Main functions#

nngt.generate(di_instructions, **kwargs)[source]#

Generate a Graph or one of its subclasses from a dict containing all the relevant informations.

Parameters:	di_instructions (`dict`) – Dictionary containing the instructions to generate the graph. It must have at least `"graph_type"` in its keys, with a value among `"distance_rule", "erdos_renyi", "fixed_degree", "newman_watts", "price_scale_free", "random_scale_free"`. Depending on the type, di_instructions should also contain at least all non-optional arguments of the generator function.

See also

generation

nngt.get_config(key=None, detailed=False)[source]#: Get the NNGT configuration as a dictionary.

Note

This function has no MPI barrier on it.

nngt.load_from_file(filename, fmt='auto', separator=' ', secondary=';', attributes=None, notifier='@', ignore='#')[source]#

Load a Graph from a file.

Parameters:

Parameters:	filename (str) – The path to the file. fmt (str, optional (default: “neighbour”)) – The format used to save the graph. Supported formats are: “neighbour” (neighbour list, default if format cannot be deduced automatically), “ssp” (scipy.sparse), “edge_list” (list of all the edges in the graph, one edge per line, represented by a `source target`-pair), “gml” (gml format, default if filename ends with ‘.gml’), “graphml” (graphml format, default if filename ends with ‘.graphml’ or ‘.xml’), “dot” (dot format, default if filename ends with ‘.dot’), “gt” (only when using graph_tool`<http://graph-tool.skewed.de/>_ as library, detected if `filename ends with ‘.gt’). separator (str, optional (default ” “)) – separator used to separate inputs in the case of custom formats (namely “neighbour” and “edge_list”) secondary (str, optional (default: “;”)) – Secondary separator used to separate attributes in the case of custom formats. attributes (list, optional (default: [])) – List of names for the attributes present in the file. If a notifier is present in the file, names will be deduced from it; otherwise the attributes will be numbered. notifier (str, optional (default: “@”)) – Symbol specifying the following as meaningfull information. Relevant information are formatted `@info_name=info_value`, where `info_name` is in (“attributes”, “directed”, “name”, “size”) and associated info_value``s are of type (``list, `bool`, `str`, `int`). Additional notifiers are `@type=SpatialGraph/Network/SpatialNetwork`, which must be followed by the relevant notifiers among `@shape`, `@population`, and `@graph`. ignore (str, optional (default: “#”)) – Ignore lines starting with the ignore string.
Returns:	graph (`Graph` or subclass) – Loaded graph.

filename (str) – The path to the file.
fmt (str, optional (default: “neighbour”)) – The format used to save the graph. Supported formats are: “neighbour” (neighbour list, default if format cannot be deduced automatically), “ssp” (scipy.sparse), “edge_list” (list of all the edges in the graph, one edge per line, represented by a source target-pair), “gml” (gml format, default if filename ends with ‘.gml’), “graphml” (graphml format, default if filename ends with ‘.graphml’ or ‘.xml’), “dot” (dot format, default if filename ends with ‘.dot’), “gt” (only when using graph_tool`<http://graph-tool.skewed.de/>_ as library, detected if `filename ends with ‘.gt’).
separator (str, optional (default ” “)) – separator used to separate inputs in the case of custom formats (namely “neighbour” and “edge_list”)
secondary (str, optional (default: “;”)) – Secondary separator used to separate attributes in the case of custom formats.
attributes (list, optional (default: [])) – List of names for the attributes present in the file. If a notifier is present in the file, names will be deduced from it; otherwise the attributes will be numbered.
notifier (str, optional (default: “@”)) – Symbol specifying the following as meaningfull information. Relevant information are formatted @info_name=info_value, where info_name is in (“attributes”, “directed”, “name”, “size”) and associated info_value``s are of type (``list, bool, str, int). Additional notifiers are @type=SpatialGraph/Network/SpatialNetwork, which must be followed by the relevant notifiers among @shape, @population, and @graph.
ignore (str, optional (default: “#”)) – Ignore lines starting with the ignore string.

Returns:

graph (Graph or subclass) – Loaded graph.

nngt.num_mpi_processes()[source]#: Returns the number of MPI processes (1 if MPI is not used)

nngt.on_master_process()[source]#

Check whether the current code is executing on the master process (rank 0) if MPI is used.

