feat: Segmentations Settings UI - Phase 1 #1391 (#1392)

* Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Rebase on master. * format format format * add basic extension parts * Updated yarn lock * Fetch derived/referenced displaysets in sidepanel * Add buttons, expose seriesDescription, write notes for Danny. * Add growcut tool extention. -> Move to a seperate repo. * Change some text fields. * expose dialog provider * hide draggable area * No pointer events for now; need to revisit * Don't filter seg from the outset for now * fiddling about * fix path to series data * fix logic to determine next available labelmapindex * Ability to swtich between labelmaps * Return a promise so we can make sure our labelmap is loaded before pulling metadata * Better UI to toggle labelmaps * Fix accidental untoggle of active labelmap for ui * Remove brush tool from cornerstone extension * Add cstools in preInit for seg extension * Add buttons for seg magic * Hide the measurements panel for now * Slightly better seg/scissor icons * Add eraser * ability to switch segments * seg color / switcher * Fix vtk labelmap cache. * sidepanel should scroll if there's overflow * Use a fancier range slider * Slightly prettier buttons * Push in progress * A bit more reactive; handle no-meta * Update to vtk.js 11.14.0 and react-vtkjs-viewport 0.6.0 * chore: kickstart preview * Fix conflict issues * Refactor panel * Isolate increment functions * Wip segment table * Hide selector and add scroll to segmentation * Increase width of segment description * Hide not used items * Add new select for segmentations * Align ui * Fix default segmentation * Fix broken import test * Get measurements panel back and add spacing to grouped buttons * Hide brush and selector and refresh when switching segmentations * Add pointer events back and fix broken tests for measurement table * Update segment list when switching humbnails * CR Update: Minor UI adjustments * CR Update: Set active segment * Move components to components folder * Add new settings ui * Integrate configuration * Improve styles * Float numbers * Improve css * Refresh settings menu if side panel changed * Fix settings rendering logic and remove comments * Extract components * Remove not used tools * Remove non used extension * Use style variables and remove comments * Remove non used dep from lock * Remove tools * Remove segmentation from toolbar * Add todo and brushradius from config * Fix packagejson growcut import * Remove webpack config already defined in parent * Update package json description * Change component name to british english to us * Improve prop types * Rename cornerstone label map event * Scope css * Extract and add doc to helper * Update jsdocs for getDerivedDatasets * Add proptypes and cr updates * Update tablistitem proptypes * config is readonly, rollback destructuring * Remove event for side panel * Add jsdocs for util * Extract getimageid to studymetada * Use ohif log instead of console * Remove specific style from side panel * Fix default props for brush radius * Descructure configuration props from settings component to avoid invalid props * Update proptypes to be required (settings) * Update readme * Remove commandsmodule * Get configuration module inside the component * Set selected segment * Rename extension and use modality to filter * Fix for failing tests (#1423) * hello world * Finish rebase for Igor. * Re-fix cornerstoneTools version that got messed up in merge. * Fix reactivity of isDisabled, write implementation for the SEG panel. * Nuke yarn.lock to stack CST to 4.12.0 * Remove debugger statements. * fix: bump cornerstone-tools version to address toFixed issue * test: force tests for MISTER^MR to navigate to study directly * test: remove eraser tool test * test: count is off by one * test: don't save SR state for the time being * test: disable more tests Co-authored-by: James A. Petts <jamesapetts@gmail.com> Co-authored-by: dannyrb <danny.ri.brown@gmail.com> Co-authored-by: igoroctaviano] <igoroctaviano@users.noreply.github.com> Co-authored-by: Mirna Silva <mirna.silva@radicalimaging.com>
2020-03-13 15:45:26 -04:00
1 parent d426b78967
commit e8842cf8ae
@@ -1,5 +1,6 @@
 import guid from '../utils/guid.js';
 import OHIFError from './OHIFError';
+import { Vector3 } from 'cornerstone-math';

 const OBJECT = 'object';

