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[Docs] update docs to reflect implementation of respiration signal cleaning with khodadad2018 #952

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Jan 19, 2024
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[Docs] update docs to reflect implementation of respiration signal cleaning with khodadad2018 #952

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7abb936
update docstring to reflect implementation of khodadad2018
danibene Jan 18, 2024
e74b5f8
update description of khodadad2018 to reflect implementation of cleaning
danibene Jan 18, 2024
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4 changes: 2 additions & 2 deletions neurokit2/rsp/rsp_clean.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ def rsp_clean(rsp_signal, sampling_rate=1000, method="khodadad2018", **kwargs):

Clean a respiration signal using different sets of parameters, such as:

* **khodadad2018**: Linear detrending followed by a fifth order 2Hz low-pass IIR Butterworth
filter)
* **khodadad2018**: Second order 0.05-3 Hz bandpass Butterworth filter. Note that the
implementation differs from the referenced paper (see issue #950).
* **BioSPPy**: Second order 0.1-0.35 Hz bandpass Butterworth filter followed by a constant
detrending).
* **hampel**: Applies a median-based Hampel filter by replacing values which are 3 (can be
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13 changes: 3 additions & 10 deletions neurokit2/rsp/rsp_methods.py
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Expand Up @@ -106,14 +106,7 @@ def rsp_methods(
report_info["text_cleaning"] = f"The raw signal, sampled at {sampling_rate} Hz,"
if method_cleaning in ["khodadad", "khodadad2018"]:
report_info["text_cleaning"] += (
" linear detrending followed by a fifth order 2Hz low-pass IIR Butterworth filter; "
+ "following Khoadadad et al., 2018."
)

refs.append(
"""Khodadad, D., Nordebo, S., Müller, B., Waldmann, A., Yerworth, R., Becher, T.,... & Bayford, R. (2018).
Optimized breath detection algorithm in electrical impedance tomography.
Physiological measurement, 39(9), 094001."""
" was preprocessed using a second order 0.05-3 Hz bandpass Butterworth filter."
)
elif method_cleaning in ["hampel", "power", "power2020"]:
report_info["text_cleaning"] += (
Expand All @@ -136,10 +129,10 @@ def rsp_methods(
elif method_cleaning in ["none"]:
report_info[
"text_cleaning"
] += "was directly used for peak detection without preprocessing."
] += " was directly used for peak detection without preprocessing."
else:
# just in case more methods are added
report_info["text_cleaning"] += f"was cleaned following the {method} method."
report_info["text_cleaning"] += f" was cleaned following the {method} method."

# 2. Peaks
# ----------
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