def nearest_neighbor_centroid(fly1, fly2, normalized=False):
"""Finds the centroid-to-centroid distance to a Fly's nearest neighbor.
Flies should be tracked from within the same movie.
Parameters
----------
fly1 : Fly object
First fly; should have n_frames == fly2.n_frames.
fly2 : Fly object
Second fly; should have n_frames == fly1.n_frames.
normalized : boolean (default = True)
Whether or not the returned array should be normalized to its
mean.
Returns
-------
distances : np.ndarray | shape = [fly1.n_frames]
Centroid-to-centroid distances between fly1 and fly2.
"""
fly1_centroids = fly1.body.centroid.coords_xy()
fly2_centroids = fly2.body.centroid.coords_xy()
distances = np.sqrt((fly1_centroids[:, 0] - fly2_centroids[:, 0])**2 +
(fly1_centroids[:, 1] - fly2_centroids[:, 1])**2)
if normalized:
return normalize(distances)
return distances
def change_in_area(fly, normalized=False):
"""Calculates the first derivative of the area
of the ellipse fitted to a fly.
Parameters
----------
fly : Fly object
normalized : boolean (default=False)
Whether or not the first derivative should be normalized to its mean.
Returns
-------
d_area : np.ndarray | shape = [fly.n_frames - 1]
"""
area = fly.body.area()
d_area = np.diff(area) / np.diff(fly.timestamps).astype(np.float)
if normalized:
return normalize(d_area)
return d_area
def change_in_minor_axis_length(fly, normalized=False):
"""Calculates the first derivative of the length
of the minor axis of the ellipse fitted to a fly.
Parameters
----------
fly : Fly object
normalized : boolean (default=False)
Whether or not the first derivative should be normalized to its mean.
Returns
-------
d_min_ax_len : np.ndarray | shape = [fly.n_frames - 1]
"""
min_ax_len = fly.body.minor_axis_length
d_min_ax_len = np.diff(min_ax_len) / np.diff(fly.timestamps).astype(
np.float)
if normalized:
return normalize(d_min_ax_len)
return d_min_ax_len
def centroid_velocity(fly, normalized=False):
"""Calculates the velocity of a fly based of the movement of its centroid.
Parameters
----------
fly : Fly object
normalized : boolean (default=False)
Whether or not the velocity should be normalized to its mean.
Returns
-------
centroid_velocity : np.ndarray | shape = [fly.n_frames]
"""
centroids = fly.body.centroid.coords_xy()
squared_differences = np.diff(centroids, axis=0)**2
distance_traveled = np.sqrt(np.sum(squared_differences, axis=1))
velocity = distance_traveled / np.diff(fly.timestamps).astype(np.float)
velocity = np.hstack((0, velocity))
if normalized:
return normalize(velocity)
return velocity