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py_mercator2roms.py
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py_mercator2roms.py
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# -*- coding: utf-8 -*-
# %run py_mercator2roms.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: emason@imedea.uib-csic.es
===========================================================================
Create a ROMS boundary file based on Mercator 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 time import strptime
from py_roms2roms import vertInterp, horizInterp, bry_flux_corr, debug0, debug1, debug2
from py_roms2roms import ROMS, RomsGrid, WestGrid, EastGrid, NorthGrid, SouthGrid, RomsData
class MercatorData (RomsData):
'''
MercatorData class (inherits from RomsData class)
'''
def __init__(self, filenames, model_type, mercator_var, romsgrd, **kwargs):
"""
Creates a new Mercator data object.
Parameters
----------
*filenames* : list of Mercator nc files.
*model_type* : string specifying Mercator model.
*romsgrd* : a `RomsGrid` instance.
"""
super(MercatorData, self).__init__(filenames[0], model_type)
self.romsfile = filenames
self.vartype = mercator_var
self.romsgrd = romsgrd
self.var_dic = {'sossheig':'SSH',
'votemper':'TEMP', 'vosaline':'SALT',
'vozocrtx':'U', 'vomecrty':'V',
'ssh':'SSH',
'temperature':'TEMP', 'salinity':'SALT',
'u':'U', 'v':'V'}
#print self.var_dic
self._set_variable_type()
try:
self._lon = self.read_nc('nav_lon', indices='[:]')
self._lat = self.read_nc('nav_lat', indices='[:]')
except Exception:
self._lon = self.read_nc('longitude', indices='[:]')
self._lat = self.read_nc('latitude', indices='[:]')
self._lon, self._lat = np.meshgrid(self._lon, self._lat)
#print self._lon.shape
#print self._lat.shape
if kwargs.has_key('i0'):
self.i0, self.i1 = kwargs['i0'], kwargs['i1']
self.j0, self.j1 = kwargs['j0'], kwargs['j1']
else:
self.set_subgrid(romsgrd, k=50)
try:
self._depths = self.read_nc('deptht', indices='[:]')
except Exception:
self._depths = self.read_nc('depth', indices='[:]')
try:
self._time_count = self.read_nc('time_counter', indices='[:]')
except Exception:
self._time_count = self.read_nc('time', indices='[:]')
self._set_data_shape()
self._set_dates()
self.datain = np.empty(self._data_shape, dtype=np.float64)
if len(self._data_shape) == 2:
self.dataout = np.ma.empty(self.romsgrd.lon().shape)
else:
tmp_shape = (self._depths.size, self.romsgrd.lon().shape[0],
self.romsgrd.lon().shape[1])
self.datatmp = np.ma.empty(tmp_shape, dtype=np.float64).squeeze()
self.dataout = np.ma.empty(self.romsgrd.mask3d().shape,
dtype=np.float64).squeeze()
self._set_maskr()
self._set_angle()
def lon(self):
return self._lon[self.j0:self.j1, self.i0:self.i1]
def lat(self):
return self._lat[self.j0:self.j1, self.i0:self.i1]
def maskr(self):
return self._maskr[self.j0:self.j1, self.i0:self.i1]
def maskr3d(self):
return self._maskr3d[:, self.j0:self.j1, self.i0:self.i1]
def angle(self):
return self._angle[self.j0:self.j1, self.i0:self.i1]
def depths(self):
return self._depths
def dates(self):
return self._time_count
def _set_data_shape(self):
ssh_varnames = ('sossheig') # clumsy; needs to be added to if they invent more names
#if kwargs.has_key('predefined_shp'):
#self._data_shape = kwargs['predefined_shp']
#if len(self._data_shape ) > 2:
#self.dimtype = '3D'
#else:
#self.dimtype = '2D'
#print 'self.varname', self.varname
if self._depths.size == 1 or self.varname in ssh_varnames:
_shp = (self.j1 - self.j0, self.i1 - self.i0)
self._data_shape = _shp
self.dimtype = '2D'
else:
_shp = (self._depths.size, self.j1 - self.j0, self.i1 - self.i0)
self._data_shape = _shp
self.dimtype = '3D'
return self
def _set_variable_type(self):
self.varname = None
for varname, vartype in zip(self.var_dic.keys(), self.var_dic.values()):
#print self.romsfile
#print varname, vartype
#print self.list_of_variables()
#print self.vartype
if varname in self.list_of_variables() and vartype in self.vartype:
self.varname = varname
return self
if self.varname is None:
raise Exception # no candidate variable identified
def _get_maskr(self, k=None):
"""
Called by _set_maskr()
"""
if '3D' in self.dimtype:
self.k = k
indices = '[0, self.k]'
else:
indices = '[0]'
try:
_mask = self.read_nc(self.varname, indices=indices).mask
except Exception: # triggered when all points are masked
_mask = np.ones(self.read_nc(self.varname, indices=indices).shape)
_mask = np.asarray(_mask, dtype=np.int)
_mask *= -1
_mask += 1
return _mask
def _set_maskr(self):
"""
Set the landsea mask (*self.maskr*) with same shape
as input Mercator nc file. If a 3D variable, then additional
attribute, self._maskr3d is set.
