def merge_atm_sfc(fsfc, fatm, fmerged):
from os import system
from netCDF4 import Dataset
import numpy as np
import subprocess
# Calendar
path_calendar = '/san0/acolmd/SVN/trunk/MESOSCALE/LMD_MM_MARS/SIMU/calendar'
gcm_sol = []
gcm_ls = []
mmm_date = []
calendar = open(path_calendar, 'r')
calendar.readline() #get rid of the first line
calendar_l = calendar.readlines()
for line in calendar_l:
s = str.split(line)
gcm_sol = np.append(gcm_sol, np.float(s[1]))
gcm_ls = np.append(gcm_ls, np.float(s[2]))
mmm_date = np.append(mmm_date, s[3])
calendar.close()
calendar_l = 0.
# Constants
grav = 3.72
# Grid properties
ls_simu_start = 147. #ls of start simu
# lt_start="07:30:00" #local time of start simu at cen_lon # read in .ctl
# NOTE: I ASSUME THE LT_START IN .CTL FOR MRAMS IS LOCAL TIME OF START AT LONGITUDE 0
dx = [240000., 80000., 26667, 8889]
dy = dx
# Date management
idx = np.abs(gcm_ls - ls_simu_start).argmin()
date_start = mmm_date[idx]
# USER: fill the date you want to analyse:
days = [16, 17, 18]
# Grid id
if 'g1' in fatm:
gid = 1
elif 'g2' in fatm:
gid = 2
elif 'g3' in fatm:
gid = 3
else:
gid = 4
# Load datasets
atm = Dataset(fatm)
sfc = Dataset(fsfc)
# reconstruct dimensions
lon = atm.variables['lon']
nlon = len(lon)
lat = atm.variables['lat']
nlat = len(lat)
lev = atm.variables['lev']
nlev = len(lev)
time = atm.variables['time']
ntime = len(time)
units_time = time.units[12:len(time.units)]
# date from mrams file:
year_mrams, month_mrams, day_mrams, hour_mrams, minute_mrams, second_mrams = date_to_time(
units_time)
lt_start = hour_mrams + ':' + minute_mrams + ':' + second_mrams
# or date from calendar with initial Ls:
year, month, day, hour, minute, second = date_to_time(date_start, lt_start)
dt = (time[1] - time[0]) * 60.
daylength = 3600. * 24. / (dt * 60.)
i = 0
imax = np.floor(len(time) / daylength)
while (i < imax + 1):
i = i + 1
dayslab = [int((i - 1) * daylength), int(daylength * i)]
if i == imax + 1: dayslab = [int((i - 1) * daylength), len(time)]
fmerged_slab = fmerged + '0' + str(gid) + '_' + time_to_date(
mmm_date[idx + i - 1], lt_start)
err = check_file(fmerged_slab)
year, month, day, hour, minute, second = date_to_time(
mmm_date[idx + i - 1], lt_start)
if int(day) in days:
print ' -->> hyperslab : ', dayslab, ' => mramsout_d0' + str(
gid) + '_' + time_to_date(mmm_date[idx + i - 1], lt_start)
else:
err = 0
print ' -->> hyperslab : ', dayslab, ' => mramsout_d0' + str(
gid) + '_' + time_to_date(mmm_date[idx + i - 1],
lt_start) + ' --> Skipped'
if err == 1:
# prepare merged file
subprocess.call(['touch', fmerged_slab], shell=False)
subprocess.call(['rm', '-rf', fmerged_slab], shell=False)
merged_file = Dataset(fmerged_slab, 'w', format='NETCDF3_64BIT')
merged_file.description = 'MRAMS merged atm and sfc converted (netcdf) file.'
