feat: cornerstone3D stack and volume viewports (#2787)

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
2022-07-27 12:39:04 -04:00
1 parent 86dcaf6293
commit bd1c38c00c
@@ -1,4 +1,12 @@
 import { api } from 'dicomweb-client';
+import {
+  DicomMetadataStore,
+  IWebApiDataSource,
+  utils,
+  errorHandler,
+  classes,
+} from '@ohif/core';
+
 import {
  mapParams,
  search as qidoSearch,
@@ -7,12 +15,6 @@ import {
  processSeriesResults,
 } from './qido.js';
 import dcm4cheeReject from './dcm4cheeReject';
-import {
-  DicomMetadataStore,
-  IWebApiDataSource,
-  utils,
-  errorHandler,
-} from '@ohif/core';

 import getImageId from './utils/getImageId';
 import dcmjs from 'dcmjs';
@@ -31,6 +33,8 @@ const ImplementationClassUID =
 const ImplementationVersionName = 'OHIF-VIEWER-2.0.0';
 const EXPLICIT_VR_LITTLE_ENDIAN = '1.2.840.10008.1.2.1';

+const metadataProvider = classes.MetadataProvider;
+
 /**
 *
 * @param {string} name - Data source name
@@ -94,7 +98,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
    query: {
      studies: {
        mapParams: mapParams.bind(),
-        search: async function (origParams) {
+        search: async function(origParams) {
          const headers = UserAuthenticationService.getAuthorizationHeader();
          if (headers) {
            qidoDicomWebClient.headers = headers;
@@ -119,7 +123,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
      },
      series: {
        // mapParams: mapParams.bind(),
-        search: async function (studyInstanceUid) {
+        search: async function(studyInstanceUid) {
          const headers = UserAuthenticationService.getAuthorizationHeader();
          if (headers) {
            qidoDicomWebClient.headers = headers;
@@ -163,13 +167,13 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
       * @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart,
       *    or is already retrieved, or a promise to a URL for such use if a BulkDataURI
       */
-      directURL: (params) => {
+      directURL: params => {
        const {
          instance,
-          tag = "PixelData",
-          defaultPath = "/pixeldata",
-          defaultType = "video/mp4",
-          singlepart: fetchPart = "video",
+          tag = 'PixelData',
+          defaultPath = '/pixeldata',
+          defaultType = 'video/mp4',
+          singlepart: fetchPart = 'video',
        } = params;
        const value = instance[tag];
        if (!value) return undefined;
@@ -180,10 +184,15 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
          value.DirectRetrieveURL = URL.createObjectURL(blob);
          return value.DirectRetrieveURL;
        }
-        if (!singlepart || singlepart !== true && singlepart.indexOf(fetchPart) === -1) {
+        if (
+          !singlepart ||
+          (singlepart !== true && singlepart.indexOf(fetchPart) === -1)
+        ) {
          if (value.retrieveBulkData) {
            return value.retrieveBulkData().then(arr => {
-              value.DirectRetrieveURL = URL.createObjectURL(new Blob([arr], { type: defaultType }));
+              value.DirectRetrieveURL = URL.createObjectURL(
+                new Blob([arr], { type: defaultType })
+              );
              return value.DirectRetrieveURL;
            });
          }
@@ -191,7 +200,11 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
          return undefined;
        }

-        const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
+        const {
+          StudyInstanceUID,
+          SeriesInstanceUID,
+          SOPInstanceUID,
+        } = instance;
        const BulkDataURI =
          (value && value.BulkDataURI) ||
          `series/${SeriesInstanceUID}/instances/${SOPInstanceUID}${defaultPath}`;
@@ -234,94 +247,27 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
            );
          }

