def CreateNewSeries(cf, ds):
'''Create a new series using the MergeSeries or AverageSeries instructions.'''
log.info(' Checking for new series to create')
for ThisOne in cf['Variables'].keys():
if 'MergeSeries' in cf['Variables'][ThisOne].keys():
qcts.MergeSeries(cf, ds, ThisOne, [0, 10])
if 'AverageSeries' in cf['Variables'][ThisOne].keys():
qcts.AverageSeriesByElements(cf, ds, ThisOne)
def l3qc(cf, ds2):
"""
Corrections
Generates L3 from L2 data
Functions performed:
qcts.AddMetVars (optional)
qcts.CorrectSWC (optional*)
qcck.do_linear (all sites)
qcutils.GetMergeList + qcts.MergeSeries Ah_EC (optional)x
qcts.TaFromTv (optional)
qcutils.GetMergeList + qcts.MergeSeries Ta_EC (optional)x
qcts.CoordRotation2D (all sites)
qcts.MassmanApprox (optional*)y
qcts.Massman (optional*)y
qcts.CalculateFluxes (used if Massman not optioned)x
qcts.CalculateFluxesRM (used if Massman optioned)y
qcts.FhvtoFh (all sites)
qcts.Fe_WPL (WPL computed on fluxes, as with Campbell algorithm)+x
qcts.Fc_WPL (WPL computed on fluxes, as with Campbell algorithm)+x
qcts.Fe_WPLcov (WPL computed on kinematic fluxes (ie, covariances), as with WPL80)+y
qcts.Fc_WPLcov (WPL computed on kinematic fluxes (ie, covariances), as with WPL80)+y
qcts.CalculateNetRadiation (optional)
qcutils.GetMergeList + qcts.MergeSeries Fsd (optional)
qcutils.GetMergeList + qcts.MergeSeries Fn (optional*)
qcts.InterpolateOverMissing (optional)
AverageSeriesByElements (optional)
qcts.CorrectFgForStorage (all sites)
qcts.Average3SeriesByElements (optional)
qcts.CalculateAvailableEnergy (optional)
qcck.do_qcchecks (all sites)
qcck.gaps (optional)
*: requires ancillary measurements for paratmerisation
+: each site requires one pair, either Fe_WPL & Fc_WPL (default) or Fe_WPLCov & FcWPLCov
x: required together in option set
y: required together in option set
"""
# make a copy of the L2 data
ds3 = copy.deepcopy(ds2)
# set some attributes for this level
qcutils.UpdateGlobalAttributes(cf, ds3, "L3")
# initialise the global attribute to document the functions used
ds3.globalattributes['Functions'] = ''
# put the control file name into the global attributes
ds3.globalattributes['controlfile_name'] = cf['controlfile_name']
# check to see if we have any imports
qcgf.ImportSeries(cf, ds3)
# correct measured soil water content using empirical relationship to collected samples
qcts.CorrectSWC(cf, ds3)
# apply linear corrections to the data
qcck.do_linear(cf, ds3)
# merge whatever humidities are available
qcts.MergeHumidities(cf, ds3, convert_units=True)
# get the air temperature from the CSAT virtual temperature
qcts.TaFromTv(cf, ds3)
# merge the HMP and corrected CSAT data
qcts.MergeSeries(cf, ds3, 'Ta', [0, 10], convert_units=True)
qcutils.CheckUnits(ds3, "Ta", "C", convert_units=True)
# calculate humidities (absolute, specific and relative) from whatever is available
qcts.CalculateHumidities(ds3)
# merge the 7500 CO2 concentration
qcts.MergeSeries(cf, ds3, 'Cc', [0, 10], convert_units=True)
qcutils.CheckUnits(ds3, "Cc", "mg/m3", convert_units=True)
# add relevant meteorological values to L3 data
qcts.CalculateMeteorologicalVariables(ds3)
