References

summary
public

C Canvas

Class for taking a CPM grid and displaying it in either browser or with nodejs.

public

This class implements a data structure with constant-time insertion, deletion, and random sampling.

public

Rendering context of canvas.

public

Hex code string for a color.

public

An object of class MersenneTwister.

public

Unique identifier of some element.

grid

summary
public

This class encapsulates a lower-resolution grid and makes it visible as a higher-resolution grid.

public

C Grid

This base class defines a general grid and provides grid methods that do not depend on the coordinate system used.

public

C Grid2D

A class containing (mostly static) utility functions for dealing with 2D grids.

public

C Grid3D

A class containing (mostly static) utility functions for dealing with 3D grids.

public

This class contains methods that should be executed once per Monte Carlo Step.

public

T Pixel: Object[]

A pixel on the grid.

public

Function that updates a gridpoint depending on its current value and that of its neighbors.

public

Array coordinates to a pixel on the grid.

public

An array with the grid size in pixels for each dimension.

public

Index coordinate to a pixel on the grid.

hamiltonian

summary
public

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

public

The ActivityMultiBackground constraint implements the activity constraint of Potts models, but allows users to specify locations on the grid where LAMBDA_ACT is different.

public

Implements the adhesion constraint of Potts models.

public

Implements bias of motion in the direction of a supplied "attraction point".

public

This constraint allows a "barrier" celltype from and into which copy attempts are forbidden.

public

This constraint allows a set of "barrier" background pixels, into which copy attempts are forbidden.

public

This class implements a constraint for cells moving up a chemotactic gradient.

public
this class is experimental.

This constraint enforces that cells stay 'connected' throughout any copy attempts.

public

This base class defines a general CPM constraint and provides methods that do not depend on the specific constraint used.

public

Extension of class Constraint used for a hard constraint.

public

This constraint forbids that cells exceed or fall below a certain size range.

public
this class is experimental.

Version of the ConnectivityConstraint which only checks local connectivity.

public

Class for checking if parameters are present in a conf object and are of the expected structure and type.

public

Implements the perimeter constraint of Potts models.

public

This is a constraint in which each cell has a preferred direction of migration.

public

Implements a global bias direction of motion.

public
this class is experimental.

This constraint encourages that cells stay 'connected' throughout any copy attempts.

public

Extension of class Constraint used for a soft constraint.

public
this class is experimental.

Soft version of the ConnectivityConstraint which only checks local connectivity.

public

Implements the volume constraint of Potts models.

public

This class enables automatic addition of Hamiltonian terms to a CPM through their parameter names.

public

Parameter structure for parameters that should come in an array with an element for each CellKind including background.

public

Parameter structure for parameters that specify interactions between two cells with each a CellKind.

public

Parameter structure for parameters that should come as a single value.

public

An array of arrays containing interaction parameter values for each CellKind - combination.

public

An array containing parameter values for each CellKind.

public

An array containing parameter values for each CellKind.

public

An array containing parameter values for each CellKind.

public

An array containing parameter values for each CellKind.

models

summary
public

C CA

Extension of the GridBasedModel class suitable for a Cellular Automaton (CA).

public

C CPM

The core CPM class.

public

Base class for grid-based models.

public

A unique identifier number of a cell on the grid.

public

Index specifying the 'kind' of cell we are dealing with.

simulation

summary
public

This class provides some boilerplate code for creating simulations easily.

stats

summary
public

This Stat creates a CellArrayObject with the border cellpixels of each cell on the grid.

public
this class is experimental.

This stat computes a list of all cell ids of the cells that border to "cell" and belong to a different cellid, also giving the interface length for each contact.

public

This Stat computes the centroid of a cell.

public

This Stat computes the centroid of a cell when grid has a torus.

public

This Stat creates an object with the connected components of each cell on the grid.

public

This Stat creates an object with the connected components of each cell's border on the grid. Keys are the CellId of all cells on the grid, corresponding values are objects where each element is a connected component. Each element of that array contains the ArrayCoordinate for that pixel.

public

This Stat computes the 'connectedness' of cells on the grid.

public

This Stat creates an object with the cellpixels of each cell on the grid.

public

C Stat

Base class for a statistic that can be computed on a GridBasedModel.

public

An object where each cell on the grid has a key (its CellId), and the corresponding value at that key is an array with some values for that cell.

public

An object where each cell on the grid has a key (its CellId), and the corresponding value at that key is single property of that cell.