def percent_to_mmolpmol(ds, MF_out, RH_in, Ta_in, ps_in):
"""
Purpose:
Calculate H2O mole fraction from relative humidity (RH).
"""
nRecs = int(ds.root["Attributes"]["nc_nrecs"])
zeros = numpy.zeros(nRecs, dtype=numpy.int32)
ones = numpy.ones(nRecs, dtype=numpy.int32)
for item in [RH_in, Ta_in, ps_in]:
if item not in list(ds.root["Variables"].keys()):
msg = " Requested series " + item + " not found, " + MF_out + " not calculated"
logger.error(msg)
return 0
# get the relative humidity and check the units
RH = pfp_utils.GetVariable(ds, RH_in)
RH = pfp_utils.convert_units_func(ds, RH, "percent")
# get the temperature and check the units
Ta = pfp_utils.GetVariable(ds, Ta_in)
Ta = pfp_utils.convert_units_func(ds, Ta, "degC")
# get the absoulte humidity
AH_data = pfp_mf.absolutehumidityfromrelativehumidity(
Ta["Data"], RH["Data"])
# get the atmospheric pressure and check the units
ps = pfp_utils.GetVariable(ds, ps_in)
ps = pfp_utils.convert_units_func(ds, ps, "kPa")
# get the output variable (created in pfp_ts.DoFunctions())
MF = pfp_utils.GetVariable(ds, MF_out)
# do the business
MF["Data"] = pfp_mf.h2o_mmolpmolfromgpm3(AH_data, Ta["Data"], ps["Data"])
MF["Flag"] = numpy.where(
numpy.ma.getmaskarray(MF["Data"]) == True, ones, zeros)
MF["Attr"]["units"] = "mmol/mol"
# put the output variable back into the data structure
pfp_utils.CreateVariable(ds, MF)
return 1
def gH2Opm3_to_mmolpmol(ds, MF_out, AH_in, Ta_in, ps_in):
"""
Purpose:
Calculate H2O mole fraction in mml/mol from absolute humidity in g/m^3.
Usage:
pfp_func_units.gH2Opm3_to_mmolpmol(ds, MF_out, AH_in, Ta_in, ps_in)
Author: PRI
Date: August 2019
"""
nRecs = int(ds.root["Attributes"]["nc_nrecs"])
zeros = numpy.zeros(nRecs, dtype=numpy.int32)
ones = numpy.ones(nRecs, dtype=numpy.int32)
for item in [AH_in, Ta_in, ps_in]:
if item not in ds.root["Variables"].keys():
msg = " Requested series " + item + " not found, " + MF_out + " not calculated"
logger.error(msg)
return 0
AH = pfp_utils.GetVariable(ds, AH_in)
AH = pfp_utils.convert_units_func(ds, AH, "g/m^3")
Ta = pfp_utils.GetVariable(ds, Ta_in)
Ta = pfp_utils.convert_units_func(ds, Ta, "degC")
ps = pfp_utils.GetVariable(ds, ps_in)
ps = pfp_utils.convert_units_func(ds, ps, "kPa")
MF = pfp_utils.GetVariable(ds, MF_out)
MF["Data"] = pfp_mf.h2o_mmolpmolfromgpm3(AH["Data"], Ta["Data"],
ps["Data"])
MF["Flag"] = numpy.where(
numpy.ma.getmaskarray(MF["Data"]) == True, ones, zeros)
MF["Attr"]["units"] = "mmol/mol"
pfp_utils.CreateVariable(ds, MF)
return 1
def mgCO2pm3_to_umolpmol(ds, MF_out, CO2_in, Ta_in, ps_in):
"""
Purpose:
Calculate CO2 mole fraction in uml/mol from mass density in mgCO2/m3.
