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 pbSave_clicked(self):
"""
save time budget analysis results in TSV, CSV, ODS, XLS format
"""
def complete(l: list, max_: int) -> list:
"""
complete list with empty string until len = max
Args:
l (list): list to complete
max_ (int): length of the returned list
Returns:
list: completed list
"""
while len(l) < max_:
l.append("")
return l
logging.debug("save time budget results to file")
extended_file_formats = [
"Tab Separated Values (*.tsv)", "Comma Separated Values (*.csv)",
"Open Document Spreadsheet ODS (*.ods)",
"Microsoft Excel Spreadsheet XLSX (*.xlsx)",
"Legacy Microsoft Excel Spreadsheet XLS (*.xls)", "HTML (*.html)"
]
file_formats = ["tsv", "csv", "ods", "xlsx", "xls", "html"]
file_name, filter_ = QFileDialog().getSaveFileName(
self, "Save Time budget analysis", "",
";;".join(extended_file_formats))
if not file_name:
return
outputFormat = file_formats[extended_file_formats.index(filter_)]
if pathlib.Path(file_name).suffix != "." + outputFormat:
file_name = str(pathlib.Path(file_name)) + "." + outputFormat
# check if file with new extension already exists
if pathlib.Path(file_name).is_file():
if dialog.MessageDialog(
programName, f"The file {file_name} already exists.",
[CANCEL, OVERWRITE]) == CANCEL:
return
rows = []
# 1 observation
if (self.lw.count() == 1 and self.config_param.get(
TIME_BUDGET_FORMAT, DEFAULT_TIME_BUDGET_FORMAT)
== COMPACT_TIME_BUDGET_FORMAT):
col1, indep_var_label = [], []
# add obs id
col1.append(self.lw.item(0).text())
# add obs date
col1.append(self.pj[OBSERVATIONS][self.lw.item(0).text()].get(
"date", ""))
# description
col1.append(
utilities.eol2space(
self.pj[OBSERVATIONS][self.lw.item(0).text()].get(
DESCRIPTION, "")))
header = ["Observation id", "Observation date", "Description"]
# indep var
for var in self.pj[OBSERVATIONS][self.lw.item(0).text()].get(
INDEPENDENT_VARIABLES, {}):
indep_var_label.append(var)
col1.append(self.pj[OBSERVATIONS][self.lw.item(0).text()]
[INDEPENDENT_VARIABLES][var])
header.extend(indep_var_label)
col1.extend([
f"{self.min_time:0.3f}", f"{self.max_time:0.3f}",
f"{self.max_time - self.min_time:0.3f}"
])
header.extend([
"Time budget start", "Time budget stop", "Time budget duration"
])
for col_idx in range(self.twTB.columnCount()):
header.append(self.twTB.horizontalHeaderItem(col_idx).text())
rows.append(header)
for row_idx in range(self.twTB.rowCount()):
values = []
for col_idx in range(self.twTB.columnCount()):
values.append(
intfloatstr(self.twTB.item(row_idx, col_idx).text()))
rows.append(col1 + values)
else:
# observations list
rows.append(["Observations:"])
for idx in range(self.lw.count()):
rows.append([""])
rows.append(["Observation id", self.lw.item(idx).text()])
rows.append([
"Observation date",
self.pj[OBSERVATIONS][self.lw.item(idx).text()].get(
"date", "")
])
rows.append([
"Description",
utilities.eol2space(
self.pj[OBSERVATIONS][self.lw.item(idx).text()].get(
DESCRIPTION, ""))
])
if INDEPENDENT_VARIABLES in self.pj[OBSERVATIONS][self.lw.item(
idx).text()]:
rows.append(["Independent variables:"])
for var in self.pj[OBSERVATIONS][self.lw.item(
idx).text()][INDEPENDENT_VARIABLES]:
rows.append([
var, self.pj[OBSERVATIONS][self.lw.item(
idx).text()][INDEPENDENT_VARIABLES][var]
])
if self.excluded_behaviors_list.text():
s1, s2 = self.excluded_behaviors_list.text().split(": ")
rows.extend([[""], [s1] + s2.split(", ")])
rows.extend([[""], [""], ["Time budget:"]])
# write header
header = []
for col_idx in range(self.twTB.columnCount()):
header.append(self.twTB.horizontalHeaderItem(col_idx).text())
rows.append(header)
rows.append([""])
for row in range(self.twTB.rowCount()):
values = []
for col_idx in range(self.twTB.columnCount()):
values.append(
intfloatstr(self.twTB.item(row, col_idx).text()))
rows.append(values)
max_row_length = max([len(r) for r in rows])
