Complete action reference¶

This page is generated from the live registry and documents all 70 callable actions. The signature and parameter tables are therefore the contract enforced by the runner, not a parallel handwritten list.

All successful actions return data, warnings, provenance, and an equivalent replay script. File-writing actions place files under root; source recordings remain read-only.

`inspect`¶

Grounding snapshot: actions, defaults, and optional recording metadata.

cw.call("inspect", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`describe_config`¶

Every config key, default, and enum domain.

cw.call("describe_config")

This action has no parameters.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`normalize_config`¶

Clamp and complete a partial config.

cw.call("normalize_config", config=None)

Name	Type	Required	Default	Units	Meaning
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`normalization_methods`¶

Every value-normalisation method, formula, alias and requirement.

cw.call("normalization_methods")

This action has no parameters.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`normalize`¶

Normalise one selected trace with an explicit, reproducible method.

cw.call("normalize", recording, config=None, normalization_method='minmax', target_min=-1.0, target_max=1.0, reference_value=None, reference_start_hours=None, reference_end_hours=None, reference_statistic='mean', standard_deviation_ddof=0, detrended=False, envelope_floor_fraction=0.1)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`normalization_method`	string	no	`"minmax"`	-	Transformation to apply. Canonical choices are none, mean_center, median_center, zscore, robust_zscore, robust_scale, own_mean, own_daily_total, minmax, max_abs, reference_delta, fold_change, delta_over_reference, log2_fold_change, percent_of_reference, percent_change, envelope and pre_treatment_cycle. Aliases include range for minmax, extreme or to_extreme for max_abs, z for zscore, dff for delta_over_reference, and fold for fold_change.
`target_min`	float	no	`-1.0`	normalised units	Lower output bound for minmax range scaling; ignored by other methods.
`target_max`	float	no	`1.0`	normalised units	Upper output bound for minmax range scaling; must exceed target_min.
`reference_value`	float	no	`null`	recording units	Explicit baseline for reference_delta, fold_change, delta_over_reference, log2_fold_change, percent_of_reference, percent_change or pre_treatment_cycle. Use this or a reference time window, never both.
`reference_start_hours`	float	no	`null`	hours	Inclusive start of the baseline window, in hours from the selected recording start. Must be paired with reference_end_hours.
`reference_end_hours`	float	no	`null`	hours	Inclusive end of the baseline window used to calculate the reference. Must exceed and be paired with reference_start_hours.
`reference_statistic`	string	no	`"mean"`	-	How a reference time window is reduced: mean or median.
`standard_deviation_ddof`	integer	no	`0`	-	Degrees of freedom removed from the z-score standard-deviation divisor: 0 for a population, 1 for a sample.
`detrended`	boolean	no	`false`	-	Whether inputs are already baseline-subtracted.
`envelope_floor_fraction`	float	no	`0.1`	fraction	For envelope normalisation, return missing values after the fitted oscillation envelope falls below this fraction of its starting amplitude. Must lie from 0 inclusive to 1 exclusive.

Config: all keys and defaults.

Result access: declared.

Figure views: processed_trace.

`load_recording`¶

Import a recording and return metadata.

cw.call("load_recording", recording)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`list_output`¶

List files written under the output root.

cw.call("list_output")

This action has no parameters.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`set_group_colours`¶

Fix the colour a named group is drawn in, overriding the house cycle.

cw.call("set_group_colours", colours=None)

Name	Type	Required	Default	Units	Meaning
`colours`	object	no	`null`	-	Group label to colour: {'WT': 'circadian_teal', 'KO': '#ff00aa'}. A house colour name, a matplotlib name, or a literal hex. Omit to read the current table; pass {} to clear it. Applies to every figure drawn afterwards, so a group keeps its colour regardless of what order the groups arrive in.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`summary`¶

Headline read on one recording: period, rhythm, quality, metrics.

cw.call("summary", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`analyze`¶

Full analysis with selectable sections.

cw.call("analyze", recording, config=None, sections=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`sections`	array of string	no	`null`	-	Analysis sections to return; use ['all'] for full output.

Config: all keys and defaults.

Result access: composite.

Figure views: activity_profile, periodograms, daily_timing, onset_interval_serial, fft_spectrum, autocorrelation, bout_lengths, interbout_serial, time_series, wavelet, actogram, period_methods.

`quality`¶

Data-quality metrics for the selected window.

cw.call("quality", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`rhythm`¶

Rhythmic/arrhythmic verdict for the configured periodogram.

cw.call("rhythm", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`periodograms`¶

Lomb-Scargle, chi-square and F periodograms.

cw.call("periodograms", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: periodograms.

`daily_measures`¶

Daily onset, offset, alpha and phase markers.

cw.call("daily_measures", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: daily_timing.

`onset_fits`¶

Regression fits through daily onsets and offsets.

cw.call("onset_fits", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`profile`¶

Folded average-day activity profile.

cw.call("profile", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: activity_profile.

`peak_aligned_profile`¶

Align an average-cycle profile to a participant morning or evening peak.

cw.call("peak_aligned_profile", recording, config=None, peak_period, anchor_amplitude=None, peak_options=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`peak_period`	string	yes	—	-	Peak to detect and align: morning (07:00-14:00) or evening (17:00-22:00).
`anchor_amplitude`	float	no	`null`	activity amplitude	Optional established participant peak amplitude. When supplied, the unsmoothed aligned profile is scaled so time zero equals this value.
`peak_options`	object	no	`null`	-	Peak-alignment options: alignment_window_hours, smoothing_window_bins, polynomial_order, minimum_peak_distance_hours, active_window_hours, and allow_window_max_fallback.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`cosinor`¶

Cosinor fit at the configured period.

cw.call("cosinor", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`period_methods`¶

Which period methods are available, and what each one can report.

cw.call("period_methods")

This action has no parameters.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`estimate_period`¶

Period, phase and amplitude by one named method.

cw.call("estimate_period", recording, config=None, method=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`method`	string	no	`null`	-	Which period method to run: lomb, chi_square, f, fft_nlls, mesa, mfourfit, spectrum_resampling, jtk or ejtk. Omit to use the config's period_method (default lomb). Run period_methods for what each one can and cannot report -- MESA and mFourFit give no error bar and no significance measure, and FFT-NLLS is the only one that yields RAE.

