pygedai 1.0.3

PyGEDAI: Generalized Eigenvalue De-Artifacting Instrument in Python

PyGEDAI Usage Guide

This library implements the Generalized Eigenvalue De-Artifacting Instrument (GEDAI) for EEG cleaning. The core API mirrors the original MATLAB tooling while embracing PyTorch tensors for efficient numerical work. This document provides a concise reference for integrating gedai() and batch_gedai() into your projects while staying faithful to the algorithmic description in Ros et al. (2025).

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What GEDAI Does

GEDAI (Generalized Eigenvalue De-Artifacting Instrument) is an unsupervised, theoretically grounded denoiser for heavily contaminated EEG. It contrasts each epoch’s covariance with a physics-based forward model (leadfield), retaining only components that behave like genuine neural activity, no clean calibration data or manual supervision required.

Core mechanism: A generalized eigenvalue decomposition (GEVD) compares the data covariance (dataCOV) with a leadfield-derived reference covariance (refCOV). Components aligned with the brain subspace are kept; orthogonal components are treated as artifacts. The Signal & Noise Subspace Alignment Index (SENSAI) automatically selects the optimal rejection threshold. See Ros et al., 2025 for full details.

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Background and References

• Ros, T., Férat, V., Huang, Y., Colangelo, C., Kia, S. M., Wolfers, T., Vulliemoz, S., & Michela, A. (2025). Return of the GEDAI: Unsupervised EEG Denoising based on Leadfield Filtering. bioRxiv. https://doi.org/10.1101/2025.10.04.680449
• Original MATLAB/EEGLAB plugin: https://github.com/neurotuning/GEDAI-master (this Python port follows the architecture and processing stages documented there).

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Quick Start

Install from PyPI for a quick start:

pip install pygedai

import torch
from pygedai import gedai, batch_gedai

eeg = torch.load("eeg.pt") # (channels, samples)
leadfield = torch.load("leadfield.pt") # (channels, channels)

# Clean a single recording
result = gedai(eeg, sfreq=100.0, leadfield=leadfield)
cleaned = result["cleaned"]

# Clean a mini-batch of trials
batch = eeg.unsqueeze(0) # add batch dimension
cleaned_batch = batch_gedai(batch, sfreq=100.0, leadfield=leadfield)

# result contains cleaned EEG, per-band thresholds, and SENSAI quality metrics
print(f"SENSAI quality score: {result['sensai_score']:.3f}")

The notebook testing/Test.ipynb covers an end-to-end example, including plots that compare raw and cleaned signals.

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Reference Covariance Without Templates

If you already know your electrode locations, you can reuse the shipped leadfield by mapping your channels with interpolate_ref_cov, no template building step required. Provide a dataframe with columns channel_name, X, Y, Z (meters in head space), call the helper and pass the returned tensor straight into gedai().

import pandas as pd
import mne
import torch
from pygedai.ref_cov import interpolate_ref_cov

montage = mne.channels.make_standard_montage("GSN-HydroCel-128")
montage_head = mne.channels.transform_to_head(montage)
ch_pos = montage_head.get_positions()["ch_pos"]

electrode_positions = (
    pd.DataFrame.from_dict(ch_pos, orient="index", columns=["X", "Y", "Z"])
      .reset_index()
      .rename(columns={"index": "channel_name"})
)

ref_cov = interpolate_ref_cov(electrode_positions, dtype=torch.float64)

raw_eeg = ... # load your EEG as a (channels, samples) torch tensor
sfreq = ... # set your sampling frequency

clean_eeg = gedai(
  raw_eeg,
  sfreq=sfreq,
  denoising_strength="auto",
  leadfield=ref_cov,
  device="cpu",
  dtype=torch.float32,
  skip_checks_and_return_cleaned_only=True, # optional if you only want cleaned EEG
)

See testing/Interpolate RefCov.ipynb for a more detailed walkthrough.

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Real Time Streaming

GEDAIStream keeps a rolling buffer of incoming EEG chunks, periodically recomputes artifact thresholds, and applies them to each new chunk without reinitializing the optimizer. Use the gedai_stream() factory to create a configured stream when you need continuous denoising or want to embed GEDAI inside acquisition software. Streaming also inherits the ENOVA-based bad-epoch rejection described later, so you can gate catastrophic artifacts online by supplying enova_threshold to the factory.

