def extrap_at_mask(self,vname,time,quiet=1,**opts):
if not quiet: print('Extrap at mask:\n loading')
v=self.use(vname,SEARCHtime=time)
x,y,h,m=self.grid.vars(vname)
if self.hasz(vname): # 3d
N=v.shape[0]
for n in range(N):
if not quiet: print(' extrap level %d of %d' % (n,N))
v[n,...]=calc.mask_extrap(x,y,np.ma.masked_where(m==0,v[n,...]))
else: # 2d
v=calc.mask_extrap(x,y,np.ma.masked_where(m==0,v))
return v
def extrap_at_mask(self, vname, time, quiet=1, **opts):
if not quiet: print('Extrap at mask:\n loading')
v = self.use(vname, SEARCHtime=time)
x, y, h, m = self.grid.vars(vname)
if self.hasz(vname): # 3d
N = v.shape[0]
for n in range(N):
if not quiet: print(' extrap level %d of %d' % (n, N))
v[n, ...] = calc.mask_extrap(
x, y, np.ma.masked_where(m == 0, v[n, ...]))
else: # 2d
v = calc.mask_extrap(x, y, np.ma.masked_where(m == 0, v))
return v
def s_levels(self,
time,
ruvpw='r',
i=False,
j=False,
k=False,
extrapZeta=False):
ruvpw = ruvpw[0]
h = self.grid.h
zeta = self.use('zeta', SEARCHtime=time)
if extrapZeta:
if not calc.ismarray(zeta):
zeta = np.ma.masked_where(self.grid.mask == 0, zeta)
zeta = calc.mask_extrap(self.grid.lon, self.grid.lat, zeta)
h = rt.rho2uvp(h, ruvpw)
zeta = rt.rho2uvp(zeta, ruvpw)
z = rt.s_levels(h, zeta, self.s_params, rw=ruvpw)
if k is False: k = slice(None)
if j is False: j = slice(None)
if i is False: i = slice(None)
return z[k, j, i]
def s_levels(self,time,loc='rr',i=False,j=False,k=False,extrapZeta=False):
## ruvpw=ruvpw[0]
try:
hLoc,vLoc=loc
except:
hLoc,vLoc=loc,'r'
h=self.grid.h
zeta=self.use('zeta',SEARCHtime=time)
if extrapZeta:
if not calc.ismarray(zeta): zeta=np.ma.masked_where(self.grid.mask==0,zeta)
zeta=calc.mask_extrap(self.grid.lon,self.grid.lat,zeta)
h=rt.rho2uvp(h,hLoc) ##########ruvpw)
zeta=rt.rho2uvp(zeta,hLoc) ###########ruvpw)
z=rt.s_levels(h,zeta,self.s_params,rw=vLoc) ##########ruvpw)
if k is False: k=slice(None)
if j is False: j=slice(None)
if i is False: i=slice(None)
return z[k,j,i]
def s_levels(self,time,loc='rr',i=False,j=False,k=False,extrapZeta=False):
try:
hLoc,vLoc=loc
except:
hLoc,vLoc=loc,'r'
h=self.grid.h
zeta=self.use('zeta',SEARCHtime=time)
if extrapZeta:
#if not calc.ismarray(zeta): zeta=np.ma.masked_where(self.grid.mask==0,zeta)
if not np.ma.is_masked(zeta): zeta=np.ma.masked_where(self.grid.mask==0,zeta)
zeta=calc.mask_extrap(self.grid.lon,self.grid.lat,zeta)
h=rt.rho2uvp(h,hLoc)
zeta=rt.rho2uvp(zeta,hLoc)
z=rt.s_levels(h,zeta,self.s_params,rw=vLoc)
if k is False: k=slice(None)
if j is False: j=slice(None)
if i is False: i=slice(None)
return z[k,j,i]
def s_levels(self, time, ruvpw="r", i=False, j=False, k=False, extrapZeta=False):
ruvpw = ruvpw[0]
h = self.grid.h
zeta = self.use("zeta", SEARCHtime=time)
if extrapZeta:
if not calc.ismarray(zeta):
zeta = np.ma.masked_where(self.grid.mask == 0, zeta)
zeta = calc.mask_extrap(self.grid.lon, self.grid.lat, zeta)
h = rt.rho2uvp(h, ruvpw)
zeta = rt.rho2uvp(zeta, ruvpw)
z = rt.s_levels(h, zeta, self.s_params, rw=ruvpw)
if k is False:
k = slice(None)
