Task files are the blueprints of AutoCleanEEG pipeline. They combine two parts:
  1. Configuration (config) – a dictionary that specifies which steps to enable and how to parameterize them.
  2. Task class (Task) – a Python class that orchestrates the execution of steps in order.

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High-Level Overview

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Why Task Files?

  • Reproducibility: The same task file always runs with the same parameters.
  • Transparency: Every step and setting is explicitly defined.
  • Flexibility: You can create different task files for different study designs or datasets (e.g., resting state vs. oddball tasks).
  • Automation: Tasks integrate with the pipeline CLI to run end-to-end preprocessing.
Task files are designed to be human-readable and editable.
While you can generate them automatically, customizing them allows you to tailor preprocessing to your study’s specific needs.

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Example Snippet

config = {
    "resample_step": {"enabled": True, "value": 250},
    "filtering": {"enabled": True, "value": {"l_freq": 1, "h_freq": 100}},
    "ICA": {"enabled": True, "value": {"method": "infomax"}},
    "epoch_settings": {"enabled": True, "value": {"tmin": -1, "tmax": 1}},
}

class RestingState_Basic(Task):
    def run(self) -> None:
        self.import_raw()
        self.resample_data()
        self.filter_data()
        self.run_ica()
        self.create_regular_epochs(export=True)
        self.generate_reports()