def l1qc_process(cf, ds1):
# get the netCDF attributes from the control file
qcts.do_attributes(cf, ds1)
# round the Python datetime to the nearest second
qcutils.round_datetime(ds1, mode="nearest_second")
#check for gaps in the Python datetime series and fix if present
fixtimestepmethod = qcutils.get_keyvaluefromcf(cf, ["options"],
"FixTimeStepMethod",
default="round")
if qcutils.CheckTimeStep(ds1):
qcutils.FixTimeStep(ds1, fixtimestepmethod=fixtimestepmethod)
# recalculate the Excel datetime
qcutils.get_xldatefromdatetime(ds1)
# get the Year, Month, Day etc from the Python datetime
qcutils.get_ymdhmsfromdatetime(ds1)
# write the processing level to a global attribute
ds1.globalattributes['nc_level'] = str("L1")
# get the start and end date from the datetime series unless they were
# given in the control file
if 'start_date' not in ds1.globalattributes.keys():
ds1.globalattributes['start_date'] = str(
ds1.series['DateTime']['Data'][0])
if 'end_date' not in ds1.globalattributes.keys():
ds1.globalattributes['end_date'] = str(
ds1.series['DateTime']['Data'][-1])
# calculate variances from standard deviations and vice versa
qcts.CalculateStandardDeviations(cf, ds1)
# create new variables using user defined functions
qcts.DoFunctions(cf, ds1)
# create a series of synthetic downwelling shortwave radiation
qcts.get_synthetic_fsd(ds1)
def interpolate_to_30minutes(ds_60minutes):
ds_30minutes = qcio.DataStructure()
# copy the global attributes
for this_attr in list(ds_60minutes.globalattributes.keys()):
ds_30minutes.globalattributes[this_attr] = ds_60minutes.globalattributes[this_attr]
# update the global attribute "time_step"
ds_30minutes.globalattributes["time_step"] = 30
# generate the 30 minute datetime series
dt_loc_60minutes = ds_60minutes.series["DateTime"]["Data"]
dt_loc_30minutes = [x for x in perdelta(dt_loc_60minutes[0],dt_loc_60minutes[-1],datetime.timedelta(minutes=30))]
nRecs_30minutes = len(dt_loc_30minutes)
dt_utc_60minutes = ds_60minutes.series["DateTime_UTC"]["Data"]
dt_utc_30minutes = [x for x in perdelta(dt_utc_60minutes[0],dt_utc_60minutes[-1],datetime.timedelta(minutes=30))]
# update the global attribute "nc_nrecs"
ds_30minutes.globalattributes['nc_nrecs'] = nRecs_30minutes
ds_30minutes.series["DateTime"] = {}
ds_30minutes.series["DateTime"]["Data"] = dt_loc_30minutes
flag = numpy.zeros(len(dt_loc_30minutes),dtype=numpy.int32)
ds_30minutes.series["DateTime"]["Flag"] = flag
ds_30minutes.series["DateTime_UTC"] = {}
ds_30minutes.series["DateTime_UTC"]["Data"] = dt_utc_30minutes
flag = numpy.zeros(len(dt_utc_30minutes),dtype=numpy.int32)
ds_30minutes.series["DateTime_UTC"]["Flag"] = flag
# get the year, month etc from the datetime
qcutils.get_xldatefromdatetime(ds_30minutes)
qcutils.get_ymdhmsfromdatetime(ds_30minutes)
# interpolate to 30 minutes
nRecs_60 = len(ds_60minutes.series["DateTime"]["Data"])
nRecs_30 = len(ds_30minutes.series["DateTime"]["Data"])
x_60minutes = numpy.arange(0,nRecs_60,1)
x_30minutes = numpy.arange(0,nRecs_60-0.5,0.5)
varlist_60 = list(ds_60minutes.series.keys())
