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# mypy: disable-error-code="attr-defined"
import warnings
import numpy as np
import scipy._lib._elementwise_iterative_method as eim
from scipy._lib._util import _RichResult
from scipy._lib._array_api import array_namespace, xp_sign, xp_copy, xp_take_along_axis
_EERRORINCREASE = -1 # used in derivative
def _derivative_iv(f, x, args, tolerances, maxiter, order, initial_step,
step_factor, step_direction, preserve_shape, callback):
# Input validation for `derivative`
xp = array_namespace(x)
if not callable(f):
raise ValueError('`f` must be callable.')
if not np.iterable(args):
args = (args,)
tolerances = {} if tolerances is None else tolerances
atol = tolerances.get('atol', None)
rtol = tolerances.get('rtol', None)
# tolerances are floats, not arrays; OK to use NumPy
message = 'Tolerances and step parameters must be non-negative scalars.'
tols = np.asarray([atol if atol is not None else 1,
rtol if rtol is not None else 1,
step_factor])
if (not np.issubdtype(tols.dtype, np.number) or np.any(tols < 0)
or np.any(np.isnan(tols)) or tols.shape != (3,)):
raise ValueError(message)
step_factor = float(tols[2])
maxiter_int = int(maxiter)
if maxiter != maxiter_int or maxiter <= 0:
raise ValueError('`maxiter` must be a positive integer.')
order_int = int(order)
if order_int != order or order <= 0:
raise ValueError('`order` must be a positive integer.')
step_direction = xp.asarray(step_direction)
initial_step = xp.asarray(initial_step)
temp = xp.broadcast_arrays(x, step_direction, initial_step)
x, step_direction, initial_step = temp
message = '`preserve_shape` must be True or False.'
if preserve_shape not in {True, False}:
raise ValueError(message)
if callback is not None and not callable(callback):
raise ValueError('`callback` must be callable.')
return (f, x, args, atol, rtol, maxiter_int, order_int, initial_step,
step_factor, step_direction, preserve_shape, callback)
def derivative(f, x, *, args=(), tolerances=None, maxiter=10,
order=8, initial_step=0.5, step_factor=2.0,
step_direction=0, preserve_shape=False, callback=None):
"""Evaluate the derivative of a elementwise, real scalar function numerically.
For each element of the output of `f`, `derivative` approximates the first
derivative of `f` at the corresponding element of `x` using finite difference
differentiation.
This function works elementwise when `x`, `step_direction`, and `args` contain
(broadcastable) arrays.
Parameters
----------
f : callable
The function whose derivative is desired. The signature must be::
f(xi: ndarray, *argsi) -> ndarray
where each element of ``xi`` is a finite real number and ``argsi`` is a tuple,
which may contain an arbitrary number of arrays that are broadcastable with
``xi``. `f` must be an elementwise function: each scalar element ``f(xi)[j]``
must equal ``f(xi[j])`` for valid indices ``j``. It must not mutate the array
``xi`` or the arrays in ``argsi``.
x : float array_like
Abscissae at which to evaluate the derivative. Must be broadcastable with
`args` and `step_direction`.
args : tuple of array_like, optional
Additional positional array arguments to be passed to `f`. Arrays
must be broadcastable with one another and the arrays of `init`.
If the callable for which the root is desired requires arguments that are
not broadcastable with `x`, wrap that callable with `f` such that `f`
accepts only `x` and broadcastable ``*args``.
tolerances : dictionary of floats, optional
Absolute and relative tolerances. Valid keys of the dictionary are:
- ``atol`` - absolute tolerance on the derivative
- ``rtol`` - relative tolerance on the derivative
Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
`atol` is the smallest normal number of the appropriate dtype, and
the default `rtol` is the square root of the precision of the
appropriate dtype.
order : int, default: 8
The (positive integer) order of the finite difference formula to be
used. Odd integers will be rounded up to the next even integer.
initial_step : float array_like, default: 0.5
The (absolute) initial step size for the finite difference derivative
approximation.
step_factor : float, default: 2.0
The factor by which the step size is *reduced* in each iteration; i.e.
the step size in iteration 1 is ``initial_step/step_factor``. If
``step_factor < 1``, subsequent steps will be greater than the initial
step; this may be useful if steps smaller than some threshold are
undesirable (e.g. due to subtractive cancellation error).
maxiter : int, default: 10
The maximum number of iterations of the algorithm to perform. See
Notes.
step_direction : integer array_like
An array representing the direction of the finite difference steps (for
use when `x` lies near to the boundary of the domain of the function.)
Must be broadcastable with `x` and all `args`.
Where 0 (default), central differences are used; where negative (e.g.
-1), steps are non-positive; and where positive (e.g. 1), all steps are
non-negative.
preserve_shape : bool, default: False
In the following, "arguments of `f`" refers to the array ``xi`` and
any arrays within ``argsi``. Let ``shape`` be the broadcasted shape
of `x` and all elements of `args` (which is conceptually
distinct from ``xi` and ``argsi`` passed into `f`).
- When ``preserve_shape=False`` (default), `f` must accept arguments
of *any* broadcastable shapes.
- When ``preserve_shape=True``, `f` must accept arguments of shape
``shape`` *or* ``shape + (n,)``, where ``(n,)`` is the number of
abscissae at which the function is being evaluated.
In either case, for each scalar element ``xi[j]`` within ``xi``, the array
returned by `f` must include the scalar ``f(xi[j])`` at the same index.
Consequently, the shape of the output is always the shape of the input
``xi``.
See Examples.
callback : callable, optional
An optional user-supplied function to be called before the first
iteration and after each iteration.