if j is False:
j = slice(None)
if i is False:
i = slice(None)
return z[k, j, i]
def ww3gb_2TPAR(datafolder,date0,date1,romsgrid,nseg=(10,10),addxy=(0.001,0.001),dspr=20,path='',name='TPAR'):
'''dspr, directional spreading; see https://www.myroms.org/forum/viewtopic.php?f=14&t=2335
'''
g=roms.Grid(romsgrid)
# loading data:
xlim=g.lon.min()-2,g.lon.max()+2
ylim=g.lat.min()-2,g.lat.max()+2
lon,lat,Time,Res=WW3Data(datafolder).data(date0,date1,xlim,ylim)
# calc spec points:
xy,ij=ww3_specpoints(romsgrid,nseg,addxy)
# interpolate data at initial point of each segment:
x=xy[:,0]
y=xy[:,1]
nt=len(Time)
nv=len(Res)
nx=xy.shape[0]
TPAR=np.zeros((nt,nv,nx),'f')
vnames='hs','tp','dp'
# Significant_height_of_combined_wind_waves_and_swell
# Primary_wave_mean_period
# Primary_wave_direction
for it in range(nt):
if it%10==0: print 'time %03d of %03d : %s'%(it,nt,Time[it].isoformat(' '))
for iv in range(nv):
vname=vnames[iv]
#print ' -- %s'%vname
v=Res[vname][it,...]
# 1st extrap masked data:
v=calc.mask_extrap(lon,lat,v)
TPAR[it,iv,:]=calc.griddata(lon,lat,v,x,y)
# create TPAR files:
for i in range(nx):
fname=name+'_seg%03d.txt'%i
j=open(fname,'w')
j.write('TPAR\n')
for it in range(nt):
# time as YYYYMMDD.HHMMSS
tiso=Time[it].strftime('%Y%m%d.%H%M%S')
j.write('%s %6.2f %6.2f %6.2f %6.2f\n'%(tiso,TPAR[it,0,i],TPAR[it,1,i],TPAR[it,2,i],dspr))
j.close()
print 'created tpar file %s'%fname
x1=xy[:,2]
y1=xy[:,3]
# add to swan INPUT:
# BOUND SHAPESPEC JONSWAP PEAK DSPR DEGREES
# BOUNDSPEC SEGMENT XY -54.3906 33.1171 -55.5271 35.8094 VARIABLE FILE 0 './forcings/TPAR2.txt'
print '\n'
print 'BOUND SHAPESPEC JONSWAP PEAK DSPR DEGREES'
for i in range(nx):
fname=os.path.join(path,name+'_seg%03d.txt'%i)
print 'BOUNDSPEC SEGMENT XY %8.4f %8.4f %8.4f %8.4f VARIABLE FILE 0 \'%s\''%(x[i],y[i],x1[i],y1[i],fname)
print '\n'
i0=ij[:,0]
j0=ij[:,1]
i1=ij[:,2]
j1=ij[:,3]
for i in range(nx):
fname=os.path.join(path,name+'_seg%03d.txt'%i)
print 'BOUNDSPEC SEGMENT IJ %3d %3d %3d %3d VARIABLE FILE 0 \'%s\''%(i0[i],j0[i],i1[i],j1[i],fname)
print '\n'
def ww3gb_2TPAR(datafolder,
date0,
date1,
romsgrid,
nseg=(10, 10),
addxy=(0.001, 0.001),
dspr=20,
path='',
name='TPAR'):
'''dspr, directional spreading; see https://www.myroms.org/forum/viewtopic.php?f=14&t=2335
'''
g = roms.Grid(romsgrid)
# loading data:
xlim = g.lon.min() - 2, g.lon.max() + 2
ylim = g.lat.min() - 2, g.lat.max() + 2
lon, lat, Time, Res = WW3Data(datafolder).data(date0, date1, xlim, ylim)
# calc spec points:
xy, ij = ww3_specpoints(romsgrid, nseg, addxy)
# interpolate data at initial point of each segment:
x = xy[:, 0]
y = xy[:, 1]
nt = len(Time)
nv = len(Res)
nx = xy.shape[0]
TPAR = np.zeros((nt, nv, nx), 'f')
vnames = 'hs', 'tp', 'dp'
# Significant_height_of_combined_wind_waves_and_swell
# Primary_wave_mean_period
# Primary_wave_direction
for it in range(nt):
if it % 10 == 0:
print 'time %03d of %03d : %s' % (it, nt, Time[it].isoformat(' '))
for iv in range(nv):
vname = vnames[iv]
#print ' -- %s'%vname
v = Res[vname][it, ...]
