fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-19 10:58:10 +08:00
Code Issues Packages Projects Releases Wiki Activity

add array type foundations (#2376)

Browse Source
This commit is contained in:
Bruce Martin
2021-08-12 07:17:05 -07:00
committed by GitHub
parent 59c475b821
commit 660dff256c
9 changed files with 103 additions and 65 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
client/src/annoMatrix/loader.ts
View File

@@ -8,7 +8,7 @@ import {
removeObsAnnoCategory,
addObsLayout,
} from "../util/stateManager/schemaHelpers";
import { isArrayOrTypedArray } from "../util/typeHelpers";
import { isAnyArray } from "../common/types/arraytypes";
import { _whereCacheCreate } from "./whereCache";
import AnnoMatrix from "./annoMatrix";
import PromiseLimit from "../util/promiseLimit";
@@ -134,7 +134,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const newAnnoMatrix = this._clone();
let data;
if (isArrayOrTypedArray(value)) {
if (isAnyArray(value)) {
if (value.constructor !== Ctor)
throw new Error("Mismatched value array type");
if (value.length !== this.nObs)

85
client/src/common/types/arraytypes.ts Normal file
View File

@@ -0,0 +1,85 @@
/**
* Utility type and interface definitions.
*/
/**
* TypedArrays that can be assigned to a number.
*/
export type TypedArray =
| Int8Array
| Uint8Array
| Int16Array
| Uint16Array
| Int32Array
| Uint32Array
| Float32Array
| Float64Array;
export type UnsignedTypedArray = Uint8Array | Uint16Array | Uint32Array;
export type FloatTypedArray = Float32Array | Float64Array;
export type TypedArrayConstructor =
| Int8ArrayConstructor
| Uint8ArrayConstructor
| Int16ArrayConstructor
| Uint16ArrayConstructor
| Int32ArrayConstructor
| Uint32ArrayConstructor
| Float32ArrayConstructor
| Float64ArrayConstructor;
export type AnyArray = Array<unknown> | TypedArray;
export type NumberArray = Array<number> | TypedArray;
export type Int8 = Int8Array[0];
export type Uint8 = Uint8Array[0];
export type Int16 = Int16Array[0];
export type Uint16 = Uint16Array[0];
export type Int32 = Int32Array[0];
export type Uint32 = Uint32Array[0];
export type Float32 = Float32Array[0];
export type Float64 = Float64Array[0];
/**
* Test if the parameter is a TypedArray.
* @param tbd - value to be tested
* @returns true if `tbd` is a TypedArray, false if not.
*/
export function isTypedArray(tbd: unknown): tbd is TypedArray {
return (
ArrayBuffer.isView(tbd) &&
Object.prototype.toString.call(tbd) !== "[object DataView]"
);
}
/**
* Test if the paramter is a float TypedArray
* @param tbd - value to be tested
* @returns - true if `tbd` is a float typed array.
*/
export function isFloatTypedArray(tbd: unknown): tbd is FloatTypedArray {
return tbd instanceof Float32Array || tbd instanceof Float64Array;
}
/**
* Test if the paramter is a float TypedArray
* @param tbd - value to be tested
* @returns - true if `tbd` is a float typed array.
*/
export function isUnsignedTypedArray(tbd: unknown): tbd is UnsignedTypedArray {
return (
tbd instanceof Uint8Array ||
tbd instanceof Uint16Array ||
tbd instanceof Uint32Array
);
}
/**
* Test if the parameter is a TypedArray or Array
* @param tbd - value to be tested
* @returns - true if `tbd` is a TypedArray or Array
*/
export function isAnyArray(tbd: unknown): tbd is AnyArray {
return Array.isArray(tbd) || isTypedArray(tbd);
}

11
client/src/util/dataframe/dataframe.ts
View File

@@ -1,12 +1,7 @@
import { IdentityInt32Index, isLabelIndex } from "./labelIndex";
// weird cross-dependency that we should clean up someday...
import {
isTypedArray,
isArrayOrTypedArray,
callOnceLazy,
memoize,
__getMemoId,
} from "./util";
import { callOnceLazy, memoize, __getMemoId } from "./util";
import { isTypedArray, isAnyArray } from "../../common/types/arraytypes";
import {
summarizeContinuous,
summarizeCategorical as _summarizeCategorical,
@@ -163,7 +158,7 @@ class Dataframe {
if (!Array.isArray(columnarData)) {
throw new TypeError("Dataframe constructor requires array of columns");
}
if (!columnarData.every((c) => isArrayOrTypedArray(c))) {
if (!columnarData.every((c) => isAnyArray(c))) {
throw new TypeError("Dataframe columns must all be Array or TypedArray");
}
if (!isLabelIndex(rowIndex)) {

2
client/src/util/dataframe/histogram.ts
View File

@@ -1,7 +1,7 @@
/*
Dataframe histogram
*/
import { isTypedArray } from "./util";
import { isTypedArray } from "../../common/types/arraytypes";
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
function _histogramContinuous(column: any, bins: any, min: any, max: any) {

2
client/src/util/dataframe/util.ts
View File

@@ -2,8 +2,6 @@
Private utility code for dataframe
*/
export { isTypedArray, isArrayOrTypedArray } from "../typeHelpers";
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function callOnceLazy(f: any) {
/*