Called as ``callback(res)``, where ``res`` is a ``_RichResult``
similar to that returned by `derivative` (but containing the current
iterate's values of all variables). If `callback` raises a
``StopIteration``, the algorithm will terminate immediately and
`derivative` will return a result. `callback` must not mutate
`res` or its attributes.
Returns
-------
res : _RichResult
An object similar to an instance of `scipy.optimize.OptimizeResult` with the
following attributes. The descriptions are written as though the values will
be scalars; however, if `f` returns an array, the outputs will be
arrays of the same shape.
success : bool array
``True`` where the algorithm terminated successfully (status ``0``);
``False`` otherwise.
status : int array
An integer representing the exit status of the algorithm.
- ``0`` : The algorithm converged to the specified tolerances.
- ``-1`` : The error estimate increased, so iteration was terminated.
- ``-2`` : The maximum number of iterations was reached.
- ``-3`` : A non-finite value was encountered.
- ``-4`` : Iteration was terminated by `callback`.
- ``1`` : The algorithm is proceeding normally (in `callback` only).
df : float array
The derivative of `f` at `x`, if the algorithm terminated
successfully.
error : float array
An estimate of the error: the magnitude of the difference between
the current estimate of the derivative and the estimate in the
previous iteration.
nit : int array
The number of iterations of the algorithm that were performed.
nfev : int array
The number of points at which `f` was evaluated.
x : float array
The value at which the derivative of `f` was evaluated
(after broadcasting with `args` and `step_direction`).
See Also
--------
jacobian, hessian
Notes
-----
The implementation was inspired by jacobi [1]_, numdifftools [2]_, and
DERIVEST [3]_, but the implementation follows the theory of Taylor series
more straightforwardly (and arguably naively so).
In the first iteration, the derivative is estimated using a finite
difference formula of order `order` with maximum step size `initial_step`.
Each subsequent iteration, the maximum step size is reduced by
`step_factor`, and the derivative is estimated again until a termination
condition is reached. The error estimate is the magnitude of the difference
between the current derivative approximation and that of the previous
iteration.
The stencils of the finite difference formulae are designed such that
abscissae are "nested": after `f` is evaluated at ``order + 1``
points in the first iteration, `f` is evaluated at only two new points
in each subsequent iteration; ``order - 1`` previously evaluated function
values required by the finite difference formula are reused, and two
function values (evaluations at the points furthest from `x`) are unused.
Step sizes are absolute. When the step size is small relative to the
magnitude of `x`, precision is lost; for example, if `x` is ``1e20``, the
default initial step size of ``0.5`` cannot be resolved. Accordingly,
consider using larger initial step sizes for large magnitudes of `x`.
The default tolerances are challenging to satisfy at points where the
true derivative is exactly zero. If the derivative may be exactly zero,
consider specifying an absolute tolerance (e.g. ``atol=1e-12``) to
improve convergence.
References
----------
.. [1] Hans Dembinski (@HDembinski). jacobi.
https://github.com/HDembinski/jacobi
.. [2] Per A. Brodtkorb and John D'Errico. numdifftools.
https://numdifftools.readthedocs.io/en/latest/
.. [3] John D'Errico. DERIVEST: Adaptive Robust Numerical Differentiation.
https://www.mathworks.com/matlabcentral/fileexchange/13490-adaptive-robust-numerical-differentiation
.. [4] Numerical Differentition. Wikipedia.
https://en.wikipedia.org/wiki/Numerical_differentiation
Examples
--------
Evaluate the derivative of ``np.exp`` at several points ``x``.
>>> import numpy as np
>>> from scipy.differentiate import derivative
>>> f = np.exp
>>> df = np.exp # true derivative
>>> x = np.linspace(1, 2, 5)
>>> res = derivative(f, x)
>>> res.df # approximation of the derivative
array([2.71828183, 3.49034296, 4.48168907, 5.75460268, 7.3890561 ])
>>> res.error # estimate of the error
array([7.13740178e-12, 9.16600129e-12, 1.17594823e-11, 1.51061386e-11,
1.94262384e-11])
>>> abs(res.df - df(x)) # true error
array([2.53130850e-14, 3.55271368e-14, 5.77315973e-14, 5.59552404e-14,
6.92779167e-14])
Show the convergence of the approximation as the step size is reduced.
Each iteration, the step size is reduced by `step_factor`, so for
sufficiently small initial step, each iteration reduces the error by a
factor of ``1/step_factor**order`` until finite precision arithmetic
inhibits further improvement.
>>> import matplotlib.pyplot as plt
>>> iter = list(range(1, 12)) # maximum iterations
>>> hfac = 2 # step size reduction per iteration
>>> hdir = [-1, 0, 1] # compare left-, central-, and right- steps
>>> order = 4 # order of differentiation formula
>>> x = 1
>>> ref = df(x)
>>> errors = [] # true error
>>> for i in iter:
... res = derivative(f, x, maxiter=i, step_factor=hfac,
... step_direction=hdir, order=order,
... # prevent early termination
... tolerances=dict(atol=0, rtol=0))
... errors.append(abs(res.df - ref))
>>> errors = np.array(errors)
>>> plt.semilogy(iter, errors[:, 0], label='left differences')
>>> plt.semilogy(iter, errors[:, 1], label='central differences')
>>> plt.semilogy(iter, errors[:, 2], label='right differences')
>>> plt.xlabel('iteration')
>>> plt.ylabel('error')
>>> plt.legend()
>>> plt.show()
>>> (errors[1, 1] / errors[0, 1], 1 / hfac**order)
(0.06215223140159822, 0.0625)
The implementation is vectorized over `x`, `step_direction`, and `args`.
The function is evaluated once before the first iteration to perform input
validation and standardization, and once per iteration thereafter.
