def main():
for expt in session.query(models.Experiment):
print('In experiment "{}"...'.format(expt.id))
for odor_state in ODOR_STATES:
print('Odor state = "{}"'.format(odor_state))
trajs = session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True)
for variable_name in QUANTITIES:
print('{}...'.format(variable_name))
traj_data = []
traj_ctr = 0
for traj in trajs:
traj_data.extend(
traj.timepoint_field(session, variable_name))
traj_ctr += 1
lb, ub = None, None
if variable_name.endswith('_a') or 'heading' in variable_name:
lb = 0
if 'heading' in variable_name:
ub = 180
cts, bins = make_distribution(np.array(traj_data),
N_BINS,
lb=lb,
ub=ub)
file_name = '{}_{}_{}.pickle'.format(expt.id, odor_state,
variable_name)
tp_dstr = models.TimepointDistribution(
figure_root_path_env_var=figure_data_env_var,
directory_path=DIRECTORY_PATH,
file_name=file_name,
variable=variable_name,
experiment_id=expt.id,
odor_state=odor_state,
n_data_points=len(traj_data),
n_trajectories=traj_ctr,
bin_min=bins[0],
bin_max=bins[-1],
n_bins=N_BINS)
tp_dstr.data = {'cts': cts, 'bins': bins}
session.add(tp_dstr)
commit(session)
def main():
# loop over all experiments
for expt in session.query(models.Experiment):
print("In experiment '{}'".format(expt.id))
dt = 1 / expt.sampling_frequency
for traj in session.query(
models.Trajectory).filter_by(experiment=expt):
positions = traj.positions(session)
velocities = traj.velocities(session)
# calculate kinematic quantities
velocities_a = kinematics.norm(velocities)
accelerations = kinematics.acceleration(velocities, dt)
accelerations_a = kinematics.norm(accelerations)
headings = kinematics.heading(velocities)
angular_velocities = kinematics.angular_velocity(velocities, dt)
angular_velocities_a = kinematics.norm(angular_velocities)
angular_accelerations = kinematics.acceleration(
angular_velocities, dt)
angular_accelerations_a = kinematics.norm(angular_accelerations)
distance_from_wall = kinematics.distance_from_wall(
positions, WALL_BOUNDS)
# store kinematic quantities in timepoints
for ctr, tp in enumerate(traj.timepoints(session)):
tp.velocity_a = velocities_a[ctr]
tp.acceleration_x, tp.acceleration_y, tp.acceleration_z = accelerations[
ctr]
tp.acceleration_a = accelerations_a[ctr]
tp.heading_xy, tp.heading_xz, tp.heading_xyz = headings[ctr]
tp.angular_velocity_x, tp.angular_velocity_y, tp.angular_velocity_z = angular_velocities[
ctr]
tp.angular_velocity_a = angular_velocities_a[ctr]
tp.angular_acceleration_x, tp.angular_acceleration_y, tp.angular_acceleration_z = angular_accelerations[
ctr]
tp.angular_acceleration_a = angular_accelerations_a[ctr]
tp.distance_from_wall = distance_from_wall[ctr]
session.add(tp)
commit(session)
def main():
for expt in session.query(models.Experiment):
threshold = session.query(models.Threshold).filter_by(experiment=expt,
determination=DETERMINATION).first()
for cg in threshold.crossing_groups:
print(cg.id)
for crossing in cg.crossings:
position_x_entry = crossing.timepoint_field(session, 'position_x', 0, 0, 'entry', 'entry')[0]
position_y_entry = crossing.timepoint_field(session, 'position_y', 0, 0, 'entry', 'entry')[0]
position_z_entry = crossing.timepoint_field(session, 'position_z', 0, 0, 'entry', 'entry')[0]
position_x_peak = crossing.timepoint_field(session, 'position_x', 0, 0, 'peak', 'peak')[0]
position_y_peak = crossing.timepoint_field(session, 'position_y', 0, 0, 'peak', 'peak')[0]
position_z_peak = crossing.timepoint_field(session, 'position_z', 0, 0, 'peak', 'peak')[0]
position_x_exit = crossing.timepoint_field(session, 'position_x', 0, 0, 'exit', 'exit')[0]
position_y_exit = crossing.timepoint_field(session, 'position_y', 0, 0, 'exit', 'exit')[0]
position_z_exit = crossing.timepoint_field(session, 'position_z', 0, 0, 'exit', 'exit')[0]
heading_xy_entry = crossing.timepoint_field(session, 'heading_xy', 0, 0, 'entry', 'entry')[0]
heading_xz_entry = crossing.timepoint_field(session, 'heading_xz', 0, 0, 'entry', 'entry')[0]
heading_xyz_entry = crossing.timepoint_field(session, 'heading_xyz', 0, 0, 'entry', 'entry')[0]
heading_xy_peak = crossing.timepoint_field(session, 'heading_xy', 0, 0, 'peak', 'peak')[0]
heading_xz_peak = crossing.timepoint_field(session, 'heading_xz', 0, 0, 'peak', 'peak')[0]
heading_xyz_peak = crossing.timepoint_field(session, 'heading_xyz', 0, 0, 'peak', 'peak')[0]
heading_xy_exit = crossing.timepoint_field(session, 'heading_xy', 0, 0, 'exit', 'exit')[0]
heading_xz_exit = crossing.timepoint_field(session, 'heading_xz', 0, 0, 'exit', 'exit')[0]
heading_xyz_exit = crossing.timepoint_field(session, 'heading_xyz', 0, 0, 'exit', 'exit')[0]
crossing.feature_set_basic = models.CrossingFeatureSetBasic(position_x_entry=position_x_entry,
position_y_entry=position_y_entry,
position_z_entry=position_z_entry,
position_x_peak=position_x_peak,
position_y_peak=position_y_peak,
position_z_peak=position_z_peak,
position_x_exit=position_x_exit,
position_y_exit=position_y_exit,
position_z_exit=position_z_exit,
heading_xy_entry=heading_xy_entry,
heading_xz_entry=heading_xz_entry,
heading_xyz_entry=heading_xyz_entry,
heading_xy_peak=heading_xy_peak,
heading_xz_peak=heading_xz_peak,
heading_xyz_peak=heading_xyz_peak,
heading_xy_exit=heading_xy_exit,
heading_xz_exit=heading_xz_exit,
heading_xyz_exit=heading_xyz_exit)
session.add(crossing)
commit(session)
def crossing_number_distributions(
CROSSING_GROUPS, AX_GRID):
"""
Plot histograms of the number of odor crossings per trajectory.
"""
crossing_numbers_all = {}
for cg_id in CROSSING_GROUPS:
# get crossing group and trajectories
cg = session.query(models.CrossingGroup).get(cg_id)
expt = cg.experiment
trajs = session.query(models.Trajectory).filter_by(
experiment=expt, odor_state='on', clean=True).all()
crossing_numbers = []
for traj in trajs:
crossing_numbers.append(len(
session.query(models.Crossing).filter_by(
crossing_group=cg, trajectory=traj).all()))
crossing_numbers_all[cg_id] = crossing_numbers
# MAKE PLOTS
fig_size = (6 * AX_GRID[1], 3 * AX_GRID[0])
fig, axs = plt.subplots(*AX_GRID,
figsize=fig_size, sharex=True, sharey=True, tight_layout=True)
for ax, cg_id in zip(axs.flatten(), CROSSING_GROUPS):
bins = np.arange(-1, np.max(crossing_numbers_all[cg_id])) + 0.5
ax.hist(crossing_numbers_all[cg_id], bins=bins, lw=0, normed=True)
ax.set_xlabel('number of crossings')
ax.set_ylabel('proportion\nof trajectories')
ax.set_title('{}...'.format(cg_id[:15]))
for ax in axs.flatten():
set_fontsize(ax, 16)
return fig
def main():
# loop over all experiments
for expt in session.query(models.Experiment):
print("In experiment '{}'".format(expt.id))
dt = 1 / expt.sampling_frequency
for traj in session.query(models.Trajectory).filter_by(experiment=expt):
positions = traj.positions(session)
velocities = traj.velocities(session)
# calculate kinematic quantities
velocities_a = kinematics.norm(velocities)
accelerations = kinematics.acceleration(velocities, dt)
accelerations_a = kinematics.norm(accelerations)
headings = kinematics.heading(velocities)
angular_velocities = kinematics.angular_velocity(velocities, dt)
angular_velocities_a = kinematics.norm(angular_velocities)
angular_accelerations = kinematics.acceleration(angular_velocities, dt)
angular_accelerations_a = kinematics.norm(angular_accelerations)
distance_from_wall = kinematics.distance_from_wall(positions, WALL_BOUNDS)
# store kinematic quantities in timepoints
for ctr, tp in enumerate(traj.timepoints(session)):
tp.velocity_a = velocities_a[ctr]
tp.acceleration_x, tp.acceleration_y, tp.acceleration_z = accelerations[ctr]
tp.acceleration_a = accelerations_a[ctr]
tp.heading_xy, tp.heading_xz, tp.heading_xyz = headings[ctr]
tp.angular_velocity_x, tp.angular_velocity_y, tp.angular_velocity_z = angular_velocities[ctr]
tp.angular_velocity_a = angular_velocities_a[ctr]
tp.angular_acceleration_x, tp.angular_acceleration_y, tp.angular_acceleration_z = angular_accelerations[ctr]
tp.angular_acceleration_a = angular_accelerations_a[ctr]
tp.distance_from_wall = distance_from_wall[ctr]
session.add(tp)
commit(session)
def main():
for expt in session.query(models.Experiment):
print('In experiment "{}"...'.format(expt.id))
for odor_state in ODOR_STATES:
print('Odor state = "{}"'.format(odor_state))
trajs = session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True)
for variable_name in QUANTITIES:
print('{}...'.format(variable_name))
traj_data = []
traj_ctr = 0
for traj in trajs:
traj_data.extend(traj.timepoint_field(session, variable_name))
traj_ctr += 1
lb, ub = None, None
if variable_name.endswith('_a') or 'heading' in variable_name:
lb = 0
if 'heading' in variable_name:
ub = 180
cts, bins = make_distribution(np.array(traj_data), N_BINS, lb=lb, ub=ub)
file_name = '{}_{}_{}.pickle'.format(expt.id, odor_state, variable_name)
tp_dstr = models.TimepointDistribution(figure_root_path_env_var=figure_data_env_var,
directory_path=DIRECTORY_PATH,
file_name=file_name,
