def __init__(self, directory, filename, constraints=None,
callback=None, tmp_directory=None):
self.directory = directory
self.filename = filename
self.tmp_directory = tmp_directory or os.path.join(directory, 'tmp')
# try to create the temporary directory
# if there are other problems (e.g. permissions) except that it already
# exists an exception will be raised
try:
os.makedirs(self.tmp_directory)
except OSError:
if not os.path.isdir(self.tmp_directory):
raise
self.cube_list = iris.load(os.path.join(directory, filename),
constraints=constraints, callback=callback)
self._orig_standard_name = self.cube_list[0].standard_name
self._orig_var_name = self.cube_list[0].var_name
self._orig_long_name = self.cube_list[0].long_name
self.calendar = self.cube_list[0].coord('time').units.calendar
self._orig_units = self.cube_list[0].units
for ndim, coord in enumerate(self.cube_list[0].dim_coords):
if coord.units.is_time_reference():
self._timeaxis = ndim
break
# save the period of the entire dataset
self._orig_period = (
self.cube_list[0].dim_coords[self._timeaxis].units.num2date(
self.cube_list[0].dim_coords[self._timeaxis].points[0]),
self.cube_list[-1].dim_coords[self._timeaxis].units.num2date(
self.cube_list[-1].dim_coords[self._timeaxis].points[-1])
)
# save the geographical extent
x = self.cube_list[0].coord(axis="X", dim_coords=True)
y = self.cube_list[0].coord(axis="Y", dim_coords=True)
# save the coordinate system
self._coord_system = x.coord_system.as_cartopy_crs()
if not x.has_bounds():
x.guess_bounds()
y.guess_bounds()
x_edges = np.concatenate((x.bounds[:,0], np.array([x.bounds[-1,-1]]*y.shape[0]),
x.bounds[:,-1], np.array([x.bounds[0,0]]*y.shape[0])))
y_edges = np.concatenate((np.array([y.bounds[0,0]]*x.shape[0]), y.bounds[:,0],
np.array([y.bounds[-1,-1]]*x.shape[0]), y.bounds[:,-1]))
ll_crs = Geodetic()
lon_lat_edges = ll_crs.transform_points(
x.coord_system.as_cartopy_crs(), x_edges, y_edges)[:,:-1]
east, west = max(lon_lat_edges[:,0]), min(lon_lat_edges[:,0])
north, south = max(lon_lat_edges[:,1]), min(lon_lat_edges[:,1])
self._orig_extent = (north, east, south, west)
x.bounds = None
y.bounds = None
def _extent_constraint(self):
"""
if Dataset has an extent set return the geographical constraint
with at least one extra line/row at the north/south- and
west/east-edge, respectively to guarantee a sufficient large
extent for interpolating on a smaller grid.
Returns:
:class:`iris.Constraint` over the x and y axis
"""
north, east, south, west = self.extent
from matplotlib.path import Path
poly = Path([[west, south], [east, south], [east, north],
[west, north], [west, south]],
closed=True)
ll_crs = Geodetic()
x = self.cube_list[0].coord(axis='X', dim_coords=True)
y = self.cube_list[0].coord(axis='Y', dim_coords=True)
dx = x.points[1] - x.points[0]
dy = y.points[1] - y.points[0]
# get the order of the spatial dimensions
xdim = 1
ydim = 0
if self.cube_list[0].coord_dims(x) < self.cube_list[0].coord_dims(y):
xdim = 0
ydim = 1
xgrid, ygrid = np.meshgrid(x.points, y.points)
ll_field = ll_crs.transform_points(self._coord_system, xgrid,
ygrid)[:, :, :2]
ll_flat = ll_field.reshape((-1, 2))
mask = poly.contains_points(ll_flat).reshape(xgrid.shape)
inside_indices = np.where(mask)
minx, maxx = inside_indices[xdim].min(), inside_indices[xdim].max()
miny, maxy = inside_indices[ydim].min(), inside_indices[ydim].max()
west_bound, east_bound = x.points[minx] - dx, x.points[maxx] + dx
south_bound, north_bound = y.points[miny] - dy, y.points[maxy] + dy
return iris.Constraint(
coord_values={
x.standard_name:
lambda cell: west_bound <= cell.point <= east_bound,
y.standard_name:
lambda cell: south_bound <= cell.point <= north_bound
})
def _extent_constraint(self):
"""
if Dataset has an extent set return the geographical constraint
with at least one extra line/row at the north/south- and
west/east-edge, respectively to guarantee a sufficient large
extent for interpolating on a smaller grid.