"""
if '3D' in self.dimtype:
self._maskr = self._get_maskr(k=0)
self._set_maskr3d()
else:
self._maskr = self._get_maskr()
return self
def _set_maskr3d(self):
"""
Called by _set_maskr()
"""
_3dshp = (self._depths.size, self._lon.shape[0], self._lon.shape[1])
#print _3dshp
self._maskr3d = np.empty(_3dshp)
for k in xrange(self._depths.size):
self._maskr3d[k] = self._get_maskr(k=k)
return self
def _set_angle(self):
'''
Compute angles of local grid positive x-axis relative to east
'''
latu = np.deg2rad(0.5 * (self._lat[:,1:] + self._lat[:,:-1]))
lonu = np.deg2rad(0.5 * (self._lon[:,1:] + self._lon[:,:-1]))
dellat = latu[:,1:] - latu[:,:-1]
dellon = lonu[:,1:] - lonu[:,:-1]
dellon[dellon > np.pi] = dellon[dellon > np.pi] - (2. * np.pi)
dellon[dellon < -np.pi] = dellon[dellon < -np.pi] + (2. * np.pi)
dellon = dellon * np.cos(0.5 * (latu[:,1:] + latu[:,:-1]))
self._angle = np.zeros_like(self._lat)
ang_s = np.arctan(dellat / (dellon + np.spacing(0.4)))
deli = np.logical_and(dellon < 0., dellat < 0.)
ang_s[deli] = ang_s[deli] - np.pi
deli = np.logical_and(dellon < 0., dellat >= 0.)
ang_s[deli] = ang_s[deli] + np.pi
ang_s[ang_s > np.pi] = ang_s[ang_s > np.pi] - np.pi
ang_s[ang_s < -np.pi] = ang_s[ang_s <- np.pi] + np.pi
self._angle[:,1:-1] = ang_s
self._angle[:,0] = self._angle[:,1]
self._angle[:,-1] = self._angle[:,-2]
return self
def get_variable(self, date):
ind = (self._time_count == date).nonzero()[0][0]
#print 'ind', ind
try:
with netcdf.Dataset(self.romsfile[ind]) as nc:
if '3D' in self.dimtype:
self.datain[:] = np.ma.masked_array(
nc.variables[self.varname][0, :, self.j0:self.j1,
self.i0:self.i1].astype(np.float64)).data
else:
self.datain[:] = np.ma.masked_array(
nc.variables[self.varname][0, self.j0:self.j1,
self.i0:self.i1].astype(np.float64)).data
except Exception:
with netcdf.Dataset(self.romsfile[0]) as nc:
if '3D' in self.dimtype:
self.datain[:] = np.ma.masked_array(
nc.variables[self.varname][ind, :, self.j0:self.j1,
self.i0:self.i1].astype(np.float64)).data
else:
self.datain[:] = np.ma.masked_array(
nc.variables[self.varname][ind, self.j0:self.j1,
self.i0:self.i1].astype(np.float64)).data
return self
def _set_time_origin(self):
try:
self._time_counter_origin = self.read_nc_att('time_counter', 'time_origin')
ymd, hms = self._time_counter_origin.split(' ')
except Exception:
try:
self._time_counter_origin = self.read_nc_att('time_counter', 'units')
junk, junk, ymd, hms = self._time_counter_origin.split(' ')
#print self._time_counter_origin
except Exception:
self._time_counter_origin = self.read_nc_att('time', 'units')
junk, junk, ymd, hms = self._time_counter_origin.split(' ')
#else: Exception
#print self._time_counter_origin
y, mo, d = ymd.split('-')
h, mi, s = hms.split(':')
#print y, mo, d, h, mi, s
try:
time_origin = datetime(int(y), strptime(mo,'%b').tm_mon, int(d),
int(h), int(mi), int(s))
except Exception:
time_origin = datetime(int(y), int(mo), int(d),
int(h), int(mi), int(s))
self.time_origin = plt.date2num(time_origin)
return self
def _set_dates(self):
self._set_time_origin()
#self._time_count = self.read_nc_mf('time_counter')
with netcdf.Dataset(self.romsfile[0]) as nc:
try:
date_start = nc.variables['time_counter'][:]
except Exception:
date_start = nc.variables['time'][:]
with netcdf.Dataset(self.romsfile[-1]) as nc:
try:
date_end = nc.variables['time_counter'][:]
except Exception:
date_end = nc.variables['time'][:]
if 'second' in self._time_counter_origin:
self._time_interval = 86400.
