WIP SR viewport.
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const path = require('path');
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const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
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const SRC_DIR = path.join(__dirname, '../src');
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const DIST_DIR = path.join(__dirname, '../dist');
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module.exports = (env, argv) => {
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return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
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};
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const webpack = require('webpack');
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const merge = require('webpack-merge');
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const path = require('path');
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const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
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const pkg = require('./../package.json');
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const ROOT_DIR = path.join(__dirname, './..');
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const SRC_DIR = path.join(__dirname, '../src');
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const DIST_DIR = path.join(__dirname, '../dist');
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module.exports = (env, argv) => {
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const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
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return merge(commonConfig, {
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devtool: 'source-map',
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stats: {
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colors: true,
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hash: true,
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timings: true,
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assets: true,
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chunks: false,
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chunkModules: false,
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modules: false,
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children: false,
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warnings: true,
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},
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optimization: {
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minimize: true,
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sideEffects: true,
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},
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output: {
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path: ROOT_DIR,
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library: 'OHIFExtCornerstone',
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libraryTarget: 'umd',
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libraryExport: 'default',
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filename: pkg.main,
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},
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plugins: [
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new webpack.optimize.LimitChunkCountPlugin({
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maxChunks: 1,
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}),
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],
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});
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};
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MIT License
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Copyright (c) 2018 Open Health Imaging Foundation
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
|
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
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SOFTWARE.
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# @ohif/extension-cornerstone
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This extension adds support for viewing and manipulating 2D medical images via a
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viewport. The underlying implementation wraps the
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`cornerstonejs/react-cornerstone-viewport`, and provides basic commands and
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toolbar buttons for common actions.
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<!-- TODO: Simple image or GIF? -->
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#### Index
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Extension Id: `cornerstone`
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- [Commands Module](#commands-module)
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- [Toolbar Module](#toolbar-module)
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- [Viewport Module](#viewport-module)
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## Commands Module
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This extensions includes the following `Commands` and `Command Definitions`.
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These can be registered with `@ohif/core`'s `CommandManager`. After registering
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the commands, they can be bound to `hotkeys` using the `HotkeysManager` and
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listed in the `UserPreferences` modal.
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You can read more about [`Commands`][docs-commands], [`Hotkeys`][docs-hotkeys],
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and the [`UserPreferences` Modal][docs-userprefs] in their respective locations
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in the OHIF Viewer's documentation.
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| Command Name | Description | Store Contexts |
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| ---------------------------- | --------------------------------------- | -------------- |
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| `rotateViewportCW` | | viewports |
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| `rotateViewportCCW` | | viewports |
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| `invertViewport` | | viewports |
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| `flipViewportVertical` | | viewports |
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| `flipViewportHorizontal` | | viewports |
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| `scaleUpViewport` | | viewports |
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| `scaleDownViewport` | | viewports |
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| `fitViewportToWindow` | | viewports |
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| `resetViewport` | | viewports |
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| clearAnnotations | TODO | |
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| next/previous Image | TODO | |
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| first/last Image | TODO | |
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| `nextViewportDisplaySet` | | |
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| `previousViewportDisplaySet` | | |
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| `setToolActive` | Activates tool for primary button/touch | |
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## Toolbar Module
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Our toolbar module contains definitions for:
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- `StackScroll`
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- `Zoom`
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- `Wwwc`
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- `Pan`
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- `Length`
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- `Angle`
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- `Reset`
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- `Cine`
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All use the `ACTIVE_VIEWPORT::CORNERSTONE` context.
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## Viewport Module
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Our Viewport wraps [cornerstonejs/react-cornerstone-viewport][react-viewport]
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and is connected the redux store. This module is the most prone to change as we
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hammer out our Viewport interface.
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## Tool Configuration
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Tools can be configured through extension configuration using the tools key:
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```js
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...
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cornerstoneExtensionConfig: {
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tools: {
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ArrowAnnotate: {
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configuration: {
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getTextCallback: (callback, eventDetails) => callback(prompt('Enter your custom annotation')),
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},
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},
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},
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},
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...
