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import { utilities } from '@cornerstonejs/core';
import { utilities as ToolsUtilities } from '@cornerstonejs/tools';
import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
import vtkPlane from '@kitware/vtk.js/Common/DataModel/Plane';
import vtkPolyData from '@kitware/vtk.js/Common/DataModel/PolyData';
import vtkContourLoopExtraction from '@kitware/vtk.js/Filters/General/ContourLoopExtraction';
import vtkCutter from '@kitware/vtk.js/Filters/Core/Cutter';
const {
math: {
polyline: { containsPoint, getAABB, projectTo2D },
},
geometricSurfaceUtils: { checkStandardBasis, rotatePoints },
boundingBox: { getBoundingBoxAroundShapeWorld },
planar: { isPlaneIntersectingAABB },
} = ToolsUtilities;
async function peerImport(moduleId) {
try {
if (moduleId === '@icr/polyseg-wasm') {
return import('@icr/polyseg-wasm');
}
} catch (error) {
console.warn('Error importing module:', error);
return null;
}
}
/**
* Object containing methods for converting between different representations of
* segmentations (e.g., contour, labelmap, surface, etc.) These logics
* are used in a webworker to avoid blocking the main thread. You can
* search for workerManager.executeTask('polySeg', ...) to see
* how these methods are used.
*
* See also the webworker docs at packages/docs/docs/concepts/cornerstone-core/web-worker.md
* to learn more about how to use web-workers in the context of Cornerstone.
*/
const polySegConverters = {
/**
* The polySeg instance that is used to convert between different representations
*/
polySeg: null,
/**
* Utilities to keep track of the initialization state of the polySeg instance
* and avoid initializing it multiple times
*/
polySegInitializing: false,
polySegInitializingPromise: null,
/**
* This method initializes the polySeg instance and sets it to this.polySeg
*/
async initializePolySeg(progressCallback) {
let ICRPolySeg;
try {
ICRPolySeg = (await peerImport('@icr/polyseg-wasm')).default;
} catch (error) {
console.error(error);
console.debug(
"Warning: '@icr/polyseg-wasm' module not found. Please install it separately."
);
return;
}
if (this.polySegInitializing) {
await this.polySegInitializingPromise;
return;
}
if (this.polySeg?.instance) {
return;
}
this.polySegInitializing = true;
this.polySegInitializingPromise = new Promise((resolve) => {
this.polySeg = new ICRPolySeg();
this.polySeg
.initialize({
updateProgress: progressCallback,
})
.then(() => {
this.polySegInitializing = false;
resolve();
});
});
await this.polySegInitializingPromise;
},
/**
* Converts a contour to a surface using the PolySeg library.
* @param {Object} args - The arguments for the conversion.
* @param {Array} args.polylines - The polylines representing the contour.
* @param {Array} args.numPointsArray - The number of points in each polyline.
* @param {...Function} callbacks - Optional callback functions.
* @returns {Promise} - A promise that resolves to the converted surface.
*/
async convertContourToSurface(args, ...callbacks) {
const { polylines, numPointsArray } = args;
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const results = await this.polySeg.instance.convertContourRoiToSurface(
polylines,
numPointsArray
);
return results;
},
/**
* Converts a labelmap to a surface using the specified arguments.
* @param {Object} args - The arguments for the conversion.
* @param {Array} args.scalarData - The scalar data of the labelmap.
* @param {Array} args.dimensions - The dimensions of the labelmap.
* @param {Array} args.spacing - The spacing of the labelmap.
* @param {Array} args.direction - The direction of the labelmap.
* @param {Array} args.origin - The origin of the labelmap.
* @param {number} args.segmentIndex - The segment index of the labelmap.
* @param {Function} progressCallback - The callback function for progress updates.
* @returns {Promise} - A promise that resolves with the converted surface results.
*/
async convertLabelmapToSurface(args, ...callbacks) {
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const results = this.polySeg.instance.convertLabelmapToSurface(
args.scalarData,
args.dimensions,
args.spacing,
args.direction,
args.origin,
[args.segmentIndex]
);
const rotationInfo = checkStandardBasis(args.direction);
if (!rotationInfo.isStandard) {
const rotatedPoints = rotatePoints(
rotationInfo.rotationMatrix,
args.origin,
results.points
);
results.points = [...rotatedPoints];
}
return results;
},
/**
* Converts a contour to a volume labelmap.
* @param {Object} args - The arguments for the conversion.
* @param {Array} args.segmentIndices - The indices of the segments.
* @param {Array} args.scalarData - The scalar data.
* @param {Map} args.annotationUIDsInSegmentMap - The map of annotation UIDs in segment.
