bep032tools.generator package

Subpackages

Submodules

bep032tools.generator.BEP032Generator module

class bep032tools.generator.BEP032Generator.BEP032Data(sub_id, ses_id, modality='ephys')

Bases: object

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

property basedir
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)
classmethod generate_struct(csv_file, pathToDir)

Create structure with csv file given in argument This file must contain a header row specifying the provided data. Accepted titles are defined in the BEP. Essential information of the following attributes needs to be present. Essential columns are ‘sub_id’ and ‘ses_id’. Optional columns are ‘runs’, ‘tasks’ and ‘data_file’ (only single file per sub_id, ses_id combination supported). ‘data_file’ needs to be a valid path to a nix or nwb file.

Parameters

  • csv_file (str) – Csv file that contains sub_id and ses_id and optional columns

  • pathToDir (str) – Path to directory where the directories will be created.

generate_structure()

Generate the required folders for storing the dataset

Returns

Path of created data folder

Return type

path

get_data_folder(mode='absolute')

Generate the relative path to the folder of the data files

Parameters

mode (str) – Return the absolute or local path to the data folder. Valid values: ‘absolute’, ‘local’

Returns

Path of the data folder

Return type

pathlib.Path

organize_data_files(mode='link')

Add datafiles to BEP032 structure

Parameters

mode (str) – Can be either ‘link’, ‘copy’ or ‘move’.

register_data_files(*files, task=None, run=None)

Register data with the BEP032 data structure.

Parameters

  • *files (path to files to be added as data files.) – If multiple files are provided they are treated as a single data files split into multiple chunks and will be enumerated according to the order they are provided in.

  • task (str) – task name used

  • run (str) – run name used

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.BEP032Generator.create_file(source, destination, mode, exist_ok=False)

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’.

  • exist_ok (bool) – If False, raise an Error if the destination already exist. Default: False

Raises

ValueError – In case of invalid creation mode.

bep032tools.generator.BEP032Generator.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.BEP032Generator.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