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Fix bandpass Butterworth filter order to get a better filter, add option to change order in CLI #90

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merged 1 commit into from
Aug 13, 2023
Merged

Fix bandpass Butterworth filter order to get a better filter, add option to change order in CLI #90

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8 changes: 8 additions & 0 deletions phys2cvr/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,6 +260,14 @@ def _get_parser():
),
default=None,
)
opt_filt.add_argument(
"-bo",
"--butter-order",
dest="butter_order",
type=int,
help=("Order of Butterworth filter. Default is 9."),
default=None,
)

opt_flow = parser.add_argument_group("Optional Arguments to modify the workflow")
opt_flow.add_argument(
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18 changes: 12 additions & 6 deletions phys2cvr/phys2cvr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,8 +62,9 @@ def phys2cvr(
n_trials=None,
abs_xcorr=False,
skip_xcorr=False,
highcut=None,
lowcut=None,
highcut=0.04,
lowcut=0.02,
butter_order=9,
apply_filter=False,
run_regression=False,
lagged_regression=True,
Expand Down Expand Up @@ -140,11 +141,14 @@ def phys2cvr(
highcut : str, int, or float, optional
High frequency limit for filter.
Required if applying a filter.
Default: empty
Default: 0.02
lowcut : str, int, or float, optional
Low frequency limit for filter.
Required if applying a filter.
Default: empty
Default: 0.04
butter_order : int, optional
Butterworth filter order.
Default: 9
apply_filter : bool, optional
Apply a Butterworth filter to the functional input.
Default: False
Expand Down Expand Up @@ -322,7 +326,9 @@ def phys2cvr(
LGR.info(f"Loading {fname_func}")
if apply_filter:
LGR.info("Applying butterworth filter to {fname_func}")
func_avg = signal.filter_signal(func_avg, tr, lowcut, highcut)
func_avg = signal.filter_signal(
func_avg, tr, lowcut, highcut, butter_order
)
else:
raise NameError(
"Provided functional signal, but no TR specified! "
Expand Down Expand Up @@ -372,7 +378,7 @@ def phys2cvr(

if apply_filter:
LGR.info(f"Obtaining filtered average signal in {roiref}")
func_filt = signal.filter_signal(func, tr, lowcut, highcut)
func_filt = signal.filter_signal(func, tr, lowcut, highcut, butter_order)
func_avg = func_filt[roi].mean(axis=0)
else:
LGR.info(f"Obtaining average signal in {roiref}")
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10 changes: 4 additions & 6 deletions phys2cvr/signal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ def create_hrf(freq=40):
return hrf


def filter_signal(data, tr, lowcut="", highcut=""):
def filter_signal(data, tr, lowcut=0.02, highcut=0.04, order=9):
"""
Create a bandpass filter given a lowcut and a highcut, then filter data.

Expand All @@ -104,20 +104,18 @@ def filter_signal(data, tr, lowcut="", highcut=""):
Lower frequency in the bandpass
highcut : float
Higher frequency in the bandpass
order : int
The order of the butterworth filter

Returns
-------
filt_data : np.ndarray
Input `data`, but filtered.
"""
if not lowcut:
lowcut = 0.02
if not highcut:
highcut = 0.04
nyq = (1 / tr) / 2
low = lowcut / nyq
high = highcut / nyq
a, b = butter(1, [low, high], btype="band")
a, b = butter(order, [low, high], btype="band")
filt_data = filtfilt(a, b, data, axis=-1)
return filt_data

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