Download rtme/lib/python3.10/site-packages/scipy/optimize/_numdiff.py from ckadirt/backup_rtme: direct link, hf CLI and curl.
- Browser
- Download file 28.7 kB
-
https://huggingface.co/ckadirt/backup_rtme/resolve/main/rtme/lib/python3.10/site-packages/scipy/optimize/_numdiff.py
- Command line
-
hf download hf://ckadirt/backup_rtme/rtme/lib/python3.10/site-packages/scipy/optimize/_numdiff.py
-
curl -L -o _numdiff.py https://huggingface.co/ckadirt/backup_rtme/resolve/main/rtme/lib/python3.10/site-packages/scipy/optimize/_numdiff.py
28.7 kB
| """Routines for numerical differentiation.""" | |
| import functools | |
| import numpy as np | |
| from numpy.linalg import norm | |
| from scipy.sparse.linalg import LinearOperator | |
| from ..sparse import issparse, csc_matrix, csr_matrix, coo_matrix, find | |
| from ._group_columns import group_dense, group_sparse | |
| from scipy._lib._array_api import atleast_nd, array_namespace | |
| def _adjust_scheme_to_bounds(x0, h, num_steps, scheme, lb, ub): | |
| """Adjust final difference scheme to the presence of bounds. | |
| Parameters | |
| ---------- | |
| x0 : ndarray, shape (n,) | |
| Point at which we wish to estimate derivative. | |
| h : ndarray, shape (n,) | |
| Desired absolute finite difference steps. | |
| num_steps : int | |
| Number of `h` steps in one direction required to implement finite | |
| difference scheme. For example, 2 means that we need to evaluate | |
| f(x0 + 2 * h) or f(x0 - 2 * h) | |
| scheme : {'1-sided', '2-sided'} | |
| Whether steps in one or both directions are required. In other | |
| words '1-sided' applies to forward and backward schemes, '2-sided' | |
| applies to center schemes. | |
| lb : ndarray, shape (n,) | |
| Lower bounds on independent variables. | |
| ub : ndarray, shape (n,) | |
| Upper bounds on independent variables. | |
| Returns | |
| ------- | |
| h_adjusted : ndarray, shape (n,) | |
| Adjusted absolute step sizes. Step size decreases only if a sign flip | |
| or switching to one-sided scheme doesn't allow to take a full step. | |
| use_one_sided : ndarray of bool, shape (n,) | |
| Whether to switch to one-sided scheme. Informative only for | |
| ``scheme='2-sided'``. | |
| """ | |
| if scheme == '1-sided': | |
| use_one_sided = np.ones_like(h, dtype=bool) | |
| elif scheme == '2-sided': | |
| h = np.abs(h) | |
| use_one_sided = np.zeros_like(h, dtype=bool) | |
| else: | |
| raise ValueError("`scheme` must be '1-sided' or '2-sided'.") | |
| if np.all((lb == -np.inf) & (ub == np.inf)): | |
| return h, use_one_sided | |
| h_total = h * num_steps | |
| h_adjusted = h.copy() | |
| lower_dist = x0 - lb | |
| upper_dist = ub - x0 | |
| if scheme == '1-sided': | |
| x = x0 + h_total | |
| violated = (x < lb) | (x > ub) | |
| fitting = np.abs(h_total) <= np.maximum(lower_dist, upper_dist) | |
| h_adjusted[violated & fitting] *= -1 | |
| forward = (upper_dist >= lower_dist) & ~fitting | |
| h_adjusted[forward] = upper_dist[forward] / num_steps | |
| backward = (upper_dist < lower_dist) & ~fitting | |
| h_adjusted[backward] = -lower_dist[backward] / num_steps | |
| elif scheme == '2-sided': | |
| central = (lower_dist >= h_total) & (upper_dist >= h_total) | |
| forward = (upper_dist >= lower_dist) & ~central | |
| h_adjusted[forward] = np.minimum( | |
| h[forward], 0.5 * upper_dist[forward] / num_steps) | |
| use_one_sided[forward] = True | |
| backward = (upper_dist < lower_dist) & ~central | |
| h_adjusted[backward] = -np.minimum( | |