elif 'hour' in self._time_counter_origin:
self._time_interval = 24.
#print 'date_start',date_start
#print 'date_end',date_end
#print 'self._time_interval',self._time_interval
try:
#print 'here 1'
self._time_count = np.arange(date_start, date_end +
self._time_interval, self._time_interval)
except:
#print 'here 2'
self._time_count = np.arange(date_start[0], date_end[-1] +
self._time_interval, self._time_interval)
#print 'date_start', date_start
#print 'date_end', date_end
#print '',
#self._time_count = self.read_nc_mf('TIME')
self._time_count /= self._time_interval #86400.
self._time_count += self.time_origin
return self
def get_date(self, ind):
return self._time_count[ind]
def get_fillmask_cofs(self):
if '3D' in self.dimtype:
self.fillmask_cof_tmp = []
for k in xrange(self._depths.size):
try:
self.get_fillmask_cof(self.maskr3d()[k])
self.fillmask_cof_tmp.append(self.fillmask_cof)
except Exception:
self.fillmask_cof_tmp.append(None)
self.fillmask_cof = self.fillmask_cof_tmp
else:
self.get_fillmask_cof(self.maskr())
return self
def _fillmask(self, dist, iquery, igood, ibad, k=None):
'''
'''
weight = dist / (dist.min(axis=1)[:,np.newaxis] * np.ones_like(dist))
np.place(weight, weight > 1., 0.)
if k is not None:
#print self.datain[k].shape
#print igood.shape
#print 'igood', igood
#print 'iquery', iquery
#print 'k', k
#print igood[:,0][iquery]
#print igood[:,1][iquery]
#aaaaaa
xfill = weight * self.datain[k][igood[:,0][iquery], igood[:,1][iquery]]
xfill = (xfill / weight.sum(axis=1)[:,np.newaxis]).sum(axis=1)
self.datain[k][ibad[:,0], ibad[:,1]] = xfill
else:
xfill = weight * self.datain[igood[:,0][iquery], igood[:,1][iquery]]
xfill = (xfill / weight.sum(axis=1)[:,np.newaxis]).sum(axis=1)
self.datain[ibad[:,0], ibad[:,1]] = xfill
return self
def fillmask(self):
'''Fill missing values in an array with an average of nearest
neighbours
From http://permalink.gmane.org/gmane.comp.python.scientific.user/19610
Order: call after self.get_fillmask_cof()
'''
if '3D' in self.dimtype:
for k in xrange(len(self.fillmask_cof)):
if self.fillmask_cof[k] is not None:
dist, iquery, igood, ibad = self.fillmask_cof[k]
#print dist, iquery, igood, ibad
try:
self._fillmask(dist, iquery, igood, ibad, k=k)
except:
self.maskr3d()[k] = 0
self._check_and_fix_deep_levels()
else:
dist, iquery, igood, ibad = self.fillmask_cof
self._fillmask(dist, iquery, igood, ibad)
return self
def _check_and_fix_deep_levels(self):
for k in xrange(self._depths.size):
if np.sum(self.maskr3d()[k]) == 0:
self.datain[k] = self.datain[k-1]
return self
def set_2d_depths(self):
'''
'''
self._2d_depths = np.tile(-self.depths()[::-1],
(self.romsgrd.h().size, 1)).T
return self
def set_3d_depths(self):
'''
'''
self._3d_depths = np.tile(-self.depths()[::-1],
(self.romsgrd.h().shape[1],
