feat: cornerstone3D stack and volume viewports (#2787)
* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
This commit is contained in:
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@@ -0,0 +1,5 @@
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import packageJson from '../package.json';
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const id = packageJson.name;
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export { id };
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@@ -0,0 +1,206 @@
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import toolbarButtons from './toolbarButtons.js';
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import { hotkeys } from '@ohif/core';
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import { id } from './id';
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const configs = {
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Length: {},
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//
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};
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const ohif = {
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layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout',
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sopClassHandler: '@ohif/extension-default.sopClassHandlerModule.stack',
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hangingProtocols: '@ohif/extension-default.hangingProtocolModule.default',
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measurements: '@ohif/extension-default.panelModule.measure',
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thumbnailList: '@ohif/extension-default.panelModule.seriesList',
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};
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const cs3d = {
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viewport: '@ohif/extension-cornerstone.viewportModule.cornerstone',
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};
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const dicomsr = {
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sopClassHandler:
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'@ohif/extension-cornerstone-dicom-sr.sopClassHandlerModule.dicom-sr',
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viewport: '@ohif/extension-cornerstone-dicom-sr.viewportModule.dicom-sr',
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};
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const dicomvideo = {
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sopClassHandler:
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'@ohif/extension-dicom-video.sopClassHandlerModule.dicom-video',
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viewport: '@ohif/extension-dicom-video.viewportModule.dicom-video',
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};
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const dicompdf = {
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sopClassHandler: '@ohif/extension-dicom-pdf.sopClassHandlerModule.dicom-pdf',
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viewport: '@ohif/extension-dicom-pdf.viewportModule.dicom-pdf',
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};
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const extensionDependencies = {
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'@ohif/extension-default': '^3.0.0',
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'@ohif/extension-cornerstone': '^3.0.0',
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'@ohif/extension-cornerstone-dicom-sr': '^3.0.0',
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'@ohif/extension-dicom-pdf': '^3.0.1',
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'@ohif/extension-dicom-video': '^3.0.1',
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};
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function modeFactory({ modeConfiguration }) {
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return {
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id,
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routeName: 'viewer',
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displayName: 'Basic Viewer CS3D',
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/**
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* Lifecycle hooks
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*/
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onModeEnter: ({ servicesManager, extensionManager }) => {
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const { ToolBarService, ToolGroupService } = servicesManager.services;
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const utilityModule = extensionManager.getModuleEntry(
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'@ohif/extension-cornerstone.utilityModule.tools'
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);
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const { toolNames, Enums } = utilityModule.exports;
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const tools = {
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active: [
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{
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toolName: toolNames.WindowLevel,
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bindings: [{ mouseButton: Enums.MouseBindings.Primary }],
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},
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{
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toolName: toolNames.Pan,
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bindings: [{ mouseButton: Enums.MouseBindings.Auxiliary }],
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},
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{
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toolName: toolNames.Zoom,
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bindings: [{ mouseButton: Enums.MouseBindings.Secondary }],
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},
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{ toolName: toolNames.StackScrollMouseWheel, bindings: [] },
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],
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passive: [
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{ toolName: toolNames.Length },
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{ toolName: toolNames.Bidirectional },
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{ toolName: toolNames.Probe },
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{ toolName: toolNames.EllipticalROI },
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{ toolName: toolNames.RectangleROI },
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{ toolName: toolNames.StackScroll },
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],
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// enabled
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// disabled
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};
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const toolGroupId = 'default';
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ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, configs);
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let unsubscribe;
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const activateTool = () => {
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ToolBarService.recordInteraction({
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groupId: 'WindowLevel',
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itemId: 'WindowLevel',
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interactionType: 'tool',
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commands: [
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{
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commandName: 'setToolActive',
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commandOptions: {
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toolName: 'WindowLevel',
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},
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context: 'CORNERSTONE',
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},
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],
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});
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// We don't need to reset the active tool whenever a viewport is getting
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// added to the toolGroup.
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unsubscribe();
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};
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// Since we only have one viewport for the basic cs3d mode and it has
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// only one hanging protocol, we can just use the first viewport
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({ unsubscribe } = ToolGroupService.subscribe(
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ToolGroupService.EVENTS.VIEWPORT_ADDED,
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activateTool
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));
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ToolBarService.init(extensionManager);
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ToolBarService.addButtons(toolbarButtons);
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ToolBarService.createButtonSection('primary', [
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'MeasurementTools',
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'Zoom',
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'WindowLevel',
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'Pan',
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'Layout',
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'MoreTools',
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]);
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},
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onModeExit: ({ servicesManager }) => {
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const {
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ToolGroupService,
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MeasurementService,
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ToolBarService,
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} = servicesManager.services;
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ToolBarService.reset();
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MeasurementService.clearMeasurements();
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ToolGroupService.destroy();
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},
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validationTags: {
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study: [],
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series: [],
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},
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isValidMode: ({ modalities }) => {
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const modalities_list = modalities.split('\\');
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// Slide Microscopy modality not supported by basic mode yet
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return !modalities_list.includes('SM');
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},
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routes: [
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{
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path: 'viewer-cs3d',
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/*init: ({ servicesManager, extensionManager }) => {
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//defaultViewerRouteInit
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},*/
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layoutTemplate: ({ location, servicesManager }) => {
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return {
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id: ohif.layout,
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props: {
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// TODO: Should be optional, or required to pass empty array for slots?
