def test_time_unit_conversion(self):
"""Test that the output cube contains the desired units and datatypes
for the time, forecast_reference_time and forecast_period coordinate,
where a unit conversion has been required for the time and forecast
reference time coordinates."""
self.cube.coord("time").convert_units("hours since 1970-01-01 00:00")
frt_coord = DimCoord(
1519099200,
standard_name="forecast_reference_time",
units="seconds since 1970-01-01 00:00:00",
)
frt_coord.convert_units("hours since 1970-01-01 00:00")
self.cube.add_aux_coord(frt_coord)
self.cube.coord("forecast_reference_time").convert_units(
"hours since 1970-01-01 00:00")
result = self.plugin.process(self.cube, self.timestep)
self.assertEqual(result.coord("forecast_period").points, 600)
# 2017-11-10 04:10:00
self.assertEqual(result.coord("time").points, 1519099800)
self.assertEqual(
result.coord("forecast_reference_time").points, 1519099200)
self.assertEqual(result.coord("forecast_period").units, "seconds")
self.assertEqual(
result.coord("time").units, "seconds since 1970-01-01 00:00:00")
self.assertEqual(
result.coord("forecast_reference_time").units,
"seconds since 1970-01-01 00:00:00",
)
self.assertEqual(result.coord("forecast_period").dtype, np.int32)
self.assertEqual(result.coord("time").dtype, np.int64)
self.assertEqual(
result.coord("forecast_reference_time").dtype, np.int64)
def create_data_object(self, filenames, variable, index_offset=1):
from cis.data_io.hdf_vd import get_data
from cis.data_io.hdf_vd import VDS
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
from iris.coords import DimCoord, AuxCoord
from iris.cube import Cube
from cis.data_io.gridded_data import GriddedData
from cis.time_util import cis_standard_time_unit
logging.debug("Creating data object for variable " + variable)
variables = ['Latitude', 'Longitude', "Profile_Time", "Pressure"]
logging.info("Listing coordinates: " + str(variables))
variables.append(variable)
# reading data from files
sdata = {}
for filename in filenames:
try:
sds_dict = hdf_sd.read(filename, variables)
except HDF4Error as e:
raise IOError(str(e))
for var in list(sds_dict.keys()):
utils.add_element_to_list_in_dict(sdata, var, sds_dict[var])
alt_name = "altitude"
logging.info("Additional coordinates: '" + alt_name + "'")
# work out size of data arrays
# the coordinate variables will be reshaped to match that.
# NOTE: This assumes that all Caliop_L1 files have the same altitudes.
# If this is not the case, then the following line will need to be changed
# to concatenate the data from all the files and not just arbitrarily pick
# the altitudes from the first file.
alt_data = get_data(VDS(filenames[0], "Lidar_Data_Altitudes"), True)
alt_coord = DimCoord(alt_data, standard_name='altitude', units='km')
alt_coord.convert_units('m')
lat_data = hdf.read_data(sdata['Latitude'], self._get_calipso_data)[:, index_offset]
lat_coord = AuxCoord(lat_data, standard_name='latitude')
pres_data = hdf.read_data(sdata['Pressure'], self._get_calipso_data)
pres_coord = AuxCoord(pres_data, standard_name='air_pressure', units='hPa')
# longitude
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, self._get_calipso_data)[:, index_offset]
lon_coord = AuxCoord(lon_data, standard_name='longitude')
# profile time, x
time = sdata['Profile_Time']
time_data = hdf.read_data(time, self._get_calipso_data)[:, index_offset]
time_coord = DimCoord(time_data, long_name='Profile_Time', standard_name='time',
units="seconds since 1993-01-01 00:00:00")
time_coord.convert_units(cis_standard_time_unit)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
if variable in MIXED_RESOLUTION_VARIABLES:
logging.warning("Using Level 2 resolution profile for mixed resolution variable {}. See CALIPSO "
"documentation for more details".format(variable))
data = hdf.read_data(var, self._get_mixed_resolution_calipso_data)
else:
data = hdf.read_data(var, self._get_calipso_data)
cube = Cube(data, long_name=metadata.long_name, units=self.clean_units(metadata.units),
dim_coords_and_dims=[(alt_coord, 1), (time_coord, 0)], aux_coords_and_dims=[(lat_coord, (0,)),
(lon_coord, (0,)),
(pres_coord, (0, 1))])
gd = GriddedData.make_from_cube(cube)
return gd
def create_data_object(self, filenames, variable, index_offset=1):
from cis.data_io.hdf_vd import get_data
from cis.data_io.hdf_vd import VDS
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
from iris.coords import DimCoord, AuxCoord
from iris.cube import Cube, CubeList
from cis.data_io.gridded_data import GriddedData
from cis.time_util import cis_standard_time_unit
from datetime import datetime
from iris.util import new_axis
import numpy as np
logging.debug("Creating data object for variable " + variable)
variables = ["Pressure_Mean"]
logging.info("Listing coordinates: " + str(variables))
variables.append(variable)
# reading data from files
sdata = {}
for filename in filenames:
try:
sds_dict = hdf_sd.read(filename, variables)
except HDF4Error as e:
raise IOError(str(e))
for var in list(sds_dict.keys()):
utils.add_element_to_list_in_dict(sdata, var, sds_dict[var])
