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 { Types, metaData, utilities as csUtils } from '@cornerstonejs/core';
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import {
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AnnotationTool,
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annotation,
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drawing,
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utilities,
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Types as cs3DToolsTypes,
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} from '@cornerstonejs/tools';
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import { getTrackingUniqueIdentifiersForElement } from './modules/dicomSRModule';
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import SCOORD_TYPES from '../constants/scoordTypes';
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export default class DICOMSRDisplayTool extends AnnotationTool {
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static toolName = 'DICOMSRDisplay';
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constructor(
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toolProps = {},
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defaultToolProps = {
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configuration: {},
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}
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) {
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super(toolProps, defaultToolProps);
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}
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_getTextBoxLinesFromLabels(labels) {
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// TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
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const labelLength = Math.min(labels.length, 3);
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const lines = [];
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for (let i = 0; i < labelLength; i++) {
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const labelEntry = labels[i];
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lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
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}
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return lines;
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}
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// This tool should not inherit from AnnotationTool and we should not need
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// to add the following lines.
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isPointNearTool = () => null;
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getHandleNearImagePoint = () => null;
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renderAnnotation = (
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enabledElement: Types.IEnabledElement,
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svgDrawingHelper: any
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): void => {
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const { viewport } = enabledElement;
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const { element } = viewport;
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let annotations = annotation.state.getAnnotations(
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element,
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this.getToolName()
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);
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// Todo: We don't need this anymore, filtering happens in triggerAnnotationRender
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if (!annotations?.length) {
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return;
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}
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annotations = this.filterInteractableAnnotationsForElement(
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element,
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annotations
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);
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if (!annotations?.length) {
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return;
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}
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const trackingUniqueIdentifiersForElement = getTrackingUniqueIdentifiersForElement(
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element
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);
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const {
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activeIndex,
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trackingUniqueIdentifiers,
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} = trackingUniqueIdentifiersForElement;
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const activeTrackingUniqueIdentifier =
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trackingUniqueIdentifiers[activeIndex];
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// Filter toolData to only render the data for the active SR.
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const filteredAnnotations = annotations.filter(annotation =>
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trackingUniqueIdentifiers.includes(
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annotation.data?.cachedStats?.TrackingUniqueIdentifier
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)
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);
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if (!viewport._actors?.size) {
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return;
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}
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const styleSpecifier: cs3DToolsTypes.AnnotationStyle.StyleSpecifier = {
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toolGroupId: this.toolGroupId,
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toolName: this.getToolName(),
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viewportId: enabledElement.viewport.id,
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};
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for (let i = 0; i < filteredAnnotations.length; i++) {
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const annotation = filteredAnnotations[i];
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const annotationUID = annotation.annotationUID;
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const { renderableData } = annotation.data.cachedStats;
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const { label, cachedStats } = annotation.data;
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const { referencedImageId } = annotation.metadata;
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styleSpecifier.annotationUID = annotationUID;
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const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
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const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
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const color =
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cachedStats.TrackingUniqueIdentifier === activeTrackingUniqueIdentifier
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? 'rgb(0, 255, 0)'
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: this.getStyle('color', styleSpecifier, annotation);
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const options = {
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color,