>>> def f(x, p):
... f.nit += 1
... return x**p
>>> f.nit = 0
>>> def df(x, p):
... return p*x**(p-1)
>>> x = np.arange(1, 5)
>>> p = np.arange(1, 6).reshape((-1, 1))
>>> hdir = np.arange(-1, 2).reshape((-1, 1, 1))
>>> res = derivative(f, x, args=(p,), step_direction=hdir, maxiter=1)
>>> np.allclose(res.df, df(x, p))
True
>>> res.df.shape
(3, 5, 4)
>>> f.nit
2
By default, `preserve_shape` is False, and therefore the callable
`f` may be called with arrays of any broadcastable shapes.
For example:
>>> shapes = []
>>> def f(x, c):
... shape = np.broadcast_shapes(x.shape, c.shape)
... shapes.append(shape)
... return np.sin(c*x)
>>>
>>> c = [1, 5, 10, 20]
>>> res = derivative(f, 0, args=(c,))
>>> shapes
[(4,), (4, 8), (4, 2), (3, 2), (2, 2), (1, 2)]
To understand where these shapes are coming from - and to better
understand how `derivative` computes accurate results - note that
higher values of ``c`` correspond with higher frequency sinusoids.
The higher frequency sinusoids make the function's derivative change
faster, so more function evaluations are required to achieve the target
accuracy:
>>> res.nfev
array([11, 13, 15, 17], dtype=int32)
The initial ``shape``, ``(4,)``, corresponds with evaluating the
function at a single abscissa and all four frequencies; this is used
for input validation and to determine the size and dtype of the arrays
that store results. The next shape corresponds with evaluating the
function at an initial grid of abscissae and all four frequencies.
Successive calls to the function evaluate the function at two more
abscissae, increasing the effective order of the approximation by two.
However, in later function evaluations, the function is evaluated at
fewer frequencies because the corresponding derivative has already
converged to the required tolerance. This saves function evaluations to
improve performance, but it requires the function to accept arguments of
any shape.
"Vector-valued" functions are unlikely to satisfy this requirement.
For example, consider
>>> def f(x):
... return [x, np.sin(3*x), x+np.sin(10*x), np.sin(20*x)*(x-1)**2]
This integrand is not compatible with `derivative` as written; for instance,
the shape of the output will not be the same as the shape of ``x``. Such a
function *could* be converted to a compatible form with the introduction of
additional parameters, but this would be inconvenient. In such cases,
a simpler solution would be to use `preserve_shape`.
>>> shapes = []
>>> def f(x):
... shapes.append(x.shape)
... x0, x1, x2, x3 = x
... return [x0, np.sin(3*x1), x2+np.sin(10*x2), np.sin(20*x3)*(x3-1)**2]
>>>
>>> x = np.zeros(4)
>>> res = derivative(f, x, preserve_shape=True)
>>> shapes
[(4,), (4, 8), (4, 2), (4, 2), (4, 2), (4, 2)]
Here, the shape of ``x`` is ``(4,)``. With ``preserve_shape=True``, the
function may be called with argument ``x`` of shape ``(4,)`` or ``(4, n)``,
and this is what we observe.
"""
# TODO (followup):
# - investigate behavior at saddle points
# - multivariate functions?
# - relative steps?
# - show example of `np.vectorize`
res = _derivative_iv(f, x, args, tolerances, maxiter, order, initial_step,
step_factor, step_direction, preserve_shape, callback)
(func, x, args, atol, rtol, maxiter, order,
h0, fac, hdir, preserve_shape, callback) = res
# Initialization
# Since f(x) (no step) is not needed for central differences, it may be
# possible to eliminate this function evaluation. However, it's useful for
# input validation and standardization, and everything else is designed to
# reduce function calls, so let's keep it simple.
temp = eim._initialize(func, (x,), args, preserve_shape=preserve_shape)
func, xs, fs, args, shape, dtype, xp = temp
finfo = xp.finfo(dtype)
atol = finfo.smallest_normal if atol is None else atol
rtol = finfo.eps**0.5 if rtol is None else rtol # keep same as `hessian`
x, f = xs[0], fs[0]
df = xp.full_like(f, xp.nan)
# Ideally we'd broadcast the shape of `hdir` in `_elementwise_algo_init`, but
# it's simpler to do it here than to generalize `_elementwise_algo_init` further.
# `hdir` and `x` are already broadcasted in `_derivative_iv`, so we know
# that `hdir` can be broadcasted to the final shape. Same with `h0`.
hdir = xp.broadcast_to(hdir, shape)
hdir = xp.reshape(hdir, (-1,))
hdir = xp.astype(xp_sign(hdir), dtype)
h0 = xp.broadcast_to(h0, shape)
h0 = xp.reshape(h0, (-1,))
h0 = xp.astype(h0, dtype)
h0[h0 <= 0] = xp.asarray(xp.nan, dtype=dtype)
status = xp.full_like(x, eim._EINPROGRESS, dtype=xp.int32) # in progress
nit, nfev = 0, 1 # one function evaluations performed above
# Boolean indices of left, central, right, and (all) one-sided steps
il = hdir < 0
ic = hdir == 0
ir = hdir > 0
io = il | ir
# Most of these attributes are reasonably obvious, but:
# - `fs` holds all the function values of all active `x`. The zeroth
# axis corresponds with active points `x`, the first axis corresponds
# with the different steps (in the order described in
# `_derivative_weights`).
# - `terms` (which could probably use a better name) is half the `order`,
# which is always even.
work = _RichResult(x=x, df=df, fs=f[:, xp.newaxis], error=xp.nan, h=h0,
df_last=xp.nan, error_last=xp.nan, fac=fac,
atol=atol, rtol=rtol, nit=nit, nfev=nfev,
status=status, dtype=dtype, terms=(order+1)//2,
hdir=hdir, il=il, ic=ic, ir=ir, io=io,
# Store the weights in an object so they can't get compressed
# Using RichResult to allow dot notation, but a dict would work
diff_state=_RichResult(central=[], right=[], fac=None))
# This is the correspondence between terms in the `work` object and the
# final result. In this case, the mapping is trivial. Note that `success`
# is prepended automatically.
res_work_pairs = [('status', 'status'), ('df', 'df'), ('error', 'error'),
('nit', 'nit'), ('nfev', 'nfev'), ('x', 'x')]
def pre_func_eval(work):
"""Determine the abscissae at which the function needs to be evaluated.
