nipype.interfaces.cmtk.nx module

AverageNetworks

Link to code

Bases: BaseInterface

Calculates and outputs the average network given a set of input NetworkX gpickle files

This interface will only keep an edge in the averaged network if that edge is present in at least half of the input networks.

Example

>>> import nipype.interfaces.cmtk as cmtk
>>> avg = cmtk.AverageNetworks()
>>> avg.inputs.in_files = ['subj1.pck', 'subj2.pck']
>>> avg.run()                 # doctest: +SKIP

in_files : a list of items which are a pathlike object or string representing an existing file

Networks for a group of subjects.

group_id : a unicode string

ID for group. (Nipype default value: group1)

out_gexf_groupavg : a pathlike object or string representing a file

Average network saved as a .gexf file.

out_gpickled_groupavg : a pathlike object or string representing a file

Average network saved as a NetworkX .pck.

resolution_network_file : a pathlike object or string representing an existing file

Parcellation files from Connectome Mapping Toolkit. This is not necessary, but if included, the interface will output the statistical maps as networkx graphs.

gexf_groupavg : a pathlike object or string representing a file

Average network saved as a .gexf file.

gpickled_groupavg : a pathlike object or string representing a file

Average network saved as a NetworkX .pck.

matlab_groupavgs : a list of items which are a pathlike object or string representing a file

NetworkXMetrics

Link to code

Bases: BaseInterface

Calculates and outputs NetworkX-based measures for an input network

Example

>>> import nipype.interfaces.cmtk as cmtk
>>> nxmetrics = cmtk.NetworkXMetrics()
>>> nxmetrics.inputs.in_file = 'subj1.pck'
>>> nxmetrics.run()                 # doctest: +SKIP

in_file : a pathlike object or string representing an existing file

Input network.

compute_clique_related_measures : a boolean

Computing clique-related measures (e.g. node clique number) can be very time consuming. (Nipype default value: False)

out_edge_metrics_matlab : a pathlike object or string representing a file

Output edge metrics in MATLAB .mat format.

out_global_metrics_matlab : a pathlike object or string representing a file

Output node metrics in MATLAB .mat format.

out_k_core : a pathlike object or string representing a file

Computed k-core network stored as a NetworkX pickle. (Nipype default value: k_core)

out_k_crust : a pathlike object or string representing a file

Computed k-crust network stored as a NetworkX pickle. (Nipype default value: k_crust)

out_k_shell : a pathlike object or string representing a file

Computed k-shell network stored as a NetworkX pickle. (Nipype default value: k_shell)

out_node_metrics_matlab : a pathlike object or string representing a file

Output node metrics in MATLAB .mat format.

out_pickled_extra_measures : a pathlike object or string representing a file

Network measures for group 1 that return dictionaries stored as a Pickle. (Nipype default value: extra_measures)

treat_as_weighted_graph : a boolean

Some network metrics can be calculated while considering only a binarized version of the graph. (Nipype default value: True)

edge_measure_networks : a list of items which are a pathlike object or string representing a file edge_measures_matlab : a pathlike object or string representing a file

Output edge metrics in MATLAB .mat format.

global_measures_matlab : a pathlike object or string representing a file

Output global metrics in MATLAB .mat format.

gpickled_network_files : a list of items which are a pathlike object or string representing a file k_core : a pathlike object or string representing a file

Computed k-core network stored as a NetworkX pickle.

k_crust : a pathlike object or string representing a file

Computed k-crust network stored as a NetworkX pickle.

k_networks : a list of items which are a pathlike object or string representing a file k_shell : a pathlike object or string representing a file

Computed k-shell network stored as a NetworkX pickle.

matlab_dict_measures : a list of items which are a pathlike object or string representing a file matlab_matrix_files : a list of items which are a pathlike object or string representing a file node_measure_networks : a list of items which are a pathlike object or string representing a file node_measures_matlab : a pathlike object or string representing a file

Output node metrics in MATLAB .mat format.

pickled_extra_measures : a pathlike object or string representing a file

Network measures for the group that return dictionaries, stored as a Pickle.

nipype.interfaces.cmtk.nx.add_dicts_by_key(in_dict1, in_dict2)

Combines two dictionaries and adds the values for those keys that are shared

nipype.interfaces.cmtk.nx.add_edge_data(edge_array, ntwk, above=0, below=0)

nipype.interfaces.cmtk.nx.add_node_data(node_array, ntwk)

nipype.interfaces.cmtk.nx.average_networks(in_files, ntwk_res_file, group_id)

Sums the edges of input networks and divides by the number of networks Writes the average network as .pck and .gexf and returns the name of the written networks

nipype.interfaces.cmtk.nx.compute_dict_measures(ntwk)

Returns a dictionary

nipype.interfaces.cmtk.nx.compute_edge_measures(ntwk)

These return edge-based measures

nipype.interfaces.cmtk.nx.compute_network_measures(ntwk)

nipype.interfaces.cmtk.nx.compute_node_measures(ntwk, calculate_cliques=False)

These return node-based measures

nipype.interfaces.cmtk.nx.compute_singlevalued_measures(ntwk, weighted=True, calculate_cliques=False)

Returns a single value per network

nipype.interfaces.cmtk.nx.fix_keys_for_gexf(orig)

GEXF Networks can be read in Gephi, however, the keys for the node and edge IDs must be converted to strings

nipype.interfaces.cmtk.nx.read_unknown_ntwk(ntwk)

nipype.interfaces.cmtk.nx.remove_all_edges(ntwk)