feat: visualize overlapping segments in cornerstone (#2185)

* feat: visualize overlapping segments

load multiple labelMaps (splitted by dcmjs because overlapping) in a segmentations [IDC2164]

Dynamically update active labelmap [IDC2164]

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>
Co-authored-by: Igor Octaviano <igoroctaviano@gmail.com>

extensions/dicom-segmentation/src/loadSegmentation.js

@@ -1,92 +1,62 @@
-import OHIF from '@ohif/core';
 import dcmjs from 'dcmjs';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';
 
-const { DicomLoaderService } = OHIF.utils;
-
 export default async function loadSegmentation(
+  imageIds,
   segDisplaySet,
-  referencedDisplaySet,
-  studies
+  labelmapBuffer,
+  segMetadata,
+  segmentsOnFrame,
+  labelmapSegments
 ) {
-  const { StudyInstanceUID } = referencedDisplaySet;
+  const { setters } = cornerstoneTools.getModule('segmentation');
 
-  // Set here is loading is asynchronous.
-  // If this function throws its set back to false.
-  segDisplaySet.isLoaded = true;
+  // TODO: Could define a color LUT based on colors in the SEG.
+  const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
+  const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
 
-  const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
-    segDisplaySet,
-    studies
+  setters.labelmap3DByFirstImageId(
+    imageIds[0],
+    labelmapBuffer,
+    labelmapIndex,
+    segMetadata,
+    imageIds.length,
+    segmentsOnFrame,
+    colorLUTIndex
   );
 
-  const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
-  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-    dicomData.dict
-  );
+  if (!segDisplaySet.labelmapSegments) {
+    segDisplaySet.labelmapSegments = {};
+  }
 
-  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
+  /**
+   * Cache each labelmap segments.
+   * This data is used to determine the active label map when a given segment is activated/clicked.
+   */
+  segDisplaySet.labelmapSegments[labelmapIndex] = labelmapSegments.length ? Array.from(new Set(labelmapSegments.filter(a => !!a).reduce((a, b) => a.concat(b)))) : [];
+  segDisplaySet.labelmapIndex = labelmapIndex;
 
-  const imageIds = _getImageIdsForDisplaySet(
-    studies,
-    StudyInstanceUID,
-    referencedDisplaySet.SeriesInstanceUID
-  );
-
-  return new Promise((resolve, reject) => {
-    let results;
-
-    try {
-      results = _parseSeg(segArrayBuffer, imageIds);
-    } catch (error) {
-      segDisplaySet.isLoaded = false;
-      segDisplaySet.loadError = true;
-      reject(error);
-    }
-
-    const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
-    const { setters } = cornerstoneTools.getModule('segmentation');
-
-    // TODO: Could define a color LUT based on colors in the SEG.
-    const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
-    const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
-
-    setters.labelmap3DByFirstImageId(
-      imageIds[0],
-      labelmapBuffer,
-      labelmapIndex,
-      segMetadata,
-      imageIds.length,
-      segmentsOnFrame,
-      colorLUTIndex
-    );
-
-    segDisplaySet.labelmapIndex = labelmapIndex;
-
-    /*
-     * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
-     *
-     * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
-     * or other components that could rely on loaded segmentations that
-     * the segments were loaded so that e.g. when the user opens the panel
-     * before the segments are fully loaded, the panel can subscribe to this custom event
-     * and update itself with the new segments.
-     *
-     * This limitation is due to the fact that the cs segmentation module is an object (which will be
-     * updated after the segments are loaded) that React its not aware of its changes
-     * because the module object its not passed in to the panel component as prop but accessed externally.
-     *
-     * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
-     * allows us to easily watch the module or the segmentations loading process in any other component
-     * without subscribing to external events.
-     */
-    console.log('Segmentation loaded.');
-    const event = new CustomEvent('extensiondicomsegmentationsegloaded');
-    document.dispatchEvent(event);
-
-    resolve(labelmapIndex);
-  });
+  /*
+   * TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
+   *
+   * Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
+   * or other components that could rely on loaded segmentations that
+   * the segments were loaded so that e.g. when the user opens the panel
+   * before the segments are fully loaded, the panel can subscribe to this custom event
+   * and update itself with the new segments.
+   *
+   * This limitation is due to the fact that the cs segmentation module is an object (which will be
+   * updated after the segments are loaded) that React its not aware of its changes
+   * because the module object its not passed in to the panel component as prop but accessed externally.
+   *
+   * Improving this event approach to something reactive that can be tracked inside the react lifecycle,
+   * allows us to easily watch the module or the segmentations loading process in any other component
+   * without subscribing to external events.
+   */
+  console.log('Segmentation loaded.');
+  const event = new CustomEvent('extensiondicomsegmentationsegloaded');
+  document.dispatchEvent(event);
 }
 
 function _getNextLabelmapIndex(firstImageId) {
@@ -172,38 +142,3 @@ function _getNextColorLUTIndex() {
 
   return colorLUTIndex;
 }
-
-function _parseSeg(arrayBuffer, imageIds) {
-  return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
-    imageIds,
-    arrayBuffer,
-    cornerstone.metaData
-  );
-}
-
-function _getImageIdsForDisplaySet(
-  studies,
-  StudyInstanceUID,
-  SeriesInstanceUID
-) {
-  const study = studies.find(
-    study => study.StudyInstanceUID === StudyInstanceUID
-  );
-
-  const displaySets = study.displaySets.filter(displaySet => {
-    return displaySet.SeriesInstanceUID === SeriesInstanceUID;
-  });
-
-  if (displaySets.length > 1) {
-    console.warn(
-      'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
-    );
-    // TODO -> We could make check the instance list and see if any match?
-    // Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
-    // ^ Will that even happen?
-  }
-
-  const referencedDisplaySet = displaySets[0];
-
-  return referencedDisplaySet.images.map(image => image.getImageId());
-}