def events_to_timed_behavioral_sequences(pj: dict,
obs_id: str,
subject: str,
parameters: dict,
precision: float,
behav_seq_separator: str) -> str:
"""
return the behavioral string for subject in obsId
Args:
pj (dict): project
obs_id (str): observation id
subj (str): subject
parameters (dict): parameters
precision (float): time value for scan sample
behav_seq_separator (str): separator of behviors in behavioral sequences
Returns:
str: behavioral string for selected subject in selected observation
"""
out = ""
current_states = []
# events_with_status = project_functions.events_start_stop(pj[ETHOGRAM], pj[OBSERVATIONS][obs_id][EVENTS])
state_behaviors_codes = utilities.state_behavior_codes(pj[ETHOGRAM])
delta = Decimal(str(round(precision, 3)))
out = ""
t = Decimal("0.000")
current = []
while t < pj[OBSERVATIONS][obs_id][EVENTS][-1][0]:
'''
if out:
out += behav_seq_separator
'''
csbs = utilities.get_current_states_modifiers_by_subject(state_behaviors_codes,
pj[OBSERVATIONS][obs_id][EVENTS],
{"": {"name": subject}},
t,
include_modifiers=False)[""]
if csbs:
if current:
if csbs == current[-1]:
current.append("+".join(csbs))
else:
out.append(current)
current = [csbs]
else:
current = [csbs]
t += delta
return out
def events_to_timed_behavioral_sequences(pj: dict, obs_id: str, subject: str,
parameters: dict, precision: float,
behav_seq_separator: str) -> str:
"""
return the behavioral string for subject in obsId
Args:
pj (dict): project
obs_id (str): observation id
subj (str): subject
parameters (dict): parameters
precision (float): time value for scan sample
behav_seq_separator (str): separator of behviors in behavioral sequences
Returns:
str: behavioral string for selected subject in selected observation
"""
out = ""
current_states = []
# events_with_status = project_functions.events_start_stop(pj[ETHOGRAM], pj[OBSERVATIONS][obs_id][EVENTS])
state_behaviors_codes = utilities.state_behavior_codes(pj[ETHOGRAM])
delta = Decimal(str(round(precision, 3)))
out = ""
t = Decimal("0.000")
current = []
while t < pj[OBSERVATIONS][obs_id][EVENTS][-1][0]:
'''
if out:
out += behav_seq_separator
'''
csbs = utilities.get_current_states_modifiers_by_subject(
state_behaviors_codes,
pj[OBSERVATIONS][obs_id][EVENTS], {"": {
"name": subject
}},
t,
include_modifiers=False)[""]
if csbs:
if current:
if csbs == current[-1]:
current.append("+".join(csbs))
else:
out.append(current)
current = [csbs]
else:
current = [csbs]
t += delta
return out
def events_start_stop(ethogram, events):
"""
returns events with status (START/STOP or POINT)
take consideration of subject
Args:
events (list): list of events
Returns:
list: list of events with type (POINT or STATE)
"""
state_events_list = utilities.state_behavior_codes(ethogram) # from utilities
events_flagged = []
for event in events:
time, subject, code, modifier = (
event[EVENT_TIME_FIELD_IDX],
event[EVENT_SUBJECT_FIELD_IDX],
event[EVENT_BEHAVIOR_FIELD_IDX],
event[EVENT_MODIFIER_FIELD_IDX],
)
# check if code is state
if code in state_events_list:
# how many code before with same subject?
if (
len(
[
x[EVENT_BEHAVIOR_FIELD_IDX]
for x in events
if x[EVENT_BEHAVIOR_FIELD_IDX] == code and
x[EVENT_TIME_FIELD_IDX] < time and
x[EVENT_SUBJECT_FIELD_IDX] == subject and
x[EVENT_MODIFIER_FIELD_IDX] == modifier
]
)
% 2
): # test if odd
flag = STOP
else:
flag = START
else:
flag = POINT
events_flagged.append(event + [flag])
return events_flagged
def events_start_stop(ethogram, events):
"""
returns events with status (START/STOP or POINT)
take consideration of subject
Args:
events (list): list of events
Returns:
list: list of events with type (POINT or STATE)
"""
state_events_list = utilities.state_behavior_codes(ethogram) # from utilities
events_flagged = []
for event in events:
time, subject, code, modifier = (
event[EVENT_TIME_FIELD_IDX],
event[EVENT_SUBJECT_FIELD_IDX],
event[EVENT_BEHAVIOR_FIELD_IDX],
event[EVENT_MODIFIER_FIELD_IDX],
)
# check if code is state
if code in state_events_list:
# how many code before with same subject?
if (
len(
[
x[EVENT_BEHAVIOR_FIELD_IDX]
for x in events
if x[EVENT_BEHAVIOR_FIELD_IDX] == code and
x[EVENT_TIME_FIELD_IDX] < time and
x[EVENT_SUBJECT_FIELD_IDX] == subject and
x[EVENT_MODIFIER_FIELD_IDX] == modifier
]
)
% 2
): # test if odd
flag = STOP
else:
flag = START
else:
flag = POINT
events_flagged.append(event + [flag])
return events_flagged
def create_behavior_binary_table(pj: dict, selected_observations: list,
parameters_obs: dict,
time_interval: float) -> dict:
"""
create behavior binary table
Args:
pj (dict): project dictionary
selected_observations (list): list of selected observations
parameters_obs (dict): dcit of parameters
time_interval (float): time interval (in seconds)
Returns:
dict: dictionary of tablib dataset
"""
results_df = {}
state_behavior_codes = [
x for x in utilities.state_behavior_codes(pj[ETHOGRAM])
if x in parameters_obs[SELECTED_BEHAVIORS]
]
point_behavior_codes = [
x for x in utilities.point_behavior_codes(pj[ETHOGRAM])
if x in parameters_obs[SELECTED_BEHAVIORS]
]
if not state_behavior_codes and not point_behavior_codes:
return {"error": True, "msg": "No state events selected"}
for obs_id in selected_observations:
if obs_id not in results_df:
results_df[obs_id] = {}
for subject in parameters_obs[SELECTED_SUBJECTS]:
# extract tuple (behavior, modifier)
behav_modif_list = [
(idx[2], idx[3]) for idx in pj[OBSERVATIONS][obs_id][EVENTS]
if idx[1] == (subject if subject != NO_FOCAL_SUBJECT else "")
and idx[2] in parameters_obs[SELECTED_BEHAVIORS]
]
# extract observed subjects NOT USED at the moment
observed_subjects = [
event[EVENT_SUBJECT_FIELD_IDX]
for event in pj[OBSERVATIONS][obs_id][EVENTS]
]
# add selected behavior if not found in (behavior, modifier)
if not parameters_obs[EXCLUDE_BEHAVIORS]:
#for behav in state_behavior_codes:
for behav in parameters_obs[SELECTED_BEHAVIORS]:
if behav not in [x[0] for x in behav_modif_list]:
behav_modif_list.append((behav, ""))
behav_modif_set = set(behav_modif_list)
if parameters_obs[INCLUDE_MODIFIERS]:
results_df[obs_id][subject] = tablib.Dataset(
headers=["time"] + [
f"{x[0]}" + f" ({x[1]})" * (x[1] != "")
for x in sorted(behav_modif_set)
])
else:
results_df[obs_id][subject] = tablib.Dataset(
headers=["time"] + [x[0] for x in sorted(behav_modif_set)])
if subject == NO_FOCAL_SUBJECT:
sel_subject_dict = {"": {SUBJECT_NAME: ""}}
else:
sel_subject_dict = dict([
(idx, pj[SUBJECTS][idx]) for idx in pj[SUBJECTS]
if pj[SUBJECTS][idx][SUBJECT_NAME] == subject
])
row_idx = 0
t = parameters_obs[START_TIME]
while t < parameters_obs[END_TIME]:
# state events
current_states = utilities.get_current_states_modifiers_by_subject(
state_behavior_codes,
pj[OBSERVATIONS][obs_id][EVENTS],
sel_subject_dict,
t,
include_modifiers=parameters_obs[INCLUDE_MODIFIERS])
# point events
current_point = utilities.get_current_points_by_subject(
point_behavior_codes,
pj[OBSERVATIONS][obs_id][EVENTS],
sel_subject_dict,
t,
time_interval,
include_modifiers=parameters_obs[INCLUDE_MODIFIERS])
cols = [float(t)] # time
for behav in results_df[obs_id][subject].headers[
1:]: # skip time
if behav in state_behavior_codes:
cols.append(
int(behav in current_states[list(
current_states.keys())[0]]))
if behav in point_behavior_codes:
cols.append(current_point[list(
current_point.keys())[0]].count(behav))
#int(behav in current_point[list(current_point.keys())[0]]))
results_df[obs_id][subject].append(cols)
t += time_interval
row_idx += 1
return results_df
def test_empty_ethogram(self):
r = utilities.state_behavior_codes({})
assert r == []
def test_1(self):
pj_float = json.loads(open("files/test.boris").read())
r = utilities.state_behavior_codes(pj_float["behaviors_conf"])
# print(r)
assert r == ['s', 'r', 'm']
def test_empty_ethogram(self):
r = utilities.state_behavior_codes({})
assert r == []
def test_1(self):
pj_float = json.loads(open("files/test.boris").read())
r = utilities.state_behavior_codes(pj_float["behaviors_conf"])
# print(r)
assert r == ['s', 'r', 'm']