* @param {Array} args.dimensions - The dimensions of the image data.
* @param {Array} args.origin - The origin of the image data.
* @param {Array} args.direction - The direction of the image data.
* @param {Array} args.spacing - The spacing of the image data.
* @param {...Function} callbacks - Optional callbacks.
* @param {Function} callbacks[0] - The progress callback.
* @returns {Array} - The scalar data of the segmentation voxel manager.
*/
async convertContourToVolumeLabelmap(args, ...callbacks) {
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const {
segmentIndices,
scalarData,
annotationUIDsInSegmentMap,
dimensions,
origin,
direction,
spacing,
} = args;
const segmentationVoxelManager =
utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions,
scalarData,
});
const imageData = vtkImageData.newInstance();
imageData.setDimensions(dimensions);
imageData.setOrigin(origin);
imageData.setDirection(direction);
imageData.setSpacing(spacing);
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: scalarData,
});
imageData.getPointData().setScalars(scalarArray);
imageData.modified();
for (const index of segmentIndices) {
const annotations = annotationUIDsInSegmentMap.get(index);
for (const annotation of annotations) {
if (!annotation.polyline) {
continue;
}
const { polyline, holesPolyline } = annotation;
const bounds = getBoundingBoxAroundShapeWorld(polyline);
const [iMin, jMin, kMin] = utilities.transformWorldToIndex(imageData, [
bounds[0][0],
bounds[1][0],
bounds[2][0],
]);
const [iMax, jMax, kMax] = utilities.transformWorldToIndex(imageData, [
bounds[0][1],
bounds[1][1],
bounds[2][1],
]);
const { projectedPolyline, sharedDimensionIndex } =
projectTo2D(polyline);
const holes = holesPolyline?.map((hole) => {
const { projectedPolyline: projectedHole } = projectTo2D(hole);
return projectedHole;
});
const firstDim = (sharedDimensionIndex + 1) % 3;
const secondDim = (sharedDimensionIndex + 2) % 3;
const voxels = utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions,
scalarData,
});
voxels.forEach(
({ pointIJK }) => {
segmentationVoxelManager.setAtIJKPoint(pointIJK, index);
},
{
imageData,
isInObject: (pointLPS) => {
const point2D = [pointLPS[firstDim], pointLPS[secondDim]];
// Check if the point is inside any of the polylines for this segment
const isInside = containsPoint(projectedPolyline, point2D, {
holes,
});
return isInside;
},
boundsIJK: [
[iMin, iMax],
[jMin, jMax],
[kMin, kMax],
],
}
);
}
}
return segmentationVoxelManager.scalarData;
},
/**
* Converts a contour to a stack labelmap.
* @param {Object} args - The arguments for the conversion.
* @param {Array} callbacks - Optional callbacks for progress updates.
* @returns {Promise<Object>} - The converted segmentations information.
*/
async convertContourToStackLabelmap(args, ...callbacks) {
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const { segmentationsInfo, annotationUIDsInSegmentMap, segmentIndices } =
args;
const segmentationVoxelManagers = new Map();
segmentationsInfo.forEach((segmentationInfo, referencedImageId) => {
const { dimensions, scalarData, direction, spacing, origin } =
segmentationInfo;
const manager = utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions,
scalarData,
});
const imageData = vtkImageData.newInstance();
imageData.setDimensions(dimensions);
imageData.setOrigin(origin);
imageData.setDirection(direction);
imageData.setSpacing(spacing);
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: scalarData,
});
imageData.getPointData().setScalars(scalarArray);
imageData.modified();
segmentationVoxelManagers.set(referencedImageId, { manager, imageData });
});
for (const index of segmentIndices) {
const annotations = annotationUIDsInSegmentMap.get(index);
for (const annotation of annotations) {
if (!annotation.polyline) {
continue;
}
const { polyline, holesPolyline, referencedImageId } = annotation;
const bounds = getBoundingBoxAroundShapeWorld(polyline);
const { manager: segmentationVoxelManager, imageData } =
segmentationVoxelManagers.get(referencedImageId);
const [iMin, jMin, kMin] = utilities.transformWorldToIndex(imageData, [
bounds[0][0],
bounds[1][0],
bounds[2][0],
]);
const [iMax, jMax, kMax] = utilities.transformWorldToIndex(imageData, [
bounds[0][1],
bounds[1][1],
bounds[2][1],
]);
const { projectedPolyline, sharedDimensionIndex } =
projectTo2D(polyline);
const holes = holesPolyline?.map((hole) => {
const { projectedPolyline: projectedHole } = projectTo2D(hole);
return projectedHole;
});
const firstDim = (sharedDimensionIndex + 1) % 3;
const secondDim = (sharedDimensionIndex + 2) % 3;
const voxels = utilities.VoxelManager.createImageVoxelManager({
width: imageData.getDimensions()[0],
height: imageData.getDimensions()[1],
scalarData: imageData.getPointData().getScalars().getData(),
});
voxels.forEach(
({ pointIJK }) => {
segmentationVoxelManager.setAtIJKPoint(pointIJK, index);
},
{
imageData,
isInObject: (pointLPS) => {
const point2D = [pointLPS[firstDim], pointLPS[secondDim]];
// Check if the point is inside any of the polylines for this segment
const isInside = containsPoint(projectedPolyline, point2D, {
holes,
});
return isInside;
},
boundsIJK: [
[iMin, iMax],
[jMin, jMax],
[kMin, kMax],
],
}
);
}
}
segmentationsInfo.forEach((segmentationInfo, referencedImageId) => {
const { manager: segmentationVoxelManager } =
segmentationVoxelManagers.get(referencedImageId);
segmentationInfo.scalarData = segmentationVoxelManager.scalarData;
});
return segmentationsInfo;
},
/**
* Converts a surface to a volume labelmap.
