def make_grid(filemesh, idm=4320, jdm=1188):
meshfile_hgr = filemesh[:-6] + "hgr.nc"
meshfile_zgr = filemesh[:-6] + "zgr.nc"
maskfile = filemesh[:-11] + "mask.nc"
ncidh = netCDF4.Dataset(meshfile_hgr, "r")
ncidz = netCDF4.Dataset(meshfile_zgr, "r")
ncidm = netCDF4.Dataset(maskfile, "r")
# Now acquire the data. P-cell data
plon = np.squeeze(ncidh.variables["glamt"][0, :, :])
plat = np.squeeze(ncidh.variables["gphit"][0, :, :])
scpx = np.squeeze(ncidh.variables["e1t"][0, :, :])
scpy = np.squeeze(ncidh.variables["e2t"][0, :, :])
# U-cell data.
ulon = np.squeeze(u_to_hycom_u(ncidh.variables["glamu"][0, :, :]))
ulat = np.squeeze(u_to_hycom_u(ncidh.variables["gphiu"][0, :, :]))
scux = np.squeeze(u_to_hycom_u(ncidh.variables["e1u"][0, :, :]))
scuy = np.squeeze(u_to_hycom_u(ncidh.variables["e2u"][0, :, :]))
# V-cell data.
# TODO: Proper extrapolation of data on grid edges (mainly bottom row)
vlon = np.squeeze(v_to_hycom_v(ncidh.variables["glamv"][0, :, :]))
vlat = np.squeeze(v_to_hycom_v(ncidh.variables["gphiu"][0, :, :]))
scvx = np.squeeze(v_to_hycom_v(ncidh.variables["e1v"][0, :, :]))
scvy = np.squeeze(v_to_hycom_v(ncidh.variables["e2v"][0, :, :]))
# Q-cell data
# TODO: Proper extrapolation of data on grid edges (mainly bottom row)
qlon = np.squeeze(f_to_hycom_q(ncidh.variables["glamf"][0, :, :]))
qlat = np.squeeze(f_to_hycom_q(ncidh.variables["gphif"][0, :, :]))
scqx = np.squeeze(f_to_hycom_q(ncidh.variables["e1f"][0, :, :]))
scqy = np.squeeze(f_to_hycom_q(ncidh.variables["e2f"][0, :, :]))
# Angle used for rotation
ulon_rgt = numpy.copy(ulon)
ulat_rgt = numpy.copy(ulat)
ulon_lft = numpy.roll(ulon, 1, axis=1)
ulat_lft = numpy.roll(ulat, 1, axis=1)
pang = modeltools.tools.p_azimuth(ulon_lft, ulat_lft, ulon_rgt, ulat_rgt)
# Aspect ratio
asp = numpy.where(scpy == 0., 99.0, scpx / scpy)
# Coriolis
corio = numpy.sin(
numpy.radians(qlat)) * 4. * numpy.pi / 86164.0 # Sidereal day
# Put inside datadict for abfile writing
ddict = {}
ddict["plon"] = plon
ddict["plat"] = plat
ddict["ulon"] = ulon
ddict["ulat"] = ulat
ddict["vlon"] = vlon
ddict["vlat"] = vlat
ddict["qlon"] = qlon
ddict["qlat"] = qlat
#
ddict["scpx"] = scpx
ddict["scpy"] = scpy
ddict["scux"] = scux
ddict["scuy"] = scuy
ddict["scvx"] = scvx
ddict["scvy"] = scvy
ddict["scqx"] = scqx
ddict["scqy"] = scqy
#
ddict["cori"] = corio
ddict["pang"] = pang
ddict["pasp"] = asp
abfile.write_regional_grid(ddict)
# Bathymetry
hdepw = np.squeeze(ncidz.variables["hdepw"][0, :, :])
mbathy = np.squeeze(ncidz.variables["mbathy"][0, :, :])
ncidt = netCDF4.Dataset(maskfile, "r")
tmask = np.squeeze(ncidt.variables["tmaskutil"][0, :, :])
tmp2 = numpy.where(mbathy > 0., hdepw, 0.)
abfile.write_bathymetry("bathy", 1, tmp2, 0.)
shutil.move("depth_bathy_01.a", './dummped_depth_NMOa0.08_01.a')
shutil.move("depth_bathy_01.b", './dummped_depth_NMOa0.08_01.b')
shutil.move("regional.grid.a", "./dummped_regional.grid.a")
shutil.move("regional.grid.b", "./dummped_regional.grid.b")
def main(meshfile, first_j=0):
nemo_mesh = modeltools.nemo.NemoMesh(meshfile, first_j=first_j)
# ncid =netCDF4.Dataset(meshfile,"r")
# plon =ncid.variables["glamt"][0,:,:]
# plat =ncid.variables["gphit"][0,:,:]
# ulon =ncid.variables["glamu"][0,:,:]
# ulat =ncid.variables["gphiu"][0,:,:]
# vlon =ncid.variables["glamv"][0,:,:]
# vlat =ncid.variables["gphiv"][0,:,:]
# jdm,idm=plon.shape
#
# # These tests are on full grid
# periodic_i = modeltools.nemo.periodic_i(plon,plat)
# arctic_patch=modeltools.nemo.arctic_patch(plon,plat)
# logger.info("Grid periodic in i :%s"%str(periodic_i))
# logger.info("Arctic Patch :%s"%str(arctic_patch))
#
# # Not difficult to extend, but for now...
# if not periodic_i and arctic_patch:
# msg="Only periodic in i and arctic patchsupported for now"
# logger.error(msg)
# raise ValueError,msg
# HYCOM stagger with same i,j index:
# -------------
#
# x----x----x
# | | |
# | | |
# U----P----x
# | | |
# | | |
# Q----V----x
#
# Procedure:
# - Shift u points 1 cell to left
# - Shift v points 1 cell down
# - Shift q points 1 cell to left and 1 cell down
# Get slices for the unique domain of the nemo mesh
#si = nemo_mesh.slicei
#sj = nemo_mesh.slicej
# Now acquire the data. P-cell data
plon = nemo_mesh.sliced(nemo_mesh["glamt"][0, :, :])
plat = nemo_mesh.sliced(nemo_mesh["gphit"][0, :, :])
scpx = nemo_mesh.sliced(nemo_mesh["e1t"][0, :, :])
scpy = nemo_mesh.sliced(nemo_mesh["e2t"][0, :, :])
# U-cell data.
ulon = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(
nemo_mesh["glamu"][0, :, :]))
ulat = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(
nemo_mesh["gphiu"][0, :, :]))
scux = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(nemo_mesh["e1u"][0, :, :]))
scuy = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(nemo_mesh["e2u"][0, :, :]))
