def get_peaks_ecg(subject, inputs, outputs, recompute, logpath):
"""Detect R-peaks in ECG.
1. Detect R-peaks
2. autocorrect artifacts in R-peaks detection.
"""
save_path = Path(
individualize_path(outputs["save_path"], subject, expand_name=True))
if save_path.exists() and not recompute: # only recompute if requested
print(f"Not re-computing {save_path}")
return
physio_path = next(
Path(".").glob(individualize_path(inputs["physio_path"], subject)))
ecg = np.ravel(pd.read_csv(physio_path, sep="\t", header=None))
# Detect R-peaks.
peaks = ecg_peaks(ecg, ECG_SFREQ_DECIMATED)
# Correct artifacts in peak detection.
peaks_corrected = correct_peaks(peaks, ECG_SFREQ_DECIMATED, iterative=True)
# Save peaks as samples.
pd.Series(peaks_corrected).to_csv(save_path,
sep="\t",
header=False,
index=False,
float_format="%.4f")
if not logpath:
return
fig, ax = plt.subplots(nrows=1, ncols=1)
sec = np.linspace(0, len(ecg) / ECG_SFREQ_DECIMATED, len(ecg))
ax.plot(sec, ecg)
ax.scatter(sec[peaks],
ecg[peaks],
zorder=3,
c="r",
marker="+",
s=300,
label="uncorrected R-peaks")
ax.scatter(sec[peaks_corrected],
ecg[peaks_corrected],
zorder=4,
c="g",
marker="x",
s=300,
label="corrected R-peaks")
ax.set_xlabel("seconds")
ax.legend(loc="upper right")
fig.savefig(logpath, dpi=200)
plt.close(fig)
def test_missed_correction_wrapper(peaks_correct, peaks_missed, iterative,
rmssd_diff):
peaks_corrected = correct_peaks(peaks_missed, sfreq=1, iterative=iterative)
rmssd_correct = compute_rmssd(peaks_correct)
rmssd_corrected = compute_rmssd(peaks_corrected)
rmssd_uncorrected = compute_rmssd(peaks_missed)
# Assert that correction does not produce peaks that exceed the temporal
# bounds of the original peaks.
assert peaks_correct[0] <= peaks_corrected[0]
assert peaks_correct[-1] >= peaks_corrected[-1]
# Assert that after artifact correction, the difference in RMSSD to the
# undistorted signal decreases. This also implicitely tests if the peak
# distortion affects the RMSSD (manipulation check).
rmssd_diff_uncorrected = np.abs(rmssd_correct - rmssd_uncorrected)
rmssd_diff_corrected = np.abs(rmssd_correct - rmssd_corrected)
assert int(rmssd_diff_uncorrected - rmssd_diff_corrected) == rmssd_diff