# check to see if the user wants to use the fluxes in the L2 file
if not qcutils.cfoptionskeylogical(cf, Key="UseL2Fluxes", default=False):
# check the covariancve units and change if necessary
qcts.CheckCovarianceUnits(ds3)
# do the 2D coordinate rotation
qcts.CoordRotation2D(cf, ds3)
# do the Massman frequency attenuation correction
qcts.MassmanStandard(cf, ds3)
# calculate the fluxes
qcts.CalculateFluxes(cf, ds3)
# approximate wT from virtual wT using wA (ref: Campbell OPECSystem manual)
qcts.FhvtoFh(cf, ds3)
# correct the H2O & CO2 flux due to effects of flux on density measurements
qcts.Fe_WPL(cf, ds3)
qcts.Fc_WPL(cf, ds3)
# convert CO2 units if required
qcutils.ConvertCO2Units(cf, ds3, Cc='Cc')
# calculate Fc storage term - single height only at present
qcts.CalculateFcStorage(cf, ds3)
# convert Fc and Fc_storage units if required
qcutils.ConvertFcUnits(cf, ds3, Fc='Fc', Fc_storage='Fc_storage')
# correct Fc for storage term - only recommended if storage calculated from profile available
qcts.CorrectFcForStorage(cf, ds3)
# merge the incoming shortwave radiation
qcts.MergeSeries(cf, ds3, 'Fsd', [0, 10])
# calculate the net radiation from the Kipp and Zonen CNR1
qcts.CalculateNetRadiation(cf,
ds3,
Fn_out='Fn_KZ',
Fsd_in='Fsd',
Fsu_in='Fsu',
Fld_in='Fld',
Flu_in='Flu')
qcts.MergeSeries(cf, ds3, 'Fn', [0, 10])
# combine wind speed from the Wind Sentry and the CSAT
qcts.MergeSeries(cf, ds3, 'Ws', [0, 10])
# combine wind direction from the Wind Sentry and the CSAT
qcts.MergeSeries(cf, ds3, 'Wd', [0, 10])
# correct soil heat flux for storage
# ... either average the raw ground heat flux, soil temperature and moisture
# and then do the correction (OzFlux "standard")
qcts.AverageSeriesByElements(cf, ds3, 'Ts')
qcts.AverageSeriesByElements(cf, ds3, 'Sws')
if qcutils.cfoptionskeylogical(cf, Key='CorrectIndividualFg'):
# ... or correct the individual ground heat flux measurements (James' method)
qcts.CorrectIndividualFgForStorage(cf, ds3)
qcts.AverageSeriesByElements(cf, ds3, 'Fg')
else:
qcts.AverageSeriesByElements(cf, ds3, 'Fg')
qcts.CorrectFgForStorage(cf,
ds3,
Fg_out='Fg',
Fg_in='Fg',
Ts_in='Ts',
Sws_in='Sws')
# calculate the available energy
qcts.CalculateAvailableEnergy(ds3, Fa_out='Fa', Fn_in='Fn', Fg_in='Fg')
# create new series using MergeSeries or AverageSeries
qcck.CreateNewSeries(cf, ds3)
# create a series of daily averaged soil moisture interpolated back to the time step
#qcts.DailyAverageSws_Interpolated(cf,ds3,Sws_out='Sws_daily',Sws_in='Sws')
# re-apply the quality control checks (range, diurnal and rules)
qcck.do_qcchecks(cf, ds3)
# coordinate gaps in the three main fluxes
qcck.CoordinateFluxGaps(cf, ds3)
# coordinate gaps in Ah_7500_Av with Fc
qcck.CoordinateAh7500AndFcGaps(cf, ds3)
# get the statistics for the QC flags and write these to an Excel spreadsheet
qcio.get_seriesstats(cf, ds3)
# write the percentage of good data as a variable attribute
qcutils.get_coverage_individual(ds3)
# write the percentage of good data for groups
qcutils.get_coverage_groups(ds3)
return ds3