data = tablib.Dataset()
data.title = "Time budget"
for row in rows:
data.append(complete(row, max_row_length))
if outputFormat in ["tsv", "csv", "html"]:
with open(file_name, "wb") as f:
f.write(str.encode(data.export(outputFormat)))
return
if outputFormat in ["ods", "xlsx", "xls"]:
with open(file_name, "wb") as f:
f.write(data.export(outputFormat))
return
def select_observations(pj: dict, mode: str, windows_title: str = "") -> tuple:
"""
allow user to select observations
mode: accepted values: OPEN, EDIT, SINGLE, MULTIPLE, SELECT1
Args:
pj (dict): BORIS project dictionary
mode (str): mode foe selection: OPEN, EDIT, SINGLE, MULTIPLE, SELECT1
windows_title (str): title for windows
Returns:
str: selected mode: OPEN, EDIT, VIEW
list: list of selected observations
"""
obsListFields = ["id", "date", "description", "subjects", "media"]
indepVarHeader, column_type = [], [TEXT] * len(obsListFields)
if INDEPENDENT_VARIABLES in pj:
for idx in utilities.sorted_keys(pj[INDEPENDENT_VARIABLES]):
indepVarHeader.append(pj[INDEPENDENT_VARIABLES][idx]["label"])
column_type.append(pj[INDEPENDENT_VARIABLES][idx]["type"])
data = []
for obs in sorted(list(pj[OBSERVATIONS].keys())):
date = pj[OBSERVATIONS][obs]["date"].replace("T", " ")
descr = utilities.eol2space(pj[OBSERVATIONS][obs][DESCRIPTION])
# subjects
observedSubjects = [NO_FOCAL_SUBJECT if x == "" else x for x in project_functions.extract_observed_subjects(pj, [obs])]
''' removed 2020-01-13
if "" in observedSubjects:
observedSubjects.remove("")
'''
subjectsList = ", ".join(observedSubjects)
mediaList = []
if pj[OBSERVATIONS][obs][TYPE] in [MEDIA]:
if pj[OBSERVATIONS][obs][FILE]:
for player in sorted(pj[OBSERVATIONS][obs][FILE].keys()):
for media in pj[OBSERVATIONS][obs][FILE][player]:
mediaList.append(f"#{player}: {media}")
if len(mediaList) > 8:
media = " ".join(mediaList)
else:
media = "\n".join(mediaList)
elif pj[OBSERVATIONS][obs][TYPE] in [LIVE]:
media = LIVE
# independent variables
indepvar = []
if INDEPENDENT_VARIABLES in pj[OBSERVATIONS][obs]:
for var_label in indepVarHeader:
if var_label in pj[OBSERVATIONS][obs][INDEPENDENT_VARIABLES]:
indepvar.append(pj[OBSERVATIONS][obs][INDEPENDENT_VARIABLES][var_label])
else:
indepvar.append("")
data.append([obs, date, descr, subjectsList, media] + indepvar)
obsList = observations_list.observationsList_widget(data,
header=obsListFields + indepVarHeader,
column_type=column_type)
if windows_title:
obsList.setWindowTitle(windows_title)
obsList.pbOpen.setVisible(False)
obsList.pbView.setVisible(False)
obsList.pbEdit.setVisible(False)
obsList.pbOk.setVisible(False)
obsList.pbSelectAll.setVisible(False)
obsList.pbUnSelectAll.setVisible(False)
obsList.mode = mode
if mode == OPEN:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOpen.setVisible(True)
if mode == VIEW:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbView.setVisible(True)
if mode == EDIT:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbEdit.setVisible(True)
if mode == SINGLE:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOpen.setVisible(True)
obsList.pbView.setVisible(True)
obsList.pbEdit.setVisible(True)
if mode == MULTIPLE:
obsList.view.setSelectionMode(QAbstractItemView.MultiSelection)
obsList.pbOk.setVisible(True)
obsList.pbSelectAll.setVisible(True)
obsList.pbUnSelectAll.setVisible(True)
if mode == SELECT1:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOk.setVisible(True)
obsList.resize(900, 600)
obsList.view.sortItems(0, Qt.AscendingOrder)
for row in range(obsList.view.rowCount()):
obsList.view.resizeRowToContents(row)
selectedObs = []
result = obsList.exec_()
if result:
if obsList.view.selectedIndexes():
for idx in obsList.view.selectedIndexes():
if idx.column() == 0: # first column
selectedObs.append(idx.data())
if result == 0: # cancel
resultStr = ""
if result == 1: # select
resultStr = "ok"
