);
+      } catch (e) {
+        console.warn(e);
+      }
+    },
   };
 
   const definitions = {
@@ -372,6 +421,9 @@ const commandsModule = ({
     storeSegmentation: {
       commandFn: actions.storeSegmentation,
     },
+    downloadRTSS: {
+      commandFn: actions.downloadRTSS,
+    },
   };
 
   return {

diff --git a/extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx b/extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx
@@ -1,7 +1,7 @@
 import { createReportAsync } from '@ohif/extension-default';
 import React, { useEffect, useState, useCallback } from 'react';
 import PropTypes from 'prop-types';
-import { SegmentationGroupTable } from '@ohif/ui';
+import { SegmentationGroupTable, LegacyButtonGroup, LegacyButton } from '@ohif/ui';
 
 import callInputDialog from './callInputDialog';
 import callColorPickerDialog from './colorPickerDialog';
@@ -215,6 +215,12 @@ export default function PanelSegmentation({
     }
   };
 
+  const onSegmentationDownloadRTSS = segmentationId => {
+    commandsManager.runCommand('downloadRTSS', {
+      segmentationId,
+    });
+  };
+
   return (
     <>
       <div className="ohif-scrollbar flex min-h-0 flex-auto select-none flex-col justify-between overflow-auto">
@@ -227,6 +233,7 @@ export default function PanelSegmentation({
           onSegmentationClick={onSegmentationClick}
           onSegmentationDelete={onSegmentationDelete}
           onSegmentationDownload={onSegmentationDownload}
+          onSegmentationDownloadRTSS={onSegmentationDownloadRTSS}
           storeSegmentation={storeSegmentation}
           onSegmentationEdit={onSegmentationEdit}
           onSegmentClick={onSegmentClick}

diff --git a/extensions/cornerstone-dicom-seg/src/panels/SegmentationToolbox.tsx b/extensions/cornerstone-dicom-seg/src/panels/SegmentationToolbox.tsx
@@ -10,9 +10,9 @@ const TOOL_TYPES = {
   SPHERE_BRUSH: 'SphereBrush',
   CIRCULAR_ERASER: 'CircularEraser',
   SPHERE_ERASER: 'SphereEraser',
-  CIRCLE_SCISSOR: 'CircleScissor',
-  RECTANGLE_SCISSOR: 'RectangleScissor',
-  SPHERE_SCISSOR: 'SphereScissor',
+  CIRCLE_SHAPE: 'CircleScissor',
+  RECTANGLE_SHAPE: 'RectangleScissor',
+  SPHERE_SHAPE: 'SphereScissor',
   THRESHOLD_CIRCULAR_BRUSH: 'ThresholdCircularBrush',
   THRESHOLD_SPHERE_BRUSH: 'ThresholdSphereBrush',
 };
@@ -31,7 +31,7 @@ const initialState = {
     brushSize: 15,
     mode: 'CircularEraser', // Can be 'CircularEraser' or 'SphereEraser'
   },
-  Scissors: {
+  Shapes: {
     brushSize: 15,
     mode: 'CircleScissor', // E.g., 'CircleScissor', 'RectangleScissor', or 'SphereScissor'
   },
@@ -301,24 +301,24 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
           ],
         },
         {
-          name: 'Scissor',
-          icon: 'icon-tool-scissor',
+          name: 'Shapes',
+          icon: 'icon-tool-shape',
           disabled: !toolsEnabled,
           active:
-            state.activeTool === TOOL_TYPES.CIRCLE_SCISSOR ||
-            state.activeTool === TOOL_TYPES.RECTANGLE_SCISSOR ||
-            state.activeTool === TOOL_TYPES.SPHERE_SCISSOR,
-          onClick: () => setToolActive(TOOL_TYPES.CIRCLE_SCISSOR),
+            state.activeTool === TOOL_TYPES.CIRCLE_SHAPE ||
+            state.activeTool === TOOL_TYPES.RECTANGLE_SHAPE ||
+            state.activeTool === TOOL_TYPES.SPHERE_SHAPE,
+          onClick: () => setToolActive(TOOL_TYPES.CIRCLE_SHAPE),
           options: [
             {
               name: 'Mode',
               type: 'radio',
-              value: state.Scissors.mode,
-              id: 'scissor-mode',
+              value: state.Shapes.mode,
+              id: 'shape-mode',
               values: [
-                { value: TOOL_TYPES.CIRCLE_SCISSOR, label: 'Circle' },
-                { value: TOOL_TYPES.RECTANGLE_SCISSOR, label: 'Rectangle' },
-                { value: TOOL_TYPES.SPHERE_SCISSOR, label: 'Sphere' },
+                { value: TOOL_TYPES.CIRCLE_SHAPE, label: 'Circle' },
+                { value: TOOL_TYPES.RECTANGLE_SHAPE, label: 'Rectangle' },
+                { value: TOOL_TYPES.SPHERE_SHAPE, label: 'Sphere' },
               ],
               onChange: value => setToolActive(value),
             },

diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json
@@ -44,9 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.19.4",
-    "@cornerstonejs/core": "^1.19.4",
-    "@cornerstonejs/tools": "^1.19.4",
+    "@cornerstonejs/adapters": "^1.20.1",
+    "@cornerstonejs/core": "^1.20.1",
+    "@cornerstonejs/tools": "^1.20.1",
     "classnames": "^2.3.2"
   }
 }
diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json
@@ -36,7 +36,7 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.2",
     "@cornerstonejs/codec-openjph": "^2.4.2",
-    "@cornerstonejs/dicom-image-loader": "^1.19.4",
+    "@cornerstonejs/dicom-image-loader": "^1.20.1",
     "@ohif/core": "3.7.0-beta.101",
     "@ohif/ui": "3.7.0-beta.101",
     "dcmjs": "^0.29.6",
@@ -52,10 +52,10 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.19.4",
-    "@cornerstonejs/core": "^1.19.4",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.19.4",
-    "@cornerstonejs/tools": "^1.19.4",
+    "@cornerstonejs/adapters": "^1.20.1",
+    "@cornerstonejs/core": "^1.20.1",
+    "@cornerstonejs/streaming-image-volume-loader": "^1.20.1",
+    "@cornerstonejs/tools": "^1.20.1",
     "@kitware/vtk.js": "27.3.1",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "4.0.8",

diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json
@@ -30,8 +30,8 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@cornerstonejs/core": "^1.19.4",
-    "@cornerstonejs/tools": "^1.19.4",
+    "@cornerstonejs/core": "^1.20.1",
+    "@cornerstonejs/tools": "^1.20.1",
     "@ohif/core": "3.7.0-beta.101",
     "@ohif/extension-cornerstone-dicom-sr": "3.7.0-beta.101",
     "@ohif/ui": "3.7.0-beta.101",