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Source code for iris.util

# Copyright Iris contributors
#
# This file is part of Iris and is released under the BSD license.
# See LICENSE in the root of the repository for full licensing details.
"""Miscellaneous utility functions."""

from __future__ import annotations

from abc import ABCMeta, abstractmethod
from collections.abc import Hashable, Iterable
import functools
import inspect
import os
import os.path
import sys
import tempfile

import cf_units
from dask import array as da
import numpy as np
import numpy.ma as ma

from iris._deprecation import warn_deprecated
from iris._lazy_data import is_lazy_data, is_lazy_masked_data
from iris._shapefiles import create_shapefile_mask
from iris.common import SERVICES
from iris.common.lenient import _lenient_client
import iris.exceptions


[docs] def broadcast_to_shape(array, shape, dim_map, chunks=None): """Broadcast an array to a given shape. Each dimension of the array must correspond to a dimension in the given shape. The result is a read-only view (see :func:`numpy.broadcast_to`). If you need to write to the resulting array, make a copy first. Parameters ---------- array : :class:`numpy.ndarray`-like An array to broadcast. shape : :class:`list`, :class:`tuple` etc The shape the array should be broadcast to. dim_map : :class:`list`, :class:`tuple` etc A mapping of the dimensions of *array* to their corresponding element in *shape*. *dim_map* must be the same length as the number of dimensions in *array*. Each element of *dim_map* corresponds to a dimension of *array* and its value provides the index in *shape* which the dimension of *array* corresponds to, so the first element of *dim_map* gives the index of *shape* that corresponds to the first dimension of *array* etc. chunks : :class:`tuple`, optional If the source array is a :class:`dask.array.Array` and a value is provided, then the result will use these chunks instead of the same chunks as the source array. Setting chunks explicitly as part of broadcast_to_shape is more efficient than rechunking afterwards. See also :func:`dask.array.broadcast_to`. Note that the values provided here will only be used along dimensions that are new on the result or have size 1 on the source array. Examples -------- Broadcasting an array of shape (2, 3) to the shape (5, 2, 6, 3) where the first dimension of the array corresponds to the second element of the desired shape and the second dimension of the array corresponds to the fourth element of the desired shape:: a = np.array([[1, 2, 3], [4, 5, 6]]) b = broadcast_to_shape(a, (5, 2, 6, 3), (1, 3)) Broadcasting an array of shape (48, 96) to the shape (96, 48, 12):: # a is an array of shape (48, 96) result = broadcast_to_shape(a, (96, 48, 12), (1, 0)) Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if isinstance(array, da.Array): if chunks is not None: chunks = list(chunks) for src_idx, tgt_idx in enumerate(dim_map): # Only use the specified chunks along new dimensions or on # dimensions that have size 1 in the source array. if array.shape[src_idx] != 1: chunks[tgt_idx] = array.chunks[src_idx] broadcast = functools.partial(da.broadcast_to, shape=shape, chunks=chunks) else: broadcast = functools.partial(np.broadcast_to, shape=shape) n_orig_dims = len(array.shape) n_new_dims = len(shape) - n_orig_dims array = array.reshape(array.shape + (1,) * n_new_dims) # Get dims in required order. array = np.moveaxis(array, range(n_orig_dims), dim_map) new_array = broadcast(array) if ma.isMA(array): # broadcast_to strips masks so we need to handle them explicitly. mask = ma.getmask(array) if mask is ma.nomask: new_mask = ma.nomask else: new_mask = broadcast(mask) new_array = ma.array(new_array, mask=new_mask) elif is_lazy_masked_data(array): # broadcast_to strips masks so we need to handle them explicitly. mask = da.ma.getmaskarray(array) new_mask = broadcast(mask) new_array = da.ma.masked_array(new_array, new_mask) return new_array
[docs] def delta(ndarray, dimension, circular=False): """Calculate the difference between values along a given dimension. Parameters ---------- ndarray : The array over which to do the difference. dimension : The dimension over which to do the difference on ndarray. circular : bool, default=False If not False then return n results in the requested dimension with the delta between the last and first element included in the result otherwise the result will be of length n-1 (where n is the length of ndarray in the given dimension's direction) If circular is numeric then the value of circular will be added to the last element of the given dimension if the last element is negative, otherwise the value of circular will be subtracted from the last element. The example below illustrates the process:: original array -180, -90, 0, 90 delta (with circular=360): 90, 90, 90, -270+360 Notes ----- .. note:: The difference algorithm implemented is forward difference: >>> import numpy as np >>> import iris.util >>> original = np.array([-180, -90, 0, 90]) >>> iris.util.delta(original, 0) array([90, 90, 90]) >>> iris.util.delta(original, 0, circular=360) array([90, 90, 90, 90]) .. note:: This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if circular is not False: _delta = np.roll(ndarray, -1, axis=dimension) last_element = [slice(None, None)] * ndarray.ndim last_element[dimension] = slice(-1, None) last_element = tuple(last_element) if not isinstance(circular, bool): result = np.where(ndarray[last_element] >= _delta[last_element])[0] _delta[last_element] -= circular _delta[last_element][result] += 2 * circular np.subtract(_delta, ndarray, _delta) else: _delta = np.diff(ndarray, axis=dimension) return _delta
[docs] def describe_diff(cube_a, cube_b, output_file=None): """Print the differences that prevent compatibility between two cubes. Print the differences that prevent compatibility between two cubes, as defined by :meth:`iris.cube.Cube.is_compatible()`. Parameters ---------- cube_a : An instance of :class:`iris.cube.Cube` or :class:`iris.cube.CubeMetadata`. cube_b : An instance of :class:`iris.cube.Cube` or :class:`iris.cube.CubeMetadata`. output_file : optional A :class:`file` or file-like object to receive output. Defaults to sys.stdout. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. .. note:: Compatibility does not guarantee that two cubes can be merged. Instead, this function is designed to provide a verbose description of the differences in metadata between two cubes. Determining whether two cubes will merge requires additional logic that is beyond the scope of this function. See Also -------- iris.cube.Cube.is_compatible : Check if a Cube is compatible with another. """ if output_file is None: output_file = sys.stdout if cube_a.is_compatible(cube_b): output_file.write("Cubes are compatible\n") else: common_keys = set(cube_a.attributes).intersection(cube_b.attributes) for key in common_keys: if np.any(cube_a.attributes[key] != cube_b.attributes[key]): output_file.write( '"%s" cube_a attribute value "%s" is not ' "compatible with cube_b " 'attribute value "%s"\n' % (key, cube_a.attributes[key], cube_b.attributes[key]) ) if cube_a.name() != cube_b.name(): output_file.write( 'cube_a name "%s" is not compatible ' 'with cube_b name "%s"\n' % (cube_a.name(), cube_b.name()) ) if cube_a.units != cube_b.units: output_file.write( 'cube_a units "%s" are not compatible with cube_b units "%s"\n' % (cube_a.units, cube_b.units) ) if cube_a.cell_methods != cube_b.cell_methods: output_file.write( "Cell methods\n%s\nand\n%s\nare not compatible\n" % (cube_a.cell_methods, cube_b.cell_methods) )
