"""
This module contains support functions and convenience methods used
throughout symfit. Some are used predominantly internally, others are
designed for users.
"""
from __future__ import print_function
from functools import wraps
from collections import OrderedDict
import sys
import warnings
import numpy as np
from sympy.utilities.lambdify import lambdify
import sympy
from sympy.tensor import IndexedBase
from sympy import Symbol
from symfit.core.argument import Parameter, Variable
if sys.version_info >= (3,0):
import inspect as inspect_sig
else:
import funcsigs as inspect_sig
[docs]def seperate_symbols(func):
"""
Seperate the symbols in symbolic function func. Return them in alphabetical
order.
:param func: scipy symbolic function.
:return: (vars, params), a tuple of all variables and parameters, each
sorted in alphabetical order.
:raises TypeError: only symfit Variable and Parameter are allowed, not sympy
Symbols.
"""
params = []
vars = []
for symbol in func.free_symbols:
if isinstance(symbol, Parameter):
params.append(symbol)
elif isinstance(symbol, (Variable, IndexedBase, Symbol)):
vars.append(symbol)
else:
raise TypeError('model contains an unknown symbol type, {}'.format(type(symbol)))
params.sort(key=lambda symbol: symbol.name)
vars.sort(key=lambda symbol: symbol.name)
return vars, params
[docs]def sympy_to_py(func, vars, params):
"""
Turn a symbolic expression into a Python lambda function,
which has the names of the variables and parameters as it's argument names.
:param func: sympy expression
:param vars: variables in this model
:param params: parameters in this model
:return: lambda function to be used for numerical evaluation of the model. Ordering of the arguments will be vars
first, then params.
"""
return lambdify((vars + params), func, modules='numpy', dummify=False)
[docs]def sympy_to_scipy(func, vars, params):
"""
Convert a symbolic expression to one scipy digs. Not used by ``symfit`` any more.
:param func: sympy expression
:param vars: variables
:param params: parameters
:return: Scipy-style function to be used for numerical evaluation of the model.
"""
lambda_func = sympy_to_py(func, vars, params)
def f(x, p):
"""
Scipy style function.
:param x: list of arrays, NxM
:param p: tuple of parameter values.
"""
x = np.atleast_2d(x)
y = [x[i] for i in range(len(x))] if len(x[0]) else []
try:
ans = lambda_func(*(y + list(p)))
except TypeError:
# Possibly this is a constant function in which case it only has Parameters.
ans = lambda_func(*list(p))# * np.ones(x_shape)
return ans
return f
[docs]def variables(names):
"""
Convenience function for the creation of multiple variables.
:param names: string of variable names. Should be comma seperated.
Example: x, y = variables('x, y')
"""
return [Variable(name=name.strip()) for name in names.split(',')]
[docs]def parameters(names):
"""
Convenience function for the creation of multiple parameters.
:param names: string of parameter names. Should be comma seperated.
Example: a, b = parameters('a, b')
"""
return [Parameter(name=name.strip()) for name in names.split(',')]
[docs]def cache(func):
"""
Decorator function that gets a method as its input and either buffers the input,
or returns the buffered output. Used in conjunction with properties to take away
the standard buffering logic.
:param func:
:return:
"""
@wraps(func)
def new_func(self):
try:
return getattr(self, '_{}'.format(func.__name__))
except AttributeError:
setattr(self, '_{}'.format(func.__name__), func(self))
return getattr(self, '_{}'.format(func.__name__))
return new_func
[docs]def jacobian(expr, symbols):
"""
Derive a symbolic expr w.r.t. each symbol in symbols. This returns a symbolic jacobian vector.
:param expr: A sympy Expr.
:param symbols: The symbols w.r.t. which to derive.
"""
jac = []
for symbol in symbols:
# Differentiate to every param
f = sympy.diff(expr, symbol)
jac.append(f)
return jac
[docs]def key2str(target):
"""
In ``symfit`` there are many dicts with symbol: value pairs.
These can not be used immediately as \*\*kwargs, even though this would make
a lot of sense from the context.
