def oxygen_concentration_correction(data, ncvar):
oxy_yaml = ncvar['oxygen_concentration']
if 'reference_salinity' not in oxy_yaml.keys():
_log.warning(
'No reference_salinity found in oxygen deployment yaml. Assuming reference salinity of 0 psu'
)
ref_sal = 0
else:
ref_sal = float(oxy_yaml['reference_salinity'])
_log.info(f'Correcting oxygen using reference salinity {ref_sal} PSU')
ds_oxy = data.oxygen_concentration[~np.isnan(data.oxygen_concentration)]
# Match the nearest temperature and salinity values from their timestamps
ds_temp = data.potential_temperature[~np.isnan(data.potential_temperature
)].reindex(time=ds_oxy.time,
method="nearest")
ds_sal = data.salinity[~np.isnan(data.salinity)].reindex(time=ds_oxy.time,
method="nearest")
o2_sol = gsw.O2sol_SP_pt(ds_sal, ds_temp)
o2_sat = ds_oxy / gsw.O2sol_SP_pt(ds_sal * 0 + ref_sal, ds_temp)
data['oxygen_concentration'].values[~np.isnan(data.oxygen_concentration
)] = o2_sat * o2_sol
data['oxygen_concentration'].attrs['oxygen_concentration_QC:RTQC_methodology'] =\
f'oxygen concentration corrected for salinity using gsw.O2sol_SP_pt with salinity and potential temperature ' \
f'from dataset. Original oxygen concentration assumed to have been calculated using salinity = {ref_sal} PSU'
return data
def add_psal(netCDFfile):
ds = Dataset(netCDFfile, 'a')
var_temp = ds.variables["TEMP"]
var_psal = ds.variables["PSAL"]
var_pres = ds.variables["PRES"]
t = var_temp[:]
SP = var_psal[:]
p = var_pres[:]
SA = gsw.SA_from_SP(SP, p, ds.longitude, ds.latitude)
pt = gsw.pt0_from_t(SA, t, p)
oxsol = gsw.O2sol_SP_pt(SP, pt)
ncVarOut = ds.createVariable("OXSOL", "f4", ("TIME",), fill_value=np.nan, zlib=True) # fill_value=nan otherwise defaults to max
ncVarOut[:] = oxsol
ncVarOut.units = "umol/kg"
ncVarOut.comment = "calculated using gsw-python https://teos-10.github.io/GSW-Python/index.html function gsw.O2sol_SP_pt"
# update the history attribute
try:
hist = ds.history + "\n"
except AttributeError:
hist = ""
ds.setncattr('history', hist + datetime.utcnow().strftime("%Y-%m-%d") + " : added oxygen solubility")
ds.close()
def add_oxsol(netCDFfile):
ds = Dataset(netCDFfile, 'a')
var_temp = ds.variables["TEMP"]
var_psal = ds.variables["PSAL"]
t = var_temp[:]
SP = var_psal[:]
if "PRES" in ds.variables:
var_pres = ds.variables["PRES"]
pres_var = "PRES"
comment = ""
p = var_pres[:]
elif "NOMINAL_DEPTH" in ds.variables:
var_pres = ds.variables["NOMINAL_DEPTH"]
pres_var = "NOMINAL_DEPTH"
comment = ", using nominal depth of " + str(var_pres[:])
p = var_pres[:]
else:
p = 0
pres_var = "nominal depth of 0 dbar"
comment = ", using nominal depth 0 dbar"
lat = -47
lon = 142
try:
lat = ds.variables["LATITUDE"][0]
lon = ds.variables["LONGITUDE"][0]
except:
pass
SA = gsw.SA_from_SP(SP, p, lon, lat)
pt = gsw.pt0_from_t(SA, t, p)
oxsol = gsw.O2sol_SP_pt(SP, pt)
if 'OXSOL' in ds.variables:
ncVarOut = ds.variables['OXSOL']