[docs] def guess_coord_axis(coord): """Return a "best guess" axis name of the coordinate. Heuristic categorisation of the coordinate into either label 'T', 'Z', 'Y', 'X' or None. Parameters ---------- coord : The :class:`iris.coords.Coord`. Returns ------- {'T', 'Z', 'Y', 'X'} or None. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. The ``guess_coord_axis`` behaviour can be skipped by setting the :attr:`~iris.coords.Coord.ignore_axis` property on `coord` to ``False``. """ axis = None if hasattr(coord, "ignore_axis") and coord.ignore_axis is True: return axis elif coord.standard_name in ( "longitude", "grid_longitude", "projection_x_coordinate", ): axis = "X" elif coord.standard_name in ( "latitude", "grid_latitude", "projection_y_coordinate", ): axis = "Y" elif coord.units.is_convertible("hPa") or coord.attributes.get("positive") in ( "up", "down", ): axis = "Z" elif coord.units.is_time_reference(): axis = "T" return axis
[docs] def rolling_window( a: np.ndarray | da.Array, window: int = 1, step: int = 1, axis: int = -1, ) -> np.ndarray | da.Array: """Make an ndarray with a rolling window of the last dimension. Parameters ---------- a : array_like Array to add rolling window to. window : int, default=1 Size of rolling window. step : int, default=1 Size of step between rolling windows. axis : int, default=-1 Axis to take the rolling window over. Returns ------- array Array that is a view of the original array with an added dimension of the size of the given window at axis + 1. Examples -------- :: >>> x = np.arange(10).reshape((2, 5)) >>> rolling_window(x, 3) array([[[0, 1, 2], [1, 2, 3], [2, 3, 4]], [[5, 6, 7], [6, 7, 8], [7, 8, 9]]]) Calculate rolling mean of last dimension:: >>> np.mean(rolling_window(x, 3), -1) array([[ 1., 2., 3.], [ 6., 7., 8.]]) Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if window < 1: raise ValueError("`window` must be at least 1.") if window > a.shape[axis]: raise ValueError("`window` is too long.") if step < 1: raise ValueError("`step` must be at least 1.") axis = axis % a.ndim array_module = da if isinstance(a, da.Array) else np steps = tuple( slice(None, None, step) if i == axis else slice(None) for i in range(a.ndim) ) def _rolling_window(array): return array_module.moveaxis( array_module.lib.stride_tricks.sliding_window_view( array, window_shape=window, axis=axis, )[steps], -1, axis + 1, ) rw = _rolling_window(a) if isinstance(da.utils.meta_from_array(a), np.ma.MaskedArray): mask = _rolling_window(array_module.ma.getmaskarray(a)) rw = array_module.ma.masked_array(rw, mask) return rw
[docs] def array_equal(array1, array2, withnans=False): """Return whether two arrays have the same shape and elements. Parameters ---------- array1, array2 : arraylike Args to be compared, normalised if necessary with :func:`np.asarray`. withnans : bool, default=False When unset (default), the result is False if either input contains NaN points. This is the normal floating-point arithmetic result. When set, return True if inputs contain the same value in all elements, _including_ any NaN values. Notes ----- This provides much the same functionality as :func:`numpy.array_equal`, but with additional support for arrays of strings and NaN-tolerant operation. This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if withnans and (array1 is array2): return True def normalise_array(array): if not is_lazy_data(array): array = np.asarray(array) return array array1, array2 = normalise_array(array1), normalise_array(array2) eq = array1.shape == array2.shape if eq: eqs = array1 == array2 if withnans and (array1.dtype.kind == "f" or array2.dtype.kind == "f"): eqs = np.where(np.isnan(array1) & np.isnan(array2), True, eqs) eq = bool(np.all(eqs)) return eq
[docs] def approx_equal(a, b, max_absolute_error=1e-10, max_relative_error=1e-10): """Check if two numbers are almost equal. Returns whether two numbers are almost equal, allowing for the finite precision of floating point numbers. Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. .. deprecated:: 3.2.0 Instead use :func:`math.isclose`. For example, rather than calling ``approx_equal(a, b, max_abs, max_rel)`` replace with ``math.isclose(a, b, max_rel, max_abs)``. Note that :func:`~math.isclose` will return True if the actual error equals the maximum, whereas :func:`util.approx_equal` will return False. """ wmsg = ( "iris.util.approx_equal has been deprecated and will be removed, " "please use math.isclose instead." ) warn_deprecated(wmsg) # Deal with numbers close to zero if abs(a - b) < max_absolute_error: return True # Ensure we get consistent results if "a" and "b" are supplied in the # opposite order. max_ab = max([a, b], key=abs) relative_error = abs(a - b) / max_ab return relative_error < max_relative_error
[docs] def between(lh, rh, lh_inclusive=True, rh_inclusive=True): """Provide convenient way of defining a 3 element inequality. Such as ``a < number < b``. Parameters ---------- lh : The left hand element of the inequality. rh : The right hand element of the inequality. lh_inclusive : bool, default=True Affects the left hand comparison operator to use in the inequality. True for ``<=`` false for ``<``. Defaults to True. rh_inclusive : bool, default=True Same as lh_inclusive but for right hand operator. Examples -------- :: between_3_and_6 = between(3, 6) for i in range(10): print(i, between_3_and_6(i)) between_3_and_6 = between(3, 6, rh_inclusive=False) for i in range(10): print(i, between_3_and_6(i)) Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if lh_inclusive and rh_inclusive: return lambda c: lh <= c <= rh elif lh_inclusive and not rh_inclusive: return lambda c: lh <= c < rh elif not lh_inclusive and rh_inclusive: return lambda c: lh < c <= rh else: return lambda c: lh < c < rh
[docs] def reverse(cube_or_array, coords_or_dims): """Reverse the cube or array along the given dimensions. Parameters ---------- cube_or_array : :class:`iris.cube.Cube` or :class:`numpy.ndarray` The cube or array to reverse. coords_or_dims : int, str, :class:`iris.coords.Coord` or sequence of these Identify one or more dimensions to reverse. If cube_or_array is a numpy array, use int or a sequence of ints, as in the examples below. If cube_or_array is a Cube, a Coord or coordinate name (or sequence of these) may be specified instead. Examples -------- :: >>> import numpy as np >>> a = np.arange(24).reshape(2, 3, 4) >>> print(a) [[[ 0 1 2 3] [ 4 5 6 7] [ 8 9 10 11]] <BLANKLINE> [[12 13 14 15] [16 17 18 19] [20 21 22 23]]] >>> print(reverse(a, 1)) [[[ 8 9 10 11] [ 4 5 6 7] [ 0 1 2 3]] <BLANKLINE> [[20 21 22 23] [16 17 18 19] [12 13 14 15]]] >>> print(reverse(a, [1, 2])) [[[11 10 9 8] [ 7 6 5 4] [ 3 2 1 0]] <BLANKLINE> [[23 22 21 20] [19 18 17 16] [15 14 13 12]]] Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ from iris.cube import Cube index = [slice(None, None)] * cube_or_array.ndim if isinstance(coords_or_dims, Cube): raise TypeError( "coords_or_dims must be int, str, coordinate or " "sequence of these. Got cube." ) if isinstance(coords_or_dims, str) or not isinstance(coords_or_dims, Iterable): coords_or_dims = [coords_or_dims] axes = set() for coord_or_dim in coords_or_dims: if isinstance(coord_or_dim, int): axes.add(coord_or_dim) elif isinstance(cube_or_array, np.ndarray): raise TypeError("To reverse an array, provide an int or sequence of ints.") else: try: axes.update(cube_or_array.coord_dims(coord_or_dim)) except AttributeError: raise TypeError( "coords_or_dims must be int, str, coordinate " "or sequence of these." ) axes = np.array(list(axes), ndmin=1) if axes.ndim != 1 or axes.size == 0: raise ValueError( "Reverse was expecting a single axis or a 1d array " "of axes, got %r" % axes ) if np.min(axes) < 0 or np.max(axes) > cube_or_array.ndim - 1: raise ValueError( "An axis value out of range for the number of " "dimensions from the given array (%s) was received. " "Got: %r" % (cube_or_array.ndim, axes) ) for axis in axes: index[axis] = slice(None, None, -1) return cube_or_array[tuple(index)]
