def _create_coord_list(self, filenames):
from cis.time_util import cis_standard_time_unit
# list of coordinate variables we are interested in
variables = ['Latitude', 'Longitude', 'TAI_start', 'Profile_time', 'Height']
# reading the various files
try:
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
# altitude coordinate
height = sdata['Height']
height_data = hdf.read_data(height, "SD")
height_metadata = hdf.read_metadata(height, "SD")
height_coord = Coord(height_data, height_metadata, "Y")
except InvalidVariableError:
# This means we are reading a Cloudsat file without height, so remove height from the variables list
variables.remove('Height')
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
height_data = None
height_coord = None
# latitude
lat = vdata['Latitude']
lat_data = hdf.read_data(lat, "VD")
if height_data is not None:
lat_data = utils.expand_1d_to_2d_array(lat_data, len(height_data[0]), axis=1)
lat_metadata = hdf.read_metadata(lat, "VD")
lat_metadata.shape = lat_data.shape
lat_coord = Coord(lat_data, lat_metadata)
# longitude
lon = vdata['Longitude']
lon_data = hdf.read_data(lon, "VD")
if height_data is not None:
lon_data = utils.expand_1d_to_2d_array(lon_data, len(height_data[0]), axis=1)
lon_metadata = hdf.read_metadata(lon, "VD")
lon_metadata.shape = lon_data.shape
lon_coord = Coord(lon_data, lon_metadata)
# time coordinate
time_data = self._generate_time_array(vdata)
if height_data is not None:
time_data = utils.expand_1d_to_2d_array(time_data, len(height_data[0]), axis=1)
time_coord = Coord(time_data, Metadata(name='Profile_time', standard_name='time', shape=time_data.shape,
units=str(cis_standard_time_unit),
calendar=cis_standard_time_unit.calendar), "X")
# create object containing list of coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
if height_coord is not None:
coords.append(height_coord)
coords.append(time_coord)
return coords
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
# reading coordinates
coords = self._create_coord_list(filenames)
# reading of variables
sdata, vdata = hdf.read(filenames, variable)
# missing values
missing_values = [0, -9999, -4444, -3333]
# retrieve data + its metadata
if variable in vdata:
# vdata should be expanded in the same way as the coordinates are expanded
try:
height_length = coords.get_coord('Height').shape[1]
var = utils.expand_1d_to_2d_array(hdf.read_data(vdata[variable], "VD", missing_values),
height_length, axis=1)
except CoordinateNotFoundError:
var = hdf.read_data(vdata[variable], "VD", missing_values)
metadata = hdf.read_metadata(vdata[variable], "VD")
elif variable in sdata:
var = hdf.read_data(sdata[variable], "SD", missing_values)
metadata = hdf.read_metadata(sdata[variable], "SD")
else:
raise ValueError("variable not found")
return UngriddedData(var, metadata, coords)
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
variables = ["Latitude", "Longitude", "Scan_Start_Time"]
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
apply_interpolation = True if scale is "1km" else False
lat = sdata["Latitude"]
sd_lat = hdf.read_data(lat, "SD")
lat_data = self.__field_interpolate(sd_lat) if apply_interpolation else sd_lat
lat_metadata = hdf.read_metadata(lat, "SD")
lat_coord = Coord(lat_data, lat_metadata, "Y")
lon = sdata["Longitude"]
lon_data = (
self.__field_interpolate(hdf.read_data(lon, "SD")) if apply_interpolation else hdf.read_data(lon, "SD")
)
lon_metadata = hdf.read_metadata(lon, "SD")
lon_coord = Coord(lon_data, lon_metadata, "X")
time = sdata["Scan_Start_Time"]
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = "time"
time_coord = Coord(time, time_metadata, "T")
time_coord.convert_TAI_time_to_std_time(dt.datetime(1993, 1, 1, 0, 0, 0))
return CoordList([lat_coord, lon_coord, time_coord])
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_one_dimensional_coord_list(self, filenames, index_offset=1):
"""
Create a set of coordinates appropriate for a ond-dimensional (column integrated) variable
:param filenames:
:param int index_offset: For 5km products this will choose the coordinates which represent the start (0),
middle (1) and end (2) of the 15 shots making up each column retrieval.
