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04-roms2swan.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Script for prepering SWAN input files from ROMS results #######
"""
__author__ = "Saeed Moghimi"
__copyright__ = "Copyright 2015, Oregon State University"
__license__ = "GPL"
__version__ = "0.1"
__email__ = "[email protected]"
##############################################
# Saeed Moghimi; [email protected]
# Logs:
# 1.0 03/25/2013 02:14:41 PM
#
#
#
##############################################
import netCDF4
import netcdftime
import pylab as pl
import numpy as np
from datetime import datetime
import os,sys
import glob
##############################################
try:
os.system('rm base_info.pyc' )
except:
pass
if 'base_info' in sys.modules:
del(sys.modules["base_info"])
import base_info
##############################################
inp_dir = local_inp = base_info.base_dir+'/inp'
real_data = base_info.real_data
final_grd = local_inp+'/const/'+base_info.grd
hisfile_name = base_info.hisfile_name
##################################################
################# Funcs ##########################
#write scaler field in file to be read by swan by idla=1
def wrt_field(outfile,name):
outf=open(outfile,'w')
ny,nx=name.shape
aa=pl.arange(ny-1,-1,-1)
for iy in aa:
str1=' '.join('%.4f' % n for n in name[iy,:])
str1=str1+'\n'
outf.write(str1)
outf.close()
#write vector field in file to be read by swan by idla=1
def wrt_vec(outfile,name1,name2):
outf=open(outfile,'w')
ny,nx=name1.shape
aa=pl.arange(ny-1,-1,-1)
for iy in aa:
str1=' '.join('%.4f' % n for n in name1[iy,:])
str1=str1+'\n'
outf.write(str1)
for iy in aa:
str1=' '.join('%.4f' % n for n in name2[iy,:])
str1=str1+'\n'
outf.write(str1)
outf.close()
######################################################
#N=100
if real_data:
print 'real data assimilation is considered'
#obs_file=inp_dir+'/obs_wave/rad/cBathy2012-05-10T05.nc'
obs_file=inp_dir+'/obs_wave/rad/cBathy.nc'
time_var='time'
else:
print 'Syn data assimilation is considered'
obs_file=inp_dir+'/obs_wave/syn/wav_syn_obs.nc'
time_var='ocean_time'
#if real:
nc = netCDF4.Dataset(obs_file)
ncv_obs = nc.variables
xr = ncv_obs['x'][:]
yr = ncv_obs['y'][:]
utim_obs = netcdftime.utime(ncv_obs[time_var].units)
sec_obs = ncv_obs[time_var][:]
date_obs = utim_obs.num2date(sec_obs)
nc.close()
##>>>> Choose which obs data going to use for assimilation.
try:
date_assim = date_obs[0]
except:
date_assim = date_obs
#ntime=12 # netcdf index
arg = sys.argv
dirin = arg[1]
#dirin ='../03_mem_inp/member'+ str(1000+n+1)
dirout = dirin.split('/')[-1]+'/'
print dirout
## Read the ROMS Data
# This is a code to manipulate the input from the NetCDF files given by
# Saeed's ROMS model.
if True:
# Enter path to the data file
#datapath = '/home/shusin3/users/moghimi/assimilation/assim_local/wave_current/seq1/every2/run_1000/03_mem_inp/member1001';
datapath = dirin;
datafile = datapath+'/'+hisfile_name;
tnc = netCDF4.Dataset(datafile)
x = tnc.variables['x_rho'][:]
y = tnc.variables['y_rho'][:]
h = tnc.variables['h'][:]
#### > find ntme based on obs time stamp
ncvar = tnc.variables
timename_sim = 'ocean_time'
utime_sim = netcdftime.utime(ncvar[timename_sim].units)
times = ncvar[timename_sim][:]
sdates_sim = utime_sim.num2date(times)
#To find closest time step to assimilation time
sec_assim = utime_sim.date2num(date_assim)
diff = np.abs(sec_assim-times)
ind = np.where(diff==diff.min())
ntime = pl.array(ind[0]).item()
print 'ntime > ',ntime,' date_simul > ',sdates_sim[ind],' date_assim > ',date_assim
z = tnc.variables['zeta'][ntime,:]
u_tmp = tnc.variables ['ubar'][ntime,:]
u_mask = tnc.variables['mask_u'][:]
u_tmp[u_mask==0]=0
#u_tmp[u_tmp.mask]=0
v_tmp = tnc.variables['vbar'][ntime,:]
v_mask = tnc.variables['mask_v'][:]
v_tmp[v_mask==0]=0
#v_tmp[v_tmp.mask]=0
#calculate u and v in rho points
u = pl.zeros_like(z)
v = pl.zeros_like(z)
u[:,1:-1] = (u_tmp[:,:-1]+u_tmp[:,1:])/2.