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leftPanels: [ohif.thumbnailList],
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rightPanels: [ohif.measurements],
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viewports: [
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{
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namespace: cs3d.viewport,
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displaySetsToDisplay: [ohif.sopClassHandler],
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},
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{
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namespace: dicomvideo.viewport,
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displaySetsToDisplay: [dicomvideo.sopClassHandler],
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},
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{
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namespace: dicompdf.viewport,
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displaySetsToDisplay: [dicompdf.sopClassHandler],
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},
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],
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},
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};
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},
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},
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],
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extensions: extensionDependencies,
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hangingProtocols: [ohif.hangingProtocols],
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sopClassHandlers: [
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dicomvideo.sopClassHandler,
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ohif.sopClassHandler,
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dicompdf.sopClassHandler,
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dicomsr.sopClassHandler,
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],
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hotkeys: [...hotkeys.defaults.hotkeyBindings],
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};
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}
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const mode = {
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id,
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modeFactory,
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extensionDependencies,
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||||
};
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export default mode;
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@@ -0,0 +1,331 @@
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// TODO: torn, can either bake this here; or have to create a whole new button type
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// Only ways that you can pass in a custom React component for render :l
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||||
import {
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// ExpandableToolbarButton,
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// ListMenu,
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WindowLevelMenuItem,
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} from '@ohif/ui';
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import { defaults } from '@ohif/core';
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const { windowLevelPresets } = defaults;
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/**
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*
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* @param {*} type - 'tool' | 'action' | 'toggle'
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* @param {*} id
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* @param {*} icon
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* @param {*} label
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||||
*/
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function _createButton(type, id, icon, label, commands, tooltip) {
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return {
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id,
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icon,
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label,
|
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type,
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commands,
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tooltip,
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};
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}
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const _createActionButton = _createButton.bind(null, 'action');
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const _createToggleButton = _createButton.bind(null, 'toggle');
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const _createToolButton = _createButton.bind(null, 'tool');
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/**
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*
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* @param {*} preset - preset number (from above import)
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* @param {*} title
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* @param {*} subtitle
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*/
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function _createWwwcPreset(preset, title, subtitle) {
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return {
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id: preset.toString(),
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title,
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subtitle,
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type: 'action',
|
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commands: [
|
||||
{
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||||
commandName: 'setWindowLevel',
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commandOptions: {
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||||
...windowLevelPresets[preset],
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||||
},
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context: 'CORNERSTONE',
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||||
},
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||||
],
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||||
};
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||||
}
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const toolbarButtons = [
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||||
// Measurement
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||||
{
|
||||
id: 'MeasurementTools',
|
||||
type: 'ohif.splitButton',
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||||
props: {
|
||||
groupId: 'MeasurementTools',
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||||
isRadio: true, // ?
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||||
// Switch?
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||||
primary: _createToolButton(
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||||
'Length',
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||||
'tool-length',
|
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'Length',
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||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'Length',
|
||||
},
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||||
context: 'CORNERSTONE',
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||||
},
|
||||
],
|
||||
'Length'
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||||
),
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||||
secondary: {
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||||
icon: 'chevron-down',
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||||
label: '',
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||||
isActive: true,
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||||
tooltip: 'More Measure Tools',
|
||||
},
|
||||
items: [
|
||||
_createToolButton(
|
||||
'Length',
|
||||
'tool-length',
|
||||
'Length',
|
||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'Length',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Length Tool'
|
||||
),
|
||||
_createToolButton(
|
||||
'Bidirectional',
|
||||
'tool-bidirectional',
|
||||
'Bidirectional',
|
||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'Bidirectional',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Bidirectional Tool'
|
||||
),
|
||||
_createToolButton(
|
||||
'EllipticalROI',
|
||||
'tool-elipse',
|
||||
'Ellipse',
|
||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'EllipticalROI',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Ellipse Tool'
|
||||
),
|
||||
],
|
||||
},
|
||||
},
|
||||
// Zoom..
