def _create_coord_list(self, filename):
import numpy as np
coords = CoordList()
time_data = read(filename, 'time')['time']
try:
alt_data = read(filename, 'altitude')['altitude']
except InvalidVariableError:
alt_data = read(filename, 'range')['range']
len_y = alt_data.shape[1]
time_arr = utils.expand_1d_to_2d_array(time_data[:], len_y, axis=1)
t_coord = Coord(time_arr, get_metadata(time_data), axis='x')
t_coord.convert_to_std_time()
coords.append(t_coord)
#alt_arr = utils.expand_1d_to_2d_array(alt_data[:], len_x, axis=0)
alt_arr = alt_data[:, :, 0] #eliminate "angle" axis
#alt_arr = alt_data #eliminate "angle" axis
coords.append(Coord(alt_arr, get_metadata(alt_data), axis='y'))
lat_data = read(filename, 'latitude')['latitude']
lat_arr = np.ones(alt_arr.shape) * lat_data[:]
coords.append(Coord(lat_arr, get_metadata(lat_data)))
lon_data = read(filename, 'longitude')['longitude']
lon_arr = np.ones(alt_arr.shape) * lon_data[:]
coords.append(Coord(lon_arr, get_metadata(lon_data)))
return coords
def can_not_convert_time_without_since_in_units_with_no_units():
times = numpy.array([0, 1])
units = ""
time_stamp_info = "1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time(time_stamp_info)
def _create_coord_list(self, filename):
import numpy as np
coords = CoordList()
time_data = read(filename, 'time')['time']
len_x = time_data.shape[0]
try:
alt_data = read(filename, 'altitude')['altitude']
except InvalidVariableError:
alt_data = read(filename, 'range')['range']
len_y = alt_data.shape[0]
time_arr = utils.expand_1d_to_2d_array(time_data[:], len_y, axis=1)
t_coord = Coord(time_arr, get_metadata(time_data), axis='x')
t_coord.convert_to_std_time()
coords.append(t_coord)
alt_arr = utils.expand_1d_to_2d_array(alt_data[:], len_x, axis=0)
coords.append(Coord(alt_arr, get_metadata(alt_data), axis='y'))
lat_data = read(filename, 'latitude')['latitude']
lat_arr = np.ones(alt_arr.shape) * lat_data[:]
coords.append(Coord(lat_arr, get_metadata(lat_data)))
lon_data = read(filename, 'longitude')['longitude']
lon_arr = np.ones(alt_arr.shape) * lon_data[:]
coords.append(Coord(lon_arr, get_metadata(lon_data)))
return coords
def _create_time_coord(self, timestamp, time_variable_name, data_variables, coord_axis='T', standard_name='time'):
"""
Create a time coordinate, taking into account the fact that each file may have a different timestamp.
:param timestamp: Timestamp or list of timestamps for
:param time_variable_name: Name of the time variable
:param data_variables: Dictionary containing one or multiple netCDF data variables for each variable name
:param coord_axis: Axis, default 'T'
:param standard_name: Coord standard name, default 'time'
:return: Coordinate
"""
from cis.data_io.Coord import Coord
from six.moves import zip_longest
timestamps = listify(timestamp)
time_variables = data_variables[time_variable_name]
time_coords = []
# Create a coordinate for each separate file to account for differing timestamps
for file_time_var, timestamp in zip_longest(time_variables, timestamps):
metadata = get_metadata(file_time_var)
metadata.standard_name = standard_name
coord = Coord(file_time_var, metadata, coord_axis)
coord.convert_to_std_time(timestamp)
time_coords.append(coord)
return Coord.from_many_coordinates(time_coords)
def can_not_convert_time_without_since_in_units_with_no_units():
times = numpy.array([0, 1])
units = ""
time_stamp_info = "1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time(time_stamp_info)
def create_coords(self, filenames, usr_variable=None):
from cis.data_io.netcdf import read_many_files_individually, get_metadata, get_netcdf_file_variables
from cis.data_io.Coord import Coord, CoordList
from cis.data_io.ungridded_data import UngriddedCoordinates, UngriddedData
from cis.exceptions import InvalidVariableError
# We have to read it once first to find out which variables are in there. We assume the set of coordinates in
# all the files are the same
file_variables = get_netcdf_file_variables(filenames[0])
def get_axis_std_name(var):
axis=None
lvar = var.lower()
if lvar.startswith('lon'):
axis = 'x', 'longitude'
if lvar.startswith('lat'):
axis = 'y', 'latitude'
if lvar == 'G_ALT' or lvar == 'altitude' or lvar == 'pressure_altitude':
axis = 'z', 'altitude'
if lvar == 'time':
axis = 't', 'time'
if lvar == 'p' or lvar == 'pressure' or lvar == 'static_pressure':
axis = 'p', 'air_pressure'
return axis
all_coord_variables = [(v, get_axis_std_name(v)) for v in file_variables if get_axis_std_name(v) is not None]
# Get rid of any duplicates
coord_variables = []