Usage:
pfp_func_units.mgCO2pm3_to_umolpmol(ds, MF_out, CO2_in, Ta_in, ps_in)
Author: PRI
Date: August 2019
"""
nRecs = int(ds.root["Attributes"]["nc_nrecs"])
zeros = numpy.zeros(nRecs, dtype=numpy.int32)
ones = numpy.ones(nRecs, dtype=numpy.int32)
for item in [CO2_in, Ta_in, ps_in]:
if item not in ds.root["Variables"].keys():
msg = " Requested series " + item + " not found, " + MF_out + " not calculated"
logger.error(msg)
return 0
CO2 = pfp_utils.GetVariable(ds, CO2_in)
CO2 = pfp_utils.convert_units_func(ds, CO2, "mg/m^3")
Ta = pfp_utils.GetVariable(ds, Ta_in)
Ta = pfp_utils.convert_units_func(ds, Ta, "degC")
ps = pfp_utils.GetVariable(ds, ps_in)
ps = pfp_utils.convert_units_func(ds, ps, "kPa")
MF = pfp_utils.GetVariable(ds, MF_out)
MF["Data"] = pfp_mf.co2_ppmfrommgCO2pm3(CO2["Data"], Ta["Data"],
ps["Data"])
MF["Flag"] = numpy.where(
numpy.ma.getmaskarray(MF["Data"]) == True, ones, zeros)
MF["Attr"]["units"] = "umol/mol"
pfp_utils.CreateVariable(ds, MF)
return 1
def gH2Opm3_to_mmolpm3(ds, H2O_out, AH_in):
"""
Purpose:
Calculate H2O molar density in mmol/m^3 from absolute humidity in g/m^3.
Usage:
pfp_func_units.gH2Opm3_to_mmolpm3(ds, MD_out, AH_in)
Author: PRI
Date: September 2020
"""
for item in [AH_in]:
if item not in ds.root["Variables"].keys():
msg = " Requested series " + item + " not found, " + H2O_out + " not calculated"
logger.error(msg)
return 0
var_in = pfp_utils.GetVariable(ds, AH_in)
got_variance = False
if var_in["Label"][-3:] == "_Vr" and var_in["Attr"]["units"] in [
"g^2/m^6", "gH2O^2/m^6"
]:
got_variance = True
var_in["Data"] = numpy.ma.sqrt(var_in["Data"])
var_in["Attr"]["units"] = "g/m^3"
var_out = pfp_utils.convert_units_func(ds,
var_in,
"mmol/m^3",
mode="quiet")
var_out["Label"] = H2O_out
if got_variance:
var_out["Data"] = var_out["Data"] * var_out["Data"]
var_out["Attr"]["units"] = "mmol^2/m^6"
pfp_utils.CreateVariable(ds, var_out)
return 1
def mmolpm3_to_gH2Opm3(ds, AH_out, H2O_in):
"""
Purpose:
Function to convert mmol/m^3 (molar density) to g/m^3 (mass density).
Usage:
pfp_func_units.mmolpm3_to_gpm3(ds, AH_out, H2O_in)
Author: PRI
Date: August 2020
"""
for item in [H2O_in]:
if item not in list(ds.root["Variables"].keys()):
msg = " Requested series " + item + " not found, " + AH_out + " not calculated"
logger.error(msg)
return 0
var_in = pfp_utils.GetVariable(ds, H2O_in)
got_variance = False
if var_in["Label"][-3:] == "_Vr" and var_in["Attr"][
"units"] == "mmol^2/m^6":
got_variance = True
var_in["Data"] = numpy.ma.sqrt(var_in["Data"])
var_in["Attr"]["units"] = "mmol/m^3"
var_out = pfp_utils.convert_units_func(ds, var_in, "g/m^3", mode="quiet")
var_out["Label"] = AH_out
if got_variance:
var_out["Data"] = var_out["Data"] * var_out["Data"]
var_out["Attr"]["units"] = "g^2/m^6"
pfp_utils.CreateVariable(ds, var_out)
return 1
def mgCO2pm3_to_mmolpm3(ds, CO2_out, CO2_in):
"""
Purpose:
Calculate CO2 molar density in mmol/m3 from CO2 concentration in mg/m3.
