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pysoda2roms.py
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pysoda2roms.py
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# -*- coding: utf-8 -*-
# %run pysoda2roms.py
'''
===========================================================================
This file is part of py-roms2roms
py-roms2roms is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
py-roms2roms is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with py-roms2roms. If not, see <http://www.gnu.org/licenses/>.
Version 1.0.1
Copyright (c) 2014 by Evan Mason, IMEDEA
Email: [email protected]
===========================================================================
Create a ROMS boundary file based on SODA data
===========================================================================
'''
import netCDF4 as netcdf
import pylab as plt
import numpy as np
import scipy.interpolate as si
import scipy.ndimage as nd
import scipy.spatial as sp
import glob as glob
import time
import scipy.interpolate.interpnd as interpnd
import collections
from mpl_toolkits.basemap import Basemap
from collections import OrderedDict
from datetime import datetime
import calendar
from py_roms2roms import vertInterp, horizInterp, bry_flux_corr, debug0, debug1, debug2
from py_roms2roms import ROMS, RomsGrid, RomsData
from py_mercator2roms import EastGrid, WestGrid, SouthGrid, NorthGrid, prepare_romsgrd
class RomsGrid(RomsGrid):
'''
Modify the RomsGrid class
'''
def lon(self):
'''
We need to override 'lon' method of pyroms2roms RomsGrid to
account for the SODA 0-360 degree grid.
'''
lon = self.read_nc('lon_rho', indices=self.indices)
# If all west of 0 degrees (e.g., for Canaries)
# then it's easy...
if np.all(lon < 0.):
lon += 360.
# Trickiest case (e.g. western Med)
# no option but to activate a flag indicating
# modification of the SODA grid and variables
elif np.logical_and(np.any(lon < 0.),
np.any(lon >= 0.)):
self.zero_crossing = True
return lon
def check_zero_crossing(self):
if np.logical_and(np.any(self.lon() < 0.),
np.any(self.lon() >= 0.)):
self.zero_crossing = True
class SodaData (RomsData):
'''
SODA data class (inherits from RomsData class)
'''
def __init__(self, filename, model_type, sodagrd):
"""
soda_file, 'SODA', sodagrd
"""
super(SodaData, self).__init__(filename, model_type)
self._lon = sodagrd._lon
self._lat = sodagrd._lat
# Update sodagrd for zero crossing
if sodagrd.zero_crossing is True:
self.fix_zero_crossing = True
# Tell SodaData object about i/j limits
self.i0, self.i1 = sodagrd.i0, sodagrd.i1
self.j0, self.j1 = sodagrd.j0, sodagrd.j1
def lon(self):
if self.fix_zero_crossing is True:
lon1 = self._lon[self.j0:self.j1, :self.i0]
lon0 = self._lon[self.j0:self.j1, self.i1:] - 360
return np.concatenate((lon0, lon1), axis=1)
else:
return self._lon[self.j0:self.j1, self.i0:self.i1]
def lat(self):
if self.fix_zero_crossing is True:
lat1 = self._lat[self.j0:self.j1, :self.i0]
lat0 = self._lat[self.j0:self.j1, self.i1:]
return np.concatenate((lat0, lat1), axis=1)
else:
return self._lat[self.j0:self.j1, self.i0:self.i1]
def ssh(self, var):
if self.fix_zero_crossing is True:
ssh1 = self.read_nc(var, indices='[self.j0:self.j1, :self.i0]')
ssh0 = self.read_nc(var, indices='[self.j0:self.j1, self.i1:]')
return np.concatenate((ssh0, ssh1), axis=1)
else:
return self.read_nc(var, indices=self.indices)
def _vars3d(self, var):
var1 = self.read_nc(var, '[::-1, self.j0:self.j1,:self.i0]')
