import ActivityConstraint from 'Artistoo/src/hamiltonian/ActivityConstraint.js'

public class | source

ActivityConstraint

Extends:

Constraint → SoftConstraint → ActivityConstraint

Direct Subclass:

ActivityMultiBackground

This class implements the activity constraint of Potts models published in:

Niculescu I, Textor J, de Boer RJ (2015) Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration. PLoS Comput Biol 11(10): e1004280.

Pixels recently added to a cell get an "activity", which then declines with every MCS. Copy attempts from more active into less active pixels have a higher success rate, which puts a positive feedback on protrusive activity and leads to cell migration.

This constraint is generally used together with Adhesion, VolumeConstraint, and PerimeterConstraint.

See:

https://doi.org/10.1371/journal.pcbi.1004280

Example:

// Build a CPM and add the constraint
let CPM = require( "path/to/build" )
let C = new CPM.CPM( [200,200], {
	T : 20,
	J : [[0,20],[20,10]],
	V : [0,500],
	LAMBDA_V : [0,5],
	P : [0,260],
	LAMBDA_P : [0,2] 	
})
C.add( new CPM.ActivityConstraint( {
	LAMBDA_ACT : [0,500],
	MAX_ACT : [0,30],
	ACT_MEAN : "geometric"
} ) )

// Or add automatically by entering the parameters in the CPM
let C2 = new CPM.CPM( [200,200], {
	T : 20,
	J : [[0,20],[20,10]],
	V : [0,500],
	LAMBDA_V : [0,5],
	P : [0,260],
	LAMBDA_P : [0,2],
	LAMBDA_ACT : [0,500],
	MAX_ACT : [0,30],
	ACT_MEAN : "geometric"	
})

Constructor Summary

Public Constructor
public	constructor(conf: object) The constructor of the ActivityConstraint requires a conf object with parameters.

Member Summary

Public Members
public	activityAt: function Wrapper: select function to compute activities based on ACT_MEAN in conf.
public	cellpixelsact: object Activity of all cellpixels with a non-zero activity is stored in this object, with the IndexCoordinate of each pixel as key and its current activity as value.

Method Summary

Public Methods
public	confChecker() This method checks that all required parameters are present in the object supplied to the constructor, and that they are of the right format.
public	deltaH(sourcei: IndexCoordinate, targeti: IndexCoordinate, src_type: CellId, tgt_type: CellId): number Method to compute the Hamiltonian for this constraint.
public	postMCSListener() The postMCSListener of the ActivityConstraint ensures that pixel activities decline with one after every MCS.
public	postSetpixListener(i: IndexCoordinate, t_old: CellId, t: CellId) The postSetpixListener of the ActivityConstraint ensures that pixels are given their maximal activity when they are freshly added to a CPM.
public	pxact(i: IndexCoordinate): number Current activity (under the Act model) of the pixel at position i.

Private Methods
private	activityAtArith(i: IndexCoordinate): number Activity mean computation methods for arithmetic mean.
private	activityAtGeom(i: IndexCoordinate): number Activity mean computation methods for geometric mean.

Inherited Summary

From class Constraint
public get abstract	CONSTRAINT_TYPE This method is actually implemented in the subclass.
public set	CPM(C: CPM) This function attaches the relevant CPM to this constraint, so that information about this cpm can be requested from the constraint.
public get	parameters: object: * Get the parameters of this constraint from the conf object.
public	C: CPM CPM on which this constraint acts.
public	conf: object Configuration object for this constraint.
public abstract	cellParameter(param: string, cid: CellId): any Get a cellid or cellkind-specific parameter for a constraint.
public abstract	confChecker() The optional confChecker method should verify that all the required conf parameters are actually present in the conf object and have the right format.
public	paramOfCell(param: string, cid: CellId): any Get a cellId specific parameter, only used if CPMEvol is used: looks whether the requested parameter is overwritten in an @object Cell and otherwise returns @function paramOfKind
public	paramOfKind(param: string, cid: CellId): any Returns a cellKind specfic variable: Assumes that the parameter is indexable by cellkind.

