Matlab Prepare Signal Data

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From the author

Use this skill when conditioning, loading, preparing, or labeling signal data for analysis or ML training. Covers: cleaning a single signal (fill gaps, remove drift, deoutlier, denoise, resample/align a time base) BEFORE analysis; building a `signalDatastore` pipeline; creating a `labeledSignalSet` for Signal Labeler; deriving labels (filename, folder, in-file, ROI, time-frequency ROI); stratified train/val/test splits; framing long signals; parallel processing; and shaping datastore output for `trainnet`. Triggers include "clean up this signal", "remove drift / detrend", "fill gaps", "remove spikes / outliers", "denoise", "resample to a uniform rate", "align channels", "labels from filenames", "stratified split", "prepare for Signal Labeler", and function names like `fillgaps`, `fillmissing`, `detrend`, `filloutliers`, `smoothdata`, `resample`, `synchronize`, `signalDatastore`, `labeledSignalSet`, `filenames2labels`, `folders2labels`, `splitlabels`, `framesig`, `framelbl`, `createDatastores`.

— the description by MathWorks

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

This skill provides a structured approach to signal data preparation, guiding users through the lifecycle of cleaning raw signals, managing datastores, applying labels, and partitioning data for machine learning. It emphasizes using high-level Signal Processing Toolbox functions to ensure readability and maintainability, while offering clear heuristics for ordering conditioning steps like detrending, smoothing, and outlier removal. The skill is designed to help users move from raw data to a ready-to-train state for models like trainnet.

What it does

Cleans signals by filling gaps, removing drift, denoising, and handling outliers.
Synchronizes and resamples multi-channel data onto a uniform time base.
Builds data pipelines using signalDatastore for efficient loading.
Creates labeledSignalSet objects for structured labeling and Signal Labeler interoperability.
Performs stratified splits and framing for long signal sequences.
Shapes and prepares datastore outputs for machine learning workflows.

When to use it

When you need to clean a single signal before analysis or training.
When preparing a dataset of signals for machine learning with specific labeling requirements.
When you need to align multiple signal channels or resample them to a uniform rate.
When you need to partition signal data into training, validation, and test sets.
When you need to frame long signals for windowed analysis or supervision.

Advantages

Promotes readable, maintainable code by preferring high-level toolbox functions.
Provides a logical, verified order for conditioning steps to prevent data corruption.
Reduces manual effort by automating common tasks like label derivation from filenames.
Ensures compatibility with Signal Labeler and deep learning training functions.
Offers clear guidance on when to escalate to lower-level methods.

Usage examples

“How do I remove a linear trend from my signal?”: The agent will recommend using detrend(x, 1) and explain why explicit degree specification is preferred for code clarity.
“I have a folder of signal files; how do I create a datastore and split them for training?”: The agent will guide you through using signalDatastore to load the files, followed by splitlabels to perform a stratified split.
“My signal has gaps; how should I fix them?”: The agent will suggest using fillmissing for short gaps or fillgaps for longer gaps in oscillatory signals, depending on the signal characteristics.
“How do I align two signals with different sampling rates?”: The agent will recommend using the synchronize function to place both signals onto a shared time grid.

Install

Download the skill as a ZIP:
https://autogineer.com/agent-skills/matlab/matlab-prepare-signal-data/download

Unzip it into the cross-client skills folder of your project:

mkdir -p .agents/skills && unzip matlab-prepare-signal-data.zip -d .agents/skills

Documentation by MathWorks

Prepare Signal Data

Look in Signal Processing Toolbox first. The conditioning, labeling, splitting, framing, and partitioning helpers here live in Signal Processing Toolbox — not in Stats & ML Toolbox or generic-MATLAB string utilities.

The arc: condition a raw signal (clean it) -> load a folder into a datastore -> label -> split / frame -> hand off to trainnet. Each stage is a workflow file; this page routes you to the right one.

