def set_to_current_time(self):
"""
set time to current media time
"""
self.teTime.setTime(
QTime.fromString(seconds2time(self.current_time), HHMMSSZZZ))
self.dsbTime.setValue(float(self.current_time))
def choose_obs_subj_behav_category(pj: dict,
selected_observations: list,
maxTime=0,
flagShowIncludeModifiers: bool = True,
flagShowExcludeBehaviorsWoEvents: bool = True,
by_category: bool = False,
show_time: bool = False,
timeFormat: str = HHMMSS):
"""
show window for:
- selection of subjects
- selection of behaviors (based on selected subjects)
- selection of time interval
- inclusion/exclusion of modifiers
- inclusion/exclusion of behaviors without events (flagShowExcludeBehaviorsWoEvents == True)
Returns:
dict: {"selected subjects": selectedSubjects,
"selected behaviors": selectedBehaviors,
"include modifiers": True/False,
"exclude behaviors": True/False,
"time": TIME_FULL_OBS / TIME_EVENTS / TIME_ARBITRARY_INTERVAL
"start time": startTime,
"end time": endTime
}
"""
paramPanelWindow = param_panel.Param_panel()
paramPanelWindow.resize(600, 500)
paramPanelWindow.setWindowTitle("Select subjects and behaviors")
paramPanelWindow.selectedObservations = selected_observations
paramPanelWindow.pj = pj
if not flagShowIncludeModifiers:
paramPanelWindow.cbIncludeModifiers.setVisible(False)
if not flagShowExcludeBehaviorsWoEvents:
paramPanelWindow.cbExcludeBehaviors.setVisible(False)
if by_category:
paramPanelWindow.cbIncludeModifiers.setVisible(False)
paramPanelWindow.cbExcludeBehaviors.setVisible(False)
paramPanelWindow.frm_time_interval.setEnabled(False)
if timeFormat == HHMMSS:
paramPanelWindow.teStartTime.setTime(QTime.fromString("00:00:00.000", "hh:mm:ss.zzz"))
paramPanelWindow.teEndTime.setTime(QTime.fromString(utilities.seconds2time(maxTime), "hh:mm:ss.zzz"))
paramPanelWindow.dsbStartTime.setVisible(False)
paramPanelWindow.dsbEndTime.setVisible(False)
if timeFormat == S:
paramPanelWindow.dsbStartTime.setValue(0.0)
paramPanelWindow.dsbEndTime.setValue(maxTime)
paramPanelWindow.teStartTime.setVisible(False)
paramPanelWindow.teEndTime.setVisible(False)
# hide max time
if not maxTime:
paramPanelWindow.frm_time.setVisible(False)
if selected_observations:
observedSubjects = project_functions.extract_observed_subjects(pj, selected_observations)
else:
# load all subjects and "No focal subject"
observedSubjects = [pj[SUBJECTS][x][SUBJECT_NAME] for x in pj[SUBJECTS]] + [""]
selectedSubjects = []
# add 'No focal subject'
if "" in observedSubjects:
selectedSubjects.append(NO_FOCAL_SUBJECT)
paramPanelWindow.item = QListWidgetItem(paramPanelWindow.lwSubjects)
paramPanelWindow.ch = QCheckBox()
paramPanelWindow.ch.setText(NO_FOCAL_SUBJECT)
paramPanelWindow.ch.stateChanged.connect(paramPanelWindow.cb_changed)
paramPanelWindow.ch.setChecked(True)
paramPanelWindow.lwSubjects.setItemWidget(paramPanelWindow.item, paramPanelWindow.ch)
all_subjects = [pj[SUBJECTS][x][SUBJECT_NAME] for x in utilities.sorted_keys(pj[SUBJECTS])]
for subject in all_subjects:
paramPanelWindow.item = QListWidgetItem(paramPanelWindow.lwSubjects)
paramPanelWindow.ch = QCheckBox()
paramPanelWindow.ch.setText(subject)
paramPanelWindow.ch.stateChanged.connect(paramPanelWindow.cb_changed)
if subject in observedSubjects:
selectedSubjects.append(subject)
paramPanelWindow.ch.setChecked(True)
paramPanelWindow.lwSubjects.setItemWidget(paramPanelWindow.item, paramPanelWindow.ch)
