import Grid2D from 'Artistoo/src/grid/Grid2D.js'

public class | source

Grid2D

Extends:

Grid → Grid2D

Direct Subclass:

CoarseGrid

A class containing (mostly static) utility functions for dealing with 2D grids. Extends the Grid class but implements functions specific to the 2D grid (such as neighborhoods).

Example:

Diffusion on a 2D chemokine grid

 let CPM = require("path/to/build")

 // Make a grid with a chemokine, add some chemokine at the middle pixel
let chemoGrid = new CPM.Grid2D( [100,100], [true,true], "Float32" )
chemoGrid.setpix( [50,50], 100 )

// Measure chemokine at different spots before and after diffusion
let p1 = [50,50], p2 = [50,51]
console.log( "p1: " + chemoGrid.pixt( p1 ) + ", p2: " + chemoGrid.pixt(p2) )
chemoGrid.diffusion( 0.001 )
console.log( "p1: " + chemoGrid.pixt( p1 ) + ", p2: " + chemoGrid.pixt(p2) )
chemoGrid.multiplyBy( 0.9 )	 // decay of the chemokine
console.log( "p1: " + chemoGrid.pixt( p1 ) + ", p2: " + chemoGrid.pixt(p2) )

Neighborhoods on a 2D grid


let CPM = require("path/to/build")

// Make a grid with a torus, and find the neighborhood of the upper left pixel [0,0]
let grid = new CPM.Grid2D( [100,100], [true,true] )
console.log( grid.neigh( [0,0] ) ) // returns coordinates of 8 neighbors

// Now try a grid without torus; the corner now has fewer neighbors.
let grid2 = new CPM.Grid2D( [100,100], [false,false] )
console.log( grid2.neigh( [0,0] ) ) // returns only 3 neighbors

// Or try a Neumann neighborhood using the iterator
for( let i of grid.neighNeumanni( 0 ) ){
	console.log( grid.i2p(i).join(" ") )
}

Test:

Constructor Summary

Public Constructor
public	constructor(extents: GridSize, torus: boolean[], datatype: string) Constructor of the Grid2D object.

Member Summary

Public Members
public	datatype: *

Private Members
private	_pixelArray: Uint16Array \| Float32Array Array with values for each pixel stored at the position of its IndexCoordinate.

Method Summary

Public Methods
public	gradienti(i: IndexCoordinate): number[] Method to compute the gradient at location i on the grid (location given as an IndexCoordinate).
public	i2p(i: IndexCoordinate): ArrayCoordinate Method for conversion from an IndexCoordinate to an ArrayCoordinate.
public	* neighNeumanni(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] Return array of IndexCoordinate of von Neumann-4 neighbor pixels of the pixel at coordinate i.
public	neighi(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] Return array of IndexCoordinate of Moore-8 neighbor pixels of the pixel at coordinate i.
public	p2i(p: ArrayCoordinate): IndexCoordinate Method for conversion from an ArrayCoordinate to an IndexCoordinate.
public	* pixels(): Pixel This iterator returns locations and values of all non-zero pixels.
public	* pixelsi(): IndexCoordinate This iterator returns locations and values of all pixels.