See `_derivative_weights` for a description of the stencil (pattern
of the abscissae).
In the first iteration, there is only one stored function value in
`work.fs`, `f(x)`, so we need to evaluate at `order` new points. In
subsequent iterations, we evaluate at two new points. Note that
`work.x` is always flattened into a 1D array after broadcasting with
all `args`, so we add a new axis at the end and evaluate all point
in one call to the function.
For improvement:
- Consider measuring the step size actually taken, since ``(x + h) - x``
is not identically equal to `h` with floating point arithmetic.
- Adjust the step size automatically if `x` is too big to resolve the
step.
- We could probably save some work if there are no central difference
steps or no one-sided steps.
"""
n = work.terms # half the order
h = work.h[:, xp.newaxis] # step size
c = work.fac # step reduction factor
d = c**0.5 # square root of step reduction factor (one-sided stencil)
# Note - no need to be careful about dtypes until we allocate `x_eval`
if work.nit == 0:
hc = h / c**xp.arange(n, dtype=work.dtype)
hc = xp.concat((-xp.flip(hc, axis=-1), hc), axis=-1)
else:
hc = xp.concat((-h, h), axis=-1) / c**(n-1)
if work.nit == 0:
hr = h / d**xp.arange(2*n, dtype=work.dtype)
else:
hr = xp.concat((h, h/d), axis=-1) / c**(n-1)
n_new = 2*n if work.nit == 0 else 2 # number of new abscissae
x_eval = xp.zeros((work.hdir.shape[0], n_new), dtype=work.dtype)
il, ic, ir = work.il, work.ic, work.ir
x_eval[ir] = work.x[ir][:, xp.newaxis] + hr[ir]
x_eval[ic] = work.x[ic][:, xp.newaxis] + hc[ic]
x_eval[il] = work.x[il][:, xp.newaxis] - hr[il]
return x_eval
def post_func_eval(x, f, work):
""" Estimate the derivative and error from the function evaluations
As in `pre_func_eval`: in the first iteration, there is only one stored
function value in `work.fs`, `f(x)`, so we need to add the `order` new
points. In subsequent iterations, we add two new points. The tricky
part is getting the order to match that of the weights, which is
described in `_derivative_weights`.
For improvement:
- Change the order of the weights (and steps in `pre_func_eval`) to
simplify `work_fc` concatenation and eliminate `fc` concatenation.
- It would be simple to do one-step Richardson extrapolation with `df`
and `df_last` to increase the order of the estimate and/or improve
the error estimate.
- Process the function evaluations in a more numerically favorable
way. For instance, combining the pairs of central difference evals
into a second-order approximation and using Richardson extrapolation
to produce a higher order approximation seemed to retain accuracy up
to very high order.
- Alternatively, we could use `polyfit` like Jacobi. An advantage of
fitting polynomial to more points than necessary is improved noise
tolerance.
"""
n = work.terms
n_new = n if work.nit == 0 else 1
il, ic, io = work.il, work.ic, work.io
# Central difference
# `work_fc` is *all* the points at which the function has been evaluated
# `fc` is the points we're using *this iteration* to produce the estimate
work_fc = (f[ic][:, :n_new], work.fs[ic], f[ic][:, -n_new:])
work_fc = xp.concat(work_fc, axis=-1)
if work.nit == 0:
fc = work_fc
else:
fc = (work_fc[:, :n], work_fc[:, n:n+1], work_fc[:, -n:])
fc = xp.concat(fc, axis=-1)
# One-sided difference
work_fo = xp.concat((work.fs[io], f[io]), axis=-1)
if work.nit == 0:
fo = work_fo
else:
fo = xp.concat((work_fo[:, 0:1], work_fo[:, -2*n:]), axis=-1)
work.fs = xp.zeros((ic.shape[0], work.fs.shape[-1] + 2*n_new), dtype=work.dtype)
work.fs[ic] = work_fc
work.fs[io] = work_fo
wc, wo = _derivative_weights(work, n, xp)
work.df_last = xp.asarray(work.df, copy=True)
work.df[ic] = fc @ wc / work.h[ic]
work.df[io] = fo @ wo / work.h[io]
