def test_obs_obsmanager_project_model():
# Load manager
manager = test_obs_obsmanager_init_surf()
# Load model
f = DS(NCFILE_MANGA0, 'mars', level='surf', logger_level='error')
temp = f('temp')
f.close()
temp.id += '_surf'
# Interpolate model
otemp = manager.project_model(temp)
assert_allclose(otemp[1][0], [12.91558515, 10.58179214])
return manager
def test_obs_ncobsplatform_surf():
# Load and stack obs
obs = NcObsPlatform(NCFILE_OBS_SURF,
logger=LOGGER,
lat=(45, 47.8),
norms=[0.2, 0.1])
stacked = obs.stacked_data.copy()
assert obs.lons.shape == (3, )
assert obs.ns == 6
assert obs.ndim == 1
assert_allclose(obs.means, [0, 0], atol=1e-7)
assert obs.depths == 'surf'
assert_allclose(stacked, [2.5, 1.5, 4., 1., 1.5, 4.])
# Named norms
notnormed = obs.set_named_norms(temp=0.1)
assert obs.norms == [0.1, 0.1]
assert_allclose(obs.stacked_data[:3], 2 * stacked[:3])
assert_allclose(obs.stacked_data[3:], stacked[3:])
obs.set_named_norms(temp=0.2)
# Interpolate model
f = DS(NCFILE_MANGA0, 'mars', level=obs.depths, logger_level='error')
temp = f('temp')
sal = f('sal')
f.close()
temp.id += '_surf'
sal.id += '_surf'
otemp = obs.project_model(temp)
osal = obs.project_model(sal)
otem_true = [12.97311556, 12.91558515, 10.58179214]
assert_allclose(otemp[0], otem_true)
# Stack model
otemp[:] -= 11.5
osal[:] -= 35.5
stacked_data = obs.restack([otemp, osal])
assert stacked_data.shape == (6, 15)
assert_allclose(stacked_data[:3, 0] * obs.norms[0] + 11.5, otem_true)
return obs
break
else:
args.var = args.var[:3]
# Reading parameters
kwread = eval('dict(%s)' % args.select)
kwread['squeeze'] = 1
for ss in 'lon', 'lat', 'dep', 'time':
if getattr(args, ss) is not None:
kwread[ss] = get_sel(getattr(args, ss))
# Read variable
vv = [f(vname, **kwread) for vname in args.var]
if args.dvar:
depth = f(args.dvar, **kwread)
f.close()
if args.verbose:
for v in vv:
v.info()
order = vv[0].getOrder()
ndim = vv[0].ndim
# Reduce rank when needed
if ndim > 2:
for i in xrange(ndim - 2):
if order[i] == 'z':
islice = -1 if isdepthup(var[0].getAxis(0)) else 0
else:
islice = 0
vv = [v[islice] for v in vv]
order = vv[0].getOrder()
break
else:
args.var = args.var[:3]
# Reading parameters
kwread = eval('dict(%s)'%args.select)
kwread['squeeze'] = 1
for ss in 'lon', 'lat', 'dep', 'time':
if getattr(args, ss) is not None:
kwread[ss] = get_sel(getattr(args, ss))
# Read variable
vv = [f(vname, **kwread) for vname in args.var]
if args.dvar:
depth = f(args.dvar, **kwread)
f.close()
if args.verbose:
for v in vv:
v.info()
order = vv[0].getOrder()
ndim = vv[0].ndim
# Reduce rank when needed
if ndim>2:
for i in xrange(ndim-2):
if order[i]=='z':
islice = -1 if isdepthup(var[0].getAxis(0)) else 0
else:
islice = 0
vv = [v[islice] for v in vv]
order = vv[0].getOrder()
class NcReader(object):
"""A generic interface to open and read a netcdf file
Examples
--------
>>> f = NcReader(ncfile, 'mars3d') # VACUMM Mars3D reader
>>> u = f('u', lon=(10, 12)) # generic var name
>>> u = f('+sst', lon=(10, 12)) # netcdf var name
>>> f.close()
>>> f = NcReader(ncfile, 'cdms2') # direct cdms2 reader
>>> u = f('u', lon=(10, 12)) # netcdf var name
>>> f.close()
>>> f = NcReader(ncfile, 'netcdf') # python netcdf4 reader
>>> u = f('u', slice(0, 10)) # <=> f['u'][:10]
>>> f.close()
"""
def __init__(self, ncfile, readertype='generic', **kwargs):
self.ncfile = ncfile
if not isinstance(readertype, basestring):
self.f = readertype(ncfile, **kwargs)
self.type = 'callable'
elif readertype=='cdms2':
self.f = cdms2.open(ncfile, **kwargs)
self.type = readertype
elif readertype=='netcdf4':
import netcdf4
self.f = netcdf4.Dataset(ncfile, **kwargs)
self.type = readertype
else:
self.f = DS(ncfile, readertype, **kwargs)
self.type = 'dataset'
def __call__(self, vname, *args, **kwargs):
if self.type=='netcdf4':
args = tuple(filter(lambda x: isinstance(x, slice), args))
return self.f[vname][args]
else:
return self.f(vname, *args, **kwargs)
def __getitem__(self, vname):
return self.f[vname]
def get_variables(self):
if self.type=='netcdf4' or self.type=='cdms2':
return self.variables.keys()
if self.type=='dataset':
return self.f.dataset[0].variables.keys()
raise SONATError('Method yet not implemented for read type "{}"'.format(self.type))
def close(self):
self.f.close()
