TenetoBIDS

class TenetoBIDS(bids_dir, selected_pipeline, bids_filter=None, bidsvalidator=False, update_pipeline=True, history=None, exist_ok=False, layout=None, nettsv='nn-t')

Bases: object

Class for analysing data in BIDS.

TenetoBIDS allows for an analysis to be performed across a dataset. All different functions from Teneto can be applied to all files in a dataset organized in BIDS. Data should be first preprocessed (e.g. fMRIPrep).

Parameters:

• bids_dir (str) – string to BIDS directory

• selected_pipeline (str or dict) –

  the directory that is in the bids_dir/derivatives/<selected_pipeline>/. This fine will be used as the input to any teneto function (first argument). If multiple inputs are required for a function, then you can specify:

  {‘netin’: ‘tvc’, ‘communities’: ‘coms’}

  With this, the input for netin with be from bids_dir/derivatives/[teneto-]tvc/, and the input for communities will be from bids_dir/derivatives/[teneto-]coms/. The keys in this dictionary must match the names of the teneto funciton inputs.

• bids_filter (dict)

• history (bool)

• update_pipeline (bool) – If true, the output_pipeline becomes the new selected_pipeline

• exist_ok (bool) – If False, will raise an error if the output directory already exist_ok. If True, will not raise an error. This can lead to files being overwritten, if desc is not set.

• nettsv (str can be nn-t or ijt.) – nn-t means networks are node-node x time. ijt means daframs are ijt columns.

Methods Summary

create_output_pipeline(runc_func, ...[, ...])	Creates the directories of the saved file.
get_aux_file(bidsfile[, filetype])	Tries to automatically get auxiliary data for input files, and loads it
get_run_options([for_selected])	Returns the different function names that can be called using TenetoBIDS.run()
get_selected_files([output])	Uses information in selected_pipeline and the bids layout and shows the files that will be processed when calling TenetoBIDS.run().
load_data([bids_filter])	Returns data, default is the input data.
load_events()	Loads event data for selected files
load_file(bidsfile)	Aux function to load the data and sidecar from a BIDSFile
run(run_func, input_params[, output_desc, ...])	Runs a runction on the selected files.
troubleshoot(stepname, status)	Prints ongoing info to assist with troubleshooting
update_bids_filter(filter_addons)	Updates TenetoBIDS.bids_filter
update_bids_layout()	Function that upddates to new bids l

Methods Documentation

create_output_pipeline(runc_func, output_pipeline_name, exist_ok=None)

Creates the directories of the saved file.

Parameters:

• output_pipeline (str) – name of output pipeline

• exist_ok (bool) – If False, will raise error if pipeline already exist_ok. If True, will not raise an error. This can lead to files being overwritten, if desc is not set. If None, will use the exist_ok set during init.

Returns:

bids_dir/teneto-[output_pipeline]/

Return type:

Creates the output pipeline directory in

get_aux_file(bidsfile, filetype='confounds')

Tries to automatically get auxiliary data for input files, and loads it

Paramters

bidsfileBIDSDataFile or BIDSImageFile

The BIDS file that the confound file is gong to be matched.

filetypestring

Can be confounds, events. Specified if you want to get the confound or events data.

get_run_options(for_selected=True)

Returns the different function names that can be called using TenetoBIDS.run()

Parameters:

for_selected (bool) – If True, only return run options for the selected files. If False, returns all options.

Returns:

options – a list of options that can be run.

Return type:

str

get_selected_files(output=None)

Uses information in selected_pipeline and the bids layout and shows the files that will be processed when calling TenetoBIDS.run().

If you specify a particular output, it will tell you which files will get selected for that output

load_data(bids_filter=None)

Returns data, default is the input data.

bids_filterdict

default is None. If set, load data will load all files found by the bids_filter. Any preset BIDS filter is used as well, but will get overwritten by this input.

load_events()

Loads event data for selected files

load_file(bidsfile)

Aux function to load the data and sidecar from a BIDSFile

Paramters

bidsfileBIDSDataFile or BIDSImageFile

The BIDS file that the confound file is gong to be matched.

run(run_func, input_params, output_desc=None, output_pipeline_name=None, bids_filter=None, update_pipeline=True, exist_ok=None, troubleshoot=False)

Runs a runction on the selected files.

Parameters:

• run_func (str) – str should correspond to a teneto function. So to run the funciton teneto.timeseries.derive_temporalnetwork the input should be: ‘timeseries.derive_temporalnetwork’

• input_params (dict) – keyword and value pairing of arguments for the function being run. The input data to each function will be located automatically. This input_params does not need to include the input network. For any other input that needs to be loaded loaded within the teneto_bidsstructure (communities, events, confounds), you can pass the value “bids” if they can be found within the current selected_pipeline. If they are found within a different selected_pipeline, type “bids_[selected_pipeline]”.

• output_desc (str) – If none, no desc is used (removed any previous file) If ‘keep’, then desc is preserved. If any other str, desc is set to that string

• output_pipeline_name (str) – If set, then the data is saved in teneto_[functionname]_[output_pipeline_name]. If run_func is teneto.timeseries.derive_temporalnetwork and output_pipeline_name is jackknife then then the pipeline the data is saved in is teneto-generatetemporalnetwork_jackknife

• update_pipeline (bool) – If set to True (default), then the selected_pipeline updates to output of function

• exist_ok (bool) – If set to True, then overwrites direcotry is possible.

• troubleshoot (bool) – If True, prints out certain information during running. Useful to run if reporting a bug.

troubleshoot(stepname, status)

Prints ongoing info to assist with troubleshooting

update_bids_filter(filter_addons)

Updates TenetoBIDS.bids_filter

Parameters:

filter_addons (dict) – dictionary that updates TenetoBIDS.bids_filter

update_bids_layout()

Function that upddates to new bids l