def main():
add_script_execution(SCRIPT_ID, session=session, notes=SCRIPT_NOTES)
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = SIMULATION_ID.format(expt, odor_state)
sim = session.query(models.Simulation).get(sim_id)
print(sim_id)
pos_idxs_start = []
for trial in sim.trials:
tp_id_start = trial.start_timepoint_id
tp = session.query(models.Timepoint).get(tp_id_start)
pos_idxs_start += [(tp.xidx, tp.yidx, tp.zidx)]
pos_start = [sim.env.pos_from_idx(idx) for idx in pos_idxs_start]
# build the histogram
bins = (sim.env.xbins, sim.env.ybins, sim.env.zbins)
hist, _ = np.histogramdd(np.array(pos_start), bins=bins)
# create the data model and store it
hist_data_model = models.SimulationAnalysisTakeOffPositionHistogram(
)
hist_data_model.simulation = sim
hist_data_model.store_data(session, hist.astype(int))
session.add(hist_data_model)
session.commit()
def main():
add_script_execution(SCRIPT_ID, session=session, notes=SCRIPT_NOTES)
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = SIMULATION_ID.format(expt, odor_state)
sim = session.query(models.Simulation).get(sim_id)
print(sim_id)
pos_idxs_start = []
for trial in sim.trials:
tp_id_start = trial.start_timepoint_id
tp = session.query(models.Timepoint).get(tp_id_start)
pos_idxs_start += [(tp.xidx, tp.yidx, tp.zidx)]
pos_start = [sim.env.pos_from_idx(idx) for idx in pos_idxs_start]
# build the histogram
bins = (sim.env.xbins, sim.env.ybins, sim.env.zbins)
hist, _ = np.histogramdd(np.array(pos_start), bins=bins)
# create the data model and store it
hist_data_model = models.SimulationAnalysisTakeOffPositionHistogram()
hist_data_model.simulation = sim
hist_data_model.store_data(session, hist.astype(int))
session.add(hist_data_model)
session.commit()
def main(traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID, session=session, multi_use=False, notes=SCRIPTNOTES)
for sim_id_template in SIMULATION_IDS:
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = sim_id_template.format(expt, odor_state)
print(sim_id)
sim = session.query(models.Simulation).get(sim_id)
# get the position indexes for all time points for all trials
pos_idxs = []
for trial in sim.trials[:traj_limit]:
tps = trial.get_timepoints(session)
pos_idxs += [np.array([(tp.xidx, tp.yidx, tp.zidx) for tp in tps])]
pos_idxs = np.concatenate(pos_idxs, axis=0)
pos = np.array([sim.env.pos_from_idx(pos_idx) for pos_idx in pos_idxs])
# build the histogram
bins = (sim.env.xbins, sim.env.ybins, sim.env.zbins)
pos_histogram, _ = np.histogramdd(pos, bins=bins)
# create the data model and store it
pos_hist_data_model = models.SimulationAnalysisPositionHistogram()
pos_hist_data_model.simulation = sim
pos_hist_data_model.store_data(session, pos_histogram.astype(int))
session.add(pos_hist_data_model)
session.commit()
def test_correct_number_of_histograms_made(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
self.assertEqual(
N_N_TIMESTEPS,
len(sim.analysis_displacement_after_n_timesteps_histograms))
def main(traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID, session=session, multi_use=False, notes=SCRIPTNOTES)
for sim_id_template in SIMULATION_IDS:
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = sim_id_template.format(expt, odor_state)
print(sim_id)
sim = session.query(models.Simulation).get(sim_id)
for n_timesteps in N_TIMESTEPSS:
# get the displacements for all trials
displacements = []
for trial in sim.trials[:traj_limit]:
tps = trial.get_timepoints(session).all()
pos_idx_start = np.array((tps[0].xidx, tps[0].yidx, tps[0].zidx))
if n_timesteps > len(tps) - 1:
# skip if the trajectory has ended by n_timesteps
continue
pos_idx_end = np.array((tps[n_timesteps].xidx,
tps[n_timesteps].yidx,
tps[n_timesteps].zidx))
displacements += [(pos_idx_end - pos_idx_start).astype(int)]
displacements = np.array(displacements)
# build the histogram
x_ub = min(n_timesteps + 1, sim.env.nx)
x_lb = -x_ub
y_ub = min(n_timesteps + 1, sim.env.ny)
y_lb = -y_ub
z_ub = min(n_timesteps + 1, sim.env.nz)
z_lb = -z_ub
x_bins = np.arange(x_lb, x_ub) + 0.5
y_bins = np.arange(y_lb, y_ub) + 0.5
z_bins = np.arange(z_lb, z_ub) + 0.5
displacement_histogram, _ = \
np.histogramdd(displacements, bins=(x_bins, y_bins, z_bins))
# create the data model and store it
displacement_hist_data_model = \
models.SimulationAnalysisDisplacementAfterNTimestepsHistogram()
displacement_hist_data_model.n_timesteps = n_timesteps
displacement_hist_data_model.simulation = sim
displacement_hist_data_model.shape = displacement_histogram.shape
displacement_hist_data_model. \
store_data(session, displacement_histogram.astype(int))
session.add(displacement_hist_data_model)
session.commit()
def test_starting_position_idxs_are_correct(self):
sims = session.query(models.Simulation).\
filter(models.Simulation.id.like(self.sim_id_pattern)).all()
for sim in sims:
for trial in sim.trials:
first_tp = trial.get_timepoints(session).first()
trial_start_idx = (first_tp.xidx, first_tp.yidx, first_tp.zidx)
self.assertEqual(trial_start_idx, trial.geom_config.start_idx)
def test_number_of_points_in_histogram_is_number_of_trials(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_displacement_total_histogram.fetch_data(session)
n_trials = len(sim.trials)
n_points = sim.analysis_displacement_total_histogram.xy.sum()
self.assertEqual(n_points, n_trials)
n_points = sim.analysis_displacement_total_histogram.xz.sum()
self.assertEqual(n_points, n_trials)
n_points = sim.analysis_displacement_total_histogram.yz.sum()
self.assertEqual(n_points, n_trials)
def test_correct_number_of_simulations_trials_and_timepoints(self):
sims = session.query(models.Simulation).\
filter(models.Simulation.id.like(self.sim_id_pattern)).all()
self.assertEqual(len(sims), 12)