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lineDash,
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lineWidth,
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};
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Object.keys(renderableData).forEach(GraphicType => {
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const renderableDataForGraphicType = renderableData[GraphicType];
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let renderMethod;
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switch (GraphicType) {
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case SCOORD_TYPES.POINT:
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renderMethod = this.renderPoint;
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break;
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case SCOORD_TYPES.MULTIPOINT:
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renderMethod = this.renderMultipoint;
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break;
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case SCOORD_TYPES.POLYLINE:
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renderMethod = this.renderPolyLine;
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break;
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case SCOORD_TYPES.CIRCLE:
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renderMethod = this.renderEllipse;
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break;
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case SCOORD_TYPES.ELLIPSE:
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renderMethod = this.renderEllipse;
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break;
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default:
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throw new Error(`Unsupported GraphicType: ${GraphicType}`);
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}
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const canvasCoordinates = renderMethod(
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svgDrawingHelper,
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viewport,
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renderableDataForGraphicType,
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annotationUID,
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referencedImageId,
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options
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);
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if (!canvasCoordinates) {
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return;
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}
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const textLines = this._getTextBoxLinesFromLabels(label);
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let canvasCornersToUseForTextBox = canvasCoordinates;
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if (GraphicType === SCOORD_TYPES.ELLIPSE) {
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canvasCornersToUseForTextBox = utilities.math.ellipse.getCanvasEllipseCorners(
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canvasCoordinates
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);
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}
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const canvasTextBoxCoords = utilities.drawing.getTextBoxCoordsCanvas(
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canvasCornersToUseForTextBox
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);
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annotation.data.handles.textBox.worldPosition = viewport.canvasToWorld(
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canvasTextBoxCoords
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);
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const textBoxPosition = viewport.worldToCanvas(
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annotation.data.handles.textBox.worldPosition
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);
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const textBoxUID = '1';
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const textBoxOptions = this.getLinkedTextBoxStyle(
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styleSpecifier,
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annotation
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);
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const boundingBox = drawing.drawLinkedTextBox(
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svgDrawingHelper,
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annotationUID,
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textBoxUID,
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textLines,
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textBoxPosition,
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canvasCoordinates,
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{},
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{
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...textBoxOptions,
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color,
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}
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);
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const { x: left, y: top, width, height } = boundingBox;
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annotation.data.handles.textBox.worldBoundingBox = {
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topLeft: viewport.canvasToWorld([left, top]),
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topRight: viewport.canvasToWorld([left + width, top]),
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bottomLeft: viewport.canvasToWorld([left, top + height]),
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bottomRight: viewport.canvasToWorld([left + width, top + height]),
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};
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});
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}
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};
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renderPolyLine(
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svgDrawingHelper,
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viewport,
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renderableData,
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annotationUID,
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referencedImageId,
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options
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) {
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// Todo: this needs to use the drawPolyLine from cs3D since it is implemented
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// now, before it was implemented with a loop over drawLine which is hacky
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let canvasCoordinates;
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renderableData.map((data, index) => {
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canvasCoordinates = data.map(p => viewport.worldToCanvas(p));
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if (canvasCoordinates.length === 2) {
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const lineUID = `${index}`;
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drawing.drawLine(
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svgDrawingHelper,
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annotationUID,
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lineUID,
