Merge branch 'master' into fix/overview-thumbnails

README.md

@@ -327,6 +327,27 @@ For more information about the motivation, design, and capabilities of Slim, ple
 
 If you use Slim in your research, please cite the above article.
 
+## Acknowledgments
+
+This software is maintained by the Imaging Data Commons (IDC) team, which has been funded in whole or
+in part with Federal funds from the NCI, NIH, under task order no. HHSN26110071
+under contract no. HHSN261201500003l.
+
+NCI Imaging Data Commons (IDC) (https://imaging.datacommons.cancer.gov/) is a cloud-based environment 
+containing publicly available cancer imaging data co-located with analysis and exploration tools and resources. 
+IDC is a node within the broader NCI Cancer Research Data Commons (CRDC) infrastructure that provides secure 
+access to a large, comprehensive, and expanding collection of cancer research data.
+
+Learn more about IDC from this publication:
+
+> Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D.,
+> Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H.
+> J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P.,
+> Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. & Kikinis, R.
+> _National Cancer Institute Imaging Data Commons: Toward Transparency,
+> Reproducibility, and Scalability in Imaging Artificial Intelligence_.
+> RadioGraphics (2023). https://doi.org/10.1148/rg.230180
+
 ## DICOM Conformance Statement
 
 The DICOM conformance statement for Slim is available in this repository [here](/DICOM-Conformance-Statement.md)

craco.config.js

@@ -69,7 +69,7 @@ module.exports = {
         '^.+\\.[t|j]sx?$': 'babel-jest'
       }
       config.transformIgnorePatterns = [
-        'node_modules/(?!(ol|dicom-microscopy-viewer|dicomweb-client|@cornerstonejs|dicomicc)/)'
+        'node_modules/(?!(ol|dicom-microscopy-viewer|dicomweb-client|@cornerstonejs|dicomicc|rbush|color-rgba|color-parse|color-name|color-space|quickselect|earcut)/)'
       ]
       config.moduleNameMapper = {
         '@cornerstonejs/codec-libjpeg-turbo-8bit/decodewasmjs': '@cornerstonejs/codec-libjpeg-turbo-8bit/dist/libjpegturbowasm_decode',

docs/CHANGELOG.md

@@ -1,3 +1,10 @@
+# [0.39.0](https://github.com/ImagingDataCommons/slim/compare/v0.38.0...v0.39.0) (2025-02-25)
+
+
+### Features
+
+* icc profiles toggle  ([#269](https://github.com/ImagingDataCommons/slim/issues/269)) ([2320267](https://github.com/ImagingDataCommons/slim/commit/23202679246d8f2dbd8ac7b741d8d970e3cb3beb))
+
 # [0.38.0](https://github.com/ImagingDataCommons/slim/compare/v0.37.0...v0.38.0) (2025-02-04)
 
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "slim",
-  "version": "0.38.0",
+  "version": "0.39.0",
   "homepage": "https://github.com/imagingdatacommons/slim",
   "private": true,
   "author": "ImagingDataCommons",

src/components/SlideViewer.tsx

@@ -28,6 +28,7 @@ import { UndoOutlined, CheckOutlined, StopOutlined } from '@ant-design/icons'
 import * as dmv from 'dicom-microscopy-viewer'
 import * as dcmjs from 'dcmjs'
 import * as dwc from 'dicomweb-client'
+import type { CheckboxChangeEvent } from 'antd/es/checkbox'
 
 import DicomWebManager from '../DicomWebManager'
 import AnnotationList from './AnnotationList'
@@ -422,6 +423,7 @@ interface SlideViewerState {
     }
   }
   loadingFrames: Set<string>
+  isICCProfilesEnabled: boolean
 }
 
