def test_read_metadata(self):
meta = self.file.read_metadata()
for k in CSV_META_TEMPLATE.keys():
assert k in meta.keys()
assert meta['lc_2010'].val == meta['lc_2005'].val == meta[
'lc_2000'].val == 130
assert meta['climate_KG'].val == 'Cfa'
assert self.file.check_metadata(filter_meta_dict={
'lc_2005': 130,
'climate_KG': 'Cfa',
'sand_fraction': 36.
})
sats = meta['saturation']
assert len(sats) == 2
assert sats[0].val == 0.46
assert sats[1].depth == Depth(0.3, 1.)
sands = meta['sand_fraction']
assert len(sands) == 2
assert sands[1].val == 29.
assert sands[0].depth == Depth(0, 0.3)
assert len(meta['silt_fraction']) == len(meta['clay_fraction']) == 2
assert len(meta['organic_carbon']) == 3
assert meta['organic_carbon'][0].val == 1.27
assert meta['organic_carbon'][0].depth == Depth(0, 0.3)
assert meta['organic_carbon'][1].depth == Depth(0.3, 1)
# todo: why is there a value for this depth even?
assert meta['organic_carbon'][2].depth == Depth(-99.9, -99.9)
assert meta['organic_carbon'][2].val == 0.59
def test_read_metadata(self):
meta = self.file.read_metadata()
for k in CSV_META_TEMPLATE.keys():
assert k in meta.keys()
assert meta["lc_2010"].val == meta["lc_2005"].val == meta[
"lc_2000"].val == 130
assert meta["climate_KG"].val == "Cfa"
assert self.file.check_metadata(filter_meta_dict={
"lc_2005": 130,
"climate_KG": "Cfa",
"sand_fraction": 36.0,
})
sats = meta["saturation"]
assert len(sats) == 2
assert sats[0].val == 0.46
assert sats[1].depth == Depth(0.3, 1.0)
sands = meta["sand_fraction"]
assert len(sands) == 2
assert sands[1].val == 29.0
assert sands[0].depth == Depth(0, 0.3)
assert len(meta["silt_fraction"]) == len(meta["clay_fraction"]) == 2
assert len(meta["organic_carbon"]) == 3
assert meta["organic_carbon"][0].val == 1.27
assert meta["organic_carbon"][0].depth == Depth(0, 0.3)
assert meta["organic_carbon"][1].depth == Depth(0.3, 1)
# todo: why is there a value for this depth even?
assert meta["organic_carbon"][2].depth == Depth(-99.9, -99.9)
assert meta["organic_carbon"][2].val == 0.59
def test_eval(self):
assert self.sensor.eval("soil_moisture", Depth(0, 5))
assert self.sensor.eval("soil_moisture", (0, 0.21),
check_only_sensor_depth_from=True)
assert self.sensor.eval("soil_moisture",
Depth(0, 0.05),
check_only_sensor_depth_from=True)
# fails because of varname:
assert not self.sensor.eval("wrongname", Depth(0, 0.21))
# fails because of depth
assert not self.sensor.eval("soil_moisture", [0, 0.05],
check_only_sensor_depth_from=False)
def setUp(self) -> None:
vars = [
MetaVar('first', 1, Depth(0, 1)),
MetaVar('second', 0),
MetaVar('neg', -99, Depth(-0.25, -1)),
MetaVar('dup', '3rd', Depth(1, 3))
]
self.dat = MetaData(vars)
self.other = MetaData(
[MetaVar('dup', '3rd', Depth(2, 4)),
MetaVar('4', 4)])
def setUp(self) -> None:
vars = [
MetaVar("first", 1, Depth(0, 1)),
MetaVar("second", 0),
MetaVar("neg", -99, Depth(-0.25, -1)),
MetaVar("dup", "3rd", Depth(1, 3)),
]
self.dat = MetaData(vars)
self.other = MetaData(
[MetaVar("dup", "3rd", Depth(2, 4)),
MetaVar("4", 4)])
def test_best_meta(self):
self.dat.merge(self.other, inplace=True)
assert len(self.dat) == 6
# no depths overlap
best_meta_9_10 = self.dat.best_meta_for_depth(Depth(9, 10))
assert sorted(best_meta_9_10.keys()) == sorted(['second', '4'])
# all depths overlap
best_meta_inf = self.dat.best_meta_for_depth(Depth(-np.inf, np.inf))
assert len(best_meta_inf) == len(self.dat) - 1 # one duplicate removed
assert sorted(best_meta_inf.keys()) == sorted(
['second', '4', 'dup', 'first', 'neg'])
# both valzes for dup where equally good, so the first was kept
assert best_meta_inf['dup'].depth.start == 1
assert best_meta_inf['dup'].depth.end == 3
# all but one dup and neg depth overlaps
best_meta_015 = self.dat.best_meta_for_depth(Depth(0, 1.5))
assert len(best_meta_015) == len(self.dat) - 2
assert best_meta_015['dup'].depth.start == 1
assert best_meta_015['dup'].depth.end == 3
# both duplicate depths overlap, but one more --> keep second, drop neg
best_meta_231 = self.dat.best_meta_for_depth(Depth(2, 3.1))
assert len(best_meta_231) == len(
self.dat) - 3 # one duplicate and first and neg
assert best_meta_231['dup'].depth.start == 2
assert best_meta_231['dup'].depth.end == 4
# both duplicate depths overlap, equally good -> keep first
best_meta_23 = self.dat.best_meta_for_depth(Depth(2, 3))
assert len(best_meta_23) == len(
self.dat) - 3 # one dup and first and neg
assert best_meta_23['dup'].depth.start == 1.
assert best_meta_23['dup'].depth.end == 3.