self.romsgrd.h().shape[0], 1)).T
return self
def set_map_coordinate_weights(self, j=None):
'''
Order : set_2d_depths or set_3d_depths
'''
if j is not None:
mercator_depths = self._3d_depths[:,j]
roms_depths = self.romsgrd.scoord2z_r()[:,j]
else:
mercator_depths = self._2d_depths
roms_depths = self.romsgrd.scoord2z_r()
self.mapcoord_weights = self.romsgrd.get_map_coordinate_weights(
roms_depths, mercator_depths)
return self
def reshape2roms(self):
'''
Following interpolation with horizInterp() we need to
include land points and reshape
'''
self.dataout = self.dataout.reshape(self.romsgrd.lon().shape)
return self
def _check_for_nans(self):
'''
'''
flat_mask = self.romsgrd.maskr().ravel()
assert not np.any(np.isnan(self.dataout[np.nonzero(flat_mask)])
), 'Nans in self.dataout sea points'
self.dataout[:] = np.nan_to_num(self.dataout)
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._vert_interp = vertInterp(self.mapcoord_weights)
return self
def _interp2romsgrd(self, k=None):
'''
'''
if k is not None:
interp = horizInterp(self.tri, self.datain[k].flat[self.ball])
interp = interp(self.romsgrd.points)
try:
self.datatmp[k] = interp
except Exception:
self.datatmp[k] = interp.reshape(self.romsgrd.maskr().shape)
else:
interp = horizInterp(self.tri, self.datain.flat[self.ball])
self.dataout = interp(self.romsgrd.points)
return self
def interp2romsgrd(self, j=None):
'''
'''
if '3D' in self.dimtype:
for k in np.arange(self._depths.size):
self._interp2romsgrd(k)
self.dataout[:] = self._vert_interp.vert_interp(self.datatmp[::-1])
else:
self._interp2romsgrd()
return self
#def _get_barotropic_velocity(self, baroclinic_velocity, cell_depths):
#sum_baroclinic = np.sum((baroclinic_velocity * cell_depths), axis=0)
#total_depth = np.sum((cell_depths), axis=0)
#sum_baroclinic /= total_depth
#return sum_baroclinic
#def set_barotropic(self): #, boundary):
#'''
#'''
#self.barotropic = self._get_barotropic_velocity(self.dataout, self.romsgrd.scoord2dz())
#return self
def debug_figure(self):
if self.var_dic[self.varname] in 'SALT':
cmin, cmax = 34, 38
elif self.var_dic[self.varname] in 'TEMP':
cmin, cmax = 5, 25
elif self.var_dic[self.varname] in ('U', 'V'):
cmin, cmax = -.4, .4
else:
raise Exception
plt.figure()
ax = plt.subplot(211)
ax.set_title('Mercator vertical grid')
pcm = ax.pcolormesh(self.romsgrd.lat(), -self.depths(), self.datatmp)
pcm.set_clim(cmin, cmax)
ax.plot(np.squeeze(self.romsgrd.lat()), -self.romsgrd.h(), c='gray', lw=3)
plt.colorbar(pcm)
ax = plt.subplot(212)
ax.set_title('ROMS vertical grid')
pcm = ax.pcolormesh(np.tile(self.romsgrd.lat(), (self.romsgrd.N, 1)),
self.romsgrd.scoord2z_r(),
self.dataout)
pcm.set_clim(cmin, cmax)
ax.plot(np.squeeze(self.romsgrd.lat()), -self.romsgrd.h(), c='gray', lw=2)
plt.colorbar(pcm)
