feat: new Total Metabolic Tumor Volume tmtv (#2866)

* fix: ptDisplaySet metadata problem * fix: typo in xhrHeader field * fix: temporary fix for crosshairs on reload data * fix hotkey bug for input fields * upgrade docusarusu to stable release * circle ci node upgrade * cypress node upgrade * bump node in netlify * bump node version * remove versioned docs * update resources * fix: webpack injection of plugins * fix meaningful label for panels * add reviews and fix cli for creation * copy over chunks if exists in the build * edit templates * edit templates * fix yarn lock * fix(plugin):Deploy on windows is broken Co-authored-by: Bill Wallace <[email protected]>
OHIF · Aug 17, 2022 · 10b4ed5 · 10b4ed5
1 parent ae897c4
commit 10b4ed5
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Showing 41 changed files with 2,033 additions and 824 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -18,17 +18,17 @@ executors:
   # Custom executor to override Cypress config
   deploy-to-prod-executor:
     docker:
-      - image: cimg/node:14.18
+      - image: cimg/node:16.14
         environment:
           CYPRESS_BASE_URL: https://ohif-staging.netlify.com/
   chrome-and-pacs:
     docker:
       # Primary container image where all steps run.
-      - image: 'cypress/browsers:node14.17.0-chrome88-ff89'
+      - image: 'cypress/browsers:node16.14.2-slim-chrome103-ff102'
 
 defaults: &defaults
   docker:
-    - image: cimg/node:14.18-browsers
+    - image: cimg/node:16.14-browsers
       environment:
         TERM: xterm # Enable colors in term
         QUICK_BUILD: true
@@ -181,7 +181,7 @@ jobs:
 
   DEPLOY_TO_DEV:
     docker:
-      - image: circleci/node:14.17.0
+      - image: circleci/node:16.14.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 32708787-c9b0-4634-b50f-7ca41952da77
@@ -196,7 +196,7 @@ jobs:
 
   DEPLOY_TO_STAGING:
     docker:
-      - image: circleci/node:14.17.0
+      - image: circleci/node:16.14.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: c7502ae3-b150-493c-8422-05701e44a969
@@ -211,7 +211,7 @@ jobs:
 
   DEPLOY_TO_PRODUCTION:
     docker:
-      - image: circleci/node:14.17.0
+      - image: circleci/node:16.14.0
         environment:
           TERM: xterm
           NETLIFY_SITE_ID: 79c4a5da-5c95-4dc9-84f7-45fd9dfe21b0

diff --git a/.node-version b/.node-version
@@ -1 +1 @@
-14.18.0
+16.14.0
diff --git a/.prettierrc b/.prettierrc
@@ -4,5 +4,6 @@
   "proseWrap": "always",
   "tabWidth": 2,
   "semi": true,
-  "singleQuote": true
+  "singleQuote": true,
+  "arrowParens": "avoid"
 }
diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json
@@ -45,7 +45,7 @@
   "dependencies": {
     "@babel/runtime": "7.16.3",
     "classnames": "^2.2.6",
-    "@cornerstonejs/core": "^0.13.11",
-    "@cornerstonejs/tools": "^0.20.15"
+    "@cornerstonejs/core": "^0.14.4",
+    "@cornerstonejs/tools": "^0.21.7"
   }
 }
diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json
@@ -29,7 +29,7 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
-    "cornerstone-wado-image-loader": "^4.2.0",
+    "cornerstone-wado-image-loader": "^4.2.1",
     "dcmjs": "^0.24.5",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
@@ -43,9 +43,9 @@
   },
   "dependencies": {
     "@babel/runtime": "7.17.9",
-    "@cornerstonejs/core": "^0.13.11",
-    "@cornerstonejs/streaming-image-volume-loader": "^0.4.10",
-    "@cornerstonejs/tools": "^0.20.15",
+    "@cornerstonejs/core": "^0.14.4",
+    "@cornerstonejs/streaming-image-volume-loader": "^0.4.16",
+    "@cornerstonejs/tools": "^0.21.7",
     "@kitware/vtk.js": "^24.18.7",
     "dom-to-image": "^2.6.0",
     "lodash.debounce": "4.0.8",

diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx
@@ -195,9 +195,11 @@ const OHIFCornerstoneViewport = React.memo(props => {
             DisplaySetService
           );
 
+          const keepCamera = true;
           CornerstoneViewportService.updateViewport(
             viewportIndex,
-            newViewportData
+            newViewportData,
+            keepCamera
           );
 
           setViewportData(newViewportData);

diff --git a/extensions/cornerstone/src/Viewport/Overlays/CornerstoneOverlays.tsx b/extensions/cornerstone/src/Viewport/Overlays/CornerstoneOverlays.tsx
@@ -41,7 +41,7 @@ function CornerstoneOverlays(props) {
       viewportIndex
     );
 
