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):
"""Read file coordinates into a CIS object"""
from cis.data_io.Coord import Coord, CoordList
from reame.utils import ncdf_read
try:
lon_data, lon_metadata = ncdf_read(self.filenames, "longitude")
lat_data, lat_metadata = ncdf_read(self.filenames, "latitude")
except IndexError:
lon_data, lon_metadata = ncdf_read(self.filenames, "lon")
lat_data, lat_metadata = ncdf_read(self.filenames, "lat")
lat = Coord(lat_data, lat_metadata, "Y")
lat.update_shape()
lat.update_range()
lon = Coord(lon_data, lon_metadata, "X")
lon.update_shape()
lat.update_range()
time_data, time_metadata = ncdf_read(self.filenames, "time")
# Ensure the standard name is set
time_metadata.standard_name = "time"
time = Coord(time_data, time_metadata, "T")
time.convert_TAI_time_to_std_time(ATSR_REFERENCE_TIME)
time.update_shape()
time.update_range()
return CoordList([lat, lon, time])
def _create_coord_list(self):
from cis.data_io.Coord import Coord, CoordList
from cis.data_io.ungridded_data import Metadata
from cis.time_util import convert_sec_since_to_std_time
from os.path import basename
lat_all = []
lon_all = []
time_all = []
for fname in self.filenames:
var_name = self.gdal_variable_name(fname, "Optical_Depth_055")
if self.grid_path:
granule = basename(fname).split(".")[2]
lat_data, lon_data = self._read_grid_centres(granule)
else:
lat_data, lon_data = self._calculate_grid_centres(var_name)
time_data = self._calculate_grid_time(var_name, lat_data, lon_data)
# Workaround files containing only one day
sh = (-1, ) + lat_data.shape
time_data = time_data.reshape(sh)
keep = np.logical_not(self._read_qcmask(fname)).reshape(sh)
for time_slice, keep_slice in zip(time_data, keep):
lat_all.extend(lat_data[keep_slice])
lon_all.extend(lon_data[keep_slice])
time_all.extend(time_slice[keep_slice])
if len(lat_all) == 0:
raise NotImplementedError("It's empty!")
lat = Coord(
np.ma.array(lat_all),
Metadata(name="lat",
standard_name="latitude",
units="degrees",
range=(-90., 90.)), "Y")
lat.update_shape()
lon = Coord(
np.ma.array(lon_all),
Metadata(name="lon",
standard_name="longitude",
units="degrees",
range=(-180., 180.)), "X")
lon.update_shape()
time = Coord(
np.ma.array(time_all),
Metadata(name="time",
standard_name="time",
units="Seconds since 1993-1-1 00:00:00.0 0"), "T")
time.convert_TAI_time_to_std_time(MODIS_REFERENCE_TIME)
time.update_shape()
# Set the QC mask as we now know how many points we have
self._qcmask = np.full(lat.shape, False)
return CoordList([lat, lon, time])
def _create_coord_list(self, filenames):
from cis.data_io.netcdf import read_many_files, get_metadata
from cis.data_io.Coord import Coord
import datetime
# FIXME: when reading an existing file variables might be "latitude", "longitude"
variables = ["lat", "lon", "time"]
logging.info("Listing coordinates: " + str(variables))
data = read_many_files(filenames, variables, dim="pixel_number")
coords = CoordList()
coords.append(Coord(data["lon"], get_metadata(data["lon"]), "X"))
coords.append(Coord(data["lat"], get_metadata(data["lat"]), "Y"))
time_coord = Coord(data["time"], get_metadata(data["time"]), "T")
time_coord.convert_TAI_time_to_std_time(datetime.datetime(1970, 1, 1))
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']
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_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_coord_list(self):
"""Read data coordinates into CIS object"""
from cis.data_io.Coord import Coord, CoordList
from reame.utils import hdf_read
lon_data, lon_metadata = hdf_read(self.filenames, "Longitude")
lon = Coord(lon_data, lon_metadata, "X")
lon.update_shape()
lon.update_range()
lat_data, lat_metadata = hdf_read(self.filenames, "Latitude")
lat = Coord(lat_data, lat_metadata, "Y")
lat.update_shape()
lat.update_range()
time_data, time_metadata = hdf_read(self.filenames, "Scan_Start_Time")
# Ensure the standard name is set
time_metadata.standard_name = "time"
time = Coord(time_data, time_metadata, "T")
time.convert_TAI_time_to_std_time(MODIS_REFERENCE_TIME)
time.update_shape()
time.update_range()
return CoordList([lat, lon, time])