for sim in sims:
self.assertEqual(len(sim.trials), TRAJ_LIMIT)
for trial in sim.trials:
self.assertEqual(len(trial.get_timepoints(session).all()), trial.trial_info.duration)
self.assertEqual(len(trial.get_timepoints(session).all()), trial.geom_config.duration)
def test_correct_number_of_geom_configs_added(self):
gcgs = session.query(models.GeomConfigGroup). \
filter(models.GeomConfigGroup.id.like('wind_tunnel_matched_discretized%'))
self.assertEqual(len(gcgs.all()), 12)
for gcg in gcgs:
self.assertEqual(len(gcg.geom_configs), TRAJ_LIMIT)
# make sure all geom_configs have geom_config_extension with all fields filled out
for gc in gcg.geom_configs:
self.assertGreater(gc.extension_real_trajectory.avg_dt, 0)
self.assertGreater(len(gc.extension_real_trajectory.real_trajectory_id), 0)
def test_windspeeds_are_correct(self):
sims = session.query(models.Simulation).\
filter(models.Simulation.id.like(self.sim_id_pattern)).all()
for sim in sims:
insect_params = {ip.name: ip.value for ip in sim.insect.insect_params}
w = insect_params['w']
if '0.3mps' in sim.id:
self.assertAlmostEqual(w, 0.3, delta=.0001)
elif '0.4mps' in sim.id:
self.assertAlmostEqual(w, 0.4, delta=.0001)
elif '0.6mps' in sim.id:
self.assertAlmostEqual(w, 0.6, delta=.0001)
def test_correct_number_of_geom_configs_added(self):
gcgs = session.query(models.GeomConfigGroup). \
filter(models.GeomConfigGroup.id.like('wind_tunnel_matched_discretized%'))
self.assertEqual(len(gcgs.all()), 12)
for gcg in gcgs:
self.assertEqual(len(gcg.geom_configs), TRAJ_LIMIT)
# make sure all geom_configs have geom_config_extension with all fields filled out
for gc in gcg.geom_configs:
self.assertGreater(gc.extension_real_trajectory.avg_dt, 0)
self.assertGreater(
len(gc.extension_real_trajectory.real_trajectory_id), 0)
def test_plot_heatmaps(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_position_histogram.fetch_data(session)
heatmap_xy = sim.analysis_position_histogram.xy
heatmap_xz = sim.analysis_position_histogram.xz
heatmap_yz = sim.analysis_position_histogram.yz
fig, axs = plt.subplots(1, 3)
axs[0].matshow(heatmap_xy.T, origin='lower', extent=sim.env.extentxy)
axs[1].matshow(heatmap_xz.T, origin='lower', extent=sim.env.extentxz)
axs[2].matshow(heatmap_yz.T, origin='lower', extent=sim.env.extentyz)
plt.show()
def test_histogram_dimensions_correct(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_position_histogram.fetch_data(session)
heatmap_xy = sim.analysis_position_histogram.xy
self.assertEqual(heatmap_xy.shape[0], sim.env.nx)
self.assertEqual(heatmap_xy.shape[1], sim.env.ny)
heatmap_xz = sim.analysis_position_histogram.xz
self.assertEqual(heatmap_xz.shape[0], sim.env.nx)
self.assertEqual(heatmap_xz.shape[1], sim.env.nz)
heatmap_yz = sim.analysis_position_histogram.yz
self.assertEqual(heatmap_yz.shape[0], sim.env.ny)
self.assertEqual(heatmap_yz.shape[1], sim.env.nz)
def test_histogram_dimensions_correct(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_position_histogram.fetch_data(session)
heatmap_xy = sim.analysis_position_histogram.xy
self.assertEqual(heatmap_xy.shape[0], sim.env.nx)
self.assertEqual(heatmap_xy.shape[1], sim.env.ny)
heatmap_xz = sim.analysis_position_histogram.xz
self.assertEqual(heatmap_xz.shape[0], sim.env.nx)
self.assertEqual(heatmap_xz.shape[1], sim.env.nz)
heatmap_yz = sim.analysis_position_histogram.yz
self.assertEqual(heatmap_yz.shape[0], sim.env.ny)
self.assertEqual(heatmap_yz.shape[1], sim.env.nz)
def test_plotting_of_histograms(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
hists = sim.analysis_displacement_after_n_timesteps_histograms
[hist.fetch_data(session) for hist in hists]
fig, axs = plt.subplots(3, 2)
axs[0, 0].matshow(hists[2].xy.T, origin='lower')
axs[1, 0].matshow(hists[2].xz.T, origin='lower')
axs[2, 0].matshow(hists[2].yz.T, origin='lower')
axs[0, 1].matshow(hists[4].xy.T, origin='lower')
axs[1, 1].matshow(hists[4].xz.T, origin='lower')
axs[2, 1].matshow(hists[4].yz.T, origin='lower')
plt.show(block=True)
def test_plotting_of_histograms(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
hists = sim.analysis_displacement_after_n_timesteps_histograms
[hist.fetch_data(session) for hist in hists]
fig, axs = plt.subplots(3, 2)
axs[0, 0].matshow(hists[2].xy.T, origin='lower')
axs[1, 0].matshow(hists[2].xz.T, origin='lower')
axs[2, 0].matshow(hists[2].yz.T, origin='lower')
axs[0, 1].matshow(hists[4].xy.T, origin='lower')
axs[1, 1].matshow(hists[4].xz.T, origin='lower')
axs[2, 1].matshow(hists[4].yz.T, origin='lower')
plt.show(block=True)
def test_correct_number_of_histograms_and_correct_size_and_count(self):
hists = session.query(models.SimulationAnalysisTakeOffPositionHistogram). \
filter(models.SimulationAnalysisTakeOffPositionHistogram.simulation_id. \
like(SIM_ID_START + '%'))
self.assertEqual(len(hists.all()), 9)
for hist in hists:
hist.fetch_data(session)
sim = hist.simulation
shape = (sim.env.nx, sim.env.ny, sim.env.nz)
self.assertEqual(shape, hist._data.shape)
self.assertEqual(len(sim.trials), hist._data.sum())
print(hist._data.sum())
def test_correct_number_of_simulations_trials_and_timepoints(self):
sims = session.query(models.Simulation). \
filter(models.Simulation.id.like(self.sim_id_pattern))
self.assertEqual(len(sims.all()), 12)
for sim in sims:
self.assertEqual(len(list(sim.trials)), TRAJ_LIMIT)
for trial in sim.trials:
# check to make sure trial info duration matches geom_config duration
self.assertEqual(trial.trial_info.duration, trial.geom_config.duration)
# check to make sure there are actually as many timepoints connected to the trial
# as there should be
self.assertEqual(trial.trial_info.duration,
len(trial.get_timepoints(session).all()))
def test_correct_number_of_histograms_and_correct_size_and_count(self):
