def test_recombination_CRDS():
get_local_bucket(empty=True)
filename = "hfd.picarro.1minute.100m.min.dat"
filepath = get_datapath(filename=filename, data_type="CRDS")
crds = CRDS()
ObsSurface.read_file(filepath, data_type="CRDS")
gas_data = crds.read_data(data_filepath=filepath, site="HFD")
ch4_data_read = gas_data["ch4"]["data"]
gas_name = "ch4"
location = "hfd"
keys = search(species=gas_name, locations=location)
to_download = keys["ch4_hfd_100m_picarro"]["keys"][
"2013-12-04-14:02:30_2019-05-21-15:46:30"]
ch4_data_recombined = recombine_sections(data_keys=to_download)
ch4_data_recombined.attrs = {}
assert ch4_data_read.time.equals(ch4_data_recombined.time)
assert ch4_data_read["ch4"].equals(ch4_data_recombined["ch4"])
def test_read_data():
crds = CRDS()
tac_filepath = get_datapath(filename="tac.picarro.1minute.100m.test.dat",
data_type="CRDS")
combined = crds.read_data(data_filepath=tac_filepath, site="tac")
assert len(combined) == 2
assert list(combined.keys()) == ["ch4", "co2"]
ch4_metadata = combined["ch4"]["metadata"]
assert ch4_metadata["site"] == "tac"
assert ch4_metadata["instrument"] == "picarro"
assert ch4_metadata["time_resolution"] == "1_minute"
assert ch4_metadata["inlet"] == "100m"
assert ch4_metadata["port"] == "9"
assert ch4_metadata["type"] == "air"
assert ch4_metadata["species"] == "ch4"
ch4_data = combined["ch4"]["data"]
assert ch4_data.time[0] == pd.Timestamp("2012-07-31 14:50:30")
assert ch4_data["ch4"][0] == pytest.approx(1905.28)
assert ch4_data["ch4 stdev"][0] == pytest.approx(0.268)
assert ch4_data["ch4 n_meas"][0] == pytest.approx(20)
def data():
crds = CRDS()
filename = "bsd.picarro.1minute.248m.dat"
filepath = get_datapath(filename=filename, data_type="CRDS")
combined_data = crds.read_data(data_filepath=filepath, site="bsd")
return combined_data
def test_gas_info(hfd_filepath):
crds = CRDS()
data = pd.read_csv(
hfd_filepath,
header=None,
skiprows=1,
sep=r"\s+",
index_col=["0_1"],
parse_dates=[[0, 1]],
)
n_gases, n_cols = crds.gas_info(data=data)
assert n_gases == 3
assert n_cols == 3
def test_get_site_attributes():
crds = CRDS()
attrs = crds.get_site_attributes(site="bsd", inlet="108m")
assert attrs == {
'data_owner': "Simon O'Doherty",
'data_owner_email': '*****@*****.**',
'inlet_height_magl': '108m',
'comment': 'Cavity ring-down measurements. Output from GCWerks'
}
attrs = crds.get_site_attributes(site="tac", inlet="50m")
assert attrs == {
'data_owner': "Simon O'Doherty",
'data_owner_email': '*****@*****.**',
'inlet_height_magl': '50m',
'comment': 'Cavity ring-down measurements. Output from GCWerks'
}
def clear_datasources(args):
from HUGS.Modules import CRDS, GC
gc = GC.load()
crds = CRDS.load()
crds.clear_datasources()
gc.clear_datasources()
crds.save()
gc.save()
def test_read_file():
hfd_filepath = get_datapath(filename="hfd.picarro.1minute.100m.min.dat",
data_type="CRDS")
crds = CRDS()
gas_data = crds.read_file(data_filepath=hfd_filepath)
ch4_data = gas_data["ch4"]["data"]
co2_data = gas_data["co2"]["data"]
co_data = gas_data["co"]["data"]
assert ch4_data["ch4"][0].values == pytest.approx(1993.83)
assert ch4_data["ch4_stdev"][0].values == pytest.approx(1.555)
assert ch4_data["ch4_n_meas"][0].values == pytest.approx(19.0)
