feat: 🎸 Seg jump to slice + show/hide
* Add segment part 2 (jump to frame and visibility toggle) * Cr updates * Filter displaysets with images * feat: 🎸 Seg jump to slice + show/hide Co-authored-by: James Petts <jamesapetts@gmail.com>
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Igor OctavianoandJames Petts authored and GitHub committed
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@@ -1,4 +1,4 @@
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import React, { useState, useEffect } from 'react';
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import React, { useState, useEffect, useCallback } from 'react';
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import PropTypes from 'prop-types';
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import cornerstoneTools from 'cornerstone-tools';
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import cornerstone from 'cornerstone-core';
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@@ -28,13 +28,20 @@ const refreshViewport = () => {
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/**
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* SegmentationPanel component
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*
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* @param {Object} props
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* @param {Array} props.studies
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* @param {Array} props.viewports - viewportSpecificData
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* @param {number} props.activeIndex - activeViewportIndex
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* @param {Array} props.studies - Studies data
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* @param {Array} props.viewports - Viewports data (viewportSpecificData)
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* @param {number} props.activeIndex - Active viewport index
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* @param {boolean} props.isOpen - Boolean that indicates if the panel is expanded
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* @param {Function} props.onSegItemClick - Segment click handler
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* @returns component
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*/
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const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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const SegmentationPanel = ({
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studies,
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viewports,
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activeIndex,
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isOpen,
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onSegItemClick,
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}) => {
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/*
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* TODO: wrap get/set interactions with the cornerstoneTools
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* store with context to make these kind of things less blurry.
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@@ -43,13 +50,14 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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const DEFAULT_BRUSH_RADIUS = configuration.radius || 10;
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const [state, setState] = useState({
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brushRadius: DEFAULT_BRUSH_RADIUS,
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brushColor: 'rgba(221, 85, 85, 1)', /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */
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brushColor:
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'rgba(221, 85, 85, 1)' /* TODO: We shouldn't hardcode this color, in the future the SEG may set the colorLUT to whatever it wants. */,
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selectedSegment: null,
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selectedSegmentation: null,
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showSegSettings: false,
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brushStackState: null,
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labelmapList: [],
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segmentList: []
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segmentList: [],
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});
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useEffect(() => {
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@@ -57,7 +65,12 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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log.warn('Segmentation Panel: labelmap modified', event);
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const module = cornerstoneTools.getModule('segmentation');
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const activeViewport = viewports[activeIndex];
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const firstImageId = studyMetadata.getFirstImageId(activeViewport.displaySetInstanceUID);
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const studyMetadata = studyMetadataManager.get(
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activeViewport.StudyInstanceUID
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);
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const firstImageId = studyMetadata.getFirstImageId(
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activeViewport.displaySetInstanceUID
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);
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updateState('brushStackState', module.state.series[firstImageId]);
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};
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@@ -86,20 +99,29 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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useEffect(() => {
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const module = cornerstoneTools.getModule('segmentation');
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const activeViewport = viewports[activeIndex];
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const studyMetadata = studyMetadataManager.get(activeViewport.StudyInstanceUID);
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const firstImageId = studyMetadata.getFirstImageId(activeViewport.displaySetInstanceUID);
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const studyMetadata = studyMetadataManager.get(
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activeViewport.StudyInstanceUID
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);
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const firstImageId = studyMetadata.getFirstImageId(
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activeViewport.displaySetInstanceUID
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);
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const brushStackState = module.state.series[firstImageId];
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if (brushStackState) {
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const labelmap3D = brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
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const labelmapList = getLabelmapList(brushStackState, firstImageId, activeViewport);
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const segmentList = getSegmentList(labelmap3D, firstImageId);
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const labelmap3D =
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brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
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const labelmapList = getLabelmapList(
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brushStackState,
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firstImageId,
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activeViewport
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);
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const segmentList = getSegmentList(labelmap3D, firstImageId, brushStackState);
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setState(state => ({
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...state,
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brushStackState,
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selectedSegmentation: brushStackState.activeLabelmapIndex,
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labelmapList,
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segmentList
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segmentList,
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}));
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} else {
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setState(state => ({
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@@ -108,126 +130,201 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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segmentList: [],
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}));
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}
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}, [studies, viewports, activeIndex]);
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}, [studies, viewports, activeIndex, getLabelmapList, getSegmentList]);
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/* Handle open/closed panel behaviour */
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useEffect(() => {
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updateState('showSegSettings', state.showSegSettings && !isOpen);
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setState(state => ({
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...state,
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showSegSettings: state.showSegSettings && !isOpen,
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}));
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}, [isOpen]);
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const getLabelmapList = (brushStackState, firstImageId, activeViewport) => {
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/* Get list of SEG labelmaps specific to active viewport (reference series) */
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const referencedSegDisplaysets = _getReferencedSegDisplaysets(
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activeViewport.StudyInstanceUID,
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activeViewport.SeriesInstanceUID
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);
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const getLabelmapList = useCallback(
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(brushStackState, firstImageId, activeViewport) => {
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/* Get list of SEG labelmaps specific to active viewport (reference series) */
