EVOLUTION-MANAGER

Edit File: _numpy_compat.py

"""Functions copypasted from newer versions of numpy. """ from __future__ import division, print_function, absolute_import import warnings from warnings import WarningMessage import re from functools import wraps import numpy as np from scipy._lib._version import NumpyVersion if NumpyVersion(np.__version__) > '1.7.0.dev': _assert_warns = np.testing.assert_warns else: def _assert_warns(warning_class, func, *args, **kw): r""" Fail unless the given callable throws the specified warning. This definition is copypasted from numpy 1.9.0.dev. The version in earlier numpy returns None. Parameters ---------- warning_class : class The class defining the warning that `func` is expected to throw. func : callable The callable to test. *args : Arguments Arguments passed to `func`. **kwargs : Kwargs Keyword arguments passed to `func`. Returns ------- The value returned by `func`. """ with warnings.catch_warnings(record=True) as l: warnings.simplefilter('always') result = func(*args, **kw) if not len(l) > 0: raise AssertionError("No warning raised when calling %s" % func.__name__) if not l[0].category is warning_class: raise AssertionError("First warning for %s is not a " "%s( is %s)" % (func.__name__, warning_class, l[0])) return result if NumpyVersion(np.__version__) >= '1.10.0': from numpy import broadcast_to else: # Definition of `broadcast_to` from numpy 1.10.0. def _maybe_view_as_subclass(original_array, new_array): if type(original_array) is not type(new_array): # if input was an ndarray subclass and subclasses were OK, # then view the result as that subclass. new_array = new_array.view(type=type(original_array)) # Since we have done something akin to a view from original_array, we # should let the subclass finalize (if it has it implemented, i.e., is # not None). if new_array.__array_finalize__: new_array.__array_finalize__(original_array) return new_array def _broadcast_to(array, shape, subok, readonly): shape = tuple(shape) if np.iterable(shape) else (shape,) array = np.array(array, copy=False, subok=subok) if not shape and array.shape: raise ValueError('cannot broadcast a non-scalar to a scalar array') if any(size < 0 for size in shape): raise ValueError('all elements of broadcast shape must be non-' 'negative') broadcast = np.nditer( (array,), flags=['multi_index', 'refs_ok', 'zerosize_ok'], op_flags=['readonly'], itershape=shape, order='C').itviews[0] result = _maybe_view_as_subclass(array, broadcast) if not readonly and array.flags.writeable: result.flags.writeable = True return result def broadcast_to(array, shape, subok=False): return _broadcast_to(array, shape, subok=subok, readonly=True) if NumpyVersion(np.__version__) >= '1.11.0': def get_randint(random_state): return random_state.randint else: # In NumPy versions previous to 1.11.0 the randint function and the randint # method of RandomState does only work with int32 values. def get_randint(random_state): def randint_patched(low, high, size, dtype=np.int32): low = max(low, np.iinfo(dtype).min, np.iinfo(np.int32).min) high = min(high, np.iinfo(dtype).max, np.iinfo(np.int32).max) integers = random_state.randint(low, high=high, size=size) return integers.astype(dtype, copy=False) return randint_patched if NumpyVersion(np.__version__) >= '1.9.0': from numpy import unique else: # the return_counts keyword was added in 1.9.0 def unique(ar, return_index=False, return_inverse=False, return_counts=False): """ Find the unique elements of an array. Returns the sorted unique elements of an array. There are three optional outputs in addition to the unique elements: the indices of the input array that give the unique values, the indices of the unique array that reconstruct the input array, and the number of times each unique value comes up in the input array. Parameters ---------- ar : array_like Input array. This will be flattened if it is not already 1-D. return_index : bool, optional If True, also return the indices of `ar` that result in the unique array. return_inverse : bool, optional If True, also return the indices of the unique array that can be used to reconstruct `ar`. return_counts : bool, optional If True, also return the number of times each unique value comes up in `ar`. .. versionadded:: 1.9.0 Returns ------- unique : ndarray The sorted unique values. unique_indices : ndarray, optional The indices of the first occurrences of the unique values in the (flattened) original array. Only provided if `return_index` is True. unique_inverse : ndarray, optional The indices to reconstruct the (flattened) original array from the unique array. Only