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run_viirs2ioda_npp.py
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run_viirs2ioda_npp.py
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#!/usr/bin/env python
# run_viirs2ioda.py
# process VIIRS files and produce JEDI/IODA compatible obs files
import os
import subprocess as sp
import datetime as dt
import glob
import sys
#import xarray as xr
#grid='96'
grid='192'
InPath='/scratch2/NCEPDEV/stmp3/Andrew.Tangborn/VIIRS/CLASS/'
OutPath='/scratch2/NCEPDEV/stmp3/Andrew.Tangborn/VIIRS/'
#FV3Grid='/scratch1/BMC/gsd-fv3-dev/MAPP_2018/pagowski/fix_fv3/C'+grid
CycleHrs=6
thinning = 0.9999
year=2019
month=6
day=27
hour=18
yymmdd_int = str(year)+str(month).zfill(2)+str(day).zfill(2)
InRoot = InPath + yymmdd_int
OutRoot1 = OutPath +'thin'+str(thinning)+'/'
if not os.path.exists(OutRoot1):
os.makedirs(OutRoot1)
OutRoot = OutRoot1 + yymmdd_int
if not os.path.exists(OutRoot):
os.makedirs(OutRoot)
date1 = dt.date(year,month,day)
print('InRoot=',InRoot)
yyyymmddhh = int(str(year)+str(month).zfill(2)+str(day).zfill(2)+str(hour).zfill(2))
print('yyyymmddhh =',yyyymmddhh)
InRoot2 = InPath + yymmdd_int
if hour==0:
date2 = dt.timedelta(days=-1) + date1
yyyymmdd2 = date2.strftime("%Y%m%d")
print('yyyymmdd2=',yyyymmdd2)
InRoot2 = InPath + yyyymmdd2
#year=2022
#month=4
#day=4
#hour=0
#yyyymmddhh = 2022040400
StartCycle=dt.datetime(year,month,day,hour)
EndCycle=dt.datetime(year,month,day,hour)
#print('StartCycle=',StartCycle)
#executable='python /scratch1/NCEPDEV/da/Andrew.Tangborn/JEDI/jan27_aod2ioda/build/bin/viirs_aod2ioda.py'
executable='python /scratch1/NCEPDEV/da/Andrew.Tangborn/JEDI/gdas_app_august5_2022/gdasapp/build/bin/viirs_aod2ioda.py'
my_env = os.environ.copy()
my_env['OMP_NUM_THREADS'] = '4' # for openmp to speed up fortran call
#./viirs2ioda.x $validtime $fv3dir $infile $outfile
HalfCycle = CycleHrs/2
NowCycle=StartCycle
while NowCycle <= EndCycle:
# print("Processing analysis cycle: "+NowCycle.strftime("%Y-%m-%d_%H:%M UTC"))
# get +- half of cycle hours
StartObs = NowCycle - dt.timedelta(hours=HalfCycle)
EndObs = NowCycle + dt.timedelta(hours=HalfCycle)
StartObs_doy = StartObs.timetuple().tm_yday
EndObs_doy = EndObs.timetuple().tm_yday
EndObs_mon = EndObs.timetuple().tm_mon
EndObs_mday = EndObs.timetuple().tm_mday
StartObs_mon = StartObs.timetuple().tm_mon
StartObs_mday = StartObs.timetuple().tm_mday
# These times are not matched up with the root directory.
# Fix this next
print('StartObs = ', StartObs)
print('EndObs_mon = ', EndObs_mon)
print('EndObs_doy = ', EndObs_doy)
print('EndObs_mday = ', EndObs_mday)
str_start_mon = str(StartObs_mon)
str_start_mon = str_start_mon.zfill(2)
str_start_mday = str(StartObs_mday)
str_start_mday = str_start_mday.zfill(2)
str_year = str(StartObs.year)
str_end = str(EndObs_doy)
str_end_mon = str(EndObs_mon)
str_end_mon = str_end_mon.zfill(2)
str_end_mday = str(EndObs_mday)
str_end_mday = str_end_mday.zfill(2)
print('str_start_mon =', str_start_mon)
print('str_start_mday =', str_start_mday)
print('str_end_mon =', str_end_mon)
print('str_end_mday = ', str_end_mday)
# str_start = 'JRR-AOD_v2r0_j01_s'+str_year+str_start_mon+str_start_mday
# str_end = 'JRR-AOD_v2r0_j01_s'+str_year+str_end_mon+str_end_mday
str_start = 'JRR-AOD_v2r0_npp_s'+str_year+str_start_mon+str_start_mday
str_end = 'JRR-AOD_v2r0_npp_s'+str_year+str_end_mon+str_end_mday
print('str_start = ', str_start)
print('str_end = ', str_end)
# get possible files to use
usefiles = []
dir1 = InRoot2+'/'+str_start
dir2 = InRoot+'/'+str_end
# dir3 = InRoot2+'/'+str_start1
# dir4 = InRoot+'/'+str_end1
if hour==0:
dir5 = InRoot2+'/'+str_start
dir6 = InRoot+'/'+str_end
# dir7 = InRoot2+'/'+str_start1
# dir8 = InRoot+'/'+str_end1
print('dir1=',dir1)
print('dir2=',dir2)
# print('dir3=',dir3)
# print('dir4=',dir4)
files1 = glob.glob(dir1+'*.nc')
print('files1=',files1)
files2 = glob.glob(dir2+'*.nc')
# files3 = glob.glob(dir3+'*.nc')
# files4 = glob.glob(dir4+'*.nc')
#allfiles = set(files1+files2+files3+files4)
allfiles = set(files1+files2)
print('allfiles = ', allfiles)
for f in allfiles:
fshort = f.split('/')[-1].split('.')
