https://github.com/int-brain-lab/iblenv/issues/261

Author: k1o0

brainbox/behavior/wheel.py

@@ -4,7 +4,7 @@
 import numpy as np
 from numpy import pi
 import scipy.interpolate as interpolate
-from scipy.signal import convolve, gaussian
+from scipy.signal import convolve, windows
 from scipy.linalg import hankel
 import matplotlib.pyplot as plt
 from matplotlib.collections import LineCollection
@@ -114,7 +114,7 @@ def velocity_smoothed(pos, freq, smooth_size=0.03):
     std_samps = np.round(smooth_size * freq)  # Standard deviation relative to sampling frequency
     N = std_samps * 6  # Number of points in the Gaussian covering +/-3 standard deviations
     gauss_std = (N - 1) / 6
-    win = gaussian(N, gauss_std)
+    win = windows.gaussian(N, gauss_std)
     win = win / win.sum()  # Normalize amplitude
 
     # Convolve and multiply by sampling frequency to restore original units
@@ -274,7 +274,7 @@ def movements(t, pos, freq=1000, pos_thresh=8, t_thresh=.2, min_gap=.1, pos_thre
     peak_amps = np.fromiter(peaks, dtype=float, count=onsets.size)
     N = 10  # Number of points in the Gaussian
     STDEV = 1.8  # Equivalent to a width factor (alpha value) of 2.5
-    gauss = gaussian(N, STDEV)  # A 10-point Gaussian window of a given s.d.
+    gauss = windows.gaussian(N, STDEV)  # A 10-point Gaussian window of a given s.d.
     vel = convolve(np.diff(np.insert(pos, 0, 0)), gauss, mode='same')
     # For each movement period, find the timestamp where the absolute velocity was greatest
     peaks = (t[m + np.abs(vel[m:n]).argmax()] for m, n in zip(onset_samps, offset_samps))

ibllib/atlas/atlas.py

@@ -781,7 +781,7 @@ def xyz2ccf(self, xyz, ccf_order='mlapdv'):
         """
         Converts coordinates to the CCF coordinates, which is assumed to be the cube indices
         times the spacing.
-        :param xyz: mlapdv coordinates in um, origin Bregma
+        :param xyz: mlapdv coordinates in meters, origin Bregma
         :param ccf_order: order that you want values returned 'mlapdv' (ibl) or 'apdvml'
         (Allen mcc vertices)
         :return: coordinates in CCF space um, origin is the front left top corner of the data