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

public class | source

Adhesion

Extends:

Constraint → SoftConstraint → Adhesion

Implements the adhesion constraint of Potts models. Each pair of neighboring pixels [n,m] gets a positive energy penalty deltaH if n and m do not belong to the same CellId.

Example:

// Build a CPM and add the constraint
let CPM = require( "path/to/build" )
let C = new CPM.CPM( [200,200], { T : 20 } )
C.add( new CPM.Adhesion( { J : [[0,20],[20,10]] } ) )

// Or add automatically by entering the parameters in the CPM
let C2 = new CPM.CPM( [200,200], {
	T : 20,
	J : [[0,20],[20,10]]
})

Constructor Summary

Public Constructor
public	constructor(conf: object) The constructor of Adhesion requires a conf object with a single parameter J.

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.

Private Methods
private	H(i: IndexCoordinate, tp: CellId): number Returns the Hamiltonian around a pixel i with cellid tp by checking all its neighbors that belong to a different cellid.
private	J(t1: CellId, t2: CellId): number Get adhesion between two cells t1,t2 from "conf".

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 Adhesion requires a conf object with a single parameter J.

Override:

Constraint#constructor

Params:

Name	Type	Attribute	Description
conf	object		parameter object for this constraint
conf.J	CellKindInteractionMatrix		J[n][m] gives the adhesion energy between a pixel of CellKind n and a pixel of CellKind m. J[n][n] is only non-zero when the pixels in question are of the same CellKind, but a different CellId. Energies are given as non-negative numbers.

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.

Private Methods

private H(i: IndexCoordinate, tp: CellId): number source

Returns the Hamiltonian around a pixel i with cellid tp by checking all its neighbors that belong to a different cellid.

Params:

Name	Type	Attribute	Description
i	IndexCoordinate		coordinate of the pixel to evaluate hamiltonian at.
tp	CellId		cellid of this pixel.

Return:

number

sum over all neighbors of adhesion energies (only non-zero for neighbors belonging to a different cellid).

private J(t1: CellId, t2: CellId): number source

Get adhesion between two cells t1,t2 from "conf".

Params:

Name	Type	Attribute	Description
t1	CellId		cellid of the first cell.
t2	CellId		cellid of the second cell.

Return:

number

adhesion between a pixel of t1 and one of t2.