logging.debug(f'selectedSubjects: {selectedSubjects}')
if selected_observations:
observedBehaviors = paramPanelWindow.extract_observed_behaviors(selected_observations, selectedSubjects) # not sorted
else:
# load all behaviors
observedBehaviors = [pj[ETHOGRAM][x][BEHAVIOR_CODE] for x in pj[ETHOGRAM]]
logging.debug(f'observed behaviors: {observedBehaviors}')
if BEHAVIORAL_CATEGORIES in pj:
categories = pj[BEHAVIORAL_CATEGORIES][:]
# check if behavior not included in a category
try:
if "" in [pj[ETHOGRAM][idx][BEHAVIOR_CATEGORY] for idx in pj[ETHOGRAM] if BEHAVIOR_CATEGORY in pj[ETHOGRAM][idx]]:
categories += [""]
except Exception:
categories = ["###no category###"]
else:
categories = ["###no category###"]
for category in categories:
if category != "###no category###":
if category == "":
paramPanelWindow.item = QListWidgetItem("No category")
paramPanelWindow.item.setData(34, "No category")
else:
paramPanelWindow.item = QListWidgetItem(category)
paramPanelWindow.item.setData(34, category)
font = QFont()
font.setBold(True)
paramPanelWindow.item.setFont(font)
paramPanelWindow.item.setData(33, "category")
paramPanelWindow.item.setData(35, False)
paramPanelWindow.lwBehaviors.addItem(paramPanelWindow.item)
for behavior in [pj[ETHOGRAM][x][BEHAVIOR_CODE] for x in utilities.sorted_keys(pj[ETHOGRAM])]:
if ((categories == ["###no category###"])
or (behavior in [pj[ETHOGRAM][x][BEHAVIOR_CODE] for x in pj[ETHOGRAM]
if BEHAVIOR_CATEGORY in pj[ETHOGRAM][x] and pj[ETHOGRAM][x][BEHAVIOR_CATEGORY] == category])):
paramPanelWindow.item = QListWidgetItem(behavior)
if behavior in observedBehaviors:
paramPanelWindow.item.setCheckState(Qt.Checked)
else:
paramPanelWindow.item.setCheckState(Qt.Unchecked)
if category != "###no category###":
paramPanelWindow.item.setData(33, "behavior")
if category == "":
paramPanelWindow.item.setData(34, "No category")
else:
paramPanelWindow.item.setData(34, category)
paramPanelWindow.lwBehaviors.addItem(paramPanelWindow.item)
if not paramPanelWindow.exec_():
return {SELECTED_SUBJECTS: [],
SELECTED_BEHAVIORS: []}
selectedSubjects = paramPanelWindow.selectedSubjects
selectedBehaviors = paramPanelWindow.selectedBehaviors
logging.debug(f"selected subjects: {selectedSubjects}")
logging.debug(f"selected behaviors: {selectedBehaviors}")
if timeFormat == HHMMSS:
startTime = utilities.time2seconds(paramPanelWindow.teStartTime.time().toString(HHMMSSZZZ))
endTime = utilities.time2seconds(paramPanelWindow.teEndTime.time().toString(HHMMSSZZZ))
if timeFormat == S:
startTime = Decimal(paramPanelWindow.dsbStartTime.value())
endTime = Decimal(paramPanelWindow.dsbEndTime.value())
if startTime > endTime:
QMessageBox.warning(None, programName, "The start time is after the end time",
QMessageBox.Ok | QMessageBox.Default, QMessageBox.NoButton)
return {SELECTED_SUBJECTS: [], SELECTED_BEHAVIORS: []}
if paramPanelWindow.rb_full.isChecked():
time_param = TIME_FULL_OBS
if paramPanelWindow.rb_limit.isChecked():
time_param = TIME_EVENTS
if paramPanelWindow.rb_interval.isChecked():
time_param = TIME_ARBITRARY_INTERVAL
return {SELECTED_SUBJECTS: selectedSubjects,
SELECTED_BEHAVIORS: selectedBehaviors,
INCLUDE_MODIFIERS: paramPanelWindow.cbIncludeModifiers.isChecked(),
EXCLUDE_BEHAVIORS: paramPanelWindow.cbExcludeBehaviors.isChecked(),
"time": time_param,
START_TIME: startTime,
END_TIME: endTime
}
def create_subtitles(pj: dict, selected_observations: list, parameters: dict,
export_dir: str) -> tuple:
"""
create subtitles for selected observations, subjects and behaviors
Args:
pj (dict): project
selected_observations (list): list of observations
parameters (dict):
export_dir (str): directory to save subtitles
Returns:
bool: True if OK else False
str: error message
"""
def subject_color(subject):
"""
subject color
Args:
subject (str): subject name
Returns:
str: HTML tag for color font (beginning)
str: HTML tag for color font (closing)
"""
if subject == NO_FOCAL_SUBJECT:
return "", ""
else:
return (
"""<font color="{}">""".format(
subtitlesColors[parameters["selected subjects"].index(
row["subject"]) % len(subtitlesColors)]),
"</font>",
)
try:
ok, msg, db_connector = db_functions.load_aggregated_events_in_db(
pj, parameters["selected subjects"], selected_observations,
parameters["selected behaviors"])
if not ok:
return False, msg
cursor = db_connector.cursor()
flag_ok = True
msg = ""
for obsId in selected_observations:
if pj[OBSERVATIONS][obsId][TYPE] in [LIVE]:
out = ""
cursor.execute(
("SELECT subject, behavior, start, stop, type, modifiers FROM aggregated_events "
"WHERE observation = ? AND subject in ({}) "
"AND behavior in ({}) "
"ORDER BY start").format(
",".join(["?"] *
len(parameters["selected subjects"])),
",".join(["?"] *
len(parameters["selected behaviors"]))),
[obsId] + parameters["selected subjects"] +
parameters["selected behaviors"],
)
for idx, row in enumerate(cursor.fetchall()):
col1, col2 = subject_color(row["subject"])
if parameters["include modifiers"]:
modifiers_str = "\n{}".format(row["modifiers"].replace(
"|", ", "))
else:
modifiers_str = ""
out += ("{idx}\n"
"{start} --> {stop}\n"
"{col1}{subject}: {behavior}"
"{modifiers}"
"{col2}\n\n").format(
idx=idx + 1,
start=utilities.seconds2time(
row["start"]).replace(".", ","),
stop=utilities.seconds2time(
row["stop"] if row["type"] ==
STATE else row["stop"] +
POINT_EVENT_ST_DURATION).replace(".", ","),
col1=col1,
col2=col2,
subject=row["subject"],
behavior=row["behavior"],
modifiers=modifiers_str,
)
file_name = str(
pathlib.Path(
pathlib.Path(export_dir) /
utilities.safeFileName(obsId)).with_suffix(".srt"))
try:
with open(file_name, "w") as f:
f.write(out)
except Exception:
flag_ok = False
msg += "observation: {}\ngave the following error:\n{}\n".format(
obsId, str(sys.exc_info()[1]))
elif pj[OBSERVATIONS][obsId][TYPE] in [MEDIA]:
for nplayer in ALL_PLAYERS:
if not pj[OBSERVATIONS][obsId][FILE][nplayer]:
continue
init = 0
for mediaFile in pj[OBSERVATIONS][obsId][FILE][nplayer]:
try:
end = init + pj[OBSERVATIONS][obsId][MEDIA_INFO][
LENGTH][mediaFile]
except KeyError:
return False, f"The length for media file {mediaFile} is not available"
out = ""
print(",".join(["?"] *
len(parameters["selected subjects"])))
print(",".join(["?"] *
len(parameters["selected behaviors"])))
print([obsId, init, end] +
parameters["selected subjects"] +
parameters["selected behaviors"])
cursor.execute(
("SELECT subject, behavior, type, start, stop, modifiers FROM aggregated_events "
"WHERE observation = ? AND start BETWEEN ? and ? "
"AND subject in ({}) "
"AND behavior in ({}) "
"ORDER BY start").format(
",".join(
["?"] *
len(parameters["selected subjects"])),
",".join(
["?"] *
len(parameters["selected behaviors"])),
),
[obsId, init, end] +
parameters["selected subjects"] +
parameters["selected behaviors"],
)
for idx, row in enumerate(cursor.fetchall()):
col1, col2 = subject_color(row["subject"])
