def test_can_load_min_len(self):
trackfile = self.tempdir / 'test.csv'
chains = tracking.link_all_chains(TRACKS,
merge_fxn='pairwise',
processes=1)
tracking.save_track_csvfile(trackfile, chains)
load_chains = tracking.load_track_csvfile(trackfile, min_len=3)
exp_chains = [
[1.0, 1.1, 1.2, 1.3, 1.4],
[2.0, 2.1, 2.2],
[3.0, 3.1, 3.2, 3.3, 3.4],
[4.0, 4.1, 4.2, 4.3],
[5.2, 5.3, 5.4],
]
self.assertEqual(len(load_chains), len(exp_chains))
for lc, exp_coords in zip(load_chains, exp_chains):
self.assertEqual(lc.line_x, exp_coords)
self.assertEqual(lc.line_y, exp_coords)
load_chains = tracking.load_track_csvfile(trackfile, min_len=4)
exp_chains = [
[1.0, 1.1, 1.2, 1.3, 1.4],
[3.0, 3.1, 3.2, 3.3, 3.4],
[4.0, 4.1, 4.2, 4.3],
]
self.assertEqual(len(load_chains), len(exp_chains))
for lc, exp_coords in zip(load_chains, exp_chains):
self.assertEqual(lc.line_x, exp_coords)
self.assertEqual(lc.line_y, exp_coords)
def test_links_tracks_different_step(self):
chains = tracking.link_all_chains(TRACKS,
link_step=2,
merge_fxn='pairwise',
processes=1)
chains = list(sorted(chains, key=lambda c: c.line_x[0]))
chain_coords = [
[1.0, 1.2, 1.4],
[1.1, 1.3],
[2.0, 2.2, 2.4],
[2.1],
[3.0, 3.2, 3.4],
[3.1, 3.3],
[4.0, 4.2],
[4.1, 4.3],
[5.0, 5.2, 5.4],
[5.3],
]
self.assertEqual(len(chains), len(chain_coords))
for coords, chain in zip(chain_coords, chains):
self.assertEqual(coords, chain.line_x)
self.assertEqual(coords, chain.line_y)
def test_can_track_save_load(self):
trackfile = self.tempdir / 'test.csv'
chains = tracking.link_all_chains(TRACKS,
merge_fxn='pairwise',
processes=1)
tracking.save_track_csvfile(trackfile, chains)
load_chains = tracking.load_track_csvfile(trackfile)
self.assertEqual(len(load_chains), len(chains))
for lc, c in zip(load_chains, chains):
self.assertEqual(lc, c)
def test_links_default_tracks_cluster(self):
chains = tracking.link_all_chains(TRACKS,
merge_fxn='cluster',
max_merge_dist=4.0,
impute_steps=3,
processes=1)
chains = list(sorted(chains, key=lambda c: c.line_x[0]))
chain_coords = [
[1.0],
[1.4],
[2.0],
[2.4],
[3.0, 3.1, 4.2, 3.55, 3.4],
[4.0],
[5.0],
[5.4],
]
self.assertEqual(len(chains), len(chain_coords))
for coords, chain in zip(chain_coords, chains):
fmt = 'Mismatched coordinates\n expected {}\n got {}\n\n'
msg = fmt.format(coords, chain.line_x)
self.assertEqual(len(coords), len(chain.line_x), msg=msg)
self.assertTrue(all([
round(c, 2) == round(x, 2)
for c, x in zip(coords, chain.line_x)
]),
msg=msg)
fmt = 'Mismatched coordinates\n expected {}\n got {}\n\n'
msg = fmt.format(coords, chain.line_y)
self.assertEqual(len(coords), len(chain.line_y), msg=msg)
self.assertTrue(all([
round(c, 2) == round(y, 2)
for c, y in zip(coords, chain.line_y)
]),
msg=msg)
def test_gets_sane_results_for_velocity(self):
chains = tracking.link_all_chains(TRACKS,
merge_fxn='pairwise',
processes=1)
chains = list(sorted(chains, key=lambda c: c.line_x[0]))
chain_vels = [
np.array([0.1, 0.1, 0.1, 0.1]),
np.array([0.1, 0.1]),
np.array([0.0]),
np.array([0.1, 0.1, 0.1, 0.1]),
np.array([0.1, 0.1, 0.1]),
np.array([0.0]),
np.array([0.1, 0.1]),
]
self.assertEqual(len(chains), len(chain_vels))
for vel, chain in zip(chain_vels, chains):
np.testing.assert_almost_equal(vel, chain.vel_x())
np.testing.assert_almost_equal(vel, chain.vel_y())
np.testing.assert_almost_equal(vel * np.sqrt(2), chain.vel_mag())