def format_axis(axis,
name=None,
force=True,
recreate=False,
format_subaxes=True,
nodef=True,
mode='warn',
**kwargs):
"""Format a MV2 axis according to its generic name
:Params:
- **axis**: A :mod:`numpy` or :mod:`MV2` variabe.
- **name**: Single or list of generic axis names. It should be one of
those listed by :attr:`CF_AXIS_SPECS`.If None, it is guessed
with :func:`match_known_axis`.
- **force**, optional: Overwrite attributes in all cases.
- **nodef**, optional: Remove location specification when it refers to the
default location (:attr:`DEFAULT_LOCATION`).
- **axes2d_<param>**, optional: <param> is passed to
:func:`~vacumm.misc.grid.misc.create_axes2d` for 2D axes.
- **recreate**, optional: Force recreation of axes using either
- Other parameters are passed as attributes.
:Examples:
>>> axis1d = format_axis(array1d, 'lon')
>>> axis2d = format_axis(array2d, 'lon_u', axes2d_iid = 'xi', axes2d_jid = 'xi', recreate=True)
"""
# Guess best generic name from a list
if name is None: return axis
if isinstance(name, (list, tuple)):
for nm in name:
if match_obj(axis, nm):
name = nm
break
# Check specs
if name is None: # guess it
name = match_known_axis(axis)
if not name:
if mode == 'warn':
warn("Can't guess CF axis name")
return axis
elif mode == 'silent':
return axis
else:
raise KeyError("Variable does not match any CF axis")
elif name not in CF_AXIS_SPECS:
if mode == 'warn':
warn("Generic axis name not found '%s'." % name)
return axis
elif mode == 'silent':
return axis
else:
raise KeyError(
"Generic axis name not found '%s'. Please choose one of: %s" %
(name, ', '.join(CF_AXIS_SPECS.keys())))
specs = CF_AXIS_SPECS[name]
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# Always a MV2 axis (1D or 2D)
axis._oldid = axis.id
kwaxed2d = kwfilter(kwargs, 'axes2d_')
if not isaxis(axis) or recreate:
if len(axis.shape) == 1:
axis = cdms2.createAxis(axis)
else:
xy = specs['axis'].lower()
kwaxed2d[xy] = axis
axis = create_axes2d(**kwaxed2d)
return axis
axis2d = len(axis.shape) == 2
# Apply specs
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# - remove default location
if nodef:
for att in 'id', 'long_name', 'standard_name':
# sname = stype+'s'
if att not in specs: continue
if get_loc(specs[att], att) == DEFAULT_LOCATION:
specs[att] = [no_loc_single(specs[att][0], att)]
# - id
if force or axis.id.startswith('variable_') or axis.id.startswith('axis_'):
axis.id = specs['id'][0]
# - attributes
for att, val in cf2atts(specs,
exclude=['axis'] if axis2d else None,
**kwargs).items():
if force or not getattr(axis, att, ''):
setattr(axis, att, val)
# - store cf name
axis._vacumm_cf_name = axis.id
# Sub-axes for 2D axes
if axis2d and format_subaxes:
format_axis(axis.getAxis(-1), specs['iaxis'])
format_axis(axis.getAxis(-2), specs['jaxis'])
return axis
def get_spec(var1, var2=None, dx=None, dy=None, verbose=False, fft=False, **kwargs):
"""Get the spectrum of a 2D variable
:Return: specvar,nbwave,dk
"""
# Get the resolution in meters
kwresol = kwfilter(kwargs, 'resol_')
if None in [dx, dy]:
if not cdms2.isVariable(var1):
raise TypeError('var1 must be a MV2 array to compute dx and dy')
kwresol.setdefault('proj', True)
ldx, ldy = resol(var1, **kwresol)
dx = dx or ldx
dy = dy or ldy
if N.ma.isMA(var1): var1= var1.filled(0.)
if N.ma.isMA(var2): var2 = var2.filled(0.)
