def open_file(myfile0,
filetype,
fieldname,
fieldlevel,
datetime1=None,
datetime2=None,
vector="",
idm=None,
jdm=None):
logger.info("Now processing %s" % myfile0)
m = re.match("(.*)\.[ab]", myfile0)
if m:
myfile = m.group(1)
else:
myfile = myfile0
ab2 = None
rdtimes = []
if filetype == "archive":
ab = abf.ABFileArchv(myfile, "r")
n_intloop = 1
elif filetype == "regional.depth":
ab = abf.ABFileBathy(myfile, "r", idm=idm, jdm=jdm)
n_intloop = 1
elif filetype == "forcing":
ab = abf.ABFileForcing(myfile, "r", idm=idm, jdm=jdm)
if vector:
file2 = myfile.replace(fieldname, vector)
logger.info("Opening file %s for vector component nr 2" % file2)
ab2 = abf.ABFileForcing(file2, "r", idm=idm, jdm=jdm)
if datetime1 is None or datetime2 is None:
raise NameError(
"datetime1 and datetime2 must be specified when plotting forcing files"
)
else:
iday1, ihour1, isec1 = modeltools.hycom.datetime_to_ordinal(
datetime1, 3)
rdtime1 = modeltools.hycom.dayfor(datetime1.year, iday1, ihour1, 3)
#
iday2, ihour2, isec2 = modeltools.hycom.datetime_to_ordinal(
datetime2, 3)
rdtime2 = modeltools.hycom.dayfor(datetime2.year, iday2, ihour2, 3)
rdtimes = sorted([
elem for elem in ab.field_times
if elem > rdtime1 and elem < rdtime2
])
n_intloop = len(rdtimes)
else:
raise NotImplementedError("Filetype %s not implemented" % filetype)
# Check that fieldname is actually in file
if fieldname not in ab.fieldnames:
logger.error("Unknown field %s at level %d" % (fieldname, fieldlevel))
logger.error("Available fields : %s" % (" ".join(ab.fieldnames)))
raise ValueError("Unknown field %s at level %d" %
(fieldname, fieldlevel))
return n_intloop, ab, ab2, rdtimes
def main(filemesh,grid2dfiles,first_j=0,mean_file=False,iexpt=10,iversn=22,yrflag=3,makegrid=None,bio_path=None) :
if mean_file :
fnametemplate="archm.%Y_%j_%H"
else :
fnametemplate="archv.%Y_%j_%H"
itest=1
jtest=200
gdept,gdepw,e3t_ps,e3w_ps,mbathy,hdepw,depth,plon,plat=read_mesh(filemesh)
if makegrid is not None:
logger.info("Making NEMO grid & bathy [ab] files ...")
make_grid(filemesh)
mbathy = mbathy -1 # python indexing starts from 0
nlev = gdept.size
mbathy_u,e3u_ps,depthu=depth_u_points(depth,mbathy,gdepw)
mbathy_v,e3v_ps,depthv=depth_v_points(depth,mbathy,gdepw)
#
mbathy_u=sliced(u_to_hycom_u(mbathy_u))
e3u_ps =sliced(u_to_hycom_u(e3u_ps ))
depthu =sliced(u_to_hycom_u(depthu ))
#
mbathy_v=sliced(v_to_hycom_v(mbathy_v))
e3v_ps =sliced(v_to_hycom_v(e3v_ps ))
depthv =sliced(v_to_hycom_v(depthv ))
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")
ncidt=netCDF4.Dataset(filet,"r")
# 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("hours 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
tmp3=int(numpy.round(tmp3))
mydt = datetime.datetime(refy,refm,refd,0,0,0) + datetime.timedelta(hours=tmp3) # Then calculate dt. Phew!
if bio_path:
jdm,idm=numpy.shape(plon)
points = numpy.transpose(((plat.flatten(),plon.flatten())))
delta = mydt.strftime( '%Y-%m-%d')
# filename format MERCATOR-BIO-14-2013-01-05-00
idx,biofname=search_biofile(bio_path,delta)
if idx >7:
msg="No available BIO file within a week difference with PHY"
logger.error(msg)
raise ValueError(msg)
logger.info("BIO file %s reading & interpolating to 1/12 deg grid cells ..."%biofname)
ncidb=netCDF4.Dataset(biofname,"r")
blon=ncidb.variables["longitude"][:];
blat=ncidb.variables["latitude"][:]
minblat=blat.min()
no3=ncidb.variables["NO3"][0,:,:,:];
no3[numpy.abs(no3)>1e+5]=numpy.nan
po4=ncidb.variables["PO4"][0,:,:,:]
si=ncidb.variables["Si"][0,:,:,:]
po4[numpy.abs(po4)>1e+5]=numpy.nan
si[numpy.abs(si)>1e+5]=numpy.nan
# TODO: The following piece will be optimised and replaced soon.
nz,ny,nx=no3.shape
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=no3;dummy[:,:,-1]=no3[:,:,-1]
no3=dummy
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=po4;dummy[:,:,-1]=po4[:,:,-1]
po4=dummy
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=si;dummy[:,:,-1]=si[:,:,-1]
si=dummy
dummy=numpy.zeros((nx+1))
dummy[:nx]=blon
blon=dummy
blon[-1]=-blon[0]
# TODO: Note that the coordinate files are for global configuration while
# the data file saved for latitude larger than 30. In the case you change your data file coordinate
# configuration you need to modify the following lines
bio_coordfile=bio_path[:-4]+"/GLOBAL_ANALYSIS_FORECAST_BIO_001_014_COORD/GLO-MFC_001_014_mask.nc"
biocrd=netCDF4.Dataset(bio_coordfile,"r")
blat2 = biocrd.variables['latitude'][:]
index=numpy.where(blat2>=minblat)[0]
depth_lev = biocrd.variables['deptho_lev'][index[0]:,:]
#
#
#
dummy=numpy.zeros((ny,nx+1))
dummy[:,:nx]=depth_lev;dummy[:,-1]=depth_lev[:,-1]
depth_lev=dummy
depth_lev[depth_lev>50]=0
depth_lev=depth_lev.astype('i')
dummy_no3=no3
dummy_po4=po4
dummy_si=si
for j in range(ny):
for i in range(nx):
dummy_no3[depth_lev[j,i]:nz-2,j,i]=no3[depth_lev[j,i]-1,j,i]
dummy_po4[depth_lev[j,i]:nz-2,j,i]=po4[depth_lev[j,i]-1,j,i]
dummy_si[depth_lev[j,i]:nz-2,j,i]=si[depth_lev[j,i]-1,j,i]
no3=dummy_no3
po4=dummy_po4
si=dummy_si
po4 = po4 * 106.0 * 12.01
si = si * 6.625 * 12.01
no3 = no3 * 6.625 * 12.01
# field_interpolator=FieldInterpolatorBilinear(blon,blat,plon.flatten(),plat.flatten())
# Read and calculculate U in hycom U-points.
logger.info("gridU, gridV, gridT & gridS file")
ncidu=netCDF4.Dataset(fileu,"r")
u=numpy.zeros((nlev,mbathy.shape[0],mbathy.shape[1]))
ncidv=netCDF4.Dataset(filev,"r")
v=numpy.zeros((nlev,mbathy.shape[0],mbathy.shape[1]))
udummy=ncidu.variables["vozocrtx"][:,:,:,:]
vdummy=ncidv.variables["vomecrty"][:,:,:,:]
tdummy=ncidt.variables["votemper"][:,:,:,:]
tdummy_fill=ncidt.variables["votemper"]._FillValue
sdummy=ncids.variables["vosaline"][:,:,:,:]
sdummy_fill=ncids.variables["vosaline"]._FillValue
for k in range(nlev) :
u[k,:,:] = sliced(u_to_hycom_u(udummy[0,k,:,:] )) # Costly, make more efficient if needed
v[k,:,:] = sliced(v_to_hycom_v(vdummy[0,k,:,:] )) # Costly, make more efficient if needed
u = numpy.where(numpy.abs(u)<1e10,u,0.)
v = numpy.where(numpy.abs(v)<1e10,v,0.)
logger.info("Calculate barotropic velocities ...")
#Calculate barotropic and baroclinic u
usum=numpy.zeros(u.shape[-2:])
dsumu=numpy.zeros(u.shape[-2:])
vsum=numpy.zeros(v.shape[-2:])
dsumv=numpy.zeros(v.shape[-2:])
for k in range(u.shape[0]-1) : # Dont include lowest layer
J,I = numpy.where(mbathy_u>k)
usum[J,I] = usum[J,I] + u[k,J,I]*dt[k]
dsumu[J,I] = dsumu[J,I] + dt[k]
J,I = numpy.where(mbathy_v>k)
vsum[J,I] = vsum[J,I] + v[k,J,I]*dt[k]
dsumv[J,I] = dsumv[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]
dsumu[J,I] = dsumu[J,I] + e3u_ps[J,I]
dsumu=numpy.where(abs(dsumu)<1e-2,0.05,dsumu)
ubaro=numpy.where(dsumu>0.1,usum/dsumu,0.)