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const referencedSegDisplaysets = _getReferencedSegDisplaysets(
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activeViewport.StudyInstanceUID,
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activeViewport.SeriesInstanceUID
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);
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return referencedSegDisplaysets.map((displaySet, index) => {
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const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
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return referencedSegDisplaysets.map((displaySet, index) => {
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const { labelmapIndex, SeriesDate, SeriesTime } = displaySet;
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/* Map to display representation */
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const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
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const date = moment(dateStr, 'YYYYMMDD:HHmmss');
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const isActiveLabelmap =
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labelmapIndex === brushStackState.activeLabelmapIndex;
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const displayDate = date.format('ddd, MMM Do YYYY');
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const displayTime = date.format('h:mm:ss a');
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const displayDescription = displaySet.SeriesDescription;
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/* Map to display representation */
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const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
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const date = moment(dateStr, 'YYYYMMDD:HHmmss');
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const isActiveLabelmap =
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labelmapIndex === brushStackState.activeLabelmapIndex;
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const displayDate = date.format('ddd, MMM Do YYYY');
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const displayTime = date.format('h:mm:ss a');
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const displayDescription = displaySet.SeriesDescription;
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return {
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value: labelmapIndex,
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title: displayDescription,
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description: displayDate,
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onClick: async () => {
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const activatedLabelmapIndex = await _setActiveLabelmap(
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activeViewport,
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studies,
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displaySet,
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firstImageId,
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brushStackState.activeLabelmapIndex
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);
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updateState('selectedSegmentation', activatedLabelmapIndex);
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},
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};
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});
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};
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return {
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value: labelmapIndex,
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title: displayDescription,
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description: displayDate,
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onClick: async () => {
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const activatedLabelmapIndex = await _setActiveLabelmap(
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activeViewport,
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studies,
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displaySet,
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firstImageId,
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brushStackState.activeLabelmapIndex
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);
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updateState('selectedSegmentation', activatedLabelmapIndex);
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},
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};
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});
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},
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[studies]
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);
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const getSegmentList = (labelmap3D, firstImageId) => {
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/*
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* Newly created segments have no `meta`
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* So we instead build a list of all segment indexes in use
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* Then find any associated metadata
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*/
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const uniqueSegmentIndexes = labelmap3D.labelmaps2D
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.reduce((acc, labelmap2D) => {
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if (labelmap2D) {
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const segmentIndexes = labelmap2D.segmentsOnLabelmap;
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const getSegmentList = useCallback(
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(labelmap3D, firstImageId, brushStackState) => {
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/*
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* Newly created segments have no `meta`
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* So we instead build a list of all segment indexes in use
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* Then find any associated metadata
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*/
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const uniqueSegmentIndexes = labelmap3D.labelmaps2D
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.reduce((acc, labelmap2D) => {
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if (labelmap2D) {
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const segmentIndexes = labelmap2D.segmentsOnLabelmap;
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for (let i = 0; i < segmentIndexes.length; i++) {
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if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
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acc.push(segmentIndexes[i]);
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for (let i = 0; i < segmentIndexes.length; i++) {
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if (!acc.includes(segmentIndexes[i]) && segmentIndexes[i] !== 0) {
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acc.push(segmentIndexes[i]);
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}
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}
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}
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return acc;
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}, [])
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.sort((a, b) => a - b);
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const module = cornerstoneTools.getModule('segmentation');
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const colorLutTable =
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module.state.colorLutTables[labelmap3D.colorLUTIndex];
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const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
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const segmentList = [];
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for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
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const segmentIndex = uniqueSegmentIndexes[i];
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const color = colorLutTable[segmentIndex];
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let segmentLabel = '(unlabeled)';
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let segmentNumber = segmentIndex;
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/* Meta */
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if (hasLabelmapMeta) {
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const segmentMeta = labelmap3D.metadata.data[segmentIndex];
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if (segmentMeta) {
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segmentNumber = segmentMeta.SegmentNumber;
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segmentLabel = segmentMeta.SegmentLabel;
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}
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}
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return acc;
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}, [])
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.sort((a, b) => a - b);
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const sameSegment = state.selectedSegment === segmentNumber;
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const setCurrentSelectedSegment = () => {
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_setActiveSegment(
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firstImageId,
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segmentNumber,
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labelmap3D.activeSegmentIndex
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);
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updateState('selectedSegment', sameSegment ? null : segmentNumber);
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const module = cornerstoneTools.getModule('segmentation');
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const colorLutTable =
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module.state.colorLutTables[labelmap3D.colorLUTIndex];
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const hasLabelmapMeta = labelmap3D.metadata && labelmap3D.metadata.data;
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const validIndexList = [];
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labelmap3D.labelmaps2D.forEach((labelMap2D, index) => {
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if (labelMap2D.segmentsOnLabelmap.includes(segmentNumber)) {
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validIndexList.push(index);