hists = session.query(models.SimulationAnalysisTakeOffPositionHistogram). \
filter(models.SimulationAnalysisTakeOffPositionHistogram.simulation_id. \
like(SIM_ID_START + '%'))
self.assertEqual(len(hists.all()), 9)
for hist in hists:
hist.fetch_data(session)
sim = hist.simulation
shape = (sim.env.nx, sim.env.ny, sim.env.nz)
self.assertEqual(shape, hist._data.shape)
self.assertEqual(len(sim.trials), hist._data.sum())
print(hist._data.sum())
def test_plot_heatmaps(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
sim.analysis_displacement_total_histogram.fetch_data(session)
heatmap_xy = sim.analysis_displacement_total_histogram.xy
heatmap_xz = sim.analysis_displacement_total_histogram.xz
heatmap_yz = sim.analysis_displacement_total_histogram.yz
extent_xy = sim.analysis_displacement_total_histogram.extent_xy
extent_xz = sim.analysis_displacement_total_histogram.extent_xz
extent_yz = sim.analysis_displacement_total_histogram.extent_yz
fig, axs = plt.subplots(1, 3)
axs[0].matshow(heatmap_xy.T, origin='lower', extent=extent_xy)
axs[1].matshow(heatmap_xz.T, origin='lower', extent=extent_xz)
axs[2].matshow(heatmap_yz.T, origin='lower', extent=extent_yz)
plt.show()
def main(traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID,
session=session,
multi_use=False,
notes=SCRIPTNOTES)
for sim_id_template in SIMULATION_IDS:
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = sim_id_template.format(expt, odor_state)
print(sim_id)
sim = session.query(models.Simulation).get(sim_id)
# get the position indexes for all time points for all trials
pos_idxs = []
for trial in sim.trials[:traj_limit]:
tps = trial.get_timepoints(session)
pos_idxs += [
np.array([(tp.xidx, tp.yidx, tp.zidx) for tp in tps])
]
pos_idxs = np.concatenate(pos_idxs, axis=0)
pos = np.array(
[sim.env.pos_from_idx(pos_idx) for pos_idx in pos_idxs])
# build the histogram
bins = (sim.env.xbins, sim.env.ybins, sim.env.zbins)
pos_histogram, _ = np.histogramdd(pos, bins=bins)
# create the data model and store it
pos_hist_data_model = models.SimulationAnalysisPositionHistogram(
)
pos_hist_data_model.simulation = sim
pos_hist_data_model.store_data(session,
pos_histogram.astype(int))
session.add(pos_hist_data_model)
session.commit()
def test_histograms_are_correct_size_and_have_correct_number_of_points(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
hists = sim.analysis_displacement_after_n_timesteps_histograms
[hist.fetch_data(session) for hist in hists]
for h_ctr, hist in enumerate(hists):
n_timesteps = hist.n_timesteps
nx = min(2 * sim.env.nx - 1, 2 * n_timesteps + 1)
ny = min(2 * sim.env.ny - 1, 2 * n_timesteps + 1)
nz = min(2 * sim.env.nz - 1, 2 * n_timesteps + 1)
self.assertEqual(hist._data.shape, (nx, ny, nz))
if n_timesteps == 1:
self.assertEqual(hist._data[1, 1, 1], 0)
print(hist._data.sum())
if h_ctr < len(hists) - 1:
self.assertGreaterEqual(hist._data.sum(), hists[h_ctr + 1]._data.sum())
def test_histograms_are_correct_size_and_have_correct_number_of_points(
self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
hists = sim.analysis_displacement_after_n_timesteps_histograms
[hist.fetch_data(session) for hist in hists]
for h_ctr, hist in enumerate(hists):
n_timesteps = hist.n_timesteps
nx = min(2 * sim.env.nx - 1, 2 * n_timesteps + 1)
ny = min(2 * sim.env.ny - 1, 2 * n_timesteps + 1)
nz = min(2 * sim.env.nz - 1, 2 * n_timesteps + 1)
self.assertEqual(hist._data.shape, (nx, ny, nz))
if n_timesteps == 1:
self.assertEqual(hist._data[1, 1, 1], 0)
print(hist._data.sum())
if h_ctr < len(hists) - 1:
self.assertGreaterEqual(hist._data.sum(),
hists[h_ctr + 1]._data.sum())
def main(traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID,
session=session,
multi_use=False,
notes=SCRIPTNOTES)
for sim_id_template in SIMULATION_IDS:
for expt in EXPERIMENTS:
for odor_state in ODOR_STATES:
sim_id = sim_id_template.format(expt, odor_state)
print(sim_id)
sim = session.query(models.Simulation).get(sim_id)
for n_timesteps in N_TIMESTEPSS:
# get the displacements for all trials
displacements = []
for trial in sim.trials[:traj_limit]:
tps = trial.get_timepoints(session).all()
pos_idx_start = np.array(
(tps[0].xidx, tps[0].yidx, tps[0].zidx))
if n_timesteps > len(tps) - 1:
# skip if the trajectory has ended by n_timesteps
continue
pos_idx_end = np.array(
(tps[n_timesteps].xidx, tps[n_timesteps].yidx,
tps[n_timesteps].zidx))
displacements += [
(pos_idx_end - pos_idx_start).astype(int)
]
displacements = np.array(displacements)
# build the histogram
x_ub = min(n_timesteps + 1, sim.env.nx)
x_lb = -x_ub
y_ub = min(n_timesteps + 1, sim.env.ny)
y_lb = -y_ub
z_ub = min(n_timesteps + 1, sim.env.nz)
z_lb = -z_ub
x_bins = np.arange(x_lb, x_ub) + 0.5
y_bins = np.arange(y_lb, y_ub) + 0.5
z_bins = np.arange(z_lb, z_ub) + 0.5
displacement_histogram, _ = \
np.histogramdd(displacements, bins=(x_bins, y_bins, z_bins))
# create the data model and store it
displacement_hist_data_model = \
models.SimulationAnalysisDisplacementAfterNTimestepsHistogram()
displacement_hist_data_model.n_timesteps = n_timesteps
displacement_hist_data_model.simulation = sim
displacement_hist_data_model.shape = displacement_histogram.shape
displacement_hist_data_model. \
store_data(session, displacement_histogram.astype(int))
session.add(displacement_hist_data_model)
session.commit()
def main(traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID, session=session, multi_use=True, notes=SCRIPTNOTES)
for expt in EXPERIMENTS:
if '0.3mps' in expt:
w = 0.3
elif '0.4mps' in expt:
w = 0.4
elif '0.6mps' in expt:
w = 0.6
insect_params = INSECT_PARAMS.copy()
insect_params['w'] = w
for odor_state in ODOR_STATES:
print('Running simulation for expt "{}" with odor "{}"...'.
