lw_pipeline.Config

class lw_pipeline.Config(config_file_path=None, verbose=False)

Bases: object

A class representing the configuration settings.

__init__(config_file_path=None, verbose=False)

Initialize the Config object.

Parameters:

• config_file_path (str, optional) – The path to the configuration file. If provided, the configuration settings will be updated based on the variables defined in the file.

• verbose (bool, optional) – If True, print messages about the configuration file being used. Default is False.

Methods

__init__([config_file_path, verbose])	Initialize the Config object.
ask(message[, default])	Ask to do something, e.g. before potentially deleting data, etc.
check_steps_dir()	Make sure steps dir is absolute.
get_version()	Get a version of the pipeline by getting last commit hash from the git.
set_variable_and_write_to_config_file(...)	Set a variable in this class and write to config file, if not defined there.
setup_logging()	Set up logging based on configuration settings.

Attributes

auto_response	Decide how questions are answered (off/y/n/default)
bids_acquisition	EEG information that should be included in the BIDS file
bids_datatype	BIDS datatype of the data created as derivatives in the pipeline
bids_extension	Extension of the BIDS files in the bids root directory
bids_root	Root directory for BIDS formatted data
config_file_path	The path to an external configuration file.
data_dir	Default data directory
deriv_root	Root directory for derivatives
eeg_path	Path to the eeg data which should be converted to BIDS
log_file	Path to the log file.
log_format	Format string for log messages
log_level	Logging level for the pipeline.
log_to_file	Whether to write logs to a file in addition to console output
n_jobs	Number of parallel jobs to run
output_profiling	Include timing and file size information in sidecar metadata
output_root	Root directory for non-BIDS outputs.
outputs_to_generate	List or dict specifying which outputs to generate.
overwrite	Overwrite existing derivative files, if False they are skipped
overwrite_mode	Overwrite mode for output files.
sessions	List of sessions to include in the pipeline processing.
sidecar_auto_generate	Automatically generate sidecar JSON files for all outputs
steps_dir	Steps directory relative to config file or current working directory if no
subjects	List of subjects to include in the pipeline processing.
tasks	List of tasks to include in the pipeline processing.

ask(message, default='n')

Ask to do something, e.g. before potentially deleting data, etc.

Make sure to specify options, e.g. (y/n), in the message.

auto_response = 'off'

Decide how questions are answered (off/y/n/default)

bids_acquisition = None

EEG information that should be included in the BIDS file

bids_datatype = 'eeg'

BIDS datatype of the data created as derivatives in the pipeline

bids_extension = '.edf'

Extension of the BIDS files in the bids root directory

bids_root = '/home/runner/data/bids'

Root directory for BIDS formatted data

check_steps_dir()

Make sure steps dir is absolute.

Notes

• If config_file_path is not None, the relative steps_dir is resolved relative to the directory containing the configuration file.

• If config_file_path is None, the relative steps_dir is resolved relative to the current working directory.

Parameters:

• steps_dir (str) – The directory path for steps, which will be converted to an absolute path.

• config_file_path (str or None) – The path to the configuration file, used to resolve relative paths.

config_file_path = None

The path to an external configuration file.

data_dir = '/home/runner/data'

Default data directory

deriv_root = '/home/runner/data/derivatives'

Root directory for derivatives

eeg_path = {}

Path to the eeg data which should be converted to BIDS

Structure: subject -> condition -> task -> list of eeg files (runs) File names expected relative to data_dir

get_version()

Get a version of the pipeline by getting last commit hash from the git.

Cave: This only works if the pipeline is in a git repository. If not, it will return “unknown”.

log_file = None

Path to the log file. If None and log_to_file is True, defaults to ‘pipeline.log’ in the deriv_root directory.

log_format = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'

Format string for log messages

log_level = 'INFO'

Logging level for the pipeline. Options: “DEBUG”, “INFO”, “WARNING”, “ERROR”, “CRITICAL”

log_to_file = True

Whether to write logs to a file in addition to console output

n_jobs = 1

Number of parallel jobs to run

output_profiling = False

Include timing and file size information in sidecar metadata

output_root = None

Root directory for non-BIDS outputs. If None, defaults to deriv_root.

outputs_to_generate = None

List or dict specifying which outputs to generate. - None: Generate all outputs enabled by default - List of patterns: Generate outputs matching patterns (e.g., [“plot*”, “stats”]) - Dict: Step-specific patterns (e.g., {“01”: [“plot”], “02”: [“*”]}) Supports wildcards via fnmatch (e.g., “*” for all, “plot*”: all starting with plot)

overwrite = False

Overwrite existing derivative files, if False they are skipped

overwrite_mode = 'never'

Overwrite mode for output files. Options: - “always”: Always overwrite existing files - “never”: Never overwrite, skip existing files - “ask”: Prompt user for each file - “ifnewer”: Overwrite if source file is newer than output

sessions = []

List of sessions to include in the pipeline processing. If empty list, include all sessions

set_variable_and_write_to_config_file(variable, value)

Set a variable in this class and write to config file, if not defined there.

For safety, only allow to write variables that are not already set.

Parameters:

• variable (str) – The name of the variable to update.

• value (mixed) – The value to set the variable to.

setup_logging()

Set up logging based on configuration settings.

This method configures the root logger with console and optionally file handlers based on the log_level, log_to_file, and log_file settings.

sidecar_auto_generate = True

Automatically generate sidecar JSON files for all outputs

steps_dir = 'steps/'

Steps directory relative to config file or current working directory if no

subjects = []

List of subjects to include in the pipeline processing. If empty list, include all subjects

tasks = []

List of tasks to include in the pipeline processing. If empty list, include all tasks