u[:,0] = u_tmp[:,0]
u[:,-1] = u_tmp[:,-1]
v[1:-1,:] = (v_tmp[:-1,:]+v_tmp[1:,:])/2.
v[0 ,:] = v_tmp [0 ,:]
v[-1 ,:] = v_tmp [-1 ,:]
#to read final mask
nco = netCDF4.Dataset(final_grd)
ncvo = nco.variables
mr = ncvo['mask_rho'][:]
nco.close()
#apply the mask
h = h * mr
z = z * mr
u = u * mr
v = v * mr
#open directory
os.system('mkdir -p '+dirout)
wrt_field(outfile = dirout+'/bathy.bot' ,name =h)
wrt_field(outfile = dirout+'/wlevel.bot',name =z)
wrt_vec(outfile = dirout+'/current.bot' ,name1=u,name2=v)
## Write the coordinate file
# Output File
outfile=dirout+'/local_rect_coords.bot'
outf=open(outfile,'w')
ny,nx=x.shape
aa=pl.arange(ny-1,-1,-1)
for iy in aa:
for ix in range(nx):
str1=('%.4f' % x[iy,ix])
str1=str1+'\n'
outf.write(str1)
for iy in aa:
for ix in range(nx):
str1=('%.4f' % y[iy,ix])
str1=str1+'\n'
outf.write(str1)
outf.close()
###############################################################################################
if real_data:
# >>> copy boundary spectra from inner model
#Find directory of inner to get BOU spectra
# Outer SWAN runs directory from Gabriel Garcia
bouSwanDir = '/home/nmg/nmg/assimilation/assimModelBoundaryConditions/nri_swanOuterBoundary/'
inner = bouSwanDir + '04-inner-tide-currents-final/03-stationary/'
##inner='/home/shusin3/users/ggarcia/projects/new_river_inlet/swan/201205/16-inner-tide-currents/steady/'
##inner='/home/shusin3/users/ggarcia/projects/new_river_inlet/swan/201205_ww3_nested/16-inner-tide-currents/steady/'
#inner='/home/shusin3/users/moghimi/coupling/wave_verification/local/01-ggarcia/04-inner-tide-currents-final/03-stationary/'
wav_base = datetime(2012,05,01,01,0,0);
units = 'seconds since '+wav_base.isoformat()[:10]+' '+wav_base.isoformat()[11:]
utwav = netcdftime.utime(units)
timvec = pl.linspace(0,500,501)*3600.0
wav_dates = utwav.num2date(timvec)
ind = pl.array(pl.where((wav_dates>=date_assim))).squeeze()
ind0 = ind[0]
if '08_forward' in dirin:
dirout = dirin.replace('08_forward','08_forward_swan/08_forward')
else:
dirout = dirin.replace('/03_mem_inp/','/04_wav_adj/')
spcdir = inner + str(ind0)
print spcdir
os.system('cp '+' '+spcdir+'/local20m.spc '+dirout+'/bnd.spc')
print 'date_assim > ',date_assim,' taken_date_wave> ',wav_dates[ind[0]],'\n',spcdir
else:
#global experiment_spc
#experiment_spc=False
#spc_file=local_inp+'/obs_wave/syn/wave_limit_test/spc_inner/local20m_hs.5_t14.spc'
#spc_file=local_inp+'/obs_wave/syn/wave_limit_test/spc_inner/local20m_hs3_t4.spc'
spc_file=local_inp+'/obs_wave/syn/wave_limit_test/spc_inner/local20m_hs1_t7.spc'
print '\n\n >>> experiment_spc is True >>>>> it should be False by default!'
print ' >>>>>>>> ******* this experimental spc is taking for swan ****** <<<<<<'
print ' >>>>>>>> ******* consider experiment_spc=False ??? ****** <<<<<<'
os.system('ln -sf '+spc_file+' '+dirout+'/bnd.spc' )
print ' global experiment_spc \n',spc_file
############################################
#os.system('mv '+' '+dirs[9]+'/tmp.inp '+dirout)
#os.system('mv '+' '+dirs[9]+'/log1.txt '+dirout)