ando.tools.generator package

Subpackages

Submodules

ando.tools.generator.AnDOGenerator module

class ando.tools.generator.AnDOGenerator.AnDOData(sub_id, ses_id, modality='ephys')

Bases: object

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

The AnDOData 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 AnDOData objects are required.

Parameters

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

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

  • tasks (list) – list of strings, the task identifiers used in the session

  • runs (list or dict) – list of integers, the run identifiers used in the session. In case of more than one task a dictionary needs to be provided with the task as keys and the list of run identifiers as corresponding values

property basedir
generate_data_files(mode='link')

Add datafiles to AnDO structure

Parameters

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

generate_metadata_files()

Copy registered metadata files into BIDS structure

This method currently only takes the file postfix into account to determine the target folder.

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

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

Register data with the AnDO 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.

register_metadata_files(*files)

Register metadata with the AnDO data structure.

Parameters

*files (list) – path to files to be added as metadata files. File content needs to be according with AnDO guidelines as files will only be moved to the their correct location based on the file name

validate()

Validate the generated structure using the AnDO validator

Returns

True if validation was successful. False if it failed.

Return type

bool

ando.tools.generator.AnDOGenerator.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.

ando.tools.generator.AnDOGenerator.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 AnDO structure

Return type

pandas.dataframe

ando.tools.generator.AnDOGenerator.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’.

Parameters

  • csv_file (str) – Csv file that contains a list of directories to create.

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

ando.tools.generator.AnDOGenerator.main()

Notes

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

positional arguments:

pathToCsv Path to your folder

pathToDir Path to your csv file

optional arguments:
-h, --help

show this help message and exit

Module contents