def call_minpack(fun, x0, jac, ftol, xtol, gtol, max_nfev, x_scale, diff_step):
n = x0.size
if diff_step is None:
epsfcn = EPS
else:
epsfcn = diff_step**2
# Compute MINPACK's `diag`, which is inverse of our `x_scale` and
# ``x_scale='jac'`` corresponds to ``diag=None``.
if isinstance(x_scale, string_types) and x_scale == 'jac':
diag = None
else:
diag = 1 / x_scale
full_output = True
col_deriv = False
factor = 100.0
if jac is None:
if max_nfev is None:
# n squared to account for Jacobian evaluations.
max_nfev = 100 * n * (n + 1)
x, info, status = _minpack._lmdif(fun, x0, (), full_output, ftol, xtol,
gtol, max_nfev, epsfcn, factor, diag)
else:
if max_nfev is None:
max_nfev = 100 * n
x, info, status = _minpack._lmder(fun, jac, x0, (), full_output,
col_deriv, ftol, xtol, gtol,
max_nfev, factor, diag)
f = info['fvec']
if callable(jac):
J = jac(x)
else:
J = np.atleast_2d(approx_derivative(fun, x))
cost = 0.5 * np.dot(f, f)
g = J.T.dot(f)
g_norm = norm(g, ord=np.inf)
nfev = info['nfev']
njev = info.get('njev', None)
status = FROM_MINPACK_TO_COMMON[status]
active_mask = np.zeros_like(x0, dtype=int)
return OptimizeResult(x=x,
cost=cost,
fun=f,
jac=J,
grad=g,
optimality=g_norm,
active_mask=active_mask,
nfev=nfev,
njev=njev,
status=status)
def call_minpack(fun, x0, jac, ftol, xtol, gtol, max_nfev, scaling, diff_step):
n = x0.size
if diff_step is None:
epsfcn = EPS
else:
epsfcn = diff_step ** 2
if isinstance(scaling, string_types) and scaling == "jac":
scaling = None
full_output = True
col_deriv = False
factor = 100.0
if jac is None:
if max_nfev is None:
# n squared to account for Jacobian evaluations.
max_nfev = 100 * n * (n + 1)
x, info, status = _minpack._lmdif(fun, x0, (), full_output, ftol, xtol, gtol, max_nfev, epsfcn, factor, scaling)
else:
if max_nfev is None:
max_nfev = 100 * n
x, info, status = _minpack._lmder(
fun, jac, x0, (), full_output, col_deriv, ftol, xtol, gtol, max_nfev, factor, scaling
)
f = info["fvec"]
if callable(jac):
J = jac(x)
else:
J = np.atleast_2d(approx_derivative(fun, x))
cost = 0.5 * np.dot(f, f)
g = J.T.dot(f)
g_norm = norm(g, ord=np.inf)
nfev = info["nfev"]
njev = info.get("njev", None)
status = FROM_MINPACK_TO_COMMON[status]
active_mask = np.zeros_like(x0, dtype=int)
return OptimizeResult(
x=x,
cost=cost,
fun=f,
jac=J,
grad=g,
optimality=g_norm,
active_mask=active_mask,
nfev=nfev,
njev=njev,
status=status,
)
def call_minpack(fun, x0, jac, ftol, xtol, gtol, max_nfev, x_scale, diff_step):
n = x0.size
if diff_step is None:
epsfcn = EPS
else:
epsfcn = diff_step**2
# Compute MINPACK's `diag`, which is inverse of our `x_scale` and
# ``x_scale='jac'`` corresponds to ``diag=None``.
if isinstance(x_scale, string_types) and x_scale == 'jac':
diag = None
else:
diag = 1 / x_scale
full_output = True
col_deriv = False
factor = 100.0
if jac is None:
if max_nfev is None:
# n squared to account for Jacobian evaluations.
max_nfev = 100 * n * (n + 1)
x, info, status = _minpack._lmdif(
fun, x0, (), full_output, ftol, xtol, gtol,
max_nfev, epsfcn, factor, diag)
else:
if max_nfev is None:
max_nfev = 100 * n
x, info, status = _minpack._lmder(
fun, jac, x0, (), full_output, col_deriv,
ftol, xtol, gtol, max_nfev, factor, diag)
f = info['fvec']
if callable(jac):
J = jac(x)
else:
J = np.atleast_2d(approx_derivative(fun, x))
cost = 0.5 * np.dot(f, f)
g = J.T.dot(f)
g_norm = norm(g, ord=np.inf)
nfev = info['nfev']
njev = info.get('njev', None)
status = FROM_MINPACK_TO_COMMON[status]
active_mask = np.zeros_like(x0, dtype=int)
return OptimizeResult(
x=x, cost=cost, fun=f, jac=J, grad=g, optimality=g_norm,
active_mask=active_mask, nfev=nfev, njev=njev, status=status)
def call_minpack(fun, x0, jac, ftol, xtol, gtol, max_nfev, scaling, diff_step):
n = x0.size
if diff_step is None:
epsfcn = EPS
else:
epsfcn = diff_step**2
if scaling == 'jac':
scaling = None
full_output = True
col_deriv = False
factor = 100.0
if jac is None:
if max_nfev is None:
# n squared to account for Jacobian evaluations.
max_nfev = 100 * n * (n + 1)
x, info, status = _minpack._lmdif(
fun, x0, (), full_output, ftol, xtol, gtol,
max_nfev, epsfcn, factor, scaling)
else:
if max_nfev is None:
max_nfev = 100 * n
x, info, status = _minpack._lmder(
fun, jac, x0, (), full_output, col_deriv,
ftol, xtol, gtol, max_nfev, factor, scaling)
f = info['fvec']
if callable(jac):
J = jac(x)
else:
J = np.atleast_2d(approx_derivative(fun, x))
cost = 0.5 * np.dot(f, f)
g = J.T.dot(f)
g_norm = norm(g, ord=np.inf)
nfev = info['nfev']
njev = info.get('njev', None)
status = FROM_MINPACK_TO_COMMON[status]
active_mask = np.zeros_like(x0, dtype=int)
return OptimizeResult(
x=x, cost=cost, fun=f, jac=J, grad=g, optimality=g_norm,
active_mask=active_mask, nfev=nfev, njev=njev, status=status)
def fit_with_gauss(x, y):
# It is better to start as close as possible to the real solution. So I
# take the maximum value of the y's as a prior for the amplitude, and
# the location of the peak as a prior for the mu
peak = np.argmax(y)
p0 = [y[peak], x[peak], 1., 0.0]
#p0 = [1., 0., 1., 0.]
#coeff, var_matrix = curve_fit(fgauss.gauss, x, y, p0=p0)
#coeff, var_matrix = curve_fit(gauss, x, y, p0=p0)
#coeff = leastsq(fgauss.gauss_res, p0, args=(x,y), maxfev=500, full_output=True)
#coeff = leastsq(fgauss.gauss_res, p0, args=(x,y), Dfun=fgauss.gauss_jacob, col_deriv=1, maxfev=500)[0]
#coeff = minpack._lmdif(fgauss.gauss_res, p0, (x,y), 0, 1.49012e-8, 1.49012e-8,
# 0.0, 500, 0.0, 100, None)[0]
coeff = minpack._lmder(fgauss.gauss_res, fgauss.gauss_jacob, p0, (x, y), 0,
1, 1.49012e-8, 1.49012e-8, 0.0, 500, 100, None)[0]
return coeff
def leastsqbound(func,
x0,
args=(),
bounds=None,
Dfun=None,
full_output=0,
col_deriv=0,
ftol=1.49012e-8,
xtol=1.49012e-8,
gtol=0.0,
maxfev=0,
epsfcn=0.0,
factor=100,
diag=None):
"""
Bounded minimization of the sum of squares of a set of equations.
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers.
x0 : ndarray
The starting estimate for the minimization.
args : tuple
Any extra arguments to func are placed in this tuple.
bounds : list
``(min, max)`` pairs for each element in ``x``, defining
the bounds on that parameter. Use None for one of ``min`` or
``max`` when there is no bound in that direction.
Dfun : callable
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
full_output : bool
non-zero to return all optional outputs.
col_deriv : bool
non-zero to specify that the Jacobian function computes derivatives
down the columns (faster, because there is no transpose operation).
ftol : float
Relative error desired in the sum of squares.
xtol : float
Relative error desired in the approximate solution.
gtol : float
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int
The maximum number of calls to the function. If zero, then 100*(N+1) is
the maximum where N is the number of elements in x0.
epsfcn : float
A suitable step length for the forward-difference approximation of the
Jacobian (for Dfun=None). If epsfcn is less than the machine precision,
it is assumed that the relative errors in the functions are of the
order of the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
Uses the fjac and ipvt optional outputs to construct an
estimate of the jacobian around the solution. ``None`` if a
singular matrix encountered (indicates very flat curvature in
some direction). This matrix must be multiplied by the
residual standard deviation to get the covariance of the
parameter estimates -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the key s::
- 'nfev' : the number of function calls
- 'fvec' : the function evaluated at the output
- 'fjac' : A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
- 'ipvt' : an integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
- 'qtf' : the vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
Contraints on the parameters are enforced using an internal parameter list
with appropiate transformations such that these internal parameters can be
optimized without constraints. The transfomation between a given internal
parameter, p_i, and a external parameter, p_e, are as follows:
With ``min`` and ``max`` bounds defined ::
p_i = arcsin((2 * (p_e - min) / (max - min)) - 1.)
p_e = min + ((max - min) / 2.) * (sin(p_i) + 1.)
With only ``max`` defined ::
p_i = sqrt((max - p_e + 1.)**2 - 1.)
p_e = max + 1. - sqrt(p_i**2 + 1.)
With only ``min`` defined ::
p_i = sqrt((p_e - min + 1.)**2 - 1.)
p_e = min - 1. + sqrt(p_i**2 + 1.)
These transfomations are used in the MINUIT package, and described in
detail in the section 1.3.1 of the MINUIT User's Guide.
To Do
-----
Currently the ``factor`` and ``diag`` parameters scale the
internal parameter list, but should scale the external parameter list.
The `qtf` vector in the infodic dictionary reflects internal parameter
list, it should be correct to reflect the external parameter list.
References
----------
* F. James and M. Winkler. MINUIT User's Guide, July 16, 2004.