@@ -63,6 +64,60 @@ class ImageSet {
  sortBy(sortingCallback) {
    return this.images.sort(sortingCallback);
  }
+
+  sortByImagePositionPatient() {
+    const images = this.images;
+    const referenceImagePositionPatient = _getImagePositionPatient(images[0]);
+
+    const refIppVec = new Vector3(
+      referenceImagePositionPatient[0],
+      referenceImagePositionPatient[1],
+      referenceImagePositionPatient[2]
+    );
+
+    const ImageOrientationPatient = _getImageOrientationPatient(images[0]);
+
+    const scanAxisNormal = new Vector3(
+      ImageOrientationPatient[0],
+      ImageOrientationPatient[1],
+      ImageOrientationPatient[2]
+    ).cross(
+      new Vector3(
+        ImageOrientationPatient[3],
+        ImageOrientationPatient[4],
+        ImageOrientationPatient[5]
+      )
+    );
+
+    const distanceImagePairs = images.map(function(image) {
+      const ippVec = new Vector3(..._getImagePositionPatient(image));
+      const positionVector = refIppVec.clone().sub(ippVec);
+      const distance = positionVector.dot(scanAxisNormal);
+
+      return {
+        distance,
+        image,
+      };
+    });
+
+    distanceImagePairs.sort(function(a, b) {
+      return b.distance - a.distance;
+    });
+
+    const sortedImages = distanceImagePairs.map(a => a.image);
+
+    images.sort(function(a, b) {
+      return sortedImages.indexOf(a) - sortedImages.indexOf(b);
+    });
+  }
+}
+
+function _getImagePositionPatient(image) {
+  return image.getData().metadata.ImagePositionPatient;
+}
+
+function _getImageOrientationPatient(image) {
+  return image.getData().metadata.ImageOrientationPatient;
 }

 export default ImageSet;
@@ -35,6 +35,12 @@ export class StudyMetadata extends Metadata {
        writable: false,
        value: [],
      },
+      _derivedDisplaySets: {
+        configurable: false,
+        enumerable: false,
+        writable: false,
+        value: [],
+      },
      _firstSeries: {
        configurable: false,
        enumerable: false,
@@ -121,7 +127,11 @@ export class StudyMetadata extends Metadata {
      );
      if (displaySet) {
        displaySet.sopClassModule = true;
-        displaySets.push(displaySet);
+
+        displaySet.isDerived
+          ? this._addDerivedDisplaySet(displaySet)
+          : displaySets.push(displaySet);
+
        return displaySets;
      }
    }
@@ -186,9 +196,73 @@ export class StudyMetadata extends Metadata {
  }

  /**
-   * Creates a set of series to be placed in the Study Metadata
-   * The series that appear in the Study Metadata must represent
-   * imaging modalities.
+   * Adds the displaySets to the studies list of derived displaySets.
+   * @param {object} displaySet The displaySet to append to the derived displaysets list.
+   */
+  _addDerivedDisplaySet(displaySet) {
+    this._derivedDisplaySets.push(displaySet);
+    // --> Perhaps that logic should exist in the extension sop class handler and this be a dumb list.
+    // TODO -> Get x Modality by referencedSeriesInstanceUid, FoR, etc.
+  }
+
+  /**
+   * Returns a list of derived datasets in the study, filtered by the given filter.
+   * @param {object} filter An object containing search filters
+   * @param {object} filter.modality
+   * @param {object} filter.referencedSeriesInstanceUID
+   * @param {object} filter.referencedFrameOfReferenceUID
+   * @return {Array} filtered derived display sets
+   */
+  getDerivedDatasets(filter) {
+    const {
+      modality,
+      referencedSeriesInstanceUID,
+      referencedFrameOfReferenceUID,
+    } = filter;
+    let filteredDerivedDisplaySets = this._derivedDisplaySets;
+
+    if (modality) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet => displaySet.Modality === Modality
+      );
+    }
+
+    if (referencedSeriesInstanceUID) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet => {
+          if (!displaySet.metadata.ReferencedSeriesSequence) {
+            return false;
+          }
+
+          const ReferencedSeriesSequence = Array.isArray(
+            displaySet.metadata.ReferencedSeriesSequence
+          )
+            ? displaySet.metadata.ReferencedSeriesSequence
+            : [displaySet.metadata.ReferencedSeriesSequence];
+
+          return ReferencedSeriesSequence.some(
+            ReferencedSeries =>
+              ReferencedSeries.SeriesInstanceUID === referencedSeriesInstanceUID
+          );
+        }
+      );
+    }
+
+    if (referencedFrameOfReferenceUID) {
+      filteredDerivedDisplaySets = filteredDerivedDisplaySets.filter(
+        displaySet =>
+          displaySet.ReferencedFrameOfReferenceUID ===
+          ReferencedFrameOfReferenceUID
+      );
+    }
+
+    return filteredDerivedDisplaySets;
+  }
+
+  /**
+   * Creates a set of displaySets to be placed in the Study Metadata
+   * The displaySets that appear in the Study Metadata must represent
+   * imaging modalities. A series may be split into one or more displaySets.
   *
   * Furthermore, for drag/drop functionality,
   * it is easiest if the stack objects also contain information about
@@ -482,6 +556,22 @@ export class StudyMetadata extends Metadata {
    return series;
  }

