Initial commit from prod-batam

extensions/cornerstone/src/getSopClassHandlerModule.js

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+import OHIF from '@ohif/core';
+import { utilities as csUtils, Enums as csEnums } from '@cornerstonejs/core';
+import dcmjs from 'dcmjs';
+import { dicomWebUtils } from '@ohif/extension-default';
+
+const { MetadataModules } = csEnums;
+const { utils } = OHIF;
+const { denaturalizeDataset } = dcmjs.data.DicomMetaDictionary;
+const { transferDenaturalizedDataset, fixMultiValueKeys } = dicomWebUtils;
+
+const SOP_CLASS_UIDS = {
+  VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6',
+};
+
+const SOPClassHandlerId =
+  '@ohif/extension-cornerstone.sopClassHandlerModule.DicomMicroscopySopClassHandler';
+
+function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
+  // If the series has no instances, stop here
+  if (!instances || !instances.length) {
+    throw new Error('No instances were provided');
+  }
+
+  const instance = instances[0];
+
+  let singleFrameInstance = instance;
+  let currentFrames = +singleFrameInstance.NumberOfFrames || 1;
+  for (const instanceI of instances) {
+    const framesI = +instanceI.NumberOfFrames || 1;
+    if (framesI < currentFrames) {
+      singleFrameInstance = instanceI;
+      currentFrames = framesI;
+    }
+  }
+  let imageIdForThumbnail = null;
+  const dataSource = extensionManager.getActiveDataSource()[0];
+  if (singleFrameInstance) {
+    if (currentFrames == 1) {
+      // Not all DICOM server implementations support thumbnail service,
+      // So if we have a single-frame image, we will prefer it.
+      imageIdForThumbnail = singleFrameInstance.imageId;
+    }
+    if (!imageIdForThumbnail) {
+      // use the thumbnail service provided by DICOM server
+      imageIdForThumbnail = dataSource.getImageIdsForInstance({
+        instance: singleFrameInstance,
+        thumbnail: true,
+      });
+    }
+  }
+
+  const {
+    FrameOfReferenceUID,
+    SeriesDescription,
+    ContentDate,
+    ContentTime,
+    SeriesNumber,
+    StudyInstanceUID,
+    SeriesInstanceUID,
+    SOPInstanceUID,
+    SOPClassUID,
+  } = instance;
+
+  instances = instances.map(inst => {
+    // NOTE: According to DICOM standard a series should have a FrameOfReferenceUID
+    // When the Microscopy file was built by certain tool from multiple image files,
+    // each instance's FrameOfReferenceUID is sometimes different.
+    // Even though this means the file was not well formatted DICOM VL Whole Slide Microscopy Image,
+    // the case is so often, so let's override this value manually here.
+    //
+    // https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.4.html#sect_C.7.4.1.1.1
+
+    inst.FrameOfReferenceUID = instance.FrameOfReferenceUID;
+
+    return inst;
+  });
+
+  const othersFrameOfReferenceUID = instances
+    .filter(v => v)
+    .map(inst => inst.FrameOfReferenceUID)
+    .filter((value, index, array) => array.indexOf(value) === index);
+  if (othersFrameOfReferenceUID.length > 1) {
+    console.warn(
+      'Expected FrameOfReferenceUID of difference instances within a series to be the same, found multiple different values',
+      othersFrameOfReferenceUID
+    );
+  }
+
+  const displaySet = {
+    plugin: 'microscopy',
+    Modality: 'SM',
+    viewportType: csEnums.ViewportType.WHOLE_SLIDE,
+    altImageText: 'Microscopy',
+    displaySetInstanceUID: utils.guid(),
+    SOPInstanceUID,
+    SeriesInstanceUID,
+    StudyInstanceUID,
+    FrameOfReferenceUID,
+    SOPClassHandlerId,
+    SOPClassUID,
+    SeriesDescription: SeriesDescription || 'Microscopy Data',
+    // Map ContentDate/Time to SeriesTime for series list sorting.
+    SeriesDate: ContentDate,
+    SeriesTime: ContentTime,
+    SeriesNumber,
+    firstInstance: singleFrameInstance, // top level instance in the image Pyramid
+    instance,
+    numImageFrames: 0,
+    numInstances: 1,
+    imageIdForThumbnail, // thumbnail image
+    others: instances, // all other level instances in the image Pyramid
+    instances,
+    othersFrameOfReferenceUID,
+    imageIds: instances.map(instance => instance.imageId),
+  };
+  // The microscopy viewer directly accesses the metadata already loaded, and
+  // uses the DICOMweb client library directly for loading, so it has to be
+  // provided here.
+  const dicomWebClient = dataSource.retrieve.getWadoDicomWebClient?.();
+  const instanceMap = new Map();
+  instances.forEach(instance => instanceMap.set(instance.imageId, instance));
+  if (dicomWebClient) {
+    const webClient = Object.create(dicomWebClient);
+    // This replaces just the dicom web metadata call with one which retrieves
+    // internally.
+    webClient.getDICOMwebMetadata = getDICOMwebMetadata.bind(webClient, instanceMap);
+
+    csUtils.genericMetadataProvider.addRaw(displaySet.imageIds[0], {
+      type: MetadataModules.WADO_WEB_CLIENT,
+      metadata: webClient,
+    });
+  } else {
+    // Might have some other way of getting the data in the future or internally?
+    // throw new Error('Unable to provide a DICOMWeb client library, microscopy will fail to view');
+  }
+
+  return [displaySet];
+}
+
+/**
+ * This method provides access to the internal DICOMweb metadata, used to avoid
+ * refetching the DICOMweb data.  It gets assigned as a member function to the
+ * dicom web client.
+ */
+function getDICOMwebMetadata(instanceMap, imageId) {
+  const instance = instanceMap.get(imageId);
+  if (!instance) {
+    console.warn('Metadata not already found for', imageId, 'in', instanceMap);
+    return this.super.getDICOMwebMetadata(imageId);
+  }
+  return transferDenaturalizedDataset(
+    denaturalizeDataset(fixMultiValueKeys(instanceMap.get(imageId)))
+  );
+}
+
+export function getDicomMicroscopySopClassHandler({ servicesManager, extensionManager }) {
+  const getDisplaySetsFromSeries = instances => {
+    return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
+  };
+
+  return {
+    name: 'DicomMicroscopySopClassHandler',
+    sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
+    getDisplaySetsFromSeries,
+  };
+}
+
+export function getSopClassHandlerModule(params) {
+  return [getDicomMicroscopySopClassHandler(params)];
+}