Fix performance issues with Microscopy extension

2019-02-04 16:45:49 +01:00
1 parent bf8f737fec
commit e3d26f2181
@@ -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 +1,82 @@
+{
+  "name": "ohif-dicom-microscopy-extension",
+  "version": "0.0.4",
+  "description": "OHIF extension for Dicom Microscopy",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/index.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": {
+    "react": "^15.0.0 || ^16.0.0",
+    "react-dom": "^15.0.0 || ^16.0.0"
+  },
+  "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": "^9.0.0",
+    "cross-env": "^5.2.0",
+    "eslint": "5.6.0",
+    "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": "^0.68.2",
+    "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": "^1.6.3",
+    "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",
+    "dicom-microscopy-viewer": "^0.2.0",
+    "ohif-core": "^0.2.4"
+  }
+}
@@ -0,0 +1,55 @@
+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';
+
+export default {
+  input: 'src/index.js',
+  output: [
+    {
+      file: pkg.main,
+      format: 'umd',
+      name: 'ohif-dicom-microscopy-extension',
+      sourcemap: true,
+      exports: 'named',
+      globals: {
+        'react': 'React',
+        'react-dom': 'ReactDOM'
+      }
+    },
+    {
+      file: pkg.module,
+      format: 'es',
+      sourcemap: true
+    }
+  ],
+  plugins: [
+    builtins(),
+    external(),
+    postcss({
+      modules: false
+    }),
+    url(),
+    svgr(),
+    babel({
+      exclude: 'node_modules/**',
+      plugins: [ '@babel/external-helpers' ],
+      externalHelpers: true,
+      runtimeHelpers: true
+    }),
+    resolve(),
+    commonjs({
+      include: 'node_modules/**',
+      namedExports: {
+          'node_modules/dicom-microscopy-viewer/build/dicom-microscopy-viewer.js': [
+            'api'
+          ]
+      }
+    })
+  ]
+}
@@ -0,0 +1,28 @@
+import OHIF from 'ohif-core';
+
+const { utils } = OHIF;
+
+const SOP_CLASS_UIDS = {
+  VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6'
+};
+
+const DicomMicroscopySopClassHandler = {
+  id: 'DicomMicroscopySopClassHandlerPlugin',
+  sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
+  getDisplaySetFromSeries(series, study, dicomWebClient) {
+    const instance = series.getFirstInstance();
+
+    // Note: We are passing the dicomweb client into each viewport!
+
+    return {
+      plugin: 'microscopy',
+      displaySetInstanceUid: utils.guid(),
+      dicomWebClient,
+      sopInstanceUid: instance.getSOPInstanceUID(),
+      seriesInstanceUid: series.getSeriesInstanceUID(),
+      studyInstanceUid: study.getStudyInstanceUID()
+    };
+  }
+};
+
+export default DicomMicroscopySopClassHandler;
@@ -0,0 +1,83 @@
+import React, { Component } from 'react';
+import { api } from 'dicom-microscopy-viewer';
+
+const microscopyViewer = api.VLWholeSlideMicroscopyImageViewer;
+
+class DicomMicroscopyViewport extends Component {
+  state = {
+    error: null
+  };
+
+  constructor(props) {
+    super(props);
+
+    this.container = React.createRef();
+  }
+
+  // install the microscopy renderer into the web page.
+  // you should only do this once.
+  installOpenLayersRenderer(container, displaySet) {
+    const dicomWebClient = displaySet.dicomWebClient;
+
+    const searchInstanceOptions = {
+      studyInstanceUID: displaySet.studyInstanceUid,
+      seriesInstanceUID: displaySet.seriesInstanceUid
+    };
+
+    dicomWebClient
+      .searchForInstances(searchInstanceOptions)
+      .then(instances => {
+        const promises = [];
+        for (let i = 0; i < instances.length; i++) {
+          const sopInstanceUID = instances[i]['00080018']['Value'][0];
+          const retrieveInstanceOptions = {
+            studyInstanceUID: displaySet.studyInstanceUid,
+            seriesInstanceUID: displaySet.seriesInstanceUid,
+            sopInstanceUID
+          };
+
+          const promise = dicomWebClient
+            .retrieveInstanceMetadata(retrieveInstanceOptions)
+            .then(metadata => {
+              const imageType = metadata[0]['00080008']['Value'];
+              if (imageType[2] === 'VOLUME') {
+                return metadata[0];
+              }
+            });
+          promises.push(promise);
+        }
+        return Promise.all(promises);
+      })
+      .then(metadata => {
+        metadata = metadata.filter(m => m);
+
+        const viewer = new microscopyViewer({
+          client: dicomWebClient,
+          metadata
+        });
+
+        viewer.render({ container });
+      });
+  }
+
+  componentDidMount() {
+    const { studies, displaySet } = this.props.viewportData;
+
+    this.installOpenLayersRenderer(this.container.current, displaySet);
+  }
+
+  render() {
+    const style = { width: '100%', height: '100%' };
+    return (
+      <div className={'DicomMicroscopyViewer'} style={style}>
+        {this.state.error ? (
+          <h2>{JSON.stringify(this.state.error)}</h2>
+        ) : (
+          <div ref={this.container} />
+        )}
+      </div>
+    );
+  }
+}
+
+export default DicomMicroscopyViewport;
@@ -0,0 +1,27 @@
+import DicomMicroscopyViewport from './DicomMicroscopyViewport.js';
+import DicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler.js';
+
+export default class OHIFDicomMicroscopyExtension {
+  /**
+   * Extension ID is a unique id, might be used for namespacing extension specific redux actions/reducers (?)
+   */
+  getExtensionId() {
+    return 'microscopy';
+  }
+
+  getViewportModule() {
+    return DicomMicroscopyViewport;
+  }
+
+  getSopClassHandler() {
+    return DicomMicroscopySopClassHandler;
+  }
+
+  getPanelModule() {
+    return null;
+  }
+
+  getToolbarModule() {
+    return null;
+  }
+}
@@ -0,0 +1,5 @@
+import OHIFDicomMicroscopyExtension from './OHIFDicomMicroscopyExtension.js';
+
+export { OHIFDicomMicroscopyExtension };
+
+export default OHIFDicomMicroscopyExtension;