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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import React, { useCallback, useContext, useEffect, useState } from 'react';
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import PropTypes from 'prop-types';
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import OHIF, { utils } from '@ohif/core';
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import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule';
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import {
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Notification,
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ViewportActionBar,
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useViewportGrid,
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useViewportDialog,
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} from '@ohif/ui';
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const { formatDate } = utils;
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const MEASUREMENT_TRACKING_EXTENSION_ID =
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'@ohif/extension-measurement-tracking';
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const SR_TOOLGROUP_BASE_NAME = 'SRToolGroup';
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function OHIFCornerstoneSRViewport(props) {
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const {
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children,
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dataSource,
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displaySets,
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viewportIndex,
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viewportLabel,
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servicesManager,
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extensionManager,
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} = props;
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const {
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DisplaySetService,
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CornerstoneViewportService,
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} = servicesManager.services;
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// SR viewport will always have a single display set
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if (displaySets.length > 1) {
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throw new Error('SR viewport should only have a single display set');
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}
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const srDisplaySet = displaySets[0];
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const [viewportGrid, viewportGridService] = useViewportGrid();
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const [viewportDialogState, viewportDialogApi] = useViewportDialog();
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const [measurementSelected, setMeasurementSelected] = useState(0);
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const [measurementCount, setMeasurementCount] = useState(1);
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const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState(
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null
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);
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const [
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referencedDisplaySetMetadata,
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setReferencedDisplaySetMetadata,
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] = useState(null);
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const [isHydrated, setIsHydrated] = useState(srDisplaySet.isHydrated);
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const [element, setElement] = useState(null);
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const { viewports, activeViewportIndex } = viewportGrid;
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// Optional hook into tracking extension, if present.
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let trackedMeasurements;
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let sendTrackedMeasurementsEvent;
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const hasMeasurementTrackingExtension = extensionManager.registeredExtensionIds.includes(
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MEASUREMENT_TRACKING_EXTENSION_ID
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);
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// TODO: this is a hook that fails if we register/de-register
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if (hasMeasurementTrackingExtension) {
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const contextModule = extensionManager.getModuleEntry(
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'@ohif/extension-measurement-tracking.contextModule.TrackedMeasurementsContext'
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);
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const useTrackedMeasurements = () => useContext(contextModule.context);
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[
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trackedMeasurements,
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sendTrackedMeasurementsEvent,
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] = useTrackedMeasurements();
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}
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/**
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* Store the tracking identifiers per viewport in order to be able to
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* show the SR measurements on the referenced image on the correct viewport,
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* when multiple viewports are used.
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*/
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const setTrackingIdentifiers = useCallback(
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measurementSelected => {
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const { measurements } = srDisplaySet;
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setTrackingUniqueIdentifiersForElement(
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element,
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measurements.map(measurement => measurement.TrackingUniqueIdentifier),
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measurementSelected
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);
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},
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[element, measurementSelected, srDisplaySet]
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);
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/**
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* OnElementEnabled callback which is called after the cornerstoneExtension
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* has enabled the element. Note: we delegate all the image rendering to
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* cornerstoneExtension, so we don't need to do anything here regarding
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* the image rendering, element enabling etc.
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*/
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const onElementEnabled = evt => {
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setElement(evt.detail.element);
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};
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const updateViewport = useCallback(
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newMeasurementSelected => {
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const {
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StudyInstanceUID,
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displaySetInstanceUID,
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sopClassUids,
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} = srDisplaySet;
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if (!StudyInstanceUID || !displaySetInstanceUID) {
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return;
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}
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if (sopClassUids && sopClassUids.length > 1) {
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// Todo: what happens if there are multiple SOP Classes? Why we are
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// not throwing an error?
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console.warn(
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'More than one SOPClassUID in the same series is not yet supported.'
