"""
This module contains support functions and convenience methods used
throughout symfit. Some are used predominantly internally, others are
designed for users.
"""
from functools import wraps
from collections import OrderedDict
import numpy as np
from symfit.core.argument import Parameter, Variable
from sympy.utilities.lambdify import lambdify
import sympy
[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 = []
from sympy.tensor import IndexedBase
from sympy import Symbol
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