# Part 1 - estimate of the wavenumbers
[kx,ky,kkx,kky,kk,Lx,Ly] = get_kxky(var1, dx, dy, verbose=verbose)
if verbose:
print "dx = %s, fy = %s " %(dx,dy)
print "kx = ",kx[0:3]
print "ky = ",ky[0:3]
print "kkx[0:3,2] = ",kkx[0:3,2]
print "kky[0:3,1] = ",kky[0:3,1]
print "kk[0:3,3] = ",kk[0:3,3]
print "shape",kx.shape,ky.shape,kkx.shape,kky.shape,kk.shape
# Part 2 - estimate of the spectrum
# - fast fourier transform
if fft:
hat_phi1=N.fft.fft2(var1)
hat_phi1=hat_phi1*hat_phi1.conj()
hat_phi1=hat_phi1.real.copy() # useless
else:
hat_phi1 = var1
if var2 is not None:
if fft:
hat_phi2=N.fft.fft2(var2)
hat_phi2=hat_phi2*hat_phi2.conj()
hat_phi2=hat_phi2.real.copy() # useless
else:
hat_phi2 = var2
hat_spec = hat_phi1 + hat_phi2
else:
hat_spec = hat_phi1
# - integration of the spectrum
# shift to have values centered on the intervals
dk = kx[1] - kx[0]
dk_half = dk/2 # half of the interval
k_= kx[0:min(var1.shape[1],var1.shape[0])/2] + dk
specvar = k_*0
for i in range(len(k_)):
# get indexes that satisfy two conditions
# integration over a spectral width
specvar[i] = ( hat_spec[ (kk<=k_[i]+dk_half) & (kk>k_[i]-dk_half) ] ).sum()
# Normalisation (Danioux 2011)
specvar /= (var1.shape[1]*var1.shape[0])**2 * dk
# Dimensionalization to be able to compare with the litterature
nbwave = k_*1000.0/2.0/N.pi # from rad/m to km/m
dk *= 1000.0/2.0/N.pi
specvar *= 2.0*N.pi/1000.0
if verbose:
if var2 is not None:
print "\n Normalized co-spectrum : \n",specvar
else:
print "\n Normalized spectrum : \n",specvar
return specvar,nbwave,dk
def format_var(var,
name=None,
force=True,
format_axes=True,
order=None,
nodef=True,
mode='warn',
**kwargs):
"""Format a MV2 variable according to its generic name
:Params:
- **var**: A :mod:`numpy` or :mod:`MV2` variabe.
- **name**: Generic name of variable. It should be one of
those listed by :attr:`CF_VAR_SPECS`. If None, it is guessed
with :func:`match_known_var`.
- **force**, optional: Overwrite attributes in all cases.
- **format_axes**, optional: Also format axes.
- **nodef**, optional: Remove location specification when it refers to the
default location (:attr:`DEFAULT_LOCATION`).
- **mode**: "silent", "warn" or "raise".
- Other parameters are passed as attributes, except those:
- present in specifications to allow overriding defaults,
- starting with 'x', 'y', or 't' which are passed
to :func:`format_axis`.
:Examples:
>>> var = format_var(myarray, 'sst', valid_min=-2, valid_max=100)
"""
# Filter keywords for axis formating
axismeths = {'t': 'getTime', 'y': 'getLatitude', 'x': 'getLongitude'}
kwaxes = {}
for k in axismeths.keys():
kwaxes[k] = kwfilter(kwargs, k + '_')
# Always a MV2 array
if not cdms2.isVariable(var):
var = MV2.asarray(var)
# Check specs
if name is None: # guess it
name = match_known_var(var)
if not name:
if mode == 'warn':
warn("Can't guess cf name")
return var
elif mode == 'silent':
return var
else:
raise KeyError("Variable does not match any CF var")
elif name not in CF_VAR_SPECS and name not in CF_AXIS_SPECS:
if var.id in CF_VAR_SPECS or var.id in CF_AXIS_SPECS:
name = var.id
elif mode == 'warn':
warn("Generic var name not found '%s'." % name)
return var
elif mode == 'silent':
return var
else:
raise KeyError(
"Generic var name not found '%s'. Please choose one of: %s" %
(name, ', '.join(CF_VAR_SPECS.keys() + CF_AXIS_SPECS.keys())))
isaxis = name in CF_AXIS_SPECS
if isaxis:
specs = CF_AXIS_SPECS[name].copy()
if 'axis' in specs:
del specs['axis']
else:
specs = CF_VAR_SPECS[name].copy()
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# - remove default location
if nodef:
refloc = specs.get('physloc', None) or DEFAULT_LOCATION
for att in 'id', 'long_name', 'standard_name':
if get_loc(specs[att], att) == refloc:
specs[att] = [no_loc_single(specs[att][0], att)]
name = specs['id'][0]
# - id
if ((force is True or force in [2, 'id', 'all'])
or var.id.startswith('variable_')