# strip out the date and time variables already done
for item in ["DateTime","DateTime_UTC","xlDateTime","Year","Month","Day","Hour","Minute","Second","Hdh","Hr_UTC"]:
if item in varlist_60: varlist_60.remove(item)
# now do the interpolation (its OK to interpolate accumulated precipitation)
for label in varlist_60:
series_60minutes,flag,attr = qcutils.GetSeries(ds_60minutes,label)
ci_60minutes = numpy.zeros(len(series_60minutes))
idx = numpy.where(abs(series_60minutes-float(c.missing_value))<c.eps)[0]
ci_60minutes[idx] = float(1)
int_fn = interp1d(x_60minutes,series_60minutes)
series_30minutes = int_fn(x_30minutes)
int_fn = interp1d(x_60minutes,ci_60minutes)
ci_30minutes = int_fn(x_30minutes)
idx = numpy.where(abs(ci_30minutes-float(0))>c.eps)[0]
series_30minutes[idx] = numpy.float64(c.missing_value)
flag_30minutes = numpy.zeros(nRecs_30, dtype=numpy.int32)
flag_30minutes[idx] = numpy.int32(1)
qcutils.CreateSeries(ds_30minutes,label,series_30minutes,Flag=flag_30minutes,Attr=attr)
# get the UTC hour
hr_utc = [float(x.hour)+float(x.minute)/60 for x in dt_utc_30minutes]
attr = qcutils.MakeAttributeDictionary(long_name='UTC hour')
flag_30minutes = numpy.zeros(nRecs_30, dtype=numpy.int32)
qcutils.CreateSeries(ds_30minutes,'Hr_UTC',hr_utc,Flag=flag_30minutes,Attr=attr)
return ds_30minutes
def l1qc(cf):
# get the data series from the Excel file
in_filename = qcio.get_infilenamefromcf(cf)
if not qcutils.file_exists(in_filename, mode="quiet"):
msg = " Input file " + in_filename + " not found ..."
logger.error(msg)
ds1 = qcio.DataStructure()
ds1.returncodes = {"value": 1, "message": msg}
return ds1
file_name, file_extension = os.path.splitext(in_filename)
if "csv" in file_extension.lower():
ds1 = qcio.csv_read_series(cf)
if ds1.returncodes["value"] != 0:
return ds1
# get a series of Excel datetime from the Python datetime objects
qcutils.get_xldatefromdatetime(ds1)
else:
ds1 = qcio.xl_read_series(cf)
if ds1.returncodes["value"] != 0:
return ds1
# get a series of Python datetime objects from the Excel datetime
qcutils.get_datetimefromxldate(ds1)
# get the netCDF attributes from the control file
qcts.do_attributes(cf, ds1)
# round the Python datetime to the nearest second
qcutils.round_datetime(ds1, mode="nearest_second")
#check for gaps in the Python datetime series and fix if present
fixtimestepmethod = qcutils.get_keyvaluefromcf(cf, ["options"],
"FixTimeStepMethod",
default="round")
if qcutils.CheckTimeStep(ds1):
qcutils.FixTimeStep(ds1, fixtimestepmethod=fixtimestepmethod)
# recalculate the Excel datetime
qcutils.get_xldatefromdatetime(ds1)
# get the Year, Month, Day etc from the Python datetime
qcutils.get_ymdhmsfromdatetime(ds1)
# write the processing level to a global attribute
ds1.globalattributes['nc_level'] = str("L1")
# get the start and end date from the datetime series unless they were
# given in the control file
if 'start_date' not in ds1.globalattributes.keys():
ds1.globalattributes['start_date'] = str(
ds1.series['DateTime']['Data'][0])
if 'end_date' not in ds1.globalattributes.keys():
ds1.globalattributes['end_date'] = str(
ds1.series['DateTime']['Data'][-1])
# calculate variances from standard deviations and vice versa
qcts.CalculateStandardDeviations(cf, ds1)