Config: all keys and defaults.

Result access: declared.

Figure views: period_methods.

`compare_periods`¶

Run several period methods over one record and return one comparison table.

cw.call("compare_periods", recording, config=None, methods=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`methods`	array of strings	no	`null`	-	Which period methods to compare, as a list of registry keys. Omit to use the config's period_methods. BioDare2's advice is to pair any method that cannot test significance (MESA, mFourFit, FFT-NLLS) with one that can (lomb), and discard the rest if the Lomb-Scargle periodogram rejects the record.

Config: all keys and defaults.

Result access: declared.

Figure views: compare_periods.

`rhythmicity`¶

JTK / eJTK rhythmicity test across sparsely sampled series, corrected together.

cw.call("rhythmicity", recordings, config=None, rhythmicity_method=None)

Name	Type	Required	Default	Units	Meaning
`recordings`	array of recording specs	yes	—	-	Recordings to pool into one group trace.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`rhythmicity_method`	string	no	`null`	-	jtk for classic JTK_CYCLE or ejtk for the permutation null (default). eJTK is the one to use; classic JTK is kept for comparability with published work and is known to be anti-conservative. Both are for sparsely sampled, omics-like data -- a densely sampled record is binned down to jtk_max_points before either sees it.

Config: all keys and defaults.

Result access: declared.

Figure views: rhythmicity.

`nonparametric`¶

IS, IV, RA, L5 and M10 metrics.

cw.call("nonparametric", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`bouts`¶

Activity bout detection and summary statistics.

cw.call("bouts", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: bout_lengths, interbout_serial.

`fft`¶

FFT amplitude or power spectrum.

cw.call("fft", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: fft_spectrum.

`autocorrelation`¶

Autocorrelation function and best period.

cw.call("autocorrelation", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: autocorrelation.

`wavelet`¶

Continuous wavelet transform power and ridge.

cw.call("wavelet", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: wavelet.

`actogram`¶

Actogram matrix and display levels (the numbers behind the plot).

cw.call("actogram", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`time_series`¶

Binned time series for every measurement channel.

cw.call("time_series", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: time_series.

`select_frame`¶

Selected sample window as records, with truncation metadata.

cw.call("select_frame", recording, config=None, limit=200)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`limit`	integer	no	`200`	rows	Maximum rows returned by select_frame.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`methods_paragraph`¶

Publication-ready Methods paragraph for the actual analysis.

cw.call("methods_paragraph", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`analysis_script`¶

Generate (but do not save) a runnable Python script that reproduces this analysis.

cw.call("analysis_script", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`write_analysis_script`¶

Write the replay script under root/scripts.

cw.call("write_analysis_script", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`render_actogram`¶

Render actogram SVG under root/figures.

cw.call("render_actogram", recording, config=None, options=None, individual_layers=False)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`options`	object	no	`null`	-	Actogram export options.
`individual_layers`	boolean	no	`false`	-	Also write one SVG per measurement channel.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`render_figures`¶

Render the full figure set under root/figures.

cw.call("render_figures", recording, config=None, interface_state=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`interface_state`	object	no	`null`	-	Figure-selection state from the UI.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`detrend`¶

Baseline subtract, smooth, optionally exclude transients, and fit damping.

cw.call("detrend", recording, config=None, detrend_method='running_mean', window_hours=24.0, polynomial_degree=3, min_valid_fraction=0.5, bandwidth_hours=None, low_cut_hours=45.0, high_cut_hours=4.0, filter_order=2, lowess_fraction=None, lowess_iterations=3, asls_smoothness=1000000.0, asls_asymmetry=0.01, asls_iterations=10, smooth_window_hours=0.0, exclude_hours=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`detrend_method`	string	no	`"running_mean"`	-	Baseline removal method: none, linear, robust_linear/Huber, first_difference, running_mean, moving_median, lowess/loess, savitzky_golay, polynomial (including cubic/bicubic and poly6), kernel/baseline, amp_baseline, asymmetric_least_squares/asls, or frequency.
`window_hours`	float	no	`24.0`	hours	Baseline window.
`polynomial_degree`	integer	no	`3`	count	Polynomial baseline degree; poly6/degree6 force 6 and cubic/poly3/bicubic force 3.
`min_valid_fraction`	float	no	`0.5`	dimensionless	Minimum finite share of a local smoothing window.
`bandwidth_hours`	float	no	`null`	hours	Gaussian kernel standard deviation; omitted uses one quarter of window_hours.
`low_cut_hours`	float	no	`45.0`	hours	Longest period retained by frequency detrending.
`high_cut_hours`	float	no	`4.0`	hours	Shortest period retained by frequency detrending.
`filter_order`	integer	no	`2`	count	Butterworth frequency-filter order.
`lowess_fraction`	float	no	`null`	dimensionless	Fraction of finite samples in each LOWESS local fit; omitted derives it from window_hours.
`lowess_iterations`	integer	no	`3`	count	LOWESS robust residual-reweighting passes after the initial local fit; 0 disables reweighting.
`asls_smoothness`	float	no	`1000000.0`	dimensionless	Positive second-difference penalty for asymmetric least squares; larger is smoother.
`asls_asymmetry`	float	no	`0.01`	dimensionless	Weight in (0, 0.5) for points above the asymmetric baseline; smaller excludes positive peaks more strongly.
`asls_iterations`	integer	no	`10`	count	Asymmetric least-squares reweighting passes, from 1 to 100.
`smooth_window_hours`	float	no	`0.0`	hours	Centred smoothing window; zero disables smoothing.
`exclude_hours`	float	no	`null`	hours	Leading hours to discard before fitting.

Config: all keys and defaults.

Result access: declared.