## Dimensions
merged_file.createDimension('Time', None)
merged_file.createDimension('bottom_top', nlev)
merged_file.createDimension('south_north', nlat)
merged_file.createDimension('west_east', nlon)
merged_file.createDimension('bottom_top_stag', nlev +
1) # very important for PHTOT in API
# merged_file.createDimension('south_north_stag',nlat+1)
# merged_file.createDimension('west_east_stag',nlon+1)
## Variables for dimensions
times = merged_file.createVariable('Time', 'f', ('Time', ))
times[:] = time[dayslab[0]:dayslab[1]]
altitudes = merged_file.createVariable('bottom_top', 'f',
('bottom_top', ))
altitudes[:] = lev[:]
latitudes = merged_file.createVariable('south_north', 'f',
('south_north', ))
latitudes[:] = lat[:]
longitudes = merged_file.createVariable('west_east', 'f',
('west_east', ))
longitudes[:] = lon[:]
## Set attributes
setattr(merged_file, 'TITLE', 'OUTPUT FROM MRAMS MODEL')
setattr(merged_file, 'START_DATE',
time_to_date(mmm_date[idx], lt_start))
setattr(merged_file, 'SIMULATION_START_DATE',
time_to_date(mmm_date[idx], lt_start))
setattr(merged_file, 'WEST-EAST_GRID_DIMENSION', nlon + 1)
setattr(merged_file, 'SOUTH-NORTH_GRID_DIMENSION', nlat + 1)
setattr(merged_file, 'BOTTOM-TOP_GRID_DIMENSION', nlev + 1)
setattr(merged_file, 'DX', np.float(dx[gid - 1]))
setattr(merged_file, 'DY', np.float(dy[gid - 1]))
setattr(merged_file, 'DT', np.float(dt))
setattr(merged_file, 'GRID_TYPE', 'C') #
setattr(merged_file, 'GRID_ID', gid)
setattr(merged_file, 'PARENT_ID', gid - 1)
setattr(merged_file, 'MAP_PROJ', 2) #
setattr(merged_file, 'JULYR', year)
setattr(merged_file, 'JULDAY', gcm_sol[idx + i - 1])
setattr(merged_file, 'WEST-EAST_PATCH_START_UNSTAG', 1)
setattr(merged_file, 'WEST-EAST_PATCH_END_UNSTAG', nlon)
setattr(merged_file, 'WEST-EAST_PATCH_START_STAG', 1)
setattr(merged_file, 'WEST-EAST_PATCH_END_STAG', nlon) ###
setattr(merged_file, 'SOUTH-NORTH_PATCH_START_UNSTAG', 1)
setattr(merged_file, 'SOUTH-NORTH_PATCH_END_UNSTAG', nlat)
setattr(merged_file, 'SOUTH-NORTH_PATCH_START_STAG', 1)
setattr(merged_file, 'SOUTH-NORTH_PATCH_END_STAG', nlat) ###
setattr(merged_file, 'BOTTOM-TOP_PATCH_START_UNSTAG', 1)
setattr(merged_file, 'BOTTOM-TOP_PATCH_END_UNSTAG', nlev)
setattr(merged_file, 'BOTTOM-TOP_PATCH_START_STAG', 1)
setattr(merged_file, 'BOTTOM-TOP_PATCH_END_STAG', nlev + 1)
## Set grid variables
xlon = merged_file.createVariable('XLONG', 'f', (
'Time',
'south_north',
'west_east',
))
xlat = merged_file.createVariable('XLAT', 'f', (
'Time',
'south_north',
'west_east',
))
print ' glon -> XLON'
xlon[:, :, :] = sfc.variables['glon'][dayslab[0]:dayslab[1], :, :]
print ' glat -> XLAT'
xlat[:, :, :] = sfc.variables['glat'][dayslab[0]:dayslab[1], :, :]
cen_lon, cen_lat = find_center(lon, lat, xlon[0, :, :],
xlat[0, :, :])
setattr(merged_file, 'CEN_LAT', cen_lat)
setattr(merged_file, 'CEN_LON', cen_lon)
## Renaming
print ' topo -> HGT'
hgt = merged_file.createVariable('HGT', 'f', (
'Time',
'south_north',
'west_east',
))
hgt[:, :, :] = sfc.variables['topo'][dayslab[0]:dayslab[1], :, :]
print ' tempk -> tk'
tk = merged_file.createVariable('tk', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
tk[:, :, :, :] = atm.variables['tempk'][
dayslab[0]:dayslab[1], :, :, :]
print ' press -> PTOT'
ptot = merged_file.createVariable('PTOT', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