provided if `return_inverse` is True. unique_counts : ndarray, optional The number of times each of the unique values comes up in the original array. Only provided if `return_counts` is True. .. versionadded:: 1.9.0 Notes ----- Taken over from numpy 1.12.0-dev (c8408bf9c). Omitted examples, see numpy documentation for those. """ ar = np.asanyarray(ar).flatten() optional_indices = return_index or return_inverse optional_returns = optional_indices or return_counts if ar.size == 0: if not optional_returns: ret = ar else: ret = (ar,) if return_index: ret += (np.empty(0, np.bool),) if return_inverse: ret += (np.empty(0, np.bool),) if return_counts: ret += (np.empty(0, np.intp),) return ret if optional_indices: perm = ar.argsort(kind='mergesort' if return_index else 'quicksort') aux = ar[perm] else: ar.sort() aux = ar flag = np.concatenate(([True], aux[1:] != aux[:-1])) if not optional_returns: ret = aux[flag] else: ret = (aux[flag],) if return_index: ret += (perm[flag],) if return_inverse: iflag = np.cumsum(flag) - 1 inv_idx = np.empty(ar.shape, dtype=np.intp) inv_idx[perm] = iflag ret += (inv_idx,) if return_counts: idx = np.concatenate(np.nonzero(flag) + ([ar.size],)) ret += (np.diff(idx),) return ret if NumpyVersion(np.__version__) > '1.12.0.dev': polyvalfromroots = np.polynomial.polynomial.polyvalfromroots else: def polyvalfromroots(x, r, tensor=True): r""" Evaluate a polynomial specified by its roots at points x. This function is copypasted from numpy 1.12.0.dev. If `r` is of length `N`, this function returns the value .. math:: p(x) = \prod_{n=1}^{N} (x - r_n) The parameter `x` is converted to an array only if it is a tuple or a list, otherwise it is treated as a scalar. In either case, either `x` or its elements must support multiplication and addition both with themselves and with the elements of `r`. If `r` is a 1-D array, then `p(x)` will have the same shape as `x`. If `r` is multidimensional, then the shape of the result depends on the value of `tensor`. If `tensor is ``True`` the shape will be r.shape[1:] + x.shape; that is, each polynomial is evaluated at every value of `x`. If `tensor` is ``False``, the shape will be r.shape[1:]; that is, each polynomial is evaluated only for the corresponding broadcast value of `x`. Note that scalars have shape (,). Parameters ---------- x : array_like, compatible object If `x` is a list or tuple, it is converted to an ndarray, otherwise it is left unchanged and treated as a scalar. In either case, `x` or its elements must support addition and multiplication with with themselves and with the elements of `r`. r : array_like Array of roots. If `r` is multidimensional the first index is the root index, while the remaining indices enumerate multiple polynomials. For instance, in the two dimensional case the roots of each polynomial may be thought of as stored in the columns of `r`. tensor : boolean, optional If True, the shape of the roots array is extended with ones on the right, one for each dimension of `x`. Scalars have dimension 0 for this action. The result is that every column of coefficients in `r` is evaluated for every element of `x`. If False, `x` is broadcast over the columns of `r` for the evaluation. This keyword is useful when `r` is multidimensional. The default value is True. Returns ------- values : ndarray, compatible object The shape of the returned array is described above. See Also -------- polyroots, polyfromroots, polyval Examples -------- >>> from numpy.polynomial.polynomial import polyvalfromroots >>> polyvalfromroots(1, [1,2,3]) 0.0 >>> a = np.arange(4).reshape(2,2) >>> a array([[0, 1], [2, 3]]) >>> polyvalfromroots(a, [-1, 0, 1]) array([[ -0., 0.], [ 6., 24.]]) >>> r = np.arange(-2, 2).reshape(2,2) # multidimensional coefficients >>> r # each column of r defines one polynomial array([[-2, -1], [ 0, 1]]) >>> b = [-2, 1] >>> polyvalfromroots(b, r, tensor=True) array([[-0., 3.], [ 3., 0.]]) >>> polyvalfromroots(b, r, tensor=False) array([-0., 0.]) """ r = np.array(r, ndmin=1, copy=0) if r.dtype.char in '?bBhHiIlLqQpP': r = r.astype(np.double) if isinstance(x, (tuple, list)): x = np.asarray(x) if isinstance(x, np.ndarray): if tensor: r = r.reshape(r.shape + (1,)*x.ndim) elif x.ndim >= r.ndim: raise ValueError("x.ndim must be < r.ndim when tensor == " "False") return np.prod(x - r, axis=0) try: from numpy.testing import suppress_warnings except ImportError: class suppress_warnings(object): """ Context manager and decorator doing much the same as ``warnings.catch_warnings``. However, it also provides a filter mechanism to work around https://bugs.python.org/issue4180. This bug causes