Moved the Cornerstone viewport code to an extension. Tons of changes to rollup and package.json files to make everything play nicely

2019-02-06 14:46:06 +01:00
1 parent 9a0f417eec
commit 22202141b8
@@ -0,0 +1,14 @@
+{
+  "presets": [
+    ["@babel/preset-env", {
+      "targets": {
+        "ie": "11"
+      }
+    }],
+    "@babel/preset-react"
+  ],
+  "plugins": [
+    "@babel/plugin-proposal-class-properties",
+    "@babel/plugin-transform-runtime"
+  ]
+}
@@ -0,0 +1,9 @@
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 2
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
@@ -0,0 +1,16 @@
+{
+  "extends": [
+  	"react-app",
+  	"eslint:recommended",
+    "plugin:react/recommended"
+  ],
+  "parser": "babel-eslint",
+  "env": {
+    "jest": true
+  },
+  "settings": {
+    "react": {
+      "version": "detect",
+    },
+  },
+}
@@ -0,0 +1,23 @@
+
+# See https://help.github.com/ignore-files/ for more about ignoring files.
+
+# dependencies
+node_modules
+
+# builds
+build
+dist
+.rpt2_cache
+
+# misc
+.DS_Store
+.env
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+.idea
@@ -0,0 +1,3 @@
+{
+  "singleQuote": true
+}
@@ -0,0 +1,4 @@
+language: node_js
+node_js:
+  - 9
+  - 8
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
@@ -0,0 +1,92 @@
+{
+  "name": "ohif-cornerstone-extension",
+  "version": "0.0.3",
+  "description": "OHIF extension for Cornerstone",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.umd.js",
+  "module": "dist/index.es.js",
+  "jsnext:main": "dist/index.es.js",
+  "engines": {
+    "node": ">=8",
+    "npm": ">=5"
+  },
+  "scripts": {
+    "build": "rollup -c",
+    "start": "rollup -c -w",
+    "lint": "eslint -c .eslintrc --fix src && prettier --single-quote --write src/**/*.{js,jsx,json,css}"
+  },
+  "peerDependencies": {
+    "cornerstone-core": "^2.2.8",
+    "cornerstone-wado-image-loader": "^2.2.3",
+    "dcmjs": "^0.3.2",
+    "dicom-parser": "^1.8.3",
+    "react": "^15.0.0 || ^16.0.0",
+    "react-dom": "^15.0.0 || ^16.0.0",
+    "react-redux": "^6.0.0",
+    "redux": "^4.0.1",
+    "ohif-core": "^0.2.6"
+  },
+  "devDependencies": {
+    "@babel/core": "^7.2.2",
+    "@babel/plugin-external-helpers": "^7.2.0",
+    "@babel/plugin-proposal-class-properties": "^7.2.3",
+    "@babel/plugin-transform-runtime": "^7.2.0",
+    "@babel/preset-env": "^7.2.3",
+    "@babel/preset-react": "^7.0.0",
+    "babel-eslint": "^10.0.1",
+    "cross-env": "^5.2.0",
+    "eslint": "5.13.0",
+    "eslint-plugin-import": "^2.14.0",
+    "eslint-plugin-node": "^8.0.0",
+    "eslint-plugin-promise": "^4.0.1",
+    "eslint-plugin-react": "^7.11.1",
+    "gh-pages": "^2.0.1",
+    "husky": "^1.3.1",
+    "lint-staged": "^8.1.0",
+    "prettier": "^1.15.3",
+    "react": "^16.6.3",
+    "react-dom": "^16.6.3",
+    "rollup": "^1.1.2",
+    "rollup-plugin-babel": "^4.2.0",
+    "rollup-plugin-commonjs": "^9.2.0",
+    "rollup-plugin-node-builtins": "^2.1.2",