plt.figure()
ax = plt.subplot(211)
ax.scatter(self._vert_interp.hweights, self._vert_interp.vweights, s=10, edgecolors='none')
ax = plt.subplot(212)
lats1 = np.tile(self.romsgrd.lat(), (self.romsgrd.N, 1))
lats2 = np.tile(self.romsgrd.lat(), (self._depths.size, 1))
ax.scatter(lats1, self.romsgrd.scoord2z_r(), s=10, c='r', edgecolors='none', label='ROMS')
ax.scatter(lats2, self._2d_depths, s=10, c='g', edgecolors='none', label='Mercator')
plt.show()
return
def check_angle(self):
'''
Check angle computation
'''
plt.pcolormesh(self.lon(), self.lat(), self.angle())
plt.axis('image')
plt.colorbar()
plt.show()
return
def prepare_romsgrd(romsgrd):
romsgrd.make_gnom_transform().proj2gnom(ignore_land_points=False)
romsgrd.make_kdetree()
return romsgrd
def prepare_mercator(mercator, balldist):
assert mercator._time_count.size == len(mercator.romsfile), "it's possible some files are missing"
mercator.proj2gnom(ignore_land_points=False, M=mercator.romsgrd.M)
mercator.child_contained_by_parent(mercator.romsgrd)
mercator.make_kdetree().get_fillmask_cofs()
ballpoints = mercator.kdetree.query_ball_tree(mercator.romsgrd.kdetree, r=balldist)
mercator.ball = np.array(np.array(ballpoints).nonzero()[0])
mercator.tri = sp.Delaunay(mercator.points[mercator.ball])
if '3D' in mercator.dimtype:
mercator.set_2d_depths().set_map_coordinate_weights()
mercator.vert_interp()
proceed = True
return mercator, proceed
if __name__ == '__main__':
'''
py_mercator2roms
Evan Mason 2014
'''
#_USER DEFINED VARIABLES_______________________________________
# Mercator information
#mercator_dir = '/marula/emason/data/mercator/nea_daily/'
#mercator_dir = '/marula/emason/data/mercator/nwmed/ORCA12/'
#mercator_dir = '/marula/emason/data/IBI_daily/'
mercator_dir = '/data_cmems/ibi_phys005001b/'
# Child ROMS information
#roms_dir = '../'
#roms_dir = '/marula/emason/runs2012/MedSea5/'
#roms_dir = '/marula/emason/runs2013/na_7pt5km_intann_5day/'
#roms_dir = '/marula/emason/runs2009/na_2009_7pt5km/'
#roms_dir = '/marula/emason/runs2014/na75/'
#roms_dir = '/Users/emason/runs/runs2014/MedCan5/'
#roms_dir = '/Users/emason/runs2009/na_2009_7pt5/'
#roms_dir = '/marula/emason/runs2014/NWMED2/'
#roms_dir = '/marula/emason/runs2014/AlbSea175/'
#roms_dir = '/marula/emason/runs2015/AlbSea500/'
roms_dir = '/marula/emason/runs2016/meddies/'
#roms_grd = 'roms_grd_NA2009_7pt5km.nc'
#roms_grd = 'grd_MedCan5.nc'
#roms_grd = 'roms_grd_NA2009_7pt5km.nc'
#roms_grd = 'grd_nwmed_2km.nc'
#roms_grd = 'grd_AlbSea175.nc'
#roms_grd = 'grd_AlbSea500.nc'
roms_grd = 'grd_meddies_1km.nc'
if 'roms_grd_NA2009_7pt5km.nc' in roms_grd:
sigma_params = dict(theta_s=6, theta_b=0, hc=120, N=32)
bry_filename = 'bry_na75_mercator.nc'
start_date = '20100106'
end_date = '20130531'
day_zero = '????????'