Figure views: processed_trace.

`group_profile`¶

Pool recordings into a mean +/- SEM group trace.

cw.call("group_profile", recordings, config=None, normalize='own_mean', time_axis='clock_time', pool_order='profile_then_pool', statistic='mean', within_recording_reducer='mean', detrended=False)

Name	Type	Required	Default	Units	Meaning
`recordings`	array of recording specs	yes	—	-	Recordings to pool into one group trace.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`normalize`	string	no	`"own_mean"`	-	Value normalisation before pooling. Accepts none, mean_center, median_center, zscore, robust_zscore, robust_scale, own_mean, own_daily_total, minmax, max_abs, reference_delta, fold_change, delta_over_reference, log2_fold_change, percent_of_reference, percent_change, envelope or pre_treatment_cycle. Reference-based methods require reference metadata on each profile; use normalization_methods for formulas.
`time_axis`	string	no	`"clock_time"`	-	clock_time, tau_scaled, or onset_aligned.
`pool_order`	string	no	`"profile_then_pool"`	-	profile_then_pool or virtual_animal.
`statistic`	string	no	`"mean"`	-	mean or median.
`within_recording_reducer`	string	no	`"mean"`	-	How each recording contributes at each phase bin before pooling: mean averages selected cycles; max retains the largest observed binned value across the selected recording.
`detrended`	boolean	no	`false`	-	Whether inputs are already baseline-subtracted.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`phase_response_curve`¶

Circadian time of a stimulus, per-animal shift, the cohort PRC and its type.

cw.call("phase_response_curve", animals, config=None)

Name	Type	Required	Default	Units	Meaning
`animals`	array of objects	yes	—	-	One entry per animal in the pulse experiment. Either a record to score -- {'recording': spec, 'stimulus': '2026-01-08 18:00', 'label': 'm01', 'config': {...}} -- or a point already scored elsewhere: {'circadian_time': 15.2, 'shift_hours': -1.4, 'label': 'm01'}. A record needs fit1_start/fit1_end before the pulse and fit2_start/fit2_end after it in its config, and 'stimulus' is the wall-clock time the pulse landed (or hours from the start of the record's first day). An animal whose pre-stimulus fit is too short is dropped with a warning rather than failing the cohort.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: phase_response_curve.

`compare_phase_response_curves`¶

Fit two cohorts' phase response curves with one model and test each difference.

cw.call("compare_phase_response_curves", shift_cohorts, config=None, unit='animal')

Name	Type	Required	Default	Units	Meaning
`shift_cohorts`	object	yes	—	-	Two labelled cohorts of pulsed animals, to test whether their phase response curves differ: {'WT': [animal, ...], 'KO': [...]}. Each animal takes the same shape phase_response_curve's `animals` does -- a record to score, or a point already scored. Exactly two cohorts: which contrast is meant is a decision about the experiment.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`unit`	string	no	`"animal"`	-	Independent animal supplying each phase-response point; the legacy default is animal.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`instantaneous_phase`¶

Hilbert phase, instantaneous period and amplitude envelope over time.

cw.call("instantaneous_phase", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: instantaneous_phase.

`phase_comparison`¶

Circular summary and between-group test for phase.

cw.call("phase_comparison", phases, config=None, period_hours=None)

Name	Type	Required	Default	Units	Meaning
`phases`	object	yes	—	hours	Phase values grouped by label: {'WT': [6.1, 5.8, ...], 'KO': [...]}. These are phases the caller already has -- onset hours from daily_measures, phase_hours from estimate_period, or their own scoring. This action does not compute phases, so the numbers may come from anywhere as long as they are clock hours on one shared period.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`period_hours`	float	no	`null`	hours	The cycle the phases live on. Omit to use the config's period_hours (24 h by default). A free-running cohort should pass its own tau, so that 'one cycle' means one of the animals' cycles rather than one solar day. `splitting` uses it for a second purpose that is the same idea: the period the resolution element P**2/T is worked out at, which sets how far apart two components must be before that record can show them to differ.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`phase_summary`¶

Circular mean, concentration and Rayleigh test for one set of phases.

cw.call("phase_summary", phase_values, config=None, period_hours=None, label='')

Name	Type	Required	Default	Units	Meaning
`phase_values`	array	yes	—	hours	Phase values for one group or tissue, expressed on one shared cycle.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`period_hours`	float	no	`null`	hours	The cycle the phases live on. Omit to use the config's period_hours (24 h by default). A free-running cohort should pass its own tau, so that 'one cycle' means one of the animals' cycles rather than one solar day. `splitting` uses it for a second purpose that is the same idea: the period the resolution element P**2/T is worked out at, which sets how far apart two components must be before that record can show them to differ.
`label`	string	no	`""`	-	Readable name returned with the single-group phase summary.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`synchrony`¶

Kuramoto coherence over single cells, and whether damping is desynchrony or amplitude loss.

cw.call("synchrony", traces, hours, config=None)

Name	Type	Required	Default	Units	Meaning
`traces`	object or array	yes	—	recording units	Single-cell traces on one shared time grid: {'roi_1': [values], ...}. Per-ROI output from a slice recording.
`hours`	array	yes	—	hours	The shared time grid the traces are sampled on, in hours from the start of the recording.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: synchrony.

`period_dispersion`¶

Whether a population lost coherence because its cells' periods diverged or because their phases were displaced.

cw.call("period_dispersion", traces, hours, config=None)

Name	Type	Required	Default	Units	Meaning
`traces`	object or array	yes	—	recording units	Single-cell traces on one shared time grid: {'roi_1': [values], ...}. Per-ROI output from a slice recording.
`hours`	array	yes	—	hours	The shared time grid the traces are sampled on, in hours from the start of the recording.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: period_dispersion.