[docs] def monotonic(array, strict=False, return_direction=False): """Return whether the given 1d array is monotonic. Note that, the array must not contain missing data. Parameters ---------- strict : bool, default=False Flag to enable strict monotonic checking. return_direction : bool, default=False Flag to change return behaviour to return (monotonic_status, direction). Direction will be 1 for positive or -1 for negative. The direction is meaningless if the array is not monotonic. Returns ------- bool Whether the array was monotonic. If the return_direction flag was given then the returned value will be: ``(monotonic_status, direction)``. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if array.ndim != 1 or len(array) <= 1: raise ValueError( "The array to check must be 1 dimensional and have more than 1 element." ) if ma.isMaskedArray(array) and ma.count_masked(array) != 0: raise ValueError("The array to check contains missing data.") # Identify the directions of the largest/most-positive and # smallest/most-negative steps. d = np.diff(array) sign_max_d = np.sign(np.max(d)) sign_min_d = np.sign(np.min(d)) if strict: monotonic = sign_max_d == sign_min_d and sign_max_d != 0 else: monotonic = ( (sign_min_d < 0 and sign_max_d <= 0) or (sign_max_d > 0 and sign_min_d >= 0) or (sign_min_d == sign_max_d == 0) ) if return_direction: if sign_max_d == 0: direction = sign_min_d else: direction = sign_max_d return monotonic, direction return monotonic
[docs] def column_slices_generator(full_slice, ndims): """Return a dictionary mapping old data dimensions to new. Given a full slice full of tuples, return a dictionary mapping old data dimensions to new and a generator which gives the successive slices needed to index correctly (across columns). This routine deals with the special functionality for tuple based indexing e.g. [0, (3, 5), :, (1, 6, 8)] by first providing a slice which takes the non tuple slices out first i.e. [0, :, :, :] then subsequently iterates through each of the tuples taking out the appropriate slices i.e. [(3, 5), :, :] followed by [:, :, (1, 6, 8)] This method was developed as numpy does not support the direct approach of [(3, 5), : , (1, 6, 8)] for column based indexing. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ list_of_slices = [] # Map current dimensions to new dimensions, or None dimension_mapping = {None: None} _count_current_dim = 0 for i, i_key in enumerate(full_slice): if isinstance(i_key, (int, np.integer)): dimension_mapping[i] = None else: dimension_mapping[i] = _count_current_dim _count_current_dim += 1 # Get all of the dimensions for which a tuple of indices were provided # (numpy.ndarrays are treated in the same way tuples in this case) def is_tuple_style_index(key): return isinstance(key, tuple) or (isinstance(key, np.ndarray) and key.ndim == 1) tuple_indices = [i for i, key in enumerate(full_slice) if is_tuple_style_index(key)] # stg1: Take a copy of the full_slice specification, turning all tuples # into a full slice if tuple_indices != list(range(len(full_slice))): first_slice = list(full_slice) for tuple_index in tuple_indices: first_slice[tuple_index] = slice(None, None) # turn first_slice back into a tuple ready for indexing first_slice = tuple(first_slice) list_of_slices.append(first_slice) # stg2 iterate over each of the tuples for tuple_index in tuple_indices: # Create a list with the indices to span the whole data array that we # currently have spanning_slice_with_tuple = [slice(None, None)] * _count_current_dim # Replace the slice(None, None) with our current tuple spanning_slice_with_tuple[dimension_mapping[tuple_index]] = full_slice[ tuple_index ] # if we just have [(0, 1)] turn it into [(0, 1), ...] as this is # Numpy's syntax. if len(spanning_slice_with_tuple) == 1: spanning_slice_with_tuple.append(Ellipsis) spanning_slice_with_tuple = tuple(spanning_slice_with_tuple) list_of_slices.append(spanning_slice_with_tuple) # return the dimension mapping and a generator of slices return dimension_mapping, iter(list_of_slices)
def _build_full_slice_given_keys(keys, ndim): """Build an equivalent tuple of keys which span ndims. Given the keys passed to a __getitem__ call, build an equivalent tuple of keys which span ndims. """ # Ensure that we always have a tuple of keys if not isinstance(keys, tuple): keys = tuple([keys]) # catch the case where an extra Ellipsis has been provided which can be # discarded iff len(keys)-1 == ndim if len(keys) - 1 == ndim and Ellipsis in filter( lambda obj: not isinstance(obj, np.ndarray), keys ): keys = list(keys) is_ellipsis = [key is Ellipsis for key in keys] keys.pop(is_ellipsis.index(True)) keys = tuple(keys) # for ndim >= 1 appending a ":" to the slice specification is allowable, # remove this now if len(keys) > ndim and ndim != 0 and keys[-1] == slice(None, None): keys = keys[:-1] if len(keys) > ndim: raise IndexError( "More slices requested than dimensions. Requested " "%r, but there were only %s dimensions." % (keys, ndim) ) # For each dimension get the slice which has been requested. # If no slice provided, then default to the whole dimension full_slice = [slice(None, None)] * ndim for i, key in enumerate(keys): if key is Ellipsis: # replace any subsequent Ellipsis objects in keys with # slice(None, None) as per Numpy keys = keys[:i] + tuple( [slice(None, None) if key is Ellipsis else key for key in keys[i:]] ) # iterate over the remaining keys in reverse to fill in # the gaps from the right hand side for j, key in enumerate(keys[:i:-1]): full_slice[-j - 1] = key # we've finished with i now so stop the iteration break else: full_slice[i] = key # remove any tuples on dimensions, turning them into numpy array's for # consistent behaviour full_slice = tuple( [ np.array(key, ndmin=1) if isinstance(key, tuple) else key for key in full_slice ] ) return full_slice def _slice_data_with_keys(data, keys): """Index an array-like object as "data[keys]", with orthogonal indexing. Parameters ---------- data : array-like Array to index. keys : list List of indexes, as received from a __getitem__ call. Returns ------- dim_map : dict A dimension map, as returned by :func:`column_slices_generator`. i.e. "dim_map[old_dim_index]" --> "new_dim_index" or None. data_region : array-like The sub-array. Notes ----- This enforces an orthogonal interpretation of indexing, which means that both 'real' (numpy) arrays and other array-likes index in the same way, instead of numpy arrays doing 'fancy indexing'. .. note:: Avoids copying the data, where possible. """ # Combines the use of _build_full_slice_given_keys and # column_slices_generator. # By slicing on only one index at a time, this also mostly avoids copying # the data, except some cases when a key contains a list of indices. n_dims = len(data.shape) full_slice = _build_full_slice_given_keys(keys, n_dims) dims_mapping, slices_iter = column_slices_generator(full_slice, n_dims) for this_slice in slices_iter: data = data[this_slice] if data.ndim > 0 and min(data.shape) < 1: # Disallow slicings where a dimension has no points, like "[5:5]". raise IndexError("Cannot index with zero length slice.") return dims_mapping, data def _wrap_function_for_method(function, docstring=None): """Return a wrapper function modified to be suitable for use as a method. The wrapper function renames the first argument as "self" and allows an alternative docstring, thus allowing the built-in help(...) routine to display appropriate output. """ # Generate the Python source for the wrapper function. # NB. The first argument is replaced with "self". args, varargs, varkw, defaults = inspect.getargspec(function) if defaults is None: basic_args = ["self"] + args[1:] default_args = [] simple_default_args = [] else: cutoff = -len(defaults) basic_args = ["self"] + args[1:cutoff] default_args = ["%s=%r" % pair for pair in zip(args[cutoff:], defaults)] simple_default_args = args[cutoff:] var_arg = [] if varargs is None else ["*" + varargs] var_kw = [] if varkw is None else ["**" + varkw] arg_source = ", ".join(basic_args + default_args + var_arg + var_kw) simple_arg_source = ", ".join(basic_args + simple_default_args + var_arg + var_kw) source = "def %s(%s):\n return function(%s)" % ( function.