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Fig_Arctic_SSHSSS_2_local.py
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#!/usr/bin/python3
import os
import xarray as xr
import numpy as np
import numpy.typing as npt
import typing as T
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
import matplotlib.tri as tri
from mpl_toolkits.axes_grid1 import make_axes_locatable
import matplotlib.patches as patches
import imageio.v2 as imageio
import matplotlib as mpl
import matplotlib.pylab as plb
def dates_range(start_date, end_date):
"""
This function takes the start and end dates and returns
all the dates in between.
"""
dates = []
for i in range(
int(
(
datetime.strptime(end_date, "%Y%m%d")
- datetime.strptime(start_date, "%Y%m%d")
).days
)
+ 1
):
date = datetime.strptime(start_date, "%Y%m%d") + timedelta(days=i)
#dates.append(date.strftime("%m/%d/%y"))
dates.append(date)
return dates
def open_schism(date, n, data_dir):
"""
"""
n=n+1
try:
ds_t = xr.open_dataset(
f"{data_dir}temperature_{n}.nc",
chunks={},
engine='h5netcdf',
drop_variables=['vvel4.5',
'uvel4.5',
'vvel_bottom',
'uvel_bottom',
'vvel_surface',
'uvel_surface',
'salt_bottom',
'temp_bottom',
'precipitationRate',
'evaporationRate',
'windSpeedX',
'windSpeedY',
'windStressX',
'windStressY',
'dryFlagElement',
'dryFlagSide',
'dryFlagNode',
]
)
print("Model TEMPERATURE data found for: ", date)
except:
print("No model TEMPERATURE data found for: ", date)
pass
try:
ds_s = xr.open_dataset(
f"{data_dir}salinity_{n}.nc",
chunks={},
engine='h5netcdf',
drop_variables=['vvel4.5',
'uvel4.5',
'vvel_bottom',
'uvel_bottom',
'vvel_surface',
'uvel_surface',
'salt_bottom',
'temp_bottom',
'precipitationRate',
'evaporationRate',
'windSpeedX',
'windSpeedY',
'windStressX',
'windStressY',
'dryFlagElement',
'dryFlagSide',
'dryFlagNode',
]
)
print("Model SALINITY data found for: ", date)
except:
print("No model SALINITY data found for: ", date)
pass
return ds_t,ds_s
def split_quads(face_nodes: npt.NDArray[np.int_]) -> npt.NDArray[np.int_]:
"""
https://gist.github.com/pmav99/5ded91f18ef096b080b2ed45598c7d1c
copied from: https://github.com/ec-jrc/Thalassa/blob/master/thalassa/utils.py
"""
if face_nodes.shape[-1] != 4:
return face_nodes
existing_triangles = face_nodes[:, :3]
quad_indexes = np.nonzero(~np.isnan(face_nodes).any(axis=1))
quads = face_nodes[quad_indexes]
quads_first_column = quads[:, 0]
quads_last_two_columns = quads[:, -2:]
new_triangles = np.c_[quads_first_column, quads_last_two_columns]
new_face_nodes = T.cast(
npt.NDArray[np.int_],
np.r_[existing_triangles, new_triangles].astype(int),
)
return new_face_nodes
def fixed_connectivity_tri(data_dir):
ds_tri = xr.open_dataset(
f"{data_dir}out2d_1.nc",
chunks={},
engine='h5netcdf',
drop_variables=['vvel4.5',
'uvel4.5',
'vvel_bottom',
'uvel_bottom',
'vvel_surface',
'uvel_surface',
'salt_bottom',
'temp_bottom',
'precipitationRate',
'evaporationRate',
'windSpeedX',
'windSpeedY',
'windStressX',
'windStressY',
'dryFlagElement',
'dryFlagSide',
'dryFlagNode',
]
)
