lw_pipeline.Pipeline_MNE_BIDS_Data#

class lw_pipeline.Pipeline_MNE_BIDS_Data(config, from_bids=False, from_deriv='', from_deriv_dir='', concatenate_runs=False)[source]#

Bases: Pipeline_Data

Data representation of eeg/ieeg/meg files for the pipeline.

Contains Path or BidsPath objects of files the pipeline should be applied to.

__init__(config, from_bids=False, from_deriv='', from_deriv_dir='', concatenate_runs=False)[source]#

Initialize the PipelineData object.

Parameters:

  • config (Config) – Configuration object.

  • from_bids (bool) – If True, the data is initialized from BIDS files located in the bids_root directory.

  • from_deriv (str) – Find bids styled files in the derivatives directory with the description from_deriv.

  • from_deriv_dir (str) – Ignore the variable config.eeg_path and construct file_paths from the derivatives directory. Requires bids styled files in the derivatives directory.

Methods

__init__(config[, from_bids, from_deriv, ...])

Initialize the PipelineData object.

apply(function[, subjects, sessions, tasks, ...])

Apply a function to each data file individually.

as_df()

Return the file_paths dictionary as a pandas DataFrame.

concatenate_runs()

Concatenate runs of the same task for each subject and session.

copy()

Create a deep copy of the Pipeline_MNE_BIDS_Data object.

get_bids_path(source, subject, session, ...)

Create a BIDSPath without actually doing sth.

get_bids_path_from_bids_root(source, bids_path)

Get BidsPath for raw data from the bids_root directory.

get_raw_from_derivatives(source, bids_path)

Get BidsPath for raw data from the derivatives directory.

get_raw_from_derivatives_dir(...)

Ignore the variable config.eeg_path and construct file_paths from deriv.

Attributes

config

Configuration of the pipeline.

file_paths

Dictionary of file paths organized by subject, session, task, and run.

from_deriv

apply(function, subjects=None, sessions=None, tasks=None, save=True, print_duration=True, suffix='eeg', description='', bids_root=None)[source]#

Apply a function to each data file individually.

Can also save the output to the derivatives directory.

Parameters:

  • function (function) – Function to apply to the data with the signature (source, bids_path).

  • subjects (list) – List of subjects to apply the function to.

  • sessions (list) – List of sessions to apply the function to.

  • tasks (list) – List of tasks to apply the function to.

  • save (bool) – Whether to save the output to the derivatives directory (in case function return a raw object, i.e. subclass of mne.io.BaseRaw or an mne.Annotations instance).

  • print_duration (bool) – Whether to print the duration of the function.

  • suffix (str) – Suffix of the output Bidspath. Default is “eeg”. For Anntations one could use “markers”. Only certain values allowed, cf. MNE-BIDS documentation (https://mne.tools/mne-bids/stable/generated/mne_bids.BIDSPath.html#mne_bids.BIDSPath). If suffix is not in [“meg”, “eeg”, “ieeg”], the output file path will not be updated in the file_paths dictionary. Annotations are saved, but not directly passed on to the next step.

  • description (str) – Description of the output Bidspath for the derivative, if none specified use PipelineStep.short_id + function name instead.

  • bids_root (str) – Root directory for the destination. If None, the bids derivatives directory from the config is used.

as_df()[source]#

Return the file_paths dictionary as a pandas DataFrame.

Returns:

df – DataFrame with columns “Subject”, “Session”, “Task”, “Run”, “Source”.

Return type:

pd.DataFrame

concatenate_runs()[source]#

Concatenate runs of the same task for each subject and session.

Creates a new run “99”.

property config#

Configuration of the pipeline.

copy()[source]#

Create a deep copy of the Pipeline_MNE_BIDS_Data object.

Returns:

A deep copy of the current object.

Return type:

Pipeline_MNE_BIDS_Data

file_paths = None#

Dictionary of file paths organized by subject, session, task, and run.

get_bids_path(source, subject, session, task, run)[source]#

Create a BIDSPath without actually doing sth. with the source file.

get_bids_path_from_bids_root(source, bids_path)[source]#

Get BidsPath for raw data from the bids_root directory.

get_raw_from_derivatives(source, bids_path)[source]#

Get BidsPath for raw data from the derivatives directory.

get_raw_from_derivatives_dir(derivative_description)[source]#

Ignore the variable config.eeg_path and construct file_paths from deriv. dir.

Requires bids styled files in the derivatives directory.