# 1st extrap masked data:
v = calc.mask_extrap(lon, lat, v)
TPAR[it, iv, :] = calc.griddata(lon, lat, v, x, y)
# create TPAR files:
for i in range(nx):
fname = name + '_seg%03d.txt' % i
j = open(fname, 'w')
j.write('TPAR\n')
for it in range(nt):
# time as YYYYMMDD.HHMMSS
tiso = Time[it].strftime('%Y%m%d.%H%M%S')
j.write(
'%s %6.2f %6.2f %6.2f %6.2f\n' %
(tiso, TPAR[it, 0, i], TPAR[it, 1, i], TPAR[it, 2, i], dspr))
j.close()
print 'created tpar file %s' % fname
x1 = xy[:, 2]
y1 = xy[:, 3]
# add to swan INPUT:
# BOUND SHAPESPEC JONSWAP PEAK DSPR DEGREES
# BOUNDSPEC SEGMENT XY -54.3906 33.1171 -55.5271 35.8094 VARIABLE FILE 0 './forcings/TPAR2.txt'
print '\n'
print 'BOUND SHAPESPEC JONSWAP PEAK DSPR DEGREES'
for i in range(nx):
fname = os.path.join(path, name + '_seg%03d.txt' % i)
print 'BOUNDSPEC SEGMENT XY %8.4f %8.4f %8.4f %8.4f VARIABLE FILE 0 \'%s\'' % (
x[i], y[i], x1[i], y1[i], fname)
print '\n'
i0 = ij[:, 0]
j0 = ij[:, 1]
i1 = ij[:, 2]
j1 = ij[:, 3]
for i in range(nx):
fname = os.path.join(path, name + '_seg%03d.txt' % i)
print 'BOUNDSPEC SEGMENT IJ %3d %3d %3d %3d VARIABLE FILE 0 \'%s\'' % (
i0[i], j0[i], i1[i], j1[i], fname)
print '\n'
def his2gnome(fname,
his,
grd=False,
nomask=False,
gshhsMask=True,
xylim=False,
dates=False,
ij=(1, 1)):
'''
Creates GNOME wind file
Ex:
his2gnome(out,his,grd,dates=dates,ij=(2,2))
if gshhsMask, the high res mask file mask_gshhs.npy will be created at 1st usage.
Mask is based on high (h) resolution gshhs data which must be available (env variable
GSHHS_MASK must be set).
'''
if not grd: grd = his
deta, dxi = ij
dims = netcdf.fdim(his)
xi, eta = dims['xi_rho'], dims['eta_rho']
xi0, eta0 = xi, eta
nc0 = netcdf.ncopen(his)
time = netcdf.nctime(nc0, 'ocean_time')
# for roms agrif:
#t=netcdf.use(nc0,'scrum_time')
#time=netcdf.num2date(t,'seconds since %d-01-01' % year0)
x0 = netcdf.use(grd, 'lon_rho')
y0 = netcdf.use(grd, 'lat_rho')
ang = netcdf.use(grd, 'angle')
if not xylim is False:
xlim = xylim[:2]
ylim = xylim[2:]
i1, i2, j1, j2 = calc.ij_limits(x0, y0, xlim, ylim)
print(i1, i2, j1, j2)
xi = i2 - i1
eta = j2 - j1
else:
i1, i2 = 0, xi
j1, j2 = 0, eta
XI = '%d:%d:%d' % (i1, i2, dxi)
ETA = '%d:%d:%d' % (j1, j2, deta)
xi = len(range(i1, i2, dxi))
eta = len(range(j1, j2, deta))
# create file:
create_uv(fname, xi, eta)
nc = netcdf.ncopen(fname, 'a')
for v0, v in ('lon_rho', 'lon'), ('lat_rho', 'lat'), ('mask_rho',
'mask'), ('h',
'depth'):
print('filling %s with %s' % (v, v0))
nc.vars[v][:] = netcdf.use(grd, v0, xi_rho=XI, eta_rho=ETA)
if nomask:
print('NO MASK !!!')
