cbmos.utils package

Module contents

cbmos.utils.generate_cartesian_coordinates(n_x, n_y, scaling=1.0)

Generate cartesian coordinates which can be used to set up a cell population.

Parameters:

• n_x (int) – number of columns

• n_y (int) – number of rows

• scaling (float) – distance between the cells, in cell diameters

cbmos.utils.generate_hcp_coordinates(n_x, n_y, n_z, scaling=1.0)

Generate coordinates from a HCP (hexagonal close-packed) grid which can be used to set up a cell population.

Parameters:

• n_x (int) – number of columns

• n_y (int) – number of rows

• n_z (int) – number of layers

• scaling (float) – distance between the cells, in cell diameters

cbmos.utils.generate_honeycomb_coordinates(n_x, n_y, scaling=1.0)

Generate coordinates from a honeycomb mesh which can be used to set up a cell population.

Parameters:

• n_x (int) – number of columns

• n_y (int) – number of rows

• scaling (float) – distance between the cells, in cell diameters

cbmos.utils.plot_2d_population(cell_list, color='blue')

Plot a two dimensional population provided as a list of Cell objects.

cbmos.utils.setup_locally_compressed_monolayer(n_x, n_y, scaling=1.0, separation=0.3, seed=None)

Set up a locally compressed monolayer where the middle cell has just divided.

Parameters:

• n_x (int) – number of columns

• n_y (int) – number of rows

• scaling (float) – distance between neighboring cells, in cell diameters

• separation (float) – distance between daughter cells, in cell diameters

Return type:

list of cells

cbmos.utils.setup_locally_compressed_spheroid(n_x, n_y, n_z, scaling=1.0, separation=0.3, seed=None)

Set up a locally compressed spheroid where the middle cell has just divided.

Parameters:

• n_x (int) – number of columns

• n_y (int) – number of rows

• n_z (int) – number of layers

• scaling (float) – distance between neighboring cells, in cell diameters

• separation (float) – distance between daughter cells, in cell diameters

Return type:

list of cells