`phase_angle`¶

How far the animal's daily marker sits from the light transition, and whether that angle held.

cw.call("phase_angle", recording, cohorts=None, config=None, marker=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`cohorts`	object	no	`null`	-	Recordings grouped by label, to test whether the groups hold different angles of entrainment: {'WT': [spec, ...], 'KO': [...]}. One angle per animal, so the unit of analysis is the animal. Omit it and only the focal recording is answered for.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`marker`	string	no	`null`	-	Which daily marker the angle of entrainment is measured from: onset, offset or acrophase. Defaults to the entrainment_marker config key, and is never guessed from the data.

Config: all keys and defaults.

Result access: declared.

Figure views: phase_angle.

`reentrainment`¶

How many cycles the animal took to catch up with a shifted schedule, and at what rate.

cw.call("reentrainment", recording, config=None, shift_day=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`shift_day`	string	no	`null`	-	The date the light schedule moved, as YYYY-MM-DD. Omit it and the date is read out of the schedule itself; supply it when the schedule in the config does not carry the move. The shift date belongs to neither side: the first full day on the new schedule is day 1.

Config: all keys and defaults.

Result access: declared.

Figure views: reentrainment.

`masking`¶

Whether a light pulse changed activity while it was on, which is not the same finding as a phase shift.

cw.call("masking", recording, pulse_start, pulse_hours, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`pulse_start`	string	yes	—	-	When the light pulse began, as an ISO date-time (2026-05-11T22:00). The same clock window on the days before it becomes the control.
`pulse_hours`	float	yes	—	hours	How long the pulse lasted. Must be greater than zero.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: masking.

`sleep`¶

Sleep scored as sustained immobility, split by light and dark, with bouts and fragmentation.

cw.call("sleep", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: sleep.

`food_anticipation`¶

Whether the animal became active before a declared mealtime, and whether that anticipation survived a fast.

cw.call("food_anticipation", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: food_anticipation.

`two_process_fit`¶

Fit the two-process model of sleep regulation to a scored record, and report which of its parameters the record does not separate.

cw.call("two_process_fit", sleep_result, period_hours=24.0, acrophase_hours=0.0, config=None)

Name	Type	Required	Default	Units	Meaning
`sleep_result`	object	yes	—	-	An immobility_sleep result, whole. A record it refused to score is refused here for the same reason rather than re-derived.
`period_hours`	float	no	`24.0`	hours	Fixed cycle of the two-process sleep fit; omitted or null uses the installed reference-cycle default, not a search range.
`acrophase_hours`	number	no	`0.0`	hours	Circadian-term acrophase of the sleep model; omitted or null uses zero on the declared cycle.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: two_process_fit.

`two_process_predict`¶

Run the fitted sleep model forward under a proposed cycle length, once per parameter set the record cannot rule out.

cw.call("two_process_predict", fit, schedule, config=None)

Name	Type	Required	Default	Units	Meaning
`fit`	object	yes	—	-	A two_process_fit result, whole. A fit with no parameters -- a record the model refused -- is refused here rather than run with defaults.
`schedule`	object	yes	—	-	The proposed schedule: `days`, `period_hours`, and optionally `acrophase_hours` and `label`. The acrophase defaults to the one the record was fitted under, which assumes the animal holds the same phase angle; where it would not, entrainment_range predicts the new one and it should be passed here.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: two_process_predict.

`entrainment_range`¶

Which zeitgeber periods a measured phase response curve predicts this animal can entrain to, and the phase angle it would sit at.

cw.call("entrainment_range", curve, tau_hours, config=None)

Name	Type	Required	Default	Units	Meaning
`curve`	object	yes	—	-	A phase_response_curve result, whole. Its `fit` is what is iterated; a curve with no fit -- too few animals -- is refused rather than predicted from.
`tau_hours`	number	yes	—	hours	The animal's own free-running period, in hours. The cohort curve does not carry it because a cohort has one per animal.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: entrainment_range.

`predicted_reentrainment`¶

How many cycles the same curve predicts a schedule shift will take, and the transient on the way.

cw.call("predicted_reentrainment", curve, tau_hours, shift_hours, t_hours=24.0, config=None)

Name	Type	Required	Default	Units	Meaning
`curve`	object	yes	—	-	A phase_response_curve result, whole. Its `fit` is what is iterated; a curve with no fit -- too few animals -- is refused rather than predicted from.
`tau_hours`	number	yes	—	hours	The animal's own free-running period, in hours. The cohort curve does not carry it because a cohort has one per animal.
`shift_hours`	number	yes	—	hours	How far the schedule moved, in hours, POSITIVE for an advance -- the transition arriving earlier -- which is the phase response curve's own sign convention.
`t_hours`	number	no	`24.0`	hours	The zeitgeber period the animal is being shifted within, in hours.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: predicted_reentrainment.

`paired_measures`¶

The same subjects measured in two epochs: what moved, by how much, and whether pairing bought any precision.

cw.call("paired_measures", epochs, config=None, circular_measures=None)

Name	Type	Required	Default	Units	Meaning
`epochs`	object	yes	—	-	The epochs of one study, each a list of subject entries: {"baseline": [{"subject_id": "m01", "measures": {"period_hours": 23.8}}, ...], "treatment": [...]}. Pairing is by subject_id, so a subject missing from any epoch is dropped and named. `paired_measures` takes exactly two and `longitudinal_measures` three or more; each refuses the other's shape by name.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`circular_measures`	array	no	`null`	-	Which measure names are clock times rather than plain numbers, e.g. ["acrophase_hours"]. Those are differenced round the circle -- 23.5 h to 00.5 h is +1 h, not -23 h -- and tested with a Rayleigh test. Nothing is inferred from a name.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`longitudinal_measures`¶

The same subjects measured at three or more ordered visits: the omnibus across visits, the linear trend along them, and the pairs.

cw.call("longitudinal_measures", epochs, config=None, circular_measures=None, order=None)

