def ncload(nc,variable,tt):
if variable=='agemean':
ac = nc.variables['agec'][tt,klayer,:]
aa = nc.variables['agealpha'][tt,klayer,:]
tmp = aa/ac
tmp[ac<1e-12]=0.
return tmp/86400.
if variable=='area':
eta = nc.variables['eta'][tt,:]
dzf = self.getdzf(eta)
dzf = Spatial.getdzf(self,eta)
return self.df*dzf
else:
if self.hasDim(variable,self.griddims['Nk']): # 3D
return nc.variables[variable][tt,klayer,:]
else:
return nc.variables[variable][tt,:]
def ncload(nc,variable,tt):
if variable=='agemean':
ac = nc.variables['agec'][tt,klayer,:]
aa = nc.variables['agealpha'][tt,klayer,:]
tmp = aa/ac
tmp[ac<1e-12]=0.
return tmp/86400.
if variable=='area':
eta = nc.variables['eta'][tt,:]
dzf = self.getdzf(eta)
dzf = Spatial.getdzf(self,eta)
return self.df*dzf
else:
if self.hasDim(variable,self.griddims['Nk']): # 3D
return nc.variables[variable][tt,klayer,:]
else:
return nc.variables[variable][tt,:]
def suntans2untrim(ncfile, outfile, tstart, tend, grdfile=None):
"""
Converts a suntans averages netcdf file into untrim format
for use in particle tracking
"""
####
# Step 1: Load the suntans data object
####
sun = Spatial(ncfile, klayer=[-99])
# Calculate some other variables
sun.de = sun.get_edgevar(sun.dv, method='min')
sun.mark[sun.mark == 5] = 0
sun.mark[sun.mark == 3] = 2
sun.facemark = np.zeros((sun.Nc, ), dtype=np.int)
# Update the grad variable from the ascii grid file if supplied
if not grdfile == None:
print('Updating grid with ascii values...')
grd = Grid(grdfile)
sun.grad = grd.grad[:, ::-1]
###
# Step 2: Write the grid variables to a netcdf file
###
nc = Dataset(outfile, 'w', format='NETCDF4_CLASSIC')
# Global variable
nc.Description = 'UnTRIM history file converted from SUNTANS output'
# Write the dimensions
for dd in list(untrim_griddims.keys()):
if dd == 'time':
nc.createDimension(untrim_griddims[dd], 0)
elif dd == 'numsides':
nc.createDimension(untrim_griddims[dd], sun.maxfaces)
else:
nc.createDimension(untrim_griddims[dd], sun[dd])
for dd in other_dims:
nc.createDimension(dd, other_dims[dd])
###
# Step 3: Initialize all of the grid variables
###
def create_nc_var(name, dimensions, attdict,data=None, \
dtype='f8',zlib=False,complevel=0,fill_value=999999.0):
tmp=nc.createVariable(name, dtype, dimensions,\
zlib=zlib,complevel=complevel,fill_value=fill_value)
for aa in list(attdict.keys()):
tmp.setncattr(aa, attdict[aa])
if not data == None:
nc.variables[name][:] = data
# Make sure the masked cells have a value of -1
mask = sun['cells'].mask.copy()
sun['cells'][mask] = FILLVALUE
sun['face'][mask] = FILLVALUE
for vv in list(untrim_gridvars.keys()):
vname = untrim_gridvars[vv]
print('Writing grid variable %s (%s)...' % (vname, vv))
if vv == 'time':
continue
# add dz_min attribute to z_r variable
if vv == 'z_r':
ugrid[vname]['attributes'].update({'dz_min': 1e-5})
#sun[vv][:]=sun[vv][::-1]
sun[vv][:] = sun['z_w'][0:-1][::-1]
