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import {
Types,
cache,
utilities,
getWebWorkerManager,
volumeLoader,
imageLoader,
metaData,
Enums,
triggerEvent,
eventTarget,
} from '@cornerstonejs/core';
import {
Annotation,
ContourAnnotation,
ContourSegmentationData,
PolySegConversionOptions,
} from '../../../../types';
import { getAnnotation } from '../../..';
import { WorkerTypes } from '../../../../enums';
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: ContourSegmentationData,
options: PolySegConversionOptions = {}
) {
const { viewport } = options;
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 volumeProps = utilities.generateVolumePropsFromImageIds(
imageIds,
segmentationVolumeId
);
const { metadata, dimensions, origin, direction, spacing, scalarData } =
volumeProps;
const segmentationVolume = await volumeLoader.createLocalSegmentationVolume(
{
dimensions,
origin,
direction,
spacing,
metadata,
imageIds: imageIds.map((imageId) => `generated://${imageId}`),
referencedImageIds: imageIds,
},
segmentationVolumeId
);
const { segmentIndices, annotationUIDsInSegmentMap } =
_getAnnotationMapFromSegmentation(contourRepresentationData, options);
triggerWorkerProgress(eventTarget, 0);
const newScalarData = await workerManager.executeTask(
'polySeg',
'convertContourToVolumeLabelmap',
{
segmentIndices,
dimensions,
scalarData,
origin,
direction,
spacing,
annotationUIDsInSegmentMap,
},
{
callbacks: [
(progress) => {
triggerWorkerProgress(eventTarget, progress);
},
],
}
);
triggerWorkerProgress(eventTarget, 1);
segmentationVolume.imageData
.getPointData()
.getScalars()
.setData(newScalarData);
segmentationVolume.imageData.modified();
// update the scalarData in the volume as well
segmentationVolume.modified();
return {
volumeId: segmentationVolume.volumeId,
};
}
export async function convertContourToStackLabelmap(
contourRepresentationData: 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 { imageIds: segmentationImageIds } =
await imageLoader.createAndCacheDerivedSegmentationImages(imageIds);
const { segmentIndices, annotationUIDsInSegmentMap } =
_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.getPixelData(),
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, 1);
const imageIdReferenceMap = new Map();
newSegmentationsScalarData.forEach(({ scalarData }, referencedImageId) => {
const segmentationInfo = segmentationsInfo.get(referencedImageId);
const { imageId: segImageId } = segmentationInfo;
const segImage = cache.getImage(segImageId);
segImage.getPixelData().set(scalarData);
segImage.imageFrame?.pixelData?.set(scalarData);
imageIdReferenceMap.set(referencedImageId, segImageId);
});
return {
imageIdReferenceMap,
};
}
function _getAnnotationMapFromSegmentation(
contourRepresentationData: ContourSegmentationData,
options: PolySegConversionOptions = {}
) {
const annotationMap = contourRepresentationData.annotationUIDsMap;
const segmentIndices = options.segmentIndices?.length
? options.segmentIndices
: Array.from(annotationMap.keys());
const annotationUIDsInSegmentMap = new Map<number, any>();
segmentIndices.forEach((index) => {
const annotationUIDsInSegment = annotationMap.get(index);
// Todo: there is a bug right now where the annotationUIDsInSegment has both
// children and parent annotations, so we need to filter out the parent
// annotations only
let uids = Array.from(annotationUIDsInSegment);
uids = uids.filter(
(uid) => !(getAnnotation(uid) as Annotation).parentAnnotationUID
);
const annotations = uids.map((uid) => {
const annotation = getAnnotation(uid) as ContourAnnotation;
const hasChildAnnotations = annotation.childAnnotationUIDs?.length;
return {
polyline: annotation.data.contour.polyline,
referencedImageId: annotation.metadata.referencedImageId,
holesPolyline:
hasChildAnnotations &&
annotation.childAnnotationUIDs.map((childUID) => {
const childAnnotation = getAnnotation(
childUID
) as ContourAnnotation;
return childAnnotation.data.contour.polyline;
}),
};
});
annotationUIDsInSegmentMap.set(index, annotations);
});
return { segmentIndices, annotationUIDsInSegmentMap };
}
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