var0 = self.read_nc(var, '[::-1, self.j0:self.j1,self.i1:]')
return np.concatenate((var0, var1), axis=2)
def temp(self, var):
if self.fix_zero_crossing is True:
return self._vars3d(var)
else:
return self.read_nc(var, '[::-1, self.j0:self.j1, self.i0:self.i1]')
def salt(self, var):
if self.fix_zero_crossing is True:
return self._vars3d(var)
else:
return self.read_nc(var, '[::-1, self.j0:self.j1, self.i0:self.i1]')
def u(self, var):
if self.fix_zero_crossing is True:
return self._vars3d(var)
else:
return self.read_nc(var, '[::-1, self.j0:self.j1, self.i0:self.i1]')
def v(self, var):
if self.fix_zero_crossing is True:
return self._vars3d(var)
else:
return self.read_nc(var, '[::-1, self.j0:self.j1, self.i0:self.i1]')
class SodaGrid (ROMS):
'''
SODA grid class
'''
def __init__(self, filename, model_type):
'''
'''
super(SodaGrid, self).__init__(filename, model_type)
print 'Initialising SodaGrid', filename
try:
self._lon = self.read_nc('lon', indices='[:]')
self._lat = self.read_nc('lat', indices='[:]')
except Exception:
self._lon = self.read_nc('LON', indices='[:]')
self._lat = self.read_nc('LAT', indices='[:]')
self._lon, self._lat = np.meshgrid(self._lon,
self._lat)
def lon(self):
if self.fix_zero_crossing is True:
lon1 = self._lon[self.j0:self.j1, :self.i0]
lon0 = self._lon[self.j0:self.j1, self.i1:] - 360
return np.concatenate((lon0, lon1), axis=1)
else:
return self._lon
def lat(self):
if self.fix_zero_crossing is True:
lat1 = self._lat[self.j0:self.j1, :self.i0]
lat0 = self._lat[self.j0:self.j1, self.i1:]
return np.concatenate((lat0, lat1), axis=1)
else:
return self._lat
#def _lonlat(self):
#try:
#lon = self.read_nc('lon', indices=''.join(('[', self.indices[18:])))
#lat = self.read_nc('lat', indices=''.join((self.indices[:16], ']')))
#except:
#lon = self.read_nc('LON', indices=''.join(('[', self.indices[18:])))
#lat = self.read_nc('LAT', indices=''.join((self.indices[:16], ']')))
#lon, lat = np.meshgrid(lon, lat)
#return lon, lat
#def lon(self):
#if self.fix_zero_crossing is True:
#try:
#lon1 = self.read_nc('lon', indices='[:self.i0]')
#lon0 = self.read_nc('lon', indices='[self.i1:]') - 360.
#lat = self.read_nc('lat', indices=''.join((self.indices[:16], ']')))
#except:
#lon1 = self.read_nc('LON', indices='[:self.i0]')
#lon0 = self.read_nc('LON', indices='[self.i1:]') - 360.
#lat = self.read_nc('LAT', indices=''.join((self.indices[:16], ']')))
#lon = np.append(lon0, lon1)
#return np.meshgrid(lon, lat)[0]
#else:
#return self._lonlat()[0]
#def lat(self):
#if self.fix_zero_crossing is True:
#try:
#lon1 = self.read_nc('lon', indices='[:self.i0]')
#lon0 = self.read_nc('lon', indices='[self.i1:]') - 360.
#lat = self.read_nc('lat', indices=''.join((self.indices[:16], ']')))
#except:
#lon1 = self.read_nc('LON', indices='[:self.i0]')
#lon0 = self.read_nc('LON', indices='[self.i1:]') - 360.
#lat = self.read_nc('LAT', indices=''.join((self.indices[:16], ']')))
#lon = np.append(lon0, lon1)
#return np.meshgrid(lon, lat)[1]
#else:
#return self._lonlat()[1]
def mask(self, var):
if self.fix_zero_crossing is True:
mask1 = self.read_nc(var, indices='[self.j0:self.j1, :self.i0]')
mask0 = self.read_nc(var, indices='[self.j0:self.j1, self.i1:]')
mask = np.concatenate((mask0, mask1), axis=1)
else:
mask = self.read_nc(var, indices=self.indices)
mask[mask > -999.] = 1.
mask[mask < -999.] = 0.
return mask
def mask3d(self, var):
'''
3d mask
var should be a string: 'temp', 'salt', etc...