ptot[:, :, :, :] = atm.variables['press'][
dayslab[0]:dayslab[1], :, :, :]
u = merged_file.createVariable('U', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
v = merged_file.createVariable('V', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
w = merged_file.createVariable('W', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
print ' u_avg -> U'
u[:, :, :, :] = atm.variables['u_avg'][
dayslab[0]:dayslab[1], :, :, :]
print ' v_avg -> V'
v[:, :, :, :] = atm.variables['v_avg'][
dayslab[0]:dayslab[1], :, :, :]
print ' w_avg -> W'
w[:, :, :, :] = atm.variables['w_avg'][
dayslab[0]:dayslab[1], :, :, :]
tke = merged_file.createVariable('TKE', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
print ' sgs_tke -> TKE'
tke[:, :, :, :] = atm.variables['sgs_tke'][
dayslab[0]:dayslab[1], :, :, :]
tau_dust = merged_file.createVariable('TAU_DUST', 'f', (
'Time',
'south_north',
'west_east',
))
print ' dust_sfc_od_vis -> TAU_DUST'
tau_dust[:, :, :] = atm.variables['dust_sfc_od_vis'][
dayslab[0]:dayslab[1], :, :]
z_lyrmid_agl = merged_file.createVariable('z_lyrmid_agl', 'f', (
'Time',
'bottom_top',
'south_north',
'west_east',
))
print ' z_lyrmid_agl -> z_lyrmid_agl'
z_lyrmid_agl[:, :, :, :] = atm.variables['z_lyrmid_agl'][
dayslab[0]:dayslab[1], :, :, :]
# Compute PHTOT for API
print ' Computing PHTOT'
phtot = merged_file.createVariable('PHTOT', 'f', (
'Time',
'bottom_top_stag',
'south_north',
'west_east',
))
phtot[:, 0:nlev, :, :] = z_lyrmid_agl[:, :, :, :] * grav
phtot[:, nlev, :, :] = 0.
for l in np.arange(nlev):
phtot[:, l, :, :] = phtot[:, l, :, :] + grav * hgt[:, :, :]
merged_file.close()
def merge_atm_sfc(fsfc,fatm,fmerged):
from os import system
from netCDF4 import Dataset
import numpy as np
import subprocess
# Calendar
path_calendar='/san0/acolmd/SVN/trunk/MESOSCALE/LMD_MM_MARS/SIMU/calendar'
gcm_sol=[]
gcm_ls=[]
mmm_date=[]
calendar = open(path_calendar, 'r')
calendar.readline() #get rid of the first line
calendar_l=calendar.readlines()
for line in calendar_l:
s=str.split(line)
gcm_sol=np.append(gcm_sol,np.float(s[1]))
gcm_ls=np.append(gcm_ls,np.float(s[2]))
mmm_date=np.append(mmm_date,s[3])
calendar.close()
calendar_l=0.
# Constants
grav=3.72
# Grid properties
ls_simu_start=147. #ls of start simu
# lt_start="07:30:00" #local time of start simu at cen_lon # read in .ctl
# NOTE: I ASSUME THE LT_START IN .CTL FOR MRAMS IS LOCAL TIME OF START AT LONGITUDE 0
dx=[240000.,80000.,26667,8889]
dy=dx
# Date management
idx=np.abs(gcm_ls - ls_simu_start).argmin()
date_start=mmm_date[idx]
# USER: fill the date you want to analyse:
days=[16,17,18]
# Grid id
if 'g1' in fatm:
gid=1
elif 'g2' in fatm:
gid=2
elif 'g3' in fatm:
gid=3
else:
gid=4
# Load datasets
atm=Dataset(fatm) ; sfc=Dataset(fsfc)
# reconstruct dimensions
lon = atm.variables['lon'] ; nlon = len(lon)
lat = atm.variables['lat'] ; nlat = len(lat)
lev = atm.variables['lev'] ; nlev = len(lev)
time = atm.variables['time'] ; ntime = len(time)
units_time=time.units[12:len(time.units)]
# date from mrams file:
year_mrams, month_mrams, day_mrams, hour_mrams, minute_mrams, second_mrams = date_to_time(units_time)
lt_start = hour_mrams+':'+minute_mrams+':'+second_mrams
# or date from calendar with initial Ls:
year, month, day, hour, minute, second = date_to_time(date_start,lt_start)
dt=(time[1]-time[0])*60.
