chore(release): publish [skip ci]

- @ohif/extension-cornerstone@2.0.0 - @ohif/extension-dicom-html@1.0.0 - @ohif/extension-dicom-pdf@1.0.0 - @ohif/extension-vtk@0.50.21 - @ohif/core@1.0.0 - @ohif/viewer@2.0.0
fix: 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases (#862 )
2019-09-27 11:58:23 +00:00 · 2019-09-27 13:47:08 +02:00 · 2019-09-27 11:10:33 +00:00 · 2019-09-27 06:54:47 -04:00
39 changed files with 775 additions and 418 deletions
@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+# [2.0.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@1.2.2...@ohif/extension-cornerstone@2.0.0) (2019-09-27)
+
+
+### Bug Fixes
+
+* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
+
+
+### BREAKING CHANGES
+
+* DICOM Seg
+
+
+
+
+
 ## [1.2.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@1.2.1...@ohif/extension-cornerstone@1.2.2) (2019-09-26)


@@ -1,6 +1,6 @@
 {
  "name": "@ohif/extension-cornerstone",
-  "version": "1.2.2",
+  "version": "2.0.0",
  "description": "OHIF extension for Cornerstone",
  "author": "OHIF",
  "license": "MIT",
@@ -4,7 +4,7 @@ import OHIF from '@ohif/core';
 import cornerstone from 'cornerstone-core';
 import cornerstoneTools from 'cornerstone-tools';

-const { StackManager } = OHIF.utils;
+const { StackManager, DicomLoaderService } = OHIF.utils;

 function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
  const study = studies.find(
@@ -52,14 +52,6 @@ function addSegMetadataToCornerstoneToolState(
  }
 }

-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,
@@ -73,8 +65,11 @@ async function handleSegmentationStorage(
    studyInstanceUid,
    displaySetInstanceUid
  );
-  const segWadoUri = displaySet.images[0].getData().wadouri;
-  const arrayBuffer = await retrieveDicomData(segWadoUri);
+
+  const arrayBuffer = await DicomLoaderService.findDicomDataPromise(
+    displaySet,
+    studies
+  );
  const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
  const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
    dicomData.dict
@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+# [1.0.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@0.50.8...@ohif/extension-dicom-html@1.0.0) (2019-09-27)
+
+
+### Bug Fixes
+
+* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
+
+
+### BREAKING CHANGES
+
+* DICOM Seg
+
+
+
+
+
 ## [0.50.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-html@0.50.7...@ohif/extension-dicom-html@0.50.8) (2019-09-26)


@@ -1,6 +1,6 @@
 {
  "name": "@ohif/extension-dicom-html",
-  "version": "0.50.8",
+  "version": "1.0.0",
  "description": "OHIF extension for rendering structured reports to HTML",
  "author": "OHIF",
  "license": "MIT",
@@ -1,46 +1,34 @@
 import React, { Component } from 'react';
 import PropTypes from 'prop-types';
 import DicomHtmlViewport from './DicomHtmlViewport';
+import OHIF from '@ohif/core';
+const { DicomLoaderService } = OHIF.utils;

 class OHIFDicomHtmlViewport extends Component {
  static propTypes = {
    studies: PropTypes.object,
    displaySet: PropTypes.object,
-    viewportIndex: PropTypes.number
+    viewportIndex: PropTypes.number,
  };

  state = {
    byteArray: null,
-    error: null
+    error: null,
  };

  componentDidMount() {
-    const { displaySet } = this.props.viewportData;
-    const {
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    } = displaySet;
+    const { displaySet, studies } = this.props.viewportData;

-    this.retrieveDicomData(
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
+      data => {
+        const byteArray = new Uint8Array(data);
        this.setState({
-          byteArray
+          byteArray: byteArray,
        });
      },
      error => {
        this.setState({
-          error
+          error,
        });

        throw new Error(error);
@@ -48,27 +36,6 @@ class OHIFDicomHtmlViewport extends Component {
    );
  }

-  retrieveDicomData(
-    studyInstanceUid,
-    seriesInstanceUid,
-    sopInstanceUid,
-    wadoRoot,
-    wadoUri,
-    authorizationHeaders
-  ) {
-    // TODO: Passing in a lot of data we aren't using
-
-    // 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: authorizationHeaders
-    })
-      .then(response => response.arrayBuffer())
-      .then(arraybuffer => {
-        return new Uint8Array(arraybuffer);
-      });
-  }
-
  render() {
    return (
      <>
@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+# [1.0.0](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@0.50.4...@ohif/extension-dicom-pdf@1.0.0) (2019-09-27)
+
+
+### Bug Fixes
+
+* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
+
+
+### BREAKING CHANGES
+
+* DICOM Seg
+
+
+
+
+
 ## [0.50.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-pdf@0.50.3...@ohif/extension-dicom-pdf@0.50.4) (2019-09-10)


@@ -1,6 +1,6 @@
 {
  "name": "@ohif/extension-dicom-pdf",
-  "version": "0.50.4",
+  "version": "1.0.0",
  "description": "OHIF extension for Dicom PDF",
  "author": "OHIF",
  "license": "MIT",
@@ -4,41 +4,46 @@ import TypedArrayProp from './TypedArrayProp';

 // TODO: Should probably use dcmjs for this
 const SOP_CLASS_UIDS = {
-  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1'
+  ENCAPSULATED_PDF: '1.2.840.10008.5.1.4.1.1.104.1',
 };

 class DicomPDFViewport extends Component {
  state = {
    fileURL: null,
-    error: null
+    error: null,
  };

  static propTypes = {
-    byteArray: TypedArrayProp.uint8
+    byteArray: TypedArrayProp.uint8,
  };

-  renderPDF = dataSet => {
-    const sopClassUid = dataSet.string('x00080016');
+  renderPDF = (dataSet, byteArray) => {
+    let pdfByteArray = byteArray;

-    if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
-      throw new Error('This is not a DICOM-encapsulated PDF');
+    if (dataSet) {
+      const sopClassUid = dataSet.string('x00080016');
+
+      if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
+        throw new Error('This is not a DICOM-encapsulated PDF');
+      }
+
+      const fileTag = dataSet.elements.x00420011;
+      const offset = fileTag.dataOffset;
+      const remainder = offset + fileTag.length;
+      pdfByteArray = dataSet.byteArray.slice(offset, remainder);
    }

-    const fileTag = dataSet.elements.x00420011;
-    const offset = fileTag.dataOffset;
-    const remainder = offset + fileTag.length;
-    const pdfByteArray = dataSet.byteArray.slice(offset, remainder);
    const PDF = new Blob([pdfByteArray], { type: 'application/pdf' });
    const fileURL = URL.createObjectURL(PDF);

    this.setState({
-      fileURL
+      fileURL,
    });
  };

  parseByteArray = byteArray => {
    const options = {
-      untilTag: ''
+      untilTag: '',
    };

    let dataSet;
@@ -47,7 +52,7 @@ class DicomPDFViewport extends Component {
      dataSet = dicomParser.parseDicom(byteArray, options);
    } catch (error) {
      this.setState({
-        error
+        error,
      });
    }