def l3qc(cf, ds2):
"""
Corrections
Generates L3 from L2 data
Functions performed:
qcts.AddMetVars (optional)
qcts.CorrectSWC (optional*)
qcck.do_linear (all sites)
qcutils.GetMergeList + qcts.MergeSeries Ah_EC (optional)x
qcts.TaFromTv (optional)
qcutils.GetMergeList + qcts.MergeSeries Ta_EC (optional)x
qcts.CoordRotation2D (all sites)
qcts.MassmanApprox (optional*)y
qcts.Massman (optional*)y
qcts.CalculateFluxes (used if Massman not optioned)x
qcts.CalculateFluxesRM (used if Massman optioned)y
qcts.FhvtoFh (all sites)
qcts.Fe_WPL (WPL computed on fluxes, as with Campbell algorithm)+x
qcts.Fc_WPL (WPL computed on fluxes, as with Campbell algorithm)+x
qcts.Fe_WPLcov (WPL computed on kinematic fluxes (ie, covariances), as with WPL80)+y
qcts.Fc_WPLcov (WPL computed on kinematic fluxes (ie, covariances), as with WPL80)+y
qcts.CalculateNetRadiation (optional)
qcutils.GetMergeList + qcts.MergeSeries Fsd (optional)
qcutils.GetMergeList + qcts.MergeSeries Fn (optional*)
qcts.InterpolateOverMissing (optional)
AverageSeriesByElements (optional)
qcts.CorrectFgForStorage (all sites)
qcts.Average3SeriesByElements (optional)
qcts.CalculateAvailableEnergy (optional)
qcck.do_qcchecks (all sites)
qcck.gaps (optional)
*: requires ancillary measurements for paratmerisation
+: each site requires one pair, either Fe_WPL & Fc_WPL (default) or Fe_WPLCov & FcWPLCov
x: required together in option set
y: required together in option set
"""
# make a copy of the L2 data
ds3 = copy.deepcopy(ds2)
ds3.globalattributes['nc_level'] = 'L3'
ds3.globalattributes['EPDversion'] = sys.version
ds3.globalattributes['QC_version_history'] = cfg.__doc__
# put the control file name into the global attributes
ds3.globalattributes['controlfile_name'] = cf['controlfile_name']
# calculate NDVI
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='NDVI') and cf['Functions']['NDVI'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', calculateNDVI'
except:
ds3.globalattributes['L3Functions'] = 'calculateNDVI'
log.info(' Calculating NDVI from component reflectances ...')
qcts.CalculateNDVI(cf, ds3)
# bypass soil temperature correction for Sws (when Ts bad)
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='BypassSwsTcorr'
) and cf['Functions']['BypassSwsTcorr'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', BypassSwsTcorr'
except:
ds3.globalattributes['L3Functions'] = 'BypassSwsTcorr'
log.info(' Re-computing Sws without temperature correction ...')
qcts.BypassTcorr(cf, ds3)
# correct measured soil water content using empirical relationship to collected samples
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='CorrectSWC') and cf['Functions']['CorrectSWC'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CorrectSWC'
except:
ds3.globalattributes['L3Functions'] = 'CorrectSWC'
log.info(' Correcting soil moisture data ...')
qcts.CorrectSWC(cf, ds3)
# apply linear corrections to the data
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', do_linear'
except:
ds3.globalattributes['L3Functions'] = 'do_linear'
log.info(' Applying linear corrections ...')