# V-cell data.
# TODO: Proper extrapolation of data on grid edges (mainly bottom row)
vlon = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(
nemo_mesh["glamv"][0, :, :]))
vlat = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(
nemo_mesh["gphiu"][0, :, :]))
scvx = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(nemo_mesh["e1v"][0, :, :]))
scvy = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(nemo_mesh["e2v"][0, :, :]))
# Q-cell data
# TODO: Proper extrapolation of data on grid edges (mainly bottom row)
qlon = nemo_mesh.sliced(nemo_mesh.f_to_hycom_q(
nemo_mesh["glamf"][0, :, :]))
qlat = nemo_mesh.sliced(nemo_mesh.f_to_hycom_q(
nemo_mesh["gphif"][0, :, :]))
scqx = nemo_mesh.sliced(nemo_mesh.f_to_hycom_q(nemo_mesh["e1f"][0, :, :]))
scqy = nemo_mesh.sliced(nemo_mesh.f_to_hycom_q(nemo_mesh["e2f"][0, :, :]))
# Angle used for rotation
ulon_rgt = numpy.copy(ulon)
ulat_rgt = numpy.copy(ulat)
ulon_lft = numpy.roll(ulon, 1, axis=1)
ulat_lft = numpy.roll(ulat, 1, axis=1)
pang = modeltools.tools.p_azimuth(ulon_lft, ulat_lft, ulon_rgt, ulat_rgt)
# Aspect ratio
asp = numpy.where(scpy == 0., 99.0, scpx / scpy)
# Coriolis
corio = numpy.sin(
numpy.radians(qlat)) * 4. * numpy.pi / 86164.0 # Sidereal day
# Put inside datadict for abfile writing
ddict = {}
ddict["plon"] = plon
ddict["plat"] = plat
ddict["ulon"] = ulon
ddict["ulat"] = ulat
ddict["vlon"] = vlon
ddict["vlat"] = vlat
ddict["qlon"] = qlon
ddict["qlat"] = qlat
#
ddict["scpx"] = scpx
ddict["scpy"] = scpy
ddict["scux"] = scux
ddict["scuy"] = scuy
ddict["scvx"] = scvx
ddict["scvy"] = scvy
ddict["scqx"] = scqx
ddict["scqy"] = scqy
#
ddict["cori"] = corio
ddict["pang"] = pang
ddict["pasp"] = asp
abfile.write_regional_grid(ddict)
# Bathymetry
hdepw = nemo_mesh.sliced(nemo_mesh["hdepw"][0, :, :])
mbathy = nemo_mesh.sliced(nemo_mesh["mbathy"][0, :, :])
tmp2 = numpy.where(mbathy > 0, hdepw, 0)
abfile.write_bathymetry("bathy", 1, tmp2, 0.)
# Total depth calc
hdept = nemo_mesh.sliced(nemo_mesh["hdept"][0, :, :])
hdepw = nemo_mesh.sliced(nemo_mesh["hdepw"][0, :, :])
e3t_ps = nemo_mesh.sliced(nemo_mesh["e3t_ps"][0, :, :])
e3w_ps = nemo_mesh.sliced(nemo_mesh["e3w_ps"][0, :, :])
nav_lev = nemo_mesh["nav_lev"][:]
gdept_0 = nemo_mesh["gdept_0"][0, :]
gdepw_0 = nemo_mesh["gdepw_0"][0, :]
e3t_0 = nemo_mesh["e3t_0"][0, :]
tmp1 = numpy.where(mbathy > 0, gdepw_0[mbathy - 1] + e3t_ps, 0)
itest = 0
jtest = 300
# KAL - my conclusions (Double check with Gilles)
# hdepw = Total water depth in t-cell
# gdepw_0[mbathy-1] Gives Water depth of full vertical cells 1 up to and including cell mbathy-1
# e3t_ps Is the fraction of cell "mbathy" that is used in the calculations'
# hdepw = gdepw_0[mbathy-1] + e3t_ps
# Diag plot of depths
figure = matplotlib.pyplot.figure(figsize=(8, 8))
ax = figure.add_subplot(111)
ax.hold(True)
ax.plot(nav_lev, "r-", label="nav_lev")
ax.plot(gdept_0, "b.", label="gdept_0")
ax.plot(gdepw_0, "g.", label="gdepw_0")
ax.plot(numpy.arange(nav_lev.size),
numpy.ones((nav_lev.size, )) * hdepw[jtest, itest],
"c",
lw=2,
label="hdepw")
ax.plot(numpy.arange(nav_lev.size),
numpy.ones((nav_lev.size, )) * hdept[jtest, itest],
"m",
lw=2,
label="hdept")
ax.plot(numpy.arange(nav_lev.size),
numpy.ones((nav_lev.size, )) * gdepw_0[mbathy[jtest, itest] - 1] +
e3t_ps[jtest, itest],
"m.",
lw=2,
label="gdepw_0[mbathy[jtest,itest]-1]+e3t_ps")
ax.legend()
ax.set_ylim(hdepw[jtest, itest] - 600, hdepw[jtest, itest] + 600)
figure.canvas.print_figure("tst.png")
# Diag plot of depths
figure = matplotlib.pyplot.figure(figsize=(8, 8))
ax = figure.add_subplot(111)
P = ax.pcolormesh(tmp2 - tmp1, vmin=-1e-2, vmax=1e-2)
figure.colorbar(P)
figure.canvas.print_figure("tst2.png")
def main(infile,blo,bla,shapiro_passes,resolution,cutoff,input_bathymetry) :
gfile=abfile.ABFileGrid("regional.grid","r")
plon=gfile.read_field("plon")
plat=gfile.read_field("plat")
scpx=gfile.read_field("scpx")
scpy=gfile.read_field("scpy")
width=numpy.median(scpx)/1000.0
logger.info("Grid median resolution:%8.2f km "%(width))
# give the bathy directory here
if input_bathymetry=="GEBCO_2021":
bathyDir="/cluster/projects/nn2993k/ModelInput/bathymetry/GEBCO_2021/"
# GEBCO only - TODO: move logic to gebco set
if resolution is None :
if width > 20 :
dfile=bathyDir+"GEBCO_2021_2D_median20km.nc"
elif width > 8 :
dfile=bathyDir+"GEBCO_2021_2D_median8km.nc"
elif width > 4 :
dfile=bathyDir+"GEBCO_2021_2D_median4km.nc"
elif width > 2 :
dfile=bathyDir+"GEBCO_2021_2D_median2km.nc"
else :
dfile=bathyDir+"GEBCO_2021_sub_ice_topo.nc"
logger.info ("Source resolution not set - choosing datafile %s"%dfile)
else :
dfile=bathyDir+"GEBCO_2021_2D_median%dkm.nc" % resolution
print(dfile)
logger.info ("Source resolution set to %d km - trying to use datafile %s"%(resolution,dfile))
elif input_bathymetry=="GEBCO_2014":
bathyDir="/cluster/projects/nn2993k/ModelInput/bathymetry/GEBCO_2014/"