Python before 3.4 to not reliably show warnings again after they have been ignored once (even within catch_warnings). It means that no "ignore" filter can be used easily, since following tests might need to see the warning. Additionally it allows easier specificity for testing warnings and can be nested. Parameters ---------- forwarding_rule : str, optional One of "always", "once", "module", or "location". Analogous to the usual warnings module filter mode, it is useful to reduce noise mostly on the outmost level. Unsuppressed and unrecorded warnings will be forwarded based on this rule. Defaults to "always". "location" is equivalent to the warnings "default", match by exact location the warning warning originated from. Notes ----- Filters added inside the context manager will be discarded again when leaving it. Upon entering all filters defined outside a context will be applied automatically. When a recording filter is added, matching warnings are stored in the ``log`` attribute as well as in the list returned by ``record``. If filters are added and the ``module`` keyword is given, the warning registry of this module will additionally be cleared when applying it, entering the context, or exiting it. This could cause warnings to appear a second time after leaving the context if they were configured to be printed once (default) and were already printed before the context was entered. Nesting this context manager will work as expected when the forwarding rule is "always" (default). Unfiltered and unrecorded warnings will be passed out and be matched by the outer level. On the outmost level they will be printed (or caught by another warnings context). The forwarding rule argument can modify this behaviour. Like ``catch_warnings`` this context manager is not threadsafe. Examples -------- >>> with suppress_warnings() as sup: ... sup.filter(DeprecationWarning, "Some text") ... sup.filter(module=np.ma.core) ... log = sup.record(FutureWarning, "Does this occur?") ... command_giving_warnings() ... # The FutureWarning was given once, the filtered warnings were ... # ignored. All other warnings abide outside settings (may be ... # printed/error) ... assert_(len(log) == 1) ... assert_(len(sup.log) == 1) # also stored in log attribute Or as a decorator: >>> sup = suppress_warnings() >>> sup.filter(module=np.ma.core) # module must match exact >>> @sup >>> def some_function(): ... # do something which causes a warning in np.ma.core ... pass """ def __init__(self, forwarding_rule="always"): self._entered = False # Suppressions are either instance or defined inside one with block: self._suppressions = [] if forwarding_rule not in {"always", "module", "once", "location"}: raise ValueError("unsupported forwarding rule.") self._forwarding_rule = forwarding_rule def _clear_registries(self): if hasattr(warnings, "_filters_mutated"): # clearing the registry should not be necessary on new pythons, # instead the filters should be mutated. warnings._filters_mutated() return # Simply clear the registry, this should normally be harmless, # note that on new pythons it would be invalidated anyway. for module in self._tmp_modules: if hasattr(module, "__warningregistry__"): module.__warningregistry__.clear() def _filter(self, category=Warning, message="", module=None, record=False): if record: record = [] # The log where to store warnings else: record = None if self._entered: if module is None: warnings.filterwarnings( "always", category=category, message=message) else: module_regex = module.__name__.replace('.', r'\.') + '$' warnings.filterwarnings( "always", category=category, message=message, module=module_regex) self._tmp_modules.add(module) self._clear_registries() self._tmp_suppressions.append( (category, message, re.compile(message, re.I), module, record)) else: self._suppressions.append( (category, message, re.compile(message, re.I), module, record)) return record def filter(self, category=Warning, message="", module=None): """ Add a new suppressing filter or apply it if the state is entered. Parameters ---------- category : class, optional Warning class to filter message : string, optional Regular expression matching the warning message. module : module, optional Module to filter for. Note that the module (and its file) must match exactly and cannot be a submodule. This may make it unreliable for external modules. Notes ----- When added within a context, filters are only added inside the context and will be forgotten when the context is exited. """ self._filter(category=category, message=message, module=module, record=False) def record(self, category=Warning, message="", module=None): """ Append a new recording filter or apply it if the state is entered. All warnings matching will be appended to the ``log`` attribute. Parameters ---------- category : class, optional Warning class to filter message : string, optional Regular expression matching the warning message. module : module, optional Module to filter for. Note that the module (and its file) must match exactly and cannot be a submodule. This may make it unreliable for external modules. Returns ------- log : list A list which will be filled with all matched warnings. Notes ----- When added within a context, filters are only added inside the context and will be forgotten when the context is exited. """ return self._filter(category=category, message=message, module=module, record=True) def __enter__(self): if self._entered: raise RuntimeError("cannot enter suppress_warnings twice.") self._orig_show = warnings.showwarning self._filters = warnings.filters warnings.filters = self._filters[:] self._entered = True self._tmp_suppressions = [] self._tmp_modules = set() self._forwarded = set() self.log = [] # reset global log (no need to keep same list) for cat, mess, _, mod, log in self._suppressions: if log is not None: del log[:] # clear the log if mod is None: warnings.filterwarnings( "always", category=cat, message=mess) else: module_regex = mod.__name__.replace('.', r'\.') + '$' warnings.filterwarnings( "always", category=cat, message=mess, module=module_regex) self._tmp_modules.add(mod) warnings.showwarning = self._showwarning self._clear_registries() return self def __exit__(self, *exc_info): warnings.showwarning = self._orig_show warnings.filters = self._filters self._clear_registries() self._entered = False del self._orig_show del self._filters def _showwarning(self, message, category, filename, lineno, *args, **kwargs): use_warnmsg = kwargs.pop("use_warnmsg", None) for cat, _, pattern, mod, rec in ( self._suppressions + self._tmp_suppressions)[::-1]: if (issubclass(category, cat) and pattern.match(message.args[0]) is not None): if mod is None: # Message and category match, either recorded or ignored if rec is not None: msg = WarningMessage(message, category, filename, lineno, **kwargs) self.log.append(msg) rec.append(msg) return # Use startswith, because warnings strips the c or o from # .pyc/.pyo files. elif mod.__file__.startswith(filename): # The message and module (filename) match if rec is not None: msg = WarningMessage(message, category, filename, lineno, **kwargs) self.log.append(msg) rec.append(msg) return # There is no filter in place, so pass to the outside handler # unless we should only pass it once if self._forwarding_rule == "always": if use_warnmsg is None: self._orig_show(message, category, filename, lineno, *args, **kwargs) else: self._orig_showmsg(use_warnmsg) return if self._forwarding_rule == "once": signature = (message.args, category) elif self._forwarding_rule == "module": signature = (message.args, category, filename) elif self._forwarding_rule == "location": signature = (message.args, category, filename, lineno) if signature in self._forwarded: return self._forwarded.add(signature) if use_warnmsg is None: self._orig_show(message, category, filename, lineno, *args, **kwargs) else: self._orig_showmsg(use_warnmsg) def __call__(self, func): """ Function decorator to apply certain suppressions to a whole function. """ @wraps(func) def new_func(*args, **kwargs): with self: return func(*args, **kwargs) return new_func if NumpyVersion(np.__version__) >= '1.10.0': from numpy import cov else: from numpy import array, average, dot def cov(m, y=None, rowvar=True, bias=False, ddof=None, fweights=None, aweights=None): """ Estimate a covariance matrix, given data and weights. Covariance indicates the level to which two variables vary together. If we examine N-dimensional samples, :math:`X = [x_1, x_2, ... x_N]^T`, then the covariance matrix element :math:`C_{ij}` is the covariance of :math:`x_i` and :math:`x_j`. The element :math:`C_{ii}` is the variance of :math:`x_i`. See the notes for an outline of the algorithm. Parameters ---------- m : array_like A 1-D or 2-D array containing multiple variables and observations. Each row of `m` represents a variable, and each column a single observation of all those variables. Also see `rowvar` below. y : array_like, optional An additional set of variables and observations. `y` has the same form as that of `m`. rowvar : bool, optional If `rowvar` is True (default), then each row represents a variable, with observations in the columns. Otherwise, the relationship is transposed: each column