Re-add extensions as top level dir

extensions/ohif-vtk-extension/src/ConnectedToolbarSection.js

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+import { connect } from 'react-redux';
+import { ToolbarSection } from 'react-viewerbase';
+import OHIF from 'ohif-core'
+
+const { setToolActive } = OHIF.redux.actions;
+const Icons = 'icons.svg';
+
+const mapStateToProps = state => {
+  const activeButton = state.tools.buttons.find(tool => tool.active === true);
+
+  return {
+    buttons: [  {
+      command: 'Rotate',
+      type: 'tool',
+      text: 'Rotate',
+      svgUrl: `${Icons}#3d-rotate`,
+      active: true
+    }],
+    activeCommand: 'Rotate'
+  };
+};
+
+const mapDispatchToProps = dispatch => {
+  return {
+    setToolActive: tool => {
+      //dispatch(setToolActive(tool.command))
+    }
+  };
+};
+
+const ConnectedToolbarSection = connect(
+  mapStateToProps,
+  mapDispatchToProps
+)(ToolbarSection);
+
+export default ConnectedToolbarSection;

extensions/ohif-vtk-extension/src/ConnectedVTKViewport.js

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+import { connect } from 'react-redux';
+import { VTKMPRViewport } from 'react-vtkjs-viewport';
+import OHIF from 'ohif-core';
+
+const {
+  setViewportActive,
+  setViewportSpecificData,
+  clearViewportSpecificData
+} = OHIF.redux.actions;
+
+const mapStateToProps = (state, ownProps) => {
+  const activeButton = state.tools.buttons.find(tool => tool.active === true);
+  let dataFromStore;
+
+  if (state.extensions && state.extensions.vtk) {
+    dataFromStore = state.extensions.vtk;
+  }
+
+  // If this is the active viewport, enable prefetching.
+  const { viewportIndex } = ownProps; //.viewportData;
+  const isActive = viewportIndex === state.viewports.activeViewportIndex;
+  const viewportSpecificData =
+    state.viewports.viewportSpecificData[viewportIndex] || {};
+
+  const viewportLayout = state.viewports.layout.viewports[viewportIndex];
+  const pluginDetails = viewportLayout.vtk || {};
+
+  return {
+    layout: state.viewports.layout,
+    isActive,
+    ...pluginDetails,
+    activeTool: activeButton && activeButton.command,
+    ...dataFromStore,
+    enableStackPrefetch: isActive,
+  };
+};
+
+const mapDispatchToProps = (dispatch, ownProps) => {
+  const { viewportIndex } = ownProps;
+
+  return {
+    setViewportActive: () => {
+      dispatch(setViewportActive(viewportIndex));
+    },
+
+    setViewportSpecificData: data => {
+      dispatch(setViewportSpecificData(viewportIndex, data));
+    },
+
+    clearViewportSpecificData: () => {
+      dispatch(clearViewportSpecificData(viewportIndex));
+    }
+  };
+};
+
+const ConnectedVTKViewport = connect(
+  mapStateToProps,
+  //mapDispatchToProps
+)(VTKMPRViewport);
+
+export default ConnectedVTKViewport;

extensions/ohif-vtk-extension/src/LoadingIndicator.css

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+.imageViewerLoadingIndicator {
+  color: #91B9CD;
+}
+
+.loadingIndicator {
+  background-color: rgba(0, 0, 0, 0.75);
+  font-size: 18px;
+  height: 100%;
+  overflow: hidden;
+  position: absolute;
+  top: 0;
+  width: 100%;
+  z-index: 1;
+
+  /* Necessary for click-through to cornerstone element below */
+  pointer-events: none;
+}

extensions/ohif-vtk-extension/src/LoadingIndicator.js

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+import React, { PureComponent } from 'react';
+import PropTypes from 'prop-types';
+
+import './LoadingIndicator.css';
+
+class LoadingIndicator extends PureComponent {
+  static propTypes = {
+    percentComplete: PropTypes.number.isRequired,
+    error: PropTypes.object
+  };
+
+  static defaultProps = {
+    percentComplete: 0,
+    error: null
+  };
+
+  render() {
+    let percComplete;
+    if (this.props.percentComplete && this.props.percentComplete !== 100) {
+      percComplete = `${this.props.percentComplete}%`;
+    }
+
+    return (
+      <React.Fragment>
+        {this.props.error ? (
+          <div className="imageViewerErrorLoadingIndicator loadingIndicator">
+            <div className="indicatorContents">
+              <h4>Error Loading Image</h4>
+              <p className="description">An error has occurred.</p>
+              <p className="details">{this.props.error.message}</p>
+            </div>
+          </div>
+        ) : (
+          <div className="imageViewerLoadingIndicator loadingIndicator">
+            <div className="indicatorContents">
+              <p>
+                Loading... <i className="fa fa-spin fa-circle-o-notch fa-fw" />{' '}
+                {percComplete}
+              </p>
+            </div>
+          </div>
+        )}
+      </React.Fragment>
+    );
+  }
+}
+
+export default LoadingIndicator;

