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_that_can_calculate_mid_point_between_two_datetime(self):
from cis.time_util import calculate_mid_time
t1 = convert_datetime_to_std_time(dt.datetime(2010, 0o2, 0o5, 0, 0, 0))
t2 = convert_datetime_to_std_time(dt.datetime(2010, 0o2, 0o6, 0, 0, 0))
tm = calculate_mid_time(t1, t2)
eq_(
tm,
convert_datetime_to_std_time(dt.datetime(2010, 0o2, 0o5, 12, 0,
0)))
def _create_coord_list(self, filenames):
import numpy as np
from cis.time_util import calculate_mid_time, cis_standard_time_unit
variables = ["XDim", "YDim"]
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
lat = sdata["YDim"]
lat_metadata = hdf.read_metadata(lat, "SD")
lon = sdata["XDim"]
lon_metadata = hdf.read_metadata(lon, "SD")
# expand lat and lon data array so that they have the same shape
lat_data = utils.expand_1d_to_2d_array(
hdf.read_data(lat, "SD"), lon_metadata.shape, axis=1
) # expand latitude column wise
lon_data = utils.expand_1d_to_2d_array(
hdf.read_data(lon, "SD"), lat_metadata.shape, axis=0
) # expand longitude row wise
lat_metadata.shape = lat_data.shape
lon_metadata.shape = lon_data.shape
# to make sure "Latitude" and "Longitude", i.e. the standard_name is displayed instead of "YDim"and "XDim"
lat_metadata.standard_name = "latitude"
lat_metadata._name = ""
lon_metadata.standard_name = "longitude"
lon_metadata._name = ""
# create arrays for time coordinate using the midpoint of the time delta between the start date and the end date
time_data_array = []
for filename in filenames:
mid_datetime = calculate_mid_time(self._get_start_date(filename), self._get_end_date(filename))
logging.debug("Using " + str(mid_datetime) + " as datetime for file " + str(filename))
# Only use part of the full lat shape as it has already been concatenated
time_data = np.empty((lat_metadata.shape[0] / len(filenames), lat_metadata.shape[1]), dtype="float64")
time_data.fill(mid_datetime)
time_data_array.append(time_data)
time_data = utils.concatenate(time_data_array)
time_metadata = Metadata(
name="DateTime",
standard_name="time",
shape=time_data.shape,
units=str(cis_standard_time_unit),
calendar=cis_standard_time_unit.calendar,
)
coords = CoordList()
coords.append(Coord(lon_data, lon_metadata, "X"))
coords.append(Coord(lat_data, lat_metadata, "Y"))
coords.append(Coord(time_data, time_metadata, "T"))
return coords
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_can_calculate_mid_point_between_two_datetime():
from cis.time_util import calculate_mid_time
t1 = convert_datetime_to_std_time(dt.datetime(2010, 02, 05, 0, 0, 0))
t2 = convert_datetime_to_std_time(dt.datetime(2010, 02, 06, 0, 0, 0))
tm = calculate_mid_time(t1, t2)
eq_(tm, convert_datetime_to_std_time(dt.datetime(2010, 02, 05, 12, 0, 0)))