# work out size of data arrays
# the coordinate variables will be reshaped to match that.
# NOTE: This assumes that all Caliop_L1 files have the same altitudes.
# If this is not the case, then the following line will need to be changed
# to concatenate the data from all the files and not just arbitrarily pick
# the altitudes from the first file.
alt_data = self._get_calipso_data(hdf_sd.HDF_SDS(filenames[0], 'Altitude_Midpoint'))[0, :]
alt_coord = DimCoord(alt_data, standard_name='altitude', units='km')
alt_coord.convert_units('m')
lat_data = self._get_calipso_data(hdf_sd.HDF_SDS(filenames[0], 'Latitude_Midpoint'))[0, :]
lat_coord = DimCoord(lat_data, standard_name='latitude', units='degrees_north')
lon_data = self._get_calipso_data(hdf_sd.HDF_SDS(filenames[0], 'Longitude_Midpoint'))[0, :]
lon_coord = DimCoord(lon_data, standard_name='longitude', units='degrees_east')
cubes = CubeList()
for f in filenames:
t = get_data(VDS(f, "Nominal_Year_Month"), True)[0]
time_data = cis_standard_time_unit.date2num(datetime(int(t[0:4]), int(t[4:6]), 15))
time_coord = AuxCoord(time_data, long_name='Profile_Time', standard_name='time',
units=cis_standard_time_unit)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
data = self._get_calipso_data(hdf_sd.HDF_SDS(f, variable))
pres_data = self._get_calipso_data(hdf_sd.HDF_SDS(f, 'Pressure_Mean'))
pres_coord = AuxCoord(pres_data, standard_name='air_pressure', units='hPa')
if data.ndim == 2:
# pres_coord = new_axis()
cube = Cube(data, long_name=metadata.long_name or variable, units=self.clean_units(metadata.units),
dim_coords_and_dims=[(lat_coord, 0), (lon_coord, 1)],
aux_coords_and_dims=[(time_coord, ())])
# Promote the time scalar coord to a length one dimension
new_cube = new_axis(cube, 'time')
cubes.append(new_cube)
elif data.ndim == 3:
# pres_coord = new_axis()
cube = Cube(data, long_name=metadata.long_name or variable, units=self.clean_units(metadata.units),
dim_coords_and_dims=[(lat_coord, 0), (lon_coord, 1), (alt_coord, 2)],
aux_coords_and_dims=[(time_coord, ())])
# Promote the time scalar coord to a length one dimension
new_cube = new_axis(cube, 'time')
# Then add the (extended) pressure coord so that it is explicitly a function of time
new_cube.add_aux_coord(pres_coord[np.newaxis, ...], (0, 1, 2, 3))
cubes.append(new_cube)
else:
raise ValueError("Unexpected number of dimensions for CALIOP data: {}".format(data.ndim))
# Concatenate the cubes from each file into a single GriddedData object
gd = GriddedData.make_from_cube(cubes.concatenate_cube())
return gd
def create_data_object(self, filenames, variable, index_offset=1):
from cis.data_io.hdf_vd import get_data
from cis.data_io.hdf_vd import VDS
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
from iris.coords import DimCoord, AuxCoord
from iris.cube import Cube
from cis.data_io.gridded_data import GriddedData
from cis.time_util import cis_standard_time_unit
logging.debug("Creating data object for variable " + variable)
variables = ['Latitude', 'Longitude', "Profile_Time", "Pressure"]
logging.info("Listing coordinates: " + str(variables))
variables.append(variable)
# reading data from files
sdata = {}
for filename in filenames:
try:
sds_dict = hdf_sd.read(filename, variables)
except HDF4Error as e:
raise IOError(str(e))
for var in list(sds_dict.keys()):
utils.add_element_to_list_in_dict(sdata, var, sds_dict[var])
alt_name = "altitude"
logging.info("Additional coordinates: '" + alt_name + "'")