if parameters["include modifiers"]:
modifiers_str = "\n{}".format(
row["modifiers"].replace("|", ", "))
else:
modifiers_str = ""
out += (
"{idx}\n"
"{start} --> {stop}\n"
"{col1}{subject}: {behavior}"
"{modifiers}"
"{col2}\n\n").format(
idx=idx + 1,
start=utilities.seconds2time(row["start"] -
init).replace(
".", ","),
stop=utilities.seconds2time(
(row["stop"] if row["type"] ==
STATE else row["stop"] +
POINT_EVENT_ST_DURATION) -
init).replace(".", ","),
col1=col1,
col2=col2,
subject=row["subject"],
behavior=row["behavior"],
modifiers=modifiers_str,
)
file_name = str(
pathlib.Path(
pathlib.Path(export_dir) /
pathlib.Path(mediaFile).name).with_suffix(
".srt"))
try:
with open(file_name, "w") as f:
f.write(out)
except Exception:
flag_ok = False
msg += "observation: {}\ngave the following error:\n{}\n".format(
obsId, str(sys.exc_info()[1]))
init = end
return flag_ok, msg
except Exception:
return False, str(sys.exc_info()[1])
def check_state_events_obs(obsId: str,
ethogram: dict,
observation: dict,
time_format: str = HHMMSS) -> tuple:
"""
check state events for the observation obsId
check if behaviors in observation are defined in ethogram
check if number is odd
Args:
obsId (str): id of observation to check
ethogram (dict): ethogram of project
observation (dict): observation to be checked
time_format (str): time format
Returns:
tuple (bool, str): if OK True else False , message
"""
out = ""
# check if behaviors are defined as "state event"
event_types = {ethogram[idx]["type"] for idx in ethogram}
if not event_types or event_types == {"Point event"}:
return (True, "No behavior is defined as `State event`")
flagStateEvent = False
subjects = [
event[EVENT_SUBJECT_FIELD_IDX] for event in observation[EVENTS]
]
ethogram_behaviors = {ethogram[idx][BEHAVIOR_CODE] for idx in ethogram}
for subject in sorted(set(subjects)):
behaviors = [
event[EVENT_BEHAVIOR_FIELD_IDX] for event in observation[EVENTS]
if event[EVENT_SUBJECT_FIELD_IDX] == subject
]
for behavior in sorted(set(behaviors)):
if behavior not in ethogram_behaviors:
# return (False, "The behaviour <b>{}</b> is not defined in the ethogram.<br>".format(behavior))
continue
else:
if STATE in event_type(behavior, ethogram).upper():
flagStateEvent = True
lst, memTime = [], {}
for event in [
event for event in observation[EVENTS]
if event[EVENT_BEHAVIOR_FIELD_IDX] == behavior
and event[EVENT_SUBJECT_FIELD_IDX] == subject
]:
behav_modif = [
event[EVENT_BEHAVIOR_FIELD_IDX],
event[EVENT_MODIFIER_FIELD_IDX]
]
if behav_modif in lst:
lst.remove(behav_modif)
del memTime[str(behav_modif)]
else:
lst.append(behav_modif)
memTime[str(
behav_modif)] = event[EVENT_TIME_FIELD_IDX]
for event in lst:
out += (
"""The behavior <b>{behavior}</b> {modifier} is not PAIRED for subject"""
""" "<b>{subject}</b>" at <b>{time}</b><br>"""
).format(
behavior=behavior,
modifier=("(modifier " + event[1] +
") ") if event[1] else "",
subject=subject if subject else NO_FOCAL_SUBJECT,
time=memTime[str(event)] if time_format == S else
utilities.seconds2time(memTime[str(event)]),
)
return (False, out) if out else (True, "No problem detected")
def test_10(self):
assert utilities.seconds2time(Decimal(10.0)) == "00:00:10.000"
def test_gt_86400(self):
assert utilities.seconds2time(
Decimal(86400.999)) == "24:00:00.999"
def test_negative(self):
assert utilities.seconds2time(
Decimal(-2.123)) == "-00:00:02.123"
def test_10(self):
