pj[SUBJECTS][k]["name"]
for k in utilities.sorted_keys(pj[SUBJECTS])
] + [NO_FOCAL_SUBJECT]
ok, msg, db_connector = db_functions.load_aggregated_events_in_db(
pj, subjects, observations_id_list, behaviors)
if not ok:
print(cleanhtml(msg))
sys.exit()
cursor = db_connector.cursor()
interval = 1
if len(args.command) > 1:
interval = utilities.float2decimal(args.command[1])
include_modifiers = True
if len(args.command) > 2:
include_modifiers = "TRUE" in args.command[2].upper()
K, out = irr.cohen_kappa(cursor, observations_id_list[0],
observations_id_list[1], interval, subjects,
include_modifiers)
print(("Cohen's Kappa - Index of Inter-Rater Reliability\n\n"
"Interval time: {interval:.3f} s\n").format(interval=interval))
print(out)
sys.exit()
def test_1(self):
r = utilities.float2decimal(0.001)
assert r == Decimal(str(0.001))
def behavior_binary_table(pj: dict):
"""
ask user for parameters for behavior binary table
call create_behavior_binary_table
"""
result, selected_observations = select_observations.select_observations(
pj, MULTIPLE, "Select observations for the behavior binary table")
if not selected_observations:
return
# check if state events are paired
out = ""
not_paired_obs_list = []
for obs_id in selected_observations:
r, msg = project_functions.check_state_events_obs(
obs_id, pj[ETHOGRAM], pj[OBSERVATIONS][obs_id])
if not r:
out += f"Observation: <strong>{obs_id}</strong><br>{msg}<br>"
not_paired_obs_list.append(obs_id)
if out:
out = f"The observations with UNPAIRED state events will be removed from the analysis<br><br>{out}"
results = dialog.Results_dialog()
results.setWindowTitle(f"{programName} - Check selected observations")
results.ptText.setReadOnly(True)
results.ptText.appendHtml(out)
results.pbSave.setVisible(False)
results.pbCancel.setVisible(True)
if not results.exec_():
return
selected_observations = [
x for x in selected_observations if x not in not_paired_obs_list
]
if not selected_observations:
return
max_obs_length, selectedObsTotalMediaLength = project_functions.observation_length(
pj, selected_observations)
if max_obs_length == -1: # media length not available, user choose to not use events
return
parameters = dialog.choose_obs_subj_behav_category(
pj,
selected_observations,
maxTime=max_obs_length,
flagShowIncludeModifiers=True,
flagShowExcludeBehaviorsWoEvents=True,
by_category=False)
if not parameters[SELECTED_SUBJECTS] or not parameters[SELECTED_BEHAVIORS]:
QMessageBox.warning(None, programName,
"Select subject(s) and behavior(s) to analyze")
return
# ask for time interval
i, ok = QInputDialog.getDouble(None, "Behavior binary table",
"Time interval (in seconds):", 1.0, 0.001,
86400, 3)
if not ok:
return
time_interval = utilities.float2decimal(i)
'''
iw = dialog.Info_widget()
iw.lwi.setVisible(False)
iw.resize(350, 200)
iw.setWindowFlags(Qt.WindowStaysOnTopHint)
iw.setWindowTitle("Behavior binary table")
iw.label.setText("Creating the behavior binary table...")
iw.show()
QApplication.processEvents()
'''
results_df = create_behavior_binary_table(pj, selected_observations,
parameters, time_interval)
'''
iw.hide()
'''
if "error" in results_df:
QMessageBox.warning(None, programName, results_df["msg"])
return
# save results
if len(selected_observations) == 1:
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(
None, "Save results", "", ";;".join(extended_file_formats))
if not file_name:
return
output_format = file_formats[extended_file_formats.index(filter_)]
if pathlib.Path(file_name).suffix != "." + output_format:
file_name = str(pathlib.Path(file_name)) + "." + output_format
# 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
else:
items = ("Tab Separated Values (*.tsv)",
"Comma separated values (*.csv)",
"Open Document Spreadsheet (*.ods)",
"Microsoft Excel Spreadsheet XLSX (*.xlsx)",
"Legacy Microsoft Excel Spreadsheet XLS (*.xls)",
"HTML (*.html)")
item, ok = QInputDialog.getItem(None, "Save results",
"Available formats", items, 0, False)
if not ok:
return
output_format = re.sub(".* \(\*\.", "", item)[:-1]
export_dir = QFileDialog().getExistingDirectory(
None,
"Choose a directory to save results",
os.path.expanduser("~"),
options=QFileDialog.ShowDirsOnly)
if not export_dir:
return
mem_command = ""
for obs_id in results_df:
for subject in results_df[obs_id]:
if len(selected_observations) > 1:
file_name_with_subject = str(
pathlib.Path(export_dir) /
utilities.safeFileName(obs_id + "_" +
subject)) + "." + output_format
else:
file_name_with_subject = str(
os.path.splitext(file_name)[0] +
utilities.safeFileName("_" +
subject)) + "." + output_format
# check if file with new extension already exists
if mem_command != OVERWRITE_ALL and pathlib.Path(
file_name_with_subject).is_file():
if mem_command == "Skip all":
continue
mem_command = dialog.MessageDialog(
programName,
f"The file {file_name_with_subject} already exists.",
[OVERWRITE, OVERWRITE_ALL, "Skip", "Skip all", CANCEL])
if mem_command == CANCEL:
return
if mem_command in ["Skip", "Skip all"]:
continue
try:
if output_format in ["csv", "tsv", "html"]:
with open(file_name_with_subject, "wb") as f:
f.write(
str.encode(results_df[obs_id][subject].export(
output_format)))
if output_format in ["ods", "xlsx", "xls"]:
with open(file_name_with_subject, "wb") as f:
f.write(
results_df[obs_id][subject].export(output_format))
except Exception:
error_type, error_file_name, error_lineno = utilities.error_info(
sys.exc_info())
logging.critical(
f"Error in behavior binary table function: {error_type} {error_file_name} {error_lineno}"
)
QMessageBox.critical(None, programName,
f"Error saving file: {error_type}")
return
def test_1(self):
r = utilities.float2decimal(0.001)
assert r == Decimal(str(0.001))
