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IOverticalGrid.py
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IOverticalGrid.py
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from datetime import datetime
import numpy as np
import warnings
__author__ = 'Trond Kristiansen'
__email__ = '[email protected]'
__created__ = datetime(2008, 8, 15)
__modified__ = datetime(2015, 7, 25)
__version__ = "1.5"
__status__ = "Development"
'''
Various vertical coordinates
Presently, only ocean s-coordinates are supported. Future plans will be to
include all of the vertical coordinate systems defined by the CF conventions.
vgrid.py function copied from https://github.com/kshedstrom/pyroms (Frederic Castruccio)
'''
def calculateVgrid(self):
print(("---> Setting up vertical coordinates using self.vtransform: %s self.vstretching: %s"%(self.vtransform,self.vstretching)))
if self.vtransform == 1:
vgrid = s_coordinate(self.h, self.theta_b, self.theta_s, self.tcline, self.nlevels, self.vtransform, self.vstretching, zeta=None)
elif self.vtransform == 2 and self.vstretching == 2:
vgrid = s_coordinate_2(self.h, self.theta_b, self.theta_s, self.tcline, self.nlevels, self.vtransform, self.vstretching, zeta=None)
elif self.vtransform == 2 and self.vstretching == 4:
vgrid = s_coordinate_4(self.h, self.theta_b, self.theta_s, self.tcline, self.nlevels, self.vtransform, self.vstretching, zeta=None)
else:
raise Warning('Unknow vertical transformation Vtrans')
self.z_r = vgrid.z_r[0,:]
self.z_w = vgrid.z_w[0,:]
self.Cs_rho = vgrid.Cs_r
self.Cs_w = vgrid.Cs_w
self.s_rho = vgrid.s_rho
self.s_w = vgrid.s_w
class s_coordinate(object):
"""
Song and Haidvogel (1994) vertical coordinate transformation (Vtransform=1) and
stretching functions (Vstretching=1).
return an object that can be indexed to return depths
s = s_coordinate(h, theta_b, theta_s, Tcline, N)
"""
def __init__(self, h, theta_b, theta_s, tcline, N, vtransform, vstretching, zeta=None):
self.h = np.asarray(h)
self.hmin = h.min()
self.theta_b = theta_b
self.theta_s = theta_s
self.tcline = tcline
self.N = int(N)
self.Np = self.N+1
self.vtransform = vtransform
self.vstretching = vstretching
self.hc = min(self.hmin, self.tcline)
self.Vtrans = 1
if self.vtransform==1:
if (self.tcline > self.hmin):
warnings.warn('Vertical transformation parameters are not defined correctly in either gridid.txt or in the history files: \n Tcline = %d and hmin = %d. \n You need to make sure that Tcline <= hmin when using transformation 1.' %(self.Tcline,self.hmin))
self.c1 = 1.0
self.c2 = 2.0
self.p5 = 0.5
if zeta is None:
self.zeta = np.zeros(h.shape)
else:
self.zeta = zeta
self._get_s_rho()
self._get_s_w()
self._get_Cs_r()
self._get_Cs_w()
self.z_r = z_r(self.h, self.hc, self.N, self.s_rho, self.Cs_r, self.zeta, self.Vtrans)
self.z_w = z_w(self.h, self.hc, self.Np, self.s_w, self.Cs_w, self.zeta, self.Vtrans)
def _get_s_rho(self):
lev = np.arange(1,self.N+1,1)
ds = 1.0 / self.N
self.s_rho = -self.c1 + (lev - self.p5) * ds
def _get_s_w(self):
lev = np.arange(0,self.Np,1)
ds = 1.0 / (self.Np-1)
self.s_w = -self.c1 + lev * ds
def _get_Cs_r(self):
if (self.theta_s >= 0):
Ptheta = np.sinh(self.theta_s * self.s_rho) / np.sinh(self.theta_s)
Rtheta = np.tanh(self.theta_s * (self.s_rho + self.p5)) / \
(self.c2 * np.tanh(self.p5 * self.theta_s)) - self.p5
self.Cs_r = (self.c1 - self.theta_b) * Ptheta + self.theta_b * Rtheta
else:
self.Cs_r = self.s_rho
def _get_Cs_w(self):
if (self.theta_s >= 0):
Ptheta = np.sinh(self.theta_s * self.s_w) / np.sinh(self.theta_s)
Rtheta = np.tanh(self.theta_s * (self.s_w + self.p5)) / \
(self.c2 * np.tanh(self.p5 * self.theta_s)) - self.p5
self.Cs_w = (self.c1 - self.theta_b) * Ptheta + self.theta_b * Rtheta
else:
self.Cs_w = self.s_w
class s_coordinate_2(s_coordinate):
"""
A. Shchepetkin (2005) UCLA-ROMS vertical coordinate transformation (Vtransform=2) and
stretching functions (Vstretching=2).