if result == 2: # open
resultStr = OPEN
if result == 3: # edit
resultStr = EDIT
if result == 4: # view
resultStr = VIEW
return resultStr, selectedObs
def test_r(self):
assert utilities.eol2space("aaa\rbbb") == "aaa bbb"
def test_r(self):
assert utilities.eol2space("aaa\rbbb") == "aaa bbb"
def select_observations(pj: dict, mode: str) -> tuple:
"""
allow user to select observations
mode: accepted values: OPEN, EDIT, SINGLE, MULTIPLE, SELECT1
Args:
pj (dict): BORIS project dictionary
mode (str): mode foe selection: OPEN, EDIT, SINGLE, MULTIPLE, SELECT1
Returns:
str: selected mode: OPEN, EDIT, VIEW
list: list of selected observations
"""
obsListFields = ["id", "date", "description", "subjects", "media"]
indepVarHeader, column_type = [], [TEXT] * len(obsListFields)
if INDEPENDENT_VARIABLES in pj:
for idx in utilities.sorted_keys(pj[INDEPENDENT_VARIABLES]):
indepVarHeader.append(pj[INDEPENDENT_VARIABLES][idx]["label"])
column_type.append(pj[INDEPENDENT_VARIABLES][idx]["type"])
data = []
for obs in sorted(list(pj[OBSERVATIONS].keys())):
date = pj[OBSERVATIONS][obs]["date"].replace("T", " ")
descr = utilities.eol2space(pj[OBSERVATIONS][obs]["description"])
# subjects
observedSubjects = project_functions.extract_observed_subjects(pj, [obs])
# remove when No focal subject
if "" in observedSubjects:
observedSubjects.remove("")
subjectsList = ", ".join(observedSubjects)
mediaList = []
if pj[OBSERVATIONS][obs][TYPE] in [MEDIA]:
if pj[OBSERVATIONS][obs][FILE]:
for player in sorted(pj[OBSERVATIONS][obs][FILE].keys()):
for media in pj[OBSERVATIONS][obs][FILE][player]:
mediaList.append("#{0}: {1}".format(player, media))
if len(mediaList) > 8:
media = " ".join(mediaList)
else:
media = "\n".join(mediaList)
elif pj[OBSERVATIONS][obs][TYPE] in [LIVE]:
media = LIVE
# independent variables
indepvar = []
if INDEPENDENT_VARIABLES in pj[OBSERVATIONS][obs]:
for var_label in indepVarHeader:
if var_label in pj[OBSERVATIONS][obs][INDEPENDENT_VARIABLES]:
indepvar.append(pj[OBSERVATIONS][obs][INDEPENDENT_VARIABLES][var_label])
else:
indepvar.append("")
data.append([obs, date, descr, subjectsList, media] + indepvar)
obsList = observations_list.observationsList_widget(data, header=obsListFields + indepVarHeader, column_type=column_type)
obsList.pbOpen.setVisible(False)
obsList.pbView.setVisible(False)
obsList.pbEdit.setVisible(False)
obsList.pbOk.setVisible(False)
obsList.pbSelectAll.setVisible(False)
obsList.pbUnSelectAll.setVisible(False)
obsList.mode = mode
if mode == OPEN:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOpen.setVisible(True)
if mode == VIEW:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbView.setVisible(True)
if mode == EDIT:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbEdit.setVisible(True)
if mode == SINGLE:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOpen.setVisible(True)
obsList.pbView.setVisible(True)
obsList.pbEdit.setVisible(True)
if mode == MULTIPLE:
obsList.view.setSelectionMode(QAbstractItemView.MultiSelection)
obsList.pbOk.setVisible(True)
obsList.pbSelectAll.setVisible(True)
obsList.pbUnSelectAll.setVisible(True)
if mode == SELECT1:
obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
obsList.pbOk.setVisible(True)
obsList.resize(900, 600)
obsList.view.sortItems(0, Qt.AscendingOrder)
for row in range(obsList.view.rowCount()):
obsList.view.resizeRowToContents(row)
selectedObs = []
result = obsList.exec_()
if result:
if obsList.view.selectedIndexes():
for idx in obsList.view.selectedIndexes():
if idx.column() == 0: # first column
selectedObs.append(idx.data())
if result == 0: # cancel
resultStr = ""
if result == 1: # select
resultStr = "ok"
if result == 2: # open
resultStr = OPEN
if result == 3: # edit
resultStr = EDIT
if result == 4: # view
resultStr = VIEW
return resultStr, selectedObs
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
