feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more (#3015)
* feat: add initial sop class handler for SEG * feat: move segmentation service * update segmentation service methods * fix: viewport data structure * feat: Add initial render for the DICOM SEG for each displaySet * fix: various wrong architectural dependencies between services * feat: initial separate SEG display in each viewport * feat: refactore viewport action bar * initial work for SEG hydration * fix: various bugs regarding drag and dropping different viewports * fix: rendering issues for multiple seg displaysets * fix: bugs for thumbnail and hydration * feat: fix the initial segment color * update after rebase * feat: initial design for the segmentation group table * feat: initial new design for the segmentation panel * feat: segmentation panel * feat: make segmentation appear on all related viewports * fix: segmentation load bug based on functional groups * initial work for segmentation crosshairs * fix: various stylings and functionality * fix: various stylings for the seg panel * fix: overflow styles * feat: add more ui components * feat: added segmentation config * feat: add jump to segment * feat: add jump to segment for DICOM SEG viewport * fix: bugs after rebase * feat: jump in segmentation viewport * fix: mpr support for seg * feat: add more icons * feat: new icons * feat: add new side panel * feat: add segmentation config * feat: add loading indicator to ohif * feat: make hanging protocols follow matching rules for viewports * feat: enhance drag and drop to be hanging protocol aware * fix: mpr restore previous layout * fix: crosshairs toggle * fix: add auth headers to the dicom loader via dicomwebclient * fix: bug for crosshairs toggle in mpr * fix: seg viewport reusing old toolGroup * feat: add loading animation with lottie * fix: various bugs for Segmentation hydration in mpr * feat: change outline alpha to outline opacity * feat: loading indicator for seg viewport * fix: various segmentation group styles * fix: local mode for seg * feat: add animation for the highlight * fix: loading indicatro to show segment indices * feat: enhance modality drop down ui * fix: panels * fix: download form * fix: layout shift in loading indicator * fix: loading indicator to have correct values * fix: update software number * fix: image jump between MPR and default * fix: segmentation cleanup and cine service cleanup * fix: segmentation toolgroup clena up * fix: highlight interval should not trigger again * fix: issue with multiframe sorting * rename: change onSeriesChange to onArrowsClick * fix: buttons for tmtv and layout shift * fix: various bugs wrt crosshairs * fix: crosshairs re init on reset camera * fix: middle slice calculation different from cs middle reset camera * fix: reset camera should reset viewport camera * fix: loading segments in MPR mode * fix: tmtv hp back to before * fix: layout shift * feat: orientation markers for volume viewport * fix: capture for volume viewports * fix: memory leak for back to worklist * fix: loading bar bg color * fix: side panel for only one panel * fix: react select style in production * fix: various styling for segmentation groups * fix: various ui styles * feat: add new segmentation config styles * fix: hover state for segmentation item * fix: side panel layout shift * temp add panels * try to fix scrollbar for thimbnail * fix: scroll not appearing for side panels * feat: changed styles for scrollbar * feat: add cpu fallback warning * fix: webworker destroy * fix: select styles * fix: orientation marker color and position * fix: capture screenshot for volume viewports * fix: hide segment visibility on mpr * fix: reloading an already loaded seg displayset * feat: add is equal * fix: mpr jump to measurements * apply review comments * fix: optimization for the segmentation load * fix: remove unnecessary context menu and hp service reset * fix: segmentation service wrt brush settings * feat: initial work for the stack synchronization * fix: add validateDisplaySetSelectorsForNewDisplaySets to make sure drag and drop can follow requirements * fix: various react proptypes * fix: thumbnails for the tmtv and change default props to default params * feat: make showing loading indicator configurable and add docs * bump versions and add more docs * fix demo * update cornerstone versions * apply review comments * feat: add reference lines * fix build * fix unit tests * add reference lines icon * fix: e2e tests * fix static wado config * docs: add segmentation service docs * fix: docker build * fix: keep camera and bump versions * Try re-enabling minification to fix deploy previews Co-authored-by: Erik Ziegler <erik.sweed@gmail.com>
This commit is contained in:
AlirezaandErik Ziegler authored and GitHub committed
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@@ -1,34 +1,44 @@
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import {
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getEnabledElement,
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StackViewport,
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volumeLoader,
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cache,
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utilities as csUtils,
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} from '@cornerstonejs/core';
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import {
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ToolGroupManager,
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Enums,
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segmentation,
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utilities as csToolsUtils,
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utilities as cstUtils,
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segmentation as cstSegmentation,
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ReferenceLinesTool,
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synchronizers as cstSynchronizers,
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} from '@cornerstonejs/tools';
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import { Types } from '@ohif/core';
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import CornerstoneViewportDownloadForm from './utils/CornerstoneViewportDownloadForm';
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import { getEnabledElement as OHIFgetEnabledElement } from './state';
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import callInputDialog from './utils/callInputDialog';
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import { setColormap } from './utils/colormap/transferFunctionHelpers';
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import getProtocolViewportStructureFromGridViewports from './utils/getProtocolViewportStructureFromGridViewports';
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import removeToolGroupSegmentationRepresentations from './utils/removeToolGroupSegmentationRepresentations';
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import calculateViewportRegistrations from './utils/calculateViewportRegistrations';
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const MPR_TOOLGROUP_ID = 'mpr';
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// [ {
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// synchronizerId: string,
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// viewports: [ { viewportId: number, renderingEngineId: string, index: number } , ...]