| h[backward], 0.5 * lower_dist[backward] / num_steps) | |
| use_one_sided[backward] = True | |
| min_dist = np.minimum(upper_dist, lower_dist) / num_steps | |
| adjusted_central = (~central & (np.abs(h_adjusted) <= min_dist)) | |
| h_adjusted[adjusted_central] = min_dist[adjusted_central] | |
| use_one_sided[adjusted_central] = False | |
| return h_adjusted, use_one_sided | |
| def _eps_for_method(x0_dtype, f0_dtype, method): | |
| """ | |
| Calculates relative EPS step to use for a given data type | |
| and numdiff step method. | |
| Progressively smaller steps are used for larger floating point types. | |
| Parameters | |
| ---------- | |
| f0_dtype: np.dtype | |
| dtype of function evaluation | |
| x0_dtype: np.dtype | |
| dtype of parameter vector | |
| method: {'2-point', '3-point', 'cs'} | |
| Returns | |
| ------- | |
| EPS: float | |
| relative step size. May be np.float16, np.float32, np.float64 | |
| Notes | |
| ----- | |
| The default relative step will be np.float64. However, if x0 or f0 are | |
| smaller floating point types (np.float16, np.float32), then the smallest | |
| floating point type is chosen. | |
| """ | |
| # the default EPS value | |
| EPS = np.finfo(np.float64).eps | |
| x0_is_fp = False | |
| if np.issubdtype(x0_dtype, np.inexact): | |
| # if you're a floating point type then over-ride the default EPS | |
| EPS = np.finfo(x0_dtype).eps | |
| x0_itemsize = np.dtype(x0_dtype).itemsize | |
| x0_is_fp = True | |
| if np.issubdtype(f0_dtype, np.inexact): | |
| f0_itemsize = np.dtype(f0_dtype).itemsize | |
| # choose the smallest itemsize between x0 and f0 | |
| if x0_is_fp and f0_itemsize < x0_itemsize: | |
| EPS = np.finfo(f0_dtype).eps | |
| if method in ["2-point", "cs"]: | |
| return EPS**0.5 | |
| elif method in ["3-point"]: | |
| return EPS**(1/3) | |
| else: | |
| raise RuntimeError("Unknown step method, should be one of " | |
| "{'2-point', '3-point', 'cs'}") | |
| def _compute_absolute_step(rel_step, x0, f0, method): | |
| """ | |
| Computes an absolute step from a relative step for finite difference | |
| calculation. | |
| Parameters | |
| ---------- | |
| rel_step: None or array-like | |
| Relative step for the finite difference calculation | |
| x0 : np.ndarray | |
| Parameter vector | |
| f0 : np.ndarray or scalar | |
| method : {'2-point', '3-point', 'cs'} | |
| Returns | |
| ------- | |
| h : float | |
| The absolute step size | |
| Notes | |
| ----- | |
| `h` will always be np.float64. However, if `x0` or `f0` are | |
| smaller floating point dtypes (e.g. np.float32), then the absolute | |
| step size will be calculated from the smallest floating point size. | |
| """ | |
| # this is used instead of np.sign(x0) because we need | |
| # sign_x0 to be 1 when x0 == 0. | |
| sign_x0 = (x0 >= 0).astype(float) * 2 - 1 | |
| rstep = _eps_for_method(x0.dtype, f0.dtype, method) | |
| if rel_step is None: | |
| abs_step = rstep * sign_x0 * np.maximum(1.0, np.abs(x0)) | |
| else: | |
| # User has requested specific relative steps. | |
| # Don't multiply by max(1, abs(x0) because if x0 < 1 then their | |
| # requested step is not used. | |
| abs_step = rel_step * sign_x0 * np.abs(x0) | |
| # however we don't want an abs_step of 0, which can happen if | |
| # rel_step is 0, or x0 is 0. Instead, substitute a realistic step | |
| dx = ((x0 + abs_step) - x0) | |
| abs_step = np.where(dx == 0, | |
| rstep * sign_x0 * np.maximum(1.0, np.abs(x0)), | |
| abs_step) | |
| return abs_step | |
| def _prepare_bounds(bounds, x0): | |