Name	Type	Required	Default	Units	Meaning
`epochs`	object	yes	—	-	The epochs of one study, each a list of subject entries: {"baseline": [{"subject_id": "m01", "measures": {"period_hours": 23.8}}, ...], "treatment": [...]}. Pairing is by subject_id, so a subject missing from any epoch is dropped and named. `paired_measures` takes exactly two and `longitudinal_measures` three or more; each refuses the other's shape by name.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`circular_measures`	array	no	`null`	-	Which measure names are clock times rather than plain numbers, e.g. ["acrophase_hours"]. Those are differenced round the circle -- 23.5 h to 00.5 h is +1 h, not -23 h -- and tested with a Rayleigh test. Nothing is inferred from a name.
`order`	array	no	`null`	-	The epoch labels in study order, e.g. ["baseline", "6_months", "12_months"]. The linear trend is fitted along this axis, so it decides what rising and falling mean. Without it the order the epochs arrived in is used and said to have been assumed.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`channel_comparison`¶

The lag between two measurement channels of one subject, with each channel's own period so the lag is not misread as a phase angle.

cw.call("channel_comparison", recording, channels, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`channels`	array	yes	—	-	Exactly two measurement channel keys from this recording, e.g. ["activity", "body_temperature"]. Use `inspect` to list what a recording carries.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: channel_comparison.

`splitting`¶

Two circadian components running at once, or the reason the record carries one.

cw.call("splitting", recording, config=None, period_hours=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`period_hours`	float	no	`null`	hours	The cycle the phases live on. Omit to use the config's period_hours (24 h by default). A free-running cohort should pass its own tau, so that 'one cycle' means one of the animals' cycles rather than one solar day. `splitting` uses it for a second purpose that is the same idea: the period the resolution element P**2/T is worked out at, which sets how far apart two components must be before that record can show them to differ.

Config: all keys and defaults.

Result access: declared.

Figure views: splitting.

`ultradian`¶

The strongest component faster than a day, and how large it is beside the daily one.

cw.call("ultradian", recording, config=None)

Name	Type	Required	Default	Units	Meaning
`recording`	recording spec	yes	—	-	The record to analyse: {'path': 'data/m01.awd'} (a bare path string also works), {'demo': true} for the built-in deterministic record, {'inline': {'filename': ..., 'text': ...}} for tabular text, {'trace': {'hours': [...], 'values': [...], 'name': ...}} for one elapsed-time trace, or {'channels': {'hours': [...], 'values': {'reporter_a': [...], 'reporter_b': [...]}}} for several measurements from one subject. A returned processed_trace spec retains transformed values, their original clock, source identity and explicit processing history. Versioned recording_snapshot specs are self-contained numeric inputs for replaying in-memory Recording objects; they do not invoke a raw-activity importer.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: ultradian.

`dose_response`¶

Phase shift against stimulus dose at one circadian time: the half-maximal dose, the saturating maximum, and what was withheld.

cw.call("dose_response", dose_points, config=None, dose_unit=None)

Name	Type	Required	Default	Units	Meaning
`dose_points`	array	yes	—	-	The phase shifts of one dose series, as [[dose, shift_hours, label, circadian_time], ...] or as objects with "dose", "shift_hours", an optional "label" naming the animal and an optional "circadian_time". One entry per animal per dose. The dose is in whatever unit the stimulus was measured in and the package never guesses which; the shift follows the Aschoff sign convention the rest of the package uses, advance positive.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`dose_unit`	string	no	`null`	-	What the dose was measured in -- lux, uW/cm2, mg, photons. A label and nothing else: it is printed wherever a dose is printed and no arithmetic is done with it. Omit it and no unit appears anywhere, which is the honest output for a package that was not told what was measured.

Config: all keys and defaults.

Result access: declared.

Figure views: dose_response.

`temperature_compensation`¶

Q10 for the period across a temperature series, and whether the clock is compensated.

cw.call("temperature_compensation", temperature_points, config=None)

Name	Type	Required	Default	Units	Meaning
`temperature_points`	array	yes	—	-	One entry per unit per temperature: [[20.0, 24.1, 'slice_1'], ...], or objects with temperature_c, period_hours and an optional label. Three slices at each of three temperatures is nine entries, and the labels are what lets the interval be clustered on the slice rather than on the measurement.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: temperature_compensation.

`phase_map`¶

Phase against position across regions: whether there is a wave, and which way and how fast it travels.

cw.call("phase_map", points, config=None, period_hours=None, position_units='um')

Name	Type	Required	Default	Units	Meaning
`points`	object or array	yes	—	hours and position units	One entry per region, each carrying a phase and a position: [{'label': 'left', 'phase_hours': 6.2, 'x': 120, 'y': 340}, ...]. A list of [label, phase_hours, x, y] arrays works too. The phases are ones the caller already measured -- acrophases from a cosinor, peak times, onsets -- and the positions are region centroids in whatever unit position_units names. Six regions is the floor; below it the plane is fitted but never tested.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`period_hours`	float	no	`null`	hours	The cycle the phases live on. Omit to use the config's period_hours (24 h by default). A free-running cohort should pass its own tau, so that 'one cycle' means one of the animals' cycles rather than one solar day. `splitting` uses it for a second purpose that is the same idea: the period the resolution element P**2/T is worked out at, which sets how far apart two components must be before that record can show them to differ.
`position_units`	string	no	`"um"`	-	What the x and y in points are measured in: 'um', 'px', 'mm'. It travels through to the reported speed, which comes back in these units per hour. Nothing is converted -- this is a label, so pass the unit the positions are actually in.

Config: all keys and defaults.

Result access: declared.

Figure views: phase_map.

`coupling`¶

How far one named trace leads another, whether that lag is a number, and whether it held.

cw.call("coupling", series_a, series_b, hours, config=None)

Name	Type	Required	Default	Units	Meaning
`series_a`	object or array	yes	—	recording units	The first trace: {'label': 'left lobe', 'values': [...]} on the shared hours grid. A [label, values] array works too. The label is reported back as the one that leads or lags, so make it the name you would use in a figure.
`series_b`	object or array	yes	—	recording units	The second trace, same shape as series_a and on the same hours grid. The reported lag is negative when series_a peaks first.
`hours`	array	yes	—	hours	The shared time grid the traces are sampled on, in hours from the start of the recording.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: coupling.