"""
# use leastsq if no bounds are present
if bounds is None:
return leastsq(func, x0, args, Dfun, full_output, col_deriv, ftol,
xtol, gtol, maxfev, epsfcn, factor, diag)
# create function which convert between internal and external parameters
i2e = _internal2external_func(bounds)
e2i = _external2internal_func(bounds)
x0 = array(x0, ndmin=1)
i0 = e2i(x0)
n = len(x0)
if len(bounds) != n:
raise ValueError('length of x0 != length of bounds')
if type(args) != type(()):
args = (args, )
m = _check_func('leastsq', 'func', func, x0, args, n)[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
# define a wrapped func which accept internal parameters, converts them
# to external parameters and calls func
def wfunc(x, *args):
return func(i2e(x), *args)
if Dfun is None:
if (maxfev == 0):
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(wfunc, i0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if (maxfev == 0):
maxfev = 100 * (n + 1)
def wDfun(x, *args): # wrapped Dfun
return Dfun(i2e(x), *args)
retval = _minpack._lmder(func, wDfun, i0, args, full_output, col_deriv,
ftol, xtol, gtol, maxfev, factor, diag)
errors = {
0: ["Improper input parameters.", TypeError],
1: [
"Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None
],
2: [
"The relative error between two consecutive "
"iterates is at most %f" % xtol, None
],
3: [
"Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None
],
4: [
"The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None
],
5: [
"Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError
],
6: [
"ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible."
"" % ftol, ValueError
],
7: [
"xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError
],
8: [
"gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError
],
'unknown': ["Unknown error.", TypeError]
}
info = retval[-1] # The FORTRAN return value
if (info not in [1, 2, 3, 4] and not full_output):
if info in [5, 6, 7, 8]:
warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0]) # internal params to external params
if full_output:
# convert fjac from internal params to external
grad = _internal2external_grad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T /
take(grad, retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except LinAlgError:
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)
def leastsqbound(func, x0, args=(), bounds=None, Dfun=None, full_output=0,
col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):
"""
Bounded minimization of the sum of squares of a set of equations.
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers.
x0 : ndarray
The starting estimate for the minimization.
args : tuple
Any extra arguments to func are placed in this tuple.
bounds : list
``(min, max)`` pairs for each element in ``x``, defining
the bounds on that parameter. Use None for one of ``min`` or
``max`` when there is no bound in that direction.
Dfun : callable
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
full_output : bool
non-zero to return all optional outputs.
col_deriv : bool
non-zero to specify that the Jacobian function computes derivatives
down the columns (faster, because there is no transpose operation).
ftol : float
Relative error desired in the sum of squares.
xtol : float
Relative error desired in the approximate solution.
gtol : float
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int
The maximum number of calls to the function. If zero, then 100*(N+1) is
the maximum where N is the number of elements in x0.
epsfcn : float
A suitable step length for the forward-difference approximation of the
Jacobian (for Dfun=None). If epsfcn is less than the machine precision,
it is assumed that the relative errors in the functions are of the
order of the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
Uses the fjac and ipvt optional outputs to construct an
estimate of the jacobian around the solution. ``None`` if a
singular matrix encountered (indicates very flat curvature in
some direction). This matrix must be multiplied by the
residual standard deviation to get the covariance of the
parameter estimates -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the key s::
- 'nfev' : the number of function calls
- 'fvec' : the function evaluated at the output
- 'fjac' : A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
- 'ipvt' : an integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
- 'qtf' : the vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
Contraints on the parameters are enforced using an internal parameter list
with appropiate transformations such that these internal parameters can be
optimized without constraints. The transfomation between a given internal
parameter, p_i, and a external parameter, p_e, are as follows:
With ``min`` and ``max`` bounds defined ::
p_i = arcsin((2 * (p_e - min) / (max - min)) - 1.)
p_e = min + ((max - min) / 2.) * (sin(p_i) + 1.)
With only ``max`` defined ::
p_i = sqrt((max - p_e + 1.)**2 - 1.)
p_e = max + 1. - sqrt(p_i**2 + 1.)
With only ``min`` defined ::
p_i = sqrt((p_e - min + 1.)**2 - 1.)
p_e = min - 1. + sqrt(p_i**2 + 1.)
These transfomations are used in the MINUIT package, and described in
detail in the section 1.3.1 of the MINUIT User's Guide.
To Do
-----
Currently the ``factor`` and ``diag`` parameters scale the
internal parameter list, but should scale the external parameter list.
The `qtf` vector in the infodic dictionary reflects internal parameter
list, it should be correct to reflect the external parameter list.
References
----------
* F. James and M. Winkler. MINUIT User's Guide, July 16, 2004.