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canvasCoordinates[0],
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canvasCoordinates[1],
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{
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color: options.color,
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width: options.lineWidth,
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}
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);
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} else {
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throw new Error('Drawing polyline for SR not yet implemented');
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}
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});
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return canvasCoordinates; // used for drawing textBox
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}
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renderMultipoint(
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svgDrawingHelper,
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viewport,
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renderableData,
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annotationUID,
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referencedImageId,
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options
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) {
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let canvasCoordinates;
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renderableData.map((data, index) => {
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canvasCoordinates = data.map(p => viewport.worldToCanvas(p));
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const handleGroupUID = '0';
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drawing.drawHandles(
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svgDrawingHelper,
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annotationUID,
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handleGroupUID,
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canvasCoordinates,
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{
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color: options.color,
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}
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);
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});
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}
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renderPoint(
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svgDrawingHelper,
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viewport,
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renderableData,
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annotationUID,
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referencedImageId,
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options
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) {
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const canvasCoordinates = [];
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renderableData.map((data, index) => {
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const point = data[0];
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// This gives us one point for arrow
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canvasCoordinates.push(viewport.worldToCanvas(point));
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// We get the other point for the arrow by using the image size
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const imagePixelModule = metaData.get(
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'imagePixelModule',
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referencedImageId
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);
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let xOffset = 10;
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let yOffset = 10;
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if (imagePixelModule) {
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const { columns, rows } = imagePixelModule;
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xOffset = columns / 10;
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yOffset = rows / 10;
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}
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const imagePoint = csUtils.worldToImageCoords(referencedImageId, point);
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const arrowEnd = csUtils.imageToWorldCoords(referencedImageId, [
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imagePoint[0] + xOffset,
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imagePoint[1] + yOffset,
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]);
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canvasCoordinates.push(viewport.worldToCanvas(arrowEnd));
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const arrowUID = `${index}`;
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// Todo: handle drawing probe as probe, currently we are drawing it as an arrow
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drawing.drawArrow(
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svgDrawingHelper,
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annotationUID,
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arrowUID,
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canvasCoordinates[1],
|
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canvasCoordinates[0],
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{
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color: options.color,
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width: options.lineWidth,
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}
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);
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});
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|
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return canvasCoordinates; // used for drawing textBox
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}
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|
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renderEllipse(
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svgDrawingHelper,
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viewport,
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renderableData,
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annotationUID,
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referencedImageId,
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options
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) {
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let canvasCoordinates;
|
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renderableData.map((data, index) => {
|
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if (data.length === 0) {
|
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// since oblique ellipse is not supported for hydration right now
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// we just return
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return;
|
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}
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const ellipsePointsWorld = data;
|
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canvasCoordinates = ellipsePointsWorld.map(p =>
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viewport.worldToCanvas(p)
|
||||
);
|
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|
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const canvasCorners = <Array<Types.Point2>>(