-          // Get Series
-          const {
-            seriesSummaryMetadata,
-            seriesPromises,
-          } = await retrieveStudyMetadata(
-            wadoDicomWebClient,
-            StudyInstanceUID,
-            enableStudyLazyLoad,
-            filters,
-            sortCriteria,
-            sortFunction
-          );
-
-          /**
-           * naturalizes the dataset, and adds a retrieve bulkdata method
-           * to any values containing BulkDataURI.
-           * @param {*} instance
-           * @returns naturalized dataset, with retrieveBulkData methods
-           */
-          const addRetrieveBulkData = instance => {
-            const naturalized = naturalizeDataset(instance);
-            Object.keys(naturalized).forEach(key => {
-              const value = naturalized[key];
-              // The value.Value will be set with the bulkdata read value
-              // in which case it isn't necessary to re-read this.
-              if (value && value.BulkDataURI && !value.Value) {
-                // Provide a method to fetch bulkdata
-                value.retrieveBulkData = () => {
-                  const options = {
-                    // The bulkdata fetches work with either multipart or
-                    // singlepart, so set multipart to false to let the server
-                    // decide which type to respond with.
-                    multipart: false,
-                    BulkDataURI: value.BulkDataURI,
-                    // The study instance UID is required if the bulkdata uri
-                    // is relative - that isn't disallowed by DICOMweb, but
-                    // isn't well specified in the standard, but is needed in
-                    // any implementation that stores static copies of the metadata
-                    StudyInstanceUID: naturalized.StudyInstanceUID,
-                  };
-                  return qidoDicomWebClient
-                    .retrieveBulkData(options)
-                    .then(val => {
-                      const ret = (val && val[0]) || undefined;
-                      value.Value = ret;
-                      return ret;
-                    });
-                };
-              }
-            });
-            return naturalized;
-          };
-
-          // Async load series, store as retrieved
-          function storeInstances(instances) {
-            const naturalizedInstances = instances.map(addRetrieveBulkData);
-
-            DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
-          }
-
-          function setSuccessFlag() {
-            const study = DicomMetadataStore.getStudy(
+          if (enableStudyLazyLoad) {
+            return implementation._retrieveSeriesMetadataAsync(
              StudyInstanceUID,
+              filters,
+              sortCriteria,
+              sortFunction,
              madeInClient
            );
-            study.isLoaded = true;
          }