-    if (viewportInfo?.viewportOptions?.customViewportOptions?.hideOverlays) {
+    if (viewportInfo?.viewportOptions?.customViewportProps?.hideOverlays) {
       return null;
     }
   }

diff --git a/extensions/cornerstone/src/commandsModule.js b/extensions/cornerstone/src/commandsModule.js
@@ -115,19 +115,18 @@ const commandsModule = ({ servicesManager }) => {
       const renderingEngine = CornerstoneViewportService.getRenderingEngine();
       const viewport = renderingEngine.getViewport(viewportId);
 
-      const lower = windowCenterNum - windowWidthNum / 2.0;
-      const upper = windowCenterNum + windowWidthNum / 2.0;
-
-      if (viewport instanceof StackViewport) {
-        viewport.setProperties({
-          voiRange: {
-            upper,
-            lower,
-          },
-        });
+      const { lower, upper } = csUtils.windowLevel.toLowHighRange(
+        windowWidthNum,
+        windowCenterNum
+      );
 
-        viewport.render();
-      }
+      viewport.setProperties({
+        voiRange: {
+          upper,
+          lower,
+        },
+      });
+      viewport.render();
     },
     toggleCrosshairs({ toolGroupId, toggledState }) {
       const toolName = 'Crosshairs';

diff --git a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts
@@ -166,14 +166,12 @@ class CornerstoneViewportService implements IViewportService {
     const viewportInfo = this.viewportsInfo.get(viewportIndex);
     viewportInfo.setRenderingEngineId(renderingEngine.id);
 
-    const {
-      viewportOptions,
-      displaySetOptions,
-    } = this._getViewportAndDisplaySetOptions(
-      publicViewportOptions,
-      publicDisplaySetOptions,
-      viewportInfo
-    );
+    const { viewportOptions, displaySetOptions } =
+      this._getViewportAndDisplaySetOptions(
+        publicViewportOptions,
+        publicDisplaySetOptions,
+        viewportInfo
+      );
 
     viewportInfo.setViewportOptions(viewportOptions);
     viewportInfo.setDisplaySetOptions(displaySetOptions);
@@ -400,48 +398,57 @@ class CornerstoneViewportService implements IViewportService {
       volume.load();
     });
 
-    this.setVolumesForViewport(viewport, volumeInputArray);
+    // This returns the async continuation only
+    return this.setVolumesForViewport(viewport, volumeInputArray);
   }
 
-  public setVolumesForViewport(viewport, volumeInputArray) {
-    viewport.setVolumes(volumeInputArray).then(() => {
-      const viewportInfo = this.getViewportInfo(viewport.id);
-      const initialImageOptions = viewportInfo.getInitialImageOptions();
-
-      if (
-        initialImageOptions &&
-        (initialImageOptions.preset !== undefined ||
-          initialImageOptions.index !== undefined)
-      ) {
-        const { index, preset } = initialImageOptions;
-
-        const { numberOfSlices } = csUtils.getImageSliceDataForVolumeViewport(
-          viewport
-        );
-
-        const imageIndex = this._getInitialImageIndex(
-          numberOfSlices,
-          index,
-          preset
-        );
-
-        csToolsUtils.jumpToSlice(viewport.element, {
-          imageIndex,
-        });
-      }
+  public async setVolumesForViewport(viewport, volumeInputArray) {
+    await viewport.setVolumes(volumeInputArray);
 
-      viewport.render();
-    });
+    const viewportInfo = this.getViewportInfo(viewport.id);
+    const initialImageOptions = viewportInfo.getInitialImageOptions();
+
+    if (
+      initialImageOptions &&
+      (initialImageOptions.preset !== undefined ||
+        initialImageOptions.index !== undefined)
+    ) {
+      const { index, preset } = initialImageOptions;
+
+      const { numberOfSlices } =
+        csUtils.getImageSliceDataForVolumeViewport(viewport);
+
+      const imageIndex = this._getInitialImageIndex(
+        numberOfSlices,
+        index,
+        preset
+      );
+
+      csToolsUtils.jumpToSlice(viewport.element, {
+        imageIndex,
+      });
+    }
+
+    viewport.render();
   }
 