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```
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## Annotate Tools Configuration
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*We currently support one property for annotation tools.*
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### Hide handles
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This extension configuration allows you to toggle on/off handle rendering for all annotate tools:
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```js
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...
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cornerstoneExtensionConfig: {
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hideHandles: true,
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},
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...
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## Resources
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### Repositories
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- [cornerstonejs/react-cornerstone-viewport][react-viewport]
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- [cornerstonejs/cornerstoneTools][cornerstone-tools]
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- [cornerstonejs/cornerstone][cornerstone]
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<!--
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Links
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-->
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<!-- prettier-ignore-start -->
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[docs-commands]: https://www.com
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[docs-hotkeys]: https://www.com
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[docs-userprefs]: htt
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[react-viewport]: https://github.com/cornerstonejs/react-cornerstone-viewport
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[cornerstone-tools]: https://github.com/cornerstonejs/cornerstoneTools
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[cornerstone]: https://github.com/cornerstonejs/cornerstone
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<!-- prettier-ignore-end -->
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@@ -0,0 +1 @@
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module.exports = require('../../babel.config.js');
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{
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"name": "@ohif/extension-dicom-sr",
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"version": "0.0.1",
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"description": "OHIF extension for an SR Cornerstone Viewport",
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"author": "OHIF",
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"license": "MIT",
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"repository": "OHIF/Viewers",
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"main": "dist/index.umd.js",
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"module": "src/index.js",
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"engines": {
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"node": ">=10",
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"npm": ">=6",
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"yarn": ">=1.16.0"
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},
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"files": [
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"dist",
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"README.md"
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],
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"publishConfig": {
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"access": "public"
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},
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"scripts": {
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"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
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"dev:cornerstone": "yarn run dev",
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"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
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"build:package": "yarn run build",
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"start": "yarn run dev",
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"test:unit": "jest --watchAll",
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"test:unit:ci": "jest --ci --runInBand --collectCoverage"
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},
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"peerDependencies": {
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"@ohif/core": "^0.50.0",
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"@ohif/ui": "^0.50.0",
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"cornerstone-core": "^2.3.0",
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"cornerstone-math": "^0.1.8",
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"cornerstone-tools": "4.15.1",
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"dcmjs": "^0.12.3",
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"cornerstone-wado-image-loader": "^3.1.2",
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"dicom-parser": "^1.8.3",
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"hammerjs": "^2.0.8",
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"prop-types": "^15.6.2",
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"react": "^16.11.0",
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"react-dom": "^16.11.0",
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"react-redux": "^6.0.0",
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"react-resize-detector": "^3.4.0",
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"redux": "^4.0.1"
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},
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"dependencies": {
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"@babel/runtime": "7.7.6",
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"classnames": "^2.2.6",
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"lodash.merge": "^4.6.2",
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"lodash.throttle": "^4.1.1",
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"react-cornerstone-viewport": "2.3.8"
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}
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}
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import React, { Component } from 'react';
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import CornerstoneViewport from 'react-cornerstone-viewport';
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//import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
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import OHIF from '@ohif/core';
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import PropTypes from 'prop-types';
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import cornerstone from 'cornerstone-core';
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import debounce from 'lodash.debounce';
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import throttle from 'lodash.throttle';
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// const {
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// onAdded,
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// onRemoved,
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// onModified,
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// } = OHIF.measurements.MeasurementHandlers;
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// // TODO: Transition to enums for the action names so that we can ensure they stay up to date
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// // everywhere they're used.
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// const MEASUREMENT_ACTION_MAP = {
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// added: onAdded,
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// removed: onRemoved,
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// modified: throttle(event => {
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// return onModified(event);
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// }, 300),
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// };
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// const cine = viewportSpecificData.cine;
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// isPlaying = cine.isPlaying === true;
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// frameRate = cine.cineFrameRate || frameRate;
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const { StackManager } = OHIF.utils;
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class OHIFCornerstoneViewport extends Component {
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state = {
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viewportData: null,
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};
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static defaultProps = {
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customProps: {},
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};
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static propTypes = {
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displaySet: PropTypes.object,
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viewportIndex: PropTypes.number,
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dataSource: PropTypes.object,
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children: PropTypes.node,
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customProps: PropTypes.object,
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};
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static name = 'OHIFCornerstoneViewport';
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static init() {
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console.log('OHIFCornerstoneViewport init()');
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}
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static destroy() {
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console.log('OHIFCornerstoneViewport destroy()');
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StackManager.clearStacks();
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}
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/**
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* Obtain the CornerstoneTools Stack for the specified display set.
