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import type { Types } from '@cornerstonejs/core';
import { vec3 } from 'gl-matrix';
import createPolylineToolData from './createPolylineToolData';
import findAnnotationsForInterpolation from './findAnnotationForInterpolation';
import type { InterpolationViewportData } from '../../../types/InterpolationTypes';
import type { InterpolationROIAnnotation } from '../../../types/ToolSpecificAnnotationTypes';
import type { AnnotationInterpolationCompletedEventDetail } from '../../../types/EventTypes';
import EventTypes from '../../../enums/Events';
import * as annotationState from '../../../stateManagement/annotation';
import selectHandles from './selectHandles';
import updateChildInterpolationUID from './updateChildInterpolationUID';
import { createPolylineHole } from '../../../eventListeners/annotations/contourSegmentation/contourSegmentationCompleted';
const { PointsManager } = utilities;
/**
* An XYZ encoded points that also includes an indicator I for whether the
* point is included in the original contour.
*/
export type PointsXYZI = Types.PointsXYZ & {
I?: boolean[];
kIndex?: number;
};
export type PointsArray3 = Types.PointsManager<Types.Point3> & {
I?: boolean[];
};
const dP = 0.2; // Aim for < 0.2mm between interpolated nodes when super-sampling.
/**
* interpolate - Interpolate missing contours in the ROIContours.
* If input is tool data collection, it is expected to be sorted in the order
* of stack image in which it was drawn.
*
* This is performed in a microtask in order to avoid delaying the event handler
* excessively, but to ensure it is completed before the data is additionally
* changed. It was originally done in a setTimeout, but that allowed the data
* to be updated between calls, causing issues with the interpolation process.
*
* @param viewportData - Object
* @returns null
*/
function interpolate(viewportData: InterpolationViewportData) {
Iif (!viewportData.annotation) {
return;
}
const { isInterpolationUpdate, annotation } = viewportData;
queueMicrotask(() => {
try {
Iif (isInterpolationUpdate) {
annotation.isInterpolationUpdate = true;
// This may not be true long term, but treat it as user generated for
// this run.
annotation.autoGenerated = false;
}
startInterpolation(viewportData);
} finally {
Iif (isInterpolationUpdate) {
// Reset the auto generated flag
annotation.autoGenerated = true;
}
}
});
}
/**
* Start the actual interpolation from the list
* @param viewportData - Object
* @returns null
*/
function startInterpolation(viewportData: InterpolationViewportData) {
const { annotation: toolData } = viewportData;
updateChildInterpolationUID(toolData);
const { interpolationData, interpolationList } =
findAnnotationsForInterpolation(toolData, viewportData) || {};
Iif (!interpolationData || !interpolationList) {
return;
}
const eventData = {
toolName: toolData.metadata.toolName,
toolType: toolData.metadata.toolName,
viewport: viewportData.viewport,
};
for (let i = 0; i < interpolationList.length; i++) {
Eif (interpolationList[i]) {
_linearlyInterpolateBetween(
interpolationList[i].list,
interpolationList[i].pair,
interpolationData,
eventData
);
}
}
const { id, renderingEngineId, element } = viewportData.viewport;
const eventDetails: AnnotationInterpolationCompletedEventDetail = {
annotation: toolData,
element,
viewportId: id,
renderingEngineId,
};
if (interpolationList.length) {
triggerEvent(
viewportData.viewport.element,
EventTypes.ANNOTATION_INTERPOLATION_PROCESS_COMPLETED,
eventDetails
);
}
}
/**
* _linearlyInterpolateBetween - Linearly interpolate all the slices in the
* indices array between the contourPair.
*
* @param indices - natural[], An array of slice indices to interpolate.
* @param annotationPair - natural[2], The slice indices of the reference contours.
* @param interpolationData - object
* @param eventData - object
* @returns null
*/
function _linearlyInterpolateBetween(
indices,
annotationPair,
interpolationData,
eventData
) {
const annotation0 = interpolationData.get(annotationPair[0])[0];
const annotation1 = interpolationData.get(annotationPair[1])[0];
const c1 = _generateClosedContour(annotation0.data.contour.polyline);
const c2 = _generateClosedContour(annotation1.data.contour.polyline);
const { c1Interp, c2Interp } = _generateInterpolationContourPair(c1, c2);
c1Interp.kIndex = annotationPair[0];
c2Interp.kIndex = annotationPair[1];
// Using the newly constructed contours, interpolate each ROI.
indices.forEach(function (index) {
_linearlyInterpolateContour(
c1Interp,
c2Interp,
index,
annotationPair,
interpolationData,
c1.x.length > c2.x.length,
eventData
);
});
}
function getPointCount(pointArray) {
let sum = 0;
for (let i = 0; i < pointArray.I.length; i++) {
if (pointArray.I[i]) {
sum++;
}
}
return sum;
}
/**
* _linearlyInterpolateContour - Inserts a linearly interpolated contour at
* specified slice index.