work.df[il] *= -1
work.h /= work.fac
work.error_last = work.error
# Simple error estimate - the difference in derivative estimates between
# this iteration and the last. This is typically conservative because if
# convergence has begin, the true error is much closer to the difference
# between the current estimate and the *next* error estimate. However,
# we could use Richarson extrapolation to produce an error estimate that
# is one order higher, and take the difference between that and
# `work.df` (which would just be constant factor that depends on `fac`.)
work.error = xp.abs(work.df - work.df_last)
def check_termination(work):
"""Terminate due to convergence, non-finite values, or error increase"""
stop = xp.astype(xp.zeros_like(work.df), xp.bool)
i = work.error < work.atol + work.rtol*abs(work.df)
work.status[i] = eim._ECONVERGED
stop[i] = True
if work.nit > 0:
i = ~((xp.isfinite(work.x) & xp.isfinite(work.df)) | stop)
work.df[i], work.status[i] = xp.nan, eim._EVALUEERR
stop[i] = True
# With infinite precision, there is a step size below which
# all smaller step sizes will reduce the error. But in floating point
# arithmetic, catastrophic cancellation will begin to cause the error
# to increase again. This heuristic tries to avoid step sizes that are
# too small. There may be more theoretically sound approaches for
# detecting a step size that minimizes the total error, but this
# heuristic seems simple and effective.
i = (work.error > work.error_last*10) & ~stop
work.status[i] = _EERRORINCREASE
stop[i] = True
return stop
def post_termination_check(work):
return
def customize_result(res, shape):
return shape
return eim._loop(work, callback, shape, maxiter, func, args, dtype,
pre_func_eval, post_func_eval, check_termination,
post_termination_check, customize_result, res_work_pairs,
xp, preserve_shape)
def _derivative_weights(work, n, xp):
# This produces the weights of the finite difference formula for a given
# stencil. In experiments, use of a second-order central difference formula
# with Richardson extrapolation was more accurate numerically, but it was
# more complicated, and it would have become even more complicated when
# adding support for one-sided differences. However, now that all the
# function evaluation values are stored, they can be processed in whatever
# way is desired to produce the derivative estimate. We leave alternative
# approaches to future work. To be more self-contained, here is the theory
# for deriving the weights below.
#
# Recall that the Taylor expansion of a univariate, scalar-values function
# about a point `x` may be expressed as:
# f(x + h) = f(x) + f'(x)*h + f''(x)/2!*h**2 + O(h**3)
# Suppose we evaluate f(x), f(x+h), and f(x-h). We have:
# f(x) = f(x)
# f(x + h) = f(x) + f'(x)*h + f''(x)/2!*h**2 + O(h**3)
# f(x - h) = f(x) - f'(x)*h + f''(x)/2!*h**2 + O(h**3)
# We can solve for weights `wi` such that:
# w1*f(x) = w1*(f(x))
# + w2*f(x + h) = w2*(f(x) + f'(x)*h + f''(x)/2!*h**2) + O(h**3)
# + w3*f(x - h) = w3*(f(x) - f'(x)*h + f''(x)/2!*h**2) + O(h**3)
# = 0 + f'(x)*h + 0 + O(h**3)
# Then
# f'(x) ~ (w1*f(x) + w2*f(x+h) + w3*f(x-h))/h
# is a finite difference derivative approximation with error O(h**2),
# and so it is said to be a "second-order" approximation. Under certain
# conditions (e.g. well-behaved function, `h` sufficiently small), the
# error in the approximation will decrease with h**2; that is, if `h` is
# reduced by a factor of 2, the error is reduced by a factor of 4.
#
# By default, we use eighth-order formulae. Our central-difference formula
# uses abscissae:
# x-h/c**3, x-h/c**2, x-h/c, x-h, x, x+h, x+h/c, x+h/c**2, x+h/c**3
# where `c` is the step factor. (Typically, the step factor is greater than
# one, so the outermost points - as written above - are actually closest to
# `x`.) This "stencil" is chosen so that each iteration, the step can be
# reduced by the factor `c`, and most of the function evaluations can be
# reused with the new step size. For example, in the next iteration, we
# will have:
# x-h/c**4, x-h/c**3, x-h/c**2, x-h/c, x, x+h/c, x+h/c**2, x+h/c**3, x+h/c**4
# We do not reuse `x-h` and `x+h` for the new derivative estimate.
# While this would increase the order of the formula and thus the
# theoretical convergence rate, it is also less stable numerically.
# (As noted above, there are other ways of processing the values that are
# more stable. Thus, even now we store `f(x-h)` and `f(x+h)` in `work.fs`
# to simplify future development of this sort of improvement.)
#
# The (right) one-sided formula is produced similarly using abscissae
# x, x+h, x+h/d, x+h/d**2, ..., x+h/d**6, x+h/d**7, x+h/d**7
# where `d` is the square root of `c`. (The left one-sided formula simply
# uses -h.) When the step size is reduced by factor `c = d**2`, we have
# abscissae:
# x, x+h/d**2, x+h/d**3..., x+h/d**8, x+h/d**9, x+h/d**9
# `d` is chosen as the square root of `c` so that the rate of the step-size
# reduction is the same per iteration as in the central difference case.
# Note that because the central difference formulas are inherently of even
# order, for simplicity, we use only even-order formulas for one-sided
# differences, too.
# It's possible for the user to specify `fac` in, say, double precision but
# `x` and `args` in single precision. `fac` gets converted to single
# precision, but we should always use double precision for the intermediate
# calculations here to avoid additional error in the weights.
fac = float(work.fac)
# Note that if the user switches back to floating point precision with
# `x` and `args`, then `fac` will not necessarily equal the (lower
# precision) cached `_derivative_weights.fac`, and the weights will
# need to be recalculated. This could be fixed, but it's late, and of
# low consequence.
diff_state = work.diff_state
if fac != diff_state.fac:
diff_state.central = []
diff_state.right = []
diff_state.fac = fac
if len(diff_state.central) != 2*n + 1:
# Central difference weights. Consider refactoring this; it could
# probably be more compact.
# Note: Using NumPy here is OK; we convert to xp-type at the end
i = np.arange(-n, n + 1)
p = np.abs(i) - 1. # center point has power `p` -1, but sign `s` is 0
s = np.sign(i)
h = s / fac ** p
A = np.vander(h, increasing=True).T
b = np.zeros(2*n + 1)
b[1] = 1
weights = np.linalg.solve(A, b)
# Enforce identities to improve accuracy
weights[n] = 0
for i in range(n):
weights[-i-1] = -weights[i]
# Cache the weights. We only need to calculate them once unless
# the step factor changes.
diff_state.central = weights
# One-sided difference weights. The left one-sided weights (with
# negative steps) are simply the negative of the right one-sided
# weights, so no need to compute them separately.
i = np.arange(2*n + 1)
p = i - 1.
