Fit functions are a set of callable classes designed to aid in fitting analytical functions to data. A fit function class combines the following functionality:
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path
from plasmapy.analysis import fit_functions as ffuncs
plt.rcParams["figure.figsize"] = [10.5, 0.56 * 10.5]
There is an ever expanding collection of fit functions, but this notebook will use ExponentialPlusLinear as an example.
A fit function class has no required arguments at time of instantiation.
# basic instantiation
explin = ffuncs.ExponentialPlusLinear()
# fit parameters are not set yet
(explin.params, explin.param_errors)
Each fit parameter is given a name.
explin.param_names
These names are used throughout the fit function's documentation, as well as in its __repr__
, __str__
, and latex_str
methods.
(explin, explin.__str__(), explin.latex_str)
Fit functions provide the curve_fit() method to fit the analytical function to a set of $(x, y)$ data. This is typically done with SciPy's curve_fit() function, but fitting is done with SciPy's linregress() for the Linear fit funciton.
Let's generate some noisy data to fit to...
params = (5.0, 0.1, -0.5, -8.0) # (a, alpha, m, b)
xdata = np.linspace(-20, 15, num=100)
ydata = explin.func(xdata, *params) + np.random.normal(0.0, 0.6, xdata.size)
plt.plot(xdata, ydata)
plt.xlabel("X", fontsize=14)
plt.ylabel("Y", fontsize=14)
The fit function curve_fit()
shares the same signature as SciPy's curve_fit(), so any **kwargs
will be passed on. By default, only the $(x, y)$ values are needed.
explin.curve_fit(xdata, ydata)
After fitting, the fitted parameters, uncertainties, and coefficient of determination, or $r^2$, values can be retrieved through their respective properties, params
, parame_errors
, and rsq
.
(explin.params, explin.params.a, explin.params.alpha)
(explin.param_errors, explin.param_errors.a, explin.param_errors.alpha)
explin.rsq
Now that parameters are set, the fit function is callable.
explin(0)
Associated errors can also be generated.
y, y_err = explin(np.linspace(-1, 1, num=10), reterr=True)
(y, y_err)
Known uncertainties in $x$ can be specified too.
y, y_err = explin(np.linspace(-1, 1, num=10), reterr=True, x_err=0.1)
(y, y_err)
# plot original data
plt.plot(xdata, ydata, marker="o", linestyle=" ", label="Data")
ax = plt.gca()
ax.set_xlabel("X", fontsize=14)
ax.set_ylabel("Y", fontsize=14)
ax.axhline(0.0, color="r", linestyle="--")
# plot fitted curve + error
yfit, yfit_err = explin(xdata, reterr=True)
ax.plot(xdata, yfit, color="orange", label="Fit")
ax.fill_between(
xdata,
yfit + yfit_err,
yfit - yfit_err,
color="orange",
alpha=0.12,
zorder=0,
label="Fit Error",
)
# plot annotations
plt.legend(fontsize=14, loc="upper left")
txt = f"$f(x) = {explin.latex_str}$\n" f"$r^2 = {explin.rsq:.3f}$\n"
for name, param, err in zip(explin.param_names, explin.params, explin.param_errors):
txt += f"{name} = {param:.3f} $\\pm$ {err:.3f}\n"
txt_loc = [-13.0, ax.get_ylim()[1]]
txt_loc = ax.transAxes.inverted().transform(ax.transData.transform(txt_loc))
txt_loc[0] -= 0.02
txt_loc[1] -= 0.05
ax.text(
txt_loc[0],
txt_loc[1],
txt,
fontsize="large",
transform=ax.transAxes,
va="top",
linespacing=1.5,
)
An exponential plus a linear offset has no analytical solutions for its roots, except for a few specific cases. To get around this, ExponentialPlusLinear().root_solve() uses SciPy's fsolve() to calculate it's roots. If a fit function has analytical solutions to its roots (e.g. Linear().root_solve()), then the method is overriden with the known solution.
root, err = explin.root_solve(-15.0)
(root, err)
Let's use Linear().root_solve() as an example for a known solution.
lin = ffuncs.Linear(params=(1.0, -5.0), param_errors=(0.1, 0.1))
root, err = lin.root_solve()
(root, err)