def getbounds(ifile, dimkey):
dim = ifile.dimensions[dimkey]
dimboundkey = dimkey + '_bounds'
dimbndkey = dimkey + '_bnds'
if dimboundkey in ifile.variables:
db = ifile.variables[dimboundkey]
elif dimbndkey in ifile.variables:
db = ifile.variables[dimbndkey]
elif dimkey in ifile.variables:
d = ifile.variables[dimkey]
dd = np.diff(d)
ddm = dd.mean()
if not (ddm == dd).all():
warn('Bounds is an approximation assuming ' +
'%s variable is cell centers' % dimkey)
db = (d[:-1] + d[1:]) / 2.
db = np.append(np.append(d[0] - dd[0] / 2., db), d[-1] + dd[-1] / 2)
return db
else:
return np.arange(0, len(dim) + 1)
if len(dim) == db.shape[0] and db.shape[1] == 2:
return np.append(db[:, 0], db[-1, 1])
elif db.ndim == 1:
return db
else:
return db[:, 0]
def getlatbnds(ifile):
if 'latitude_bounds' in ifile.variables:
latb = ifile.variables['latitude_bounds']
unit = latb.units.strip()
if 'nv' in latb.dimensions:
if latb[:].ndim == 2 and len(ifile.dimensions['nv']) == 2:
latb = np.append(latb[:][:, 0], latb[:][-1, 1])
elif latb[:].ndim == 2 and len(ifile.dimensions['nv']) == 4:
latb = np.append(latb[:][:, 0], latb[:][-1, 1])
elif latb.ndim == 3:
latb = latb[:, :, 0]
elif 'latitude' in ifile.variables:
latb = ifile.variables['latitude']
unit = latb.units.strip()
latb = latb[:]
latdiff = np.diff(latb, axis=0)
if not (latdiff == latdiff[[0]]).all():
warn('Latitude bounds are approximate')
latb = np.apply_along_axis(np.convolve, 0, latb, [0.5, 0.5])
latb[0] *= 2
latb[-1] *= 2
if latb.ndim == 2:
latb = np.append(latb, latb[:, [-1]], axis=1)
elif 'ROW' in ifile.dimensions:
unit = 'x (m)'
latb = (np.arange(len(ifile.dimensions['ROW']) + 1) *
getattr(ifile, 'YCELL', 1) / 1000.)
else:
raise KeyError('latitude bounds not found')
return latb, unit
def getsigmabnds(ifile):
if hasattr(ifile, 'VGLVLS'):
return ifile.VGLVLS[:]
elif 'etai_pressure' in ifile.variables:
etai_pressure = ifile.variables['etai_pressure']
return ((etai_pressure - etai_pressure[-1]) /
(etai_pressure[0] - etai_pressure[-1]))
elif 'layer_bounds' in ifile.variables:
lay = ifile.variables['layer_bounds']
if lay.units.strip() in ('Pa', 'hPa'):
sigma = (lay[:] - lay[-1]) / (lay[0] - lay[-1])
return sigma
else:
warn("Unknown tranform of layer to sigma; " +
"sigma units %s" % lay.units)
return lay
else:
warn("Unknown vertical coordinate")
if hasattr(ifile, 'NLAYS'):
nlays = ifile.NLAYS
elif 'LAY' in ifile.dimensions:
nlays = len(ifile.dimensions['LAY'])
elif 'lev' in ifile.dimensions:
nlays = len(ifile.dimensions['lev'])
elif 'layer' in ifile.dimensions:
nlays = len(ifile.dimensions['layer'])
else:
nlays = 1
return np.arange(nlays)
def getsigmabnds(ifile):
if hasattr(ifile, 'VGLVLS'):
return ifile.VGLVLS[:]
elif 'etai_pressure' in ifile.variables:
etai_pressure = ifile.variables['etai_pressure']
return (etai_pressure - etai_pressure[-1]) / (etai_pressure[0] - etai_pressure[-1])
elif 'layer_bounds' in ifile.variables:
lay = ifile.variables['layer_bounds']
if lay.units.strip() in ('Pa', 'hPa'):
sigma = (lay[:] -lay[-1]) / (lay[0] - lay[-1])
return sigma
else:
warn("Unknown tranform of layer to sigma; sigma units %s" % lay.units)
return lay
else:
warn("Unknown vertical coordinate")
if hasattr(ifile, 'NLAYS'):
nlays = ifile.NLAYS
elif 'LAY' in ifile.dimensions:
nlays = len(ifile.dimensions['LAY'])
elif 'lev' in ifile.dimensions:
nlays = len(ifile.dimensions['lev'])
elif 'layer' in ifile.dimensions:
nlays = len(ifile.dimensions['layer'])
else:
nlays = 1
return np.arange(nlays)
def getlonbnds(ifile):
if 'longitude_bounds' in ifile.variables:
lonb = ifile.variables['longitude_bounds']
unit = lonb.units.strip()
if 'nv' in lonb.dimensions:
if lonb[:].ndim == 2 and len(ifile.dimensions['nv']) == 2:
lonb = np.append(lonb[:][:, 0], lonb[:][-1, 1])
elif lonb[:].ndim == 3:
lonb = lonb[:][:, :, 0]
elif 'longitude' in ifile.variables:
lonb = ifile.variables['longitude']
unit = lonb.units.strip()
lonb = lonb[:]
if lonb.ndim > 1:
londiff = np.diff(lonb, axis = 1)
alldiffsame = (londiff == londiff[:, [0]]).all()
elif lonb.ndim == 1:
alldiffsame = True
londiff = np.diff(lonb)
else:
raise ValueError("Cannot infer longitude bounds when dimensions >2")
if not alldiffsame:
londiff = np.diff(lonb, axis = 1)
if not (londiff == londiff[:, [0]]).all():
warn('Longitude bounds are approximate')
lonb = np.concatenate([lonb, lonb[:, [-1]]], axis = 1) - .5 * np.concatenate([londiff[:, :], londiff[:, [-1]], -londiff[:, [-1]]], axis = 1)
lonb = np.append(lonb, lonb[[-1], :], axis = 0)
else:
londiff = np.diff(lonb, axis = 0)
lonb = np.concatenate([lonb, lonb[[-1]]], axis = 0) - .5 * np.concatenate([londiff[:], londiff[[-1]], -londiff[[-1]]], axis = 0)
else:
raise KeyError('longitude bounds not found')
return lonb, unit
def getlatbnds(ifile):
if 'latitude_bounds' in ifile.variables:
latb = ifile.variables['latitude_bounds']
unit = latb.units.strip()
if 'nv' in latb.dimensions:
if latb[:].ndim == 2 and len(ifile.dimensions['nv']) == 2:
latb = np.append(latb[:][:, 0], latb[:][-1, 1])
elif latb[:].ndim == 2 and len(ifile.dimensions['nv']) == 4:
latb = np.append(latb[:][:, 0], latb[:][-1, 1])
elif latb.ndim == 3:
latb = latb[:, :, 0]
elif 'latitude' in ifile.variables:
latb = ifile.variables['latitude']
unit = latb.units.strip()
latb = latb[:]
latdiff = np.diff(latb, axis = 0)
if not (latdiff == latdiff[[0]]).all():
warn('Latitude bounds are approximate')
latb = np.apply_along_axis(np.convolve, 0, latb, [0.5, 0.5])
latb[0] *= 2
latb[-1] *= 2
#latb = np.concatenate([latb, latb[[-1]]], axis = 0) - .5 * np.concatenate([latdiff[:], latdiff[[-1]], -latdiff[[-1]]], axis = 0)
#latb = np.minimum(90, latb)
#latb = np.maximum(-90, latb)
if latb.ndim == 2:
latb = np.append(latb, latb[:, [-1]], axis = 1)
elif 'ROW' in ifile.dimensions:
unit = 'x (m)'
latb = np.arange(len(ifile.dimensions['ROW']) + 1) * getattr(ifile, 'YCELL', 1) / 1000.