qcck.do_linear(cf, ds3)
# determine HMP Ah if not output by datalogger
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='CalculateAh'
) and cf['Functions']['CalculateAh'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateAh'
except:
ds3.globalattributes['L3Functions'] = 'CalculateAh'
log.info(' Adding HMP Ah to database')
qcts.CalculateAhHMP(cf, ds3)
# merge the HMP and corrected 7500 data
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='MergeSeriesAhTa'
) and cf['Functions']['MergeSeriesAhTa'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', MergeSeriesAhTaCc'
except:
ds3.globalattributes['L3Functions'] = 'MergeSeriesAhTaCc'
qcts.MergeSeries(cf, ds3, 'Ah', [0, 10])
qcts.MergeSeries(cf, ds3, 'Cc', [0, 10])
# get the air temperature from the CSAT virtual temperature
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', TaFromTv'
except:
ds3.globalattributes['L3Functions'] = 'TaFromTv'
qcts.TaFromTv(cf, ds3)
# merge the HMP and corrected CSAT data
qcts.MergeSeries(cf, ds3, 'Ta', [0, 10])
# add relevant meteorological values to L3 data
if (qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections')
and cf['Functions']['Corrections']
== 'True') or (qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='CalculateMetVars')
and cf['Functions']['CalculateMetVars'] == 'True'):
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateMetVars'
except:
ds3.globalattributes['L3Functions'] = 'CalculateMetVars'
log.info(' Adding standard met variables to database')
qcts.CalculateMeteorologicalVariables(ds3)
# do the 2D coordinate rotation
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CoordRotation2D'
except:
ds3.globalattributes['L3Functions'] = 'CoordRotation2D'
qcts.CoordRotation2D(cf, ds3)
# do the Massman frequency attenuation correction
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', Massman'
except:
ds3.globalattributes['L3Functions'] = 'Massman'
qcts.MassmanStandard(cf, ds3)
# calculate the fluxes
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateFluxes'
except:
ds3.globalattributes['L3Functions'] = 'CalculateFluxes'
qcts.CalculateFluxes(cf, ds3)
# approximate wT from virtual wT using wA (ref: Campbell OPECSystem manual)
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', FhvtoFh'
except:
ds3.globalattributes['L3Functions'] = 'FhvtoFh'
qcts.FhvtoFh(cf, ds3)
# correct the H2O & CO2 flux due to effects of flux on density measurements
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='WPLcov') and cf['Functions']['WPLcov'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', WPLcov'
except:
ds3.globalattributes['L3Functions'] = 'WPLcov'
qcts.do_WPL(cf, ds3, cov='True')
else:
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', WPL'
except:
ds3.globalattributes['L3Functions'] = 'WPL'
qcts.do_WPL(cf, ds3)
# calculate the net radiation from the Kipp and Zonen CNR1
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='CalculateNetRadiation'
) and cf['Functions']['CalculateNetRadiation'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateNetRadiation'
except:
ds3.globalattributes['L3Functions'] = 'CalculateNetRadiation'
qcts.MergeSeries(cf, ds3, 'Fsd', [0, 10])
qcts.CalculateNetRadiation(ds3, 'Fn_KZ', 'Fsd', 'Fsu', 'Fld', 'Flu')
qcts.MergeSeries(cf, ds3, 'Fn', [0, 10])
# combine wind speed from the CSAT and the Wind Sentry
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='MergeSeriesWS'
) and cf['Functions']['MergeSeriesWS'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', MergeSeriesWS'
except:
ds3.globalattributes['L3Functions'] = 'MergeSeriesWS'
qcts.MergeSeries(cf, ds3, 'Ws', [0, 10])
# average the soil temperature data
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
if 'SoilAverage' not in ds3.globalattributes['L3Functions']:
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', SoilAverage'
