Re IDC #3077: Seg series thumbnail selection

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();
+                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,
-              });
-              }
-            }
+            }}
             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/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