format(expt, odor_state))
# get geom_config_group for this experiment and odor state
geom_config_group_id = GEOM_CONFIG_GROUP_ID.format(expt, odor_state)
geom_config_group = session.query(models.GeomConfigGroup).get(geom_config_group_id)
# get wind tunnel copy simulation so we can match plume and insect
# note we select the first simulation that is of this type and corresponds to the
# right geom_config_group, since we only use the plume from it, which is independent
# of what insect parameters were used
#
# for instance, the plume bound to a simulation in which the insect had D = 0.6 and that
# bound to a simulation where D = 0.4 will be the same, since it is only the insect's
# internal model that has changed
wt_copy_sims = session.query(models.Simulation).\
filter(models.Simulation.geom_config_group == geom_config_group).\
filter(models.Simulation.id.like(WIND_TUNNEL_DISCRETIZED_SIMULATION_ID_PATTERN))
# get plume from corresponding discretized real wind tunnel trajectory
if 'fruitfly' in expt:
pl = CollimatedPlume(env=ENV, dt=-1, orm=wt_copy_sims.first().plume)
elif 'mosquito' in expt:
pl = SpreadingGaussianPlume(env=ENV, dt=-1, orm=wt_copy_sims.first().plume)
# create insect
# note: we will actually make a new insect for each trial, since the dt's vary;
# here we just set dt=-1, since this doesn't get stored in the db anyhow
ins = Insect(env=ENV, dt=-1)
ins.set_params(**insect_params)
ins.generate_orm(models)
# create simulation
sim_id = SIMULATION_ID.format(insect_params['r'],
insect_params['d'],
expt, odor_state)
sim_desc = SIMULATION_DESCRIPTION.format(expt, odor_state)
sim = models.Simulation(id=sim_id, description=sim_desc)
sim.env = ENV
sim.dt = -1
sim.total_trials = len(geom_config_group.geom_configs)
sim.heading_smoothing = 0
sim.geom_config_group = geom_config_group
sim.plume = pl.orm
sim.insect = ins.orm
session.add(sim)
# create ongoing run
ongoing_run = models.OngoingRun(trials_completed=0, simulations=[sim])
session.add(ongoing_run)
session.commit()
# generate trials
for gctr, geom_config in enumerate(geom_config_group.geom_configs):
if gctr == traj_limit:
break
# make new plume and insect with proper dts
ins = Insect(env=ENV, dt=geom_config.extension_real_trajectory.avg_dt)
ins.set_params(**insect_params)
ins.loglike_function = LOGLIKE
# set insect starting position
ins.set_pos(geom_config.start_idx, is_idx=True)
# initialize plume and insect and create trial
pl.initialize()
ins.initialize()
trial = Trial(pl=pl, ins=ins, nsteps=geom_config.duration)
# run trial
for step in xrange(geom_config.duration - 1):
trial.step()
# save trial
trial.add_timepoints(models, session=session, heading_smoothing=sim.heading_smoothing)
trial.generate_orm(models)
trial.orm.geom_config = geom_config
trial.orm.simulation = sim
session.add(trial.orm)
# update ongoing_run
ongoing_run.trials_completed = gctr + 1
session.add(ongoing_run)
session.commit()
def main(traj_limit=None):
# add script execution to infotaxis database
add_script_execution(script_id=SCRIPT_ID,
session=session,
multi_use=True,
notes=SCRIPT_NOTES)
session.commit()
# get wind tunnel connection and models
wt_session = imp.load_source('connect',
os.path.join(WT_REPO, 'db_api',
'connect.py')).session
wt_models = imp.load_source('models',
os.path.join(WT_REPO, 'db_api', 'models.py'))
for experiment_id in EXPERIMENT_IDS:
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 = session.query(
models.GeomConfigGroup).get(geom_config_group_id)
# make simulation
r = INSECT_PARAMS_DICT[experiment_id]['r']
d = INSECT_PARAMS_DICT[experiment_id]['d']
sim_id = SIMULATION_ID.format(r, d, experiment_id, odor_state)
sim_description = SIMULATION_DESCRIPTION.format(
experiment_id, odor_state)
sim = models.Simulation(id=sim_id, description=sim_description)
sim.env, sim.dt = ENV, DT
sim.heading_smoothing = 0
sim.geom_config_group = geom_config_group
# make plume
if 'fruitfly' in experiment_id:
pl = CollimatedPlume(env=ENV, dt=DT)
elif 'mosquito' in experiment_id:
pl = SpreadingGaussianPlume(env=ENV, dt=DT)
pl.set_params(**PLUME_PARAMS_DICT[experiment_id])
if odor_state in ('none', 'afterodor'):
pl.set_params(threshold=-1)
pl.initialize()
pl.generate_orm(models, sim=sim)
# make insect
ins = Insect(env=ENV, dt=DT)
ins.set_params(**INSECT_PARAMS_DICT[experiment_id])
ins.loglike_function = LOGLIKE
ins.initialize()
ins.generate_orm(models, sim=sim)
# add simulation and ongoing run
sim.ongoing_run = models.OngoingRun(trials_completed=0)
session.add(sim)
session.commit()
# loop through all geom_configs in group, look up corresponding trajectory,
# and discretize it
for gctr, geom_config in enumerate(geom_config_group.geom_configs):
# get trajectory id from geom_config and trajectory from wind tunnel database
traj_id = geom_config.extension_real_trajectory.real_trajectory_id
traj = wt_session.query(wt_models.Trajectory).get(traj_id)