'''
if self.fix_zero_crossing is True:
mask1 = self.read_nc(var, indices='[::-1, self.j0:self.j1, :self.i0]')
mask0 = self.read_nc(var, indices='[::-1, self.j0:self.j1, self.i1:]')
mask3d = np.concatenate((mask0, mask1), axis=2)
else:
mask3d = self.read_nc(var, indices='[::-1, self.j0:self.j1, selfi0:self.i1]')
mask3d[mask3d > -999.] = 1.
mask3d[mask3d < -999.] = 0.
return mask3d
def depths(self):
try:
return self.read_nc('depth', indices='[:]')
except:
return self.read_nc('DEPTH', indices='[:]')
def set_2d_depths(self, romsgrd):
'''
'''
self._2d_depths = np.tile(-self.depths()[::-1],
(romsgrd.h().size, 1)).T
return self
def set_3d_depths(self, romsgrd):
'''
'''
self._3d_depths = np.tile(-self.depths()[::-1],
(romsgrd.h().shape[1],
romsgrd.h().shape[0], 1)).T
return self
def set_map_coordinate_weights(self, romsgrd, j=None):
'''
Order : set_2d_depths or set_3d_depths
'''
#self.set_2d_depths(romsgrd)
if j is not None:
soda_depths = self._3d_depths[:,j]
roms_depths = romsgrd.scoord2z_r()[:,j]
else:
soda_depths = self._2d_depths
roms_depths = romsgrd.scoord2z_r()
self.mapcoord_weights = romsgrd.get_map_coordinate_weights(
roms_depths, soda_depths)
return self
def vert_interp(self):
'''
Vertical interpolation using ndimage.map_coordinates()
See vertInterp class in py_roms2roms.py
Requires self.mapcoord_weights set by set_map_coordinate_weights()
'''
self.vinterp = vertInterp(self.mapcoord_weights)
return self
def prepare_sodagrd(sodagrd, romsgrd):
'''
'''
if sodagrd.zero_crossing is True: # Update sodagrd for zero crossing
sodagrd.fix_zero_crossing = True
#sodagrd.proj2gnom(ignore_land_points=False, M=romsgrd.M)
#sodagrd.child_contained_by_parent(romsgrd)
#sodagrd.make_kdetree()#.get_fillmask_cofs()
return sodagrd
if __name__ == '__main__':
'''
pysoda2roms
Information about SODA:
http://www.atmos.umd.edu/~carton/index2_files/soda.htm
SODA may be downloaded from:
http://soda.tamu.edu/assim
Evan Mason 2012
'''
#_USER DEFINED VARIABLES_______________________________________
# SODA information
version = '2.1.6' # Note, uses m for u, v, ssh
#version = '1.4.3' # Note, uses cm for u, v, ssh
#version = '2.2.8'
monthly = False # True for MONTHLY data, else 5DAY
#soda_dir = '/Users/emason/data/SODA_2.1.6/'
#soda_dir = '/marula/emason/data/SODA/2.1.6/'
#soda_dir = '/marula/emason/data/SODA/2.1.6/MONTHLY/'
<<<<<<< local
#soda_dir = '/marula/emason/data/SODA/2.1.6/5DAY/'
=======
soda_dir = '/marula/emason/data/SODA/2.1.6/5DAY/'
>>>>>>> other
#soda_dir = '/shared/emason/SODA/2.2.8/MONTHLY/'
<<<<<<< local
soda_dir = '/Users/emason/data/SODA_2.2.8/'
=======
#soda_dir = '/Users/emason/data/SODA_2.2.8/'
>>>>>>> other
soda_grd = ''.join(('SODA_', version))
# Child ROMS information
#roms_dir = '../'
#roms_dir = '/marula/emason/runs2012/MedSea5/'
#roms_dir = '/marula/emason/runs2013/na_7pt5km_intann_5day/'
#roms_dir = '/home/emason/'