variable=variable_name,
experiment_id=expt.id,
odor_state=odor_state,
n_data_points=len(traj_data),
n_trajectories=traj_ctr,
bin_min=bins[0],
bin_max=bins[-1],
n_bins=N_BINS)
tp_dstr.data = {'cts': cts, 'bins': bins}
session.add(tp_dstr)
commit(session)
def main():
for expt in session.query(models.Experiment):
print('In experiment "{}"...'.format(expt.id))
for odor_state in ODOR_STATES:
print('Odor state = "{}"'.format(odor_state))
trajs = session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True)
for variable in QUANTITIES:
print('{}...'.format(variable))
tp_data = [
traj.timepoint_field(session, variable) for traj in trajs
]
n_data_points = np.sum([len(d) for d in tp_data])
window_len = N_LAGS / expt.sampling_frequency
acor, p_value, conf_lb, conf_ub = \
time_series.xcov_multi_with_confidence(tp_data, tp_data, 0, N_LAGS, normed=True)
time_vector = np.arange(len(acor)) / expt.sampling_frequency
file_name = '{}_{}_{}.pickle'.format(expt.id, odor_state,
variable)
tp_acor = models.TimepointAutocorrelation(
figure_root_path_env_var=figure_data_env_var,
directory_path=DIRECTORY_PATH,
file_name=file_name,
variable=variable,
experiment_id=expt.id,
odor_state=odor_state,
n_data_points=n_data_points,
n_trajectories=len(tp_data),
window_len=window_len)
tp_acor.data = {
'time_vector': time_vector,
'autocorrelation': acor,
'p_value': p_value,
'confidence_lower': conf_lb,
'confidence_upper': conf_ub
}
session.add(tp_acor)
commit(session)
def main():
for th_ctr in range(2):
for expt in session.query(models.Experiment):
print('Experiment "{}"'.format(expt.id))
threshold_value = THRESHOLD_VALUES[expt.insect][th_ctr]
# make threshold
threshold = models.Threshold(experiment=expt,
determination='arbitrary',
value=threshold_value)
session.add(threshold)
# loop over odor states
for odor_state in ODOR_STATES:
print('Odor "{}"'.format(odor_state))
# make crossing group
cg_id = '{}_{}_th{}'.format(expt.id, odor_state, threshold_value)
cg = models.CrossingGroup(id=cg_id,
experiment=expt,
odor_state=odor_state,
threshold=threshold)
session.add(cg)
# get crossings for each trajectory
for traj in session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True):
segments, peaks = time_series.segment_by_threshold(traj.odors(session),
threshold_value,
traj.timepoint_ids_extended)
# add crossings
for s_ctr, (segment, peak) in enumerate(zip(segments, peaks)):
crossing = models.Crossing(trajectory=traj,
crossing_number=s_ctr + 1,
crossing_group=cg)
crossing.start_timepoint_id = segment[0]
crossing.entry_timepoint_id = segment[1]
crossing.peak_timepoint_id = segment[2]
crossing.exit_timepoint_id = segment[3] - 1
crossing.end_timepoint_id = segment[4] - 1
crossing.max_odor = peak
session.add(crossing)
commit(session)
def trajectory_duration_distributions(
EXPERIMENTS, AX_GRID):
"""
Plot histogram of trajectory lengths.
"""
traj_durations = {}
for expt_id in EXPERIMENTS:
trajs = session.query(models.Trajectory).filter_by(
experiment_id=expt_id, odor_state='on', clean=True).all()
traj_durations[expt_id] = [traj.duration for traj in trajs]
fig_size = (6 * AX_GRID[1], 3 * AX_GRID[0])
fig, axs = plt.subplots(*AX_GRID,
figsize=fig_size, sharex=True, sharey=True, tight_layout=True)
for ax, expt_id in zip(axs.flatten(), EXPERIMENTS):
ax.hist(traj_durations[expt_id], bins=50, lw=0, normed=True)
ax.set_xlabel('duration (s)')
ax.set_ylabel('proportion\nof trajectories')
ax.set_title(expt_id)
for ax in axs.flatten():
set_fontsize(ax, 16)
return fig
def test_segments_correctly_loaded(self):
trial = session.query(models.Trial).get(1)
trial.ignored_segments = []
trial.ignored_segments += [models.IgnoredSegment(start_time=10, end_time=20)]
trial.ignored_segments += [models.IgnoredSegment(start_time=100, end_time=200)]
# make sure segments load correctly with one dt
data, _, _, _ = edr_handling.load_from_trial(trial, dt=.01)
self.assertEqual(len(data), 3)
self.assertAlmostEqual(data[0][0, 0], 0, delta=.00001)
self.assertAlmostEqual(data[0][-1, 0], 9.99, delta=.03)
self.assertAlmostEqual(data[1][0, 0], 20, delta=.03)
self.assertAlmostEqual(data[1][-1, 0], 99.99, delta=.03)
# make sure segments load correctly with another dt
data, _, _, _ = edr_handling.load_from_trial(trial, dt=.005)
self.assertEqual(len(data), 3)
self.assertAlmostEqual(data[0][0, 0], 0, delta=.00001)
self.assertAlmostEqual(data[0][-1, 0], 9.99, delta=.03)
self.assertAlmostEqual(data[1][0, 0], 20, delta=.03)
self.assertAlmostEqual(data[1][-1, 0], 99.99, delta=.03)
session.rollback()
def main():
for expt in session.query(models.Experiment):
if 'mosquito' in expt.id:
baseline = MOSQUITO_BASELINE_ODOR
else:
baseline = 0
trajs = session.query(models.Trajectory).filter_by(experiment=expt, clean=True)
for traj in trajs:
odor = traj.odors(session)
integrated_odor = (odor - baseline).sum() / 100
traj.odor_stats = models.TrajectoryOdorStats(integrated_odor=integrated_odor)
session.add(traj)
commit(session)
def main():
for expt in session.query(models.Experiment):
print('Experiment "{}"'.format(expt.id))
threshold = session.query(models.Threshold).\
filter_by(experiment=expt, determination=DETERMINATION).first()
# loop over odor states
for odor_state in ODOR_STATES:
print('Odor "{}"'.format(odor_state))
# make crossing group
cg_id = '{}_{}_th{}_{}'.format(expt.id, odor_state,
threshold.value, DETERMINATION)
cg = models.CrossingGroup(id=cg_id,
experiment=expt,
odor_state=odor_state,
threshold=threshold)
session.add(cg)
# get crossings for each trajectory
for traj in session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True):
segments, peaks = time_series.segment_by_threshold(
traj.odors(session), threshold.value,
traj.timepoint_ids_extended)
# add crossings
for s_ctr, (segment, peak) in enumerate(zip(segments, peaks)):
crossing = models.Crossing(trajectory=traj,
crossing_number=s_ctr + 1,
crossing_group=cg)
crossing.start_timepoint_id = segment[0]
crossing.entry_timepoint_id = segment[1]
crossing.peak_timepoint_id = segment[2]
crossing.exit_timepoint_id = segment[3] - 1
crossing.end_timepoint_id = segment[4] - 1
crossing.max_odor = peak
session.add(crossing)
commit(session)
def main():
for expt in session.query(models.Experiment):
if 'mosquito' in expt.id:
baseline = MOSQUITO_BASELINE_ODOR
else:
baseline = 0
trajs = session.query(models.Trajectory).filter_by(experiment=expt,
clean=True)
for traj in trajs:
odor = traj.odors(session)
integrated_odor = (odor - baseline).sum() / 100
traj.odor_stats = models.TrajectoryOdorStats(
integrated_odor=integrated_odor)
session.add(traj)
commit(session)
def main():
for expt in session.query(models.Experiment):
print('In experiment "{}"...'.format(expt.id))
for odor_state in ODOR_STATES:
print('Odor state = "{}"'.format(odor_state))
trajs = session.query(models.Trajectory).\
filter_by(experiment=expt, odor_state=odor_state, clean=True)
for variable in QUANTITIES:
print('{}...'.format(variable))
tp_data = [traj.timepoint_field(session, variable) for traj in trajs]
n_data_points = np.sum([len(d) for d in tp_data])
window_len = N_LAGS / expt.sampling_frequency
acor, p_value, conf_lb, conf_ub = \
time_series.xcov_multi_with_confidence(tp_data, tp_data, 0, N_LAGS, normed=True)
time_vector = np.arange(len(acor)) / expt.sampling_frequency
file_name = '{}_{}_{}.pickle'.format(expt.id, odor_state, variable)
tp_acor = models.TimepointAutocorrelation(figure_root_path_env_var=figure_data_env_var,
directory_path=DIRECTORY_PATH,
file_name=file_name,
variable=variable,
experiment_id=expt.id,
odor_state=odor_state,
n_data_points=n_data_points,
n_trajectories=len(tp_data),
window_len=window_len)
tp_acor.data = {'time_vector': time_vector,
'autocorrelation': acor,
'p_value': p_value,
'confidence_lower': conf_lb,
'confidence_upper': conf_ub}
session.add(tp_acor)
commit(session)
def main():
for insect in INSECTS:
cleaning_params_list = session.query(models.TrajectoryCleaningParameter.param,
models.TrajectoryCleaningParameter.value).\
filter_by(insect=insect).all()
cleaning_params = dict(cleaning_params_list)
for expt in session.query(models.Experiment).filter_by(insect=insect):
for traj in expt.trajectories:
clean_portions = clean_traj(traj, cleaning_params)
for ctr, clean_portion in enumerate(clean_portions):
if clean_portion[
0] == traj.start_timepoint_id and clean_portion[
1] == traj.end_timepoint_id:
traj.clean = True
portion_traj = traj
else:
stp_id, etp_id = clean_portion
# make new trajectory
id = traj.id + '_c{}'.format(ctr)
portion_traj = models.Trajectory(
id=id,
start_timepoint_id=stp_id,
end_timepoint_id=etp_id,
experiment=expt,
raw=False,
clean=True,
odor_state=traj.odor_state)
session.add(portion_traj)
portion_traj.basic_info = make_trajectory_basic_info(
portion_traj)
session.add(portion_traj)
commit(session)
def main():
instructions = ('Right click on trial to mark starts and ends of segments.\n'
'Close window to move on to next trial.')
