def animate_and_follow(individual=0, num_neighbours=15):
test_trajectories_file = os.path.join(dir_of_data, 'test_trajectories.npy')
t = np.load(test_trajectories_file)
tt.interpolate_nans(t)
tt.center_trajectories_and_normalise(t)
s_ = tt.smooth(t)
v_ = tt.smooth_velocity(t)
e_ = tt.normalise(v_[:, individual, :])
s = tt.center_in_individual(s_, individual)
s = tt.fixed_to_comoving(s, e_)
v = tt.fixed_to_comoving(v_, e_)
center = tt.fixed_to_comoving(-s_[:, [individual], :], e_)
indices = ttsocial.give_indices(s, num_neighbours)
sn = ttsocial.restrict(s, indices, individual)
vn = ttsocial.restrict(v, indices, individual)
sf = s[:, [individual], :]
vf = v[:, [individual], :]
anim = ttanimation.scatter_vectors(s, velocities=v, k=10)
anim += ttanimation.scatter_ellipses(s, velocities=v, color='c')
anim += ttanimation.scatter_ellipses(sn, velocities=vn, color='b')
anim += ttanimation.scatter_ellipses(sf, velocities=vf, color='r')
anim += ttanimation.scatter_circle(center)
anim.prepare()
anim.show()
def from_positions(cls, t, interpolate_nans=True, smooth_params=None):
"""Trajectory from positions
:param t: Positions nd.array.
:param interpolate_nans: whether to interpolate NaNs
:param smooth_params: Arguments for smoothing (see tt.smooth)
"""
if smooth_params is None:
smooth_params = {"sigma": -1, "only_past": False}
# Interpolate trajectories
if interpolate_nans:
tt.interpolate_nans(t)
displacement = np.array([0.0, 0.0])
# Smooth trajectories
if smooth_params["sigma"] > 0:
t_smooth = tt.smooth(t, **smooth_params)
else:
t_smooth = t
trajectories = {}
if smooth_params.get("only_past", False):
[
trajectories["_s"],
trajectories["_v"],
trajectories["_a"],
] = tt.velocity_acceleration_backwards(t_smooth)
else:
[
trajectories["_s"],
trajectories["_v"],
trajectories["_a"],
] = tt.velocity_acceleration(t_smooth)
# TODO: Organise the params dictionary more hierarchically
# Maybe in the future add a "how_construct" key being a dictionary
# with the classmethod called, path, interpolate_nans,
# and smooth_params
params = {
"displacement": displacement, # Units: pixels
"length_unit": 1, # Units: pixels
"length_unit_name": "px",
"time_unit": 1, # In frames
"time_unit_name": "frames",
"interpolate_nans": interpolate_nans,
"smooth_params": smooth_params,
"construct_method": "from_positions",
}
return cls(trajectories, params)
def from_positions(cls,
t,
interpolate_nans=True,
smooth_sigma=0,
only_past=True,
unit_length=None,
frame_rate=None,
arena_radius=None):
trajectories = Namespace()
trajectories.raw = t.copy()
if interpolate_nans:
tt.interpolate_nans(t)
radius, center_x, center_y, unit_length = \
tt.center_trajectories_and_normalise(t, unit_length=unit_length,
forced_radius=arena_radius)
if smooth_sigma > 0:
t_smooth = tt.smooth(t, sigma=smooth_sigma, only_past=only_past)
else:
t_smooth = t
if only_past:
[trajectories.s, trajectories.v, trajectories.a] = \
tt.velocity_acceleration_backwards(t_smooth)
else:
[trajectories.s, trajectories.v, trajectories.a] = \
tt.velocity_acceleration(t_smooth)
trajectories.speed = tt.norm(trajectories.v)
trajectories.acceleration = tt.norm(trajectories.a)
trajectories.distance_to_center = tt.norm(trajectories.s)
trajectories.e = tt.normalise(trajectories.v)
trajectories.tg_acceleration = tt.dot(trajectories.a, trajectories.e)
trajectories.curvature = tt.curvature(trajectories.v, trajectories.a)
trajectories.normal_acceleration = \
np.square(trajectories.speed)*trajectories.curvature
traj = cls(trajectories)
traj.params = {
"frame_rate": frame_rate,
"center_x": center_x, # Units: unit_length
"center_y": center_y, # Units: unit length
"radius": radius, # Units: unit length
"unit_length": unit_length
} # Units: pixels
return traj
import os
import matplotlib as mpl
import numpy as np
import trajectorytools as tt
import trajectorytools.animation as ttanimation
from trajectorytools.constants import dir_of_data
if __name__ == "__main__":
test_trajectories_file = os.path.join(dir_of_data, "test_trajectories.npy")
t = np.load(test_trajectories_file)
tt.center_trajectories_and_normalise(t)
tt.interpolate_nans(t)
t = tt.smooth(t, sigma=0.5)
s_, v_, a_ = tt.velocity_acceleration(t)
speed = tt.norm(v_)
colornorm = mpl.colors.Normalize(vmin=speed.min(),
vmax=speed.max(),
clip=True)
mapper = mpl.cm.ScalarMappable(norm=colornorm, cmap=mpl.cm.hot)
color = mapper.to_rgba(speed)
anim1 = ttanimation.scatter_vectors(s_, velocities=v_, k=10)
anim2 = ttanimation.scatter_ellipses_color(s_, v_, color)
anim = anim1 + anim2
anim.prepare()
anim.show()