s = np.sign(i)
h = s / np.sqrt(fac) ** p
A = np.vander(h, increasing=True).T
b = np.zeros(2 * n + 1)
b[1] = 1
weights = np.linalg.solve(A, b)
diff_state.right = weights
return (xp.asarray(diff_state.central, dtype=work.dtype),
xp.asarray(diff_state.right, dtype=work.dtype))
def jacobian(f, x, *, tolerances=None, maxiter=10, order=8, initial_step=0.5,
step_factor=2.0, step_direction=0):
r"""Evaluate the Jacobian of a function numerically.
Parameters
----------
f : callable
The function whose Jacobian is desired. The signature must be::
f(xi: ndarray) -> ndarray
where each element of ``xi`` is a finite real. If the function to be
differentiated accepts additional arguments, wrap it (e.g. using
`functools.partial` or ``lambda``) and pass the wrapped callable
into `jacobian`. `f` must not mutate the array ``xi``. See Notes
regarding vectorization and the dimensionality of the input and output.
x : float array_like
Points at which to evaluate the Jacobian. Must have at least one dimension.
See Notes regarding the dimensionality and vectorization.
tolerances : dictionary of floats, optional
Absolute and relative tolerances. Valid keys of the dictionary are:
- ``atol`` - absolute tolerance on the derivative
- ``rtol`` - relative tolerance on the derivative
Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
`atol` is the smallest normal number of the appropriate dtype, and
the default `rtol` is the square root of the precision of the
appropriate dtype.
maxiter : int, default: 10
The maximum number of iterations of the algorithm to perform. See
Notes.
order : int, default: 8
The (positive integer) order of the finite difference formula to be
used. Odd integers will be rounded up to the next even integer.
initial_step : float array_like, default: 0.5
The (absolute) initial step size for the finite difference derivative
approximation. Must be broadcastable with `x` and `step_direction`.
step_factor : float, default: 2.0
The factor by which the step size is *reduced* in each iteration; i.e.
the step size in iteration 1 is ``initial_step/step_factor``. If
``step_factor < 1``, subsequent steps will be greater than the initial
step; this may be useful if steps smaller than some threshold are
undesirable (e.g. due to subtractive cancellation error).
step_direction : integer array_like
An array representing the direction of the finite difference steps (e.g.
for use when `x` lies near to the boundary of the domain of the function.)
Must be broadcastable with `x` and `initial_step`.
Where 0 (default), central differences are used; where negative (e.g.
-1), steps are non-positive; and where positive (e.g. 1), all steps are
non-negative.
Returns
-------
res : _RichResult
An object similar to an instance of `scipy.optimize.OptimizeResult` with the
following attributes. The descriptions are written as though the values will
be scalars; however, if `f` returns an array, the outputs will be
arrays of the same shape.
success : bool array
``True`` where the algorithm terminated successfully (status ``0``);
``False`` otherwise.
status : int array
An integer representing the exit status of the algorithm.
- ``0`` : The algorithm converged to the specified tolerances.
- ``-1`` : The error estimate increased, so iteration was terminated.
- ``-2`` : The maximum number of iterations was reached.
- ``-3`` : A non-finite value was encountered.
df : float array
The Jacobian of `f` at `x`, if the algorithm terminated
successfully.
error : float array
An estimate of the error: the magnitude of the difference between
the current estimate of the Jacobian and the estimate in the
previous iteration.
nit : int array
The number of iterations of the algorithm that were performed.
nfev : int array
The number of points at which `f` was evaluated.
Each element of an attribute is associated with the corresponding
element of `df`. For instance, element ``i`` of `nfev` is the
number of points at which `f` was evaluated for the sake of
computing element ``i`` of `df`.
See Also
--------
derivative, hessian
Notes
-----
Suppose we wish to evaluate the Jacobian of a function
:math:`f: \mathbf{R}^m \rightarrow \mathbf{R}^n`. Assign to variables
``m`` and ``n`` the positive integer values of :math:`m` and :math:`n`,
respectively, and let ``...`` represent an arbitrary tuple of integers.
If we wish to evaluate the Jacobian at a single point, then:
- argument `x` must be an array of shape ``(m,)``
- argument `f` must be vectorized to accept an array of shape ``(m, ...)``.
The first axis represents the :math:`m` inputs of :math:`f`; the remainder
are for evaluating the function at multiple points in a single call.
- argument `f` must return an array of shape ``(n, ...)``. The first
axis represents the :math:`n` outputs of :math:`f`; the remainder
are for the result of evaluating the function at multiple points.
- attribute ``df`` of the result object will be an array of shape ``(n, m)``,
the Jacobian.
This function is also vectorized in the sense that the Jacobian can be
evaluated at ``k`` points in a single call. In this case, `x` would be an
array of shape ``(m, k)``, `f` would accept an array of shape
``(m, k, ...)`` and return an array of shape ``(n, k, ...)``, and the ``df``
attribute of the result would have shape ``(n, m, k)``.