print(instructions)
# get trials
trials = session.query(models.Trial). \
filter(models.Trial.experiment_id == EXPERIMENT_ID). \
filter(models.Trial.recording_start >= EARLIEST_DATETIME)
for trial in trials[:N_TRIALS]:
fig = plt.figure(facecolor='white', figsize=FIG_SIZE)
fig, axs, edr_data = plot_trial_basic(trial, fig, cols=COLS, dt=.02)
# define previously specified ignored segments if there are any
if trial.ignored_segments:
ignored_segments_simple = [(i_s.start_time, i_s.end_time) for i_s in trial.ignored_segments]
else:
ignored_segments_simple = None
t_min = edr_data[0, 0]
t_max = edr_data[-1, 0]
# create segment selector
segment_selector = SegmentSelector(fig, axs, t_min, t_max, segments=ignored_segments_simple)
plt.show(block=True)
# remove all ignored segments that were previously bound to this trial
[session.delete(i_s) for i_s in trial.ignored_segments]
trial.ignored_segments = []
# add all ignored segments that we've created in the segment selector
for segment in segment_selector.segments_simple:
ignored_segment = models.IgnoredSegment()
# convert time to time idx
ignored_segment.start_time = segment[0]
ignored_segment.end_time = segment[1]
trial.ignored_segments += [ignored_segment]
save = raw_input('Save [y or n]?')
if save.lower() == 'y':
# add all updated trials to database
for trial in trials:
session.add(trial)
session.commit()
else:
print('Data not saved.')
session.rollback()
def main(traj_limit=None):
# add script execution to infotaxis database
add_script_execution(script_id=SCRIPT_ID,
notes=SCRIPT_NOTES,
session=session)
session.commit()
for experiment_id in EXPERIMENT_IDS:
print experiment_id
for odor_state in ODOR_STATES:
# make geom_config_group
geom_config_group_id = '{}_{}_odor_{}'.format(
GEOM_CONFIG_GROUP_ID, experiment_id, odor_state)
geom_config_group_desc = GEOM_CONFIG_GROUP_DESC.format(
experiment_id, odor_state)
geom_config_group = models.GeomConfigGroup(
id=geom_config_group_id, description=geom_config_group_desc)
# get all wind tunnel trajectories of interest
trajs = wt_session.query(wt_models.Trajectory).\
filter_by(
experiment_id=experiment_id,
odor_state=odor_state,
clean=True
)
for tctr, traj in enumerate(trajs):
positions = traj.positions(wt_session)
discrete_trajectory = ENV.discretize_position_sequence(
positions)
discrete_duration = len(discrete_trajectory)
avg_dt = .01 * len(positions) / discrete_duration
geom_config = models.GeomConfig(duration=discrete_duration)
geom_config.start_idx = discrete_trajectory[0]
geom_config.geom_config_group = geom_config_group
# add extension containing extra data about this geom_config
ext = models.GeomConfigExtensionRealTrajectory(
real_trajectory_id=traj.id, avg_dt=avg_dt)
geom_config.extension_real_trajectory = ext
if traj_limit and (tctr == traj_limit - 1):
break
session.add(geom_config_group)
session.commit()
def test_segments_correctly_loaded_with_beginning_ignored_segments(self):
trial = session.query(models.Trial).get(1)
trial.ignored_segments = []
trial.ignored_segments += [models.IgnoredSegment(start_time=0, end_time=20)]
trial.ignored_segments += [models.IgnoredSegment(start_time=100, end_time=200)]
data, _, _, _ = edr_handling.load_from_trial(trial, dt=.01)
self.assertEqual(len(data), 2)
session.rollback()
trial = session.query(models.Trial).get(1)
trial.ignored_segments = []
trial.ignored_segments += [models.IgnoredSegment(start_time=0.05, end_time=20)]
trial.ignored_segments += [models.IgnoredSegment(start_time=100, end_time=200)]
data, _, _, _ = edr_handling.load_from_trial(trial, dt=.01)
self.assertEqual(len(data), 2)
session.rollback()
trial = session.query(models.Trial).get(1)
trial.ignored_segments = []
trial.ignored_segments += [models.IgnoredSegment(start_time=0.11, end_time=20)]
trial.ignored_segments += [models.IgnoredSegment(start_time=100, end_time=200)]
data, _, _, _ = edr_handling.load_from_trial(trial, dt=.01)
self.assertEqual(len(data), 3)
session.rollback()
def main(traj_limit=None):
# add script execution to infotaxis database
add_script_execution(script_id=SCRIPT_ID, notes=SCRIPT_NOTES, session=session)
session.commit()
for experiment_id in EXPERIMENT_IDS:
print experiment_id
for odor_state in ODOR_STATES:
# make geom_config_group
geom_config_group_id = '{}_{}_odor_{}'.format(GEOM_CONFIG_GROUP_ID, experiment_id, odor_state)
geom_config_group_desc = GEOM_CONFIG_GROUP_DESC.format(experiment_id, odor_state)
geom_config_group = models.GeomConfigGroup(id=geom_config_group_id,
description=geom_config_group_desc)
# get all wind tunnel trajectories of interest
trajs = wt_session.query(wt_models.Trajectory).\
filter_by(
experiment_id=experiment_id,
odor_state=odor_state,
clean=True
)
for tctr, traj in enumerate(trajs):
positions = traj.positions(wt_session)
discrete_trajectory = ENV.discretize_position_sequence(positions)
discrete_duration = len(discrete_trajectory)
avg_dt = .01 * len(positions) / discrete_duration
geom_config = models.GeomConfig(duration=discrete_duration)
geom_config.start_idx = discrete_trajectory[0]
geom_config.geom_config_group = geom_config_group
# add extension containing extra data about this geom_config
ext = models.GeomConfigExtensionRealTrajectory(real_trajectory_id=traj.id,
avg_dt=avg_dt)
geom_config.extension_real_trajectory = ext
if traj_limit and (tctr == traj_limit - 1):
break
session.add(geom_config_group)
session.commit()
def main():
# get or create experiment
experiment = get_or_create(session, models.Experiment,
id=EXPERIMENT_ID,
directory_path=EXPERIMENT_DIRECTORY_PATH)
full_directory_path = os.path.join(ARENA_DATA_DIRECTORY, EXPERIMENT_DIRECTORY_PATH)
edr_files = [file_name for file_name in os.listdir(full_directory_path)
if file_name.lower().endswith('.edr')]
# get all trials and add them to database
for file_name in edr_files:
print('Attempting to load file "{}"'.format(file_name))
# skip if file already added
if session.query(models.Trial).filter_by(file_name=file_name).first():
print('Skipping file "{}" because it is already in the database.'.format(file_name))
continue
try:
file_path = os.path.join(full_directory_path, file_name)
_, recording_start, _, header = edr_handling.load_edr(file_path)
recording_duration = header['recording_duration']
# get insect number from file name using regex
insect_number = re.findall(INSECT_NUMBER_EXPRESSION, file_name)[0]
insect_id = '{}_{}'.format(recording_start.strftime('%Y%m%d'), insect_number)
# get/create insect
insect = get_or_create(session, models.Insect, id=insect_id)
trial = models.Trial(file_name=file_name,
recording_start=recording_start,
recording_duration=recording_duration)
trial.insect = insect
trial.experiment = experiment
session.add(trial)
except Exception, e:
print('Error: "{}"'.format(e))
def show_distributions(EXPERIMENTS, VARIABLES, ODOR_STATES, AX_GRID):
AX_SIZE = (6, 4)
LW = 2
COLORS = ('b', 'g', 'r')
fig_size = (AX_SIZE[0] * AX_GRID[1], AX_SIZE[1] * AX_GRID[0])
fig, axs = plt.subplots(*AX_GRID, figsize=fig_size, tight_layout=True)
for ax, (expt_id, variable) in zip(axs.flatten(),
cproduct(EXPERIMENTS, VARIABLES)):
handles = []
for odor_state, color in zip(ODOR_STATES, COLORS):
tp_dstr = session.query(models.TimepointDistribution).filter_by(
variable=variable,
experiment_id=expt_id,
odor_state=odor_state).first()
handles.append(
ax.plot(tp_dstr.bincs,
tp_dstr.cts,
lw=LW,
color=color,
label=odor_state)[0])
ax.set_xlabel(variable)
ax.set_ylabel('counts')
ax.legend(handles=handles)
ax.set_title('{}\n{}'.format(expt_id, variable))
for ax in axs.flatten():
set_font_size(ax, 16)
return fig
def get_trajs_with_integrated_odor_above_threshold(experiment_id, odor_state, integrated_odor_threshold, max_trajs=np.inf):
"""
Return all trajectories from a given experiment/odor state that have a certain minimum odor.
