def coriolis_parameter(lat,
gravity=default_gravity,
fromvar=False,
format_axes=False):
"""Get the coriolis parameters computed at each latitude
:Params:
- **lat**: Latitude or a variable with latitude coordinates.
- **gravity**, optional: Gravity.
- **fromvar**, optional: If True, lat is supposed to be a MV2
array with latitude coordinates.
"""
# Latitude
if fromvar:
if not cdms2.isVariable(lat):
raise VACUMMError('lat must a MV2 array because fromvar is True')
latv = lat * 0
lat = lat.getLatitude()
if lat is None:
raise VACUMMError(
'lat must a MV2 array with a latitude axis because fromvar is True'
)
if cdms2.isVariable(lat): lat = lat.asma() # 2D axes
if lat.shape != latv.shape:
if len(lat.shape) == 2:
latv[:] = N.ma.resize(lat, latv.shape)
else:
yaxis = latv.getOrder().index('y')
new_shape = len(latv.shape) * [1]
new_shape[yaxis] = latv.shape[yaxis]
tile_shape = list(latv.shape)
tile_shape[yaxis] = 1
latv[:] = N.tile(lat[:].reshape(new_shape), tile_shape)
else:
latv = lat if not N.ndim(lat) else lat[:]
# Compute
f0 = 2 * N.ma.sin(N.pi * latv / 180.)
# f0 *= 2*N.pi/(24.*3600.)
f0 *= 2 * N.pi / (86164.) # 86164 = sidereal day....
# Format
if N.isscalar(f0): return f0
f0 = MV2.asarray(f0)
if not fromvar and isaxis(lat) and f0.ndim == 1:
f0.setAxis(0, lat)
return format_var(f0, 'corio', format_axes=format_axes)
def coriolis_parameter(lat, gravity=default_gravity, fromvar=False, format_axes=False):
"""Get the coriolis parameters computed at each latitude
:Params:
- **lat**: Latitude or a variable with latitude coordinates.
- **gravity**, optional: Gravity.
- **fromvar**, optional: If True, lat is supposed to be a MV2
array with latitude coordinates.
"""
# Latitude
if fromvar:
if not cdms2.isVariable(lat):
raise VACUMMError('lat must a MV2 array because fromvar is True')
latv = lat*0
lat = lat.getLatitude()
if lat is None:
raise VACUMMError('lat must a MV2 array with a latitude axis because fromvar is True')
if cdms2.isVariable(lat): lat=lat.asma() # 2D axes
if lat.shape!=latv.shape:
if len(lat.shape)==2:
latv[:] = N.ma.resize(lat, latv.shape)
else:
yaxis = latv.getOrder().index('y')
new_shape = len(latv.shape)*[1]
new_shape[yaxis] = latv.shape[yaxis]
tile_shape = list(latv.shape)
tile_shape[yaxis] = 1
latv[:] = N.tile(lat[:].reshape(new_shape), tile_shape)
else:
latv = lat if N.isscalar(lat) else lat[:]
# Compute
f0 = 2*N.ma.sin(N.pi*latv/180.)
# f0 *= 2*N.pi/(24.*3600.)
f0 *= 2*N.pi/(86164.) # 86164 = sidereal day....
# Format
if N.isscalar(f0): return f0
f0 = MV2.asarray(f0)
if not fromvar and isaxis(lat) and f0.ndim==1:
f0.setAxis(0, lat)
return format_var(f0, 'corio', format_axes=format_axes)
def _format_var_(vv, name, mask=None, prefix=True, suffix=True, templates=None,
htemplates=None, attributes=None, single=True, **kwargs):
# Some inits
ist = name.startswith('t')
name = name[1:]
if prefix is True:
prefix = 'Temporal ' if ist else 'Spatial '
elif not prefix:
prefix = ''
kwargs['copy'] = 0
# Aways have a list
if isinstance(vv, tuple):
vv = list(vv)
single = False
elif not isinstance(vv, list):
vv = [vv]
single = True
elif single:
single = len(vv)==1
else:
single = False
dual = len(vv)==2
if templates is not None and not isinstance(templates, (list, tuple)):
templates = [templates]*len(vv)
if htemplates is not None and not isinstance(htemplates, (list, tuple)):
htemplates = [htemplates]*len(vv)
if attributes is None:
attributes = ({}, {})
elif not isinstance(attributes, (list, tuple)):
attributes = [attributes]*len(vv)
# Long_name
long_name = prefix
if name=='avail':
long_name += 'availability'
if name=='count':
long_name += 'count'
elif name=='mean':
long_name += 'average'
elif name=='std':
long_name += 'standard deviation'
elif name=='bias':
long_name += 'bias'
elif name=='rms':
long_name += 'absolute RMS difference'
elif name=='crms':
long_name += 'centered RMS difference'
elif name=='corr':
long_name += 'correlation'
elif name=='hist':
long_name += 'histogram'
# Type change
if 'count' in name:
dtype = 'l'
else:
dtype = None
for i, v in enumerate(vv):
# From template or not
hvar = v.ndim==2 # Histogram-like variables: first axis = bins
hist = htemplates and hvar
if templates is not None:
# From axis (sstats)
if isaxis(templates[i]):
# if hvar and not ist:
# v = N.ma.transpose(v) # time first, not bins
var = MV2.asarray(v)
var.setAxis(0, templates[i])