Inherited Summary

From class Grid
private get	_pixels: Uint16Array \| Float32Array: * Return the array this._pixelArray, which should be set in the grid subclass.
private set	_pixels(pixels: Uint16Array \| Float32Array) Set or update the private this._pixelArray.
public	datatype: *
public	extents: GridSize field_size array of field size in each dimension.
public	midpoint: ArrayCoordinate Array coordinates to the middle pixel on the grid.
public	ndim: number Number of dimensions of the grid.
public	torus: boolean[] Should the borders of the grid be linked, so that a cell moving out on the left reappears on the right? Warning: setting to false can give artifacts if done incorrectly.
private	_pixelArray: * Array with values for each pixel stored at the position of its IndexCoordinate.
private	_pixelsbuffer: Uint16Array \| Float32Array For storing a copy of all pixel values; eg for synchronous updating of some sort.
public	applyLocally(f: updatePixelFunction) Apply a function to all pixel values on the grid.
public	checkOnGrid(p: ArrayCoordinate) Method to check if a given ArrayCoordinate falls within the bounds of this grid.
public	correctPosition(p: ArrayCoordinate): ArrayCoordinate Method to correct an ArrayCoordinate outside the grid dimensions when the grid is wrapped (torus = true).
public	diffusion(D: number) Perform a diffusion step on the grid, updating the values of all pixels according to Fick's second law of diffusion.
public	gradient(p: ArrayCoordinate): number Method to compute the gradient at location p on the grid (location given in array coordinates).
public	gradienti(i: IndexCoordinate): number[] Template method to compute the gradient at location i on the grid (location given in index coordinates).
public abstract	i2p(i: IndexCoordinate): ArrayCoordinate Method for conversion from an IndexCoordinate to an ArrayCoordinate.
public	laplacian(p: ArrayCoordinate): number Method to compute the laplacian at location p on the grid (location given in array coordinates).
public	laplaciani(i: IndexCoordinate): number Method to compute the laplacian at location i on the grid (location given in index coordinates).
public	multiplyBy(r: number) Multiply all pixel values on the grid with a constant factor r.
public	neigh(p: ArrayCoordinate, torus: boolean[]): ArrayCoordinate[] The neigh method returns the neighborhood of a pixel p.
public abstract	* neighNeumanni(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] A method to compute the Neumann neighborhood should be implemented in the Grid subclass if the laplacian (see below) is used.
public abstract	neighi(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] Method returning the (Moore) neighborhood of a pixel based on its IndexCoordinate.
public abstract	p2i(p: ArrayCoordinate): IndexCoordinate Method for conversion from an ArrayCoordinate to an IndexCoordinate.
public abstract	* pixels(): Pixel This iterator returns locations and values of all non-zero pixels.
public	pixelsBuffer(): Uint16Array \| Float32Array This method pre-allocates an array of the correct datatype to make a copy of the current pixel values.
public abstract	* pixelsi(): IndexCoordinate This iterator returns locations all pixels including background.
public	pixt(p: ArrayCoordinate): number The pixt method finds the current value of a pixel p on the grid.
public	pixti(i: IndexCoordinate): number The pixti method finds the current value of a pixel i on the grid.
public	setpix(p: ArrayCoordinate, t: number) The setpix method changes the value of a pixel p on the grid to t.
public	setpixi(i: IndexCoordinate, t: number) The setpixi method changes the value of a pixel i on the grid to t.
private	_isValidValue(t: number, tol: number): void Check if a value is valid on this type of grid.

Public Constructors

public constructor(extents: GridSize, torus: boolean[], datatype: string) source

Constructor of the Grid2D object.

Override:

Grid#constructor

Params:

Name	Type	Attribute	Description
extents	GridSize		the size of the grid in each dimension
torus	boolean[]	optional default: [true,true]	should the borders of the grid be linked, so that a cell moving out on the left reappears on the right? Should be an array specifying whether the torus holds in each dimension; eg [true,false] for a torus in x but not y dimension. Warning: setting the torus to false can give artifacts if not done properly, see Grid#torus.
datatype	string	optional default: "Uint16"	What datatype are the values associated with each pixel on the grid? Choose from "Uint16" or "Float32".

Public Members

public datatype: * source

Override:

Grid#datatype

Private Members

private _pixelArray: Uint16Array | Float32Array source

Array with values for each pixel stored at the position of its IndexCoordinate. E.g. the value of pixel with coordinate i is stored as this._pixelArray[i]. Note that this array is accessed indirectly via the _pixels set- and get methods.

Override:

Grid#_pixelArray

Public Methods

public gradienti(i: IndexCoordinate): number[] source

Method to compute the gradient at location i on the grid (location given as an IndexCoordinate).

Override:

Grid#gradienti

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		index coordinate of a pixel to compute the gradient at

Return:

number[]

the gradient at position i.

