def _create_cube(self, filenames, variable):
import numpy as np
from cis.data_io.hdf import _read_hdf4
from iris.cube import Cube, CubeList
from iris.coords import DimCoord, AuxCoord
from cis.time_util import calculate_mid_time, cis_standard_time_unit
from cis.data_io.hdf_sd import get_metadata
from cf_units import Unit
variables = ['XDim', 'YDim', variable]
logging.info("Listing coordinates: " + str(variables))
cube_list = CubeList()
# Read each file individually, let Iris do the merging at the end.
for f in filenames:
sdata, vdata = _read_hdf4(f, variables)
lat_coord = DimCoord(_get_MODIS_SDS_data(sdata['YDim']),
standard_name='latitude',
units='degrees')
lon_coord = DimCoord(_get_MODIS_SDS_data(sdata['XDim']),
standard_name='longitude',
units='degrees')
# create time coordinate using the midpoint of the time delta between the start date and the end date
start_datetime = self._get_start_date(f)
end_datetime = self._get_end_date(f)
mid_datetime = calculate_mid_time(start_datetime, end_datetime)
logging.debug("Using {} as datetime for file {}".format(
mid_datetime, f))
time_coord = AuxCoord(mid_datetime,
standard_name='time',
units=cis_standard_time_unit,
bounds=[start_datetime, end_datetime])
var = sdata[variable]
metadata = get_metadata(var)
try:
units = Unit(metadata.units)
except ValueError:
logging.warning(
"Unable to parse units '{}' in {} for {}.".format(
metadata.units, f, variable))
units = None
cube = Cube(_get_MODIS_SDS_data(sdata[variable]),
dim_coords_and_dims=[(lon_coord, 1), (lat_coord, 0)],
aux_coords_and_dims=[(time_coord, None)],
var_name=metadata._name,
long_name=metadata.long_name,
units=units)
cube_list.append(cube)
# Merge the cube list across the scalar time coordinates before returning a single cube.
return cube_list.merge_cube()
def test_read_hdf4():
filename = escape_colons(valid_hdf_sd_file)
sds, vds = _read_hdf4(filename, ['Solution_Ocean', 'Path_Radiance_Land', 'Mean_Reflectance_Land'])
# VD variable are listed in the VD part of the tuple, but not in the SD part
eq_(True, 'Solution_Ocean' in vds)
eq_(False, 'Solution_Ocean' in sds)
# SD variable are listed in the SD part of the tuple, but not in the VD part
eq_(True, 'Path_Radiance_Land' in sds)
eq_(False, 'Path_Radiance_Land' in vds)
eq_(True, 'Mean_Reflectance_Land' in sds)
eq_(False, 'Mean_Reflectance_Land' in vds)
def _create_cube(self, filenames, variable):
import numpy as np
from cis.data_io.hdf import _read_hdf4
from cis.data_io import hdf_vd
from iris.cube import Cube, CubeList
from iris.coords import DimCoord, AuxCoord
from cis.time_util import calculate_mid_time, cis_standard_time_unit
from cis.data_io.hdf_sd import get_metadata
from cf_units import Unit
variables = ['XDim:GlobalGrid', 'YDim:GlobalGrid', variable]
logging.info("Listing coordinates: " + str(variables))
cube_list = CubeList()
# Read each file individually, let Iris do the merging at the end.
for f in filenames:
sdata, vdata = _read_hdf4(f, variables)
lat_points = np.linspace(-90., 90., hdf_vd.get_data(vdata['YDim:GlobalGrid']))
lon_points = np.linspace(-180., 180., hdf_vd.get_data(vdata['XDim:GlobalGrid']))
lat_coord = DimCoord(lat_points, standard_name='latitude', units='degrees')
lon_coord = DimCoord(lon_points, standard_name='longitude', units='degrees')
# create time coordinate using the midpoint of the time delta between the start date and the end date
start_datetime = self._get_start_date(f)
end_datetime = self._get_end_date(f)
mid_datetime = calculate_mid_time(start_datetime, end_datetime)
logging.debug("Using {} as datetime for file {}".format(mid_datetime, f))
time_coord = AuxCoord(mid_datetime, standard_name='time', units=cis_standard_time_unit,
bounds=[start_datetime, end_datetime])
var = sdata[variable]
metadata = get_metadata(var)
try:
units = Unit(metadata.units)
except ValueError:
logging.warning("Unable to parse units '{}' in {} for {}.".format(metadata.units, f, variable))
units = None
cube = Cube(_get_MODIS_SDS_data(sdata[variable]),
dim_coords_and_dims=[(lon_coord, 1), (lat_coord, 0)],
aux_coords_and_dims=[(time_coord, None)],
var_name=metadata._name, long_name=metadata.long_name, units=units)
cube_list.append(cube)
# Merge the cube list across the scalar time coordinates before returning a single cube.
return cube_list.merge_cube()
def test_that_cannot_read_unknown_variables_and_valid_variables():
filename = escape_colons(valid_hdf_sd_file)
sds, vds = _read_hdf4(filename, ['someBizarreVariableNobodyKnowsAbout', 'Solution_Ocean', 'Path_Radiance_Land',
'Mean_Reflectance_Land'])
def test_that_cannot_read_unknown_variables():
filename = escape_colons(valid_hdf_sd_file)
sds, vds = _read_hdf4(filename, ['athing', 'unechose', 'einding'])
def should_raise_io_error_with_non_hdf_file():
_read_hdf4(valid_cloud_cci_filename, valid_cloud_cci_variable)