print('fshort = ', fshort[0][:])
print('fshort[0][26:30]=',fshort[0][26:30])
yyyymmdd=fshort[0][18:26]
print('yyyymmdd=',yyyymmdd)
hhmm=fshort[0][26:30]
print('hhmm=',hhmm)
yyyymmddhhmmss=yyyymmdd+hhmm+'00'
yyyymmddhhmmss=dt.datetime.strptime(yyyymmddhhmmss, '%Y%m%d%H%M%S')
print('yyyymmddhhmmss=',yyyymmddhhmmss)
fstart = yyyymmddhhmmss #dt.datetime.strptime(yyyymmddhhmmss,"%Y%m%d%H%M%S")
# print('fstart, StartObs, EndObs',fstart,StartObs,EndObs)
# print('fstart=',fstart)
# fend = dt.datetime.strptime(fshort[4][1:-1],"%Y%m%d%H%M%S")
# Determine which files are within the assimilation window by comparing time/date
print('StartObs=', StartObs)
print('fstart=', fstart)
if (fstart > StartObs) and (fstart < EndObs):
print('f=',f)
print('StartObs, fstart, EndObs', StartObs, fstart, EndObs)
usefiles.append(f)
validtime=NowCycle.strftime("%Y%m%d%H")
#print('validtime=',validtime)
input_flag='-i'
output_flag='-o'
OutDir = OutRoot
output_file = OutDir+'/gdas.t'+str(hour).zfill(2)+'z.viirs_npp.'+validtime+'.nc4'
method_flag = '-m'
method = 'nesdis'
mask_flag = '-k'
mask = 'maskout'
thin_flag = '-n'
thin_value = str(thinning)
usefiles_str = ""
for ele in usefiles:
usefiles_str += ele+' '
args=' '+input_flag+' '+usefiles_str+' '+method_flag+' '+method+' '+mask_flag+' '+mask+' '+thin_flag+' '+thin_value+' '+output_flag+' '+output_file
cmd = executable+args
print('cmd=',cmd)
# with open('test.txt', 'w') as f:
# print(cmd,file=f)
# print('output_file=',output_file)
proc = sp.Popen(cmd,env=my_env,shell=True)
if not os.path.exists(OutDir):
os.makedirs(OutDir)
# for f in usefiles:
# fout = OutDir+'/'+f.split('/')[-1]
# args = ' 'input_flag' 'usefiles' '+f+' '+-o+' '+fout
# print('args=',args)
# cmd = executable+args
# print('cmd = ', cmd)
# proc = sp.Popen(cmd,env=my_env,shell=True)
# proc.wait() # so that it doesn't overload the system
# concatenate them
# cmd = 'ncrcat -O '+OutDir+'/*.nc '+OutDir+'/MODIS_C61.'+validtime+'.nc'
# print('cmd=',cmd )
# proc = sp.Popen(cmd,env=my_env,shell=True)
# proc.wait()
#creates larger files with confused dimensions
# ncfiles = glob.glob(OutDir+'/JRR-AOD_v1r1_npp_*.nc')
##ds = xr.open_mfdataset(outfiles, combine='nested', concat_dim=['nlocs'])
# ds = xr.open_mfdataset(ncfiles, concat_dim=['nlocs'])
##ds = xr.open_mfdataset(ncfiles)
# ds.to_netcdf(OutDir+'/viirs_aod_snpp.'+validtime+'-Xarray.nc')
NowCycle = NowCycle + dt.timedelta(hours=CycleHrs)