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>
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@@ -0,0 +1,296 @@
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import { eventTarget } from '@cornerstonejs/core';
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import { Enums, annotation } from '@cornerstonejs/tools';
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import { DicomMetadataStore } from '@ohif/core';
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import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
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const { removeAnnotation } = annotation.state;
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const csToolsEvents = Enums.Events;
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const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
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const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
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const initMeasurementService = (
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MeasurementService,
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DisplaySetService,
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CornerstoneViewportService
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) => {
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/* Initialization */
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const {
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Length,
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Bidirectional,
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EllipticalROI,
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ArrowAnnotate,
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} = measurementServiceMappingsFactory(
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MeasurementService,
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DisplaySetService,
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CornerstoneViewportService
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);
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const csTools3DVer1MeasurementSource = MeasurementService.createSource(
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CORNERSTONE_3D_TOOLS_SOURCE_NAME,
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CORNERSTONE_3D_TOOLS_SOURCE_VERSION
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);
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/* Mappings */
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MeasurementService.addMapping(
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csTools3DVer1MeasurementSource,
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'Length',
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Length.matchingCriteria,
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Length.toAnnotation,
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Length.toMeasurement
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);
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MeasurementService.addMapping(
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csTools3DVer1MeasurementSource,
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'Bidirectional',
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Bidirectional.matchingCriteria,
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Bidirectional.toAnnotation,
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Bidirectional.toMeasurement
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);
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MeasurementService.addMapping(
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csTools3DVer1MeasurementSource,
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'EllipticalROI',
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EllipticalROI.matchingCriteria,
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EllipticalROI.toAnnotation,
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EllipticalROI.toMeasurement
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);
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MeasurementService.addMapping(
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csTools3DVer1MeasurementSource,
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'ArrowAnnotate',
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ArrowAnnotate.matchingCriteria,
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ArrowAnnotate.toAnnotation,
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ArrowAnnotate.toMeasurement
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);
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return csTools3DVer1MeasurementSource;
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};
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const connectToolsToMeasurementService = (
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MeasurementService,
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DisplaySetService,
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CornerstoneViewportService
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) => {
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const csTools3DVer1MeasurementSource = initMeasurementService(
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MeasurementService,
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DisplaySetService,
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CornerstoneViewportService
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);
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connectMeasurementServiceToTools(
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MeasurementService,
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CornerstoneViewportService,
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csTools3DVer1MeasurementSource
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);
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const { annotationToMeasurement, remove } = csTools3DVer1MeasurementSource;
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//
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function addMeasurement(csToolsEvent) {
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try {
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const annotationAddedEventDetail = csToolsEvent.detail;
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const {
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annotation: { metadata, annotationUID },
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} = annotationAddedEventDetail;
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const { toolName } = metadata;
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// To force the measurementUID be the same as the annotationUID
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// Todo: this should be changed when a measurement can include multiple annotations
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// in the future
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annotationAddedEventDetail.uid = annotationUID;
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annotationToMeasurement(toolName, annotationAddedEventDetail);
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} catch (error) {
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console.warn('Failed to update measurement:', error);
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}
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}
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function updateMeasurement(csToolsEvent) {
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try {
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const annotationModifiedEventDetail = csToolsEvent.detail;
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const {
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annotation: { metadata, annotationUID },
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} = annotationModifiedEventDetail;
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// If the measurement hasn't been added, don't modify it
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const measurement = MeasurementService.getMeasurement(annotationUID);
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if (!measurement) {
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return;
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}
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const { toolName } = metadata;
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annotationModifiedEventDetail.uid = annotationUID;
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annotationToMeasurement(toolName, annotationModifiedEventDetail);
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} catch (error) {
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console.warn('Failed to update measurement:', error);
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}
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}
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/**
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* When csTools fires a removed event, remove the same measurement
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* from the measurement service
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*
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* @param {*} csToolsEvent
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*/
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function removeMeasurement(csToolsEvent) {
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try {
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try {
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const annotationRemovedEventDetail = csToolsEvent.detail;
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const {
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annotation: { annotationUID },
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} = annotationRemovedEventDetail;
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const measurement = MeasurementService.getMeasurement(annotationUID);
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if (measurement) {
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console.log('~~ removeEvt', csToolsEvent);