except:
ds3.globalattributes['L3Functions'] = 'SoilAverage'
# interpolate over any ramaining gaps up to 3 hours in length
qcts.AverageSeriesByElementsI(cf, ds3, 'Ts')
qcts.AverageSeriesByElementsI(cf, ds3, 'Sws')
# correct the measured soil heat flux for storage in the soil layer above the sensor
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CorrectFgForStorage'
except:
ds3.globalattributes['L3Functions'] = 'CorrectFgForStorage'
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='IndividualFgCorrection'
) and cf['Functions']['IndividualFgCorrection'] == 'True':
qcts.CorrectIndividualFgForStorage(cf, ds3)
qcts.AverageSeriesByElementsI(cf, ds3, 'Fg')
else:
qcts.AverageSeriesByElementsI(cf, ds3, 'Fg')
qcts.CorrectGroupFgForStorage(cf, ds3)
# calculate the available energy
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='CalculateAvailableEnergy'
) and cf['Functions']['CalculateAvailableEnergy'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateAvailableEnergy'
except:
ds3.globalattributes['L3Functions'] = 'CalculateAvailableEnergy'
qcts.CalculateAvailableEnergy(ds3)
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='DiagnosticMode'):
if cf['Functions']['DiagnosticMode'] == 'False':
qcutils.prepOzFluxVars(cf, ds3)
else:
qcutils.prepOzFluxVars(cf, ds3)
# calculate specific humidity and saturated specific humidity profile
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='qTprofile') and cf['Functions']['qTprofile'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', qTprofile'
except:
ds3.globalattributes['L3Functions'] = 'qTprofile'
qcts.CalculateSpecificHumidityProfile(cf, ds3)
# calculate Penman-Monteith inversion
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='PenmanMonteith'
) and cf['Functions']['PenmanMonteith'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', PenmanMonteith'
except:
ds3.globalattributes['L3Functions'] = 'PenmanMonteith'
qcts.do_PenmanMonteith(cf, ds3)
# calculate bulk Richardson numbers
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='bulkRichardson'
) and cf['Functions']['bulkRichardson'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', bulkRichardson'
except:
ds3.globalattributes['L3Functions'] = 'bulkRichardson'
qcts.do_bulkRichardson(cf, ds3)
# re-apply the quality control checks (range, diurnal and rules)
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', do_qccheck(RangeCheck, diurnalcheck, excludedates, excludehours)'
qcck.do_qcchecks(cf, ds3)
# quality control checks (range, diurnal and rules) without flux post-processing
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='QCChecks') and cf['Functions']['QCChecks'] == 'True':
qcck.do_qcchecks(cf, ds3)
# apply the ustar filter
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='ustarFilter'
) and cf['Functions']['ustarFilter'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', ustarFilter'
except:
ds3.globalattributes['L3Functions'] = 'ustarFilter'
qcts.FilterFcByUstar(cf, ds3)
# coordinate gaps in the three main fluxes
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='CoordinateFluxGaps'
) and cf['Functions']['CoordinateFluxGaps'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CoordinateFluxGaps'
except:
ds3.globalattributes['L3Functions'] = 'CoordinateFluxGaps'
qcck.CoordinateFluxGaps(cf, ds3)
# coordinate gaps in Ah_7500_Av with Fc
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CoordinateAh7500AndFcGaps'
except:
ds3.globalattributes['L3Functions'] = 'CoordinateAh7500AndFcGaps'
qcck.CoordinateAh7500AndFcGaps(cf, ds3)
# calcluate ET at observation interval
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='CalculateET'
) and cf['Functions']['CalculateET'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', CalculateET'
except:
ds3.globalattributes['L3Functions'] = 'CalculateET'
log.info(' Calculating ET')
qcts.CalculateET(cf, ds3, 'L3')
# run MOST (Buckingham Pi) 2d footprint model (Kljun et al. 2004)
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='footprint') and cf['Functions']['footprint'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', footprint'
except:
ds3.globalattributes['L3Functions'] = 'footprint'
qcts.do_footprint_2d(cf, ds3)
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='Corrections'
) and cf['Functions']['Corrections'] == 'True':
qcio.get_seriesstats(cf, ds3)
# convert Fc [mgCO2 m-2 s-1] to Fc_co2 [mgCO2 m-2 s-1], Fc_c [mgC m-2 s-1], NEE [umol m-2 s-1] and NEP = - NEE
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='convertFc') and cf['Functions']['convertFc'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', convertFc'
except:
ds3.globalattributes['L3Functions'] = 'convertFc'
qcts.ConvertFc(cf, ds3)
# convert Fc [mgCO2 m-2 s-1] to Fc [umol m-2 s-1]
if qcutils.cfkeycheck(
cf, Base='Functions',
ThisOne='JasonFc') and cf['Functions']['JasonFc'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', convertFc (umol only)'
except:
ds3.globalattributes['L3Functions'] = 'convertFc (umol only)'
qcts.ConvertFcJason(cf, ds3)
# write the percentage of good data as a variable attribute
qcutils.get_coverage_individual(ds3)
# write the percentage of good data for groups
qcutils.get_coverage_groups(ds3)
# compute water-use efficiency from flux-gradient similarity (appendix A, Scanlon & Sahu 2008)
if qcutils.cfkeycheck(cf, Base='Functions',
ThisOne='wue') and cf['Functions']['wue'] == 'True':
try:
ds3.globalattributes[
'L3Functions'] = ds3.globalattributes['L3Functions'] + ', wue'
except:
ds3.globalattributes['L3Functions'] = 'wue'
log.info(
' Calculating water-use efficiency from flux-gradient similarity')
qcts.CalculateWUEfromSimilarity(cf, ds3)
# compute climatology for L3 data
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='climatology'
) and cf['Functions']['climatology'] == 'True':
try:
ds3.globalattributes['L3Functions'] = ds3.globalattributes[
'L3Functions'] + ', climatology'
except:
ds3.globalattributes['L3Functions'] = 'climatology'
qcts.do_climatology(cf, ds3)
if qcutils.cfkeycheck(cf, Base='Functions',
ThisOne='Sums') and cf['Functions']['Sums'] == 'L3':
try:
ds3.globalattributes[
'L3Functions'] = ds3.globalattributes['L5Functions'] + ', Sums'
except:
ds3.globalattributes['L3Functions'] = 'Sums'
qcts.do_sums(cf, ds3)
try:
ds3.globalattributes['Functions'] = ds3.globalattributes[
'Functions'] + ', ' + ds3.globalattributes['L3Functions']
except:
ds3.globalattributes['Functions'] = ds3.globalattributes['L3Functions']
return ds3
def l3qc(cf, ds2):
"""
"""
# make a copy of the L2 data
ds3 = copy.deepcopy(ds2)
# set some attributes for this level
qcutils.UpdateGlobalAttributes(cf, ds3, "L3")
# put the control file name into the global attributes
ds3.globalattributes['controlfile_name'] = cf['controlfile_name']
# check to see if we have any imports
qcgf.ImportSeries(cf, ds3)
# apply linear corrections to the data
qcck.do_linear(cf, ds3)
# ************************
# *** Merge humidities ***
# ************************
# merge whatever humidities are available
qcts.MergeHumidities(cf, ds3, convert_units=True)
# **************************
# *** Merge temperatures ***
# **************************
# get the air temperature from the CSAT virtual temperature
qcts.TaFromTv(cf, ds3)
# merge the HMP and corrected CSAT data
qcts.MergeSeries(cf, ds3, "Ta", convert_units=True)
qcutils.CheckUnits(ds3, "Ta", "C", convert_units=True)
# ***************************
# *** Calcuate humidities ***
# ***************************
# calculate humidities (absolute, specific and relative) from whatever is available
qcts.CalculateHumidities(ds3)
