init

modes/microscopy/.gitignore

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+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# TypeScript v1 declaration files
+typings/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Microbundle cache
+.rpt2_cache/
+.rts2_cache_cjs/
+.rts2_cache_es/
+.rts2_cache_umd/
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+.env.test
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+
+# Next.js build output
+.next
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and *not* Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# TernJS port file
+.tern-port

modes/microscopy/.prettierrc

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+{
+  "plugins": ["prettier-plugin-tailwindcss"],
+  "trailingComma": "es5",
+  "printWidth": 100,
+  "proseWrap": "always",
+  "tabWidth": 2,
+  "semi": true,
+  "singleQuote": true,
+  "arrowParens": "avoid",
+  "endOfLine": "auto"
+}

modes/microscopy/.webpack/webpack.dev.js

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+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+const ENTRY = {
+  app: `${SRC_DIR}/index.js`,
+};
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+};

modes/microscopy/.webpack/webpack.prod.js

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+const webpack = require('webpack');
+const { merge } = require('webpack-merge');
+const path = require('path');
+const MiniCssExtractPlugin = require('mini-css-extract-plugin');
+
+const pkg = require('./../package.json');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+
+const ROOT_DIR = path.join(__dirname, './../');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+const ENTRY = {
+  app: `${SRC_DIR}/index.tsx`,
+};
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+
+  return merge(commonConfig, {
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: false,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'ohif-mode-microscopy',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+      // new MiniCssExtractPlugin({
+      //   filename: './dist/[name].css',
+      //   chunkFilename: './dist/[id].css',
+      // }),
+    ],
+  });
+};

modes/microscopy/LICENSE

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+MIT License
+
+Copyright (c) 2023 microscopy (26860200+md-prog@users.noreply.github.com)
+
+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.

modes/microscopy/README.md

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+# OHIF mode for microscopy
+Mode for *DICOM VL Whole Slide Microscopy Image*.
+This mode uses [OHIF extension for microscopy](../../extensions/dicom-microscopy/).
+
+
+## Acknowledgements
+
+- [DICOM Microscopy Viewer](https://github.com/ImagingDataCommons/dicom-microscopy-viewer) is a Vanilla JS library for web-based visualization of DICOM VL Whole Slide Microscopy Image datasets and derived information.
+- [SLIM Viewer](https://github.com/imagingdatacommons/slim) is a single-page application for interactive visualization and annotation of digital whole slide microscopy images and derived image analysis results in standard DICOM format. The application is based on the dicom-microscopy-viewer JavaScript library and runs fully client side without any custom server components.
+
+
+## License
+MIT

modes/microscopy/babel.config.js

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+module.exports = {
+  plugins: ['@babel/plugin-proposal-class-properties'],
+  env: {
+    test: {
+      presets: [
+        [
+          // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2
+          '@babel/preset-env',
+          {
+            modules: 'commonjs',
+            debug: false,
+          },
+          '@babel/preset-typescript',
+        ],
+        '@babel/preset-react',
+      ],
+      plugins: [
+        '@babel/plugin-proposal-object-rest-spread',
+        '@babel/plugin-syntax-dynamic-import',
+        '@babel/plugin-transform-regenerator',
+        '@babel/plugin-transform-runtime',
+      ],
+    },
+    production: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        '@babel/preset-typescript',
+      ],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+    development: {
+      presets: [
+        // WebPack handles ES6 --> Target Syntax
+        ['@babel/preset-env', { modules: false }],
+        '@babel/preset-react',
+        '@babel/preset-typescript',
+      ],
+      plugins: ['react-refresh/babel'],
+      ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'],
+    },
+  },
+};

modes/microscopy/package.json

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+{
+  "name": "@ohif/mode-microscopy",
+  "version": "3.9.1",
+  "description": "OHIF mode for DICOM microscopy",
+  "author": "OHIF",
+  "license": "MIT",
+  "main": "dist/ohif-mode-microscopy.umd.js",
+  "files": [
+    "dist/**",
+    "public/**",
+    "README.md"
+  ],
+  "repository": "OHIF/Viewers",
+  "keywords": [
+    "ohif-mode"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "module": "src/index.tsx",
+  "engines": {
+    "node": ">=14",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "scripts": {
+    "clean": "shx rm -rf dist",
+    "clean:deep": "yarn run clean && shx rm -rf node_modules",
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
+    "dev:cornerstone": "yarn run dev",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "start": "yarn run dev",
+    "test:unit": "jest --watchAll",
+    "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
+  },
+  "peerDependencies": {
+    "@ohif/core": "3.9.1",
+    "@ohif/extension-dicom-microscopy": "3.9.1"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.20.13",
+    "i18next": "^17.0.3"
+  }
+}