*
* @param c1Interp - object, The first reference contour.
* @param c2Interp - object, The second reference contour.
* @param sliceIndex - Number, The slice index to interpolate.
* @param annotationPair - Number[], The slice indices of the reference contours.
* @param interpolationData - object[], Data for the slice location of contours
* for the ROIContour.
* @param c1HasMoreNodes - boolean, True if c1 has more nodes than c2.
* @param eventData - object
* @returns null
*/
function _linearlyInterpolateContour(
c1Interp,
c2Interp,
sliceIndex,
annotationPair,
interpolationData,
c1HasMoreNodes,
eventData
) {
const [startIndex, endIndex] = annotationPair;
const zInterp = (sliceIndex - startIndex) / (endIndex - startIndex);
const annotation0 = interpolationData.get(startIndex)[0];
const annotation1 = interpolationData.get(endIndex)[0];
const interpolated3DPoints = _generateInterpolatedOpenContour(
c1Interp,
c2Interp,
zInterp,
c1HasMoreNodes
);
const nearestAnnotation = zInterp > 0.5 ? annotation1 : annotation0;
const handlePoints = selectHandles(interpolated3DPoints);
Iif (interpolationData.has(sliceIndex)) {
_editInterpolatedContour(
interpolated3DPoints,
handlePoints,
sliceIndex,
nearestAnnotation,
eventData
);
} else {
_addInterpolatedContour(
interpolated3DPoints,
handlePoints,
sliceIndex,
nearestAnnotation,
eventData
);
}
}
/**
* _addInterpolatedContour - Adds a new contour to the imageId.
*
* @param interpolated3DPoints - object, The polygon to add to the ROIContour.
* @param sliceIndex - Number, The slice index to interpolate..
* @param referencedToolData - The toolData of another polygon in the
* ROIContour, to assign appropriate metadata to the new polygon.
* @param eventData - object
* @returns null
*/
function _addInterpolatedContour(
interpolated3DPoints: PointsArray3,
handlePoints: PointsArray3,
sliceIndex: number,
referencedToolData,
eventData
) {
const points = interpolated3DPoints.points;
const { viewport } = eventData;
const interpolatedAnnotation = createPolylineToolData(
points,
handlePoints,
referencedToolData
);
const viewRef = viewport.getViewReference({ sliceIndex });
Iif (!viewRef) {
throw new Error(`Can't find slice ${sliceIndex}`);
}
Object.assign(interpolatedAnnotation.metadata, viewRef);
annotationState.state.addAnnotation(interpolatedAnnotation, viewport.element);
referencedToolData.onInterpolationComplete?.(
interpolatedAnnotation,
referencedToolData
);
const { parentAnnotationUID } = referencedToolData;
Iif (parentAnnotationUID) {
const parentReferenced =
annotationState.state.getAnnotation(parentAnnotationUID);
const parentAnnotation = _findExistingAnnotation(
parentReferenced,
sliceIndex,
eventData
);
createPolylineHole(viewport, parentAnnotation, interpolatedAnnotation);
}
}
/**
* Finds an existing annotation on the given slide, with the interpolation UID as
* specified in the referenced tool data.
*/
function _findExistingAnnotation(referencedToolData, sliceIndex, eventData) {
const { viewport } = eventData;
const annotations = annotationState.state.getAnnotations(
referencedToolData.metadata.toolName,
viewport.element
);
for (let i = 0; i < annotations.length; i++) {
const annotation = annotations[i] as InterpolationROIAnnotation;
if (
annotation.interpolationUID === referencedToolData.interpolationUID &&
annotation.metadata.sliceIndex === sliceIndex
) {
return annotation;
}
}
}
/**
* _editInterpolatedContour - Edits an interpolated polygon on the imageId
* that corresponds to the specified ROIContour.
*
* @param interpolated3DPoints - object, The polygon to add to the ROIContour.
* @param sliceIndex - Number, The slice index to interpolate.