# create new variables using user defined functions
qcts.DoFunctions(cf, ds1)
# create a series of synthetic downwelling shortwave radiation
qcts.get_synthetic_fsd(ds1)
# check missing data and QC flags are consistent
qcutils.CheckQCFlags(ds1)
return ds1
def interpolate_to_30minutes(ds_60minutes):
ds_30minutes = qcio.DataStructure()
# copy the global attributes
for this_attr in ds_60minutes.globalattributes.keys():
ds_30minutes.globalattributes[this_attr] = ds_60minutes.globalattributes[this_attr]
# update the global attribute "time_step"
ds_30minutes.globalattributes["time_step"] = 30
# generate the 30 minute datetime series
dt_loc_60minutes = ds_60minutes.series["DateTime"]["Data"]
dt_loc_30minutes = [x for x in perdelta(dt_loc_60minutes[0],dt_loc_60minutes[-1],datetime.timedelta(minutes=30))]
nRecs_30minutes = len(dt_loc_30minutes)
dt_utc_60minutes = ds_60minutes.series["DateTime_UTC"]["Data"]
dt_utc_30minutes = [x for x in perdelta(dt_utc_60minutes[0],dt_utc_60minutes[-1],datetime.timedelta(minutes=30))]
# update the global attribute "nc_nrecs"
ds_30minutes.globalattributes['nc_nrecs'] = nRecs_30minutes
flag_30minutes = numpy.zeros(nRecs_30minutes)
ds_30minutes.series["DateTime"] = {}
ds_30minutes.series["DateTime"]["Data"] = dt_loc_30minutes
ds_30minutes.series["DateTime_UTC"] = {}
ds_30minutes.series["DateTime_UTC"]["Data"] = dt_utc_30minutes
# get the year, month etc from the datetime
qcutils.get_xldatefromdatetime(ds_30minutes)
qcutils.get_ymdhmsfromdatetime(ds_30minutes)
# interpolate to 30 minutes
nRecs_60 = len(ds_60minutes.series["DateTime"]["Data"])
nRecs_30 = len(ds_30minutes.series["DateTime"]["Data"])
x_60minutes = numpy.arange(0,nRecs_60,1)
x_30minutes = numpy.arange(0,nRecs_60-0.5,0.5)
varlist_60 = ds_60minutes.series.keys()
# strip out the date and time variables already done
for item in ["DateTime","DateTime_UTC","xlDateTime","Year","Month","Day","Hour","Minute","Second","Hdh","Hr_UTC"]:
if item in varlist_60: varlist_60.remove(item)
# now do the interpolation (its OK to interpolate accumulated precipitation)
for label in varlist_60:
series_60minutes,flag,attr = qcutils.GetSeries(ds_60minutes,label)
ci_60minutes = numpy.zeros(len(series_60minutes))
idx = numpy.where(abs(series_60minutes-float(c.missing_value))<c.eps)[0]
ci_60minutes[idx] = float(1)
int_fn = interp1d(x_60minutes,series_60minutes)
series_30minutes = int_fn(x_30minutes)
int_fn = interp1d(x_60minutes,ci_60minutes)
ci_30minutes = int_fn(x_30minutes)
idx = numpy.where(abs(ci_30minutes-float(0))>c.eps)[0]
series_30minutes[idx] = numpy.float64(c.missing_value)
qcutils.CreateSeries(ds_30minutes,label,series_30minutes,Flag=flag_30minutes,Attr=attr)
# get the UTC hour
hr_utc = [float(x.hour)+float(x.minute)/60 for x in dt_utc_30minutes]
attr = qcutils.MakeAttributeDictionary(long_name='UTC hour')
qcutils.CreateSeries(ds_30minutes,'Hr_UTC',hr_utc,Flag=flag_30minutes,Attr=attr)
return ds_30minutes
def l1qc(cf):
# get the data series from the Excel file
in_filename = qcio.get_infilenamefromcf(cf)
if not qcutils.file_exists(in_filename,mode="quiet"):
msg = " Input file "+in_filename+" not found ..."