When to Use

Cleaning a single signal before analysis: fill gaps, remove drift, deoutlier, denoise, put it on a uniform time base, align multiple channels.
Loading / preparing signal data for ML training: datastores, labels from filenames or folders, stratified splits, framing, parallel processing.
Structured labeling: labeledSignalSet for Signal Labeler, all label types.

When NOT to Use

Raw .wav audio classification with Audio Toolbox available. audioDatastore is the canonical path (this skill's custom-ReadFcn workflow handles .wav only when Audio Toolbox is absent — references/wf-custom-readfcn.md).
Frequency-selective filter DESIGN (band isolation, notch, custom FIR/IIR) — see the matlab-design-digital-filter skill. This skill's conditioning is about cleaning, not designing filters.
Computing per-frame features (RMS, crest factor, spectral / bandwidth, time-frequency features) from an already-conditioned signal — see the matlab-extract-signal-features skill. This skill's framesig / framelbl are for manual per-window labeling / supervision, not for deriving a feature table; the signal*FeatureExtractor objects window internally and emit the table.

Best practices

Deliverable is a runnable .m script the user can save, version, and re-run — not workspace state.
Prefer the highest-level function that does the job. detrend / smoothdata / fillmissing / resample read cleanly and are easy for a non-expert to follow. Drop to a lower-level / more-configurable path (designfilt + filtfilt, a hand-built AR model, a named primitive) only when you need control the high-level call cannot give, or when the user asks. Readability first; escalate to low-level for necessity, not by default.
- The high-level call usually exposes the control you think you need. In particular smoothdata(x, "sgolay", fl) takes the frame length fl as an argument — it does NOT hide it — so prefer it over calling sgolayfilt directly. Reach for sgolayfilt only for what the dispatcher genuinely lacks (derivative output via dn, or an unusual polynomial order).

0. Common reflexes

If your first instinct is one of these, the canonical replacement is one row away.

Reflex	Canonical	Detail
Hand-design a highpass/`designfilt` to remove a smooth drift	`detrend(x, n)` — escalate `n` = 1 -> 2 -> 3 before reaching for a filter; polynomial detrend has unity passband gain	references/fn-detrend.md
Invent a gap-filler (`regularizeNaNs`, `inpaintn` — not real)	`fillmissing` (interp) for short gaps; `fillgaps` (SPT, AR) for long gaps in oscillatory signals	references/wf-repair-missing.md
Hand-roll `retime` + shift + `retime` + concat to align channels	`synchronize(A, B, ...)` — one call to a shared grid	references/wf-align-channels.md
Custom `ReadFcn` for a `.csv`	`signalDatastore` default reader + `SignalVariableNames`	references/fn-signaldatastore.md
`cvpartition` for a datastore split	`splitlabels` + `subset(ds, idx{k})`	references/fn-splitlabels.md
`regexp` / `extractBefore` / `fileparts` for labels from filenames	`filenames2labels(sds, Extract=...)`	references/fn-filenames2labels.md
`regexp` / nested `fileparts` for labels from subfolders	`folders2labels(sds.Files)`	references/fn-folders2labels.md
Manual framing loop with `(i-1)*hop+1`	`framesig(x, fl, OverlapLength=...)`	references/wf-frame-and-label.md
Manual ROI-to-frame vote with `containers.Map`	`framelbl(rois, ...)`	references/wf-frame-and-label.md
`for` loop `load(file)` to read in-file label variables	`signalDatastore(folder, SignalVariableNames=["x","label"])`	references/fn-signaldatastore.md
`signalMask` when you need Signal Labeler interop	`labeledSignalSet` with ROI labels (signalMask can't import)	references/fn-labeledsignalset.md
`signalLabeler(lss)` (pass the set as an arg)	Launch bare `signalLabeler` (zero args), then Import -> From Workspace or From File	references/wf-label-and-export.md

SPT-specialized functions exist — reach for them, don't reinvent. fillgaps (AR gap fill), medfilt1 / hampel (impulse handling), sgolayfilt / smoothdata(...,"sgolay") (feature-preserving smoothing) are in Signal Processing Toolbox.

1. Workflows

Each workflow file is the entry point and lists the functions it uses. Start here.