obc_dict = dict(south=1, east=1, north=1, west=1) # 1=open, 0=closed
elif 'grd_nwmed_2km.nc' in roms_grd:
sigma_params = dict(theta_s=6.5, theta_b=0, hc=110, N=36)
bry_filename = 'bry_nwmed_2km.nc'
start_date = '20100106'
end_date = '20130531'
day_zero = '19850101'
obc_dict = dict(south=1, east=1, north=1, west=1) # 1=open, 0=closed
elif 'grd_AlbSea175.nc' in roms_grd:
sigma_params = dict(theta_s=7., theta_b=0.25, hc=90., N=32)
bry_filename = 'bry_AlbSea175.nc'
start_date = '20131230'
end_date = '20140602'
day_zero = '20140101'
obc_dict = dict(south=0, east=1, north=1, west=1) # 1=open, 0=closed
elif 'grd_AlbSea500.nc' in roms_grd:
sigma_params = dict(theta_s=6., theta_b=0.25, hc=100., N=32)
bry_filename = 'bry_AlbSea500_NOPREFILTER.nc'
start_date = '20131230'
end_date = '20140602'
day_zero = '20140101'
obc_dict = dict(south=0, east=1, north=1, west=1) # 1=open, 0=closed
elif 'grd_meddies_1km.nc' in roms_grd:
sigma_params = dict(theta_s=7, theta_b=6, hc=300, N=50)
#ini_filename = 'ini_meddies_ecco_198501.nc'
#bry_filename = 'bry_meddies_IBI_4r1M_20160120.nc'
#bry_filename = 'bry_meddies_IBI_3r1M_20130422.nc'
bry_filename = 'bry_meddies_IBI_2r1M_20120109.nc'
#bry_filename = 'bry_meddies_IBI_1rM_20120109.nc'
#ini_date = '20131130'
#start_date, end_date, day_zero = '20130422', '20140413', '20130422'
start_date, end_date, day_zero = '20120109', '20130421', '20120109'
#start_date, end_date, day_zero = '20111231', '20120108', '20111231'
obc_dict = dict(south=1, east=1, north=1, west=1) # 1=open, 0=closed
else:
raise Exception('No sigma params defined for grid: %s' % roms_grd)
# Child ROMS boundary file information
bry_cycle = 0. # days, 0 means no cycle
if 'ORCA' in mercator_dir:
#mercator_ssh_files = sorted(glob.glob(mercator_dir + '*_gridT*.nc'))
mercator_ssh_files = sorted(glob.glob(mercator_dir + '*_grid2D*.nc'))
mercator_temp_files = sorted(glob.glob(mercator_dir + '*_gridT*.nc'))
mercator_salt_files = sorted(glob.glob(mercator_dir + '*_gridS*.nc'))
mercator_u_files = sorted(glob.glob(mercator_dir + '*_gridU*.nc'))
mercator_v_files = sorted(glob.glob(mercator_dir + '*_gridV*.nc'))
balldist = 50000. # meters
elif 'PSY2V4R4' in mercator_dir:
to_be_done
balldist = 50000. # meters
elif 'IBI_daily' in mercator_dir or 'ibi' in mercator_dir:
print 'Warning: check version numbers in filenames'
#mercator_ssh_files = glob.glob(mercator_dir + 'pde_ibi36v?r1_ibisr_01dav_*_HC01.nc')
#mercator_ssh_files = glob.glob(mercator_dir +
#'CMEMS_4r1M_IBI_PHY_NRT_PdE_01dav_????????_????????_R*_HC01.nc')
#mercator_ssh_files = glob.glob(mercator_dir +
#'CMEMS_3r1M_IBI_PHY_NRT_PdE_01dav_????????_????????_R*_HC01.nc')
mercator_ssh_files = glob.glob(mercator_dir +
'CMEMS_2r1M_IBI_PHY_NRT_PdE_01dav_????????_????????_R*_HC01.nc')
#mercator_ssh_files = glob.glob(mercator_dir +
#'CMEMS_1r1M_IBI_PHY_NRT_PdE_01dav_????????_????????_R*_HC01.nc')
mercator_temp_files = \
mercator_salt_files = \
mercator_u_files = \
mercator_v_files = sorted(mercator_ssh_files)
balldist = 20000. # meters
#aaaaaa
#_END USER DEFINED VARIABLES_______________________________________
plt.close('all')
assert len(start_date) == 8, '*start_date* must be a length 8 string'
assert len(end_date) == 8, '*end_date* must be a length 8 string'
fillval = 9999.