#roms_dir = '/marula/emason/runs2014/MedCan5/'
#roms_dir = '/Users/emason/runs/runs2014/MedCan5/'
roms_dir = '/Users/emason/runs2009/na_2009_7pt5/'
#roms_dir = '/marula/emason/runs2014/NA75_IA/'
#roms_grd = 'roms_grd_NA2009_7pt5km.nc'
#roms_grd = 'grd_MedCan5.nc'
roms_grd = 'roms_grd_NA2009_7pt5km.nc'
if 'roms_grd_NA2009_7pt5km.nc' in roms_grd:
sigma_params = dict(theta_s=6, theta_b=0, hc=120, N=32)
elif 'grd_nwmed_2km.nc' in roms_grd:
sigma_params = dict(theta_s=6, theta_b=0, hc=250, N=40)
else:
print 'No sigma params defined for grid: %s' %roms_grd
raise Exception
# Child ROMS boundary file information
obc_dict = dict(south=1, east=1, north=1, west=1) # 1=open, 0=closed
bry_cycle = 0. # days, 0 means no cycle
#bry_filename = 'bry_SODA5day_NA7pt5km.nc' # bry filename
#bry_filename = 'bry_MedCan5_SODA_2.2.8_MONTHLY.nc'
<<<<<<< local
bry_filename = 'bry_NA75_SODA_2.2.8_MONTHLY.nc.CORRECTED'
first_file = '198412' # first/last SODA file,
last_file = '201112'
#first_file = '19850104-19850109' # first/last SODA file,
#last_file = '20081224-20081229'
=======
#bry_filename = 'bry_NA75_SODA_2.2.8_MONTHLY.nc.CORRECTED'
bry_filename = 'bry_NA75_SODA_2.1.6_5DAY.nc'
#first_file = '198412' # first/last SODA file,
#last_file = '201101'
first_file = '19850104-19850109' # first/last SODA file,
last_file = '20081224-20081229'
>>>>>>> other
day_zero = '19850101'
balldist = 250000. # meters
#_END USER DEFINED VARIABLES_______________________________________
plt.close('all')
if monthly:
assert len(first_file) == 6, 'first_file must be a length six string'
assert len(last_file) == 6, 'last_file must be a length six string'
else:
assert len(first_file) == 17, 'first_file must be a length seventeen string'
assert len(last_file) == 17, 'last_file must be a length seventeen string'
fillval = 9999.
if '2.2.8' in version:
ssh_str = 'SSH'
temp_str = 'TEMP'
salt_str = 'SALT'
u_str = 'U'
v_str = 'V'
else:
ssh_str = 'ssh'
temp_str = 'temp'
salt_str = 'salt'
u_str = 'u'
v_str = 'v'
day_zero = datetime(int(day_zero[:4]), int(day_zero[4:6]), int(day_zero[6:]))
day_zero = plt.date2num(day_zero)
# Initialise SodaGrid and RomsGrid objects for both parent and child grids
romsgrd = RomsGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
romsgrd = prepare_romsgrd(romsgrd)
romsgrd.set_bry_dx()
romsgrd.set_bry_maskr()
romsgrd.set_bry_areas()
# Get surface areas of open boundaries and prepare boundary grids
chd_bry_surface_areas = []
boundary_grids = []
for open_boundary, flag in zip(obc_dict.keys(), obc_dict.values()):
if 'west' in open_boundary and flag:
chd_bry_surface_areas.append(romsgrd.area_west.sum(axis=0) * romsgrd.maskr_west)
boundary_grids.append(WestGrid(roms_dir + roms_grd, sigma_params, 'ROMS'))
elif 'east' in open_boundary and flag:
chd_bry_surface_areas.append(romsgrd.area_east.sum(axis=0) * romsgrd.maskr_east)