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}
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});
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const avg = array => array.reduce((a, b) => a + b) / array.length;
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const average = avg(validIndexList);
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const closest = validIndexList.reduce((prev, curr) => {
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return Math.abs(curr - average) < Math.abs(prev - average)
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? curr
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: prev;
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});
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const segmentList = [];
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for (let i = 0; i < uniqueSegmentIndexes.length; i++) {
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const segmentIndex = uniqueSegmentIndexes[i];
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const enabledElements = cornerstone.getEnabledElements();
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const element = enabledElements[activeIndex].element;
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const toolState = cornerstoneTools.getToolState(element, 'stack');
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const color = colorLutTable[segmentIndex];
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let segmentLabel = '(unlabeled)';
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let segmentNumber = segmentIndex;
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if (!toolState) {
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return;
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}
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/* Meta */
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if (hasLabelmapMeta) {
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const segmentMeta = labelmap3D.metadata.data[segmentIndex];
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const imageIds = toolState.data[0].imageIds;
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const imageId = imageIds[closest];
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const frameIndex = imageIds.indexOf(imageId);
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if (segmentMeta) {
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segmentNumber = segmentMeta.SegmentNumber;
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segmentLabel = segmentMeta.SegmentLabel;
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const SOPInstanceUID = cornerstone.metaData.get(
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'SOPInstanceUID',
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imageId
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);
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const StudyInstanceUID = cornerstone.metaData.get(
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'StudyInstanceUID',
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imageId
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);
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onSegItemClick({
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StudyInstanceUID,
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SOPInstanceUID,
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frameIndex,
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activeViewportIndex: activeIndex,
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});
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};
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const enabledElements = cornerstone.getEnabledElements();
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const enabledElementViewport = enabledElements[activeIndex];
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let isVisible = true;
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if (enabledElementViewport) {
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const element = enabledElementViewport.element;
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const module = cornerstoneTools.getModule('segmentation');
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isVisible = module.getters.isSegmentVisible(
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element,
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segmentNumber,
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brushStackState.activeLabelmapIndex
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);
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}
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segmentList.push(
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<SegmentItem
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key={segmentNumber}
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itemClass={`segment-item ${sameSegment && 'selected'}`}
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onClick={setCurrentSelectedSegment}
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label={segmentLabel}
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index={segmentNumber}
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color={color}
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visible={isVisible}
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onVisibilityChange={() => {
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const element = enabledElements[activeIndex].element;
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module.setters.toggleSegmentVisibility(
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element,
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segmentNumber,
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brushStackState.activeLabelmapIndex
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);
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refreshViewport();
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}}
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/>
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);
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}
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const sameSegment = state.selectedSegment === segmentNumber;
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const setCurrentSelectedSegment = () => {
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_setActiveSegment(
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firstImageId,
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segmentNumber,
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labelmap3D.activeSegmentIndex
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);
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updateState('selectedSegment', sameSegment ? null : segmentNumber);
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};
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return segmentList;
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segmentList.push(
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<SegmentItem
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key={segmentNumber}
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itemClass={`segment-item ${sameSegment && 'selected'}`}
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onClick={setCurrentSelectedSegment}
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label={segmentLabel}
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index={segmentNumber}
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color={color}
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/>
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);
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}
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return segmentList;
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/*
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* Let's iterate over segmentIndexes ^ above
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* If meta has a match, use it to show info
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* If now, add "no-meta" class
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* Show default name
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*/
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};
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/*
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* Let's iterate over segmentIndexes ^ above
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* If meta has a match, use it to show info
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* If now, add "no-meta" class
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* Show default name
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*/
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},
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[activeIndex, onSegItemClick, state.selectedSegment]
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);
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const updateState = (field, value) => {
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setState(state => ({ ...state, [field]: value }));
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@@ -270,8 +367,7 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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}
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const module = cornerstoneTools.getModule('segmentation');
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const colorLutTable =
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module.state.colorLutTables[labelmap3D.colorLUTIndex];
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const colorLutTable = module.state.colorLutTables[labelmap3D.colorLUTIndex];
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const color = colorLutTable[labelmap3D.activeSegmentIndex];
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return `rgba(${color.join(',')})`;
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@@ -329,7 +425,9 @@ const SegmentationPanel = ({ studies, viewports, activeIndex, isOpen }) => {
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<div className="segmentations">
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<SegmentationSelect
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value={
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state.labelmapList.find(i => i.value === state.selectedSegmentation) || null
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state.labelmapList.find(
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i => i.value === state.selectedSegmentation
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) || null
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}
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formatOptionLabel={SegmentationItem}
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options={state.labelmapList}
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