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

.webpack/rules/transpileJavaScript.js

@@ -25,7 +25,7 @@ function transpileJavaScript(mode) {
     // These are packages that are not transpiled to our lowest supported
     // JS version (currently ES5). Most of these leverage ES6+ features,
     // that we need to transpile to a different syntax.
-    exclude,
+    exclude: [/(codecs)/, /(dicomicc)/, exclude],
     loader: 'babel-loader',
     options: {
       // Find babel.config.js in monorepo root

.webpack/webpack.base.js

@@ -78,6 +78,7 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
       },
     },
     module: {
+      noParse: [/(codec)/, /(dicomicc)/],
       rules: [
         transpileJavaScriptRule(mode),
         loadWebWorkersRule,
@@ -89,6 +90,10 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
           },
         },
         cssToJavaScript,
+        {
+          test: /\.wasm/,
+          type: 'asset/resource',
+        },
       ], //.concat(vtkRules),
     },
     resolve: {
@@ -103,6 +108,8 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => {
         '@hooks': path.resolve(__dirname, '../platform/viewer/src/hooks'),
         '@routes': path.resolve(__dirname, '../platform/viewer/src/routes'),
         '@state': path.resolve(__dirname, '../platform/viewer/src/state'),
+        'dicom-microscopy-viewer':
+          'dicom-microscopy-viewer/dist/dynamic-import/dicomMicroscopyViewer.min.js',
         '@cornerstonejs/dicom-image-loader':
           '@cornerstonejs/dicom-image-loader/dist/dynamic-import/cornerstoneDICOMImageLoader.min.js',
       },