J,I = numpy.where(mbathy_v>=0)
vsum[J,I] = vsum[J,I] + v[mbathy_v[J,I],J,I]*e3v_ps[J,I]
dsumv[J,I] = dsumv[J,I] + e3v_ps[J,I]
dsumv=numpy.where(abs(dsumv)<1e-2,0.05,dsumv)
vbaro=numpy.where(dsumv>.1,vsum/dsumv,0.)
fnametemplate="archv.%Y_%j"
deltat=datetime.datetime(refy,refm,refd,0,0,0)+datetime.timedelta(hours=tmp3)
oname=deltat.strftime(fnametemplate)+"_00"
# model day
refy, refm, refd=(1900,12,31)
model_day= deltat-datetime.datetime(refy,refm,refd,0,0,0)
model_day=model_day.days
logger.info("Model day in HYCOM is %s"%str(model_day))
# Masks (land:True)
if mask_method == 1 :
ip = mbathy == -1
iu = mbathy_u == -1
iv = mbathy_v == -1
else :
ip = depth == 0
iu = depthu == 0
iv = depthv == 0
# 2D data
ncid2d=netCDF4.Dataset(file2d,"r")
ssh = sliced(ncid2d.variables["sossheig"][0,:,:])
ssh = numpy.where(ssh==ncid2d.variables["sossheig"]._FillValue,0.,ssh)
ssh = numpy.where(ssh>1e10,0.,ssh*9.81) # NB: HYCOM srfhgt is in geopotential ...
montg1=numpy.zeros(ssh.shape)
# Write to abfile
outfile = abf.ABFileArchv("./data/"+oname,"w",iexpt=iexpt,iversn=iversn,yrflag=yrflag,)
logger.info("Writing 2D variables")
outfile.write_field(montg1, ip,"montg1" ,0,model_day,1,0)
outfile.write_field(ssh, ip,"srfhgt" ,0,model_day,0,0)
outfile.write_field(numpy.zeros(ssh.shape),ip,"surflx" ,0,model_day,0,0) # Not used
outfile.write_field(numpy.zeros(ssh.shape),ip,"salflx" ,0,model_day,0,0) # Not used
outfile.write_field(numpy.zeros(ssh.shape),ip,"bl_dpth" ,0,model_day,0,0) # Not used
outfile.write_field(numpy.zeros(ssh.shape),ip,"mix_dpth",0,model_day,0,0) # Not used
outfile.write_field(ubaro ,iu,"u_btrop" ,0,model_day,0,0) # u: nemo in cell i is hycom in cell i+1
outfile.write_field(vbaro ,iv,"v_btrop" ,0,model_day,0,0) # v: nemo in cell j is hycom in cell j+1
ny=mbathy.shape[0];nx=mbathy.shape[1]
error=numpy.zeros((ny,nx))
for k in numpy.arange(u.shape[0]) :
if bio_path:
no3k=interpolate2d(blat, blon, no3[k,:,:], points).reshape((jdm,idm))
no3k = maplev(no3k)
po4k=interpolate2d(blat, blon, po4[k,:,:], points).reshape((jdm,idm))
po4k = maplev(po4k)
si_k=interpolate2d(blat, blon, si[k,:,:], points).reshape((jdm,idm))
si_k = maplev(si_k)
if k%10==0 : logger.info("Writing 3D variables including BIO, level %d of %d"%(k+1,u.shape[0]))
else:
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
# 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]
tmpfill=sdummy_fill#ncids.variables["vosaline"]._FillValue
sl = sliced(sdummy[0,k,:,:])
tmpfill=tdummy_fill#ncidt.variables["votemper"]._FillValue
tl = sliced(tdummy[0,k,:,:])
sl = numpy.where(numpy.abs(sl)<1e2,sl,numpy.nan)
sl = numpy.minimum(numpy.maximum(maplev(sl),25),80.)
tl = numpy.where(numpy.abs(tl)<=5e2,tl,numpy.nan)
tl = numpy.minimum(numpy.maximum(maplev(tl),-5.),50.)
# Fill empty layers with values from above
if k > 0 :
K= numpy.where(dtl < 1e-4)
tl[K] = tl_above[K]
onem=9806.
outfile.write_field(ul ,iu,"u-vel.",0,model_day,k+1,0) # u: nemo in cell i is hycom in cell i+1
outfile.write_field(vl ,iv,"v-vel.",0,model_day,k+1,0) # v: nemo in cell j is hycom in cell j+1
outfile.write_field(dtl*onem,ip,"thknss",0,model_day,k+1,0)
outfile.write_field(tl ,ip,"temp" ,0,model_day,k+1,0)
outfile.write_field(sl ,ip,"salin" ,0,model_day,k+1,0)
if bio_path :
outfile.write_field(no3k ,ip,"ECO_no3" ,0,model_day,k+1,0)
outfile.write_field(po4k ,ip,"ECO_pho" ,0,model_day,k+1,0)
outfile.write_field(si_k ,ip,"ECO_sil" ,0,model_day,k+1,0)
tl_above=numpy.copy(tl)
sl_above=numpy.copy(sl)
# TODO: Process ice data
ncid2d.close()
outfile.close()
ncidt.close()
ncids.close()
ncidu.close()
ncidv.close()
if bio_path:ncidb.close()
nemo_mesh = []
def main(lon1,
lat1,
lon2,
lat2,
variable,
files,
filetype="archive",
clim=None,
sectionid="",
ijspace=False,
xaxis="distance",
section_map=False,
dens=False,
dpi=180):
logger.info("Filetype is %s" % filetype)
gfile = abf.ABFileGrid("regional.grid", "r")
plon = gfile.read_field("plon")
plat = gfile.read_field("plat")
# Set up section info
if ijspace:
sec = gridxsec.SectionIJSpace([lon1, lon2], [lat1, lat2], plon, plat)
else:
sec = gridxsec.Section([lon1, lon2], [lat1, lat2], plon, plat)
I, J = sec.grid_indexes
dist = sec.distance
print('dit.shae=', dist.shape)
slon = sec.longitude
slat = sec.latitude
logger.info("Min max I-index (starts from 0):%d %d" % (I.min(), I.max()))
logger.info("Min max J-index (starts from 0):%d %d" % (J.min(), J.max()))
#
#
if section_map:
ll_lon = slon.min() - 10.
ur_lon = slon.max() + 10.
ll_lat = np.maximum(-90., slat.min() - 10.)
ur_lat = np.minimum(90., slat.max() + 10.)
proj = ccrs.Stereographic(central_latitude=90.0,
central_longitude=-40.0)
pxy = proj.transform_points(ccrs.PlateCarree(), plon, plat)
px = pxy[:, :, 0]
py = pxy[:, :, 1]
x, y = np.meshgrid(np.arange(slon.shape[0]), np.arange(slat.shape[0]))
figure = plt.figure(figsize=(10, 8))
ax = figure.add_subplot(111)
ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_extent([-179, 179, 53, 85], ccrs.PlateCarree())
ax.add_feature(cfeature.GSHHSFeature('auto', edgecolor='grey'))
ax.add_feature(cfeature.GSHHSFeature('auto', facecolor='grey'))
ax.gridlines()
ax.plot(slon, slat, "r-", lw=1)
pos = ax.get_position()
asp = pos.height / pos.width
w = figure.get_figwidth()
h = asp * w
figure.set_figheight(h)
if sectionid:
figure.canvas.print_figure("map_%s.png" % sectionid, dpi=dpi)
else:
figure.canvas.print_figure("map.png", dpi=dpi)
# Get layer thickness variable used in hycom
dpname = modeltools.hycom.layer_thickness_variable[filetype]
logger.info("Filetype %s: layer thickness variable is %s" %
(filetype, dpname))
if xaxis == "distance":
x = dist / 1000.
xlab = "Distance along section[km]"
elif xaxis == "i":
x = I
xlab = "i-index"
elif xaxis == "j":
x = J
xlab = "j-index"
elif xaxis == "lon":
x = slon
xlab = "longitude"
elif xaxis == "lat":
x = slat
xlab = "latitude"
else:
logger.warning("xaxis must be i,j,lo,lat or distance")
x = dist / 1000.