connect=np.array(ds_tri['SCHISM_hgrid_face_nodes'][:])-1
connect_tri=split_quads(np.array(connect))
x, y = np.array(ds_tri['SCHISM_hgrid_node_x']), np.array(ds_tri['SCHISM_hgrid_node_y'])
depth=np.array(ds_tri.variables['depth'])
return x,y,connect_tri,depth
def concat_LEO(sat_date, path_sat):
"""
concatenates all LEO sat data on path_sat directory,
sat_date is the list of names of the files to be concat, e.g. 20180801.nc
"""
ds_sat=[]
for date in sat_date:
try:
ds_sat.append(xr.open_dataset(r"{}/leosst_{}.nc".format(path_sat,date),engine='h5netcdf'))
except:
print("No satellite data found for: ", date)
ds_sat = xr.concat(ds_sat,dim="time",data_vars="all")
return ds_sat
def plot_arctic(
triangulation,
z_th,
z_sh,
z_tr,
z_sr,
depth=None,
isobaths=None,
output_dir="",
n=0,
long_name_t="name of the var",
long_name_s="name of the var",
time_str="time str",
vmin_t=None,
vmax_t=None,
vmin_s=None,
vmax_s=None,
latmin=None,
latmax=None,
lonmin=None,
lonmax=None,
interv_t=None,
interv_s=None):
cmap = plb.cm.jet
cmaplist = [cmap(i) for i in range(cmap.N)]
cmap = mpl.colors.LinearSegmentedColormap.from_list(
'Custom cmap', cmaplist, cmap.N)
## SST Plots
bounds_t = np.linspace(vmin_t, vmax_t, len([i for i in np.arange(vmin_t, vmax_t, interv_t)])+1)
norm_t = mpl.colors.BoundaryNorm(bounds_t, cmap.N)
fig = plt.figure(figsize=(20,9))
ax = fig.add_subplot(221)
tp = ax.tripcolor(triangulation,z_th,shading='flat',cmap=cmap,norm=norm_t)
div = make_axes_locatable(ax)
cax = div.append_axes("right", size="5%", pad=0.2)
cb = fig.colorbar(tp,
cax=cax,
boundaries=np.arange(vmin_t,vmax_t,interv_t),
cmap=cmap,norm=norm_t,
ticks=np.linspace(vmin_t,vmax_t,len([i for i in np.arange(vmin_t,vmax_t,1)])+1))
cb.set_label(long_name_t)
ax.set_title(time_str+" HYCOM Hotstart")
ax.set_xlim(lonmin,lonmax)
ax.set_ylim(latmin,latmax)
ax.set_xlim(lonmin,lonmax)
ax.set_ylim(latmin,latmax)
#plot3
ax3 = fig.add_subplot(223)
tp3 = ax3.tripcolor(triangulation,z_tr,shading='flat',cmap=cmap,norm=norm_t)
div3 = make_axes_locatable(ax3)
cax3 = div3.append_axes("right", size="5%", pad=0.2)
cb3 = fig.colorbar(tp3,
cax=cax3,
boundaries=np.arange(vmin_t,vmax_t,interv_t),
cmap=cmap,norm=norm_t,
ticks=np.linspace(vmin_t,vmax_t,len([i for i in np.arange(vmin_t,vmax_t,1)])+1))
cb3.set_label(long_name_t)
ax3.set_title(time_str+" ROMS Hotstart")
# ax.set_facecolor('grey')
ax3.set_xlim(lonmin,lonmax)
ax3.set_ylim(latmin,latmax)
ax3.set_xlim(lonmin,lonmax)
ax3.set_ylim(latmin,latmax)
## SSS Plots
bounds_s = np.linspace(vmin_s, vmax_s, len([i for i in np.arange(vmin_s, vmax_s, interv_s)])+1)
norm_s = mpl.colors.BoundaryNorm(bounds_s, cmap.N)
ax2 = fig.add_subplot(222)
tp2 = ax2.tripcolor(triangulation,z_sh,shading='flat',cmap=cmap,norm=norm_s)
div2 = make_axes_locatable(ax2)
cax2 = div2.append_axes("right", size="5%", pad=0.2)
cb2 = fig.colorbar(tp2,
cax=cax2,
boundaries=np.arange(vmin_s,vmax_s,interv_s),
cmap=cmap,norm=norm_s,
ticks=np.linspace(vmin_s,vmax_s,len([i for i in np.arange(vmin_s,vmax_s,1)])+1))
cb2.set_label(long_name_s)
ax2.set_title(time_str+" HYCOM Hotstart")
