def events_to_behavioral_sequences_all_subj(pj, obs_id: str,
subjects_list: list,
parameters: dict,
behav_seq_separator: str) -> str:
"""
return the behavioral sequences for all selected subjects in obs_id
Args:
pj (dict): project
obs_id (str): observation id
subjects_list (list): list of subjects
parameters (dict): parameters
behav_seq_separator (str): separator of behviors in behavioral sequences
Returns:
str: behavioral sequences for all selected subjects in selected observation
"""
out = ""
current_states = {i: [] for i in subjects_list}
events_with_status = project_functions.events_start_stop(
pj[ETHOGRAM], pj[OBSERVATIONS][obs_id][EVENTS])
for event in events_with_status:
# check if event in selected behaviors
if event[EVENT_BEHAVIOR_FIELD_IDX] not in parameters[
SELECTED_BEHAVIORS]:
continue
if (event[EVENT_SUBJECT_FIELD_IDX]
in subjects_list) or (event[EVENT_SUBJECT_FIELD_IDX] == ""
and NO_FOCAL_SUBJECT in subjects_list):
subject = event[EVENT_SUBJECT_FIELD_IDX] if event[
EVENT_SUBJECT_FIELD_IDX] else NO_FOCAL_SUBJECT
if event[-1] == POINT:
if current_states[subject]:
out += f"[{subject}]" + "+".join(
current_states[subject]
) + "+" + event[EVENT_BEHAVIOR_FIELD_IDX]
else:
out += f"[{subject}]" + event[EVENT_BEHAVIOR_FIELD_IDX]
if parameters[INCLUDE_MODIFIERS]:
out += "&" + event[EVENT_MODIFIER_FIELD_IDX].replace(
"|", "+")
out += behav_seq_separator
if event[-1] == START:
if parameters[INCLUDE_MODIFIERS]:
current_states[subject].append(
(f"{event[EVENT_BEHAVIOR_FIELD_IDX]}"
f"{'&' if event[EVENT_MODIFIER_FIELD_IDX] else ''}"
f"{event[EVENT_MODIFIER_FIELD_IDX].replace('|', ';')}"
))
else:
current_states[subject].append(
event[EVENT_BEHAVIOR_FIELD_IDX])
out += f"[{subject}]" + "+".join(
sorted(current_states[subject]))
out += behav_seq_separator
if event[-1] == STOP:
if parameters[INCLUDE_MODIFIERS]:
behav_modif = (
f"{event[EVENT_BEHAVIOR_FIELD_IDX]}"
f"{'&' if event[EVENT_MODIFIER_FIELD_IDX] else ''}"
f"{event[EVENT_MODIFIER_FIELD_IDX].replace('|', ';')}")
else:
behav_modif = event[EVENT_BEHAVIOR_FIELD_IDX]
if behav_modif in current_states[subject]:
current_states[subject].remove(behav_modif)
if current_states[subject]:
out += f"[{subject}]" + "+".join(
sorted(current_states[subject]))
out += behav_seq_separator
# remove last separator (if separator not empty)
if behav_seq_separator:
out = out[0:-len(behav_seq_separator)]
return out
def export_events(parameters, obsId, observation, ethogram, file_name,
output_format):
"""
export events
Args:
parameters (dict): subjects, behaviors
obsId (str): observation id
observation (dict): observation
ethogram (dict): ethogram of project
file_name (str): file name for exporting events
output_format (str): output for exporting events
Returns:
bool: result: True if OK else False
str: error message
"""
total_length = f"{project_functions.observation_total_length(observation):.3f}"
eventsWithStatus = project_functions.events_start_stop(
ethogram, observation[EVENTS])
# check max number of modifiers
max_modifiers = 0
for event in eventsWithStatus:
for c in pj_events_fields:
if c == "modifier" and event[pj_obs_fields[c]]:
max_modifiers = max(max_modifiers,
len(event[pj_obs_fields[c]].split("|")))
# media file number
mediaNb = 0
if observation["type"] == MEDIA:
for player in observation[FILE]:
mediaNb += len(observation[FILE][player])
rows = []
# observation id
rows.append(["Observation id", obsId])
rows.append([""])
# media file name
if observation["type"] in [MEDIA]:
rows.append(["Media file(s)"])
elif observation["type"] in [LIVE]:
rows.append(["Live observation"])
else:
rows.append(["?"])