xlab = "Distance along section[km]"
# Loop over archive files
figure = plt.figure()
ax = figure.add_subplot(111)
pos = ax.get_position()
for fcnt, myfile0 in enumerate(files):
# Remove [ab] ending if present
m = re.match("(.*)\.[ab]", myfile0)
if m:
myfile = m.group(1)
else:
myfile = myfile0
# Add more filetypes if needed. By def we assume archive
if filetype == "archive":
i_abfile = abf.ABFileArchv(myfile, "r")
elif filetype == "restart":
i_abfile = abf.ABFileRestart(myfile,
"r",
idm=gfile.idm,
jdm=gfile.jdm)
else:
raise NotImplementedError("Filetype %s not implemented" % filetype)
# kdm assumed to be max level in ab file
kdm = max(i_abfile.fieldlevels)
# Set up interface and daat arrays
xx = np.zeros((kdm + 1, I.size))
intfsec = np.zeros((kdm + 1, I.size))
datasec = np.zeros((kdm + 1, I.size))
if dens:
datasec_sal = np.zeros((kdm + 1, I.size))
sigma_sec = np.zeros((kdm + 1, I.size))
# Loop over layers in file.
logger.info("File %s" % (myfile))
for k in range(kdm):
logger.debug("File %s, layer %03d/%03d" % (myfile, k, kdm))
# Get 2D fields
dp2d = i_abfile.read_field(dpname, k + 1)
data2d = i_abfile.read_field(variable, k + 1)
dp2d = np.ma.filled(dp2d, 0.) / modeltools.hycom.onem
data2d = np.ma.filled(data2d, 1e30)
# Place data into section arrays
intfsec[k + 1, :] = intfsec[k, :] + dp2d[J, I]
if k == 0: datasec[k, :] = data2d[J, I]
datasec[k + 1, :] = data2d[J, I]
if dens:
data2d_sal = i_abfile.read_field('salin', k + 1)
data2d_sal = np.ma.filled(data2d_sal, 1e30)
datasec_sal[k + 1, :] = data2d_sal[J, I]
i_maxd = np.argmax(np.abs(intfsec[kdm, :]))
for k in range(kdm + 1):
xx[k, :] = x[:]
datasec = np.ma.masked_where(datasec > 0.5 * 1e30, datasec)
print("datasec min, max=", datasec.min(), datasec.max())
if dens:
datasec_sal = np.ma.masked_where(datasec_sal > 0.5 * 1e30,
datasec_sal)
print("datasec_sal min, max=", datasec_sal.min(),
datasec_sal.max())
sigma_sec = mod_hyc2plot.sig(datasec, datasec_sal)
sigma_sec = np.ma.masked_where(sigma_sec < 0.0, sigma_sec)
datasec = sigma_sec
# Set up section plot
datasec = np.ma.masked_where(datasec > 0.5 * 1e30, datasec)
print("min, max=", datasec.min(), datasec.max())
if clim is None:
clim = [datasec.min(), datasec.max()]
#clim=[0.0,13]
print("clim=", clim[0], clim[1])
if clim is not None:
lvls = MaxNLocator(nbins=70).tick_values(clim[0], clim[1])
mf = 'sawtooth_fc100.txt'
LinDic = mod_hyc2plot.cmap_dict(mf)
my_cmap = matplotlib.colors.LinearSegmentedColormap(
'my_colormap', LinDic)
cmap = my_cmap
norm = BoundaryNorm(lvls, ncolors=cmap.N, clip=True)
P = ax.contourf(xx, -intfsec, datasec, cmap=cmap, levels=lvls)
# Plot layer interfaces
for k in range(1, kdm + 1):
if k % 100 == 0:
PL = ax.plot(x, -intfsec[k, :], "-", color="k")
textx = x[i_maxd]
texty = -0.5 * (intfsec[k - 1, i_maxd] + intfsec[k, i_maxd])
ax.text(textx,
texty,
str(k),
verticalalignment="center",
horizontalalignment="center",
fontsize=6)
elif k % 5 == 0:
PL = ax.plot(x, -intfsec[k, :], "--", color="k", linewidth=0.5)
textx = x[i_maxd]
texty = -0.5 * (intfsec[k - 1, i_maxd] + intfsec[k, i_maxd])
ax.text(textx,
texty,
str(k),
verticalalignment="center",
horizontalalignment="center",
fontsize=6)
else:
if k > 2 and k % 2 == 0:
PL = ax.plot(x,
-intfsec[k, :],
"-",
color=".5",
linewidth=0.5)
textx = x[i_maxd]
texty = -0.5 * (intfsec[k - 1, i_maxd] +
intfsec[k, i_maxd])
ax.text(textx,
texty,
str(k),
verticalalignment="center",
horizontalalignment="center",
fontsize=6)
else:
continue
# Print figure
ax.set_facecolor('xkcd:gray')
aspect = 90
pad_fraction = 0.25
divider = make_axes_locatable(ax)
width = axes_size.AxesY(ax, aspect=1. / aspect)
pad = axes_size.Fraction(pad_fraction, width)
cax = divider.append_axes("right", size=width, pad=pad)
cb = ax.figure.colorbar(P, cax=cax)
if clim is not None: P.set_clim(clim)
if dens:
ax.set_title('[P. density ]: ' + myfile)
else:
ax.set_title('[' + variable + ']: ' + myfile)
ax.set_ylabel('Depth [m]')
ax.set_xlabel(xlab)
# Print in different y-lims
suff = os.path.basename(myfile)
if sectionid: suff = suff + "_" + sectionid
if dens: variable = "dens"
figure.canvas.print_figure("sec_%s_full_%s.png" % (variable, suff),
dpi=dpi)
ax.set_ylim(-1000, 0)
figure.canvas.print_figure("sec_%s_1000m_%s.png" % (variable, suff),
dpi=dpi)
# Close input file
i_abfile.close()
#
ax.clear()
cb.remove()
def main(lon1,lat1,lon2,lat2,variable,files,filetype="archive",clim=None,sectionid="",
ijspace=False,xaxis="distance",section_map=False,ncfiles="",dpi=180) :
#TP4Grd='/cluster/work/users/aal069/TP4a0.12/mfile/'
logger.info("Filetype is %s"% filetype)
gfile = abf.ABFileGrid("regional.grid","r")
plon=gfile.read_field("plon")
plat=gfile.read_field("plat")
# Set up section info
if ijspace :
sec = gridxsec.SectionIJSpace([lon1,lon2],[lat1,lat2],plon,plat)
else :
sec = gridxsec.Section([lon1,lon2],[lat1,lat2],plon,plat)
I,J=sec.grid_indexes
dist=sec.distance
print('dit.shae=',dist.shape)
slon=sec.longitude
slat=sec.latitude
# In testing
#J,I,slon,slat,case,dist=sec.find_intersection(qlon,qlat)
#print I,J
#raise NameError,"test"
logger.info("Min max I-index (starts from 0):%d %d"%(I.min(),I.max()))
logger.info("Min max J-index (starts from 0):%d %d"%(J.min(),J.max()))
#
#
if section_map :
ll_lon=slon.min()-10.
ur_lon=slon.max()+10.
ll_lat=np.maximum(-90.,slat.min()-10.)
ur_lat=np.minimum(90. ,slat.max()+10.)
proj=ccrs.Stereographic(central_latitude=90.0,central_longitude=-40.0)
#pxy = proj.transform_points(ccrs.PlateCarree(), plon, plat)
#px=pxy[:,:,0]
#py=pxy[:,:,1]
#x,y=np.meshgrid(np.arange(slon.shape[0]),np.arange(slat.shape[0]))
figure =plt.figure(figsize=(8,8))
ax=figure.add_subplot(111,projection=proj)
#ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_extent([-179, 179, 53, 85],ccrs.PlateCarree())
#ax = plt.axes(projection=ccrs.Stereographic())
ax.add_feature(cfeature.GSHHSFeature('auto', edgecolor='grey'))
ax.add_feature(cfeature.GSHHSFeature('auto', facecolor='grey'))
ax.gridlines()
#ax.coastlines(resolution='110m')
ax.plot(slon,slat,"r-",lw=1,transform=ccrs.PlateCarree())
pos = ax.get_position()
asp=pos.height/pos.width
w=figure.get_figwidth()
h=asp*w
figure.set_figheight(h)
if sectionid :
figure.canvas.print_figure("map_%s.png"%sectionid,dpi=dpi,bbox_inches='tight')
else :
figure.canvas.print_figure("map.png",dpi=dpi,bbox_inches='tight')
# Get layer thickness variable used in hycom
dpname = modeltools.hycom.layer_thickness_variable[filetype]
logger.info("Filetype %s: layer thickness variable is %s"%(filetype,dpname))
if xaxis == "distance" :
x=dist/1000.
xlab="Distance along section[km]"
elif xaxis == "i" :
x=I
xlab="i-index"
elif xaxis == "j" :
x=J
xlab="j-index"
elif xaxis == "lon" :
x=slon
xlab="longitude"
elif xaxis == "lat" :
x=slat
xlab="latitude"
else :
logger.warning("xaxis must be i,j,lo,lat or distance")
x=dist/1000.