# try:
# var.setAxis(int(hist), templates[i])
# except:
# pass
if hist:
var.setAxis(1, htemplates[i])
# From variable (tstats)
else:
try:
var = (htemplates if hvar else templates)[i].clone()
except:
pass
try:
var[:] = v.reshape(var.shape)
except:
pass
else:
var = MV2.asarray(v)
del v
# Type
if dtype:
var = var.astype(dtype)
# Mask
if mask is not None:
func = N.resize if var.size!=mask.size else N.reshape
var[:] = MV2.masked_where(func(mask, var.shape), var, copy=0)
# Attributes
# - id and long_name
var.id = attributes[i]['id']+'_'+name
var.long_name = long_name
if suffix and isinstance(suffix, basestring):
var.long_name += suffix
# - single stats
if name in ['mean', 'std', 'hist', 'min', 'max']:
if "units" in attributes[i]:
var.units = attributes[i]['units']
if suffix is True and "long_name" in attributes[i]:
var.long_name += ' of '+attributes[i]['long_name']
# - dual stats
elif name in ['bias', 'rms', 'crms']:
for attr in attributes: # loop on both variables attributes
if "units" in attr and not hasattr(var, 'units'):
var.units = attr['units']
if suffix is True and "long_name" in attr and var.long_name==long_name:
var.long_name += ' of '+attr['long_name']
vv[i] = var
if single:
return vv[0]
return tuple(vv)
def _format_var_(vv, name, mask=None, prefix=True, suffix=True, templates=None,
htemplates=None, attributes=None, single=True, **kwargs):
if name=='tstd':
pass
# Some inits
ist = name.startswith('t')
name = name[1:]
if prefix is True:
prefix = 'Temporal ' if ist else 'Spatial '
elif not prefix:
prefix = ''
kwargs['copy'] = 0
# Aways have a list
if isinstance(vv, tuple):
vv = list(vv)
single = False
elif not isinstance(vv, list):
vv = [vv]
single = True
elif single:
single = len(vv)==1
else:
single = False
dual = len(vv)==2
if templates is not None and not isinstance(templates, (list, tuple)):
templates = [templates]*len(vv)
if htemplates is not None and not isinstance(htemplates, (list, tuple)):
htemplates = [htemplates]*len(vv)
if attributes is None:
attributes = ({}, {})
elif not isinstance(attributes, (list, tuple)):
attributes = [attributes]*len(vv)
# Long_name
long_name = prefix
if name=='avail':
long_name += 'availability'
elif name=='mean':
long_name += 'average'
elif name=='std':
long_name += 'standard deviation'
elif name=='bias':
long_name += 'bias'
elif name=='rms':
long_name += 'absolute RMS difference'
elif name=='crms':
long_name += 'centered RMS difference'
elif name=='corr':
long_name += 'correlation'
elif name=='hist':
long_name += 'histogram'
# Type change
if 'count' in name:
dtype = 'l'
else:
dtype = None
for i, v in enumerate(vv):
# From template or not
hvar = v.ndim==2 # Histogram-like variables: first axis = bins
hist = htemplates and hvar
if templates is not None:
# From axis (sstats)
if isaxis(templates[i]):
# if hvar and not ist:
# v = N.ma.transpose(v) # time first, not bins
var = MV2.asarray(v)
var.setAxis(0, templates[i])
# try:
# var.setAxis(int(hist), templates[i])
# except:
# pass
if hist:
var.setAxis(1, htemplates[i])
# From variable (tstats)
else:
try:
var = (htemplates if hvar else templates)[i].clone()
except:
pass
try:
var[:] = v.reshape(var.shape)
except:
pass
else:
var = MV2.asarray(v)
del v
# Type
if dtype:
var = var.astype(dtype)
# Mask
if mask is not None:
func = N.resize if var.size!=mask.size else N.reshape
var[:] = MV2.masked_where(func(mask, var.shape), var, copy=0)
# Attributes
# - id and long_name
var.id = attributes[i]['id']+'_'+name
var.long_name = long_name
if suffix and isinstance(suffix, basestring):
var.long_name += suffix
# - single stats
if name in ['mean', 'std', 'hist', 'min', 'max']:
if "units" in attributes[i]:
var.units = attributes[i]['units']
if suffix is True and "long_name" in attributes[i]:
var.long_name += ' of '+attributes[i]['long_name']
# - dual stats
elif name in ['bias', 'rms', 'crms']:
for attr in attributes: # loop on both variables attributes
if "units" in attr and not hasattr(var, 'units'):
var.units = attr['units']
if suffix is True and "long_name" in attr and var.long_name==long_name:
var.long_name += ' of '+attr['long_name']
vv[i] = var
if single:
return vv[0]
return tuple(vv)
def change_loc(var, toloc, axes=True, squeeze=True):
"""Change location specifications of a variable and its axes
It affects the id, the standard_name and the long_name when they are defined.
