feat: cornerstone3D stack and volume viewports (#2787)

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <[email protected]> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <[email protected]> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <[email protected]> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <[email protected]> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <[email protected]> Co-authored-by: Bill Wallace <[email protected]>
OHIF · Jul 27, 2022 · bd1c38c · bd1c38c
1 parent 86dcaf6
commit bd1c38c
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diff --git a/.eslintrc.json b/.eslintrc.json
@@ -1,11 +1,18 @@
 {
+  "plugins": [
+    "@typescript-eslint",
+    "import",
+    "eslint-plugin-tsdoc",
+    "prettier"
+  ],
   "extends": [
     "react-app",
     "eslint:recommended",
     "plugin:react/recommended",
+    "plugin:@typescript-eslint/recommended",
     "plugin:prettier/recommended"
   ],
-  "parser": "babel-eslint",
+  "parser": "@typescript-eslint/parser",
   "env": {
     "jest": true
   },

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -11,5 +11,18 @@
       "url": "http://localhost:3000",
       "webRoot": "${workspaceFolder}"
     }
+    // {
+    //   "name": "Debug Jest Tests",
+    //   "type": "node",
+    //   "request": "launch",
+    //   "runtimeArgs": [
+    //     "--inspect-brk",
+    //     "${workspaceRoot}/node_modules/.bin/jest",
+    //     "--runInBand"
+    //   ],
+    //   "console": "integratedTerminal",
+    //   "internalConsoleOptions": "neverOpen",
+    //   "port": 9229
+    // }
   ]
 }
diff --git a/.webpack/rules/transpileJavaScript.js b/.webpack/rules/transpileJavaScript.js
@@ -4,7 +4,6 @@ function transpileJavaScript(mode) {
   const exclude =
     mode === 'production'
       ? excludeNodeModulesExcept([
-          'vtk.js',
           // 'dicomweb-client',
           // https://github.com/react-dnd/react-dnd/blob/master/babel.config.js
           'react-dnd',
@@ -21,7 +20,8 @@ function transpileJavaScript(mode) {
       : excludeNodeModulesExcept([]);
 
   return {
-    test: /\.(mjs|js|jsx)?$/,
+    // Include mjs, ts, tsx, js, and jsx files.
+    test: /\.(mjs|ts|js)x?$/,
     // These are packages that are not transpiled to our lowest supported
     // JS version (currently ES5). Most of these leverage ES6+ features,
     // that we need to transpile to a different syntax.

diff --git a/.webpack/webpack.base.js b/.webpack/webpack.base.js
@@ -12,6 +12,8 @@ const CopyPlugin = require('copy-webpack-plugin');
 
 // ~~ PackageJSON
 const PACKAGE = require('../platform/viewer/package.json');
+// const vtkRules = require('vtk.js/Utilities/config/dependency.js').webpack.core
+//   .rules;
 // ~~ RULES
 const loadShadersRule = require('./rules/loadShaders.js');
 const loadWebWorkersRule = require('./rules/loadWebWorkers.js');
@@ -66,19 +68,28 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
       children: false,
       warnings: true,
     },
+    devServer: {
+      open: true,
+      port: 3000,
+      historyApiFallback: true,
+      headers: {
+        'Cross-Origin-Embedder-Policy': 'require-corp',
+        'Cross-Origin-Opener-Policy': 'same-origin',
+      },
+    },
     module: {
       rules: [
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
-        loadShadersRule,
+        // loadShadersRule,
         {
           test: /\.m?js/,
           resolve: {
             fullySpecified: false,
           },
         },
         cssToJavaScript,
-      ],
+      ], //.concat(vtkRules),
     },
     resolve: {
       mainFields: ['module', 'browser', 'main'],
@@ -106,7 +117,7 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
         SRC_DIR,
       ],
       // Attempt to resolve these extensions in order.
-      extensions: ['.js', '.jsx', '.json', '*'],
+      extensions: ['.js', '.jsx', '.json', '.ts', '.tsx', '*'],
       // symlinked resources are resolved to their real path, not their symlinked location
       symlinks: true,
       fallback: { fs: false, path: false, zlib: false },

diff --git a/README.md b/README.md
@@ -190,13 +190,14 @@ you'll see the following:
 ├── extensions               #
 │   ├── _example             # Skeleton of example extension
 │   ├── default              #
-│   ├── cornerstone          # 2D images w/ Cornerstone.js
-│   ├── dicom-sr             #
+│   ├── cornerstone       # image rendering and tools w/ Cornerstone
+│   ├── cornerstone- dicom-sr #
 │   └── measurement-tracking #
 │
 ├── modes                    #
 │   ├── _example             # Skeleton of example mode
-│   └── longitudinal         #
+│   ├── basic-dev-mode       # Basic development mode
+│   └── longitudinal         # Longitudinal mode (measurement tracking)
 │
 ├── platform                 #
 │   ├── core                 # Business Logic