• sfreq: Sampling frequency in Hz.
• leadfield: Square reference covariance (channels × channels) that anchors the GEVD.
• threshold_update_interval_sec: How often (seconds of streamed data) to refresh artifact thresholds once the initial pass has completed.
• initial_threshold_delay_sec: Minimum buffered duration before the first threshold computation, letting the optimizer see a representative window.
• buffer_max_sec: Size cap (seconds) on the rolling buffer used for threshold estimation to keep memory usage bounded.
• processing_window_sec: Optional batching window (seconds) for cleaning. When set, incoming chunks are concatenated until the window length is reached, then processed as a single batch; synchronous calls return None until enough data is accumulated.
• moving_window_chunk_sec: Size of the raw-history tail (seconds) that is prepended to every chunk before cleaning. GEDAI uses this overlapping context to avoid boundary artifacts; when both options are set the moving-window duration must exceed processing_window_sec so enough historical context is available beyond the active chunk.
• denoising_strength: Same semantics as gedai() ("auto", "auto-", "auto+", or numeric); governs artifact rejection aggressiveness.
• enova_threshold: Optional float in [0, 1] describing the maximum explained noise variance tolerated per epoch. Values near 0.9 reject epochs whose noise accounts for >=90% of their variance, whereas a tighter cutoff such as 0.3 removes any epoch dominated by artifacts.
• epoch_size_in_cycles, lowcut_frequency, wavelet_levels, matlab_levels: Wavelet configuration forwarded to gedai(), controlling frequency resolution and band selection.
• device, dtype: Target torch device/dtype for buffering and computation.
• TolX, maxiter: Convergence tolerance and iteration cap for SENSAI's golden-section search during threshold discovery.
• max_concurrent_chunks: Upper bound on how many chunks are allowed to be in-flight at once when using callbacks. Set to -1 to disable back-pressure entirely and let submissions proceed without waiting.
• num_workers: Thread pool size used for asynchronous cleaning; pass an explicit value to cap executor threads even when max_concurrent_chunks=-1. When omitted it mirrors max_concurrent_chunks, or falls back to Python's default when back-pressure is disabled.

import torch
from pygedai import gedai_stream

leadfield = torch.load("leadfield_61ch.pt")
stream = gedai_stream(sfreq=250.0, leadfield=leadfield, device="cpu", threshold_update_interval_sec=10.0, initial_threshold_delay_sec=5.0)

with stream:
  for chunk in acquire_eeg_chunks():
    cleaned_chunk = stream.next(chunk)
    handle_cleaned_eeg(cleaned_chunk)

When you need non-blocking streaming, pass a callback to stream.next, control back-pressure with max_concurrent_chunks, and adjust num_workers to set the thread count. Setting max_concurrent_chunks=-1 disables back-pressure entirely so the main loop never waits, while num_workers caps the executor's parallelism when provided.

cleaned_chunks: dict[int, torch.Tensor] = {}

def handle_cleaned_chunk(cleaned_chunk: torch.Tensor, chunk_index: int, raw_chunk: torch.Tensor) -> None:
  # Cache results while the main loop keeps submitting new chunks.
  cleaned_chunks[chunk_index] = cleaned_chunk.detach().cpu()

stream = gedai_stream(
  sfreq=fs,
  leadfield=leadfield_cov,
  initial_threshold_delay_sec=10.0,
  threshold_update_interval_sec=10.0,
  max_concurrent_chunks=-1,
  num_workers=4,
)

with stream:
  for idx, chunk in enumerate(eeg_chunks):
    stream.next(chunk, callback=handle_cleaned_chunk)
    # Perform logging, plotting, or acquisition work while GEDAI runs on a worker thread.

# Cleaned tensors are available in cleaned_chunks once the callbacks have fired.

If you set processing_window_sec, the stream buffers consecutive chunks until that many seconds of data are collected. Each window is cleaned (and delivered via callback, if provided) as a single block so downstream consumers always see window-aligned segments. When callback is omitted, next() returns None until a full window has been accumulated and then yields the cleaned window-sized tensor.

Configure moving_window_chunk_sec when you want each chunk (or processing window) to include a short tail of the immediately preceding raw data. This overlapping context keeps GEDAI’s wavelet bands from seeing abrupt edges, reduces artifacts near chunk boundaries, and determines how much history is stored in the stream’s state. Leave it unset to run on non-overlapping chunks, or choose a value strictly greater than processing_window_sec to keep extra historical context beyond the active window.

Threshold updates run on the main streaming thread. When it's time to refresh, the stream waits for all currently running cleaning jobs to finish, then recomputes the thresholds, and only after that lets new chunks be processed. Jobs that were already running use the old thresholds. All chunks after the update use the new ones.

The notebook testing/RealTimeEEG.ipynb contains a full example that pairs this pattern with a queue.Queue to plot real-time updates while GEDAI runs concurrently.