* @param referencedToolData - type, The toolData of another polygon in the
* ROIContour, to assign appropriate metadata to the new polygon.
* @param eventData - object
*/
function _editInterpolatedContour(
interpolated3DPoints: PointsArray3,
handlePoints: PointsArray3,
sliceIndex,
referencedToolData,
eventData
) {
const oldAnnotationData = _findExistingAnnotation(
referencedToolData,
sliceIndex,
eventData
);
const points = interpolated3DPoints.points;
const interpolatedAnnotation = createPolylineToolData(
points,
handlePoints,
oldAnnotationData
);
// Does a real update here instead of an add/remove, which caused delete issues in child annotations
Object.assign(oldAnnotationData, {
metadata: interpolatedAnnotation.metadata,
data: interpolatedAnnotation.data,
});
}
/**
* _generateInterpolatedOpenContour - Interpolate an open contour between c1ir
* and c2ir at the zInterp position.
*
* @param c1ir - object, The interpolated c1 contour with
* superfluous nodes removed.
* @param c2ir - object, The interpolated c2 contour with
* superfluous nodes removed.
* @param zInterp - Number, The z- coordinate of the desired
* interpolation.
* @param c1HasMoreNodes - boolean, True if c1 has more original nodes
* than c2.
* @returns object, The interpolated contour at z=zInterp.
*/
function _generateInterpolatedOpenContour(
c1ir,
c2ir,
zInterp,
c1HasMoreNodes
): PointsArray3 {
const indices = c1HasMoreNodes ? c1ir.I : c2ir.I;
const c1 = PointsManager.fromXYZ(c1ir);
const c2 = PointsManager.fromXYZ(c2ir);
const { length } = c1;
const cInterp = PointsManager.create3(length) as PointsArray3;
const vecSubtract = vec3.create();
const vecResult = vec3.create();
const c1Source = PointsManager.create3(length);
c1Source.kIndex = c1ir.kIndex;
const c2Source = PointsManager.create3(length);
c2Source.kIndex = c2ir.kIndex;
for (let i = 0; i < c1ir.x.length; i++) {
if (indices[i]) {
const c1point = c1.getPoint(i);
const c2point = c2.getPoint(i);
c1Source.push(c1point);
c2Source.push(c2point);
vec3.sub(vecSubtract, c2point, c1point);
cInterp.push(
vec3.scaleAndAdd(
vecResult,
c1point,
vecSubtract,
zInterp
) as Types.Point3
);
}
}
cInterp.sources = [c1Source, c2Source];
return cInterp;
}
/**
* _generateInterpolationContourPair - generates two aligned contours with an
* equal number of nodes from which an intermediate contour may be interpolated.
*
* @param c1 - The first contour.
* @param c2 - The second contour.
* @returns - An object containing the two contours.
*/
function _generateInterpolationContourPair(c1, c2) {
const cumPerim1 = _getCumulativePerimeter(c1);
const cumPerim2 = _getCumulativePerimeter(c2);
const interpNodes = Math.max(
Math.ceil(cumPerim1[cumPerim1.length - 1] / dP),
Math.ceil(cumPerim2[cumPerim2.length - 1] / dP)
);
const cumPerim1Norm = _normalisedCumulativePerimeter(cumPerim1);
const cumPerim2Norm = _normalisedCumulativePerimeter(cumPerim2);
const numNodes1 = interpNodes + c2.x.length;
const numNodes2 = interpNodes + c1.x.length;
// concatenate p && cumPerimNorm
const perim1Interp = _getInterpolatedPerim(numNodes1, cumPerim1Norm);
const perim2Interp = _getInterpolatedPerim(numNodes2, cumPerim2Norm);
const perim1Ind = _getIndicatorArray(numNodes1 - 2, c1.x.length);
const perim2Ind = _getIndicatorArray(numNodes2 - 2, c2.x.length);
const nodesPerSegment1 = _getNodesPerSegment(perim1Interp, perim1Ind);
const nodesPerSegment2 = _getNodesPerSegment(perim2Interp, perim2Ind);
const c1i = _getSuperSampledContour(c1, nodesPerSegment1);
const c2i = _getSuperSampledContour(c2, nodesPerSegment2);
// Keep c2i fixed and shift the starting node of c1i to minimise the total length of segments.
_shiftSuperSampledContourInPlace(c1i, c2i);
return _reduceContoursToOriginNodes(c1i, c2i);
}
/**
* _reduceContoursToOriginNodes - Removes any nodes from the contours that don't
* correspond to an original contour node.