diff --git a/babel.config.js b/babel.config.js
@@ -1,10 +1,16 @@
-const aliases = require('./aliases.config');
-const path = require('path');
-
 // https://babeljs.io/docs/en/options#babelrcroots
 module.exports = {
   babelrcRoots: ['./platform/*', './extensions/*', './modes/*'],
-  plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'],
+  presets: [
+    '@babel/preset-env',
+    '@babel/preset-react',
+    '@babel/preset-typescript',
+  ],
+  plugins: [
+    'inline-react-svg',
+    '@babel/plugin-proposal-class-properties',
+    '@babel/plugin-transform-typescript',
+  ],
   env: {
     test: {
       presets: [
@@ -17,19 +23,22 @@ module.exports = {
           },
         ],
         '@babel/preset-react',
+        '@babel/preset-typescript',
       ],
       plugins: [
         '@babel/plugin-proposal-object-rest-spread',
         '@babel/plugin-syntax-dynamic-import',
         '@babel/plugin-transform-regenerator',
         '@babel/plugin-transform-runtime',
+        '@babel/plugin-transform-typescript',
       ],
     },
     production: {
       presets: [
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
+        '@babel/preset-typescript',
       ],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
     },
@@ -38,6 +47,7 @@ module.exports = {
         // WebPack handles ES6 --> Target Syntax
         ['@babel/preset-env', { modules: false }],
         '@babel/preset-react',
+        '@babel/preset-typescript',
       ],
       plugins: ['react-hot-loader/babel'],
       ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],

diff --git a/extensions/dicom-sr/.webpack/webpack.dev.js → ...nerstone-dicom-sr/.webpack/webpack.dev.js b/extensions/dicom-sr/.webpack/webpack.dev.js → ...nerstone-dicom-sr/.webpack/webpack.dev.js
diff --git a/extensions/dicom-sr/.webpack/webpack.prod.js → ...erstone-dicom-sr/.webpack/webpack.prod.js b/extensions/dicom-sr/.webpack/webpack.prod.js → ...erstone-dicom-sr/.webpack/webpack.prod.js
@@ -14,7 +14,6 @@ module.exports = (env, argv) => {
   const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
 
   return merge(commonConfig, {
-    devtool: 'source-map',
     stats: {
       colors: true,
       hash: true,