daylength=3600.*24./(dt*60.)
i=0
imax=np.floor(len(time)/daylength)
while (i < imax+1):
i=i+1
dayslab=[int((i-1)*daylength),int(daylength*i)]
if i==imax+1: dayslab=[int((i-1)*daylength),len(time)]
fmerged_slab=fmerged+'0'+str(gid)+'_'+time_to_date(mmm_date[idx+i-1],lt_start)
err=check_file(fmerged_slab)
year, month, day, hour, minute, second = date_to_time(mmm_date[idx+i-1],lt_start)
if int(day) in days:
print ' -->> hyperslab : ',dayslab,' => mramsout_d0'+str(gid)+'_'+time_to_date(mmm_date[idx+i-1],lt_start)
else:
err=0
print ' -->> hyperslab : ',dayslab,' => mramsout_d0'+str(gid)+'_'+time_to_date(mmm_date[idx+i-1],lt_start)+' --> Skipped'
if err == 1:
# prepare merged file
subprocess.call(['touch',fmerged_slab],shell=False)
subprocess.call(['rm','-rf',fmerged_slab],shell=False)
merged_file = Dataset(fmerged_slab, 'w', format='NETCDF3_64BIT')
merged_file.description = 'MRAMS merged atm and sfc converted (netcdf) file.'
## Dimensions
merged_file.createDimension('Time', None)
merged_file.createDimension('bottom_top',nlev)
merged_file.createDimension('south_north',nlat)
merged_file.createDimension('west_east',nlon)
merged_file.createDimension('bottom_top_stag',nlev+1) # very important for PHTOT in API
# merged_file.createDimension('south_north_stag',nlat+1)
# merged_file.createDimension('west_east_stag',nlon+1)
## Variables for dimensions
times = merged_file.createVariable('Time', 'f', ('Time',))
times[:] = time[dayslab[0]:dayslab[1]]
altitudes = merged_file.createVariable('bottom_top', 'f', ('bottom_top',))
altitudes[:] = lev[:]
latitudes = merged_file.createVariable('south_north', 'f', ('south_north',))
latitudes[:] = lat[:]
longitudes = merged_file.createVariable('west_east', 'f', ('west_east',))
longitudes[:] = lon[:]
## Set attributes
setattr(merged_file, 'TITLE', 'OUTPUT FROM MRAMS MODEL')
setattr(merged_file, 'START_DATE', time_to_date(mmm_date[idx],lt_start))
setattr(merged_file, 'SIMULATION_START_DATE', time_to_date(mmm_date[idx],lt_start))
setattr(merged_file, 'WEST-EAST_GRID_DIMENSION', nlon+1)
setattr(merged_file, 'SOUTH-NORTH_GRID_DIMENSION', nlat+1)
setattr(merged_file, 'BOTTOM-TOP_GRID_DIMENSION', nlev+1)
setattr(merged_file, 'DX', np.float(dx[gid-1]))
setattr(merged_file, 'DY', np.float(dy[gid-1]))
setattr(merged_file, 'DT', np.float(dt))
setattr(merged_file, 'GRID_TYPE', 'C') #
setattr(merged_file, 'GRID_ID', gid)
setattr(merged_file, 'PARENT_ID', gid-1)
setattr(merged_file, 'MAP_PROJ', 2) #
setattr(merged_file, 'JULYR', year)
setattr(merged_file, 'JULDAY', gcm_sol[idx+i-1])
setattr(merged_file, 'WEST-EAST_PATCH_START_UNSTAG' , 1)
setattr(merged_file, 'WEST-EAST_PATCH_END_UNSTAG' , nlon)
setattr(merged_file, 'WEST-EAST_PATCH_START_STAG' , 1)
setattr(merged_file, 'WEST-EAST_PATCH_END_STAG' , nlon) ###
setattr(merged_file, 'SOUTH-NORTH_PATCH_START_UNSTAG' , 1)