Call stream.reset() to clear thresholds while keeping the leadfield or stream.close() when shutting down the pipeline. The state property surfaces the current buffer and thresholds so you can checkpoint progress between sessions.

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Deployment & Local Testing

Build source and wheel distributions

Use the existing setup.py helper to create both source (sdist) and wheel (bdist_wheel) artifacts before publishing or sharing locally:

python setup.py sdist bdist_wheel

The resulting archives land in dist/ and are ready for installation in any compatible Python environment.

As a final step to publish the built artifacts to PyPI, upload them with Twine:

twine upload dist/*

Install into a fresh environment (example with conda)

conda create -n pygedai python=3.12 -y
conda activate pygedai
pip install mne
pip install "torch==2.2.2"
pip install "numpy==1.26.4"
pip install dist/pygedai-1.0.3-py3-none-any.whl --force-reinstall

Adjust the Python version and dependency pins as needed for your platform (the above works well on Intel macOS).

Verify dependency versions

python - <<'PY'
import torch, numpy as np
print("torch:", torch.__version__, "numpy:", np.__version__)
PY

No errors should be emitted; the versions printed should match your expectations.

Install from PyPI instead

Once a release is published, install the public package (with optional Torch extras) directly:

pip install mne
pip install "numpy==1.26.4"
pip install "pygedai[torch]"

Smoke-test the pipeline locally

Run this script to ensure PyGEDAI processes bundled sample data end to end:

python - <<'PY'
import pathlib
import torch
import mne
import numpy as np
from pygedai import gedai

root = pathlib.Path.cwd()
raw_filepath = root / "testing" / "samples" / "with_artifacts" / "artifact_jumps.set"
print(raw_filepath)
raw = mne.io.read_raw_eeglab(str(raw_filepath), preload=True)
raw.set_eeg_reference(ref_channels="average", projection=False, verbose=False)

device = "cuda" if torch.cuda.is_available() else "cpu"

eeg = torch.from_numpy(raw.get_data(picks="eeg")).to(device=device, dtype=torch.float32)

leadfield_filepath = root / "testing" / "leadfield_calibrated" / "leadfield4GEDAI_eeg_61ch.npy"
leadfield = torch.from_numpy(np.load(str(leadfield_filepath))).to(device=device, dtype=torch.float32)

result = gedai(
  eeg,
  sfreq=raw.info["sfreq"],
  denoising_strength="auto",
  leadfield=leadfield,
  device=device,
)

cleaned = result["cleaned"].detach().cpu().numpy()

print("cleaned shape:", cleaned.shape)
print("SENSAI score:", float(result["sensai_score"]))
PY

Successful execution prints the cleaned array shape and a SENSAI quality score.

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gedai()

gedai(eeg, sfreq, denoising_strength="auto", leadfield=None, *, epoch_size_in_cycles=12.0, lowcut_frequency=0.5, wavelet_levels=9, matlab_levels=None, chanlabels=None, device="cpu", dtype=torch.float32, skip_checks_and_return_cleaned_only=False, batched=False, verbose_timing=False, TolX=1e-1, maxiter=500)

Purpose

Execute the GEDAI pipeline on a single EEG recording shaped (channels, samples) by applying rank-safe referencing, broadband denoising, multi-resolution wavelet cleaning, and artifact scoring.

Required Parameters

• eeg: PyTorch tensor or array-like with shape (channels, samples). For best performance convert to a torch tensor before calling.
• sfreq: Sampling frequency in Hertz. Guides epoch sizing and band selection.
• leadfield: (channels, channels) reference covariance matrix derived from your EEG forward model (leadfield) that defines the theoretical brain signal subspace. Accepts a filepath, numpy array, or torch tensor. The row and column order must match the EEG channel ordering because tensors carry no channel labels.