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// ]}
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let STACK_IMAGE_SYNC_GROUPS_INFO = [];
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const commandsModule = ({ servicesManager }) => {
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const {
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ViewportGridService,
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ToolGroupService,
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DisplaySetService,
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SyncGroupService,
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CineService,
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ToolBarService,
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UIDialogService,
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CornerstoneViewportService,
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SegmentationService,
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DisplaySetService,
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HangingProtocolService,
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UINotificationService,
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} = servicesManager.services;
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@@ -133,34 +143,23 @@ const commandsModule = ({ servicesManager }) => {
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});
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viewport.render();
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},
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toggleCrosshairs({ toolGroupId, toggledState }) {
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const toolName = 'Crosshairs';
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// If it is Enabled
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if (toggledState) {
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actions.setToolActive({ toolName, toolGroupId });
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return;
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}
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const toolGroup = _getToolGroup(toolGroupId);
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if (!toolGroup) {
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return;
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}
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toolGroup.setToolDisabled(toolName);
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// Get the primary toolId from the ToolBarService and set it to active
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// Since it was set to passive if not already active
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const primaryActiveTool = ToolBarService.state.primaryToolId;
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if (
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toolGroup?.toolOptions[primaryActiveTool]?.mode ===
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Enums.ToolModes.Passive
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) {
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toolGroup.setToolActive(primaryActiveTool, {
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bindings: [{ mouseButton: Enums.MouseBindings.Primary }],
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});
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}
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},
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setToolActive: ({ toolName, toolGroupId = null }) => {
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if (toolName === 'Crosshairs') {
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const activeViewportToolGroup = _getToolGroup(null);
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if (!activeViewportToolGroup._toolInstances.Crosshairs) {
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UINotificationService.show({
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title: 'Crosshairs',
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message:
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'You need to be in a MPR view to use Crosshairs. Click on MPR button in the toolbar to activate it.',
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type: 'info',
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duration: 3000,
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});
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throw new Error('Crosshairs tool is not available in this viewport');
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}
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}
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const toolGroup = _getToolGroup(toolGroupId);
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if (!toolGroup) {
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@@ -298,8 +297,12 @@ const commandsModule = ({ servicesManager }) => {
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if (viewport instanceof StackViewport) {
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viewport.resetProperties();
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viewport.resetCamera();
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viewport.render();
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} else {
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// Todo: add reset properties for volume viewport
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viewport.resetCamera();
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}
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viewport.render();
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},
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scaleViewport: ({ direction }) => {
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const enabledElement = _getActiveViewportEnabledElement();
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@@ -331,59 +334,7 @@ const commandsModule = ({ servicesManager }) => {
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const { viewport } = enabledElement;
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const options = { delta: direction };
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csToolsUtils.scroll(viewport, options);
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},
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async createSegmentationForDisplaySet({ displaySetInstanceUID }) {
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const volumeId = displaySetInstanceUID;
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const segmentationUID = csUtils.uuidv4();
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const segmentationId = `${volumeId}::${segmentationUID}`;
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await volumeLoader.createAndCacheDerivedVolume(volumeId, {
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volumeId: segmentationId,
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});
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// Add the segmentations to state
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segmentation.addSegmentations([
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{
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segmentationId,
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representation: {
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// The type of segmentation
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type: Enums.SegmentationRepresentations.Labelmap,
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// The actual segmentation data, in the case of labelmap this is a
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// reference to the source volume of the segmentation.
