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.