# get positions from traj
positions = traj.positions(wt_session)
# create discretized version of trajectory
trial = TrialFromPositionSequence(positions, pl, ins)
# add timepoints to trial and generate data model
trial.add_timepoints(models,
session=session,
heading_smoothing=sim.heading_smoothing)
trial.generate_orm(models)
# bind simulation, geom_config
trial.orm.simulation = sim
trial.orm.geom_config = geom_config
# update ongoing run
sim.ongoing_run.trials_completed += 1
session.add(sim)
session.commit()
if traj_limit and (gctr == traj_limit - 1):
break
# update total number of trials
sim.total_trials = gctr + 1
session.add(sim)
session.commit()
def infotaxis_analysis(
WIND_TUNNEL_CG_IDS,
INFOTAXIS_WIND_SPEED_CG_IDS,
MAX_CROSSINGS,
INFOTAXIS_HISTORY_DEPENDENCE_CG_IDS,
MAX_CROSSINGS_EARLY,
X_0_MIN, X_0_MAX, H_0_MIN, H_0_MAX,
X_0_MIN_SIM, X_0_MAX_SIM,
X_0_MIN_SIM_HISTORY, X_0_MAX_SIM_HISTORY,
T_BEFORE_EXPT, T_AFTER_EXPT,
TS_BEFORE_SIM, TS_AFTER_SIM, HEADING_SMOOTHING_SIM,
HEAT_MAP_EXPT_ID, HEAT_MAP_SIM_ID,
N_HEAT_MAP_TRAJS,
X_BINS, Y_BINS,
FIG_SIZE, FONT_SIZE,
EXPT_LABELS,
EXPT_COLORS,
SIM_LABELS):
"""
Show infotaxis-generated trajectories alongside empirical trajectories. Show wind-speed
dependence and history dependence.
"""
from db_api.infotaxis import models as models_infotaxis
from db_api.infotaxis.connect import session as session_infotaxis
ts_before_expt = int(round(T_BEFORE_EXPT / DT))
ts_after_expt = int(round(T_AFTER_EXPT / DT))
headings = {}
# get headings for wind tunnel plume crossings
headings['wind_tunnel'] = {}
for cg_id in WIND_TUNNEL_CG_IDS:
crossings_all = session.query(models.Crossing).filter_by(crossing_group_id=cg_id).all()
headings['wind_tunnel'][cg_id] = []
cr_ctr = 0
for crossing in crossings_all:
if cr_ctr >= MAX_CROSSINGS:
break
# skip this crossing if it doesn't meet our inclusion criteria
x_0 = crossing.feature_set_basic.position_x_peak
h_0 = crossing.feature_set_basic.heading_xyz_peak
if not (X_0_MIN <= x_0 <= X_0_MAX):
continue
if not (H_0_MIN <= h_0 <= H_0_MAX):
continue
# store crossing heading
temp = crossing.timepoint_field(
session, 'heading_xyz', -ts_before_expt, ts_after_expt - 1,
'peak', 'peak', nan_pad=True)
# subtract initial heading
temp -= temp[ts_before_expt]
headings['wind_tunnel'][cg_id].append(temp)
cr_ctr += 1
headings['wind_tunnel'][cg_id] = np.array(headings['wind_tunnel'][cg_id])
# get headings from infotaxis plume crossings
headings['infotaxis'] = {}
for cg_id in INFOTAXIS_WIND_SPEED_CG_IDS:
crossings_all = list(session_infotaxis.query(models_infotaxis.Crossing).filter_by(
crossing_group_id=cg_id).all())
print('{} crossings for infotaxis crossing group: "{}"'.format(
len(crossings_all), cg_id))
headings['infotaxis'][cg_id] = []
cr_ctr = 0
for crossing in crossings_all:
if cr_ctr >= MAX_CROSSINGS:
break
# skip this crossing if it doesn't meet our inclusion criteria
x_0 = crossing.feature_set_basic.position_x_peak
h_0 = crossing.feature_set_basic.heading_xyz_peak
if not (X_0_MIN_SIM <= x_0 <= X_0_MAX_SIM):
continue
if not (H_0_MIN <= h_0 <= H_0_MAX):
continue
# store crossing heading
temp = crossing.timepoint_field(
session_infotaxis, 'hxyz', -TS_BEFORE_SIM, TS_AFTER_SIM - 1,
'peak', 'peak', nan_pad=True)
temp[~np.isnan(temp)] = gaussian_filter1d(
temp[~np.isnan(temp)], HEADING_SMOOTHING_SIM)
# subtract initial heading and store result
temp -= temp[TS_BEFORE_SIM]
headings['infotaxis'][cg_id].append(temp)
cr_ctr += 1
headings['infotaxis'][cg_id] = np.array(headings['infotaxis'][cg_id])
# get history dependences for infotaxis simulations
headings['it_hist_dependence'] = {}
for cg_id in INFOTAXIS_HISTORY_DEPENDENCE_CG_IDS:
crossings_all = list(session_infotaxis.query(models_infotaxis.Crossing).filter_by(
crossing_group_id=cg_id).all())
headings['it_hist_dependence'][cg_id] = {'early': [], 'late': []}
cr_ctr = 0
for crossing in crossings_all:
if cr_ctr >= MAX_CROSSINGS:
break
# skip this crossing if it doesn't meet our inclusion criteria
x_0 = crossing.feature_set_basic.position_x_peak
h_0 = crossing.feature_set_basic.heading_xyz_peak
if not (X_0_MIN_SIM_HISTORY <= x_0 <= X_0_MAX_SIM_HISTORY):
continue
if not (H_0_MIN <= h_0 <= H_0_MAX):
continue
# store crossing heading
temp = crossing.timepoint_field(
session_infotaxis, 'hxyz', -TS_BEFORE_SIM, TS_AFTER_SIM - 1,
'peak', 'peak', nan_pad=True)
temp[~np.isnan(temp)] = gaussian_filter1d(
temp[~np.isnan(temp)], HEADING_SMOOTHING_SIM)
# subtract initial heading
temp -= temp[TS_BEFORE_SIM]
# store according to its crossing number
if crossing.crossing_number <= MAX_CROSSINGS_EARLY:
headings['it_hist_dependence'][cg_id]['early'].append(temp)
elif crossing.crossing_number > MAX_CROSSINGS_EARLY:
headings['it_hist_dependence'][cg_id]['late'].append(temp)
else:
raise Exception('crossing number is not early or late for crossing {}'.format(
crossing.id))
cr_ctr += 1
headings['it_hist_dependence'][cg_id]['early'] = np.array(