else:
raise KeyError('latitude bounds not found')
return latb, unit
def getproj4_from_cf_var(gridmapping, withgrid=False):
mapstr_bits = OrderedDict()
gname = getattr(gridmapping, 'grid_mapping_name')
pv4s = dict(lambert_conformal_conic='lcc',
rotated_latitude_longitude='ob_tran',
latitude_longitude='lonlat',
transverse_mercator='tmerc',
equatorial_mercator='merc',
mercator='merc',
polar_stereographic='stere')
pv4name = pv4s[gname]
for pk in gridmapping.ncattrs():
pv = getattr(gridmapping, pk)
if pk == 'grid_mapping_name':
pv4 = pv4s[pv]
mapstr_bits['proj'] = pv4
if pv == 'rotated_latitude_longitude':
mapstr_bits['o_proj'] = 'eqc'
elif pk == 'standard_parallel':
if pv4name == 'stere':
mapstr_bits['lat_ts'] = pv[0]
else:
mapstr_bits['lat_1'] = pv[0]
if len(pv) > 1:
mapstr_bits['lat_2'] = pv[1]
elif pk == 'longitude_of_central_meridian':
mapstr_bits['lon_0'] = pv
elif pk == 'latitude_of_projection_origin':
mapstr_bits['lat_0'] = pv
elif pk == 'false_easting':
mapstr_bits['x_0'] = pv
elif pk == 'false_northing':
mapstr_bits['y_0'] = pv
elif pk == 'scale_factor_at_projection_origin':
mapstr_bits['k_0'] = pv
elif pk == 'earth_radius':
mapstr_bits['a'] = pv
mapstr_bits['b'] = pv
elif pk == 'semi_major_axis':
mapstr_bits['a'] = pv
elif pk == 'semi_minor_axis':
mapstr_bits['b'] = pv
elif pk == 'inverse_flattening':
mapstr_bits['f'] = 1 / pv
elif pk == 'grid_north_pole_latitude':
mapstr_bits['o_lat_p'] = pv
elif pk == 'grid_north_pole_longitude':
mapstr_bits['lon_0'] = pv
else:
warn('Currently not using:' + str(pk) + ' ' + str(pv))
# repr is required to prevent rounding of numpy array values
mapstr = ' '.join([
'+%s=%s' % (k, v if isinstance(v, str) else repr(v))
for k, v in mapstr_bits.items()
])
return mapstr
def getpresbnds(ifile, pref=101325., ptop=None):
if 'etai_pressure' in ifile.variables:
return ifile.variables['etai_pressure'][:]
elif 'layer_bounds' in ifile.variables:
return ifile.variables['layer_bounds'][:]
else:
sigma = getsigmabnds(ifile)
if ptop is None:
if hasattr(ifile, 'VGTOP'):
ptop = ifile.VGTOP
else:
warn("Assuming VGTOP = 10000 Pa")
ptop = 10000
return pres_from_sigma(sigma, pref=pref, ptop=ptop)
def getpresbnds(ifile, pref = 101325., ptop = None):
if 'etai_pressure' in ifile.variables:
return ifile.variables['etai_pressure'][:]
elif 'layer_bounds' in ifile.variables:
return ifile.variables['layer_bounds'][:]
else:
sigma = getsigmabnds(ifile)
if ptop is None:
if hasattr(ifile, 'VGTOP'):
ptop = ifile.VGTOP
else:
warn("Assuming VGTOP = 10000 Pa")
ptop = 10000
return pres_from_sigma(sigma, pref = pref, ptop = ptop)
def getproj4(ifile, withgrid=False):
"""
Arguments:
ifile - PseudoNetCDF file
withgrid - True to include gridding parameters
Returns:
proj4str - string with proj4 parameters
"""
from .conventions.ioapi import getmapdef
if (getattr(ifile, 'GDTYP', 0) in (1, 2, 6, 7) and all([
hasattr(ifile, k)
for k in 'P_GAM P_ALP P_BET XORIG YORIG XCELL YCELL'.split()
])):
gridmapping = getmapdef(ifile, add=False)
mapstr = getproj4_from_cf_var(gridmapping, withgrid=withgrid)
if withgrid:
mapstr += ' +to_meter=%s' % ifile.XCELL
elif (getattr(ifile, 'Conventions', getattr(ifile, 'CONVENTIONS',
''))[:2].upper() == 'CF'):
gridmappings = []
for k, v in ifile.variables.items():
if hasattr(v, 'grid_mapping'):
gridmappings.append(getattr(v, 'grid_mapping'))
if len(gridmappings) == 0:
warn('No known grid mapping; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmappings = list(set(gridmappings))
if len(gridmappings) > 1:
warn('Using first grid mapping of ' + str(gridmappings))
if not gridmappings[0] in ifile.variables:
warn(gridmappings[0] + ' could not be found; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmapping = ifile.variables[gridmappings[0]]
mapstr = getproj4_from_cf_var(gridmapping, withgrid=withgrid)
else:
warn('No known grid mapping; assuming lonlat')
mapstr = '+proj=lonlat'
mapstr += ' +no_defs'
return mapstr
def getproj4(ifile, withgrid=False):
"""
Arguments:
ifile - PseudoNetCDF file
withgrid - True to include gridding parameters
Returns:
proj4str - string with proj4 parameters
"""
from .conventions.ioapi import get_ioapi_sphere
if getattr(ifile, 'GDTYP', 0) in (2, 7) and all([
hasattr(ifile, k)
for k in 'P_GAM P_ALP P_BET XORIG YORIG XCELL YCELL'.split()
]):
semi_major_axis, semi_minor_axis = get_ioapi_sphere()
if ifile.GDTYP == 2:
mapstr = '+proj=lcc +a=%s +b=%s +lon_0=%s +lat_1=%s +lat_2=%s +lat_0=%s' % (
semi_major_axis, semi_minor_axis, ifile.P_GAM, ifile.P_ALP,
ifile.P_BET, ifile.YCENT)
elif ifile.GDTYP == 7:
mapstr = '+proj=merc +a=%s +b=%s +lat_ts=0 +lon_0=%s' % (
semi_major_axis, semi_minor_axis, ifile.XCENT)
if withgrid:
mapstr += ' +x_0=%s +y_0=%s +to_meter=%sm' % (
-ifile.XORIG, -ifile.YORIG, ifile.XCELL)
elif getattr(ifile, 'Conventions', getattr(ifile, 'CONVENTIONS',
''))[:2].upper() == 'CF':
gridmappings = []
for k, v in ifile.variables.items():
if hasattr(v, 'grid_mapping'):
gridmappings.append(getattr(v, 'grid_mapping'))
if len(gridmappings) == 0:
warn('No known grid mapping; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmappings = list(set(gridmappings))
if len(gridmappings) > 1:
warn('Using first grid mapping of ' + str(gridmappings))
if not gridmappings[0] in ifile.variables:
warn(gridmappings[0] + ' could not be found; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmapping = ifile.variables[gridmappings[0]]
mapstr = getproj4_from_cf_var(gridmapping, withgrid=withgrid)
mapstr += ' +no_defs'
return mapstr
def getproj4(ifile, withgrid=False):
"""
Arguments:
ifile - PseudoNetCDF file
withgrid - True to include gridding parameters
Returns:
proj4str - string with proj4 parameters
"""
from .conventions.ioapi import getmapdef
if (getattr(ifile, 'GDTYP', 0) in (1, 2, 6, 7) and all([
hasattr(ifile, k)
for k in 'P_GAM P_ALP P_BET XORIG YORIG XCELL YCELL'.split()
])):
gridmapping = getmapdef(ifile, add=False)
mapstr = getproj4_from_cf_var(gridmapping, withgrid=withgrid)
if withgrid:
dx = min(ifile.XCELL, ifile.YCELL)
if ifile.XCELL != ifile.YCELL:
warn('Grid is not regular: using minimum {}'.format(dx))
if gridmapping.grid_mapping_name == 'latitude_longitude':
er = min(gridmapping.semi_minor_axis,
gridmapping.semi_major_axis)
if (gridmapping.semi_minor_axis !=
gridmapping.semi_major_axis):
warn('Earth not a perfect sphere: using minimum ' +
'{}'.format(er))
mapstr += ' +to_meter=%s' % (np.radians(1) * er * dx)
else:
mapstr += ' +to_meter=%s' % ifile.XCELL
elif (getattr(ifile, 'Conventions', getattr(ifile, 'CONVENTIONS',
''))[:2].upper() == 'CF'):
gridmappings = []
for k, v in ifile.variables.items():
if hasattr(v, 'grid_mapping'):
gridmappings.append(getattr(v, 'grid_mapping'))
if len(gridmappings) == 0:
warn('No known grid mapping; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmappings = list(set(gridmappings))
if len(gridmappings) > 1:
warn('Using first grid mapping of ' + str(gridmappings))
if not gridmappings[0] in ifile.variables:
warn(gridmappings[0] + ' could not be found; assuming lonlat')
mapstr = '+proj=lonlat'
else:
gridmapping = ifile.variables[gridmappings[0]]
mapstr = getproj4_from_cf_var(gridmapping, withgrid=withgrid)
else:
warn('No known grid mapping; assuming lonlat')
mapstr = '+proj=lonlat'
mapstr += ' +no_defs'
return mapstr