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import { utilities as csUtils, cache, volumeLoader } from '@cornerstonejs/core';
import type { Types } from '@cornerstonejs/core';
import { run, type GrowCutOptions } from './runGrowCut';
import type { SphereBoundsInfo } from '../../getSphereBoundsInfo';
import { getSphereBoundsInfo } from '../../getSphereBoundsInfo';
const { transformWorldToIndex } = csUtils;
const POSITIVE_SEED_VALUE = 254;
const NEGATIVE_SEED_VALUE = 255;
const POSITIVE_SEED_VARIANCE = 0.1;
const NEGATIVE_SEED_VARIANCE = 0.8;
type SphereInfo = {
center: Types.Point3;
radius: number;
};
type GrowCutSphereBoundsInfo = SphereBoundsInfo & {
topLeftIJK: Types.Point3;
bottomRightIJK: Types.Point3;
};
function _getGrowCutSphereBoundsInfo(
referencedVolume: Types.IImageVolume,
sphereBoundsInfo: SphereBoundsInfo
): GrowCutSphereBoundsInfo {
const { topLeftWorld, bottomRightWorld } = sphereBoundsInfo;
const topLeftIJK = transformWorldToIndex(
referencedVolume.imageData,
topLeftWorld
);
const bottomRightIJK = transformWorldToIndex(
referencedVolume.imageData,
bottomRightWorld
);
return {
...sphereBoundsInfo,
topLeftIJK,
bottomRightIJK,
};
}
function _getSphereBoundsInfo(
referencedVolume: Types.IImageVolume,
sphereInfo: SphereInfo
): SphereBoundsInfo {
const direction = referencedVolume.imageData.getDirection();
const vecColumn = vec3.fromValues(direction[3], direction[4], direction[5]);
const { center: sphereCenterPoint, radius: sphereRadius } = sphereInfo;
const refVolImageData = referencedVolume.imageData;
const topCirclePoint = vec3.scaleAndAdd(
vec3.create(),
sphereCenterPoint,
vecColumn,
-sphereRadius
) as Types.Point3;
const bottomCirclePoint = vec3.scaleAndAdd(
vec3.create(),
sphereCenterPoint,
vecColumn,
sphereRadius
) as Types.Point3;
// Gets the sphere bounds info in acquired orientation (no viewport needed)
const sphereBoundsInfo = getSphereBoundsInfo(
[bottomCirclePoint, topCirclePoint],
refVolImageData
);
return _getGrowCutSphereBoundsInfo(referencedVolume, sphereBoundsInfo);
}
function _createSubVolumeFromSphere(
referencedVolume: Types.IImageVolume,
sphereInfo: SphereInfo,
viewport: Types.IViewport
) {
const refVolImageData = referencedVolume.imageData;
const camera = viewport.getCamera();
const { ijkVecRowDir, ijkVecColDir } = csUtils.getVolumeDirectionVectors(
refVolImageData,
camera
);
// If two of the three vectors are aligned to X, Y or Z then the 3rd vector
// is also aligned (non-oblique)
const obliqueView = [ijkVecRowDir, ijkVecColDir].some(
(vec) =>
!csUtils.isEqual(Math.abs(vec[0]), 1) &&
!csUtils.isEqual(Math.abs(vec[1]), 1) &&
!csUtils.isEqual(Math.abs(vec[2]), 1)
);
if (obliqueView) {
console.warn('Oblique view is not supported!');
return;
}
const { boundsIJK: sphereBoundsIJK /*, topLeftWorld, bottomRightWorld */ } =
_getSphereBoundsInfo(referencedVolume, sphereInfo);
const subVolumeBoundsIJK: Types.AABB3 = {
minX: sphereBoundsIJK[0][0],
maxX: sphereBoundsIJK[0][1] + 1,
minY: sphereBoundsIJK[1][0],
maxY: sphereBoundsIJK[1][1] + 1,
minZ: sphereBoundsIJK[2][0],
maxZ: sphereBoundsIJK[2][1] + 1,
};
return csUtils.createSubVolume(
referencedVolume.volumeId,
subVolumeBoundsIJK,
{
targetBuffer: {
type: 'Float32Array',
},
}
);
}
function _setPositiveSeedValues(
referencedVolume: Types.IImageVolume,
