interfaces.cmtk.nx¶
AverageNetworks¶
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
Inputs:
[Mandatory]
in_files: (a list of items which are a pathlike object or string
representing an existing file)
Networks for a group of subjects
[Optional]
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.
group_id: (a unicode string, nipype default value: group1)
ID for group
out_gpickled_groupavg: (a pathlike object or string representing a
file)
Average network saved as a NetworkX .pck
out_gexf_groupavg: (a pathlike object or string representing a file)
Average network saved as a .gexf file
Outputs:
gpickled_groupavg: (a pathlike object or string representing a file)
Average network saved as a NetworkX .pck
gexf_groupavg: (a pathlike object or string representing a file)
Average network saved as a .gexf file
matlab_groupavgs: (a list of items which are a pathlike object or
string representing a file)
NetworkXMetrics¶
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
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
Input network
[Optional]
out_k_core: (a pathlike object or string representing a file, nipype
default value: k_core)
Computed k-core network stored as a NetworkX pickle.
out_k_shell: (a pathlike object or string representing a file, nipype
default value: k_shell)
Computed k-shell network stored as a NetworkX pickle.
out_k_crust: (a pathlike object or string representing a file, nipype
default value: k_crust)
Computed k-crust network stored as a NetworkX pickle.
treat_as_weighted_graph: (a boolean, nipype default value: True)
Some network metrics can be calculated while considering only a
binarized version of the graph
compute_clique_related_measures: (a boolean, nipype default value:
False)
Computing clique-related measures (e.g. node clique number) can be
very time consuming
out_global_metrics_matlab: (a pathlike object or string representing
a file)
Output node metrics in MATLAB .mat format
out_node_metrics_matlab: (a pathlike object or string representing a
file)
Output node metrics in MATLAB .mat format
out_edge_metrics_matlab: (a pathlike object or string representing a
file)
Output edge metrics in MATLAB .mat format
out_pickled_extra_measures: (a pathlike object or string representing
a file, nipype default value: extra_measures)
Network measures for group 1 that return dictionaries stored as a
Pickle.
Outputs:
gpickled_network_files: (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)
global_measures_matlab: (a pathlike object or string representing a
file)
Output global metrics in MATLAB .mat format
node_measures_matlab: (a pathlike object or string representing a
file)
Output node metrics in MATLAB .mat format
edge_measures_matlab: (a pathlike object or string representing a
file)
Output edge metrics in MATLAB .mat format
node_measure_networks: (a list of items which are a pathlike object
or string representing a file)
edge_measure_networks: (a list of items which are a pathlike object
or string representing a file)
k_networks: (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_shell: (a pathlike object or string representing a file)
Computed k-shell 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.
pickled_extra_measures: (a pathlike object or string representing a
file)
Network measures for the group that return dictionaries, stored as a
Pickle.
matlab_dict_measures: (a list of items which are a pathlike object or
string representing a file)
add_dicts_by_key()
¶
Combines two dictionaries and adds the values for those keys that are shared
add_edge_data()
¶
add_node_data()
¶
average_networks()
¶
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
compute_network_measures()
¶
fix_keys_for_gexf()
¶
GEXF Networks can be read in Gephi, however, the keys for the node and edge IDs must be converted to strings