__name__, arg_source, simple_arg_source, ) # Compile the wrapper function # NB. There's an outstanding bug with "exec" where the locals and globals # dictionaries must be the same if we're to get closure behaviour. my_locals = {"function": function} exec(source, my_locals, my_locals) # Update the docstring if required, and return the modified function wrapper = my_locals[function.__name__] if docstring is None: wrapper.__doc__ = function.__doc__ else: wrapper.__doc__ = docstring return wrapper class _MetaOrderedHashable(ABCMeta): """Ensures that non-abstract subclasses are given a default __init__ method. A metaclass that ensures that non-abstract subclasses of _OrderedHashable without an explicit __init__ method are given a default __init__ method with the appropriate method signature. Also, an _init method is provided to allow subclasses with their own __init__ constructors to initialise their values via an explicit method signature. NB. This metaclass is used to construct the _OrderedHashable class as well as all its subclasses. """ def __new__(cls, name, bases, namespace): # We only want to modify concrete classes that have defined the # "_names" property. if "_names" in namespace and not getattr( namespace["_names"], "__isabstractmethod__", False ): args = ", ".join(namespace["_names"]) # Ensure the class has a constructor with explicit arguments. if "__init__" not in namespace: # Create a default __init__ method for the class method_source = ( "def __init__(self, %s):\n " "self._init_from_tuple((%s,))" % (args, args) ) exec(method_source, namespace) # Ensure the class has a "helper constructor" with explicit # arguments. if "_init" not in namespace: # Create a default _init method for the class method_source = ( "def _init(self, %s):\n " "self._init_from_tuple((%s,))" % (args, args) ) exec(method_source, namespace) return super().__new__(cls, name, bases, namespace) @functools.total_ordering class _OrderedHashable(Hashable, metaclass=_MetaOrderedHashable): """Convenience class for creating "immutable", hashable, and ordered classes. Instance identity is defined by the specific list of attribute names declared in the abstract attribute "_names". Subclasses must declare the attribute "_names" as an iterable containing the names of all the attributes relevant to equality/hash-value/ordering. Initial values should be set by using :: self._init(self, value1, value2, ..) .. note:: It's the responsibility of the subclass to ensure that the values of its attributes are themselves hashable. """ @property @abstractmethod def _names(self): """Override this attribute to declare the names of all the attributes relevant. Override this attribute to declare the names of all the attributes relevant to the hash/comparison semantics. """ pass def _init_from_tuple(self, values): for name, value in zip(self._names, values): object.__setattr__(self, name, value) def __repr__(self): class_name = type(self).__name__ attributes = ", ".join( "%s=%r" % (name, value) for (name, value) in zip(self._names, self._as_tuple()) ) return "%s(%s)" % (class_name, attributes) def _as_tuple(self): return tuple(getattr(self, name) for name in self._names) # Prevent attribute updates def __setattr__(self, name, value): raise AttributeError("Instances of %s are immutable" % type(self).__name__) def __delattr__(self, name): raise AttributeError("Instances of %s are immutable" % type(self).__name__) # Provide hash semantics def _identity(self): return self._as_tuple() def __hash__(self): return hash(self._identity()) def __eq__(self, other): return isinstance(other, type(self)) and self._identity() == other._identity() def __ne__(self, other): # Since we've defined __eq__ we should also define __ne__. return not self == other # Provide default ordering semantics def __lt__(self, other): if isinstance(other, _OrderedHashable): return self._identity() < other._identity() else: return NotImplemented
[docs] def create_temp_filename(suffix=""): """Return a temporary file name. Parameters ---------- suffix : str, optional, default="" Filename extension. """ temp_file = tempfile.mkstemp(suffix) os.close(temp_file[0]) return temp_file[1]
[docs] def clip_string(the_str, clip_length=70, rider="..."): """Return clipped version of the string based on the specified clip length. Return a clipped version of the string based on the specified clip length and whether or not any graceful clip points can be found. If the string to be clipped is shorter than the specified clip length, the original string is returned. If the string is longer than the clip length, a graceful point (a space character) after the clip length is searched for. If a graceful point is found the string is clipped at this point and the rider is added. If no graceful point can be found, then the string is clipped exactly where the user requested and the rider is added. Parameters ---------- the_str : str The string to be clipped. clip_length : int, default=70 The length in characters that the input string should be clipped to. Defaults to a preconfigured value if not specified. rider : str, default="..." A series of characters appended at the end of the returned string to show it has been clipped. Defaults to a preconfigured value if not specified. Returns ------- str The string clipped to the required length with a rider appended. If the clip length was greater than the original string, the original string is returned unaltered. Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if clip_length >= len(the_str) or clip_length <= 0: return the_str else: if the_str[clip_length].isspace(): return the_str[:clip_length] + rider else: first_part = the_str[:clip_length] remainder = the_str[clip_length:] # Try to find a graceful point at which to trim i.e. a space # If no graceful point can be found, then just trim where the user # specified by adding an empty slice of the remainder ( [:0] ) termination_point = remainder.find(" ") if termination_point == -1: termination_point = 0 return first_part + remainder[:termination_point] + rider
[docs] def format_array(arr): """Create a new axis as the leading dimension of the cube. Returns the given array as a string, using the python builtin str function on a piecewise basis. Useful for xml representation of arrays. For customisations, use the :mod:`numpy.core.arrayprint` directly. Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ max_line_len = 50 result = np.array2string( arr, max_line_len, separator=", ", threshold=85, ) return result