boundary_grids.append(EastGrid(roms_dir + roms_grd, sigma_params, 'ROMS'))
elif 'south' in open_boundary and flag:
chd_bry_surface_areas.append(romsgrd.area_south.sum(axis=0) * romsgrd.maskr_south)
boundary_grids.append(SouthGrid(roms_dir + roms_grd, sigma_params, 'ROMS'))
elif 'north' in open_boundary and flag:
chd_bry_surface_areas.append(romsgrd.area_north.sum(axis=0) * romsgrd.maskr_north)
boundary_grids.append(NorthGrid(roms_dir + roms_grd, sigma_params, 'ROMS'))
# Get total surface of open boundaries
chd_bry_total_surface_area = np.array([area.sum() for area in chd_bry_surface_areas]).sum()
soda_grd = soda_grd + '_' + first_file + '.cdf'
sodagrd = SodaGrid(''.join((soda_dir, soda_grd)), 'SODA')
# Activate flag for SODA zero crossing trickery
romsgrd.check_zero_crossing()
if romsgrd.zero_crossing is True:
print 'The ROMS domain straddles the zero-degree meridian'
sodagrd.zero_crossing = True
else:
sodagrd.zero_crossing = False
# Set sodagrd indices (i0:i1, j0:j1) for minimal subgrid around chd
sodagrd.set_subgrid(romsgrd, k=40)
sodagrd = prepare_sodagrd(sodagrd, romsgrd)
if True: # check the result of set_subgrid()
debug0(sodagrd.lon(), sodagrd.lat(), sodagrd.mask(ssh_str),
romsgrd.boundary()[0], romsgrd.boundary()[1])
# Set up a RomsData object for the boundary file
romsbry = RomsData(roms_dir + bry_filename, 'ROMS')
romsbry.first_file = first_file
romsbry.last_file = last_file
# Create the boundary file
romsbry.create_bry_nc(romsgrd, obc_dict, bry_cycle, fillval, 'pysoda2roms')
# Gnomonic projections for horizontal interpolations
#romsgrd.make_gnom_transform() # make Gnomonic basemap object, called as romsgrd.M
#romsgrd.proj2gnom(ignore_land_points=True) # no_mask == True as we only want data points
# Get depths
#pzr = -sodagrd.depths()[::-1]
#czr = romsgrd.scoord2z_r()
## debug1 shows results of get_strip_indices() at each open boundary
#if True:
#debug1(sodagrd.lon(), sodagrd.lat(), sodagrd.mask(ssh_str),
#par_bry_indices, romsgrd.boundary())
# Get list of roms parent data files
if monthly:
soda_files = sorted(glob.glob(soda_dir + 'SODA_' + version + '_??????.cdf'))
else:
soda_files = sorted(glob.glob(soda_dir + 'SODA_' + version +
'_????????-????????.cdf'))
tind = 0 # index for writing records to bry file
if monthly:
bry_time = 0 # bry_time in days
else:
bry_time = -2.5
active = False # flag to soda_files for loop
fm_weights = False # flag, if False then compute fillmask weights
'''
Start main loop over soda_files list here
'''
for soda_file in soda_files:
if first_file in soda_file:
active = True
if active:
print 'Opening file', soda_file
sodadata = SodaData(soda_file, 'SODA', sodagrd)
# Time loop over ocean_time
ot_loop_start = time.time()
# Get bry time (days)
if monthly:
# Monthly SODA
stime = soda_file.split('/')[-1].split('_')[-1].split('.')[0]
mid_month = 0.5 * calendar.monthrange(int(stime[:4]), int(stime[4:]))[1]