Usage:
pfp_func_units.mgCO2pm3_to_mmolpm3(ds, CO2_out, CO2_in)
Author: PRI
Date: September 2020
"""
for item in [CO2_in]:
if item not in ds.root["Variables"].keys():
msg = " Requested series " + item + " not found, " + CO2_out + " not calculated"
logger.error(msg)
return 0
var_in = pfp_utils.GetVariable(ds, CO2_in)
got_variance = False
if var_in["Label"][-3:] == "_Vr" and var_in["Attr"]["units"] in [
"mg^2/m^6", "mgCO2^2/m^6"
]:
got_variance = True
var_in["Data"] = numpy.ma.sqrt(var_in["Data"])
var_in["Attr"]["units"] = "mg/m^3"
var_out = pfp_utils.convert_units_func(ds,
var_in,
"mmol/m^3",
mode="quiet")
var_out["Label"] = CO2_out
if got_variance:
var_out["Data"] = var_out["Data"] * var_out["Data"]
var_out["Attr"]["units"] = "mmol^2/m^6"
pfp_utils.CreateVariable(ds, var_out)
return 1
def percent_to_m3pm3(ds, Sws_out, Sws_in):
"""
Purpose:
Function to convert Sws in units of "percent" (1 to 100) to "frac" (0 to 1).
Usage:
pfp_func_units.percent_to_m3pm3(ds, Sws_out, Sws_in)
Author: PRI
Date: April 2020
"""
var_in = pfp_utils.GetVariable(ds, Sws_in)
var_out = pfp_utils.convert_units_func(ds, var_in, "m^3/m^3", mode="quiet")
var_out["Label"] = Sws_out
pfp_utils.CreateVariable(ds, var_out)
return 1
def Pa_to_kPa(ds, ps_out, ps_in):
"""
Purpose:
Function to convert pressure from Pa to kPa.
Usage:
pfp_func_units.Pa_to_kPa(ds, ps_out, ps_in)
Author: PRI
Date: February 2018
"""
var_in = pfp_utils.GetVariable(ds, ps_in)
var_out = pfp_utils.convert_units_func(ds, var_in, "kPa", mode="quiet")
var_out["Label"] = ps_out
pfp_utils.CreateVariable(ds, var_out)
return 1
def kgpm3_to_gpm3(ds, AH_out, AH_in):
"""
Purpose:
Function to convert absolute humidity from kg/m^3 to g/m^3.
Usage:
pfp_func_units.kgpm3_to_gpm3(ds, AH_out, AH_in)
Author: PRI
Date: August 2020
"""
var_in = pfp_utils.GetVariable(ds, AH_in)
var_out = pfp_utils.convert_units_func(ds, var_in, "g/m^3", mode="quiet")
var_out["Label"] = AH_out
pfp_utils.CreateVariable(ds, var_out)
return 1
def fraction_to_percent(ds, RH_out, RH_in):
"""
Purpose:
Function to convert RH in units of "frac" (0 to 1) to "percent" (1 to 100).
Usage:
pfp_func_units.fraction_to_percent(ds, RH_out, RH_in)
Author: PRI
Date: August 2019
"""
var_in = pfp_utils.GetVariable(ds, RH_in)
var_out = pfp_utils.convert_units_func(ds, var_in, "percent", mode="quiet")
var_out["Label"] = RH_out
pfp_utils.CreateVariable(ds, var_out)
return 1
def percent_to_gH2Opm3(ds, AH_out, RH_in, Ta_in):
"""
Purpose:
Function to calculate absolute humidity given relative humidity and
air temperature. Absolute humidity is not calculated if any of the
input series are missing or if the specified output series already
exists in the data structure.
The calculated absolute humidity is created as a new series in the
data structure.
Usage:
pfp_func_units.percent_to_gpm3(ds,"AH_HMP_2m","RH_HMP_2m","Ta_HMP_2m")
Author: PRI
Date: September 2015
"""
nRecs = int(ds.root["Attributes"]["nc_nrecs"])
zeros = numpy.zeros(nRecs, dtype=numpy.int32)
ones = numpy.ones(nRecs, dtype=numpy.int32)
for item in [RH_in, Ta_in]:
if item not in ds.root["Variables"].keys():
msg = " Requested series " + item + " not found, " + AH_out + " not calculated"
logger.error(msg)
return 0
# get the relative humidity and check the units
RH = pfp_utils.GetVariable(ds, RH_in)
RH = pfp_utils.convert_units_func(ds, RH, "percent")
# get the temperature and check the units
Ta = pfp_utils.GetVariable(ds, Ta_in)
Ta = pfp_utils.convert_units_func(ds, Ta, "degC")
# get the absolute humidity
AH = pfp_utils.GetVariable(ds, AH_out)
AH["Data"] = pfp_mf.absolutehumidityfromrelativehumidity(
Ta["Data"], RH["Data"])
AH["Flag"] = numpy.where(
numpy.ma.getmaskarray(AH["Data"]) == True, ones, zeros)
AH["Attr"]["units"] = "g/m^3"
pfp_utils.CreateVariable(ds, AH)
return 1
def mmolpmol_to_gH2Opm3(ds, AH_out, MF_in, Ta_in, ps_in):
"""
Purpose:
Function to calculate absolute humidity given the water vapour mole
fraction, air temperature and pressure. Absolute humidity is not calculated
if any of the input series are missing or if the specified output series
already exists in the data structure.
