crag666/dotfiles/neurokit2

NeuroKit2

Scope and evidence cutoff

Use this skill for method-aware, reproducible biosignal research with NeuroKit2. The snapshot was checked on 2026-07-23 against:

• stable PyPI 0.2.13, released 2026-03-02;
• Python metadata (>=3.10; classifiers 3.10–3.14) and wheel dependencies;
• GitHub release notes/tags, NEWS.rst, source at tag v0.2.13;
• official API pages/examples (the live site identified itself as

0.2.13.dev214); and

• pinned 0.2.13 runtime signatures and synthetic output schemas.

The live documentation can be ahead of the stable wheel. Prefer the pinned runtime for reproducible work and name both versions if consulting development docs.

Boundary

NeuroKit2 is a research and educational toolbox. Do not present its output as:

• a diagnosis, treatment recommendation, patient-monitoring decision, or alarm;
• validation, certification, or regulatory evidence for a medical device; or
• proof that a physiological construct is measured validly in a new sensor,

protocol, environment, population, or disease group.

Validate acquisition hardware, electrode/optode placement, units, sampling and clock accuracy, preprocessing, detector/decomposition method, population, task, and outcomes for the intended study. Preserve raw data and an auditable exclusion log. Use deidentified local files only; do not place PHI in prompts, logs, examples, or bundled fixtures.

Reproducible installation

uv pip install "neurokit2==0.2.13"

For optional features, create a uv project, add only the packages actually required at reviewed exact versions, and commit/review the resulting uv.lock before uv sync --locked. NeuroKit2 exposes an upstream full extra, but this skill intentionally does not install that floating transitive set in an automated workflow. Optional capabilities can require MNE, cvxopt, Plotly, PyEMD, pyRQA, Pillow, OpenCV, or file readers. Record the resolved environment with the analysis. Provision any MNE data/template download as an explicit, checksummed study input. Do not install a moving development branch for a reproducible study.

Required data contract

Before processing, record:

1. signal identity and sensor/channel configuration;
2. native sampling rate in Hz and physical unit (or explicitly arbitrary_unit);
3. clock, timestamp origin, drift correction, and synchronization evidence;
4. polarity/orientation and acquisition-side filters/gain;
5. missing samples, discontinuities, saturation, flatlines, motion, and annotations;
6. whether event onsets are zero-based sample indices or seconds;
7. planned preprocessing order, methods, parameters, exclusions, and outputs; and
8. participant-level grouping needed to prevent leakage in later statistics.

Never infer units from a column name. Do not silently treat samples as milliseconds, volts, microsiemens, or arbitrary units.

Core workflow

1. Inspect before transforming

python skills/neurokit2/scripts/inspect_signal.py \
  --input recording.csv --root . --deidentified \
  --columns ECG,RSP,EDA --time-column time_s \
  --units ECG=mV,RSP=a.u.,EDA=uS

The inspector is bounded and emits no row values or paths. Resolve non-monotonic time, duplicate samples, gaps, non-finite values, flat runs, and sampling-rate disagreement before filtering.

2. Preserve preprocessing order

Use this default reasoning order, adapting it to the acquisition and cited method:

1. preserve immutable raw signal and annotations;
2. verify time base, units, polarity, clipping, gaps, and artifacts;
3. segment at long gaps; only interpolate short gaps under a declared policy;
4. apply modality-specific cleaning at the native sampling rate;
5. detect peaks/onsets or decompose components;
6. inspect quality outputs and raw overlays;
7. correct peaks only with logged categories and sensitivity checks;
8. derive rates/features;
9. align continuous modalities on a declared common time grid; and
10. map event indices to that grid, epoch, baseline, and analyze.

Do not resample binary markers or peak-index arrays as ordinary continuous signals. Map their timestamps to the target grid. Filtering and interpolation can create edge artifacts and false precision; retain masks for padded, missing, and rejected regions.

3. Treat schemas as runtime observations

Return columns depend on NeuroKit2 version, function, method, signal availability, and analysis mode. Never claim that one column list is universal.

signals, info = nk.ecg_process(ecg, sampling_rate=250)
observed_schema = {
    "columns": list(signals.columns),
    "info_keys": sorted(info),
}

Persist the observed schema with package version, method parameters, sampling rate, and quality/exclusion summary. Reference files list verified default schemas for 0.2.13, not guarantees for every method.

Current patterns

ECG, corrected peaks, and duration-aware HRV

In stable 0.2.13, ecg_process() performs cleaning, R-peak detection with correct_artifacts=True, rate, default averageQRS quality, DWT delineation, and phase.

signals, info = nk.ecg_process(ecg, sampling_rate=250, method="neurokit")
time_hrv = nk.hrv_time(info, sampling_rate=250)

Inspect ECG_R_Peaks_Uncorrected and ECG_fixpeaks_*; a corrected series is not automatically a valid NN series. For frequency/nonlinear HRV, enforce metric-specific duration and beat-count requirements. Five minutes is the conventional short-term reference; ULF is a long-recording measure, and VLF interpretation from short records is unsafe. Do not interpret LF/HF as a direct sympathovagal balance. PPG pulse-rate variability is not interchangeable with ECG HRV.

