feat(microscopy): add dicom microscopy extension and mode (#3247)

* skeleton for dicom-microscopy extension * skeleton for microscopy mode * [feat] ported @radicalimaging/microscopy-dicom to OHIF's default extension * [feat] ported microscopy mode from private repo * added new definitions to the package.json * webpack configuration update for microscopy extension * register new icons for microscopy tools * fixes to the microscopy extension and mode * trivial error fix - typescript type import error * link microscopy extension with default OHIF app plugin config * demo config fix * fix logs * remove unsed imports * [fix] loading of microscopy * [fix] webworker script loading, normalizing denaturalized dataset * found the latest version of dicom-microscopy-viewer that works with current OHIF extension : 0.35.2 * hide thumbnail pane by default, as we have issues with * comments * remove unused code * [feat] microscopy - annotation selection * [feat] microscopy - edit annotation label * wip * [bugfix] dicom-microscopy tool * [bugfix] dicom microscopy annotations * [fix] mixed-content blocking caused by BulkDataURI * [fix] microscopy measurements panel - center button * [fix] microscopy measurements panel - styling * [fix] microscopy - controls * fix local loading of microscopy * fix local loading of dicom microscopy * fix typo - indexof to indexOf * [fix] remove unused icons * remove commented out lines from webpack configuration * platform/viewer/public/config/default.js - revert accidental changes * [refactor] redirecting to microscopy mode on Local mode * attribution to DMV and SLIM viewer * [fix] code review feedbacks * fix thumbnails * [fix] microscopy - fix old publisher.publish() to PubSubService._broadcastEvent() * [fix] interactions, webpack config, roi selection * [feat] microscopy - remove select tool from UI * microscopy author * [fix] saving and loading SR * [bugfix] - missing publish() function in MicroscopyService, replace with _broadcastEvent * remove author section from readme * refactor SR saving feature * fix webpack config after merge * [bugfix] repeated import * fix e2e * webpack configuration * hide "Create report" button for microscopy
2023-04-27 20:53:52 -04:00
1 parent dd3944a87c
commit 075008c674
@@ -10,7 +10,6 @@ const CopyWebpackPlugin = require('copy-webpack-plugin');
 const HtmlWebpackPlugin = require('html-webpack-plugin');
 const { InjectManifest } = require('workbox-webpack-plugin');
 const MiniCssExtractPlugin = require('mini-css-extract-plugin');
-const CopyPlugin = require('copy-webpack-plugin');
 // ~~ Directories
 const SRC_DIR = path.join(__dirname, '../src');
 const DIST_DIR = path.join(__dirname, '../dist');
@@ -101,6 +100,21 @@ module.exports = (env, argv) => {
            from: `${PUBLIC_DIR}/${APP_CONFIG}`,
            to: `${DIST_DIR}/app-config.js`,
          },
+          // Copy Dicom Microscopy Viewer build files
+          {
+            from:
+              '../../../node_modules/dicom-microscopy-viewer/dist/dynamic-import',
+            to: DIST_DIR,
+            globOptions: {
+              ignore: ['*.js.map'],
+            },
+          },
+          // Copy dicom-image-loader build files
+          {
+            from:
+              '../../../node_modules/@cornerstonejs/dicom-image-loader/dist/dynamic-import',
+            to: DIST_DIR,
+          },
        ],
      }),
      // Generate "index.html" w/ correct includes/imports
@@ -120,15 +134,6 @@ module.exports = (env, argv) => {
        // Need to exclude the theme as it is updated independently
        exclude: [/theme/],
      }),
-      new CopyPlugin({
-        patterns: [
-          {
-            from:
-              '../../../node_modules/@cornerstonejs/dicom-image-loader/dist/dynamic-import',
-            to: DIST_DIR,
-          },
-        ],
-      }),
    ],
    // https://webpack.js.org/configuration/dev-server/
    devServer: {
@@ -55,11 +55,13 @@
    "@ohif/extension-default": "^3.0.0",
    "@ohif/extension-dicom-pdf": "^3.0.1",
    "@ohif/extension-dicom-video": "^3.0.1",
+    "@ohif/extension-dicom-microscopy": "^3.0.0",
    "@ohif/extension-test": "0.0.1",
    "@ohif/i18n": "^1.0.0",
    "@ohif/mode-basic-dev-mode": "^3.0.0",
    "@ohif/mode-test": "^0.0.1",
    "@ohif/mode-longitudinal": "^3.0.0",
+    "@ohif/mode-microscopy": "^3.0.0",
    "@ohif/ui": "^2.0.0",
    "@types/react": "^17.0.38",
    "classnames": "^2.3.2",
@@ -16,6 +16,10 @@
      "packageName": "@ohif/extension-default",
      "version": "3.0.0"
    },
+    {
+      "packageName": "@ohif/extension-dicom-microscopy",
+      "version": "3.0.0"
+    },
    {
      "packageName": "@ohif/extension-dicom-pdf",
      "version": "3.0.1"
@@ -42,6 +46,10 @@
      "packageName": "@ohif/mode-longitudinal",
      "version": "3.0.0"
    },
+    {
+      "packageName": "@ohif/mode-microscopy",
+      "version": "3.0.0"
+    },
    {
      "packageName": "@ohif/mode-tmtv",
      "version": "3.0.0"
@@ -1,5 +1,6 @@
 window.config = {
  routerBasename: '/',
+  modes: [],
  extensions: [],
  showStudyList: true,
  // below flag is for performance reasons, but it might not work for all servers
@@ -7,21 +8,24 @@ window.config = {
  showWarningMessageForCrossOrigin: true,
  strictZSpacingForVolumeViewport: true,
  showCPUFallbackMessage: true,
-  servers: {
-    dicomWeb: [
-      {
+  dataSources: [
+    {
+      friendlyName: 'DCM4CHEE Server',
+      namespace: '@ohif/extension-default.dataSourcesModule.dicomweb',
+      sourceName: 'dicomweb',
+      configuration: {
        name: 'DCM4CHEE',
        wadoUriRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
        qidoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
        wadoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb',
        qidoSupportsIncludeField: true,
        imageRendering: 'wadors',
-        thumbnailRendering: 'wadors',
        enableStudyLazyLoad: true,
        useBulkDataURI: false,
      },
-    ],
-  },
+    },
+  ],
+  defaultDataSourceName: 'dicomweb',
  hotkeys: [
    {
      commandName: 'incrementActiveViewport',
@@ -1,7 +1,7 @@
 import React, { useEffect, useRef } from 'react';
 import classnames from 'classnames';
 import { useNavigate } from 'react-router-dom';
-import { MODULE_TYPES } from '@ohif/core';
+import { DicomMetadataStore, MODULE_TYPES } from '@ohif/core';