xlab="Distance along section[km]"
# get kdm from the first file:
# Remove [ab] ending if present
print('firstfilw', files[0])
m=re.match("(.*)\.[ab]",files[0])
print('m=',m.group(1))
myf=m.group(1)
fi_abfile = abf.ABFileArchv(myf,"r")
kdm=max(fi_abfile.fieldlevels)
# Loop over archive files
figure = plt.figure()
ax=figure.add_subplot(111)
pos = ax.get_position()
count_sum=0
intfsec_sum=np.zeros((kdm+1,I.size))
datasec_sum=np.zeros((kdm+1,I.size))
for fcnt,myfile0 in enumerate(files) :
count_sum=count_sum+1
print('count_sum==', count_sum)
print('fcnt=', fcnt)
print('mfile0=', myfile0)
# Remove [ab] ending if present
m=re.match("(.*)\.[ab]",myfile0)
if m :
myfile=m.group(1)
else :
myfile=myfile0
# Add more filetypes if needed. By def we assume archive
if filetype == "archive" :
i_abfile = abf.ABFileArchv(myfile,"r")
elif filetype == "restart" :
i_abfile = abf.ABFileRestart(myfile,"r",idm=gfile.idm,jdm=gfile.jdm)
else :
raise NotImplementedError("Filetype %s not implemented"%filetype)
# kdm assumed to be max level in ab file
kdm=max(i_abfile.fieldlevels)
# Set up interface and daat arrays
xx=np.zeros((kdm+1,I.size))
intfsec=np.zeros((kdm+1,I.size))
datasec=np.zeros((kdm+1,I.size))
# Loop over layers in file.
logger.info("File %s"%(myfile))
for k in range(kdm) :
logger.debug("File %s, layer %03d/%03d"%(myfile,k,kdm))
# Get 2D fields
dp2d=i_abfile.read_field(dpname,k+1)
data2d=i_abfile.read_field(variable,k+1)
#print('---mn,mx data=', data2d.min(),data2d.max())
if (k%kdm==49):
print("---Reach bottom layer" )
dp2d=np.ma.filled(dp2d,0.)/modeltools.hycom.onem
data2d=np.ma.filled(data2d,1e30)
# Place data into section arrays
intfsec[k+1,:] = intfsec[k,:] + dp2d[J,I]
if k==0 : datasec[k,:] = data2d[J,I]
datasec[k+1,:] = data2d[J,I]
intfsec_sum=intfsec_sum + intfsec
datasec_sum=datasec_sum + datasec
#print 'prs_intafce=', np.transpose(intfsec[:,15])
i_abfile.close()
# end loop over files
intfsec_avg=intfsec_sum/count_sum
datasec_avg=datasec_sum/count_sum
if ncfiles :
MLDGS_sum=np.zeros((1,I.size))
count_sum=0
for fcnt,ncfile in enumerate(ncfiles) :
count_sum=count_sum+1
print('ncfile count_sum==', count_sum)
print('ncfile fcnt=', fcnt)
print('ncfilefile=', ncfile)
MLDGS=np.zeros((1,I.size))
ncfile0 = netCDF4.Dataset(ncfile,'r')
MLD_2D = ncfile0.variables['GS_MLD'][:]
#MLD_2D = ncfile0.variables['mlp'][:]
MLDGS[0,:]=MLD_2D[0,J,I]
MLDGS_sum= MLDGS_sum + MLDGS
ncfile0.close()
# end loop over files
MLDGS_avg=MLDGS_sum/count_sum
#
#-----------------------------------------------------------------
# read from clim mld TP5netcdf
if ncfiles :
if 'TP2' in files[0]:
fh=netCDF4.Dataset('mld_dr003_l3_modif_Interp_TP2grd.nc')
else:
fh=netCDF4.Dataset('mld_dr003_l3_modif_Interp_TP5grd.nc')
fhmldintrp = fh.variables['TP5mld'][:]
fh.close()
#fhMLDintrp_sum=np.zeros((760,800))
MLDclim_sum=np.zeros((1,I.size))
cunt_sum=0
for ii in range(12) :
cunt_sum=cunt_sum +1
MLDclim=np.zeros((1,I.size))
MLDclim[0,:]=fhmldintrp[ii,J,I]
MLDclim_sum= MLDclim_sum + MLDclim
print('clim count_sum==', cunt_sum)
MLDclim_avg=MLDclim_sum/cunt_sum
#-----------------------------------------------------------------
i_maxd=np.argmax(np.abs(intfsec_avg[kdm,:]))
#print i_maxd
for k in range(kdm+1) :
xx[k,:] = x[:]
# Set up section plot
#datasec = np.ma.masked_where(datasec==1e30,datasec)
datasec_avg = np.ma.masked_where(datasec_avg>0.5*1e30,datasec_avg)
#print datasec.min(),datasec.max()
#P=ax.pcolormesh(dist/1000.,-intfsec,datasec)
#print i_maxd
for k in range(kdm+1) :
xx[k,:] = x[:]
if clim is not None : lvls = MaxNLocator(nbins=30).tick_values(clim[0], clim[1])
#print 'levels=', lvls
mf='sawtooth_0-1.txt'
LinDic=mod_hyc2plot.cmap_dict(mf)
my_cmap = matplotlib.colors.LinearSegmentedColormap('my_colormap',LinDic)
cmap=my_cmap
#cmap = matplotlib.pyplot.get_cmap('gist_rainbow_r')
norm = BoundaryNorm(lvls, ncolors=cmap.N, clip=True)
print('x.shape=' , x.shape)
print('x.min,xmax=' , x.min(),x.max())
print('xx.shape=' , xx.shape)
print('xx.min,xxmax=' , xx.min(),xx.max())
print('intfsec_avg.shape=', intfsec_avg.shape)
print('datasec_avg.shape=', datasec_avg.shape)
#P=ax.pcolormesh(x,-intfsec,datasec,cmap=cmap)
P=ax.contourf(xx,-intfsec_avg,datasec_avg,extend='both',cmap=cmap,levels=lvls)
if 'sal' in variable:
P1=ax.contour(xx,-intfsec_avg,datasec_avg,levels=[32.0,33.0,34.0,35.0,35.5],
colors=('k',),linestyles=('-',),linewidths=(1.5,))
else:
P1=ax.contour(xx,-intfsec_avg,datasec_avg,levels=[-1,0.0,2.0],
colors=('k',),linestyles=('-',),linewidths=(1.5,))
matplotlib.pyplot.clabel(P1, fmt = '%2.1d', colors = 'k', fontsize=10) #contour line labels
# Plot layer interfaces
for k in range(1,kdm+1) :
if k%100 == 0 :
PL=ax.plot(x,-intfsec_avg[k,:],"-",color="k")
elif k%5 == 0 and k <= 10:
PL=ax.plot(x,-intfsec_avg[k,:],"--",color="k", linewidth=0.5)
textx = x[i_maxd]
texty = -0.5*(intfsec_avg[k-1,i_maxd] + intfsec_avg[k,i_maxd])
ax.text(textx,texty,str(k),verticalalignment="center",horizontalalignment="center",fontsize=6)
elif k%2 and k > 10 :
PL=ax.plot(x,-intfsec_avg[k,:],"--",color="k", linewidth=0.5)
textx = x[i_maxd]
texty = -0.5*(intfsec_avg[k-1,i_maxd] + intfsec_avg[k,i_maxd])
ax.text(textx,texty,str(k),verticalalignment="center",horizontalalignment="center",fontsize=6)
if ncfiles :
PL=ax.plot(x,-MLDGS_avg[0,:],"-",color="w", linewidth=1.50)
PL=ax.plot(x,-MLDclim_avg[0,:],"--",color="r", linewidth=1.50)
### else :
### PL=ax.plot(x,-intfsec_avg[k,:],"-",color=".5")
# Print figure and remove wite space.
aspect = 50
pad_fraction = 0.25
divider = make_axes_locatable(ax)
width = axes_size.AxesY(ax, aspect=1./aspect)
pad = axes_size.Fraction(pad_fraction, width)
cax = divider.append_axes("right", size=width, pad=pad)
cb=ax.figure.colorbar(P,cax=cax,extend='both')
#cb=ax.figure.colorbar(P,extend='both')
if clim is not None : P.set_clim(clim)
#cb=ax.figure.colorbar(P,extend='both')
ax.set_title(variable+':'+myfile+'AVG-')
ax.set_ylabel('Depth [m]')
ax.set_xlabel(xlab)
#ax.set_position(pos)
#matplotlib.pyplot.tight_layout()
# Print in different y-lims
suff=os.path.basename(myfile)
if sectionid : suff=suff+"_"+sectionid
figure.canvas.print_figure("sec_AVG_%s_full_%s.png"%(variable,suff),dpi=dpi)
#ax.set_ylim(-1000,0)
if 'Fram' in sectionid or 'Svin' in sectionid:
print('sectionid=', sectionid)
ax.set_ylim(-600,0)
figure.canvas.print_figure("sec_AVG_%s_600m_%s.png"%(variable,suff),dpi=dpi)
else:
#ax.set_ylim(-2500,0)
#figure.canvas.print_figure("sec_AVG_%s_2500m_%s.png"%(variable,suff),dpi=dpi)
ax.set_ylim(-3000,0)
figure.canvas.print_figure("sec_AVG_%s_3000m_%s.png"%(variable,suff),dpi=dpi)
# Close input file
#i_abfile.close()
#
ax.clear()
cb.remove()
def main(meshfile,file,iexpt=10,iversn=22,yrflag=3,bio_path=None) :
#
# Trim input netcdf file name being appropriate for reading
#
meshfile=str(meshfile)[2:-2]
logger.info("Reading mesh information from %s."%(meshfile))
#
# Read mesh file containing grid and coordinate information.
# Note that for now, we are using T-grid in vertical which may need
# to be improved by utilizing W-point along the vertical axis.
#
hdept,gdept,mbathy,mbathy_u,mbathy_v,mask,e3t,plon,plat=read_grid(meshfile)
logger.warning("Reading grid information from regional.grid.[ab] (not completed)")
#
# Convert from P-point (i.e. NEMO grid) to U and V HYCOM grids
#
mask_u=p2u_2d(mask)
mask_v=p2v_2d(mask)
#
# Read regional.grid.[ab]
# Grid angle is not used for this product because all quantities are
# on regular rectangular grid points.
#
angle=numpy.zeros(plon.shape)
#
# Number vertical layers in T-point.
#
nlev=gdept.size
#
# layer thickness in the absence of layer partial steps.
#
dt = gdept[1:] - gdept[:-1]
#
# Prepare/read input data file (in netcdf format). Reference time is 1950-01-01
#
logger.info("Reading data files.")