# work out size of data arrays
# the coordinate variables will be reshaped to match that.
# NOTE: This assumes that all Caliop_L1 files have the same altitudes.
# If this is not the case, then the following line will need to be changed
# to concatenate the data from all the files and not just arbitrarily pick
# the altitudes from the first file.
alt_data = get_data(VDS(filenames[0], "Lidar_Data_Altitudes"), True)
alt_coord = DimCoord(alt_data, standard_name='altitude', units='km')
alt_coord.convert_units('m')
lat_data = hdf.read_data(sdata['Latitude'],
self._get_calipso_data)[:, index_offset]
lat_coord = AuxCoord(lat_data, standard_name='latitude')
pres_data = hdf.read_data(sdata['Pressure'], self._get_calipso_data)
pres_coord = AuxCoord(pres_data,
standard_name='air_pressure',
units='hPa')
# longitude
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, self._get_calipso_data)[:, index_offset]
lon_coord = AuxCoord(lon_data, standard_name='longitude')
# profile time, x
time = sdata['Profile_Time']
time_data = hdf.read_data(time, self._get_calipso_data)[:,
index_offset]
time_coord = DimCoord(time_data,
long_name='Profile_Time',
standard_name='time',
units="seconds since 1993-01-01 00:00:00")
time_coord.convert_units(cis_standard_time_unit)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
if variable in MIXED_RESOLUTION_VARIABLES:
logging.warning(
"Using Level 2 resolution profile for mixed resolution variable {}. See CALIPSO "
"documentation for more details".format(variable))
data = hdf.read_data(var, self._get_mixed_resolution_calipso_data)
else:
data = hdf.read_data(var, self._get_calipso_data)
cube = Cube(data,
long_name=metadata.long_name,
units=self.clean_units(metadata.units),
dim_coords_and_dims=[(alt_coord, 1), (time_coord, 0)],
aux_coords_and_dims=[(lat_coord, (0, )),
(lon_coord, (0, )),
(pres_coord, (0, 1))])
gd = GriddedData.make_from_cube(cube)
return gd
def create_data_object(self, filenames, variable, index_offset=1):
from cis.data_io.hdf_vd import get_data
from cis.data_io.hdf_vd import VDS
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
from iris.coords import DimCoord, AuxCoord
from iris.cube import Cube, CubeList
from cis.data_io.gridded_data import GriddedData
from cis.time_util import cis_standard_time_unit
from datetime import datetime
from iris.util import new_axis
import numpy as np
logging.debug("Creating data object for variable " + variable)
variables = ["Pressure_Mean"]
logging.info("Listing coordinates: " + str(variables))
variables.append(variable)
# reading data from files
sdata = {}
for filename in filenames:
try:
sds_dict = hdf_sd.read(filename, variables)
except HDF4Error as e:
raise IOError(str(e))
for var in list(sds_dict.keys()):
utils.add_element_to_list_in_dict(sdata, var, sds_dict[var])
# work out size of data arrays
# the coordinate variables will be reshaped to match that.
# NOTE: This assumes that all Caliop_L1 files have the same altitudes.
# If this is not the case, then the following line will need to be changed
# to concatenate the data from all the files and not just arbitrarily pick
# the altitudes from the first file.
alt_data = self._get_calipso_data(
hdf_sd.HDF_SDS(filenames[0], 'Altitude_Midpoint'))[0, :]
alt_coord = DimCoord(alt_data, standard_name='altitude', units='km')
alt_coord.convert_units('m')
lat_data = self._get_calipso_data(
hdf_sd.HDF_SDS(filenames[0], 'Latitude_Midpoint'))[0, :]
lat_coord = DimCoord(lat_data,
standard_name='latitude',
units='degrees_north')
lon_data = self._get_calipso_data(
hdf_sd.HDF_SDS(filenames[0], 'Longitude_Midpoint'))[0, :]
lon_coord = DimCoord(lon_data,
standard_name='longitude',
units='degrees_east')
cubes = CubeList()
for f in filenames:
t = get_data(VDS(f, "Nominal_Year_Month"), True)[0]
time_data = cis_standard_time_unit.date2num(
datetime(int(t[0:4]), int(t[4:6]), 15))
time_coord = AuxCoord(time_data,
long_name='Profile_Time',
standard_name='time',
units=cis_standard_time_unit)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
data = self._get_calipso_data(hdf_sd.HDF_SDS(f, variable))
pres_data = self._get_calipso_data(
hdf_sd.HDF_SDS(f, 'Pressure_Mean'))
pres_coord = AuxCoord(pres_data,
standard_name='air_pressure',
units='hPa')
if data.ndim == 2:
# pres_coord = new_axis()
cube = Cube(data,
long_name=metadata.long_name or variable,
units=self.clean_units(metadata.units),
dim_coords_and_dims=[(lat_coord, 0),
(lon_coord, 1)],
aux_coords_and_dims=[(time_coord, ())])
# Promote the time scalar coord to a length one dimension
new_cube = new_axis(cube, 'time')
cubes.append(new_cube)
elif data.ndim == 3:
# pres_coord = new_axis()
cube = Cube(data,
long_name=metadata.long_name or variable,
units=self.clean_units(metadata.units),
dim_coords_and_dims=[(lat_coord, 0),
(lon_coord, 1),
(alt_coord, 2)],
aux_coords_and_dims=[(time_coord, ())])
# Promote the time scalar coord to a length one dimension
new_cube = new_axis(cube, 'time')
# Then add the (extended) pressure coord so that it is explicitly a function of time
new_cube.add_aux_coord(pres_coord[np.newaxis, ...],
(0, 1, 2, 3))
cubes.append(new_cube)
else:
raise ValueError(
"Unexpected number of dimensions for CALIOP data: {}".
format(data.ndim))
# Concatenate the cubes from each file into a single GriddedData object
gd = GriddedData.make_from_cube(cubes.concatenate_cube())
return gd