Suppose the desired callable ``f_not_vectorized`` is not vectorized; it can
only accept an array of shape ``(m,)``. A simple solution to satisfy the required
interface is to wrap ``f_not_vectorized`` as follows::
def f(x):
return np.apply_along_axis(f_not_vectorized, axis=0, arr=x)
Alternatively, suppose the desired callable ``f_vec_q`` is vectorized, but
only for 2-D arrays of shape ``(m, q)``. To satisfy the required interface,
consider::
def f(x):
m, batch = x.shape[0], x.shape[1:] # x.shape is (m, ...)
x = np.reshape(x, (m, -1)) # `-1` is short for q = prod(batch)
res = f_vec_q(x) # pass shape (m, q) to function
n = res.shape[0]
return np.reshape(res, (n,) + batch) # return shape (n, ...)
Then pass the wrapped callable ``f`` as the first argument of `jacobian`.
References
----------
.. [1] Jacobian matrix and determinant, *Wikipedia*,
https://en.wikipedia.org/wiki/Jacobian_matrix_and_determinant
Examples
--------
The Rosenbrock function maps from :math:`\mathbf{R}^m \rightarrow \mathbf{R}`;
the SciPy implementation `scipy.optimize.rosen` is vectorized to accept an
array of shape ``(m, p)`` and return an array of shape ``p``. Suppose we wish
to evaluate the Jacobian (AKA the gradient because the function returns a scalar)
at ``[0.5, 0.5, 0.5]``.
>>> import numpy as np
>>> from scipy.differentiate import jacobian
>>> from scipy.optimize import rosen, rosen_der
>>> m = 3
>>> x = np.full(m, 0.5)
>>> res = jacobian(rosen, x)
>>> ref = rosen_der(x) # reference value of the gradient
>>> res.df, ref
(array([-51., -1., 50.]), array([-51., -1., 50.]))
As an example of a function with multiple outputs, consider Example 4
from [1]_.
>>> def f(x):
... x1, x2, x3 = x
... return [x1, 5*x3, 4*x2**2 - 2*x3, x3*np.sin(x1)]
The true Jacobian is given by:
>>> def df(x):
... x1, x2, x3 = x
... one = np.ones_like(x1)
... return [[one, 0*one, 0*one],
... [0*one, 0*one, 5*one],
... [0*one, 8*x2, -2*one],
... [x3*np.cos(x1), 0*one, np.sin(x1)]]
Evaluate the Jacobian at an arbitrary point.
>>> rng = np.random.default_rng(389252938452)
>>> x = rng.random(size=3)
>>> res = jacobian(f, x)
>>> ref = df(x)
>>> res.df.shape == (4, 3)
True
>>> np.allclose(res.df, ref)
True
Evaluate the Jacobian at 10 arbitrary points in a single call.
>>> x = rng.random(size=(3, 10))
>>> res = jacobian(f, x)
>>> ref = df(x)
>>> res.df.shape == (4, 3, 10)
True
>>> np.allclose(res.df, ref)
True
"""
xp = array_namespace(x)
x = xp.asarray(x)
int_dtype = xp.isdtype(x.dtype, 'integral')
x0 = xp.asarray(x, dtype=xp.asarray(1.0).dtype) if int_dtype else x
if x0.ndim < 1:
message = "Argument `x` must be at least 1-D."
raise ValueError(message)
m = x0.shape[0]
i = xp.arange(m)
def wrapped(x):
p = () if x.ndim == x0.ndim else (x.shape[-1],) # number of abscissae
new_shape = (m, m) + x0.shape[1:] + p
xph = xp.expand_dims(x0, axis=1)
if x.ndim != x0.ndim:
xph = xp.expand_dims(xph, axis=-1)
xph = xp_copy(xp.broadcast_to(xph, new_shape), xp=xp)
xph[i, i] = x
return f(xph)
res = derivative(wrapped, x, tolerances=tolerances,
maxiter=maxiter, order=order, initial_step=initial_step,
step_factor=step_factor, preserve_shape=True,
step_direction=step_direction)
del res.x # the user knows `x`, and the way it gets broadcasted is meaningless here
return res
def hessian(f, x, *, tolerances=None, maxiter=10,
order=8, initial_step=0.5, step_factor=2.0):
r"""Evaluate the Hessian of a function numerically.
Parameters
----------
f : callable
The function whose Hessian is desired. The signature must be::
f(xi: ndarray) -> ndarray
where each element of ``xi`` is a finite real. If the function to be
differentiated accepts additional arguments, wrap it (e.g. using
`functools.partial` or ``lambda``) and pass the wrapped callable
into `hessian`. `f` must not mutate the array ``xi``. See Notes
regarding vectorization and the dimensionality of the input and output.
x : float array_like
Points at which to evaluate the Hessian. Must have at least one dimension.
See Notes regarding the dimensionality and vectorization.
tolerances : dictionary of floats, optional
Absolute and relative tolerances. Valid keys of the dictionary are:
- ``atol`` - absolute tolerance on the derivative
- ``rtol`` - relative tolerance on the derivative
Iteration will stop when ``res.error < atol + rtol * abs(res.df)``. The default
`atol` is the smallest normal number of the appropriate dtype, and
the default `rtol` is the square root of the precision of the
appropriate dtype.
order : int, default: 8
The (positive integer) order of the finite difference formula to be
used. Odd integers will be rounded up to the next even integer.
initial_step : float, default: 0.5
The (absolute) initial step size for the finite difference derivative
approximation.
step_factor : float, default: 2.0
The factor by which the step size is *reduced* in each iteration; i.e.
the step size in iteration 1 is ``initial_step/step_factor``. If
``step_factor < 1``, subsequent steps will be greater than the initial
step; this may be useful if steps smaller than some threshold are
undesirable (e.g. due to subtractive cancellation error).
maxiter : int, default: 10
The maximum number of iterations of the algorithm to perform. See
Notes.