:param experiment_id: experiment id
:param odor_state: odor state
:param integrated_odor_threshold: threshold
:return: list of trajectories
"""
trajs_all = session.query(models.Trajectory).filter(
models.Trajectory.experiment_id == experiment_id,
models.Trajectory.odor_state == odor_state,
models.Trajectory.clean,
)
trajs = []
for traj in trajs_all:
if traj.odor_stats.integrated_odor > integrated_odor_threshold:
trajs.append(traj)
if len(trajs) >= max_trajs:
break
return trajs
def show_distributions(EXPERIMENTS, VARIABLES, ODOR_STATES, AX_GRID):
AX_SIZE = (6, 4)
LW = 2
COLORS = ('b', 'g', 'r')
fig_size = (AX_SIZE[0] * AX_GRID[1], AX_SIZE[1] * AX_GRID[0])
fig, axs = plt.subplots(*AX_GRID,
figsize=fig_size,
tight_layout=True)
for ax, (expt_id, variable) in zip(axs.flatten(), cproduct(EXPERIMENTS, VARIABLES)):
handles = []
for odor_state, color in zip(ODOR_STATES, COLORS):
tp_dstr = session.query(models.TimepointDistribution).filter_by(
variable=variable, experiment_id=expt_id,
odor_state=odor_state).first()
handles.append(ax.plot(
tp_dstr.bincs, tp_dstr.cts, lw=LW, color=color, label=odor_state)[0])
ax.set_xlabel(variable)
ax.set_ylabel('counts')
ax.legend(handles=handles)
ax.set_title('{}\n{}'.format(expt_id, variable))
for ax in axs.flatten():
set_font_size(ax, 16)
return fig
import matplotlib.cm as cm
from db_api import models
from db_api.connect import session
ODOR_STATES = ('on', 'none', 'afterodor')
THRESHOLDS = {'fruit_fly': (0.01, 0.1), 'mosquito': (401, 410)}
DTH = 0.0001
TIMEPOINTS_BEFORE_ENTRY = 50
TIMEPOINTS_AFTER_EXIT = 50
FACE_COLOR = 'white'
FIG_SIZE = (8, 10)
LW = 2
plt.ion()
expts = session.query(models.Experiment).all()
keep_going = True
e_ctr = 0
o_ctr = 0
th_ctr = 0
fig, axs = plt.subplots(3,
1,
facecolor=FACE_COLOR,
figsize=FIG_SIZE,
tight_layout=True)
axs[2].twin = axs[2].twinx()
while keep_going:
# get new crossing group
def main():
for expt in session.query(models.Experiment):
threshold = session.query(models.Threshold).filter_by(
experiment=expt, determination=DETERMINATION).first()
for cg in threshold.crossing_groups:
print(cg.id)
for crossing in cg.crossings:
position_x_entry = crossing.timepoint_field(
session, 'position_x', 0, 0, 'entry', 'entry')[0]
position_y_entry = crossing.timepoint_field(
session, 'position_y', 0, 0, 'entry', 'entry')[0]
position_z_entry = crossing.timepoint_field(
session, 'position_z', 0, 0, 'entry', 'entry')[0]
position_x_peak = crossing.timepoint_field(
session, 'position_x', 0, 0, 'peak', 'peak')[0]
position_y_peak = crossing.timepoint_field(
session, 'position_y', 0, 0, 'peak', 'peak')[0]
position_z_peak = crossing.timepoint_field(
session, 'position_z', 0, 0, 'peak', 'peak')[0]
position_x_exit = crossing.timepoint_field(
session, 'position_x', 0, 0, 'exit', 'exit')[0]
position_y_exit = crossing.timepoint_field(
session, 'position_y', 0, 0, 'exit', 'exit')[0]
position_z_exit = crossing.timepoint_field(
session, 'position_z', 0, 0, 'exit', 'exit')[0]
heading_xy_entry = crossing.timepoint_field(
session, 'heading_xy', 0, 0, 'entry', 'entry')[0]
heading_xz_entry = crossing.timepoint_field(
session, 'heading_xz', 0, 0, 'entry', 'entry')[0]
heading_xyz_entry = crossing.timepoint_field(
session, 'heading_xyz', 0, 0, 'entry', 'entry')[0]
heading_xy_peak = crossing.timepoint_field(
session, 'heading_xy', 0, 0, 'peak', 'peak')[0]
heading_xz_peak = crossing.timepoint_field(
session, 'heading_xz', 0, 0, 'peak', 'peak')[0]
heading_xyz_peak = crossing.timepoint_field(
session, 'heading_xyz', 0, 0, 'peak', 'peak')[0]
heading_xy_exit = crossing.timepoint_field(
session, 'heading_xy', 0, 0, 'exit', 'exit')[0]
heading_xz_exit = crossing.timepoint_field(
session, 'heading_xz', 0, 0, 'exit', 'exit')[0]
heading_xyz_exit = crossing.timepoint_field(
session, 'heading_xyz', 0, 0, 'exit', 'exit')[0]
crossing.feature_set_basic = models.CrossingFeatureSetBasic(
position_x_entry=position_x_entry,
position_y_entry=position_y_entry,
position_z_entry=position_z_entry,
position_x_peak=position_x_peak,
position_y_peak=position_y_peak,
position_z_peak=position_z_peak,
position_x_exit=position_x_exit,
position_y_exit=position_y_exit,
position_z_exit=position_z_exit,
heading_xy_entry=heading_xy_entry,
heading_xz_entry=heading_xz_entry,
heading_xyz_entry=heading_xyz_entry,
heading_xy_peak=heading_xy_peak,
heading_xz_peak=heading_xz_peak,
heading_xyz_peak=heading_xyz_peak,
heading_xy_exit=heading_xy_exit,
heading_xz_exit=heading_xz_exit,
heading_xyz_exit=heading_xyz_exit)
session.add(crossing)
commit(session)
THRESHOLD_ID = 4 # look up in threshold table
DISCRIMINATION_THRESHOLD = 450
DISPLAY_START = -50
DISPLAY_END = 150
INTEGRAL_START = 0 # timepoints (fs 100 Hz) relative to peak
INTEGRAL_END = 100
VARIABLE = 'heading_xyz'
FACE_COLOR = 'white'
FIG_SIZE = (10, 10)
LW = 2
COLORS = ['k', 'r'] # [below, above] discrimination threshold
# get threshold and crossing group for odor on trajectories
threshold = session.query(models.Threshold).get(THRESHOLD_ID)
cg = session.query(models.CrossingGroup).\
filter_by(threshold=threshold, odor_state='on').first()
all_crossings = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).all()
# get all crossings where max odor is below/above discrimination threshold
crossings_below = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor < DISCRIMINATION_THRESHOLD).all()
crossings_above = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor >= DISCRIMINATION_THRESHOLD).all()
# make array for storing crossing-specific time-series
figsize=FIG_SIZE_POS,
facecolor=FACE_COLOR,
sharex=True,
sharey=True,
tight_layout=True)
fig_pos, axs_pos = plt.subplots(4,
1,
figsize=FIG_SIZE_POS,
facecolor=FACE_COLOR,
sharex=True,
tight_layout=True)
wind_speed_handles = []
wind_speed_labels = []
for expt_ctr, expt in enumerate(session.query(models.Experiment)):
print(expt.id)
if 'fruitfly' in expt.id:
wind_speed_labels.append('f {} m/s'.format(expt.wind_speed))
elif 'mosquito' in expt.id:
wind_speed_labels.append('m {} m/s'.format(expt.wind_speed))
subset_handles = []
subset_labels = []
subset_handles_pos = []
subset_labels_pos = []
X_LIM = 0, 30
Y_LIM = 40, 130
fig, axs = plt.subplots(2,
3,
facecolor='white',
figsize=FIG_SIZE,
tight_layout=True)
for s_ctr, sg_id_template in enumerate(
(SEGMENT_GROUP_ID_EMPIRICAL, SEGMENT_GROUP_ID_INFOTAXIS)):
for e_ctr, expt in enumerate(EXPERIMENTS):
for o_ctr, odor_state in enumerate(ODOR_STATES):
sg_id = sg_id_template.format(expt, odor_state)
seg_group = session.query(models.SegmentGroup).get(sg_id)
heading_ensemble = None
for ens in seg_group.analysis_triggered_ensembles:
# only get the heading ensemble if it has no conditions
if ens.variable == 'heading' and ens.trigger_start == 'exit':
heading_ensemble = ens
break
heading_ensemble.fetch_data(session)
if heading_ensemble._data is None:
continue
time_vector = np.arange(len(heading_ensemble.mean))
ax = axs[s_ctr, o_ctr]
def optimize_model_params(
SEED,
DURATION, DT, BOUNDS,
EXPERIMENT, ODOR_STATE,
MAX_TRAJS_EMPIRICAL,
N_TIME_POINTS_EMPIRICAL,
SAVE_FILE_PREFIX,
INITIAL_PARAMS, MAX_ITERS):
"""
Find optimal model parameters by fitting speed and angular velocity distributions of empirical
data.