@@ -57,7 +62,7 @@ class DicomPDFViewport extends Component {
  componentDidMount() {
    const dataSet = this.parseByteArray(this.props.byteArray);

-    this.renderPDF(dataSet);
+    this.renderPDF(dataSet, this.props.byteArray);
  }

  render() {
@@ -1,60 +1,54 @@
-import React, { Component } from "react";
-import PropTypes from "prop-types";
-import OHIF from "@ohif/core";
-import OHIFComponentPlugin from "./OHIFComponentPlugin.js";
-import DicomPDFViewport from "./DicomPDFViewport";
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import OHIF from '@ohif/core';
+import OHIFComponentPlugin from './OHIFComponentPlugin.js';
+import DicomPDFViewport from './DicomPDFViewport';

-const { DICOMWeb } = OHIF;
+const { DicomLoaderService } = OHIF.utils;

 class OHIFDicomPDFViewport extends Component {
  static propTypes = {
    studies: PropTypes.object,
    displaySet: PropTypes.object,
-    viewportIndex: PropTypes.number
+    viewportIndex: PropTypes.number,
  };

  state = {
    byteArray: null,
-    error: null
+    error: null,
  };

-  static id = "DicomPDFViewportPDF";
+  static id = 'DicomPDFViewportPDF';

  static init() {
-    console.log("DicomPDFViewport init()");
+    console.log('DicomPDFViewport init()');
  }

  static destroy() {
-    console.log("DicomPDFViewport destroy()");
+    console.log('DicomPDFViewport destroy()');
  }

  componentDidMount() {
-    const { displaySet } = this.props.viewportData;
+    const { displaySet, studies } = this.props.viewportData;
    const {
      studyInstanceUid,
      seriesInstanceUid,
      sopInstanceUid,
      wadoRoot,
      wadoUri,
-      authorizationHeaders
+      authorizationHeaders,
    } = displaySet;

-    this.retrieveDicomData(
-      studyInstanceUid,
-      seriesInstanceUid,
-      sopInstanceUid,
-      wadoRoot,
-      wadoUri,
-      authorizationHeaders
-    ).then(
-      byteArray => {
+    DicomLoaderService.findDicomDataPromise(displaySet, studies).then(
+      data => {
+        const byteArray = new Uint8Array(data);
        this.setState({
-          byteArray
+          byteArray: byteArray,
        });
      },
      error => {
        this.setState({
-          error
+          error,
        });

        throw new Error(error);
@@ -62,27 +56,6 @@ class OHIFDicomPDFViewport extends Component {
    );
  }

-  retrieveDicomData(
-    studyInstanceUid,
-    seriesInstanceUid,
-    sopInstanceUid,
-    wadoRoot,
-    wadoUri,
-    authorizationHeaders
-  ) {
-    // TODO: Passing in a lot of data we aren't using
-
-    // 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: authorizationHeaders
-    })
-      .then(response => response.arrayBuffer())
-      .then(arraybuffer => {
-        return new Uint8Array(arraybuffer);
-      });
-  }
-
  render() {
    const { id, init, destroy } = OHIFDicomPDFViewport;
    const pluginProps = { id, init, destroy };
@@ -3,6 +3,14 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+## [0.50.21](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.20...@ohif/extension-vtk@0.50.21) (2019-09-27)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [0.50.20](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@0.50.19...@ohif/extension-vtk@0.50.20) (2019-09-26)

 **Note:** Version bump only for package @ohif/extension-vtk
@@ -1,6 +1,6 @@
 {
  "name": "@ohif/extension-vtk",
-  "version": "0.50.20",
+  "version": "0.50.21",
  "description": "OHIF extension for VTK.js",
  "author": "OHIF",
  "license": "MIT",
@@ -51,7 +51,7 @@
    "react-vtkjs-viewport": "0.1.0"
  },
  "devDependencies": {
-    "@ohif/core": "^0.50.10",
+    "@ohif/core": "^1.0.0",
    "@ohif/ui": "^0.51.2",
    "cornerstone-tools": "^4.0.9",
    "cornerstone-wado-image-loader": "^3.0.0",
@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+# [1.0.0](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.10...@ohif/core@1.0.0) (2019-09-27)
+
+
+### Bug Fixes
+
+* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
+
+
+### BREAKING CHANGES
+
+* DICOM Seg
+
+
+
+
+
 ## [0.50.10](https://github.com/OHIF/Viewers/compare/@ohif/core@0.50.9...@ohif/core@0.50.10) (2019-09-23)


@@ -1,6 +1,6 @@
 {
  "name": "@ohif/core",
-  "version": "0.50.10",
+  "version": "1.0.0",
  "description": "Generic business logic for web-based medical imaging applications",
  "author": "OHIF Core Team",
  "license": "MIT",
@@ -129,6 +129,7 @@ export class StudyMetadata extends Metadata {
        );

        if (displaySet) {
+          displaySet.sopClassModule = true;
          displaySets.push(displaySet);