# Reverse the order of grad(???)
if vv == 'grad':
sun[vv][:] = sun[vv][:, ::-1]
## Fix one-based indexing
#if vv in ['cells','edges','grad']:
# mask = sun[vv][:]==-1
# tmp = sun[vv][:]+1
# tmp[mask]=-1
# #sun[vv][:]=sun[vv][:]+1
# create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
# data=tmp,dtype=ugrid[vname]['dtype'])
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
data=sun[vv],dtype=ugrid[vname]['dtype'])
# Initialize the two time variables
vname = untrim_gridvars['time']
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'])
vname = 'Mesh2_data_time_string'
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'])
###
# Step 4: Initialize all of the time-varying variables (but don't write)
###
for vname in varnames:
print('Creating variable %s...' % (vname))
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'],zlib=True,complevel=1,fill_value=999999.)
###
# Step 5: Loop through all of the time steps and write the variables
###
tsteps = sun.getTstep(tstart, tend)
tdays = othertime.DaysSince(sun.time, basetime=datetime(1899, 12, 31))
for ii, tt in enumerate(tsteps):
# Convert the time to the untrim formats
timestr = datetime.strftime(sun.time[tt], '%Y-%m-%d %H:%M:%S')
print('Writing data at time %s (%d of %d)...' %
(timestr, tt, tsteps[-1]))
#Write the time variables
nc.variables['Mesh2_data_time'][ii] = tdays[ii]
nc.variables['Mesh2_data_time_string'][:, ii] = timestr
# Load each variable or calculate it and convert it to the untrim format
sun.tstep = [tt]
###
# Compute a few terms first
eta = sun.loadData(variable='eta')
U = sun.loadData(variable='U_F')
dzz = sun.getdzz(eta)
dzf = sun.getdzf(eta)
vname = 'Mesh2_sea_surface_elevation'
#print '\tVariable: %s...'%vname
nc.variables[vname][:, ii] = eta
vname = 'Mesh2_salinity_3d'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='salt')
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
vname = 'Mesh2_vertical_diffusivity_3d'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='nu_v')
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
vname = 'h_flow_avg'
#print '\tVariable: %s...'%vname
nc.variables[vname][:, :, ii] = U.swapaxes(0, 1)[:, ::-1]
vname = 'v_flow_avg'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='w') * sun.Ac # m^3/s
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
# Need to calculate a few terms for the other variables
vname = 'Mesh2_edge_wet_area'
#print '\tVariable: %s...'%vname
#dzf = sun.loadData(variable='dzf')
tmp3d = dzf * sun.df
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
vname = 'Mesh2_face_water_volume'
#print '\tVariable: %s...'%vname
#dzz = sun.loadData(variable='dzz')
tmp3d = dzz * sun.Ac
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
vname = 'Mesh2_face_wet_area'
#print '\tVariable: %s...'%vname
tmp3d = np.repeat(sun.Ac[np.newaxis, ...], sun.Nkmax, axis=0)
nc.variables[vname][:, :, ii] = tmp3d.swapaxes(0, 1)[:, ::-1]
