feat(segmentation mode): Add create, and export SEG with Brushes (OHI…

…F#3632)
Sofien-Sellami · Oct 5, 2023 · 32c2abe · 32c2abe
1 parent 6244ac2
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -13,18 +13,18 @@ version: 2.1
 ##
 orbs:
   codecov: codecov/[email protected]
-  cypress: cypress-io/cypress@1.26.0
-executors:
-  # Custom executor to override Cypress config
-  deploy-to-prod-executor:
-    docker:
-      - 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:node16.14.2-slim-chrome103-ff102'
+  cypress: cypress-io/cypress@3
+# executors:
+#   # Custom executor to override Cypress config
+#   deploy-to-prod-executor:
+#     docker:
+#       - 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:node18.12.0-chrome106-ff106'
 
 defaults: &defaults
   docker:
@@ -363,32 +363,20 @@ jobs:
             fi
 
 workflows:
-  version: 2
-
   PR_CHECKS:
     jobs:
       - UNIT_TESTS
 
-      # E2E: PWA
       - cypress/run:
           name: 'E2E: PWA'
-          executor: chrome-and-pacs
-          browser: chrome
-          pre-steps:
-            - run: |
-                # Clear yarn cache; use yarn from image (update image to update yarn)
-                rm -rf ~/.yarn
-                yarn -v
-          yarn: true
-          record: true
-          store_artifacts: true
-          working_directory: platform/app
-          build: yarn test:data
-          start: yarn run test:e2e:serve
-          spec: 'cypress/integration/**/*'
-          wait-on: 'http://localhost:3000'
-          cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
-          no-workspace: true # Don't persist workspace
+          start-command: yarn run test:data && yarn run test:e2e:serve
+          install-browsers: true
+          cypress-command:
+            'npx wait-on@latest http://localhost:3000 && cd platform/app &&  npx cypress run
+            --record --browser chrome --parallel'
+          package-manager: 'yarn'
+          cypress-cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
+          cypress-cache-path: '~/.cache/Cypress'
           post-steps:
             - store_artifacts:
                 path: platform/app/cypress/screenshots
@@ -399,34 +387,34 @@ workflows:
           requires:
             - UNIT_TESTS
 
-  PR_OPTIONAL_VISUAL_TESTS:
-    jobs:
-      - AWAIT_APPROVAL:
-          type: approval
-      # Update hub.docker.org
-      - cypress/run:
-          name: 'Generate Percy Snapshots'
-          executor: cypress/browsers-chrome76
-          browser: chrome
-          pre-steps:
-            - run: 'rm -rf ~/.yarn && yarn -v && yarn global add wait-on'
-          yarn: true
-          store_artifacts: false
-          working_directory: platform/app
-          build:
-            yarn test:data && npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
-            yarn run build
-          # start server --> verify running --> percy + chrome + cypress
-          command: yarn run test:e2e:dist
-          cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
-          no-workspace: true # Don't persist workspace
-          post-steps:
-            - store_artifacts:
-                path: platform/app/cypress/screenshots
-            - store_artifacts:
-                path: platform/app/cypress/videos
-          requires:
-            - AWAIT_APPROVAL
+  # PR_OPTIONAL_VISUAL_TESTS:
+  #   jobs:
+  #     - AWAIT_APPROVAL:
+  #         type: approval
+  #     # Update hub.docker.org
+  #     - cypress/run:
+  #         name: 'Generate Percy Snapshots'
+  #         executor: cypress/browsers-chrome76
+  #         browser: chrome
+  #         pre-steps:
+  #           - run: 'rm -rf ~/.yarn && yarn -v && yarn global add wait-on'
+  #         yarn: true
+  #         store_artifacts: false
+  #         working_directory: platform/app
+  #         build:
+  #           yarn test:data && npx cross-env QUICK_BUILD=true APP_CONFIG=config/dicomweb-server.js
+  #           yarn run build
+  #         # start server --> verify running --> percy + chrome + cypress
+  #         command: yarn run test:e2e:dist
+  #         cache-key: 'yarn-packages-{{ checksum "yarn.lock" }}'
+  #         no-workspace: true # Don't persist workspace
+  #         post-steps:
+  #           - store_artifacts:
+  #               path: platform/app/cypress/screenshots
+  #           - store_artifacts:
+  #               path: platform/app/cypress/videos
+  #         requires:
+  #           - AWAIT_APPROVAL
 