labelmap: Types.IImageVolume,
sphereInfo: SphereInfo,
options?: GrowCutOptions
) {
const refVolumePixelData =
referencedVolume.voxelManager.getCompleteScalarDataArray();
const worldStartPos = sphereInfo.center;
const [width, height, numSlices] = referencedVolume.dimensions;
const numPixelsPerSlice = width * height;
const ijkStartPosition = transformWorldToIndex(
referencedVolume.imageData,
worldStartPos
);
const referencePixelValue =
refVolumePixelData[
ijkStartPosition[2] * numPixelsPerSlice +
ijkStartPosition[1] * width +
ijkStartPosition[0]
];
const positiveSeedValue = options.positiveSeedValue ?? POSITIVE_SEED_VALUE;
const positiveSeedVariance =
options.positiveSeedVariance ?? POSITIVE_SEED_VARIANCE;
const positiveSeedVarianceValue = Math.abs(
referencePixelValue * positiveSeedVariance
);
const minPositivePixelValue = referencePixelValue - positiveSeedVarianceValue;
const maxPositivePixelValue = referencePixelValue + positiveSeedVarianceValue;
// Neighbors distance that will be visited for every pixel
const neighborsCoordDelta = [
[-1, 0, 0],
[1, 0, 0],
[0, -1, 0],
[0, 1, 0],
[0, 0, -1],
[0, 0, 1],
];
const startVoxelIndex =
ijkStartPosition[2] * numPixelsPerSlice +
ijkStartPosition[1] * width +
ijkStartPosition[0];
// Update the label map for the start voxel
// labelmapData[startVoxelIndex] = positiveSeedValue;
labelmap.voxelManager.setAtIndex(startVoxelIndex, positiveSeedValue);
// Add the start point to the queue and traverse all neighbor pixels that are not visited yet and within the positive range
const queue = [ijkStartPosition];
// Run breadth first search in 3D space to update the positive and negative seed values
while (queue.length) {
const ijkVoxel = queue.shift();
const [x, y, z] = ijkVoxel;
for (let i = 0, len = neighborsCoordDelta.length; i < len; i++) {
const neighborCoordDelta = neighborsCoordDelta[i];
const nx = x + neighborCoordDelta[0];
const ny = y + neighborCoordDelta[1];
const nz = z + neighborCoordDelta[2];
// Continue if it is out of bounds.
if (
nx < 0 ||
nx >= width ||
ny < 0 ||
ny >= height ||
nz < 0 ||
nz >= numSlices
) {
continue;
}
const neighborVoxelIndex = nz * numPixelsPerSlice + ny * width + nx;
const neighborPixelValue = refVolumePixelData[neighborVoxelIndex];
// const neighborLabelmapValue = labelmapData[neighborVoxelIndex];
const neighborLabelmapValue =
labelmap.voxelManager.getAtIndex(neighborVoxelIndex);
if (
neighborLabelmapValue === positiveSeedValue ||
neighborPixelValue < minPositivePixelValue ||
neighborPixelValue > maxPositivePixelValue
) {
continue;
}
// labelmapData[neighborVoxelIndex] = positiveSeedValue;
labelmap.voxelManager.setAtIndex(neighborVoxelIndex, positiveSeedValue);
queue.push([nx, ny, nz]);
}
}
}
function _setNegativeSeedValues(
subVolume: Types.IImageVolume,
labelmap: Types.IImageVolume,
sphereInfo: SphereInfo,
viewport: Types.IViewport,
options: GrowCutOptions
) {
const subVolPixelData = subVolume.voxelManager.getCompleteScalarDataArray();
const [columns, rows, numSlices] = labelmap.dimensions;
const numPixelsPerSlice = columns * rows;
// The camera has the same orientation for the labelmap volume because this
// volume has the same orientation as the referenced volume and there is no
// need to convert from refVolume to labelmap spaces.
