chore(release): publish [skip ci]

- @ohif/extension-dicom-segmentation@0.7.21
 - @ohif/viewer@4.12.50

.github/ISSUE_TEMPLATE/---bug-report.md

@@ -2,23 +2,21 @@
 name: "\U0001F41B Bug report"
 about: Create a report to help us improve
 title: ''
-labels: 'Community: Report :bug:, Awaiting Reproduction, Triage :white_flag:'
+labels: 'Community: Report :bug:, Awaiting Reproduction'
 assignees: ''
 ---
 
-> **Before Creating an issue**
->
-> - Are you running the latest version?
-> - Are you reporting to the correct repository?
-> - Did you search existing issues?
-
-## Bug Report
+<!-- ⚠️⚠️ Do Not Delete This! bug_report_template ⚠️⚠️ -->
+<!-- Please read our Rules of Conduct: https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md -->
+<!-- 🕮 Read our guide about our process: https://v3-docs.ohif.org/development/our-process -->
+<!-- 🔎 Search existing issues to avoid creating duplicates. -->
+<!-- 🧪 Test using the latest version -->
 
 ### Describe the Bug
 
 _A clear and concise description of what the bug is._
 
-### What steps can we follow to reproduce the bug?
+### Steps to Reproduce:
 
 1. First step
 2. Second step
@@ -28,6 +26,15 @@ _A clear and concise description of what the bug is._
 Please use code blocks to show formatted errors or code snippets
 ```
 
+### The current behavior
+
+_A clear and concise description of what happens instead of the expected
+behavior._
+
+### The expected behavior
+
+_A clear and concise description of what you expected to happen._
+
 > :warning: Reports we cannot reproduce are at risk of being marked stale and
 > closed. The more information you can provide, the more likely we are to look
 > into and address your issue.

.github/ISSUE_TEMPLATE/---feature-request.md

@@ -2,19 +2,28 @@
 name: "\U0001F680 Feature request"
 about: Suggest an idea for this project
 title: ''
-labels: 'Community: Request :hand:, Triage :white_flag:'
+labels: 'Community: Request :hand:'
 assignees: ''
 ---
 
-> :hand: Many people requests features. Tell us why yours is important to the
+<!-- ⚠️⚠️ Do Not Delete This! feature_request_template ⚠️⚠️ -->
+<!-- Please read our Rules of Conduct: https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md -->
+
+<!-- :hand: Many people requests features. Tell us why yours is important to the
 > community. How does it add value? Why _this feature_?
 >
 > Is your request very specific to your needs? Consider
-> [contributing it](https://docs.ohif.org/contributing.html) yourself! Or reach
-> out to a community member that offers
+> [contributing it](https://v3-docs.ohif.org/development/contributing) yourself!
+> Or reach out to a community member that offers
 > [consulting services](https://docs.ohif.org/help.html#paid--commercial).
+-->
 
-## Request
+### Request
+
+<!--
+Please include as much detail as possible including possibly mock up screen shots, workflow or logic flow diagrams etc.
+Discuss if and how the requested feature interacts with existing features
+-->
 
 **What feature or change would you like to see made?**
 

.github/pull_request_template.md

@@ -1,14 +1,91 @@
-### PR Checklist
-
-- [ ] Brief description of changes
-- [ ] Links to any relevant issues
-- [ ] Required status checks are passing
-- [ ] User cases if changes impact the user's experience
-- [ ] `@mention` a maintainer to request a review
+<!-- Do Not Delete This! pr_template -->
+<!-- Please read our Rules of Conduct: https://github.com/OHIF/Viewers/blob/master/CODE_OF_CONDUCT.md -->
+<!-- 🕮 Read our guide about our Contributing Guide here https://v3-docs.ohif.org/development/contributing -->
+<!-- :hand: Thank you for starting this amazing contribution! -->
 
 <!--
-  Links
-  -->
+⚠️⚠️ Please make sure the checklist section below is complete before submitting your PR.
+To complete the checklist, add an 'x' to each item: [] -> [x]
+(PRs that do not have all the checkboxes marked will not be approved)
+-->
+
+### Context
+
+<!--
+Provide a clear explanation of the reasoning behind this change, such as:
+- A link to the issue being addressed, using the format "Fixes #ISSUE_NUMBER"
+- An image showing the issue or problem being addressed (if not already in the issue)
+- Error logs or callStacks to help with the understanding of the problem (if not already in the issue)
+-->
+
+### Changes & Results