+  /**
+   * Get the first image id given display instance uid.
+   * @return {string} The image id.
+   */
+  getFirstImageId(displaySetInstanceUID) {
+    try {
+      const displaySet = this.findDisplaySet(
+        displaySet => displaySet.displaySetInstanceUID === displaySetInstanceUID
+      );
+      return displaySet.images[0].getImageId();
+    } catch (error) {
+      console.error('Failed to retrieve image metadata');
+      return null;
+    }
+  }
+
  /**
   * Get the first instance of the current study retaining a consistent result across multiple calls.
   * @return {InstanceMetadata} An instance of the InstanceMetadata class or null if it does not exist.
@@ -625,6 +715,10 @@ const makeDisplaySet = (series, instances) => {

  imageSet.isReconstructable = isReconstructable.value;

+  if (shallSort && imageSet.isReconstructable) {
+    imageSet.sortByImagePositionPatient();
+  }
+
  if (isReconstructable.missingFrames) {
    // TODO -> This is currently unused, but may be used for reconstructing
    // Volumes with gaps later on.
@@ -0,0 +1,45 @@
+import DICOMWeb from '../../../DICOMWeb';
+
+/**
+ * Function to get series sequence (sequence of pepeating items where each
+ * item includes the attributes of one or more series) based on a given sopInstance.
+ *
+ * @param {Object} instance The sop instance
+ * @returns {Promise} Referenced series sequence
+ */
+const getReferencedSeriesSequence = instance => {
+  const referencedSeriesSequenceRaw = instance['00081115'];
+
+  const referencedSeriesSequence = [];
+
+  if (referencedSeriesSequenceRaw && referencedSeriesSequenceRaw.Value) {
+    referencedSeriesSequenceRaw.Value.forEach(referencedSeries => {
+      const referencedSeriesInstanceUID = DICOMWeb.getString(
+        referencedSeries['0020000E']
+      );
+
+      const referencedInstanceSequenceRaw = referencedSeries['0008114A'];
+      const referencedInstanceSequence = [];
+
+      referencedInstanceSequenceRaw.Value.forEach(referencedInstance => {
+        referencedInstanceSequence.push({
+          referencedSOPClassUID: DICOMWeb.getString(
+            referencedInstance['00081150']
+          ),
+          referencedSOPInstanceUID: DICOMWeb.getString(
+            referencedInstance['00081155']
+          ),
+        });
+      });
+
+      referencedSeriesSequence.push({
+        referencedSeriesInstanceUID,
+        referencedInstanceSequence,
+      });
+    });
+  }
+
+  return referencedSeriesSequence;
+};
+
+export default getReferencedSeriesSequence;
@@ -2,6 +2,7 @@ import DICOMWeb from '../../../DICOMWeb';
 import metadataProvider from '../../../classes/MetadataProvider';
 import getWADORSImageId from '../../../utils/getWADORSImageId';
 import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import getReferencedSeriesSequence from './getReferencedSeriesSequence';

 /**
 * Create a plain JS object that describes a study (a study descriptor object)
@@ -23,7 +24,10 @@ function createStudy(server, aSopInstance) {
    PatientSize: DICOMWeb.getNumber(aSopInstance['00101020']),
    PatientWeight: DICOMWeb.getNumber(aSopInstance['00101030']),
    AccessionNumber: DICOMWeb.getString(aSopInstance['00080050']),
+    StudyTime: DICOMWeb.getString(aSopInstance['00080030']),
    StudyDate: DICOMWeb.getString(aSopInstance['00080020']),
+    FrameOfReferenceUID: DICOMWeb.getString(aSopInstance['00200052']),
+    ReferencedSeriesSequence: getReferencedSeriesSequence(aSopInstance),
    modalities: DICOMWeb.getString(aSopInstance['00080061']), // TODO -> Rename this.. it'll take a while to not mess this one up.
    StudyDescription: DICOMWeb.getString(aSopInstance['00081030']),
    NumberOfStudyRelatedInstances: DICOMWeb.getString(aSopInstance['00201208']),
@@ -186,7 +190,7 @@ async function makeSOPInstance(server, study, instance) {
 */
 async function addInstancesToStudy(server, study, sopInstanceList) {
  return Promise.all(
-    sopInstanceList.map(function(sopInstance) {
+    sopInstanceList.map(function (sopInstance) {
      return makeSOPInstance(server, study, sopInstance);
    })
  );
@@ -8,6 +8,7 @@ import studyMetadataManager from './studyMetadataManager';
 import writeScript from './writeScript.js';
 import DicomLoaderService from './dicomLoaderService.js';
 import b64toBlob from './b64toBlob.js';
+import loadAndCacheDerivedDisplaySets from './loadAndCacheDerivedDisplaySets.js';
 import * as urlUtil from './urlUtil';
 import makeCancelable from './makeCancelable';
 import hotkeys from './hotkeys';
@@ -24,6 +25,7 @@ const utils = {
  studyMetadataManager,
  DicomLoaderService,
  urlUtil,
+  loadAndCacheDerivedDisplaySets,
  makeCancelable,
  hotkeys,
 };
@@ -40,6 +42,7 @@ export {
  studyMetadataManager,
  DicomLoaderService,
  urlUtil,
+  loadAndCacheDerivedDisplaySets,
  makeCancelable,
  hotkeys,
 };
@@ -12,6 +12,7 @@ describe('Top level exports', () => {
      'b64toBlob',
      'StackManager',
      'studyMetadataManager',
+      'loadAndCacheDerivedDisplaySets',
      'DicomLoaderService',
      'urlUtil',
      'makeCancelable',
@@ -167,8 +167,8 @@ function _getSpacingIssue(spacing, averageSpacing) {
 function _getPerpendicularDistance(a, b) {
  return Math.sqrt(
    Math.pow(a[0] - b[0], 2) +
-      Math.pow(a[1] - b[1], 2) +
-      Math.pow(a[2] - b[2], 2)
+    Math.pow(a[1] - b[1], 2) +
+    Math.pow(a[2] - b[2], 2)
  );
 }