"""
# use leastsq if no bounds are present
if bounds is None:
return leastsq(func, x0, args, Dfun, full_output, col_deriv,
ftol, xtol, gtol, maxfev, epsfcn, factor, diag)
# create function which convert between internal and external parameters
i2e = _internal2external_func(bounds)
e2i = _external2internal_func(bounds)
x0 = asarray(x0).flatten()
i0 = e2i(x0)
n = len(x0)
if len(bounds) != n:
raise ValueError('length of x0 != length of bounds')
if not isinstance(args, tuple):
args = (args,)
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = finfo(dtype).eps
# define a wrapped func which accept internal parameters, converts them
# to external parameters and calls func
def wfunc(x, *args):
return func(i2e(x), *args)
if Dfun is None:
if (maxfev == 0):
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(wfunc, i0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if (maxfev == 0):
maxfev = 100 * (n + 1)
def wDfun(x, *args): # wrapped Dfun
return Dfun(i2e(x), *args)
retval = _minpack._lmder(wfunc, wDfun, i0, args, full_output,
col_deriv, ftol, xtol, gtol, maxfev,
factor, diag)
errors = {0: ["Improper input parameters.", TypeError],
1: ["Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None],
2: ["The relative error between two consecutive "
"iterates is at most %f" % xtol, None],
3: ["Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None],
4: ["The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None],
5: ["Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError],
6: ["ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible.""" % ftol,
ValueError],
7: ["xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol,
ValueError],
8: ["gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError],
'unknown': ["Unknown error.", TypeError]}
info = retval[-1] # The FORTRAN return value
if (info not in [1, 2, 3, 4] and not full_output):
if info in [5, 6, 7, 8]:
warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0]) # internal params to external params
if full_output:
# convert fjac from internal params to external
grad = _internal2external_grad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T / take(grad,
retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except LinAlgError:
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)
def leastsqBound(func, x0, args=(), bounds=None, Dfun=None, full_output=0,
col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):
from scipy.optimize import _minpack
"""
Non-linear least square fitting (Levenberg-Marquardt method) with
bounded parameters.
the codes of transformation between int <-> ext refers to the work of
Jonathan J. Helmus: https://github.com/jjhelmus/leastsqbound-scipy
other codes refers to the source code of minpack.py:
..\Lib\site-packages\scipy\optimize\minpack.py
An internal parameter list is used to enforce contraints on the fitting
parameters. The transfomation is based on that of MINUIT package.
please see: F. James and M. Winkler. MINUIT User's Guide, 2004.
bounds : list
(min, max) pairs for each parameter, use None for 'min' or 'max'
when there is no bound in that direction.
For example: if there are two parameters needed to be fitting, then
bounds is [(min1,max1), (min2,max2)]
This function is based on 'leastsq' of minpack.py, the annotation of
other parameters can be found in 'leastsq'.
..\Lib\site-packages\scipy\optimize\minpack.py
"""
def _check_func(checker, argname, thefunc, x0, args, numinputs,
output_shape=None):
"""The same as that of minpack.py"""
res = np.atleast_1d(thefunc(*((x0[:numinputs],) + args)))
if (output_shape is not None) and (shape(res) != output_shape):
if (output_shape[0] != 1):
if len(output_shape) > 1:
if output_shape[1] == 1:
return shape(res)
msg = "%s: there is a mismatch between the input and output " \
"shape of the '%s' argument" % (checker, argname)
func_name = getattr(thefunc, '__name__', None)
if func_name:
msg += " '%s'." % func_name
else:
msg += "."
raise TypeError(msg)
if np.issubdtype(res.dtype, np.inexact):
dt = res.dtype
else:
dt = dtype(float)
return shape(res), dt
def _int2extGrad(p_int, bounds):
"""Calculate the gradients of transforming the internal (unconstrained) to external (constrained) parameter."""
grad = np.empty_like(p_int)
for i, (x, bound) in enumerate(zip(p_int, bounds)):
lower, upper = bound
if lower is None and upper is None: # No constraints
grad[i] = 1.0
elif upper is None: # only lower bound
grad[i] = x/np.sqrt(x*x + 1.0)
elif lower is None: # only upper bound
grad[i] = -x/np.sqrt(x*x + 1.0)
else: # lower and upper bounds
grad[i] = (upper - lower)*np.cos(x)/2.0
return grad
def _int2extFunc(bounds):
"""transform internal parameters into external parameters."""
local = [_int2extLocal(b) for b in bounds]
def _transform_i2e(p_int):
p_ext = np.empty_like(p_int)
p_ext[:] = [i(j) for i, j in zip(local, p_int)]
return p_ext
return _transform_i2e
def _ext2intFunc(bounds):
"""transform external parameters into internal parameters."""
local = [_ext2intLocal(b) for b in bounds]
def _transform_e2i(p_ext):
p_int = np.empty_like(p_ext)
p_int[:] = [i(j) for i, j in zip(local, p_ext)]
return p_int
return _transform_e2i
def _int2extLocal(bound):
"""transform a single internal parameter to an external parameter."""
lower, upper = bound
if lower is None and upper is None: # no constraints
return lambda x: x
elif upper is None: # only lower bound
return lambda x: lower - 1.0 + np.sqrt(x*x + 1.0)
elif lower is None: # only upper bound
return lambda x: upper + 1.0 - np.sqrt(x*x + 1.0)
else:
return lambda x: lower + ((upper - lower)/2.0)*(np.sin(x) + 1.0)
def _ext2intLocal(bound):
"""transform a single external parameter to an internal parameter."""