:return:
"""
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
import datetime as dt
from cis.time_util import convert_sec_since_to_std_time, cis_standard_time_unit
variables = ['Latitude', 'Longitude', "Profile_Time"]
logging.info("Listing coordinates: " + str(variables))
# 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])
# latitude
lat_data = hdf.read_data(sdata['Latitude'], self._get_calipso_data)[:, index_offset]
lat_metadata = hdf.read_metadata(sdata['Latitude'], "SD")
lat_coord = Coord(lat_data, lat_metadata, 'Y')
# longitude
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, self._get_calipso_data)[:, index_offset]
lon_metadata = hdf.read_metadata(lon, "SD")
lon_coord = Coord(lon_data, lon_metadata, 'X')
# profile time, x
time = sdata['Profile_Time']
time_data = hdf.read_data(time, self._get_calipso_data)[:, index_offset]
time_data = convert_sec_since_to_std_time(time_data, dt.datetime(1993, 1, 1, 0, 0, 0))
time_coord = Coord(time_data, Metadata(name='Profile_Time', standard_name='time', shape=time_data.shape,
units=cis_standard_time_unit), "T")
# create the object containing all coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
coords.append(time_coord)
return coords
def create_data_object(self, filenames, variable):
from pywork.CALIOP_utils import mask_data
logging.debug("Creating *QC'd* data object for variable " + variable)
# reading of variables
sdata, vdata = hdf.read(filenames, [variable, "Pressure", "Extinction_QC_Flag_532", "CAD_Score"])
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
# reading coordinates
# See if the variable is one dimensional (check the length of shape, neglecting length 1 dimensions)
if len([l for l in metadata.shape if l > 1]) == 1:
coords = self._create_one_dimensional_coord_list(filenames, index_offset=1)
else:
coords = self._create_coord_list(filenames, index_offset=1)
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))
callback = self._get_mixed_resolution_calipso_data
else:
callback = self._get_calipso_data
var_data = hdf.read_data(sdata[variable], callback)
extinction_qc = hdf.read_data(sdata["Extinction_QC_Flag_532"], self._get_mixed_resolution_calipso_data)
cad_score = hdf.read_data(sdata["CAD_Score"], self._get_mixed_resolution_calipso_data)
qcd_var_data, = mask_data(var_data, cad_score, extinction_qc)
# reading coordinates
if variable.startswith('Column'):
coords = self._create_one_dimensional_coord_list(filenames, index_offset=1)
else:
coords = self._create_coord_list(filenames, index_offset=1)
pres_data = hdf.read_data(sdata['Pressure'], self._get_calipso_data)
pres_metadata = hdf.read_metadata(sdata['Pressure'], "SD")
# Fix badly formatted units which aren't CF compliant and will break if they are aggregated
if str(pres_metadata.units) == "hPA":
pres_metadata.units = "hPa"
qcd_pres_data = mask_data(pres_data, cad_score, extinction_qc)
pres_coord = Coord(qcd_pres_data, pres_metadata, 'P')
coords.append(pres_coord)
return UngriddedData(qcd_var_data, metadata, coords)
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
from cis.time_util import convert_time_since_to_std_time, cis_standard_time_unit
from cis.utils import concatenate
from cf_units import Unit
from geotiepoints import modis5kmto1km
variables = ['Latitude', 'Longitude', 'View_time']
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
apply_interpolation = True if scale is "1km" else False
lat_data = hdf.read_data(sdata['Latitude'], _get_MODIS_SDS_data)
lat_metadata = hdf.read_metadata(sdata['Latitude'], "SD")
lon_data = hdf.read_data(sdata['Longitude'], _get_MODIS_SDS_data)
lon_metadata = hdf.read_metadata(sdata['Longitude'], "SD")
if apply_interpolation:
lon_data, lat_data = modis5kmto1km(lon_data, lat_data)
lat_coord = Coord(lat_data, lat_metadata, 'Y')