or (isaxis and var.id.startswith('axis_'))): # FIXME: use regexp
var.id = name
# - attributes
forceatts = (force is True or force in ['atts', 'all']
or (isinstance(force, int) and force > 0))
for att, val in cf2atts(specs, **kwargs).items():
if forceatts or not getattr(var, att, ''):
setattr(var, att, val)
# - physical location
loc = get_loc(var, mode='ext')
if not loc and 'physloc' in specs:
loc = specs['physloc']
if loc:
if 'physloc' in specs and loc == specs['physloc']:
var._vacumm_cf_physloc = loc.lower()
set_loc(var, loc)
# - store cf name
var._vacumm_cf_name = name
# Axes
if format_axes:
# Order
order = var.getOrder() if not isinstance(order, basestring) else order
if order is not None:
if not re.match('^[xyzt-]+$', order):
raise VACUMMError("Wrong cdms order type: " + order)
if len(order) != var.ndim:
raise VACUMMError(
"Cdms order should be of length %s instead of %s" %
(var.ndim, len(order)))
# First check
if 'axes' in specs:
axspecs = specs['axes']
formatted = []
for key, meth in axismeths.items():
axis = getattr(var, meth)()
if order is not None: order.replace(key, '-')
if axis is not None:
format_axis(axis, axspecs[key], **kwaxes[key])
formatted.append(key)
# Check remaining simple axes (DOES NOT WORK FOR 2D AXES)
if order is not None and order != '-' * len(order):
for key in axismeths.keys():
if key in order and key not in formatted:
axis = var.getAxis(order.index(key))
format_axis(axis, axspecs[key], **kwaxes[key])
return var
def plot(self, var=None, orig=True, tide=True, cotes=True, highs=True, lows=True, zeros=True, legend=True, title=None, savefig=None, savefigs=None, show=True, marker='o', **kwargs):
# Which variable?
vtypes = 'orig', 'tide', 'highs', 'lows', 'zeros', 'cotes'
if var is not None:
assert var in vtypes
for vt in vtypes:
exec "%s = %s"%(vt, vt==var)
# Plot params
# - specific
kwplot = {}
for vt in vtypes:
kwplot[vt] = kwfilter(kwargs, vt)
kwplot[vt].update(show=False)
kwplot[vt].update(title=False)
# - global
nt = self.data['base'].shape[0]
times = T.mpl(self.data['base'][0:nt:nt-1].getTime())
kwargs.setdefault('xmin', times[0])
kwargs.setdefault('xmax', times[1])
# - complete
for vt in vtypes:
tmp = kwargs.copy()
tmp.update(kwplot[vt])
kwplot[vt] = tmp
anom = not (orig or highs or lows or zeros)
# Original signal
if orig:
kwplot['orig'].setdefault('color', '#888888')
kwplot['orig'].setdefault('zorder', '10')
curve(self.sea_level(), **kwplot['orig'])
# High tides
if highs:
kwplot['highs'].setdefault('color', 'r')
kwplot['highs'].setdefault('linewidth', 0)
kwplot['highs'].setdefault('markersize', 5)
kwplot['highs'].setdefault('zorder', '12')
curve(self.highs(), marker, **kwplot['highs'])
# Low tides
if lows:
kwplot['lows'].setdefault('color', 'b')
kwplot['lows'].setdefault('linewidth', 0)
kwplot['lows'].setdefault('markersize', 5)
kwplot['lows'].setdefault('zorder', '12')
curve(self.lows(), marker, **kwplot['lows'])
# Zeros
if zeros:
kwplot['zeros'].setdefault('color', 'k')
kwplot['zeros'].setdefault('linewidth', 0)
kwplot['zeros'].setdefault('markersize', 5)
kwplot['zeros'].setdefault('zorder', '12')
curve(self.zeros(), marker, **kwplot['zeros'])
# Tidal signal
if tide:
kwplot['orig'].setdefault('color', 'k')
kwplot['orig'].setdefault('zorder', '11')
curve(self.tide(anom=anom), **kwplot['tide'])
# Surcote/decotes
if cotes:
kwplot['cotes'].setdefault('color', 'g')
kwplot['cotes'].setdefault('zorder', '12')
curve(self.cotes(anom=anom), **kwplot['cotes'])
# Misc
if title is None:
if var is not None:
title = var.title()
else:
title = 'Marigraph'
if title:
P.title(title)
if savefig:
P.savefig(savefig, **kwfilter(kwargs, 'savefig'))
if savefigs:
Savefigs(savefigs, **kwfilter(kwargs, 'savefigs'))
if show:
P.show()
def plot(self, var=None, orig=True, tide=True, cotes=True, highs=True, lows=True, zeros=True, legend=True, title=None, savefig=None, savefigs=None, show=True, marker='o', **kwargs):