-          // Google Cloud Healthcare doesn't return StudyInstanceUID, so we need to add
-          // it manually here
-          seriesSummaryMetadata.forEach(aSeries => {
-            aSeries.StudyInstanceUID = StudyInstanceUID;
-          });
-
-          DicomMetadataStore.addSeriesMetadata(
-            seriesSummaryMetadata,
+          return implementation._retrieveSeriesMetadataSync(
+            StudyInstanceUID,
+            filters,
+            sortCriteria,
+            sortFunction,
            madeInClient
          );
-
-          const numberOfSeries = seriesPromises.length;
-          seriesPromises.forEach(async (seriesPromise, index) => {
-            const instances = await seriesPromise;
-            storeInstances(instances);
-            if (index === numberOfSeries - 1) setSuccessFlag();
-          });
        },
      },
    },
+
    store: {
      dicom: async dataset => {
        const headers = UserAuthenticationService.getAuthorizationHeader();
@@ -353,6 +299,187 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
        await wadoDicomWebClient.storeInstances(options);
      },
    },
+    _retrieveSeriesMetadataSync: async (
+      StudyInstanceUID,
+      filters,
+      sortCriteria,
+      sortFunction,
+      madeInClient
+    ) => {
+      const enableStudyLazyLoad = false;
+
+      // data is all SOPInstanceUIDs
+      const data = await retrieveStudyMetadata(
+        wadoDicomWebClient,
+        StudyInstanceUID,
+        enableStudyLazyLoad,
+        filters,
+        sortCriteria,
+        sortFunction
+      );
+
+      // first naturalize the data
+      const naturalizedInstancesMetadata = data.map(naturalizeDataset);
+
+      const seriesSummaryMetadata = {};
+      const instancesPerSeries = {};
+
+      naturalizedInstancesMetadata.forEach(instance => {
+        if (!seriesSummaryMetadata[instance.SeriesInstanceUID]) {
+          seriesSummaryMetadata[instance.SeriesInstanceUID] = {
+            StudyInstanceUID: instance.StudyInstanceUID,
+            StudyDescription: instance.StudyDescription,
+            SeriesInstanceUID: instance.SeriesInstanceUID,
+            SeriesDescription: instance.SeriesDescription,
+            SeriesNumber: instance.SeriesNumber,
+            SeriesTime: instance.SeriesTime,
+            SOPClassUID: instance.SOPClassUID,
+            ProtocolName: instance.ProtocolName,
+            Modality: instance.Modality,
+          };
+        }
+
+        if (!instancesPerSeries[instance.SeriesInstanceUID]) {
+          instancesPerSeries[instance.SeriesInstanceUID] = [];
+        }
+
+        const imageId = implementation.getImageIdsForInstance({
+          instance,
+        });
+
+        instance.imageId = imageId;
+
+        metadataProvider.addImageIdToUIDs(imageId, {
+          StudyInstanceUID,
+          SeriesInstanceUID: instance.SeriesInstanceUID,
+          SOPInstanceUID: instance.SOPInstanceUID,
+        });
+
+        instancesPerSeries[instance.SeriesInstanceUID].push(instance);
+      });
+
+      // grab all the series metadata
+      const seriesMetadata = Object.values(seriesSummaryMetadata);
+      DicomMetadataStore.addSeriesMetadata(seriesMetadata, madeInClient);
+
+      Object.keys(instancesPerSeries).forEach(seriesInstanceUID =>
+        DicomMetadataStore.addInstances(
+          instancesPerSeries[seriesInstanceUID],
+          madeInClient
+        )
+      );
+    },
+
+    _retrieveSeriesMetadataAsync: async (
+      StudyInstanceUID,
+      filters,
+      sortCriteria,
+      sortFunction,
+      madeInClient = false
+    ) => {
+      const enableStudyLazyLoad = true;
+      // Get Series
+      const {
+        preLoadData: seriesSummaryMetadata,
+        promises: seriesPromises,
+      } = await retrieveStudyMetadata(
+        wadoDicomWebClient,
+        StudyInstanceUID,
+        enableStudyLazyLoad,
+        filters,
+        sortCriteria,
+        sortFunction
+      );
+
+      /**
+       * naturalizes the dataset, and adds a retrieve bulkdata method
+       * to any values containing BulkDataURI.
+       * @param {*} instance
+       * @returns naturalized dataset, with retrieveBulkData methods
+       */
+      const addRetrieveBulkData = instance => {
+        const naturalized = naturalizeDataset(instance);
+        Object.keys(naturalized).forEach(key => {
+          const value = naturalized[key];
+          // The value.Value will be set with the bulkdata read value
+          // in which case it isn't necessary to re-read this.
+          if (value && value.BulkDataURI && !value.Value) {
+            // Provide a method to fetch bulkdata
+            value.retrieveBulkData = () => {
+              const options = {
+                // The bulkdata fetches work with either multipart or
+                // singlepart, so set multipart to false to let the server
+                // decide which type to respond with.
+                multipart: false,
+                BulkDataURI: value.BulkDataURI,
+                // The study instance UID is required if the bulkdata uri
+                // is relative - that isn't disallowed by DICOMweb, but
+                // isn't well specified in the standard, but is needed in
+                // any implementation that stores static copies of the metadata
+                StudyInstanceUID: naturalized.StudyInstanceUID,
+              };
+              return qidoDicomWebClient.retrieveBulkData(options).then(val => {
+                const ret = (val && val[0]) || undefined;
+                value.Value = ret;
+                return ret;
+              });
+            };
+          }
+        });
+        return naturalized;
+      };
+
+      // Async load series, store as retrieved
+      function storeInstances(instances) {
+        const naturalizedInstances = instances.map(addRetrieveBulkData);
+
+        // Adding instanceMetadata to OHIF MetadataProvider
+        naturalizedInstances.forEach((instance, index) => {
+          const imageId = implementation.getImageIdsForInstance({
+            instance,
+          });
+
+          // Adding imageId to each instance
+          // Todo: This is not the best way I can think of to let external
+          // metadata handlers know about the imageId that is stored in the store
+          instance.imageId = imageId;
+
+          // Adding UIDs to metadataProvider
+          // Note: storing imageURI in metadataProvider since stack viewports
+          // will use the same imageURI
+          metadataProvider.addImageIdToUIDs(imageId, {
+            StudyInstanceUID,
+            SeriesInstanceUID: instance.SeriesInstanceUID,
+            SOPInstanceUID: instance.SOPInstanceUID,
+          });
+        });
+
+        DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
+      }
+
+      function setSuccessFlag() {
+        const study = DicomMetadataStore.getStudy(
+          StudyInstanceUID,
+          madeInClient
+        );
+        study.isLoaded = true;
+      }
+
+      // Google Cloud Healthcare doesn't return StudyInstanceUID, so we need to add
+      // it manually here
+      seriesSummaryMetadata.forEach(aSeries => {
+        aSeries.StudyInstanceUID = StudyInstanceUID;
+      });
+
+      DicomMetadataStore.addSeriesMetadata(seriesSummaryMetadata, madeInClient);
+
+      const numberOfSeries = seriesPromises.length;
+      seriesPromises.forEach(async (seriesPromise, index) => {
+        const instances = await seriesPromise;
+        storeInstances(instances);
+        if (index === numberOfSeries - 1) setSuccessFlag();
+      });
+    },
    deleteStudyMetadataPromise,
    getImageIdsForDisplaySet(displaySet) {
      const images = displaySet.images;
@@ -25,7 +25,7 @@ const seriesSortCriteria = {
 };

