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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 | import { utilities, cache, Types } from '@cornerstonejs/core';
/**
* 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('No ROI provided');
}
if (options.maskVolumeId && options.imageCoordinate) {
throw new Error('Please provide only one ROI');
}
if (options.maskVolumeId) {
const segmentationVolume = cache.getVolume(options.maskVolumeId);
// Get the index of every non-zero voxel in mask by mapping indexes to
// new array, then using the array to filter
const indexArray = segmentationVolume
.getScalarData()
.map((_, i) => i)
.filter((i) => segmentationVolume.getScalarData()[i] !== 0);
const dataInTime = _getTimePointDataMask(frames, indexArray, dynamicVolume);
return dataInTime;
}
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, indexArray, volume) {
const allScalarData = volume.getScalarDataArrays();
const value = [];
for (let i = 0; i < indexArray.length; i++) {
const indexValues = [];
frames.forEach((frame) => {
const activeScalarData = allScalarData[frame];
indexValues.push(activeScalarData[indexArray[i]]);
});
value.push(indexValues);
}
return value;
}
export default getDataInTime;
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