+
+<!--
+List all the changes that have been done, such as:
+- Add new components
+- Remove old components
+- Update dependencies
+
+What are the effects of this change?
+- Before vs After
+- Screenshots / GIFs / Videos
+-->
+
+### Testing
+
+<!--
+Describe how we can test your changes.
+- open a URL
+- visit a page
+- click on a button
+- etc.
+-->
+
+### Checklist
+
+#### PR
+
+<!--
+https://semantic-release.gitbook.io/semantic-release/#how-does-it-work
+
+Examples:
+Please note the letter casing in the provided examples (upper or lower).
+
+- feat(MeasurementService): add ...
+- fix(Toolbar): fix ...
+- docs(Readme): update ...
+- style(Whitespace): fix ...
+- refactor(ExtensionManager): ...
+- test(HangingProtocol): Add test ...
+- chore(git): update ...
+- perf(VolumeLoader): ...
+
+You don't need to have each commit within the Pull Request follow the rule,
+but the PR title must comply with it, as it will be used as the commit message
+after the commits are squashed.
+-->
+
+- [] My Pull Request title is descriptive, accurate and follows the
+  semantic-release format and guidelines.
+
+#### Code
+
+- [] My code has been well-documented (function documentation, inline comments,
+  etc.)
+
+#### Public Documentation Updates
+
+<!-- https://v3-docs.ohif.org/ -->
+
+- [] The documentation page has been updated as necessary for any public API
+  additions or removals.
+
+#### Tested Environment
+
+- [] "OS: <!--[e.g. Windows 10, macOS 10.15.4]"-->
+- [] "Node version: <!--[e.g. 16.14.0]"-->
+- [] "Browser:
+  <!--[e.g. Chrome 83.0.4103.116, Firefox 77.0.1, Safari 13.1.1]"-->
 
 <!-- prettier-ignore-start -->
 [blog]: https://circleci.com/blog/triggering-trusted-ci-jobs-on-untrusted-forks/

.github/stale.yml

@@ -4,23 +4,17 @@
 # Number of days of inactivity before an issue becomes stale
 daysUntilStale: 180
 # Number of days of inactivity before a stale issue is closed
-daysUntilClose: 9000
+daysUntilClose: 60
 # Issues with these labels will never be considered stale
 exemptLabels:
-  - 'Story :raised_hands:'
   - 'Bug: Verified :bug:'
-  - 'Task: CI/Tooling :robot:'
-  - 'Task: Docs 📖'
-  - 'Task: Docs :book:'
-  - 'Task: Refactor :hammer_and_wrench:'
-  - 'Task: Tests :microscope:'
   - 'PR: Awaiting Review 👀'
-  - 'Triage :white_flag:'
-  - 'Extension: Discussion'
   - 'Announcement 🎉'
   - 'IDC:priority'
   - 'IDC:candidate'
   - 'IDC:collaboration'
+  - 'Community: Request :hand:'
+  - 'Community: Report :bug:'
 # Label to use when marking an issue as stale
 staleLabel: 'Stale :baguette_bread:'
 # Comment to post when marking an issue as stale. Set to `false` to disable

extensions/dicom-segmentation/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [0.7.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.20...@ohif/extension-dicom-segmentation@0.7.21) (2023-01-17)
+
+**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+
+
+
+
+
 ## [0.7.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.7.19...@ohif/extension-dicom-segmentation@0.7.20) (2023-01-10)
 
 **Note:** Version bump only for package @ohif/extension-dicom-segmentation

extensions/dicom-segmentation/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-dicom-segmentation",
-  "version": "0.7.20",
+  "version": "0.7.21",
   "description": "OHIF extension for viewing segmentations in the 2D MPR view",
   "author": "OHIF",
   "license": "MIT",

extensions/dicom-segmentation/src/commandsModule.js

@@ -0,0 +1,100 @@
+import csTools from 'cornerstone-tools';
+import cs from 'cornerstone-core';
+import OHIF from '@ohif/core';
+
+import DICOMSegTempCrosshairsTool from './tools/DICOMSegTempCrosshairsTool';
+import refreshViewports from './utils/refreshViewports';
+
+const { studyMetadataManager } = OHIF.utils;
+
+const commandsModule = ({ commandsManager }) => {
+  const actions = {
+    jumpToFirstSegment: ({ viewports }) => {
+      try {
+        const { activeViewportIndex, viewportSpecificData } = viewports;
+        const viewport = viewportSpecificData[activeViewportIndex];
+        const { StudyInstanceUID, displaySetInstanceUID } = viewport;
+        const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+        const firstImageId = studyMetadata.getFirstImageId(
+          displaySetInstanceUID
+        );
+
+        const module = csTools.getModule('segmentation');