ax2.set_xlim(lonmin,lonmax)
ax2.set_ylim(latmin,latmax)
ax2.set_xlim(lonmin,lonmax)
ax2.set_ylim(latmin,latmax)
#plot4
ax4 = fig.add_subplot(224)
tp4 = ax4.tripcolor(triangulation,z_sr,shading='flat',cmap=cmap,norm=norm_s)
div4 = make_axes_locatable(ax4)
cax4 = div4.append_axes("right", size="5%", pad=0.2)
cb4 = fig.colorbar(tp4,
cax=cax4,
boundaries=np.arange(vmin_s,vmax_s,interv_s),
cmap=cmap,norm=norm_s,
ticks=np.linspace(vmin_s,vmax_s,len([i for i in np.arange(vmin_s,vmax_s,1)])+1))
cb4.set_label(long_name_s)
ax4.set_title(time_str+" ROMS Hotstart")
ax4.set_xlim(lonmin,lonmax)
ax4.set_ylim(latmin,latmax)
ax4.set_xlim(lonmin,lonmax)
ax4.set_ylim(latmin,latmax)
if depth is not None and isobaths is not None:
depth[np.isnan(depth)] = -9999
ax.tricontour(triangulation, depth, levels=isobaths, linewidths=.5, colors="k")
ax2.tricontour(triangulation, depth, levels=isobaths, linewidths=.5, colors="k")
ax3.tricontour(triangulation, depth, levels=isobaths, linewidths=.5, colors="k")
ax4.tricontour(triangulation, depth, levels=isobaths, linewidths=.5, colors="k")
fig.tight_layout()
fig.savefig(output_dir+'{:04d}.jpeg'.format(n))
plt.close()
plt.clf()
def main(start_date,end_date,output_dir,isobaths,data_dir_h,data_dir_r):
long_name_t="Sea Surface Temperature (degC)"
long_name_s="Sea Surface Salinity (PSU)"
dates = dates_range(start_date, end_date)
times = [dd.strftime("%m/%d/%y") for dd in dates]
x,y,connect_tri,depth = fixed_connectivity_tri(data_dir_h)
lonmin,lonmax=x.min(),x.max()
latmin,latmax=y.min(),y.max()
triangulation = tri.Triangulation(x=x, y=y, triangles=connect_tri)
for n, date in enumerate(dates):
ds_th,ds_sh = open_schism(date, n, data_dir_h)
ds_th = np.array(ds_th.variables["temperature"][0,:,-1])
ds_sh = np.array(ds_sh.variables["salinity"][0,:,-1])
ds_tr,ds_sr = open_schism(date, n, data_dir_r)
ds_tr = np.array(ds_tr.variables["temperature"][0,:,-1])
ds_sr = np.array(ds_sr.variables["salinity"][0,:,-1])
print("creating plot ",n," of ", len(dates))
time_str=times[n]
z_th = ds_th
z_sh = ds_sh
z_tr = ds_tr
z_sr = ds_sr
plot_arctic(triangulation,
z_th,
z_sh,
z_tr,
z_sr,
depth=depth,
isobaths=isobaths,
output_dir=output_dir,
n=n,
long_name_t=long_name_t,
long_name_s=long_name_s,
time_str=time_str,
latmin=latmin,
latmax=latmax,
lonmin=lonmin,
lonmax=lonmax,
vmin_t=0,
vmax_t=15,
vmin_s=29,
vmax_s=34,
interv_t=.5,
interv_s=.25)
files = os.listdir(output_dir)
files = sorted(files)
images = []
for file in files:
images.append(imageio.imread(output_dir+file))
# os.remove(output_dir/file)
imageio.mimsave(output_dir+f'{start_date}_{end_date}_sstsss.gif',images, fps = 2)
if __name__ == '__main__':
# Enter your inputs here:
# var = 'temperature'
start_date='20190702'
end_date='20191030'
isobaths=[200,2000]#None
data_dir_h=r"/work2/noaa/nosofs/felicioc/BeringSea/O04a_hychot/"
data_dir_r=r"/work2/noaa/nosofs/felicioc/BeringSea/O04/"
output_dir=r"/work2/noaa/nosofs/felicioc/BeringSea/P04/sst_sst_roms_hycom/"
main(start_date,end_date,output_dir,isobaths,data_dir_h,data_dir_r)