          return;
@@ -214,7 +215,7 @@ export class StudyMetadata extends Metadata {
   * @returns {boolean} True on success, false on failure.
   */
  addDisplaySet(displaySet) {
-    if (displaySet instanceof ImageSet) {
+    if (displaySet instanceof ImageSet || displaySet.sopClassModule) {
      this._displaySets.push(displaySet);
      return true;
    }
@@ -402,6 +402,7 @@ async function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
        baseWadoRsUri: baseWadoRsUri,
        wadouri: WADOProxy.convertURL(wadouri, server),
        wadorsuri: WADOProxy.convertURL(wadorsuri, server),
+        wadoRoot: server.wadoRoot,
        imageRendering: server.imageRendering,
        thumbnailRendering: server.thumbnailRendering,
      };
@@ -0,0 +1,199 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import { api } from 'dicomweb-client';
+import DICOMWeb from '../DICOMWeb';
+
+const getImageId = imageObj => {
+  if (!imageObj) {
+    return;
+  }
+
+  return typeof imageObj.getImageId === 'function'
+    ? imageObj.getImageId()
+    : imageObj.url;
+};
+
+const findImageIdOnStudies = (studies, displaySetInstanceUid) => {
+  const study = studies.find(study => {
+    const displaySet = study.displaySets.some(
+      displaySet => displaySet.displaySetInstanceUid === displaySetInstanceUid
+    );
+    return displaySet;
+  });
+  const { seriesList = [] } = study;
+  const { instances = [] } = seriesList[0] || {};
+  const instance = instances[0];
+
+  return getImageId(instance);
+};
+
+const someInvalidStrings = strings => {
+  const stringsArray = Array.isArray(strings) ? strings : [strings];
+  const emptyString = string => !string;
+  let invalid = stringsArray.some(emptyString);
+  return invalid;
+};
+
+const getImageInstance = dataset => {
+  return dataset && dataset.images && dataset.images[0];
+};
+
+const getImageInstanceId = imageInstance => {
+  return getImageId(imageInstance);
+};
+
+const fetchIt = (url, headers = DICOMWeb.getAuthorizationHeader()) => {
+  return fetch(url, headers).then(response => response.arrayBuffer());
+};
+
+const cornerstoneRetriever = imageId => {
+  return cornerstone.loadAndCacheImage(imageId).then(image => {
+    return image && image.data && image.data.byteArray.buffer;
+  });
+};
+
+const wadorsRetriever = (
+  url,
+  studyInstanceUID,
+  seriesInstanceUID,
+  sopInstanceUID,
+  headers = DICOMWeb.getAuthorizationHeader()
+) => {
+  const config = {
+    url,
+    headers,
+  };
+  const dicomWeb = new api.DICOMwebClient(config);
+
+  return dicomWeb.retrieveInstance({
+    studyInstanceUID,
+    seriesInstanceUID,
+    sopInstanceUID,
+  });
+};
+
+const getImageLoaderType = imageId => {
+  const loaderRegExp = /^\w+\:/;
+  const loaderType = loaderRegExp.exec(imageId);
+
+  return (
+    (loaderRegExp.lastIndex === 0 &&
+      loaderType &&
+      loaderType[0] &&
+      loaderType[0].replace(':', '')) ||
+    ''
+  );
+};
+
+const DicomLoaderService = new (class {
+  getLocalData(dataset, studies) {
+    if (dataset && dataset.localFile) {
+      // Use referenced imageInstance
+      const imageInstance = getImageInstance(dataset);
+      let imageId = getImageInstanceId(imageInstance);
+
+      // or Try to get it from studies
+      if (someInvalidStrings(imageId)) {
+        imageId = findImageIdOnStudies(studies, dataset.displaySetInstanceUid);
+      }
+
+      if (!someInvalidStrings(imageId)) {
+        return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+      }
+    }
+  }
+
+  getDataByImageType(dataset) {
+    const imageInstance = getImageInstance(dataset);
+
+    if (imageInstance) {
+      const imageId = getImageInstanceId(imageInstance);
+      let getDicomDataMethod = fetchIt;
+      const loaderType = getImageLoaderType(imageId);
+
+      switch (loaderType) {
+        case 'dicomfile':
+          getDicomDataMethod = cornerstoneRetriever.bind(this, imageId);
+          break;
+        case 'wadors':
+          const url = imageInstance.getData().wadoRoot;
+          const studyInstanceUID = imageInstance.getStudyInstanceUID();
+          const seriesInstanceUID = imageInstance.getSeriesInstanceUID();
+          const sopInstanceUID = imageInstance.getSOPInstanceUID();
+          const invalidParams = someInvalidStrings([
+            url,
+            studyInstanceUID,
+            seriesInstanceUID,
+            sopInstanceUID,
+          ]);
+          if (invalidParams) {
+            return;
+          }
+
+          getDicomDataMethod = wadorsRetriever.bind(
+            this,
+            url,
+            studyInstanceUID,
+            seriesInstanceUID,
+            sopInstanceUID
+          );
+          break;
+        case 'wadouri':
+          // Strip out the image loader specifier
+          imageId = imageId.substring(imageId.indexOf(':') + 1);
+
+          if (someInvalidStrings(imageId)) {
+            return;
+          }
+          getDicomDataMethod = fetchIt.bind(this, imageId);
+          break;
+      }
+
+      return getDicomDataMethod();
+    }
+  }
+
+  getDataByDatasetType(dataset) {
+    const {
+      studyInstanceUid,
+      seriesInstanceUid,
+      sopInstanceUid,
+      authorizationHeaders,
+      wadoRoot,
+      wadoUri,
+    } = dataset;
+    // Retrieve wadors or just try to fetch wadouri
+    if (!someInvalidStrings(wadoRoot)) {
+      return wadorsRetriever(
+        wadoRoot,
+        studyInstanceUid,
+        seriesInstanceUid,
+        sopInstanceUid,
+        authorizationHeaders
+      );
+    } else if (!someInvalidStrings(wadoUri)) {
+      return fetchIt(wadoUri, { headers: authorizationHeaders });
+    }
+  }
+
+  *getLoaderIterator(dataset, studies) {
+    yield this.getLocalData(dataset, studies);
+    yield this.getDataByImageType(dataset);
+    yield this.getDataByDatasetType(dataset);
+  }
+
+  findDicomDataPromise(dataset, studies) {
+    const loaderIterator = this.getLoaderIterator(dataset, studies);
+    // it returns first valid retriever method.
+    for (const loader of loaderIterator) {
+      if (loader) {
+        return loader;
+      }
+    }
+
+    // in case of no valid loader
+    throw new Error('Invalid dicom data loader');
+  }
+})();
+
+export default DicomLoaderService;
@@ -5,11 +5,16 @@ function getWADORSImageUrl(instance, frame) {
    return;
  }

-  // We need to sum 1 because WADO-RS frame number is 1-based
-  frame = frame ? parseInt(frame) + 1 : 1;
+  // Use null to obtain an imageId which represents the instance
+  if (frame === null) {
+    wadorsuri = wadorsuri.replace(/frames\/(\d+)/, '');
+  } else {
+    // We need to sum 1 because WADO-RS frame number is 1-based
+    frame = frame ? parseInt(frame) + 1 : 1;

-  // Replaces /frame/1 by /frame/{frame}
-  wadorsuri = wadorsuri.replace(/frames\/(\d+)/, `frames/${frame}`);
+    // Replaces /frame/1 by /frame/{frame}
+    wadorsuri = wadorsuri.replace(/frames\/(\d+)/, `frames/${frame}`);
+  }

  return wadorsuri;
 }
@@ -8,6 +8,7 @@ import sortBy from './sortBy.js';
 import studyMetadataManager from './studyMetadataManager';
 import updateMetaDataManager from './updateMetaDataManager.js';
 import writeScript from './writeScript.js';
+import DicomLoaderService from './dicomLoaderService.js';

 const utils = {
  guid,
@@ -21,6 +22,7 @@ const utils = {
  // Updates WADO-RS metaDataManager
  updateMetaDataManager,
  DICOMTagDescriptions,
+  DicomLoaderService,
 };

 export {
@@ -35,6 +37,7 @@ export {
  // Updates WADO-RS metaDataManager
  updateMetaDataManager,
  DICOMTagDescriptions,
+  DicomLoaderService,
 };

 export default utils;
@@ -14,6 +14,7 @@ describe('Top level exports', () => {
      // Updates WADO-RS metaDataManager
      'updateMetaDataManager',
      'DICOMTagDescriptions',
+      'DicomLoaderService',
    ].sort();

    const exports = Object.keys(utils.default).sort();
@@ -102,32 +102,6 @@ module.exports = (env, argv) => {
        swDest: 'sw.js',
        clientsClaim: true,
        skipWaiting: true,
-        exclude: [
-          new RegExp('^https://fonts.googleapis.com/'),
-          new RegExp('^https://fonts.gstatic.com/'),
-        ],
-        runtimeCaching: [
-          {
-            urlPattern: new RegExp('^https://fonts.googleapis.com/'),
-            handler: 'StaleWhileRevalidate',
-            options: {
-              cacheName: 'google-fonts-stylesheets',
-            },
-          },
-          {
-            urlPattern: new RegExp('^https://fonts.gstatic.com/'),
-            handler: 'CacheFirst',
-            options: {
-              cacheName: 'google-fonts-webfonts',
-
-              // Only cache 30 images / one year.
-              expiration: {
-                maxAgeSeconds: 60 * 60 * 24 * 365,
-                maxEntries: 30,
-              },
-            },
-          },
-        ],
      }),
    ],
    // https://webpack.js.org/configuration/dev-server/
@@ -3,6 +3,30 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.