"""
# check to see if empirical time points have already been saved
file_name = '{}_{}_odor_{}.npy'.format(SAVE_FILE_PREFIX, EXPERIMENT, ODOR_STATE)
if os.path.isfile(file_name):
empirical = np.load(file_name)[0]
else:
print('extracting time points from data')
# get all trajectories
trajs = session.query(models.Trajectory).filter_by(
experiment_id=EXPERIMENT, odor_state=ODOR_STATE, clean=True).\
limit(MAX_TRAJS_EMPIRICAL).all()
# get all speeds and angular velocities
cc = np.concatenate
speeds_empirical = cc([traj.velocities_a(session) for traj in trajs])
ws_empirical = cc([traj.angular_velocities_a(session) for traj in trajs])
ys_empirical = cc([traj.timepoint_field(session, 'position_y') for traj in trajs])
# sample a set of speeds and ws
np.random.seed(SEED)
speeds_empirical = np.random.choice(speeds_empirical, N_TIME_POINTS_EMPIRICAL, replace=False)
ws_empirical = np.random.choice(ws_empirical, N_TIME_POINTS_EMPIRICAL, replace=False)
ys_empirical = np.random.choice(ys_empirical, N_TIME_POINTS_EMPIRICAL, replace=False)
empirical = {'speeds': speeds_empirical, 'ws': ws_empirical, 'ys': ys_empirical}
# save them for easy access next time
np.save(file_name, np.array([empirical]))
print('performing optimization')
# make a plume
pl = GaussianLaminarPlume(0, np.zeros((2,)), np.ones((2,)))
# define function to be optimized
def optim_fun(p):
np.random.seed(SEED)
start_pos = np.array([
np.random.uniform(*BOUNDS[0]),
np.random.uniform(*BOUNDS[1]),
np.random.uniform(*BOUNDS[2]),
])
# make agent and trajectory
ag = CenterlineInferringAgent(
tau=p[0], noise=p[1], bias=p[2], threshold=np.inf,
hit_trigger='peak', hit_influence=0,
k_0=np.eye(2), k_s=np.eye(2), tau_memory=1, bounds=BOUNDS)
traj = ag.track(pl, start_pos, DURATION, DT)
speeds = np.linalg.norm(traj['vs'], axis=1)
ws = np.linalg.norm(angular_velocity(traj['vs'], DT), axis=1)
ws = ws[~np.isnan(ws)]
ys = traj['xs'][:, 1]
ks_speeds = stats.ks_2samp(speeds, empirical['speeds'])[0]
ks_ws = stats.ks_2samp(ws, empirical['ws'])[0]
ks_ys = stats.ks_2samp(ys, empirical['ys'])[0]
val = ks_speeds + ks_ws + ks_ys
# punish unallowable values
if np.any(p < 0):
val += 10000
return val
# optimize it
p_best = optimize.fmin(optim_fun, np.array(INITIAL_PARAMS), maxiter=MAX_ITERS)
# generate one final trajectory
np.random.seed(SEED)
start_pos = np.array([
np.random.uniform(*BOUNDS[0]),
np.random.uniform(*BOUNDS[1]),
np.random.uniform(*BOUNDS[2]),
])
ag = CenterlineInferringAgent(
tau=p_best[0], noise=p_best[1], bias=p_best[2], threshold=np.inf,
hit_trigger='peak', hit_influence=0,
k_0=np.eye(2), k_s=np.eye(2), tau_memory=1, bounds=BOUNDS)
traj = ag.track(pl, start_pos, DURATION, DT)
speeds = np.linalg.norm(traj['vs'], axis=1)
ws = np.linalg.norm(angular_velocity(traj['vs'], DT), axis=1)
ws = ws[~np.isnan(ws)]
ys = traj['xs'][:, 1]
# make plots of things that have been optimized
## get bins
speed_max = max(speeds.max(), empirical['speeds'].max())
bins_speed = np.linspace(0, speed_max, 41, endpoint=True)
bincs_speed = 0.5 * (bins_speed[:-1] + bins_speed[1:])
w_max = max(ws.max(), empirical['ws'].max())
bins_w = np.linspace(0, w_max, 41, endpoint=True)
bincs_w = 0.5 * (bins_w[:-1] + bins_w[1:])
bins_y = np.linspace(BOUNDS[1][0], BOUNDS[1][1], 41, endpoint=True)
bincs_y = 0.5 * (bins_y[:-1] + bins_y[1:])
cts_speed, _ = np.histogram(speeds, bins=bins_speed, normed=True)
cts_speed_empirical, _ = np.histogram(empirical['speeds'], bins=bins_speed, normed=True)
cts_w, _ = np.histogram(ws, bins=bins_w, normed=True)
cts_w_empirical, _ = np.histogram(empirical['ws'], bins=bins_w, normed=True)
cts_y, _ = np.histogram(ys, bins=bins_y, normed=True)
cts_y_empirical, _ = np.histogram(empirical['ys'], bins=bins_y, normed=True)
fig = plt.figure(figsize=(15, 8), tight_layout=True)
axs = []
axs.append(fig.add_subplot(2, 3, 1))
axs.append(fig.add_subplot(2, 3, 2))
axs.append(fig.add_subplot(2, 3, 3))
axs[0].plot(bincs_speed, cts_speed_empirical, lw=2, color='k')
axs[0].plot(bincs_speed, cts_speed, lw=2, color='r')
axs[0].set_xlabel('speed (m/s)')
axs[0].set_ylabel('rel. counts')
axs[0].legend(['data', 'model'], fontsize=16)
axs[1].plot(bincs_w, cts_w_empirical, lw=2, color='k')
axs[1].plot(bincs_w, cts_w, lw=2, color='r')
axs[1].set_xlabel('ang. vel. (rad/s)')
axs[2].plot(bincs_y, cts_y_empirical, lw=2, color='k')
axs[2].plot(bincs_y, cts_y, lw=2, color='r')
axs[2].set_xlabel('y (m)')
axs.append(fig.add_subplot(2, 1, 2))
axs[3].plot(traj['xs'][:500, 0], traj['xs'][:500, 1], lw=2, color='k', zorder=0)
axs[3].scatter(traj['xs'][0, 0], traj['xs'][0, 1], lw=0, c='r', zorder=1, s=100)
axs[3].set_xlim(*BOUNDS[0])
axs[3].set_ylim(*BOUNDS[1])
axs[3].set_xlabel('x (m)')
axs[3].set_ylabel('y (m)')
axs[3].set_title('example trajectory')
for ax in axs:
set_font_size(ax, 16)
# print out parameters
print('best params:')
print('tau = {}'.format(p_best[0]))
print('noise = {}'.format(p_best[1]))
print('bias = {}'.format(p_best[2]))
return fig
Y_LIM = 40, 150
figs = []
axss = []
for _ in range(3):
fig, axs = plt.subplots(2, 3, facecolor=FACE_COLOR, figsize=FIG_SIZE, tight_layout=True)
figs += [fig]
axss += [axs]
for s_ctr, sg_id_template in enumerate((SEGMENT_GROUP_ID_EMPIRICAL, SEGMENT_GROUP_ID_INFOTAXIS)):
for e_ctr, expt in enumerate(EXPERIMENTS):
for o_ctr, odor_state in enumerate(ODOR_STATES):
for c in ('early', 'late'):
sg_id = sg_id_template.format(expt, odor_state)
seg_group = session.query(models.SegmentGroup).get(sg_id)
heading_ensemble = None
for ens in seg_group.analysis_triggered_ensembles:
# only get the heading ensemble if it has correct conditions
conditions = (ens.variable == 'heading',
ens.trigger_start == 'exit',
59 < ens.heading_min < 61,
119 < ens.heading_max < 121,
ens.x_idx_max == 50,
ens.x_idx_min == 15)
if c == 'early':
conditions += (ens.encounter_number_min == 1,
ens.encounter_number_max == 2,)
elif c == 'late':
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from db_api import models
from db_api.connect import session
ODOR_STATES = ('on', 'none', 'afterodor')
TIMEPOINTS_BEFORE_ENTRY = 50
TIMEPOINTS_AFTER_EXIT = 50
FACE_COLOR = 'white'
FIG_SIZE = (8, 10)
LW = 2
plt.ion()
expts = session.query(models.Experiment).all()
keep_going = True
e_ctr = 0
o_ctr = 0
fig, axs = plt.subplots(3, 1, facecolor=FACE_COLOR, figsize=FIG_SIZE, tight_layout=True)
axs[2].twin = axs[2].twinx()
while keep_going:
# get new crossing group
expt = expts[e_ctr]
odor_state = ODOR_STATES[o_ctr]
threshold = session.query(models.Threshold).\
filter_by(experiment=expt, determination='chosen')
def main():
n_timesteps = TIME_AVG_END - TIME_AVG_START
for expt in session.query(models.Experiment):
for cg in session.query(models.CrossingGroup).\
filter(models.CrossingGroup.experiment == expt).\
filter(models.CrossingGroup.odor_state == 'on').\
filter(models.Threshold.determination == 'arbitrary'):
print('Crossings group: "{}"'.format(cg.id))
for th_val in DISCRIMINATION_THRESHOLD_VALUES[expt.insect]:
crossings_below = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor < th_val).all()
crossings_above = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor >= th_val).all()
responses_below = np.nan * np.ones((len(crossings_below), n_timesteps), dtype=float)
responses_above = np.nan * np.ones((len(crossings_above), n_timesteps), dtype=float)
# fill in values
for crossing, response in zip(crossings_below, responses_below):
response_var = crossing.timepoint_field(session, RESPONSE_VAR,
first=TIME_AVG_START,
last=TIME_AVG_END - 1,
first_rel_to=TIME_AVG_REL_TO,
last_rel_to=TIME_AVG_REL_TO)
response[:len(response_var)] = response_var
for crossing, response in zip(crossings_above, responses_above):
response_var = crossing.timepoint_field(session, RESPONSE_VAR,
first=TIME_AVG_START,
last=TIME_AVG_END - 1,
first_rel_to=TIME_AVG_REL_TO,
last_rel_to=TIME_AVG_REL_TO)
response[:len(response_var)] = response_var
diff, lb, ub = get_time_avg_response_diff_and_bounds(responses_below,
responses_above)
if len(crossings_below) == 0 or len(crossings_above) == 0:
diff = None
lb = None
ub = None
disc_th = models.DiscriminationThreshold(crossing_group=cg,
odor_threshold=th_val,
n_crossings_below=len(crossings_below),
n_crossings_above=len(crossings_above),
time_avg_start=TIME_AVG_START,
time_avg_end=TIME_AVG_END,
time_avg_rel_to=TIME_AVG_REL_TO,
variable=RESPONSE_VAR,
time_avg_difference=diff,
lower_bound=lb,
upper_bound=ub)
session.add(disc_th)
commit(session)
}
fig, axs_unflat = plt.subplots(3,
2,
facecolor=FACE_COLOR,
figsize=FIG_SIZE,
sharex=True,
tight_layout=True)
axs = axs_unflat.flatten()
axs_twin = [ax.twinx() for ax in axs[2:]]
wind_speed_handles = []
wind_speed_labels = []
for expt in session.query(models.Experiment):
if 'fly' in expt.id:
wind_speed_label = 'fly {} m/s'.format(expt.wind_speed)
elif 'mosquito' in expt.id:
wind_speed_label = 'mosquito {} m/s'.format(expt.wind_speed)
print(expt.id)
# get threshold and crossing group for this experiment
threshold = session.query(models.Threshold).filter_by(
experiment=expt, determination=DETERMINATION).first()
THRESHOLD_ID = 4 # look up in threshold table
DISCRIMINATION_THRESHOLD = 450
DISPLAY_START = -50
DISPLAY_END = 150
INTEGRAL_START = 0 # timepoints (fs 100 Hz) relative to peak
INTEGRAL_END = 100
VARIABLE = 'heading_xyz'
FACE_COLOR = 'white'
FIG_SIZE = (10, 10)
LW = 2
COLORS = ['k', 'r'] # [below, above] discrimination threshold
# get threshold and crossing group for odor on trajectories
threshold = session.query(models.Threshold).get(THRESHOLD_ID)
cg = session.query(models.CrossingGroup).\
filter_by(threshold=threshold, odor_state='on').first()
all_crossings = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).all()
# get all crossings where max odor is below/above discrimination threshold
crossings_below = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor < DISCRIMINATION_THRESHOLD).all()
crossings_above = session.query(models.Crossing).\
filter(models.Crossing.crossing_group == cg).\
filter(models.Crossing.max_odor >= DISCRIMINATION_THRESHOLD).all()
# make array for storing crossing-specific time-series
def response_discrimination_via_thresholds(
RESPONSE_VAR,
CROSSING_GROUP_IDS,
CROSSING_GROUP_LABELS,
CROSSING_GROUP_X_LIMS,
AX_SIZE, FONT_SIZE):
"""
Plot the difference between the mean time-averaged headings for plume-crossings
above and below an odor concentration threshold as a function of that threshold.