This function wraps such dict to make them usable as \*\*kwargs immidiately.
:param target: dict to be made save
:return: dict of str(symbol): value pairs.
"""
return {str(symbol): value for symbol, value in target.items()}
[docs]class RequiredKeyword(object):
""" Flag variable to indicate that this is a required keyword. """
[docs]class RequiredKeywordError(Exception):
""" Error raised in case a keyword-only argument is not treated as such. """
[docs]class keywordonly(object):
"""
Decorator class which wraps a python 2 function into one with keyword-only arguments.
Example::
@keywordonly(floor=True)
def f(x, **kwargs):
floor = kwargs.pop('floor')
return np.floor(x**2) if floor else x**2
This decorator is not much more than::
floor = kwargs.pop('floor') if 'floor' in kwargs else True
However, I prefer it's usage because:
- it's clear from reading the function declaration there is an option to provide this
argument. The information on possible keywords is where you'd expect it to be.
- you're guaranteed that the pop works.
- Perhaps in the future I will make this inspect-compatible so then we come full circle.
Please note that this decorator needs a ** argument on the wrapped function
in order to work.
"""
def __init__(self, **kwonly_arguments):
self.kwonly_arguments = kwonly_arguments
# Mark which are required
self.required_keywords = {
kw for kw, value in kwonly_arguments.items() if value is RequiredKeyword
}
# Transform all into keywordonly inspect.Parameter objects.
self.keywordonly_parameters = OrderedDict(
(kw, inspect_sig.Parameter(kw,
kind=inspect_sig.Parameter.KEYWORD_ONLY,
default=value)
)
for kw, value in kwonly_arguments.items()
)
[docs] def __call__(self, func):
"""
Returns a decorated version of `func`, who's signature now includes the
keyword-only arguments.
:param func: the function to be decorated
:return: the decorated function
"""
sig = inspect_sig.signature(func)
params = []
# A var keyword has to be found for this function to be decorated
for name, param in sig.parameters.items():
if param.kind == param.VAR_KEYWORD:
# Keyword only's go before the **kwargs parameter.
params.extend(self.keywordonly_parameters.values())
params.append(param)
break
params.append(param)
else:
raise RequiredKeywordError(
'The keywordonly decorator requires the function to '
'accept a **kwargs argument.'
)
# Update signature
sig = sig.replace(parameters=params)
func.__signature__ = sig
@wraps(func)
def wrapped_func(*args, **kwargs):
"""
:param args: args used to call the function
:param kwargs: kwargs used to call the function
:return: Wrapped function which behaves like it has keyword-only arguments.
:raises: ``RequiredKeywordError`` if not all required keywords were specified.
"""
bound_args = func.__signature__.bind(*args, **kwargs)
# Apply defaults
for param in sig.parameters.values():
if param.name not in bound_args.arguments:
if param.default is RequiredKeyword:
raise RequiredKeywordError(
'Keyword `{}` is a required keyword. '
'Please provide a value.'.format(param.name)
)
elif param.kind == inspect_sig.Parameter.VAR_KEYWORD:
bound_args.arguments[param.name] = {}
elif param.kind == inspect_sig.Parameter.VAR_POSITIONAL:
bound_args.arguments[param.name] = tuple()
else:
bound_args.arguments[param.name] = param.default
return func(*bound_args.args, **bound_args.kwargs)
return wrapped_func
[docs]class deprecated(object):
"""
Decorator to raise a DeprecationWarning.
"""
[docs] def __init__(self, replacement=None):
"""
:param replacement: The function which should now be used instead.
"""
self.replacement = replacement
def __call__(self, func):
@wraps(func)
def deprecated_func(*args, **kwargs):
warnings.warn(DeprecationWarning(
'`{}` has been deprecated.'.format(func.__name__)
+ ' Use `{}` instead.'.format(self.replacement)) if self.replacement else ''
)
return func(*args, **kwargs)
return deprecated_func
[docs]class D(sympy.Derivative):
"""
Convenience wrapper for ``sympy.Derivative``. Used most notably in defining
``ODEModel``'s.
"""