+    "rollup-plugin-node-resolve": "^4.0.0",
+    "rollup-plugin-peer-deps-external": "^2.2.0",
+    "rollup-plugin-postcss": "^2.0.3",
+    "rollup-plugin-url": "^2.1.0",
+    "stylelint": "^9.9.0",
+    "stylelint-config-recommended": "^2.1.0",
+    "stylus": "^0.54.5"
+  },
+  "husky": {
+    "hooks": {
+      "pre-commit": "lint-staged"
+    }
+  },
+  "lint-staged": {
+    "src/**/*.{js,jsx,json,css}": [
+      "prettier --single-quote --write",
+      "git add"
+    ]
+  },
+  "browserslist": [
+    ">0.2%",
+    "not dead",
+    "not ie <= 11",
+    "not op_mini all"
+  ],
+  "files": [
+    "dist"
+  ],
+  "dependencies": {
+    "@babel/runtime": "^7.2.0",
+    "classnames": "^2.2.6",
+    "cornerstone-tools": "3.0.1",
+    "cornerstone-math": "^0.1.8",
+    "dcmjs": "^0.3.2",
+    "hammerjs": "^2.0.8",
+    "react-cornerstone-viewport": "^0.1.9"
+  }
+}
@@ -0,0 +1,62 @@
+import babel from 'rollup-plugin-babel'
+import commonjs from 'rollup-plugin-commonjs'
+import external from 'rollup-plugin-peer-deps-external'
+import postcss from 'rollup-plugin-postcss'
+import resolve from 'rollup-plugin-node-resolve'
+import url from 'rollup-plugin-url'
+import pkg from './package.json'
+// Deal with https://github.com/rollup/rollup-plugin-commonjs/issues/297
+import builtins from 'rollup-plugin-node-builtins';
+
+const globals =  {
+  'react': 'React',
+  'react-dom': 'ReactDOM',
+  'react-redux': 'ReactRedux',
+  'cornerstone-core': 'cornerstone',
+  'cornerstone-wado-image-loader': 'cornerstoneWADOImageLoader',
+  'dcmjs': 'dcmjs',
+  'dicom-parser': 'dicomParser',
+  'ohif-core': 'OHIF'
+};
+
+export default {
+  input: 'src/index.js',
+  output: [
+    {
+      file: pkg.main,
+      format: 'umd',
+      name: 'ohif-cornerstone-extension',
+      sourcemap: true,
+      globals
+    },
+    {
+      file: pkg.module,
+      format: 'es',
+      sourcemap: true,
+      globals
+    }
+  ],
+  plugins: [
+    builtins(),
+    external(),
+    postcss({
+      modules: false
+    }),
+    url(),
+    babel({
+      exclude: 'node_modules/**',
+      externalHelpers: true,
+      runtimeHelpers: true
+    }),
+    resolve(),
+    commonjs({
+      include: 'node_modules/**',
+      namedExports: {
+          'node_modules/react-is/index.js': [
+            'isValidElementType'
+          ]
+      }
+    })
+  ],
+  external: Object.keys(pkg.peerDependencies || {}),
+}
@@ -0,0 +1,52 @@
+import { connect } from 'react-redux';
+import CornerstoneViewport from 'react-cornerstone-viewport';
+import OHIF from 'ohif-core'
+import cornerstone from "cornerstone-core";
+import cornerstoneTools from "cornerstone-tools";
+
+const { setViewportActive, setViewportSpecificData, clearViewportSpecificData } = OHIF.redux.actions;
+
+const mapStateToProps = (state, ownProps) => {
+    const activeButton = state.tools.buttons.find(tool => tool.active === true);
+
+    // If this is the active viewport, enable prefetching.
