* Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Rebase on master. * format format format * add basic extension parts * Updated yarn lock * Fetch derived/referenced displaysets in sidepanel * Add buttons, expose seriesDescription, write notes for Danny. * Add growcut tool extention. -> Move to a seperate repo. * Change some text fields. * expose dialog provider * hide draggable area * No pointer events for now; need to revisit * Don't filter seg from the outset for now * fiddling about * fix path to series data * fix logic to determine next available labelmapindex * Ability to swtich between labelmaps * Return a promise so we can make sure our labelmap is loaded before pulling metadata * Better UI to toggle labelmaps * Fix accidental untoggle of active labelmap for ui * Remove brush tool from cornerstone extension * Add cstools in preInit for seg extension * Add buttons for seg magic * Hide the measurements panel for now * Slightly better seg/scissor icons * Add eraser * ability to switch segments * seg color / switcher * Fix vtk labelmap cache. * sidepanel should scroll if there's overflow * Use a fancier range slider * Slightly prettier buttons * Push in progress * A bit more reactive; handle no-meta * Update to vtk.js 11.14.0 and react-vtkjs-viewport 0.6.0 * chore: kickstart preview * Fix conflict issues * Refactor panel * Isolate increment functions * Wip segment table * Hide selector and add scroll to segmentation * Increase width of segment description * Hide not used items * Add new select for segmentations * Align ui * Fix default segmentation * Fix broken import test * Get measurements panel back and add spacing to grouped buttons * Hide brush and selector and refresh when switching segmentations * Add pointer events back and fix broken tests for measurement table * Update segment list when switching humbnails * CR Update: Minor UI adjustments * CR Update: Set active segment * Move components to components folder * Add new settings ui * Integrate configuration * Improve styles * Float numbers * Improve css * Refresh settings menu if side panel changed * Fix settings rendering logic and remove comments * Extract components * Remove not used tools * Remove non used extension * Use style variables and remove comments * Remove non used dep from lock * Remove tools * Remove segmentation from toolbar * Add todo and brushradius from config * Fix packagejson growcut import * Remove webpack config already defined in parent * Update package json description * Change component name to british english to us * Improve prop types * Rename cornerstone label map event * Scope css * Extract and add doc to helper * Update jsdocs for getDerivedDatasets * Add proptypes and cr updates * Update tablistitem proptypes * config is readonly, rollback destructuring * Remove event for side panel * Add jsdocs for util * Extract getimageid to studymetada * Use ohif log instead of console * Remove specific style from side panel * Fix default props for brush radius * Descructure configuration props from settings component to avoid invalid props * Update proptypes to be required (settings) * Update readme * Remove commandsmodule * Get configuration module inside the component * Set selected segment * Rename extension and use modality to filter * Fix for failing tests (#1423) * hello world * Finish rebase for Igor. * Re-fix cornerstoneTools version that got messed up in merge. * Fix reactivity of isDisabled, write implementation for the SEG panel. * Nuke yarn.lock to stack CST to 4.12.0 * Remove debugger statements. * fix: bump cornerstone-tools version to address toFixed issue * test: force tests for MISTER^MR to navigate to study directly * test: remove eraser tool test * test: count is off by one * test: don't save SR state for the time being * test: disable more tests Co-authored-by: James A. Petts <jamesapetts@gmail.com> Co-authored-by: dannyrb <danny.ri.brown@gmail.com> Co-authored-by: igoroctaviano] <igoroctaviano@users.noreply.github.com> Co-authored-by: Mirna Silva <mirna.silva@radicalimaging.com>
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@@ -34,7 +34,7 @@
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"@ohif/ui": "^0.50.0",
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"cornerstone-core": "^2.2.8",
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"cornerstone-math": "^0.1.8",
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"cornerstone-tools": "4.12.0",
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"cornerstone-tools": "4.12.5",
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"cornerstone-wado-image-loader": "^3.0.0",
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"dcmjs": "^0.10.1",
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"dicom-parser": "^1.8.3",
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@@ -4,19 +4,9 @@ import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
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import OHIF from '@ohif/core';
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import PropTypes from 'prop-types';
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import cornerstone from 'cornerstone-core';
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import handleSegmentationStorage from './handleSegmentationStorage.js';
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const { StackManager } = OHIF.utils;
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const SOP_CLASSES = {
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SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4',
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};
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const specialCaseHandlers = {};
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specialCaseHandlers[
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SOP_CLASSES.SEGMENTATION_STORAGE
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] = handleSegmentationStorage;
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class OHIFCornerstoneViewport extends Component {
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state = {
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viewportData: null,
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@@ -124,42 +114,24 @@ class OHIFCornerstoneViewport extends Component {
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studies,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPClassUID,
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SOPInstanceUID,
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frameIndex
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) => {
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let viewportData;
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switch (SOPClassUID) {
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case SOP_CLASSES.SEGMENTATION_STORAGE:
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const specialCaseHandler =
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specialCaseHandlers[SOP_CLASSES.SEGMENTATION_STORAGE];
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const stack = OHIFCornerstoneViewport.getCornerstoneStack(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPInstanceUID,
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frameIndex
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);
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viewportData = await specialCaseHandler(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPInstanceUID,
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frameIndex
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);
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break;
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default:
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const stack = OHIFCornerstoneViewport.getCornerstoneStack(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPInstanceUID,
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frameIndex
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);
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viewportData = {
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StudyInstanceUID,
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displaySetInstanceUID,
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stack,
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};
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break;
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}
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viewportData = {
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StudyInstanceUID,
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displaySetInstanceUID,
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stack,
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};
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return viewportData;
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};
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@@ -184,13 +156,10 @@ class OHIFCornerstoneViewport extends Component {
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);
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}
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const SOPClassUID = sopClassUIDs && sopClassUIDs[0];
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this.getViewportData(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPClassUID,
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SOPInstanceUID,
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frameIndex
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).then(viewportData => {