represents a variable, while the rows contain observations. bias : bool, optional Default normalization (False) is by ``(N - 1)``, where ``N`` is the number of observations given (unbiased estimate). If `bias` is True, then normalization is by ``N``. These values can be overridden by using the keyword ``ddof`` in numpy versions >= 1.5. ddof : int, optional If not ``None`` the default value implied by `bias` is overridden. Note that ``ddof=1`` will return the unbiased estimate, even if both `fweights` and `aweights` are specified, and ``ddof=0`` will return the simple average. See the notes for the details. The default value is ``None``. .. versionadded:: 1.5 fweights : array_like, int, optional 1-D array of integer freguency weights; the number of times each observation vector should be repeated. .. versionadded:: 1.10 aweights : array_like, optional 1-D array of observation vector weights. These relative weights are typically large for observations considered "important" and smaller for observations considered less "important". If ``ddof=0`` the array of weights can be used to assign probabilities to observation vectors. .. versionadded:: 1.10 Returns ------- out : ndarray The covariance matrix of the variables. See Also -------- corrcoef : Normalized covariance matrix Notes ----- Assume that the observations are in the columns of the observation array `m` and let ``f = fweights`` and ``a = aweights`` for brevity. The steps to compute the weighted covariance are as follows:: >>> w = f * a >>> v1 = np.sum(w) >>> v2 = np.sum(w * a) >>> m -= np.sum(m * w, axis=1, keepdims=True) / v1 >>> cov = np.dot(m * w, m.T) * v1 / (v1**2 - ddof * v2) Note that when ``a == 1``, the normalization factor ``v1 / (v1**2 - ddof * v2)`` goes over to ``1 / (np.sum(f) - ddof)`` as it should. Examples -------- Consider two variables, :math:`x_0` and :math:`x_1`, which correlate perfectly, but in opposite directions: >>> x = np.array([[0, 2], [1, 1], [2, 0]]).T >>> x array([[0, 1, 2], [2, 1, 0]]) Note how :math:`x_0` increases while :math:`x_1` decreases. The covariance matrix shows this clearly: >>> np.cov(x) array([[ 1., -1.], [-1., 1.]]) Note that element :math:`C_{0,1}`, which shows the correlation between :math:`x_0` and :math:`x_1`, is negative. Further, note how `x` and `y` are combined: >>> x = [-2.1, -1, 4.3] >>> y = [3, 1.1, 0.12] >>> X = np.stack((x, y), axis=0) >>> print(np.cov(X)) [[ 11.71 -4.286 ] [ -4.286 2.14413333]] >>> print(np.cov(x, y)) [[ 11.71 -4.286 ] [ -4.286 2.14413333]] >>> print(np.cov(x)) 11.71 """ # Check inputs if ddof is not None and ddof != int(ddof): raise ValueError( "ddof must be integer") # Handles complex arrays too m = np.asarray(m) if m.ndim > 2: raise ValueError("m has more than 2 dimensions") if y is None: dtype = np.result_type(m, np.float64) else: y = np.asarray(y) if y.ndim > 2: raise ValueError("y has more than 2 dimensions") dtype = np.result_type(m, y, np.float64) X = array(m, ndmin=2, dtype=dtype) if not rowvar and X.shape[0] != 1: X = X.T if X.shape[0] == 0: return np.array([]).reshape(0, 0) if y is not None: y = array(y, copy=False, ndmin=2, dtype=dtype) if not rowvar and y.shape[0] != 1: y = y.T X = np.concatenate((X, y), axis=0) if ddof is None: if bias == 0: ddof = 1 else: ddof = 0 # Get the product of frequencies and weights w = None if fweights is not None: fweights = np.asarray(fweights, dtype=float) if not np.all(fweights == np.around(fweights)): raise TypeError( "fweights must be integer") if fweights.ndim > 1: raise RuntimeError( "cannot handle multidimensional fweights") if fweights.shape[0] != X.shape[1]: raise RuntimeError( "incompatible numbers of samples and fweights") if any(fweights < 0): raise ValueError( "fweights cannot be negative") w = fweights if aweights is not None: aweights = np.asarray(aweights, dtype=float) if aweights.ndim > 1: raise RuntimeError( "cannot handle multidimensional aweights") if aweights.shape[0] != X.shape[1]: raise RuntimeError( "incompatible numbers of samples and aweights") if any(aweights < 0): raise ValueError( "aweights cannot be negative") if w is None: w = aweights else: w *= aweights avg, w_sum = average(X, axis=1, weights=w, returned=True) w_sum = w_sum[0] # Determine the normalization if w is None: fact = X.shape[1] - ddof elif ddof == 0: fact = w_sum elif aweights is None: fact = w_sum - ddof else: fact = w_sum - ddof*sum(w*aweights)/w_sum if fact <= 0: warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning, stacklevel=2) fact = 0.0 X -= avg[:, None] if w is None: X_T = X.T else: X_T = (X*w).T c = dot(X, X_T.conj()) c *= 1. / np.float64(fact) return c.squeeze()