assert utilities.seconds2time(Decimal(10.0)) == "00:00:10.000"
def test_gt_86400(self):
assert utilities.seconds2time(
Decimal(86400.999)) == "24:00:00.999"
def test_negative(self):
assert utilities.seconds2time(
Decimal(-2.123)) == "-00:00:02.123"
def create_subtitles(pj: dict,
selected_observations: list,
parameters: dict,
export_dir: str) -> tuple:
"""
create subtitles for selected observations, subjects and behaviors
Args:
pj (dict): project
selected_observations (list): list of observations
parameters (dict):
export_dir (str): directory to save subtitles
Returns:
bool: True if OK else False
str: error message
"""
def subject_color(subject):
"""
subject color
Args:
subject (str): subject name
Returns:
str: HTML tag for color font (beginning)
str: HTML tag for color font (closing)
"""
if subject == NO_FOCAL_SUBJECT:
return "", ""
else:
return (
"""<font color="{}">""".format(
subtitlesColors[parameters["selected subjects"].index(row["subject"]) % len(subtitlesColors)]
),
"</font>",
)
try:
ok, msg, db_connector = db_functions.load_aggregated_events_in_db(
pj, parameters["selected subjects"], selected_observations, parameters["selected behaviors"]
)
if not ok:
return False, msg
cursor = db_connector.cursor()
flag_ok = True
msg = ""
for obsId in selected_observations:
if pj[OBSERVATIONS][obsId][TYPE] in [LIVE]:
out = ""
cursor.execute(
(
"SELECT subject, behavior, start, stop, type, modifiers FROM aggregated_events "
"WHERE observation = ? AND subject in ({}) "
"AND behavior in ({}) "
"ORDER BY start"
).format(",".join(["?"] * len(parameters["selected subjects"])),
",".join(["?"] * len(parameters["selected behaviors"]))),
[obsId] + parameters["selected subjects"] + parameters["selected behaviors"],
)
for idx, row in enumerate(cursor.fetchall()):
col1, col2 = subject_color(row["subject"])
if parameters["include modifiers"]:
modifiers_str = "\n{}".format(row["modifiers"].replace("|", ", "))
else:
modifiers_str = ""
out += ("{idx}\n" "{start} --> {stop}\n" "{col1}{subject}: {behavior}" "{modifiers}" "{col2}\n\n").format(
idx=idx + 1,
start=utilities.seconds2time(row["start"]).replace(".", ","),
stop=utilities.seconds2time(row["stop"] if row["type"] == STATE else row["stop"] + POINT_EVENT_ST_DURATION).replace(
".", ","
),
col1=col1,
col2=col2,
subject=row["subject"],
behavior=row["behavior"],
modifiers=modifiers_str,
)
file_name = str(pathlib.Path(pathlib.Path(export_dir) / utilities.safeFileName(obsId)).with_suffix(".srt"))
try:
with open(file_name, "w") as f:
f.write(out)
except Exception:
flag_ok = False
msg += "observation: {}\ngave the following error:\n{}\n".format(obsId, str(sys.exc_info()[1]))
elif pj[OBSERVATIONS][obsId][TYPE] in [MEDIA]:
for nplayer in ALL_PLAYERS:
if not pj[OBSERVATIONS][obsId][FILE][nplayer]:
continue
init = 0
for mediaFile in pj[OBSERVATIONS][obsId][FILE][nplayer]:
try:
end = init + pj[OBSERVATIONS][obsId][MEDIA_INFO][LENGTH][mediaFile]
except KeyError:
return False, f"The length for media file {mediaFile} is not available"
out = ""
print(",".join(["?"] * len(parameters["selected subjects"])))
print(",".join(["?"] * len(parameters["selected behaviors"])))
print([obsId, init, end] + parameters["selected subjects"] + parameters["selected behaviors"])
cursor.execute(
(
"SELECT subject, behavior, type, start, stop, modifiers FROM aggregated_events "
"WHERE observation = ? AND start BETWEEN ? and ? "
"AND subject in ({}) "
"AND behavior in ({}) "