file=str(file).strip()[2:-2]
dirname=os.path.dirname(file)
logger.debug("file name is {}".format(file))
logger.debug("dirname is {}".format(dirname))
logger.debug("basename is {}".format(os.path.basename(file)))
m=re.match("(MERCATOR-PHY-24-)(.*\.nc)",os.path.basename(file))
logger.debug("file prefix is {}".format(file_pre))
### m=re.match(file_pre,os.path.basename(file))
if not m:
msg="File %s is not a grid2D file, aborting"%file
logger.error(msg)
raise ValueError(msg)
#fileinput0=os.path.join(dirname+"/"+"MERCATOR-PHY-24-"+m.group(2))
file_date=file[-16:-6]
fileinput0=file
print((file_date,file))
next_day=datetime.datetime.strptime(file_date, '%Y-%m-%d')+datetime.timedelta(days=1)
fileinput1=datetime.datetime.strftime(next_day,'%Y%m%d')
fileinput1=os.path.join(dirname+"/"+file_pre+fileinput1+'.nc')
logger.info("Reading from %s"%(fileinput0))
ncid0=netCDF4.Dataset(fileinput0,"r")
if timeavg_method==1 and os.path.isfile(fileinput1) :
logger.info("timeavg_method=1, Reading from %s"%(fileinput1))
ncid1=netCDF4.Dataset(fileinput1,"r")
#
# Calculate temporal averaged temperature, salinity, and velocity
#
uo = 0.5*(ncid0.variables["uo"][0,:,:,:]+ ncid1.variables["uo"][0,:,:,:])
vo = 0.5*(ncid0.variables["vo"][0,:,:,:]+ ncid1.variables["vo"][0,:,:,:])
salt = 0.5*(ncid0.variables["so"][0,:,:,:]+ ncid1.variables["so"][0,:,:,:])
temp = 0.5*(ncid0.variables["thetao"][0,:,:,:]+ncid1.variables["thetao"][0,:,:,:])
ssh = numpy.squeeze(0.5*(ncid0.variables["zos"][0,:,:]+ncid1.variables["zos"][0,:,:]))
else:
#
# Set variables based on current file when timeavg_method ~=1 or the next netcdf file is not available
logger.debug("time average method set to {}".format(timeavg_method))
uo = ncid0.variables["uo"][0,:,:,:]
vo = ncid0.variables["vo"][0,:,:,:]
salt = ncid0.variables["so"][0,:,:,:]
temp = ncid0.variables["thetao"][0,:,:,:]
ssh = numpy.squeeze(ncid0.variables["zos"][0,:,:])
#
# I will account these values afterward. Because in the current version, I am accounting for missing values using a gap-filling methodology.
#
logger.debug("getting _FillValue")
uofill=ncid0.variables["uo"]._FillValue
vofill=ncid0.variables["vo"]._FillValue
slfill=ncid0.variables["so"]._FillValue
tlfill=ncid0.variables["thetao"]._FillValue
shfill=ncid0.variables["zos"]._FillValue
# Set time
logger.info("Set time.")
time=ncid0.variables["time"][0]
unit=ncid0.variables["time"].units
tmp=cfunits.Units(unit)
refy,refm,refd=(1950,1,1)
tmp2=cfunits.Units("hours since %d-%d-%d 00:00:00"%(refy,refm,refd))
tmp3=int(numpy.round(cfunits.Units.conform(time,tmp,tmp2)))
mydt = datetime.datetime(refy,refm,refd,0,0,0) + datetime.timedelta(hours=tmp3) # Then calculate dt. Phew!
if timeavg_method==1 and os.path.isfile(fileinput1) :
fnametemplate="archv.%Y_%j_%H"
deltat=datetime.datetime(refy,refm,refd,0,0,0) + \
datetime.timedelta(hours=tmp3) + \
datetime.timedelta(hours=12)
oname=deltat.strftime(fnametemplate)
else:
#
# I am assuming that daily mean can be set at 00 instead of 12
# for cases that there is no information of next day.
#
fnametemplate="archv.%Y_%j"
deltat=datetime.datetime(refy,refm,refd,0,0,0) + \
datetime.timedelta(hours=tmp3)
oname=deltat.strftime(fnametemplate) + '_00'
# model day
refy, refm, refd=(1900,12,31)
model_day= deltat-datetime.datetime(refy,refm,refd,0,0,0)
model_day=model_day.days
logger.info("Model day in HYCOM is %s"%str(model_day))
if bio_path:
jdm,idm=numpy.shape(plon)
points = numpy.transpose(((plat.flatten(),plon.flatten())))
delta = mydt.strftime( '%Y-%m-%d')
# filename format MERCATOR-BIO-14-2013-01-05-00
print((bio_path,delta))
idx,biofname=search_biofile(bio_path,delta)
if idx >7:
msg="No available BIO file within a week difference with PHY"
logger.error(msg)
raise ValueError(msg)
logger.info("BIO file %s reading & interpolating to 1/12 deg grid cells ..."%biofname)
ncidb=netCDF4.Dataset(biofname,"r")
blon=ncidb.variables["longitude"][:];
blat=ncidb.variables["latitude"][:]
minblat=blat.min()
no3=ncidb.variables["NO3"][0,:,:,:];
no3[numpy.abs(no3)>1e+10]=numpy.nan
po4=ncidb.variables["PO4"][0,:,:,:]
si=ncidb.variables["Si"][0,:,:,:]
po4[numpy.abs(po4)>1e+10]=numpy.nan
si[numpy.abs(si)>1e+10]=numpy.nan
# TODO: Ineed to improve this part
nz,ny,nx=no3.shape
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=no3;dummy[:,:,-1]=no3[:,:,-1]
no3=dummy
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=po4;dummy[:,:,-1]=po4[:,:,-1]
po4=dummy
dummy=numpy.zeros((nz,ny,nx+1))
dummy[:,:,:nx]=si;dummy[:,:,-1]=si[:,:,-1]
si=dummy
dummy=numpy.zeros((nx+1))
dummy[:nx]=blon
blon=dummy
blon[-1]=-blon[0]
# TODO: Note that the coordinate files are for global configuration while
# the data file saved for latitude larger than 30. In the case you change your data file coordinate
# configuration you need to modify the following lines
bio_coordfile=bio_path[:-4]+"/GLOBAL_ANALYSIS_FORECAST_BIO_001_014_COORD/GLO-MFC_001_014_mask.nc"
biocrd=netCDF4.Dataset(bio_coordfile,"r")
blat2 = biocrd.variables['latitude'][:]
index=numpy.where(blat2>=minblat)[0]
depth_lev = biocrd.variables['deptho_lev'][index[0]:,:]
#
#
#
dummy=numpy.zeros((ny,nx+1))
dummy[:,:nx]=depth_lev;dummy[:,-1]=depth_lev[:,-1]
depth_lev=dummy
depth_lev[depth_lev>50]=0
depth_lev=depth_lev.astype('i')
dummy_no3=no3
dummy_po4=po4
dummy_si=si
for j in range(ny):
for i in range(nx):
dummy_no3[depth_lev[j,i]:nz-2,j,i]=no3[depth_lev[j,i]-1,j,i]
dummy_po4[depth_lev[j,i]:nz-2,j,i]=po4[depth_lev[j,i]-1,j,i]
dummy_si[depth_lev[j,i]:nz-2,j,i]=si[depth_lev[j,i]-1,j,i]
no3=dummy_no3
po4=dummy_po4
si=dummy_si
#
po4 = po4 * 106.0 * 12.01
si = si * 6.625 * 12.01
no3 = no3 * 6.625 * 12.01
logger.info("Read, trim, rotate NEMO velocities.")
u=numpy.zeros((nlev,mbathy.shape[0],mbathy.shape[1]))
v=numpy.zeros((nlev,mbathy.shape[0],mbathy.shape[1]))
utmp=numpy.zeros((mbathy.shape))
vtmp=numpy.zeros((mbathy.shape))
#
# Metrices to detect carrefully bottom at p-, u-, and v-grid points.While I have used 3D, mask data,following methods are good enough for now.