# ********************************
# *** Merge CO2 concentrations ***
# ********************************
# merge the 7500 CO2 concentration
# PRI 09/08/2017 possibly the ugliest thing I have done yet
# This needs to be abstracted to a general alias checking routine at the
# start of the L3 processing so that possible aliases are mapped to a single
# set of variable names.
if "CO2" in cf["Variables"]:
CO2 = "CO2"
elif "Cc" in cf["Variables"]:
CO2 = "Cc"
else:
msg = "Label for CO2 ('CO2','Cc') not found in control file"
logger.error(msg)
return
qcts.MergeSeries(cf, ds3, CO2, convert_units=True)
# ******************************************
# *** Calculate meteorological variables ***
# ******************************************
# Update meteorological variables
qcts.CalculateMeteorologicalVariables(ds3)
# *************************************************
# *** Calculate fluxes from covariances section ***
# *************************************************
# check to see if the user wants to use the fluxes in the L2 file
if not qcutils.cfoptionskeylogical(cf, Key="UseL2Fluxes", default=False):
# check the covariance units and change if necessary
qcts.CheckCovarianceUnits(ds3)
# do the 2D coordinate rotation
qcts.CoordRotation2D(cf, ds3)
# do the Massman frequency attenuation correction
qcts.MassmanStandard(cf, ds3)
# calculate the fluxes
qcts.CalculateFluxes(cf, ds3)
# approximate wT from virtual wT using wA (ref: Campbell OPECSystem manual)
qcts.FhvtoFh(cf, ds3)
# correct the H2O & CO2 flux due to effects of flux on density measurements
qcts.Fe_WPL(cf, ds3)
qcts.Fc_WPL(cf, ds3)
# **************************************
# *** Calculate Monin-Obukhov length ***
# **************************************
qcts.CalculateMoninObukhovLength(ds3)
# **************************
# *** CO2 and Fc section ***
# **************************
# convert CO2 units if required
qcutils.ConvertCO2Units(cf, ds3, CO2=CO2)
# calculate Fc storage term - single height only at present
qcts.CalculateFcStorageSinglePoint(cf, ds3, Fc_out='Fc_single', CO2_in=CO2)
# convert Fc and Fc_storage units if required
qcutils.ConvertFcUnits(cf, ds3)
# merge Fc and Fc_storage series if required
merge_list = [
label for label in cf["Variables"].keys() if label[0:2] == "Fc"
and "MergeSeries" in cf["Variables"][label].keys()
]
for label in merge_list:
qcts.MergeSeries(cf, ds3, label, save_originals=True)
# correct Fc for storage term - only recommended if storage calculated from profile available
qcts.CorrectFcForStorage(cf, ds3)
# *************************
# *** Radiation section ***
# *************************
# merge the incoming shortwave radiation
qcts.MergeSeries(cf, ds3, 'Fsd')
# calculate the net radiation from the Kipp and Zonen CNR1
qcts.CalculateNetRadiation(cf,
ds3,
Fn_out='Fn_KZ',
Fsd_in='Fsd',
Fsu_in='Fsu',
Fld_in='Fld',
Flu_in='Flu')
qcts.MergeSeries(cf, ds3, 'Fn')
# ****************************************
# *** Wind speed and direction section ***
# ****************************************
# combine wind speed from the Wind Sentry and the SONIC
qcts.MergeSeries(cf, ds3, 'Ws')
# combine wind direction from the Wind Sentry and the SONIC
qcts.MergeSeries(cf, ds3, 'Wd')
# ********************
# *** Soil section ***
# ********************
# correct soil heat flux for storage
# ... either average the raw ground heat flux, soil temperature and moisture
# and then do the correction (OzFlux "standard")
qcts.AverageSeriesByElements(cf, ds3, 'Ts')
qcts.AverageSeriesByElements(cf, ds3, 'Sws')
if qcutils.cfoptionskeylogical(cf, Key='CorrectIndividualFg'):
# ... or correct the individual ground heat flux measurements (James' method)
qcts.CorrectIndividualFgForStorage(cf, ds3)
qcts.AverageSeriesByElements(cf, ds3, 'Fg')
else:
qcts.AverageSeriesByElements(cf, ds3, 'Fg')
qcts.CorrectFgForStorage(cf,
ds3,