lon_coord = Coord(lon_data, lon_metadata, 'X')
time = sdata['View_time']
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = 'time'
time_metadata.units = cis_standard_time_unit
t_arrays = []
for f, d in zip(filenames, time):
time_start = self._get_start_date(f)
t_data = _get_MODIS_SDS_data(
d) / 24.0 # Convert hours since to days since
t_offset = time_start - dt.datetime(1600, 1,
1) # Convert to CIS time
t_arrays.append(t_data + t_offset.days)
time_coord = Coord(concatenate(t_arrays), time_metadata, "T")
return CoordList([lat_coord, lon_coord, time_coord])
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
from cis.time_util import convert_time_since_to_std_time, cis_standard_time_unit
from cis.utils import concatenate
from cf_units import Unit
from geotiepoints import modis5kmto1km
variables = ['Latitude', 'Longitude', 'View_time']
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
apply_interpolation = True if scale is "1km" else False
lat_data = hdf.read_data(sdata['Latitude'], _get_MODIS_SDS_data)
lat_metadata = hdf.read_metadata(sdata['Latitude'], "SD")
lon_data = hdf.read_data(sdata['Longitude'], _get_MODIS_SDS_data)
lon_metadata = hdf.read_metadata(sdata['Longitude'], "SD")
if apply_interpolation:
lon_data, lat_data = modis5kmto1km(lon_data, lat_data)
lat_coord = Coord(lat_data, lat_metadata, 'Y')
lon_coord = Coord(lon_data, lon_metadata, 'X')
time = sdata['View_time']
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = 'time'
time_metadata.units = cis_standard_time_unit
t_arrays = []
for f, d in zip(filenames, time):
time_start = self._get_start_date(f)
t_data = _get_MODIS_SDS_data(d) / 24.0 # Convert hours since to days since
t_offset = time_start - dt.datetime(1600, 1, 1) # Convert to CIS time
t_arrays.append(t_data + t_offset.days)
time_coord = Coord(concatenate(t_arrays), time_metadata, "T")
return CoordList([lat_coord, lon_coord, time_coord])
def _create_one_dimensional_coord_list(self, filenames):
from cis.time_util import cis_standard_time_unit
# list of coordinate variables we are interested in
variables = [
'MODIS_latitude', 'MODIS_longitude', 'TAI_start', 'Profile_time'
]
# reading the various files
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
# latitude
lat = sdata['MODIS_latitude']
lat_data = hdf.read_data(lat, self._get_cloudsat_sds_data)
lat_metadata = hdf.read_metadata(lat, "SD")
lat_metadata.shape = lat_data.shape
lat_metadata.standard_name = 'latitude'
lat_coord = Coord(lat_data, lat_metadata)
# longitude
lon = sdata['MODIS_longitude']
lon_data = hdf.read_data(lon, self._get_cloudsat_sds_data)
lon_metadata = hdf.read_metadata(lon, "SD")
lon_metadata.shape = lon_data.shape
lon_metadata.standard_name = 'longitude'
lon_coord = Coord(lon_data, lon_metadata)
# time coordinate
time_data = self._generate_time_array(vdata)
time_coord = Coord(
time_data,
Metadata(name='Profile_time',
standard_name='time',
shape=time_data.shape,
units=cis_standard_time_unit), "X")
# create object containing list of coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
coords.append(time_coord)
return coords
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
# reading of variables
sdata, vdata = hdf.read(filenames, variable)
# reading (un-expanded) coordinates, since the data is 1-dimensional
coords = self._create_one_dimensional_coord_list(filenames)
# retrieve data + its metadata
if variable in vdata:
var = hdf.read_data(vdata[variable], self._get_cloudsat_vds_data)
metadata = hdf.read_metadata(vdata[variable], "VD")
elif variable in sdata:
var = hdf.read_data(sdata[variable], self._get_cloudsat_sds_data)
metadata = hdf.read_metadata(sdata[variable], "SD")
else:
raise ValueError("variable not found")
return UngriddedData(var, metadata, coords)
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