rows.append([""])
if observation[TYPE] in [MEDIA]:
for player in sorted(list(observation[FILE].keys())):
for media in observation[FILE][player]:
rows.append([f"Player #{player}", media])
rows.append([""])
# date
if "date" in observation:
rows.append(
["Observation date", observation["date"].replace("T", " ")])
rows.append([""])
# description
if "description" in observation:
rows.append(
["Description",
utilities.eol2space(observation["description"])])
rows.append([""])
# time offset
if "time offset" in observation:
rows.append(["Time offset (s)", observation["time offset"]])
rows.append([""])
# independent variables
if INDEPENDENT_VARIABLES in observation:
rows.extend([["independent variables"], ["variable", "value"]])
for variable in observation[INDEPENDENT_VARIABLES]:
rows.append(
[variable, observation[INDEPENDENT_VARIABLES][variable]])
rows.append([""])
# write table header
col = 0
header = ["Time"]
header.extend(["Media file path", "Total length", "FPS"])
header.extend(["Subject", "Behavior", "Behavioral category"])
behavioral_category = project_functions.behavior_category(ethogram)
for x in range(1, max_modifiers + 1):
header.append(f"Modifier {x}")
header.extend(["Comment", "Status"])
rows.append(header)
duration1 = [] # in seconds
if observation["type"] in [MEDIA]:
try:
for mediaFile in observation[FILE][PLAYER1]:
duration1.append(observation[MEDIA_INFO]["length"][mediaFile])
except KeyError:
pass
for event in eventsWithStatus:
if (((event[SUBJECT_EVENT_FIELD] in parameters["selected subjects"]) or
(event[SUBJECT_EVENT_FIELD] == ""
and NO_FOCAL_SUBJECT in parameters["selected subjects"])) and
(event[BEHAVIOR_EVENT_FIELD] in parameters["selected behaviors"])):
fields = []
fields.append(
utilities.intfloatstr(str(event[EVENT_TIME_FIELD_IDX])))
if observation["type"] in [MEDIA]:
time_ = event[EVENT_TIME_FIELD_IDX] - observation[TIME_OFFSET]
if time_ < 0:
time_ = 0
if duration1:
mediaFileIdx = [
idx1 for idx1, x in enumerate(duration1)
if time_ >= sum(duration1[0:idx1])
][-1]
fields.append(observation[FILE][PLAYER1][mediaFileIdx])
fields.append(total_length)
# FPS
try:
fields.append(observation[MEDIA_INFO]["fps"][
observation[FILE][PLAYER1][mediaFileIdx]]) # fps
except KeyError:
fields.append("NA")
else:
fields.append("NA") # media file
fields.append("NA") # FPS
if observation["type"] in [LIVE]:
fields.append(LIVE) # media
fields.append(total_length) # total length
fields.append("NA") # FPS
fields.append(event[EVENT_SUBJECT_FIELD_IDX])
fields.append(event[EVENT_BEHAVIOR_FIELD_IDX])
# behavioral category
try:
behav_category = behavioral_category[
event[EVENT_BEHAVIOR_FIELD_IDX]]
except Exception:
behav_category = ""
fields.append(behav_category)
# modifiers
if max_modifiers:
modifiers = event[EVENT_MODIFIER_FIELD_IDX].split("|")
while len(modifiers) < max_modifiers:
modifiers.append("")
for m in modifiers:
fields.append(m)
# comment
fields.append(event[EVENT_COMMENT_FIELD_IDX].replace(
os.linesep, " "))
# status
fields.append(event[-1])
rows.append(fields)
maxLen = max([len(r) for r in rows])
data = tablib.Dataset()
data.title = utilities.safe_xl_worksheet_title(obsId, output_format)
'''
if output_format in ["xls", "xlsx"]:
for forbidden_char in EXCEL_FORBIDDEN_CHARACTERS:
data.title = data.title.replace(forbidden_char, " ")
if output_format in ["xls"]:
if len(data.title) > 31:
data.title = data.title[0:31]
'''
for row in rows:
data.append(utilities.complete(row, maxLen))
r, msg = dataset_write(data, file_name, output_format)
return r, msg
def events_to_behavioral_sequences(pj,
obs_id: str,
subj: str,
parameters: dict,
behav_seq_separator: str) -> str:
"""
return the behavioral sequence (behavioral string) for subject in obsId
Args:
pj (dict): project
obs_id (str): observation id
subj (str): subject
parameters (dict): parameters
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])
for event in events_with_status:
# check if event in selected behaviors
if event[EVENT_BEHAVIOR_FIELD_IDX] not in parameters[SELECTED_BEHAVIORS]:
continue
if event[EVENT_SUBJECT_FIELD_IDX] == subj or (subj == NO_FOCAL_SUBJECT and event[EVENT_SUBJECT_FIELD_IDX] == ""):
if event[-1] == POINT:
if current_states:
out += "+".join(current_states) + "+" + event[EVENT_BEHAVIOR_FIELD_IDX]
else:
out += event[EVENT_BEHAVIOR_FIELD_IDX]
if parameters[INCLUDE_MODIFIERS]:
out += "&" + event[EVENT_MODIFIER_FIELD_IDX].replace("|", "+")
out += behav_seq_separator
if event[-1] == START:
if parameters[INCLUDE_MODIFIERS]:
current_states.append("{}{}{}".format(event[EVENT_BEHAVIOR_FIELD_IDX],
"&" if event[EVENT_MODIFIER_FIELD_IDX] else "",
event[EVENT_MODIFIER_FIELD_IDX].replace("|", ";")))
else:
current_states.append(event[EVENT_BEHAVIOR_FIELD_IDX])
out += "+".join(sorted(current_states))
out += behav_seq_separator
if event[-1] == STOP:
if parameters[INCLUDE_MODIFIERS]:
behav_modif = "{}{}{}".format(event[EVENT_BEHAVIOR_FIELD_IDX],
"&" if event[EVENT_MODIFIER_FIELD_IDX] else "",
event[EVENT_MODIFIER_FIELD_IDX].replace("|", ";"))
else:
behav_modif = event[EVENT_BEHAVIOR_FIELD_IDX]
if behav_modif in current_states:
current_states.remove(behav_modif)
if current_states:
out += "+".join(sorted(current_states))
out += behav_seq_separator
# remove last separator (if separator not empty)
if behav_seq_separator:
out = out[0: -len(behav_seq_separator)]
return out
def events_to_behavioral_sequences(pj, obs_id: str, subj: str,
parameters: dict,
behav_seq_separator: str) -> str:
"""
return the behavioral sequence (behavioral string) for subject in obsId
Args:
pj (dict): project
obs_id (str): observation id
subj (str): subject
parameters (dict): parameters
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])
for event in events_with_status:
# check if event in selected behaviors
if event[EVENT_BEHAVIOR_FIELD_IDX] not in parameters[
SELECTED_BEHAVIORS]:
continue
if event[EVENT_SUBJECT_FIELD_IDX] == subj or (
subj == NO_FOCAL_SUBJECT
and event[EVENT_SUBJECT_FIELD_IDX] == ""):
if event[-1] == POINT:
if current_states:
out += "+".join(
current_states) + "+" + event[EVENT_BEHAVIOR_FIELD_IDX]
else:
out += event[EVENT_BEHAVIOR_FIELD_IDX]
if parameters[INCLUDE_MODIFIERS]:
out += "&" + event[EVENT_MODIFIER_FIELD_IDX].replace(
"|", "+")
out += behav_seq_separator
if event[-1] == START:
if parameters[INCLUDE_MODIFIERS]:
current_states.append("{}{}{}".format(
event[EVENT_BEHAVIOR_FIELD_IDX],
"&" if event[EVENT_MODIFIER_FIELD_IDX] else "",
event[EVENT_MODIFIER_FIELD_IDX].replace("|", ";")))
else:
current_states.append(event[EVENT_BEHAVIOR_FIELD_IDX])
out += "+".join(sorted(current_states))
out += behav_seq_separator
if event[-1] == STOP:
if parameters[INCLUDE_MODIFIERS]:
behav_modif = "{}{}{}".format(
event[EVENT_BEHAVIOR_FIELD_IDX],
"&" if event[EVENT_MODIFIER_FIELD_IDX] else "",
event[EVENT_MODIFIER_FIELD_IDX].replace("|", ";"))
else:
behav_modif = event[EVENT_BEHAVIOR_FIELD_IDX]
if behav_modif in current_states:
current_states.remove(behav_modif)
if current_states:
out += "+".join(sorted(current_states))
out += behav_seq_separator
# remove last separator (if separator not empty)
if behav_seq_separator:
out = out[0:-len(behav_seq_separator)]
return out
def export_events(parameters, obsId, observation, ethogram, file_name, output_format):
"""
export events
Args:
parameters (dict): subjects, behaviors
obsId (str): observation id
observation (dict): observation
ethogram (dict): ethogram of project
file_name (str): file name for exporting events
output_format (str): output for exporting events
Returns:
bool: result: True if OK else False
str: error message
"""
total_length = "{0:.3f}".format(project_functions.observation_total_length(observation))
eventsWithStatus = project_functions.events_start_stop(ethogram, observation[EVENTS])
# check max number of modifiers
max_modifiers = 0
for event in eventsWithStatus:
for c in pj_events_fields:
if c == "modifier" and event[pj_obs_fields[c]]:
max_modifiers = max(max_modifiers, len(event[pj_obs_fields[c]].split("|")))
# media file number
mediaNb = 0
if observation["type"] == MEDIA:
for player in observation[FILE]:
mediaNb += len(observation[FILE][player])
rows = []
# observation id
rows.append(["Observation id", obsId])
rows.append([""])
# media file name
if observation["type"] in [MEDIA]:
rows.append(["Media file(s)"])
elif observation["type"] in [LIVE]:
rows.append(["Live observation"])
else:
rows.append(["?"])
