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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 | 428x 428x 428x 428x | import { volumeLoader, utilities as csUtils } from '@cornerstonejs/core';
import type { Types } from '@cornerstonejs/core';
import { run } from './runGrowCut';
import type { GrowCutOptions } from './runGrowCut';
const POSITIVE_SEED_VALUE = 254;
const NEGATIVE_SEED_VALUE = 255;
// Positive and negative threshold/range (defaults to CT hounsfield ranges)
// //www.sciencedirect.com/topics/medicine-and-dentistry/hounsfield-scale
const NEGATIVE_PIXEL_RANGE = [-Infinity, -995];
const POSITIVE_PIXEL_RANGE = [0, 1900];
type BoundingBoxInfo = {
boundingBox: {
ijkTopLeft: Types.Point3;
ijkBottomRight: Types.Point3;
};
};
type GrowCutBoundingBoxOptions = GrowCutOptions & {
negativePixelRange?: [number, number];
positivePixelRange?: [number, number];
};
function _setNegativeSeedValues(
subVolume: Types.IImageVolume,
labelmap: Types.IImageVolume,
options?: GrowCutBoundingBoxOptions
) {
const {
negativeSeedValue = NEGATIVE_SEED_VALUE,
negativePixelRange = NEGATIVE_PIXEL_RANGE,
} = options;
const subVolPixelData = subVolume.voxelManager.getCompleteScalarDataArray();
const [width, height, numSlices] = labelmap.dimensions;
const middleSliceIndex = Math.floor(numSlices / 2);
const visited = new Array(width * height).fill(false);
const sliceOffset = middleSliceIndex * width * height;
// Run Breadth First Search to set some voxels to negative only for the current slice (performance).
const bfs = (startX: number, startY: number) => {
const queue = [[startX, startY]];
while (queue.length) {
const [x, y] = queue.shift();
const slicePixelIndex = y * width + x;
// Continue if it is out of bounds or it has been already visited.
if (
x < 0 ||
x >= width ||
y < 0 ||
y >= height ||
visited[slicePixelIndex]
) {
continue;
}
// Mark the pixel as visited
visited[slicePixelIndex] = true;
const volumeVoxelIndex = sliceOffset + slicePixelIndex;
const volumeVoxelValue = subVolPixelData[volumeVoxelIndex];
// Does not do anything if it is not air or any value below (eg: minPixelValue)
if (
volumeVoxelValue < negativePixelRange[0] ||
volumeVoxelValue > negativePixelRange[1]
) {
continue;
}
labelmap.voxelManager.setAtIndex(volumeVoxelIndex, negativeSeedValue);
queue.push([x - 1, y]);
queue.push([x + 1, y]);
queue.push([x, y - 1]);
queue.push([x, y + 1]);
}
};
// Check each pixel from left-right or right-left and stop once it reach a pixel value
// that is greater than the threshold value
const scanLine = (startX, limitX, incX, y) => {
for (let x = startX; x !== limitX; x += incX) {
const slicePixelIndex = y * width + x;
const volumeVoxelIndex = sliceOffset + slicePixelIndex;
const volumeVoxelValue = subVolPixelData[volumeVoxelIndex];
if (
volumeVoxelValue < negativePixelRange[0] ||
volumeVoxelValue > negativePixelRange[1]
) {
break;
}
if (!visited[slicePixelIndex]) {
bfs(x, y);
}
}
};
for (let y = 0; y < height; y++) {
scanLine(0, width - 1, 1, y);
scanLine(width - 1, 0, -1, y);
}
}
function _setPositiveSeedValues(
subVolume: Types.IImageVolume,
labelmap: Types.IImageVolume,
options?: GrowCutBoundingBoxOptions
) {
const {
positiveSeedValue = POSITIVE_SEED_VALUE,
positivePixelRange = POSITIVE_PIXEL_RANGE,
} = options;
const subVolPixelData = subVolume.voxelManager.getCompleteScalarDataArray();
const labelmapData = labelmap.voxelManager.getCompleteScalarDataArray();
const [width, height, numSlices] = labelmap.dimensions;
const middleSliceIndex = Math.floor(numSlices / 2);
const startSliceIndex = Math.max(middleSliceIndex - 3, 0);
const stopSliceIndex = Math.max(startSliceIndex + 5, numSlices);
const pixelsPerSlice = width * height;
for (let z = startSliceIndex; z < stopSliceIndex; z++) {
const zOffset = z * pixelsPerSlice;
for (let y = 0; y < height; y++) {
const yOffset = y * width;
for (let x = 0; x < width; x++) {
const index = zOffset + yOffset + x;
const pixelValue = subVolPixelData[index];
// CT specific values
// https://www.sciencedirect.com/topics/medicine-and-dentistry/hounsfield-scale
const isPositiveValue =
pixelValue >= positivePixelRange[0] &&
pixelValue <= positivePixelRange[1];
if (isPositiveValue) {
labelmap.voxelManager.setAtIndex(index, positiveSeedValue);
}
}
}
}
}
async function _createAndCacheSegmentationSubVolumeForBoundingBox(
subVolume: Types.IImageVolume,
options?: GrowCutBoundingBoxOptions
): Promise<Types.IImageVolume> {
const labelmap = volumeLoader.createAndCacheDerivedLabelmapVolume(
subVolume.volumeId
);
_setPositiveSeedValues(subVolume, labelmap, options);
_setNegativeSeedValues(subVolume, labelmap, options);
return labelmap;
}
/**
* Run grow cut for a given volume and a bounding box whithin that volume. The
* positive and negative seed values are set based on positive/negative pixel
* value ranges that can be passed in the `options` (`positivePixelRange` and
* `negativePixelRange`). By default it uses some CT pixel values ranges.
*
* @param referencedVolumeId - Referenced volume id
* @param boundingBoxInfo - Bounding box (top-left and bottom-right corners)
* @param options - Options
* @returns A new labelmap created that shall have the size of the bounding box
*/
async function runGrowCutForBoundingBox(
referencedVolumeId: string,
boundingBoxInfo: BoundingBoxInfo,
options?: GrowCutBoundingBoxOptions
): Promise<Types.IImageVolume> {
const { boundingBox } = boundingBoxInfo;
const { ijkTopLeft, ijkBottomRight } = boundingBox;
const subVolumeBoundsIJK: Types.AABB3 = {
minX: ijkTopLeft[0],
maxX: ijkBottomRight[0],
minY: ijkTopLeft[1],
maxY: ijkBottomRight[1],
minZ: ijkTopLeft[2],
maxZ: ijkBottomRight[2],
};
const subVolume = csUtils.createSubVolume(
referencedVolumeId,
subVolumeBoundsIJK,
{
targetBuffer: {
type: 'Float32Array',
},
}
);
const labelmap = await _createAndCacheSegmentationSubVolumeForBoundingBox(
subVolume,
options
);
await run(subVolume.volumeId, labelmap.volumeId);
return labelmap;
}
export { runGrowCutForBoundingBox as default, runGrowCutForBoundingBox };
export type { BoundingBoxInfo, GrowCutBoundingBoxOptions };
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