Split packages into platform and extensions

extensions/vtk/src/handleSegmentationStorage.js

@@ -0,0 +1,150 @@
+import * as dcmjs from 'dcmjs';
+
+import OHIF from 'ohif-core';
+import { api } from 'dicomweb-client';
+
+const { StackManager } = OHIF.utils;
+
+function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
+  const study = studies.find(
+    study => study.studyInstanceUid === studyInstanceUid
+  );
+
+  const displaySet = study.displaySets.find(set => {
+    return set.displaySetInstanceUid === displaySetInstanceUid;
+  });
+
+  return displaySet;
+}
+
+function getDisplaySetsBySeries(studies, studyInstanceUid, seriesInstanceUid) {
+  const study = studies.find(
+    study => study.studyInstanceUid === studyInstanceUid
+  );
+
+  return study.displaySets.filter(set => {
+    return set.seriesInstanceUid === seriesInstanceUid;
+  });
+}
+
+function getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
+  const study = studies.find(
+    study => study.studyInstanceUid === studyInstanceUid
+  );
+
+  // Create shortcut to displaySet
+  const displaySet = getDisplaySet(
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid
+  );
+
+  // Get stack from Stack Manager
+  const stack = StackManager.findOrCreateStack(study, displaySet);
+
+  // Clone the stack here so we don't mutate it later
+  const stackClone = Object.assign({}, stack);
+  stackClone.currentImageIdIndex = 0;
+
+  return stackClone;
+}
+
+function retrieveDicomData(
+  studyInstanceUID,
+  seriesInstanceUID,
+  sopInstanceUID,
+  wadoRoot
+) {
+  const config = {
+    url: wadoRoot,
+    headers: DICOMWeb.getAuthorizationHeader(),
+  };
+
+  const dicomWeb = new api.DICOMwebClient(config);
+  const options = {
+    studyInstanceUID,
+    seriesInstanceUID,
+    sopInstanceUID,
+  };
+
+  return dicomWeb.retrieveInstance(options);
+}
+
+async function handleSegmentationStorage(
+  studies,
+  studyInstanceUid,
+  displaySetInstanceUid
+) {
+  const study = studies.find(
+    study => study.studyInstanceUid === studyInstanceUid
+  );
+  const displaySet = getDisplaySet(
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid
+  );
+
+  // TODO: This is terrible but we need to use WADO-RS or we can't retrieve the SEG
+  // from google cloud
+  const wadoRoot = displaySet.images[0].getData().wadoRoot;
+
+  const StudyInstanceUID = displaySet.images[0].getStudyInstanceUID();
+  const SeriesInstanceUID = displaySet.images[0].getSeriesInstanceUID();
+  const SOPInstanceUID = displaySet.images[0].getSOPInstanceUID();
+
+  const arrayBuffer = await retrieveDicomData(
+    StudyInstanceUID,
+    SeriesInstanceUID,
+    SOPInstanceUID,
+    wadoRoot
+  );
+
+  const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
+  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+    dicomData.dict
+  );
+
+  const segments = dcmjs.adapters.VTKjs.Segmentation.generateSegments(dataset);
+
+  dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
+
+  const seriesInstanceUid = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
+  const displaySets = getDisplaySetsBySeries(
+    studies,
+    studyInstanceUid,
+    seriesInstanceUid
+  );
+
+  if (displaySets.length > 1) {
+    console.warn(
+      'More than one display set with the same seriesInstanceUid. This is not supported yet...'
+    );
+  }
+
+  const referenceDisplaySet = displaySets[0];
+  const imageIds = referenceDisplaySet.images.map(image => image.getImageId());
+
+  if (!results) {
+    throw new Error('Fractional segmentations are not supported');
+  }
+
+  const cachedStack = StackManager.findOrCreateStack(
+    study,
+    referenceDisplaySet
+  );
+  const stack = Object.assign({}, cachedStack);
+  stack.currentImageIdIndex = 0;
+
+  return {
+    referenceDataObject,
+    labelmapDataObject,
+  };
+
+  return {
+    studyInstanceUid,
+    displaySetInstanceUid,
+    stack,
+  };
+}
+
+export default handleSegmentationStorage;