| """ | |
| Prepares new-style bounds from a two-tuple specifying the lower and upper | |
| limits for values in x0. If a value is not bound then the lower/upper bound | |
| will be expected to be -np.inf/np.inf. | |
| Examples | |
| -------- | |
| >>> _prepare_bounds([(0, 1, 2), (1, 2, np.inf)], [0.5, 1.5, 2.5]) | |
| (array([0., 1., 2.]), array([ 1., 2., inf])) | |
| """ | |
| lb, ub = (np.asarray(b, dtype=float) for b in bounds) | |
| if lb.ndim == 0: | |
| lb = np.resize(lb, x0.shape) | |
| if ub.ndim == 0: | |
| ub = np.resize(ub, x0.shape) | |
| return lb, ub | |
| def group_columns(A, order=0): | |
| """Group columns of a 2-D matrix for sparse finite differencing [1]_. | |
| Two columns are in the same group if in each row at least one of them | |
| has zero. A greedy sequential algorithm is used to construct groups. | |
| Parameters | |
| ---------- | |
| A : array_like or sparse matrix, shape (m, n) | |
| Matrix of which to group columns. | |
| order : int, iterable of int with shape (n,) or None | |
| Permutation array which defines the order of columns enumeration. | |
| If int or None, a random permutation is used with `order` used as | |
| a random seed. Default is 0, that is use a random permutation but | |
| guarantee repeatability. | |
| Returns | |
| ------- | |
| groups : ndarray of int, shape (n,) | |
| Contains values from 0 to n_groups-1, where n_groups is the number | |
| of found groups. Each value ``groups[i]`` is an index of a group to | |
| which ith column assigned. The procedure was helpful only if | |
| n_groups is significantly less than n. | |
| References | |
| ---------- | |
| .. [1] A. Curtis, M. J. D. Powell, and J. Reid, "On the estimation of | |
| sparse Jacobian matrices", Journal of the Institute of Mathematics | |
| and its Applications, 13 (1974), pp. 117-120. | |
| """ | |
| if issparse(A): | |
| A = csc_matrix(A) | |
| else: | |
| A = np.atleast_2d(A) | |
| A = (A != 0).astype(np.int32) | |
| if A.ndim != 2: | |
| raise ValueError("`A` must be 2-dimensional.") | |
| m, n = A.shape | |
| if order is None or np.isscalar(order): | |
| rng = np.random.RandomState(order) | |
| order = rng.permutation(n) | |
| else: | |
| order = np.asarray(order) | |
| if order.shape != (n,): | |
| raise ValueError("`order` has incorrect shape.") | |
| A = A[:, order] | |
| if issparse(A): | |
| groups = group_sparse(m, n, A.indices, A.indptr) | |
| else: | |
| groups = group_dense(m, n, A) | |
| groups[order] = groups.copy() | |
| return groups | |
| def approx_derivative(fun, x0, method='3-point', rel_step=None, abs_step=None, | |
| f0=None, bounds=(-np.inf, np.inf), sparsity=None, | |
| as_linear_operator=False, args=(), kwargs={}): | |
| """Compute finite difference approximation of the derivatives of a | |
| vector-valued function. | |
| If a function maps from R^n to R^m, its derivatives form m-by-n matrix | |
| called the Jacobian, where an element (i, j) is a partial derivative of | |
| f[i] with respect to x[j]. | |
| Parameters | |
| ---------- | |
| fun : callable | |
| Function of which to estimate the derivatives. The argument x | |
| passed to this function is ndarray of shape (n,) (never a scalar | |
| even if n=1). It must return 1-D array_like of shape (m,) or a scalar. | |
| x0 : array_like of shape (n,) or float | |
| Point at which to estimate the derivatives. Float will be converted | |
| to a 1-D array. | |
| method : {'3-point', '2-point', 'cs'}, optional | |