nc.vars['mask'][:] = 1
if gshhsMask:
try:
mask = np.load('mask_gshhs.npy')
except:
mask = 1 + 0 * netcdf.use(nc0, 'mask_rho', xi_rho=XI, eta_rho=ETA)
mask = mask.astype('bool')
x = netcdf.use(grd, 'lon_rho', xi_rho=XI, eta_rho=ETA)
y = netcdf.use(grd, 'lat_rho', xi_rho=XI, eta_rho=ETA)
from okean import gshhs
axis = x.min(), x.max(), y.min(), y.max()
g = gshhs.gshhs(axis,
resolution='h',
area_thresh=0.,
max_level=2,
clip=True)
for lon, lat, level in zip(g.lon, g.lat, g.level):
if level == 1: # land
print('mask ', lon.shape)
i = calc.inpolygon(x, y, lon, lat)
mask = mask & ~i
mask.dump('mask_gshhs.npy')
nc.vars['mask'][:] = mask
x = x0[j1:j2:deta, i1:i2:dxi]
y = y0[j1:j2:deta, i1:i2:dxi]
ang = ang[j1:j2:deta, i1:i2:dxi]
n = -1
for it in range(len(time)):
if not dates is False:
d0, d1 = dates
if time[it] < d0 or time[it] >= d1: continue
n += 1
U = np.zeros((eta0, xi0), 'f')
V = np.zeros((eta0, xi0), 'f')
nc.vars['time'][n] = netcdf.date2num(time[it], tunits)
# for roms agrif:
#u=netcdf.use(nc0,'u',time=it,s_rho=-1)
#v=netcdf.use(nc0,'v',time=it,s_rho=-1)
u = netcdf.use(nc0, 'u', ocean_time=it, s_rho=-1)
v = netcdf.use(nc0, 'v', ocean_time=it, s_rho=-1)
# mask extrap:
print('mask extrap...')
u = calc.mask_extrap(x0, y0, np.ma.masked_where(u == 0, u))
v = calc.mask_extrap(x0, y0, np.ma.masked_where(v == 0, v))
U[:, 1:-1] = 0.5 * (u[:, :-1] + u[:, 1:])
U[:, 0] = u[:, 0]
U[:, -1] = u[:, -1]
V[1:-1, :] = 0.5 * (v[:-1.:] + v[1:, :])
V[0, :] = v[0, :]
V[-1, :] = v[-1, :]
U = U[j1:j2, i1:i2]
V = V[j1:j2, i1:i2]
U = U[j1:j2:deta, i1:i2:dxi]
V = V[j1:j2:deta, i1:i2:dxi]
# rotate uv:
print('rotating ...')
U, V = calc.rot2d(U, V, -ang)
print('filling uv', n, time[it])
nc.vars['u'][n, ...] = U
nc.vars['v'][n, ...] = V
nc.close()
nc0.close()
def his2gnome(fname,his,grd=False,nomask=False,gshhsMask=True,xylim=False,dates=False,ij=(1,1)):
'''
Creates GNOME wind file
Ex:
his2gnome(out,his,grd,dates=dates,ij=(2,2))
if gshhsMask, the high res mask file mask_gshhs.npy will be created at 1st usage.
Mask is based on high (h) resolution gshhs data which must be available (env variable
GSHHS_MASK must be set).
