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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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2 changes: 1 addition & 1 deletion phys2denoise/metrics/cardiac.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ def _crf(t):

dt = tr / oversampling
time_stamps = np.linspace(
0, time_length, np.rint(float(time_length) / dt).astype(np.int)
0, time_length, np.rint(float(time_length) / dt).astype(int)
)
time_stamps -= onset
crf_arr = _crf(time_stamps)
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4 changes: 2 additions & 2 deletions phys2denoise/metrics/chest_belt.py
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Expand Up @@ -162,7 +162,7 @@ def env(resp, samplerate, window=10):


@due.dcite(references.CHANG_GLOVER_2009)
def rv(resp, samplerate, window=6, lags=(0,)):
def rv(resp, samplerate, window=6):
"""Calculate respiratory variance.

Parameters
Expand Down Expand Up @@ -260,7 +260,7 @@ def _rrf(t):

dt = tr / oversampling
time_stamps = np.linspace(
0, time_length, np.rint(float(time_length) / dt).astype(np.int)
0, time_length, np.rint(float(time_length) / dt).astype(int)
)
time_stamps -= onset
rrf_arr = _rrf(time_stamps)
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4 changes: 2 additions & 2 deletions phys2denoise/metrics/utils.py
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Expand Up @@ -116,9 +116,9 @@ def apply_lags(arr1d, lags):
arr_with_lags = np.zeros((arr1d.shape[0], len(lags)))
for i_lag, lag in enumerate(lags):
if lag < 0:
arr_delayed = np.hstack((arr1d[lag:], np.zeros(lag)))
arr_delayed = np.hstack((arr1d[abs(lag):], np.zeros(abs(lag))))
elif lag > 0:
arr_delayed = np.hstack((np.zeros(lag), arr1d[lag:]))
arr_delayed = np.hstack((np.zeros(lag), arr1d[:-lag]))
else:
arr_delayed = arr1d.copy()
arr_with_lags[:, i_lag] = arr_delayed
Expand Down