log.error(msg)
ds1 = qcio.DataStructure()
ds1.returncodes = {"value":1,"message":msg}
return ds1
file_name,file_extension = os.path.splitext(in_filename)
if "csv" in file_extension.lower():
ds1 = qcio.csv_read_series(cf)
if ds1.returncodes["value"] != 0:
return ds1
# get a series of Excel datetime from the Python datetime objects
qcutils.get_xldatefromdatetime(ds1)
else:
ds1 = qcio.xl_read_series(cf)
if ds1.returncodes["value"] != 0:
return ds1
# get a series of Python datetime objects from the Excel datetime
qcutils.get_datetimefromxldate(ds1)
# get the netCDF attributes from the control file
qcts.do_attributes(cf,ds1)
# round the Python datetime to the nearest second
qcutils.round_datetime(ds1,mode="nearest_second")
#check for gaps in the Python datetime series and fix if present
fixtimestepmethod = qcutils.get_keyvaluefromcf(cf,["options"],"FixTimeStepMethod",default="round")
if qcutils.CheckTimeStep(ds1): qcutils.FixTimeStep(ds1,fixtimestepmethod=fixtimestepmethod)
# recalculate the Excel datetime
qcutils.get_xldatefromdatetime(ds1)
# get the Year, Month, Day etc from the Python datetime
qcutils.get_ymdhmsfromdatetime(ds1)
# write the processing level to a global attribute
ds1.globalattributes['nc_level'] = str("L1")
# get the start and end date from the datetime series unless they were
# given in the control file
if 'start_date' not in ds1.globalattributes.keys():
ds1.globalattributes['start_date'] = str(ds1.series['DateTime']['Data'][0])
if 'end_date' not in ds1.globalattributes.keys():
ds1.globalattributes['end_date'] = str(ds1.series['DateTime']['Data'][-1])
# calculate variances from standard deviations and vice versa
qcts.CalculateStandardDeviations(cf,ds1)
# create new variables using user defined functions
qcts.DoFunctions(cf,ds1)
# create a series of synthetic downwelling shortwave radiation
qcts.get_synthetic_fsd(ds1)
return ds1
dt_utc = [x.replace(tzinfo=pytz.utc) for x in dt_UTC]
# convert from UTC to local time
dt_loc = [x.astimezone(site_tz) for x in dt_utc]
# remove any daylight saving adjustments (towers run on standard time)
dt_loc = [x - x.dst() for x in dt_loc]
# strip the time zone from the local datetime series
dt_loc = [x.replace(tzinfo=None) for x in dt_loc]
ds.series["DateTime"]["Data"] = dt_loc
# update global attributes
ds.globalattributes["nc_nrecs"] = len(dt_loc)
ds.globalattributes["start_datetime"] = str(dt_loc[0])
ds.globalattributes["end_datetime"] = str(dt_loc[-1])
# get the Excel datetime
qcutils.get_xldatefromdatetime(ds)
# get the year, month, day, hour, minute and second
qcutils.get_ymdhmsfromdatetime(ds)
# put the QC'd, smoothed and interpolated EVI into the data structure
flag = numpy.zeros(len(dt_loc), dtype=numpy.int32)
attr = qcutils.MakeAttributeDictionary(
long_name="MODIS EVI, smoothed and interpolated",
units="none",
horiz_resolution="250m",
cutout_size=str(site_cutout),
evi_quality_threshold=str(evi_quality_threshold),
evi_sd_threshold=str(evi_sd_threshold),
evi_interpolate=str(evi_interpolate),
evi_smooth_filter=str(evi_smooth_filter),
sg_num_points=str(sg_num_points),
sg_order=str(sg_num_points))
qcutils.CreateSeries(ds, "EVI", evi_interp2_smooth, Flag=flag, Attr=attr)
erai_time_tts = netCDF4.date2num(tmp, time_units)
# local datetime series at tower time step
dt_erai_loc_tts = [x.astimezone(site_tz) for x in dt_erai_utc_tts]
# NOTE: will have to disable daylight saving at some stage, towers stay on Standard Time
# PRI hopes that the following line will do this ...
dt_erai_loc_tts = [x - x.dst() for x in dt_erai_loc_tts]
# make the datetime series timezone naive and put it in data structure
dt_erai_loc_tts = [x.replace(tzinfo=None) for x in dt_erai_loc_tts]
ds_erai.series["DateTime"]["Data"] = dt_erai_loc_tts
ds_erai.globalattributes["nc_nrecs"] = len(dt_erai_loc_tts)
ds_erai.globalattributes["start_datetime"] = str(dt_erai_loc_tts[0])
ds_erai.globalattributes["end_datetime"] = str(dt_erai_loc_tts[-1])
# get the Excel datetime
qcutils.get_xldatefromdatetime(ds_erai)
# get the year, month, day, hour, minute and second
qcutils.get_ymdhmsfromdatetime(ds_erai)