headings['it_hist_dependence'][cg_id]['early'])
headings['it_hist_dependence'][cg_id]['late'] = np.array(
headings['it_hist_dependence'][cg_id]['late'])
# get heatmaps
if N_HEAT_MAP_TRAJS:
trajs_expt = session.query(models.Trajectory).\
filter_by(experiment_id=HEAT_MAP_EXPT_ID, odor_state='on').limit(N_HEAT_MAP_TRAJS)
trials_sim = session_infotaxis.query(models_infotaxis.Trial).\
filter_by(simulation_id=HEAT_MAP_SIM_ID).limit(N_HEAT_MAP_TRAJS)
else:
trajs_expt = session.query(models.Trajectory).\
filter_by(experiment_id=HEAT_MAP_EXPT_ID, odor_state='on')
trials_sim = session_infotaxis.query(models_infotaxis.Trial).\
filter_by(simulation_id=HEAT_MAP_SIM_ID)
expt_xs = []
expt_ys = []
sim_xs = []
sim_ys = []
for traj in trajs_expt:
expt_xs.append(traj.timepoint_field(session, 'position_x'))
expt_ys.append(traj.timepoint_field(session, 'position_y'))
for trial in trials_sim:
sim_xs.append(trial.timepoint_field(session_infotaxis, 'xidx'))
sim_ys.append(trial.timepoint_field(session_infotaxis, 'yidx'))
expt_xs = np.concatenate(expt_xs)
expt_ys = np.concatenate(expt_ys)
sim_xs = np.concatenate(sim_xs) * 0.02 - 0.3
sim_ys = np.concatenate(sim_ys) * 0.02 - 0.15
## MAKE PLOTS
fig, axs = plt.figure(figsize=FIG_SIZE, tight_layout=True), []
axs.append(fig.add_subplot(4, 3, 1))
axs.append(fig.add_subplot(4, 3, 2, sharey=axs[0]))
# plot wind-speed dependence of wind tunnel trajectories
t = np.arange(-ts_before_expt, ts_after_expt) * DT
handles = []
for cg_id in WIND_TUNNEL_CG_IDS:
label = EXPT_LABELS[cg_id]
color = EXPT_COLORS[cg_id]
headings_mean = np.nanmean(headings['wind_tunnel'][cg_id], axis=0)
headings_sem = stats.nansem(headings['wind_tunnel'][cg_id], axis=0)
# plot mean and sem
handles.append(
axs[0].plot(t, headings_mean, lw=3, color=color, zorder=1, label=label)[0])
axs[0].fill_between(
t, headings_mean - headings_sem, headings_mean + headings_sem,
color=color, alpha=0.2)
axs[0].set_xlabel('time since odor peak (s)')
axs[0].set_ylabel('$\Delta$ heading (degrees)')
axs[0].set_title('experimental data\n(wind speed comparison)')
axs[0].legend(handles=handles, loc='best')
t = np.arange(-TS_BEFORE_SIM, TS_AFTER_SIM)
for cg_id, wt_cg_id in zip(INFOTAXIS_WIND_SPEED_CG_IDS, WIND_TUNNEL_CG_IDS):
label = EXPT_LABELS[wt_cg_id]
color = EXPT_COLORS[wt_cg_id]
headings_mean = np.nanmean(headings['infotaxis'][cg_id], axis=0)
headings_sem = stats.nansem(headings['infotaxis'][cg_id], axis=0)
# plot mean and sem
axs[1].plot(t, headings_mean, lw=3, color=color, zorder=1, label=label)
axs[1].fill_between(
t, headings_mean - headings_sem, headings_mean + headings_sem,
color=color, alpha=0.2)
axs[1].set_xlabel('time steps since odor peak (s)')
axs[1].set_title('infotaxis simulations\n(wind speed comparison)')
# add axes for infotaxis history dependence and make plots
[axs.append(fig.add_subplot(4, 3, 3 + ctr)) for ctr in range(4)]
for (ax, cg_id) in zip(axs[-4:], INFOTAXIS_HISTORY_DEPENDENCE_CG_IDS):
mean_early = np.nanmean(headings['it_hist_dependence'][cg_id]['early'], axis=0)
sem_early = stats.nansem(headings['it_hist_dependence'][cg_id]['early'], axis=0)
mean_late = np.nanmean(headings['it_hist_dependence'][cg_id]['late'], axis=0)
sem_late = stats.nansem(headings['it_hist_dependence'][cg_id]['late'], axis=0)
# plot means and stds
try:
handle_early = ax.plot(t, mean_early, lw=3, color='b', zorder=0, label='early')[0]
ax.fill_between(
t, mean_early - sem_early, mean_early + sem_early,
color='b', alpha=0.2)
except:
pass
try:
handle_late = ax.plot(t, mean_late, lw=3, color='g', zorder=0, label='late')[0]
ax.fill_between(
t, mean_late - sem_late, mean_late + sem_late,
color='g', alpha=0.2)
except:
pass
ax.set_xlabel('time steps since odor peak (s)')
ax.set_title(SIM_LABELS[cg_id])
try:
ax.legend(handles=[handle_early, handle_late])
except:
pass
axs[3].set_ylabel('$\Delta$ heading (degrees)')
# plot heat maps
axs.append(fig.add_subplot(4, 1, 3))
axs.append(fig.add_subplot(4, 1, 4))
axs[6].hist2d(expt_xs, expt_ys, bins=(X_BINS, Y_BINS))
axs[7].hist2d(sim_xs, sim_ys, bins=(X_BINS, Y_BINS))
axs[6].set_ylabel('y (m)')
axs[7].set_ylabel('y (m)')
axs[7].set_xlabel('x (m)')
axs[6].set_title('experimental data (fly 0.4 m/s)')
axs[7].set_title('infotaxis simulation')
for ax in axs:
set_fontsize(ax, FONT_SIZE)
return fig
def main(SIM_PREFIX=None, sim_ids=None, thresholds=None, trial_limit=None):
if thresholds is None:
thresholds = THRESHOLDS
SCRIPTNOTES = ('Identify plume crossings for simulations with prefix "{}" '
'using heading smoothing "{}" and thresholds "{}"'.format(
SIM_PREFIX, HEADING_SMOOTHING, thresholds))
if sim_ids is None:
SIM_SUFFIXES = [
'fruitfly_0.3mps_checkerboard_floor_odor_on',
'fruitfly_0.3mps_checkerboard_floor_odor_none',
'fruitfly_0.3mps_checkerboard_floor_odor_afterodor',
'fruitfly_0.4mps_checkerboard_floor_odor_on',
'fruitfly_0.4mps_checkerboard_floor_odor_none',
