Main module¶
For more details regarding the main classes, see:
NNGT¶
Package aimed at facilitating the analysis of Neural Networks Growth and Topology.
The library mainly provides algorithms for
- generating networks
- analyzing their activity
- studying the graph theoretical properties of those networks
Available modules¶
- analysis
- Tools to study graph topology and neuronal activity.
- core
- Where the main classes are coded; however, most useful classes and methods for users are loaded at the main level (nngt) when the library is imported, so nngt.core should generally not be used.
- generation
- Functions to generate specific networks.
- geometry
- Tools to work on metric graphs (see PyNCulture).
- io
- Tools for input/output operations.
- lib
- Basic functions used by several most other modules.
- simulation
- Tools to provide complex network generation with NEST and help analyze the influence of the network structure on neuronal activity.
- plot
- plot data or graphs using matplotlib and graph_tool.
Units¶
Functions related to spatial embedding of networks are using micrometers (um) as default unit; other units from the metric system can also be provided:
- mm for milimeters
- cm centimeters
- dm for decimeters
- m for meters
Main classes and functions¶
nngt.Graph ([nodes, name, weighted, ...]) |
The basic graph class, which inherits from a library class such as gt.Graph , networkx.DiGraph , or igraph.Graph. |
nngt.GroupProperty (size[, constraints, ...]) |
Class defining the properties needed to create groups of neurons from an existing GraphClass or one of its subclasses. |
nngt.Network ([name, weighted, directed, ...]) |
The detailed class that inherits from Graph and implements additional properties to describe various biological functions and interact with the NEST simulator. |
nngt.NeuralGroup ([nodes, ntype, model, ...]) |
Class defining groups of neurons. |
nngt.NeuralPop (size[, parent, with_models]) |
The basic class that contains groups of neurons and their properties. |
nngt.SpatialGraph ([nodes, name, weighted, ...]) |
The detailed class that inherits from Graph and implements additional properties to describe spatial graphs (i.e. |
nngt.SpatialNetwork (population[, name, ...]) |
Class that inherits from Network and SpatialGraph to provide a detailed description of a real neural network in space, i.e. |
nngt.generate (di_instructions, **kwargs) |
Generate a Graph or one of its subclasses from a dict containing all the relevant informations. |
nngt.get_config ([key]) |
Get the NNGT configuration as a dictionary. |
nngt.load_from_file (filename[, fmt, ...]) |
Load the main properties (edges, attributes...) from a file. |
nngt.save_to_file (graph, filename[, fmt, ...]) |
Save a graph to file. |
nngt.seed ([seed]) |
Seed the random generator used by NNGT (i.e. |
nngt.set_config (config[, value]) |
Set NNGT’s configuration. |
nngt.use_library (library[, reloading]) |
Allows the user to switch to a specific graph library. |