*
* @param c1i - The first super-sampled contour.
* @param c2i - The second super-sampled contour.
* @returns An object containing the two reduced contours.
*/
function _reduceContoursToOriginNodes(c1i: PointsXYZI, c2i: PointsXYZI) {
const c1Interp: PointsXYZI = {
x: [],
y: [],
z: [],
I: [],
};
const c2Interp: PointsXYZI = {
x: [],
y: [],
z: [],
I: [],
};
for (let i = 0; i < c1i.x.length; i++) {
if (c1i.I[i] || c2i.I[i]) {
c1Interp.x.push(c1i.x[i]);
c1Interp.y.push(c1i.y[i]);
c1Interp.z.push(c1i.z[i]);
c1Interp.I.push(c1i.I[i]);
c2Interp.x.push(c2i.x[i]);
c2Interp.y.push(c2i.y[i]);
c2Interp.z.push(c2i.z[i]);
c2Interp.I.push(c2i.I[i]);
}
}
return {
c1Interp,
c2Interp,
};
}
/**
* _shiftSuperSampledContourInPlace - Shifts the indices of c1i around to
* minimize: SUM (|c1i[i]-c2i[i]|) from 0 to N.
*
* @param c1i - The contour to shift.
* @param c2i - The reference contour.
* modifies c1i
* @returns null
*/
function _shiftSuperSampledContourInPlace(c1i, c2i) {
const c1iLength = c1i.x.length;
const optimal = {
startingNode: 0,
totalSquaredXYLengths: Infinity,
};
for (let startingNode = 0; startingNode < c1iLength; startingNode++) {
let node = startingNode;
// NOTE: 1) Ignore calculating Z, as the sum of all squared Z distances will always be a constant.
// NOTE: 2) Don't need actual length, so don't worry about square rooting.
let totalSquaredXYLengths = 0;
for (let iteration = 0; iteration < c1iLength; iteration++) {
totalSquaredXYLengths +=
(c1i.x[node] - c2i.x[iteration]) ** 2 +
(c1i.y[node] - c2i.y[iteration]) ** 2 +
(c1i.z[node] - c2i.z[iteration]) ** 2;
node++;
if (node === c1iLength) {
node = 0;
}
}
if (totalSquaredXYLengths < optimal.totalSquaredXYLengths) {
optimal.totalSquaredXYLengths = totalSquaredXYLengths;
optimal.startingNode = startingNode;
}
}
const node = optimal.startingNode;
_shiftCircularArray(c1i.x, node);
_shiftCircularArray(c1i.y, node);
_shiftCircularArray(c1i.z, node);
_shiftCircularArray(c1i.I, node);
}
/**
* _shiftCircularArray - Shift the circular array by the count.
*
* @param arr - Array, The array.
* @param count - Number, The shift.
* @returns The shifted array.
*/
function _shiftCircularArray(arr, count) {
count -= arr.length * Math.floor(count / arr.length);
const slicedArray = arr.splice(0, count);
arr.push(...slicedArray);
return arr;
}
/**
* _getSuperSampledContour - Generates a super sampled contour with additional
* nodes added per segment.
*
* @param c - object, The original contour.
* @param nodesPerSegment - Number[], An array of the number of nodes to add
* per line segment.
* @returns object, The super sampled contour.
*/
function _getSuperSampledContour(c, nodesPerSegment): PointsXYZI {
const ci = {
x: [],
y: [],
z: [],
I: [],
};
// Length - 1, produces 'open' polygon.
for (let n = 0; n < c.x.length - 1; n++) {
// Add original node.
ci.x.push(c.x[n]);
ci.y.push(c.y[n]);
ci.z.push(c.z[n]);
ci.I.push(true);
// Add linearly interpolated nodes.
const xSpacing = (c.x[n + 1] - c.x[n]) / (nodesPerSegment[n] + 1);
const ySpacing = (c.y[n + 1] - c.y[n]) / (nodesPerSegment[n] + 1);
const zSpacing = (c.z[n + 1] - c.z[n]) / (nodesPerSegment[n] + 1);
// Add other nodesPerSegment - 1 other nodes (as already put in original node).
for (let i = 0; i < nodesPerSegment[n] - 1; i++) {
ci.x.push(ci.x[ci.x.length - 1] + xSpacing);
ci.y.push(ci.y[ci.y.length - 1] + ySpacing);
ci.z.push(ci.z[ci.z.length - 1] + zSpacing);
ci.I.push(false);
}
}
return ci;
}
/**
* _getNodesPerSegment - Returns an array of the number of interpolated nodes
* to be added along each line segment of a polygon.