[docs] def new_axis(src_cube, scalar_coord=None, expand_extras=()): # maybe not lazy """Create a new axis as the leading dimension of the cube. Create a new axis as the leading dimension of the cube, promoting a scalar coordinate if specified. Parameters ---------- src_cube : :class:`iris.cube.Cube` Source cube on which to generate a new axis. scalar_coord : :class:`iris.coord.Coord` or str, optional Scalar coordinate to promote to a dimension coordinate. expand_extras : iterable, optional Auxiliary coordinates, ancillary variables and cell measures which will be expanded so that they map to the new dimension as well as the existing dimensions. Returns ------- :class:`iris.cube.Cube` A new :class:`iris.cube.Cube` instance with one extra leading dimension (length 1). Chosen auxiliary coordinates, cell measures and ancillary variables will also be given an additional dimension, associated with the leading dimension of the cube. Examples -------- :: >>> cube.shape (360, 360) >>> ncube = iris.util.new_axis(cube, 'time') >>> ncube.shape (1, 360, 360) Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ def _reshape_data_array(data_manager): # Indexing numpy arrays requires loading deferred data here returning a # copy of the data with a new leading dimension. # If the data of the source cube (or values of the dimensional metadata # object) is a Masked Constant, it is changed here to a Masked Array to # allow the mask to gain an extra dimension with the data. if data_manager.has_lazy_data(): new_data = data_manager.lazy_data()[None] else: if isinstance(data_manager.data, ma.core.MaskedConstant): new_data = ma.array([np.nan], mask=[True]) else: new_data = data_manager.data[None] return new_data def _handle_dimensional_metadata(cube, dm_item, cube_add_method, expand_extras): cube_dims = dm_item.cube_dims(cube) if dm_item in expand_extras: if cube_dims == (): new_dm_item, new_dims = dm_item.copy(), 0 else: new_dims = np.concatenate([(0,), np.array(cube_dims) + 1]) new_values = _reshape_data_array(dm_item._values_dm) kwargs = dm_item.metadata._asdict() new_dm_item = dm_item.__class__(new_values, **kwargs) try: if dm_item.has_bounds(): new_dm_item.bounds = _reshape_data_array(dm_item._bounds_dm) except AttributeError: pass else: new_dims = np.array(cube_dims) + 1 new_dm_item = dm_item.copy() cube_add_method(new_dm_item, new_dims) if scalar_coord is not None: scalar_coord = src_cube.coord(scalar_coord) try: src_cube.coord(scalar_coord, dim_coords=False) except iris.exceptions.CoordinateNotFoundError: emsg = scalar_coord.name() + " is already a dimension coordinate." raise ValueError(emsg) if not scalar_coord.shape == (1,): emsg = scalar_coord.name() + " is not a scalar coordinate." raise ValueError(emsg) expand_extras = [src_cube._dimensional_metadata(item) for item in expand_extras] new_cube = iris.cube.Cube(_reshape_data_array(src_cube._data_manager)) new_cube.metadata = src_cube.metadata for coord in src_cube.dim_coords: coord_dims = np.array(src_cube.coord_dims(coord)) + 1 new_cube.add_dim_coord(coord.copy(), coord_dims) for coord in src_cube.aux_coords: if scalar_coord and scalar_coord == coord: dim_coord = iris.coords.DimCoord.from_coord(coord) new_cube.add_dim_coord(dim_coord, 0) else: _handle_dimensional_metadata( src_cube, coord, new_cube.add_aux_coord, expand_extras ) for cm in src_cube.cell_measures(): _handle_dimensional_metadata( src_cube, cm, new_cube.add_cell_measure, expand_extras ) for av in src_cube.ancillary_variables(): _handle_dimensional_metadata( src_cube, av, new_cube.add_ancillary_variable, expand_extras ) nonderived_coords = src_cube.dim_coords + src_cube.aux_coords coord_mapping = {id(old_co): new_cube.coord(old_co) for old_co in nonderived_coords} for factory in src_cube.aux_factories: new_factory = factory.updated(coord_mapping) new_cube.add_aux_factory(new_factory) return new_cube
[docs] def squeeze(cube): """Remove any dimension of length one. Remove any dimension of length one. If it has an associated DimCoord or AuxCoord, this becomes a scalar coord. Parameters ---------- cube : :class:`iris.cube.Cube` Source cube to remove length 1 dimension(s) from. Returns ------- :class:`iris.cube.Cube` A new :class:`iris.cube.Cube` instance without any dimensions of length 1. Examples -------- For example:: >>> cube.shape (1, 360, 360) >>> ncube = iris.util.squeeze(cube) >>> ncube.shape (360, 360) Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ slices = [0 if cube.shape[dim] == 1 else slice(None) for dim in range(cube.ndim)] squeezed = cube[tuple(slices)] return squeezed
[docs] def file_is_newer_than(result_path, source_paths): """Determine if the 'result' file was modified last. Return whether the 'result' file has a later modification time than all of the 'source' files. If a stored result depends entirely on known 'sources', it need only be re-built when one of them changes. This function can be used to test that by comparing file timestamps. Parameters ---------- result_path : str The filepath of a file containing some derived result data. source_paths : str or iterable of str The path(s) to the original datafiles used to make the result. May include wildcards and '~' expansions (like Iris load paths), but not URIs. Returns ------- bool True if all the sources are older than the result, else False. If any of the file paths describes no existing files, an exception will be raised. Notes ----- .. note:: There are obvious caveats to using file timestamps for this, as correct usage depends on how the sources might change. For example, a file could be replaced by one of the same name, but an older timestamp. If wildcards and '~' expansions are used, this introduces even more uncertainty, as then you cannot even be sure that the resulting list of file names is the same as the originals. For example, some files may have been deleted or others added. .. note:: The result file may often be a :mod:`pickle` file. In that case, it also depends on the relevant module sources, so extra caution is required. Ideally, an additional check on iris.__version__ is advised. """ # Accept a string as a single source path if isinstance(source_paths, str): source_paths = [source_paths] # Fix our chosen timestamp function file_date = os.path.getmtime # Get the 'result file' time result_timestamp = file_date(result_path) # Get all source filepaths, with normal Iris.io load helper function source_file_paths = iris.io.expand_filespecs(source_paths) # Compare each filetime, for each spec, with the 'result time' for path in source_file_paths: source_timestamp = file_date(path) if source_timestamp >= result_timestamp: return False return True
[docs] def is_regular(coord): """Determine if the given coord is regular. Notes ----- This function does not maintain laziness when called; it realises data. See more at :doc:`/userguide/real_and_lazy_data`. """ try: regular_step(coord) except iris.exceptions.CoordinateNotRegularError: return False except (TypeError, ValueError): return False return True
[docs] def regular_step(coord): """Return the regular step from a coord or fail. Notes ----- This function does not maintain laziness when called; it realises data. See more at :doc:`/userguide/real_and_lazy_data`. """ if coord.ndim != 1: raise iris.exceptions.CoordinateMultiDimError("Expected 1D coord") if coord.shape[0] < 2: raise ValueError("Expected a non-scalar coord") avdiff, regular = points_step(coord.points) if not regular: msg = "Coord %s is not regular" % coord.name() raise iris.exceptions.CoordinateNotRegularError(msg) return avdiff.astype(coord.points.dtype)