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data: {
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volumeId: segmentationId,
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},
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},
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},
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]);
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return segmentationId;
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},
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async addSegmentationRepresentationToToolGroup({
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segmentationId,
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toolGroupId,
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representationType,
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}) {
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// // Add the segmentation representation to the toolgroup
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await segmentation.addSegmentationRepresentations(toolGroupId, [
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{
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segmentationId,
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type: representationType,
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},
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]);
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},
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getLabelmapVolumes: ({ segmentations }) => {
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if (!segmentations || !segmentations.length) {
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segmentations = SegmentationService.getSegmentations();
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}
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const labelmapVolumes = segmentations.map(segmentation => {
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return cache.getVolume(segmentation.id);
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});
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return labelmapVolumes;
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cstUtils.scroll(viewport, options);
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},
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setViewportColormap: ({
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viewportIndex,
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@@ -398,7 +349,7 @@ const commandsModule = ({ servicesManager }) => {
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const actorEntries = viewport.getActors();
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const actorEntry = actorEntries.find(actorEntry => {
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return actorEntry.uid === displaySetInstanceUID;
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return actorEntry.uid.includes(displaySetInstanceUID);
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});
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const { actor: volumeActor } = actorEntry;
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@@ -423,6 +374,254 @@ const commandsModule = ({ servicesManager }) => {
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setHangingProtocol: ({ protocolId }) => {
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HangingProtocolService.setProtocol(protocolId);
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},
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toggleMPR: ({ toggledState }) => {
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const { activeViewportIndex, viewports } = ViewportGridService.getState();
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const viewportDisplaySetInstanceUIDs =
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viewports[activeViewportIndex].displaySetInstanceUIDs;
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const errorCallback = error => {
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UINotificationService.show({
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title: 'Multiplanar reconstruction (MPR) ',
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message:
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'Cannot create MPR for this DisplaySet since it is not reconstructable.',
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type: 'info',
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duration: 3000,
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});
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};
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const cacheId = 'beforeMPR';
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if (toggledState) {
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ViewportGridService.setCachedLayout({
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cacheId,
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cachedLayout: ViewportGridService.getState(),
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});
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const matchDetails = {
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displaySetInstanceUIDs: viewportDisplaySetInstanceUIDs,
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};
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HangingProtocolService.setProtocol(
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MPR_TOOLGROUP_ID,
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matchDetails,
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errorCallback
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);
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return;
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}
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const { cachedLayout } = ViewportGridService.getState();
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if (!cachedLayout || !cachedLayout[cacheId]) {
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return;
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}
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const { viewports: cachedViewports, numRows, numCols } = cachedLayout[
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cacheId
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];
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// Todo: The following assumes that when turning off MPR we are applying the default
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// protocol which might not be the one that was used before MPR was turned on
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// In order to properly implement this logic, we should modify the hanging protocol
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// upon layout change with layout selector, and cache and restore it when turning
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// MPR on and off
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const viewportStructure = getProtocolViewportStructureFromGridViewports({
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viewports: cachedViewports,
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numRows,
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numCols,
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});
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const viewportSpecificMatch = cachedViewports.reduce(
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(acc, viewport, index) => {
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const {
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displaySetInstanceUIDs,
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viewportOptions,
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displaySetOptions,
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} = viewport;
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acc[index] = {
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displaySetInstanceUIDs,
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viewportOptions,
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displaySetOptions,
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};
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return acc;
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},
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{}
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);
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const defaultProtocol = HangingProtocolService.getProtocolById('default');
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// Todo: this assumes there is only one stage in the default protocol
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const defaultProtocolStage = defaultProtocol.stages[0];
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defaultProtocolStage.viewportStructure = viewportStructure;
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const { primaryToolId } = ToolBarService.state;
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const mprToolGroup = _getToolGroup(MPR_TOOLGROUP_ID);
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// turn off crosshairs if it is on
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if (
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primaryToolId === 'Crosshairs' ||
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mprToolGroup.getToolInstance('Crosshairs')?.mode ===
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Enums.ToolModes.Active
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) {
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const toolGroup = _getToolGroup(MPR_TOOLGROUP_ID);
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toolGroup.setToolDisabled('Crosshairs');
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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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}
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// clear segmentations if they exist
