import GridManipulator from 'Artistoo/src/grid/GridManipulator.js'
public class | source

GridManipulator

This class contains methods that should be executed once per Monte Carlo Step. Examples are cell division, cell death etc.

It also contains methods to seed new cells in certain shapes and configurations. Methods are written for CPMs, but some of the methods may also apply to other models of class (GridBasedModel, e.g. the cell seeding methods) or even a general grid (Grid, e.g. the makeLine and assignCellPixels methods).

Example:

// Build CPM and attach a gridmanipulator
let C = new CPM.CPM( [100,100], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )

Test:

Constructor Summary

Public Constructor
public

Constructor of class GridManipulator.

Member Summary

Public Members
public

The model whose grid we are manipulating.

Method Summary

Public Methods
public

assignCellPixels(voxels: ArrayCoordinate[], cellkind: CellKind, newID: CellId)

Helper method that assigns all pixels in a given array to a cell of a given cellkind: changes the pixels defined by voxels (array of coordinates p) into the given cellKind and a corresponding cellID.

public

changeKind(voxels: *, cellkind: *, newid: *)

Abrogated; this is now assignCellPixels.

public

Let cell "id" divide by splitting it along a line perpendicular to its major axis.

public

killCell(cellID: *)

this method is experimental.
public

makeBox(bottomLeft: ArrayCoordinate[], boxSize: number[], pixels: ArrayCoordinate[]): ArrayCoordinate[]

Helper method to return a rectangle (or in 3D: box) of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once.

public

Helper method to return a circle (in 3D: sphere) of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once.

public

makeLine(dimension: number, coordinateValue: number, pixels: ArrayCoordinate[]): ArrayCoordinate[]

Helper method to return an entire plane or line of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once.

public

makePlane(dim: number, coordinateValue: number, pixels: ArrayCoordinate[]): ArrayCoordinate[]

Deprecated method, please use makeLine instead.

public

seedCell(kind: CellKind, max_attempts: number): CellId

Seed a new cell at a random position.

public

Seed a new cell of celltype "kind" onto position "p".

public

seedCellsInCircle(kind: CellKind, n: number, center: ArrayCoordinate, radius: number, max_attempts: number)

Seed "n" cells of celltype "kind" at random points lying within a circle surrounding "center" with radius "radius".

Public Constructors

public constructor(C: CPM | GridBasedModel | Grid) source

Constructor of class GridManipulator.

Params:

NameTypeAttributeDescription
C CPM | GridBasedModel | Grid

the model whose grid you wish to manipulate. Methods are written for CPMs, but some of the methods may also apply to other models of class (GridBasedModel, e.g. the cell seeding methods) or even a general grid (Grid, e.g. the makeLine and assignCellPixels methods).

Public Members

public C: CPM | GridBasedModel | Grid source

The model whose grid we are manipulating.

Public Methods

public assignCellPixels(voxels: ArrayCoordinate[], cellkind: CellKind, newID: CellId) source

Helper method that assigns all pixels in a given array to a cell of a given cellkind: changes the pixels defined by voxels (array of coordinates p) into the given cellKind and a corresponding cellID.

Params:

NameTypeAttributeDescription
voxels ArrayCoordinate[]

Array of pixels to change.

cellkind CellKind

cellkind to change these pixels into.

newID CellId
  • optional

(Optional) id of the cell to assign the pixels to; if this is unspecified, a new cellID is generated for this purpose.

Example:

	let C = new CPM.CPM( [10,10], {T:20, J:[[0,20],[20,10]]} )
	let gm = new CPM.GridManipulator( C )
	let myLine = gm.makeLine( 0, 2 )
	gm.assignCellPixels( myLine, 1 )

public changeKind(voxels: *, cellkind: *, newid: *) source

Abrogated; this is now assignCellPixels. *

Params:

NameTypeAttributeDescription
voxels *
cellkind *
newid *

public divideCell(id: CellId): CellId source

Let cell "id" divide by splitting it along a line perpendicular to its major axis.

Params:

NameTypeAttributeDescription
id CellId

the id of the cell that needs to divide.