# Which variable?
vtypes = 'orig', 'tide', 'highs', 'lows', 'zeros', 'cotes'
if var is not None:
assert var in vtypes
for vt in vtypes:
exec("%s = %s"%(vt, vt==var))
# Plot params
# - specific
kwplot = {}
for vt in vtypes:
kwplot[vt] = kwfilter(kwargs, vt)
kwplot[vt].update(show=False)
kwplot[vt].update(title=False)
# - global
nt = self.data['base'].shape[0]
times = T.mpl(self.data['base'][0:nt:nt-1].getTime())
kwargs.setdefault('xmin', times[0])
kwargs.setdefault('xmax', times[1])
# - complete
for vt in vtypes:
tmp = kwargs.copy()
tmp.update(kwplot[vt])
kwplot[vt] = tmp
anom = not (orig or highs or lows or zeros)
# Original signal
if orig:
kwplot['orig'].setdefault('color', '#888888')
kwplot['orig'].setdefault('zorder', '10')
curve(self.sea_level(), **kwplot['orig'])
# High tides
if highs:
kwplot['highs'].setdefault('color', 'r')
kwplot['highs'].setdefault('linewidth', 0)
kwplot['highs'].setdefault('markersize', 5)
kwplot['highs'].setdefault('zorder', '12')
curve(self.highs(), marker, **kwplot['highs'])
# Low tides
if lows:
kwplot['lows'].setdefault('color', 'b')
kwplot['lows'].setdefault('linewidth', 0)
kwplot['lows'].setdefault('markersize', 5)
kwplot['lows'].setdefault('zorder', '12')
curve(self.lows(), marker, **kwplot['lows'])
# Zeros
if zeros:
kwplot['zeros'].setdefault('color', 'k')
kwplot['zeros'].setdefault('linewidth', 0)
kwplot['zeros'].setdefault('markersize', 5)
kwplot['zeros'].setdefault('zorder', '12')
curve(self.zeros(), marker, **kwplot['zeros'])
# Tidal signal
if tide:
kwplot['orig'].setdefault('color', 'k')
kwplot['orig'].setdefault('zorder', '11')
curve(self.tide(anom=anom), **kwplot['tide'])
# Surcote/decotes
if cotes:
kwplot['cotes'].setdefault('color', 'g')
kwplot['cotes'].setdefault('zorder', '12')
curve(self.cotes(anom=anom), **kwplot['cotes'])
# Misc
if title is None:
if var is not None:
title = var.title()
else:
title = 'Marigraph'
if title:
P.title(title)
if savefig:
P.savefig(savefig, **kwfilter(kwargs, 'savefig'))
if savefigs:
Savefigs(savefigs, **kwfilter(kwargs, 'savefigs'))
if show:
P.show()
def format_axis(axis, name, force=True, recreate=False, format_subaxes=True,
nodef=True, **kwargs):
"""Format a MV2 axis according to its generic name
:Params:
- **var**: A :mod:`numpy` or :mod:`MV2` variabe.
- **name**: Single or list of generic axis names. It should be one of
those listed by :attr:`GENERIC_AXIS_NAMES`.
- **force**, optional: Overwrite attributes in all cases.
- **nodef**, optional: Remove location specification when it refers to the
default location (:attr:`DEFAULT_LOCATION`).
- **axes2d_<param>**, optional: <param> is passed to
:func:`~vacumm.misc.grid.misc.create_axes2d` for 2D axes.
- **recreate**, optional: Force recreation of axes using either
- Other parameters are passed as attributes.