# UnTRIM references from bottom to top i.e.
# k = 0 @ bed ; k = Nkmax-1 @ top
vname = 'Mesh2_edge_bottom_layer'
#print '\tVariable: %s...'%vname
#tmp2d = sun.Nkmax-sun.Nke # zero based
tmp2d = sun.Nkmax - sun.Nke + 1 # one based
nc.variables[vname][:, ii] = tmp2d
vname = 'Mesh2_edge_top_layer'
#print '\tVariable: %s...'%vname
etop = sun.loadData(variable='etop')
#tmp2d = sun.Nkmax-etop-1 # zero based
tmp2d = sun.Nkmax - etop # one based
nc.variables[vname][:, ii] = tmp2d
vname = 'Mesh2_face_bottom_layer'
#print '\tVariable: %s...'%vname
#tmp2d = sun.Nkmax-sun.Nk + 1 # zero based
tmp2d = sun.Nkmax - sun.Nk # one based
nc.variables[vname][:, ii] = tmp2d
vname = 'Mesh2_face_top_layer'
#print '\tVariable: %s...'%vname
ctop = sun.loadData(variable='ctop')
#tmp2d = sun.Nkmax-ctop-1 # zero based
tmp2d = sun.Nkmax - ctop # one based
nc.variables[vname][:, ii] = tmp2d
print(72 * '#')
print('\t Finished SUNTANS->UnTRIM conversion')
print(72 * '#')
# close the file
nc.close()
def getdzf(self,eta):
""" Get the cell thickness along each edge of the slice"""
dzf = Spatial.getdzf(self,eta,j=self.j)
dzf[self.maskslice]=0
return dzf
def suntans2untrim(ncfile,outfile,tstart,tend,grdfile=None):
"""
Converts a suntans averages netcdf file into untrim format
for use in particle tracking
"""
####
# Step 1: Load the suntans data object
####
sun = Spatial(ncfile,klayer=[-99])
# Calculate some other variables
sun.de = sun.get_edgevar(sun.dv,method='min')
sun.mark[sun.mark==5]=0
sun.mark[sun.mark==3]=2
sun.facemark = np.zeros((sun.Nc,),dtype=np.int)
# Update the grad variable from the ascii grid file if supplied
if not grdfile == None:
print 'Updating grid with ascii values...'
grd = Grid(grdfile)
sun.grad = grd.grad[:,::-1]
###
# Step 2: Write the grid variables to a netcdf file
###
nc = Dataset(outfile,'w',format='NETCDF4_CLASSIC')
# Global variable
nc.Description = 'UnTRIM history file converted from SUNTANS output'
# Write the dimensions
for dd in untrim_griddims.keys():
if dd == 'time':
nc.createDimension(untrim_griddims[dd],0)
elif dd =='numsides':
nc.createDimension(untrim_griddims[dd],sun.maxfaces)
else:
nc.createDimension(untrim_griddims[dd],sun[dd])
for dd in other_dims:
nc.createDimension(dd,other_dims[dd])
###
# Step 3: Initialize all of the grid variables
###
def create_nc_var(name, dimensions, attdict,data=None, \
dtype='f8',zlib=False,complevel=0,fill_value=999999.0):
tmp=nc.createVariable(name, dtype, dimensions,\
zlib=zlib,complevel=complevel,fill_value=fill_value)
for aa in attdict.keys():
tmp.setncattr(aa,attdict[aa])
if not data==None:
nc.variables[name][:] = data
# Make sure the masked cells have a value of -1
mask = sun['cells'].mask.copy()
sun['cells'][mask]=FILLVALUE
sun['face'][mask]=FILLVALUE
for vv in untrim_gridvars.keys():
vname = untrim_gridvars[vv]
print 'Writing grid variable %s (%s)...'%(vname,vv)
if vv=='time':
continue
# add dz_min attribute to z_r variable
if vv == 'z_r':
ugrid[vname]['attributes'].update({'dz_min':1e-5})
#sun[vv][:]=sun[vv][::-1]
sun[vv][:]=sun['z_w'][0:-1][::-1]
# Reverse the order of grad(???)
if vv=='grad':
sun[vv][:]=sun[vv][:,::-1]
## Fix one-based indexing
#if vv in ['cells','edges','grad']:
# mask = sun[vv][:]==-1
# tmp = sun[vv][:]+1
# tmp[mask]=-1
# #sun[vv][:]=sun[vv][:]+1
# create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
# data=tmp,dtype=ugrid[vname]['dtype'])
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
data=sun[vv],dtype=ugrid[vname]['dtype'])
# Initialize the two time variables
vname=untrim_gridvars['time']
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'])
vname = 'Mesh2_data_time_string'
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'])
###
# Step 4: Initialize all of the time-varying variables (but don't write)
###
for vname in varnames:
print 'Creating variable %s...'%(vname)
create_nc_var(vname,ugrid[vname]['dimensions'],ugrid[vname]['attributes'],\
dtype=ugrid[vname]['dtype'],zlib=True,complevel=1,fill_value=999999.)