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remove(annotationUID, annotationRemovedEventDetail);
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}
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} catch (error) {
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console.warn('Failed to update measurement:', error);
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}
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} catch (error) {
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console.warn('Failed to remove measurement:', error);
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}
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}
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// on display sets added, check if there are any measurements in measurement service that need to be
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// put into cornerstone tools
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const completedEvt = csToolsEvents.ANNOTATION_COMPLETED;
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const updatedEvt = csToolsEvents.ANNOTATION_MODIFIED;
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const removedEvt = csToolsEvents.ANNOTATION_REMOVED;
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eventTarget.addEventListener(completedEvt, addMeasurement);
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eventTarget.addEventListener(updatedEvt, updateMeasurement);
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eventTarget.addEventListener(removedEvt, removeMeasurement);
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return csTools3DVer1MeasurementSource;
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};
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const connectMeasurementServiceToTools = (
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MeasurementService,
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CornerstoneViewportService,
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measurementSource
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) => {
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const {
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MEASUREMENT_REMOVED,
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MEASUREMENTS_CLEARED,
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MEASUREMENT_UPDATED,
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RAW_MEASUREMENT_ADDED,
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} = MeasurementService.EVENTS;
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const csTools3DVer1MeasurementSource = MeasurementService.getSource(
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CORNERSTONE_3D_TOOLS_SOURCE_NAME,
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CORNERSTONE_3D_TOOLS_SOURCE_VERSION
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);
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MeasurementService.subscribe(MEASUREMENTS_CLEARED, ({ measurements }) => {
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if (!Object.keys(measurements).length) {
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return;
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}
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for (const measurement of Object.values(measurements)) {
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const { uid, source } = measurement;
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if (source.name !== CORNERSTONE_3D_TOOLS_SOURCE_NAME) {
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continue;
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}
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removeAnnotation(uid);
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}
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});
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MeasurementService.subscribe(
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MEASUREMENT_UPDATED,
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({ source, measurement, notYetUpdatedAtSource }) => {
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if (source.name !== CORNERSTONE_3D_TOOLS_SOURCE_NAME) {
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return;
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}
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if (notYetUpdatedAtSource === false) {
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// This event was fired by cornerstone telling the measurement service to sync.
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// Already in sync.
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return;
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}
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const { uid, label } = measurement;
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const sourceAnnotation = annotation.state.getAnnotation(uid);
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const { data, metadata } = sourceAnnotation;
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if (!data) {
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return;
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}
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if (data.label !== label) {
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data.label = label;
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}
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if (metadata.toolName === 'ArrowAnnotate') {
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data.text = label;
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}
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// Todo: trigger render for annotation
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}
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);
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MeasurementService.subscribe(
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RAW_MEASUREMENT_ADDED,
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({ source, measurement, data, dataSource }) => {
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if (source.name !== CORNERSTONE_3D_TOOLS_SOURCE_NAME) {
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return;
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}
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const {
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referenceSeriesUID,
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referenceStudyUID,
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SOPInstanceUID,
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} = measurement;
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const instance = DicomMetadataStore.getInstance(
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referenceStudyUID,
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referenceSeriesUID,
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SOPInstanceUID
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);
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const imageId = dataSource.getImageIdsForInstance({ instance });
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const annotationManager = annotation.state.getDefaultAnnotationManager();
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annotationManager.addAnnotation({
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annotationUID: measurement.uid,
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highlighted: false,
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isLocked: false,
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invalidated: false,
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metadata: {
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toolName: measurement.toolName,
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FrameOfReferenceUID: measurement.FrameOfReferenceUID,
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referencedImageId: imageId,
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},
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data: {
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text: data.annotation.data.text,
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handles: { ...data.annotation.data.handles },
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cachedStats: { ...data.annotation.data.cachedStats },
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label: data.annotation.data.label,
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},
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});
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}
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);
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MeasurementService.subscribe(
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MEASUREMENT_REMOVED,
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({ source, measurement: removedMeasurementId }) => {
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if (source?.name && source.name !== CORNERSTONE_3D_TOOLS_SOURCE_NAME) {
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return;
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}
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removeAnnotation(removedMeasurementId);
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const renderingEngine = CornerstoneViewportService.getRenderingEngine();
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// Note: We could do a better job by triggering the render on the
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// viewport itself, but the removeAnnotation does not include that info...
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renderingEngine.render();
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}
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);
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};
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export {
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initMeasurementService,
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connectToolsToMeasurementService,
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connectMeasurementServiceToTools,
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};
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