:Examples:
>>> axis1d = format_axis(array1d, 'lon')
>>> axis2d = format_axis(array2d, 'lon_u', axes2d_iid = 'xi', axes2d_jid = 'xi', recreate=True)
"""
# Guess best generic name from a list
if name is None: return axis
if isinstance(name, (list, tuple)):
for nm in name:
if match_obj(axis, nm):
name = nm
break
# Check specs
if name not in GENERIC_AXIS_NAMES:
raise KeyError("Generic axis name not found '%s'. Please choose one of: %s"%(
name, ', '.join(GENERIC_AXIS_NAMES)))
specs = AXIS_SPECS[name]
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# Always a MV2 axis (1D or 2D)
axis._oldid = axis.id
kwaxed2d = kwfilter(kwargs, 'axes2d_')
if not isaxis(axis) or recreate:
if len(axis.shape)==1:
axis = cdms2.create_axis(axis)
else:
xy = specs['axis'].lower()
kwaxed2d[xy] = axis
axis = create_axes2d(**kwaxed2d)
return axis
axis2d = len(axis.shape)==2
# Apply specs
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# - remove default location
if nodef:
for stype in 'name', 'long_name', 'standard_name':
sname = stype+'s'
if sname not in specs: continue
if get_loc(specs[sname], stype)==DEFAULT_LOCATION:
specs[sname] = [no_loc_single(specs[sname][0], stype)]
# - id
if force or axis.id.startswith('variable_') or axis.id.startswith('axis_'):
axis.id = specs['names'][0]
# - attributes
for att, val in cf2atts(specs, exclude=['axis'] if axis2d else None, **kwargs).items():
if force or not getattr(axis, att, ''):
setattr(axis, att, val)
# - store cf name
axis._vacumm_cf_name = axis.id
# Sub-axes for 2D axes
if axis2d and format_subaxes:
format_axis(axis.getAxis(-1), specs['iaxis'][0])
format_axis(axis.getAxis(-2), specs['jaxis'][0])
return axis
def format_var(var, name, force=True, format_axes=True, order=None, nodef=True, **kwargs):
"""Format a MV2 variable according to its generic name
:Params:
- **var**: A :mod:`numpy` or :mod:`MV2` variabe.
- **name**: Generic name of variable. It should be one of
those listed by :attr:`GENERIC_VAR_NAMES`.
- **force**, optional: Overwrite attributes in all cases.
- **format_axes**, optional: Also format axes.
- **nodef**, optional: Remove location specification when it refers to the
default location (:attr:`DEFAULT_LOCATION`).
- Other parameters are passed as attributes, except those:
- present in specifications to allow overriding defaults,
- starting with 'x', 'y', or 't' which are passed
to :func:`format_axis`.
:Examples:
>>> var = format_var(myarray, 'sst', valid_min=-2, valid_max=100)
"""
# Filter keywords for axis formating
axismeths = {'t':'getTime', 'y':'getLatitude', 'x':'getLongitude'}
kwaxes = {}
for k in axismeths.keys():
kwaxes[k] = kwfilter(kwargs, k+'_')
# Always a MV2 array
var = MV2.asarray(var)
# Check specs
if name not in GENERIC_VAR_NAMES:
if var.id in GENERIC_VAR_NAMES:
name = var.id
else:
raise KeyError("Generic var name not found '%s'. Please choose one of: %s"%(
name, ', '.join(GENERIC_VAR_NAMES)))
specs = VAR_SPECS[name].copy()
# - merge kwargs and specs
for key, val in kwargs.items():
if val is None or key not in specs: continue
# Check type
if not isinstance(val, list) and isinstance(specs[key], list):
val = [val]
# Set
specs[key] = val
del kwargs[key]
# - remove default location
if nodef:
refloc = specs.get('physloc', DEFAULT_LOCATION)
for stype in 'name', 'long_name', 'standard_name':
sname = stype+'s'
if sname not in specs: continue
if get_loc(specs[sname], stype)==refloc:
specs[sname] = [no_loc_single(specs[sname][0], stype)]
name = specs['names'][0]
# - id
if force or var.id.startswith('variable_'):
var.id = name
# - attributes
for att, val in cf2atts(specs, **kwargs).items():
if force or not getattr(var, att, ''):
setattr(var, att, val)
# - physical location
loc = get_loc(var, mode='ext')
if not loc and 'physloc' in specs:
loc = specs['physloc']
if loc:
if 'physloc' in specs and loc in specs['physloc']:
var._vacumm_cf_physloc = loc.lower()
set_loc(var, loc)
# - store cf name
var._vacumm_cf_name = name
# Axes
if format_axes:
# Order
order = var.getOrder() if not isinstance(order, basestring) else order
if order is not None:
if not re.match('^[xyzt-]+$', order):
raise VACUMMError("Wrong cdms order type: "+order)
if len(order)!=var.ndim:
raise VACUMMError("Cdms order should be of length %s instead of %s"%(var.ndim, len(order)))
# First check
axspecs = specs['axes']
formatted = []
for key, meth in axismeths.items():
axis = getattr(var, meth)()
if order is not None: order.replace(key, '-')
if axis is not None:
format_axis(axis, axspecs[key], **kwaxes[key])
formatted.append(key)
# Check remaining simple axes (DOES NOT WORK FOR 2D AXES)
if order is not None and order!='-'*len(order):
for key in axismeths.keys():
if key in order and key not in formatted:
axis = var.getAxis(order.index(key))
format_axis(axis, axspecs[key], **kwaxes[key])
return var