# Note that the second half of the month (mid_month) is added to bry_time
bry_time += mid_month # *after* bry_time has been written to bry file
bry_time = datetime(int(stime[:4]), int(stime[4:]), int(np.round(mid_month)))
bry_time = plt.date2num(bry_time) - day_zero
else:
# 5-day SODA
stime = soda_file.split('/')[-1].split('_')[-1].split('.')[0].split('-')[0]
bry_time = datetime(int(stime[:4]), int(stime[4:6]), int(stime[6:]))
bry_time = plt.date2num(bry_time)
bry_time += 2.5 # add 2.5 days
bry_time -= day_zero
# Read in variables
ptemp = sodadata.temp(temp_str)
psalt = sodadata.salt(salt_str)
pu = sodadata.u(u_str)
pv = sodadata.v(v_str)
if '1.4.3' in version: # cm to m
pu *= 0.01
pv *= 0.01
# Get weights for fillmask
if fm_weights is False:
fm_temp = np.array([])
fm_salt = np.array([])
fm_u = np.array([])
fm_v = np.array([])
for k in np.arange(sodagrd.depths().size):
junk, t_wt = sodadata.fillmask(ptemp[k], sodagrd.mask3d(temp_str)[k])
junk, s_wt = sodadata.fillmask(psalt[k], sodagrd.mask3d(salt_str)[k])
junk, u_wt = sodadata.fillmask(pu[k], sodagrd.mask3d(u_str)[k])
junk, v_wt = sodadata.fillmask(pv[k], sodagrd.mask3d(v_str)[k])
fm_temp = np.append(fm_temp, t_wt)
fm_salt = np.append(fm_salt, s_wt)
fm_u = np.append(fm_u, u_wt)
fm_v = np.append(fm_v, v_wt)
fm_temp = fm_temp.reshape(fm_temp.size / 4., 4)
fm_salt = fm_salt.reshape(fm_salt.size / 4., 4)
fm_u = fm_u.reshape(fm_u.size / 4., 4)
fm_v = fm_v.reshape(fm_v.size / 4., 4)
junk, z_wt = sodadata.fillmask(sodadata.ssh(ssh_str), sodagrd.mask(ssh_str))
fm_weights = True
for k in np.arange(sodagrd.depths().size):
ptemp[k] = sodadata.fillmask( ptemp[k], sodagrd.mask3d(temp_str)[k], fm_temp[k] )
psalt[k] = sodadata.fillmask( psalt[k], sodagrd.mask3d(salt_str)[k], fm_salt[k] )
pu[k] = sodadata.fillmask( pu[k], sodagrd.mask3d(u_str)[k], fm_u[k] )
pv[k] = sodadata.fillmask( pv[k], sodagrd.mask3d(v_str)[k], fm_v[k] )
if '1.4.3' in version: # cm to m
pzeta = 0.01 * sodadata.fillmask(sodadata.ssh(ssh_str), sodagrd.mask(ssh_str), z_wt)
else:
pzeta = sodadata.fillmask(sodadata.ssh(ssh_str), sodagrd.mask(ssh_str), z_wt)
# Initialise lists to be used during bry flux correction
boundarylist = []
uvlist = []
uvbarlist = []
# Loop over boundaries
bryind1 = 0
for open_boundary, flag in zip(obc_dict.keys(), obc_dict.values()):
print '------ processing %sern boundary' %open_boundary
if 'west' in open_boundary and flag:
bry_romsgrd = boundary_grids[bryind1]
elif 'east' in open_boundary and flag:
bry_romsgrd = boundary_grids[bryind1]
elif 'north' in open_boundary and flag:
bry_romsgrd = boundary_grids[bryind1]
elif 'south' in open_boundary and flag:
bry_romsgrd = boundary_grids[bryind1]
bry_romsgrd = prepare_romsgrd(bry_romsgrd)
sodagrd.set_2d_depths(bry_romsgrd).set_map_coordinate_weights(bry_romsgrd)
sodagrd.vert_interp()
sodagrd.proj2gnom(ignore_land_points=False, M=bry_romsgrd.M)