`sample_size`¶

How many units a difference needs, or what power a given n has, by simulating the test that will actually be run.

cw.call("sample_size", question='phase_difference', difference, resultant_length=None, n_per_group=None, target_power=None, config=None)

Name	Type	Required	Default	Units	Meaning
`question`	string	no	`"phase_difference"`	-	Which power question to answer: 'phase_difference' for two groups of phases compared on the circle, or 'mesor', 'amplitude' or 'rhythm_phase' for a cosinor parameter compared between two cohorts. 'observed' asks for post-hoc observed power and is refused with the reason, because it is a restatement of the p-value you already have.
`difference`	float	yes	—	hours or recording units	The smallest difference worth detecting, in the parameter's own units: hours for a phase, recording units for a mesor or an amplitude. Not the difference you observed -- the one that would change your mind.
`resultant_length`	float	no	`null`	-	Within-group phase concentration for the phase-difference question; omitted uses the shared resultant-length default.
`n_per_group`	integer	no	`null`	units per group	Give it to ask 'what power do I have at this n'. Leave it out to ask 'how many do I need', which searches over n instead.
`target_power`	float	no	`null`	-	Prospective target power; omitted follows config.power_target. Ignored when a fixed sample size is evaluated.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.

Config: all keys and defaults.

Result access: declared.

Figure views: sample_size.

`compare_rhythms`¶

Fit one cosinor to two groups and test which rhythm parameter differs.

cw.call("compare_rhythms", groups, config=None, unit='subject')

Name	Type	Required	Default	Units	Meaning
`groups`	object	yes	—	-	Recordings grouped by label: {'WT': [spec, ...], 'KO': [...]}.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`unit`	string	no	`"subject"`	-	Unit of analysis: subject, slice, or cell.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`group_comparison`¶

Two-way mixed RM ANOVA with pointwise post-hoc across groups.

cw.call("group_comparison", groups, config=None, alpha=0.05, correction='sidak', unit='subject', sphericity='greenhouse_geisser')

Name	Type	Required	Default	Units	Meaning
`groups`	object	yes	—	-	Recordings grouped by label: {'WT': [spec, ...], 'KO': [...]}.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`alpha`	float	no	`0.05`	-	Group-comparison significance threshold.
`correction`	string	no	`"sidak"`	-	sidak, bonferroni, or none.
`unit`	string	no	`"subject"`	-	Unit of analysis: subject, slice, or cell.
`sphericity`	string	no	`"greenhouse_geisser"`	-	greenhouse_geisser, huynh_feldt, or none.

Config: all keys and defaults.

Result access: declared.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`render_group_figure`¶

Render the group overlay and optional significance bar to SVG.

cw.call("render_group_figure", groups, config=None, normalize='own_mean', time_axis='clock_time', pool_order='profile_then_pool', statistic='mean', within_recording_reducer='mean', detrended=False, alpha=0.05, correction='sidak', unit='subject', sphericity='greenhouse_geisser', statistics=True, figure_options=None)

Name	Type	Required	Default	Units	Meaning
`groups`	object	yes	—	-	Recordings grouped by label: {'WT': [spec, ...], 'KO': [...]}.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`normalize`	string	no	`"own_mean"`	-	Value normalisation before pooling. Accepts none, mean_center, median_center, zscore, robust_zscore, robust_scale, own_mean, own_daily_total, minmax, max_abs, reference_delta, fold_change, delta_over_reference, log2_fold_change, percent_of_reference, percent_change, envelope or pre_treatment_cycle. Reference-based methods require reference metadata on each profile; use normalization_methods for formulas.
`time_axis`	string	no	`"clock_time"`	-	clock_time, tau_scaled, or onset_aligned.
`pool_order`	string	no	`"profile_then_pool"`	-	profile_then_pool or virtual_animal.
`statistic`	string	no	`"mean"`	-	mean or median.
`within_recording_reducer`	string	no	`"mean"`	-	How each recording contributes at each phase bin before pooling: mean averages selected cycles; max retains the largest observed binned value across the selected recording.
`detrended`	boolean	no	`false`	-	Whether inputs are already baseline-subtracted.
`alpha`	float	no	`0.05`	-	Group-comparison significance threshold.
`correction`	string	no	`"sidak"`	-	sidak, bonferroni, or none.
`unit`	string	no	`"subject"`	-	Unit of analysis: subject, slice, or cell.
`sphericity`	string	no	`"greenhouse_geisser"`	-	greenhouse_geisser, huynh_feldt, or none.
`statistics`	boolean	no	`true`	-	Whether to compute and render group statistics.
`figure_options`	object	no	`null`	-	Optional group SVG presentation options: colors/color_map, x_bounds, x_ticks or x_tick_step, x_tick_label_offset, x_label, y_label, title, margin, legend, text_scale, title_scale, axis_scale, tick_scale, legend_scale, show_grid, group_order/order, style/house_style. style defaults to 'pyflash' for PyFLASH-compatible typography, outward ticks, frameless legends and left/bottom spines.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`diagnosis_groups`¶

Resolve cohort metadata into diagnosis-labelled recording groups.

cw.call("diagnosis_groups", cohort)

Name	Type	Required	Default	Units	Meaning
`cohort`	object	yes	—	-	Metadata-driven cohort spec. Requires metadata_csv plus either a recording_column or recording_pattern; groups rows by diagnosis_column, defaulting to a diagnosis/condition/group-like column. Optional exclude_subjects removes participant IDs without editing source metadata. Optional mask_csv supplies one start/end analysis interval per subject; mask_subject_column, mask_start_column, and mask_end_column override its inferred columns.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`study_report`¶

One document for a whole study: the named analyses run on every recording of a cohort, the scalar table they produce, the group and paired comparisons, and every recording's checksum.

cw.call("study_report", cohort, analyses, config=None, epoch_column=None)

Name	Type	Required	Default	Units	Meaning
`cohort`	object	yes	—	-	Metadata-driven cohort spec. Requires metadata_csv plus either a recording_column or recording_pattern; groups rows by diagnosis_column, defaulting to a diagnosis/condition/group-like column. Optional exclude_subjects removes participant IDs without editing source metadata. Optional mask_csv supplies one start/end analysis interval per subject; mask_subject_column, mask_start_column, and mask_end_column override its inferred columns.
`analyses`	array	yes	—	-	Action names to run on every recording of the study, e.g. ["cosinor", "sleep"]. Each is dispatched through this same registry, so a number in the report is the number that action returns on its own; run discover for the list of names.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`epoch_column`	string	no	`null`	-	Metadata column naming which epoch each recording belongs to, e.g. "epoch" holding baseline/treatment. Where it names exactly two epochs and subjects appear in both, the report runs the paired comparison; where it does not, the report says which of those it was. Omit it for a study with one epoch.

