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
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commit 075008c674
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+import { hotkeys } from '@ohif/core';
+
+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() {
+  return {
+    // TODO: We're using this as a route segment
+    // We should not be.
+    id,
+    routeName: 'microscopy',
+    displayName: 'Microscopy',
+
+    /**
+     * Lifecycle hooks
+     */
+    onModeEnter: ({ servicesManager, extensionManager, commandsManager }) => {
+      const { toolbarService } = servicesManager.services;
+
+      toolbarService.init(extensionManager);
+      toolbarService.addButtons(toolbarButtons);
+      toolbarService.createButtonSection('primary', [
+        'MeasurementTools',
+        'dragPan',
+      ]);
+    },
+
+    onModeExit: ({ servicesManager }) => {
+      const { toolbarService } = servicesManager.services;
+
+      toolbarService.reset();
+    },
+
+    validationTags: {
+      study: [],
+      series: [],
+    },
+
+    isValidMode: ({ modalities }) => {
+      const modalities_list = modalities.split('\\');
+
+      // Slide Microscopy and ECG modality not supported by basic mode yet
+      return modalities_list.includes('SM');
+    },
+
+    routes: [
+      {
+        path: 'microscopy',
+        /*init: ({ servicesManager, extensionManager }) => {
+          //defaultViewerRouteInit
+        },*/
+        layoutTemplate: ({ location, servicesManager }) => {
+          return {
+            id: ohif.layout,
+            props: {
+              leftPanels: [ohif.leftPanel],
+              leftPanelDefaultClosed: true, // we have problem with rendering thumbnails for microscopy images
+              rightPanelDefaultClosed: 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: [
+                    '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler',
+                    '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler',
+                  ],
+                },
+                {
+                  namespace: dicomvideo.viewport,
+                  displaySetsToDisplay: [dicomvideo.sopClassHandler],
+                },
+                {
+                  namespace: dicompdf.viewport,
+                  displaySetsToDisplay: [dicompdf.sopClassHandler],
+                },
+              ],
+            },
+          };
+        },
+      },
+    ],
+    extensions: extensionDependencies,
+    hangingProtocols: [ohif.hangingProtocols],
+    hangingProtocol: ['default'],
+
+    // Order is important in sop class handlers when two handlers both use
+    // the same sop class under different situations.  In that case, the more
+    // general handler needs to come last.  For this case, the dicomvideo must
+    // come first to remove video transfer syntax before ohif uses images
+    sopClassHandlers: [
+      '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler',
+      '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler',
+      dicomvideo.sopClassHandler,
+      dicompdf.sopClassHandler,
+    ],
+    hotkeys: [...hotkeys.defaults.hotkeyBindings],
+  };
+}
+
+const mode = {
+  id,
+  modeFactory,
+  extensionDependencies,
+};
+
+export default mode;