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optimize centroid util (#1147)
* move unvarying evaluations outside of loop * refactoring * remove perf checks * commenting * minor fix + renaming * small fix * benchmarking * merge master * Revert pref checks * renaming and comment * remove redundant sets in Map
This commit is contained in:
Severiano Badajoz
+104
-71
@@ -4,13 +4,92 @@ import { unassignedCategoryLabel } from "../globals";
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/*
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Centroid coordinate calculation
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Calculates centroids for displaying
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In the case that a category is truncated, the truncated labels will not have
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centroids calculated
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*/
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/*
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calcMedianCentroid goes through a given metadata category
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fetches each cell's coordinates grouping by category value.
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/*
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Generates a mapping of categorical values to data needed to calculate centroids
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categoricalValue -> {
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length: int,
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holdsFinite: Boolean,
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xCoordinates: Float32Array,
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yCoordinates: Float32Array
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}
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*/
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const getCoordinatesByCategoricalValues = (
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obsAnnotations,
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obsLayout,
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categoryName,
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layoutDimNames,
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categoricalSelection,
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schemaObsByName
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) => {
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const coordsByCategoryLabel = new Map();
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It then calculates the median value and puts that in the array
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const categoryArray = obsAnnotations.col(categoryName).asArray();
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const layoutXArray = obsLayout.col(layoutDimNames[0]).asArray();
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const layoutYArray = obsLayout.col(layoutDimNames[1]).asArray();
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const { categoryValueIndices, categoryValueCounts } = categoricalSelection[
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categoryName
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];
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// Check to see if the current category is a user created annotation
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const isUserAnno = schemaObsByName[categoryName].writable;
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// Iterate over all cells
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for (let i = 0, len = categoryArray.length; i < len; i += 1) {
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// Fetch the categorical value of the current cell
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const categoryValue = categoryArray[i];
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// Get the index of the categoryValue within the category
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const categoryValueIndex = categoryValueIndices.get(categoryValue);
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// If the category is truncated and this value is removed,
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// it will not be assigned a category value and will not be
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// labeled on the graph
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// If the user created this category,
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// do not create a label for the `unassigned` value
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if (
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categoryValueIndex !== undefined &&
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!(isUserAnno && categoryValue === unassignedCategoryLabel)
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) {
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// Create/fetch the scratchpad value
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let coords = coordsByCategoryLabel.get(categoryValue);
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if (coords === undefined) {
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// Get the number of cells which are in the categorical value
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const numInCategoricalValue = categoryValueCounts[categoryValueIndex];
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coords = {
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hasFinite: false,
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xCoordinates: new Float32Array(numInCategoricalValue),
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yCoordinates: new Float32Array(numInCategoricalValue),
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length: 0
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};
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coordsByCategoryLabel.set(categoryValue, coords);
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}
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coords.hasFinite =
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coords.hasFinite ||
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(Number.isFinite(layoutXArray[i]) && Number.isFinite(layoutYArray[i]));
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const coordinatesLength = coords.length;
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coords.xCoordinates[coordinatesLength] = layoutXArray[i];
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coords.yCoordinates[coordinatesLength] = layoutYArray[i];
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coords.length = coordinatesLength + 1;
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}
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}
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return coordsByCategoryLabel;
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};
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/*
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calcMedianCentroid calculates the median coordinates for categorical values in a given metadata field
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categoricalValue -> [x-Coordinate, y-Coordinate]
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*/
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const calcMedianCentroid = (
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@@ -21,85 +100,39 @@ const calcMedianCentroid = (
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categoricalSelection,
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schemaObsByName
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) => {
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const categoryArray = obsAnnotations.col(categoryName).asArray();
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// generate a map describing the coordinates for each value within the given category
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const dataMap = getCoordinatesByCategoricalValues(
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obsAnnotations,
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obsLayout,
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categoryName,
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layoutDimNames,
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categoricalSelection,
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schemaObsByName
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);
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const layoutXArray = obsLayout.col(layoutDimNames[0]).asArray();
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const layoutYArray = obsLayout.col(layoutDimNames[1]).asArray();
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// categoricalValue => [medianXCoordinate, medianYCoordinate]
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const coordinates = new Map();
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// Iterate over all the cells in the category
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for (let i = 0, len = categoryArray.length; i < len; i += 1) {
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const categoryValue = categoryArray[i];
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// Get the index of the categoryValue within the category
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// If the category is truncated and this value is removed,
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// it will not be assigned a category value and will not be
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// labeled on the graph
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const categoryValueIndex = categoricalSelection[
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categoryName
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].categoryValueIndices.get(categoryValue);
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// Check to see if the current category is a user created annotation
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// if the user created this category, do not create a label for the `unassigned` value
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const isUserAnno = schemaObsByName[categoryName].writable;
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if (
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categoryValueIndex !== undefined &&
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!(isUserAnno && categoryValue === unassignedCategoryLabel)
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) {
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// Get the number of cells which are in the category value
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const numInCategoryValue =
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categoricalSelection[categoryName].categoryValueCounts[
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categoryValueIndex
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];
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// Create/fetch the valueArray,
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// which is what the key points to in the `coordinates` hashmap
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const valueArray = coordinates.get(categoryValue) || [
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false, // hasFinite
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0, // index
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new Float32Array(numInCategoryValue), // x coordinates
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new Float32Array(numInCategoryValue) // y coordinates
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];
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const index = valueArray[1];
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let hasFinite = valueArray[0];
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hasFinite =
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hasFinite ||
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(Number.isFinite(layoutXArray[i]) && Number.isFinite(layoutYArray[i]));
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valueArray[0] = hasFinite;
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valueArray[1] = index + 1;
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valueArray[2][index] = layoutXArray[i];
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valueArray[3][index] = layoutYArray[i];
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coordinates.set(categoryValue, valueArray);
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}
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}
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// Iterate over the recently created map
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coordinates.forEach((value, key) => {
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// If there are coordinates for this cateogrical value,
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dataMap.forEach((value, key) => {
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// If there are coordinates for this categorical value,
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// and there is a finite coordinate for the category value
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if (value[2].length > 0 && value[3].length > 0 && value[0]) {
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// Find the median x and y coordinate
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// and insert them into the first two indices
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value[0] = quantile([0.5], value[2])[0];
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value[1] = quantile([0.5], value[3])[0];
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// Remove the last two elements (where the arrays of coordinates were)
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value.pop();
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value.pop();
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} else {
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// remove the entry if not
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coordinates.delete(key);
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if (value.length > 0 && value.hasFinite) {
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const calculatedCoordinates = [];
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// Find and store the median x and y coordinate
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calculatedCoordinates[0] = quantile([0.5], value.xCoordinates)[0];
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calculatedCoordinates[1] = quantile([0.5], value.yCoordinates)[0];
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coordinates.set(key, calculatedCoordinates);
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}
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});
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// return the map: categoricalValue -> [medianXCoordinate, medianYCoordinate]
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return coordinates;
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};
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// A simple function to hash the parameters
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// (not 100% on world hash, Bruce will have to check this one out)
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const hashMedianCentroid = (
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obsAnnotations,
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obsLayout,
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