:Params:
-
:Example:
>>> change_loc(sst, 'u').id
'sst_u'
>>> change_loc(sst, 't', squeeze=True).id
'sst'
"""
# Squeeze physloc
if not isinstance(squeeze, basestring):
if squeeze:
squeeze = get_physloc(var)
else:
squeeze = None
# Change attributes
# - get
specs = change_loc_specs(
toloc,
squeeze=squeeze,
id=var.id,
standard_name=getattr(var, 'standard_name', None),
long_name=getattr(var, 'long_name', None),
)
# - set
var.id = specs['id']
for att in 'standard_name', 'long_name':
if att in specs:
setattr(var, att, specs[att])
# - cf name
if hasattr(var, '_vacumm_cf_name'):
var._vacumm_cf_name = change_loc_single(var._vacumm_cf_name,
'id',
toloc,
squeeze=squeeze)
# Change axes and grid attributes
if axes and cdms2.isVariable(var) or cdms2.isGrid(var):
# Axes
# - usual
for meth in 'Longitude', 'Latitude', 'Time', 'Level':
if hasattr(var, 'get' + meth):
axismet = getattr(var, 'get' + meth) # var.getLongitude
if axismet() is not None:
change_loc(axismet(), toloc, squeeze=squeeze)
# - 2d axes
if cdms2.isVariable(var) and isaxis(var) and var.ndim > 2:
for i in -1, -2:
change_loc(var.getAxis(i), toloc, squeeze=squeeze)
# Grid
if cdms2.isVariable(var) and var.getGrid() is not None:
change_loc(var.getGrid(), toloc, squeeze=squeeze)
# Reference attribute
set_loc(var, toloc)
return var
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 change_loc(var, toloc, axes=True, squeeze=True):
"""Change location specifications of a variable and its axes
It affects the id, the standard_name and the long_name when they are defined.
:Params:
-
:Example:
>>> change_loc(sst, 'u').id
'sst_u'
>>> change_loc(sst, 't', squeeze=True).id
'sst'
"""
# Squeeze physloc
if not isinstance(squeeze, basestring):
if squeeze:
squeeze = get_physloc(var)
else:
squeeze = None
# Change attributes
# - get
specs = change_loc_specs(toloc, squeeze=squeeze,
names=var.id,
standard_names = getattr(var, 'standard_name', None),
long_names = getattr(var, 'long_name', None),
)
# - set
var.id = specs['names']
for att in 'standard_name', 'long_name':
if att+'s' in specs:
setattr(var, att, specs[att+'s'])
# - cf name
if hasattr(var, '_vacumm_cf_name'):
var._vacumm_cf_name = change_loc_single(var._vacumm_cf_name, 'name', toloc,
squeeze=squeeze)
# Change axes and grid attributes
if axes and cdms2.isVariable(var) or cdms2.isGrid(var):
# Axes
# - usual
for meth in 'Longitude', 'Latitude', 'Time', 'Level':
if hasattr(var, 'get'+meth):
axismet = getattr(var, 'get'+meth) # var.getLongitude
if axismet() is not None:
change_loc(axismet(), toloc, squeeze=squeeze)
# - 2d axes
if cdms2.isVariable(var) and isaxis(var) and var.ndim>2:
for i in -1, -2:
change_loc(var.getAxis(i), toloc, squeeze=squeeze)
# Grid
if cdms2.isVariable(var) and var.getGrid() is not None:
change_loc(var.getGrid(), toloc, squeeze=squeeze)
# Reference attribute
set_loc(var, toloc)
return var
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