"""
concentration_factor = 0.0476 / 526
fig, axs = plt.subplots(
2, 2, facecolor='white',
figsize=(7.5, 5), tight_layout=True)
axs = axs.flatten()
for cg_id, ax in zip(CROSSING_GROUP_IDS, axs):
cg = session.query(models.CrossingGroup).filter_by(id=cg_id).first()
disc_ths = session.query(models.DiscriminationThreshold).\
filter_by(crossing_group=cg, variable=RESPONSE_VAR)
ths = np.array([disc_th.odor_threshold for disc_th in disc_ths])
if 'fly' in cg_id:
ths *= concentration_factor
means = np.array([disc_th.time_avg_difference for disc_th in disc_ths], dtype=float)
lbs = np.array([disc_th.lower_bound for disc_th in disc_ths], dtype=float)
ubs = np.array([disc_th.upper_bound for disc_th in disc_ths], dtype=float)
ax.plot(ths, means, color='k', lw=3)
ax.fill_between(ths, lbs, ubs, color='k', alpha=.3)
ax.set_xlim(CROSSING_GROUP_X_LIMS[cg.id])
if 'fly' in cg_id:
ax.set_xlabel('threshold (% ethanol)')
else:
ax.set_xlabel('threshold (ppm CO2)')
for xtl in ax.get_xticklabels():
xtl.set_rotation(60)
ax.set_ylabel('mean heading diff.\nbetween groups')
ax.set_title(CROSSING_GROUP_LABELS[cg.id])
for ax in axs:
set_fontsize(ax, FONT_SIZE)
return fig
above_z, below_z])
return np.min(dist_all_walls, axis=0)
plt.ion()
fig, axs = plt.subplots(4, 1, facecolor=FACE_COLOR, figsize=FIG_SIZE, tight_layout=True)
axs[3].twin = axs[3].twinx()
# loop through odor states
for odor_state in ODOR_STATES:
print('Current odor state: {}'.format(odor_state))
sample_group = '_'.join([EXPERIMENT_ID, 'odor', odor_state])
trajs = session.query(models.Trajectory).filter_by(experiment_id=EXPERIMENT_ID,
odor_state=odor_state,
raw=True).all()
# loop through trajectories
t_ctr = 0
n_trajs = len(trajs)
if trajs:
keep_going = True
else:
keep_going = False
while keep_going:
t_ctr %= n_trajs
row_labels = ('0.3 m/s', '0.4 m/s', '0.6 m/s')
col_labels = ('on', 'none', 'afterodor')
for sim_id_template in (SIMULATION_ID_EMPIRICAL, SIMULATION_ID_INFOTAXIS):
fig, axs = plt.subplots(3,
3,
facecolor='white',
figsize=FIG_SIZE,
tight_layout=True)
for e_ctr, expt in enumerate(EXPERIMENTS):
for o_ctr, odor_state in enumerate(ODOR_STATES):
sim_id = sim_id_template.format(expt, odor_state)
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_displacement_total_histogram.fetch_data(session)
if PROJECTION == 'xy':
heatmap = sim.analysis_displacement_total_histogram.xy
extent = sim.analysis_displacement_total_histogram.extent_xy
xlabel = 'x'
ylabel = 'y'
elif PROJECTION == 'xz':
heatmap = sim.analysis_displacement_total_histogram.xz
extent = sim.analysis_displacement_total_histogram.extent_xz
xlabel = 'x'
ylabel = 'z'
elif PROJECTION == 'yz':
heatmap = sim.analysis_displacement_total_histogram.yz
def main(n_trials, n_train_max, n_test_max, root_dir_env_var):
# make basis functions
basis_ins, basis_outs, max_filter_length = igfh.make_exponential_basis_functions(
INPUT_TAUS, OUTPUT_TAUS, DOMAIN_FACTOR
)
for expt_id in EXPERIMENT_IDS:
for odor_state in ODOR_STATES:
trajs = igfh.get_trajs_with_integrated_odor_above_threshold(
expt_id, odor_state, INTEGRATED_ODOR_THRESHOLD
)
train_test_ratio = (n_train_max / (n_train_max + n_test_max))
test_train_ratio = (n_test_max / (n_train_max + n_test_max))
n_train = min(n_train_max, np.floor(len(trajs) * train_test_ratio))
n_test = min(n_test_max, np.floor(len(trajs) * test_train_ratio))
trajs_trains = []
trajs_tests = []
glmss = []
residualss = []
for trial_ctr in range(n_trials):
print('{}: odor {} (trial number: {})'.format(expt_id, odor_state, trial_ctr))
# get random set of training and test trajectories
perm = np.random.permutation(len(trajs))
train_idxs = perm[:n_train]
test_idxs = perm[-n_test:]
trajs_train = list(np.array(trajs)[train_idxs])
trajs_test = list(np.array(trajs)[test_idxs])
# do some more stuff
glms = []
residuals = []
for input_set, output, basis_in, basis_out in zip(INPUT_SETS, OUTPUTS, basis_ins, basis_outs):
# get relevant time-series data from each trajectory set
data_train = igfh.time_series_from_trajs(
trajs_train,
inputs=input_set,
output=output
)
data_test = igfh.time_series_from_trajs(
trajs_test,
inputs=input_set,
output=output
)
glm = fitting.GLMFitter(link=LINK, family=FAMILY)
glm.set_params(DELAY, basis_in=basis_in, basis_out=False)
glm.input_set = input_set
glm.output = output
# fit to training data
glm.fit(data=data_train, start=START_TIMEPOINT)
# predict test data
prediction = glm.predict(data=data_test, start=START_TIMEPOINT)
_, ground_truth = glm.make_feature_matrix_and_response_vector(data_test, START_TIMEPOINT)
# calculate residual
residual = np.sqrt(((prediction - ground_truth)**2).mean())
# clear out feature matrix and response from glm for efficient storage
glm.feature_matrix = None
glm.response_vector = None
glm.results.remove_data()
# store things
glms.append(glm)
residuals.append(residual)
trajs_train_ids = [traj.id for traj in trajs_train]
trajs_test_ids = [traj.id for traj in trajs_test]
trajs_trains.append(trajs_train_ids)
trajs_tests.append(trajs_test_ids)
glmss.append(glms)
residualss.append(residuals)
# save a glm fit set
glm_fit_set = models.GlmFitSet()
# add data to it
glm_fit_set.root_dir_env_var = root_dir_env_var
glm_fit_set.path_relative = 'glm_fit'
glm_fit_set.file_name = '{}_{}_odor_{}.pickle'.format(FIT_NAME, expt_id, odor_state)
glm_fit_set.experiment = session.query(models.Experiment).get(expt_id)
glm_fit_set.odor_state = odor_state
glm_fit_set.name = FIT_NAME
glm_fit_set.link = LINK
glm_fit_set.family = FAMILY
glm_fit_set.integrated_odor_threshold = INTEGRATED_ODOR_THRESHOLD
glm_fit_set.predicted = PREDICTED
glm_fit_set.delay = DELAY
glm_fit_set.start_time_point = START_TIMEPOINT
glm_fit_set.n_glms = len(glms)
glm_fit_set.n_train = n_train
glm_fit_set.n_test = n_test
glm_fit_set.n_trials = n_trials
# save data file
glm_fit_set.save_to_file(
input_sets=INPUT_SETS,
outputs=OUTPUTS,
basis_in=basis_ins,
basis_out=basis_outs,
trajs_train=trajs_trains,
trajs_test=trajs_tests,
glms=glmss,
residuals=residualss
)
# save everything else (+ link to data file) in database
session.add(glm_fit_set)
commit(session)
from db_api.connect import session
from config import *
from config.position_heatmap import *
row_labels = ('0.3 m/s', '0.4 m/s', '0.6 m/s')
col_labels = ('on', 'none', 'afterodor')
for sim_id_template in (SIMULATION_ID_EMPIRICAL, SIMULATION_ID_INFOTAXIS):
fig, axs = plt.subplots(3, 3, facecolor='white', figsize=FIG_SIZE, tight_layout=True)
for e_ctr, expt in enumerate(EXPERIMENTS):
for o_ctr, odor_state in enumerate(ODOR_STATES):
sim_id = sim_id_template.format(expt, odor_state)
sim = session.query(models.Simulation).get(sim_id)
# get histogram
hist = None
for h in sim.analysis_displacement_after_n_timesteps_histograms:
if h.n_timesteps == N_TIMESTEPS:
hist = h
break
hist.fetch_data(session)
if PROJECTION == 'xy':
heatmap = hist.xy
extent = hist.extent_xy
xlabel = 'x'
ylabel = 'y'
for ii in range(1, 5):
axs[ii, 0] = fig.add_subplot(5, 2, 2*ii + 1, sharex=axs[0, 0], sharey=axs[0, 0])
axs[ii, 1] = fig.add_subplot(5, 2, 2*(ii + 1), sharex=axs[0, 0], sharey=axs[0, 1])
fig_tp, axs_tp = plt.subplots(
4, 1, figsize=FIG_SIZE_POS, facecolor=FACE_COLOR, sharex=True, sharey=True, tight_layout=True
)
fig_pos, axs_pos = plt.subplots(
4, 1, figsize=FIG_SIZE_POS, facecolor=FACE_COLOR, sharex=True, tight_layout=True
)
wind_speed_handles = []
wind_speed_labels = []
for expt_ctr, expt in enumerate(session.query(models.Experiment)):
print(expt.id)
if 'fruitfly' in expt.id:
wind_speed_labels.append('f {} m/s'.format(expt.wind_speed))
elif 'mosquito' in expt.id:
wind_speed_labels.append('m {} m/s'.format(expt.wind_speed))
subset_handles = []
subset_labels = []
subset_handles_pos = []
from db_api.connect import session
from db_api import models
from config.wind_tunnel_discretized_matched_hit_number_histogram import *
hit_numbers = {expt: {} for expt in EXPERIMENTS}
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
# get all trials for the simulation from this odor state and experiment
sim_id = SIMULATION_ID.format(expt, odor_state)
print('Getting hit number distribution from simulation "{}" ...'.format(sim_id))