setattr(merged_file, 'SOUTH-NORTH_PATCH_END_UNSTAG' , nlat)
setattr(merged_file, 'SOUTH-NORTH_PATCH_START_STAG' , 1)
setattr(merged_file, 'SOUTH-NORTH_PATCH_END_STAG' , nlat) ###
setattr(merged_file, 'BOTTOM-TOP_PATCH_START_UNSTAG' , 1)
setattr(merged_file, 'BOTTOM-TOP_PATCH_END_UNSTAG' , nlev)
setattr(merged_file, 'BOTTOM-TOP_PATCH_START_STAG' , 1)
setattr(merged_file, 'BOTTOM-TOP_PATCH_END_STAG' , nlev+1)
## Set grid variables
xlon = merged_file.createVariable('XLONG', 'f', ('Time','south_north','west_east',))
xlat = merged_file.createVariable('XLAT', 'f', ('Time','south_north','west_east',))
print ' glon -> XLON' ; xlon[:,:,:] = sfc.variables['glon'][dayslab[0]:dayslab[1],:,:]
print ' glat -> XLAT' ; xlat[:,:,:] = sfc.variables['glat'][dayslab[0]:dayslab[1],:,:]
cen_lon, cen_lat = find_center(lon,lat,xlon[0,:,:],xlat[0,:,:])
setattr(merged_file, 'CEN_LAT', cen_lat)
setattr(merged_file, 'CEN_LON', cen_lon)
## Renaming
print ' topo -> HGT' ; hgt = merged_file.createVariable('HGT', 'f', ('Time','south_north','west_east',))
hgt[:,:,:] = sfc.variables['topo'][dayslab[0]:dayslab[1],:,:]
print ' tempk -> tk' ; tk = merged_file.createVariable('tk', 'f', ('Time','bottom_top','south_north','west_east',))
tk[:,:,:,:] = atm.variables['tempk'][dayslab[0]:dayslab[1],:,:,:]
print ' press -> PTOT' ; ptot = merged_file.createVariable('PTOT', 'f', ('Time','bottom_top','south_north','west_east',))
ptot[:,:,:,:] = atm.variables['press'][dayslab[0]:dayslab[1],:,:,:]
u = merged_file.createVariable('U', 'f', ('Time','bottom_top','south_north','west_east',))
v = merged_file.createVariable('V', 'f', ('Time','bottom_top','south_north','west_east',))
w = merged_file.createVariable('W', 'f', ('Time','bottom_top','south_north','west_east',))
print ' u_avg -> U' ; u[:,:,:,:] = atm.variables['u_avg'][dayslab[0]:dayslab[1],:,:,:]
print ' v_avg -> V' ; v[:,:,:,:] = atm.variables['v_avg'][dayslab[0]:dayslab[1],:,:,:]
print ' w_avg -> W' ; w[:,:,:,:] = atm.variables['w_avg'][dayslab[0]:dayslab[1],:,:,:]
tke = merged_file.createVariable('TKE', 'f', ('Time','bottom_top','south_north','west_east',))
print ' sgs_tke -> TKE' ; tke[:,:,:,:] = atm.variables['sgs_tke'][dayslab[0]:dayslab[1],:,:,:]
tau_dust = merged_file.createVariable('TAU_DUST', 'f', ('Time','south_north','west_east',))
print ' dust_sfc_od_vis -> TAU_DUST' ; tau_dust[:,:,:] = atm.variables['dust_sfc_od_vis'][dayslab[0]:dayslab[1],:,:]
z_lyrmid_agl = merged_file.createVariable('z_lyrmid_agl', 'f', ('Time','bottom_top','south_north','west_east',))
print ' z_lyrmid_agl -> z_lyrmid_agl' ; z_lyrmid_agl[:,:,:,:] = atm.variables['z_lyrmid_agl'][dayslab[0]:dayslab[1],:,:,:]
# Compute PHTOT for API
print ' Computing PHTOT'
phtot = merged_file.createVariable('PHTOT', 'f', ('Time','bottom_top_stag','south_north','west_east',))
phtot[:,0:nlev,:,:]=z_lyrmid_agl[:,:,:,:]*grav ; phtot[:,nlev,:,:]=0.
