Options¶

This module contains the configuration options for neural network models, including options for nodes, edges, integration, and visualization.

NetworkOptions Class¶

class farms_network.core.options.NetworkOptions(**kwargs)¶

Base class for neural network options

Attributes:

directed (bool): Whether the network is directed. Default is True.
multigraph (bool): Whether the network allows multiple edges between nodes. Default is False.
graph (dict): Graph properties (e.g., name). Default is {“name”: “”}.
units (optional): Units for the network. Default is None.
integration (IntegrationOptions): Options for numerical integration. Default values shown in the table below.

add_edge(options: EdgeOptions)¶: Add a node if it does not already exist in the list

add_edges(options: Iterable[EdgeOptions])¶: Add a collection of edges

add_node(options: NodeOptions)¶: Add a node if it does not already exist in the list

add_nodes(options: Iterable[NodeOptions])¶: Add a collection of nodes

classmethod from_options(kwargs)¶: From options

IntegrationOptions Class¶

class farms_network.core.options.IntegrationOptions(**kwargs)¶

Class to set the options for numerical integration

The default values for IntegrationOptions are as follows:

Parameter	Default Value
timestep	`1e-3`
integrator	`"dopri5"`
method	`"adams"`
atol	`1e-12`
rtol	`1e-6`
max_step	`0.0`
checks	`True`

classmethod defaults(**kwargs)¶

classmethod from_options(kwargs: Dict)¶: From options

NodeOptions Class¶

class farms_network.core.options.NodeOptions(**kwargs)¶

Base class for defining node options

Attributes:

name (str): Name of the node.
model (str): Node model type.
parameters (NodeParameterOptions): Node-specific parameters.
state (NodeStateOptions): Node state options.

classmethod from_options(kwargs: Dict)¶: Load from options

NodeParameterOptions Class¶

class farms_network.core.options.NodeParameterOptions¶

Base class for node specific parameters

The default values for NodeParameterOptions are as follows:

Parameter	Default Value
c_m	`10.0` pF
g_leak	`2.8` nS
e_leak	`-60.0` mV
v_max	`0.0` mV
v_thr	`-50.0` mV
g_syn_e	`10.0` nS
g_syn_i	`10.0` nS
e_syn_e	`-10.0` mV
e_syn_i	`-75.0` mV

classmethod from_options(kwargs: Dict)¶: From options

NodeStateOptions Class¶

class farms_network.core.options.NodeStateOptions(**kwargs)¶

Base class for node specific state options

Attributes:

initial (list of float): Initial state values.
names (list of str): State variable names.

classmethod from_kwargs(**kwargs)¶: From node specific name-value kwargs

classmethod from_options(kwargs: Dict)¶: From options

EdgeOptions Class¶

class farms_network.core.options.EdgeOptions(**kwargs)¶

Base class for defining edge options between nodes

Attributes:

from_node (str): Source node of the edge.
to_node (str): Target node of the edge.
weight (float): Weight of the edge.
type (str): Edge type (e.g., excitatory, inhibitory).

classmethod from_options(kwargs: Dict)¶: From options

EdgeVisualOptions Class¶

class farms_network.core.options.EdgeVisualOptions(**kwargs)¶

Base class for edge visualization parameters

Attributes:

color (list of float): Color of the edge.
label (str): Label for the edge.
layer (str): Layer in which the edge is displayed.

classmethod from_options(kwargs: Dict)¶: From options

LIDannerParameterOptions Class¶

class farms_network.core.options.LIDannerParameterOptions(**kwargs)¶

Class to define the parameters of Leaky Integrator Danner node model.

Attributes:: c_m (float): Membrane capacitance (in pF). g_leak (float): Leak conductance (in nS). e_leak (float): Leak reversal potential (in mV). v_max (float): Maximum voltage (in mV). v_thr (float): Threshold voltage (in mV). g_syn_e (float): Excitatory synaptic conductance (in nS). g_syn_i (float): Inhibitory synaptic conductance (in nS). e_syn_e (float): Excitatory synaptic reversal potential (in mV). e_syn_i (float): Inhibitory synaptic reversal potential (in mV).

The default values for LIDannerParameterOptions are as follows:

Parameter	Default Value
c_m	`10.0` pF
g_leak	`2.8` nS
e_leak	`-60.0` mV
v_max	`0.0` mV
v_thr	`-50.0` mV
g_syn_e	`10.0` nS
g_syn_i	`10.0` nS
e_syn_e	`-10.0` mV
e_syn_i	`-75.0` mV

classmethod defaults(**kwargs)¶: Get the default parameters for LI Danner Node model

LINaPDannerParameterOptions Class¶

class farms_network.core.options.LINaPDannerParameterOptions(**kwargs)¶

Class to define the parameters of Leaky integrator danner node model

The default values for LIDannerNaPParameterOptions are as follows:

Parameter	Default Value
c_m	`10.0` pF
g_nap	`4.5` nS
e_na	`50.0` mV
v1_2_m	`-40.0` mV
k_m	`-6.0`
v1_2_h	`-45.0` mV
k_h	`4.0`
v1_2_t	`-35.0` mV
k_t	`15.0`
g_leak	`4.5` nS
e_leak	`-62.5` mV
tau_0	`80.0` ms
tau_max	`160.0` ms
v_max	`0.0` mV
v_thr	`-50.0` mV
g_syn_e	`10.0` nS
g_syn_i	`10.0` nS
e_syn_e	`-10.0` mV
e_syn_i	`-75.0` mV

classmethod defaults(**kwargs)¶: Get the default parameters for LI NaP Danner Node model