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@@ -205,7 +174,7 @@ class OHIFCornerstoneViewport extends Component {
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}
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componentDidUpdate(prevProps) {
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const { studies, displaySet } = this.props.viewportData;
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const { displaySet } = this.props.viewportData;
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const prevDisplaySet = prevProps.viewportData.displaySet;
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if (
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@@ -1,128 +0,0 @@
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import * as dcmjs from 'dcmjs';
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import OHIF from '@ohif/core';
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import cornerstone from 'cornerstone-core';
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import cornerstoneTools from 'cornerstone-tools';
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const { StackManager, DicomLoaderService } = OHIF.utils;
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function getDisplaySet(studies, StudyInstanceUID, displaySetInstanceUID) {
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const study = studies.find(
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study => study.StudyInstanceUID === StudyInstanceUID
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);
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const displaySet = study.displaySets.find(set => {
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return set.displaySetInstanceUID === displaySetInstanceUID;
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});
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return displaySet;
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}
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function getDisplaySetsBySeries(studies, StudyInstanceUID, SeriesInstanceUID) {
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const study = studies.find(
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study => study.StudyInstanceUID === StudyInstanceUID
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);
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return study.displaySets.filter(set => {
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return set.SeriesInstanceUID === SeriesInstanceUID;
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});
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}
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function parseSeg(arrayBuffer, imageIds) {
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return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
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imageIds,
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arrayBuffer,
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cornerstone.metaData
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);
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}
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function addSegMetadataToCornerstoneToolState(
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segMetadata,
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toolState,
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displaySetInstanceUID
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) {
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cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
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toolState
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);
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const brushModule = cornerstoneTools.store.modules.brush;
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for (let i = 0; i < segMetadata.length; i++) {
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brushModule.setters.metadata(displaySetInstanceUID, i, segMetadata[i]);
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}
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}
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async function handleSegmentationStorage(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID
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) {
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const study = studies.find(
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study => study.StudyInstanceUID === StudyInstanceUID
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);
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const displaySet = getDisplaySet(
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studies,
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StudyInstanceUID,
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displaySetInstanceUID
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);
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const arrayBuffer = await DicomLoaderService.findDicomDataPromise(
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displaySet,
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studies
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);
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const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
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const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
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dicomData.dict
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);
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dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
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const SeriesInstanceUID = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
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const displaySets = getDisplaySetsBySeries(
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studies,
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StudyInstanceUID,
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SeriesInstanceUID
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);
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if (displaySets.length > 1) {
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console.warn(
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'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
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);
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}
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const referenceDisplaySet = displaySets[0];
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const imageIds = referenceDisplaySet.images.map(image => image.getImageId());
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const results = parseSeg(arrayBuffer, imageIds);
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if (!results) {
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throw new Error('Fractional segmentations are not supported');
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}
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const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
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const { setters } = cornerstoneTools.getModule('segmentation');
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setters.labelmap3DByFirstImageId(
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imageIds[0],
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labelmapBuffer,
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0, // TODO -> Can define a color LUT based on colors in the SEG later.
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segMetadata,
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imageIds.length,
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segmentsOnFrame
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);
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const cachedStack = StackManager.findOrCreateStack(
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study,
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referenceDisplaySet
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);
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const stack = Object.assign({}, cachedStack);
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stack.currentImageIdIndex = 0;
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return {
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StudyInstanceUID,
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displaySetInstanceUID,
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stack,
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};
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}
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export default handleSegmentationStorage;
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@@ -66,7 +66,6 @@ export default function init({ servicesManager, configuration }) {
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csTools.DragProbeTool,
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csTools.RectangleRoiTool,
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],
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segmentation: [csTools.BrushTool],
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other: [
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csTools.PanTool,
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csTools.ZoomTool,
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