Use the bounded pipeline:

python skills/neurokit2/scripts/ecg_hrv_pipeline.py \
  --synthetic --sampling-rate 250 --duration 300 \
  --domains time,frequency,nonlinear

EDA with explicit decomposition

The stable default eda_process(method="neurokit") uses high-pass tonic/phasic decomposition, not cvxEDA. Choose and report decomposition explicitly:

clean = nk.eda_clean(eda, sampling_rate=100, method="neurokit")
components = nk.eda_phasic(clean, sampling_rate=100, method="highpass")
markers, info = nk.eda_peaks(
    components["EDA_Phasic"],
    sampling_rate=100,
    method="neurokit",
    amplitude_min=0.1,
)

For neurokit/kim2004, amplitude_min is relative to the largest detected response; it is not an absolute microsiemens threshold. cvxEDA needs optional cvxopt.

python skills/neurokit2/scripts/eda_pipeline.py \
  --synthetic --sampling-rate 100 --duration 60 \
  --phasic-method highpass --peak-method neurokit

Events, epochs, and baseline

events_find() reports zero-based sample onsets; duration/spacing arguments are in samples. epochs_create() takes epoch limits in seconds.

events = nk.events_find(trigger, threshold=0.5, duration_min=2)
epochs = nk.epochs_create(
    signals,
    events,
    sampling_rate=100,
    epochs_start=-0.2,
    epochs_end=0.8,
    baseline_correction=False,
)

Plan sample-exact windows first:

python skills/neurokit2/scripts/plan_epochs.py \
  --events 1000,2500,4000 --event-unit samples \
  --sampling-rate 100 --recording-samples 5000 \
  --epoch-start -0.2 --epoch-end 0.8 \
  --baseline-start -0.2 --baseline-end 0

In 0.2.13 the epoch slice is end-exclusive, but the generated floating time index includes epochs_end. Built-in baseline correction subtracts the epoch mean from its start through t=0; use manual correction for a narrower prespecified baseline. Boundary epochs are padded and can contain NaN. Decide drop/pad/error before analysis.

RSA and multimodal processing

bio_process() assumes all inputs already share one sampling rate and alignment. It does not resample, synchronize, estimate drift, or create nested modality dictionaries; its info output is flat. Unequal lengths are concatenated by index and can introduce NaN. RSA is added only when synchronized ECG and RSP are present.

Validate a strict local manifest before calling it:

python skills/neurokit2/scripts/validate_multimodal.py \
  --manifest streams.json --root . --deidentified

After independent modality QC and alignment:

bio_signals, bio_info = nk.bio_process(
    ecg=ecg_aligned,
    rsp=rsp_aligned,
    eda=eda_aligned,
    sampling_rate=common_rate,
)
rsa_summary = nk.hrv_rsa(
    bio_signals,
    bio_signals,
    rpeaks=bio_info,
    sampling_rate=common_rate,
    continuous=False,
)

Summary RSA is a dictionary; continuous=True returns a DataFrame with RSA_P2T and RSA_Gates in the verified default workflow. Co-record respiration and report its rate/depth/context; RSA is not a direct, context-free measure of vagal tone.

Complexity returns values plus metadata

Most complexity functions in 0.2.13 return (value, info). The convenience function also returns two objects:

features, details = nk.complexity(signal)  # default which="makowski2022"
sampen, sampen_info = nk.entropy_sample(signal)
dfa, dfa_info = nk.fractal_dfa(signal)

The default convenience selection is not “all measures.” Complexity estimates are sensitive to length, stationarity, normalization, delay, dimension, tolerance, scale, and implementation. Predefine them and run sensitivity/surrogate analyses.

Bundled command-line helpers

All helpers reject URLs, path traversal, and symlinks; bound bytes/rows/channels; refuse overwrite unless --force; use lazy scientific imports so --help works without NeuroKit2; never use pickle; and produce deterministic JSON/CSV. Real-data commands require --deidentified.

Generate a fixture without exposing participant data:

python skills/neurokit2/scripts/generate_synthetic.py \
  --output synthetic.csv --root . --duration 30 \
  --sampling-rate 250 --seed 42

Security note

No example or helper uses Python eval() or exec(). NeuroKit2 names such as eeg_*, events_*, and *_eventrelated() are ordinary library calls. If a static scanner reports an eval/exec pattern based on a substring, inspect the exact line and record it as a scanner false positive only after confirming no dynamic execution exists.

References

Read only the files needed for the modality or decision: All bundled Markdown paths below are under references/; this skill has no templates/ or assets/ reference paths.

Primary sources checked 2026-07-23