| Finite difference method to use: | |
| - '2-point' - use the first order accuracy forward or backward | |
| difference. | |
| - '3-point' - use central difference in interior points and the | |
| second order accuracy forward or backward difference | |
| near the boundary. | |
| - 'cs' - use a complex-step finite difference scheme. This assumes | |
| that the user function is real-valued and can be | |
| analytically continued to the complex plane. Otherwise, | |
| produces bogus results. | |
| rel_step : None or array_like, optional | |
| Relative step size to use. If None (default) the absolute step size is | |
| computed as ``h = rel_step * sign(x0) * max(1, abs(x0))``, with | |
| `rel_step` being selected automatically, see Notes. Otherwise | |
| ``h = rel_step * sign(x0) * abs(x0)``. For ``method='3-point'`` the | |
| sign of `h` is ignored. The calculated step size is possibly adjusted | |
| to fit into the bounds. | |
| abs_step : array_like, optional | |
| Absolute step size to use, possibly adjusted to fit into the bounds. | |
| For ``method='3-point'`` the sign of `abs_step` is ignored. By default | |
| relative steps are used, only if ``abs_step is not None`` are absolute | |
| steps used. | |
| f0 : None or array_like, optional | |
| If not None it is assumed to be equal to ``fun(x0)``, in this case | |
| the ``fun(x0)`` is not called. Default is None. | |
| bounds : tuple of array_like, optional | |
| Lower and upper bounds on independent variables. Defaults to no bounds. | |
| Each bound must match the size of `x0` or be a scalar, in the latter | |
| case the bound will be the same for all variables. Use it to limit the | |
| range of function evaluation. Bounds checking is not implemented | |
| when `as_linear_operator` is True. | |
| sparsity : {None, array_like, sparse matrix, 2-tuple}, optional | |
| Defines a sparsity structure of the Jacobian matrix. If the Jacobian | |
| matrix is known to have only few non-zero elements in each row, then | |
| it's possible to estimate its several columns by a single function | |
| evaluation [3]_. To perform such economic computations two ingredients | |
| are required: | |
| * structure : array_like or sparse matrix of shape (m, n). A zero | |
| element means that a corresponding element of the Jacobian | |
| identically equals to zero. | |
| * groups : array_like of shape (n,). A column grouping for a given | |
| sparsity structure, use `group_columns` to obtain it. | |
| A single array or a sparse matrix is interpreted as a sparsity | |
| structure, and groups are computed inside the function. A tuple is | |
| interpreted as (structure, groups). If None (default), a standard | |
| dense differencing will be used. | |
| Note, that sparse differencing makes sense only for large Jacobian | |
| matrices where each row contains few non-zero elements. | |
| as_linear_operator : bool, optional | |
| When True the function returns an `scipy.sparse.linalg.LinearOperator`. | |
| Otherwise it returns a dense array or a sparse matrix depending on | |
| `sparsity`. The linear operator provides an efficient way of computing | |
| ``J.dot(p)`` for any vector ``p`` of shape (n,), but does not allow | |
| direct access to individual elements of the matrix. By default | |
| `as_linear_operator` is False. | |
| args, kwargs : tuple and dict, optional | |
| Additional arguments passed to `fun`. Both empty by default. | |
| The calling signature is ``fun(x, *args, **kwargs)``. | |