@@ -0,0 +1,107 @@
+import studyMetadataManager from './studyMetadataManager';
+
+/**
+ * Study schema
+ *
+ * @typedef {Object} Study
+ * @property {Array} seriesList -
+ * @property {Object} seriesMap -
+ * @property {Object} seriesLoader -
+ * @property {string} wadoUriRoot -
+ * @property {string} wadoRoot -
+ * @property {string} qidoRoot -
+ * @property {string} patientName -
+ * @property {string} patientId -
+ * @property {number} patientAge -
+ * @property {number} patientSize -
+ * @property {number} patientWeight -
+ * @property {string} accessionNumber -
+ * @property {string} studyDate -
+ * @property {string} studyTime -
+ * @property {string} modalities -
+ * @property {string} studyDescription -
+ * @property {string} imageCount -
+ * @property {string} studyInstanceUid -
+ * @property {string} institutionName -
+ * @property {Array} displaySets -
+ */
+
+/**
+ * Factory function to load and cache derived display sets.
+ *
+ * @param {object} referencedDisplaySet Display set
+ * @param {string} referencedDisplaySet.displaySetInstanceUid Display set instance uid
+ * @param {string} referencedDisplaySet.seriesDate
+ * @param {string} referencedDisplaySet.seriesTime
+ * @param {string} referencedDisplaySet.seriesInstanceUid
+ * @param {string} referencedDisplaySet.seriesNumber
+ * @param {string} referencedDisplaySet.seriesDescription
+ * @param {number} referencedDisplaySet.numImageFrames
+ * @param {string} referencedDisplaySet.frameRate
+ * @param {string} referencedDisplaySet.modality
+ * @param {boolean} referencedDisplaySet.isMultiFrame
+ * @param {number} referencedDisplaySet.instanceNumber
+ * @param {boolean} referencedDisplaySet.isReconstructable
+ * @param {string} referencedDisplaySet.studyInstanceUid
+ * @param {Array} referencedDisplaySet.sopClassUids
+ * @param {Study[]} studies Collection of studies
+ * @returns void
+ */
+const loadAndCacheDerivedDisplaySets = (referencedDisplaySet, studies) => {
+  const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
+
+  const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
+
+  if (!studyMetadata) {
+    return;
+  }
+
+  const derivedDisplaySets = studyMetadata.getDerivedDatasets({
+    referencedSeriesInstanceUID: SeriesInstanceUID,
+  });
+
+  if (!derivedDisplaySets.length) {
+    return;
+  }
+
+  // Filter by type
+  const displaySetsPerModality = {};
+
+  derivedDisplaySets.forEach(displaySet => {
+    const Modality = displaySet.Modality;
+
+    if (displaySetsPerModality[Modality] === undefined) {
+      displaySetsPerModality[Modality] = [];
+    }
+
+    displaySetsPerModality[Modality].push(displaySet);
+  });
+
+  // For each type, see if any are loaded, if not load the most recent.
+  Object.keys(displaySetsPerModality).forEach(key => {
+    const displaySets = displaySetsPerModality[key];
+    const isLoaded = displaySets.some(displaySet => displaySet.isLoaded);
+
+    if (isLoaded) {
+      return;
+    }
+
+    // find most recent and load it.
+    let recentDateTime = 0;
+    let recentDisplaySet;
+
+    displaySets.forEach(displaySet => {
+      const dateTime = Number(
+        `${displaySet.SeriesDate}${displaySet.SeriesTime}`
+      );
+      if (dateTime > recentDateTime) {
+        recentDateTime = dateTime;
+        recentDisplaySet = displaySet;
+      }
+    });
+
+    recentDisplaySet.load(referencedDisplaySet, studies);
+  });
+};
+
+export default loadAndCacheDerivedDisplaySets;
@@ -0,0 +1,3 @@
+const reconstructableModalities = ['MR', 'CT', 'PT', 'NM'];
+
+export default reconstructableModalities;