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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 | 428x 428x 428x 428x | import { vec3 } from 'gl-matrix';
import type { Types } from '@cornerstonejs/core';
import {
cache,
utilities,
getWebWorkerManager,
volumeLoader,
imageLoader,
metaData,
Enums,
triggerEvent,
eventTarget,
} from '@cornerstonejs/core';
import type { Types as ToolsTypes } from '@cornerstonejs/tools';
import * as cornerstoneTools from '@cornerstonejs/tools';
import type { PolySegConversionOptions } from '../types';
const { WorkerTypes } = cornerstoneTools.Enums;
const { segmentation } = cornerstoneTools;
const workerManager = getWebWorkerManager();
const triggerWorkerProgress = (eventTarget, progress) => {
triggerEvent(eventTarget, Enums.Events.WEB_WORKER_PROGRESS, {
progress,
type: WorkerTypes.POLYSEG_CONTOUR_TO_LABELMAP,
});
};
export async function convertContourToVolumeLabelmap(
contourRepresentationData: ToolsTypes.ContourSegmentationData,
options: PolySegConversionOptions = {}
) {
const viewport = options.viewport as Types.IVolumeViewport;
const volumeId = viewport.getVolumeId();
const imageIds = utilities.getViewportImageIds(viewport);
if (!imageIds) {
throw new Error(
'No imageIds found, labelmap computation from contour requires viewports with imageIds'
);
}
const segmentationVolumeId = utilities.uuidv4();
const segmentationVolume = volumeLoader.createAndCacheDerivedLabelmapVolume(
volumeId,
{
volumeId: segmentationVolumeId,
}
);
const { dimensions, origin, direction, spacing, voxelManager } =
segmentationVolume;
const { segmentIndices, annotationUIDsInSegmentMap } =
segmentation.utilities.getAnnotationMapFromSegmentation(
contourRepresentationData,
options
);
triggerWorkerProgress(eventTarget, 0);
const newScalarData = await workerManager.executeTask(
'polySeg',
'convertContourToVolumeLabelmap',
{
segmentIndices,
dimensions,
scalarData: voxelManager.getCompleteScalarDataArray?.(),
origin,
direction,
spacing,
annotationUIDsInSegmentMap,
},
{
callbacks: [
(progress) => {
triggerWorkerProgress(eventTarget, progress);
},
],
}
);
triggerWorkerProgress(eventTarget, 100);
voxelManager.setCompleteScalarDataArray(newScalarData);
segmentationVolume.modified();
return {
volumeId: segmentationVolume.volumeId,
};
}
export async function convertContourToStackLabelmap(
contourRepresentationData: ToolsTypes.ContourSegmentationData,
options: PolySegConversionOptions = {}
) {
if (!options.viewport) {
throw new Error(
'No viewport provided, labelmap computation from contour requires viewports'
);
}
const viewport = options.viewport as Types.IStackViewport;
const imageIds = viewport.getImageIds();
if (!imageIds) {
throw new Error(
'No imageIds found, labelmap computation from contour requires viewports with imageIds'
);
}
// check if the imageIds are already cached
imageIds.forEach((imageId) => {
if (!cache.getImageLoadObject(imageId)) {
throw new Error(
'ImageIds must be cached before converting contour to labelmap'
);
}
});
// create
const segImages =
await imageLoader.createAndCacheDerivedLabelmapImages(imageIds);
const segmentationImageIds = segImages.map((it) => it.imageId);
const { segmentIndices, annotationUIDsInSegmentMap } =
segmentation.utilities.getAnnotationMapFromSegmentation(
contourRepresentationData,
options
);
// information for the referenced to the segmentation image
// Define constant to hold segmentation information
const segmentationsInfo = new Map();
// Loop through each segmentation image ID
segmentationImageIds.forEach((segImageId, index) => {
// Fetch the image from cache
const segImage = cache.getImage(segImageId);
// Fetch metadata for the image
const imagePlaneModule = metaData.get(
Enums.MetadataModules.IMAGE_PLANE,
segImageId
);
// Extract properties from image metadata
let {
columnCosines,
rowCosines,
rowPixelSpacing,
columnPixelSpacing,
imagePositionPatient,
} = imagePlaneModule;
// Set defaults if necessary
columnCosines = columnCosines ?? [0, 1, 0];
rowCosines = rowCosines ?? [1, 0, 0];
rowPixelSpacing = rowPixelSpacing ?? 1;
columnPixelSpacing = columnPixelSpacing ?? 1;
imagePositionPatient = imagePositionPatient ?? [0, 0, 0];
// Create vector from row and column cosines
const rowCosineVec = vec3.fromValues(
rowCosines[0],
rowCosines[1],
rowCosines[2]
);
const colCosineVec = vec3.fromValues(
columnCosines[0],
columnCosines[1],
columnCosines[2]
);
// Calculate scan axis normal
const scanAxisNormal = vec3.create();
vec3.cross(scanAxisNormal, rowCosineVec, colCosineVec);
// Define direction and spacing
const direction = [...rowCosineVec, ...colCosineVec, ...scanAxisNormal];
const spacing = [rowPixelSpacing, columnPixelSpacing, 1];
// Set origin
const origin = imagePositionPatient;
// Store segmentation information
segmentationsInfo.set(imageIds[index], {
direction,
spacing,
origin,
scalarData: segImage.voxelManager.getScalarData(),
imageId: segImageId,
dimensions: [segImage.width, segImage.height, 1],
});
});
triggerWorkerProgress(eventTarget, 0);
const newSegmentationsScalarData = await workerManager.executeTask(
'polySeg',
'convertContourToStackLabelmap',
{
segmentationsInfo,
annotationUIDsInSegmentMap,
segmentIndices,
},
{
callbacks: [
(progress) => {
triggerWorkerProgress(eventTarget, progress);
},
],
}
);
triggerWorkerProgress(eventTarget, 100);
const segImageIds = [];
newSegmentationsScalarData.forEach(({ scalarData }, referencedImageId) => {
const segmentationInfo = segmentationsInfo.get(referencedImageId);
const { imageId: segImageId } = segmentationInfo;
const segImage = cache.getImage(segImageId);
segImage.voxelManager.getScalarData().set(scalarData);
segImage.imageFrame?.pixelData?.set(scalarData);
segImageIds.push(segImageId);
});
return {
imageIds: segImageIds,
};
}
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