feat: cornerstone3D stack and volume viewports (#2787)
* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
This commit is contained in:
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+41669
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+11
-6
@@ -1,5 +1,5 @@
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import React from 'react';
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import { DICOMSR, DicomMetadataStore } from '@ohif/core';
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import { DicomMetadataStore } from '@ohif/core';
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/**
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*
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@@ -11,6 +11,7 @@ import { DICOMSR, DicomMetadataStore } from '@ohif/core';
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*/
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async function createReportAsync(
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servicesManager,
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commandsManager,
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dataSource,
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measurements,
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options
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@@ -29,11 +30,15 @@ async function createReportAsync(
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});
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try {
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const naturalizedReport = await DICOMSR.storeMeasurements(
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measurements,
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dataSource,
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['ArrowAnnotate'],
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options
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const naturalizedReport = await commandsManager.runCommand(
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'storeMeasurements',
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{
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measurementData: measurements,
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dataSource,
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additionalFindingTypes: ['ArrowAnnotate'],
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options,
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},
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'CORNERSTONE_STRUCTURED_REPORT'
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);
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// The "Mode" route listens for DicomMetadataStore changes
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File renamed without changes.
@@ -1,165 +0,0 @@
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import { DicomMetadataStore } from '@ohif/core';
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export default function downloadCSVReport(
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measurementData,
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StudyInstanceUID,
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referencedSeriesInstanceUIDs,
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MeasurementService
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) {
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const { VALUE_TYPES } = MeasurementService;
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if (measurementData.length === 0) {
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// Prevent download of report with no measurements.
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return;
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}
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const seriesMetadataMap = {};
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referencedSeriesInstanceUIDs.forEach(SeriesInstanceUID => {
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seriesMetadataMap[SeriesInstanceUID] = DicomMetadataStore.getSeries(
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StudyInstanceUID,
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SeriesInstanceUID
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);
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});
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const rows = [
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[
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'Patient ID',
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'Patient Name',
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'StudyInstanceUID',
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'SeriesInstanceUID',
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'SOPInstanceUID',
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'Label',
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'Long Axis (mm)',
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'Short Axis (mm)',
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'Length (mm)',
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'Area (mmˆ2)',
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'Mean',
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'StDev',
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'Units',
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],
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];
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measurementData.forEach(measurement => {
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switch (measurement.type) {
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case VALUE_TYPES.BIDIRECTIONAL:
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rows.push(_getBidirectionalRow(measurement, seriesMetadataMap));
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break;
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case VALUE_TYPES.ELLIPSE:
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rows.push(_getEllipseRow(measurement, seriesMetadataMap));
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break;
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case VALUE_TYPES.POINT:
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rows.push(_getAdditionalFindingRow(measurement, seriesMetadataMap));
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break;
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case VALUE_TYPES.POLYLINE:
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rows.push(_getLengthRow(measurement, seriesMetadataMap));
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}
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});
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let csvContent =
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'data:text/csv;charset=utf-8,' + rows.map(row => row.join(',')).join('\n');
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_createAndDownloadFile(csvContent);
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}
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function _getBidirectionalRow(measurement, seriesMetadataMap) {
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const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
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return [
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...commonRowItems,
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measurement.longestDiameter, // Long Axis (mm)
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measurement.shortestDiameter, // Short Axis (mm)
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];
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}
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function _getCommonRowItems(measurement, seriesMetadataMap) {
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const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
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const firstInstance = seriesMetadata.instances[0];
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const row = [
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firstInstance.PatientID, // Patient ID
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firstInstance.PatientName.Alphabetic, // PatientName
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measurement.referenceStudyUID, // StudyInstanceUID
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measurement.referenceSeriesUID, // SeriesInstanceUID
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measurement.SOPInstanceUID, // SOPInstanceUID
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measurement.label || '', // Label
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];
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return row;
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}
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function _getAdditionalFindingRow(measurement, seriesMetadataMap) {
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const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
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return [...commonRowItems];
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}
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function _getEllipseRow(measurement, seriesMetadataMap) {
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const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
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const blankColumns = ['', '', ''];
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const { area, mean, stdDev, unit } = _getEllipseStatsWithUnits(
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measurement,
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seriesMetadataMap
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);
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return [
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...commonRowItems,
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...blankColumns,
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area, // Area (mmˆ2)
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mean, // Mean
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stdDev, // StDev
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unit,
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];
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}
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function _getEllipseStatsWithUnits(measurement, seriesMetadataMap) {
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const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
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const firstInstance = seriesMetadata.instances[0];
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const modality = firstInstance.Modality;
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switch (modality) {
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case 'CT':
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return {
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mean: `${measurement.mean.toFixed(1)}`,
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stdDev: `${measurement.stdDev.toFixed(1)}`,
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area: measurement.area.toFixed(1),
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unit: 'HU',
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};
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case 'PT':
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if (measurement.meanSUV) {
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return {
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mean: `${measurement.meanSUV.toFixed(1)}`,
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stdDev: `${measurement.stdDevSUV.toFixed(1)}`,
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area: measurement.area.toFixed(1),
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unit: 'SUV',
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};
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}
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// If no SUV calculation then fallback to default.