-  public updateViewport(viewportIndex, viewportData) {
+  // Todo: keepCamera is an interim solution until we have a better solution for
+  // keeping the camera position when the viewport data is changed
+  public updateViewport(viewportIndex, viewportData, keepCamera = false) {
     const viewportInfo = this.getViewportInfoByIndex(viewportIndex);
 
     const viewportId = viewportInfo.getViewportId();
     const viewport = this.getCornerstoneViewport(viewportId);
+    const viewportCamera = viewport.getCamera();
 
     if (viewport instanceof VolumeViewport) {
-      this._setVolumeViewport(viewport, viewportData, viewportInfo);
+      this._setVolumeViewport(viewport, viewportData, viewportInfo).then(() => {
+        if (keepCamera) {
+          viewport.setCamera(viewportCamera);
+          viewport.render();
+        }
+      });
+
       return;
     }
 

diff --git a/extensions/cornerstone/src/services/ViewportService/Viewport.ts b/extensions/cornerstone/src/services/ViewportService/Viewport.ts
@@ -19,7 +19,7 @@ export type ViewportOptions = {
   initialView?: string;
   syncGroups?: SyncGroup[];
   initialImageOptions?: InitialImageOptions;
-  customViewportOptions?: Record<string, unknown>;
+  customViewportProps?: Record<string, unknown>;
 };
 
 export type PublicViewportOptions = {
@@ -31,7 +31,7 @@ export type PublicViewportOptions = {
   initialView?: string;
   syncGroups?: SyncGroup[];
   initialImageOptions?: InitialImageOptions;
-  customViewportOptions?: Record<string, unknown>;
+  customViewportProps?: Record<string, unknown>;
 };
 
 export type PublicDisplaySetOptions = {

diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.js b/extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.js
@@ -172,8 +172,8 @@ function getDisplayText(mappedAnnotations, displaySet) {
 
   // Area is the same for all series
   const { length, width, SeriesNumber, SOPInstanceUID } = mappedAnnotations[0];
-  const roundedLength = utils.roundNumber(length, 1);
-  const roundedWidth = utils.roundNumber(width, 1);
+  const roundedLength = utils.roundNumber(length, 2);
+  const roundedWidth = utils.roundNumber(width, 2);
 
   const instance = displaySet.images.find(
     image => image.SOPInstanceUID === SOPInstanceUID

diff --git a/extensions/default/src/getPTImageIdInstanceMetadata.ts b/extensions/default/src/getPTImageIdInstanceMetadata.ts
@@ -23,7 +23,6 @@ export default function getPTImageIdInstanceMetadata(
     dicomMetaData.CorrectedImage === undefined ||
     dicomMetaData.Units === undefined ||
     !dicomMetaData.RadiopharmaceuticalInformationSequence ||
-    !dicomMetaData.RadiopharmaceuticalInformationSequence.length ||
     dicomMetaData.RadiopharmaceuticalInformationSequence[0]
       .RadionuclideHalfLife === undefined ||
     dicomMetaData.RadiopharmaceuticalInformationSequence[0]

diff --git a/extensions/default/src/init.js b/extensions/default/src/init.js
@@ -36,22 +36,22 @@ const handlePETImageMetadata = ({ SeriesInstanceUID, StudyInstanceUID }) => {
     return;
   }
   const imageIds = instances.map(instance => instance.imageId);
-  const InstanceMetadataArray = [];
+  const instanceMetadataArray = [];
   imageIds.forEach(imageId => {
     const instanceMetadata = getPTImageIdInstanceMetadata(imageId);
     if (instanceMetadata) {
-      InstanceMetadataArray.push(instanceMetadata);
+      instanceMetadataArray.push(instanceMetadata);
     }
   });
 
-  if (!InstanceMetadataArray.length) {
+  if (!instanceMetadataArray.length) {
     return;
   }
 
   // try except block to prevent errors when the metadata is not correct
   let suvScalingFactors;
   try {
-    suvScalingFactors = calculateSUVScalingFactors(InstanceMetadataArray);
+    suvScalingFactors = calculateSUVScalingFactors(instanceMetadataArray);
   } catch (error) {
     console.log(error);
   }
@@ -60,7 +60,7 @@ const handlePETImageMetadata = ({ SeriesInstanceUID, StudyInstanceUID }) => {
     return;
   }
 
-  InstanceMetadataArray.forEach((instanceMetadata, index) => {
+  instanceMetadataArray.forEach((instanceMetadata, index) => {
     metadataProvider.addCustomMetadata(
       imageIds[index],
       'scalingModule',

diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json
@@ -32,8 +32,8 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "classnames": "^2.2.6",
-    "@cornerstonejs/core": "^0.13.11",
-    "@cornerstonejs/tools": "^0.20.15",
+    "@cornerstonejs/core": "^0.14.4",
+    "@cornerstonejs/tools": "^0.21.7",
     "@ohif/extension-cornerstone-dicom-sr": "^3.0.0",
     "dcmjs": "^0.24.5",
     "prop-types": "^15.6.2",