extensions/ohif-vtk-extension/src/OHIFVTKExtension.js

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+import React, { Component } from 'react';
+import OHIFVTKViewport from './OHIFVTKViewport.js';
+import ToolbarModule from './ToolbarModule.js';
+
+/**
+ * Pass in 'children' to a React component. The purpose of this is to
+ * allow end users of this extension to pass in components which will
+ * be rendered on top of the base components.
+ *
+ * @param WrappedComponent
+ * @param children
+ * @return {function(*): *}
+ */
+function withChildren(WrappedComponent, children) {
+  return function(props) {
+    return <WrappedComponent children={children} { ...props } />;
+  };
+}
+
+// Note: If you are authoring extensions which use stateful libraries (e.g. cornerstone-core, react-redux) as peerDependencies and are also duplicated at the application level, try using 'yalc' to link it to the application, rather than yarn link. This can help fix 'module not found' issues.
+// https://github.com/whitecolor/yalc
+
+export default class OHIFVTKExtension {
+  constructor(children) {
+    this.children = children;
+  }
+
+  /**
+   * Extension ID is a unique id, might be used for namespacing extension specific redux actions/reducers (?)
+   */
+  getExtensionId() {
+    return 'vtk';
+  }
+
+  getViewportModule() {
+    if (this.children && this.children.viewport) {
+      return withChildren(OHIFVTKViewport, this.children.viewport);
+    }
+
+    return OHIFVTKViewport;
+  }
+
+  getSopClassHandler() {
+    return null;
+  }
+
+  getPanelModule() {
+    return null;
+  }
+
+  getToolbarModule() {
+    return ToolbarModule;
+  }
+}