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*
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* @param {Object} displaySet
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* @param {Object} dataSource
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* @return {Object} CornerstoneTools Stack
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*/
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static getCornerstoneStack(displaySet, dataSource) {
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const { frameIndex } = displaySet;
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// Get stack from Stack Manager
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const storedStack = StackManager.findOrCreateStack(displaySet, dataSource);
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// Clone the stack here so we don't mutate it
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const stack = Object.assign({}, storedStack);
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stack.currentImageIdIndex = frameIndex;
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// TODO -> Do we ever use this like this?
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// if (SOPInstanceUID) {
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// const index = stack.imageIds.findIndex(imageId => {
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// const imageIdSOPInstanceUID = cornerstone.metaData.get(
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// 'SOPInstanceUID',
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// imageId
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// );
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// return imageIdSOPInstanceUID === SOPInstanceUID;
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// });
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// if (index > -1) {
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// stack.currentImageIdIndex = index;
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// } else {
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// console.warn(
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// 'SOPInstanceUID provided was not found in specified DisplaySet'
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// );
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// }
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// }
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return stack;
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}
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getViewportData = async displaySet => {
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let viewportData;
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const { dataSource } = this.props;
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const stack = OHIFCornerstoneViewport.getCornerstoneStack(
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displaySet,
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dataSource
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);
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viewportData = {
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StudyInstanceUID: displaySet.StudyInstanceUID,
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displaySetInstanceUID: displaySet.displaySetInstanceUID,
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stack,
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};
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return viewportData;
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};
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setStateFromProps() {
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const { displaySet } = this.props;
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const {
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StudyInstanceUID,
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displaySetInstanceUID,
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sopClassUids,
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} = displaySet;
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if (!StudyInstanceUID || !displaySetInstanceUID) {
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return;
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}
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if (sopClassUids && sopClassUids.length > 1) {
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console.warn(
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'More than one SOPClassUID in the same series is not yet supported.'
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);
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}
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this.getViewportData(displaySet).then(viewportData => {
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this.setState({
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viewportData,
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});
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});
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}
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componentDidMount() {
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this.setStateFromProps();
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}
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componentDidUpdate(prevProps) {
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const { displaySet } = this.props;
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const prevDisplaySet = prevProps.displaySet;
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if (
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displaySet.displaySetInstanceUID !==
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prevDisplaySet.displaySetInstanceUID ||
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displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
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displaySet.frameIndex !== prevDisplaySet.frameIndex
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) {
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this.setStateFromProps();
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||||
}
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||||
}
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||||
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render() {
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let childrenWithProps = null;
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||||
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||||
if (!this.state.viewportData) {
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return null;
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||||
}
|
||||
const { viewportIndex } = this.props;
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||||
const {
|
||||
imageIds,
|
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currentImageIdIndex,
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||||
// If this comes from the instance, would be a better default
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// `FrameTime` in the instance
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// frameRate = 0,
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} = this.state.viewportData.stack;
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||||
|
||||
// TODO: Does it make more sense to use Context?
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if (this.props.children && this.props.children.length) {
|
||||
childrenWithProps = this.props.children.map((child, index) => {
|
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return (
|
||||
child &&
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||||
React.cloneElement(child, {
|
||||
viewportIndex: this.props.viewportIndex,
|
||||
key: index,
|
||||
})
|
||||
);
|
||||
});
|
||||
}
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||||
|
||||
const debouncedNewImageHandler = debounce(
|
||||
({ currentImageIdIndex, sopInstanceUid }) => {
|
||||
const { displaySet } = this.props;
|
||||
const { StudyInstanceUID } = displaySet;
|
||||
if (currentImageIdIndex > 0) {
|
||||
this.props.onNewImage({
|
||||
StudyInstanceUID,
|
||||
SOPInstanceUID: sopInstanceUid,
|
||||
frameIndex: currentImageIdIndex,
|
||||
activeViewportIndex: viewportIndex,
|
||||
});
|
||||
}
|
||||
},
|
||||
700
|
||||
);
|
||||
|
||||
// TODO -> We may still want a wrapped component to define all the measurement api stuff.