The calculated absolute humidity is created as a new series in the
data structure.
Usage:
pfp_func_units.mmolpmol_to_gpm3(ds,"AH_IRGA_Av","H2O_IRGA_Av","Ta_HMP_2m","ps")
Author: PRI
Date: September 2015
"""
nRecs = int(ds.root["Attributes"]["nc_nrecs"])
zeros = numpy.zeros(nRecs, dtype=numpy.int32)
ones = numpy.ones(nRecs, dtype=numpy.int32)
for item in [MF_in, Ta_in, ps_in]:
if item not in list(ds.root["Variables"].keys()):
msg = " Requested series " + item + " not found, " + AH_out + " not calculated"
logger.error(msg)
return 0
MF = pfp_utils.GetVariable(ds, MF_in)
MF = pfp_utils.convert_units_func(ds, MF, "mmol/mol")
Ta = pfp_utils.GetVariable(ds, Ta_in)
Ta = pfp_utils.convert_units_func(ds, Ta, "degC")
ps = pfp_utils.GetVariable(ds, ps_in)
ps = pfp_utils.convert_units_func(ds, ps, "kPa")
AH = pfp_utils.GetVariable(ds, AH_out)
AH["Data"] = pfp_mf.h2o_gpm3frommmolpmol(MF["Data"], Ta["Data"],
ps["Data"])
AH["Flag"] = numpy.where(
numpy.ma.getmaskarray(AH["Data"]) == True, ones, zeros)
AH["Attr"]["units"] = "g/m^3"
pfp_utils.CreateVariable(ds, AH)
return 1
def K_to_C(ds, T_out, T_in):
"""
Purpose:
Function to convert temperature from K to C.
Usage:
pfp_func_units.K_to_C(ds, T_out, T_in)
Author: PRI
Date: February 2018
"""
if T_in not in list(ds.root["Variables"].keys()):
msg = " Convert_K_to_C: variable " + T_in + " not found, skipping ..."
logger.warning(msg)
return 0
if "<" in T_out or ">" in T_out:
logger.warning(" ***")
msg = " *** " + T_in + ": illegal name (" + T_out + ") in function, skipping ..."
logger.warning(msg)
logger.warning(" ***")
return 0
var_in = pfp_utils.GetVariable(ds, T_in)
var_out = pfp_utils.convert_units_func(ds, var_in, "degC", mode="quiet")
var_out["Label"] = T_out
pfp_utils.CreateVariable(ds, var_out)
return 1
"Attr":
data[site][label + "_" + str(i) + str(j)]["Attr"]
}
# put it into the data structure
pfp_utils.CreateVariable(dss_ats[site], variable)
# do the units conversion
msg = " Converting units for ps, Ta, Ts and Sws"
logger.info(msg)
for site in sites:
for i in range(3):
for j in range(3):
# surface pressure units Pa to kPa
ps = pfp_utils.GetVariable(dss_ats[site],
"ps" + "_" + str(i) + str(j))
ps = pfp_utils.convert_units_func(dss_ats[site], ps, "kPa")
pfp_utils.CreateVariable(dss_ats[site], ps)
# air temperature
Ta = pfp_utils.GetVariable(dss_ats[site],
"Ta" + "_" + str(i) + str(j))
Ta = pfp_utils.convert_units_func(dss_ats[site], Ta, "degC")
pfp_utils.CreateVariable(dss_ats[site], Ta)
# soil temperature
Ts = pfp_utils.GetVariable(dss_ats[site],
"Ts" + "_" + str(i) + str(j))
Ts = pfp_utils.convert_units_func(dss_ats[site], Ts, "degC")
pfp_utils.CreateVariable(dss_ats[site], Ts)
# soil moisture
Sws = pfp_utils.GetVariable(dss_ats[site],
"Sws" + "_" + str(i) + str(j))
Sws = pfp_utils.convert_units_func(dss_ats[site], Sws, "m^3/m^3")
pfp_utils.CreateVariable(dss_ats[site], Fh)
# latent heat flux
Fe = pfp_utils.GetVariable(dss_ats[site], "Fe")
Fe["Data"] = float(-1)*Fe["Data"]/(era5_timestep*60.0)
pfp_utils.CreateVariable(dss_ats[site], Fe)
# Precipitation is in m, convert to mm
Precip = pfp_utils.GetVariable(dss_ats[site], "Precip")
Precip["Data"] = Precip["Data"]*float(1000)
pfp_utils.CreateVariable(dss_ats[site], Precip)
# do the units conversion
msg = " Converting units for ps, Ta, Td, Ts and Sws"
logger.info(msg)
for site in sites:
# surface pressure units Pa to kPa
ps = pfp_utils.GetVariable(dss_ats[site], "ps")
ps = pfp_utils.convert_units_func(dss_ats[site], ps, "kPa")
pfp_utils.CreateVariable(dss_ats[site], ps)
# air temperature
Ta = pfp_utils.GetVariable(dss_ats[site], "Ta")
Ta = pfp_utils.convert_units_func(dss_ats[site], Ta, "degC")
pfp_utils.CreateVariable(dss_ats[site], Ta)
# dew point temperature
Td = pfp_utils.GetVariable(dss_ats[site], "Td")
Td = pfp_utils.convert_units_func(dss_ats[site], Td, "degC")
pfp_utils.CreateVariable(dss_ats[site], Td)
# soil temperature level 1
Ts = pfp_utils.GetVariable(dss_ats[site], "Ts")
Ts = pfp_utils.convert_units_func(dss_ats[site], Ts, "degC")
pfp_utils.CreateVariable(dss_ats[site], Ts)
# soil temperature level 2
Ts2 = pfp_utils.GetVariable(dss_ats[site], "Ts2")
def change_variable_attributes(std, ds):
"""
Purpose:
Clean up the variable attributes.
Usage:
Author: PRI
Date: November 2018
"""
# coerce units into a standard form
msg = " Parse variable attributes"
logger.info(msg)
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
# parse variable attributes to new format
variable["Attr"] = parse_variable_attributes(variable["Attr"])
pfp_utils.CreateVariable(ds, variable)
# coerce units into a standard form
msg = " Changing variable units"
logger.info(msg)
old_units = list(std["Variables"]["units_map"].keys())
deprecated_units = pfp_utils.string_to_list(std["Variables"]["deprecated"]["units"])
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
old_unit = variable["Attr"]["units"]
if old_unit in old_units:
variable["Attr"]["units"] = std["Variables"]["units_map"][old_unit]
pfp_utils.CreateVariable(ds, variable)
elif old_unit in deprecated_units or len(old_unit) == 0:
variable["Attr"]["units"] = "1"
pfp_utils.CreateVariable(ds, variable)
# do any units conversion required
msg = " Converting units"
logger.info(msg)
stdv = std["Variables"]
stdva = std["Variables"]["attributes"]
labels = list(ds.series.keys())
vattrs = pfp_utils.string_to_list(stdv["units_convert"]["labels"])
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
for vattr in vattrs:
#if label[:len(vattr)] == vattr:
if label.split("_")[0] == vattr:
old_units = variable["Attr"]["units"]
std_units = stdva[vattr]["units"]
if old_units != std_units:
msg = " Converting " + label + " to units of " + std_units
logger.info(msg)
variable = pfp_utils.convert_units_func(ds, variable, std_units)
pfp_utils.CreateVariable(ds, variable)
# rename existing long_name to description, introduce a
# consistent long_name attribute
msg = " Long name, description and units"
logger.info(msg)
stdva = std["Variables"]["attributes"]
vattr_list = list(stdva.keys())
labels = list(ds.series.keys())
descr = "description_" + ds.globalattributes["processing_level"]
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
# existing long_name to description
variable["Attr"][descr] = variable["Attr"]["long_name"]
for item in vattr_list:
if label == item:
for key in list(stdva[item].keys()):
if key == "units":
if "_Sd" not in label and "_Vr" not in label:
old_units = variable["Attr"]["units"]
new_units = pfp_utils.string_to_list(stdva[item]["units"])
if old_units not in new_units and old_units != "1":
msg = "Units '" + old_units + "' not found for variable " + label
logger.warning(msg)
continue
if old_units in new_units:
if "standard_name" in stdva[item]:
idx = new_units.index(old_units)
standard_names = pfp_utils.string_to_list(stdva[item]["standard_name"])
variable["Attr"]["standard_name"] = standard_names[idx]
elif key == "standard_name":
if "_Sd" in label or "_Vr" in label:
# remove standard_name for standard deviations and variances
if "standard_name" in variable["Attr"]:
variable["Attr"].pop("standard_name")
else:
variable["Attr"][key] = stdva[item][key]
# remove standard_name attribute if not defined for this variable
if (("standard_name" in variable["Attr"]) and ("standard_name" not in stdva[item])):
variable["Attr"].pop("standard_name")
elif label.split("_")[0] == item:
for key in list(stdva[item].keys()):
if key == "units":
if "_Sd" not in label and "_Vr" not in label:
old_units = variable["Attr"]["units"]
new_units = pfp_utils.string_to_list(stdva[item]["units"])
if old_units not in new_units and old_units != "1":
msg = "Units '" + old_units + "' not found for variable " + label
logger.warning(msg)
continue
if old_units in new_units:
if "standard_name" in stdva[item]:
idx = new_units.index(old_units)
standard_names = pfp_utils.string_to_list(stdva[item]["standard_name"])
variable["Attr"]["standard_name"] = standard_names[idx]
elif key == "standard_name":
if "_Sd" in label or "_Vr" in label:
# remove standard_name for standard deviations and variances
if "standard_name" in variable["Attr"]:
variable["Attr"].pop("standard_name")
else:
variable["Attr"][key] = stdva[item][key]
# remove standard_name attribute if not defined for this variable
if (("standard_name" in variable["Attr"]) and ("standard_name" not in stdva[item])):
variable["Attr"].pop("standard_name")
pfp_utils.CreateVariable(ds, variable)
# parse variable attributes to new format, remove deprecated variable attributes
# and fix valid_range == "-1e+35,1e+35"
msg = " Remove deprecated, check valid_range"
logger.info(msg)
tmp = std["Variables"]["deprecated"]["attributes"]
deprecated = pfp_utils.string_to_list(tmp)
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
## parse variable attributes to new format
#variable["Attr"] = parse_variable_attributes(variable["Attr"])
# remove deprecated variable attributes
for vattr in deprecated:
if vattr in list(variable["Attr"].keys()):
del variable["Attr"][vattr]
# fix valid_range == "-1e+35,1e+35"
if "valid_range" in variable["Attr"]:
valid_range = variable["Attr"]["valid_range"]
if valid_range == "-1e+35,1e+35":
d = numpy.ma.min(variable["Data"])
mn = pfp_utils.round2significant(d, 4, direction='down')
d = numpy.ma.max(variable["Data"])
mx = pfp_utils.round2significant(d, 4, direction='up')
variable["Attr"]["valid_range"] = repr(mn) + "," + repr(mx)
pfp_utils.CreateVariable(ds, variable)
# ugly hack to deal with CO2_IRGA_Av, CO2_IRGA_Sd and CO2_IRGA_Vr units
msg = " Converting CO2 units"
logger.info(msg)
labels = list(ds.series.keys())
for label in labels:
if (label.split("_")[0] == "CO2"):
co2 = pfp_utils.GetVariable(ds, label)
if ((label == "CO2") and (co2["Attr"]["units"] == "mg/m^3")):
co2 = pfp_utils.convert_units_func(ds, co2, "umol/mol")
pfp_utils.CreateVariable(ds, co2)
elif ((label[-3:] == "_Av") and (co2["Attr"]["units"] == "mg/m^3")):
co2 = pfp_utils.convert_units_func(ds, co2, "umol/mol")
pfp_utils.CreateVariable(ds, co2)
elif ((label[-3:] == "_Sd") and (co2["Attr"]["units"] == "mg/m^3")):
