def setUpClass(cls):
config = SetupConfig()
path = os.path.join(data_path, "weird_short_3_mice")
raw_data = uf.read_single_file(path, "20101010_110000.txt")
data = uf.from_raw_data(raw_data)
cls.mismatch1 = uf.antenna_mismatch(data, config)
cls.presences1 = uf.check_antenna_presence(data, config, 24 * 3600)
res_path = os.path.join(path, "Results")
files = glob.glob(os.path.join(res_path + "/diagnostics/*.csv"))
for f in files:
print("rm ", f)
cls.length = len(data["Antenna"])
out1 = uf.run_diagnostics(data, 24 * 3600, res_path, config)
cls.str11, cls.str12, cls.str13, cls.str14, cls.str15 = out1
path = os.path.join(data_path, "weird_short")
raw_data = uf.read_single_file(path, "20101010_110000.txt")
data = uf.from_raw_data(raw_data)
cls.mismatch2 = uf.antenna_mismatch(data, config)
cls.presences2 = uf.check_antenna_presence(data, config, 24 * 3600)
res_path = os.path.join(path, "Results")
files = glob.glob(os.path.join(res_path + "/diagnostics/*.csv"))
for f in files:
os.remove(f)
out2 = uf.run_diagnostics(data, 24 * 3600, res_path, config)
cls.str21, cls.str22, cls.str23, cls.str24, cls.str25 = out2
path1 = os.path.join(data_path, "weird_very_short_3_mice")
raw_data1 = uf.read_single_file(path1, "20101010_110000.txt")
data1 = uf.from_raw_data(raw_data1)
config1 = SetupConfig()
res_path1 = os.path.join(path1, "Results")
out = uf.run_diagnostics(data1, 24 * 3600, res_path1, config1)
cls.incorr_tunnel = out[-1]
def setUpClass(cls):
cls.path1 = os.path.join(data_path, "modular_1",
"data_setup_additional")
cls.dataset1 = Loader(cls.path1, visit_threshold=1.5, prefix="gugu")
cls.setup1 = SetupConfig(cls.path1)
cls.dataset1_standard = Loader(cls.path1)
cls.path2 = os.path.join(data_path, "weird_very_short")
cls.dataset2 = Loader(cls.path2, visit_threshold=2)
cls.setup3 = SetupConfig(path=data_path, fname="setup_short.txt")
cls.dataset3 = Loader(cls.path1,
visit_threshold=1.5,
setup_config=cls.setup3,
remove_antennas=["8"])
cls.path_empty = os.path.join(data_path, "empty")
def setUpClass(cls):
path = os.path.join(data_path, "weird_short")
raw_data = uf.read_single_file(path, "20101010_110000.txt")
data = uf.from_raw_data(raw_data)
setup_config = SetupConfig()
cls.data = EcoHabDataBase(data, None, 2, setup_config)
cls.config = Timeline(path)
def setUpClass(cls):
config = SetupConfig()
cls.mismatched_pairs = config.mismatched_pairs
path = os.path.join(data_path, "weird_short_3_mice")
raw_data1 = uf.read_single_file(path, "20101010_110000.txt")
cls.data1 = uf.from_raw_data(raw_data1)
cls.mismatch1 = uf.antenna_mismatch(cls.data1, config)
path = os.path.join(data_path, "weird_short")
raw_data2 = uf.read_single_file(path, "20101010_110000.txt")
cls.data2 = uf.from_raw_data(raw_data2)
cls.mismatch2 = uf.antenna_mismatch(cls.data2, config)
def __init__(self, path, **kwargs):
# Read in parameters
self.path = path
setup_config = kwargs.pop('setup_config', None)
if isinstance(setup_config, SetupConfig):
antennas = setup_config
elif isinstance(setup_config, str):
antennas = SetupConfig(path=setup_config)
else:
antennas = SetupConfig(path=self.path)
self.mask = kwargs.pop('mask', None)
self.visit_threshold = kwargs.pop('visit_threshold', 2.)
add_date = kwargs.pop('add_date', True)
res_dir = kwargs.pop("res_dir", "Results")
self.prefix = kwargs.pop("prefix", ufl.make_prefix(self.path))
self.max_break = kwargs.pop("max_break", self.MAX_BREAK)
remove_antennas = kwargs.pop('remove_antennas', [])
tags = kwargs.pop('legal_tags', "ALL")
if add_date:
today = date.today().strftime("%d.%m.%y")
res_dir = "%s_%s" % (res_dir, today)
self.res_dir = ufl.results_path(self.path, res_dir)
# Read in data
rawdata = self._read_in_raw_data(tags)
data = ufl.from_raw_data(rawdata)
data = ufl.remove_antennas(data, remove_antennas)
# As in antenna registrations
ufl.run_diagnostics(data, self.max_break, self.res_dir, antennas)
super(Loader, self).__init__(data, self.mask, self.visit_threshold,
antennas)
self.cages = antennas.cages
self.directions = antennas.directions
self.setup_config = antennas
self.all_antennas = antennas.all_antennas
self.internal_antennas = antennas.internal_antennas
self.setup_name = antennas.name
self.home_antenna = antennas.homecage_antenna
self.home_internal_antennas = antennas.homecage_internal_antennas
self.stimulus_internal_antennas = antennas.stimCage_internal_antennas
def setUpClass(cls):
antennas = ["1", "2", "1", "2", "3", "4", "5", "6", "7"]
times = [1, 2, 2.5, 3, 4.5, 5.5, 6.5, 7.5, 10.5]
durations = [3, 600, 3, 34, 55, 66, 1999, 200, 100]
cls.pred_out = {"1 2": 1, "3 4": 0, "5 6": 1, "7 8": 0}
keys = cls.pred_out.keys()
cls.out, cls.tot = uf.incorrect_tunnel_single_mouse(
keys, antennas, times, durations)
cls.pred_tot = {"1 2": 3, "3 4": 1, "5 6": 1, "7 8": 0}
path = os.path.join(data_path, "weird_very_short_3_mice")
cls.raw_data = uf.read_single_file(path, "20101010_110000.txt")
cls.data = uf.from_raw_data(cls.raw_data)
config = SetupConfig()
cls.out_i, cls.out_tot_i = uf.incorrect_tunnel_registrations(
cls.data, config)
cls.pred_out_i = {"1 2": 0, "3 4": 0, "5 6": 2, "7 8": 0}
cls.pred_tot_i = {"1 2": 2, "3 4": 1, "5 6": 7, "7 8": 0}
def setUpClass(cls):
path = os.path.join(data_path, "weird_short_3_mice")
raw_data = uf.read_single_file(path, "20101010_110000.txt")
data = uf.from_raw_data(raw_data)
cls.config = SetupConfig()
cls.presences = uf.check_antenna_presence(data, cls.config, 24 * 3600)
cls.end = data["Time"][-1]
cls.begs = []
for key in cls.presences.keys():
if len(cls.presences[key]):
cls.begs.append(cls.presences[key][0][0])
cls.begs_data = []
for antenna in ["1", "2", "3", "4", "5", "6", "7", "8"]:
if antenna == "4":
continue
idx = np.where(data["Antenna"] == antenna)[0][-1]
cls.begs_data.append(np.round(data["Time"][idx]))
def setUpClass(cls):
path = os.path.join(data_path, "weird_short_3_mice")
raw_data = uf.read_single_file(path, "20101010_110000.txt")
data = uf.from_raw_data(raw_data)
config = SetupConfig()
cls.mismatch1 = uf.skipped_registrations(data, config)