# GEBCO only - TODO: move logic to gebco set
if resolution is None :
if width > 20 :
dfile=bathyDir+"GEBCO_2014_2D_median20km.nc"
elif width > 8 :
dfile=bathyDir+"GEBCO_2014_2D_median8km.nc"
elif width > 4 :
dfile=bathyDir+"GEBCO_2014_2D_median4km.nc"
else :
dfile=bathyDir+"GEBCO_2014_2D.nc"
logger.info ("Source resolution not set - choosing datafile %s"%dfile)
else :
dfile=bathyDir+"GEBCO_2014_2D_median%dkm.nc" % resolution
logger.info ("Source resolution set to %d km - trying to use datafile %s"%(resolution,dfile))
else:
print("Input grid not defined, cuttetn opotion GEBCO_2014 and GEBCO_2021")
gebco = modeltools.forcing.bathy.GEBCO(filename=dfile)
w2=gebco.regrid(plon,plat,width=width)
print(w2.min(),w2.max())
# Run shapiro filter on interpolated data to remove 2 DeltaX noise
w3=numpy.copy(w2)
for i in range(shapiro_passes):
logger.info("Shapiro filter ... pass %d"%(i+1))
w3=modeltools.tools.shapiro_filter(w3,threshold=cutoff)
#print w3.min(),w3.max()
# Modify basin
w4=numpy.copy(-w3)
it=1
while it==1 or numpy.count_nonzero(w4-w4old) > 0 :
w4old = numpy.copy(w4)
logger.info("Basin modifications ... pass %d"%(it))
w4=modeltools.tools.remove_isolated_basins(plon,plat,w4,blo,bla,threshold=cutoff)
w4=modeltools.tools.remove_islets(w4,threshold=cutoff)
w4=modeltools.tools.remove_one_neighbour_cells(w4,threshold=cutoff)
logger.info("Modified %d points "%numpy.count_nonzero(w4-w4old) )
it+=1
w5=numpy.copy(w4)
#print w5.min(),w5.max()
# Mask data where depth below threshold
w5=numpy.ma.masked_where(w5<=cutoff,w5)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to file hycom_bathymetry.nc")
ncid = netCDF4.Dataset("hycom_bathymetry.nc","w")
ncid.createDimension("idm",w5.shape[1])
ncid.createDimension("jdm",w5.shape[0])
ncid.createVariable("lon","f8",("jdm","idm"))
ncid.createVariable("lat","f8",("jdm","idm"))
ncid.createVariable("h_1","f8",("jdm","idm"))
ncid.createVariable("h_2","f8",("jdm","idm"))
ncid.createVariable("h_3","f8",("jdm","idm"))
ncid.variables["lon"][:]=plon
ncid.variables["lat"][:]=plat
ncid.variables["h_1"][:]=w2
ncid.variables["h_2"][:]=w3
ncid.variables["h_3"][:]=w5
ncid.close()
# Print to HYCOM and CICE bathymetry files
abfile.write_bathymetry("bathy",1,w5,cutoff)
# Show some grid statistics
sx = (w2[1:,:-1]-w2[:-1,:-1])/scpy[1:,:-1]
sy = (w2[:-1,1:]-w2[:-1,:-1])/scpx[:-1,1:]
grad = sx + sy
slopefac=numpy.sqrt(sx**2+sy**2)
logger.info("Maximum slope factor after interpolation =%.4f"%slopefac.max())
sx = (w5[1:,:-1]-w5[:-1,:-1])/scpy[1:,:-1]
sy = (w5[:-1,1:]-w5[:-1,:-1])/scpx[:-1,1:]
grad = sx + sy
slopefac=numpy.sqrt(sx**2+sy**2)
logger.info("Maximum slope factor after smoothing =%.4f"%slopefac.max())
figure = matplotlib.pyplot.figure(figsize=(8,8))
ax=figure.add_subplot(111)
P=ax.pcolor(slopefac)
figure.colorbar(P,norm=matplotlib.colors.LogNorm(vmin=w5.min(), vmax=w5.max()))
#ax.contour(w5)#,[-10.,-100.,-500.,-1000.])
#ax.set_title("Slope fac in color, depth contours in black")
logger.info("Slope factor in slopefac.png")
figure.canvas.print_figure("slopefac.png")
def main(infile_coarse,infile_fine,ncells_linear=20,ncells_exact=3) :
bathy_threshold=0. # TODO
# Read plon,plat
gfile=abfile.ABFileGrid("regional.grid","r")
plon=gfile.read_field("plon")
plat=gfile.read_field("plat")
gfile.close()
# Read input bathymetry - fine version
bfile=abfile.ABFileBathy(infile_fine,"r",idm=gfile.idm,jdm=gfile.jdm)
fine_depth_m=bfile.read_field("depth")
fine_depth_m=numpy.ma.masked_where(fine_depth_m<=bathy_threshold,fine_depth_m)
fine_depth=numpy.ma.filled(fine_depth_m,bathy_threshold)
bfile.close()
# Read input bathymetry - coarse version
bfile=abfile.ABFileBathy(infile_coarse,"r",idm=gfile.idm,jdm=gfile.jdm)
coarse_depth_m=bfile.read_field("depth")
coarse_depth_m=numpy.ma.masked_where(coarse_depth_m<=bathy_threshold,coarse_depth_m)
coarse_depth=numpy.ma.filled(coarse_depth_m,bathy_threshold)
bfile.close()
# create relaxation mask (rmu)
tmp=numpy.linspace(0.,1.,ncells_linear)
tmp=numpy.concatenate((numpy.zeros((ncells_exact,)),tmp)) # ie: hree first cells will match outer bathymetry
ncells=ncells_linear+ncells_exact
rmu=numpy.ones(coarse_depth.shape)
rmu[:,0:ncells] = numpy.minimum(tmp,rmu[:,0:ncells])
rmu[0:ncells,:] = numpy.minimum(tmp,rmu[0:ncells,:].transpose()).transpose()
rmu[:,-ncells:] = numpy.minimum(tmp[::-1],rmu[:,-ncells:])
rmu[-ncells:,:] = numpy.minimum(tmp[::-1],rmu[-ncells:,:].transpose()).transpose()
## Only allow points where both models are defined in the boundaruy
rmumask=fine_depth_m.mask
rmumask[:,0:ncells] = numpy.logical_or(rmumask[:,0:ncells],coarse_depth_m.mask[:,0:ncells])
rmumask[0:ncells,:] = numpy.logical_or(rmumask[0:ncells,:],coarse_depth_m.mask[0:ncells,:])
rmumask[:,-ncells:] = numpy.logical_or(rmumask[:,-ncells:],coarse_depth_m.mask[:,-ncells:])
rmumask[-ncells:,:] = numpy.logical_or(rmumask[-ncells:,:],coarse_depth_m.mask[-ncells:,:])