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removeToolGroupSegmentationRepresentations(MPR_TOOLGROUP_ID);
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HangingProtocolService.setProtocol(
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'default',
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viewportSpecificMatch,
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error => {
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UINotificationService.show({
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title: 'Multiplanar reconstruction (MPR) ',
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message:
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'Something went wrong while trying to restore the previous layout.',
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type: 'info',
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duration: 3000,
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});
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}
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);
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},
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toggleStackImageSync: ({ toggledState }) => {
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if (!toggledState) {
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STACK_IMAGE_SYNC_GROUPS_INFO.forEach(syncGroupInfo => {
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const { viewports, synchronizerId } = syncGroupInfo;
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viewports.forEach(({ viewportId, renderingEngineId }) => {
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SyncGroupService.removeViewportFromSyncGroup(
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viewportId,
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renderingEngineId,
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synchronizerId
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);
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});
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});
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return;
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}
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STACK_IMAGE_SYNC_GROUPS_INFO = [];
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// create synchronization groups and add viewports
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let { viewports } = ViewportGridService.getState();
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// filter empty viewports
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viewports = viewports.filter(
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viewport =>
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viewport.displaySetInstanceUIDs &&
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viewport.displaySetInstanceUIDs.length
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);
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// filter reconstructable viewports
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viewports = viewports.filter(viewport => {
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const { displaySetInstanceUIDs } = viewport;
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for (const displaySetInstanceUID of displaySetInstanceUIDs) {
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const displaySet = DisplaySetService.getDisplaySetByUID(
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displaySetInstanceUID
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);
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if (displaySet && displaySet.isReconstructable) {
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return true;
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}
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return false;
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}
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});
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const viewportsByOrientation = viewports.reduce((acc, viewport) => {
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const { viewportId, viewportType } = viewport.viewportOptions;
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if (viewportType !== 'stack') {
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console.warn('Viewport is not a stack, cannot sync images yet');
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return acc;
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}
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const { element } = CornerstoneViewportService.getViewportInfo(
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viewportId
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);
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const { viewport: csViewport, renderingEngineId } = getEnabledElement(
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element
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);
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const { viewPlaneNormal } = csViewport.getCamera();
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// Should we round here? I guess so, but not sure how much precision we need
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const orientation = viewPlaneNormal.map(v => Math.round(v)).join(',');
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if (!acc[orientation]) {
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acc[orientation] = [];
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}
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acc[orientation].push({ viewportId, renderingEngineId });
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return acc;
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}, {});
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// create synchronizer for each group
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Object.values(viewportsByOrientation).map(viewports => {
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let synchronizerId = viewports
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.map(({ viewportId }) => viewportId)
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.join(',');
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synchronizerId = `imageSync_${synchronizerId}`;
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calculateViewportRegistrations(viewports);
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viewports.forEach(({ viewportId, renderingEngineId }) => {
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SyncGroupService.addViewportToSyncGroup(
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viewportId,
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renderingEngineId,
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{
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type: 'stackimage',
|
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id: synchronizerId,
|
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source: true,
|
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target: true,
|
||||
}
|
||||
);
|
||||
});
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STACK_IMAGE_SYNC_GROUPS_INFO.push({
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synchronizerId,
|
||||
viewports,
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||||
});
|
||||
});
|
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},
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toggleReferenceLines: ({ toggledState }) => {
|
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const { activeViewportIndex } = ViewportGridService.getState();
|
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const viewportInfo = CornerstoneViewportService.getViewportInfoByIndex(
|
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activeViewportIndex
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);
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const viewportId = viewportInfo.getViewportId();
|
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const toolGroup = ToolGroupService.getToolGroupForViewport(viewportId);
|
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|
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if (!toggledState) {
|
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toolGroup.setToolDisabled(ReferenceLinesTool.toolName);
|
||||
}
|
||||
|
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toolGroup.setToolConfiguration(
|
||||
ReferenceLinesTool.toolName,
|
||||
{
|
||||
sourceViewportId: viewportId,
|
||||
},
|
||||
true // overwrite
|
||||
);
|
||||
toolGroup.setToolEnabled(ReferenceLinesTool.toolName);
|
||||
},
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||||
};
|
||||
|
||||
const definitions = {
|
||||
@@ -524,22 +723,6 @@ const commandsModule = ({ servicesManager }) => {
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
createSegmentationForDisplaySet: {
|
||||
commandFn: actions.createSegmentationForDisplaySet,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
addSegmentationRepresentationToToolGroup: {
|
||||
commandFn: actions.addSegmentationRepresentationToToolGroup,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
|
||||
getLabelmapVolumes: {
|
||||
commandFn: actions.getLabelmapVolumes,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
setViewportColormap: {
|
||||
commandFn: actions.setViewportColormap,
|
||||
storeContexts: [],
|
||||
@@ -550,6 +733,21 @@ const commandsModule = ({ servicesManager }) => {
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
toggleMPR: {
|
||||
commandFn: actions.toggleMPR,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
toggleStackImageSync: {
|
||||
commandFn: actions.toggleStackImageSync,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
toggleReferenceLines: {
|
||||
commandFn: actions.toggleReferenceLines,
|
||||
storeContexts: [],
|
||||
options: {},
|
||||
},
|
||||
};
|
||||
|
||||
return {
|
||||
|
||||
Reference in new issue
Block a user