Config: all keys and defaults.

Result access: composite.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`render_diagnosis_profile`¶

Render a diagnosis-condition average activity profile overlay from cohort metadata.

cw.call("render_diagnosis_profile", cohort, config=None, normalize='own_mean', time_axis='clock_time', pool_order='profile_then_pool', statistic='mean', within_recording_reducer='mean', detrended=False, alpha=0.05, correction='sidak', unit='subject', sphericity='greenhouse_geisser', statistics=True, figure_options=None)

Name	Type	Required	Default	Units	Meaning
`cohort`	object	yes	—	-	Metadata-driven cohort spec. Requires metadata_csv plus either a recording_column or recording_pattern; groups rows by diagnosis_column, defaulting to a diagnosis/condition/group-like column. Optional exclude_subjects removes participant IDs without editing source metadata. Optional mask_csv supplies one start/end analysis interval per subject; mask_subject_column, mask_start_column, and mask_end_column override its inferred columns.
`config`	object	no	`null`	-	Partial scientific settings. Omitted or None values use the shared installed defaults; invalid fresh values are rejected. Run describe_config for names, meanings, units, bounds and choices. Explicitly load old saved mappings with load_saved_settings to report compatibility conversions.
`normalize`	string	no	`"own_mean"`	-	Value normalisation before pooling. Accepts none, mean_center, median_center, zscore, robust_zscore, robust_scale, own_mean, own_daily_total, minmax, max_abs, reference_delta, fold_change, delta_over_reference, log2_fold_change, percent_of_reference, percent_change, envelope or pre_treatment_cycle. Reference-based methods require reference metadata on each profile; use normalization_methods for formulas.
`time_axis`	string	no	`"clock_time"`	-	clock_time, tau_scaled, or onset_aligned.
`pool_order`	string	no	`"profile_then_pool"`	-	profile_then_pool or virtual_animal.
`statistic`	string	no	`"mean"`	-	mean or median.
`within_recording_reducer`	string	no	`"mean"`	-	How each recording contributes at each phase bin before pooling: mean averages selected cycles; max retains the largest observed binned value across the selected recording.
`detrended`	boolean	no	`false`	-	Whether inputs are already baseline-subtracted.
`alpha`	float	no	`0.05`	-	Group-comparison significance threshold.
`correction`	string	no	`"sidak"`	-	sidak, bonferroni, or none.
`unit`	string	no	`"subject"`	-	Unit of analysis: subject, slice, or cell.
`sphericity`	string	no	`"greenhouse_geisser"`	-	greenhouse_geisser, huynh_feldt, or none.
`statistics`	boolean	no	`true`	-	Whether to compute and render group statistics.
`figure_options`	object	no	`null`	-	Optional group SVG presentation options: colors/color_map, x_bounds, x_ticks or x_tick_step, x_tick_label_offset, x_label, y_label, title, margin, legend, text_scale, title_scale, axis_scale, tick_scale, legend_scale, show_grid, group_order/order, style/house_style. style defaults to 'pyflash' for PyFLASH-compatible typography, outward ticks, frameless legends and left/bottom spines.

Config: all keys and defaults.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

`clear_output`¶

Delete generated files under the output root after confirmation.

cw.call("clear_output", confirm=False)

Name	Type	Required	Default	Units	Meaning
`confirm`	boolean	no	`false`	-	Explicit confirmation for a destructive action.

Result access: raw.

Figure views: No Result.plot adapter; use the declared result or the separate export action.

Period estimator settings¶

These references come from each installed method definition; their defaults, units and constraints come from the shared configuration reference. A template-period grid is distinct from a numeric search range. Batch multiple-testing correction is not an individual estimator setting.

ER Periodogram (`chi_square`)¶

Fold-and-compare periodogram: how much of the variance a given period explains, against a chi-square critical value.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, periodogram_alpha, chi_square_spline_interval_hours, chi_square_normalisation.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

eJTK (`ejtk`)¶

The same template match with the null built by permutation, which is better calibrated than the analytic one. The rhythmicity test to reach for on sparsely sampled data.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: jtk_periods, jtk_asymmetries, jtk_phase_step_hours, jtk_max_points, jtk_alpha, ejtk_permutations, jtk_seed.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

F Periodogram (`f`)¶

The chi-square periodogram's variance ratio tested as an F statistic. BioDare2 has no equivalent; it is kept because it handles unequal sample counts per phase bin.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, periodogram_alpha, chi_square_spline_interval_hours, chi_square_normalisation.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

FFT NLLS (`fft_nlls`)¶

Sum of independent cosines fitted by non-linear least squares from FFT starting values. The only method that reports an error for period, phase and amplitude, and so the only source of RAE.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, period_hours, nlls_max_components, nlls_improvement_alpha, nlls_circadian_min, nlls_circadian_max.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

JTK_CYCLE (`jtk`)¶

Rank correlation against a library of cosine templates, with an analytic null. Kept for comparability with published work; it is known to be anti-conservative, which is why eJTK exists.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: jtk_periods, jtk_asymmetries, jtk_phase_step_hours, jtk_max_points, jtk_alpha.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

LS Periodogram (`lomb`)¶

Least-squares spectral estimate that tolerates gaps and uneven sampling, and carries a false-alarm probability.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, periodogram_alpha.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

MESA (`mesa`)¶

Maximum entropy spectrum of an autoregressive model. Shares no assumptions with the curve-fitting methods and is the most resilient of the six to baseline trend, so it is the one to validate the others against.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, mesa_model_length.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

MFourFit (`mfourfit`)¶

A main cosine plus up to four harmonics of it, grid-searched over period. BioDare2 rates it the most accurate of the six on entrained data, but it returns a period even for noise, so it needs a significance test beside it.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, mfourfit_step_hours, mfourfit_harmonics.