[docs] def regular_points(zeroth, step, count): """Make an array of regular points. Create an array of `count` points from `zeroth` + `step`, adding `step` each time. In float32 if this gives a sufficiently regular array (tested with points_step) and float64 if not. Parameters ---------- zeroth : number The value *prior* to the first point value. step : number The numeric difference between successive point values. count : number The number of point values. Notes ----- This function does maintain laziness when called; it doesn't realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ points = (zeroth + step) + step * np.arange(count, dtype=np.float32) _, regular = iris.util.points_step(points) if not regular: points = (zeroth + step) + step * np.arange(count, dtype=np.float64) return points
[docs] def points_step(points): """Determine whether `points` has a regular step. Parameters ---------- points : numeric, array-like The sequence of values to check for a regular difference. Returns ------- numeric, bool A tuple containing the average difference between values, and whether the difference is regular. Notes ----- This function does not maintain laziness when called; it realises data. See more at :doc:`/userguide/real_and_lazy_data`. """ # Calculations only make sense with multiple points points = np.asanyarray(points) if points.size >= 2: diffs = np.diff(points) avdiff = np.mean(diffs) # TODO: This value for `rtol` is set for test_analysis to pass... regular = np.allclose(diffs, avdiff, rtol=0.001) else: avdiff = np.nan regular = True return avdiff, regular
[docs] def unify_time_units(cubes): """Perform an in-place conversion of the time units. Perform an in-place conversion of the time units of all time coords in the cubes in a given iterable. One common epoch is defined for each calendar found in the cubes to prevent units being defined with inconsistencies between epoch and calendar. During this process, all time coordinates have their data type converted to 64-bit floats to allow for smooth concatenation. Each epoch is defined from the first suitable time coordinate found in the input cubes. Parameters ---------- cubes : An iterable containing :class:`iris.cube.Cube` instances. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ epochs = {} for cube in cubes: for time_coord in cube.coords(): if time_coord.units.is_time_reference(): time_coord.points = time_coord.core_points().astype("float64") if time_coord.bounds is not None: time_coord.bounds = time_coord.core_bounds().astype("float64") epoch = epochs.setdefault( time_coord.units.calendar, time_coord.units.origin ) new_unit = cf_units.Unit(epoch, time_coord.units.calendar) time_coord.convert_units(new_unit)
def _is_circular(points, modulus, bounds=None): """Determine whether the provided points or bounds are circular. Determine whether the provided points or bounds are circular in nature relative to the modulus value. If the bounds are provided then these are checked for circularity rather than the points. Parameters ---------- points : :class:`numpy.ndarray` :class:`numpy.ndarray` of point values. modulus : Circularity modulus value. bounds : :class:`numpy.ndarray`, optional :class:`numpy.ndarray` of bound values. Returns ------- bool """ circular = False if bounds is not None: # Set circular to True if the bounds ends are equivalent. first_bound = last_bound = None if bounds.ndim == 1 and bounds.shape[-1] == 2: first_bound = bounds[0] % modulus last_bound = bounds[1] % modulus elif bounds.ndim == 2 and bounds.shape[-1] == 2: first_bound = bounds[0, 0] % modulus last_bound = bounds[-1, 1] % modulus if first_bound is not None and last_bound is not None: circular = np.allclose(first_bound, last_bound, rtol=1.0e-5) else: # set circular if points are regular and last+1 ~= first if len(points) > 1: diffs = list(set(np.diff(points))) diff = np.mean(diffs) abs_tol = np.abs(diff * 1.0e-4) diff_approx_equal = np.max(np.abs(diffs - diff)) < abs_tol if diff_approx_equal: circular_value = (points[-1] + diff) % modulus try: np.testing.assert_approx_equal( points[0], circular_value, significant=4 ) circular = True except AssertionError: if points[0] == 0: try: np.testing.assert_approx_equal( modulus, circular_value, significant=4 ) circular = True except AssertionError: pass else: # XXX - Inherited behaviour from NetCDF PyKE rules. # We need to decide whether this is valid! circular = points[0] >= modulus return circular
[docs] def promote_aux_coord_to_dim_coord(cube, name_or_coord): r"""Promote an auxiliary to a dimension coordinate on the cube. This AuxCoord must be associated with a single cube dimension. If the AuxCoord is associated with a dimension that already has a DimCoord, that DimCoord gets demoted to an AuxCoord. Parameters ---------- cube : An instance of :class:`iris.cube.Cube`. name_or_coord : * \(a) An instance of :class:`iris.coords.AuxCoord` * \(b) the :attr:`standard_name`, :attr:`long_name`, or :attr:`var_name` of an instance of an instance of :class:`iris.coords.AuxCoord`. Examples -------- .. testsetup:: promote import iris from iris.coord_categorisation import add_year from iris.util import demote_dim_coord_to_aux_coord, promote_aux_coord_to_dim_coord cube = iris.load_cube(iris.sample_data_path("E1_north_america.nc")) cube.remove_coord("forecast_reference_time") cube.remove_coord("height") cube.attributes = {} cube.cell_methods = () add_year(cube, "time") .. doctest:: promote >>> print(cube) air_temperature / (K) (time: 240; latitude: 37; longitude: 49) Dimension coordinates: time x - - latitude - x - longitude - - x Auxiliary coordinates: forecast_period x - - year x - - >>> promote_aux_coord_to_dim_coord(cube, "year") >>> print(cube) air_temperature / (K) (year: 240; latitude: 37; longitude: 49) Dimension coordinates: year x - - latitude - x - longitude - - x Auxiliary coordinates: forecast_period x - - time x - - Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ from iris.coords import Coord, DimCoord if isinstance(name_or_coord, str): aux_coord = cube.coord(name_or_coord) elif isinstance(name_or_coord, Coord): aux_coord = name_or_coord else: # Don't know how to handle this type msg = ( "Don't know how to handle coordinate of type {}. " "Ensure all coordinates are of type str or " "iris.coords.Coord." ) msg = msg.format(type(name_or_coord)) raise TypeError(msg) if aux_coord in cube.dim_coords: # nothing to do return if aux_coord not in cube.aux_coords: msg = ( "Attempting to promote an AuxCoord ({}) " "which does not exist in the cube." ) msg = msg.format(aux_coord.name()) raise ValueError(msg) coord_dim = cube.coord_dims(aux_coord) if len(coord_dim) != 1: msg = ( "Attempting to promote an AuxCoord ({}) " "which is associated with {} dimensions." ) msg = msg.format(aux_coord.name(), len(coord_dim)) raise ValueError(msg) try: dim_coord = DimCoord.from_coord(aux_coord) except ValueError as valerr: msg = ( "Attempt to promote an AuxCoord ({}) fails " "when attempting to create a DimCoord from the " "AuxCoord because: {}" ) msg = msg.format(aux_coord.name(), str(valerr)) raise ValueError(msg) old_dim_coord = cube.coords(dim_coords=True, contains_dimension=coord_dim[0]) if len(old_dim_coord) == 1: demote_dim_coord_to_aux_coord(cube, old_dim_coord[0]) # order matters here: don't want to remove # the aux_coord before have tried to make # dim_coord in case that fails cube.remove_coord(aux_coord) cube.add_dim_coord(dim_coord, coord_dim)