Return:

CellId

the id of the newly generated daughter cell.

Example:

let C = new CPM.CPM( [10,10], {
	T:20, 
J:[[0,20],[20,10]], 
V:[0,200], 
LAMBDA_V:[0,2] 
})
let gm = new CPM.GridManipulator( C )

// Seed a single cell
gm.seedCell( 1 )

// Perform some Monte Carlo Steps before dividing the cell
for( let t = 0; t < 100; t++ ){
	C.timeStep()
}
gm.divideCell( 1 )

// Check which pixels belong to which cell. Should be roughly half half.
C.getStat( PixelsByCell )

public killCell(cellID: *) source

this method is experimental.

Params:

NameTypeAttributeDescription
cellID *

Test:

public makeBox(bottomLeft: ArrayCoordinate[], boxSize: number[], pixels: ArrayCoordinate[]): ArrayCoordinate[] source

Helper method to return a rectangle (or in 3D: box) of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once. (See also makeLine and makeCircle). The method takes an existing array of coordinates (which can be empty) and adds the pixels of the specified rectangle/box to it. See assignCellPixels for a method that sets such a pixel set to a new value.

The box/rectangle is specified by its bottom left corner (x,y,z) and size (dx, dy, dz).

Params:

NameTypeAttributeDescription
bottomLeft ArrayCoordinate[]

the coordinate of the bottom left corner of the rectangle/box.

boxSize number[]

the size of the rectangle in each dimension: [dx,dy,dz].

pixels ArrayCoordinate[]
  • optional

(Optional) existing array of pixels; if given, the line will be added to this set.

Return:

ArrayCoordinate[]

the updated array of pixels.

Example:

let C = new CPM.CPM( [10,10], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )
let rect = gm.makeBox( [50,50], [10,10] )
gm.assignCellPixels( rect, 1 )

public makeCircle(center: ArrayCoordinate[], radius: number, pixels: ArrayCoordinate[]): ArrayCoordinate[] source

Helper method to return a circle (in 3D: sphere) of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once. (See also makeLine and makeBox). The method takes an existing array of coordinates (which can be empty) and adds the pixels of the specified circle/sphere to it. See assignCellPixels for a method that sets such a pixel set to a new value.

The circle/sphere is specified by its center (x,y,z) and radius.

Params:

NameTypeAttributeDescription
center ArrayCoordinate[]

the coordinate of the center of the circle/sphere.

radius number

the radius of the circle/sphere.

pixels ArrayCoordinate[]
  • optional

(Optional) existing array of pixels; if given, the circle/sphere pixels will be added to this set.

Return:

ArrayCoordinate[]

the updated array of pixels.

Example:

let C = new CPM.CPM( [10,10], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )
let circ = gm.makeCircle( [50,50], 10 )
gm.assignCellPixels( circ, 1 )

public makeLine(dimension: number, coordinateValue: number, pixels: ArrayCoordinate[]): ArrayCoordinate[] source

Helper method to return an entire plane or line of pixels; can be used in conjunction with assignCellPixels to assign all these pixels to a given CellId at once. (See also makeBox and makeCircle). The method takes an existing array of coordinates (which can be empty) and adds the pixels of the specified plane to it. See assignCellPixels for a method that sets such a pixel set to a new value.

The plane is specified by fixing one coordinate (x,y,or z) to a fixed value, and letting the others range from their min value 0 to their max value. In 3D, this returns a plane.

Params:

NameTypeAttributeDescription
dimension number

the dimension to fix the coordinate of: 0 = x, 1 = y, 2 = z. (E.g. for a straight vertical line, we fix the x-coordinate).

coordinateValue number

the value of the coordinate in the fixed dimension; location of the plane. (E.g. for our straight vertical line, the x-value where the line should be placed).

pixels ArrayCoordinate[]
  • optional

(Optional) existing array of pixels; if given, the line will be added to this set.

Return:

ArrayCoordinate[]

the updated array of pixels.