+# [2.0.0](https://github.com/OHIF/Viewers/compare/@ohif/viewer@1.2.3...@ohif/viewer@2.0.0) (2019-09-27)
+
+
+### Bug Fixes
+
+* 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases ([#862](https://github.com/OHIF/Viewers/issues/862)) ([e7e1a8a](https://github.com/OHIF/Viewers/commit/e7e1a8a)), closes [#838](https://github.com/OHIF/Viewers/issues/838)
+
+
+### BREAKING CHANGES
+
+* DICOM Seg
+
+
+
+
+
+## [1.2.3](https://github.com/OHIF/Viewers/compare/@ohif/viewer@1.2.2...@ohif/viewer@1.2.3) (2019-09-27)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
 ## [1.2.2](https://github.com/OHIF/Viewers/compare/@ohif/viewer@1.2.1...@ohif/viewer@1.2.2) (2019-09-27)

 **Note:** Version bump only for package @ohif/viewer
@@ -1,6 +1,6 @@
 {
  "name": "@ohif/viewer",
-  "version": "1.2.2",
+  "version": "2.0.0",
  "description": "OHIF Viewer",
  "author": "OHIF Contributors",
  "license": "MIT",
@@ -46,12 +46,12 @@
  },
  "dependencies": {
    "@babel/runtime": "^7.5.5",
-    "@ohif/core": "^0.50.10",
-    "@ohif/extension-cornerstone": "^1.2.2",
-    "@ohif/extension-dicom-html": "^0.50.8",
+    "@ohif/core": "^1.0.0",
+    "@ohif/extension-cornerstone": "^2.0.0",
+    "@ohif/extension-dicom-html": "^1.0.0",
    "@ohif/extension-dicom-microscopy": "^0.50.6",
-    "@ohif/extension-dicom-pdf": "^0.50.4",
-    "@ohif/extension-vtk": "^0.50.20",
+    "@ohif/extension-dicom-pdf": "^1.0.0",
+    "@ohif/extension-vtk": "^0.50.21",
    "@ohif/i18n": "^0.50.4",
    "@ohif/ui": "^0.51.2",
    "@tanem/react-nprogress": "^1.1.25",
@@ -1,47 +1,53 @@
 <!DOCTYPE html>
 <html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta
+      name="viewport"
+      content="width=device-width, initial-scale=1, shrink-to-fit=no"
+    />
+    <meta name="theme-color" content="#000000" />

-<head>
-  <meta charset="utf-8" />
-  <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
-  <meta name="theme-color" content="#000000" />
+    <link rel="manifest" href="<%= PUBLIC_URL %>manifest.json" />
+    <!-- Built with: https://polyfill.io/v3/url-builder/ -->
+    <!-- Targets IE11 -->
+    <script src="https://polyfill.io/v3/polyfill.min.js?flags=gated&features=default%2CObject.values%2CArray.prototype.flat%2CObject.entries%2CSymbol%2CArray.prototype.includes%2CString.prototype.repeat%2CArray.prototype.find"></script>
+    <script type="text/javascript" src="<%= PUBLIC_URL %>app-config.js"></script>

-  <link rel="manifest" href="<%= PUBLIC_URL %>manifest.json" />
-  <!-- Built with: https://polyfill.io/v3/url-builder/ -->
-  <!-- Targets IE11 -->
-  <script
-    src="https://polyfill.io/v3/polyfill.min.js?flags=gated&features=default%2CObject.values%2CArray.prototype.flat%2CObject.entries%2CSymbol%2CArray.prototype.includes%2CString.prototype.repeat%2CArray.prototype.find"></script>
-  <script type="text/javascript" src="<%= PUBLIC_URL %>app-config.js"></script>
+    <title>OHIF Viewer</title>

-  <title>OHIF Viewer</title>
+    <!-- WEB FONTS -->
+    <link
+      href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,700|Sanchez&display=swap"
+      rel="stylesheet"
+    />

-  <!-- EXTENSIONS -->
-  <!-- <script type="text/javascript" src="path/to/some-extension.js"></script>
+    <!-- EXTENSIONS -->
+    <!-- <script type="text/javascript" src="path/to/some-extension.js"></script>

    <script>
      window.config.extensions = [SomeExtension];
    </script> -->
-</head>
+  </head>

-<body>
-  <noscript> You need to enable JavaScript to run this app. </noscript>
+  <body>
+    <noscript> You need to enable JavaScript to run this app. </noscript>