Workflow	Use when	Reference
Repair missing samples	NaN gaps / dropouts to fill.	references/wf-repair-missing.md
Detrend, smooth, deoutlier	Drift, spikes, and/or broadband noise on one signal (smoothing/denoising lives here).	references/wf-detrend-smooth-deoutlier.md
Align multi-rate / offset channels	Several channels onto a shared time base.	references/wf-align-channels.md
Put one channel on a uniform rate	One channel -> uniform grid at a chosen rate: jittery timestamps to regularize, OR already uniform but the wrong rate to `resample`.	references/wf-uniform-rate.md
Wavelet denoising (escalation)	Non-stationary/multi-scale noise a tuned `sgolayfilt` can't remove; `wdenoise` (Wavelet TB).	references/wf-denoise.md
Envelope extraction	Amplitude outline (AM demod, peak hull) — not cleaning.	references/wf-envelope.md
Load + label + split	Folder of files -> datastore for training.	references/wf-load-and-split.md
Frame long signals + per-frame labels	Long signals, per-window supervision.	references/wf-frame-and-label.md
Label + export (all label types)	Structured labels (attribute/ROI/point/TF-ROI), export to Signal Labeler / DL.	references/wf-label-and-export.md
Parallel processing across a parpool	Per-signal work across workers.	references/wf-parallel-process.md
Custom ReadFcn (only when needed)	Format isn't `.mat` / `.csv`, or has a metadata prelude.	references/wf-custom-readfcn.md
Hand-off to `trainnet`	Datastore ready; shape for `trainnet` / `combine`.	references/wf-handoff-to-dl.md

Each workflow file names the fn- reference pages for the functions it uses; there is no separate function index — enter through the workflow that matches your task, or the reflex table above.

2. Ordering when a signal needs several conditioning steps

The governing principle (this is the real rule): order the steps so an earlier operation does not corrupt the input to a later one. Spikes bias least-squares fits and get smeared by filters/resamplers; an un-removed trend gets averaged into the signal by a smoother; most operations choke on NaN. Reason from that for the signal in front of you — do not follow a fixed chain blindly.

Default heuristic (a good starting order, not a universal law):

outliers -> detrend -> smooth, with fill and align placed by the principle above.

outliers -> detrend -> smooth is the verified core: remove spikes before a polynomial detrend (a spike biases the fit) and before a smoother (a smoother spreads the spike across its window); detrend before smooth so the smoother isn't averaging across a trend.
Fill NaN before any step that can't handle missing data (detrend, filters, most smoothers).
Align / resample: putting a signal on a new grid (retime/synchronize) creates NaN at non-overlapping times, so fill after aligning. BUT if the signal has spikes, deoutlier before resampling — resample's anti-alias filter will smear an un-removed spike. So align-vs-outliers order depends on the signal; the principle decides, not a fixed sequence.

Not every signal needs every step — identify which apply, order them by the principle, and each workflow file has an off-ramp if your problem is actually a different family.

Files

ATTRIBUTION.mdAdded by AutoGineer1.0 KiB
LICENSELicence file added by AutoGineer1.4 KiB
SKILL.md9.5 KiB
manifest.yaml650 B
references/fn-countlabels.md2.1 KiB
references/fn-detrend.md4.6 KiB
references/fn-filenames2labels.md4.8 KiB
references/fn-fillgaps.md3.3 KiB
references/fn-fillmissing.md4.2 KiB
references/fn-filloutliers.md5.0 KiB
references/fn-folders2labels.md3.4 KiB
references/fn-framelbl.md7.1 KiB
references/fn-framesig.md4.1 KiB
references/fn-hampel.md3.3 KiB
references/fn-labeledsignalset.md9.1 KiB
references/fn-labelspectrogramoptions.md4.6 KiB
references/fn-medfilt1.md3.3 KiB
references/fn-partition.md4.6 KiB
references/fn-resample.md4.6 KiB
references/fn-retime.md4.7 KiB
references/fn-sgolayfilt.md3.5 KiB
references/fn-signaldatastore.md11.9 KiB
references/fn-signallabeldefinition.md5.9 KiB
references/fn-signalmask-getmask.md8.6 KiB
references/fn-smoothdata.md4.8 KiB
references/fn-splitlabels.md5.3 KiB
references/fn-subset.md3.9 KiB
references/fn-synchronize.md4.7 KiB
references/fn-wdenoise.md5.2 KiB
references/wf-align-channels.md6.6 KiB
references/wf-custom-readfcn.md5.0 KiB
references/wf-denoise.md2.6 KiB
references/wf-detrend-smooth-deoutlier.md6.6 KiB
references/wf-envelope.md5.3 KiB
references/wf-frame-and-label.md4.7 KiB
references/wf-handoff-to-dl.md9.1 KiB
references/wf-label-and-export.md8.7 KiB
references/wf-load-and-split.md4.6 KiB
references/wf-parallel-process.md4.8 KiB
references/wf-repair-missing.md6.7 KiB
references/wf-uniform-rate.md4.2 KiB