modes/microscopy/src/id.js

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+import packageJson from '../package.json';
+
+const id = packageJson.name;
+
+export { id };

modes/microscopy/src/index.tsx

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+import { hotkeys } from '@ohif/core';
+import i18n from 'i18next';
+
+import { id } from './id';
+import toolbarButtons from './toolbarButtons';
+
+const ohif = {
+  layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout',
+  sopClassHandler: '@ohif/extension-default.sopClassHandlerModule.stack',
+  hangingProtocols: '@ohif/extension-default.hangingProtocolModule.default',
+  leftPanel: '@ohif/extension-default.panelModule.seriesList',
+  rightPanel: '@ohif/extension-default.panelModule.measure',
+};
+
+export const cornerstone = {
+  viewport: '@ohif/extension-cornerstone.viewportModule.cornerstone',
+};
+
+const dicomvideo = {
+  sopClassHandler: '@ohif/extension-dicom-video.sopClassHandlerModule.dicom-video',
+  viewport: '@ohif/extension-dicom-video.viewportModule.dicom-video',
+};
+
+const dicompdf = {
+  sopClassHandler: '@ohif/extension-dicom-pdf.sopClassHandlerModule.dicom-pdf',
+  viewport: '@ohif/extension-dicom-pdf.viewportModule.dicom-pdf',
+};
+
+const extensionDependencies = {
+  // Can derive the versions at least process.env.from npm_package_version
+  '@ohif/extension-default': '^3.0.0',
+  '@ohif/extension-cornerstone': '^3.0.0',
+  '@ohif/extension-cornerstone-dicom-sr': '^3.0.0',
+  '@ohif/extension-dicom-pdf': '^3.0.1',
+  '@ohif/extension-dicom-video': '^3.0.1',
+  '@ohif/extension-dicom-microscopy': '^3.0.0',
+};
+
+function modeFactory({ modeConfiguration }) {
+  return {
+    // TODO: We're using this as a route segment
+    // We should not be.
+    id,
+    routeName: 'microscopy',
+    displayName: i18n.t('Modes:Microscopy'),
+
+    /**
+     * Lifecycle hooks
+     */
+    onModeEnter: ({ servicesManager, extensionManager, commandsManager }: withAppTypes) => {
+      const { toolbarService } = servicesManager.services;
+
+      toolbarService.addButtons(toolbarButtons);
+      toolbarService.createButtonSection('primary', ['MeasurementTools', 'dragPan', 'TagBrowser']);
+    },
+
+    onModeExit: ({ servicesManager }: withAppTypes) => {
+      const { toolbarService, uiDialogService, uiModalService } = servicesManager.services;
+
+      uiDialogService.dismissAll();
+      uiModalService.hide();
+      toolbarService.reset();
+    },
+
+    validationTags: {
+      study: [],
+      series: [],
+    },
+
+    isValidMode: ({ modalities }) => {
+      const modalities_list = modalities.split('\\');
+
+      return {
+        valid: modalities_list.includes('SM'),
+        description: 'Microscopy mode only supports the SM modality',
+      };
+    },
+
+    routes: [
+      {
+        path: 'microscopy',
+        /*init: ({ servicesManager, extensionManager }) => {
+          //defaultViewerRouteInit
+        },*/
+        layoutTemplate: ({ location, servicesManager }) => {
+          return {
+            id: ohif.layout,
+            props: {
+              leftPanels: [ohif.leftPanel],
+              leftPanelClosed: true, // we have problem with rendering thumbnails for microscopy images
+              rightPanelClosed: true, // we do not have the save microscopy measurements yet
+              rightPanels: ['@ohif/extension-dicom-microscopy.panelModule.measure'],
+              viewports: [
+                {
+                  namespace: '@ohif/extension-dicom-microscopy.viewportModule.microscopy-dicom',
+                  displaySetsToDisplay: [
+                    // Share the sop class handler with cornerstone version of it
+                    '@ohif/extension-cornerstone.sopClassHandlerModule.DicomMicroscopySopClassHandler',
+                    '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler',
+                  ],
+                },
+                {
+                  namespace: dicomvideo.viewport,
+                  displaySetsToDisplay: [dicomvideo.sopClassHandler],
+                },
+                {
+                  namespace: dicompdf.viewport,
+                  displaySetsToDisplay: [dicompdf.sopClassHandler],
+                },
+              ],
+            },
+          };
+        },
+      },
+    ],
+    extensions: extensionDependencies,
+    hangingProtocol: 'default',
+    sopClassHandlers: [
+      '@ohif/extension-cornerstone.sopClassHandlerModule.DicomMicroscopySopClassHandler',
+      '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler',
+      dicomvideo.sopClassHandler,
+      dicompdf.sopClassHandler,
+    ],
+    hotkeys: [...hotkeys.defaults.hotkeyBindings],
+    ...modeConfiguration,
+  };
+}
+
+const mode = {
+  id,
+  modeFactory,
+  extensionDependencies,
+};
+
+export default mode;