if 'IBI_daily' in mercator_dir or 'ibi' in mercator_dir:
k2c = -273.15
day_zero = datetime(int(day_zero[:4]), int(day_zero[4:6]), int(day_zero[6:]))
day_zero = plt.date2num(day_zero)
start_date += '12'
end_date += '12'
dtstrdt = plt.datetime.datetime(np.int(start_date[:4]),
np.int(start_date[4:6]),
np.int(start_date[6:8]),
np.int(start_date[8:]))
dtenddt = plt.datetime.datetime(np.int(end_date[:4]),
np.int(end_date[4:6]),
np.int(end_date[6:8]),
np.int(end_date[8:]))
dtstr, dtend = plt.date2num(dtstrdt), plt.date2num(dtenddt)
# Set up a RomsGrid object
romsgrd = RomsGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
romsgrd.set_bry_dx()
romsgrd.set_bry_maskr()
romsgrd.set_bry_areas()
# Get surface areas of open boundaries
chd_bry_surface_areas = []
for boundary, is_open in zip(obc_dict.keys(), obc_dict.values()):
if 'west' in boundary and is_open:
chd_bry_surface_areas.append(romsgrd.area_west.sum(axis=0) * romsgrd.maskr_west)
elif 'east' in boundary and is_open:
chd_bry_surface_areas.append(romsgrd.area_east.sum(axis=0) * romsgrd.maskr_east)
elif 'south' in boundary and is_open:
chd_bry_surface_areas.append(romsgrd.area_south.sum(axis=0) * romsgrd.maskr_south)
elif 'north' in boundary and is_open:
chd_bry_surface_areas.append(romsgrd.area_north.sum(axis=0) * romsgrd.maskr_north)
# Get total surface of open boundaries
chd_bry_total_surface_area = np.array([area.sum() for area in chd_bry_surface_areas]).sum()
# Set up a RomsData object for creation of the boundary file
romsbry = RomsData(roms_dir + bry_filename, 'ROMS')
romsbry.create_bry_nc(romsgrd, obc_dict, bry_cycle, fillval, 'py_mercator2roms')
mercator_vars = dict(SSH = mercator_ssh_files,
TEMP = mercator_temp_files,
SALT = mercator_salt_files,
U = mercator_u_files)
for mercator_var, mercator_files in zip(mercator_vars.keys(), mercator_vars.values()):
print '\nProcessing variable *%s*' % mercator_var
proceed = False
with netcdf.Dataset(mercator_files[0]) as nc:
try:
mercator_date_start = nc.variables['time_counter'][:]
mercator_time_units = nc.variables['time_counter'].units
mercator_time_origin = nc.variables['time_counter'].time_origin
mercator_time_origin = plt.date2num(plt.datetime.datetime.strptime(
mercator_time_origin, '%Y-%b-%d %H:%M:%S'))
except Exception:
mercator_date_start = nc.variables['time'][:]
mercator_time_units = nc.variables['time'].units
mercator_time_origin = mercator_time_units.partition(' ')[-1].partition(' ')[-1]
mercator_time_origin = plt.date2num(plt.datetime.datetime.strptime(
mercator_time_origin, '%Y-%m-%d %H:%M:%S'))
with netcdf.Dataset(mercator_files[-1]) as nc:
try:
mercator_date_end = nc.variables['time_counter'][:]
except Exception:
mercator_date_end = nc.variables['time'][:]
if 'seconds' in mercator_time_units:
mercator_dates = np.arange(mercator_date_start, mercator_date_end + 86400, 86400)
mercator_dates /= 86400.
elif 'hours' in mercator_time_units:
mercator_dates = np.arange(mercator_date_start, mercator_date_end + 24, 24)
mercator_dates /= 24.
else:
raise Exception('deal_with_when_a_problem')
mercator_dates += mercator_time_origin
mercator_dates = mercator_dates[np.logical_and(mercator_dates >= dtstr,
mercator_dates <= dtend)]
for boundary, is_open in zip(obc_dict.keys(), obc_dict.values()):
print '\n--- processing %sern boundary' % boundary
if 'west' in boundary and is_open:
romsgrd_at_bry = WestGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
proceed = True
elif 'north' in boundary and is_open:
romsgrd_at_bry = NorthGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
proceed = True
elif 'east' in boundary and is_open:
romsgrd_at_bry = EastGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
proceed = True
elif 'south' in boundary and is_open:
romsgrd_at_bry = SouthGrid(''.join((roms_dir, roms_grd)), sigma_params, 'ROMS')
proceed = True
else:
proceed = False #raise Exception
if proceed:
romsgrd_at_bry = prepare_romsgrd(romsgrd_at_bry)