*
* @param perimInterp - Number[], Normalized array of original and added nodes.
* @param perimInd - boolean[], The indicator array describing the location of
* the original contour's nodes.
* @returns Number[], An array containing the number of nodes to be
* added per original line segment.
*/
function _getNodesPerSegment(perimInterp, perimInd) {
const idx = [];
for (let i = 0; i < perimInterp.length; ++i) {
idx[i] = i;
}
idx.sort(function (a, b) {
return perimInterp[a] < perimInterp[b] ? -1 : 1;
});
const perimIndSorted = [];
for (let i = 0; i < perimInd.length; i++) {
perimIndSorted.push(perimInd[idx[i]]);
}
const indicesOfOriginNodes = perimIndSorted.reduce(function (
arr,
elementValue,
i
) {
if (elementValue) {
arr.push(i);
}
return arr;
},
[]);
const nodesPerSegment = [];
for (let i = 0; i < indicesOfOriginNodes.length - 1; i++) {
nodesPerSegment.push(indicesOfOriginNodes[i + 1] - indicesOfOriginNodes[i]);
}
return nodesPerSegment;
}
/**
* _getIndicatorArray - Produces an array of the location of the original nodes
* in a super sampled contour.
*
* @param contour - object, The original contour.
* @param numNodes - Number, The number of nodes added.
* @returns boolean[], The indicator array of original node locations.
*/
function _getIndicatorArray(numFalse, numTrue) {
const perimInd = new Array(numFalse + numTrue);
perimInd.fill(false, 0, numFalse);
perimInd.fill(true, numFalse, numFalse + numTrue);
return perimInd;
}
/**
* _getInterpolatedPerim - Adds additional interpolated nodes to the
* normalized perimeter array.
*
* @param numNodes - object, The number of nodes to add.
* @param cumPerimNorm - The cumulative perimeter array.
* @returns Number[], The array of nodes.
*/
function _getInterpolatedPerim(numNodes, cumPerimNorm) {
const diff = 1 / (numNodes - 1);
const linspace = [diff];
// Length - 2 as we are discarding 0 and 1 for efficiency (no need to calculate them).
for (let i = 1; i < numNodes - 2; i++) {
linspace.push(linspace[linspace.length - 1] + diff);
}
return linspace.concat(cumPerimNorm);
}
/**
* _normalizedCumulativePerimeter - Normalizes the cumulative perimeter array.
*
* @param cumPerim - An array of the cumulative perimeter at each of a contour.
* @returns The normalized array.
*/
function _normalisedCumulativePerimeter(cumPerim) {
const cumPerimNorm = [];
for (let i = 0; i < cumPerim.length; i++) {
cumPerimNorm.push(cumPerim[i] / cumPerim[cumPerim.length - 1]);
}
return cumPerimNorm;
}
/**
* _getCumulativePerimeter - Returns an array of the the cumulative perimeter at
* each node of the contour.
*
* @param contour - The contour.
* @returns An array of the cumulative perimeter at each node.
*/
function _getCumulativePerimeter(contour: Types.PointsXYZ): number[] {
const cumulativePerimeter = [0];
for (let i = 1; i < contour.x.length; i++) {
const lengthOfSegment = Math.sqrt(
(contour.x[i] - contour.x[i - 1]) ** 2 +
(contour.y[i] - contour.y[i - 1]) ** 2 +
(contour.z[i] - contour.z[i - 1]) ** 2
);
cumulativePerimeter.push(cumulativePerimeter[i - 1] + lengthOfSegment);
}
return cumulativePerimeter;
}
/**
* _generateClosedContour - Generate a clockwise contour object from the points
* of a clockwise or anti-clockwise polygon.
*
* @param points - The points to generate the contour from.
* @returns The generated contour object.
*/
function _generateClosedContour(points): Types.PointsXYZ {
const c = {
x: [],
y: [],
z: [],
};
for (let i = 0; i < points.length; i++) {
c.x[i] = points[i][0];
c.y[i] = points[i][1];
c.z[i] = points[i][2];
}
// Push last node to create closed contour.
c.x.push(c.x[0]);
c.y.push(c.y[0]);
c.z.push(c.z[0]);
return c;
}
export default interpolate;
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