| Returns | |
| ------- | |
| J : {ndarray, sparse matrix, LinearOperator} | |
| Finite difference approximation of the Jacobian matrix. | |
| If `as_linear_operator` is True returns a LinearOperator | |
| with shape (m, n). Otherwise it returns a dense array or sparse | |
| matrix depending on how `sparsity` is defined. If `sparsity` | |
| is None then a ndarray with shape (m, n) is returned. If | |
| `sparsity` is not None returns a csr_matrix with shape (m, n). | |
| For sparse matrices and linear operators it is always returned as | |
| a 2-D structure, for ndarrays, if m=1 it is returned | |
| as a 1-D gradient array with shape (n,). | |
| See Also | |
| -------- | |
| check_derivative : Check correctness of a function computing derivatives. | |
| Notes | |
| ----- | |
| If `rel_step` is not provided, it assigned as ``EPS**(1/s)``, where EPS is | |
| determined from the smallest floating point dtype of `x0` or `fun(x0)`, | |
| ``np.finfo(x0.dtype).eps``, s=2 for '2-point' method and | |
| s=3 for '3-point' method. Such relative step approximately minimizes a sum | |
| of truncation and round-off errors, see [1]_. Relative steps are used by | |
| default. However, absolute steps are used when ``abs_step is not None``. | |
| If any of the absolute or relative steps produces an indistinguishable | |
| difference from the original `x0`, ``(x0 + dx) - x0 == 0``, then a | |
| automatic step size is substituted for that particular entry. | |
| A finite difference scheme for '3-point' method is selected automatically. | |
| The well-known central difference scheme is used for points sufficiently | |
| far from the boundary, and 3-point forward or backward scheme is used for | |
| points near the boundary. Both schemes have the second-order accuracy in | |
| terms of Taylor expansion. Refer to [2]_ for the formulas of 3-point | |
| forward and backward difference schemes. | |
| For dense differencing when m=1 Jacobian is returned with a shape (n,), | |
| on the other hand when n=1 Jacobian is returned with a shape (m, 1). | |
| Our motivation is the following: a) It handles a case of gradient | |
| computation (m=1) in a conventional way. b) It clearly separates these two | |
| different cases. b) In all cases np.atleast_2d can be called to get 2-D | |
| Jacobian with correct dimensions. | |
| References | |
| ---------- | |
| .. [1] W. H. Press et. al. "Numerical Recipes. The Art of Scientific | |
| Computing. 3rd edition", sec. 5.7. | |
| .. [2] A. Curtis, M. J. D. Powell, and J. Reid, "On the estimation of | |
| sparse Jacobian matrices", Journal of the Institute of Mathematics | |
| and its Applications, 13 (1974), pp. 117-120. | |
| .. [3] B. Fornberg, "Generation of Finite Difference Formulas on | |
| Arbitrarily Spaced Grids", Mathematics of Computation 51, 1988. | |
| Examples | |
| -------- | |
| >>> import numpy as np | |
| >>> from scipy.optimize._numdiff import approx_derivative | |
| >>> | |
| >>> def f(x, c1, c2): | |
| ... return np.array([x[0] * np.sin(c1 * x[1]), | |
| ... x[0] * np.cos(c2 * x[1])]) | |
| ... | |
| >>> x0 = np.array([1.0, 0.5 * np.pi]) | |
| >>> approx_derivative(f, x0, args=(1, 2)) | |
| array([[ 1., 0.], | |
| [-1., 0.]]) | |
| Bounds can be used to limit the region of function evaluation. | |
| In the example below we compute left and right derivative at point 1.0. | |
| >>> def g(x): | |
| ... return x**2 if x >= 1 else x | |
| ... | |
| >>> x0 = 1.0 | |
| >>> approx_derivative(g, x0, bounds=(-np.inf, 1.0)) | |