figure = matplotlib.pyplot.figure(figsize=(8,8))
ax=figure.add_subplot(111)
P=ax.pcolormesh(rmu)
figure.colorbar(P)#,norm=matplotlib.colors.LogNorm(vmin=mask.min(), vmax=mask.max()))
figure.canvas.print_figure("tst.png")
# Modify bathy in mask region
newbathy = (1.-rmu) * coarse_depth + rmu * fine_depth
newbathy[rmumask] = bathy_threshold
newbathy[:,0]=bathy_threshold
newbathy[:,-1]=bathy_threshold
newbathy[0,:]=bathy_threshold
newbathy[-1,:]=bathy_threshold
#print newbathy.min(),newbathy.max()
# Mask data where depth below threshold
newbathy_m=numpy.ma.masked_where(newbathy<=bathy_threshold,newbathy)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to diagnostic file bathy_merged.nc")
ncid = netCDF4.Dataset("bathy_merged.nc","w")
ncid.createDimension("idm",newbathy.shape[1])
ncid.createDimension("jdm",newbathy.shape[0])
ncid.createVariable("lon","f8",("jdm","idm"))
ncid.createVariable("lat","f8",("jdm","idm"))
ncid.createVariable("coarse","f8",("jdm","idm"))
ncid.createVariable("coarse_masked","f8",("jdm","idm"))
ncid.createVariable("fine","f8",("jdm","idm"))
ncid.createVariable("fine_masked","f8",("jdm","idm"))
ncid.createVariable("final","f8",("jdm","idm"))
ncid.createVariable("final_masked","f8",("jdm","idm"))
ncid.createVariable("rmu","f8",("jdm","idm"))
ncid.createVariable("modified","f8",("jdm","idm"))
ncid.variables["lon"][:]=plon
ncid.variables["lat"][:]=plat
ncid.variables["coarse"][:]=coarse_depth
ncid.variables["coarse_masked"][:]=coarse_depth_m
ncid.variables["fine"][:]=fine_depth
ncid.variables["fine_masked"][:]=fine_depth_m
ncid.variables["final"][:]=newbathy
ncid.variables["final_masked"][:]=newbathy_m
modmask=newbathy-fine_depth
ncid.variables["modified"][:] = modmask
ncid.variables["rmu"][:] = rmu
ncid.close()
logger.info("Writing bathymetry plot to file newbathy.png")
figure = matplotlib.pyplot.figure(figsize=(8,8))
ax=figure.add_subplot(111)
P=ax.pcolormesh(newbathy)
figure.colorbar(P,norm=matplotlib.colors.LogNorm(vmin=newbathy.min(), vmax=newbathy.max()))
I,J=numpy.where(numpy.abs(modmask)>.1)
ax.scatter(J,I,20,"r")
figure.canvas.print_figure("newbathy.png")
# Print to HYCOM
abfile.write_bathymetry("MERGED",0,newbathy,bathy_threshold)
def main(intopo):
bathy_threshold = 0. # TODO
# Read plon,plat
gfile = abfile.ABFileGrid("regional.grid", "r")
plon = gfile.read_field("plon")
plat = gfile.read_field("plat")
gfile.close()
# Read input bathymetri
bfile = abfile.ABFileBathy(intopo,
"r",
idm=gfile.idm,
jdm=gfile.jdm,
mask=True)
in_depth_m = bfile.read_field("depth")
bfile.close()
# Modify basin
in_depth = numpy.ma.filled(in_depth_m, bathy_threshold)
depth = numpy.copy(in_depth)
# Open stdin
logger.info("Reading input data")
for line in sys.stdin.readlines():
logger.info(line.strip())
ifirst, ilast, jfirst, jlast, d = line.split()
ifirst = int(ifirst) - 1 # Fortran indexing -> C
ilast = int(ilast) # Fortran indexing -> C
jfirst = int(jfirst) - 1 # Fortran indexing -> C
jlast = int(jlast) # Fortran indexing -> C
d = float(d)
logger.info(
"ifirst=%5d, ilast=%5d, jfirst=%5d, jlast=%5d : depth=%6.2f" %
(ifirst, ilast, jfirst, jlast, d))
depth[jfirst:jlast, ifirst:ilast] = d
# Mask data where depth below thresholddata = sys.stdin.readlines()
depth_m = numpy.ma.masked_where(depth <= bathy_threshold, depth)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to file bathy_modify.nc")
ncid = netCDF4.Dataset("bathy_modify.nc", "w")
ncid.createDimension("idm", depth.shape[1])
ncid.createDimension("jdm", depth.shape[0])
ncid.createVariable("lon", "f8", ("jdm", "idm"))
ncid.createVariable("lat", "f8", ("jdm", "idm"))
ncid.createVariable("old", "f8", ("jdm", "idm"))
ncid.createVariable("old_masked", "f8", ("jdm", "idm"))
ncid.createVariable("new", "f8", ("jdm", "idm"))
ncid.createVariable("new_masked", "f8", ("jdm", "idm"))
ncid.createVariable("modified", "i4", ("jdm", "idm"))
ncid.variables["lon"][:] = plon
ncid.variables["lat"][:] = plat
ncid.variables["old"][:] = in_depth
ncid.variables["old_masked"][:] = in_depth_m
ncid.variables["new"][:] = depth
ncid.variables["new_masked"][:] = depth_m
modmask = numpy.abs(in_depth - depth) > .1
ncid.variables["modified"][:] = modmask.astype("i4")
ncid.close()
# Print to HYCOM and CICE bathymetry files
abfile.write_bathymetry("MODIFIED", 0, depth, bathy_threshold)
def main(infile,
blo,
bla,
remove_isolated_basins=True,
remove_one_neighbour_cells=True,
remove_islets=True):
bathy_threshold = 0. # TODO
# Read plon,plat
gfile = abfile.ABFileGrid("regional.grid", "r")
plon = gfile.read_field("plon")
plat = gfile.read_field("plat")
gfile.close()
# Read input bathymetri
bfile = abfile.ABFileBathy(infile,
"r",
idm=gfile.idm,
jdm=gfile.jdm,
mask=True)
in_depth_m = bfile.read_field("depth")
print "in_depth_m type, min, max:", type(
in_depth_m), in_depth_m.min(), in_depth_m.max()
bfile.close()