+        const brushStackState = module.state.series[firstImageId];
+        const { labelmaps3D, activeLabelmapIndex } = brushStackState;
+        const { labelmaps2D } = labelmaps3D[activeLabelmapIndex];
+
+        const firstLabelMap2D = labelmaps2D.find(value => !!value);
+        const firstSegment = firstLabelMap2D.segmentsOnLabelmap[0];
+        const segmentNumber = firstSegment;
+
+        const validIndexList = [];
+        labelmaps2D.forEach((labelMap2D, index) => {
+          if (labelMap2D.segmentsOnLabelmap.includes(segmentNumber)) {
+            validIndexList.push(index);
+          }
+        });
+
+        const avg = array => array.reduce((a, b) => a + b) / array.length;
+        const average = avg(validIndexList);
+        const closest = validIndexList.reduce((prev, curr) => {
+          return Math.abs(curr - average) < Math.abs(prev - average)
+            ? curr
+            : prev;
+        });
+
+        const enabledElements = cs.getEnabledElements();
+        const element = enabledElements[activeViewportIndex].element;
+
+        const toolState = csTools.getToolState(element, 'stack');
+        if (!toolState) return;
+
+        const imageIds = toolState.data[0].imageIds;
+        const imageId = imageIds[closest];
+        const frameIndex = imageIds.indexOf(imageId);
+        const SOPInstanceUID = cs.metaData.get('SOPInstanceUID', imageId);
+
+        cs.getEnabledElements().forEach(enabledElement => {
+          cs.updateImage(enabledElement.element);
+        });
+
+        DICOMSegTempCrosshairsTool.addCrosshair(
+          element,
+          imageId,
+          segmentNumber
+        );
+
+        cs.getEnabledElements().forEach(enabledElement => {
+          cs.updateImage(enabledElement.element);
+        });
+
+        const refreshViewports = false;
+
+        commandsManager.runCommand('jumpToImage', {
+          StudyInstanceUID,
+          SOPInstanceUID,
+          frameIndex,
+          activeViewportIndex,
+          refreshViewports,
+        });
+      } catch (error) {
+        console.log('Error in moving to the first segment slice');
+      }
+    },
+  };
+
+  const definitions = {
+    jumpToFirstSegment: {
+      commandFn: actions.jumpToFirstSegment,
+      storeContexts: ['viewports'],
+      options: {},
+    },
+  };
+
+  return {
+    definitions,
+    defaultContext: 'VIEWER',
+  };
+};
+
+export default commandsModule;

extensions/dicom-segmentation/src/components/SegmentationSettings/SegmentationSettings.js

@@ -29,6 +29,32 @@ const SegmentationSettings = ({ configuration, onBack, onChange, servicesManager
     setState(state => ({ ...state, [field]: value }));
   };
 
+  const once = fn => (...args) => {
+    if (!fn) return;
+    fn(...args);
+    fn = null;
+  };
+
+  const segTolValue = document.getElementById('segToleranceValue');
+  if (segTolValue) {
+    segTolValue.onchange = once(function() {
+      const { UINotificationService, LoggerService } = servicesManager.services;
+
+      const error = new Error(
+        'Segmentation loader tolerance changed.\
+        This operation can potentially generate errors in the Segmentation parsing.'
+      );
+
+      LoggerService.error({ error, message: error.message });
+      UINotificationService.show({
+        title: 'Segmentation panel',
+        message: error.message,
+        type: 'warning',
+        autoClose: true,
+      });
+  });
+}
+
   const toFloat = value => parseFloat(value / 100).toFixed(2);
 
   return (
@@ -138,32 +164,23 @@ const SegmentationSettings = ({ configuration, onBack, onChange, servicesManager
         <label style={{ margin: '0 15px' }}>
           Tolerance:
           <input
+            id="segToleranceValue"
             style={{ margin: '0 15px' }}
             label="Tolerance"
             onKeyPress={event => {
-              const validate = string => {
-                let rgx = /[^-.e0-9]+/g;
-                return string.match(rgx);
-              };
+                const validate = string => {
+                  let rgx = /[^-.e0-9]+/g;
+                  return string.match(rgx);
+                };
 
-              if (validate(event.key)) {
-                event.preventDefault();
-              }
-            }}
-            onChange={event => {
