def fix_bpch2nc(cube, field, filename):
"""
An Iris load callback for properly loading the NetCDF files
created by BPCH2NC (GAMAP v2-12+).
"""
global _coordcache
# units
units = field.unit.strip()
try:
cube.units = units
except ValueError:
# Try to get equivalent units compatible with udunits.
# Store original unit as cube attribute
conform_units = ctm2cf.get_cfcompliant_units(units)
try:
cube.units = conform_units
except ValueError:
warnings.warn("Invalid udunits2 '{0}'".format(units))
cube.attributes["ctm_units"] = units
# a hack for keeping cube's long_name but show var_name in cube summary
iris.std_names.STD_NAMES[cube.var_name] = {'canonical_units': cube.units}
cube.standard_name = cube.var_name
# add spatial coordinates
modelname = cube.attributes.get('Model')
res = cube.attributes.get('Delta_Lon'), cube.attributes.get('Delta_Lat')
nlayers = cube.attributes.get('NLayers')
cache_key = modelname, res, nlayers
if _coordcache.get(cache_key) is None:
ctm_grid = grid.CTMGrid.from_model(modelname, resolution=res)
coord_names = ('longitude', 'latitude', 'levels')
lon, lat, lev = irisutil.coord_from_grid(ctm_grid, coord=coord_names)
_coordcache[cache_key] = {'lon': lon, 'lat': lat, 'lev': lev}
if cube.ndim == 3:
cube.add_dim_coord(_coordcache[cache_key]['lon'], 2)
cube.add_dim_coord(_coordcache[cache_key]['lat'], 1)
if cube.shape[0] == nlayers:
cube.add_dim_coord(_coordcache[cache_key]['lev'], 0)
# add time scalar coordinate (get info from global attributes)
tstart = (str(cube.attributes['Start_Date']) +
str(cube.attributes['Start_Time']))
tstart = datetime.datetime.strptime(tstart, "%Y%m%d%H")
tstart = timeutil.time2tau(tstart)
tend = (str(cube.attributes['End_Date']) +
str(cube.attributes['End_Time']))
tend = datetime.datetime.strptime(tend, "%Y%m%d%H")
tend = timeutil.time2tau(tend)
time_coord = iris.coords.DimCoord(points=tstart,
bounds=(tstart, tend),
standard_name='time',
units=irisutil.CTM_TIME_UNIT_IRIS)
cube.add_aux_coord(time_coord)
# attributes
# TODO: don't remove all attributes
cube.attributes.clear()
# handle 2D fields (remove 1-sized 1st dimension)
if cube.ndim == 3 and cube.shape[0] == 1:
#dummy_coord = iris.coords.DimCoord([0], long_name='dummy',
# bounds=[0, 1])
#cube.add_dim_coord(dummy_coord, 0)
return cube.slices(range(1, cube.ndim)).next()
def fix_bpch2coards(cube, field, filename):
"""
An Iris load callback for properly loading the NetCDF files
created by BPCH2COARDS (GAMAP v2-17+).
"""
global _coordcache2
# units
units = field.units
try:
cube.units = units
except ValueError:
# Try to get equivalent units compatible with udunits.
# Store original unit as cube attribute
conform_units = ctm2cf.get_cfcompliant_units(units)
try:
cube.units = conform_units
except ValueError:
warnings.warn("Invalid udunits2 '{0}'".format(units))
cube.attributes["ctm_units"] = units
# a hack for keeping cube's long_name but show var_name in cube summary
iris.std_names.STD_NAMES[cube.var_name] = {'canonical_units': cube.units}
cube.standard_name = cube.var_name
# attributes
# TODO: don't remove all attributes
cube.attributes.clear()
# longitude coordinate (non strictly monotonic) degrees -> degrees_east
try:
lon = cube.coord('longitude')
lon_dim = cube.coord_dims(lon)[0]
cache_key = 'longitude', filename
if _coordcache2.get(cache_key) is None:
west_ind = np.nonzero(lon.points >= 180.)