'fruitfly_0.4mps_checkerboard_floor_odor_afterodor',
'fruitfly_0.6mps_checkerboard_floor_odor_on',
'fruitfly_0.6mps_checkerboard_floor_odor_none',
'fruitfly_0.6mps_checkerboard_floor_odor_afterodor',
'mosquito_0.4mps_checkerboard_floor_odor_on',
'mosquito_0.4mps_checkerboard_floor_odor_none',
'mosquito_0.4mps_checkerboard_floor_odor_afterodor',]
sim_ids = [
'{}_{}'.format(SIM_PREFIX, sim_suffix)
for sim_suffix in SIM_SUFFIXES
]
# add script execution to database
add_script_execution(
SCRIPTID, session=session, multi_use=True, notes=SCRIPTNOTES)
for sim_id in sim_ids:
print('Identifying crossings from simulation: "{}"'.format(sim_id))
# get simulation
sim = session.query(models.Simulation).filter_by(id=sim_id).first()
# get all trials from this simulation
trials = session.query(models.Trial).filter_by(simulation=sim).all()
# make crossing group
if 'fly' in sim_id:
threshold = thresholds['fly']
elif 'mosq' in sim_id:
threshold = thresholds['mosq']
cg_id = '{}_th_{}_hsmoothing_{}'.format(
sim_id, threshold, HEADING_SMOOTHING)
print('Storing in crossing group:')
print(cg_id)
cg = models.CrossingGroup(
id=cg_id,
simulation=sim,
threshold=threshold,
heading_smoothing=HEADING_SMOOTHING)
session.add(cg)
# loop through trials and identify crossings
trial_ctr = 0
for trial in trials:
if trial_limit and trial_ctr >= trial_limit:
break
# get relevant time-series
odors = trial.timepoint_field(session, 'odor')
xs = trial.timepoint_field(session, 'xidx')
ys = trial.timepoint_field(session, 'yidx')
zs = trial.timepoint_field(session, 'zidx')
# get smoothed headings
hs = smooth(trial.timepoint_field(session, 'hxyz'), HEADING_SMOOTHING)
# identify crossings
crossing_lists, peaks = time_series.segment_by_threshold(
odors, threshold)
tr_start = trial.start_timepoint_id
# add crossings
for c_ctr, (crossing_list, peak) in enumerate(zip(crossing_lists, peaks)):
crossing = models.Crossing(
trial=trial,
crossing_number=c_ctr+1,
crossing_group=cg,
start_timepoint_id=crossing_list[0] + tr_start,
entry_timepoint_id=crossing_list[1] + tr_start,
peak_timepoint_id=crossing_list[2] + tr_start,
exit_timepoint_id=crossing_list[3] + tr_start - 1,
end_timepoint_id=crossing_list[4] + tr_start - 1,
max_odor=peak,)
session.add(crossing)
# create this crossing's basic feature set
crossing.feature_set_basic = models.CrossingFeatureSetBasic(
position_x_entry=xs[crossing_list[1]],
position_y_entry=ys[crossing_list[1]],
position_z_entry=zs[crossing_list[1]],
heading_xyz_entry=hs[crossing_list[1]],
position_x_peak=xs[crossing_list[2]],
position_y_peak=ys[crossing_list[2]],
position_z_peak=zs[crossing_list[2]],
heading_xyz_peak=hs[crossing_list[2]],
position_x_exit=xs[crossing_list[3] - 1],
position_y_exit=ys[crossing_list[3] - 1],
position_z_exit=zs[crossing_list[3] - 1],
heading_xyz_exit=hs[crossing_list[3] - 1],
)
session.add(crossing)
trial_ctr += 1
# commit after all crossings from all trials from a simulation have been added
session.commit()
def test_correct_simulations_analyzed(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
self.assertEqual(sim.analysis_position_histogram.simulation, sim)
def main(INSECT_PARAMS,
SCRIPTNOTES,
threshold=None,
sim_ids=None,
sim_descs=None,
expts=None,
odor_states=None,
traj_limit=None):
# add script execution to database
add_script_execution(SCRIPTID,
session=session,
multi_use=True,
notes=SCRIPTNOTES)
if expts is None:
expts = EXPERIMENTS
if odor_states is None:
odor_states = ODOR_STATES
for expt in expts:
if '0.3mps' in expt:
w = 0.3
elif '0.4mps' in expt:
w = 0.4
elif '0.6mps' in expt:
w = 0.6
insect_params = INSECT_PARAMS.copy()
insect_params['w'] = w
for odor_state in odor_states:
print('Running simulation for expt "{}" with odor "{}"...'.format(
expt, odor_state))
# get geom_config_group for this experiment and odor state
geom_config_group_id = GEOM_CONFIG_GROUP_ID.format(
expt, odor_state)
geom_config_group = session.query(
models.GeomConfigGroup).get(geom_config_group_id)
# get wind tunnel copy simulation so we can match plume and insect
# note we select the first simulation that is of this type and
# corresponds to the right geom_config_group, since we only use the
# plume from it, which is independent of insect parameters used
#
# for instance, the plume bound to a simulation in which the insect
# had D = 0.6 and that bound to a simulation where D = 0.4 will be
# the same, since it is only the insect's
# internal model that has changed
wt_copy_sims = session.query(models.Simulation).\
filter(models.Simulation.geom_config_group == geom_config_group).\
filter(models.Simulation.id.like(
WIND_TUNNEL_DISCRETIZED_SIMULATION_ID_PATTERN))
# get plume from corresponding discretized real wind tunnel trajectory
if 'fruitfly' in expt:
pl = CollimatedPlume(env=ENV,
dt=-1,
orm=wt_copy_sims.first().plume)
elif 'mosquito' in expt:
pl = SpreadingGaussianPlume(env=ENV,
dt=-1,
orm=wt_copy_sims.first().plume)