 import Dropzone from 'react-dropzone';
 import filesToStudies from './filesToStudies';
@@ -60,12 +60,41 @@ function Local() {
  const firstLocalDataSource = localDataSources[0];
  const dataSource = firstLocalDataSource.createDataSource({});

+  const microscopyExtensionLoaded = extensionManager.registeredExtensionIds.includes(
+    '@ohif/extension-dicom-microscopy'
+  );
+
+  let modePath = 'viewer';
+
  const onDrop = async acceptedFiles => {
    const studies = await filesToStudies(acceptedFiles, dataSource);
-    // Todo: navigate to work list and let user select a mode
+
    const query = new URLSearchParams();
+
+    if (microscopyExtensionLoaded) {
+      // TODO: for microscopy, we are forcing microscopy mode, which is not ideal.
+      //     we should make the local drag and drop navigate to the worklist and
+      //     there user can select microscopy mode
+      const smStudies = studies.filter(id => {
+        const study = DicomMetadataStore.getStudy(id);
+        return (
+          study.series.findIndex(
+            s => s.Modality === 'SM' || s.instances[0].Modality === 'SM'
+          ) >= 0
+        );
+      });
+
+      if (smStudies.length > 0) {
+        smStudies.forEach(id => query.append('StudyInstanceUIDs', id));
+
+        modePath = 'microscopy';
+      }
+    }
+
+    // Todo: navigate to work list and let user select a mode
    studies.forEach(id => query.append('StudyInstanceUIDs', id));
-    navigate(`/viewer/dicomlocal?${decodeURIComponent(query.toString())}`);
+
+    navigate(`/${modePath}/dicomlocal?${decodeURIComponent(query.toString())}`);
  };

  // Set body style