#include <ca.h>
Public Member Functions | |
CellularPotts (std::vector< Cell > *cells, const int sizex=200, const int sizey=200) | |
Constructs a CA field. This should be done in "Dish". | |
CellularPotts (void) | |
virtual void | AllocateSigma (int sx, int sy) |
virtual | ~CellularPotts () |
int ** | SearchNandPlot (Graphics *g=0, bool get_neighbours=true) |
Plots the dish to the screen or to a movie and searches the neighbours. | |
void | Plot (Graphics *g) |
Plot the dish to Graphics window g. | |
int ** | SearchNeighbours (void) |
Searches the cells' neighbors without plotting. | |
int | Mass (void) |
Return the total area occupied by the cells. | |
void | PlotSigma (Graphics *g, int mag=2) |
void | DivideCells (void) |
Divide all cells. | |
void | DivideCells (std::vector< bool > which_cells) |
int | AmoebaeMove (PDE *PDEfield=0) |
Monte Carlo Step. Returns summed energy change. | |
void | ReadZygotePicture (void) |
Read initial cell shape from XPM file. Reads the initial cell shape from an include xpm picture called "ZYGXPM(ZYGOTE)", and it allocates enough cells for it to the Dish. | |
void | ConstructInitCells (Dish &beast) |
int | Time () const |
Returns the number of completed Monte Carlo steps. | |
int | ZygoteArea () const |
int | SizeX () const |
Return the horizontal size of the CA plane. | |
int | SizeY () const |
Return the vertical size of the CA plane. | |
int | Sigma (const int x, const int y) const |
Return the value of lattice site (x,y). | |
void | Replace (Graphics *g) |
Dir * | FindCellDirections (void) const |
int | ThrowInCells (int n, int cellsize) |
Initialize the CA plane with n circular cells fitting in a cellsize^2 square. | |
int | GrowInCells (int n_cells, int cellsize, double subfield=1.) |
Initialize the CA plane with n cells using an Eden growth algorithm. | |
int | GrowInCells (int n_cells, int cell_size, int sx, int sy, int offset_x, int offset_y) |
Cell & | AddCell (Dish &beast) |
Adds a new Cell and returns a reference to it. | |
void | ShowDirections (Graphics &g, const Dir *celldir) const |
Display the division planes returned by FindCellDirections. | |
double | MeanCellArea (void) const |
Returns the mean area of the cells. | |
double | CellDensity (void) const |
Returns the cell density. | |
void | ResetTargetLengths (void) |
Set target lengths of all cells to the value given in parameter file. | |
void | SetRandomTypes (void) |
Give each cell a random cell type. | |
void | GrowAndDivideCells (int growth_rate) |
Cell & | getCell (int c) |
double | DrawConvexHull (Graphics *g, int color=1) |
double | Compactness (double *res_compactness=0, double *res_area=0, double *res_cell_area=0) |
Public Attributes | |
int | spins_converted |
Protected Member Functions | |
void | BaseInitialisation (std::vector< Cell > *cell) |
Protected Attributes | |
int ** | sigma |
int | sizex |
int | sizey |
Friends | |
class | Info |
class | Morphometry |
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Constructs a CA field. This should be done in "Dish".
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Adds a new Cell and returns a reference to it.
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Monte Carlo Step. Returns summed energy change. Implements the core CPM algorithm. Carries out one MCS.
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Returns the cell density. Cell density is defined as the area occupied by cells divided by the size of the field. |
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Calculate compactness (summed_area/hull_area) of all cells. This is a good measure for the density.
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Divide all cells marked "true" in which_cells.
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Divide all cells.
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Draw convex hull around all cells.
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In this method the principal axes of the cells are computed using the method described in "Biometry", box 15.5
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Cells grow until twice their original target_length, then divide, with rate "growth_rate" |
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Initialize the CA plane with n cells using an Eden growth algorithm.
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Return the total area occupied by the cells.
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Returns the mean area of the cells.
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Plot the dish to Graphics window g.
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Plot the cells according to their cell identity, not their type. The black lines are omitted. |
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Read initial cell shape from XPM file. Reads the initial cell shape from an include xpm picture called "ZYGXPM(ZYGOTE)", and it allocates enough cells for it to the Dish.
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Set target lengths of all cells to the value given in parameter file.
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Plots the dish to the screen or to a movie and searches the neighbours. These distinct tasks have been lumped together in the same method because both for drawing the black lines between the cells and for searching the neighbours the cell borders have to be determined. |
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Searches the cells' neighbors without plotting.
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Give each cell a random cell type. The number of cell types is defined by the J parameter file. (See Jtable in parameter file). |
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Display the division planes returned by FindCellDirections.
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Return the value of lattice site (x,y). i.e. This will return the index of the cell which occupies site (x,y). |
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Return the horizontal size of the CA plane.
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Return the vertical size of the CA plane.
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Initialize the CA plane with n circular cells fitting in a cellsize^2 square. ! Fill the plane with initial cells
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Returns the number of completed Monte Carlo steps.
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