def test_system_grouped_dimension_map(self):
initial_data = {
DMK.X: {
DMK.VARIABLE: 'longitude'
},
DMK.GROUPS: {
'nested': {
DMK.Y: {
DMK.VARIABLE: 'latitude'
},
DMK.GROUPS: {
'nested_in_nested': {
DMK.CRS: {
DMK.VARIABLE: 'coord_sys'
}
}
}
}
}
}
dmap = DimensionMap.from_dict(initial_data)
nested = dmap.get_group('nested')
self.assertEqual(nested.get_variable(DMK.Y), 'latitude')
self.assertIsNone(dmap.get_variable(DMK.Y))
self.assertEqual(
dmap.get_group([None, 'nested', 'nested_in_nested']).get_crs(),
'coord_sys')
def create_dimension_map(self, group_metadata):
ret = {DMK.GEOM: {DMK.VARIABLE: VariableName.GEOMETRY_VARIABLE,
DMK.DIMENSION: DimensionName.GEOMETRY_DIMENSION}}
ret = DimensionMap.from_dict(ret)
crs = self.get_crs(group_metadata)
if crs is not None:
ret.set_crs(crs)
return ret
def get_dimension_map(self, group_metadata, strict=False):
# Get dimension variable metadata. This involves checking for the presence of any bounds variables.
variables = group_metadata['variables']
dimensions = group_metadata['dimensions']
axes = {
'realization': 'R',
'time': 'T',
'level': 'Z',
'x': 'X',
'y': 'Y'
}
check_bounds = list(axes.keys())
check_bounds.pop(check_bounds.index('realization'))
# Get the main entry for each axis.
for k, v in list(axes.items()):
axes[k] = get_dimension_map_entry(v,
variables,
dimensions,
strict=strict)
# Attempt to find bounds for each entry (ignoring realizations).
for k in check_bounds:
if axes[k] is not None:
keys = ['bounds']
if k == 'time':
keys += ['climatology']
bounds_var = get_by_key_list(
variables[axes[k]['variable']]['attrs'], keys)
if bounds_var is not None:
if bounds_var not in variables:
msg = 'Bounds listed for variable "{0}" but the destination bounds variable "{1}" does not exist.'. \
format(axes[k]['variable'], bounds_var)
ocgis_lh(msg,
logger='nc.driver',
level=logging.WARNING)
bounds_var = None
axes[k]['bounds'] = bounds_var
# Create the template dimension map dictionary.
ret = {k: v for k, v in list(axes.items()) if v is not None}
# Check for coordinate system variables. This will check every variable.
crs_name = get_coordinate_system_variable_name(self, group_metadata)
if crs_name is not None:
ret[DimensionMapKey.CRS] = {DimensionMapKey.VARIABLE: crs_name}
ret = DimensionMap.from_dict(ret)
# Check for a spatial mask.
for varname, var in group_metadata['variables'].items():
if 'ocgis_role' in var.get('attrs', {}):
if var['attrs']['ocgis_role'] == 'spatial_mask':
ret.set_spatial_mask(varname, attrs=var['attrs'])
return ret
def test_system_grouped_dimension_map(self):
initial_data = {DMK.X: {DMK.VARIABLE: 'longitude'},
DMK.GROUPS: {'nested': {DMK.Y: {DMK.VARIABLE: 'latitude'},
DMK.GROUPS: {
'nested_in_nested': {DMK.CRS: {DMK.VARIABLE: 'coord_sys'}}}}}}
dmap = DimensionMap.from_dict(initial_data)
nested = dmap.get_group('nested')
self.assertEqual(nested.get_variable(DMK.Y), 'latitude')
self.assertIsNone(dmap.get_variable(DMK.Y))
self.assertEqual(dmap.get_group([None, 'nested', 'nested_in_nested']).get_crs(), 'coord_sys')
def create_dimension_map(self, group_metadata):
ret = {
DMK.GEOM: {
DMK.VARIABLE: VariableName.GEOMETRY_VARIABLE,
DMK.DIMENSION: DimensionName.GEOMETRY_DIMENSION
}
}
ret = DimensionMap.from_dict(ret)
crs = self.get_crs(group_metadata)
if crs is not None:
ret.set_crs(crs)
return ret
def test_get_data_variable_names(self):
driver = self.get_drivernetcdf()
dvars = driver.get_data_variable_names(driver.rd.metadata, driver.rd.dimension_map)
self.assertEqual(len(dvars), 0)