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);
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}
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_getViewportReferencedDisplaySetData(
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srDisplaySet,
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newMeasurementSelected,
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DisplaySetService
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).then(({ referencedDisplaySet, referencedDisplaySetMetadata }) => {
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setMeasurementSelected(newMeasurementSelected);
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setActiveImageDisplaySetData(referencedDisplaySet);
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setReferencedDisplaySetMetadata(referencedDisplaySetMetadata);
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if (
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referencedDisplaySet.displaySetInstanceUID ===
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activeImageDisplaySetData?.displaySetInstanceUID
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) {
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const { measurements } = srDisplaySet;
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// it means that we have a new referenced display set, and the
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// imageIdIndex will handle it by updating the viewport, but if they
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// are the same we just need to use MeasurementService to jump to the
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// new measurement
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const viewportInfo = CornerstoneViewportService.getViewportInfoByIndex(
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viewportIndex
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);
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const csViewport = CornerstoneViewportService.getCornerstoneViewport(
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viewportInfo.getViewportId()
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);
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const imageIds = csViewport.getImageIds();
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const imageIdIndex = imageIds.indexOf(
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measurements[newMeasurementSelected].imageId
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);
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if (imageIdIndex !== -1) {
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csViewport.setImageIdIndex(imageIdIndex);
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}
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}
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});
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},
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[dataSource, srDisplaySet, activeImageDisplaySetData, viewportIndex]
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);
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const getCornerstoneViewport = useCallback(() => {
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if (!activeImageDisplaySetData) {
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return null;
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}
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const { component: Component } = extensionManager.getModuleEntry(
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'@ohif/extension-cornerstone.viewportModule.cornerstone'
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);
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const { measurements } = srDisplaySet;
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const measurement = measurements[measurementSelected];
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if (!measurement) {
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return null;
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}
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const initialImageIndex = activeImageDisplaySetData.images.findIndex(
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image => image.imageId === measurement.imageId
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);
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return (
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<Component
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{...props}
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// should be passed second since we don't want SR displaySet to
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// override the activeImageDisplaySetData
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displaySets={[activeImageDisplaySetData]}
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viewportOptions={{
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toolGroupId: `${SR_TOOLGROUP_BASE_NAME}`,
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}}
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onElementEnabled={onElementEnabled}
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initialImageIndex={initialImageIndex}
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></Component>
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);
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}, [activeImageDisplaySetData, viewportIndex, measurementSelected]);
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const onMeasurementChange = useCallback(
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direction => {
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let newMeasurementSelected = measurementSelected;
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if (direction === 'right') {
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newMeasurementSelected++;
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if (newMeasurementSelected >= measurementCount) {
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newMeasurementSelected = 0;
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}
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} else {
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newMeasurementSelected--;
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if (newMeasurementSelected < 0) {
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newMeasurementSelected = measurementCount - 1;
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}
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}
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setTrackingIdentifiers(newMeasurementSelected);
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updateViewport(newMeasurementSelected);
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},
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[
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measurementSelected,
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measurementCount,
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updateViewport,
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setTrackingIdentifiers,
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]
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);
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/**
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Cleanup the SR viewport when the viewport is destroyed
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*/
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useEffect(() => {
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const onDisplaySetsRemovedSubscription = DisplaySetService.subscribe(
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DisplaySetService.EVENTS.DISPLAY_SETS_REMOVED,
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({ displaySetInstanceUIDs }) => {
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const activeViewport = viewports[activeViewportIndex];
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if (
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displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)
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) {
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viewportGridService.setDisplaySetsForViewport({
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viewportIndex: activeViewportIndex,
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displaySetInstanceUIDs: [],
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});
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}
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}
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);
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return () => {
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onDisplaySetsRemovedSubscription.unsubscribe();
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};
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}, []);
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/**
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* Loading the measurements from the SR viewport, which goes through the
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* isHydratable check, the outcome for the isHydrated state here is always FALSE
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* since we don't do the hydration here. Todo: can't we just set it as false? why
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* we are changing the state here? isHydrated is always false at this stage, and
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* if it is hydrated we don't event use the SR viewport.
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*/
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useEffect(() => {
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if (!srDisplaySet.isLoaded) {
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srDisplaySet.load();
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}
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setIsHydrated(srDisplaySet.isHydrated);
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const numMeasurements = srDisplaySet.measurements.length;
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setMeasurementCount(numMeasurements);
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}, [srDisplaySet]);
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/**
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* Hook to update the tracking identifiers when the selected measurement changes or
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* the element changes
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*/
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useEffect(() => {
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if (!element || !srDisplaySet.isLoaded) {
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return;
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}
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setTrackingIdentifiers(measurementSelected);
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}, [measurementSelected, element, setTrackingIdentifiers, srDisplaySet]);
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/**
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* Todo: what is this, not sure what it does regarding the react aspect,
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* it is updating a local variable? which is not state.
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*/
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let isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
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useEffect(() => {
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isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
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}, [trackedMeasurements]);
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/**
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* Data fetching for the SR displaySet, which updates the measurements and
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* also gets the referenced image displaySet that SR is based on.
