General signal processing

Checked 2026-07-23 against NeuroKit2 0.2.13, its stable wheel, tagged source, and the live signal API page (0.2.13.dev214).

Start with a signal contract

For every channel retain:

sensor/channel identity and physical unit;
native sampling rate and timestamps;
polarity, gain, acquisition filters, and ADC range;
missing/discontinuous intervals and artifact annotations;
expected physiological bandwidth; and
the exact NeuroKit2 function, method, parameters, and package version.

signal_sanitize() does not clean artifacts or interpolate missing values. In 0.2.13 it resets an indexed pandas Series to a default index.

Safe preprocessing order

Preserve the original samples and time axis.
Check timestamp order, rate, clipping, flatlines, non-finite values, and gaps.
Split at long gaps. Interpolate only short, prespecified gaps and retain a mask.
Remove offsets/trends only when justified.
Apply a modality/method-specific filter at the native rate.
Trim or flag filter transients.
Detect/correct peaks or derive features.
Resample continuous outputs only when alignment or modeling requires it.

Do not use a filter to “fix” clipping, sensor detachment, dropped packets, or motion. Do not interpolate event markers, quality flags, or peak indicator vectors as continuous amplitudes.

Verified 0.2.13 interfaces

Function	Stable behavior relevant to schemas
`signal_filter()`	Returns one array. Default is order-2 Butterworth; available behavior depends on `method`, cutoffs, and sampling rate.
`signal_sanitize()`	Resets pandas Series indexing; it is not a NaN/artifact cleaner.
`signal_fillmissing()`	Forward, backward, or both-direction fill only (`method="forward"`, `"backward"`, or `"both"`).
`signal_resample()`	Returns one array; accepts target length or source/target rates. Methods include interpolation, FFT, polyphase, NumPy, and pandas paths.
`signal_interpolate()`	Returns interpolated values; explicitly provide source and target coordinates for irregular time.
`signal_findpeaks()`	Returns a dict. The pinned default synthetic probe observed `Peaks`, `Height`, `Distance`, `Onsets`, `Offsets`, and `Width`; keys can change with input/method.
`signal_fixpeaks()`	Returns `(info, corrected_peaks)` in stable source. Default Kubios `info` includes artifact categories and diagnostics.
`signal_period()`	Takes peak locations and returns period in seconds, optionally interpolated to a requested sample length.
`signal_rate()`	Takes peak locations and returns events/minute, optionally interpolated.
`signal_psd()`	Returns a DataFrame; the pinned Welch probe observed `Frequency` and `Power`.
`signal_power()`	Returns a one-row DataFrame with band-derived names such as `Hz_0.5_2`; names depend on requested bands.
`signal_timefrequency()`	Returns `(frequency, time, representation)`; frequency is the first object.
`signal_synchrony()`	Returns an array; supported methods are Hilbert phase synchrony and rolling correlation.
`signal_decompose()`	Returns a component array; stable methods are EMD and SSA, not a component dictionary.
`signal_changepoints()`	Implements PELT and returns change-point sample indices.

Never unpack signal_psd() into (psd, frequencies) in 0.2.13:

python

psd = nk.signal_psd(
    signal,
    sampling_rate=250,
    method="welch",
    normalize=False,
    show=False,
)
frequency_hz = psd["Frequency"]
power = psd["Power"]

normalize=True scales by maximum PSD power. It is not physical calibration. Use normalize=False when absolute spectral units are required and derive those units from the acquisition and estimator.

Filtering and resampling

Cutoffs are in Hz and must lie below Nyquist. Report:

filter family and implementation (butterworth, FIR, Savitzky–Golay, powerline);
order, low/high cutoff, notch frequency, and whether processing is zero phase;
padding/edge handling and samples discarded; and
source and target sampling rates plus resampling method.

Example:

python

filtered = nk.signal_filter(
    signal,
    sampling_rate=250,
    lowcut=0.5,
    highcut=40,
    method="butterworth",
    order=2,
)
resampled = nk.signal_resample(
    filtered,
    sampling_rate=250,
    desired_sampling_rate=100,
    method="poly",
)

Downsampling requires anti-alias filtering. Resampling cannot recover timing precision or bandwidth absent from the acquisition. For multimodal data, preserve native processing and timestamps first; choose a common grid only after clock alignment.

Missing data

Forward/backward fill can create artificial constant segments. Generic interpolation can create smooth but fictional morphology and peaks. Record:

count and maximum run of missing samples;
gap durations in seconds;
whether each gap was segmented, excluded, padded, or interpolated;
interpolation method and maximum allowed gap; and
whether downstream quality and uncertainty include the imputed mask.

Most modality pipelines may warn and internally forward-fill some missing samples. That convenience is not a study-level missing-data policy.

Peak correction

python

info, corrected = nk.signal_fixpeaks(
    peaks,
    sampling_rate=250,
    method="Kubios",
    iterative=True,
)

The Kubios/Lipponen–Tarvainen path is intended for ECG/PPG beats. method="neurokit" supports explicit interval limits and can be used more generically. Always retain raw and corrected peaks, counts by artifact category, affected time ranges, and results with and without correction. Do not call corrected beat intervals “normal-to-normal” unless the study actually identifies non-sinus/ectopic beats.

Quality and reproducibility

Useful QC is multimodal and method-specific:

raw/clean overlays and filter-edge review;
missing, flatline, clipping, and saturation fractions;
peak/onset overlays and interval distributions;
quality values with their method-specific direction and scale;
sensitivity to plausible filter/detector settings; and
synthetic fixtures plus labeled empirical validation data.

The bundled inspector is dependency-free:

bash

python skills/neurokit2/scripts/inspect_signal.py \
  --input signal.csv --root . --deidentified \
  --columns ECG --time-column time_s --units ECG=mV

General signal processing

General signal processing

Start with a signal contract

Safe preprocessing order

Verified 0.2.13 interfaces

Filtering and resampling

Missing data

Peak correction

Quality and reproducibility

Sources checked 2026-07-23