lower, upper = bound
if lower is None and upper is None: # no constraints
return lambda x: x
elif upper is None: # only lower bound
return lambda x: np.sqrt((x - lower + 1.0)**2 - 1.0)
elif lower is None: # only upper bound
return lambda x: np.sqrt((x - upper - 1.0)**2 - 1.0)
else:
return lambda x: np.arcsin((2.0*(x - lower)/(upper - lower)) - 1.0)
i2e = _int2extFunc(bounds)
e2i = _ext2intFunc(bounds)
x0 = np.asarray(x0).flatten()
n = len(x0)
if len(bounds) != n:
raise ValueError('the length of bounds is inconsistent with the number of parameters ')
if not isinstance(args, tuple):
args = (args,)
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = np.finfo(dtype).eps
def funcWarp(x, *args):
return func(i2e(x), *args)
xi0 = e2i(x0)
if Dfun is None:
if maxfev == 0:
maxfev = 200*(n + 1)
retval = _minpack._lmdif(funcWarp, xi0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if maxfev == 0:
maxfev = 100*(n + 1)
def DfunWarp(x, *args):
return Dfun(i2e(x), *args)
retval = _minpack._lmder(funcWarp, DfunWarp, xi0, args, full_output, col_deriv,
ftol, xtol, gtol, maxfev, factor, diag)
errors = {0: ["Improper input parameters.", TypeError],
1: ["Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None],
2: ["The relative error between two consecutive "
"iterates is at most %f" % xtol, None],
3: ["Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None],
4: ["The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None],
5: ["Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError],
6: ["ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible.""" % ftol,
ValueError],
7: ["xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol,
ValueError],
8: ["gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError],
'unknown': ["Unknown error.", TypeError]}
info = retval[-1] # The FORTRAN return value
if info not in [1, 2, 3, 4] and not full_output:
if info in [5, 6, 7, 8]:
np.warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0])
if full_output:
grad = _int2extGrad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T / np.take(grad,
retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = np.take(np.eye(n), retval[1]['ipvt'] - 1, 0)
r = np.triu(np.transpose(retval[1]['fjac'])[:n, :])
R = np.dot(r, perm)
try:
cov_x = inv(np.dot(np.transpose(R), R))
except LinAlgError as inverror:
print(inverror)
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)
def leastsq(func,
x0,
args=(),
Dfun=None,
full_output=0,
col_deriv=0,
ftol=1.49012e-8,
xtol=1.49012e-8,
gtol=0.0,
maxfev=0,
epsfcn=None,
factor=100,
diag=None):
"""
Minimize the sum of squares of a set of equations.
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers. It must not return NaNs or
fitting might fail.
x0 : ndarray
The starting estimate for the minimization.
args : tuple, optional
Any extra arguments to func are placed in this tuple.
Dfun : callable, optional
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
full_output : bool, optional
non-zero to return all optional outputs.
col_deriv : bool, optional
non-zero to specify that the Jacobian function computes derivatives
down the columns (faster, because there is no transpose operation).
ftol : float, optional
Relative error desired in the sum of squares.
xtol : float, optional
Relative error desired in the approximate solution.
gtol : float, optional
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int, optional
The maximum number of calls to the function. If `Dfun` is provided
then the default `maxfev` is 100*(N+1) where N is the number of elements
in x0, otherwise the default `maxfev` is 200*(N+1).
epsfcn : float, optional
A variable used in determining a suitable step length for the forward-
difference approximation of the Jacobian (for Dfun=None).
Normally the actual step length will be sqrt(epsfcn)*x
If epsfcn is less than the machine precision, it is assumed that the
relative errors are of the order of the machine precision.
factor : float, optional
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence, optional
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
The inverse of the Hessian. `fjac` and `ipvt` are used to construct an
estimate of the Hessian. A value of None indicates a singular matrix,
which means the curvature in parameters `x` is numerically flat. To
obtain the covariance matrix of the parameters `x`, `cov_x` must be
multiplied by the variance of the residuals -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the keys:
``nfev``
The number of function calls
``fvec``
The function evaluated at the output
``fjac``
A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
``ipvt``
An integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
``qtf``
The vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
See Also
--------
least_squares : Newer interface to solve nonlinear least-squares problems
with bounds on the variables. See ``method=='lm'`` in particular.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
The solution, `x`, is always a 1D array, regardless of the shape of `x0`,
or whether `x0` is a scalar.
"""
x0 = asarray(x0).flatten()
n = len(x0)
if not isinstance(args, tuple):
args = (args, )
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = finfo(dtype).eps
if Dfun is None:
if maxfev == 0:
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, gtol,
maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if maxfev == 0:
maxfev = 100 * (n + 1)
retval = _minpack._lmder(func, Dfun, x0, args, full_output, col_deriv,
ftol, xtol, gtol, maxfev, factor, diag)
errors = {
0: ["Improper input parameters.", TypeError],
1: [
"Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None
],
2: [
"The relative error between two consecutive "
"iterates is at most %f" % xtol, None
],
3: [
"Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None
],
4: [
"The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None
],
5: [
"Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError
],
6: [
"ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible." % ftol, ValueError
],
7: [
"xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError
],
8: [
"gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError
]
}
# The FORTRAN return value (possible return values are >= 0 and <= 8)
info = retval[-1]
if full_output:
cov_x = None
if info in LEASTSQ_SUCCESS:
from numpy.dual import inv
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except (LinAlgError, ValueError):
pass
return (retval[0], cov_x) + retval[1:-1] + (errors[info][0], info)
else:
if info in LEASTSQ_FAILURE:
warnings.warn(errors[info][0], RuntimeWarning)
elif info == 0:
raise errors[info][1](errors[info][0])
return retval[0], info
def leastsq(func,
x0,
args=(),
Dfun=None,
ftol=1.e-7,
xtol=1.e-7,
gtol=1.e-7,
maxfev=0,
epsfcn=None,
factor=100,
diag=None):
"""
Minimize the sum of squares of a set of equations.
Adopted from scipy.optimize.leastsq
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers.
x0 : ndarray
The starting estimate for the minimization.
args : tuple
Any extra arguments to func are placed in this tuple.