trials = session.query(models.Trial).filter_by(simulation_id=sim_id)
# get the number of hits in each trial
hits_per_trial = []
for trial in trials:
n_hits = np.sum([tp.detected_odor for tp in trial.get_timepoints(session)])
hits_per_trial += [n_hits]
hit_numbers[expt][odor_state] = hits_per_trial
# plot hit number histogram for each experiment and odor_state
fig, axs = plt.subplots(3, 3, facecolor='white', tight_layout=True)
for e_ctr, expt in enumerate(EXPERIMENTS):
'angular_velocity_x',
'angular_velocity_y',
'angular_velocity_z',
'angular_velocity_a',
'angular_acceleration_x',
'angular_acceleration_y',
'angular_acceleration_z',
'angular_acceleration_a',
'distance_from_wall']
FACE_COLOR = 'white'
AX_SIZE = (8, 4)
DATA_COLORS = ('b', 'g', 'r')
LW = 2
expts = list(session.query(models.Experiment))
fig_size = (AX_SIZE[0], AX_SIZE[1] * len(expts))
fig, axs = plt.subplots(len(expts), 1, facecolor=FACE_COLOR, figsize=fig_size, tight_layout=True)
for quantity in QUANTITIES:
print('Showing distributions of "{}"'.format(quantity))
[ax.cla() for ax in axs]
for ax, expt in zip(axs, expts):
for color, odor_state in zip(DATA_COLORS, ODOR_STATES):
# get the distribution meta data from the database
tpa = session.query(models.TimepointAutocorrelation).\
filter_by(variable=quantity, experiment=expt, odor_state=odor_state).first()
FIG_SIZE_EXAMPLES = (18, 15)
FIG_SIZE_FILTERS = (14, 15)
FIG_SIZE_RESIDUALS = (14, 15)
FACE_COLOR = 'w'
FONT_SIZE = 16
MODEL_LABELS = (
'constant',
'x',
'x, odor',
'x, odor_short',
'x, odor_long',
)
glm_fit_set = session.query(models.GlmFitSet).filter_by(
name=FIT_NAME, experiment_id=EXPERIMENT, odor_state=ODOR_STATE).first()
start_time_point = glm_fit_set.start_time_point
delay = glm_fit_set.delay
n_glms = glm_fit_set.n_glms
# get GLMs for example trial
glms = glm_fit_set.glms[EXAMPLE_TRIAL]
# plot example trajectories
traj_train_id = glm_fit_set.trajs_train[EXAMPLE_TRIAL][EXAMPLE_TRAIN]
traj_test_id = glm_fit_set.trajs_test[EXAMPLE_TRIAL][EXAMPLE_TEST]
traj_train = session.query(models.Trajectory).get(traj_train_id)
traj_test = session.query(models.Trajectory).get(traj_test_id)
from __future__ import print_function, division
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from db_api import models
from db_api.connect import session
ODOR_STATES = ('on', 'none', 'afterodor')
TIMEPOINTS_BEFORE_ENTRY = 50
TIMEPOINTS_AFTER_EXIT = 50
FACE_COLOR = 'white'
FIG_SIZE = (8, 10)
LW = 2
plt.ion()
expts = session.query(models.Experiment).all()
keep_going = True
e_ctr = 0
o_ctr = 0
fig, axs = plt.subplots(3,
1,
facecolor=FACE_COLOR,
figsize=FIG_SIZE,
tight_layout=True)
axs[2].twin = axs[2].twinx()
while keep_going:
# get new crossing group
expt = expts[e_ctr]
def early_vs_late_heading_timecourse_x0_accounted_for(
CROSSING_GROUP_IDS, CROSSING_GROUP_LABELS,
X_0_MIN, X_0_MAX, H_0_MIN, H_0_MAX, CROSSING_NUMBER_MAX,
MAX_CROSSINGS_EARLY, SUBTRACT_INITIAL_HEADING,
T_BEFORE, T_AFTER, SCATTER_INTEGRATION_WINDOW,
AX_SIZE, AX_GRID, EARLY_LATE_COLORS, ALPHA,
P_VAL_COLOR, P_VAL_Y_LIM, LEGEND_CROSSING_GROUP_ID,
FONT_SIZE):
"""
Show early vs. late headings for different experiments, along with a plot of the
p-values for the difference between the two means.
"""
# convert times to time steps
ts_before = int(round(T_BEFORE / DT))
ts_after = int(round(T_AFTER / DT))
scatter_ts = [ts_before + int(round(t / DT)) for t in SCATTER_INTEGRATION_WINDOW]
# loop over crossing groups
x_0s_dict = {}
headings_dict = {}
residuals_dict = {}
p_vals_dict = {}
scatter_ys_dict = {}
crossing_ns_dict = {}
for cg_id in CROSSING_GROUP_IDS:
# get crossing group
crossing_group = session.query(models.CrossingGroup).filter_by(id=cg_id).first()
# get early and late crossings
crossings_dict = {}
crossings_all = session.query(models.Crossing).filter_by(
crossing_group=crossing_group)
crossings_dict['early'] = crossings_all.filter(
models.Crossing.crossing_number <= MAX_CROSSINGS_EARLY)
crossings_dict['late'] = crossings_all.filter(
models.Crossing.crossing_number > MAX_CROSSINGS_EARLY,
models.Crossing.crossing_number <= CROSSING_NUMBER_MAX)
x_0s_dict[cg_id] = {}
headings_dict[cg_id] = {}
scatter_ys_dict[cg_id] = {}
crossing_ns_dict[cg_id] = {}
for label in ['early', 'late']:
x_0s = []
headings = []
scatter_ys = []
crossing_ns = []
# get all initial headings, initial xs, peak concentrations, and heading time-series
for crossing in crossings_dict[label]:
assert crossing.crossing_number > 0
if label == 'early':
assert 0 < crossing.crossing_number <= MAX_CROSSINGS_EARLY
elif label == 'late':
assert MAX_CROSSINGS_EARLY < crossing.crossing_number
assert crossing.crossing_number <= CROSSING_NUMBER_MAX
# throw away crossings that do not meet trigger criteria
x_0 = getattr(
crossing.feature_set_basic, 'position_x_{}'.format('peak'))
h_0 = getattr(
crossing.feature_set_basic, 'heading_xyz_{}'.format('peak'))
if not (X_0_MIN <= x_0 <= X_0_MAX): continue
if not (H_0_MIN <= h_0 <= H_0_MAX): continue
# store x_0 (uw/dw position)
x_0s.append(x_0)
# get and store headings
temp = crossing.timepoint_field(
session, 'heading_xyz', -ts_before, ts_after - 1,
'peak', 'peak', nan_pad=True)
# subtract initial heading if desired
if SUBTRACT_INITIAL_HEADING: temp -= temp[ts_before]
# store headings
headings.append(temp)
# calculate mean heading over integration window for scatter plot
scatter_ys.append(np.nanmean(temp[scatter_ts[0]:scatter_ts[1]]))
crossing_ns.append(crossing.crossing_number)
x_0s_dict[cg_id][label] = np.array(x_0s).copy()
headings_dict[cg_id][label] = np.array(headings).copy()
scatter_ys_dict[cg_id][label] = np.array(scatter_ys).copy()
crossing_ns_dict[cg_id][label] = np.array(crossing_ns).copy()
x_early = x_0s_dict[cg_id]['early']
x_late = x_0s_dict[cg_id]['late']
h_early = headings_dict[cg_id]['early']
h_late = headings_dict[cg_id]['late']
x0s_all = np.concatenate([x_early, x_late])
hs_all = np.concatenate([h_early, h_late], axis=0)
residuals_dict[cg_id] = {
'early': np.nan * np.zeros(h_early.shape),
'late': np.nan * np.zeros(h_late.shape),
}
# fit heading linear prediction from x0 at each time point
# and subtract from original heading
for t_step in range(ts_before + ts_after):
# get all headings for this time point
hs_t = hs_all[:, t_step]
residuals = np.nan * np.zeros(hs_t.shape)
# only use headings that exist
not_nan = ~np.isnan(hs_t)
# fit linear model
rgr = linear_model.LinearRegression()
rgr.fit(x0s_all[not_nan][:, None], hs_t[not_nan])
residuals[not_nan] = hs_t[not_nan] - rgr.predict(x0s_all[not_nan][:, None])
assert np.all(np.isnan(residuals) == np.isnan(hs_t))
r_early, r_late = np.split(residuals, [len(x_early)])
residuals_dict[cg_id]['early'][:, t_step] = r_early
residuals_dict[cg_id]['late'][:, t_step] = r_late
# loop through all time points and calculate p-value (ks-test)
# between early and late
p_vals = []
for t_step in range(ts_before + ts_after):
early_with_nans = residuals_dict[cg_id]['early'][:, t_step]
late_with_nans = residuals_dict[cg_id]['late'][:, t_step]
early_no_nans = early_with_nans[~np.isnan(early_with_nans)]
late_no_nans = late_with_nans[~np.isnan(late_with_nans)]
# calculate statistical significance
p_vals.append(ks_2samp(early_no_nans, late_no_nans)[1])
p_vals_dict[cg_id] = p_vals
## MAKE PLOTS
t = np.arange(-ts_before, ts_after) * DT
# history-dependence
fig_size = (AX_SIZE[0] * AX_GRID[1], AX_SIZE[1] * AX_GRID[0])
fig_0, axs_0 = plt.subplots(*AX_GRID, figsize=fig_size, tight_layout=True)
for cg_id, ax in zip(CROSSING_GROUP_IDS, axs_0.flat):
# get mean and sem of headings for early and late groups
handles = []
for label, color in EARLY_LATE_COLORS.items():
headings_mean = np.nanmean(residuals_dict[cg_id][label], axis=0)
headings_sem = stats.nansem(residuals_dict[cg_id][label], axis=0)
handles.append(ax.plot(
t, headings_mean, color=color, lw=2, label=label, zorder=1)[0])
ax.fill_between(
t, headings_mean - headings_sem, headings_mean + headings_sem,
color=color, alpha=ALPHA, zorder=1)
ax.set_xlabel('time since crossing (s)')
if SUBTRACT_INITIAL_HEADING: ax.set_ylabel('heading* (deg.)')