|
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utilities.math.ellipse.getCanvasEllipseCorners(canvasCoordinates)
|
||||
);
|
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|
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const lineUID = `${index}`;
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drawing.drawEllipse(
|
||||
svgDrawingHelper,
|
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annotationUID,
|
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lineUID,
|
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canvasCorners[0],
|
||||
canvasCorners[1],
|
||||
{
|
||||
color: options.color,
|
||||
width: options.lineWidth,
|
||||
}
|
||||
);
|
||||
});
|
||||
|
||||
return canvasCoordinates;
|
||||
}
|
||||
}
|
||||
|
||||
const SHORT_HAND_MAP = {
|
||||
'Short Axis': 'W ',
|
||||
'Long Axis': 'L ',
|
||||
AREA: 'Area ',
|
||||
Length: '',
|
||||
CORNERSTONEFREETEXT: '',
|
||||
};
|
||||
|
||||
function _labelToShorthand(label) {
|
||||
const shortHand = SHORT_HAND_MAP[label];
|
||||
|
||||
if (shortHand !== undefined) {
|
||||
return shortHand;
|
||||
}
|
||||
|
||||
return label;
|
||||
}
|
||||
@@ -0,0 +1,64 @@
|
||||
import { getEnabledElement } from '@cornerstonejs/core';
|
||||
|
||||
const state = {
|
||||
TrackingUniqueIdentifier: null,
|
||||
trackingIdentifiersByViewportId: {},
|
||||
};
|
||||
|
||||
/**
|
||||
* This file is being used to store the per-viewport state of the SR tools,
|
||||
* Since, all the toolStates are added to the cornerstoneTools, when displaying the SRTools,
|
||||
* if there are two viewports rendering the same imageId, we don't want to show
|
||||
* the same SR annotation twice on irrelevant viewport, hence, we are storing the state
|
||||
* of the SR tools in state here, so that we can filter them later.
|
||||
*/
|
||||
|
||||
function setTrackingUniqueIdentifiersForElement(
|
||||
element,
|
||||
trackingUniqueIdentifiers,
|
||||
activeIndex = 0
|
||||
) {
|
||||
const enabledElement = getEnabledElement(element);
|
||||
const { viewport } = enabledElement;
|
||||
|
||||
state.trackingIdentifiersByViewportId[viewport.id] = {
|
||||
trackingUniqueIdentifiers,
|
||||
activeIndex,
|
||||
};
|
||||
}
|
||||
|
||||
function setActiveTrackingUniqueIdentifierForElement(
|
||||
element,
|
||||
TrackingUniqueIdentifier
|
||||
) {
|
||||
const enabledElement = getEnabledElement(element);
|
||||
const { viewport } = enabledElement;
|
||||
|
||||
const trackingIdentifiersForElement =
|
||||
state.trackingIdentifiersByViewportId[viewport.id];
|
||||
|
||||
if (trackingIdentifiersForElement) {
|
||||
const activeIndex = trackingIdentifiersForElement.trackingUniqueIdentifiers.findIndex(
|
||||
tuid => tuid === TrackingUniqueIdentifier
|
||||
);
|
||||
|
||||
trackingIdentifiersForElement.activeIndex = activeIndex;
|
||||
}
|
||||
}
|
||||
|
||||
function getTrackingUniqueIdentifiersForElement(element) {
|
||||
const enabledElement = getEnabledElement(element);
|
||||
const { viewport } = enabledElement;
|
||||
|
||||
if (state.trackingIdentifiersByViewportId[viewport.id]) {
|
||||
return state.trackingIdentifiersByViewportId[viewport.id];
|
||||
}
|
||||
|
||||
return { trackingUniqueIdentifiers: [] };
|
||||
}
|
||||
|
||||
export {
|
||||
setTrackingUniqueIdentifiersForElement,
|
||||
setActiveTrackingUniqueIdentifierForElement,
|
||||
getTrackingUniqueIdentifiersForElement,
|
||||
};
|
||||
@@ -0,0 +1,15 @@
|
||||
import DICOMSRDisplayTool from './DICOMSRDisplayTool';
|
||||
import SRLengthTool from './tools/SRLength';
|
||||
import SRBidirectional from './tools/SRBidirectional';
|
||||
import SREllipticalROI from './tools/SREllipticalROI';
|
||||
import SRArrowAnnotate from './tools/SRArrowAnnotate';
|
||||
|
||||
const toolNames = {
|
||||
DICOMSRDisplay: DICOMSRDisplayTool.toolName,
|
||||
SRLength: SRLengthTool.toolName,
|
||||
SRBidirectional: SRBidirectional.toolName,
|
||||
SREllipticalROI: SREllipticalROI.toolName,
|
||||
SRArrowAnnotate: SRArrowAnnotate.toolName,
|
||||
};
|
||||
|
||||
export default toolNames;
|
||||
@@ -0,0 +1,16 @@
|
||||
import { ArrowAnnotateTool } from '@cornerstonejs/tools';
|
||||
|
||||
/**
|
||||
* The reason we are extending ArrowAnnotateTool is to create a new tool for SR
|
||||
* viewport which basically has a different name. This is done since Cornerstone
|
||||
* has shifted from creating tool instances for each annotation, and we have ArrowAnnotate
|
||||
* mappers at the MeasurementService, so if we didn't do this, we would be mapping
|
||||
* the SR annotation to the MeasurementService (since there is a ArrowAnnotateTool mapper),
|
||||
* but with extending and renaming it, there is not mapper for SRArrowAnnotateTool; hence
|
||||
* no mapping; hence no new measurement, just temporary ones for the SR viewport.
|
||||
*/
|
||||
class SRArrowAnnotateTool extends ArrowAnnotateTool {
|
||||
static toolName = 'SRArrowAnnotate';
|
||||
}
|
||||
|
||||
export default SRArrowAnnotateTool;
|
||||
@@ -0,0 +1,16 @@
|
||||
import { BidirectionalTool } from '@cornerstonejs/tools';
|
||||
|
||||
/**
|
||||
* The reason we are extending BidirectionalTool is to create a new tool for SR
|
||||
* viewport which basically has a different name. This is done since Cornerstone
|
||||
* has shifted from creating tool instances for each annotation, and we have Bidirectional
|
||||
* mappers at the MeasurementService, so if we didn't do this, we would be mapping
|
||||
* the SR annotation to the MeasurementService (since there is a BidirectionalTool mapper),
|
||||
* but with extending and renaming it, there is not mapper for SRBidirectionalTool; hence
|
||||
* no mapping; hence no new measurement, just temporary ones for the SR viewport.
|
||||
*/
|
||||
class SRBidirectional extends BidirectionalTool {
|
||||
static toolName = 'SRBidirectional';
|
||||
}
|
||||
|
||||
export default SRBidirectional;
|
||||
@@ -0,0 +1,16 @@
|
||||
import { EllipticalROITool } from '@cornerstonejs/tools';
|
||||
|
||||
/**
|
||||
* The reason we are extending EllipticalROITool is to create a new tool for SR
|
||||
* viewport which basically has a different name. This is done since Cornerstone
|
||||
* has shifted from creating tool instances for each annotation, and we have EllipticalROI
|
||||
* mappers at the MeasurementService, so if we didn't do this, we would be mapping
|
||||
* the SR annotation to the MeasurementService (since there is a EllipticalROITool mapper),
|
||||
* but with extending and renaming it, there is not mapper for SREllipticalROITool; hence
|
||||
* no mapping; hence no new measurement, just temporary ones for the SR viewport.
|
||||
*/
|
||||
class SREllipticalROI extends EllipticalROITool {
|
||||
static toolName = 'SREllipticalROI';
|
||||
}
|
||||
|
||||
export default SREllipticalROI;
|
||||
@@ -0,0 +1,16 @@
|
||||
import { LengthTool } from '@cornerstonejs/tools';
|
||||
|
||||
/**
|
||||
* The reason we are extending LengthTool is to create a new tool for SR
|
||||
* viewport which basically has a different name. This is done since Cornerstone
|
||||
* has shifted from creating tool instances for each annotation, and we have Length
|
||||
* mappers at the MeasurementService, so if we didn't do this, we would be mapping
|
||||
* the SR annotation to the MeasurementService (since there is a LengthTool mapper),
|
||||
* but with extending and renaming it, there is not mapper for SRLengthTool; hence
|
||||
* no mapping; hence no new measurement, just temporary ones for the SR viewport.
|
||||
*/
|
||||
class SRLengthTool extends LengthTool {
|
||||
static toolName = 'SRLength';
|
||||
}
|
||||
|
||||
export default SRLengthTool;
|
||||
Reference in new issue
Block a user