-  <div id="root"></div>
+    <div id="root"></div>

-  <script>
-    // Note: This is a client access token so there is no issue with having it publicly available
-    var _rollbarConfig = {
-      accessToken: "739c64cd39e84592ba062bc29aac9769",
-      captureUncaught: true,
-      captureUnhandledRejections: true,
-      payload: {
-        environment: "viewer.ohif.org"
-      }
-    };
-    // Rollbar Snippet
-    !function (r) { var e = {}; function o(n) { if (e[n]) return e[n].exports; var t = e[n] = { i: n, l: !1, exports: {} }; return r[n].call(t.exports, t, t.exports, o), t.l = !0, t.exports } o.m = r, o.c = e, o.d = function (r, e, n) { o.o(r, e) || Object.defineProperty(r, e, { enumerable: !0, get: n }) }, o.r = function (r) { "undefined" != typeof Symbol && Symbol.toStringTag && Object.defineProperty(r, Symbol.toStringTag, { value: "Module" }), Object.defineProperty(r, "__esModule", { value: !0 }) }, o.t = function (r, e) { if (1 & e && (r = o(r)), 8 & e) return r; if (4 & e && "object" == typeof r && r && r.__esModule) return r; var n = Object.create(null); if (o.r(n), Object.defineProperty(n, "default", { enumerable: !0, value: r }), 2 & e && "string" != typeof r) for (var t in r) o.d(n, t, function (e) { return r[e] }.bind(null, t)); return n }, o.n = function (r) { var e = r && r.__esModule ? function () { return r.default } : function () { return r }; return o.d(e, "a", e), e }, o.o = function (r, e) { return Object.prototype.hasOwnProperty.call(r, e) }, o.p = "", o(o.s = 0) }([function (r, e, o) { var n = o(1), t = o(4); _rollbarConfig = _rollbarConfig || {}, _rollbarConfig.rollbarJsUrl = _rollbarConfig.rollbarJsUrl || "https://cdnjs.cloudflare.com/ajax/libs/rollbar.js/2.7.1/rollbar.min.js", _rollbarConfig.async = void 0 === _rollbarConfig.async || _rollbarConfig.async; var a = n.setupShim(window, _rollbarConfig), l = t(_rollbarConfig); window.rollbar = n.Rollbar, a.loadFull(window, document, !_rollbarConfig.async, _rollbarConfig, l) }, function (r, e, o) { var n = o(2); function t(r) { return function () { try { return r.apply(this, arguments) } catch (r) { try { console.error("[Rollbar]: Internal error", r) } catch (r) { } } } } var a = 0; function l(r, e) { this.options = r, this._rollbarOldOnError = null; var o = a++; this.shimId = function () { return o }, "undefined" != typeof window && window._rollbarShims && (window._rollbarShims[o] = { handler: e, messages: [] }) } var i = o(3), d = function (r, e) { return new l(r, e) }, c = function (r) { return new i(d, r) }; function s(r) { return t(function () { var e = Array.prototype.slice.call(arguments, 0), o = { shim: this, method: r, args: e, ts: new Date }; window._rollbarShims[this.shimId()].messages.push(o) }) } l.prototype.loadFull = function (r, e, o, n, a) { var l = !1, i = e.createElement("script"), d = e.getElementsByTagName("script")[0], c = d.parentNode; i.crossOrigin = "", i.src = n.rollbarJsUrl, o || (i.async = !0), i.onload = i.onreadystatechange = t(function () { if (!(l || this.readyState && "loaded" !== this.readyState && "complete" !== this.readyState)) { i.onload = i.onreadystatechange = null; try { c.removeChild(i) } catch (r) { } l = !0, function () { var e; if (void 0 === r._rollbarDidLoad) { e = new Error("rollbar.js did not load"); for (var o, n, t, l, i = 0; o = r._rollbarShims[i++];)for (o = o.messages || []; n = o.shift();)for (t = n.args || [], i = 0; i < t.length; ++i)if ("function" == typeof (l = t[i])) { l(e); break } } "function" == typeof a && a(e) }() } }), c.insertBefore(i, d) }, l.prototype.wrap = function (r, e, o) { try { var n; if (n = "function" == typeof e ? e : function () { return e || {} }, "function" != typeof r) return r; if (r._isWrap) return r; if (!r._rollbar_wrapped && (r._rollbar_wrapped = function () { o && "function" == typeof o && o.apply(this, arguments); try { return r.apply(this, arguments) } catch (o) { var e = o; throw e && ("string" == typeof e && (e = new String(e)), e._rollbarContext = n() || {}, e._rollbarContext._wrappedSource = r.toString(), window._rollbarWrappedError = e), e } }, r._rollbar_wrapped._isWrap = !0, r.hasOwnProperty)) for (var t in r) r.hasOwnProperty(t) && (r._rollbar_wrapped[t] = r[t]); return r._rollbar_wrapped } catch (e) { return r } }; for (var p = "log,debug,info,warn,warning,error,critical,global,configure,handleUncaughtException,handleUnhandledRejection,captureEvent,captureDomContentLoaded,captureLoad".split(","), u = 0; u < p.length; ++u)l.prototype[p[u]] = s(p[u]); r.exports = { setupShim: function (r, e) { if (r) { var o = e.globalAlias || "Rollbar"; if ("object" == typeof r[o]) return r[o]; r._rollbarShims = {}, r._rollbarWrappedError = null; var a = new c(e); return t(function () { e.captureUncaught && (a._rollbarOldOnError = r.onerror, n.captureUncaughtExceptions(r, a, !0), n.wrapGlobals(r, a, !0)), e.captureUnhandledRejections && n.captureUnhandledRejections(r, a, !0); var t = e.autoInstrument; return !1 !== e.enabled && (void 0 === t || !0 === t || "object" == typeof t && t.network) && r.addEventListener && (r.addEventListener("load", a.captureLoad.bind(a)), r.addEventListener("DOMContentLoaded", a.captureDomContentLoaded.bind(a))), r[o] = a, a })() } }, Rollbar: c } }, function (r, e) { function o(r, e, o) { if (e.hasOwnProperty && e.hasOwnProperty("addEventListener")) { for (var n = e.addEventListener; n._rollbarOldAdd && n.belongsToShim;)n = n._rolLine truncated
+    <script>
+      // Note: This is a client access token so there is no issue with having it publicly available
+      var _rollbarConfig = {
+          accessToken: "739c64cd39e84592ba062bc29aac9769",
+          captureUncaught: true,
+          captureUnhandledRejections: true,
+          payload: {
+              environment: "viewer.ohif.org"
+          }
+      };
+      // Rollbar Snippet
+      !function(r){var e={};function o(n){if(e[n])return e[n].exports;var t=e[n]={i:n,l:!1,exports:{}};return r[n].call(t.exports,t,t.exports,o),t.l=!0,t.exports}o.m=r,o.c=e,o.d=function(r,e,n){o.o(r,e)||Object.defineProperty(r,e,{enumerable:!0,get:n})},o.r=function(r){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(r,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(r,"__esModule",{value:!0})},o.t=function(r,e){if(1&e&&(r=o(r)),8&e)return r;if(4&e&&"object"==typeof r&&r&&r.__esModule)return r;var n=Object.create(null);if(o.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:r}),2&e&&"string"!=typeof r)for(var t in r)o.d(n,t,function(e){return r[e]}.bind(null,t));return n},o.n=function(r){var e=r&&r.__esModule?function(){return r.default}:function(){return r};return o.d(e,"a",e),e},o.o=function(r,e){return Object.prototype.hasOwnProperty.call(r,e)},o.p="",o(o.s=0)}([function(r,e,o){var 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      // End Rollbar Snippet
-  </script>
-</body>
-
+    </script>
+  </body>
 </html>
@@ -79,6 +79,9 @@ class ViewerLocalFileData extends Component {
        studyMetadata.createDisplaySets(sopClassHandlerModules);
      studyMetadata.setDisplaySets(study.displaySets);

+      studyMetadata.forEachDisplaySet(displayset => {
+        displayset.localFile = true;
+      });
      // Updates WADO-RS metaDataManager
      updateMetaDataManager(study);

@@ -1,74 +0,0 @@
-/* cyrillic-ext */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu72xKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F,
-    U+FE2E-FE2F;
-}
-/* cyrillic */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu5mxKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
-}
-/* greek-ext */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu7mxKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+1F00-1FFF;
-}
-/* greek */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu4WxKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+0370-03FF;
-}
-/* vietnamese */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu7WxKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+0102-0103, U+0110-0111, U+1EA0-1EF9, U+20AB;
-}
-/* latin-ext */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu7GxKKTU1Kvnz.woff2') format('woff2');
-  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB,
-    U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
-}
-/* latin */
-@font-face {
-  font-family: 'Roboto';
-  font-style: normal;
-  font-weight: 400;
-  font-display: swap;
-  src: local('Roboto'), local('Roboto-Regular'),
-    url('./KFOmCnqEu92Fr1Mu4mxKKTU1Kg.woff2') format('woff2');
-  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA,
-    U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215,
-    U+FEFF, U+FFFD;
-}
@@ -7,8 +7,6 @@ import React from 'react';
 import ReactDOM from 'react-dom';
 import App from './App.js';

-import './fonts/fonts.css';
-
 function installViewer(props, containerId = 'root', callback) {
  const container = document.getElementById(containerId);

@@ -1,160 +1,26 @@
-import cornerstone from 'cornerstone-core';
-import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
-import * as dcmjs from 'dcmjs';
+import FileLoaderService from './localFileLoaders/fileLoaderService';