else: ax.set_ylabel('heading (deg.)')
ax.set_title(CROSSING_GROUP_LABELS[cg_id])
if cg_id == LEGEND_CROSSING_GROUP_ID:
ax.legend(handles=handles, loc='upper right')
set_fontsize(ax, FONT_SIZE)
# plot p-value
ax_twin = ax.twinx()
ax_twin.plot(t, p_vals_dict[cg_id], color=P_VAL_COLOR, lw=2, ls='--', zorder=0)
ax_twin.axhline(0.05, ls='-', lw=2, color='gray')
ax_twin.set_ylim(*P_VAL_Y_LIM)
ax_twin.set_ylabel('p-value (KS test)', fontsize=FONT_SIZE)
set_fontsize(ax_twin, FONT_SIZE)
fig_1, axs_1 = plt.subplots(*AX_GRID, figsize=fig_size, tight_layout=True)
cc = np.concatenate
colors = get_n_colors(CROSSING_NUMBER_MAX, colormap='jet')
for cg_id, ax in zip(CROSSING_GROUP_IDS, axs_1.flat):
# make scatter plot of x0s vs integrated headings vs crossing number
x_0s_all = cc([x_0s_dict[cg_id]['early'], x_0s_dict[cg_id]['late']])
ys_all = cc([scatter_ys_dict[cg_id]['early'], scatter_ys_dict[cg_id]['late']])
cs_all = cc([crossing_ns_dict[cg_id]['early'], crossing_ns_dict[cg_id]['late']])
cs = np.array([colors[c-1] for c in cs_all])
hs = []
for c in sorted(np.unique(cs_all)):
label = 'cn = {}'.format(c)
mask = cs_all == c
h = ax.scatter(x_0s_all[mask], ys_all[mask],
s=20, c=cs[mask], lw=0, label=label)
hs.append(h)
# calculate partial correlation between crossing number and heading given x
not_nan = ~np.isnan(ys_all)
r, p = stats.partial_corr(
cs_all[not_nan], ys_all[not_nan], controls=[x_0s_all[not_nan]])
ax.set_xlabel('x')
ax.set_ylabel(r'$\Delta$h_mean({}:{}) (deg)'.format(
*SCATTER_INTEGRATION_WINDOW))
title = CROSSING_GROUP_LABELS[cg_id] + \
', R = {0:.2f}, P = {1:.3f}'.format(r, p)
ax.set_title(title)
ax.legend(handles=hs, loc='upper center', ncol=3)
set_fontsize(ax, 16)
return fig_0
def main():
# get or create experiment
experiment = get_or_create(session, models.Experiment,
id=EXPERIMENT_ID,
description=EXPERIMENT_DESCRIPTION,
directory_path=EXPERIMENT_DIRECTORY_PATH)
full_directory_path = os.path.join(ARENA_DATA_DIRECTORY, EXPERIMENT_DIRECTORY_PATH)
edr_file_names = [file_name for file_name in os.listdir(full_directory_path)
if file_name.lower().endswith('.edr')]
# get all trials and add them to database
for file_name in edr_file_names:
print('Attempting to load file "{}"'.format(file_name))
# skip if file already added
if session.query(models.Trial).filter_by(file_name=file_name).all():
print('Skipping file "{}" because it is already in the database.'.format(file_name))
continue
try:
file_path = os.path.join(full_directory_path, file_name)
_, recording_start, _, header = edr_handling.load_edr(file_path)
recording_duration = header['recording_duration']
# get datetime for trial pair id using regex
trial_pair_id = re.findall(DATETIME_EXPRESSION, file_name)[0]
# get or create trial pair
trial_pair = get_or_create(session, models.TrialPair, id=trial_pair_id)
# get odor
odor = re.findall(ODOR_TYPE_EXPRESSION, file_name)[0]
# get solenoid status
if re.findall(SOLENOID_STATUS_EXPRESSION, file_name)[0] == 'off':
solenoid_active = False
else:
solenoid_active = True
odor_status = models.TrialOdorStatus(odor=odor, solenoid_active=solenoid_active)
session.add(odor_status)
# get insect number from file name using regex
insect_number = re.findall(INSECT_NUMBER_EXPRESSION, file_name)[0]
insect_id = '{}_{}'.format(recording_start.strftime('%Y%m%d'), insect_number)
# get/create insect
insect = get_or_create(session, models.Insect, id=insect_id)
trial = models.Trial(file_name=file_name,
recording_start=recording_start,
recording_duration=recording_duration)
trial.insect = insect
trial.experiment = experiment
trial.odor_status = odor_status
trial.pair = trial_pair
session.add(trial)
except Exception, e:
print('Error: "{}"'.format(e))
QUANTITIES = [
'odor', 'position_x', 'position_y', 'position_z', 'velocity_x',
'velocity_y', 'velocity_z', 'velocity_a', 'acceleration_x',
'acceleration_y', 'acceleration_z', 'acceleration_a', 'heading_xy',
'heading_xz', 'heading_xyz', 'angular_velocity_x', 'angular_velocity_y',
'angular_velocity_z', 'angular_velocity_a', 'angular_acceleration_x',
'angular_acceleration_y', 'angular_acceleration_z',
'angular_acceleration_a', 'distance_from_wall'
]
FACE_COLOR = 'white'
AX_SIZE = (8, 4)
DATA_COLORS = ('b', 'g', 'r')
LW = 2
expts = list(session.query(models.Experiment))
fig_size = (AX_SIZE[0], AX_SIZE[1] * len(expts))
fig, axs = plt.subplots(len(expts),
1,
facecolor=FACE_COLOR,
figsize=fig_size,
tight_layout=True)
for quantity in QUANTITIES:
print('Showing distributions of "{}"'.format(quantity))
[ax.cla() for ax in axs]
for ax, expt in zip(axs, expts):
for color, odor_state in zip(DATA_COLORS, ODOR_STATES):
'fruitfly_0.6mps_checkerboard_floor': 4,
'mosquito_0.4mps_checkerboard_floor': 5,}
fig, axs_unflat = plt.subplots(
3, 2, facecolor=FACE_COLOR, figsize=FIG_SIZE, sharex=True,
tight_layout=True
)
axs = axs_unflat.flatten()
axs_twin = [ax.twinx() for ax in axs[2:]]
wind_speed_handles = []
wind_speed_labels = []
for expt in session.query(models.Experiment):
if 'fly' in expt.id:
wind_speed_label = 'fly {} m/s'.format(expt.wind_speed)
elif 'mosquito' in expt.id:
wind_speed_label = 'mosquito {} m/s'.format(expt.wind_speed)
print(expt.id)
# get threshold and crossing group for this experiment
threshold = session.query(models.Threshold).filter_by(
experiment=expt, determination=DETERMINATION
).first()
"""
Plot the discriminability of two response sets when they are classified by thresholding.
"""
from __future__ import print_function, division
import numpy as np
import matplotlib.pyplot as plt
from db_api.connect import session
from db_api import models
RESPONSE_VAR = 'heading_xyz'
FACE_COLOR = 'white'
AX_SIZE = (6, 3)
expts = session.query(models.Experiment).all()
fig_size = (2 * AX_SIZE[0], len(expts) * AX_SIZE[1])
fig, axs = plt.subplots(len(expts),
2,
facecolor=FACE_COLOR,
figsize=fig_size,
tight_layout=True)
for expt, ax_row in zip(expts, axs):
cgs = session.query(models.CrossingGroup).filter_by(experiment=expt,
odor_state='on')
for cg, ax in zip(cgs, ax_row):
disc_ths = session.query(models.DiscriminationThreshold).\
filter_by(crossing_group=cg, variable=RESPONSE_VAR)