 /**
@@ -582,6 +584,7 @@ class SlideViewer extends React.Component<SlideViewerProps, SlideViewerState> {
     this.handleOpticalPathActivityChange = this.handleOpticalPathActivityChange.bind(this)
     this.handlePresentationStateSelection = this.handlePresentationStateSelection.bind(this)
     this.handlePresentationStateReset = this.handlePresentationStateReset.bind(this)
+    this.handleICCProfilesToggle = this.handleICCProfilesToggle.bind(this)
 
     const { volumeViewer, labelViewer } = _constructViewers({
       clients: this.props.clients,
@@ -638,7 +641,8 @@ class SlideViewer extends React.Component<SlideViewerProps, SlideViewerState> {
       areRoisHidden: false,
       pixelDataStatistics: {},
       selectedPresentationStateUID: this.props.selectedPresentationStateUID,
-      loadingFrames: new Set()
+      loadingFrames: new Set(),
+      isICCProfilesEnabled: true
     }
   }
 
@@ -3167,6 +3171,16 @@ class SlideViewer extends React.Component<SlideViewerProps, SlideViewerState> {
     }
   }
 
+  /**
+   * Handler that will toggle the ICC profile color management, i.e., either
+   * enable or disable it, depending on its current state.
+   */
+  handleICCProfilesToggle = (event: CheckboxChangeEvent): void => {
+    const checked = event.target.checked
+    this.setState({ isICCProfilesEnabled: checked })
+    this.volumeViewer.toggleICCProfiles()
+  }
+
   render (): React.ReactNode {
     const rois: dmv.roi.ROI[] = []
     const segments: dmv.segment.Segment[] = []
@@ -3757,6 +3771,17 @@ class SlideViewer extends React.Component<SlideViewerProps, SlideViewerState> {
       )
     }
 
+    const iccProfilesMenu = this.volumeViewer.getICCProfiles().length > 0 && (
+      <div style={{ margin: '0.9rem' }}>
+        <Checkbox
+          checked={this.state.isICCProfilesEnabled}
+          onChange={this.handleICCProfilesToggle}
+        >
+          ICC Profiles
+        </Checkbox>
+      </div>
+    )
+
     return (
       <Layout style={{ height: '100%' }} hasSider>
         <Layout.Content style={{ height: '100%' }}>
@@ -3914,6 +3939,7 @@ class SlideViewer extends React.Component<SlideViewerProps, SlideViewerState> {
               </Menu.SubMenu>
             )}
             {specimenMenu}
+            {iccProfilesMenu}
             {equipmentMenu}
             {opticalPathMenu}
             {presentationStateMenu}

types/dicom-microscopy-viewer/index.d.ts

@@ -222,6 +222,8 @@ declare module 'dicom-microscopy-viewer' {
       getAnnotationGroupMetadata (
         annotationGroupUID: string
       ): metadata.MicroscopyBulkSimpleAnnotations
+      toggleICCProfiles(): void;
+      getICCProfiles(): any[];
     }
 
     export interface OverviewImageViewerOptions {

yarn.lock

@@ -11408,9 +11408,9 @@ semver@^7.1.2, semver@^7.5.2:
     lru-cache "^6.0.0"
 
 semver@^7.3.5, semver@^7.3.7:
-  version "7.6.3"
-  resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.3.tgz#980f7b5550bc175fb4dc09403085627f9eb33143"
-  integrity sha512-oVekP1cKtI+CTDvHWYFUcMtsK/00wmAEfyqKfNdARm8u1wNVhSgaX7A8d4UuIlUI5e84iEwOhs7ZPYRmzU9U6A==
+  version "7.7.1"
+  resolved "https://registry.yarnpkg.com/semver/-/semver-7.7.1.tgz#abd5098d82b18c6c81f6074ff2647fd3e7220c9f"
+  integrity sha512-hlq8tAfn0m/61p4BVRcPzIGr6LKiMwo4VM6dGi6pt4qcRkmNzTcWq6eCEjEh+qXjkMDvPlOFFSGwQjoEa6gyMA==
 
 [email protected]:
   version "0.19.0"