# get the solar altitude, we will use this later to interpolate the ERA Interim solar
# data from the ERA-I 3 hour time step to the tower time step.
# NOTE: alt_solar is in degrees
alt_solar_3hr = numpy.array([
pysolar.GetAltitude(erai_latitude, erai_longitude, dt)
for dt in dt_erai_utc_cor
])
# get the solar altitude at the tower time step
alt_solar_tts = numpy.array([
pysolar.GetAltitude(erai_latitude, erai_longitude, dt)
for dt in dt_erai_utc_tts
])
idx = numpy.where(alt_solar_tts <= 0)[0]
alt_solar_tts[idx] = float(0)
# get local time from UTC
dt_loc_60minutes=[x.astimezone(site_tz) for x in dt_utc_60minutes]
# NOTE: will have to disable daylight saving at some stage, towers stay on Standard Time
# PRI hopes that the following line will do this ...
dt_loc_60minutes=[x-x.dst() for x in dt_loc_60minutes]
# make local time timezone naive to match datetimes in OzFluxQC
dt_loc_60minutes=[x.replace(tzinfo=None) for x in dt_loc_60minutes]
ds_60minutes.series["DateTime"] = {}
ds_60minutes.series["DateTime"]["Data"] = dt_loc_60minutes
ds_60minutes.series["DateTime_UTC"] = {}
ds_60minutes.series["DateTime_UTC"]["Data"] = dt_utc_60minutes
# get the year, month etc from the datetime
flag_60minutes = numpy.zeros(nRecs,dtype=numpy.int32)
ds_60minutes.series["DateTime"]["Flag"] = flag_60minutes
qcutils.get_xldatefromdatetime(ds_60minutes)
qcutils.get_ymdhmsfromdatetime(ds_60minutes)
# get derived quantities and adjust units
# air temperature from K to C
attr = qcutils.GetAttributeDictionary(ds_60minutes,"Ta_00")
if attr["units"] == "K":
for i in range(0,3):
for j in range(0,3):
label = "Ta_"+str(i)+str(j)
Ta,f,a = qcutils.GetSeriesasMA(ds_60minutes,label)
Ta = Ta - c.C2K
attr["units"] = "C"
qcutils.CreateSeries(ds_60minutes,label,Ta,Flag=flag_60minutes,Attr=attr)
# soil temperature from K to C
attr = qcutils.GetAttributeDictionary(ds_60minutes,"Ts_00")
if attr["units"] == "K":
for i in range(0,3):
logging.info('Reading the netCDF files for '+info["site_name"])
f = access_read_mfiles2(file_list,var_list=var_list)
# get the data from the netCDF files and write it to the 60 minute data structure
logging.info('Getting the ACCESS data')
get_accessdata(cf,ds_60minutes,f,info)
# set some global attributes
logging.info('Setting global attributes')
set_globalattributes(ds_60minutes,info)
# check for time gaps in the file
logging.info("Checking for time gaps")
if qcutils.CheckTimeStep(ds_60minutes):
qcutils.FixTimeStep(ds_60minutes)
# get the datetime in some different formats
logging.info('Getting xlDateTime and YMDHMS')
qcutils.get_xldatefromdatetime(ds_60minutes)
qcutils.get_ymdhmsfromdatetime(ds_60minutes)
#f.close()
# get derived quantities and adjust units
logging.info("Changing units and getting derived quantities")
# air temperature from K to C
changeunits_airtemperature(ds_60minutes)
# soil temperature from K to C
changeunits_soiltemperature(ds_60minutes)
# pressure from Pa to kPa
changeunits_pressure(ds_60minutes)
# wind speed from components
get_windspeedanddirection(ds_60minutes)
