Script Reference

This page contains the documentation of modules needed to run as a script.

Main entrypoint

Main entrypoint for LABNIRS to SNIRF conversion when run as a script.

labnirs2snirf.labnirs2snirf.main() → int[source]

LABNIRS to SNIRF conversion script.

This function coordinates the full conversion workflow when run as python -m labnirs2snirf on the command line:

Parse command-line arguments
Configure logging based on user preferences
Read and parse LABNIRS data file
Optionally add probe position information
Write output in SNIRF format

Returns:: Exit code: 0 for success, 1 for failure.
Return type:: int

Notes

Exception handling is designed with the intention to reduce end-user exposure to stack traces and technical details. Most exceptions are hidden from end users, providing only a concise error message. Detailed error information can be obtained by increasing verbosity with -v flags and/or using –log to write to a log file.

Parsing command-line arguments

Module for handling command-line arguments.

exception labnirs2snirf.args.ArgumentError[source]

Bases: Labnirs2SnirfError

Error indicating invalid command-line arguments.

class labnirs2snirf.args.Arguments(progname: str | None = 'labnirs2snirf')[source]

Bases: object

Class to handle configuration and parsing of command-line arguments.

Parameters:: progname (str or None, default=__package__) – Program name to display in help message. If None, defaults to package name.

__init__(progname: str | None = 'labnirs2snirf')[source]

Initialize the Arguments parser.

Parameters:: progname (str or None, default=__package__) – Program name to display in help message. If None, defaults to package name.

__repr__() → str[source]

Return a detailed string representation of the Arguments object.

Returns:: String showing arguments stored.
Return type:: str

__str__() → str[source]

Return a string representation of the Arguments object.

Returns:: String showing arguments stored.
Return type:: str

drop: set[str] | None

locations: Path | None

log: bool

parse(args: list[str]) → Self[source]

Parse command-line arguments and populate the Arguments object.

Parameters:: args (list[str]) – List of command-line arguments to parse. If empty, shows help.
Returns:: Self with parsed argument values set as attributes.
Return type:: Self

Notes

If –log is specified, verbosity is automatically set to at least 1. Drop values are converted to a set to avoid duplicates.

parser: ArgumentParser

source_file: Path

target_file: Path

type: str

verbosity: int

Logging

Logging configuration utilities for the labnirs2snirf package.

labnirs2snirf.log.config_logger(file_logging: bool = False, verbosity_level: int = 0) → None[source]

Configure the root logger for the application.

Parameters:

file_logging (bool, default = False) – If True, log messages will be written to a file. If False, log messages will be printed to the console.
verbosity_level (int, default = 0) – The verbosity level of the log messages. Must be between 0 and 3. Possible values: - 0: disabled (no logging) - 1: WARNING (warnings and above) - 2: INFO (informational messages and above) - 3: DEBUG (debugging messages and above)

Notes

This function should be called only once, at the start of the application, and only if it’s run as a script, not as a library. Most modules should invoke getLogger(__name__) to get a module-specific logger, which will inherit the configuration set here.