[docs] def demote_dim_coord_to_aux_coord(cube, name_or_coord): r"""Demote a dimension coordinate on the cube to an auxiliary coordinate. The DimCoord is demoted to an auxiliary coordinate on the cube. The dimension of the cube that was associated with the DimCoord becomes anonymous. The class of the coordinate is left as DimCoord, it is not recast as an AuxCoord instance. Parameters ---------- cube : An instance of :class:`iris.cube.Cube`. name_or_coord : * \(a) An instance of :class:`iris.coords.DimCoord` * \(b) the :attr:`standard_name`, :attr:`long_name`, or :attr:`var_name` of an instance of an instance of :class:`iris.coords.DimCoord`. Examples -------- .. testsetup:: demote import iris from iris.coord_categorisation import add_year from iris.util import demote_dim_coord_to_aux_coord, promote_aux_coord_to_dim_coord cube = iris.load_cube(iris.sample_data_path("E1_north_america.nc")) cube.remove_coord("forecast_reference_time") cube.remove_coord("height") cube.attributes = {} cube.cell_methods = () add_year(cube, "time") .. doctest:: demote >>> print(cube) air_temperature / (K) (time: 240; latitude: 37; longitude: 49) Dimension coordinates: time x - - latitude - x - longitude - - x Auxiliary coordinates: forecast_period x - - year x - - >>> demote_dim_coord_to_aux_coord(cube, "time") >>> print(cube) air_temperature / (K) (-- : 240; latitude: 37; longitude: 49) Dimension coordinates: latitude - x - longitude - - x Auxiliary coordinates: forecast_period x - - time x - - year x - - Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ from iris.coords import Coord if isinstance(name_or_coord, str): dim_coord = cube.coord(name_or_coord) elif isinstance(name_or_coord, Coord): dim_coord = name_or_coord else: # Don't know how to handle this type msg = ( "Don't know how to handle coordinate of type {}. " "Ensure all coordinates are of type str or " "iris.coords.Coord." ) msg = msg.format(type(name_or_coord)) raise TypeError(msg) if dim_coord not in cube.dim_coords: # nothing to do return coord_dim = cube.coord_dims(dim_coord) cube.remove_coord(dim_coord) cube.add_aux_coord(dim_coord, coord_dim)
@functools.wraps(np.meshgrid) def _meshgrid(*xi, **kwargs): """Ensure consistent meshgrid behaviour across numpy versions. @numpy v1.13, the dtype of each output n-D coordinate is the same as its associated input 1D coordinate. This is not the case prior to numpy v1.13, where the output dtype is cast up to its highest resolution, regardlessly. Reference: https://github.com/numpy/numpy/pull/5302 """ mxi = np.meshgrid(*xi, **kwargs) for i, (mxii, xii) in enumerate(zip(mxi, xi)): if mxii.dtype != xii.dtype: mxi[i] = mxii.astype(xii.dtype) return mxi
[docs] def find_discontiguities(cube, rel_tol=1e-5, abs_tol=1e-8): """Identify spatial discontiguities. Searches the 'x' and 'y' coord on the cube for discontiguities in the bounds array, returned as a boolean array (True for all cells which are discontiguous with the cell immediately above them or to their right). Parameters ---------- cube : `iris.cube.Cube` The cube to be checked for discontinuities in its 'x' and 'y' coordinates. These coordinates must be 2D. rel_tol : float, default=1e-5 The relative equality tolerance to apply in coordinate bounds checking. abs_tol : float, default=1e-8 The absolute value tolerance to apply in coordinate bounds checking. Returns ------- numpy.ndarray Boolean True/false map of which cells in the cube XY grid have discontiguities in the coordinate points array. This can be used as the input array for :func:`iris.util.mask_cube`. Examples -------- :: # Find any unknown discontiguities in your cube's x and y arrays: discontiguities = iris.util.find_discontiguities(cube) # Pass the resultant boolean array to `iris.util.mask_cube` # with a cube slice; this will use the boolean array to mask # any discontiguous data points before plotting: masked_cube_slice = iris.util.mask_cube(cube[0], discontiguities) # Plot the masked cube slice: iplt.pcolormesh(masked_cube_slice) Notes ----- This function does not maintain laziness when called; it realises data. See more at :doc:`/userguide/real_and_lazy_data`. """ lats_and_lons = [ "latitude", "grid_latitude", "longitude", "grid_longitude", ] spatial_coords = [ coord for coord in cube.aux_coords if coord.name() in lats_and_lons ] dim_err_msg = ( "Discontiguity searches are currently only supported for " "2-dimensional coordinates." ) if len(spatial_coords) != 2: raise NotImplementedError(dim_err_msg) # Check which dimensions are spanned by each coordinate. for coord in spatial_coords: if coord.ndim != 2: raise NotImplementedError(dim_err_msg) else: span = set(cube.coord_dims(coord)) if not span: msg = "The coordinate {!r} doesn't span a data dimension." raise ValueError(msg.format(coord.name())) # Check that the 2d coordinate arrays are the same shape as each other if len(spatial_coords) == 2: assert spatial_coords[0].points.shape == spatial_coords[1].points.shape # Set up unmasked boolean array the same size as the coord points array: bad_points_boolean = np.zeros(spatial_coords[0].points.shape, dtype=bool) for coord in spatial_coords: _, (diffs_x, diffs_y) = coord._discontiguity_in_bounds( rtol=rel_tol, atol=abs_tol ) bad_points_boolean[:, :-1] = np.logical_or(bad_points_boolean[:, :-1], diffs_x) # apply mask for y-direction discontiguities: bad_points_boolean[:-1, :] = np.logical_or(bad_points_boolean[:-1, :], diffs_y) return bad_points_boolean
def _mask_array(array, points_to_mask, in_place=False): """Apply masking to array where points_to_mask is True/non-zero. Designed to work with iris.analysis.maths._binary_op_common so array and points_to_mask will be broadcastable to each other. array and points_to_mask may be numpy or dask types (or one of each). If array is lazy then in_place is ignored: _math_op_common will use the returned value regardless of in_place, so we do not need to implement it here. If in_place is True then array must be a :class:`numpy.ma.MaskedArray` or :class:`dask.array.Array` (must be a dask array if points_to_mask is lazy). """ # Decide which array library to use. if is_lazy_data(points_to_mask) or is_lazy_data(array): al = da if not is_lazy_data(array) and in_place: # Non-lazy array and lazy mask should not come up for in_place # case, due to _binary_op_common handling added at #3790. raise TypeError("Cannot apply lazy mask in-place to a non-lazy array.") in_place = False elif in_place and not isinstance(array, ma.MaskedArray): raise TypeError("Cannot apply a mask in-place to a plain numpy array.") else: al = np points_to_mask = points_to_mask.astype(bool) # Treat any masked points on our mask as False. points_to_mask = al.ma.filled(points_to_mask, False) # Get broadcasted views of the arrays. Note that broadcast_arrays does not # preserve masks, so we need to explicitly handle any existing mask on array. array_mask = al.ma.getmaskarray(array) array_data, array_mask, points_to_mask = al.broadcast_arrays( array, array_mask, points_to_mask ) new_mask = al.logical_or(array_mask, points_to_mask) if in_place: array.mask = new_mask result = array # Resolve uses returned value even if working in place. else: # Return a new, independent array. result = al.ma.masked_array(array_data.copy(), mask=new_mask) return result