# reading of variables
sdata, vdata = hdf.read(filenames, variable)
# reading (un-expanded) coordinates, since the data is 1-dimensional
coords = self._create_one_dimensional_coord_list(filenames)
# retrieve data + its metadata
if variable in vdata:
var = hdf.read_data(vdata[variable], self._get_cloudsat_vds_data)
metadata = hdf.read_metadata(vdata[variable], "VD")
elif variable in sdata:
var = hdf.read_data(sdata[variable], self._get_cloudsat_sds_data)
metadata = hdf.read_metadata(sdata[variable], "SD")
else:
raise ValueError("variable not found")
return UngriddedData(var, metadata, coords)
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
variables = ['Latitude', 'Longitude', 'Scan_Start_Time']
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
apply_interpolation = True if scale is "1km" else False
lat = sdata['Latitude']
sd_lat = hdf.read_data(lat, _get_MODIS_SDS_data)
lat_data = self.__field_interpolate(
sd_lat) if apply_interpolation else sd_lat
lat_metadata = hdf.read_metadata(lat, "SD")
lat_coord = Coord(lat_data, lat_metadata, 'Y')
lon = sdata['Longitude']
if apply_interpolation:
lon_data = self.__field_interpolate(
hdf.read_data(lon, _get_MODIS_SDS_data))
else:
lon_data = hdf.read_data(lon, _get_MODIS_SDS_data)
lon_metadata = hdf.read_metadata(lon, "SD")
lon_coord = Coord(lon_data, lon_metadata, 'X')
time = sdata['Scan_Start_Time']
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = 'time'
time_coord = Coord(time, time_metadata, "T", _get_MODIS_SDS_data)
time_coord.convert_TAI_time_to_std_time(
dt.datetime(1993, 1, 1, 0, 0, 0))
return CoordList([lat_coord, lon_coord, time_coord])
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
variables = ['Latitude', 'Longitude', 'Scan_Start_Time']
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
self.apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
self.apply_interpolation = scale == "1km"
lat = sdata['Latitude']
lat_data = hdf.read_data(lat, _get_MODIS_SDS_data)
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, _get_MODIS_SDS_data)
if self.apply_interpolation:
lon_data, lat_data = modis5kmto1km(lon_data[:], lat_data[:])
lat_metadata = hdf.read_metadata(lat, "SD")
lat_coord = Coord(lat_data, lat_metadata, 'Y')
lon_metadata = hdf.read_metadata(lon, "SD")
lon_coord = Coord(lon_data, lon_metadata, 'X')
time = sdata['Scan_Start_Time']
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = 'time'
time_data = hdf.read_data(time, _get_MODIS_SDS_data)
if self.apply_interpolation:
time_data = np.repeat(np.repeat(time_data, 5, axis=0), 5, axis=1)
time_coord = Coord(time_data, time_metadata, "T")
time_coord.convert_TAI_time_to_std_time(
dt.datetime(1993, 1, 1, 0, 0, 0))
return CoordList([lat_coord, lon_coord, time_coord])
def _create_one_dimensional_coord_list(self, filenames):
from cis.time_util import cis_standard_time_unit
# list of coordinate variables we are interested in
variables = ['MODIS_latitude', 'MODIS_longitude', 'TAI_start', 'Profile_time']
# reading the various files
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
# latitude
lat = sdata['MODIS_latitude']
lat_data = hdf.read_data(lat, self._get_cloudsat_sds_data)
lat_metadata = hdf.read_metadata(lat, "SD")
lat_metadata.shape = lat_data.shape
lat_metadata.standard_name = 'latitude'
lat_coord = Coord(lat_data, lat_metadata)
# longitude
lon = sdata['MODIS_longitude']
lon_data = hdf.read_data(lon, self._get_cloudsat_sds_data)
lon_metadata = hdf.read_metadata(lon, "SD")
lon_metadata.shape = lon_data.shape
lon_metadata.standard_name = 'longitude'
lon_coord = Coord(lon_data, lon_metadata)
# time coordinate
time_data = self._generate_time_array(vdata)
time_coord = Coord(time_data, Metadata(name='Profile_time', standard_name='time', shape=time_data.shape,