*
* @param {Object} args - The arguments for the conversion.
* @param {Array} args.points - The points defining the surface.
* @param {Array} args.polys - The polygons defining the surface.
* @param {Array} args.dimensions - The dimensions of the volume.
* @param {Array} args.spacing - The spacing between voxels in the volume.
* @param {Array} args.direction - The direction of the volume.
* @param {Array} args.origin - The origin of the volume.
* @param {Function} progressCallback - The callback function for reporting progress.
* @returns {Promise} - A promise that resolves with the converted labelmap.
*/
async convertSurfaceToVolumeLabelmap(args, ...callbacks) {
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const results = this.polySeg.instance.convertSurfaceToLabelmap(
args.points,
args.polys,
args.dimensions,
args.spacing,
args.direction,
args.origin
);
return results;
},
/**
* Converts surfaces to a volume labelmap.
* @param {Object} args - The arguments for the conversion.
* @param {Map} args.segmentsInfo - A map containing information about the segments.
* @param {Function} progressCallback - A callback function for reporting progress.
* @returns {Uint8Array} - The resulting volume labelmap.
*/
async convertSurfacesToVolumeLabelmap(args, ...callbacks) {
const [progressCallback] = callbacks;
await this.initializePolySeg(progressCallback);
const { segmentsInfo } = args;
const promises = Array.from(segmentsInfo.keys()).map((segmentIndex) => {
const { points, polys } = segmentsInfo.get(segmentIndex);
const result = this.polySeg.instance.convertSurfaceToLabelmap(
points,
polys,
args.dimensions,
args.spacing,
args.direction,
args.origin
);
return {
...result,
segmentIndex,
};
});
const results = await Promise.all(promises);
const targetImageData = vtkImageData.newInstance();
targetImageData.setDimensions(args.dimensions);
targetImageData.setOrigin(args.origin);
targetImageData.setSpacing(args.spacing);
targetImageData.setDirection(args.direction);
const totalSize =
args.dimensions[0] * args.dimensions[1] * args.dimensions[2];
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: new Uint8Array(totalSize),
});
targetImageData.getPointData().setScalars(scalarArray);
targetImageData.modified();
// we need to then consolidate the results into a single volume
// by looping into each voxel with voxelmanager for each
// and check if the voxel is inside any of the reconstructed
// labelmaps
const { dimensions } = args;
const scalarData = targetImageData.getPointData().getScalars().getData();
const segmentationVoxelManager =
utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions,
scalarData,
});
const outputVolumesInfo = results.map((result) => {
const { data, dimensions, direction, origin, spacing } = result;
const volume = vtkImageData.newInstance();
volume.setDimensions(dimensions);
volume.setOrigin(origin);
volume.setSpacing(spacing);
volume.setDirection(direction);
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: data,
});
volume.getPointData().setScalars(scalarArray);
volume.modified();
const voxelManager =
utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions,
scalarData: data,
});
const extent = volume.getExtent(); // e.g., [0, 176, 0, 268, 0, 337] for dimensions of [177, 269, 338]
return {
volume,
voxelManager,
extent,
scalarData: data,
segmentIndex: result.segmentIndex,
};
});
const voxels = utilities.VoxelManager.createScalarVolumeVoxelManager({
dimensions: targetImageData.getDimensions(),
scalarData: targetImageData.getPointData().getScalars().getData(),
});
voxels.forEach(
({ pointIJK, pointLPS }) => {
// Check if the point is inside any of the reconstructed labelmaps
// Todo: we can optimize this by returning early if the bounding box
// of the point is outside the bounding box of the labelmap
try {
for (const volumeInfo of outputVolumesInfo) {
const { volume, extent, voxelManager, segmentIndex } = volumeInfo;
const index = volume.worldToIndex(pointLPS);
// check if the ijk point is inside the volume
if (
index[0] < extent[0] ||
index[0] > extent[1] ||
index[1] < extent[2] ||
index[1] > extent[3] ||
index[2] < extent[4] ||
index[2] > extent[5]
) {
continue;
}
const roundedIndex = index.map(Math.round);
const value = voxelManager.getAtIJK(...roundedIndex);
if (value > 0) {
segmentationVoxelManager.setAtIJKPoint(pointIJK, segmentIndex);
break;
}
}
} catch (error) {
// right now there is weird error if the point is outside the volume
}
},
{ imageData: targetImageData }
);
return segmentationVoxelManager.scalarData;
},
getSurfacesAABBs({ surfacesInfo }) {
const aabbs = new Map();
for (const { points, id } of surfacesInfo) {
const aabb = getAABB(points, { numDimensions: 3 });
aabbs.set(id, aabb);
}
return aabbs;
},
/**
* Cuts the surfaces into planes.