for v in all_coord_variables:
if v is None or v[1][1] not in [x[1][1] for x in coord_variables]:
coord_variables.append(v)
all_variables = coord_variables.copy()
if usr_variable is not None:
all_variables.append((usr_variable, ''))
logging.info("Listing coordinates: " + str(all_variables))
coords = CoordList()
var_data = read_many_files_individually(filenames, [v[0] for v in all_variables])
for name, axis_std_name in coord_variables:
try:
meta = get_metadata(var_data[name][0])
if meta.standard_name is None:
meta.standard_name = axis_std_name[1]
coord = Coord(var_data[name], meta, axis=axis_std_name[0])
if meta.standard_name == 'time':
# Converting units to CIS std time
coord.convert_to_std_time()
coords.append(coord)
except InvalidVariableError:
pass
if usr_variable is None:
res = UngriddedCoordinates(coords)
else:
res = UngriddedData(var_data[usr_variable], get_metadata(var_data[usr_variable][0]), coords)
return res
def can_convert_time_with_since_in_units():
times = numpy.array([0, 1])
units = "Days since 1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time()
assert_that(coord.data_flattened[0], is_(366.0), "time point")
def can_convert_time_with_since_in_units():
times = numpy.array([0, 1])
units = "days since 1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time()
assert_that(coord.data_flattened[0], is_(366.0), "time point")
def can_convert_time_without_since_in_units():
times = numpy.array([0, 1])
units = "Days from the file reference point 1601-01-01"
time_stamp_info = "1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time(time_stamp_info)
assert_that(coord.data_flattened[0], is_(366.0), "time point")
def can_convert_time_without_since_in_units():
times = numpy.array([0, 1])
units = "Days from the file reference point 1601-01-01"
time_stamp_info = "1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time(time_stamp_info)
assert_that(coord.data_flattened[0], is_(366.0), "time point")
def create_coords(self, filenames, usr_variable=None):
from cis.data_io.netcdf import read_many_files_individually, get_metadata, get_netcdf_file_variables
from cis.data_io.Coord import Coord, CoordList
from cis.data_io.ungridded_data import UngriddedCoordinates, UngriddedData
from cis.exceptions import InvalidVariableError
# We have to read it once first to find out which variables are in there. We assume the set of coordinates in
# all the files are the same
file_variables = get_netcdf_file_variables(filenames[0])
def get_axis_std_name(var):
axis = None
lvar = var.lower()
if lvar.startswith('lon'):
axis = 'x', 'longitude'
if lvar.startswith('lat'):
axis = 'y', 'latitude'
if lvar == 'G_ALT' or lvar == 'altitude' or lvar == 'pressure_altitude':
axis = 'z', 'altitude'
if lvar == 'time':
axis = 't', 'time'
if lvar == 'p' or lvar == 'pressure' or lvar == 'static_pressure':
axis = 'p', 'air_pressure'
return axis
all_coord_variables = [(v, get_axis_std_name(v))
for v in file_variables
if get_axis_std_name(v) is not None]
# Get rid of any duplicates
coord_variables = []
for v in all_coord_variables:
if v is None or v[1][1] not in [x[1][1] for x in coord_variables]:
coord_variables.append(v)
all_variables = coord_variables.copy()
if usr_variable is not None:
all_variables.append((usr_variable, ''))
logging.info("Listing coordinates: " + str(all_variables))
coords = CoordList()
var_data = read_many_files_individually(filenames,
[v[0] for v in all_variables])
for name, axis_std_name in coord_variables:
try:
meta = get_metadata(var_data[name][0])
if meta.standard_name is None:
meta.standard_name = axis_std_name[1]
coord = Coord(var_data[name], meta, axis=axis_std_name[0])
if meta.standard_name == 'time':
# Remove the mask from the time coordinate since this screws up date conversion...
coord.data = coord.data.data
# Converting units to CIS std time
coord.convert_to_std_time()
coords.append(coord)
except InvalidVariableError:
pass
if usr_variable is None:
res = UngriddedCoordinates(coords)
else:
res = UngriddedData(var_data[usr_variable][0][0, ...],
get_metadata(var_data[usr_variable][0]),
coords)
return res
def can_not_convert_time_without_since_in_units_but_no_timestamp():
times = numpy.array([0, 1])
units = "Days from the file reference point 1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time()
def can_not_convert_time_without_since_in_units_but_no_timestamp():
times = numpy.array([0, 1])
units = "Days from the file reference point 1601-01-01"
coord = Coord(times, Metadata(units=units))
coord.convert_to_std_time()