+    const { viewportIndex } = ownProps;//.viewportData;
+    const isActive = viewportIndex === state.viewports.activeViewportIndex;
+    const viewportSpecificData = state.viewports.viewportSpecificData[viewportIndex] || {};
+
+    return {
+        layout: state.viewports.layout,
+        isActive,
+        activeTool: activeButton && activeButton.command,
+        enableStackPrefetch: isActive,
+        //stack: viewportSpecificData.stack,
+        cineToolData: viewportSpecificData.cine,
+        cornerstone,
+        cornerstoneTools
+    };
+};
+
+const mapDispatchToProps = (dispatch, ownProps) => {
+    const { viewportIndex } = ownProps;
+
+    return {
+        setViewportActive: () => {
+            dispatch(setViewportActive(viewportIndex))
+        },
+
+        setViewportSpecificData: (data) => {
+            dispatch(setViewportSpecificData(viewportIndex, data))
+        },
+
+        clearViewportSpecificData: () => {
+            dispatch(clearViewportSpecificData(viewportIndex));
+        }
+    };
+};
+
+const ConnectedCornerstoneViewport = connect(
+    mapStateToProps,
+    mapDispatchToProps
+)(CornerstoneViewport);
+
+export default ConnectedCornerstoneViewport;
@@ -0,0 +1,26 @@
+import OHIFCornerstoneViewport from './OHIFCornerstoneViewport.js';
+
+export default class OHIFCornerstoneExtension {
+  /**
+   * Extension ID is a unique id, might be used for namespacing extension specific redux actions/reducers (?)
+   */
+  getExtensionId() {
+    return 'cornerstone';
+  }
+
+  getViewportModule() {
+    return OHIFCornerstoneViewport;
+  }
+
+  getSopClassHandler() {
+    return null;
+  }
+
+  getPanelModule() {
+    return null;
+  }
+
+  getToolbarModule() {
+    return null;
+  }
+}
@@ -0,0 +1,168 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import OHIF from 'ohif-core';
+import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
+import cornerstoneTools from 'cornerstone-tools';
+import cornerstone from 'cornerstone-core';
+import './config';
+import handleSegmentationStorage from './handleSegmentationStorage.js';
+
+const { StackManager } = OHIF.utils;
+
+// Create the synchronizer used to update reference lines
+OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer(
+  'cornerstonenewimage',
+  cornerstoneTools.updateImageSynchronizer
+);
+
+// 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 OHIFCornerstoneViewport extends Component {
+  state = {
+    viewportData: null
+  };
+
+  static propTypes = {
+    studies: PropTypes.object,
+    displaySet: PropTypes.object,
+    viewportIndex: PropTypes.number
+  };
+
+  static id = 'OHIFCornerstoneViewport';
+
+  static init() {
+    console.log('OHIFCornerstoneViewport init()');
+  }
+
+  static destroy() {
+    console.log('OHIFCornerstoneViewport destroy()');
+    StackManager.clearStacks();
+  }
+
+  static getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
+    // 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
+    return StackManager.findOrCreateStack(study, displaySet);
+  }
+
+  static getViewportData = (
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid
+  ) => {
+    const currentStack = OHIFCornerstoneViewport.getCornerstoneStack(
+      studies,
+      studyInstanceUid,
+      displaySetInstanceUid
+    );
+
+    // Clone the stack here so we don't mutate it later
+    const stack = Object.assign({}, currentStack);
+    stack.currentImageIdIndex = 0;
+
+    return stack;
+  };
+
+  getViewportData = async (
+    studies,
+    studyInstanceUid,
+    displaySetInstanceUid,
+    sopClassUid
+  ) => {
+    let viewportData;
+
+    switch (sopClassUid) {
+      case SOP_CLASSES.SEGMENTATION_STORAGE:
+        const specialCaseHandler =
+          specialCaseHandlers[SOP_CLASSES.SEGMENTATION_STORAGE];
+
+        viewportData = await specialCaseHandler(
+          studies,
+          studyInstanceUid,
+          displaySetInstanceUid
+        );