return an object that can be indexed to return depths
s = s_coordinate_2(h, theta_b, theta_s, Tcline, N)
"""
def __init__(self, h, theta_b, theta_s, tcline, N, vtransform, vstretching, zeta=None):
self.h = np.asarray(h)
self.hmin = h.min()
self.theta_b = theta_b
self.theta_s = theta_s
self.tcline = tcline
self.N = int(N)
self.Np = self.N+1
self.vtransform = vtransform
self.vstretching = vstretching
self.hc = self.tcline
self.Vtrans = 2
self.Aweight = 1.0
self.Bweight = 1.0
self.c1 = 1.0
self.c2 = 2.0
self.p5 = 0.5
if zeta is None:
self.zeta = np.zeros(h.shape)
else:
self.zeta = zeta
self._get_s_rho()
self._get_s_w()
self._get_Cs_r()
self._get_Cs_w()
self.z_r = z_r(self.h, self.hc, self.N, self.s_rho, self.Cs_r, self.zeta, self.Vtrans)
self.z_w = z_w(self.h, self.hc, self.Np, self.s_w, self.Cs_w, self.zeta, self.Vtrans)
def _get_s_rho(self):
super(s_coordinate_2, self)._get_s_rho()
def _get_s_w(self):
super(s_coordinate_2, self)._get_s_w()
def _get_Cs_r(self):
if (self.theta_s >= 0):
Csur = (self.c1 - np.cosh(self.theta_s * self.s_rho)) / \
(np.cosh(self.theta_s) - self.c1)
if (self.theta_b >= 0):
Cbot = np.sinh(self.theta_b * (self.s_rho + self.c1)) / \
np.sinh(self.theta_b) - self.c1
Cweight = (self.s_rho + self.c1)**self.Aweight * \
(self.c1 + (self.Aweight / self.Bweight) * \
(self.c1 - (self.s_rho + self.c1)**self.Bweight))
self.Cs_r = Cweight * Csur + (self.c1 - Cweight) * Cbot
else:
self.Cs_r = Csur
else:
self.Cs_r = self.s_rho
def _get_Cs_w(self):
if (self.theta_s >= 0):
Csur = (self.c1 - np.cosh(self.theta_s * self.s_w)) / \
(np.cosh(self.theta_s) - self.c1)
if (self.theta_b >= 0):
Cbot = np.sinh(self.theta_b * (self.s_w + self.c1)) / \
np.sinh(self.theta_b) - self.c1
Cweight = (self.s_w + self.c1)**self.Aweight * \
(self.c1 + (self.Aweight / self.Bweight) * \
(self.c1 - (self.s_w + self.c1)**self.Bweight))
self.Cs_w = Cweight * Csur + (self.c1 - Cweight) * Cbot
else:
self.Cs_w = Csur
else:
self.Cs_w = self.s_w
class s_coordinate_4(s_coordinate):
"""
A. Shchepetkin (2005) UCLA-ROMS vertical coordinate transformation (Vtransform=2) and
stretching functions (Vstretching=4).