units=cis_standard_time_unit), "X")
# create object containing list of coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
coords.append(time_coord)
return coords
def _create_coord_list(self, filenames, variable=None):
import datetime as dt
variables = ['Latitude', 'Longitude', 'Scan_Start_Time']
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
apply_interpolation = False
if variable is not None:
scale = self.__get_data_scale(filenames[0], variable)
apply_interpolation = True if scale is "1km" else False
lat = sdata['Latitude']
lat_data = hdf.read_data(lat, _get_MODIS_SDS_data)
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, _get_MODIS_SDS_data)
if apply_interpolation:
lon_data, lat_data = modis5kmto1km(lon_data[:], lat_data[:])
lat_metadata = hdf.read_metadata(lat, "SD")
lat_coord = Coord(lat_data, lat_metadata, 'Y')
lon_metadata = hdf.read_metadata(lon, "SD")
lon_coord = Coord(lon_data, lon_metadata, 'X')
time = sdata['Scan_Start_Time']
time_metadata = hdf.read_metadata(time, "SD")
# Ensure the standard name is set
time_metadata.standard_name = 'time'
time_data = hdf.read_data(time, _get_MODIS_SDS_data)
time_data = np.repeat(np.repeat(time_data, 5, axis=0), 5, axis=1)
time_coord = Coord(time_data, time_metadata, "T")
time_coord.convert_TAI_time_to_std_time(dt.datetime(1993, 1, 1, 0, 0, 0))
return CoordList([lat_coord, lon_coord, time_coord])
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
# reading coordinates
# the variable here is needed to work out whether to apply interpolation to the lat/lon data or not
coords = self._create_coord_list(filenames, variable)
# reading of variables
sdata, vdata = hdf.read(filenames, variable)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
# cut off the edges of the data...
# TODO CHECK THIS IS ACTUALLY VALID BEFORE PUBLISHING ANYTHING WITH THIS
d = hdf.read_data(var, _get_MODIS_SDS_data)[:, 2:-2]
return UngriddedData(d, metadata, coords, _get_MODIS_SDS_data)
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
# reading coordinates
# the variable here is needed to work out whether to apply interpolation to the lat/lon data or not
coords = self._create_coord_list(filenames, variable)
# reading of variables
sdata, vdata = hdf.read(filenames, variable)
# retrieve data + its metadata
var = sdata[variable]
metadata = hdf.read_metadata(var, "SD")
# cut off the edges of the data...
# TODO CHECK THIS IS ACTUALLY VALID BEFORE PUBLISHING ANYTHING WITH THIS
d = hdf.read_data(var, _get_MODIS_SDS_data)
if self.apply_interpolation:
d = d[:, 2:-2]
return UngriddedData(d, metadata, coords, _get_MODIS_SDS_data)
def _create_coord_list(self, filenames, index_offset=0):
import logging
from cis.data_io import hdf as hdf
from cis.data_io.Coord import Coord, CoordList
from cis.data_io.ungridded_data import Metadata
import cis.utils as utils
from cis.data_io.hdf_vd import VDS
from pyhdf.error import HDF4Error
from cis.data_io import hdf_sd
import datetime as dt
from cis.time_util import convert_sec_since_to_std_time, cis_standard_time_unit
variables = ['Latitude', 'Longitude', "Profile_Time", "Pressure"]
logging.info("Listing coordinates: " + str(variables))
# 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_data *= 1000.0 # Convert to m
len_x = alt_data.shape[0]
lat_data = hdf.read_data(sdata['Latitude'], self._get_calipso_data)
len_y = lat_data.shape[0]
new_shape = (len_x, len_y)
# altitude
alt_data = utils.expand_1d_to_2d_array(alt_data, len_y, axis=0)
alt_metadata = Metadata(name=alt_name, standard_name=alt_name, shape=new_shape)
alt_coord = Coord(alt_data, alt_metadata)
# pressure
if self.include_pressure:
pres_data = hdf.read_data(sdata['Pressure'], self._get_calipso_data)
pres_metadata = hdf.read_metadata(sdata['Pressure'], "SD")