-function datasetsToStudies(datasets) {
-  const StudyInstanceUIDs = new Set();
-  datasets.forEach(ds => {
-    StudyInstanceUIDs.add(ds.StudyInstanceUID);
-  });
+const processFile = async file => {
+  try {
+    const fileLoaderService = new FileLoaderService(file);
+    const imageId = fileLoaderService.addFile(file);
+    const image = await fileLoaderService.loadFile(file, imageId);
+    const dataset = await fileLoaderService.getDataset(image, imageId);
+    const studies = await fileLoaderService.getStudies(dataset, imageId);

-  const studies = [];
-  Array.from(StudyInstanceUIDs).forEach(studyInstanceUid => {
-    const studyDatasets = datasets.filter(
-      ds => ds.StudyInstanceUID === studyInstanceUid
+    return studies;
+  } catch (error) {
+    console.log(
+      error.name,
+      ':Error when trying to load and process local files:',
+      error.message
    );
-    const firstDataset = studyDatasets[0];
-    const study = {
-      studyInstanceUid: firstDataset.StudyInstanceUID,
-      studyDate: firstDataset.StudyDate,
-      studyTime: firstDataset.StudyTime,
-      accessionNumber: firstDataset.AccessionNumber,
-      referringPhysicianName: firstDataset.ReferringPhysicianName,
-      patientName: firstDataset.PatientName,
-      patientId: firstDataset.PatientID,
-      patientBirthdate: firstDataset.PatientBirthDate,
-      patientSex: firstDataset.PatientSex,
-      studyId: firstDataset.StudyID,
-      studyDescription: firstDataset.StudyDescription,
-      //numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
-      //numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
-      // modality: DICOMWeb.getString(study['00080060']),
-      // modalitiesInStudy: DICOMWeb.getString(study['00080061']),
-      //modalities:
-      seriesList: [],
-    };
-
-    const SeriesInstanceUIDs = new Set();
-    studyDatasets.forEach(ds => {
-      SeriesInstanceUIDs.add(ds.SeriesInstanceUID);
-    });
-
-    Array.from(SeriesInstanceUIDs).forEach(seriesInstanceUid => {
-      const seriesDatasets = studyDatasets.filter(
-        ds => ds.SeriesInstanceUID === seriesInstanceUid
-      );
-
-      const SOPInstanceUIDs = new Set();
-      seriesDatasets.forEach(ds => {
-        SOPInstanceUIDs.add(ds.SOPInstanceUID);
-
-        study.seriesList.push({
-          seriesInstanceUid: ds.SeriesInstanceUID,
-          seriesDescription: ds.SeriesDescription,
-          seriesNumber: ds.SeriesNumber,
-          instances: [],
-        });
-      });
-
-      Array.from(SOPInstanceUIDs).forEach(sopInstanceUid => {
-        const instance = seriesDatasets.find(
-          a => a.SOPInstanceUID === sopInstanceUid
-        );
-        const series = study.seriesList.find(
-          a => a.seriesInstanceUid === seriesInstanceUid
-        );
-
-        series.instances.push({
-          sopInstanceUid: instance.SOPInstanceUID,
-          sopClassUid: instance.SOPClassUID,
-          rows: instance.Rows,
-          columns: instance.Columns,
-          numberOfFrames: instance.NumberOfFrames,
-          instanceNumber: instance.InstanceNumber,
-          getImageId: () => instance.imageId, // TODO: Change getImageId to check for instance.imageId property first.
-          /*imageType: DICOMWeb.getString(instance['00080008']),
-          modality: DICOMWeb.getString(instance['00080060']),
-          instanceNumber: DICOMWeb.getNumber(instance['00200013']),
-          imagePositionPatient: DICOMWeb.getString(instance['00200032']),
-          imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
-          frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
-          sliceLocation: DICOMWeb.getNumber(instance['00201041']),
-          samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
-          photometricInterpretation: DICOMWeb.getString(instance['00280004']),
-          planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
-          pixelSpacing: DICOMWeb.getString(instance['00280030']),
-          pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
-          bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
-          bitsStored: DICOMWeb.getNumber(instance['00280101']),
-          highBit: DICOMWeb.getNumber(instance['00280102']),
-          pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
-          smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
-          largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
-          windowCenter: DICOMWeb.getString(instance['00281050']),
-          windowWidth: DICOMWeb.getString(instance['00281051']),
-          rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
-          rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
-          rescaleType: DICOMWeb.getNumber(instance['00281054']),
-          sourceImageInstanceUid: getSourceImageInstanceUid(instance),
-          laterality: DICOMWeb.getString(instance['00200062']),
-          viewPosition: DICOMWeb.getString(instance['00185101']),
-          acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
-          frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
-          frameTime: DICOMWeb.getNumber(instance['00181063']),
-          frameTimeVector: parseFloatArray(
-            DICOMWeb.getString(instance['00181065'])
-          ),
-          sliceThickness: DICOMWeb.getNumber(instance['00180050']),
-          spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
-          lossyImageCompression: DICOMWeb.getString(instance['00282110']),
-          derivationDescription: DICOMWeb.getString(instance['00282111']),
-          lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
-          lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
-          echoNumber: DICOMWeb.getString(instance['00180086']),
-          contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
-          radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
-          wadouri: WADOProxy.convertURL(wadouri, server),
-          wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
-        });
-      });
-    });
-
-    studies.push(study);
-  });
-
-  console.warn(studies);
-
-  return studies;
-}
+  }
+};

 export default async function filesToStudies(files) {
-  const imagePromises = files.map(file => {
-    const imageId = cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
-    return cornerstone
-      .loadAndCacheImage(imageId)
-      .catch(error => console.warn(error));
-  });
+  const processFilesPromises = files.map(processFile);
+  const studies = await Promise.all(processFilesPromises);