| array([ 1.]) | |
| >>> approx_derivative(g, x0, bounds=(1.0, np.inf)) | |
| array([ 2.]) | |
| """ | |
| if method not in ['2-point', '3-point', 'cs']: | |
| raise ValueError("Unknown method '%s'. " % method) | |
| xp = array_namespace(x0) | |
| _x = atleast_nd(x0, ndim=1, xp=xp) | |
| _dtype = xp.float64 | |
| if xp.isdtype(_x.dtype, "real floating"): | |
| _dtype = _x.dtype | |
| # promotes to floating | |
| x0 = xp.astype(_x, _dtype) | |
| if x0.ndim > 1: | |
| raise ValueError("`x0` must have at most 1 dimension.") | |
| lb, ub = _prepare_bounds(bounds, x0) | |
| if lb.shape != x0.shape or ub.shape != x0.shape: | |
| raise ValueError("Inconsistent shapes between bounds and `x0`.") | |
| if as_linear_operator and not (np.all(np.isinf(lb)) | |
| and np.all(np.isinf(ub))): | |
| raise ValueError("Bounds not supported when " | |
| "`as_linear_operator` is True.") | |
| def fun_wrapped(x): | |
| # send user function same fp type as x0. (but only if cs is not being | |
| # used | |
| if xp.isdtype(x.dtype, "real floating"): | |
| x = xp.astype(x, x0.dtype) | |
| f = np.atleast_1d(fun(x, *args, **kwargs)) | |
| if f.ndim > 1: | |
| raise RuntimeError("`fun` return value has " | |
| "more than 1 dimension.") | |
| return f | |
| if f0 is None: | |
| f0 = fun_wrapped(x0) | |
| else: | |
| f0 = np.atleast_1d(f0) | |
| if f0.ndim > 1: | |
| raise ValueError("`f0` passed has more than 1 dimension.") | |
| if np.any((x0 < lb) | (x0 > ub)): | |
| raise ValueError("`x0` violates bound constraints.") | |
| if as_linear_operator: | |
| if rel_step is None: | |
| rel_step = _eps_for_method(x0.dtype, f0.dtype, method) | |
| return _linear_operator_difference(fun_wrapped, x0, | |
| f0, rel_step, method) | |
| else: | |
| # by default we use rel_step | |
| if abs_step is None: | |
| h = _compute_absolute_step(rel_step, x0, f0, method) | |
| else: | |
| # user specifies an absolute step | |
| sign_x0 = (x0 >= 0).astype(float) * 2 - 1 | |
| h = abs_step | |
| # cannot have a zero step. This might happen if x0 is very large | |
| # or small. In which case fall back to relative step. | |
| dx = ((x0 + h) - x0) | |
| h = np.where(dx == 0, | |
| _eps_for_method(x0.dtype, f0.dtype, method) * | |
| sign_x0 * np.maximum(1.0, np.abs(x0)), | |
| h) | |
| if method == '2-point': | |
| h, use_one_sided = _adjust_scheme_to_bounds( | |
| x0, h, 1, '1-sided', lb, ub) | |
| elif method == '3-point': | |
| h, use_one_sided = _adjust_scheme_to_bounds( | |
| x0, h, 1, '2-sided', lb, ub) | |
| elif method == 'cs': | |
| use_one_sided = False | |
| if sparsity is None: | |
| return _dense_difference(fun_wrapped, x0, f0, h, | |
| use_one_sided, method) | |
| else: | |
| if not issparse(sparsity) and len(sparsity) == 2: | |
| structure, groups = sparsity | |
| else: | |
| structure = sparsity | |
| groups = group_columns(sparsity) | |
| if issparse(structure): | |
| structure = csc_matrix(structure) | |
| else: | |
| structure = np.atleast_2d(structure) | |
| groups = np.atleast_1d(groups) | |
| return _sparse_difference(fun_wrapped, x0, f0, h, | |
| use_one_sided, structure, | |
| groups, method) | |
| def _linear_operator_difference(fun, x0, f0, h, method): | |
| m = f0.size | |
| n = x0.size | |
| if method == '2-point': | |
| def matvec(p): | |
| if np.array_equal(p, np.zeros_like(p)): | |
| return np.zeros(m) | |
| dx = h / norm(p) | |
| x = x0 + dx*p | |
| df = fun(x) - f0 | |
| return df / dx | |
| elif method == '3-point': | |