# relative humidity from temperature, specific humidity and pressure
get_relativehumidity(ds_60minutes)
# absolute humidity from temperature and relative humidity
get_absolutehumidity(ds_60minutes)
if not os.path.exists("../scripts/"):
print("erai2nc: the scripts directory is missing")
sys.exit()
# since the scripts directory is there, try importing the modules
sys.path.append('../scripts')
import qcio
import qcutils
aws_name = qcio.get_filename_dialog(path="/mnt/OzFlux/Sites")
ds_aws_30minute = qcio.nc_read_series(aws_name)
has_gaps = qcutils.CheckTimeStep(ds_aws_30minute)
if has_gaps:
print("Problems found with time step")
qcutils.FixTimeStep(ds_aws_30minute)
qcutils.get_ymdhmsfromdatetime(ds_aws_30minute)
dt_aws_30minute = ds_aws_30minute.series["DateTime"]["Data"]
ddt = [
dt_aws_30minute[i + 1] - dt_aws_30minute[i]
for i in range(0,
len(dt_aws_30minute) - 1)
]
print("Minimum time step is", min(ddt), " Maximum time step is", max(ddt))
dt_aws_30minute = ds_aws_30minute.series["DateTime"]["Data"]
start_date = dt_aws_30minute[0]
end_date = dt_aws_30minute[-1]
si_wholehour = qcutils.GetDateIndex(dt_aws_30minute,
str(start_date),
ts=30,
match="startnexthour")
bom_dist=bom_sites_info[site_name][str(bom_id)]["distance"])
qcutils.CreateSeries(ds,'Wd',data_dict[bom_id][:,11],Flag=flag,Attr=attr)
attr=qcutils.MakeAttributeDictionary(long_name='Wind gust',units='m/s',
bom_id=str(bom_id),bom_name=bom_sites_info[site_name][str(bom_id)]["site_name"],
bom_dist=bom_sites_info[site_name][str(bom_id)]["distance"])
qcutils.CreateSeries(ds,'Wg',data_dict[bom_id][:,12],Flag=flag,Attr=attr)
data_dict[bom_id][:,13] = data_dict[bom_id][:,13]/float(10)
attr=qcutils.MakeAttributeDictionary(long_name='Air Pressure',units='kPa',
bom_id=str(bom_id),bom_name=bom_sites_info[site_name][str(bom_id)]["site_name"],
bom_dist=bom_sites_info[site_name][str(bom_id)]["distance"])
qcutils.CreateSeries(ds,'ps',data_dict[bom_id][:,13],Flag=flag,Attr=attr)
# fix any time stamp issues
if qcutils.CheckTimeStep(ds):
qcutils.FixTimeStep(ds)
# update the Year, Month, Day etc from the Python datetime
qcutils.get_ymdhmsfromdatetime(ds)
# now interpolate
for label in ["Precip","Ta","Td","RH","Ws","Wd","Wg","ps"]:
qcts.InterpolateOverMissing(ds,series=label,maxlen=2)
# put this stations data into the data structure dictionary
ds_dict[bom_id] = ds
# get the earliest start datetime and the latest end datetime
log.info("Finding the start and end dates")
bom_id_list = ds_dict.keys()
ds0 = ds_dict[bom_id_list[0]]
ldt = ds0.series["DateTime"]["Data"]
#print bom_id_list[0],":",ldt[0],ldt[-1]
start_date = ldt[0]
end_date = ldt[-1]
bom_id_list.remove(bom_id_list[0])
ds_30.globalattributes["nc_nrecs"] = nRecs
ds_30.globalattributes["xl_datemode"] = str(0)
ds_30.globalattributes["site_name"] = cf["Sites"][site]["site_name"]
time_units = getattr(bios_ncfile.variables["time"],"units")
qcutils.get_datetimefromnctime(ds_30,time,time_units)
qcutils.round_datetime(ds_30,mode="nearest_timestep")