-              save('segsTolerance', event.target.value);
-
-              const { UINotificationService, LoggerService } = servicesManager.services;
-              const error = new Error('Segmentation loader tolerance changed. This operation can potentially generate errors in the Segmentation parsing.');
-              LoggerService.error({ error, message: error.message });
-              UINotificationService.show({
-                title: 'Segmentation panel',
-                message: error.message,
-                type: 'warning',
-                autoClose: true,
-              });
+                if (validate(event.key)) {
+                  event.preventDefault();
+                }
               }
             }
+            onChange={event => {
+              save('segsTolerance', event.target.value);
+            }}
             value={state.segsTolerance}
           />
         </label>

extensions/dicom-segmentation/src/index.js

@@ -6,6 +6,7 @@ import toolbarModule from './toolbarModule.js';
 import getSopClassHandlerModule from './getOHIFDicomSegSopClassHandler.js';
 import SegmentationPanel from './components/SegmentationPanel/SegmentationPanel.js';
 import { version } from '../package.json';
+import commandsModule from './commandsModule.js';
 const { studyMetadataManager } = OHIF.utils;
 
 export default {
@@ -121,6 +122,15 @@ export default {
       });
     };
 
+    const onSegmentationsCompletelyLoaded = () => {
+      commandsManager.runCommand('jumpToFirstSegment');
+    };
+
+    document.addEventListener(
+      'segseriesselected',
+      onSegmentationsCompletelyLoaded
+    );
+
     document.addEventListener(
       'extensiondicomsegmentationsegloaded',
       onSegmentationsLoaded
@@ -182,5 +192,8 @@ export default {
       defaultContext: ['VIEWER'],
     };
   },
+  getCommandsModule({ commandsManager, servicesManager }) {
+    return commandsModule({ commandsManager, servicesManager });
+  },
   getSopClassHandlerModule,
 };

platform/viewer/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [4.12.50](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.49...@ohif/viewer@4.12.50) (2023-01-17)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
 ## [4.12.49](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.12.48...@ohif/viewer@4.12.49) (2023-01-10)
 
 **Note:** Version bump only for package @ohif/viewer

platform/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/viewer",
-  "version": "4.12.49",
+  "version": "4.12.50",
   "description": "OHIF Viewer",
   "author": "OHIF Contributors",
   "license": "MIT",
@@ -54,7 +54,7 @@
     "@ohif/extension-dicom-microscopy": "^0.52.0",
     "@ohif/extension-dicom-pdf": "^1.1.2",
     "@ohif/extension-dicom-rt": "^0.7.14",
-    "@ohif/extension-dicom-segmentation": "^0.7.20",
+    "@ohif/extension-dicom-segmentation": "^0.7.21",
     "@ohif/extension-lesion-tracker": "^0.2.2",
     "@ohif/extension-vtk": "^1.12.41",
     "@ohif/i18n": "^0.53.0",

platform/viewer/src/connectedComponents/ConnectedStudyBrowser.js

@@ -54,7 +54,9 @@ const mapDispatchToProps = (dispatch, ownProps) => {
                 detail: { activatedLabelmapIndex: activatedLabelmapIndex },
               }
             );
+            const segThumbnailSelected = new CustomEvent('segseriesselected');
             document.dispatchEvent(selectionFired);
+            document.dispatchEvent(segThumbnailSelected);
           });
         } else if (Modality !== 'SR') {
           displaySet = displaySet.getSourceDisplaySet(ownProps.studyMetadata);

platform/viewer/src/connectedComponents/Viewer.js

@@ -505,14 +505,14 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
  * @returns {[string]} an array of strings containing the warnings
  */
 const _checkForSeriesInconsistencesWarnings = async function(displaySet) {
-  if (displaySet.inconsistencyWarnings) {
-    // warnings already checked and cached in displaySet
-    return displaySet.inconsistencyWarnings;
-  }
-
   const inconsistencyWarnings = [];
 
   if (displaySet.Modality !== 'SEG') {
+    // warnings already checked and cached in displaySet
+    if (displaySet.inconsistencyWarnings) {
+      return displaySet.inconsistencyWarnings;
+    }
+
     if (
       displaySet.reconstructionIssues &&
       displaySet.reconstructionIssues.length !== 0