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Documentation Index

Fetch the complete documentation index at: https://docs.autocleaneeg.org/llms.txt

Use this file to discover all available pages before exploring further.

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How the Python Task Class Works

At the core of AutoCleanEEG is the Task class. Every task is just a Python class that inherits from autoclean.core.task.Task and defines a sequence of steps in its run() method. For new users: think of it as a recipe. Each line in run() is an instruction that takes the current EEG dataset, applies some transformation, and passes it along to the next step.

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Under the Hood: MNE Objects

AutoCleanEEG builds on MNE-Python, which provides data objects for EEG/MEG:
  • Raw – continuous EEG recordings.
  • Epochs – segmented trials or fixed-length windows.
  • Evoked – averaged responses (like ERPs).
Each function in your Task class takes one of these MNE objects, transforms it (e.g., filters it, runs ICA, drops bad epochs), and then returns it for the next step. This makes the pipeline flexible: at every stage, you’re just manipulating an EEG object in memory.

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Why It’s Powerful

  • Chainable – You can call one function after another (resample → filter → ICA → epoch) and the data flows through.
  • Customizable – You can add, skip, or branch steps as needed.
  • Interoperable – Anything you can do in Python with an MNE object can be slotted into a Task step.
  • Not Limited to Python – With proper wrappers, you can even call MATLAB functions (e.g., via matlab.engine or exporting files to EEGLAB) inside a step.
That means the Task framework doesn’t limit you to built-in methods — you can plug in custom filters, artifact rejection methods, or ML models.

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Example: Transform Flow

class MyCustomTask(Task):
    def run(self):
        self.import_raw()                 # Raw object
        self.resample_data()              # Raw → resampled Raw
        self.filter_data()                # Raw → filtered Raw
        self.run_ica()                    # Raw → ICA-cleaned Raw
        self.create_regular_epochs()      # Raw → Epochs
        self.gfp_clean_epochs()           # Epochs → cleaned Epochs
        self.generate_reports()           # Produce QC reports
Here the same dataset (Raw → Epochs) is transformed step by step. At any point, you could insert your own function (e.g., a MATLAB-based algorithm) as long as you return a valid MNE object.

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Branching & Customization

You’re not locked into a fixed sequence. You can:
  • Skip steps (by disabling them in the config or removing from run()).
  • Branch (e.g., create epochs two different ways, then compare results).
  • Insert custom steps (e.g., your own artifact detector).
For example: 
if self.config["ICA"]["enabled"]:
    self.run_ica()
else:
    self.skip("ICA disabled in config")

# Branch into task-specific preprocessing
if self.task_name == "RestingState":
    self.create_regular_epochs()
elif self.task_name == "Oddball":
    self.create_eventid_epochs()

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Big Picture

The Task class is both approachable for beginners (just follow the template) and extremely powerful for advanced users (because it exposes full MNE objects at every step). That means you can start with defaults and gradually extend your pipeline as your research questions demand.