Returns:
iris.Constraint over the x and y axis
"""
north, east, south, west = self.extent
from matplotlib.path import Path
poly = Path([[west, south], [east, south],
[east, north], [west, north],
[west,south]], closed=True)
ll_crs = Geodetic()
x = self.cube_list[0].coord(axis='X', dim_coords=True)
y = self.cube_list[0].coord(axis='Y', dim_coords=True)
dx = x.points[1] - x.points[0]
dy = y.points[1] - y.points[0]
# get the order of the spatial dimensions
xdim = 1
ydim = 0
if self.cube_list[0].coord_dims(x) < self.cube_list[0].coord_dims(y):
xdim = 0
ydim = 1
xgrid, ygrid = np.meshgrid(x.points, y.points)
ll_field = ll_crs.transform_points(self._coord_system, xgrid, ygrid)[:,:,:2]
ll_flat = ll_field.reshape((-1,2))
mask = poly.contains_points(ll_flat).reshape(xgrid.shape)
inside_indices = np.where(mask)
minx, maxx = inside_indices[xdim].min(), inside_indices[xdim].max()
miny, maxy = inside_indices[ydim].min(), inside_indices[ydim].max()
west_bound, east_bound = x.points[minx]-dx, x.points[maxx]+dx
south_bound, north_bound = y.points[miny]-dy, y.points[maxy]+dy
return iris.Constraint(coord_values={
x.standard_name: lambda cell: west_bound <= cell.point <= east_bound,
y.standard_name: lambda cell: south_bound <= cell.point <= north_bound
})
def __init__(self, directory, filename, constraints=None, callback=None):
"""
Args:
* directory (str):
path to the data
* filename (str):
glob pattern of data files
Kwargs:
* constraints (:class:`iris.Constraint`):
any valid constraint on the data
* callback (callable):
a function to add metadata to the cube
| *function signature*: (cube, field, filename)
"""
from cartopy.crs import Geodetic
self.directory = directory
self.filename = filename
self.cube_list = iris.load(os.path.join(directory, filename),
constraints=constraints,
callback=callback)
self._orig_standard_name = self.cube_list[0].standard_name
self._orig_var_name = self.cube_list[0].var_name
self._orig_long_name = self.cube_list[0].long_name
self.calendar = self.cube_list[0].coord('time').units.calendar
self._orig_units = self.cube_list[0].units
for ndim, coord in enumerate(self.cube_list[0].dim_coords):
if coord.units.is_time_reference():
self._timeaxis = ndim
break
# save the period of the entire dataset
self._orig_period = (
self.cube_list[0].dim_coords[self._timeaxis].units.num2date(
self.cube_list[0].dim_coords[self._timeaxis].points[0]),
self.cube_list[-1].dim_coords[self._timeaxis].units.num2date(
self.cube_list[-1].dim_coords[self._timeaxis].points[-1] +
np.diff(self.cube_list[-1].dim_coords[
self._timeaxis].points)[-1]))
# save the geographical extent
x = self.cube_list[0].coord(axis="X", dim_coords=True)
y = self.cube_list[0].coord(axis="Y", dim_coords=True)
# save the coordinate system
self._coord_system = x.coord_system.as_cartopy_crs()
# make a bounding box in lon/lat
# if the dataset consists only of one cell/row/column draw a large
# box around it
remove_bounds = False
if not x.has_bounds():
remove_bounds = True
try:
x.guess_bounds()
except ValueError:
x.bounds = np.repeat(x.points, 2) + np.array([-1, 1]) * 30000
try:
y.guess_bounds()
except ValueError:
y.bounds = np.repeat(y.points, 2) + np.array([-1, 1]) * 30000
x_edges = np.concatenate(
(x.bounds[:, 0], np.array([x.bounds[-1, -1]] * y.shape[0]),
x.bounds[:, -1], np.array([x.bounds[0, 0]] * y.shape[0])))
y_edges = np.concatenate(
(np.array([y.bounds[0, 0]] * x.shape[0]), y.bounds[:, 0],
np.array([y.bounds[-1, -1]] * x.shape[0]), y.bounds[:, -1]))
ll_crs = Geodetic()
lon_lat_edges = ll_crs.transform_points(
