ccstools 0.1.2

A toolbox for EEG analysis at CCS, NIMHANS.

CCS EEG Toolbox (ccstools)

ccstools is a Python research toolbox for EEG and related physiology workflows at CCS, NIMHANS. It collects utilities for feature extraction, signal processing, file conversion, plotting, EEG cleaning, ASR/GEDAI-style artefact handling, sleep/HRV features, real-time acquisition helpers, and connectivity/statistical analysis.

The package is intentionally organised as a set of importable modules rather than one monolithic API. Existing function names and module paths are kept stable because notebooks, scripts, and analysis pipelines often import these functions directly.

What Is Included

• EEG feature extraction: PSD, FOOOF-style aperiodic fits, IRASA, ACW, Catch22, entropy, fractal dimension, Lempel-Ziv complexity, and multi-epoch feature tables.
• Faster feature extraction paths in eegfeatures_fast.py and eegfeatures_fast_v01.py for workflows that benefit from vectorisation or Numba-style acceleration.
• Signal processing helpers for ERP bootstrapping, PCA, sine-wave and wavelet generation, smoothing, instantaneous amplitude/phase extraction, delta-wave detection, and ERP peak detection.
• File I/O and conversion helpers for BESS waveform text, Curry files, EDF writing, MNE-to-EDF export, E-Prime text parsing, and EMBLA sleep files.
• EEG cleaning and preprocessing under ccstools.ccs_eeg, including bad-channel detection, ICA-based cleaning helpers, montage utilities, and GEDAI/SENSAI-style cleaning code.
• Plotting utilities for EEG waveforms, hypnograms, and head maps.
• Non-EEG physiology features for ECG, HRV, respiration, PSV/SDG modelling, and sleep-analysis workflows.
• Real-time and device-facing helpers for Muse, Xampl10, stimulation devices, and streaming model workflows.

Installation

For active development, install the package in editable mode:

git clone https://github.com/arunsasidharan84/ccs_toolbox.git
cd ccs_toolbox
python -m pip install -e .

For a fuller environment with scientific dependencies, use one of the provided environment files:

python -m pip install -r ccs_requirements.txt

or, with conda/mamba:

conda env create -f ccs_environment.yml
conda activate ccs_toolbox

The package metadata requires Python 3.9 or newer.

Quick Start

import numpy as np
from ccstools.eegfeatures import generate_multieegfeatures

# Shape expected by many feature helpers: epochs x channels x samples
data = np.random.randn(5, 3, 1000)
srate = 500
chanlist = ["Fz", "Cz", "Pz"]

features = generate_multieegfeatures(data, srate, chanlist)
print(features.head())

Common direct imports are also exposed from the package root:

from ccstools import compute_psd, compute_fooof, compute_irasa, compute_nonlinear, compute_acw
from ccstools import bootstrapERP, pca, smooth, detecterppeak

Repository Layout

Path	Purpose
ccstools/eegfeatures.py	Main EEG feature extraction functions, including PSD, FOOOF, IRASA, ACW, Catch22, nonlinear features, and connectivity helpers.
ccstools/eegfeatures_fast.py	Faster multi-feature extraction implementation for larger EEG feature tables.
ccstools/yasafeatures.py	YASA-oriented PSD, IRASA, FOOOF, nonlinear, and PAC feature helpers.
ccstools/sigproc.py	General signal-processing utilities: ERP bootstrapping, PCA, wavelets, amplitude/phase, delta waves, and ERP peaks.
ccstools/fileio.py, curryreader.py, embla.py, read_eprimetxt.py, save_edf.py, mne2EDF.py	File import/export and parser utilities.
ccstools/ccs_eeg/	MNE-oriented EEG preprocessing, channel-location utilities, plotting helpers, and GEDAI/SENSAI cleaning code.
ccstools/plot.py	Waveform, hypnogram, and head-map plotting utilities.
ccstools/noneegfeatures.py	ECG, HRV, respiratory, and quadrant HRV features.
ccstools/psv_sdg_brain_heart_model.py	Brain-heart modelling helpers around PSV/SDG-style analyses.
ccstools/mne_asr.py, mne_asr_utils.py	Artifact Subspace Reconstruction implementation and support routines.
ccstools/recording.py, ml_realtime.py, stimulation.py	Device, streaming, real-time model, and stimulation helpers.
verify_ccstools.py	Lightweight import/verification script.
docs/module_index.md	Human-readable module index generated from the local source tree.

Main Workflows

EEG Feature Extraction

Use ccstools.eegfeatures for the most complete API:

from ccstools.eegfeatures import compute_psd, compute_irasa, compute_acw

psdvals, freqs = compute_psd(data, srate)
irasa_features = compute_irasa(data, srate)
acw_features = compute_acw(data, srate)

For large feature tables, start with ccstools.eegfeatures_fast.generate_multieegfeatures if the local dependency stack supports it.

Signal Processing

from ccstools.sigproc import generate_sinewave, wavelet_amplitudephase, detecterppeak

sinewave, timepoints = generate_sinewave(frequency=10, amplitude=1, samplingrate=500, duration=2)

generate_moreletwavelet keeps its historical function name for compatibility, but the comments describe the underlying Morlet wavelet concept.

File I/O

from ccstools.fileio import importBessWaveform
from ccstools.read_eprimetxt import read_eprimetxt

EEGdata, srate, chanlist, times = importBessWaveform("waveform.txt")
eprime_df = read_eprimetxt("experiment.txt")

CCS EEG Pipeline

from ccstools.ccs_eeg.pipeline import run_ccs_pipeline

clean_raw, report = run_ccs_pipeline(raw_input, output_dir="outputs")

The pipeline utilities are MNE-oriented and may require channel locations, ICALABEL-compatible dependencies, and configured output folders depending on the workflow.

Dependency Notes

Core package dependencies are listed in pyproject.toml; environment-level dependencies are also captured in ccs_requirements.txt and ccs_environment.yml. Some optional workflows require hardware-specific or heavier libraries. If an import fails, first confirm that the relevant optional stack is installed for that workflow.

The toolbox includes bundled resources under ccstools/ccs_eeg/resources/, including channel-location and lead-field support files used by plotting and GEDAI-related routines.

Development Notes

• Keep public function names, module paths, argument order, and return order stable unless all dependent notebooks/scripts are updated together.
• Prefer adding docstrings, examples, and small compatibility wrappers over renaming existing functions.
• Keep device-specific code isolated from pure analysis functions so offline workflows remain importable.
• Run lightweight syntax/import checks before committing documentation or comment updates.
• Review file-level licence and authorship comments before redistributing bundled or adapted code.

Verification

A quick local check is:

python -m compileall ccstools
python verify_ccstools.py

compileall catches syntax errors without requiring the full scientific stack to run every workflow. verify_ccstools.py performs a higher-level package check and may require installed dependencies.

Licence

This project is released under the MIT License. See LICENSE for details.