|
||||
|
||||
return (
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||||
<>
|
||||
<CornerstoneViewport
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||||
viewportIndex={viewportIndex}
|
||||
imageIds={imageIds}
|
||||
imageIdIndex={currentImageIdIndex}
|
||||
onNewImage={debouncedNewImageHandler}
|
||||
// TODO: ViewportGrid Context?
|
||||
isActive={true} // todo
|
||||
isStackPrefetchEnabled={true} // todo
|
||||
isPlaying={false}
|
||||
frameRate={24}
|
||||
/>
|
||||
{childrenWithProps}
|
||||
</>
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
const temp = () => <div>Hello SR Viewport!</div>;
|
||||
|
||||
//export default OHIFCornerstoneViewport;
|
||||
export default temp;
|
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@@ -0,0 +1,146 @@
|
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import id from './id';
|
||||
import { utils } from '@ohif/core';
|
||||
|
||||
const sopClassHandlerName = 'dicom-sr';
|
||||
|
||||
const sopClassUids = [
|
||||
'1.2.840.10008.5.1.4.1.1.88.11', //BASIC_TEXT_SR:
|
||||
'1.2.840.10008.5.1.4.1.1.88.22', //ENHANCED_SR:
|
||||
'1.2.840.10008.5.1.4.1.1.88.33', //COMPREHENSIVE_SR:
|
||||
];
|
||||
|
||||
const scoordTypes = ['POINT', 'MULTIPOINT', 'POLYLINE', 'CIRCLE', 'ELLIPSE'];
|
||||
|
||||
const CodeNameCodeSequenceValues = {
|
||||
ImagingMeasurementReport: '126000',
|
||||
ImageLibrary: '111028',
|
||||
ImagingMeasurements: '126010',
|
||||
MeasurementGroup: '125007',
|
||||
ImageLibraryGroup: '126200',
|
||||
};
|
||||
|
||||
/**
|
||||
* Basic SOPClassHandler:
|
||||
* - For all Image types that are stackable, create
|
||||
* a displaySet with a stack of images
|
||||
*
|
||||
* @param {Array} sopClassHandlerModules List of SOP Class Modules
|
||||
* @param {SeriesMetadata} series The series metadata object from which the display sets will be created
|
||||
* @returns {Array} The list of display sets created for the given series object
|
||||
*/
|
||||
function getDisplaySetsFromSeries(instances) {
|
||||
// If the series has no instances, stop here
|
||||
if (!instances || !instances.length) {
|
||||
throw new Error('No instances were provided');
|
||||
}
|
||||
|
||||
const instance = instances[0];
|
||||
|
||||
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
|
||||
|
||||
const { ConceptNameCodeSequence, ContentSequence } = instance;
|
||||
|
||||
if (
|
||||
ConceptNameCodeSequence.CodeValue !==
|
||||
CodeNameCodeSequenceValues.ImagingMeasurementReport
|
||||
) {
|
||||
console.warn(
|
||||
'Only support Imaging Measurement Report SRs (TID1500) for now'
|
||||
);
|
||||
return [];
|
||||
}
|
||||
|
||||
const referencedImages = _getReferencedImagesList(ContentSequence);
|
||||
|
||||
const measurements = _getMeasurements(ContentSequence, SOPInstanceUID);
|
||||
|
||||
const displaySet = {
|
||||
plugin: id,
|
||||
Modality: 'SR',
|
||||
displaySetInstanceUID: utils.guid(),
|
||||
SOPInstanceUID,
|
||||
SeriesInstanceUID,
|
||||
StudyInstanceUID,
|
||||
SOPClassHandlerId: `${id}.sopClassHandlerModule.${sopClassHandlerName}`,
|
||||
referencedImages,
|
||||
};
|
||||
|
||||
return [displaySet];
|
||||
}
|
||||
|
||||
function getSopClassHandlerModule() {
|
||||
return [
|
||||
{
|
||||
name: sopClassHandlerName,
|
||||
sopClassUids,
|
||||
getDisplaySetsFromSeries,