#
if mbathy_method == 1 :
ip = mbathy == -1
iu = mbathy_u == -1
iv = mbathy_v == -1
else:
ip = mask == 0
iu = mask_u == 0
iv = mask_v == 0
#
# Read 3D velocity field to calculate barotropic velocity
#
# Estimate barotropic velocities using partial steps along the vertical axis. Note that for the early version of this code,
# I used dt = gdept[1:] - gdept[:-1] on NEMO t-grid. Furthermore, you may re-calculate this part on vertical grid cells for future.
#
logger.info("Calculate barotropic velocities.")
ubaro,vbaro=calc_uvbaro(uo,vo,e3t,iu,iv)
#
# Save 2D fields (here only ubaro & vbaro)
#
zeros=numpy.zeros(mbathy.shape)
#flnm = open(oname+'.txt', 'w')
#flnm.write(oname)
#flnm.close()
ssh = numpy.where(numpy.abs(ssh)>1000,0.,ssh*9.81) # NB: HYCOM srfhgt is in geopotential ...
#
outfile = abf.ABFileArchv("./data/"+oname,"w",iexpt=iexpt,iversn=iversn,yrflag=yrflag,)
outfile.write_field(zeros, ip,"montg1" ,0,model_day,1,0)
outfile.write_field(ssh, ip,"srfhgt" ,0,model_day,0,0)
outfile.write_field(zeros, ip,"surflx" ,0,model_day,0,0) # Not used
outfile.write_field(zeros, ip,"salflx" ,0,model_day,0,0) # Not used
outfile.write_field(zeros, ip,"bl_dpth" ,0,model_day,0,0) # Not used
outfile.write_field(zeros, ip,"mix_dpth",0,model_day,0,0) # Not used
outfile.write_field(ubaro, iu,"u_btrop" ,0,model_day,0,0)
outfile.write_field(vbaro, iv,"v_btrop" ,0,model_day,0,0)
#
if bio_path:
logger.info("Calculate baroclinic velocities, temperature, and salinity data as well as BIO field.")
else:
logger.info("Calculate baroclinic velocities, temperature, and salinity data.")
for k in numpy.arange(u.shape[0]) :
if bio_path:
no3k=interpolate2d(blat, blon, no3[k,:,:], points).reshape((jdm,idm))
no3k = maplev(no3k)
po4k=interpolate2d(blat, blon, po4[k,:,:], points).reshape((jdm,idm))
po4k = maplev(po4k)
si_k=interpolate2d(blat, blon, si[k,:,:], points).reshape((jdm,idm))
si_k = maplev(si_k)
if k%10==0 : logger.info("Writing 3D variables including BIO, level %d of %d"%(k+1,u.shape[0]))
else:
if k%10==0 : logger.info("Writing 3D variables, level %d of %d"%(k+1,u.shape[0]))
#
#
uo[k,:,:]=numpy.where(numpy.abs(uo[k,:,:])<10,uo[k,:,:],0)
vo[k,:,:]=numpy.where(numpy.abs(vo[k,:,:])<10,vo[k,:,:],0)
# Baroclinic velocity (in HYCOM U- and V-grid)
ul = p2u_2d(numpy.squeeze(uo[k,:,:])) - ubaro
vl = p2v_2d(numpy.squeeze(vo[k,:,:])) - vbaro
ul[iu]=spval
vl[iv]=spval
# Layer thickness
dtl=numpy.zeros(mbathy.shape)
# Use dt for the water column except the nearest cell to bottom
if thickness_method==1:
if k < u.shape[0]-1 :
J,I = numpy.where(mbathy>k)
e3=(e3t[k,:,:])
dtl[J,I]=dt[k]
J,I = numpy.where(mbathy==k)
dtl[J,I]=e3[J,I]
else:
e3=(e3t[k,:,:])
J,I = numpy.where(mbathy==k)
dtl[J,I]=e3[J,I]
# Use partial cells for the whole water column.
else :
J,I = numpy.where(mbathy>=k)
dtl[J,I]=e3t[k,J,I]
# Salinity
sl = salt[k,:,:]
# Temperature
tl = temp[k,:,:]
# Need to be carefully treated in order to minimize artifacts to the resulting [ab] files.
if fillgap_method==1:
J,I= numpy.where(mbathy<k)
sl = maplev(numpy.where(numpy.abs(sl)<1e2,sl,numpy.nan))
sl[J,I]=spval
J,I= numpy.where(mbathy<k)
tl = maplev(numpy.where(numpy.abs(tl)<1e2,tl,numpy.nan))
tl[J,I]=spval
else:
sl = numpy.where(numpy.abs(sl)<1e2,sl,numpy.nan)
sl = numpy.minimum(numpy.maximum(maplev(sl),25),80.)
tl = numpy.where(numpy.abs(tl)<=5e2,tl,numpy.nan)
tl = numpy.minimum(numpy.maximum(maplev(tl),-5.),50.)
# Thickness
dtl = maplev(dtl)
if k > 0 :
with numpy.errstate(invalid='ignore'):
K= numpy.where(dtl < 1e-4)
sl[K] = sl_above[K]
tl[K] = tl_above[K]
#
sl[ip]=spval
tl[ip]=spval
# Save 3D fields
outfile.write_field(ul ,iu,"u-vel.",0,model_day,k+1,0)
outfile.write_field(vl ,iv,"v-vel.",0,model_day,k+1,0)
outfile.write_field(dtl*onem,ip,"thknss",0,model_day,k+1,0)
outfile.write_field(tl ,ip,"temp" , 0,model_day,k+1,0)
outfile.write_field(sl ,ip,"salin" ,0,model_day,k+1,0)
if bio_path :
outfile.write_field(no3k ,ip,"ECO_no3" ,0,model_day,k+1,0)
outfile.write_field(po4k ,ip,"ECO_pho" ,0,model_day,k+1,0)
outfile.write_field(si_k ,ip,"ECO_sil" ,0,model_day,k+1,0)
tl_above=numpy.copy(tl)
sl_above=numpy.copy(sl)
outfile.close()
ncid0.close()
if timeavg_method==1 and os.path.isfile(fileinput1) :
ncid1.close()
if bio_path :
ncidb.close()
def main(psikk_file, archv_files, psikk_file_type="restart", month=1):
logger.info("psikk file type is %s" % psikk_file_type)
from_relax_archv = psikk_file_type == "relax_archv"
from_relax = psikk_file_type == "relax"
from_restart = psikk_file_type == "restart"
if not from_relax_archv and not from_relax and not from_restart:
msg = "psikk_file_type must be either restart relax or relax_archv"
logger.error(msg)
raise ValueError(msg)
# Open blkdat files. Get some properties
bp = modeltools.hycom.BlkdatParser("blkdat.input")
idm = bp["idm"]
jdm = bp["jdm"]
kdm = bp["kdm"]
thflag = bp["thflag"]
thbase = bp["thbase"]
kapref = bp["kapref"]
iversn = bp["iversn"]
iexpt = bp["iexpt"]
yrflag = bp["yrflag"]
thref = modeltools.hycom.thref
if kapref == -1:
kapnum = 2
msg = "Only kapref>=0 is implemented for now"
logger.error(msg)
raise ValueError(msg)
else:
kapnum = 1
if kapnum > 1:
msg = "Only kapnum=1 is implemented for now"
logger.error(msg)
raise ValueError(msg)
path0 = os.path.join(".", "montg1")
if os.path.exists(path0) and os.path.isdir(path0):
pass
else:
os.mkdir(path0)
# hycom sigma and kappa, written in python. NB: sigver is not used here.
# Modify to use other equations of state. For now we assume sigver is:
# 1 (7-term eqs referenced to 0 bar)
# 2 (7-term eqs referenced to 2000 bar)
if thflag == 0:
sigver = 1
else:
sigver = 2
sig = modeltools.hycom.Sigma(thflag)
if kapref > 0: kappa = modeltools.hycom.Kappa(kapref, thflag * 1000.0e4) #
# Option 1: Get psikk and thkk directly from a restart file
if from_restart:
# Read input variables from lowest layer of a restart file
m = re.match("^(.*)(\.[ab])", psikk_file)
if m: psikk_file = m.group(1)
rfile = abf.ABFileRestart(psikk_file, "r", idm=idm, jdm=jdm)
psikk = rfile.read_field("psikk", 0)
thkk = rfile.read_field("thkk", 0)
rfile.close()
# Option 2: Get temp, salinity and dp from relaxaiton fields. Estimate thkk and psikk
elif from_relax:
pattern = "^(.*)_(tem|int|sal)"
psikk_file = abf.ABFile.strip_ab_ending(psikk_file)
m = re.match(pattern, psikk_file)
if m:
relaxtem = abf.ABFileRelax(m.group(1) + "_tem", "r")
relaxsal = abf.ABFileRelax(m.group(1) + "_sal", "r")
relaxint = abf.ABFileRelax(m.group(1) + "_int", "r")
else:
msg = """Input hycom relaxation file %s does not match pattern
%s""" % (psikk_file, pattern)
logger.error(msg)
raise ValueError(msg)
# Option 3: Get temp, salinity and dp from relaxation fields (archive files generated during relaxation setup). Estimate thkk and psikk
elif from_relax_archv:
arcfile0 = abf.ABFileArchv(psikk_file, "r")
else:
msg = "No way of estimating psikk and thkk. Aborting ..."