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*/
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useEffect(() => {
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updateViewport(measurementSelected);
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}, [dataSource, srDisplaySet]);
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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let childrenWithProps = null;
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if (!activeImageDisplaySetData || !referencedDisplaySetMetadata) {
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return null;
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}
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if (children && children.length) {
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childrenWithProps = children.map((child, index) => {
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return (
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child &&
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React.cloneElement(child, {
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viewportIndex,
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key: index,
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})
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);
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});
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}
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const { Modality } = srDisplaySet;
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const {
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PatientID,
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PatientName,
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PatientSex,
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PatientAge,
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SliceThickness,
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ManufacturerModelName,
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StudyDate,
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SeriesDescription,
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SpacingBetweenSlices,
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SeriesNumber,
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} = referencedDisplaySetMetadata;
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// TODO -> disabled double click for now: onDoubleClick={_onDoubleClick}
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return (
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<>
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<ViewportActionBar
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onDoubleClick={evt => {
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evt.stopPropagation();
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evt.preventDefault();
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}}
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onPillClick={() => {
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sendTrackedMeasurementsEvent('RESTORE_PROMPT_HYDRATE_SR', {
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displaySetInstanceUID: srDisplaySet.displaySetInstanceUID,
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viewportIndex,
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});
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}}
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onSeriesChange={onMeasurementChange}
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studyData={{
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label: viewportLabel,
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useAltStyling: true,
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isTracked: false,
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isLocked,
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isRehydratable: srDisplaySet.isRehydratable,
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isHydrated,
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studyDate: formatDate(StudyDate),
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currentSeries: SeriesNumber,
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seriesDescription: SeriesDescription,
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modality: Modality,
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patientInformation: {
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patientName: PatientName
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? OHIF.utils.formatPN(PatientName.Alphabetic)
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: '',
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patientSex: PatientSex || '',
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patientAge: PatientAge || '',
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MRN: PatientID || '',
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thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
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spacing:
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SpacingBetweenSlices !== undefined
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? `${SpacingBetweenSlices.toFixed(2)}mm`
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: '',
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scanner: ManufacturerModelName || '',
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},
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}}
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/>
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<div className="relative flex flex-row w-full h-full overflow-hidden">
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{getCornerstoneViewport()}
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<div className="absolute w-full">
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{viewportDialogState.viewportIndex === viewportIndex && (
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<Notification
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message={viewportDialogState.message}
|
||||
type={viewportDialogState.type}
|
||||
actions={viewportDialogState.actions}
|
||||
onSubmit={viewportDialogState.onSubmit}
|
||||
onOutsideClick={viewportDialogState.onOutsideClick}
|
||||
/>
|
||||
)}
|
||||
</div>
|
||||
{childrenWithProps}
|
||||
</div>
|
||||
</>
|
||||
);
|
||||
}
|
||||
|
||||
OHIFCornerstoneSRViewport.propTypes = {
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||||
displaySets: PropTypes.arrayOf(PropTypes.object),
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viewportIndex: PropTypes.number.isRequired,
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||||
dataSource: PropTypes.object,
|
||||
children: PropTypes.node,
|
||||
customProps: PropTypes.object,
|
||||
};
|
||||
|
||||
OHIFCornerstoneSRViewport.defaultProps = {
|
||||
customProps: {},
|
||||
};
|
||||
|
||||
async function _getViewportReferencedDisplaySetData(
|
||||
displaySet,
|
||||
measurementSelected,
|
||||
DisplaySetService
|
||||
) {
|
||||
const { measurements } = displaySet;
|
||||
const measurement = measurements[measurementSelected];
|
||||
|
||||
const { displaySetInstanceUID } = measurement;
|
||||
|
||||
const referencedDisplaySet = DisplaySetService.getDisplaySetByUID(
|
||||
displaySetInstanceUID
|
||||
);
|
||||
|
||||
const image0 = referencedDisplaySet.images[0];
|
||||
const referencedDisplaySetMetadata = {
|
||||
PatientID: image0.PatientID,
|
||||
PatientName: image0.PatientName,
|
||||
PatientSex: image0.PatientSex,
|
||||
PatientAge: image0.PatientAge,
|
||||
SliceThickness: image0.SliceThickness,
|
||||
StudyDate: image0.StudyDate,
|
||||
SeriesDescription: image0.SeriesDescription,
|
||||
SeriesInstanceUID: image0.SeriesInstanceUID,
|
||||
SeriesNumber: image0.SeriesNumber,
|
||||
ManufacturerModelName: image0.ManufacturerModelName,
|
||||
SpacingBetweenSlices: image0.SpacingBetweenSlices,
|
||||
};
|
||||
|
||||
return { referencedDisplaySetMetadata, referencedDisplaySet };
|
||||
}
|
||||
|
||||
// function _onDoubleClick() {
|
||||
// const cancelActiveManipulatorsForElement = cornerstoneTools.getModule(
|
||||
// 'manipulatorState'
|
||||
// ).setters.cancelActiveManipulatorsForElement;
|
||||
// const enabledElements = cornerstoneTools.store.state.enabledElements;
|
||||
// enabledElements.forEach(element => {
|
||||
// cancelActiveManipulatorsForElement(element);
|
||||
// });
|
||||
// }
|
||||
|
||||
export default OHIFCornerstoneSRViewport;
|
||||
Reference in new issue
Block a user