references/fn-framelbl.md

Function: `framelbl`

Used in: wf-frame-and-label.md Toolbox: Signal Processing Toolbox

Collapse a per-sample ROI label table into per-frame labels, using a frame schedule that matches framesig. Replaces the hand-rolled containers.Map accumulator and the most-prevalent voting loop.

Signature

frameLabels = framelbl(x, frameLength)
frameLabels = framelbl(x, frameLength, Name=Value, ...)
[frameLabels, fnlcond] = framelbl(___)               % final condition for streaming (overlap)
[frameLabels, fnlcond, fnlidx] = framelbl(___)       % + final index for streaming (underlap)

x is the input label sequence — accepts:

categorical vector
string array
numeric array
logical matrix (one column per category)
ROI table (start/end limits + label per row — the most common form)

Output shape depends on ConsolidationMethod:

Consolidated (ConsolidationMethod set to "mode" / "priority" / "max" / "median" / "mean"): returns a 1 × numFrames row vector of per-frame consolidated labels, aligned with framesig's column index.
Non-consolidated (ConsolidationMethod="none", the default): returns an fl × numFrames matrix for string / numeric / logical inputs (one column per frame, one row per sample within that frame). Categorical input returns the same per-sample-per-frame layout as a categorical matrix.

Name-value arguments (all 11)

Valid combinations depend on input type — see the cross-table below.

NV-pair	Default	Purpose
`InputLabelMode`	`"mask"`	`"mask"` = each element of `x` is a per-sample label; `"attribute"` = `x` is a single label that applies to every sample (requires `SignalLength`).
`SignalLength`	inferred from ROI / required for `"attribute"`	Length of the underlying signal in samples. Must exceed `frameLength`. For ROI tables, defaults to `max(ROILimits)`.
`SampleRate`	unset	Positive scalar; only valid when `x` is an ROI table. When set, ROI limits are interpreted in seconds and converted to sample indices (rounded to nearest integer).
`Categories`	inferred	String array naming logical-matrix columns. Only valid when `x` is a logical matrix.
`ConsolidationMethod`	`"none"`	How to collapse multiple labels in a frame: `"none"` (no collapse — return raw per-frame), `"mode"` (most-prevalent vote), `"priority"` (rank-based, requires `PriorityList`), `"max"` (numeric / ordinal categorical), `"median"` (numeric / ordinal), `"mean"` (numeric only). Type restrictions: categorical/string allow only `"mode"` / `"priority"` (or `"median"` / `"max"` for ordinal); numeric forbids `"priority"`.
`PriorityList`	inferred	Rank-ordered list of unique labels for `ConsolidationMethod="priority"` (or for ROI / logical inputs). Highest priority first. Defaults to lex-ordered for non-logical, or `Categories` for logical.
`OverlapLength`	`0`	Samples shared between adjacent frames. Must match `framesig`'s `OverlapLength`. Mutually exclusive with `UnderlapLength`.
`UnderlapLength`	`0`	Samples skipped between adjacent frames. Mutually exclusive with `OverlapLength`.
`InitialCondition`	`[]`	Stacks on top of `x` along the framing dimension. Must match `x`'s data type and shape. For ROI-table inputs, must also be an ROI table whose limits don't overlap the input. Forbidden when `InputLabelMode="attribute"`.
`InitialIndex`	`1`	Index of the first sample to start framing from. `InitialIndex - 1` samples at the start are discarded.
`IncompleteFrameRule`	`"drop"`	What to do with the trailing partial frame: `"drop"` discards it; `"padwithmissing"` pads with `<undefined>` / `<missing>` / `<false>` / `NaN` depending on label type. (Note: this is `"padwithmissing"`, not `"zeropad"` as in `framesig`.)