Test:

Rigorous tests for Grid2D-specific methods. See GridExtensionSpec.js for more general tests. [ unit tests ] gradienti method should return correct gradients

See:

https://en.wikipedia.org/wiki/Gradient

public i2p(i: IndexCoordinate): ArrayCoordinate source

Method for conversion from an IndexCoordinate to an ArrayCoordinate. See also Grid2D#p2i for the backward conversion.

Override:

Grid#i2p

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		the coordinate of the pixel to convert

Return:

ArrayCoordinate

the converted coordinate.

Example:

let grid = new CPM.Grid2D( [100,100], [true,true] )
let p = grid.i2p( 5 )
console.log( p )
console.log( grid.p2i( p ))

Test:

General tests that every Grid subclass should pass i2p and p2i should be inverse for valid grid coordinates

public * neighNeumanni(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] source

Return array of IndexCoordinate of von Neumann-4 neighbor pixels of the pixel at coordinate i. This function takes the 2D Neumann-4 neighborhood, excluding the pixel itself.

Override:

Grid#neighNeumanni

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		location of the pixel to get neighbors of.
torus	boolean[]	optional default: [true,true]	does the grid have linked borders? Defaults to the setting on this grid, see torus

Return:

IndexCoordinate[]

an array of coordinates for all the neighbors of i.

Test:

See:

https://en.wikipedia.org/wiki/Von_Neumann_neighborhood

public neighi(i: IndexCoordinate, torus: boolean[]): IndexCoordinate[] source

Return array of IndexCoordinate of Moore-8 neighbor pixels of the pixel at coordinate i. This function takes the 2D Moore-8 neighborhood, excluding the pixel itself.

Override:

Grid#neighi

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		location of the pixel to get neighbors of.
torus	boolean[]	optional	does the grid have linked borders? Defaults to the setting on this grid, see torus

Return:

IndexCoordinate[]

an array of coordinates for all the neighbors of i.

Test:

See:

https://en.wikipedia.org/wiki/Moore_neighborhood

public p2i(p: ArrayCoordinate): IndexCoordinate source

Method for conversion from an ArrayCoordinate to an IndexCoordinate.

See also Grid2D#i2p for the backward conversion.

Override:

Grid#p2i

Params:

Name	Type	Attribute	Description
p	ArrayCoordinate		the coordinate of the pixel to convert

Return:

IndexCoordinate

the converted coordinate.

Example:

let grid = new CPM.Grid2D( [100,100], [true,true] )
let p = grid.i2p( 5 )
console.log( p )
console.log( grid.p2i( p ))

Test:

General tests that every Grid subclass should pass i2p and p2i should be inverse for valid grid coordinates

public * pixels(): Pixel source

This iterator returns locations and values of all non-zero pixels.

Override:

Grid#pixels

Return:

Pixel

for each pixel, return an array [p,v] where p are the pixel's array coordinates on the grid, and v its value.

Example:

let CPM = require( "path/to/build" )
// make a grid and set some values
let grid = new CPM.Grid2D( [100,100], [true,true] )
grid.setpix( [0,0], 1 )
grid.setpix( [0,1], 5 )

// iterator
for( let p of grid.pixels() ){
	console.log( p )
}

public * pixelsi(): IndexCoordinate source

This iterator returns locations and values of all pixels. Whereas the pixels generator yields only non-background pixels and specifies both their ArrayCoordinate and value, this generator yields all pixels by IndexCoordinate and does not report value.

Override:

Grid#pixelsi

Return:

IndexCoordinate

for each pixel on the grid (including background pixels).

Example:

let CPM = require( "path/to/build" )
// make a grid and set some values
let grid = new CPM.Grid2D( [100,100], [true,true] )
grid.setpixi( 0, 1 )
grid.setpixi( 1, 5 )

// iterator
for( let i of grid.pixelsi() ){
	console.log( i )
}

Test:

Rigorous tests for Grid2D-specific methods. See GridExtensionSpec.js for more general tests. [ unit tests ] pixelsi generator reports correct IndexCoordinates