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04-simplify_swan.py
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04-simplify_swan.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Script for preparing SWAN results for assimilation
"""
__author__ = "Saeed Moghimi"
__copyright__ = "Copyright 2015, Oregon State University"
__license__ = "GPL"
__version__ = "0.1"
__email__ = "moghimis@gmail.com"
#####################################################################
# Saeed Moghimi; moghimis@gmail.com
# Logs:
# 1.0 03/25/2013 02:14:41 PM
#
#
#
import netCDF4
from numpy import ma
import numpy as np
import datetime as datetime
import netcdftime
import pylab as pl
import sys,os
#swan2netcdf
arg = sys.argv
dir_in = arg[1]
##############################################
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
hisfile_name = base_info.hisfile_name
base_dir = base_info.base_dir
##################################################
#which time is the wave assimilation time?
if real_data:
#obs_file=inp_dir+'/obs_wave/rad/cBathy2012-05-10T05.nc'
obs_file = inp_dir+'/obs_wave/rad/cBathy.nc'
time_var = 'time'
else:
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)
##>>>> Choose which obs data going to use for assimilation.
try:
date_assim = date_obs[0]
tim = sec_obs [0]
except:
date_assim = date_obs
tim = sec_obs
units=ncv_obs[time_var].units
nc.close()
#read bathy file size
local_inp = base_info.base_dir+'/inp'
ncf = local_inp + '/const/' + base_info.grd
#ncf = base + '/03_mem_inp/member1004/'+hisfile_name
nc = netCDF4.Dataset(ncf)
ncv = nc.variables
bathy = ncv['h'][:]
nc.close()
row,col = bathy.shape
outfile = dir_in+'/swout.nc'
print outfile,date_assim
## read swan data
# preallocate variables for speed
xp = pl.loadtxt(dir_in + '/xp.blkout' )
yp = pl.loadtxt(dir_in + '/yp.blkout' )
hsign = pl.loadtxt(dir_in + '/swh.blkout' )
pdir = pl.loadtxt(dir_in + '/pdir.blkout' )
tm01 = pl.loadtxt(dir_in + '/tm01.blkout' )
depth = pl.loadtxt(dir_in + '/depth.blkout' )
botlev = pl.loadtxt(dir_in + '/bottom.blkout')
force = pl.loadtxt(dir_in + '/force.blkout' )
dir = pl.loadtxt(dir_in + '/dir.blkout' )
rtp = pl.loadtxt(dir_in + '/rtp.blkout' )
dissip = pl.loadtxt(dir_in + '/dissip.blkout')
ubot = pl.loadtxt(dir_in + '/ubot.blkout' )
wlen = pl.loadtxt(dir_in + '/wlen.blkout' )
qb = pl.loadtxt(dir_in + '/qb.blkout' )
transp = pl.loadtxt(dir_in + '/wp.blkout' )
vel = pl.loadtxt(dir_in + '/vel.blkout' )
if False:
figure()
teta=270-dir
teta[teta<360]=teta[teta<360]+360
hsign=ma.masked_where(hsign==-9.0,hsign)
hsx=hsign*cos(teta)
hsy=hsign*sin(teta)
pcolor(xp,yp,dir)
kk=3
quiver(xp[::kk,::kk],yp[::kk,::kk],hsx[::kk,::kk],hsy[::kk,::kk],scale=0.8)
# clean up swan data
# clean up the variables
mask = hsign.copy()
mask[mask>-5]=1.0
mask[mask<-5]=0.0
hsign [hsign <-5.] = 0.0;
pdir [pdir <-5.] = 0.0;
tm01 [tm01 <-5.] = 0.0;
depth [depth <-5.] = 0.0;
botlev[botlev<-5.] = 0.0;
force [force <-5.] = 0.0;
dir [dir <-5.] = 0.0;
rtp [rtp <-5.] = 0.0;
dissip[dissip<-5.] = 0.0;
wlen [wlen <-5] = 0.0;
qb [qb <-1] = 0.0;
# decompose vectors
velx = vel [0:row ,:];
vely = vel [row: ,:];
forcex = force [0:row ,:];
forcey = force [row: ,:];
transpx = transp[0:row ,:];
transpy = transp[row: ,:];
hsign =np.ma.masked_where(mask ==0.0, hsign)
pdir =np.ma.masked_where(mask ==0.0, pdir)
tm01 =np.ma.masked_where(mask ==0.0, tm01)
depth =np.ma.masked_where(mask ==0.0, depth)
botlev=np.ma.masked_where(mask ==0.0, botlev)
dir =np.ma.masked_where(mask ==0.0, dir)
rtp =np.ma.masked_where(mask ==0.0, rtp)
dissip=np.ma.masked_where(mask ==0.0, dissip)
wlen =np.ma.masked_where(mask ==0.0, wlen)
velx =np.ma.masked_where(mask ==0.0, velx)
