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import { getVoxelOverlap } from '../segmentation/utilities';
import pointInShapeCallback from '../pointInShapeCallback';
/**
* Gets the scalar data for a series of time points 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 time point data from
* @param options - frameNumbers: which frames to use as timepoints, if left
* blank, gets data timepoints over all frames
* maskVolumeId: segmentationId to get timepoint data of
* imageCoordinate: world coordinate to get timepoint data of
* @returns
*/
function getDataInTime(
dynamicVolume: Types.IDynamicImageVolume,
options: {
frameNumbers?;
maskVolumeId?;
imageCoordinate?;
}
): number[] | number[][] {
let dataInTime;
// if frameNumbers is not provided, all frames are selected
const frames = options.frameNumbers || [
...Array(dynamicVolume.numTimePoints).keys(),
];
// You only need to provide either maskVolumeId OR imageCoordinate.
// Throws error if neither maskVolumeId or imageCoordinate is given,
// throws error if BOTH maskVolumeId and imageCoordinate is given
if (!options.maskVolumeId && !options.imageCoordinate) {
throw new Error(
'You should provide either maskVolumeId or imageCoordinate'
);
}
if (options.maskVolumeId && options.imageCoordinate) {
throw new Error('You can only use one of maskVolumeId or imageCoordinate');
}
if (options.maskVolumeId) {
const segmentationVolume = cache.getVolume(options.maskVolumeId);
const [dataInTime, ijkCoords] = _getTimePointDataMask(
frames,
dynamicVolume,
segmentationVolume
);
return [dataInTime, ijkCoords];
}
if (options.imageCoordinate) {
const dataInTime = _getTimePointDataCoordinate(
frames,
options.imageCoordinate,
dynamicVolume
);
return dataInTime;
}
return dataInTime;
}
function _getTimePointDataCoordinate(frames, 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 allScalarData = volume.getScalarDataArrays();
const value = [];
frames.forEach((frame) => {
const activeScalarData = allScalarData[frame];
const scalarIndex = index[2] * zMultiple + index[1] * yMultiple + index[0];
value.push(activeScalarData[scalarIndex]);
});
return value;
}
function _getTimePointDataMask(frames, dynamicVolume, segmentationVolume) {
const { imageData: maskImageData } = segmentationVolume;
const segScalarData = segmentationVolume.getScalarData();
const len = segScalarData.length;
// Pre-allocate memory for array
const nonZeroVoxelIndices = [];
nonZeroVoxelIndices.length = len;
const ijkCoords = [];
const dimensions = segmentationVolume.dimensions;
// Get the index of every non-zero voxel in mask
let actualLen = 0;
for (let i = 0, len = segScalarData.length; i < len; i++) {
if (segScalarData[i] !== 0) {
ijkCoords.push([
i % dimensions[0],
Math.floor((i / dimensions[0]) % dimensions[1]),
Math.floor(i / (dimensions[0] * dimensions[1])),
]);
nonZeroVoxelIndices[actualLen++] = i;
}
}
// Trim the array to actual size
nonZeroVoxelIndices.length = actualLen;
const dynamicVolumeScalarDataArray = dynamicVolume.getScalarDataArrays();
const values = [];
const isSameVolume =
dynamicVolumeScalarDataArray[0].length === len &&
JSON.stringify(dynamicVolume.spacing) ===
JSON.stringify(segmentationVolume.spacing);
// if the segmentation mask is the same size as the dynamic volume (one frame)
// means we can just return the scalar data for the non-zero voxels
if (isSameVolume) {
for (let i = 0; i < nonZeroVoxelIndices.length; i++) {
const indexValues = [];
frames.forEach((frame) => {
const activeScalarData = dynamicVolumeScalarDataArray[frame];
indexValues.push(activeScalarData[nonZeroVoxelIndices[i]]);
});
values.push(indexValues);
}
return [values, ijkCoords];
}
// In case that the segmentation mask is not the same size as the dynamic volume (one frame)
// 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,
}) => {
// see if the value is non-zero
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 perFrameSum = new Map();
// Pre-initialize the Map
frames.forEach((frame) => perFrameSum.set(frame, 0));
const averageCallback = ({ index }) => {
for (let i = 0; i < frames.length; i++) {
const value = dynamicVolumeScalarDataArray[i][index];
const frame = frames[i];
perFrameSum.set(frame, perFrameSum.get(frame) + value);
}
count++;
};
pointInShapeCallback(
dynamicVolume.imageData,
() => true,
averageCallback,
overlapIJKMinMax
);
// average the values
const averageValues = [];
perFrameSum.forEach((sum) => {
averageValues.push(sum / count);
});
ijkCoords.push(segPointIJK);
values.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
pointInShapeCallback(maskImageData, () => true, callback);
return [values, ijkCoords];
}
export default getDataInTime;
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