x.coord_system.as_cartopy_crs(), x_edges, y_edges)[:, :-1]
east, west = max(lon_lat_edges[:, 0]), min(lon_lat_edges[:, 0])
north, south = max(lon_lat_edges[:, 1]), min(lon_lat_edges[:, 1])
self._orig_extent = (north, east, south, west)
if remove_bounds:
x.bounds = None
y.bounds = None
# set the initial temporal and spatial extent
self.period = self._orig_period
self.extent = self._orig_extent
def __init__(self, directory, filename, constraints=None,
callback=None, tmp_directory=None):
"""
Args:
* directory (str):
path to the data
* filename (str):
glob pattern of data files
Kwargs:
* constraints (:class:`iris.Constraint`):
any valid constraint on the data
* callback (callable):
a function to add metadata to the cube
| *function signature*: (cube, field, filename)
* tmp_directory (str):
path to a write-able directory where intermediate data can be saved
defaults to directory/tmp
"""
from cartopy.crs import Geodetic
self.directory = directory
self.filename = filename
self.tmp_directory = tmp_directory or os.path.join(directory, 'tmp')
# try to create the temporary directory
# if there are other problems (e.g. permissions) except that it already
# exists an exception will be raised
try:
os.makedirs(self.tmp_directory)
except OSError:
if not os.path.isdir(self.tmp_directory):
raise
self.cube_list = iris.load(os.path.join(directory, filename),
constraints=constraints, callback=callback)
self._orig_standard_name = self.cube_list[0].standard_name
self._orig_var_name = self.cube_list[0].var_name
self._orig_long_name = self.cube_list[0].long_name
self.calendar = self.cube_list[0].coord('time').units.calendar
self._orig_units = self.cube_list[0].units
for ndim, coord in enumerate(self.cube_list[0].dim_coords):
if coord.units.is_time_reference():
self._timeaxis = ndim
break
# save the period of the entire dataset
self._orig_period = (
self.cube_list[0].dim_coords[self._timeaxis].units.num2date(
self.cube_list[0].dim_coords[self._timeaxis].points[0]),
self.cube_list[-1].dim_coords[self._timeaxis].units.num2date(
self.cube_list[-1].dim_coords[self._timeaxis].points[-1] +
np.diff(
self.cube_list[-1].dim_coords[self._timeaxis].points)[-1]
)
)
# save the geographical extent
x = self.cube_list[0].coord(axis="X", dim_coords=True)
y = self.cube_list[0].coord(axis="Y", dim_coords=True)
# Determine source coordinate system
if x.coord_system is None:
# Assume WGS84 latlon if unspecified
warnings.warn('Coordinate system of latitude and longitude '
'coordinates is not specified. Assuming WGS84 Geodetic.')
self._coord_system = iris.coord_systems.GeogCS(semi_major_axis=6378137.0,
inverse_flattening=298.257223563).as_cartopy_crs()
else:
# save the coordinate system
self._coord_system = x.coord_system.as_cartopy_crs()
remove_bounds = False
if not x.has_bounds():
x.guess_bounds()
y.guess_bounds()
remove_bounds = True
x_edges = np.concatenate(
(x.bounds[:, 0], np.array([x.bounds[-1, -1]] * y.shape[0]),
x.bounds[:, -1], np.array([x.bounds[0, 0]] * y.shape[0])))
y_edges = np.concatenate(
(np.array([y.bounds[0, 0]] * x.shape[0]), y.bounds[:, 0],
np.array([y.bounds[-1, -1]] * x.shape[0]), y.bounds[:, -1]))
ll_crs = Geodetic()
lon_lat_edges = ll_crs.transform_points(
# x.coord_system.as_cartopy_crs(), x_edges, y_edges)[:, :-1]
self._coord_system, x_edges, y_edges)[:, :-1]
east, west = max(lon_lat_edges[:, 0]), min(lon_lat_edges[:, 0])
north, south = max(lon_lat_edges[:, 1]), min(lon_lat_edges[:, 1])
self._orig_extent = (north, east, south, west)
if remove_bounds:
x.bounds = None
y.bounds = None