return an object that can be indexed to return depths
s = s_coordinate_4(h, theta_b, theta_s, Tcline, N)
"""
def __init__(self, h, theta_b, theta_s, tcline, N, vtransform, vstretching, zeta=None):
self.h = np.asarray(h)
self.hmin = h.min()
self.theta_b = theta_b
self.theta_s = theta_s
self.tcline = tcline
self.N = int(N)
self.Np = self.N+1
self.vtransform = vtransform
self.vstretching = vstretching
self.hc = self.tcline
self.Vtrans = 4
self.c1 = 1.0
self.c2 = 2.0
self.p5 = 0.5
if zeta is None:
self.zeta = np.zeros(h.shape)
else:
self.zeta = zeta
self._get_s_rho()
self._get_s_w()
self._get_Cs_r()
self._get_Cs_w()
self.z_r = z_r(self.h, self.hc, self.N, self.s_rho, self.Cs_r, self.zeta, self.Vtrans)
self.z_w = z_w(self.h, self.hc, self.Np, self.s_w, self.Cs_w, self.zeta, self.Vtrans)
def _get_s_rho(self):
super(s_coordinate_4, self)._get_s_rho()
def _get_s_w(self):
super(s_coordinate_4, self)._get_s_w()
def _get_Cs_r(self):
if (self.theta_s > 0):
Csur = (self.c1 - np.cosh(self.theta_s * self.s_rho)) / \
(np.cosh(self.theta_s) - self.c1)
else:
Csur = -self.s_rho**2
if (self.theta_b > 0):
Cbot = (np.exp(self.theta_b * Csur) - self.c1 ) / \
(self.c1 - np.exp(-self.theta_b))
self.Cs_r = Cbot
else:
self.Cs_r = Csur
def _get_Cs_w(self):
if (self.theta_s > 0):
Csur = (self.c1 - np.cosh(self.theta_s * self.s_w)) / \
(np.cosh(self.theta_s) - self.c1)
else:
Csur = -self.s_w**2
if (self.theta_b > 0):
Cbot = (np.exp(self.theta_b * Csur) - self.c1 ) / \
( self.c1 - np.exp(-self.theta_b) )
self.Cs_w = Cbot
else:
self.Cs_w = Csur
class z_r(object):
"""
return an object that can be indexed to return depths of rho point
z_r = z_r(h, hc, N, s_rho, Cs_r, zeta, Vtrans)
"""
def __init__(self, h, hc, N, s_rho, Cs_r, zeta, Vtrans):
self.h = h
self.hc = hc
self.N = N
self.s_rho = s_rho
self.Cs_r = Cs_r
self.zeta = zeta
self.Vtrans = Vtrans
def __getitem__(self, key):
if isinstance(key, tuple) and len(self.zeta.shape) > len(self.h.shape):
zeta = self.zeta[key[0]]
res_index = (slice(None),) + key[1:]
elif len(self.zeta.shape) > len(self.h.shape):
zeta = self.zeta[key]
res_index = slice(None)
else:
zeta = self.zeta
res_index = key
if self.h.ndim == zeta.ndim: # Assure a time-dimension exists
zeta = zeta[np.newaxis, :]
ti = zeta.shape[0]
z_r = np.empty((ti, self.N) + self.h.shape, 'd')
if self.Vtrans == 1:
for n in range(ti):
for k in range(self.N):
z0 = self.hc * self.s_rho[k] + (self.h - self.hc) * self.Cs_r[k]
z_r[n,k,:] = z0 + zeta[n,:] * (1.0 + z0 / self.h)
elif self.Vtrans == 2 or self.Vtrans == 4:
for n in range(ti):
for k in range(self.N):
z0 = (self.hc * self.s_rho[k] + self.h * self.Cs_r[k]) / \
(self.hc + self.h)
z_r[n,k,:] = zeta[n,:] + (zeta[n,:] + self.h) * z0
return np.squeeze(z_r[res_index])
class z_w(object):
"""
return an object that can be indexed to return depths of w point
z_w = z_w(h, hc, Np, s_w, Cs_w, zeta, Vtrans)
"""
def __init__(self, h, hc, Np, s_w, Cs_w, zeta, Vtrans):
self.h = h
self.hc = hc
self.Np = Np
self.s_w = s_w
self.Cs_w = Cs_w
self.zeta = zeta
self.Vtrans = Vtrans
def __getitem__(self, key):
if isinstance(key, tuple) and len(self.zeta.shape) > len(self.h.shape):
zeta = self.zeta[key[0]]
res_index = (slice(None),) + key[1:]
elif len(self.zeta.shape) > len(self.h.shape):
zeta = self.zeta[key]
res_index = slice(None)
else:
zeta = self.zeta
res_index = key
if self.h.ndim == zeta.ndim: # Assure a time-dimension exists
zeta = zeta[np.newaxis, :]
ti = zeta.shape[0]
z_w = np.empty((ti, self.Np) + self.h.shape, 'd')
if self.Vtrans == 1:
for n in range(ti):
for k in range(self.Np):
z0 = self.hc * self.s_w[k] + (self.h - self.hc) * self.Cs_w[k]
z_w[n,k,:] = z0 + zeta[n,:] * (1.0 + z0 / self.h)
elif self.Vtrans == 2 or self.Vtrans == 4:
for n in range(ti):
for k in range(self.Np):
z0 = (self.hc * self.s_w[k] + self.h * self.Cs_w[k]) / \
(self.hc + self.h)
z_w[n,k,:] = zeta[n,:] + (zeta[n,:] + self.h) * z0
return np.squeeze(z_w[res_index])
def get_z_levels(self):
"""
Get a list of all the variables contained in netCDF file "filename"
"""
self.z_r=-self.h
if len(self.z_r)==0:
print(("No depth matrix found in file %s"%(self.selffilename)))