###
# Step 5: Loop through all of the time steps and write the variables
###
tsteps = sun.getTstep(tstart,tend)
tdays = othertime.DaysSince(sun.time,basetime=datetime(1899,12,31))
for ii, tt in enumerate(tsteps):
# Convert the time to the untrim formats
timestr = datetime.strftime(sun.time[tt],'%Y-%m-%d %H:%M:%S')
print 'Writing data at time %s (%d of %d)...'%(timestr,tt,tsteps[-1])
#Write the time variables
nc.variables['Mesh2_data_time'][ii]=tdays[ii]
nc.variables['Mesh2_data_time_string'][:,ii]=timestr
# Load each variable or calculate it and convert it to the untrim format
sun.tstep=[tt]
###
# Compute a few terms first
eta = sun.loadData(variable='eta' )
U = sun.loadData(variable='U_F' )
dzz = sun.getdzz(eta)
dzf = sun.getdzf(eta)
vname='Mesh2_sea_surface_elevation'
#print '\tVariable: %s...'%vname
nc.variables[vname][:,ii]=eta
vname = 'Mesh2_salinity_3d'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='salt' )
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
vname = 'Mesh2_vertical_diffusivity_3d'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='nu_v' )
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
vname = 'h_flow_avg'
#print '\tVariable: %s...'%vname
nc.variables[vname][:,:,ii]=U.swapaxes(0,1)[:,::-1]
vname = 'v_flow_avg'
#print '\tVariable: %s...'%vname
tmp3d = sun.loadData(variable='w' ) * sun.Ac # m^3/s
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
# Need to calculate a few terms for the other variables
vname = 'Mesh2_edge_wet_area'
#print '\tVariable: %s...'%vname
#dzf = sun.loadData(variable='dzf')
tmp3d = dzf*sun.df
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
vname = 'Mesh2_face_water_volume'
#print '\tVariable: %s...'%vname
#dzz = sun.loadData(variable='dzz')
tmp3d = dzz*sun.Ac
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
vname = 'Mesh2_face_wet_area'
#print '\tVariable: %s...'%vname
tmp3d = np.repeat(sun.Ac[np.newaxis,...],sun.Nkmax,axis=0)
nc.variables[vname][:,:,ii]=tmp3d.swapaxes(0,1)[:,::-1]
# UnTRIM references from bottom to top i.e.
# k = 0 @ bed ; k = Nkmax-1 @ top
vname = 'Mesh2_edge_bottom_layer'
#print '\tVariable: %s...'%vname
#tmp2d = sun.Nkmax-sun.Nke # zero based
tmp2d = sun.Nkmax-sun.Nke+1 # one based
nc.variables[vname][:,ii]=tmp2d
vname = 'Mesh2_edge_top_layer'
#print '\tVariable: %s...'%vname
etop = sun.loadData(variable='etop')
#tmp2d = sun.Nkmax-etop-1 # zero based
tmp2d = sun.Nkmax-etop # one based
nc.variables[vname][:,ii]=tmp2d
vname = 'Mesh2_face_bottom_layer'
#print '\tVariable: %s...'%vname
#tmp2d = sun.Nkmax-sun.Nk + 1 # zero based
tmp2d = sun.Nkmax-sun.Nk # one based
nc.variables[vname][:,ii]=tmp2d
vname = 'Mesh2_face_top_layer'
#print '\tVariable: %s...'%vname
ctop = sun.loadData(variable='ctop')
#tmp2d = sun.Nkmax-ctop-1 # zero based
tmp2d = sun.Nkmax-ctop # one based
nc.variables[vname][:,ii]=tmp2d
print 72*'#'
print '\t Finished SUNTANS->UnTRIM conversion'
print 72*'#'
# close the file
nc.close()
def getdzf(self,eta):
""" Get the cell thickness along each edge of the slice"""
dzf = Spatial.getdzf(self,eta,j=self.j)
dzf[self.maskslice]=0
return dzf