   # Our master branch deploys to viewer-dev.ohif.org, the viewer.ohif.org is
   # deployed from the release branch which is more stable and less frequently updated.

diff --git a/extensions/cornerstone-dicom-rt/src/index.tsx b/extensions/cornerstone-dicom-rt/src/index.tsx
@@ -2,7 +2,6 @@ import { id } from './id';
 import React from 'react';
 import { Types } from '@ohif/core';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import hydrateRTDisplaySet from './utils/_hydrateRT';
 
 const Component = React.lazy(() => {
   return import(/* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport');
@@ -60,4 +59,3 @@ const extension: Types.Extensions.Extension = {
 };
 
 export default extension;
-export { hydrateRTDisplaySet };
diff --git a/extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts b/extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts
diff --git a/extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts b/extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts
@@ -1,7 +1,7 @@
 function createRTToolGroupAndAddTools(ToolGroupService, customizationService, toolGroupId) {
   const { tools } = customizationService.get('cornerstone.overlayViewportTools') ?? {};
 
-  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
+  return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools);
 }
 
 export default createRTToolGroupAndAddTools;
diff --git a/extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts b/extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts
@@ -1,5 +1,4 @@
 import { ButtonEnums } from '@ohif/ui';
-import hydrateRTDisplaySet from './_hydrateRT';
 
 const RESPONSE = {
   NO_NEVER: -1,
@@ -13,6 +12,7 @@ function promptHydrateRT({
   viewportId,
   toolGroupId = 'default',
   preHydrateCallbacks,
+  hydrateRTDisplaySet,
 }) {
   const { uiViewportDialogService } = servicesManager.services;
 

diff --git a/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx b/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx
@@ -3,11 +3,9 @@ import PropTypes from 'prop-types';
 import OHIF, { utils } from '@ohif/core';
 import { ViewportActionBar, useViewportGrid, LoadingIndicatorTotalPercent } from '@ohif/ui';
 
-import _hydrateRTdisplaySet from '../utils/_hydrateRT';
 import promptHydrateRT from '../utils/promptHydrateRT';
 import _getStatusComponent from './_getStatusComponent';
 import createRTToolGroupAndAddTools from '../utils/initRTToolGroup';
-import _hydrateRTDisplaySet from '../utils/_hydrateRT';
 
 const { formatDate } = utils;
 const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup';
@@ -95,6 +93,13 @@ function OHIFCornerstoneRTViewport(props) {
     });
   }, [viewportGrid]);
 
+  const hydrateRTDisplaySet = ({ rtDisplaySet, viewportId }) => {
+    commandsManager.runCommand('loadSegmentationDisplaySetsForViewport', {
+      displaySets: [rtDisplaySet],
+      viewportId,
+    });
+  };
+
   const getCornerstoneViewport = useCallback(() => {
     const { component: Component } = extensionManager.getModuleEntry(
       '@ohif/extension-cornerstone.viewportModule.cornerstone'
@@ -154,6 +159,7 @@ function OHIFCornerstoneRTViewport(props) {
       viewportId,
       rtDisplaySet,
       preHydrateCallbacks: [storePresentationState],
+      hydrateRTDisplaySet,
     }).then(isHydrated => {
       if (isHydrated) {
         setIsHydrated(true);
@@ -295,10 +301,9 @@ function OHIFCornerstoneRTViewport(props) {
     // presentation state (w/l and invert) and then opens the RT. If we don't store
     // the presentation state, the viewport will be reset to the default presentation
     storePresentationState();
-    const isHydrated = await _hydrateRTDisplaySet({
+    const isHydrated = await hydrateRTDisplaySet({
       rtDisplaySet,
       viewportId,
-      servicesManager,
     });
 
     setIsHydrated(isHydrated);

diff --git a/extensions/cornerstone-dicom-seg/package.json b/extensions/cornerstone-dicom-seg/package.json
@@ -43,6 +43,7 @@
     "react-router-dom": "^6.8.1"
   },
   "dependencies": {
+    "@cornerstonejs/tools": "^1.16.4",
     "@babel/runtime": "^7.20.13",
     "react-color": "^2.19.3"
   }