const { worldVecRowDir, worldVecSliceDir } =
csUtils.getVolumeDirectionVectors(labelmap.imageData, viewport.getCamera());
const ijkSphereCenter = transformWorldToIndex(
subVolume.imageData,
sphereInfo.center
);
const referencePixelValue =
subVolPixelData[
ijkSphereCenter[2] * columns * rows +
ijkSphereCenter[1] * columns +
ijkSphereCenter[0]
];
const negativeSeedVariance =
options.negativeSeedVariance ?? NEGATIVE_SEED_VARIANCE;
const negativeSeedValue = options?.negativeSeedValue ?? NEGATIVE_SEED_VALUE;
const negativeSeedVarianceValue = Math.abs(
referencePixelValue * negativeSeedVariance
);
const minNegativePixelValue = referencePixelValue - negativeSeedVarianceValue;
const maxNegativePixelValue = referencePixelValue + negativeSeedVarianceValue;
const numCirclePoints = 360;
const rotationAngle = (2 * Math.PI) / numCirclePoints;
const worldQuat = quat.setAxisAngle(
quat.create(),
worldVecSliceDir,
rotationAngle
);
const vecRotation = vec3.clone(worldVecRowDir);
for (let i = 0; i < numCirclePoints; i++) {
const worldCircleBorderPoint = vec3.scaleAndAdd(
vec3.create(),
sphereInfo.center,
vecRotation,
sphereInfo.radius
);
const ijkCircleBorderPoint = transformWorldToIndex(
labelmap.imageData,
worldCircleBorderPoint as Types.Point3
);
const [x, y, z] = ijkCircleBorderPoint;
vec3.transformQuat(vecRotation, vecRotation, worldQuat);
if (
x < 0 ||
x >= columns ||
y < 0 ||
y >= rows ||
z < 0 ||
z >= numSlices
) {
continue;
}
const offset = x + y * columns + z * numPixelsPerSlice;
const pixelValue = subVolPixelData[offset];
if (
pixelValue < minNegativePixelValue ||
pixelValue > maxNegativePixelValue
) {
// labelmapData[offset] = negativeSeedValue;
labelmap.voxelManager.setAtIndex(offset, negativeSeedValue);
}
}
}
async function _createAndCacheSegmentationSubVolumeForSphere(
subVolume: Types.IImageVolume,
sphereInfo: SphereInfo,
viewport: Types.IViewport,
options?: GrowCutOptions
): Promise<Types.IImageVolume> {
const labelmap = await volumeLoader.createAndCacheDerivedLabelmapVolume(
subVolume.volumeId
);
_setPositiveSeedValues(subVolume, labelmap, sphereInfo, options);
_setNegativeSeedValues(subVolume, labelmap, sphereInfo, viewport, options);
return labelmap;
}
/**
* Run grow cut for a given volume and a sphere. A new sub-volume is created
* based on sphere's AABB, a labelmap is created for that sub-volume, some pixels
* are set as positive/negative and the labelmap is then updated in the gpu. The
* positive and negative seed pixels are set based on the center and radius of
* the sphere where pixels close o the center of the sphere are set as positive
* and up to 360 pixels at the border are set as negative.
*
* @param referencedVolumeId - Referenced volume id
* @param sphereInfo - Sphere information (center and radius)
* @param viewport - Viewport
* @param options - Options
* @returns A new labelmap created that shall have the size of the sphere's AABB
*/
async function runGrowCutForSphere(
referencedVolumeId: string,
sphereInfo: SphereInfo,
viewport: Types.IViewport,
options?: GrowCutOptions
): Promise<Types.IImageVolume> {
const referencedVolume = cache.getVolume(referencedVolumeId);
const subVolume = _createSubVolumeFromSphere(
referencedVolume,
sphereInfo,
viewport
);
const labelmap = await _createAndCacheSegmentationSubVolumeForSphere(
subVolume,
sphereInfo,
viewport,
options
);
await run(subVolume.volumeId, labelmap.volumeId);
return labelmap;
}
export { runGrowCutForSphere as default, runGrowCutForSphere };
export type { SphereInfo, GrowCutOptions as GrowCutSphereOptions };
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