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
@@ -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);
    })
  );