Key Optional Parameters

• denoising_strength: Controls artifact suppression aggressiveness.
  • "auto" (default): SENSAI-optimized threshold (noise multiplier = 3.0).
  • "auto-": More aggressive filtering (noise multiplier = 6.0).
  • "auto+": More conservative filtering (noise multiplier = 1.0).
  • Numeric value (0.0–12.0 typical): Manual threshold passed directly to the optimizer. Internally this value is forwarded to artifact_threshold_type in gedai_per_band().
• epoch_size_in_cycles: Number of wave cycles to cover when determining per-band epoch lengths (default 12.0). Lower values shorten high-frequency epochs; higher values lengthen low-frequency epochs.
• lowcut_frequency: Exclude wavelet bands whose upper frequency bound is at or below this threshold (Hz). Defaults to 0.5 to remove slow drifts.
• wavelet_levels: Number of Haar MODWT levels when matlab_levels is None. Typical values fall between 7 and 9.
• matlab_levels: Alternative to wavelet_levels, recreating MATLAB level numbering with 2**matlab_levels + 1 bands. Leave None unless porting MATLAB scripts directly.
• chanlabels: Placeholder for channel label remapping. Currently not implemented and raises an error when supplied.
• device: Target torch device such as "cpu" or "cuda". EEG data, leadfield, and internal buffers move to this device.
• dtype: Torch dtype used during computation, defaulting to torch.float32 for a balanced memory and compute footprint; set torch.float64 when maximum numerical accuracy is required and resources permit.
• skip_checks_and_return_cleaned_only: When True, bypass validation and return only the cleaned tensor to reduce overhead.
• batched: Internal flag used by batch_gedai(). Leave False in user-facing calls.
• verbose_timing: Enables profiling markers emitted by profiling.py, useful for benchmarking.
• TolX: Convergence tolerance for the golden-section search used during automatic thresholding (default 1e-1).
• maxiter: Maximum iterations allowed for the threshold optimizer (default 500).
• enova_threshold: Optional float between 0 and 1. When set, GEDAI removes entire epochs whose explained noise variance exceeds the threshold after SENSAI scoring. This is helpful for preventing severely corrupted segments from being reintroduced during reconstruction.

The broadband stage follows MATLAB by using a 1 s epoch (rounded to an even number of samples) before the wavelet decomposition step.

Returns

By default returns a dictionary with:

• cleaned: Denoised EEG (channels, samples).
• artifacts: Removed components (input_referenced - cleaned).
• sensai_score: Overall quality metric (higher means better alignment with the brain subspace).
• sensai_score_per_band: Per-band SENSAI scores (length = number of wavelet bands plus the broadband pass).
• artifact_threshold_per_band: Thresholds applied to each wavelet band.
• artifact_threshold_broadband: Threshold used during the initial broadband pass.
• epoch_size_used: Actual epoch duration in seconds after enforcing an even sample count.
• refCOV: Reference covariance matrix used for GEVD.
• epoch_sizes_per_band: Per-band epoch durations (seconds) derived from epoch_size_in_cycles.
• lowcut_frequency_used: Effective low-cut frequency after adjusting for data length constraints.
• mean_enova: Average explained noise variance across all epochs.
• enova_per_epoch: Vector of ENOVA scores produced by SENSAI_basic.
• enova_threshold_used: Echoes the threshold argument when provided.
• enova_rejected_epochs: Indices of epochs that were excised because they exceeded the ENOVA threshold.

When skip_checks_and_return_cleaned_only=True, the function returns only the cleaned tensor.

Typical Workflow

1. Load or calculate a (channels, channels) leadfield covariance from leadfield_calibrated/ or your own pipeline.
2. Convert raw EEG to a torch tensor and send it to the intended device and dtype.
3. Call gedai(...) and capture the cleaned signal along with diagnostics.
4. Visualize the results using utilities such as plot_eeg in testing/Test.ipynb.

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batch_gedai()

batch_gedai(eeg_batch, sfreq, denoising_strength="auto", leadfield=None, *, epoch_size_in_cycles=12.0, lowcut_frequency=0.5, wavelet_levels=9, matlab_levels=None, chanlabels=None, device="cpu", dtype=torch.float32, parallel=True, max_workers=None, verbose_timing=False, TolX=1e-1, maxiter=500)

Purpose

Vectorize the GEDAI pipeline across a batch dimension. Input tensors must be shaped (batch, channels, samples). Each sample is processed independently, optionally in parallel via a thread pool.

Required Parameters

• eeg_batch: PyTorch tensor containing EEG recordings arranged as (batch, channels, samples).
• sfreq: Sampling frequency shared across the batch.
• leadfield: (channels, channels) reference covariance matrix reused for every batch element. Ensure its row and column order mirrors the channel order in eeg_batch.

Key Optional Parameters

• denoising_strength, epoch_size_in_cycles, lowcut_frequency, wavelet_levels, matlab_levels, chanlabels, device, dtype, TolX, maxiter: Match the semantics of the corresponding arguments on gedai() and are forwarded per sample.
• parallel: When True, executes each batch element in a ThreadPoolExecutor. Set to False for serial execution or debugging.
• max_workers: Overrides the number of worker threads when parallel is enabled. Defaults to Python's heuristic based on CPU count.
• verbose_timing: Aggregates profiling information across the batch to assist throughput measurements.

Returns

PyTorch tensor shaped (batch, channels, samples) containing the cleaned EEG for each input sample. Internally the function gathers the cleaned value from each gedai() call and stacks the results.