Dfun : callable
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
ftol : float
Relative error desired in the sum of squares.
xtol : float
Relative error desired in the approximate solution.
gtol : float
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int
The maximum number of calls to the function. If zero, then 100*(N+1) is
the maximum where N is the number of elements in x0.
epsfcn : float
A suitable step length for the forward-difference approximation of the
Jacobian (for Dfun=None). If epsfcn is less than the machine precision,
it is assumed that the relative errors in the functions are of the
order of the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
Uses the fjac and ipvt optional outputs to construct an
estimate of the jacobian around the solution. ``None`` if a
singular matrix encountered (indicates very flat curvature in
some direction). This matrix must be multiplied by the
residual variance to get the covariance of the
parameter estimates -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the key s::
- 'nfev' : the number of function calls
- 'fvec' : the function evaluated at the output
- 'fjac' : A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
- 'ipvt' : an integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
- 'qtf' : the vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
"""
x0 = asarray(x0).flatten()
n = len(x0)
if not isinstance(args, tuple):
args = (args, )
shape = _check_func('leastsq', 'func', func, x0, args, n)
if isinstance(shape, tuple) and len(shape) > 1:
# older versions returned only shape
# newer versions return (shape, dtype)
shape = shape[0]
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if maxfev == 0:
maxfev = 200 * (n + 1)
if epsfcn is None:
epsfcn = 2.e-5 # a relatively large value!!
if Dfun is None:
retval = _minpack._lmdif(func, x0, args, 1, ftol, xtol, gtol, maxfev,
epsfcn, factor, diag)
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
retval = _minpack._lmder(func, Dfun, x0, args, 1, 0, ftol, xtol, gtol,
maxfev, factor, diag)
errors = {
0: ["Improper input parameters.", TypeError],
1: [
"Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None
],
2: [
"The relative error between two consecutive "
"iterates is at most %f" % xtol, None
],
3: [
"Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None
],
4: [
"The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None
],
5: [
"Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError
],
6: [
"ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible."
"" % ftol, ValueError
],
7: [
"xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError
],
8: [
"gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError
],
'unknown': ["Unknown error.", TypeError]
}
info = retval[-1] # The FORTRAN return value
mesg = errors[info][0]
cov_x = None
if info in [1, 2, 3, 4]:
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except (LinAlgError, ValueError):
pass
return (retval[0], cov_x) + retval[1:-1] + (mesg, info)
def leastsqBound(func,
x0,
args=(),
bounds=None,
Dfun=None,
full_output=0,
col_deriv=0,
ftol=1.49012e-8,
xtol=1.49012e-8,
gtol=0.0,
maxfev=0,
epsfcn=None,
factor=100,
diag=None):
from scipy.optimize import _minpack
"""
Non-linear least square fitting (Levenberg-Marquardt method) with
bounded parameters.
the codes of transformation between int <-> ext refers to the work of
Jonathan J. Helmus: https://github.com/jjhelmus/leastsqbound-scipy
other codes refers to the source code of minpack.py:
..\Lib\site-packages\scipy\optimize\minpack.py
An internal parameter list is used to enforce contraints on the fitting
parameters. The transfomation is based on that of MINUIT package.
please see: F. James and M. Winkler. MINUIT User's Guide, 2004.
bounds : list
(min, max) pairs for each parameter, use None for 'min' or 'max'
when there is no bound in that direction.
For example: if there are two parameters needed to be fitting, then
bounds is [(min1,max1), (min2,max2)]
This function is based on 'leastsq' of minpack.py, the annotation of
other parameters can be found in 'leastsq'.
..\Lib\site-packages\scipy\optimize\minpack.py
"""
def _check_func(checker,
argname,
thefunc,
x0,
args,
numinputs,
output_shape=None):
"""The same as that of minpack.py"""
res = np.atleast_1d(thefunc(*((x0[:numinputs], ) + args)))
if (output_shape is not None) and (shape(res) != output_shape):
if (output_shape[0] != 1):
if len(output_shape) > 1:
if output_shape[1] == 1:
return shape(res)
msg = "%s: there is a mismatch between the input and output " \
"shape of the '%s' argument" % (checker, argname)
func_name = getattr(thefunc, '__name__', None)
if func_name:
msg += " '%s'." % func_name
else:
msg += "."
raise TypeError(msg)
if np.issubdtype(res.dtype, np.inexact):
dt = res.dtype
else:
dt = dtype(float)
return shape(res), dt
def _int2extGrad(p_int, bounds):
"""Calculate the gradients of transforming the internal (unconstrained) to external (constrained) parameter."""
grad = np.empty_like(p_int)
for i, (x, bound) in enumerate(zip(p_int, bounds)):
lower, upper = bound
if lower is None and upper is None: # No constraints
grad[i] = 1.0
elif upper is None: # only lower bound
grad[i] = x / np.sqrt(x * x + 1.0)
elif lower is None: # only upper bound
grad[i] = -x / np.sqrt(x * x + 1.0)
else: # lower and upper bounds
grad[i] = (upper - lower) * np.cos(x) / 2.0
return grad
def _int2extFunc(bounds):
"""transform internal parameters into external parameters."""
