def main():
for expt_id, value in THRESHOLDS_DICT.iteritems():
threshold = models.Threshold(experiment_id=expt_id,
determination='chosen40_500',
value=value)
session.add(threshold)
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):
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):
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 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):
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 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(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)
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)
from db_api.connect import session, commit
from db_api import models
FRUIT_FLY_PARAMS = {
'speed_threshold': 0.03, # m/s
'dist_from_wall_threshold': 0.01, # m
'min_pause_length': 10, # hundredths of a second
'min_trajectory_length': 50, # hundredths of a second
}
MOSQUITO_PARAMS = {
'speed_threshold': 0.03, # m/s
'dist_from_wall_threshold': 0.01, # m
'min_pause_length': 10, # hundredths of a second
'min_trajectory_length': 50, # hundredths of a second
}
for param, value in FRUIT_FLY_PARAMS.items():
tcp = models.TrajectoryCleaningParameter(insect='fruit_fly',
param=param,
value=value)
session.add(tcp)
for param, value in MOSQUITO_PARAMS.items():
tcp = models.TrajectoryCleaningParameter(insect='mosquito',
param=param,
value=value)
session.add(tcp)
commit(session)
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)