Fg_out='Fg',
Fg_in='Fg',
Ts_in='Ts',
Sws_in='Sws')
# calculate the available energy
qcts.CalculateAvailableEnergy(ds3, Fa_out='Fa', Fn_in='Fn', Fg_in='Fg')
# create new series using MergeSeries or AverageSeries
qcck.CreateNewSeries(cf, ds3)
# re-apply the quality control checks (range, diurnal and rules)
qcck.do_qcchecks(cf, ds3)
# coordinate gaps in the three main fluxes
qcck.CoordinateFluxGaps(cf, ds3)
# coordinate gaps in Ah_7500_Av with Fc
qcck.CoordinateAh7500AndFcGaps(cf, ds3)
# check missing data and QC flags are consistent
qcutils.CheckQCFlags(ds3)
# get the statistics for the QC flags and write these to an Excel spreadsheet
qcio.get_seriesstats(cf, ds3)
# write the percentage of good data as a variable attribute
qcutils.get_coverage_individual(ds3)
# write the percentage of good data for groups
qcutils.get_coverage_groups(ds3)
return ds3
def l4qc(cf, ds3, InLevel, x):
ds4 = copy.deepcopy(ds3)
ds4.globalattributes['nc_level'] = 'L4'
if (qcutils.cfkeycheck(cf, Base='Functions', ThisOne='L4_offline') and
cf['Functions']['L4_offline'] == 'True') and qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='L4_keys'):
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', ' + cf['Functions']['L4_keys']
except:
ds4.globalattributes['L4Functions'] = cf['Functions']['L4_keys']
x = x + 1
# determine HMP Ah if not output by datalogger
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='CalculateAh'
) and cf['Functions']['CalculateAh'] == 'True':
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', CalculateAh'
except:
ds4.globalattributes['L4Functions'] = 'CalculateAh'
log.info(' Adding HMP Ah to database')
qcts.CalculateAhHMP(cf, ds4)
# add relevant meteorological values to L4 data
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='CalculateMetVars'
) and cf['Functions']['CalculateMetVars'] == 'True':
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', CalculateMetVars'
except:
ds4.globalattributes['L4Functions'] = 'CalculateMetVars'
log.info(' Adding standard met variables to database')
qcts.CalculateMeteorologicalVariables(ds4)
# merge CSAT and wind sentry wind speed
if qcutils.cfkeycheck(cf, Base='Functions', ThisOne='MergeSeriesWS'
) and cf['Functions']['MergeSeriesWS'] == 'True':
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', MergeSeriesWS'
except:
ds4.globalattributes['L4Functions'] = 'MergeSeriesWS'
qcts.MergeSeries(cf, ds4, 'Ws', [0, 10])
# linear interpolation to fill missing values over gaps of 1 hour
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='InterpolateOverMissing'
) and cf['Functions']['InterpolateOverMissing'] == 'True':
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', InterpolateOverMissing'
except:
ds4.globalattributes['L4Functions'] = 'InterpolateOverMissing'
log.info(
' Gap filling by linear interpolation to fill missing values over gaps of 1 hour'
)
for ThisOne in cf['InterpolateVars'].keys():
qcts.InterpolateOverMissing(cf, ds4, series=ThisOne, maxlen=2)
x = x + 1
# re-apply the quality control checks (range, diurnal and rules)
if x > 0:
log.info(' Doing QC checks on L4 data')
qcck.do_qcchecks(cf, ds4)
try:
ds4.globalattributes['L4Functions'] = ds4.globalattributes[
'L4Functions'] + ', do_qccheck(RangeCheck, diurnalcheck, excludedates, excludehours)'
except:
ds4.globalattributes[
'L4Functions'] = 'do_qccheck(RangeCheck, diurnalcheck, excludedates, excludehours)'
# interpolate over any ramaining gaps up to 3 hours in length
if qcutils.cfkeycheck(
cf, Base='Functions', ThisOne='InterpolateOverMissing'
) and cf['Functions']['InterpolateOverMissing'] == 'True':
for ThisOne in cf['InterpolateVars'].keys():
qcts.InterpolateOverMissing(cf, ds4, series=ThisOne, maxlen=6)
ds4.globalattributes['Functions'] = ds4.globalattributes[
'Functions'] + ', ' + ds4.globalattributes['L4Functions']
return ds4, x