Returns
-------
res : _RichResult
An object similar to an instance of `scipy.optimize.OptimizeResult` with the
following attributes. The descriptions are written as though the values will
be scalars; however, if `f` returns an array, the outputs will be
arrays of the same shape.
success : bool array
``True`` where the algorithm terminated successfully (status ``0``);
``False`` otherwise.
status : int array
An integer representing the exit status of the algorithm.
- ``0`` : The algorithm converged to the specified tolerances.
- ``-1`` : The error estimate increased, so iteration was terminated.
- ``-2`` : The maximum number of iterations was reached.
- ``-3`` : A non-finite value was encountered.
ddf : float array
The Hessian of `f` at `x`, if the algorithm terminated
successfully.
error : float array
An estimate of the error: the magnitude of the difference between
the current estimate of the Hessian and the estimate in the
previous iteration.
nfev : int array
The number of points at which `f` was evaluated.
Each element of an attribute is associated with the corresponding
element of `ddf`. For instance, element ``[i, j]`` of `nfev` is the
number of points at which `f` was evaluated for the sake of
computing element ``[i, j]`` of `ddf`.
See Also
--------
derivative, jacobian
Notes
-----
Suppose we wish to evaluate the Hessian of a function
:math:`f: \mathbf{R}^m \rightarrow \mathbf{R}`, and we assign to variable
``m`` the positive integer value of :math:`m`. If we wish to evaluate
the Hessian at a single point, then:
- argument `x` must be an array of shape ``(m,)``
- argument `f` must be vectorized to accept an array of shape
``(m, ...)``. The first axis represents the :math:`m` inputs of
:math:`f`; the remaining axes indicated by ellipses are for evaluating
the function at several abscissae in a single call.
- argument `f` must return an array of shape ``(...)``.
- attribute ``dff`` of the result object will be an array of shape ``(m, m)``,
the Hessian.
This function is also vectorized in the sense that the Hessian can be
evaluated at ``k`` points in a single call. In this case, `x` would be an
array of shape ``(m, k)``, `f` would accept an array of shape
``(m, ...)`` and return an array of shape ``(...)``, and the ``ddf``
attribute of the result would have shape ``(m, m, k)``. Note that the
axis associated with the ``k`` points is included within the axes
denoted by ``(...)``.
Currently, `hessian` is implemented by nesting calls to `jacobian`.
All options passed to `hessian` are used for both the inner and outer
calls with one exception: the `rtol` used in the inner `jacobian` call
is tightened by a factor of 100 with the expectation that the inner
error can be ignored. A consequence is that `rtol` should not be set
less than 100 times the precision of the dtype of `x`; a warning is
emitted otherwise.
References
----------
.. [1] Hessian matrix, *Wikipedia*,
https://en.wikipedia.org/wiki/Hessian_matrix
Examples
--------
The Rosenbrock function maps from :math:`\mathbf{R}^m \rightarrow \mathbf{R}`;
the SciPy implementation `scipy.optimize.rosen` is vectorized to accept an
array of shape ``(m, ...)`` and return an array of shape ``...``. Suppose we
wish to evaluate the Hessian at ``[0.5, 0.5, 0.5]``.
>>> import numpy as np
>>> from scipy.differentiate import hessian
>>> from scipy.optimize import rosen, rosen_hess
>>> m = 3
>>> x = np.full(m, 0.5)
>>> res = hessian(rosen, x)
>>> ref = rosen_hess(x) # reference value of the Hessian
>>> np.allclose(res.ddf, ref)
True
`hessian` is vectorized to evaluate the Hessian at multiple points
in a single call.
>>> rng = np.random.default_rng(4589245925010)
>>> x = rng.random((m, 10))
>>> res = hessian(rosen, x)
>>> ref = [rosen_hess(xi) for xi in x.T]
>>> ref = np.moveaxis(ref, 0, -1)
>>> np.allclose(res.ddf, ref)
True
"""
# todo:
# - add ability to vectorize over additional parameters (*args?)
# - error estimate stack with inner jacobian (or use legit 2D stencil)
kwargs = dict(maxiter=maxiter, order=order, initial_step=initial_step,
step_factor=step_factor)
tolerances = {} if tolerances is None else tolerances
atol = tolerances.get('atol', None)
rtol = tolerances.get('rtol', None)
xp = array_namespace(x)
x = xp.asarray(x)
dtype = x.dtype if not xp.isdtype(x.dtype, 'integral') else xp.asarray(1.).dtype
finfo = xp.finfo(dtype)
rtol = finfo.eps**0.5 if rtol is None else rtol # keep same as `derivative`
# tighten the inner tolerance to make the inner error negligible
rtol_min = finfo.eps * 100
message = (f"The specified `{rtol=}`, but error estimates are likely to be "
f"unreliable when `rtol < {rtol_min}`.")
if 0 < rtol < rtol_min: # rtol <= 0 is an error
warnings.warn(message, RuntimeWarning, stacklevel=2)
rtol = rtol_min
def df(x):
tolerances = dict(rtol=rtol/100, atol=atol)
temp = jacobian(f, x, tolerances=tolerances, **kwargs)
nfev.append(temp.nfev if len(nfev) == 0 else temp.nfev.sum(axis=-1))
return temp.df
nfev = [] # track inner function evaluations
res = jacobian(df, x, tolerances=tolerances, **kwargs) # jacobian of jacobian
nfev = xp.cumulative_sum(xp.stack(nfev), axis=0)
res_nit = xp.astype(res.nit[xp.newaxis, ...], xp.int64) # appease torch
res.nfev = xp_take_along_axis(nfev, res_nit, axis=0)[0]
res.ddf = res.df
del res.df # this is renamed to ddf
del res.nit # this is only the outer-jacobian nit
return res
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