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default:
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return {
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mean: `${measurement.mean.toFixed(1)}`,
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stdDev: `${measurement.stdDev.toFixed(1)}`,
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area: measurement.area.toFixed(1),
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unit: 'Pixel Values',
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};
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}
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}
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function _getLengthRow(measurement, seriesMetadataMap) {
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const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
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const blankColumns = ['', ''];
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return [...commonRowItems, ...blankColumns, measurement.length.toFixed(1)];
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}
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function _createAndDownloadFile(csvContent) {
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const encodedUri = encodeURI(csvContent);
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const link = document.createElement('a');
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link.setAttribute('href', encodedUri);
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link.setAttribute('download', 'MeasurementReport.csv');
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document.body.appendChild(link);
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link.click();
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document.body.removeChild(link);
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}
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@@ -1,36 +0,0 @@
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import csTools from 'cornerstone-tools';
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const toolsGroupedByType = {
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touch: [csTools.PanMultiTouchTool, csTools.ZoomTouchPinchTool],
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annotations: [
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csTools.ArrowAnnotateTool,
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csTools.BidirectionalTool,
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csTools.LengthTool,
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csTools.AngleTool,
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csTools.FreehandRoiTool,
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csTools.EllipticalRoiTool,
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csTools.DragProbeTool,
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csTools.RectangleRoiTool,
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],
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other: [
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csTools.PanTool,
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csTools.ZoomTool,
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csTools.WwwcTool,
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csTools.WwwcRegionTool,
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csTools.MagnifyTool,
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csTools.StackScrollTool,
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csTools.StackScrollMouseWheelTool,
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csTools.OverlayTool,
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],
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};
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export default function getTools() {
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const tools = [];
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Object.keys(toolsGroupedByType).forEach(toolsGroup =>
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tools.push(...toolsGroupedByType[toolsGroup])
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);
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return tools;
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}
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export { toolsGroupedByType };
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@@ -1,21 +0,0 @@
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import csTools from 'cornerstone-tools';
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export default function _setActiveAndPassiveToolsForElement(element, tools) {
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const BaseAnnotationTool = csTools.importInternal('base/BaseAnnotationTool');
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tools.forEach(tool => {
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if (tool.prototype instanceof BaseAnnotationTool) {
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// BaseAnnotationTool would likely come from csTools lib exports
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const toolName = new tool().name;
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csTools.setToolPassiveForElement(element, toolName); // there may be a better place to determine name; may not be on uninstantiated class
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}
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});
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csTools.setToolActiveForElement(element, 'Pan', { mouseButtonMask: 4 });
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csTools.setToolActiveForElement(element, 'Zoom', { mouseButtonMask: 2 });
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csTools.setToolActiveForElement(element, 'Wwwc', { mouseButtonMask: 1 });
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csTools.setToolActiveForElement(element, 'StackScrollMouseWheel', {}); // TODO: Empty options should not be required
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csTools.setToolActiveForElement(element, 'PanMultiTouch', { pointers: 2 }); // TODO: Better error if no options
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csTools.setToolActiveForElement(element, 'ZoomTouchPinch', {});
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csTools.setToolEnabledForElement(element, 'Overlay', {});
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}
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@@ -1,39 +0,0 @@
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import cornerstone from 'cornerstone-core';
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import cornerstoneTools from 'cornerstone-tools';
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const { globalImageIdSpecificToolStateManager } = cornerstoneTools;
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export default function setCornerstoneMeasurementActive(measurement) {
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const { id } = measurement;
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const toolState = globalImageIdSpecificToolStateManager.saveToolState();
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Object.keys(toolState).forEach(imageId => {
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const imageIdSpecificToolState = toolState[imageId];
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Object.keys(imageIdSpecificToolState).forEach(toolType => {
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const toolSpecificToolState = imageIdSpecificToolState[toolType];
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const toolSpecificToolData = toolSpecificToolState.data;
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if (toolSpecificToolData && toolSpecificToolData.length) {
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toolSpecificToolData.forEach(data => {
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data.active = data.id === id ? true : false;
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});
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}
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});
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});
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const enabledElements = cornerstoneTools.store.state.enabledElements;
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enabledElements.forEach(element => {
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try {
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cornerstone.updateImage(element);
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} catch (ex) {
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// https://github.com/cornerstonejs/cornerstone/blob/master/src/updateImage.js#L16
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// This fails if enabledElement.image is undefined and we have no layers
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// Instead of throwing, it should _probably_ do nothing.
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// We'll just swallow the exception
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}
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});
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}
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