# -*- coding: utf-8 -*-
from typing import Optional, List, Tuple
import warnings
import numpy as np
from lmfit import Model, Parameters
from lmfit.models import LinearModel
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class CurveFit:
"""
Base class for fitting curves, subclasses have specific tools, plot and attributes
"""
default_fit_kws = {
'method': 'lstsq',
'max_nfev': 5000
}
def_limit = (-np.inf, np.inf)
# limits = defaultdict(default_factory=def_limit)
def __init__(self, x, y, name=None, function=None, ic=None, limits=None, ):
"""
:param x: 1D array
:param y: 1D array
:param name: str
:param model: lmfit.models.Model (or None)
"""
self.x = x
self.y = y
self.name = name
self.model = Model(function)
self.function = function
self.params = Parameters()
self.fitted_params = None
if ic is None:
self.ic = {}
else:
self.ic = ic
if limits is None:
self.limits = {}
else:
self.limits = limits
self.result = None
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def guess_ic(self,guess=None):
pass # do nothing, can't guess. Subclass override
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def guess_limit(self):
pass # do nothing, can't guess. Subclass override
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def make_params(self):
params = Parameters()
for param, value in self.ic.items():
limit = self.limits.get(param, self.def_limit)
params.add(param, value=float(value), min=limit[0], max=limit[1],
vary=not isinstance(value, str)) # no vary if value is string
self.params = params
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def fit_model(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# Ignore UserWarning: Using UFloat objects with std_dev==0 may give unexpected results.
result = self.model.fit(self.y, self.params, x=self.x, **self.default_fit_kws)
self.result = result
fitted_params = self.get_fit_params()
return fitted_params, result
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def get_fit_params(self):
fitted_params = {}
for key, param in self.result.params.items():
fitted_params[key] = param.value
self.fitted_params = fitted_params
return self.fitted_params
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def run_default(self):
if not self.ic:
self.guess_ic()
if not self.ic: # if above cannot make IC ...
raise Exception('ic is required, no parameters to fit')
if not self.limits:
self.guess_limit()
self.make_params()
fitted_params, result = self.fit_model()
return fitted_params, result
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def best_guess(self, guess_list=None, mode='r2'):
if guess_list is None:
return self.run_default()
residuals = []
fits = []
results = []
for guess in guess_list:
self.guess_ic(guess)
self.guess_limit()
self.make_params()
fitted_params, result = self.run_default()
fits.append(fitted_params)
results.append(result)
if mode == 'r': # closest area
residuals.append(np.sum(result.residual))
elif mode == 'r2': # smallest error
residuals.append(np.sum(result.residual * result.residual))
## something based on number of args?
min_ind = np.argmin(residuals)
self.fitted_params = fits[min_ind]
self.result = results[min_ind]
return self.fitted_params, self.result
def __call__(self, x):
if self.result is None:
return None # default param call?
else:
return self.result.eval(x=x)
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class Linear(CurveFit):
"""
Linear Function Fit
"""
def __init__(self, x, y, name=None, function=None, ic=None, limits=None, ):
self.x = x
self.y = y
self.name = name
self.model = LinearModel()
self.function = function
self.params = Parameters()
self.fitted_params = None
result = self.model.fit(y, x=x)
self.result = result
fitted_params = self.get_fit_params()
self.fitted_params = fitted_params