# Test a found variable.
dimension_map = {'time': {'variable': 'the_time', DimensionMapKey.DIMENSION: ['tt', 'ttt']},
'x': {'variable': 'xx', DimensionMapKey.DIMENSION: ['xx', 'xxx']},
'y': {'variable': 'yy', DimensionMapKey.DIMENSION: ['yy', 'yyy']}}
metadata = {'variables': {'tas': {'dimensions': ('xx', 'ttt', 'yyy')},
'pr': {'dimensions': ('foo',)}}}
dimension_map = DimensionMap.from_dict(dimension_map)
dvars = driver.get_data_variable_names(metadata, dimension_map)
self.assertEqual(dvars, ('tas',))
# Test request dataset uses the dimensioned variables.
driver = self.get_drivernetcdf()
with self.assertRaises(NoDataVariablesFound):
assert driver.rd.variable
def test_get_data_variable_names(self):
driver = self.get_drivernetcdf()
dvars = driver.get_data_variable_names(driver.rd.metadata,
driver.rd.dimension_map)
self.assertEqual(len(dvars), 0)
# Test a found variable.
dimension_map = {
'time': {
'variable': 'the_time',
DimensionMapKey.DIMENSION: ['tt', 'ttt']
},
'x': {
'variable': 'xx',
DimensionMapKey.DIMENSION: ['xx', 'xxx']
},
'y': {
'variable': 'yy',
DimensionMapKey.DIMENSION: ['yy', 'yyy']
}
}
metadata = {
'variables': {
'tas': {
'dimensions': ('xx', 'ttt', 'yyy')
},
'pr': {
'dimensions': ('foo', )
}
}
}
dimension_map = DimensionMap.from_dict(dimension_map)
dvars = driver.get_data_variable_names(metadata, dimension_map)
self.assertEqual(dvars, ('tas', ))
# Test request dataset uses the dimensioned variables.
driver = self.get_drivernetcdf()
with self.assertRaises(NoDataVariablesFound):
assert driver.rd.variable
def __init__(self,
uri=None,
variable=None,
units=None,
time_range=None,
time_region=None,
time_subset_func=None,
level_range=None,
conform_units_to=None,
crs='auto',
t_units=None,
t_calendar=None,
t_conform_units_to=None,
grid_abstraction='auto',
grid_is_isomorphic='auto',
dimension_map=None,
field_name=None,
driver=None,
regrid_source=True,
regrid_destination=False,
metadata=None,
format_time=True,
opened=None,
uid=None,
rename_variable=None,
predicate=None,
rotated_pole_priority=False,
driver_kwargs=None):
self._is_init = True
self._field_name = field_name
self._level_range = None
self._time_range = None
self._time_region = None
self._time_subset_func = None
self._driver_kwargs = driver_kwargs
if rename_variable is not None:
rename_variable = get_tuple(rename_variable)
self._rename_variable = rename_variable
self.rotated_pole_priority = rotated_pole_priority
self.predicate = predicate
if dimension_map is not None and isinstance(dimension_map, dict):
dimension_map = DimensionMap.from_dict(dimension_map)
self._dimension_map = dimension_map
self._metadata = deepcopy(metadata)
self._uri = None
self.uid = uid
# This is an "open" file-like object that may be passed in-place of file location parameters.
self._opened = opened
if opened is not None and driver is None:
msg = 'If "opened" is not None, then a "driver" must be provided.'
ocgis_lh(logger='request',
exc=RequestValidationError('driver', msg))
# Field creation options.
self.format_time = format_time
self.grid_abstraction = grid_abstraction
self.grid_is_isomorphic = grid_is_isomorphic
# Flag used for regridding to determine if the coordinate system was assigned during initialization.
self._has_assigned_coordinate_system = False if crs == 'auto' else True
if uri is None:
# Fields may be created from pure metadata.
if metadata is not None:
# The default OCGIS driver is NetCDF.
if driver is None:
driver = DriverKey.NETCDF_CF
elif opened is None:
ocgis_lh(logger='request',
exc=RequestValidationError('uri', 'Cannot be None'))
else:
self._uri = get_uri(uri)
if driver is None:
klass = get_autodiscovered_driver(uri)
else:
klass = get_driver(driver)
self._driver = klass(self)
if variable is not None:
variable = get_tuple(variable)
self._variable = variable
self.time_range = time_range
self.time_region = time_region
self.time_subset_func = time_subset_func
self.level_range = level_range
self._crs = deepcopy(crs)
self.regrid_source = regrid_source
self.regrid_destination = regrid_destination
self.units = units
self.conform_units_to = conform_units_to
self._is_init = False
self._validate_time_subset_()
# Update metadata for time variable.
tvar = self.dimension_map.get_variable(DMK.TIME)
if tvar is not None:
m = self.metadata['variables'][tvar]
if t_units is not None:
m['attrs']['units'] = t_units
if t_calendar is not None:
m['attrs']['calendar'] = t_calendar
if t_conform_units_to is not None:
from ocgis.util.units import get_units_object
t_calendar = m['attrs'].get(
'calendar', constants.DEFAULT_TEMPORAL_CALENDAR)
t_conform_units_to = get_units_object(t_conform_units_to,
calendar=t_calendar)
m['conform_units_to'] = t_conform_units_to
def __init__(self, uri=None, variable=None, units=None, time_range=None, time_region=None,
time_subset_func=None, level_range=None, conform_units_to=None, crs='auto', t_units=None,
t_calendar=None, t_conform_units_to=None, grid_abstraction='auto', grid_is_isomorphic='auto',
dimension_map=None, field_name=None, driver=None, regrid_source=True, regrid_destination=False,
metadata=None, format_time=True, opened=None, uid=None, rename_variable=None, predicate=None,
rotated_pole_priority=False, driver_kwargs=None, decomp_type=DecompositionType.OCGIS):
self._is_init = True
self._field_name = field_name
self._level_range = None
self._time_range = None
self._time_region = None
self._time_subset_func = None
self._driver_kwargs = driver_kwargs
self._decomp_type = decomp_type
if rename_variable is not None:
rename_variable = get_tuple(rename_variable)
self._rename_variable = rename_variable
self.rotated_pole_priority = rotated_pole_priority
self.predicate = predicate
if dimension_map is not None and isinstance(dimension_map, dict):
dimension_map = DimensionMap.from_dict(dimension_map)
self._dimension_map = dimension_map
self._metadata = deepcopy(metadata)
self._uri = None
self.uid = uid
# This is an "open" file-like object that may be passed in-place of file location parameters.
self._opened = opened
if opened is not None and driver is None:
msg = 'If "opened" is not None, then a "driver" must be provided.'
ocgis_lh(logger='request', exc=RequestValidationError('driver', msg))
# Field creation options.
self.format_time = format_time
self.grid_abstraction = grid_abstraction
self.grid_is_isomorphic = grid_is_isomorphic
# Flag used for regridding to determine if the coordinate system was assigned during initialization.
self._has_assigned_coordinate_system = False if crs == 'auto' else True
if uri is None:
# Fields may be created from pure metadata.
if metadata is not None:
# The default OCGIS driver is NetCDF.
if driver is None:
driver = DriverKey.NETCDF_CF
elif opened is None:
ocgis_lh(logger='request', exc=RequestValidationError('uri', 'Cannot be None'))
else:
self._uri = get_uri(uri)
if driver is None:
klass = get_autodiscovered_driver(uri)
else:
klass = get_driver(driver)
self._driver = klass(self)
if variable is not None:
variable = get_tuple(variable)
self._variable = variable
self.time_range = time_range
self.time_region = time_region
self.time_subset_func = time_subset_func
self.level_range = level_range
self._crs = deepcopy(crs)
self.regrid_source = regrid_source
self.regrid_destination = regrid_destination
self.units = units
self.conform_units_to = conform_units_to
self._is_init = False
self._validate_time_subset_()
# Update metadata for time variable.
tvar = self.dimension_map.get_variable(DMK.TIME)
if tvar is not None:
m = self.metadata['variables'][tvar]
if t_units is not None:
m['attrs']['units'] = t_units
if t_calendar is not None:
m['attrs']['calendar'] = t_calendar
if t_conform_units_to is not None:
from ocgis.util.units import get_units_object
t_calendar = m['attrs'].get('calendar', constants.DEFAULT_TEMPORAL_CALENDAR)
t_conform_units_to = get_units_object(t_conform_units_to, calendar=t_calendar)
m['conform_units_to'] = t_conform_units_to