# Modify basin
in_depth = numpy.ma.filled(in_depth_m, bathy_threshold)
depth = numpy.copy(in_depth)
print "depth min max", depth.min(), depth.max()
it = 1
while it == 1 or numpy.count_nonzero(numpy.abs(depth - depth_old)) > 0:
depth_old = numpy.copy(depth)
logger.info("Basin modifications ... pass %d" % (it))
if remove_isolated_basins:
depth = modeltools.tools.remove_isolated_basins(
plon, plat, depth, blo, bla, threshold=bathy_threshold)
if remove_islets:
depth = modeltools.tools.remove_islets(depth,
threshold=bathy_threshold)
if remove_one_neighbour_cells:
depth = modeltools.tools.remove_one_neighbour_cells(
depth, threshold=bathy_threshold)
logger.info("Modified %d points " %
numpy.count_nonzero(depth - depth_old))
it += 1
w5 = numpy.copy(depth)
w5[:, 0] = bathy_threshold
w5[:, -1] = bathy_threshold
w5[0, :] = bathy_threshold
w5[-1, :] = bathy_threshold
print "w5 type min max", type(w5), w5.min(), w5.max()
# Mask data where depth below threshold
w5_m = numpy.ma.masked_where(w5 <= bathy_threshold, w5)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to file bathy_consistency.nc")
ncid = netCDF4.Dataset("bathy_consistency.nc", "w")
ncid.createDimension("idm", w5.shape[1])
ncid.createDimension("jdm", w5.shape[0])
ncid.createVariable("lon", "f8", ("jdm", "idm"))
ncid.createVariable("lat", "f8", ("jdm", "idm"))
ncid.createVariable("old", "f8", ("jdm", "idm"))
ncid.createVariable("old_masked", "f8", ("jdm", "idm"))
ncid.createVariable("new", "f8", ("jdm", "idm"))
ncid.createVariable("new_masked", "f8", ("jdm", "idm"))
ncid.createVariable("modified", "i4", ("jdm", "idm"))
ncid.variables["lon"][:] = plon
ncid.variables["lat"][:] = plat
ncid.variables["old"][:] = in_depth
ncid.variables["old_masked"][:] = in_depth_m
ncid.variables["new"][:] = w5
ncid.variables["new_masked"][:] = w5_m
modmask = numpy.abs(in_depth - depth) > .1
ncid.variables["modified"][:] = modmask.astype("i4")
ncid.close()
logger.info("Writing bathymetry plot to file newbathy.png")
figure = matplotlib.pyplot.figure(figsize=(8, 8))
ax = figure.add_subplot(111)
P = ax.pcolormesh(w5_m)
figure.colorbar(P,
norm=matplotlib.colors.LogNorm(vmin=w5_m.min(),
vmax=w5_m.max()))
I, J = numpy.where(numpy.abs(modmask) > .1)
ax.scatter(J, I, 20, "r")
figure.canvas.print_figure("newbathy.png")
# Print to HYCOM and CICE bathymetry files
abfile.write_bathymetry("CONSISTENT", 0, w5, bathy_threshold)
def main(intopo) :
bathy_threshold=0. # TODO
# Read plon,plat
gfile=abfile.ABFileGrid("regional.grid","r")
plon=gfile.read_field("plon")
plat=gfile.read_field("plat")
gfile.close()
# Read input bathymetri
bfile=abfile.ABFileBathy(intopo,"r",idm=gfile.idm,jdm=gfile.jdm,mask=True)
in_depth_m=bfile.read_field("depth")
bfile.close()
# Modify basin
in_depth=numpy.ma.filled(in_depth_m,bathy_threshold)
depth=numpy.copy(in_depth)
# Open stdin
logger.info("Reading input data")
for line in sys.stdin.readlines() :
logger.info(line.strip())
ifirst,ilast,jfirst,jlast,d = line.split()
ifirst=int(ifirst)-1 # Fortran indexing -> C
ilast =int(ilast) # Fortran indexing -> C
jfirst=int(jfirst)-1 # Fortran indexing -> C
jlast =int(jlast) # Fortran indexing -> C
d =float(d)
logger.info("ifirst=%5d, ilast=%5d, jfirst=%5d, jlast=%5d : depth=%6.2f"%(ifirst,ilast,jfirst,jlast,d))
depth[jfirst:jlast,ifirst:ilast]=d
# Mask data where depth below thresholddata = sys.stdin.readlines()
depth_m=numpy.ma.masked_where(depth<=bathy_threshold,depth)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to file bathy_modify.nc")
ncid = netCDF4.Dataset("bathy_modify.nc","w")
ncid.createDimension("idm",depth.shape[1])
ncid.createDimension("jdm",depth.shape[0])
ncid.createVariable("lon","f8",("jdm","idm"))
ncid.createVariable("lat","f8",("jdm","idm"))
ncid.createVariable("old","f8",("jdm","idm"))
ncid.createVariable("old_masked","f8",("jdm","idm"))
ncid.createVariable("new","f8",("jdm","idm"))
ncid.createVariable("new_masked","f8",("jdm","idm"))
ncid.createVariable("modified","i4",("jdm","idm"))
ncid.variables["lon"][:]=plon
ncid.variables["lat"][:]=plat
ncid.variables["old"][:]=in_depth
ncid.variables["old_masked"][:]=in_depth_m
ncid.variables["new"][:]=depth
ncid.variables["new_masked"][:]=depth_m
modmask=numpy.abs(in_depth-depth)>.1
ncid.variables["modified"][:]=modmask.astype("i4")
ncid.close()
# Print to HYCOM and CICE bathymetry files
abfile.write_bathymetry("MODIFIED",0,depth,bathy_threshold)
def main(infile,blo,bla,remove_isolated_basins=True,remove_one_neighbour_cells=True,remove_islets=True) :
bathy_threshold=0. # TODO
# Read plon,plat
gfile=abfile.ABFileGrid("regional.grid","r")
plon=gfile.read_field("plon")
plat=gfile.read_field("plat")
gfile.close()
# Read input bathymetri
bfile=abfile.ABFileBathy(infile,"r",idm=gfile.idm,jdm=gfile.jdm,mask=True)
in_depth_m=bfile.read_field("depth")
print "in_depth_m type, min, max:",type(in_depth_m),in_depth_m.min(),in_depth_m.max()