| def matvec(p): | |
| if np.array_equal(p, np.zeros_like(p)): | |
| return np.zeros(m) | |
| dx = 2*h / norm(p) | |
| x1 = x0 - (dx/2)*p | |
| x2 = x0 + (dx/2)*p | |
| f1 = fun(x1) | |
| f2 = fun(x2) | |
| df = f2 - f1 | |
| return df / dx | |
| elif method == 'cs': | |
| def matvec(p): | |
| if np.array_equal(p, np.zeros_like(p)): | |
| return np.zeros(m) | |
| dx = h / norm(p) | |
| x = x0 + dx*p*1.j | |
| f1 = fun(x) | |
| df = f1.imag | |
| return df / dx | |
| else: | |
| raise RuntimeError("Never be here.") | |
| return LinearOperator((m, n), matvec) | |
| def _dense_difference(fun, x0, f0, h, use_one_sided, method): | |
| m = f0.size | |
| n = x0.size | |
| J_transposed = np.empty((n, m)) | |
| h_vecs = np.diag(h) | |
| for i in range(h.size): | |
| if method == '2-point': | |
| x = x0 + h_vecs[i] | |
| dx = x[i] - x0[i] # Recompute dx as exactly representable number. | |
| df = fun(x) - f0 | |
| elif method == '3-point' and use_one_sided[i]: | |
| x1 = x0 + h_vecs[i] | |
| x2 = x0 + 2 * h_vecs[i] | |
| dx = x2[i] - x0[i] | |
| f1 = fun(x1) | |
| f2 = fun(x2) | |
| df = -3.0 * f0 + 4 * f1 - f2 | |
| elif method == '3-point' and not use_one_sided[i]: | |
| x1 = x0 - h_vecs[i] | |
| x2 = x0 + h_vecs[i] | |
| dx = x2[i] - x1[i] | |
| f1 = fun(x1) | |
| f2 = fun(x2) | |
| df = f2 - f1 | |
| elif method == 'cs': | |
| f1 = fun(x0 + h_vecs[i]*1.j) | |
| df = f1.imag | |
| dx = h_vecs[i, i] | |
| else: | |
| raise RuntimeError("Never be here.") | |
| J_transposed[i] = df / dx | |
| if m == 1: | |
| J_transposed = np.ravel(J_transposed) | |
| return J_transposed.T | |
| def _sparse_difference(fun, x0, f0, h, use_one_sided, | |
| structure, groups, method): | |
| m = f0.size | |
| n = x0.size | |
| row_indices = [] | |
| col_indices = [] | |
| fractions = [] | |
| n_groups = np.max(groups) + 1 | |
| for group in range(n_groups): | |
| # Perturb variables which are in the same group simultaneously. | |
| e = np.equal(group, groups) | |
| h_vec = h * e | |
| if method == '2-point': | |
| x = x0 + h_vec | |
| dx = x - x0 | |
| df = fun(x) - f0 | |
| # The result is written to columns which correspond to perturbed | |
| # variables. | |
| cols, = np.nonzero(e) | |
| # Find all non-zero elements in selected columns of Jacobian. | |
| i, j, _ = find(structure[:, cols]) | |
| # Restore column indices in the full array. | |
| j = cols[j] | |
| elif method == '3-point': | |
| # Here we do conceptually the same but separate one-sided | |
| # and two-sided schemes. | |
| x1 = x0.copy() | |
| x2 = x0.copy() | |
| mask_1 = use_one_sided & e | |
| x1[mask_1] += h_vec[mask_1] | |
| x2[mask_1] += 2 * h_vec[mask_1] | |
| mask_2 = ~use_one_sided & e | |
| x1[mask_2] -= h_vec[mask_2] | |
| x2[mask_2] += h_vec[mask_2] | |
| dx = np.zeros(n) | |
| dx[mask_1] = x2[mask_1] - x0[mask_1] | |
| dx[mask_2] = x2[mask_2] - x1[mask_2] | |
| f1 = fun(x1) | |
| f2 = fun(x2) | |
| cols, = np.nonzero(e) | |
| i, j, _ = find(structure[:, cols]) | |
| j = cols[j] | |
| mask = use_one_sided[j] | |
| df = np.empty(m) | |
| rows = i[mask] | |
| df[rows] = -3 * f0[rows] + 4 * f1[rows] - f2[rows] | |
| rows = i[~mask] | |
| df[rows] = f2[rows] - f1[rows] | |
| elif method == 'cs': | |
| f1 = fun(x0 + h_vec*1.j) | |
| df = f1.imag | |
| dx = h_vec | |
| cols, = np.nonzero(e) | |
| i, j, _ = find(structure[:, cols]) | |
| j = cols[j] | |
| else: | |
| raise ValueError("Never be here.") | |
| # All that's left is to compute the fraction. We store i, j and | |