co2 = pfp_utils.convert_units_func(ds, co2, "mmol/m^3")
# convert_units_func() will add a standard name when units=mmol/m^3
# here we dump standard_name for a standard deviation
if "standard_name" in co2["Attr"]:
co2["Attr"].pop("standard_name")
pfp_utils.CreateVariable(ds, co2)
elif ((label[-3:] == "_Vr") and (co2["Attr"]["units"] == "mg^2/m^6")):
msg = " Converting " + label + " from " + co2["Attr"]["units"]
msg += " to mmol^2/m^6"
logger.info(msg)
co2["Data"] = numpy.ma.sqrt(co2["Data"])
co2["Attr"]["units"] = "mg/m^3"
co2 = pfp_utils.convert_units_func(ds, co2, "mmol/m^3")
co2["Data"] = co2["Data"]*co2["Data"]
co2["Attr"]["units"] = "mmol^2/m^6"
# convert_units_func() will add a standard name when units=mmol/m^3
# here we dump standard_name for a variance
if "standard_name" in co2["Attr"]:
co2["Attr"].pop("standard_name")
pfp_utils.CreateVariable(ds, co2)
else:
if co2["Attr"]["units"] not in ["umol/mol", "mmol/m^3", "mmol^2/m^6", "1"]:
msg = " Unrecognised units for " + label
msg += " (" + co2["Attr"]["units"] + ")"
logger.warning(msg)
# set the statistic_type variable attribute for standard deviations and
# variances and remove standard_name if present
msg = " Setting statistic_type"
logger.info(msg)
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
if label[-3:] == "_Sd":
variable["Attr"]["statistic_type"] = "standard_deviation"
if "standard_name" in variable["Attr"]:
variable["Attr"].pop("standard_name")
pfp_utils.CreateVariable(ds, variable)
elif label[-3:] == "_Vr":
variable["Attr"]["statistic_type"] = "variance"
if "standard_name" in variable["Attr"]:
variable["Attr"].pop("standard_name")
pfp_utils.CreateVariable(ds, variable)
else:
pass
# remove undefined attributes
msg = " Remove undefined attributes"
logger.info(msg)
stdvd = std["Variables"]["deprecated"]
units_deprecated = pfp_utils.string_to_list(stdvd["units"])
height_deprecated = pfp_utils.string_to_list(stdvd["height"])
miscellaneous_deprecated = pfp_utils.string_to_list(stdvd["miscellaneous"])
standard_name_deprecated = pfp_utils.string_to_list(stdvd["standard_name"])
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
attrs = list(variable["Attr"].keys())
for attr in attrs:
if attr == "units":
if ((variable["Attr"][attr] in units_deprecated) or
(len(str(variable["Attr"][attr])) == 0)):
variable["Attr"].pop(attr)
elif attr == "height":
if ((variable["Attr"][attr] in height_deprecated) or
(len(str(variable["Attr"][attr])) == 0)):
variable["Attr"].pop(attr)
elif attr == "standard_name":
if ((variable["Attr"][attr] in standard_name_deprecated) or
(len(str(variable["Attr"][attr])) == 0)):
variable["Attr"].pop(attr)
elif len(str(variable["Attr"][attr])) == 0:
variable["Attr"].pop(attr)
else:
if ((variable["Attr"][attr] in miscellaneous_deprecated) or
(len(str(variable["Attr"][attr])) == 0)):
variable["Attr"].pop(attr)
pfp_utils.CreateVariable(ds, variable)
# append '%' symbol to coverage_L2 and coverage_L3 variable sttributes
msg = " Appending % to coverage statistics"
logger.info(msg)
labels = list(ds.series.keys())
for label in labels:
variable = pfp_utils.GetVariable(ds, label)
attrs = list(variable["Attr"].keys())
for attr in attrs:
if "coverage_" in attr:
if "%" not in variable["Attr"][attr]:
variable["Attr"][attr] += "%"
pfp_utils.CreateVariable(ds, variable)
return