|
||||
{
|
||||
id: 'Zoom',
|
||||
type: 'ohif.radioGroup',
|
||||
props: {
|
||||
type: 'tool',
|
||||
icon: 'tool-zoom',
|
||||
label: 'Zoom',
|
||||
commands: [
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'Zoom',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
},
|
||||
},
|
||||
// Window Level + Presets...
|
||||
{
|
||||
id: 'WindowLevel',
|
||||
type: 'ohif.splitButton',
|
||||
props: {
|
||||
groupId: 'WindowLevel',
|
||||
primary: _createToolButton(
|
||||
'WindowLevel',
|
||||
'tool-window-level',
|
||||
'Window Level',
|
||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'WindowLevel',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Window Level'
|
||||
),
|
||||
secondary: {
|
||||
icon: 'chevron-down',
|
||||
label: 'W/L Manual',
|
||||
isActive: true,
|
||||
tooltip: 'W/L Presets',
|
||||
},
|
||||
isAction: true, // ?
|
||||
renderer: WindowLevelMenuItem,
|
||||
items: [
|
||||
_createWwwcPreset(1, 'Soft tissue', '400 / 40'),
|
||||
_createWwwcPreset(2, 'Lung', '1500 / -600'),
|
||||
_createWwwcPreset(3, 'Liver', '150 / 90'),
|
||||
_createWwwcPreset(4, 'Bone', '80 / 40'),
|
||||
_createWwwcPreset(5, 'Brain', '2500 / 480'),
|
||||
],
|
||||
},
|
||||
},
|
||||
// Pan...
|
||||
{
|
||||
id: 'Pan',
|
||||
type: 'ohif.radioGroup',
|
||||
props: {
|
||||
type: 'tool',
|
||||
icon: 'tool-move',
|
||||
label: 'Pan',
|
||||
commands: [
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'Pan',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
},
|
||||
},
|
||||
{
|
||||
id: 'Capture',
|
||||
type: 'ohif.action',
|
||||
props: {
|
||||
icon: 'tool-capture',
|
||||
label: 'Capture',
|
||||
type: 'action',
|
||||
commands: [
|
||||
{
|
||||
commandName: 'showDownloadViewportModal',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
},
|
||||
},
|
||||
{
|
||||
id: 'Layout',
|
||||
type: 'ohif.layoutSelector',
|
||||
},
|
||||
// More...
|
||||
{
|
||||
id: 'MoreTools',
|
||||
type: 'ohif.splitButton',
|
||||
props: {
|
||||
isRadio: true, // ?
|
||||
groupId: 'MoreTools',
|
||||
primary: _createActionButton(
|
||||
'Reset',
|
||||
'tool-reset',
|
||||
'Reset View',
|
||||
[
|
||||
{
|
||||
commandName: 'resetViewport',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Reset'
|
||||
),
|
||||
secondary: {
|
||||
icon: 'chevron-down',
|
||||
label: '',
|
||||
isActive: true,
|
||||
tooltip: 'More Tools',
|
||||
},
|
||||
items: [
|
||||
_createActionButton(
|
||||
'Reset',
|
||||
'tool-reset',
|
||||
'Reset View',
|
||||
[
|
||||
{
|
||||
commandName: 'resetViewport',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Reset'
|
||||
),
|
||||
_createActionButton(
|
||||
'rotate-right',
|
||||
'tool-rotate-right',
|
||||
'Rotate Right',
|
||||
[
|
||||
{
|
||||
commandName: 'rotateViewportCW',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Rotate +90'
|
||||
),
|
||||
_createActionButton(
|
||||
'flip-horizontal',
|
||||
'tool-flip-horizontal',
|
||||
'Flip Horizontally',
|
||||
[
|
||||
{
|
||||
commandName: 'flipViewportHorizontal',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Flip Horizontal'
|
||||
),
|
||||
_createToolButton(
|
||||
'StackScroll',
|
||||
'tool-stack-scroll',
|
||||
'Stack Scroll',
|
||||
[
|
||||
{
|
||||
commandName: 'setToolActive',
|
||||
commandOptions: {
|
||||
toolName: 'StackScroll',
|
||||
},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Stack Scroll'
|
||||
),
|
||||
_createActionButton(
|
||||
'invert',
|
||||
'tool-invert',
|
||||
'Invert',
|
||||
[
|
||||
{
|
||||
commandName: 'invertViewport',
|
||||
commandOptions: {},
|
||||
context: 'CORNERSTONE',
|
||||
},
|
||||
],
|
||||
'Invert Colors'
|
||||
),
|
||||
],
|
||||
},
|
||||
},
|
||||
];
|
||||
|
||||
export default toolbarButtons;
|
||||
Reference in new issue
Block a user