# one matches perfectly
best_meta_13 = self.dat.best_meta_for_depth(Depth(1, 3))
assert len(best_meta_13) == len(self.dat) - 2 # one dup only, no neg
assert best_meta_13['dup'].depth.start == 1.
assert best_meta_13['dup'].depth.end == 3.
# check with negative
best_meta_neg = self.dat.best_meta_for_depth(Depth(-0.5, 2.))
# one dup was outside depth and is dropped, rest remains
assert sorted(best_meta_neg.keys()) == sorted(
['first', 'second', 'dup', '4', 'neg'])
assert best_meta_neg['dup'].depth.start == 1.
assert best_meta_neg['dup'].depth.end == 3.
# check with negative
best_meta_only_neg = self.dat.best_meta_for_depth(Depth(-0.5, -1.))
# only keep meta without depths and for neg depth
assert sorted(best_meta_only_neg.keys()) == sorted(
['second', 'neg', '4'])
assert best_meta_only_neg['neg'].depth.start == -0.25
assert best_meta_only_neg['neg'].depth.end == -1
def test_sensor_attributes(self):
"""
Test sensor attributes.
"""
assert self.sensor.instrument == "Cosmic-ray-Probe"
assert self.sensor.variable == "soil_moisture"
assert self.sensor.depth == Depth(0, 0.21)
def test_MetaVar(self):
var = MetaVar('myvar', 1.1, Depth(0, 1))
assert str(var) == "myvar (0.0 to 1.0 [m]): 1.1"
assert tuple(var) == ('myvar', 1.1, 0, 1)
assert var == var
nvar = MetaVar('negmyvar', 1.1, Depth(0, -1))
assert str(nvar) == "negmyvar (0.0 to -1.0 [m]): 1.1"
assert tuple(nvar) == ('negmyvar', 1.1, -0, -1)
assert nvar != var
other = MetaVar('other', 99)
assert str(other) == "other (no depth): 99"
assert tuple(other) == ('other', 99, None, None)
assert other != var
def test_get_sensors(self):
variable, depth = 'soil_moisture', Depth(0, 0.05)
sensors = self.station.get_sensors(variable,
depth_from=depth.start,
depth_to=depth.end)
assert len(sensors) == len([
s
for s in self.station.iter_sensors(variable=variable, depth=depth)
])
def test_iter_sensors(self):
"""
Test if sensor1 one is found when iteration over all sensors in 0-0.05 m.
"""
for sen in self.station.iter_sensors(
variable='sm',
depth=Depth(0, 0.05),
check_only_sensor_depth_from=False):
assert sen.name == 'sensor1_sm_0.000000_0.050000'
def setUp(self) -> None:
"""
Setup test data.
"""
net1 = Network('Net1')
net1.add_station('station_1_1', 0, 0, 0)
net1.stations['station_1_1'].add_sensor('sens_1_1_1', 'var1',
Depth(0.5, 1), None)
net1.stations['station_1_1'].add_sensor('sens_1_1_2', 'var1',
Depth(1, 2), None)
net2 = Network('Net2')
net2.add_station('station_2_1', 1, 1, 1)
net2.stations['station_2_1'].add_sensor('sens_2_1_1', 'var1',
Depth(0.5, 1), None)
net2.stations['station_2_1'].add_sensor('sens_2_1_2', 'var1',
Depth(1, 2), None)
self.netcol = NetworkCollection([net1, net2])
def test_get_sensors(self):
with pytest.deprecated_call():
variable, depth = "soil_moisture", Depth(0, 0.05)
sensors = self.station.get_sensors(variable,
depth_from=depth.start,
depth_to=depth.end)
assert len(sensors) == len([
s for s in self.station.iter_sensors(variable=variable,
depth=depth)
])
def test_add_sensor(self):
"""
Test adding sensors.
"""
name = "sensor3"
d = Depth(0, 0.1)
variable = "sm"
self.station.add_sensor(name, variable, d, None)
assert self.station.n_sensors == 3
def setUp(self) -> None:
"""
Setup test data.