-  const images = await Promise.all(imagePromises);
-  const datasets = [];
-
-  images.forEach(image => {
-    if (!image || !image.data) {
-      return;
-    }
-
-    const arrayBuffer = image.data.byteArray.buffer;
-    const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
-    const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
-      dicomData.dict
-    );
-    dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
-      dicomData.meta
-    );
-    dataset.imageId = image.imageId;
-
-    datasets.push(dataset);
-  });
-
-  return datasetsToStudies(datasets);
+  return FileLoaderService.groupSeries(studies.flat());
 }
@@ -0,0 +1,192 @@
+import * as dcmjs from 'dcmjs';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+
+const DICOMFileLoader = new (class extends FileLoader {
+  fileType = 'application/dicom';
+  loadFile(file, imageId) {
+    return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+  }
+
+  getDataset(image, imageId) {
+    let dataset = {};
+    try {
+      const dicomData = dcmjs.data.DicomMessage.readFile(image);
+      dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+        dicomData.dict
+      );
+      dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
+        dicomData.meta
+      );
+    } catch (e) {
+      console.log('Error on getting dicom file dataset. It defaults to empty');
+    }
+    // Set imageId on dataset to be consumed later on
+    dataset.imageId = imageId;
+
+    return dataset;
+  }
+
+  getStudies(dataset, imageId) {
+    return this.getStudyFromDataset(dataset);
+  }
+
+  getStudyFromDataset(dataset = {}) {
+    const {
+      StudyInstanceUID,
+      StudyDate,
+      StudyTime,
+      AccessionNumber,
+      ReferringPhysicianName,
+      PatientName,
+      PatientID,
+      PatientBirthDate,
+      PatientSex,
+      StudyID,
+      StudyDescription,
+      /*
+      NumberOfStudyRelatedSeries,
+      NumberOfStudyRelatedInstances,
+      Modality,
+      ModalitiesInStudy,
+      */
+      SeriesInstanceUID,
+      SeriesDescription,
+      SeriesNumber,
+      SOPInstanceUID,
+      SOPClassUID,
+      Rows,
+      Columns,
+      NumberOfFrames,
+      InstanceNumber,
+      imageId,
+      Modality,
+      /*ImageType,
+        InstanceNumber,
+        ImagePositionPatient,
+        ImageOrientationPatient,
+        FrameOfReferenceUID,
+        SliceLocation,
+        SamplesPerPixel,
+        PhotometricInterpretation,
+        PlanarConfiguration,
+        PixelSpacing,
+        PixelAspectRatio,
+        BitsAllocated,
+        BitsStored,
+        HighBit,
+        PixelRepresentation,
+        SmallestPixelValue,
+        LargestPixelValue,
+        WindowCenter,
+        WindowWidth,
+        RescaleIntercept,
+        RescaleSlope,
+        RescaleType,
+        Laterality,
+        ViewPosition,
+        AcquisitionDateTime,
+        FrameIncrementPointer,
+        FrameTime,
+        FrameTimeVector,
+        SliceThickness,
+        SpacingBetweenSlices,
+        LossyImageCompression,
+        DerivationDescription,
+        LossyImageCompressionRatio,
+        LossyImageCompressionMethod,
+        EchoNumber,
+        ContrastBolusAgent,
+        */
+    } = dataset;
+
+    const instance = {
+      sopInstanceUid: SOPInstanceUID,
+      sopClassUid: SOPClassUID,
+      rows: Rows,
+      columns: Columns,
+      numberOfFrames: NumberOfFrames,
+      instanceNumber: InstanceNumber,
+      url: imageId,
+      modality: Modality,
+      /*
+        TODO: in case necessary to uncoment this block, double check every property
+        imageType: ImageType || DICOMWeb.getString(dataset['00080008']),
+        instanceNumber: InstanceNumber || DICOMWeb.getNumber(dataset['00200013']),
+        imagePositionPatient: ImagePositionPatient || DICOMWeb.getString(dataset['00200032']),
+        imageOrientationPatient: ImageOrientationPatient || DICOMWeb.getString(dataset['00200037']),
+        frameOfReferenceUID: FrameOfReferenceUID || DICOMWeb.getString(dataset['00200052']),
+        sliceLocation: SliceLocation || DICOMWeb.getNumber(dataset['00201041']),
+        samplesPerPixel: SamplesPerPixel || DICOMWeb.getNumber(dataset['00280002']),
+        photometricInterpretation: PhotometricInterpretation || DICOMWeb.getString(dataset['00280004']),
+        planarConfiguration: PlanarConfiguration || DICOMWeb.getNumber(dataset['00280006']),
+        pixelSpacing: PixelSpacing || DICOMWeb.getString(dataset['00280030']),
+        pixelAspectRatio: PixelAspectRatio || DICOMWeb.getString(dataset['00280034']),
+        bitsAllocated: BitsAllocated || DICOMWeb.getNumber(dataset['00280100']),
+        bitsStored: BitsStored || DICOMWeb.getNumber(dataset['00280101']),
+        highBit: HighBit || DICOMWeb.getNumber(dataset['00280102']),
+        pixelRepresentation: PixelRepresentation || DICOMWeb.getNumber(dataset['00280103']),
+        smallestPixelValue: SmallestPixelValue || DICOMWeb.getNumber(dataset['00280106']),
+        largestPixelValue: LargestPixelValue || DICOMWeb.getNumber(dataset['00280107']),
+        windowCenter: WindowCenter || DICOMWeb.getString(dataset['00281050']),
+        windowWidth: WindowWidth || DICOMWeb.getString(dataset['00281051']),
+        rescaleIntercept: RescaleIntercept || DICOMWeb.getNumber(dataset['00281052']),
+        rescaleSlope: RescaleSlope || DICOMWeb.getNumber(dataset['00281053']),
+        rescaleType: RescaleType || DICOMWeb.getNumber(dataset['00281054']),
+        sourceImageInstanceUid: getSourceImageInstanceUid(dataset),
+        laterality: Laterality || DICOMWeb.getString(dataset['00200062']),
+        viewPosition: ViewPosition || DICOMWeb.getString(dataset['00185101']),
+        acquisitionDateTime: AcquisitionDateTime || DICOMWeb.getString(dataset['0008002A']),
+        frameIncrementPointer: FrameIncrementPointer || getFrameIncrementPointer(dataset['00280009']),
+        frameTime: FrameTime || DICOMWeb.getNumber(dataset['00181063']),
+        frameTimeVector: FrameTimeVector || parseFloatArray(
+          DICOMWeb.getString(dataset['00181065'])
+        ),
+        sliceThickness: SliceThickness || DICOMWeb.getNumber(dataset['00180050']),
+        spacingBetweenSlices: SpacingBetweenSlices || DICOMWeb.getString(dataset['00180088']),
+        lossyImageCompression: LossyImageCompression || DICOMWeb.getString(dataset['00282110']),
+        derivationDescription: DerivationDescription || DICOMWeb.getString(dataset['00282111']),
+        lossyImageCompressionRatio: LossyImageCompressionRatio || DICOMWeb.getString(dataset['00282112']),
+        lossyImageCompressionMethod: LossyImageCompressionMethod || DICOMWeb.getString(dataset['00282114']),
+        echoNumber: EchoNumber || DICOMWeb.getString(dataset['00180086']),
+        contrastBolusAgent: ContrastBolusAgent || DICOMWeb.getString(dataset['00180010']),
+        radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(dataset),
+        wadouri: WADOProxy.convertURL(wadouri, server),
+        wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
+    };
+
+    const series = {
+      seriesInstanceUid: SeriesInstanceUID,
+      seriesDescription: SeriesDescription,
+      seriesNumber: SeriesNumber,