Example:

let C = new CPM.CPM( [10,10], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )
let myLine = gm.makeLine( 0, 2 )
gm.assignCellPixels( myLine, 1 )

public makePlane(dim: number, coordinateValue: number, pixels: ArrayCoordinate[]): ArrayCoordinate[] source

Deprecated method, please use makeLine instead. Old method just links to the new method for backwards-compatibility.

Params:

NameTypeAttributeDescription
dim number

the dimension to fix the coordinate of: 0 = x, 1 = y, 2 = z. (E.g. for a straight vertical line, we fix the x-coordinate).

coordinateValue number

the value of the coordinate in the fixed dimension; location of the plane. (E.g. for our straight vertical line, the x-value where the line should be placed).

pixels ArrayCoordinate[]
  • optional

(Optional) existing array of pixels; if given, the line will be added to this set.

Return:

ArrayCoordinate[]

the updated array of pixels.

public seedCell(kind: CellKind, max_attempts: number): CellId source

Seed a new cell at a random position. Return 0 if failed, ID of new cell otherwise. Try a specified number of times, then give up if grid is too full. The first cell will always be seeded at the midpoint of the grid.

See also seedCellAt to seed a cell on a predefined position.

Params:

NameTypeAttributeDescription
kind CellKind

what kind of cell should be seeded? This determines the CPM parameters that will be used for that cell.

max_attempts number
  • optional
  • default: 10000

number of tries allowed. The method will attempt to seed a cell at a random position, but this will fail if the position is already occupied. After max_attempts fails, it will not try again. This can happen if the grid is very full.

Return:

CellId

the CellId of the newly seeded cell, or 0 if the seeding has failed.

Example:

// Build CPM and attach a gridmanipulator
let C = new CPM.CPM( [100,100], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )

// Seed some cells
gm.seedCell( 1 )
gm.seedCell( 1 )

// Check which pixels are nonzero. One is always the grid midpoint.
for( let p of C.pixels() ){
	console.log( p )
}

public seedCellAt(kind: CellKind, p: ArrayCoordinate): CellId source

Seed a new cell of celltype "kind" onto position "p". This succeeds regardless of whether there is already a cell there. See also seedCell to seed a cell on a random position.

Params:

NameTypeAttributeDescription
kind CellKind

what kind of cell should be seeded? This determines the CPM parameters that will be used for that cell.

p ArrayCoordinate

position to seed the cell at.

Return:

CellId

the CellId of the newly seeded cell, or 0 if the seeding has failed.

Example:

// Build CPM and attach a gridmanipulator
let C = new CPM.CPM( [100,100], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )

// Seed some cells
gm.seedCellAt( 1, [2,4] )
gm.seedCellAt( 1, [9,3] )

// Check which pixels are nonzero. These should be the positions defined above.
for( let p of C.pixels() ){
	console.log( p )
}

Test:

public seedCellsInCircle(kind: CellKind, n: number, center: ArrayCoordinate, radius: number, max_attempts: number) source

Seed "n" cells of celltype "kind" at random points lying within a circle surrounding "center" with radius "radius".

See also seedCell to seed a cell on a random position in the entire grid, and seedCellAt to seed a cell at a specific position.

Params:

NameTypeAttributeDescription
kind CellKind

what kind of cell should be seeded? This determines the CPM parameters that will be used for that cell.

n number

the number of cells to seed (must be integer).

center ArrayCoordinate

position on the grid where the center of the circle should be.

radius number

the radius of the circle to seed cells in.

max_attempts number

the maximum number of attempts to seed a cell. Seeding can fail if the randomly chosen position is outside the circle, or if there is already a cell there. After max_attempts the method will stop trying and throw an error.

Example:

// Build CPM and attach a gridmanipulator
let C = new CPM.CPM( [100,100], {T:20, J:[[0,20],[20,10]]} )
let gm = new CPM.GridManipulator( C )

// Seed cells within a circle
gm.seedCellsInCircle( 1, 10, [50,30], 20 )

// Check which pixels are nonzero. These should be within the circle.
for( let p of C.pixels() ){
	console.log( p )
}