Returns:	True if rank is 0, if mpi4py is not present or if MPI is not used, otherwise False.

nngt.save_to_file(graph, filename, fmt='auto', separator=' ', secondary=';', attributes=None, notifier='@')[source]#

Save a graph to file.

Changed in version 0.7: Added support to write position and Shape when saving SpatialGraph. Note that saving Shape requires shapely.

@todo: implement gml, dot, xml, gt formats

Parameters:

Parameters:	graph (`Graph` or subclass) – Graph to save. filename (str) – The path to the file. fmt (str, optional (default: “auto”)) – The format used to save the graph. Supported formats are: “neighbour” (neighbour list, default if format cannot be deduced automatically), “ssp” (scipy.sparse), “edge_list” (list of all the edges in the graph, one edge per line, represented by a `source target`-pair), “gml” (gml format, default if filename ends with ‘.gml’), “graphml” (graphml format, default if filename ends with ‘.graphml’ or ‘.xml’), “dot” (dot format, default if filename ends with ‘.dot’), “gt” (only when using graph_tool`<http://graph-tool.skewed.de/>_ as library, detected if `filename ends with ‘.gt’). separator (str, optional (default ” “)) – separator used to separate inputs in the case of custom formats (namely “neighbour” and “edge_list”) secondary (str, optional (default: “;”)) – Secondary separator used to separate attributes in the case of custom formats. attributes (list, optional (default: `None`)) – List of names for the edge attributes present in the graph that will be saved to disk; by default (`None`), all attributes will be saved. notifier (str, optional (default: “@”)) – Symbol specifying the following as meaningfull information. Relevant information are formatted `@info_name=info_value`, with `info_name` in (“attributes”, “attr_types”, “directed”, “name”, “size”). Additional notifiers are `@type=SpatialGraph/Network/SpatialNetwork`, which are followed by the relevant notifiers among `@shape`, `@population`, and `@graph` to separate the sections.

graph (Graph or subclass) – Graph to save.
filename (str) – The path to the file.
fmt (str, optional (default: “auto”)) – The format used to save the graph. Supported formats are: “neighbour” (neighbour list, default if format cannot be deduced automatically), “ssp” (scipy.sparse), “edge_list” (list of all the edges in the graph, one edge per line, represented by a source target-pair), “gml” (gml format, default if filename ends with ‘.gml’), “graphml” (graphml format, default if filename ends with ‘.graphml’ or ‘.xml’), “dot” (dot format, default if filename ends with ‘.dot’), “gt” (only when using graph_tool`<http://graph-tool.skewed.de/>_ as library, detected if `filename ends with ‘.gt’).
separator (str, optional (default ” “)) – separator used to separate inputs in the case of custom formats (namely “neighbour” and “edge_list”)
secondary (str, optional (default: “;”)) – Secondary separator used to separate attributes in the case of custom formats.
attributes (list, optional (default: None)) – List of names for the edge attributes present in the graph that will be saved to disk; by default (None), all attributes will be saved.
notifier (str, optional (default: “@”)) – Symbol specifying the following as meaningfull information. Relevant information are formatted @info_name=info_value, with info_name in (“attributes”, “attr_types”, “directed”, “name”, “size”). Additional notifiers are @type=SpatialGraph/Network/SpatialNetwork, which are followed by the relevant notifiers among @shape, @population, and @graph to separate the sections.

Note

Positions are saved as bytes by numpy.nparray.tostring()

nngt.seed(msd=None, seeds=None)[source]#

Seed the random generator used by NNGT (i.e. the numpy RandomState: for details, see numpy.random.RandomState).

..versionchanged:: 0.8: Renamed seed to msd, added seeds for multithreading.

Parameters:	msd (int, optional) – Master seed for numpy RandomState. Must be convertible to 32-bit unsigned integers. seeds (array of ints, optional) – Seeds for for RandomState. Must be convertible to 32-bit unsigned integers.

nngt.set_config(config, value=None, silent=False)[source]#

Set NNGT’s configuration.

Parameters:	config (dict or str) – Either a full configuration dictionary or one key to be set together with its associated value. value (object, optional (default: None)) – Value associated to config if config is a key.

Examples

>>> nngt.set_config({'multithreading': True, 'omp': 4})
>>> nngt.set_config('multithreading', False)

Notes

See the config file nngt/nngt.conf.default or ~/.nngt/nngt.conf for details about your configuration.

This function has an MPI barrier on it, so it must always be called on all processes.