bfile.close()
# Modify basin
in_depth=numpy.ma.filled(in_depth_m,bathy_threshold)
depth=numpy.copy(in_depth)
print "depth min max",depth.min(),depth.max()
it=1
while it==1 or numpy.count_nonzero(numpy.abs(depth-depth_old)) > 0 :
depth_old = numpy.copy(depth)
logger.info("Basin modifications ... pass %d"%(it))
if remove_isolated_basins : depth=modeltools.tools.remove_isolated_basins(plon,plat,depth,blo,bla,threshold=bathy_threshold)
if remove_islets : depth=modeltools.tools.remove_islets(depth,threshold=bathy_threshold)
if remove_one_neighbour_cells : depth=modeltools.tools.remove_one_neighbour_cells(depth,threshold=bathy_threshold)
logger.info("Modified %d points "%numpy.count_nonzero(depth-depth_old) )
it+=1
w5=numpy.copy(depth)
w5[:,0]=bathy_threshold
w5[:,-1]=bathy_threshold
w5[0,:]=bathy_threshold
w5[-1,:]=bathy_threshold
print "w5 type min max",type(w5),w5.min(),w5.max()
# Mask data where depth below threshold
w5_m=numpy.ma.masked_where(w5<=bathy_threshold,w5)
# Create netcdf file with all stages for analysis
logger.info("Writing bathymetry to file bathy_consistency.nc")
ncid = netCDF4.Dataset("bathy_consistency.nc","w")
ncid.createDimension("idm",w5.shape[1])
ncid.createDimension("jdm",w5.shape[0])
ncid.createVariable("lon","f8",("jdm","idm"))
ncid.createVariable("lat","f8",("jdm","idm"))
ncid.createVariable("old","f8",("jdm","idm"))
ncid.createVariable("old_masked","f8",("jdm","idm"))
ncid.createVariable("new","f8",("jdm","idm"))
ncid.createVariable("new_masked","f8",("jdm","idm"))
ncid.createVariable("modified","i4",("jdm","idm"))
ncid.variables["lon"][:]=plon
ncid.variables["lat"][:]=plat
ncid.variables["old"][:]=in_depth
ncid.variables["old_masked"][:]=in_depth_m
ncid.variables["new"][:]=w5
ncid.variables["new_masked"][:]=w5_m
modmask=numpy.abs(in_depth-depth)>.1
ncid.variables["modified"][:]=modmask.astype("i4")
ncid.close()
logger.info("Writing bathymetry plot to file newbathy.png")
figure = matplotlib.pyplot.figure(figsize=(8,8))
ax=figure.add_subplot(111)
P=ax.pcolormesh(w5_m)
figure.colorbar(P,norm=matplotlib.colors.LogNorm(vmin=w5_m.min(), vmax=w5_m.max()))
I,J=numpy.where(numpy.abs(modmask)>.1)
ax.scatter(J,I,20,"r")
figure.canvas.print_figure("newbathy.png")
# Print to HYCOM and CICE bathymetry files
abfile.write_bathymetry("CONSISTENT",0,w5,bathy_threshold)
def main(startdate, enddate, first_j=0):
soda_template = "/work/shared/nersc/msc/SODA/3.3.1/monthly/soda3.3.1_mn_ocean_reg_%Y.nc"
# open blkdat.input. Get nesting frequency
bp = modeltools.hycom.BlkdatParser("blkdat.input")
nestfq = bp["nestfq"]
bnstfq = bp["bnstfq"]
# Read soda-grid and topo from first file
fid = netCDF4.Dataset(startdate.strftime(soda_template), "r")
depth = fid["depth"][:]
soda_to_regional_grid(fid)
# Get bathymetry. Set to 0 wherever salinit in top layer is undefined.
bathy = numpy.zeros(fid["salt"].shape[-2:])
for k in range(depth.size):
bathy[~numpy.squeeze(fid["salt"][0, k, :, :].mask)] = depth[k]
abfile.write_bathymetry("SODA", 22, bathy, 0.)
fid.close()
# TODO:
ip = bathy == 0.
iu = bathy == 0.
iv = bathy == 0.
onem = 9806
#if mean_file :
# fnametemplate_out="archm.%Y_%j_%H"
#else :
hycom_template = "archv.%Y_%j_%H"
# Loop over nestfq, bnstfq.
deltat = enddate - startdate
dsec = deltat.days * 86400 + deltat.seconds
baroclinic_nest_times = [
startdate + datetime.timedelta(seconds=s)
for s in numpy.arange(0, dsec, nestfq * 86400)
]
barotropic_nest_times = [
startdate + datetime.timedelta(seconds=s)
for s in numpy.arange(0, dsec, bnstfq * 86400)
]
tmp = sorted(set(barotropic_nest_times + baroclinic_nest_times))
for dt in tmp:
logger.info("Processing time %s" % str(dt))
# Get "mid-month" dates
if dt.day >= 15:
nm = 1 + dt.month % 12
ny = dt.year + dt.month / 12
mm0 = datetime.datetime(dt.year, dt.month, 15, 0, 0, 0)
mm1 = datetime.datetime(ny, nm, 15, 0, 0, 0)
else:
lm = 1 + (12 + dt.month - 2) % 12
ly = dt.year - lm / 12
print dt.month, lm, ly
mm0 = datetime.datetime(ly, lm, 15, 0, 0, 0)
mm1 = datetime.datetime(dt.year, dt.month, 15, 0, 0, 0)
# Linear interpolation weights
deltat = mm1 - mm0
deltat = deltat.days + deltat.seconds / 86400.
w1 = dt - mm0
w1 = w1.days + w1.seconds / 86400.
w1 = w1 / deltat
w0 = 1. - w1
flnm0 = mm0.strftime(soda_template)
flnm1 = mm1.strftime(soda_template)
logger.info("Time %s, file %s at %s(w=%.4f) , file %s at %s(w=%.4f)" %
(str(dt), flnm0, str(mm0), w0, flnm1, str(mm1), w1))
# Open files
# TODO: reuse pointers/fields
fid0 = netCDF4.Dataset(flnm0, "r")
fid1 = netCDF4.Dataset(flnm1, "r")
# Calculate temperature, velocity
temp = w0 * fid0["temp"][0, :, :, :] + w1 * fid1["temp"][0, :, :, :]
salt = w0 * fid0["salt"][0, :, :, :] + w1 * fid1["salt"][0, :, :, :]
utot = w0 * fid0["u"][0, :, :, :] + w1 * fid1["u"][0, :, :, :]
vtot = w0 * fid0["v"][0, :, :, :] + w1 * fid1["v"][0, :, :, :]
#NB: No checks for missing values yet !