if qcutils.CheckTimeStep(ds_30): qcutils.FixTimeStep(ds_30)
ldt_30 = ds_30.series["DateTime"]["Data"]
si = qcutils.GetDateIndex(ldt_30,start_date,default=0,ts=ts,match="startnexthour")
ei = qcutils.GetDateIndex(ldt_30,end_date,default=len(ldt_30),ts=ts,match="endprevioushour")
ds_30.series["DateTime"]["Data"] = ds_30.series["DateTime"]["Data"][si:ei+1]
ds_30.series["DateTime"]["Flag"] = ds_30.series["DateTime"]["Flag"][si:ei+1]
ldt_30 = ds_30.series["DateTime"]["Data"]
nRecs = ds_30.globalattributes["nc_nrecs"] = len(ldt_30)
flag = numpy.zeros(nRecs)
qcutils.get_ymdhmsfromdatetime(ds_30)
xl_date_loc = qcutils.get_xldatefromdatetime(ds_30)
attr = qcutils.MakeAttributeDictionary(long_name="Date/time (local) in Excel format",units="days since 1899-12-31 00:00:00")
qcutils.CreateSeries(ds_30,"xlDateTime",xl_date_loc,flag,attr)
# get the data
for label in var_list:
bios_name = cf["Variables"][label]["bios_name"]
if len(bios_ncfile.variables[bios_name].shape)==1:
#print label+" has 1 dimension"
data = bios_ncfile.variables[bios_name][:][si:ei+1]
elif len(bios_ncfile.variables[bios_name].shape)==2:
#print label+" has 2 dimensions"
data = bios_ncfile.variables[bios_name][:,0][si:ei+1]
elif len(bios_ncfile.variables[bios_name].shape)==3:
#print label+" has 3 dimensions"
data = bios_ncfile.variables[bios_name][:,0,0][si:ei+1]
ds_30.globalattributes["nc_nrecs"] = nRecs
ds_30.globalattributes["xl_datemode"] = str(0)
ds_30.globalattributes["site_name"] = cf["Sites"][site]["site_name"]
time_units = getattr(bios_ncfile.variables["time"],"units")
qcutils.get_datetimefromnctime(ds_30,time,time_units)
qcutils.round_datetime(ds_30,mode="nearest_timestep")
if qcutils.CheckTimeStep(ds_30): qcutils.FixTimeStep(ds_30)
ldt_30 = ds_30.series["DateTime"]["Data"]
si = qcutils.GetDateIndex(ldt_30,start_date,default=0,ts=ts,match="startnexthour")
ei = qcutils.GetDateIndex(ldt_30,end_date,default=len(ldt_30),ts=ts,match="endprevioushour")
ds_30.series["DateTime"]["Data"] = ds_30.series["DateTime"]["Data"][si:ei+1]
ds_30.series["DateTime"]["Flag"] = ds_30.series["DateTime"]["Flag"][si:ei+1]
ldt_30 = ds_30.series["DateTime"]["Data"]
nRecs = ds_30.globalattributes["nc_nrecs"] = len(ldt_30)
flag = numpy.zeros(nRecs)
qcutils.get_ymdhmsfromdatetime(ds_30)
xl_date_loc = qcutils.get_xldatefromdatetime(ds_30)
attr = qcutils.MakeAttributeDictionary(long_name="Date/time (local) in Excel format",units="days since 1899-12-31 00:00:00")
qcutils.CreateSeries(ds_30,"xlDateTime",xl_date_loc,Flag=flag,Attr=attr)
# get the data
for label in var_list:
bios_name = cf["Variables"][label]["bios_name"]
if len(bios_ncfile.variables[bios_name].shape)==1:
#print label+" has 1 dimension"
data = bios_ncfile.variables[bios_name][:][si:ei+1]
elif len(bios_ncfile.variables[bios_name].shape)==2:
#print label+" has 2 dimensions"
data = bios_ncfile.variables[bios_name][:,0][si:ei+1]
elif len(bios_ncfile.variables[bios_name].shape)==3:
#print label+" has 3 dimensions"
data = bios_ncfile.variables[bios_name][:,0,0][si:ei+1]
