hbp_nrp_cle.brainsim.pynn.H5PyNNBrainLoader module

Load a brain network

class Brain(circuit)[source]

Bases: object

Represents a simple model of a generic brain.

property circuit

Gets the circuit brain region

load_h5_network(path, sim, **populations)[source]

Load a h5 brain network file.

Parameters

  • path – path to the .h5 file.

  • sim – The simulator module

load_pointneuron_circuit(h5_filename, sim, neuron_ids=None, synapse_model='TsodyksMarkramMechanism')[source]

Loads the h5 point-neuron circuit into PyNN. The result dictionary will contain a set of PyNN neurons that are correctly connected together.

Warning

The output NEST neurons will be of type ‘aeif_cond_exp’ and will have the default NEST parameters. The dictionary that is returned by this function will contains a set of better parameter that can be used (mtype, a, b, V_th, Delta_T, C_m, g_L, V_reset, tau_w, t_ref, V_peak, E_L, E_ex, E_in, excitatory).

Warning

If the input file has been collapsed using ‘convert_h5_to_collapsed_h5’, collapsed need to be set to True. The synapse model will then be forced to ‘quantal_stp_synapse’.

Warning

This function will not reset NEST kernel. GIDs of NEST neurons and bluepy neurons might be different.

Parameters

  • h5_filename (str) – Name of the h5 datafile.

  • sim – The simulator module

  • neuron_ids (list of ids) – The list of neurons ids for which connection will be done (inbetween them and also from them to the others. This can be feed for example with the results of the get_target() function from bluepy.)

  • synapse_model (str) – Specifies the synapse model that will be used.