if first_file in soda_file:
sodagrd.child_contained_by_parent(bry_romsgrd)
sodagrd.make_kdetree()#.get_fillmask_cofs()
ballpoints = sodagrd.kdetree.query_ball_tree(bry_romsgrd.kdetree, r=balldist)
sodagrd.ball = np.array(np.array(ballpoints).nonzero()[0])
sodagrd.tri = sp.Delaunay(sodagrd.points[sodagrd.ball])
czeta = horizInterp(sodagrd.tri, pzeta.flat[sodagrd.ball])(bry_romsgrd.points)
htemp = np.ma.zeros((sodagrd.depths().size, czeta.size))
hsalt = htemp.copy()
hu = htemp.copy()
hv = htemp.copy()
for k in np.arange(sodagrd.depths().size):
htemp[k] = horizInterp(sodagrd.tri, ptemp[k].flat[sodagrd.ball])(bry_romsgrd.points)
hsalt[k] = horizInterp(sodagrd.tri, psalt[k].flat[sodagrd.ball])(bry_romsgrd.points)
hu[k] = horizInterp(sodagrd.tri, pu[k].flat[sodagrd.ball])(bry_romsgrd.points)
hv[k] = horizInterp(sodagrd.tri, pv[k].flat[sodagrd.ball])(bry_romsgrd.points)
hu[k], hv[k] = bry_romsgrd.rotate(hu[k],
hv[k], sign=1) # rotate to child angle
# Prepare for vertical interpolations
htemp = np.vstack((htemp[0], htemp, htemp[-1]))
hsalt = np.vstack((hsalt[0], hsalt, hsalt[-1]))
hu = np.vstack((hu[0], hu, hu[-1]))
hv = np.vstack((hv[0], hv, hv[-1]))
# Do vertical interpolations with map_coordinates
ctemp = sodagrd.vinterp.vert_interp(htemp)
csalt = sodagrd.vinterp.vert_interp(hsalt)
cu = sodagrd.vinterp.vert_interp(hu)
cv = sodagrd.vinterp.vert_interp(hv)
if 0:
# debug_ind is index along boundary
debug_ind = 10
debug2(debug_ind, boundary)
# Calculate barotropic velocity
H_u = np.sum((bry_romsgrd.scoord2dz() * cu), axis=0)
D_u = np.sum((bry_romsgrd.scoord2dz()), axis=0)
cubar = H_u / D_u
H_v = np.sum((bry_romsgrd.scoord2dz() * cv), axis=0)
D_v = np.sum((bry_romsgrd.scoord2dz()), axis=0)
cvbar = H_v / D_v
# From horizontal rho to u, v points
if open_boundary in ('north', 'south'):
cu = 0.5 * (cu[:,:-1] + cu[:,1:])
cubar = 0.5 * (cubar[:-1] + cubar[1:])
elif open_boundary in ('east', 'west'):
cv = 0.5 * (cv[:,:-1] + cv[:,1:])
cvbar = 0.5 * (cvbar[:-1] + cvbar[1:])
# Apply the masking
#czeta = np.ma.masked_where(mask[0] == True, czeta)
#ctemp = np.ma.masked_where(mask == True, ctemp)
#csalt = np.ma.masked_where(mask == True, csalt)
#if boundary in ('north', 'south'):
#cu = np.ma.masked_where(mask[:,:-1] == True, cu)
#cv = np.ma.masked_where(mask == True, cv)
#cubar = np.ma.masked_where(mask[0,:-1] == True, cubar)
#cvbar = np.ma.masked_where(mask[0] == True, cvbar)
#elif boundary in ('east', 'west'):
#cu = np.ma.masked_where(mask == True, cu)
#cv = np.ma.masked_where(mask[:,:-1] == True, cv)
#cubar = np.ma.masked_where(mask[0] == True, cubar)
#cvbar = np.ma.masked_where(mask[0,:-1] == True, cvbar)
# Write to boundary file
nc = netcdf.Dataset(romsbry.romsfile, 'a')
if bryind1 == 0:
nc.variables['bry_time'][tind] = np.float(bry_time)
# Fill masked areas with 0
czeta = np.ma.filled(czeta, 0.)
