Re-add extensions as top level dir

extensions/ohif-dicom-microscopy-extension/src/DicomMicroscopySopClassHandler.js

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+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 DicomMicroscopySopClassHandler = {
+  id: 'DicomMicroscopySopClassHandlerPlugin',
+  sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
+  getDisplaySetFromSeries(series, study, dicomWebClient) {
+    const instance = series.getFirstInstance();
+
+    // Note: We are passing the dicomweb client into each viewport!
+
+    return {
+      plugin: 'microscopy',
+      displaySetInstanceUid: utils.guid(),
+      dicomWebClient,
+      sopInstanceUid: instance.getSOPInstanceUID(),
+      seriesInstanceUid: series.getSeriesInstanceUID(),
+      studyInstanceUid: study.getStudyInstanceUID()
+    };
+  }
+};
+
+export default DicomMicroscopySopClassHandler;

extensions/ohif-dicom-microscopy-extension/src/DicomMicroscopyViewport.js

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+import React, { Component } from 'react';
+import { api } from 'dicom-microscopy-viewer';
+
+const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
+
+class DicomMicroscopyViewport extends Component {
+  state = {
+    error: null
+  };
+
+  constructor(props) {
+    super(props);
+
+    this.container = React.createRef();
+  }
+
+  // install the microscopy renderer into the web page.
+  // you should only do this once.
+  installOpenLayersRenderer(container, displaySet) {
+    const dicomWebClient = displaySet.dicomWebClient;
+
+    const searchInstanceOptions = {
+      studyInstanceUID: displaySet.studyInstanceUid,
+      seriesInstanceUID: displaySet.seriesInstanceUid
+    };
+
+    dicomWebClient
+      .searchForInstances(searchInstanceOptions)
+      .then(instances => {
+        const promises = [];
+        for (let i = 0; i < instances.length; i++) {
+          const sopInstanceUID = instances[i]['00080018']['Value'][0];
+          const retrieveInstanceOptions = {
+            studyInstanceUID: displaySet.studyInstanceUid,
+            seriesInstanceUID: displaySet.seriesInstanceUid,
+            sopInstanceUID
+          };
+
+          const promise = dicomWebClient
+            .retrieveInstanceMetadata(retrieveInstanceOptions)
+            .then(metadata => {
+              const imageType = metadata[0]['00080008']['Value'];
+              if (imageType[2] === 'VOLUME') {
+                return metadata[0];
+              }
+            });
+          promises.push(promise);
+        }
+        return Promise.all(promises);
+      })
+      .then(metadata => {
+        metadata = metadata.filter(m => m);
+
+        const viewer = new microscopyViewer({
+          client: dicomWebClient,
+          metadata
+        });
+
+        viewer.render({ container });
+      });
+  }
+
+  componentDidMount() {
+    const { studies, displaySet } = this.props.viewportData;
+
+    this.installOpenLayersRenderer(this.container.current, displaySet);
+  }
+
+  render() {
+    const style = { width: '100%', height: '100%' };
+    return (
+      <div className={'DicomMicroscopyViewer'} style={style}>
+        {this.state.error ? (
+          <h2>{JSON.stringify(this.state.error)}</h2>
+        ) : (
+          <div style={style} ref={this.container} />
+        )}
+      </div>
+    );
+  }
+}
+
+export default DicomMicroscopyViewport;

extensions/ohif-dicom-microscopy-extension/src/OHIFDicomMicroscopyExtension.js

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+import DicomMicroscopyViewport from './DicomMicroscopyViewport.js';
+import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
+
+export default class OHIFDicomMicroscopyExtension {
+  /**
+   * Extension ID is a unique id, might be used for namespacing extension specific redux actions/reducers (?)
+   */
+  getExtensionId() {
+    return 'microscopy';
+  }
+
+  getViewportModule() {
+    return DicomMicroscopyViewport;
+  }
+
+  getSopClassHandler() {
+    return DicomMicroscopySopClassHandler;
+  }
+
+  getPanelModule() {
+    return null;
+  }
+
+  getToolbarModule() {
+    return null;
+  }
+}

extensions/ohif-dicom-microscopy-extension/src/index.js

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+import OHIFDicomMicroscopyExtension from './OHIFDicomMicroscopyExtension.js';
+
+export default OHIFDicomMicroscopyExtension;