snudda.init.init

class snudda.init.init.SnuddaInit(network_path=None, struct_def=None, snudda_data=None, neurons_dir=None, config_file=None, random_seed=None, connection_override_file=None, honor_stay_inside=False)[source]

Creates network-config.json in network_path.

Constructor

Args: network_path (str): location of network files struct_def (dict, optional): definition of struct to create snudda_data (str, optional): Path to SNUDDA_DATA neurons_dir (str, optional): path to neurons, default is $SNUDDA_DATA/neurons (DEPRECATED) config_file (str, optional): name of network config file, default network-config.json random_seed (int, optional): random seed

define_structure(struct_name, struct_mesh, d_min=None, struct_centre=None, side_len=None, slice_depth=None, mesh_bin_width=None, num_neurons=None, n_putative_points=None)[source]

Sets up definition for a brain structure (e.g. Cortex, Striatum, …).

Parameters:

  • struct_name (str) – Name of brain structure

  • struct_mesh (str) – Path to wavefront obj file with 3D mesh of structure or ‘cube’ or ‘slice’

  • d_min (float) – Minimum distance between somas (puts upper limit on neuron density)

  • struct_centre ((float, float, float)) – Location of brain structure (centre)

  • side_len (float, optional) – side of cube, or slice

  • slice_depth (float, optional) – depth of slice

  • mesh_bin_width (float) – discretisation of 3D mesh during cell placement

  • n_putative_points (int) – Number of putative locations (Before d_min filtering), upper limit on number of neuron positions in volume (real number will be lower)

get_morphologies(neuron_dir)[source]

Returns SWC morphology(s) path or file, depending on ‘morphology’ if specified in parameters.json or not.

If ‘morphology’ in parameters.json exists then the path where these morphologies are stored is returned. If it does not exist it is assumed that there is exactly one SWC file present in the neuron_dir, and that is then returned.

Parameters:

neuron_dir (str) – Path to neuron directory, may contain $SNUDDA_DATA, shorthand for SNUDDA_DATA directory

replace_connectivity(connection_file=None, connection_dict=None)[source]

Replaces the default connectivity.

Parameters:

  • connection_file – Path to JSON file with connection block

  • connection_dict – dict with connection block