'''
if not grd: grd=his
deta,dxi=ij
dims=netcdf.fdim(his)
xi,eta=dims['xi_rho'],dims['eta_rho']
xi0,eta0=xi,eta
nc0=netcdf.ncopen(his)
time=netcdf.nctime(nc0,'ocean_time')
# for roms agrif:
#t=netcdf.use(nc0,'scrum_time')
#time=netcdf.num2date(t,'seconds since %d-01-01' % year0)
x0=netcdf.use(grd,'lon_rho')
y0=netcdf.use(grd,'lat_rho')
ang=netcdf.use(grd,'angle')
if not xylim is False:
xlim=xylim[:2]
ylim=xylim[2:]
i1,i2,j1,j2=calc.ij_limits(x0,y0,xlim,ylim)
print i1,i2,j1,j2
xi=i2-i1
eta=j2-j1
else:
i1,i2=0,xi
j1,j2=0,eta
XI ='%d:%d:%d' %(i1,i2,dxi)
ETA ='%d:%d:%d' %(j1,j2,deta)
xi=len(range(i1,i2,dxi))
eta=len(range(j1,j2,deta))
# create file:
create_uv(fname,xi,eta)
nc=netcdf.ncopen(fname,'a')
for v0,v in ('lon_rho','lon'),('lat_rho','lat'),('mask_rho','mask'),('h','depth'):
print 'filling %s with %s' % (v,v0)
nc.vars[v][:]=netcdf.use(grd,v0,xi_rho=XI,eta_rho=ETA)
if nomask:
print 'NO MASK !!!'
nc.vars['mask'][:]=1
if gshhsMask:
try:
mask=np.load('mask_gshhs.npy')
except:
mask=1+0*netcdf.use(nc0,'mask_rho',xi_rho=XI,eta_rho=ETA)
mask=mask.astype('bool')
x=netcdf.use(grd,'lon_rho',xi_rho=XI,eta_rho=ETA)
y=netcdf.use(grd,'lat_rho',xi_rho=XI,eta_rho=ETA)
from okean import gshhs
axis=x.min(),x.max(),y.min(),y.max()
g=gshhs.gshhs(axis, resolution='h',area_thresh=0., max_level=2,clip=True)
for lon, lat, level in zip(g.lon, g.lat, g.level):
if level == 1: # land
print 'mask ',lon.shape
i=calc.inpolygon(x,y,lon,lat)
mask=mask & ~i
mask.dump('mask_gshhs.npy')
nc.vars['mask'][:]=mask
x=x0[j1:j2:deta,i1:i2:dxi]
y=y0[j1:j2:deta,i1:i2:dxi]
ang=ang[j1:j2:deta,i1:i2:dxi]
n=-1
for it in range(len(time)):
if not dates is False:
d0,d1=dates
if time[it]<d0 or time[it]>=d1: continue
n+=1
U=np.zeros((eta0,xi0),'f')
V=np.zeros((eta0,xi0),'f')
nc.vars['time'][n]=netcdf.date2num(time[it],tunits)
# for roms agrif:
#u=netcdf.use(nc0,'u',time=it,s_rho=-1)
#v=netcdf.use(nc0,'v',time=it,s_rho=-1)
u=netcdf.use(nc0,'u',ocean_time=it,s_rho=-1)
v=netcdf.use(nc0,'v',ocean_time=it,s_rho=-1)
# mask extrap:
print 'mask extrap...'
u=calc.mask_extrap(x0,y0,np.ma.masked_where(u==0,u))
v=calc.mask_extrap(x0,y0,np.ma.masked_where(v==0,v))
U[:,1:-1]=0.5*(u[:,:-1]+u[:,1:])
U[:,0]=u[:,0]
U[:,-1]=u[:,-1]
V[1:-1,:]=0.5*(v[:-1.:]+v[1:,:])
V[0,:]=v[0,:]
V[-1,:]=v[-1,:]
U=U[j1:j2,i1:i2]
V=V[j1:j2,i1:i2]
U=U[j1:j2:deta,i1:i2:dxi]
V=V[j1:j2:deta,i1:i2:dxi]
# rotate uv:
print 'rotating ...'
U,V=calc.rot2d(U,V,-ang)
print 'filling uv', n, time[it]
nc.vars['u'][n,...]=U
nc.vars['v'][n,...]=V
nc.close()
nc0.close()