for l in np.arange(nlev):
phtot[:,l,:,:]=phtot[:,l,:,:] + grav*hgt[:,:,:]
merged_file.close()
subprocess.call(['touch', 'converted_files/mramsout_d_dummy'],
shell=False)
for f in glob('converted_files/mramsout_d*'):
unlink(f)
if opt.generate:
opath = './converted_files/'
ipath = './vis/'
# for grid in ['g1','g2','g3','g4']: ## INDEX 4 OF TEST CASE HOLDEN DOES NOT WORK (CDO ERROR)
for grid in ['g1', 'g2', 'g3']:
outfileatm = 'holden_ls150-atm-S-' + grid + '.nc'
outfilesfc = 'holden_ls150-sfc-S-' + grid + '.nc'
outfilecat = 'mramsout_d'
infileatm = 'holden_ls150-atm-S-' + grid + '.ctl'
infilesfc = 'holden_ls150-sfc-S-' + grid + '.ctl'
print '- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -'
err = check_file(opath + outfileatm)
print '=> Begining conversion for File ' + infileatm + ' -> in -> ' + outfileatm
if err == 1:
subprocess.call([
'cdo', '-f', 'nc', 'import_binary', ipath + infileatm,
opath + outfileatm
],
shell=False)
print '=> File ' + infileatm + ' -> converted in -> ' + outfileatm
err = check_file(opath + outfilesfc)
print '=> Begining conversion for File ' + infilesfc + ' -> in -> ' + outfilesfc
if err == 1:
subprocess.call([
'cdo', '-f', 'nc', 'import_binary', ipath + infilesfc,
opath + outfilesfc
],
if opt.clean:
subprocess.call(['touch','converted_files/mramsout_d_dummy'],shell=False)
for f in glob ('converted_files/mramsout_d*'):
unlink(f)
if opt.generate:
opath='./converted_files/'
ipath='./vis/'
# for grid in ['g1','g2','g3','g4']: ## INDEX 4 OF TEST CASE HOLDEN DOES NOT WORK (CDO ERROR)
for grid in ['g1','g2','g3']:
outfileatm='holden_ls150-atm-S-'+grid+'.nc'
outfilesfc='holden_ls150-sfc-S-'+grid+'.nc'
outfilecat='mramsout_d'
infileatm='holden_ls150-atm-S-'+grid+'.ctl'
infilesfc='holden_ls150-sfc-S-'+grid+'.ctl'
print '- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -'
err=check_file(opath+outfileatm)
print '=> Begining conversion for File '+infileatm+' -> in -> '+outfileatm
if err == 1: subprocess.call(['cdo','-f','nc','import_binary',ipath+infileatm,opath+outfileatm],shell=False)
print '=> File '+infileatm+' -> converted in -> '+outfileatm
err=check_file(opath+outfilesfc)
print '=> Begining conversion for File '+infilesfc+' -> in -> '+outfilesfc
if err == 1: subprocess.call(['cdo','-f','nc','import_binary',ipath+infilesfc,opath+outfilesfc],shell=False)
print '=> File '+infilesfc+' -> converted in -> '+outfilesfc
print '- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -'
print '=> Begining concatenation for Files '+outfilesfc+' and '+outfileatm
merge_atm_sfc(opath+outfilesfc,opath+outfileatm,opath+outfilecat)
print '=> Files concatenated !'
print '- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -'
# subprocess.call(cmdstring,shell=False)