Usage Example

from pathlib import Path
import torch
from pygedai import batch_gedai

project_root = Path.cwd()
eeg_trial = torch.load(project_root / "testing" / "samples" / "with_artifacts" / "artifact_jumps_tensor.pt")
leadfield = torch.from_numpy(np.load(project_root / "testing" / "leadfield_calibrated" / "leadfield4GEDAI_eeg_61ch.npy")).to(device)
batch = eeg_trial.unsqueeze(0)
cleaned = batch_gedai(batch, sfreq=125.0, leadfield=leadfield, verbose_timing=True)

This mirrors the workflow shown in testing/Test.ipynb, where the cleaned batch is plotted against the raw recording.

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Tips and Troubleshooting

• Ensure the leadfield reference covariance shape matches the EEG channel count. The functions raise a ValueError when dimensions disagree.
• Channel order is critical: Double-check that the row and column order of the reference covariance matches your EEG channel order (e.g., channel index 0 in both tensors corresponds to C1); misalignment silently degrades cleaning quality.
• The leadfield parameter should be a reference covariance computed from a forward model of your montage. Precomputed examples are available in leadfield_calibrated/.
• Average referencing: GEDAI applies a non-rank-deficient average reference (dividing by n_channels + 1) to prevent ICA ghost components (see Kim et al., 2023). Do not apply standard average referencing before calling GEDAI.
• The default threshold search uses golden-section ("parabolic"). An optional debug mode ("grid") exhaustively evaluates thresholds from 0.0 to 12.0 in 0.1 steps and is roughly 100× slower.
• Use the ENOVA gate when you want GEDAI to skip exceptionally noisy segments entirely. Start with enova_threshold=0.9 (90% noise) to only drop catastrophic segments or tighten to 0.3 when you prefer to analyze strictly high-quality intervals. The metric is bounded between 0 (no noise removed) and 1 (all variance explained by removed noise).
• GEDAI typically processes ~1 s of 64-channel EEG in 0.5–2 s on CPU, depending on wavelet_levels and denoising_strength. CPU execution is usually faster than GPU because the sensai_fminbnd minimization dominates runtime and benefits little from GPU acceleration.
• Use batch_gedai() for multiple independent trials or subjects; with parallel=True and adequate CPU cores, throughput scales nearly linearly with batch size.
• If thread-pool contention or hangs arise when running batch_gedai() in parallel mode, set single-threaded math libraries before importing torch:

  import os
  os.environ["OMP_NUM_THREADS"] = "1"
  os.environ["MKL_NUM_THREADS"] = "1"
  os.environ["OPENBLAS_NUM_THREADS"] = "1"
  os.environ["NUMEXPR_NUM_THREADS"] = "1"
  os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
  os.environ["BLIS_NUM_THREADS"] = "1"
  
  import torch
  try:
      torch.set_num_threads(1) # intra-op
      torch.set_num_interop_threads(1) # inter-op
  except RuntimeError:
      pass # torch was already initialised
  

  The set_num_threads calls must run before PyTorch initialises; future Python 3.14+ releases are expected to reduce the need for this workaround.
• The pipeline enforces even epoch lengths. Incomplete epochs are padded via reflection rather than cropped, and the padding is trimmed after denoising.
• Adjust epoch_size_in_cycles or lowcut_frequency when targeting specific bandwidths: higher cycle counts improve low-frequency stability while higher low-cut values skip slow drifts and reduce required epoch durations.
• When running on GPU, move both EEG data and leadfield tensors to the target device prior to calling the API.
• Enable verbose_timing=True during development to gather profiling markers such as start_batch, modwt_analysis, and batch_done.
• If you only require cleaned signals, set skip_checks_and_return_cleaned_only=True to avoid collecting diagnostic metadata.
• Automatic threshold selection relies on sensai_fminbnd (golden-section minimization) and may run up to maxiter iterations; supplying fixed thresholds dramatically reduces runtime.

License

This port follows the PolyForm Noncommercial License 1.0.0, identical to the original GEDAI plugin. The core algorithms are patent pending; commercial use requires obtaining the appropriate license from the patent holders. See LICENSE for full terms and contact information.

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Further Resources

• GEDAI.py: Core implementation with inline comments describing the Haar MODWT pipeline, SENSAI scoring, and artifact reconstruction.
• auxiliaries/: Helper modules including GEDAI_per_band.py, SENSAI_basic.py, and clean_EEG.py, which provide per-band denoisers and optimization routines.
• testing/Test.ipynb: Practical notebook demonstrating data loading, covariance handling, calls to batch_gedai(), and visualization of results.

For issues or feature requests, please open a GitHub issue in this repository.