 const instancesSortCriteria = {
-  default: (a, b) => a.InstanceNumber - b.InstanceNumber,
+  default: (a, b) => parseInt(a.InstanceNumber) - parseInt(b.InstanceNumber),
 };

 const sortingCriteria = {
@@ -1,4 +1,4 @@
-//import RetrieveMetadataLoaderSync from './retrieveMetadataLoaderSync';
+import RetrieveMetadataLoaderSync from './retrieveMetadataLoaderSync';
 import RetrieveMetadataLoaderAsync from './retrieveMetadataLoaderAsync';

 /**
@@ -19,12 +19,10 @@ async function RetrieveMetadata(
  sortCriteria,
  sortFunction
 ) {
-  // const RetrieveMetadataLoader =
-  //   enableStudyLazyLoad !== false
-  //     ? RetrieveMetadataLoaderAsync
-  //     : RetrieveMetadataLoaderSync;
-
-  const RetrieveMetadataLoader = RetrieveMetadataLoaderAsync;
+  const RetrieveMetadataLoader =
+    enableStudyLazyLoad !== false
+      ? RetrieveMetadataLoaderAsync
+      : RetrieveMetadataLoaderSync;

  const retrieveMetadataLoader = new RetrieveMetadataLoader(
    dicomWebClient,
@@ -33,12 +31,9 @@ async function RetrieveMetadata(
    sortCriteria,
    sortFunction
  );
-  const { preLoadData, promises } = await retrieveMetadataLoader.execLoad();
+  const data = await retrieveMetadataLoader.execLoad();

-  return {
-    seriesSummaryMetadata: preLoadData,
-    seriesPromises: promises,
-  };
+  return data;
 }

 export default RetrieveMetadata;
@@ -2,7 +2,6 @@ import dcmjs from 'dcmjs';
 import { sortStudySeries, sortingCriteria } from '../utils/sortStudy';
 import RetrieveMetadataLoader from './retrieveMetadataLoader';

-
 /**
 * Creates an immutable series loader object which loads each series sequentially using the iterator interface
 * @param {DICOMWebClient} dicomWebClient The DICOMWebClient instance to be used for series load
@@ -60,7 +60,6 @@ export default class RetrieveMetadataLoaderSync extends RetrieveMetadataLoader {
  }

  async posLoad(loadData) {
-    const { server } = this;
-    return createStudyFromSOPInstanceList(server, loadData);
+    return loadData;
  }
 }