|
||||
},
|
||||
];
|
||||
}
|
||||
|
||||
function _getMeasurements(
|
||||
ImagingMeasurementReportContentSequence,
|
||||
SOPInstanceUID
|
||||
) {
|
||||
const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.ImagingMeasurements
|
||||
);
|
||||
|
||||
if (SOPInstanceUID === '2.25.435452399240481307327287169369305113868') {
|
||||
debugger;
|
||||
}
|
||||
|
||||
const MeasurementGroup = _getSequenceAsArray(
|
||||
ImagingMeasurements.ContentSequence
|
||||
).find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.MeasurementGroup
|
||||
);
|
||||
|
||||
const Measurements = _getSequenceAsArray(
|
||||
MeasurementGroup.ContentSequence
|
||||
).filter(group => group.ValueType === 'NUM');
|
||||
|
||||
debugger;
|
||||
|
||||
_getSequenceAsArray(MeasurementGroup.ContentSequence).forEach(item => {});
|
||||
}
|
||||
|
||||
function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
|
||||
const ImageLibrary = ImagingMeasurementReportContentSequence.find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.ImageLibrary
|
||||
);
|
||||
|
||||
const ImageLibraryGroup = _getSequenceAsArray(
|
||||
ImageLibrary.ContentSequence
|
||||
).find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.ImageLibraryGroup
|
||||
);
|
||||
|
||||
const referencedImages = [];
|
||||
|
||||
_getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
|
||||
const { ReferencedSOPSequence } = item;
|
||||
const {
|
||||
ReferencedSOPClassUID,
|
||||
ReferencedSOPInstanceUID,
|
||||
} = ReferencedSOPSequence;
|
||||
|
||||
referencedImages.push({ ReferencedSOPClassUID, ReferencedSOPInstanceUID });
|
||||
});
|
||||
|
||||
return referencedImages;
|
||||
}
|
||||
|
||||
function _getSequenceAsArray(sequence) {
|
||||
return Array.isArray(sequence) ? sequence : [sequence];
|
||||
}
|
||||
|
||||
export default getSopClassHandlerModule;
|
||||
@@ -0,0 +1 @@
|
||||
export default 'org.ohif.dicom-sr';
|
||||
@@ -0,0 +1,45 @@
|
||||
import React from 'react';
|
||||
import getSopClassHandlerModule from './getSopClassHandlerModule';
|
||||
import id from './id.js';
|
||||
|
||||
const Component = React.lazy(() => {
|
||||
return import('./OHIFCornerstoneSRViewport');
|
||||
});
|
||||
|
||||
const OHIFCornerstoneSRViewport = props => {
|
||||
return (
|
||||
<React.Suspense fallback={<div>Loading...</div>}>
|
||||
<Component {...props} />
|
||||
</React.Suspense>
|
||||
);
|
||||
};
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
export default {
|
||||
/**
|
||||
* Only required property. Should be a unique value across all extensions.
|
||||
*/
|
||||
id,
|
||||
|
||||
/**
|
||||
*
|
||||
*
|
||||
* @param {object} [configuration={}]
|
||||
* @param {object|array} [configuration.csToolsConfig] - Passed directly to `initCornerstoneTools`
|
||||
*/
|
||||
getViewportModule({ commandsManager }) {
|
||||
const ExtendedOHIFCornerstoneSRViewport = props => {
|
||||
const onNewImageHandler = jumpData => {
|
||||
commandsManager.runCommand('jumpToImage', jumpData);
|
||||
};
|
||||
return (
|
||||
<OHIFCornerstoneSRViewport {...props} onNewImage={onNewImageHandler} />
|
||||
);
|
||||
};
|
||||
|
||||
return [{ name: 'dicom-sr', component: ExtendedOHIFCornerstoneSRViewport }];
|
||||
},
|
||||
getSopClassHandlerModule,
|
||||
};
|
||||
Reference in new issue
Block a user