"ORDER BY start"
).format(
",".join(["?"] * len(parameters["selected subjects"])),
",".join(["?"] * len(parameters["selected behaviors"])),
),
[obsId, init, end] + parameters["selected subjects"] + parameters["selected behaviors"],
)
for idx, row in enumerate(cursor.fetchall()):
col1, col2 = subject_color(row["subject"])
if parameters["include modifiers"]:
modifiers_str = "\n{}".format(row["modifiers"].replace("|", ", "))
else:
modifiers_str = ""
out += ("{idx}\n" "{start} --> {stop}\n" "{col1}{subject}: {behavior}" "{modifiers}" "{col2}\n\n").format(
idx=idx + 1,
start=utilities.seconds2time(row["start"] - init).replace(".", ","),
stop=utilities.seconds2time(
(row["stop"] if row["type"] == STATE else row["stop"] + POINT_EVENT_ST_DURATION) - init
).replace(".", ","),
col1=col1,
col2=col2,
subject=row["subject"],
behavior=row["behavior"],
modifiers=modifiers_str,
)
file_name = str(pathlib.Path(pathlib.Path(export_dir) / pathlib.Path(mediaFile).name).with_suffix(".srt"))
try:
with open(file_name, "w") as f:
f.write(out)
except Exception:
flag_ok = False
msg += "observation: {}\ngave the following error:\n{}\n".format(obsId, str(sys.exc_info()[1]))
init = end
return flag_ok, msg
except Exception:
return False, str(sys.exc_info()[1])
def check_state_events_obs(obsId: str, ethogram: dict, observation: dict, time_format: str = HHMMSS) -> tuple:
"""
check state events for the observation obsId
check if behaviors in observation are defined in ethogram
check if number is odd
Args:
obsId (str): id of observation to check
ethogram (dict): ethogram of project
observation (dict): observation to be checked
time_format (str): time format
Returns:
tuple (bool, str): if OK True else False , message
"""
out = ""
# check if behaviors are defined as "state event"
event_types = {ethogram[idx]["type"] for idx in ethogram}
if not event_types or event_types == {"Point event"}:
return (True, "No behavior is defined as `State event`")
flagStateEvent = False
subjects = [event[EVENT_SUBJECT_FIELD_IDX] for event in observation[EVENTS]]
ethogram_behaviors = {ethogram[idx][BEHAVIOR_CODE] for idx in ethogram}
for subject in sorted(set(subjects)):
behaviors = [event[EVENT_BEHAVIOR_FIELD_IDX] for event in observation[EVENTS] if event[EVENT_SUBJECT_FIELD_IDX] == subject]
for behavior in sorted(set(behaviors)):
if behavior not in ethogram_behaviors:
# return (False, "The behaviour <b>{}</b> is not defined in the ethogram.<br>".format(behavior))
continue
else:
if STATE in event_type(behavior, ethogram).upper():
flagStateEvent = True
lst, memTime = [], {}
for event in [
event
for event in observation[EVENTS]
if event[EVENT_BEHAVIOR_FIELD_IDX] == behavior and event[EVENT_SUBJECT_FIELD_IDX] == subject
]:
behav_modif = [event[EVENT_BEHAVIOR_FIELD_IDX], event[EVENT_MODIFIER_FIELD_IDX]]
if behav_modif in lst:
lst.remove(behav_modif)
del memTime[str(behav_modif)]
else:
lst.append(behav_modif)
memTime[str(behav_modif)] = event[EVENT_TIME_FIELD_IDX]
for event in lst:
out += (
"""The behavior <b>{behavior}</b> {modifier} is not PAIRED for subject"""
""" "<b>{subject}</b>" at <b>{time}</b><br>"""
).format(
behavior=behavior,
modifier=("(modifier " + event[1] + ") ") if event[1] else "",
subject=subject if subject else NO_FOCAL_SUBJECT,
time=memTime[str(event)] if time_format == S else utilities.seconds2time(memTime[str(event)]),
)
return (False, out) if out else (True, "No problem detected")