ubaro = numpy.sum(utot, 0)
vbaro = numpy.sum(vtot, 0)
u = utot - ubaro
v = vtot - vbaro
# 2D vars
anompb = w0 * fid0["anompb"][0, :, :] + w1 * fid1["anompb"][0, :, :]
ssh = w0 * fid0["ssh"][0, :, :] + w1 * fid1["ssh"][0, :, :]
salflx = w0 * fid0["salt_flux_total"][
0, :, :] + w1 * fid1["salt_flux_total"][0, :, :]
surflx = w0 * fid0["net_heating"][
0, :, :] + w1 * fid1["salt_flux_total"][0, :, :]
montg1 = numpy.zeros(ssh.shape)
# Write to abfile
outfile = abfile.ABFileArchv(dt.strftime(hycom_template),
"w",
iexpt=10,
iversn=22,
yrflag=3)
logger.info("Writing 2D variables")
outfile.write_field(montg1, ip, "montg1", 0, 0, 1, 0)
outfile.write_field(ssh, ip, "srfhgt", 0, 0, 0, 0)
outfile.write_field(surflx, ip, "surflx", 0, 0, 0, 0)
outfile.write_field(salflx, ip, "salflx", 0, 0, 0, 0)
outfile.write_field(numpy.zeros(ssh.shape), ip, "bl_dpth", 0, 0, 0, 0)
outfile.write_field(numpy.zeros(ssh.shape), ip, "mix_dpth", 0, 0, 0, 0)
outfile.write_field(ubaro, iu, "u_btrop", 0, 0, 0, 0)
outfile.write_field(vbaro, iv, "v_btrop", 0, 0, 0, 0)
#outfile.close() ; raise NameError,"test"
for k in numpy.arange(u.shape[0]):
if k % 10 == 0:
logger.info("Writing 3D variables, level %d of %d" %
(k + 1, u.shape[0]))
if k == 0:
dtl = depth[0] * numpy.where(bathy >= depth[k], 1, 0)
else:
dtl = (depth[k] - depth[k - 1]) * numpy.where(
bathy >= depth[k], 1, 0)
print dtl.min(), dtl.max()
templ = temp[k, :, :]
saltl = salt[k, :, :]
# Set to layer above if undefined
templ[dtl <= 0.] = 20.
saltl[dtl <= 0.] = 35.
outfile.write_field(u[k, :, :], iu, "u-vel.", 0, 0, k + 1, 0)
outfile.write_field(v[k, :, :], iv, "v-vel.", 0, 0, k + 1, 0)
outfile.write_field(dtl * onem, ip, "thknss", 0, 0, k + 1, 0)
outfile.write_field(saltl, ip, "salin", 0, 0, k + 1, 0)
outfile.write_field(templ, ip, "temp", 0, 0, k + 1, 0)
oldsaltl = saltl
oldtempl = templ
# TODO: reuse pointers/fields
outfile.close()
fid0.close()
fid1.close()
raise NameError, "check vals"
raise NameError, "test"
itest = 1
jtest = 200
logger.info("Mean file:%s" % str(mean_file))
logger.info("Output file template:%s" % str(fnametemplate))
# Write regional files
nemo_mesh_to_hycom.main(filemesh, first_j=first_j)
nemo_mesh = modeltools.nemo.NemoMesh(filemesh, first_j=first_j)
#ncidmesh=netCDF4.Dataset(filemesh,"r")
gdept = nemo_mesh["gdept_0"][0, :] # Depth of t points
gdepw = nemo_mesh["gdepw_0"][0, :] # Depth of w points
e3t_ps = nemo_mesh.sliced(
nemo_mesh["e3t_ps"][0, :, :]) # Partial steps of t cell
e3w_ps = nemo_mesh.sliced(
nemo_mesh["e3w_ps"][0, :, :]) # Partial steps of w cell
mbathy = nemo_mesh.sliced(nemo_mesh["mbathy"][0, :, :]) # bathy index
hdepw = nemo_mesh.sliced(
nemo_mesh["hdepw"][0, :, :]) # Total depth of w points
mbathy = mbathy - 1 # python indexing starts from 0
nlev = gdept.size
mbathy_u, e3u_ps, depthu = nemo_mesh.depth_u_points()
mbathy_v, e3v_ps, depthv = nemo_mesh.depth_v_points()
#
mbathy_u = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(mbathy_u))
e3u_ps = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(e3u_ps))
depthu = nemo_mesh.sliced(nemo_mesh.u_to_hycom_u(depthu))
#
mbathy_v = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(mbathy_v))
e3v_ps = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(e3v_ps))
depthv = nemo_mesh.sliced(nemo_mesh.v_to_hycom_v(depthv))
# Thickness of t layers (NB: 1 less than gdepw dimension)
dt = gdepw[1:] - gdepw[:-1]
# Loop over input files. All must be in same directory
for file2d in grid2dfiles:
# See if actually a grid2D file
dirname = os.path.dirname(file2d)
m = re.match("(.*_)(grid2D)(_.*\.nc)", os.path.basename(file2d))
if not m:
msg = "File %s is not a grid2D file, aborting" % file2d
logger.error(msg)
raise ValueError, msg
# Construct remaining files
filet = os.path.join(dirname, m.group(1) + "gridT" + m.group(3))
files = os.path.join(dirname, m.group(1) + "gridS" + m.group(3))
fileu = os.path.join(dirname, m.group(1) + "gridU" + m.group(3))
filev = os.path.join(dirname, m.group(1) + "gridV" + m.group(3))
filew = os.path.join(dirname, m.group(1) + "gridW" + m.group(3))
fileice = os.path.join(dirname, m.group(1) + "icemod" + m.group(3))
logger.info("grid2D file: %s" % file2d)
# P-points
logger.info("gridS file: %s" % files)
logger.info("gridT file: %s" % filet)
ncids = netCDF4.Dataset(files, "r")
s = numpy.zeros((nlev, mbathy.shape[0], mbathy.shape[1]))
for k in range(nlev): # Dont include lowest layer
s[k, :, :] = nemo_mesh.sliced(ncids.variables["vosaline"][0,
k, :, :])
s = numpy.where(s < 1e30, s, 0.)
s = numpy.where(s == ncids.variables["vosaline"]._FillValue, 0., s)
ncidt = netCDF4.Dataset(filet, "r")
t = numpy.zeros((nlev, mbathy.shape[0], mbathy.shape[1]))
for k in range(nlev): # Dont include lowest layer
t[k, :, :] = nemo_mesh.sliced(ncidt.variables["votemper"][0,
k, :, :])
t = numpy.where(t == ncidt.variables["votemper"]._FillValue, 0., t)
t = numpy.where(t < 1e30, t, 0.)
# time from gridT file.
time = ncidt.variables["time_counter"][0]
tunit = ncidt.variables["time_counter"].units
tmp = cfunits.Units(tunit)
refy, refm, refd = (1958, 1, 1)
tmp2 = cfunits.Units("seconds since %d-%d-%d 00:00:00" %
(refy, refm, refd)) # Units from CF convention
tmp3 = cfunits.Units.conform(time, tmp,
tmp2) # Transform to new new unit
mydt = datetime.datetime(refy, refm,
refd, 0, 0, 0) + datetime.timedelta(
seconds=tmp3) # Then calculate dt. Phew!
# Read and calculculate U in hycom U-points.
logger.info("gridU file: %s" % fileu)
ncidu = netCDF4.Dataset(fileu, "r")
u = numpy.zeros((nlev, mbathy.shape[0], mbathy.shape[1]))
for k in range(nlev):
u[k, :, :] = nemo_mesh.sliced(
nemo_mesh.u_to_hycom_u(ncidu.variables["vozocrtx"][
0, k, :, :])) # Costly, make more efficient if needed
u = numpy.where(numpy.abs(u) < 1e10, u, 0.)