6
client/src/util/stateManager/matrix.ts
View File

@@ -1,6 +1,6 @@
import { flatbuffers } from "flatbuffers";
import { NetEncoding } from "./matrix_generated";
import { isTypedArray, isFpTypedArray } from "../typeHelpers";
import { isTypedArray, isFloatTypedArray } from "../../common/types/arraytypes";
import {
Dataframe,
IdentityInt32Index,
@@ -188,7 +188,7 @@ function promoteTypedArray(o: any) {
TODO - future optimization: not all int32/uint32 data series require
promotion to float64. We COULD simply look at the data to decide.
*/
if (isFpTypedArray(o) || Array.isArray(o)) return o;
if (isFloatTypedArray(o) || Array.isArray(o)) return o;
let TypedArrayCtor;
switch (o.constructor) {
@@ -246,7 +246,7 @@ export function matrixFBSToDataframe(arrayBuffers: any) {
.map((fb: any) =>
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
fb.columns.map((c: any) => {
if (isFpTypedArray(c) || Array.isArray(c)) return c;
if (isFloatTypedArray(c) || Array.isArray(c)) return c;
return promoteTypedArray(c);
})
)

32
client/src/util/typeHelpers.ts
View File

@@ -1,32 +0,0 @@
/*
Various type and schema related helper functions.
*/
/*
Utility function to test for a typed array
*/
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function isTypedArray(x: any) {
return (
ArrayBuffer.isView(x) &&
Object.prototype.toString.call(x) !== "[object DataView]"
);
}
/*
Test for float typed array, ie, Float32TypedArray or Float64TypedArray
*/
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function isFpTypedArray(x: any) {
let constructor;
const isFloatArray =
x &&
({ constructor } = x) &&
(constructor === Float32Array || constructor === Float64Array);
return isFloatArray;
}
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function isArrayOrTypedArray(x: any) {
return Array.isArray(x) || isTypedArray(x);
}

12
client/src/util/typedCrossfilter/crossfilter.ts
View File

@@ -9,6 +9,7 @@ import {
upperBoundIndirect,
} from "./sort";
import { makeSortIndex } from "./util";
import { isAnyArray } from "../../common/types/arraytypes";
class NotImplementedError extends Error {
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
@@ -450,7 +451,7 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension {
value,
new ValueArrayType(data.length)
);
} else if (isArrayOrTypedArray(value)) {
} else if (isAnyArray(value)) {
// Create value array from user-provided array. Typically used
// only by enumerated dimensions
array = this._createValueArray(
@@ -729,15 +730,6 @@ export const DimTypes = {
spatial: ImmutableSpatialDimension,
};
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
function isArrayOrTypedArray(x: any) {
return (
Array.isArray(x) ||
(ArrayBuffer.isView(x) &&
Object.prototype.toString.call(x) !== "[object DataView]")
);
}
/* return bounding box of the polygon */
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
function polygonBoundingBox(polygon: any) {

14
client/src/util/typedCrossfilter/sort.ts
View File

@@ -1,4 +1,4 @@
import { isTypedArray, isFpTypedArray } from "../typeHelpers";
import { isTypedArray, isFloatTypedArray } from "../../common/types/arraytypes";
/* eslint-disable no-bitwise -- code relies on bitwise ops */
@@ -219,7 +219,7 @@ export function sortArray(arr: any) {
return quicksort(arr, 0, arr.length - 1);
}
if (isTypedArray(arr)) {
if (isFpTypedArray(arr)) {
if (isFloatTypedArray(arr)) {
return quicksortFloats(arr, 0, arr.length - 1);
}
return quicksort(arr, 0, arr.length - 1);
@@ -230,7 +230,7 @@ export function sortArray(arr: any) {
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function sortIndex(index: any, source: any) {
if (isFpTypedArray(source))
if (isFloatTypedArray(source))
return quicksortFloatsIndirect(index, source, 0, index.length - 1);
return quicksortIndirect(index, source, 0, index.length - 1);
}
@@ -293,7 +293,7 @@ function lowerBoundFloat(valueArray: any, value: any, first: any, last: any) {
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function lowerBound(valueArray: any, value: any, first: any, last: any) {
if (isFpTypedArray(valueArray)) {
if (isFloatTypedArray(valueArray)) {
return lowerBoundFloat(valueArray, value, first, last);
}
return lowerBoundNonFloat(valueArray, value, first, last);
@@ -366,7 +366,7 @@ export function lowerBoundIndirect(
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
last: any
) {
if (isFpTypedArray(valueArray)) {
if (isFloatTypedArray(valueArray)) {
return lowerBoundFloatIndirect(valueArray, indexArray, value, first, last);
}
return lowerBoundNonFloatIndirect(valueArray, indexArray, value, first, last);
@@ -425,7 +425,7 @@ function upperBoundFloat(valueArray: any, value: any, first: any, last: any) {
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
export function upperBound(valueArray: any, value: any, first: any, last: any) {
if (isFpTypedArray(valueArray)) {
if (isFloatTypedArray(valueArray)) {
return upperBoundFloat(valueArray, value, first, last);
}
return upperBoundNonFloat(valueArray, value, first, last);
@@ -498,7 +498,7 @@ export function upperBoundIndirect(
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
last: any
) {
if (isFpTypedArray(valueArray)) {
if (isFloatTypedArray(valueArray)) {
return upperBoundFloatIndirect(valueArray, indexArray, value, first, last);
}
return upperBoundNonFloatIndirect(valueArray, indexArray, value, first, last);