if threshold is not None:
print('Setting plume detectability threshold to '
'{}'.format(threshold))
pl.set_params(threshold=threshold)
# create insect
# note: we will actually make a new insect for each trial,
# since the dt's vary;
# here we set dt=-1, since this doesn't get stored in the db anyhow
ins = Insect(env=ENV, dt=-1)
ins.set_params(**insect_params)
ins.generate_orm(models)
# create simulation
if sim_ids is None:
sim_id = SIMULATION_ID.format(insect_params['r'],
insect_params['d'], expt,
odor_state)
else:
sim_id = sim_ids[(expt, odor_state)]
if sim_descs is None:
sim_desc = SIMULATION_DESCRIPTION.format(expt, odor_state)
else:
sim_desc = sim_descs[(expt, odor_state)]
sim = models.Simulation(id=sim_id, description=sim_desc)
sim.env = ENV
sim.dt = -1
sim.total_trials = len(geom_config_group.geom_configs)
sim.heading_smoothing = 0
sim.geom_config_group = geom_config_group
sim.plume = pl.orm
sim.insect = ins.orm
session.add(sim)
# create ongoing run
ongoing_run = models.OngoingRun(trials_completed=0,
simulations=[sim])
session.add(ongoing_run)
session.commit()
# generate trials
for gctr, geom_config in enumerate(geom_config_group.geom_configs):
if gctr == traj_limit:
break
# make new plume and insect with proper dts
ins = Insect(env=ENV,
dt=geom_config.extension_real_trajectory.avg_dt)
ins.set_params(**insect_params)
ins.loglike_function = LOGLIKE
# set insect starting position
ins.set_pos(geom_config.start_idx, is_idx=True)
# initialize plume and insect and create trial
pl.initialize()
ins.initialize()
trial = Trial(pl=pl, ins=ins, nsteps=geom_config.duration)
# run trial
for step in xrange(geom_config.duration - 1):
trial.step()
# save trial
trial.add_timepoints(models,
session=session,
heading_smoothing=sim.heading_smoothing)
trial.generate_orm(models)
trial.orm.geom_config = geom_config
trial.orm.simulation = sim
session.add(trial.orm)
# update ongoing_run
ongoing_run.trials_completed = gctr + 1
session.add(ongoing_run)
session.commit()
def main(trial_limit=None):
# add script execution to database
add_script_execution(SCRIPTID, session=session, multi_use=True, notes=SCRIPTNOTES)
for sim_id in SIM_IDS:
print('Identifying crossings from simulation: "{}"'.format(sim_id))
# get simulation
sim = session.query(models.Simulation).filter_by(id=sim_id).first()
# get all trials from this simulation
trials = session.query(models.Trial).filter_by(simulation=sim).all()
# make crossing group
if 'fly' in sim_id:
threshold = THRESHOLDS['fly']
elif 'mosq' in sim_id:
threshold = THRESHOLDS['mosq']
cg_id = '{}_th_{}_hsmoothing_{}'.format(sim_id, threshold, HEADING_SMOOTHING)
cg = models.CrossingGroup(
id=cg_id,
simulation=sim,
threshold=threshold,
heading_smoothing=HEADING_SMOOTHING)
session.add(cg)
# loop through trials and identify crossings
trial_ctr = 0
for trial in trials:
if trial_limit and trial_ctr >= trial_limit:
break
# get relevant time-series
odors = trial.timepoint_field(session, 'odor')
xs = trial.timepoint_field(session, 'xidx')
ys = trial.timepoint_field(session, 'yidx')
zs = trial.timepoint_field(session, 'zidx')
# get smoothed headings
hs = smooth(trial.timepoint_field(session, 'hxyz'), HEADING_SMOOTHING)
# identify crossings
crossing_lists, peaks = time_series.segment_by_threshold(
odors, threshold)
tr_start = trial.start_timepoint_id
# add crossings
for c_ctr, (crossing_list, peak) in enumerate(zip(crossing_lists, peaks)):
crossing = models.Crossing(
trial=trial,
crossing_number=c_ctr+1,
crossing_group=cg,
start_timepoint_id=crossing_list[0] + tr_start,
entry_timepoint_id=crossing_list[1] + tr_start,
peak_timepoint_id=crossing_list[2] + tr_start,
exit_timepoint_id=crossing_list[3] + tr_start - 1,
end_timepoint_id=crossing_list[4] + tr_start - 1,
max_odor=peak,)
session.add(crossing)
# create this crossing's basic feature set
crossing.feature_set_basic = models.CrossingFeatureSetBasic(
position_x_entry=xs[crossing_list[1]],
position_y_entry=ys[crossing_list[1]],
position_z_entry=zs[crossing_list[1]],
heading_xyz_entry=hs[crossing_list[1]],
position_x_peak=xs[crossing_list[2]],
position_y_peak=ys[crossing_list[2]],
position_z_peak=zs[crossing_list[2]],
heading_xyz_peak=hs[crossing_list[2]],
position_x_exit=xs[crossing_list[3] - 1],
position_y_exit=ys[crossing_list[3] - 1],
position_z_exit=zs[crossing_list[3] - 1],
heading_xyz_exit=hs[crossing_list[3] - 1],
)
session.add(crossing)
trial_ctr += 1
# commit after all crossings from all trials from a simulation have been added
session.commit()
def test_correct_number_of_histograms_made(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
self.assertEqual(N_N_TIMESTEPS,
len(sim.analysis_displacement_after_n_timesteps_histograms))
def test_correct_simulations_analyzed(self):
for sim_id in [SIM_ID_0, SIM_ID_1]:
sim = session.query(models.Simulation).get(sim_id)
self.assertEqual(sim.analysis_position_histogram.simulation, sim)