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POscipy.optimize.curve_fit unable to fit shifted skewed gaussian curve
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  1. POscipy.optimize.curve_fit unable to fit shifted skewed gaussian curve
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    copied!<p>I am trying to fit a skewed and shifted Gaussian curve using scipy's <a href="http://docs.scipy.org/doc/scipy-0.15.1/reference/generated/scipy.optimize.curve_fit.html" rel="nofollow">curve_fit</a> function, but I find that under certain conditions the fitting is quite poor, often giving me close to or exactly a straight line.</p> <p>The code below is derived from the <code>curve_fit</code> documentation. The code provided is an arbitrary set of data for test purposes but displays the issue quite well.</p> <pre><code>import numpy as np from scipy.optimize import curve_fit import matplotlib.pyplot as plt import math as math import scipy.special as sp #def func(x, a, b, c): # return a*np.exp(-b*x) + c def func(x, sigmag, mu, alpha, c,a): #normal distribution normpdf = (1/(sigmag*np.sqrt(2*math.pi)))*np.exp(-(np.power((x-mu),2)/(2*np.power(sigmag,2)))) normcdf = (0.5*(1+sp.erf((alpha*((x-mu)/sigmag))/(np.sqrt(2))))) return 2*a*normpdf*normcdf + c x = np.linspace(0,100,100) y = func(x, 10,30, 0,0,1) yn = y + 0.001*np.random.normal(size=len(x)) popt, pcov = curve_fit(func, x, yn,) #p0=(9,35,0,9,1)) y_fit= func(x,popt[0],popt[1],popt[2],popt[3],popt[4]) plt.plot(x,yn) plt.plot(x,y_fit) </code></pre> <p>The issue seems to pop up when I shift the gaussian too far from zero (using <code>mu</code>). I have tried giving initial values, even those identical to my original function, but it does not solve the problem. For a value of <code>mu=10</code>, <code>curve_fit</code> works perfectly, but if I use <code>mu&gt;=30</code> it not longer fits the data.</p>
 

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