bmtk.builder.auxi package

Submodules

bmtk.builder.auxi.edge_connectors module

bmtk.builder.auxi.edge_connectors.connect_random(source, target, nsyn_min=0, nsyn_max=10, distribution=None)

bmtk.builder.auxi.edge_connectors.distance_connector(source, target, d_weight_min, d_weight_max, d_max, nsyn_min, nsyn_max)

bmtk.builder.auxi.node_params module

bmtk.builder.auxi.node_params.positions_columinar(N=1, center=[0.0, 50.0, 0.0], height=100.0, min_radius=0.0, max_radius=1.0, distribution='uniform')

Returns a set of random x,y,z coordinates within a given sphere. Height is given as the y (index 1) coordates

Parameters:

• N – Number of points to return
• center – center of sphere
• height – maximum length of sphere (y coord)
• min_radius – minimum horizontal radius on x-z plane
• max_radius – maximum horizontal radius on x-z plane
• distribution – Not yet implementd

Returns:

A (N, 3) matrix

bmtk.builder.auxi.node_params.positions_cuboid(N=1, center=[0.0, 0.0, 0.0], height=100.0, xside_length=100.0, yside_length=100.0, min_dist=20.0)

This function distributes the cells in a 3D cuboid (x,y,z sides may have different lengths). The method used assures cells cannot be placed too close to one another (must be > min_dist apart) WARNING: If cell density is high and there is more than 1 population of cells, there is a high chance cells will be placed on top of one another. You can use positions_list() to avoid this…

Written by Ben Latimer at University of Missouri (latimerb@missouri.edu)

Returns:A (N, 3) matrix

bmtk.builder.auxi.node_params.positions_list(positions=array([[0, 0, 0], [0, 0, 1]]))

This function is designed to be used with an externally supplied array of x,y,z coordinates. It is useful to avoid cell overlap in high density situations or to make some unique geometry. After you create each population, delete those positions from the “master” list of coordinates. This will assure that no cells are placed on top of one another.

Written by Ben Latimer at University of Missouri (latimerb@missouri.edu)

Parameters:positions – Returns:

bmtk.builder.auxi.node_params.xiter_random(N=1, min_x=0.0, max_x=1.0)

Module contents