Comparing

traja allows comparing trajectories using various methods.

import traja

df = traja.generate(seed=0)
df.traja.plot()

<matplotlib.collections.PathCollection object at 0x795026e92ef0>

Fast Dynamic Time Warping of Trajectories

Fast dynamic time warping can be performed using fastdtw. Source article: link.

import numpy as np

rotated = traja.rotate(df, angle=np.pi / 10)
rotated.traja.plot()

<matplotlib.collections.PathCollection object at 0x7950269fdb10>

Compare trajectories hierarchically

Hierarchical agglomerative clustering allows comparing trajectories as actograms and finding nearest neighbors. This is useful for comparing circadian rhythms, for example.

# Generate random trajectories
trjs = [traja.generate(seed=i) for i in range(20)]

# Calculate displacement
displacements = [trj.traja.calc_displacement() for trj in trjs]

traja.plot_clustermap(displacements)

/home/docs/checkouts/readthedocs.org/user_builds/traja/envs/latest/lib/python3.10/site-packages/seaborn/matrix.py:560: UserWarning: Clustering large matrix with scipy. Installing `fastcluster` may give better performance.
  warnings.warn(msg)

<seaborn.matrix.ClusterGrid object at 0x795026e707c0>

Compare trajectories point-wise

dist = traja.distance_between(df.traja.xy, rotated.traja.xy)

print(f"Distance between the two trajectories is {dist}")

Distance between the two trajectories is 27254.161638114736