rows.append([""])
if observation[TYPE] in [MEDIA]:
for player in sorted(list(observation[FILE].keys())):
for media in observation[FILE][player]:
rows.append(["Player #{0}".format(player), media])
rows.append([""])
# date
if "date" in observation:
rows.append(["Observation date", observation["date"].replace("T", " ")])
rows.append([""])
# description
if "description" in observation:
rows.append(["Description", utilities.eol2space(observation["description"])])
rows.append([""])
# time offset
if "time offset" in observation:
rows.append(["Time offset (s)", observation["time offset"]])
rows.append([""])
# independent variables
if INDEPENDENT_VARIABLES in observation:
rows.extend([["independent variables"], ["variable", "value"]])
for variable in observation[INDEPENDENT_VARIABLES]:
rows.append([variable, observation[INDEPENDENT_VARIABLES][variable]])
rows.append([""])
# write table header
col = 0
header = ["Time"]
header.extend(["Media file path", "Total length", "FPS"])
header.extend(["Subject", "Behavior", "Behavioral category"])
behavioral_category = project_functions.behavior_category(ethogram)
for x in range(1, max_modifiers + 1):
header.append("Modifier {}".format(x))
header.extend(["Comment", "Status"])
rows.append(header)
duration1 = [] # in seconds
if observation["type"] in [MEDIA]:
try:
for mediaFile in observation[FILE][PLAYER1]:
duration1.append(observation[MEDIA_INFO]["length"][mediaFile])
except KeyError:
pass
for event in eventsWithStatus:
if (((event[SUBJECT_EVENT_FIELD] in parameters["selected subjects"]) or
(event[SUBJECT_EVENT_FIELD] == "" and NO_FOCAL_SUBJECT in parameters["selected subjects"])) and
(event[BEHAVIOR_EVENT_FIELD] in parameters["selected behaviors"])):
fields = []
fields.append(utilities.intfloatstr(str(event[EVENT_TIME_FIELD_IDX])))
if observation["type"] in [MEDIA]:
time_ = event[EVENT_TIME_FIELD_IDX] - observation[TIME_OFFSET]
if time_ < 0:
time_ = 0
if duration1:
mediaFileIdx = [idx1 for idx1, x in enumerate(duration1) if time_ >= sum(duration1[0:idx1])][-1]
fields.append(observation[FILE][PLAYER1][mediaFileIdx])
fields.append(total_length)
# FPS
try:
fields.append(observation[MEDIA_INFO]["fps"][observation[FILE][PLAYER1][mediaFileIdx]]) # fps
except KeyError:
fields.append("NA")
else:
fields.append("NA") # media file
fields.append("NA") # FPS
if observation["type"] in [LIVE]:
fields.append(LIVE) # media
fields.append(total_length) # total length
fields.append("NA") # FPS
fields.append(event[EVENT_SUBJECT_FIELD_IDX])
fields.append(event[EVENT_BEHAVIOR_FIELD_IDX])
# behavioral category
try:
behav_category = behavioral_category[event[EVENT_BEHAVIOR_FIELD_IDX]]
except Exception:
behav_category = ""
fields.append(behav_category)
# modifiers
if max_modifiers:
modifiers = event[EVENT_MODIFIER_FIELD_IDX].split("|")
while len(modifiers) < max_modifiers:
modifiers.append("")
for m in modifiers:
fields.append(m)
# comment
fields.append(event[EVENT_COMMENT_FIELD_IDX].replace(os.linesep, " "))
# status
fields.append(event[-1])
rows.append(fields)
maxLen = max([len(r) for r in rows])
data = tablib.Dataset()
data.title = obsId
# check if worksheet name will be > 31 char
if output_format in ["xls", "xlsx"]:
for forbidden_char in EXCEL_FORBIDDEN_CHARACTERS:
data.title = data.title.replace(forbidden_char, " ")
if output_format in ["xls"]:
if len(data.title) > 31:
data.title = data.title[0:31]
for row in rows:
data.append(utilities.complete(row, maxLen))
r, msg = dataset_write(data, file_name, output_format)
return r, msg