assert co2_data["co2"][0] == pytest.approx(414.21)
assert co2_data["co2_stdev"][0] == pytest.approx(0.109)
assert co2_data["co2_n_meas"][0] == pytest.approx(19.0)
assert co_data["co"][0] == pytest.approx(214.28)
assert co_data["co_stdev"][0] == pytest.approx(4.081)
assert co_data["co_n_meas"][0] == pytest.approx(19.0)
def test_read_data_no_inlet_raises():
crds = CRDS()
filepath = Path("tac.picarro.1minute.no_inlet.dat")
with pytest.raises(ValueError):
crds.read_data(data_filepath=filepath, site="tac")
def test_get_site_attributes_unknown_site_raises():
crds = CRDS()
with pytest.raises(ValueError):
_ = crds.get_site_attributes(site="jupiter", inlet="10008m")
def test_crds_attributes():
_ = get_local_bucket(empty=True)
crds = CRDS()
filepath = get_datapath(filename="tac.picarro.1minute.100m.test.dat",
data_type="CRDS")
combined = crds.read_data(data_filepath=filepath, site="tac")
combined_attributes = assign_attributes(data=combined, site="tac")
# for key in combined_attributes:
# ds = combined_attributes[key]["data"]
# ds.to_netcdf(f"/tmp/testfile_{key}.nc")
ch4_data = combined_attributes["ch4"]["data"]
co2_data = combined_attributes["co2"]["data"]
ch4_attr = ch4_data.attrs
co2_attr = co2_data.attrs
ch4_attr_complete = ch4_attr.copy()
co2_attr_complete = co2_attr.copy()
del ch4_attr["File created"]
del co2_attr["File created"]
del ch4_attr["species"]
del co2_attr["species"]
del ch4_attr["Calibration_scale"]
del co2_attr["Calibration_scale"]
del ch4_attr["data_owner_email"]
del co2_attr["data_owner_email"]
del ch4_attr["data_owner"]
del co2_attr["data_owner"]
global_attributes = {
"inlet_height_magl": "100m",
"comment": "Cavity ring-down measurements. Output from GCWerks",
"Conditions of use":
"Ensure that you contact the data owner at the outset of your project.",
"Source": "In situ measurements of air",
"Conventions": "CF-1.6",
"Processed by": "*****@*****.**",
"station_longitude": 1.13872,
"station_latitude": 52.51775,
"station_long_name": "Tacolneston Tower, UK",
"station_height_masl": 50.0,
}
assert ch4_attr == global_attributes
assert co2_attr == global_attributes
assert ch4_attr_complete["species"] == "ch4"
assert co2_attr_complete["species"] == "co2"
# Check the individual variables attributes
time_attributes = {
"label":
"left",
"standard_name":
"time",
"comment":
"Time stamp corresponds to beginning of sampling period. Time since midnight UTC of reference date. Note that sampling periods are approximate.",
}
assert ch4_data.time.attrs == time_attributes
assert co2_data.time.attrs == time_attributes
# Check individual variables
assert ch4_data["ch4"].attrs == {
"long_name": "mole_fraction_of_methane_in_air",
"units": "1e-9",
}
assert ch4_data["ch4_stdev"].attrs == {
"long_name": "mole_fraction_of_methane_in_air_stdev",
"units": "1e-9",
}
assert ch4_data["ch4_n_meas"].attrs == {
"long_name": "mole_fraction_of_methane_in_air_n_meas"
}
assert co2_data["co2"].attrs == {
"long_name": "mole_fraction_of_carbon_dioxide_in_air",
"units": "1e-6",
}
assert co2_data["co2_stdev"].attrs == {
"long_name": "mole_fraction_of_carbon_dioxide_in_air_stdev",
"units": "1e-6",
}
assert co2_data["co2_n_meas"].attrs == {
"long_name": "mole_fraction_of_carbon_dioxide_in_air_n_meas"
}