# Fix badly formatted units which aren't CF compliant and will break if they are aggregated
if str(pres_metadata.units) == "hPA":
pres_metadata.units = "hPa"
pres_metadata.shape = new_shape
pres_coord = Coord(pres_data, pres_metadata, 'P')
# latitude
lat_data = utils.expand_1d_to_2d_array(lat_data[:, index_offset], len_x, axis=1)
lat_metadata = hdf.read_metadata(sdata['Latitude'], "SD")
lat_metadata.shape = new_shape
lat_coord = Coord(lat_data, lat_metadata, 'Y')
# longitude
lon = sdata['Longitude']
lon_data = hdf.read_data(lon, self._get_calipso_data)
lon_data = utils.expand_1d_to_2d_array(lon_data[:, index_offset], len_x, axis=1)
lon_metadata = hdf.read_metadata(lon, "SD")
lon_metadata.shape = new_shape
lon_coord = Coord(lon_data, lon_metadata, 'X')
# profile time, x
time = sdata['Profile_Time']
time_data = hdf.read_data(time, self._get_calipso_data)
time_data = convert_sec_since_to_std_time(time_data, dt.datetime(1993, 1, 1, 0, 0, 0))
time_data = utils.expand_1d_to_2d_array(time_data[:, index_offset], len_x, axis=1)
time_coord = Coord(time_data, Metadata(name='Profile_Time', standard_name='time', shape=time_data.shape,
units=cis_standard_time_unit), "T")
# create the object containing all coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
coords.append(time_coord)
coords.append(alt_coord)
if self.include_pressure and (pres_data.shape == alt_data.shape):
# For MODIS L1 this may is not be true, so skips the air pressure reading. If required for MODIS L1 then
# some kind of interpolation of the air pressure would be required, as it is on a different (smaller) grid
# than for the Lidar_Data_Altitudes.
coords.append(pres_coord)
return coords
def _create_coord_list(self, filenames):
from cis.time_util import cis_standard_time_unit
# list of coordinate variables we are interested in
variables = [
'Latitude', 'Longitude', 'TAI_start', 'Profile_time', 'Height'
]
# reading the various files
try:
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
# altitude coordinate
height = sdata['Height']
height_data = hdf.read_data(height, self._get_cloudsat_sds_data)
height_metadata = hdf.read_metadata(height, "SD")
height_coord = Coord(height_data, height_metadata, "Y")
except InvalidVariableError:
# This means we are reading a Cloudsat file without height, so remove height from the variables list
variables.remove('Height')
logging.info("Listing coordinates: " + str(variables))
sdata, vdata = hdf.read(filenames, variables)
height_data = None
height_coord = None
# latitude
lat = vdata['Latitude']
lat_data = hdf.read_data(lat, self._get_cloudsat_vds_data)
if height_data is not None:
lat_data = utils.expand_1d_to_2d_array(lat_data,
len(height_data[0]),
axis=1)
lat_metadata = hdf.read_metadata(lat, "VD")
lat_metadata.shape = lat_data.shape
lat_coord = Coord(lat_data, lat_metadata)
# longitude
lon = vdata['Longitude']
lon_data = hdf.read_data(lon, self._get_cloudsat_vds_data)
if height_data is not None:
lon_data = utils.expand_1d_to_2d_array(lon_data,
len(height_data[0]),
axis=1)
lon_metadata = hdf.read_metadata(lon, "VD")
lon_metadata.shape = lon_data.shape
lon_coord = Coord(lon_data, lon_metadata)
# time coordinate
time_data = self._generate_time_array(vdata)
if height_data is not None:
time_data = utils.expand_1d_to_2d_array(time_data,
len(height_data[0]),
axis=1)
time_coord = Coord(
time_data,
Metadata(name='Profile_time',
standard_name='time',
shape=time_data.shape,
units=cis_standard_time_unit), "X")
# create object containing list of coordinates
coords = CoordList()
coords.append(lat_coord)
coords.append(lon_coord)
if height_coord is not None:
coords.append(height_coord)
coords.append(time_coord)
return coords
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
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