#Calculate barotropic and baroclinic u
usum = numpy.zeros(u.shape[-2:])
dsum = numpy.zeros(u.shape[-2:])
for k in range(u.shape[0] - 1): # Dont include lowest layer
# TODO: Mid-layer depths seem to be undefined - figure out why ...
logger.debug(
"k=%3d, u=%10.3g, mbathy_u[jtest,itest]=%3d,gdepw[k]=%8.2f, depthu[jtest,itest]=%8.2f"
% (k, u[k, jtest, itest], mbathy_u[jtest, itest], gdepw[k],
depthu[jtest, itest]))
J, I = numpy.where(mbathy_u > k)
usum[J, I] = usum[J, I] + u[k, J, I] * dt[k]
dsum[J, I] = dsum[J, I] + dt[k]
J, I = numpy.where(mbathy >= 0)
usum[J, I] = usum[J, I] + u[mbathy_u[J, I], J, I] * e3u_ps[J, I]
dsum[J, I] = dsum[J, I] + e3u_ps[J, I]
ubaro = numpy.where(dsum > 0.1, usum / dsum, 0.)
# Read and calculculate V in hycom V-points.
logger.info("gridV file: %s" % filev)
ncidv = netCDF4.Dataset(filev, "r")
v = numpy.zeros((nlev, mbathy.shape[0], mbathy.shape[1]))
for k in range(nlev):
v[k, :, :] = nemo_mesh.sliced(
nemo_mesh.v_to_hycom_v(ncidv.variables["vomecrty"][
0, k, :, :])) # Costly, make more efficient if needed
v = numpy.where(numpy.abs(v) < 1e10, v, 0.)
#Calculate barotropic and baroclinic v
vsum = numpy.zeros(v.shape[-2:])
dsum = numpy.zeros(v.shape[-2:])
for k in range(v.shape[0] - 1): # Dont include lowest layer
logger.debug(
"k=%3d, v=%10.3g, mbathy_v[jtest,itest]=%3d,gdepw[k]=%8.2f, depthv[jtest,itest]=%8.2f"
% (k, v[k, jtest, itest], mbathy_v[jtest, itest], gdepw[k],
depthv[jtest, itest]))
J, I = numpy.where(mbathy_v > k)
vsum[J, I] = vsum[J, I] + v[k, J, I] * dt[k]
dsum[J, I] = dsum[J, I] + dt[k]
J, I = numpy.where(mbathy_u >= 0)
vsum[J, I] = vsum[J, I] + v[mbathy_u[J, I], J, I] * e3v_ps[J, I]
dsum[J, I] = dsum[J, I] + e3v_ps[J, I]
vbaro = numpy.where(dsum > .1, vsum / dsum, 0.)
# Masks (land:True)
#print mbathy.min(),mbathy.max()
ip = mbathy == -1
iu = mbathy_u == -1
iv = mbathy_v == -1
#iu = nemo_mesh.periodic_i_shift_right(iu,1) # u: nemo in cell i is hycom in cell i+1
#iv = nemo_mesh.arctic_patch_shift_up(iu,1) # v: nemo in cell j is hycom in cell j+1
#ip = nemo_mesh.sliced(ip)
#iu = nemo_mesh.sliced(iu)
#iv = nemo_mesh.sliced(iv)
#raise NameError,"test"
# 2D data
ncid2d = netCDF4.Dataset(file2d, "r")
ssh = nemo_mesh.sliced(ncid2d.variables["sossheig"][0, :, :])
ssh = numpy.where(ssh == ncid2d.variables["sossheig"]._FillValue, 0.,
ssh)
ssh = numpy.where(ssh > 1e30, 0., ssh) # Hmmmmm
#bar_height = nemo_mesh.sliced(ncid2d.variables["sobarhei"][0,:,:] )
#dyn_height = nemo_mesh.sliced(ncid2d.variables["sodynhei"][0,:,:]
montg1 = ssh * 9.81 #* 1e-3 # Approx
logger.warning("TODO:montg pot calculation must be checked...")
# Write to abfile
outfile = abfile.ABFileArchv(
mydt.strftime(fnametemplate),
"w",
iexpt=10,
iversn=22,
yrflag=3,
)
logger.info("Writing 2D variables")
outfile.write_field(montg1, ip, "montg1", 0, 0, 1, 0)
outfile.write_field(ssh, ip, "srfhgt", 0, 0, 0, 0)
outfile.write_field(numpy.zeros(ssh.shape), ip, "surflx", 0, 0, 0,
0) # Not used
outfile.write_field(numpy.zeros(ssh.shape), ip, "salflx", 0, 0, 0,
0) # Not used
outfile.write_field(numpy.zeros(ssh.shape), ip, "bl_dpth", 0, 0, 0,
0) # Not used
outfile.write_field(numpy.zeros(ssh.shape), ip, "mix_dpth", 0, 0, 0,
0) # Not used
outfile.write_field(ubaro, iu, "u_btrop", 0, 0, 0,
0) # u: nemo in cell i is hycom in cell i+1
outfile.write_field(vbaro, iv, "v_btrop", 0, 0, 0,
0) # v: nemo in cell j is hycom in cell j+1
#outfile.close() ; raise NameError,"test"
for k in numpy.arange(u.shape[0]):
if k % 10 == 0:
logger.info("Writing 3D variables, level %d of %d" %
(k + 1, u.shape[0]))
ul = numpy.squeeze(u[k, :, :]) - ubaro # Baroclinic velocity
vl = numpy.squeeze(v[k, :, :]) - vbaro # Baroclinic velocity
sl = numpy.squeeze(s[k, :, :])
tl = numpy.squeeze(t[k, :, :])
# Layer thickness
dtl = numpy.zeros(ul.shape)
if k < u.shape[0] - 1:
J, I = numpy.where(mbathy > k)
dtl[J, I] = dt[k]
J, I = numpy.where(mbathy == k)
dtl[J, I] = e3t_ps[J, I]
else:
J, I = numpy.where(mbathy == k)
dtl[J, I] = e3t_ps[J, I]
onem = 9806.
outfile.write_field(ul, iu, "u-vel.", 0, 0, k + 1,
0) # u: nemo in cell i is hycom in cell i+1
outfile.write_field(vl, iv, "v-vel.", 0, 0, k + 1,
0) # v: nemo in cell j is hycom in cell j+1
outfile.write_field(dtl * onem, ip, "thknss", 0, 0, k + 1, 0)
outfile.write_field(sl, ip, "salin", 0, 0, k + 1, 0)
outfile.write_field(tl, ip, "temp", 0, 0, k + 1, 0)
# TODO: Process ice data
ncid2d.close()
ncids.close()
ncidt.close()
ncidu.close()
ncidv.close()
outfile.close()
logger.info("Finished writing %s.[ab] " % mydt.strftime(fnametemplate))
nemo_mesh = []