[docs] @_lenient_client(services=SERVICES) def mask_cube(cube, points_to_mask, in_place=False, dim=None): """Mask any cells in the cube's data array. Masks any cells in the cube's data array which correspond to cells marked ``True`` (or non zero) in ``points_to_mask``. ``points_to_mask`` may be specified as a :class:`numpy.ndarray`, :class:`dask.array.Array`, :class:`iris.coords.Coord` or :class:`iris.cube.Cube`, following the same broadcasting approach as cube arithmetic (see :ref:`cube maths`). Parameters ---------- cube : iris.cube.Cube Cube containing data that requires masking. points_to_mask : numpy.ndarray, dask.array.Array, iris.coords.Coord or iris.cube.Cube Specifies booleans (or ones and zeros) indicating which points will be masked. in_place : bool, default=False If `True`, masking is applied to the input cube. Otherwise a copy is masked and returned. dim : int, optional If `points_to_mask` is a coord which does not exist on the cube, specify the dimension to which it should be mapped. Returns ------- iris.cube.Cube A cube whose data array is masked at points specified by ``points_to_mask``. Notes ----- If either ``cube`` or ``points_to_mask`` is lazy, the result will be lazy. This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if in_place and not cube.has_lazy_data(): # Ensure cube data is masked type so we can work on it in-place. cube.data = ma.asanyarray(cube.data) mask_function = functools.partial(_mask_array, in_place=True) else: mask_function = _mask_array input_metadata = cube.metadata result = iris.analysis.maths._binary_op_common( mask_function, "mask", cube, points_to_mask, cube.units, in_place=in_place, dim=dim, sanitise_metadata=False, ) # Resolve combines the metadata from the two operands, but we want to # preserve the metadata from the (first) input cube. result.metadata = input_metadata if not in_place: return result
[docs] def equalise_attributes(cubes): """Delete cube attributes that are not identical over all cubes in a group. This function deletes any attributes which are not the same for all the given cubes. The cubes will then have identical attributes, and the removed attributes are returned. The given cubes are modified in-place. Parameters ---------- cubes : iterable of :class:`iris.cube.Cube` A collection of cubes to compare and adjust. Returns ------- list A list of dicts holding the removed attributes. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ # deferred import to avoid circularity problem from iris.common._split_attribute_dicts import ( _convert_splitattrs_to_pairedkeys_dict, ) cube_attrs = [cube.attributes for cube in cubes] # Convert all the input dictionaries to ones with 'paired' keys, so each key # becomes a pair, ('local'/'global', attribute-name), making them specific to each # "type", i.e. global or local. # This is needed to ensure that afterwards all cubes will have identical # attributes, E.G. it treats an attribute which is global on one cube and local # on another as *not* the same. This is essential to its use in making merges work. # # This approach does also still function with "ordinary" dictionaries, or # :class:`iris.common.mixin.LimitedAttributeDict`, though somewhat inefficiently, # so the routine works on *other* objects bearing attributes, i.e. not just Cubes. # That is also important since the original code allows that (though the docstring # does not admit it). cube_attrs = [_convert_splitattrs_to_pairedkeys_dict(dic) for dic in cube_attrs] # Work out which attributes are identical across all the cubes. common_keys = list(cube_attrs[0].keys()) keys_to_remove = set(common_keys) for attrs in cube_attrs[1:]: cube_keys = list(attrs.keys()) keys_to_remove.update(cube_keys) common_keys = [ key for key in common_keys if (key in cube_keys and np.all(attrs[key] == cube_attrs[0][key])) ] keys_to_remove.difference_update(common_keys) # Convert back from the resulting 'paired' keys set, extracting just the # attribute-name parts, as a set of names to be discarded. # Note: we don't care any more what type (global/local) these were : we will # simply remove *all* attributes with those names. keys_to_remove = set(key_pair[1] for key_pair in keys_to_remove) # Remove all the non-matching attributes. removed = [] for cube in cubes: deleted_attributes = { key: cube.attributes.pop(key) for key in keys_to_remove if key in cube.attributes } removed.append(deleted_attributes) return removed
[docs] def is_masked(array): """Equivalent to :func:`numpy.ma.is_masked`, but works for both lazy AND realised arrays. Parameters ---------- array : :class:`numpy.Array` or :class:`dask.array.Array` The array to be checked for masks. Returns ------- bool Whether or not the array has any masks. Notes ----- This function maintains laziness when called; it does not realise data. See more at :doc:`/userguide/real_and_lazy_data`. """ if is_lazy_data(array): result = da.ma.getmaskarray(array).any().compute() else: result = ma.is_masked(array) return result
def _strip_metadata_from_dims(cube, dims): """Remove ancillary variables and cell measures that map to specific dimensions. Returns a cube copy with (possibly) some cell-measures and ancillary variables removed. To be used by operations that modify or remove dimensions. Note: does nothing to (aux)-coordinates. Those would be handled explicitly by the calling operation. """ reduced_cube = cube.copy() # Remove any ancillary variables that span the dimension(s) being collapsed for ancil in reduced_cube.ancillary_variables(): ancil_dims = reduced_cube.ancillary_variable_dims(ancil) if set(dims).intersection(ancil_dims): reduced_cube.remove_ancillary_variable(ancil) # Remove any cell measures that span the dimension(s) being collapsed for cm in reduced_cube.cell_measures(): cm_dims = reduced_cube.cell_measure_dims(cm) if set(dims).intersection(cm_dims): reduced_cube.remove_cell_measure(cm) return reduced_cube
[docs] def mask_cube_from_shapefile(cube, shape, minimum_weight=0.0, in_place=False): """Take a shape object and masks all points not touching it in a cube. Finds the overlap between the `shape` and the `cube` in 2D xy space and masks out any cells with less % overlap with shape than set. Default behaviour is to count any overlap between shape and cell as valid Parameters ---------- cube : :class:`~iris.cube.Cube` object The `Cube` object to masked. Must be singular, rather than a `CubeList`. shape : Shapely.Geometry object A single `shape` of the area to remain unmasked on the `cube`. If it a line object of some kind then minimum_weight will be ignored, because you cannot compare the area of a 1D line and 2D Cell. minimum_weight : float , default=0.0 A number between 0-1 describing what % of a cube cell area must the shape overlap to include it. in_place : bool, default=False Whether to mask the `cube` in-place or return a newly masked `cube`. Defaults to False. Returns ------- iris.Cube A masked version of the input cube, if in_place is False. See Also -------- :func:`~iris.util.mask_cube` Mask any cells in the cube’s data array. Notes ----- This function allows masking a cube with any cartopy projection by a shape object, most commonly from Natural Earth Shapefiles via cartopy. To mask a cube from a shapefile, both must first be on the same coordinate system. Shapefiles are mostly on a lat/lon grid with a projection very similar to GeogCS The shapefile is projected to the coord system of the cube using cartopy, then each cell is compared to the shapefile to determine overlap and populate a true/false array This array is then used to mask the cube using the `iris.util.mask_cube` function This uses numpy arithmetic logic for broadcasting, so you may encounter unexpected results if your cube has other dimensions the same length as the x/y dimensions Examples -------- >>> import shapely >>> from iris.util import mask_cube_from_shapefile >>> cube = iris.load_cube(iris.sample_data_path("E1_north_america.nc")) >>> shape = shapely.geometry.box(-100,30, -80,40) # box between 30N-40N 100W-80W >>> masked_cube = mask_cube_from_shapefile(cube, shape) """ shapefile_mask = create_shapefile_mask(shape, cube, minimum_weight) masked_cube = mask_cube(cube, shapefile_mask, in_place=in_place) if not in_place: return masked_cube