Documentation per Class

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

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

Rendering context of canvas.

Hex code string for a color.

An object of class MersenneTwister.

Unique identifier of some element.

Implements a basic holder for a model with internal products, which can be stochastically divided between daughter cells.

This class is meant as a bridge to convert between model frameworks.

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

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

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

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

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

A pixel on the grid.

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

Array coordinates to a pixel on the grid.

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

Index coordinate to a pixel on the grid.

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

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

Implements the adhesion constraint of Potts models.

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

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

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

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

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

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

Extension of class Constraint used for a hard constraint.

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

Version of the ConnectivityConstraint which only checks local connectivity.

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

Implements the perimeter constraint of Potts models.

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

Implements a global bias direction of motion.

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

Extension of class Constraint used for a soft constraint.

Soft version of the ConnectivityConstraint which only checks local connectivity.

Implements the volume constraint of Potts models.

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

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

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

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

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

An array containing parameter values for each CellKind.

An array containing parameter values for each CellKind.

An array containing parameter values for each CellKind.

An array containing parameter values for each CellKind.

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

The core CPM class.

Extension of the CPM class that uses Cell objects to track internal state of Cells Cell objects can override conf parameters, and track their lineage.

Base class for grid-based models.

A unique identifier number of a cell on the grid.

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

This class provides some boilerplate code for creating simulations easily.

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

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.

This Stat computes the centroid of a cell.

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

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

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.

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

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

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

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.

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.