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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 | import { cache } from '@cornerstonejs/core';
import type { Types } from '@cornerstonejs/core';
import { getUniqueSegmentIndices } from '../../../../utilities/segmentation';
import {
getSegmentation,
setSegmentationRepresentationSpecificConfig,
} from '../../segmentationState';
import { PolySegConversionOptions } from '../../../../types';
import { computeSurfaceFromLabelmapSegmentation } from '../Surface/surfaceComputationStrategies';
import {
SurfaceClipResult,
clipAndCacheSurfacesForViewport,
} from '../../helpers/clipAndCacheSurfacesForViewport';
import { extractContourData } from './utils/extractContourData';
import { createAndAddContourSegmentationsFromClippedSurfaces } from './utils/createAndAddContourSegmentationsFromClippedSurfaces';
import { getToolGroupForViewport } from '../../../../store/ToolGroupManager';
// the map between segment index and the intersection points and lines
export type RawContourData = Map<number, SurfaceClipResult[]>;
/**
* Computes contour data for a given segmentation.
* @param segmentationId - The ID of the segmentation.
* @param options - Optional parameters for the computation.
* @returns An object containing the annotation UIDs map.
* @throws Error if there is not enough data to convert to contour.
*/
export async function computeContourData(
segmentationId: string,
options: PolySegConversionOptions = {}
) {
const segmentIndices = options.segmentIndices?.length
? options.segmentIndices
: getUniqueSegmentIndices(segmentationId);
let rawContourData: RawContourData;
const segmentation = getSegmentation(segmentationId);
const representationData = segmentation.representationData;
try {
if (representationData.SURFACE) {
rawContourData = await computeContourFromSurfaceSegmentation(
segmentationId,
{
segmentIndices,
...options,
}
);
} else if (representationData.LABELMAP) {
rawContourData = await computeContourFromLabelmapSegmentation(
segmentationId,
{
segmentIndices,
...options,
}
);
}
} catch (error) {
console.error(error);
throw error;
}
if (!rawContourData) {
throw new Error(
'Not enough data to convert to contour, currently only support converting volume labelmap to contour if available'
);
}
const { viewport, segmentationRepresentationUID } = options;
// create the new annotations and add them to the segmentation state representation
// data for the contour representation
const annotationUIDsMap = createAndAddContourSegmentationsFromClippedSurfaces(
rawContourData,
viewport,
segmentationId
);
// make the segmentation configuration fillAlpha 0 since
// we don't have proper hole support right now
// Todo: add hole support
const toolGroupId = getToolGroupForViewport(viewport.id)?.id;
setSegmentationRepresentationSpecificConfig(
toolGroupId,
segmentationRepresentationUID,
{
CONTOUR: {
fillAlpha: 0,
},
}
);
return {
annotationUIDsMap,
};
}
/**
* Computes the contour from a labelmap segmentation.
* @param segmentationId - The ID of the segmentation.
* @param options - The options for the contour computation.
* @returns The raw contour data.
*/
async function computeContourFromLabelmapSegmentation(
segmentationId,
options: PolySegConversionOptions = {}
) {
if (!options.viewport) {
throw new Error('Viewport is required to compute contour from labelmap');
}
const results = await computeSurfaceFromLabelmapSegmentation(
segmentationId,
options
);
if (!results?.length) {
console.error('Failed to convert labelmap to surface or labelmap is empty');
return;
}
const { viewport, segmentationRepresentationUID } = options;
const pointsAndPolys = results.map((surface) => {
return {
id: surface.segmentIndex.toString(),
points: surface.data.points,
polys: surface.data.polys,
segmentIndex: surface.segmentIndex,
};
});
const polyDataCache = await clipAndCacheSurfacesForViewport(
pointsAndPolys,
viewport as Types.IVolumeViewport,
segmentationRepresentationUID
);
const rawResults = extractContourData(polyDataCache);
return rawResults;
}
/**
* Computes the contour from a surface segmentation.
* @param segmentationId - The ID of the segmentation.
* @param options - The options for the contour computation.
* @returns A promise that resolves to the raw contour data.
* @throws An error if the viewport is not provided.
*/
async function computeContourFromSurfaceSegmentation(
segmentationId,
options: PolySegConversionOptions = {}
): Promise<RawContourData> {
if (!options.viewport) {
throw new Error('Viewport is required to compute contour from surface');
}
const { viewport, segmentationRepresentationUID } = options;
const segmentIndices = options.segmentIndices?.length
? options.segmentIndices
: getUniqueSegmentIndices(segmentationId);
const segmentIndexToSurfaceId = new Map() as Map<number, string>;
const surfaceIdToSegmentIndex = new Map() as Map<string, number>;
const segmentation = getSegmentation(segmentationId);
const representationData = segmentation.representationData.SURFACE;
const surfacesInfo = [];
representationData.geometryIds.forEach((geometryId, segmentIndex) => {
if (segmentIndices.includes(segmentIndex)) {
segmentIndexToSurfaceId.set(segmentIndex, geometryId);
const surface = cache.getGeometry(geometryId)?.data as Types.ISurface;
if (surface) {
surfacesInfo.push({
id: geometryId,
points: surface.getPoints(),
polys: surface.getPolys(),
});
}
}
});
segmentIndexToSurfaceId.forEach((surfaceId, segmentIndex) => {
surfaceIdToSegmentIndex.set(surfaceId, segmentIndex);
});
const polyDataCache = await clipAndCacheSurfacesForViewport(
surfacesInfo,
viewport as Types.IVolumeViewport,
segmentationRepresentationUID
);
const rawResults = extractContourData(polyDataCache, surfaceIdToSegmentIndex);
return rawResults;
}
export { computeContourFromLabelmapSegmentation };
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