local = [_int2extLocal(b) for b in bounds]
def _transform_i2e(p_int):
p_ext = np.empty_like(p_int)
p_ext[:] = [i(j) for i, j in zip(local, p_int)]
return p_ext
return _transform_i2e
def _ext2intFunc(bounds):
"""transform external parameters into internal parameters."""
local = [_ext2intLocal(b) for b in bounds]
def _transform_e2i(p_ext):
p_int = np.empty_like(p_ext)
p_int[:] = [i(j) for i, j in zip(local, p_ext)]
return p_int
return _transform_e2i
def _int2extLocal(bound):
"""transform a single internal parameter to an external parameter."""
lower, upper = bound
if lower is None and upper is None: # no constraints
return lambda x: x
elif upper is None: # only lower bound
return lambda x: lower - 1.0 + np.sqrt(x * x + 1.0)
elif lower is None: # only upper bound
return lambda x: upper + 1.0 - np.sqrt(x * x + 1.0)
else:
return lambda x: lower + (
(upper - lower) / 2.0) * (np.sin(x) + 1.0)
def _ext2intLocal(bound):
"""transform a single external parameter to an internal parameter."""
lower, upper = bound
if lower is None and upper is None: # no constraints
return lambda x: x
elif upper is None: # only lower bound
return lambda x: np.sqrt((x - lower + 1.0)**2 - 1.0)
elif lower is None: # only upper bound
return lambda x: np.sqrt((x - upper - 1.0)**2 - 1.0)
else:
return lambda x: np.arcsin((2.0 * (x - lower) /
(upper - lower)) - 1.0)
i2e = _int2extFunc(bounds)
e2i = _ext2intFunc(bounds)
x0 = np.asarray(x0).flatten()
n = len(x0)
if len(bounds) != n:
raise ValueError(
'the length of bounds is inconsistent with the number of parameters '
)
if not isinstance(args, tuple):
args = (args, )
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = np.finfo(dtype).eps
def funcWarp(x, *args):
return func(i2e(x), *args)
xi0 = e2i(x0)
if Dfun is None:
if maxfev == 0:
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(funcWarp, xi0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if maxfev == 0:
maxfev = 100 * (n + 1)
def DfunWarp(x, *args):
return Dfun(i2e(x), *args)
retval = _minpack._lmder(funcWarp, DfunWarp, xi0, args, full_output,
col_deriv, ftol, xtol, gtol, maxfev, factor,
diag)
errors = {
0: ["Improper input parameters.", TypeError],
1: [
"Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None
],
2: [
"The relative error between two consecutive "
"iterates is at most %f" % xtol, None
],
3: [
"Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None
],
4: [
"The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None
],
5: [
"Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError
],
6: [
"ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible."
"" % ftol, ValueError
],
7: [
"xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError
],
8: [
"gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError
],
'unknown': ["Unknown error.", TypeError]
}
info = retval[-1] # The FORTRAN return value
if info not in [1, 2, 3, 4] and not full_output:
if info in [5, 6, 7, 8]:
np.warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0])
if full_output:
grad = _int2extGrad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T /
np.take(grad, retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = np.take(np.eye(n), retval[1]['ipvt'] - 1, 0)
r = np.triu(np.transpose(retval[1]['fjac'])[:n, :])
R = np.dot(r, perm)
try:
cov_x = inv(np.dot(np.transpose(R), R))
except LinAlgError as inverror:
print(inverror)
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)
def leastsqbound(func,
x0,
args=(),
bounds=None,
Dfun=None,
full_output=0,
col_deriv=0,
ftol=1.49012e-8,
xtol=1.49012e-8,
gtol=0.0,
maxfev=0,
epsfcn=None,
factor=100,
diag=None):
# use leastsq if no bounds are present
if bounds is None:
return leastsq(func, x0, args, Dfun, full_output, col_deriv, ftol,
xtol, gtol, maxfev, epsfcn, factor, diag)
# create function which convert between internal and external parameters
i2e = _internal2external_func(bounds)
e2i = _external2internal_func(bounds)
x0 = asarray(x0).flatten()
i0 = e2i(x0)
n = len(x0)
if len(bounds) != n:
raise ValueError('length of x0 != length of bounds')
if not isinstance(args, tuple):
args = (args, )
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = finfo(dtype).eps
# define a wrapped func which accept internal parameters, converts them
# to external parameters and calls func
def wfunc(x, *args):
return func(i2e(x), *args)
if Dfun is None:
if (maxfev == 0):
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(wfunc, i0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if (maxfev == 0):
maxfev = 100 * (n + 1)
def wDfun(x, *args): # wrapped Dfun
return Dfun(i2e(x), *args)
retval = _minpack._lmder(wfunc, wDfun, i0, args, full_output,
col_deriv, ftol, xtol, gtol, maxfev, factor,
diag)
errors = {
0: ["Improper input parameters.", TypeError],
1: [
"Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None
],
2: [
"The relative error between two consecutive "
"iterates is at most %f" % xtol, None
],
3: [
"Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None
],
4: [
"The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None
],
5: [
"Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError
],
6: [
"ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible."
"" % ftol, ValueError
],
7: [
"xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError
],
8: [
"gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError
],
'unknown': ["Unknown error.", TypeError]
}
info = retval[-1] # The FORTRAN return value
if (info not in [1, 2, 3, 4] and not full_output):
if info in [5, 6, 7, 8]:
pass #warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0]) # internal params to external params
if full_output:
# convert fjac from internal params to external
grad = _internal2external_grad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T /
take(grad, retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except LinAlgError:
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)
def leastsq(func, x0, args=(), Dfun=None, ftol=1.e-7, xtol=1.e-7,
gtol=1.e-7, maxfev=0, epsfcn=None, factor=100, diag=None):
"""
Minimize the sum of squares of a set of equations.