lon.points[west_ind] = -1. * (360. - lon.points)
lon.units = 'degrees_east'
_coordcache2[cache_key] = iris.coords.DimCoord.from_coord(lon)
cube.remove_coord(lon)
cube.add_dim_coord(_coordcache2[cache_key], lon_dim)
except iris.exceptions.CoordinateNotFoundError:
pass
# levels coordinate
# 'sigma_level' depreciated in the CF standard (not supported by UDUNITS)
try:
lev = cube.coord('Eta Centers')
lev_dim = cube.coord_dims(lev)[0]
lev_std_name = 'atmosphere_hybrid_sigma_pressure_coordinate'
cache_key = lev_std_name, filename
if _coordcache2.get(cache_key) is None:
lev.standard_name = lev_std_name
lev.units = iris.unit.Unit('1')
d = nc.Dataset(filename)
elev = d.variables['edge'][:]
lev.bounds = np.column_stack((elev[:-1], elev[1:]))
_coordcache2[cache_key] = iris.coords.DimCoord.from_coord(lev)
cube.remove_coord(lev)
cube.add_dim_coord(_coordcache2[cache_key], lev_dim)
except iris.exceptions.CoordinateNotFoundError:
pass
# time: dimension -> scalar coordinate (+ add bounds)
try:
time_coord = cube.coord('time')
time_dim = cube.coord_dims(time_coord)[0]
with iris.FUTURE.context(cell_datetime_objects=True):
tstart = time_coord.cell(0).point
delta_t = time_coord.attributes.pop('delta_t')
tend = tstart + timeutil.strp_relativedelta(delta_t)
time_coord.bounds = [timeutil.time2tau(tstart),
timeutil.time2tau(tend)]
if cube.shape[time_dim] == 1:
slices_dims = [d for d in range(cube.ndim) if d != time_dim]
return cube.slices(slices_dims).next()
except iris.exceptions.CoordinateNotFoundError:
pass
def _datablock_to_cube(datablock, dim_coords_and_dims=None,
aux_coords_and_dims=None, aux_factories=None,
coords_from_model=True, errcoord='error',
**kwargs):
"""
Create a :class:`iris.cubes.Cube` object given a datablock dict.
"""
# TODO: cell methods, aux_factories
# Create cube with data or data proxy, but no metadata
if isinstance(datablock['data'], bpch.BPCHDataProxy):
data = biggus.OrthoArrayAdapter(datablock['data'])
else:
data = datablock['data']
cube = iris.cube.Cube(data)
# units
units = datablock['unit'].strip()
# Try to get equivalent units compatible with udunits.
# Store original unit as cube attribute
conform_units = ctm2cf.get_cfcompliant_units(units)
try:
cube.units = conform_units
except ValueError:
warnings.warn("Invalid udunits2 '{0}'".format(units))
cube.attributes["ctm_units"] = units
# set the cube's name ('category__name')
name = "__".join([datablock['category'], datablock['name']])
name = ctm2cf.get_valid_varname(name)
# a hack for keeping cube's long_name but show var_name in cube summary
iris.std_names.STD_NAMES[name] = {'canonical_units': cube.units}
cube.standard_name = name
cube.var_name = name
cube.long_name = datablock['tracerinfo'].get('full_name')
# set coordinates from datablock metadata
if coords_from_model:
ctm_grid = grid.CTMGrid.from_model(datablock['modelname'],
resolution=datablock['resolution'])
coord_names = ('longitude', 'latitude', 'levels')
lon, lat, lev = coord_from_grid(ctm_grid, coord=coord_names)
cube.add_dim_coord(lon, 0)
cube.add_dim_coord(lat, 1)
if cube.ndim > 2:
add_dim_aux_coord(cube, lev, 2, err='pass')
# add given dimension coordinates if any
if dim_coords_and_dims:
for coord, dim in dim_coords_and_dims:
add_dim_aux_coord(cube, coord, dim, err=errcoord)
# add given auxiliary coordinates if any
if aux_coords_and_dims:
for coord, dim in aux_coords_and_dims:
add_dim_aux_coord(cube, coord, dim, err=errcoord)
# add given aux coordinates factories if any
if aux_factories:
for aux_factory in aux_factories:
cube.add_aux_factory(aux_factory)
# time coordinates
point = timeutil.time2tau(datablock['times'][0])
bounds = [timeutil.time2tau(t) for t in datablock['times']]
time_coord = iris.coords.DimCoord(points=point,
bounds=bounds,
standard_name='time',
units=CTM_TIME_UNIT_IRIS)
cube.add_aux_coord(time_coord)
# attributes
# TODO: proper attribute handling (several issues)
# 1. avoid duplicating the space domain information
# 2. keep somewhere the metadata in its original format (for further export)
# 3. deal with simple types only (e.g., tuple not valid as cube attribute)
# 4. limit the number of cube attributes (slows down the cube merging)
cube.attributes['model'] = datablock.get('modelname')
#if isinstance(datablock['tracerinfo'], dict):
# cube.attributes.update(datablock['tracerinfo'])
# cube.attributes.pop('unit')
#for attr_name in ('name', 'number', 'category', 'modelname', 'resolution'):
# cube.attributes[attr_name] = datablock.get(attr_name, None)
cube.attributes.update(kwargs)
return cube
