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Fix lag application for negative lags #36

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Fix lag application for negative lags #36

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a872bca
Improve docstrings.
tsalo Jun 28, 2021
a1648da
Remove unused argument from env.
tsalo Jun 28, 2021
b5611e3
Support negative lags in rv.
tsalo Jun 28, 2021
b9b12b4
Merge remote-tracking branch 'upstream/master' into rv-negative-lags
tsalo Mar 15, 2023
827e081
Remove lags from rv.
tsalo Mar 15, 2023
8e467e6
Fix lag implementation.
tsalo Mar 15, 2023
f7c85b1
Use int instead of numpy.int (deprecated).
tsalo Mar 15, 2023
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12 changes: 5 additions & 7 deletions phys2denoise/metrics/chest_belt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def rpv(belt_ts, window):


@due.dcite(references.POWER_2020)
def env(belt_ts, samplerate, out_samplerate, window=10, lags=(0,)):
def env(belt_ts, samplerate, out_samplerate, window=10):
"""Calculate respiratory pattern variability across a sliding window.

Parameters
Expand All @@ -69,9 +69,6 @@ def env(belt_ts, samplerate, out_samplerate, window=10, lags=(0,)):
window : :obj:`int`, optional
Size of the sliding window, in the same units as out_samplerate.
Default is 6.
lags : (Y,) :obj:`tuple` of :obj:`int`, optional
List of lags to apply to the rv estimate. In the same units as
out_samplerate.

Returns
-------
Expand Down Expand Up @@ -118,8 +115,9 @@ def rv(belt_ts, samplerate, out_samplerate, window=6, lags=(0,)):
Size of the sliding window, in the same units as out_samplerate.
Default is 6.
lags : (Y,) :obj:`tuple` of :obj:`int`, optional
List of lags to apply to the rv estimate. In the same units as
out_samplerate.
List of lags to apply to the rv estimate.
Lags can be negative, zero, and/or positive.
In seconds (like out_samplerate).

Returns
-------
Expand Down Expand Up @@ -152,7 +150,7 @@ def rv(belt_ts, samplerate, out_samplerate, window=6, lags=(0,)):
# Apply lags
n_out_samples = int((belt_ts.shape[0] / samplerate) / out_samplerate)
# convert lags from out_samplerate to samplerate
delays = [abs(int(lag * samplerate)) for lag in lags]
delays = [int(lag * samplerate) for lag in lags]
rv_with_lags = utils.apply_lags(rv_arr, lags=delays)

# Downsample to out_samplerate
Expand Down