def test_time_budget1(self):
pj = json.loads(open("files/test.boris").read())
ethogram = pj[ETHOGRAM]
selected_observations = ["observation #1"]
parameters = {
"selected subjects": ["subject1", "subject2"],
"selected behaviors": ["p", "s"],
INCLUDE_MODIFIERS: False,
EXCLUDE_BEHAVIORS: False,
"start time": 0,
"end time": 100.0
}
cursor = db_functions.load_events_in_db(pj,
parameters[SELECTED_SUBJECTS],
selected_observations,
parameters[SELECTED_BEHAVIORS])
out, categories = time_budget_functions.time_budget_analysis(
ethogram,
cursor,
selected_observations,
parameters,
by_category=False)
# open("files/test_time_budget1new.json", "w").write(json.dumps(out))
assert json.loads(open("files/test_time_budget1.json").read()) == out
def test_1(self):
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["subject1"], ["observation #1"], ["s"])
cursor.execute("SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?", ("observation #1", "subject1", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """3.3\n7.75\n9.9\n16.2\n18.35\n24.475\n"""
assert out == REF
def test_time_budget2(self):
VERIF = [{
"subject": "subject1",
"behavior": "p",
"modifiers": "",
"duration": 0,
"duration_mean": 0,
"duration_stdev": "NA",
"number": "0",
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}, {
"subject": "subject2",
"behavior": "p",
"modifiers": "",
"duration": 0,
"duration_mean": 0,
"duration_stdev": 0,
"number": 2,
"inter_duration_mean": 0.0,
"inter_duration_stdev": "NA"
}]
pj = json.loads(open("files/test.boris").read())
ethogram = pj[ETHOGRAM]
selected_observations = ["observation #2"]
parameters = {
SELECTED_SUBJECTS: ["subject1", "subject2"],
SELECTED_BEHAVIORS: ["p"],
INCLUDE_MODIFIERS: False,
EXCLUDE_BEHAVIORS: False,
"start time": 0,
"end time": 100.0
}
cursor = db_functions.load_events_in_db(pj,
parameters[SELECTED_SUBJECTS],
selected_observations,
parameters[SELECTED_BEHAVIORS])
out, categories = time_budget_functions.time_budget_analysis(
ethogram,
cursor,
selected_observations,
parameters,
by_category=False)
# open("files/test_time_budget2.json", "w").write(json.dumps(out))
assert out == VERIF
def test_time_budget3(self):
VERIF = [{
"subject": "No focal subject",
"behavior": "s",
"modifiers": "",
"duration": 59.625,
"duration_mean": 9.937,
"duration_stdev": 8.395,
"number": 6,
"inter_duration_mean": 49.268,
"inter_duration_stdev": 84.012
}, {
"subject": "No focal subject",
"behavior": "p",
"modifiers": "",
"duration": 0,
"duration_mean": 0,
"duration_stdev": "NA",
"number": 6,
"inter_duration_mean": 54.083,
"inter_duration_stdev": 117.79
}]
pj = json.loads(open("files/test.boris").read())
ethogram = pj[ETHOGRAM]
selected_observations = ["observation #2"]
parameters = {
SELECTED_SUBJECTS: ["No focal subject"],
SELECTED_BEHAVIORS: ["s", "p"],
INCLUDE_MODIFIERS: True,
EXCLUDE_BEHAVIORS: True,
"start time": 0,
"end time": 320.0
}
cursor = db_functions.load_events_in_db(pj,
parameters[SELECTED_SUBJECTS],
selected_observations,
parameters[SELECTED_BEHAVIORS])
out, categories = time_budget_functions.time_budget_analysis(
ethogram,
cursor,
selected_observations,
parameters,
by_category=False)
# open("files/test_time_budget3.json", "w").write(json.dumps(out))
assert out == VERIF
def test_time_budget4(self):
VERIF = [{
"subject": "No focal subject",
"behavior": "s",
"modifiers": "",
"duration": "UNPAIRED",
"duration_mean": "UNPAIRED",
"duration_stdev": "UNPAIRED",
"number": "UNPAIRED",
"inter_duration_mean": "UNPAIRED",
"inter_duration_stdev": "UNPAIRED"
}, {
"subject": "No focal subject",
"behavior": "p",
"modifiers": "",
"duration": "NA",
"duration_mean": "NA",
"duration_stdev": "NA",
"number": 5,