else:
ncVarOut = ds.createVariable(
"OXSOL", "f4", ("TIME", ), fill_value=np.nan,
zlib=True) # fill_value=nan otherwise defaults to max
ncVarOut[:] = oxsol
ncVarOut.units = "umol/kg"
ncVarOut.long_name = "moles_of_oxygen_per_unit_mass_in_sea_water_at_saturation"
ncVarOut.comment = "calculated using gsw-python https://teos-10.github.io/GSW-Python/index.html function gsw.O2sol_SP_pt" + comment
ncVarOut.coordinates = 'TIME LATITUDE LONGITUDE NOMINAL_DEPTH'
# update the history attribute
try:
hist = ds.history + "\n"
except AttributeError:
hist = ""
ds.setncattr(
'history', hist + datetime.utcnow().strftime("%Y-%m-%d") +
" added oxygen solubility")
ds.close()
return netCDFfile
def add_optode_oxygen(netCDFfile):
ds = Dataset(netCDFfile, 'a')
var_temp = ds.variables["TEMP"]
var_psal = ds.variables["PSAL"]
var_bphase = ds.variables["BPHASE"]
var_otemp = ds.variables["OTEMP"]
#var_otemp = ds.variables["TEMP"]
t = var_temp[:]
SP = var_psal[:]
phase = var_bphase[:]
otemp = var_otemp[:]
try:
var_pres = ds.variables["PRES"]
p = var_pres[:]
except:
p = 0
lat = -47
lon = 142
try:
lat = ds.variables["LATITUDE"][0]
lon = ds.variables["LONGITUDE"][0]
except:
pass
SA = gsw.SA_from_SP(SP, p, lon, lat)
pt = gsw.pt0_from_t(SA, t, p)
sigmat = gsw.sigma0(SA, t)
oxsol = gsw.O2sol_SP_pt(SP, pt)
if 'OXSOL' in ds.variables:
out_oxsol_var = ds.variables['OXSOL']
else:
out_oxsol_var = ds.createVariable(
"OXSOL", "f4", ("TIME", ), fill_value=np.nan,
zlib=True) # fill_value=nan otherwise defaults to max
out_oxsol_var[:] = oxsol
out_oxsol_var.units = "umol/kg"
out_oxsol_var.comment = "calculated using gsw-python https://teos-10.github.io/GSW-Python/index.html function gsw.O2sol_SP_pt"
C0 = var_bphase.calibration_C0
C1 = var_bphase.calibration_C1
C2 = var_bphase.calibration_C2
A0 = var_bphase.calibration_A0
A1 = var_bphase.calibration_A1
B0 = var_bphase.calibration_B0
B1 = var_bphase.calibration_B1
if 'DOX2_RAW' in ds.variables:
out_ox_var = ds.variables['DOX2_RAW']
else:
out_ox_var = ds.createVariable(
"DOX2_RAW", "f4", ("TIME", ), fill_value=np.nan,
zlib=True) # fill_value=nan otherwise defaults to max
oxygen = (
(A0 + A1 * otemp) /
(B0 + B1 * phase) - 1) / (C0 + C1 * otemp + C2 * np.power(otemp, 2))
out_ox_var[:] = oxygen
out_ox_var.comment_calc1 = 'calculated using ((A0 + A1 * otemp)/(B0 + B1 * phase) - 1)/(C0 + C1 * otemp + C2 * otemp * otemp)'
out_ox_var.units = "umol"
out_ox_var.long_name = "mole_concentration_of_dissolved_molecular_oxygen_in_sea_water (not salinity or pressure corrected)"
out_ox_var.valid_max = np.float32(400)
out_ox_var.valid_min = np.float32(0)
out_ox_var.coordinates = "TIME LATITUDE LONGITUDE NOMINAL_DEPTH"
# update the history attribute
try:
hist = ds.history + "\n"
except AttributeError:
hist = ""
ds.setncattr(
'history', hist + datetime.utcnow().strftime("%Y-%m-%d") +
" : calculated optode oxygen and oxygen solubility")
ds.close()