*
* @param {Object} options - The options object.
* @param {Array} options.planesInfo - The information about the planes.
* @param {Array} options.surfacesInfo - The information about the surfaces.
* @param {Function} progressCallback - The callback function for progress updates.
* @param {Function} updateCacheCallback - The callback function for updating the cache.
*/
cutSurfacesIntoPlanes(
{ planesInfo, surfacesInfo, surfacesAABB = new Map() },
progressCallback,
updateCacheCallback
) {
const numberOfPlanes = planesInfo.length;
const cutter = vtkCutter.newInstance();
const plane1 = vtkPlane.newInstance();
cutter.setCutFunction(plane1);
const surfacePolyData = vtkPolyData.newInstance();
try {
for (const [index, planeInfo] of planesInfo.entries()) {
const { sliceIndex, planes } = planeInfo;
const polyDataResults = new Map();
for (const polyDataInfo of surfacesInfo) {
const { points, polys, id, segmentIndex } = polyDataInfo;
const aabb3 =
surfacesAABB.get(id) || getAABB(points, { numDimensions: 3 });
if (!surfacesAABB.has(id)) {
surfacesAABB.set(id, aabb3);
}
const { minX, minY, minZ, maxX, maxY, maxZ } = aabb3;
const { origin, normal } = planes[0];
// Check if the plane intersects the AABB
if (
!isPlaneIntersectingAABB(
origin,
normal,
minX,
minY,
minZ,
maxX,
maxY,
maxZ
)
) {
continue;
}
// Set up the initial polydata
surfacePolyData.getPoints().setData(points, 3);
surfacePolyData.getPolys().setData(polys);
surfacePolyData.modified();
cutter.setInputData(surfacePolyData);
plane1.setOrigin(origin);
plane1.setNormal(normal);
try {
cutter.update();
} catch (e) {
console.warn('Error during clipping', e);
continue;
}
const polyData = cutter.getOutputData();
// Additional validation of cutter output
if (
!polyData ||
!polyData.getPoints() ||
polyData.getPoints().getNumberOfPoints() === 0
) {
continue;
}
const cutterOutput = polyData;
cutterOutput.buildLinks();
const loopExtraction = vtkContourLoopExtraction.newInstance();
loopExtraction.setInputData(cutterOutput);
try {
loopExtraction.update();
const loopOutput = loopExtraction.getOutputData();
if (
loopOutput &&
loopOutput.getPoints() &&
loopOutput.getLines() &&
loopOutput.getPoints().getNumberOfPoints() > 0 &&
loopOutput.getLines().getNumberOfCells() > 0
) {
polyDataResults.set(segmentIndex, {
points: loopOutput.getPoints().getData(),
lines: loopOutput.getLines().getData(),
numberOfCells: loopOutput.getLines().getNumberOfCells(),
segmentIndex,
});
}
} catch (loopError) {
console.warn('Error during loop extraction:', loopError);
continue;
}
}
progressCallback({ progress: (index + 1) / numberOfPlanes });
updateCacheCallback({ sliceIndex, polyDataResults });
}
} catch (e) {
console.warn('Error during processing', e);
} finally {
// Cleanup on completion
surfacesInfo = null;
plane1.delete();
}
},
};
expose(polySegConverters);
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