Adopted from scipy.optimize.leastsq
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers.
x0 : ndarray
The starting estimate for the minimization.
args : tuple
Any extra arguments to func are placed in this tuple.
Dfun : callable
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
ftol : float
Relative error desired in the sum of squares.
xtol : float
Relative error desired in the approximate solution.
gtol : float
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int
The maximum number of calls to the function. If zero, then 100*(N+1) is
the maximum where N is the number of elements in x0.
epsfcn : float
A suitable step length for the forward-difference approximation of the
Jacobian (for Dfun=None). If epsfcn is less than the machine precision,
it is assumed that the relative errors in the functions are of the
order of the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
Uses the fjac and ipvt optional outputs to construct an
estimate of the jacobian around the solution. ``None`` if a
singular matrix encountered (indicates very flat curvature in
some direction). This matrix must be multiplied by the
residual variance to get the covariance of the
parameter estimates -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the key s::
- 'nfev' : the number of function calls
- 'fvec' : the function evaluated at the output
- 'fjac' : A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
- 'ipvt' : an integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
- 'qtf' : the vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
"""
x0 = asarray(x0).flatten()
n = len(x0)
if not isinstance(args, tuple):
args = (args,)
shape = _check_func('leastsq', 'func', func, x0, args, n)
if isinstance(shape, tuple) and len(shape) > 1:
# older versions returned only shape
# newer versions return (shape, dtype)
shape = shape[0]
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if maxfev == 0:
maxfev = 200*(n + 1)
if epsfcn is None:
epsfcn = 2.e-5 # a relatively large value!!
if Dfun is None:
retval = _minpack._lmdif(func, x0, args, 1, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
retval = _minpack._lmder(func, Dfun, x0, args, 1, 0, ftol, xtol,
gtol, maxfev, factor, diag)
errors = {0:["Improper input parameters.", TypeError],
1:["Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None],
2:["The relative error between two consecutive "
"iterates is at most %f" % xtol, None],
3:["Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol,xtol), None],
4:["The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None],
5:["Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError],
6:["ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible.""" % ftol, ValueError],
7:["xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError],
8:["gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError],
'unknown':["Unknown error.", TypeError]}
info = retval[-1] # The FORTRAN return value
mesg = errors[info][0]
cov_x = None
if info in [1,2,3,4]:
perm = take(eye(n),retval[1]['ipvt']-1,0)
r = triu(transpose(retval[1]['fjac'])[:n,:])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R),R))
except (LinAlgError, ValueError):
pass
return (retval[0], cov_x) + retval[1:-1] + (mesg, info)
def leastsqbound(func, x0, args=(), bounds=None, Dfun=None, full_output=0,
col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):
# use leastsq if no bounds are present
if bounds is None:
return leastsq(func, x0, args, Dfun, full_output, col_deriv,
ftol, xtol, gtol, maxfev, epsfcn, factor, diag)
# create function which convert between internal and external parameters
i2e = _internal2external_func(bounds)
e2i = _external2internal_func(bounds)
x0 = asarray(x0).flatten()
i0 = e2i(x0)
n = len(x0)
if len(bounds) != n:
raise ValueError('length of x0 != length of bounds')
if not isinstance(args, tuple):
args = (args,)
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
m = shape[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n, m))
if epsfcn is None:
epsfcn = finfo(dtype).eps
# define a wrapped func which accept internal parameters, converts them
# to external parameters and calls func
def wfunc(x, *args):
return func(i2e(x), *args)
if Dfun is None:
if (maxfev == 0):
maxfev = 200 * (n + 1)
retval = _minpack._lmdif(wfunc, i0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
if (maxfev == 0):
maxfev = 100 * (n + 1)
def wDfun(x, *args): # wrapped Dfun
return Dfun(i2e(x), *args)
retval = _minpack._lmder(wfunc, wDfun, i0, args, full_output,
col_deriv, ftol, xtol, gtol, maxfev,
factor, diag)
errors = {0: ["Improper input parameters.", TypeError],
1: ["Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None],
2: ["The relative error between two consecutive "
"iterates is at most %f" % xtol, None],
3: ["Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol, xtol), None],
4: ["The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None],
5: ["Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError],
6: ["ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible.""" % ftol,
ValueError],
7: ["xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol,
ValueError],
8: ["gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError],
'unknown': ["Unknown error.", TypeError]}
info = retval[-1] # The FORTRAN return value
if (info not in [1, 2, 3, 4] and not full_output):
if info in [5, 6, 7, 8]:
pass #warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
x = i2e(retval[0]) # internal params to external params
if full_output:
# convert fjac from internal params to external
grad = _internal2external_grad(retval[0], bounds)
retval[1]['fjac'] = (retval[1]['fjac'].T / take(grad,
retval[1]['ipvt'] - 1)).T
cov_x = None
if info in [1, 2, 3, 4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
r = triu(transpose(retval[1]['fjac'])[:n, :])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R), R))
except LinAlgError:
pass
return (x, cov_x) + retval[1:-1] + (mesg, info)
else:
return (x, info)