ctemp = np.ma.filled(ctemp, 0.)
csalt = np.ma.filled(csalt, 0.)
nc.variables['zeta_%s' % open_boundary][tind] = np.ma.squeeze(czeta)
nc.variables['temp_%s' % open_boundary][tind] = np.ma.squeeze(ctemp)
nc.variables['salt_%s' % open_boundary][tind] = np.ma.squeeze(csalt)
# Save only tangential velocities for now because we
# need to apply bry flux correction to normal velocities
if open_boundary in ('north', 'south'):
cu = np.ma.filled(cu, 0.)
cubar = np.ma.filled(cubar, 0.)
nc.variables['u_%s' % open_boundary][tind] = cu
nc.variables['ubar_%s' % open_boundary][tind] = cubar
elif open_boundary in ('east', 'west'):
cv = np.ma.filled(cv, 0.)
cvbar = np.ma.filled(cvbar, 0.)
nc.variables['v_%s' % open_boundary][tind] = cv
nc.variables['vbar_%s' % open_boundary][tind] = cvbar
'''
Once all boundaries in obc_dict computed then apply volume
conservation to normal velocities and save
'''
if bryind1 == np.sum(obc_dict.values()) - 1: # all boundaries processed
boundarylist.append(open_boundary)
# Collect only normal velocities
if open_boundary in ('north', 'south'):
uvlist.append(cv)
uvbarlist.append(cvbar)
elif open_boundary in ('east', 'west'):
uvlist.append(cu)
uvbarlist.append(cubar)
fc = bry_flux_corr(boundarylist,
chd_bry_surface_areas,
chd_bry_total_surface_area,
uvbarlist)
print '------ barotropic velocity correction:', fc, 'm/s'
for fcind, fc_boundary in enumerate(boundarylist):
# Correct and save the normal velocities
if 'north' in fc_boundary:
c_fc = np.ma.filled(uvlist[fcind] + fc, 0.)
cbar_fc = np.ma.filled(uvbarlist[fcind] + fc, 0.)
nc.variables['v_north'][tind] = c_fc
nc.variables['vbar_north'][tind] = cbar_fc
elif 'south' in fc_boundary:
c_fc = np.ma.filled(uvlist[fcind] - fc, 0.)
cbar_fc = np.ma.filled(uvbarlist[fcind] - fc, 0.)
nc.variables['v_south'][tind] = c_fc
nc.variables['vbar_south'][tind] = cbar_fc
elif 'west' in fc_boundary:
c_fc = np.ma.filled(uvlist[fcind] - fc, 0.)
cbar_fc = np.ma.filled(uvbarlist[fcind] - fc, 0.)
nc.variables['u_west'][tind] = c_fc
nc.variables['ubar_west'][tind] = cbar_fc
elif 'east' in fc_boundary:
c_fc = np.ma.filled(uvlist[fcind] + fc, 0.)
cbar_fc = np.ma.filled(uvbarlist[fcind] + fc, 0.)
nc.variables['u_east'][tind] = c_fc
nc.variables['ubar_east'][tind] = cbar_fc
else: # add to the list until all boundaries accounted for
boundarylist.append(open_boundary)
# Collect only normal velocities
if open_boundary in ('north', 'south'):
uvlist.append(cv)
uvbarlist.append(cvbar)
elif open_boundary in ('east', 'west'):
uvlist.append(cu)
uvbarlist.append(cubar)
# Update cycle length to be always 'mid_month' days greater
# than bry_time
if bry_cycle == 0.:
if monthly:
nc.variables['bry_time'].cycle_length = bry_time + mid_month # days
else:
nc.variables['bry_time'].cycle_length = bry_time
nc.close()
bryind1 += 1
# Update tind for each record
tind += 1
# Update bry_time (brings it to end of current month)
#bry_time += mid_month
print '---time to process', time.time() - ot_loop_start, 'seconds'
if last_file in soda_file: active = False
print 'all done'