diff --git a/extensions/dicom-sr/LICENSE → extensions/cornerstone-dicom-sr/LICENSE b/extensions/dicom-sr/LICENSE → extensions/cornerstone-dicom-sr/LICENSE
diff --git a/extensions/dicom-sr/README.md → extensions/cornerstone-dicom-sr/README.md b/extensions/dicom-sr/README.md → extensions/cornerstone-dicom-sr/README.md
diff --git a/extensions/dicom-sr/babel.config.js → ...ions/cornerstone-dicom-sr/babel.config.js b/extensions/dicom-sr/babel.config.js → ...ions/cornerstone-dicom-sr/babel.config.js
diff --git a/extensions/dicom-sr/package.json → extensions/cornerstone-dicom-sr/package.json b/extensions/dicom-sr/package.json → extensions/cornerstone-dicom-sr/package.json
@@ -1,12 +1,12 @@
 {
-  "name": "@ohif/extension-dicom-sr",
+  "name": "@ohif/extension-cornerstone-dicom-sr",
   "version": "3.0.0",
   "description": "OHIF extension for an SR Cornerstone Viewport",
   "author": "OHIF",
   "license": "MIT",
   "repository": "OHIF/Viewers",
   "main": "dist/index.umd.js",
-  "module": "src/index.js",
+  "module": "src/index.tsx",
   "engines": {
     "node": ">=14",
     "npm": ">=6",
@@ -34,21 +34,18 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
-    "cornerstone-core": "^2.6.0",
-    "cornerstone-math": "^0.1.9",
-    "cornerstone-tools": "6.0.2",
-    "cornerstone-wado-image-loader": "4.0.4",
-    "dcmjs": "0.16.1",
+    "dcmjs": "^0.24.5",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",
     "react": "^17.0.2",
-    "react-cornerstone-viewport": "4.1.2",
     "@ohif/extension-cornerstone": "^3.0.0",
     "@ohif/extension-measurement-tracking": "^3.0.0"
   },
   "dependencies": {
     "@babel/runtime": "7.16.3",
-    "classnames": "^2.2.6"
+    "classnames": "^2.2.6",
+    "@cornerstonejs/core": "^0.13.11",
+    "@cornerstonejs/tools": "^0.20.15"
   }
 }
diff --git a/extensions/cornerstone-dicom-sr/src/commandsModule.js b/extensions/cornerstone-dicom-sr/src/commandsModule.js
@@ -0,0 +1,143 @@
+import { metaData, utilities } from '@cornerstonejs/core';
+
+import OHIF from '@ohif/core';
+import dcmjs from 'dcmjs';
+
+import getFilteredCornerstoneToolState from './utils/getFilteredCornerstoneToolState';
+
+const { MeasurementReport } = dcmjs.adapters.Cornerstone3D;
+const { log } = OHIF;
+
+/**
+ *
+ * @param measurementData An array of measurements from the measurements service
+ * that you wish to serialize.
+ * @param additionalFindingTypes toolTypes that should be stored with labels as Findings
+ * @param options Naturalized DICOM JSON headers to merge into the displaySet.
+ *
+ */
+const _generateReport = (
+  measurementData,
+  additionalFindingTypes,
+  options = {}
+) => {
+  const filteredToolState = getFilteredCornerstoneToolState(
+    measurementData,
+    additionalFindingTypes
+  );
+
+  const report = MeasurementReport.generateReport(
+    filteredToolState,
+    metaData,
+    utilities.worldToImageCoords
+  );
+
+  const { dataset } = report;
+
+  // Add in top level series options
+  Object.assign(dataset, options);
+
+  return dataset;
+};
+
+const commandsModule = ({}) => {
+  const actions = {
+    /**
+     *
+     * @param measurementData An array of measurements from the measurements service
+     * @param additionalFindingTypes toolTypes that should be stored with labels as Findings
+     * @param options Naturalized DICOM JSON headers to merge into the displaySet.
+     * as opposed to Finding Sites.
+     * that you wish to serialize.
+     */
+    downloadReport: ({
+      measurementData,
+      additionalFindingTypes,
+      options = {},
+    }) => {
+      const srDataset = actions.generateReport(
+        measurementData,
+        additionalFindingTypes,
+        options
+      );
+      const reportBlob = dcmjs.data.datasetToBlob(srDataset);
+
+      //Create a URL for the binary.
+      var objectUrl = URL.createObjectURL(reportBlob);
+      window.location.assign(objectUrl);
+    },
+
+    /**
+     *
+     * @param measurementData An array of measurements from the measurements service
+     * that you wish to serialize.
+     * @param dataSource The dataSource that you wish to use to persist the data.
+     * @param additionalFindingTypes toolTypes that should be stored with labels as Findings
+     * @param options Naturalized DICOM JSON headers to merge into the displaySet.
+     * @return The naturalized report
+     */
+    storeMeasurements: async ({
+      measurementData,
+      dataSource,
+      additionalFindingTypes,
+      options = {},
+    }) => {
+      // TODO -> Eventually use the measurements directly and not the dcmjs adapter,
+      // But it is good enough for now whilst we only have cornerstone as a datasource.
+      log.info('[DICOMSR] storeMeasurements');
+
+      if (!dataSource || !dataSource.store || !dataSource.store.dicom) {
+        log.error(
+          '[DICOMSR] datasource has no dataSource.store.dicom endpoint!'
+        );
+        return Promise.reject({});
+      }
+
+      try {
+        const naturalizedReport = _generateReport(
+          measurementData,
+          additionalFindingTypes,
+          options
+        );
+        const { StudyInstanceUID } = naturalizedReport;
+
+        await dataSource.store.dicom(naturalizedReport);
+
+        if (StudyInstanceUID) {
+          dataSource.deleteStudyMetadataPromise(StudyInstanceUID);
+        }
+
+        return naturalizedReport;
+      } catch (error) {
+        console.warn(error);
+        log.error(
+          `[DICOMSR] Error while saving the measurements: ${error.message}`
+        );
+        throw new Error(
+          error.message || 'Error while saving the measurements.'
+        );
+      }
+    },
+  };
+
+  const definitions = {
+    downloadReport: {
+      commandFn: actions.downloadReport,
+      storeContexts: [],
+      options: {},
+    },
+    storeMeasurements: {
+      commandFn: actions.storeMeasurements,
+      storeContexts: [],
+      options: {},
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+    defaultContext: 'CORNERSTONE_STRUCTURED_REPORT',
+  };
+};
+
+export default commandsModule;
diff --git a/...ons/dicom-sr/src/constants/scoordTypes.js → ...one-dicom-sr/src/constants/scoordTypes.js b/...ons/dicom-sr/src/constants/scoordTypes.js → ...one-dicom-sr/src/constants/scoordTypes.js