bep032tools.generator.BEP032Templater module

class bep032tools.generator.BEP032Templater.BEP032TemplateData(sub_id, ses_id)

Bases: BEP032Data

Representation of a BEP032 Data, as specified by in the [ephys BEP](https://bids.neuroimaging.io/bep032)

The BEP032Data object can track multiple realizations of split, run, task but only a single realization of session and subject, i.e. to represent multiple session folders, multiple BEP032Data objects are required. To include multiple realizations of tasks or runs, call the register_data method for each set of parameters separately.

Parameters:

• sub_id (str) – subject identifier, e.g. ‘0012’ or ‘j.s.smith’

• ses-id (str) – session identifier, e.g. ‘20210101’ or ‘007’

• tasks (str) – task identifier of data files

• runs (str) – run identifier of data files

generate_all_metadata_files()

generate_metadata_file_channels(output)

generate_metadata_file_contacts(output)

generate_metadata_file_dataset_description(output)

generate_metadata_file_ephys(output)

generate_metadata_file_participants(output)

generate_metadata_file_probes(output)

generate_metadata_file_scans(output)

generate_metadata_file_sessions(output)

generate_metadata_file_tasks(output)

validate()

Validate the generated structure using the BEP032 validator

Parameters:

output_folder (str) – path to the folder to validate

Returns:

True if validation was successful. False if it failed.

Return type:

bool

bep032tools.generator.BEP032Templater.create_file(source, destination, mode)

Create a file at a destination location

Parameters:

• source (str) – Source location of the file.

• destination (str) – Destination location of the file.

• mode (str) – File creation mode. Valid parameters are ‘copy’, ‘link’ and ‘move’.

Raises:

ValueError – In case of invalid creation mode.

bep032tools.generator.BEP032Templater.extract_structure_from_csv(csv_file)

Load csv file that contains folder structure information and return it as pandas.datafram.

Parameters:

csv_file (str) – The file to be loaded.

Returns:

A dataframe containing the essential columns for creating an BEP032 structure

Return type:

pandas.dataframe

bep032tools.generator.BEP032Templater.main()

Notes

Usage via command line: BEP032Generator.py [-h] pathToCsv pathToDir

positional arguments:

pathToCsv Path to your csv file

pathToDir Path to your folder

optional arguments:

-h, --help

show this help message and exit

Module contents