+      instances: [instance],
+    };
+
+    const study = {
+      studyInstanceUid: StudyInstanceUID,
+      studyDate: StudyDate,
+      studyTime: StudyTime,
+      accessionNumber: AccessionNumber,
+      referringPhysicianName: ReferringPhysicianName,
+      patientName: PatientName,
+      patientId: PatientID,
+      patientBirthdate: PatientBirthDate,
+      patientSex: PatientSex,
+      studyId: StudyID,
+      studyDescription: StudyDescription,
+      /*
+      TODO: in case necessary to uncomment this block, double check every property
+      numberOfStudyRelatedSeries: NumberOfStudyRelatedSeries || DICOMWeb.getString(dataset['00201206']),
+      numberOfStudyRelatedInstances: NumberOfStudyRelatedInstances || DICOMWeb.getString(dataset['00201208']),
+      modality: Modality || DICOMWeb.getString(dataset['00080060']),
+      modalitiesInStudy: ModalitiesInStudy || DICOMWeb.getString(dataset['00080061']),
+      modalities:
+      */
+      seriesList: [series],
+    };
+
+    return study;
+  }
+})();
+
+export default DICOMFileLoader;
@@ -0,0 +1,6 @@
+export default class FileLoader {
+  fileType;
+  loadFile(file, imageId) { }
+  getDataset(image, imageId) { }
+  getStudies(dataset, imageId) { }
+}
@@ -0,0 +1,82 @@
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+import PDFFileLoader from './pdfFileLoader';
+import DICOMFileLoader from './dicomFileLoader';
+
+class FileLoaderService extends FileLoader {
+  fileType;
+  loader;
+  constructor(file) {
+    super();
+    const fileType = file && file.type;
+    this.loader = this.getLoader(fileType);
+    this.fileType = this.loader.fileType;
+  }
+
+  static groupSeries(studies) {
+    const groupBy = (list, groupByKey, listKey) => {
+      let nonKeyCounter = 1;
+
+      return list.reduce((acc, obj) => {
+        let key = obj[groupByKey];
+        const list = obj[listKey];
+
+        // in case key not found, group it using counter
+        key = !!key ? key : '' + nonKeyCounter++;
+
+        if (!acc[key]) {
+          acc[key] = { ...obj };
+          acc[key][listKey] = [];
+        }
+
+        acc[key][listKey].push(...list);
+
+        return acc;
+      }, {});
+    };
+
+    const studiesGrouped = Object.values(
+      groupBy(studies, 'studyInstanceUid', 'seriesList')
+    );
+
+    const result = studiesGrouped.map(studyGroup => {
+      const seriesGrouped = groupBy(
+        studyGroup.seriesList,
+        'seriesInstanceUid',
+        'instances'
+      );
+      studyGroup.seriesList = Object.values(seriesGrouped);
+
+      return studyGroup;
+    });
+
+    return result;
+  }
+
+  addFile(file) {
+    return cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
+  }
+
+  loadFile(file, imageId) {
+    return this.loader.loadFile(file, imageId);
+  }
+
+  getDataset(image, imageId) {
+    return this.loader.getDataset(image, imageId);
+  }
+
+  getStudies(dataset, imageId) {
+    return this.loader.getStudies(dataset, imageId);
+  }
+
+  getLoader(fileType) {
+    if (fileType === 'application/pdf') {
+      return PDFFileLoader;
+    } else {
+      // Default to dicom loader
+      return DICOMFileLoader;
+    }
+  }
+}
+
+export default FileLoaderService;
@@ -0,0 +1,58 @@
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import FileLoader from './fileLoader';
+
+const PDFFileLoader = new (class extends FileLoader {
+  fileType = 'application/pdf';
+  loadFile(file, imageId) {
+    return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId);
+  }
+
+  getDataset(image, imageId) {
+    const dataset = {};
+    dataset.imageId = image.imageId || imageId;
+    return dataset;
+  }
+
+  getStudies(dataset, imageId) {
+    return this.getDefaultStudy(imageId);
+  }
+
+  getDefaultStudy(imageId) {
+    const study = {
+      studyInstanceUid: '',
+      studyDate: '',
+      studyTime: '',
+      accessionNumber: '',
+      referringPhysicianName: '',
+      patientName: '',
+      patientId: '',
+      patientBirthdate: '',
+      patientSex: '',
+      studyId: '',
+      studyDescription: '',
+      seriesList: [
+        {
+          seriesInstanceUid: '',
+          seriesDescription: '',
+          seriesNumber: '',
+          instances: [
+            {
+              sopInstanceUid: '',
+              sopClassUid: '1.2.840.10008.5.1.4.1.1.104.1',
+              rows: '',
+              columns: '',
+              numberOfFrames: 0,
+              instanceNumber: 1,
+              getImageId: () => imageId,
+              isLocalFile: true,
+            },
+          ],
+        },
+      ],
+    };
+
+    return study;
+  }
+})();
+
+export default PDFFileLoader;
Author	SHA1	Message	Date
ohif-bot	aa7dc1e2c1	chore(release): publish [skip ci] - @ohif/extension-cornerstone@2.0.0 - @ohif/extension-dicom-html@1.0.0 - @ohif/extension-dicom-pdf@1.0.0 - @ohif/extension-vtk@0.50.21 - @ohif/core@1.0.0 - @ohif/viewer@2.0.0	2019-09-27 11:58:23 +00:00
ladeirarodolfo	e7e1a8a6cd	fix: 🐛 Add DicomLoaderService & FileLoaderService to fix SR, PDF, and SEG support in local file and WADO-RS-only use cases (#862 ) * fix: 🐛 Local file: failing when retrieving segmentation data Fix segmentation data retrieval issues for local file. Changed from fecthing to use cornerstone loadAndCache method BREAKING CHANGE: DICOM Seg Closes: part of #838 * Switch SEG retrieval to WADO-RS * Forgot a debugger * refactor: 💡 Code refactor. Minor changes into methods * fix: 🐛 Load local files: PDF Items: 1. FileLoaderService: used for serveral operations on local files(load it, get list of studies, group them, accepting dicom and pdf) 2. DicomLoaderService: used for loading dicom based on dataset and studies. Depending on type of dicom loader might change. WIP 3. Refactor PDF and handleSegmentationStorage to use DicomLoaderService * fix: 🐛 Code review * fix: 🐛 Code review. Changed:Folder organization and dicom file Move fileLoaderService and others to a specific folder. When loading dicom file change to only retrieve the file(not use cornerstone to cache or anything else). * fix: 🐛 Code review. Move dicomLoaderService to core Moved dicomLoaderService to ohif/core and localFileLoaders to a specific folder. * fix: 🐛 Code review Simplified method to get study for dicom file. Added error handling on file loading. DicomLoaderService to be exposed on ohif/core/utils instead. * fix: 🐛 Reduce local load to one method only Reduced local file load to one method only * fix: 🐛 HTML to use dicomLoaderService. Prefer wadors than (uri) * fix: 🐛 Code implementation for multiframe files * fix: 🐛 Code review. Default local loader to dicom Closes: 838 * fix: 🐛 Code review. Use relative path to require DICOMWeb Closes: 838 * fix: 🐛 Code review. Fix unit test. Added DicomLoaderService mod Closes: 838 * fix: 🐛 Code review. Add 'Seg' on left thumb When getting/creating dataset get modality for file/image read Closes: 838	2019-09-27 13:47:08 +02:00
ohif-bot	e66c27affb	chore(release): publish [skip ci] - @ohif/viewer@1.2.3	2019-09-27 11:10:33 +00:00
Danny Brown	ae26904885	Revert "* fix: 🐛 Enabling workbox to cache webfonts and fonts-stylesheets, add local fonts for UMD build (#906 )" (#961 ) This reverts commit `69b96478cb`.	2019-09-27 06:54:47 -04:00