Detrending: linear (forced by method).

Spectrum Resampling (`spectrum_resampling`)¶

Bootstraps the smoothed FFT spectrum and averages where the peak lands, which recovers periods finer than the FFT grid can hold. The only method whose confidence interval comes from the data rather than from a fit.

Shared inputs: start, end, exclusions, analysis_channel, bin_minutes, phase_reference, phase_units.

Method settings: period_min_hours, period_max_hours, sr_grid_points, sr_trim_high_frequency, sr_bandwidth, sr_iterations, sr_seed.

Detrending: explicit period_detrend, with the applicable settings below.

none: no additional controls
linear: no additional controls
robust_linear: no additional controls
first_difference: no additional controls
polynomial: period_detrend_polynomial_degree
running_mean: period_detrend_window_hours, period_detrend_min_valid_fraction
moving_median: period_detrend_window_hours, period_detrend_min_valid_fraction
kernel: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
amp_baseline: period_detrend_window_hours, period_detrend_bandwidth_hours, period_detrend_min_valid_fraction
lowess: period_detrend_window_hours, period_detrend_lowess_fraction, period_detrend_lowess_iterations
savitzky_golay: period_detrend_window_hours, period_detrend_polynomial_degree
asymmetric_least_squares: period_detrend_asls_smoothness, period_detrend_asls_asymmetry, period_detrend_asls_iterations
frequency: period_detrend_low_cut_hours, period_detrend_high_cut_hours, period_detrend_filter_order

Complete action reference¶

inspect¶

describe_config¶

normalize_config¶

normalization_methods¶

normalize¶

load_recording¶

list_output¶

set_group_colours¶

summary¶

analyze¶

quality¶

rhythm¶

periodograms¶

daily_measures¶

onset_fits¶

profile¶

peak_aligned_profile¶

cosinor¶

period_methods¶

estimate_period¶

compare_periods¶

rhythmicity¶

nonparametric¶

bouts¶

fft¶

autocorrelation¶

wavelet¶

actogram¶

time_series¶

select_frame¶

methods_paragraph¶

analysis_script¶

write_analysis_script¶

render_actogram¶

render_figures¶

detrend¶

group_profile¶

phase_response_curve¶

compare_phase_response_curves¶

instantaneous_phase¶

phase_comparison¶

phase_summary¶

synchrony¶

period_dispersion¶

phase_angle¶

reentrainment¶

masking¶

sleep¶

food_anticipation¶

two_process_fit¶

two_process_predict¶

entrainment_range¶

predicted_reentrainment¶

paired_measures¶

longitudinal_measures¶

channel_comparison¶

splitting¶

ultradian¶

dose_response¶

temperature_compensation¶

phase_map¶

coupling¶

sample_size¶

compare_rhythms¶

group_comparison¶

render_group_figure¶

diagnosis_groups¶

study_report¶

render_diagnosis_profile¶

clear_output¶

Period estimator settings¶

ER Periodogram (chi_square)¶

eJTK (ejtk)¶

F Periodogram (f)¶

FFT NLLS (fft_nlls)¶

JTK_CYCLE (jtk)¶

LS Periodogram (lomb)¶

MESA (mesa)¶

MFourFit (mfourfit)¶

`inspect`¶

`describe_config`¶

`normalize_config`¶

`normalization_methods`¶

`normalize`¶

`load_recording`¶

`list_output`¶

`set_group_colours`¶

`summary`¶

`analyze`¶

`quality`¶

`rhythm`¶

`periodograms`¶

`daily_measures`¶

`onset_fits`¶

`profile`¶

`peak_aligned_profile`¶

`cosinor`¶

`period_methods`¶

`estimate_period`¶

`compare_periods`¶

`rhythmicity`¶

`nonparametric`¶

`bouts`¶

`fft`¶

`autocorrelation`¶

`wavelet`¶

`actogram`¶

`time_series`¶

`select_frame`¶

`methods_paragraph`¶

`analysis_script`¶

`write_analysis_script`¶

`render_actogram`¶

`render_figures`¶

`detrend`¶

`group_profile`¶

`phase_response_curve`¶

`compare_phase_response_curves`¶

`instantaneous_phase`¶

`phase_comparison`¶

`phase_summary`¶

`synchrony`¶

`period_dispersion`¶

`phase_angle`¶

`reentrainment`¶

`masking`¶

`sleep`¶

`food_anticipation`¶

`two_process_fit`¶

`two_process_predict`¶

`entrainment_range`¶

`predicted_reentrainment`¶

`paired_measures`¶

`longitudinal_measures`¶

`channel_comparison`¶

`splitting`¶

`ultradian`¶

`dose_response`¶

`temperature_compensation`¶

`phase_map`¶

`coupling`¶

`sample_size`¶

`compare_rhythms`¶

`group_comparison`¶

`render_group_figure`¶

`diagnosis_groups`¶

`study_report`¶

`render_diagnosis_profile`¶

`clear_output`¶

ER Periodogram (`chi_square`)¶

eJTK (`ejtk`)¶

F Periodogram (`f`)¶

FFT NLLS (`fft_nlls`)¶

JTK_CYCLE (`jtk`)¶

LS Periodogram (`lomb`)¶

MESA (`mesa`)¶

MFourFit (`mfourfit`)¶

Spectrum Resampling (`spectrum_resampling`)¶