From class SoftConstraint
public get	CONSTRAINT_TYPE: string: string Let the CPM know that this is a soft constraint, so return 'soft'.
public abstract	deltaH(src_i: IndexCoordinate, tgt_i: IndexCoordinate, src_type: CellId, tgt_type: CellId): number Soft constraints must have a deltaH method to compute the Hamiltonian.

Public Constructors

public constructor(conf: object) source

The constructor of the ActivityConstraint requires a conf object with parameters.

Override:

Constraint#constructor

Params:

Name	Type	Attribute	Description
conf	object		parameter object for this constraint
conf.ACT_MEAN	string	optional default: "geometric"	should local mean activity be measured with an "arithmetic" or a "geometric" mean?
conf.LAMBDA_ACT	PerKindNonNegative		strength of the activityconstraint per cellkind.
conf.MAX_ACT	PerKindNonNegative		how long do pixels remember their activity? Given per cellkind.

Public Members

public activityAt: function source

Wrapper: select function to compute activities based on ACT_MEAN in conf. Default is to use the activityAtGeom for a geometric mean.

public cellpixelsact: object source

Activity of all cellpixels with a non-zero activity is stored in this object, with the IndexCoordinate of each pixel as key and its current activity as value. When the activity reaches 0, the pixel is removed from the object until it is added again.

Public Methods

public confChecker() source

This method checks that all required parameters are present in the object supplied to the constructor, and that they are of the right format. It throws an error when this is not the case.

Override:

Constraint#confChecker

public deltaH(sourcei: IndexCoordinate, targeti: IndexCoordinate, src_type: CellId, tgt_type: CellId): number source

Method to compute the Hamiltonian for this constraint.

Override:

SoftConstraint#deltaH

Params:

Name	Type	Attribute	Description
sourcei	IndexCoordinate		coordinate of the source pixel that tries to copy.
targeti	IndexCoordinate		coordinate of the target pixel the source is trying to copy into.
src_type	CellId		cellid of the source pixel.
tgt_type	CellId		cellid of the target pixel.

Return:

number

the change in Hamiltonian for this copy attempt and this constraint.

public postMCSListener() source

The postMCSListener of the ActivityConstraint ensures that pixel activities decline with one after every MCS.

Listen:

timeStep

because when the CPM has finished an MCS, the activities must go down.

public postSetpixListener(i: IndexCoordinate, t_old: CellId, t: CellId) source

The postSetpixListener of the ActivityConstraint ensures that pixels are given their maximal activity when they are freshly added to a CPM.

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		the coordinate of the pixel that is changed.
t_old	CellId		the cellid of this pixel before the copy
t	CellId		the cellid of this pixel after the copy.

Listen:

setpixi

because when a new pixel is set (which is determined in the CPM), its activity must change so that this class knows about the update.

public pxact(i: IndexCoordinate): number source

Current activity (under the Act model) of the pixel at position i.

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		the position of the pixel to evaluate the activity of.

Return:

number

the current activity of this pixel, which is >= 0.

Private Methods

private activityAtArith(i: IndexCoordinate): number source

Activity mean computation methods for arithmetic mean. It computes the mean activity of a pixel and all its neighbors belonging to the same cell.

This method is generally called indirectly via activityAt, which is set based on the value of ACT_MEAN in the configuration object given to the constructor.

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		pixel to evaluate local activity at.

Return:

number

the arithmetic mean of activities in this part of the cell.

private activityAtGeom(i: IndexCoordinate): number source

Activity mean computation methods for geometric mean. It computes the mean activity of a pixel and all its neighbors belonging to the same cell.

This method is generally called indirectly via activityAt, which is set based on the value of ACT_MEAN in the configuration object given to the constructor.

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		pixel to evaluate local activity at.

Return:

number

the geometric mean of activities in this part of the cell.