logger(msg)
raise ValueError(msg)
# Estimate psikk, thkk from climatology. (Option 1 or option 2)
if from_relax or from_relax_archv:
logger.info("Estimating psikk and thkk from climatology")
p = numpy.ma.zeros((jdm, idm))
pup = numpy.ma.zeros((jdm, idm))
montg = numpy.ma.zeros((jdm, idm))
for k in range(kdm):
logger.debug("Reading layer %d from climatology" % k)
if k > 0: thstarup = numpy.ma.copy(thstar)
if from_relax:
saln = relaxsal.read_field("sal", k + 1, month)
temp = relaxtem.read_field("tem", k + 1, month)
plo = relaxint.read_field("int", k + 1,
month) # lowest interface of layer
dp = plo - pup
pup = numpy.copy(plo) # Next loop, pup = plo of this loop
elif from_relax_archv:
saln = arcfile0.read_field("salin", k + 1)
temp = arcfile0.read_field("temp", k + 1)
dp = arcfile0.read_field("thknss", k + 1)
else:
msg = "No way of estimating sal, tem and dp. Aborting ..."
logger(msg)
raise ValueError(msg)
th3d = sig.sig(temp, saln) - thbase
thstar = numpy.ma.copy(th3d)
if kapref > 0:
thstar = thstar + kappa.kappaf(temp[:, :], saln[:, :],
th3d[:, :] + thbase, p[:, :])
elif kapref < 0:
msg = "Only kapref>=0 is implemented for now"
logger.error(msg)
raise ValueError(msg)
# From hycom inicon.f
# montg(i,j,1,kkap)=0.0
# do k=1,kk-1
# montg(i,j,k+1,kkap)=montg(i,j,k,kkap)-
# & p(i,j,k+1)*(thstar(i,j,k+1,kkap)-thstar(i,j,k,kkap))*thref**2
# enddo
#c
# thkk( i,j,kkap)=thstar(i,j,kk,kkap)
# psikk(i,j,kkap)=montg( i,j,kk,kkap)
if k > 0:
#print (thstar - thstarup).min(), (thstar - thstarup).min()
montg = montg - p * (thstar - thstarup) * thref**2
p = p + dp
thkk = thstar
psikk = montg
if from_relax:
relaxtem.close()
relaxsal.close()
relaxint.close()
elif from_relax_archv:
arcfile0.close()
else:
pass
logger.info("Min max of thkk: %12.6g %12.6g" % (thkk.min(), thkk.max()))
logger.info("Min max of psikk: %12.6g %12.6g" % (psikk.min(), psikk.max()))
# Loop through archive files
for archv_file in archv_files:
logger.debug("Processing %s" % (archv_file))
arcfile = abf.ABFileArchv(archv_file, "r")
# Read all layers .. (TODO: If there is memory problems, read and estimate sequentially)
temp = numpy.ma.zeros(
(jdm, idm)) # Only needed when calculating density
saln = numpy.ma.zeros(
(jdm, idm)) # Only needed when calculating density
th3d = numpy.ma.zeros((kdm, jdm, idm))
thstar = numpy.ma.zeros((kdm, jdm, idm))
dp = numpy.ma.zeros((jdm, idm))
p = numpy.ma.zeros((kdm + 1, jdm, idm))
for k in range(kdm):
logger.info("Reading layer %d from %s" % (k, archv_file))
temp = arcfile.read_field("temp", k + 1)
saln = arcfile.read_field("salin", k + 1)
#dp [k ,:,:]=arcfile.read_field("thknss",k+1)
dp[:, :] = arcfile.read_field("thknss", k + 1)
th3d[k, :, :] = sig.sig(temp, saln) - thbase
p[k + 1, :, :] = p[k, :, :] + dp[:, :]
thstar[k, :, :] = numpy.ma.copy(th3d[k, :, :])
if kapref > 0:
thstar[k, :, :] = thstar[k, :, :] + kappa.kappaf(
temp[:, :], saln[:, :], th3d[k, :, :] + thbase, p[k, :, :])
elif kapref < 0:
msg = "Only kapref>=0 is implemented for now"
logger.error(msg)
raise ValueError(msg)
# This part of montg1 does nto depend on pbavg
montg1c = modeltools.hycom.montg1_pb(thstar, p)
# This part depends linearly on pbavg
montg1pb = modeltools.hycom.montg1_no_pb(psikk, thkk, thstar, p)
print montg1c.min(), montg1c.max()
print montg1pb.min(), montg1pb.max()
# ... we have ...
# montg1 = montgc + montgpb * pbavg
# srfhgt = montg1 + thref*pbavg = montgc + montgpb * pbavg + thref*pbavg
# ... which gives new montg1n for srfhgtn
# pbavgn = (srfhgtn-montgc) / (montgpb+thref)
# montg1n = montgc + montgpb*pbavgn
# Systematic differences due to choice of sigma and or eq of state is not taken into account ...
# Barotropic pressure. NB: srfhgt is in geopotential height :
srfhgt = arcfile.read_field("srfhgt", 0)
pbavg = (srfhgt - montg1c) / (montg1pb + thref)
print pbavg.min(), pbavg.max()
montg1 = montg1pb * pbavg + montg1c
logger.info("Estimated montg1 ")
print montg1.min(), montg1.max()
# Open new archive file, and write montg1 to it.
fnameout = os.path.join(path0, os.path.basename(arcfile.basename))
arcfile_out = abf.ABFileArchv(fnameout,
"w",
iversn=iversn,
yrflag=yrflag,
iexpt=iexpt,
mask=False)
for key in sorted(arcfile.fields.keys()):
fieldname = arcfile.fields[key]["field"]
time_step = arcfile.fields[key]["step"]
model_day = arcfile.fields[key]["day"]
k = arcfile.fields[key]["k"]
dens = arcfile.fields[key]["dens"]
fld = arcfile.read_field(fieldname, k)
if fieldname == "montg1":
logger.info(
"Writing field %10s at level %3d to %s (modified)" %
(fieldname, k, fnameout))
arcfile_out.write_field(montg1, None, fieldname, time_step,
model_day, sigver, thbase)
else:
arcfile_out.write_field(fld, None, fieldname, time_step,
model_day, k, dens)
#logger.info("Writing field %10s at level %3d to %s (copy from original)"%(fieldname,k,fnameout))
logger.info("Finished writing to %s" % fnameout)
arcfile_out.close()
arcfile.close()
logger.warning("Sigver assumed to be those of 7 term eqs")
logger.warning(" 1 for sigma-0/thflag=0, 2 for sigma-2/thflag=2")
logger.warning(
"For other eqs, you need to modify the code so that sigver is set correctly in the archv file"
"")
logger.warning(
"psikk and thkk from relaxation fields is beta. Preferred method is restart"
)
logger.info("Finito")
def main(archv_files,opath,header_line1=cline1,header_line2=cline2,header_line3=cline3 ) :
# Open blkdat files. Get some properties
bp=modeltools.hycom.BlkdatParser("blkdat.input")
idm = bp["idm"]
jdm = bp["jdm"]
kdm = bp["kdm"]
thflag = bp["thflag"]
thbase = numpy.float(bp["thbase"])
kapref = bp["kapref"]
iversn = bp["iversn"]
iexpt = bp["iexpt"]
yrflag = bp["yrflag"]
#thref=modeltools.hycom.thref
thref=1e-3
if kapref == -1 :
kapnum = 2
msg="Only kapref>=0 is implemented for now"
logger.error(msg)
raise ValueError(msg)
else :
kapnum = 1
if kapnum > 1 :
msg="Only kapnum=1 is implemented for now"
logger.error(msg)
raise ValueError(msg)
