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import { utilities, cache } from '@cornerstonejs/core';
import { getVoxelOverlap } from '../segmentation/utilities';
/**
* Gets the scalar data for a series of dimension groups for either a single
* coordinate or a segmentation mask, it will return the an array of scalar
* data for a single coordinate or an array of arrays for a segmentation.
*
* @param dynamicVolume - 4D volume to compute dimension group data from
* @param options - dimensionGroupNumbers: which dimension groups to use (1-based), if left
* blank, gets data over all dimension groups
* Note: dimensionGroupNumber starts at 1 in 4D DICOM specification
* maskVolumeId: segmentationId to get dimension group data of
* worldCoordinate: world coordinate to get dimension group data of
* @returns
*/
function getDataInTime(
dynamicVolume: Types.IDynamicImageVolume,
options: {
dimensionGroupNumbers?: number[];
// @deprecated
frameNumbers?: number[];
maskVolumeId?: string;
worldCoordinate?: Types.Point3;
}
): number[] | number[][] {
let dataInTime;
// if dimensionGroupNumbers is not provided, all dimension groups are selected (1-based)
const dimensionGroups =
options.dimensionGroupNumbers ||
options.frameNumbers ||
Array.from({ length: dynamicVolume.numDimensionGroups }, (_, i) => i + 1);
if (options.frameNumbers) {
console.warn(
'Warning: frameNumbers parameter is deprecated. Please use dimensionGroupNumbers instead.'
);
}
// You only need to provide either maskVolumeId OR worldCoordinate.
// Throws error if neither maskVolumeId or worldCoordinate is given,
// throws error if BOTH maskVolumeId and worldCoordinate is given
if (!options.maskVolumeId && !options.worldCoordinate) {
throw new Error(
'You should provide either maskVolumeId or imageCoordinate'
);
}
if (options.maskVolumeId && options.worldCoordinate) {
throw new Error('You can only use one of maskVolumeId or imageCoordinate');
}
if (options.maskVolumeId) {
const segmentationVolume = cache.getVolume(options.maskVolumeId);
if (!segmentationVolume) {
throw new Error('Segmentation volume not found');
}
const [dataInTime, ijkCoords] = _getDimensionGroupDataMask(
dimensionGroups,
dynamicVolume,
segmentationVolume
);
return [dataInTime, ijkCoords];
}
if (options.worldCoordinate) {
const dataInTime = _getDimensionGroupDataCoordinate(
dimensionGroups,
options.worldCoordinate,
dynamicVolume
);
return dataInTime;
}
return dataInTime;
}
function _getDimensionGroupDataCoordinate(dimensionGroups, coordinate, volume) {
const { dimensions, imageData } = volume;
const index = imageData.worldToIndex(coordinate);
index[0] = Math.floor(index[0]);
index[1] = Math.floor(index[1]);
index[2] = Math.floor(index[2]);
if (!utilities.indexWithinDimensions(index, dimensions)) {
throw new Error('outside bounds');
}
// calculate offset for index
const yMultiple = dimensions[0];
const zMultiple = dimensions[0] * dimensions[1];
const value = [];
dimensionGroups.forEach((dimensionGroupNumber) => {
const scalarIndex = index[2] * zMultiple + index[1] * yMultiple + index[0];
value.push(
volume.voxelManager.getAtIndexAndDimensionGroup(
scalarIndex,
dimensionGroupNumber
)
);
});
return value;
}
function _getDimensionGroupDataMask(
dimensionGroups,
dynamicVolume,
segmentationVolume
) {
const { imageData: maskImageData } = segmentationVolume;
const segVoxelManager = segmentationVolume.voxelManager;
const scalarDataLength = segVoxelManager.getScalarDataLength();
// Pre-allocate memory for array
const nonZeroVoxelIndices = [];
nonZeroVoxelIndices.length = scalarDataLength;
// Get the index of every non-zero voxel in mask
let actualLen = 0;
for (let i = 0, len = scalarDataLength; i < len; i++) {
if (segVoxelManager.getAtIndex(i) !== 0) {
nonZeroVoxelIndices[actualLen++] = i;
}
}
// Trim the array to actual size
nonZeroVoxelIndices.length = actualLen;
const nonZeroVoxelValuesInTime = [];
const isSameVolume =
dynamicVolume.voxelManager.getScalarDataLength() === scalarDataLength &&
JSON.stringify(dynamicVolume.spacing) ===
JSON.stringify(segmentationVolume.spacing);
const ijkCoords = [];
// if the segmentation mask is the same size as the dynamic volume (one dimension group)
// means we can just return the scalar data for the non-zero voxels
if (isSameVolume) {
for (let i = 0; i < nonZeroVoxelIndices.length; i++) {
const valuesInTime = [];
const index = nonZeroVoxelIndices[i];
for (let j = 0; j < dimensionGroups.length; j++) {
valuesInTime.push(
dynamicVolume.voxelManager.getAtIndexAndDimensionGroup(
index,
dimensionGroups[j]
)
);
}
nonZeroVoxelValuesInTime.push(valuesInTime);
ijkCoords.push(segVoxelManager.toIJK(index));
}
return [nonZeroVoxelValuesInTime, ijkCoords];
}
// In case that the segmentation mask is not the same size as the dynamic volume (one dimension group)
// then we need to consider each voxel in the segmentation mask and check if it
// overlaps with the other volume, and if so we need to average the values of the
// overlapping voxels.
const callback = ({
pointLPS: segPointLPS,
value: segValue,
pointIJK: segPointIJK,
}) => {
if (segValue === 0) {
// not interested
return;
}
// Then for each non-zero voxel in the segmentation mask, we should
// again perform the pointInShapeCallback to run the averaging callback
// function to get the average value of the overlapping voxels.
const overlapIJKMinMax = getVoxelOverlap(
dynamicVolume.imageData,
dynamicVolume.dimensions,
dynamicVolume.spacing,
segPointLPS
);
// count represents the number of voxels of the dynamic volume that represents
// one voxel of the segmentation mask
let count = 0;
const perDimensionGroupSum = new Map();
// Pre-initialize the Map
dimensionGroups.forEach((dimensionGroupNumber) =>
perDimensionGroupSum.set(dimensionGroupNumber, 0)
);
const averageCallback = ({ index }) => {
for (let i = 0; i < dimensionGroups.length; i++) {
const value = dynamicVolume.voxelManager.getAtIndexAndDimensionGroup(
index,
dimensionGroups[i]
);
const dimensionGroupNumber = dimensionGroups[i];
perDimensionGroupSum.set(
dimensionGroupNumber,
perDimensionGroupSum.get(dimensionGroupNumber) + value
);
}
count++;
};
dynamicVolume.voxelManager.forEach(averageCallback, {
imageData: dynamicVolume.imageData,
boundsIJK: overlapIJKMinMax,
});
// average the values
const averageValues = [];
perDimensionGroupSum.forEach((sum) => {
averageValues.push(sum / count);
});
ijkCoords.push(segPointIJK);
nonZeroVoxelValuesInTime.push(averageValues);
};
// Since we have the non-zero voxel indices of the segmentation mask,
// we theoretically can use them, however, we kind of need to compute the
// pointLPS for each of the non-zero voxel indices, which is a bit of a pain.
// Todo: consider using the nonZeroVoxelIndices to compute the pointLPS
segmentationVolume.voxelManager.forEach(callback, {
imageData: maskImageData,
});
return [nonZeroVoxelValuesInTime, ijkCoords];
}
export default getDataInTime;
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