def test_example_trajectories_were_cleaned_correctly(self):
trajs_raw_not_clean = session.query(models.Trajectory).filter_by(raw=True, clean=False).all()
for traj in trajs_raw_not_clean[:N_EXAMPLE_TRAJS_TO_CLEAN]:
# get cleaning parameters
insect = traj.experiment.insect
cleaning_params_list = session.query(models.TrajectoryCleaningParameter.param,
models.TrajectoryCleaningParameter.value).\
filter_by(insect=insect).all()
cleaning_params = dict(cleaning_params_list)
# clean traj
clean_portions = clean_traj(traj, cleaning_params)
# check to make sure the correct number of clean trajectories were generated with the right ids
# and that they have the right timepoint indicators
for ctr, clean_portion in enumerate(clean_portions):
clean_id = traj.id + '_c{}'.format(ctr)
traj_cleaned = session.query(models.Trajectory).get(clean_id)
self.assertFalse(traj_cleaned is None)
self.assertEqual(traj_cleaned.start_timepoint_id, clean_portion[0])
self.assertEqual(traj_cleaned.end_timepoint_id, clean_portion[1])
# make sure that there is no additional trajectory that was created
self.assertTrue(session.query(models.Trajectory). \
get(traj.id + '_c{}'.format(len(clean_portions))) is None)
def test_example_trajectories_were_cleaned_correctly(self):
trajs_raw_not_clean = session.query(models.Trajectory).filter_by(
raw=True, clean=False).all()
for traj in trajs_raw_not_clean[:N_EXAMPLE_TRAJS_TO_CLEAN]:
# get cleaning parameters
insect = traj.experiment.insect
cleaning_params_list = session.query(models.TrajectoryCleaningParameter.param,
models.TrajectoryCleaningParameter.value).\
filter_by(insect=insect).all()
cleaning_params = dict(cleaning_params_list)
# clean traj
clean_portions = clean_traj(traj, cleaning_params)
# check to make sure the correct number of clean trajectories were generated with the right ids
# and that they have the right timepoint indicators
for ctr, clean_portion in enumerate(clean_portions):
clean_id = traj.id + '_c{}'.format(ctr)
traj_cleaned = session.query(models.Trajectory).get(clean_id)
self.assertFalse(traj_cleaned is None)
self.assertEqual(traj_cleaned.start_timepoint_id,
clean_portion[0])
self.assertEqual(traj_cleaned.end_timepoint_id,
clean_portion[1])
# make sure that there is no additional trajectory that was created
self.assertTrue(session.query(models.Trajectory). \
get(traj.id + '_c{}'.format(len(clean_portions))) is None)
def test_two_long_pauses_in_middle_with_too_short_traj_between_is_cleaned_correctly(self):
speeds = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 30) + 3, # short trajectory
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3])
dists = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 30) + 3, # short trajectory
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3])
start_timepoint_id = 1003
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 2)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], start_timepoint_id + 100 -1)
self.assertEqual(clean_portions[1, 0], start_timepoint_id + 170)
self.assertEqual(clean_portions[1, 1], traj.end_timepoint_id)
def test_traj_with_three_pauses_is_cleaned_correctly(self):
speeds = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3,
np.random.uniform(0, 0.01, 5), # short pause
np.random.uniform(0, 1, 95) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3])
dists = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3,
np.random.uniform(0, 0.01, 5), # short pause
np.random.uniform(0, 1, 95) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3])
start_timepoint_id = 98
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 3)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], start_timepoint_id + 100 - 1)
self.assertEqual(clean_portions[1, 0], start_timepoint_id + 120)
self.assertEqual(clean_portions[1, 1], start_timepoint_id + 300 - 1)
self.assertEqual(clean_portions[2, 0], start_timepoint_id + 320)
self.assertEqual(clean_portions[2, 1], traj.end_timepoint_id)
def test_good_trajectory_but_too_short(self):
speeds = np.random.uniform(0, 1, 10) + 3
dists = np.random.uniform(0, 5, 10) + 9
start_timepoint_id = 4000
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 0)
def test_traj_starting_with_short_pause_is_untouched(self):
speeds = cc([np.random.uniform(0, 0.01, 5), np.random.uniform(0, 1, 500) + 3])
dists = cc([np.random.uniform(0, 0.003, 5), np.random.uniform(0, 1, 500) + 9])
start_timepoint_id = 20010
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 1)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], traj.end_timepoint_id)
def test_good_trajectory_is_left_untouched(self):
speeds = np.random.uniform(0, 1, 500) + 3
dists = np.random.uniform(0, 5, 500) + 9
start_timepoint_id = 1790
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 1)
self.assertEqual(clean_portions[0, 0], traj.start_timepoint_id)
self.assertEqual(clean_portions[0, 1], traj.end_timepoint_id)
def test_traj_ends_with_long_pause_has_pause_removed(self):
speeds = cc([np.random.uniform(0, 1, 500) + 3, np.random.uniform(0, 0.01, 20)])
dists = cc([np.random.uniform(0, 1, 500) + 9, np.random.uniform(0, 0.003, 20)])
start_timepoint_id = 1008
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 1)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], traj.end_timepoint_id - 20)
def test_trajectory_with_speed_pause_but_not_distance_pause_is_left_untouched(self):
speeds = cc([np.random.uniform(0, 1, 500) + 3,
np.random.uniform(0, 0.01, 20),
np.random.uniform(0, 1, 500) + 3])
dists = cc([np.random.uniform(0, 1, 500) + 9,
np.random.uniform(0, 0.003, 20) + 4,
np.random.uniform(0, 1, 500) + 9])
start_timepoint_id = 10883
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 1)
self.assertEqual(clean_portions[0, 0], traj.start_timepoint_id)
self.assertEqual(clean_portions[0, 1], traj.end_timepoint_id)
def test_traj_with_pause_in_middle_has_pause_removed(self):
speeds = cc([np.random.uniform(0, 1, 500) + 3,
np.random.uniform(0, 0.01, 20),
np.random.uniform(0, 1, 500) + 3])
dists = cc([np.random.uniform(0, 1, 500) + 9,
np.random.uniform(0, 0.003, 20),
np.random.uniform(0, 1, 500) + 9])
start_timepoint_id = 10883
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 2)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], start_timepoint_id + 500 - 1)
self.assertEqual(clean_portions[1, 0], start_timepoint_id + 520)
self.assertEqual(clean_portions[1, 1], traj.end_timepoint_id)
def test_traj_with_middle_and_end_pause_is_cleaned_correctly(self):
speeds = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3,
np.random.uniform(0, 0.01, 20)]) # long pause
dists = cc([np.random.uniform(0, 1, 100) + 3,
np.random.uniform(0, 0.01, 20), # long pause
np.random.uniform(0, 1, 80) + 3,
np.random.uniform(0, 0.01, 20)]) # long pause
start_timepoint_id = 9809
traj = Trajectory(start_timepoint_id, speeds, dists)
clean_portions = clean_trajectories.clean_traj(traj, CLEANING_PARAMS)
self.assertEqual(len(clean_portions), 2)
self.assertEqual(clean_portions[0, 0], start_timepoint_id)
self.assertEqual(clean_portions[0, 1], start_timepoint_id + 100 - 1)
self.assertEqual(clean_portions[1, 0], start_timepoint_id + 120)
self.assertEqual(clean_portions[1, 1], traj.end_timepoint_id - 20)