"inter_duration_mean": 3.272,
"inter_duration_stdev": 0.309
}]
pj = json.loads(open("files/test.boris").read())
ethogram = pj[ETHOGRAM]
selected_observations = ["live not paired"]
parameters = {
SELECTED_SUBJECTS: ["No focal subject"],
SELECTED_BEHAVIORS: ["s", "p"],
INCLUDE_MODIFIERS: True,
EXCLUDE_BEHAVIORS: True,
"start time": 0,
"end time": 26.862
}
cursor = db_functions.load_events_in_db(pj,
parameters[SELECTED_SUBJECTS],
selected_observations,
parameters[SELECTED_BEHAVIORS])
out, categories = time_budget_functions.time_budget_analysis(
ethogram,
cursor,
selected_observations,
parameters,
by_category=False)
# open("/tmp/test_time_budget4.json", "w").write(json.dumps(out))
assert out == VERIF
def test_2(self):
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["subject2"], ["live"], ["s", "p"])
cursor.execute("SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
("live", "subject2", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """12.509\n20.685\n"""
assert out == REF
def test_1(self):
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["subject1"],
["observation #1"], ["s"])
cursor.execute(
"SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
("observation #1", "subject1", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """3.3\n7.75\n9.9\n16.2\n18.35\n24.475\n"""
assert out == REF
def test_2(self):
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["subject2"], ["live"],
["s", "p"])
cursor.execute(
"SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
("live", "subject2", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """12.509\n20.685\n"""
assert out == REF
def test_3(self):
"""
no focal subject, observation with not paired events
"""
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["No focal subject"], ["live not paired"], ["s", "p"])
cursor.execute("SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
("live not paired", "No focal subject", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """2.718\n10.478\n12.926\n17.47\n19.502\n24.318\n26.862\n"""
assert out == REF
def test_3(self):
"""
no focal subject, observation with not paired events
"""
pj = json.loads(open("files/test.boris").read())
cursor = db_functions.load_events_in_db(pj, ["No focal subject"],
["live not paired"],
["s", "p"])
cursor.execute(
"SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
("live not paired", "No focal subject", "s"))
out = ""
for r in cursor.fetchall():
out += '{}\n'.format(r[0])
REF = """2.718\n10.478\n12.926\n17.47\n19.502\n24.318\n26.862\n"""
assert out == REF
def export_aggregated_events(pj, parameters, obsId):
"""
export aggregated events
Args:
pj (dict): BORIS project
parameters (dict): subjects, behaviors
obsId (str): observation id
Returns:
tablib.Dataset:
"""
data = tablib.Dataset()
observation = pj[OBSERVATIONS][obsId]
duration1 = [] # in seconds
if observation[TYPE] in [MEDIA]:
try:
for mediaFile in observation[FILE][PLAYER1]:
if "media_info" in observation:
duration1.append(
observation["media_info"]["length"][mediaFile])
except:
duration1 = []
total_length = "{0:.3f}".format(
project_functions.observation_total_length(observation))
cursor = db_functions.load_events_in_db(pj,
parameters["selected subjects"],
[obsId],
parameters["selected behaviors"])
for subject in parameters["selected subjects"]:
for behavior in parameters["selected behaviors"]:
cursor.execute(
"SELECT occurence, modifiers, comment FROM events WHERE observation = ? AND subject = ? AND code = ? ORDER by occurence",
(obsId, subject, behavior))
rows = list(cursor.fetchall())
for idx, row in enumerate(rows):
if observation[TYPE] in [MEDIA]:
if duration1:
mediaFileIdx = [