extensions/ohif-vtk-extension/src/OHIFVTKViewport.js

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+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import OHIF from 'ohif-core';
+import ConnectedVTKViewport from './ConnectedVTKViewport';
+import cornerstone from 'cornerstone-core';
+import handleSegmentationStorage from './handleSegmentationStorage.js';
+import { getImageData, loadImageData } from 'react-vtkjs-viewport';
+import LoadingIndicator from './LoadingIndicator.js';
+
+const { StackManager } = OHIF.utils;
+
+// Metadata configuration
+const metadataProvider = new OHIF.cornerstone.MetadataProvider();
+
+cornerstone.metaData.addProvider(
+  metadataProvider.provider.bind(metadataProvider)
+);
+
+StackManager.setMetadataProvider(metadataProvider);
+
+const SOP_CLASSES = {
+  SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4'
+};
+
+const specialCaseHandlers = {};
+specialCaseHandlers[
+  SOP_CLASSES.SEGMENTATION_STORAGE
+] = handleSegmentationStorage;
+
+class OHIFVTKViewport extends Component {
+  state = {
+    viewportData: null
+  };
+
+  static propTypes = {
+    studies: PropTypes.object,
+    displaySet: PropTypes.object,
+    viewportIndex: PropTypes.number,
+    children: PropTypes.node
+  };
+
+  static id = 'OHIFCornerstoneViewport';
+
+  static init() {
+    console.log('OHIFCornerstoneViewport init()');
+  }
+
+  static destroy() {
+    console.log('OHIFCornerstoneViewport destroy()');
+    StackManager.clearStacks();
+  }
+
+  static getCornerstoneStack(
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid,
+    sopInstanceUid,
+    frameIndex
+  ) {
+    // Create shortcut to displaySet
+    const study = studies.find(
+      study => study.studyInstanceUid === studyInstanceUid
+    );
+
+    const displaySet = study.displaySets.find(set => {
+      return set.displaySetInstanceUid === displaySetInstanceUid;
+    });
+
+    // Get stack from Stack Manager
+    const storedStack = StackManager.findOrCreateStack(study, displaySet);
+
+    // Clone the stack here so we don't mutate it
+    const stack = Object.assign({}, storedStack);
+
+    if (frameIndex !== undefined) {
+      stack.currentImageIdIndex = frameIndex;
+    } else if (sopInstanceUid) {
+      const index = stack.imageIds.findIndex(imageId => {
+        const sopCommonModule = cornerstone.metaData.get(
+          'sopCommonModule',
+          imageId
+        );
+        if (!sopCommonModule) {
+          return;
+        }
+
+        return sopCommonModule.sopInstanceUID === sopInstanceUid;
+      });
+
+      if (index > -1) {
+        stack.currentImageIdIndex = index;
+      }
+    } else {
+      stack.currentImageIdIndex = 0;
+    }
+
+    return stack;
+  }
+
+  static getViewportData = (
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid,
+    sopInstanceUid,
+    frameIndex
+  ) => {
+    return OHIFVTKViewport.getCornerstoneStack(
+      studies,
+      studyInstanceUid,
+      displaySetInstanceUid,
+      sopInstanceUid,
+      frameIndex
+    );
+  };
+
+  getViewportData = (
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid,
+    sopClassUid,
+    sopInstanceUid,
+    frameIndex
+  ) => {
+    return new Promise((resolve, reject) => {
+      const stack = OHIFVTKViewport.getViewportData(
+        studies,
+        studyInstanceUid,
+        displaySetInstanceUid,
+        sopClassUid,
+        sopInstanceUid,
+        frameIndex
+      );
+
+      let imageDataObject;
+      let labelmapDataObject;
+      let doneLoadingCallback;
+      let callbacks;
+
+      switch (sopClassUid) {
+        case SOP_CLASSES.SEGMENTATION_STORAGE:
+          throw new Error("Not yet implemented");
+
+          const data = handleSegmentationStorage(stack.imageIds, displaySetInstanceUid, cornerstone);
+          imageDataObject = data.referenceDataObject;
+          labelmapDataObject = data.labelmapDataObject;
+
+          doneLoadingCallback = () => {
+            resolve({
+              data: imageDataObject.vtkImageData,
+              labelmap: labelmapDataObject
+            });
+          };
+
+          callbacks = [
+            doneLoadingCallback
+          ];
+
+          loadImageData(imageDataObject, callbacks, cornerstone);
+
+          break;
+        default:
+          imageDataObject = getImageData(stack.imageIds, displaySetInstanceUid, cornerstone);
+          doneLoadingCallback = () => {
+            resolve({
+              data: imageDataObject.vtkImageData,
+            });
+          };
+
+          callbacks = [
+            doneLoadingCallback
+          ];
+
+          loadImageData(imageDataObject, callbacks, cornerstone);
+
+          break;
+      }
+    });
+  };
+
+  setStateFromProps() {
+    const { studies, displaySet } = this.props.viewportData;
+    const {
+      studyInstanceUid,
+      displaySetInstanceUid,
+      sopClassUids,
+      sopInstanceUid,
+      frameIndex
+    } = displaySet;
+
+    if (sopClassUids.length > 1) {
+      console.warn(
+        'More than one SOPClassUid in the same series is not yet supported.'
+      );
+    }
+
+    const sopClassUid = sopClassUids[0];
+
+    this.getViewportData(
+      studies,
+      studyInstanceUid,
+      displaySetInstanceUid,
+      sopClassUid,
+      sopInstanceUid,
+      frameIndex
+    ).then(({ data, labelmap })=> {
+      this.setState({
+        viewportData: data,
+        labelmap
+      });
+    });
+  }
+
+  componentDidMount() {
+    this.setStateFromProps();
+  }
+
+  componentDidUpdate(prevProps) {
+    const { studies, displaySet } = this.props.viewportData;
+    const prevDisplaySet = prevProps.viewportData.displaySet;
+
+    if (
+      displaySet.displaySetInstanceUid !==
+        prevDisplaySet.displaySetInstanceUid ||
+      displaySet.sopInstanceUid !== prevDisplaySet.sopInstanceUid ||
+      displaySet.frameIndex !== prevDisplaySet.frameIndex
+    ) {
+      this.setStateFromProps();
+    }
+  }
+
+  render() {
+    let childrenWithProps = null;
+
+    // TODO: Does it make more sense to use Context?
+    if (this.props.children && this.props.children.length) {
+      childrenWithProps = this.props.children.map((child, index) => {
+        return React.cloneElement(child, {
+          viewportIndex: this.props.viewportIndex,
+          key: index
+        });
+      });
+    }
+
+    const style = { width: '100%', height: '100%', position: 'relative' };
+
+    return (
+      <>
+        {this.state.viewportData ? (
+          <ConnectedVTKViewport
+            data={this.state.viewportData}
+            labelmap={this.state.labelmap}
+            viewportIndex={this.props.viewportIndex}
+          />
+        ) : <div style={style}>
+          <LoadingIndicator/>
+        </div>}
+        {childrenWithProps}
+      </>
+    );
+  }
+}
+
+export default OHIFVTKViewport;

extensions/ohif-vtk-extension/src/ToolbarModule.js

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+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import ConnectedToolbarSection from './ConnectedToolbarSection';
+
+class ToolbarModule extends Component {
+  render() {
+    return (
+      <div className="ToolbarModule">
+        <ConnectedToolbarSection />
+      </div>
+    );
+  }
+}
+
+export default ToolbarModule;

extensions/ohif-vtk-extension/src/handleSegmentationStorage.js

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+import OHIF from 'ohif-core';
+import * as dcmjs from 'dcmjs';
+
+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(wadoUri) {
+  // TODO: Authorization header depends on the server. If we ever have multiple servers
+  // we will need to figure out how / when to pass this information in.
+  return fetch(wadoUri, {
+    headers: OHIF.DICOMWeb.getAuthorizationHeader()
+  }).then(response => response.arrayBuffer());
+}
+
+async function handleSegmentationStorage(
+  studies,
+  studyInstanceUid,
+  displaySetInstanceUid
+) {
+  const study = studies.find(
+    study => study.studyInstanceUid === studyInstanceUid
+  );
+  const displaySet = getDisplaySet(
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid
+  );
+  const segWadoUri = displaySet.images[0].getData().wadouri;
+  const arrayBuffer = await retrieveDicomData(segWadoUri);
+  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;

extensions/ohif-vtk-extension/src/index.js

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