# hycom sigma and kappa, written in python. NB: sigver is not used here.
# Modify to use other equations of state. For now we assume sigver is:
# 1 (7-term eqs referenced to 0 bar)
# 2 (7-term eqs referenced to 2000 bar)
if thflag == 0 :
sigver=1
else :
sigver=2
sig = modeltools.hycom.Sigma(thflag)
if kapref > 0 : kappa = modeltools.hycom.Kappa(kapref,thflag*1000.0e4) #
# Loop through archive files
for archv_file in archv_files :
archv_file=archv_file[:-2]
logger.debug("Processing %s"%(archv_file))
arcfile=abf.ABFileArchv(archv_file,"r")
temp = numpy.ma.zeros((jdm,idm)) # Only needed when calculating density
saln = numpy.ma.zeros((jdm,idm)) # Only needed when calculating density
th3d =numpy.ma.zeros((kdm,jdm,idm))
thstar=numpy.ma.zeros((kdm,jdm,idm))
dp =numpy.ma.zeros((jdm,idm))
p =numpy.ma.zeros((kdm+1,jdm,idm))
pup =numpy.ma.zeros((jdm,idm))
montg=numpy.ma.zeros((jdm,idm))
for k in range(kdm) :
logger.info("Reading layer %d from %s"%(k,archv_file))
temp =arcfile.read_field("temp",k+1)
saln =arcfile.read_field("salin",k+1)
dp [:,:]=arcfile.read_field("thknss",k+1)
th3d [k ,:,:]=sig.sig(temp,saln) - thbase
p [k+1,:,:]= p[k,:,:] + dp[:,:]
if k>0 : thstarup =numpy.ma.copy(thstar[k ,:,:])
thstar[k ,:,:]=numpy.ma.copy(th3d [k ,:,:])
if kapref > 0 :
thstar[k ,:,:]=thstar [k ,:,:] + kappa.kappaf(temp[:,:],
saln[:,:],
th3d[k,:,:]+thbase,
p[k,:,:])
elif kapref < 0 :
msg="Only kapref>=0 is implemented for now"
logger.error(msg)
raise ValueError(msg)
if k > 0 :
montg = montg - p[k,:,:] * (thstar[k ,:,:] - thstarup) * thref**2
thkk = thstar[k ,:,:]
psikk = montg
# This part of montg1 does nto depend on pbavg
montg1c = montg1_pb(thstar,p)
# This part depends linearly on pbavg
montg1pb = montg1_no_pb(psikk,thkk,thstar,p)
# Barotropic pressure. NB: srfhgt is in geopotential height :
srfhgt=arcfile.read_field("srfhgt",0)
pbavg = (srfhgt - montg1c) / (montg1pb+thref)
montg1 = montg1pb*pbavg + montg1c
logger.info("Estimated montg1 ")
# Apply mask
#montg1=numpy.ma.masked_where(srfhgt.mask,montg1)
#montg1[~msk]=2**100
#montg1 = numpy.ma.masked_where(srfhgt<2.0**99,montg1)
msk=numpy.where(srfhgt>2.0**99,1,0)
# Open new archive file, and write montg1 to it.
fnameout = opath+str(archv_file[-17:])
arcfile_out=abf.ABFileArchv(fnameout,"w",iversn=iversn,yrflag=yrflag,iexpt=iexpt,mask=False,cline1=header_line1,cline2=header_line2,cline3=header_line3)
fields=arcfile.get_fields()
for key in sorted(fields.keys()) :
fieldname = fields[key]["field"]
time_step = fields[key]["step"]
model_day = fields[key]["day"]
k = fields[key]["k"]
dens = fields[key]["dens"]
fld =arcfile.read_field(fieldname,k)
if fieldname == "montg1" :
logger.info("Writing field %10s at level %3d to %s (modified)"%(fieldname,k,fnameout))
arcfile_out.write_field(montg1,None,fieldname,time_step,model_day,k,dens)
else :
arcfile_out.write_field(fld ,None,fieldname,time_step,model_day,k,dens)
logger.info("Finished writing to %s"%fnameout)
arcfile_out.close()
arcfile.close()
def main(lon1,
lat1,
lon2,
lat2,
variable,
files,
filetype="archive",
clim=None,
sectionid="",
ijspace=False,
xaxis="distance",
section_map=False,
dpi=180):
logger.info("Filetype is %s" % filetype)
gfile = abf.ABFileGrid("regional.grid", "r")
plon = gfile.read_field("plon")
plat = gfile.read_field("plat")
# Set up section info
if ijspace:
sec = gridxsec.SectionIJSpace([lon1, lon2], [lat1, lat2], plon, plat)
else:
sec = gridxsec.Section([lon1, lon2], [lat1, lat2], plon, plat)
I, J = sec.grid_indexes
dist = sec.distance
slon = sec.longitude
slat = sec.latitude
print(slon.shape)
print(slat.shape)
logger.info("Min max I-index (starts from 0):%d %d" % (I.min(), I.max()))
logger.info("Min max J-index (starts from 0):%d %d" % (J.min(), J.max()))
if section_map:
ll_lon = slon.min() - 10.
ur_lon = slon.max() + 10.
ll_lat = np.maximum(-90., slat.min() - 10.)
ur_lat = np.minimum(90., slat.max() + 10.)
proj = ccrs.Stereographic(central_latitude=90.0,
central_longitude=-40.0)
pxy = proj.transform_points(ccrs.PlateCarree(), plon, plat)
px = pxy[:, :, 0]
py = pxy[:, :, 1]
x, y = np.meshgrid(np.arange(slon.shape[0]), np.arange(slat.shape[0]))
figure = plt.figure(figsize=(10, 8))
ax = figure.add_subplot(111)
ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_extent([-179, 179, 53, 85], ccrs.PlateCarree())
ax.add_feature(cfeature.GSHHSFeature('auto', edgecolor='grey'))
ax.add_feature(cfeature.GSHHSFeature('auto', facecolor='grey'))
ax.gridlines()
ax.plot(slon, slat, "r-", lw=1)
pos = ax.get_position()
asp = pos.height / pos.width
w = figure.get_figwidth()
h = asp * w
figure.set_figheight(h)
if sectionid:
figure.canvas.print_figure("map_%s.png" % sectionid, dpi=dpi)
else:
figure.canvas.print_figure("map.png", dpi=dpi)
# Get layer thickness variable used in hycom
dpname = modeltools.hycom.layer_thickness_variable[filetype]
logger.info("Filetype %s: layer thickness variable is %s" %
(filetype, dpname))
if xaxis == "distance":
x = dist / 1000.
xlab = "Distance along section[km]"
elif xaxis == "i":
x = I
xlab = "i-index"
elif xaxis == "j":
x = J
xlab = "j-index"
elif xaxis == "lon":
x = slon
xlab = "longitude"
elif xaxis == "lat":
x = slat
xlab = "latitude"
else:
logger.warning("xaxis must be i,j,lo,lat or distance")
x = dist / 1000.
xlab = "Distance along section[km]"
# Loop over archive files
figure = plt.figure()
ax = figure.add_subplot(111)
pos = ax.get_position()
for fcnt, myfile0 in enumerate(files):
# Remove [ab] ending if present
m = re.match("(.*)\.[ab]", myfile0)
if m:
myfile = m.group(1)
else:
myfile = myfile0
# Add more filetypes if needed. By def we assume archive
if filetype == "archive":
i_abfile = abf.ABFileArchv(myfile, "r")
elif filetype == "restart":
i_abfile = abf.ABFileRestart(myfile,
"r",
idm=gfile.idm,
jdm=gfile.jdm)
else:
raise NotImplementedError("Filetype %s not implemented" % filetype)
# kdm assumed to be max level in ab file
kdm = max(i_abfile.fieldlevels)
# Set up interface and daat arrays
intfsec = np.zeros((kdm + 1, I.size))
datasec = np.zeros((kdm + 1, I.size))
# Loop over layers in file.
logger.info("File %s" % (myfile))
for k in range(kdm):
logger.debug("File %s, layer %03d/%03d" % (myfile, k, kdm))
# Get 2D fields
dp2d = i_abfile.read_field(dpname, k + 1)
data2d = i_abfile.read_field(variable, k + 1)
dp2d = np.ma.filled(dp2d, 0.) / modeltools.hycom.onem
data2d = np.ma.filled(data2d, 1e30)
# Place data into section arrays
intfsec[k + 1, :] = intfsec[k, :] + dp2d[J, I]
if k == 0: datasec[k, :] = data2d[J, I]
datasec[k + 1, :] = data2d[J, I]
i_maxd = np.argmax(np.abs(intfsec[kdm, :]))
# Set up section plot
datasec = np.ma.masked_where(datasec > 0.5 * 1e30, datasec)
P = plt.pcolormesh(x, -intfsec, datasec, cmap="jet", shading='auto')
if clim is not None: P.set_clim(clim)
# Plot layer interfaces
for k in range(1, kdm + 1):
if k % 10 == 0:
PL = ax.plot(x, -intfsec[k, :], "--", color="k", lw=.5)
elif k % 5 == 0:
PL = ax.plot(x, -intfsec[k, :], "--", color="k", lw=.5)
else:
PL = ax.plot(x, -intfsec[k, :], "--", color=".5", lw=.5)
textx = x[i_maxd]
texty = -0.5 * (intfsec[k - 1, i_maxd] + intfsec[k, i_maxd])
ax.text(textx,
texty,
str(k),
verticalalignment="center",
horizontalalignment="center",
fontsize=6)
cb = ax.figure.colorbar(P)
ax.set_title(myfile)
ax.set_ylabel(variable)
ax.set_xlabel(xlab)
# Print in different y-lims
suff = os.path.basename(myfile)
if sectionid: suff = suff + "_" + sectionid
figure.canvas.print_figure("sec_%s_full_%s.png" % (variable, suff),
dpi=dpi)
ax.set_ylim(-1000, 0)
figure.canvas.print_figure("sec_%s_1000m_%s.png" % (variable, suff),
dpi=dpi)
ax.set_ylim(-300, 0)
figure.canvas.print_figure("sec_%s_300m_%s.png" % (variable, suff),
dpi=dpi)
# Close input file
i_abfile.close()
#
ax.clear()
cb.remove()