idx1 for idx1, x in enumerate(duration1)
if row["occurence"] >= sum(duration1[0:idx1])
][-1]
mediaFileString = observation[FILE][PLAYER1][
mediaFileIdx]
fpsString = observation["media_info"]["fps"][
observation[FILE][PLAYER1][mediaFileIdx]]
else:
mediaFileString = "-"
fpsString = "NA"
if observation[TYPE] in [LIVE]:
mediaFileString = "LIVE"
fpsString = "NA"
if POINT in project_functions.event_type(
behavior, pj[ETHOGRAM]):
row_data = []
row_data.extend([
obsId, observation["date"].replace("T", " "),
mediaFileString, total_length, fpsString
])
# independent variables
if INDEPENDENT_VARIABLES in pj:
for idx_var in utilities.sorted_keys(
pj[INDEPENDENT_VARIABLES]):
if pj[INDEPENDENT_VARIABLES][idx_var][
"label"] in observation[
INDEPENDENT_VARIABLES]:
row_data.append(
observation[INDEPENDENT_VARIABLES][
pj[INDEPENDENT_VARIABLES][idx_var]
["label"]])
else:
row_data.append("")
row_data.extend([
subject,
behavior,
row["modifiers"].strip(),
POINT,
"{0:.3f}".format(row["occurence"]), # start
"NA", # stop
"NA", # duration
row["comment"],
""
])
data.append(row_data)
if STATE in project_functions.event_type(
behavior, pj[ETHOGRAM]):
if idx % 2 == 0:
row_data = []
row_data.extend([
obsId, observation["date"].replace("T", " "),
mediaFileString, total_length, fpsString
])
# independent variables
if INDEPENDENT_VARIABLES in pj:
for idx_var in utilities.sorted_keys(
pj[INDEPENDENT_VARIABLES]):
if pj[INDEPENDENT_VARIABLES][idx_var][
"label"] in observation[
INDEPENDENT_VARIABLES]:
row_data.append(
observation[INDEPENDENT_VARIABLES][
pj[INDEPENDENT_VARIABLES][idx_var]
["label"]])
else:
row_data.append("")
row_data.extend([
subject, behavior, row["modifiers"].strip(), STATE,
"{0:.3f}".format(row["occurence"]),
"{0:.3f}".format(rows[idx + 1]["occurence"]),
"{0:.3f}".format(rows[idx + 1]["occurence"] -
row["occurence"]), row["comment"],
rows[idx + 1]["comment"]
])
data.append(row_data)
return data
def test_time_budget5(self):
"""
test time budget with modifiers
"""
VERIF = [{
"subject": "No focal subject",
"behavior": "q",
"modifiers": "m1",
"duration": 0,
"duration_mean": 0,
"duration_stdev": "NA",
"number": 1,
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}, {
"subject": "No focal subject",
"behavior": "q",
"modifiers": "m2",
"duration": 0,
"duration_mean": 0,
"duration_stdev": "NA",
"number": 1,
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}, {
"subject": "No focal subject",
"behavior": "q",
"modifiers": "m3",
"duration": 0,
"duration_mean": 0,
"duration_stdev": "NA",
"number": 1,
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}, {
"subject": "No focal subject",
"behavior": "r",
"modifiers": "m1",
"duration": 8.775,
"duration_mean": 8.775,
"duration_stdev": "NA",
"number": 1,
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}, {
"subject": "No focal subject",
"behavior": "r",
"modifiers": "None",
"duration": 10.4,
"duration_mean": 10.4,
"duration_stdev": "NA",
"number": 1,
"inter_duration_mean": "NA",
"inter_duration_stdev": "NA"
}]
pj = json.loads(open("files/test.boris").read())
ethogram = pj[ETHOGRAM]
selected_observations = ["modifiers"]
parameters = {
SELECTED_SUBJECTS: ["No focal subject"],
SELECTED_BEHAVIORS: ["q", "r"],
INCLUDE_MODIFIERS: True,
EXCLUDE_BEHAVIORS: False,
"start time": 0,
"end time": 180
}
cursor = db_functions.load_events_in_db(
pj,
parameters[SELECTED_SUBJECTS],
selected_observations,
parameters[SELECTED_BEHAVIORS],
time_interval=TIME_ARBITRARY_INTERVAL)
out, categories = time_budget_functions.time_budget_analysis(
ethogram,
cursor,
selected_observations,
parameters,
by_category=False)
# open("files/1.json", "w").write(json.dumps(out))
assert out == VERIF