| # fractions as separate arrays and later construct coo_matrix. | |
| row_indices.append(i) | |
| col_indices.append(j) | |
| fractions.append(df[i] / dx[j]) | |
| row_indices = np.hstack(row_indices) | |
| col_indices = np.hstack(col_indices) | |
| fractions = np.hstack(fractions) | |
| J = coo_matrix((fractions, (row_indices, col_indices)), shape=(m, n)) | |
| return csr_matrix(J) | |
| def check_derivative(fun, jac, x0, bounds=(-np.inf, np.inf), args=(), | |
| kwargs={}): | |
| """Check correctness of a function computing derivatives (Jacobian or | |
| gradient) by comparison with a finite difference approximation. | |
| Parameters | |
| ---------- | |
| fun : callable | |
| Function of which to estimate the derivatives. The argument x | |
| passed to this function is ndarray of shape (n,) (never a scalar | |
| even if n=1). It must return 1-D array_like of shape (m,) or a scalar. | |
| jac : callable | |
| Function which computes Jacobian matrix of `fun`. It must work with | |
| argument x the same way as `fun`. The return value must be array_like | |
| or sparse matrix with an appropriate shape. | |
| x0 : array_like of shape (n,) or float | |
| Point at which to estimate the derivatives. Float will be converted | |
| to 1-D array. | |
| bounds : 2-tuple of array_like, optional | |
| Lower and upper bounds on independent variables. Defaults to no bounds. | |
| Each bound must match the size of `x0` or be a scalar, in the latter | |
| case the bound will be the same for all variables. Use it to limit the | |
| range of function evaluation. | |
| args, kwargs : tuple and dict, optional | |
| Additional arguments passed to `fun` and `jac`. Both empty by default. | |
| The calling signature is ``fun(x, *args, **kwargs)`` and the same | |
| for `jac`. | |
| Returns | |
| ------- | |
| accuracy : float | |
| The maximum among all relative errors for elements with absolute values | |
| higher than 1 and absolute errors for elements with absolute values | |
| less or equal than 1. If `accuracy` is on the order of 1e-6 or lower, | |
| then it is likely that your `jac` implementation is correct. | |
| See Also | |
| -------- | |
| approx_derivative : Compute finite difference approximation of derivative. | |
| Examples | |
| -------- | |
| >>> import numpy as np | |
| >>> from scipy.optimize._numdiff import check_derivative | |
| >>> | |
| >>> | |
| >>> def f(x, c1, c2): | |
| ... return np.array([x[0] * np.sin(c1 * x[1]), | |
| ... x[0] * np.cos(c2 * x[1])]) | |
| ... | |
| >>> def jac(x, c1, c2): | |
| ... return np.array([ | |
| ... [np.sin(c1 * x[1]), c1 * x[0] * np.cos(c1 * x[1])], | |
| ... [np.cos(c2 * x[1]), -c2 * x[0] * np.sin(c2 * x[1])] | |
| ... ]) | |
| ... | |
| >>> | |
| >>> x0 = np.array([1.0, 0.5 * np.pi]) | |
| >>> check_derivative(f, jac, x0, args=(1, 2)) | |
| 2.4492935982947064e-16 | |
| """ | |
| J_to_test = jac(x0, *args, **kwargs) | |
| if issparse(J_to_test): | |
| J_diff = approx_derivative(fun, x0, bounds=bounds, sparsity=J_to_test, | |
| args=args, kwargs=kwargs) | |
| J_to_test = csr_matrix(J_to_test) | |
| abs_err = J_to_test - J_diff | |
| i, j, abs_err_data = find(abs_err) | |
| J_diff_data = np.asarray(J_diff[i, j]).ravel() | |
| return np.max(np.abs(abs_err_data) / | |
| np.maximum(1, np.abs(J_diff_data))) | |
| else: | |
| J_diff = approx_derivative(fun, x0, bounds=bounds, | |
| args=args, kwargs=kwargs) | |
| abs_err = np.abs(J_to_test - J_diff) | |
| return np.max(abs_err / np.maximum(1, np.abs(J_diff))) | |