vely =np.ma.masked_where(mask ==0.0, vely)
forcex=np.ma.masked_where(mask ==0.0, forcex)
forcey=np.ma.masked_where(mask ==0.0, forcey)
transpx =np.ma.masked_where(mask ==0.0, transpx)
transpy =np.ma.masked_where(mask ==0.0, transpy)
#
if True:
#Cut to smaller region
i1,i2,j1,j2=pl.loadtxt('param.inp')
i1=int(i1)
i2=int(i2)
j1=int(j1)
j2=int(j2)
print i1,i2,j1,j2
#cut to smaller region
#i1=60
#i2=150
#j1=30
#j2=180
k=1
xp=xp [j1:j2:k,i1:i2:k]
yp=yp [j1:j2:k,i1:i2:k]
hsign=hsign [j1:j2:k,i1:i2:k]
pdir=pdir [j1:j2:k,i1:i2:k]
tm01=tm01 [j1:j2:k,i1:i2:k]
depth=depth[j1:j2:k,i1:i2:k]
botlev=botlev [j1:j2:k,i1:i2:k]
forcex=forcex [j1:j2:k,i1:i2:k]
forcey=forcey [j1:j2:k,i1:i2:k]
dir=dir [j1:j2:k,i1:i2:k]
rtp=rtp [j1:j2:k,i1:i2:k]
dissip=dissip[j1:j2:k,i1:i2:k]
ubot=ubot [j1:j2:k,i1:i2:k]
wlen=wlen [j1:j2:k,i1:i2:k]
qb=qb [j1:j2:k,i1:i2:k]
transpx=transpx [j1:j2:k,i1:i2:k]
transpy=transpy [j1:j2:k,i1:i2:k]
velx=velx [j1:j2:k,i1:i2:k]
vely=vely [j1:j2:k,i1:i2:k]
mask=mask [j1:j2:k,i1:i2:k]
#print('writing netcdf file')
##________netcdf writing________________
ny,nx = pl.shape(xp)
missing_value=0
nc = netCDF4.Dataset(outfile, 'w', format='NETCDF3_CLASSIC')
nc.createDimension('x', nx)
nc.createDimension('y', ny)
nc.createDimension('ocean_time',None)
timea = nc.createVariable('ocean_time','f8',('ocean_time',))
timea.units = units
timea[:]=tim
x_nc = nc.createVariable('x', 'float', ('y','x',))
x_nc.long_name = 'x positions'
x_nc[:] = xp[:]
y_nc = nc.createVariable('y', 'float', ('y','x',))
y_nc.long_name = 'y positions'
y_nc[:] = yp[:] #[:,1]
p10 = nc.createVariable('hsig', 'float', ('ocean_time','y','x',))
p10.long_name = 'significant wave height'
p10.units = 'm'
p10[0,:] = hsign[:]
p11 = nc.createVariable('pdir', 'float', ('ocean_time','y','x',))
p11.long_name = 'peak wave direction'
p11.units = 'deg'
p11[0,:] = pdir[:]
p12 = nc.createVariable('tm01', 'float', ('ocean_time','y','x',))
p12.long_name = 'mean wave period'
p12.units = 's'
p12[0,:] = tm01[:]
p13 = nc.createVariable('dep', 'float', ('ocean_time','y','x',))
p13.long_name = 'water depth'
p13.units = 'm'
p13[0,:] = depth[:]
p14 = nc.createVariable('forcex', 'float', ('ocean_time','y','x',))
p14.long_name = 'wave-induced force x'
p14.units = 'nm-2'
p14[0,:] = forcex[:]
p142 = nc.createVariable('forcey', 'float', ('ocean_time','y','x',))
p142.long_name = 'wave-induced force y'
p142.units = 'nm-2'
p142[0,:] = forcey[:]
p15 = nc.createVariable('dir', 'float', ('ocean_time','y','x',))
p15.long_name = 'mean wave direction'
p15.units = 'deg'
p15[0,:] = dir[:]
p16 = nc.createVariable('rtp', 'float', ('ocean_time','y','x',))
p16.long_name = 'peak wave period'
p16.units = 's'
p16[0,:] = rtp[:]
p17 = nc.createVariable('dissip', 'float', ('ocean_time','y','x',))
p17.long_name = 'dissipation'
p17.units = 'wm-2'
p17[0,:] = dissip[:]
p18 = nc.createVariable('ubot', 'float', ('ocean_time','y','x',))
p18.long_name = 'orbital velocity'
p18.units = 'ms-1'
p18[0,:] = ubot[:]
p19 = nc.createVariable('wlen', 'float', ('ocean_time','y','x',))
p19.long_name = 'wave length'
p19.units = 'm'
p19[0,:] = wlen[:]
p21 = nc.createVariable('qb', 'float', ('ocean_time','y','x',))
p21.long_name = 'franction of breaking waves'
p21.units = '0 ~ 1'
p21[0,:] = qb[:]
p22 = nc.createVariable('velx', 'float', ('ocean_time','y','x',))
p22.long_name = 'current velocity x'
p22.units = 'ms-1'
p22[0,:] = velx[:]
p23 = nc.createVariable('vely', 'float', ('ocean_time','y','x',))
p23.long_name = 'current velocity y'
p23.units = 'ms-1'
p23[0,:] = vely[:]
p24 = nc.createVariable('mask', 'float', ('ocean_time','y','x',))
p24.long_name = 'mask hs'
p24[0,:] = mask[:]
nc.created = datetime.datetime.now().isoformat()
nc.close()