modes/microscopy/src/toolbarButtons.js

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+import { ToolbarService } from '@ohif/core';
+
+const toolbarButtons = [
+  {
+    id: 'MeasurementTools',
+    uiType: 'ohif.splitButton',
+    props: {
+      groupId: 'MeasurementTools',
+      // group evaluate to determine which item should move to the top
+      evaluate: 'evaluate.group.promoteToPrimary',
+      primary: ToolbarService.createButton({
+        id: 'line',
+        icon: 'tool-length',
+        label: 'Line',
+        tooltip: 'Line',
+        commands: [
+          {
+            commandName: 'setToolActive',
+            commandOptions: { toolName: 'line' },
+            context: 'MICROSCOPY',
+          },
+        ],
+        evaluate: 'evaluate.microscopyTool',
+      }),
+      secondary: {
+        icon: 'chevron-down',
+        tooltip: 'More Measure Tools',
+      },
+      items: [
+        ToolbarService.createButton({
+          id: 'line',
+          icon: 'tool-length',
+          label: 'Line',
+          tooltip: 'Line',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'line' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        ToolbarService.createButton({
+          id: 'point',
+          icon: 'tool-point',
+          label: 'Point',
+          tooltip: 'Point Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'point' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        // Point Tool was previously defined
+        ToolbarService.createButton({
+          id: 'polygon',
+          icon: 'tool-polygon',
+          label: 'Polygon',
+          tooltip: 'Polygon Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'polygon' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        ToolbarService.createButton({
+          id: 'circle',
+          icon: 'tool-circle',
+          label: 'Circle',
+          tooltip: 'Circle Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'circle' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        ToolbarService.createButton({
+          id: 'box',
+          icon: 'tool-rectangle',
+          label: 'Box',
+          tooltip: 'Box Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'box' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        ToolbarService.createButton({
+          id: 'freehandpolygon',
+          icon: 'tool-freehand-polygon',
+          label: 'Freehand Polygon',
+          tooltip: 'Freehand Polygon Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'freehandpolygon' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+        ToolbarService.createButton({
+          id: 'freehandline',
+          icon: 'tool-freehand-line',
+          label: 'Freehand Line',
+          tooltip: 'Freehand Line Tool',
+          commands: [
+            {
+              commandName: 'setToolActive',
+              commandOptions: { toolName: 'freehandline' },
+              context: 'MICROSCOPY',
+            },
+          ],
+          evaluate: 'evaluate.microscopyTool',
+        }),
+      ],
+    },
+  },
+  {
+    id: 'dragPan',
+    uiType: 'ohif.radioGroup',
+    props: {
+      icon: 'tool-move',
+      label: 'Pan',
+      commands: [
+        {
+          commandName: 'setToolActive',
+          commandOptions: { toolName: 'dragPan' },
+          context: 'MICROSCOPY',
+        },
+      ],
+      evaluate: 'evaluate.microscopyTool',
+    },
+  },
+  {
+    id: 'TagBrowser',
+    uiType: 'ohif.radioGroup',
+    props: {
+      icon: 'dicom-tag-browser',
+      label: 'Dicom Tag Browser',
+      commands: [
+        {
+          commandName: 'openDICOMTagViewer',
+        },
+      ],
+      evaluate: 'evaluate.action',
+    },
+  },
+];
+
+export default toolbarButtons;