Setting both OverlapLength and UnderlapLength is an error — they are alternative scheduling modes, not stackable. Don't pass both names even at default values (e.g. OverlapLength=0, UnderlapLength=4 errors too). Pass at most one.

Canonical pattern

% Frame the signal:
frames = framesig(x, 1024, OverlapLength=512);

% Frame the labels with the same schedule:
frameLabels = framelbl(rois, 1024, OverlapLength=512, ...
    ConsolidationMethod="mode");

% frames(:, k) and frameLabels(k) are aligned.

`ConsolidationMethod` — the default surprises you

The default is "none", which returns an fl × numFrames matrix of raw per-sample labels, not the 1 × numFrames row of one-label-per-frame a training pipeline usually wants. Pass an explicit ConsolidationMethod (and read it as a named arg so the choice is visible), e.g.:

frameLabels = framelbl(rois, 1024, OverlapLength=512, ConsolidationMethod="mode");

Choosing which method - "mode" (most-prevalent vote) vs "priority" (when labels nest), and the ROI-containment check that decides it - is the workflow decision: see wf-frame-and-label.md ("Decision point — ConsolidationMethod"). The mechanism that forces "priority" when labels nest is the containment trap below.

Anti-pattern — hand-rolled most-prevalent voting

Don't accumulate per-sample labels into a containers.Map and pick the most-prevalent — that has a containment trap.

% Bad — hand-rolled voting buries the containment trap:
labelMap = containers.Map();
for k = 1:numFrames
    frameStart = (k-1)*hopSize + 1;
    frameEnd   = frameStart + frameLength - 1;
    % ... look up labels in [frameStart, frameEnd], count, pick max ...
end

% Good:
frameLabels = framelbl(rois, frameLength, OverlapLength=overlap, ...
    ConsolidationMethod="mode");

The containment trap

If label A's ROI fully contains label B's ROI inside a frame, a most-prevalent vote always picks A — label B never wins, even when B is the more semantically important class (e.g. "voiced speech" inside "speech"). When labels nest, use ConsolidationMethod="priority" with an explicit PriorityList, not most-prevalent.

% Containment-trap-safe — voiced wins inside speech:
frameLabels = framelbl(rois, 1024, OverlapLength=512, ...
    ConsolidationMethod="priority", ...
    PriorityList=["voiced", "unvoiced", "speech", "silence"]);

Gotchas

OverlapLength must match framesig. The two functions schedule frames independently; only matching parameters keep them aligned.
Output shape depends on ConsolidationMethod. With a consolidation method set, the output is 1 × numFrames — index with the same k you'd use into framesig's column index. With the default "none", the output is fl × numFrames (sample-within-frame down rows, frames across columns); index frame k as out(:, k). Don't expect a row vector in the default case.
An ROI shorter than a hop can fall in zero frames if the hop steps over it. Tighten the hop or pre-validate ROI durations.
An ROI longer than the signal is silently clamped — no error.

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

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Attribution and licence

Created by

MathWorks

Publisher

MathWorks (Official)

Source

matlab/matlab-agentic-toolkit · skills-catalog/signal-processing/matlab-prepare-signal-data · commit 2a7f215

Licence

BSD 2-Clause License (redistribution allowed)

LICENSE (added by AutoGineer from LICENSE.md)
ATTRIBUTION.md (written by AutoGineer)

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2026-11-09

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