"""
net1 = Network("Net1")
net1.add_station("station_1_1", 0, 0, 0)
net1.stations["station_1_1"].add_sensor("sens_1_1_1", "var1",
Depth(0.5, 1), None)
net1.stations["station_1_1"].add_sensor("sens_1_1_2", "var1",
Depth(1, 2), None)
net2 = Network("Net2")
net2.add_station("station_2_1", 1, 1, 1)
net2.stations["station_2_1"].add_sensor("sens_2_1_1", "var1",
Depth(0.5, 1), None)
net2.stations["station_2_1"].add_sensor("sens_2_1_2", "var1",
Depth(1, 2), None)
self.netcol = NetworkCollection([net1, net2])
def setUp(self):
"""
Setup test data.
"""
self.station = Station('station1', 0, 0, 0)
name = 'sensor1'
d = Depth(0, 0.05)
variable = 'sm'
se_name = '{}_{}_{:1.6f}_{:1.6f}'.format(name, variable, d.start,
d.end)
self.station.add_sensor(name, variable, d, None)
assert self.station.sensors[se_name].variable == 'sm'
name = 'sensor2'
d = Depth(0, 0.1)
variable = 'sm2'
self.station.add_sensor(name, variable, d, None)
assert self.station.n_sensors == 2
def setUp(self):
"""
Setup test data.
"""
self.station = Station("station1", 0, 0, 0)
name = "sensor1"
d = Depth(0, 0.05)
variable = "sm"
se_name = "{}_{}_{:1.6f}_{:1.6f}".format(name, variable, d.start,
d.end)
self.station.add_sensor(name, variable, d, None)
assert self.station.sensors[se_name].variable == "sm"
name = "sensor2"
d = Depth(0, 0.1)
variable = "sm2"
self.station.add_sensor(name, variable, d, None)
assert self.station.n_sensors == 2
def test_metadata_for_depth(self):
"""Check finding best matching metadata for file"""
allmeta = self.file.read_metadata()
meta_for_depth = allmeta.best_meta_for_depth(Depth(0.0, 0.21))
assert allmeta != meta_for_depth
assert len([k for k in allmeta.keys() if k == "saturation"]) > 1
assert len([k for k in meta_for_depth.keys()
if k == "saturation"]) == 1
assert (meta_for_depth["saturation"].depth.start ==
meta_for_depth["sand_fraction"].depth.start == 0.0)
assert (meta_for_depth["saturation"].depth.end ==
meta_for_depth["sand_fraction"].depth.end == 0.3)
assert allmeta["saturation"][0].depth == meta_for_depth[
"saturation"].depth
assert allmeta["saturation"][1].depth.start == 0.3
assert allmeta["saturation"][1].depth.end == 1.0
def setUp(self):
"""
Setup test data.
"""
instrument = 'Cosmic-ray-Probe'
d = Depth(0, 0.21)
variable = 'soil_moisture'
root = os.path.join(rpath, "Data_seperate_files_20170810_20180809")
subpath = os.path.join(
"COSMOS", "Barrow-ARM",
"COSMOS_COSMOS_Barrow-ARM_sm_0.000000_0.210000_Cosmic-ray-Probe_20170810_20180809.stm"
)
self.sensor = Sensor(instrument,
variable,
d,
filehandler=DataFile(root, subpath))
name = '{}_{}_{:1.6f}_{:1.6f}'.format(instrument, variable, d.start,
d.end)
assert self.sensor.name == name
def test_iter_stations(self):
self.network.add_station("station1", 0, 0, 0)
self.network.stations["station1"].add_sensor("sens1", "var1",
Depth(0.5, 1), None)
self.network.stations["station1"].add_sensor("sens2", "var1",
Depth(1, 2), None)
for s in self.network.iter_stations(variable="var1", depth=Depth(0,
1)):
# sensor 1 applies to conditions, therefore station is found.
assert s.name == "station1"
self.network.add_station("station2", 1, 1, 1)
self.network.stations["station2"].add_sensor("sens1", "var1",
Depth(0, 1), None)
self.network.stations["station2"].add_sensor("sens2", "var2",
Depth(1, 2), None)
for s in self.network.iter_stations(variable="var1",
depth=Depth(0, 0.5)):
raise ValueError("Found station but shouldn't ..."
) # this should never be reached
def test_iter_stations(self):
self.network.add_station('station1', 0, 0, 0)
self.network.stations['station1'].add_sensor('sens1', 'var1',
Depth(0.5, 1), None)
self.network.stations['station1'].add_sensor('sens2', 'var1',
Depth(1, 2), None)
for s in self.network.iter_stations(variable='var1', depth=Depth(0,
1)):
# sensor 1 applies to conditions, therefore station is found.
assert s.name == 'station1'
self.network.add_station('station2', 1, 1, 1)
self.network.stations['station2'].add_sensor('sens1', 'var1',
Depth(0, 1), None)
self.network.stations['station2'].add_sensor('sens2', 'var2',
Depth(1, 2), None)
for s in self.network.iter_stations(variable='var1',
depth=Depth(0, 0.5)):
raise ValueError("Found station but shouldn't ..."
) # this should never be reached
def test_get_depths(self):
"""
Test deriving the depths of all sensors measuring a variable at station
"""
assert self.station.get_depths("sm") == [Depth(0, 0.05)]