+        break;
+      default:
+        const stack = OHIFCornerstoneViewport.getViewportData(
+          studies,
+          studyInstanceUid,
+          displaySetInstanceUid
+        );
+        viewportData = {
+          studyInstanceUid,
+          displaySetInstanceUid,
+          stack
+        };
+
+        break;
+    }
+
+    return viewportData;
+  };
+
+  componentDidMount() {
+    const { studies, displaySet } = this.props.viewportData;
+    const {
+      studyInstanceUid,
+      displaySetInstanceUid,
+      sopClassUids
+    } = 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
+    ).then(viewportData => {
+      this.setState({
+        viewportData
+      });
+    });
+  }
+
+  render() {
+    return (<>
+      {this.state.viewportData && (
+        <ConnectedCornerstoneViewport
+          viewportData={this.state.viewportData}
+          viewportIndex={this.props.viewportIndex}
+        />
+      )}
+      </>
+    );
+  }
+}
+
+export default OHIFCornerstoneViewport;
@@ -0,0 +1,31 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneMath from 'cornerstone-math';
+import cornerstoneTools from 'cornerstone-tools';
+import Hammer from 'hammerjs';
+import OHIF from 'ohif-core';
+
+// For debugging
+window.cornerstoneTools = cornerstoneTools;
+
+cornerstoneTools.external.cornerstone = cornerstone;
+cornerstoneTools.external.Hammer = Hammer;
+cornerstoneTools.external.cornerstoneMath = cornerstoneMath;
+cornerstoneTools.init();
+
+OHIF.external.cornerstoneTools = cornerstoneTools;
+
+// Set the tool font and font size
+// context.font = "[style] [variant] [weight] [size]/[line height] [font family]";
+const fontFamily =
+  'Roboto, OpenSans, HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif';
+cornerstoneTools.textStyle.setFont(`16px ${fontFamily}`);
+
+// Set the tool width
+cornerstoneTools.toolStyle.setToolWidth(2);
+// Set color for inactive tools
+cornerstoneTools.toolColors.setToolColor('rgb(255, 255, 0)');
+
+// Set color for active tools
+cornerstoneTools.toolColors.setActiveColor('rgb(0, 255, 0)');
+
+cornerstoneTools.store.state.touchProximity = 40;
@@ -0,0 +1,155 @@
+import OHIF from 'ohif-core';
+import cornerstone from 'cornerstone-core';
+import cornerstoneTools from 'cornerstone-tools';
+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 parseSeg(arrayBuffer, imageIds, firstImagePlane) {
+  return dcmjs.adapters.Cornerstone.Segmentation.readToolState(
+    imageIds,
+    arrayBuffer,
+    firstImagePlane
+  );
+}
+
+function addSegMetadataToCornerstoneToolState(
+  segMetadata,
+  toolState,
+  displaySetInstanceUid
+) {
+  cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
+    toolState
+  );
+
+  const brushModule = cornerstoneTools.store.modules.brush;
+
+  for (let i = 0; i < segMetadata.length; i++) {
+    brushModule.setters.metadata(displaySetInstanceUid, i, segMetadata[i]);
+  }
+}
+
+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
+  );
+
+  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());
+  debugger;
+
+  const firstImagePlane = cornerstone.metadata.get('imagePlane', imageIds[0]);
+
+  const results = parseSeg(arrayBuffer, imageIds, firstImagePlane);
+
+  if (!results) {
+    throw new Error('Fractional segmentations are not supported');
+  }
+
+  const { segMetadata, toolState } = results;
+
+  segMetadata.seriesInstanceUid = seriesInstanceUid;
+
+  addSegMetadataToCornerstoneToolState(
+    segMetadata,
+    toolState,
+    displaySetInstanceUid
+  );
+
+  const cachedStack = StackManager.findOrCreateStack(
+    study,
+    referenceDisplaySet
+  );
+  const stack = Object.assign({}, cachedStack);
+  stack.currentImageIdIndex = 0;
+
+  return {
+    studyInstanceUid,
+    displaySetInstanceUid,
+    stack
+  };
+}
+
+export default handleSegmentationStorage;
@@ -0,0 +1,3 @@
+import OHIFCornerstoneExtension from './OHIFCornerstoneExtension.js';
+
+export default OHIFCornerstoneExtension;