feat: Add CS3D WSI and Video Viewports and add annotation navigation for MPR (#4182)

extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js

@@ -1,121 +0,0 @@
-import OHIF from '@ohif/core';
-
-const { utils } = OHIF;
-
-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-dicom-microscopy.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;
-  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
-      const dataSource = extensionManager.getActiveDataSource()[0];
-      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',
-    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
-    othersFrameOfReferenceUID,
-  };
-
-  return [displaySet];
-}
-
-export default 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,
-  };
-}

extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx

@@ -1,12 +1,12 @@
 import React, { Component } from 'react';
 import PropTypes from 'prop-types';
 import { LoadingIndicatorProgress } from '@ohif/ui';
+import { cleanDenaturalizedDataset } from '@ohif/extension-default';
 
 import './DicomMicroscopyViewport.css';
 import ViewportOverlay from './components/ViewportOverlay';
 import getDicomWebClient from './utils/dicomWebClient';
 import dcmjs from 'dcmjs';
-import cleanDenaturalizedDataset from './utils/cleanDenaturalizedDataset';
 import MicroscopyService from './services/MicroscopyService';
 
 class DicomMicroscopyViewport extends Component {

extensions/dicom-microscopy/src/index.tsx

@@ -5,7 +5,6 @@ import getCommandsModule from './getCommandsModule';
 import { Types } from '@ohif/core';
 
 import { useViewportGrid } from '@ohif/ui';
-import getDicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler';
 import getDicomMicroscopySRSopClassHandler from './DicomMicroscopySRSopClassHandler';
 import MicroscopyService from './services/MicroscopyService';
 import { useResizeDetector } from 'react-resize-detector';
@@ -153,17 +152,8 @@ const extension: Types.Extensions.Extension = {
    * Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}.
    * Examples include the default sop class handler provided by the default extension
    */
-  getSopClassHandlerModule({ servicesManager, commandsManager, extensionManager }) {
-    return [
-      getDicomMicroscopySopClassHandler({
-        servicesManager,
-        extensionManager,
-      }),
-      getDicomMicroscopySRSopClassHandler({
-        servicesManager,
-        extensionManager,
-      }),
-    ];
+  getSopClassHandlerModule(params) {
+    return [getDicomMicroscopySRSopClassHandler(params)];
   },
 
   getPanelModule,

extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts

@@ -1,66 +0,0 @@
-import { dicomWebUtils } from '@ohif/extension-default';
-
-function isPrimitive(v: any) {
-  return !(typeof v == 'object' || Array.isArray(v));
-}
-
-const vrNumerics = [
-  'DS',
-  'FL',
-  'FD',
-  'IS',
-  'OD',
-  'OF',
-  'OL',
-  'OV',
-  'SL',
-  'SS',
-  'SV',
-  'UL',
-  'US',
-  'UV',
-];
-
-/**
- * Specialized for DICOM JSON format dataset cleaning.
- * @param obj
- * @returns
- */
-export default function cleanDenaturalizedDataset(
-  obj: any,
-  options: {
-    StudyInstanceUID: string;
-    SeriesInstanceUID: string;
-    dataSourceConfig: unknown;
-  }
-): any {
-  if (Array.isArray(obj)) {
-    const newAry = obj.map(o => (isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)));
-    return newAry;
-  } else if (isPrimitive(obj)) {
-    return obj;
-  } else {
-    Object.keys(obj).forEach(key => {
-      if (obj[key].Value === null && obj[key].vr) {
-        delete obj[key].Value;
-      } else if (Array.isArray(obj[key].Value) && obj[key].vr) {
-        if (obj[key].Value.length === 1 && obj[key].Value[0].BulkDataURI) {
-          dicomWebUtils.fixBulkDataURI(obj[key].Value[0], options, options.dataSourceConfig);
-
-          obj[key].BulkDataURI = obj[key].Value[0].BulkDataURI;
-
-          // prevent mixed-content blockage
-          if (window.location.protocol === 'https:' && obj[key].BulkDataURI.startsWith('http:')) {
-            obj[key].BulkDataURI = obj[key].BulkDataURI.replace('http:', 'https:');
-          }
-          delete obj[key].Value;
-        } else if (vrNumerics.includes(obj[key].vr)) {
-          obj[key].Value = obj[key].Value.map(v => +v);
-        } else {
-          obj[key].Value = obj[key].Value.map(entry => cleanDenaturalizedDataset(entry, options));
-        }
-      }
-    });
-    return obj;
-  }
-}