mercator = MercatorData(mercator_files, 'Mercator', mercator_var, romsgrd_at_bry)
mercator, proceed = prepare_mercator(mercator, balldist)
if 'U' in mercator_var:
mercator_v = MercatorData(mercator_v_files, 'Mercator', 'V', romsgrd_at_bry,
i0=mercator.i0, i1=mercator.i1, j0=mercator.j0, j1=mercator.j1)
mercator_v, junk = prepare_mercator(mercator_v, balldist)
tind = 0 # index for writing records to bry file
for dt in mercator_dates:
dtnum = dt - day_zero
# Read in variables
mercator.get_variable(dt).fillmask()
# Calculate barotropic velocities
if mercator.vartype in 'U':
mercator_v.get_variable(dt).fillmask()
# Rotate to zero angle
for k in np.arange(mercator.depths().size):
u, v = mercator.datain[k], mercator_v.datain[k]
mercator.datain[k], mercator_v.datain[k] = mercator.rotate(u, v, sign=-1)
mercator.interp2romsgrd()
mercator_v.interp2romsgrd()
# Rotate u, v to child angle
for k in np.arange(romsgrd.N).astype(np.int):
u, v = mercator.dataout[k], mercator_v.dataout[k]
mercator.dataout[k], mercator_v.dataout[k] = romsgrd.rotate(u, v, sign=1,
ob=boundary)
mercator.set_barotropic()
mercator_v.set_barotropic()
else:
mercator.interp2romsgrd()
# Write to boundary file
with netcdf.Dataset(romsbry.romsfile, 'a') as nc:
if mercator.vartype in 'U':
if boundary in ('north', 'south'):
u = romsgrd.half_interp(mercator.dataout[:,:-1],
mercator.dataout[:,1:])
ubar = romsgrd.half_interp(mercator.barotropic[:-1],
mercator.barotropic[1:])
nc.variables['u_%s' % boundary][tind] = u
nc.variables['ubar_%s' % boundary][tind] = ubar
nc.variables['v_%s' %boundary][tind] = mercator_v.dataout
nc.variables['vbar_%s' % boundary][tind] = mercator_v.barotropic
elif boundary in ('east', 'west'):
v = romsgrd.half_interp(mercator_v.dataout[:,:-1],
mercator_v.dataout[:,1:])
vbar = romsgrd.half_interp(mercator_v.barotropic[:-1],
mercator_v.barotropic[1:])
nc.variables['v_%s' % boundary][tind] = v
nc.variables['vbar_%s' % boundary][tind] = vbar
nc.variables['u_%s' % boundary][tind] = mercator.dataout
nc.variables['ubar_%s' % boundary][tind] = mercator.barotropic
else:
raise Exception('Unknown boundary: %s' % boundary)
elif mercator.vartype in 'SSH':
nc.variables['zeta_%s' % boundary][tind] = mercator.dataout
nc.variables['bry_time'][tind] = np.float(dtnum)
elif mercator.vartype in 'TEMP':
if (mercator.dataout > 100.).any():
mercator.dataout += k2c # Kelvin to Celcius
#mercator.dataout *= romsgrd.mask3d()
nc.variables['temp_%s' % boundary][tind] = mercator.dataout
else:
varname = mercator.vartype.lower() + '_%s' % boundary
nc.variables[varname][tind] = mercator.dataout
#if 'east' in boundary:
#print plt.num2date(dt)
#plt.figure(99)
#plt.subplot(121)
#plt.pcolormesh(mercator.mapcoord_weights)
#plt.colorbar()
#plt.subplot(122)
#plt.pcolormesh(mercator.dataout)
##plt.pcolormesh(np.log(mercator.mapcoord_weights))
#plt.clim(34, 39)
#plt.colorbar()
#plt.show()
tind += 1
#proceed = False
# Correct volume fluxes and write to boundary file
print '\nProcessing volume flux correction'
with netcdf.Dataset(romsbry.romsfile, 'a') as nc:
bry_times = nc.variables['bry_time'][:]
boundarylist = []
for bry_ind in xrange(bry_times.size):
uvbarlist = []
for boundary, is_open in zip(obc_dict.keys(), obc_dict.values()):
if 'west' in boundary and is_open:
uvbarlist.append(nc.variables['ubar_west'][bry_ind])
elif 'east' in boundary and is_open:
uvbarlist.append(nc.variables['ubar_east'][bry_ind])
elif 'north' in boundary and is_open:
uvbarlist.append(nc.variables['vbar_north'][bry_ind])
elif 'south' in boundary and is_open:
uvbarlist.append(nc.variables['vbar_south'][bry_ind])
if bry_ind == 0 and is_open:
boundarylist.append(boundary)
fc = bry_flux_corr(boundarylist,
chd_bry_surface_areas,
chd_bry_total_surface_area,
uvbarlist)
print '------ barotropic velocity correction:', fc, 'm/s'
for boundary, is_open in zip(obc_dict.keys(), obc_dict.values()):
if 'west' in boundary and is_open:
nc.variables['u_west'][bry_ind] -= fc