gaussian fit with scipy.optimize.curve_fit in python with wrong results
Your problem is with the initial parameters of the curve_fit. By default, if no other information is given, it will start with an array of 1, but this obviously lead to a radically wrong result. This can be corrected simply by giving a reasonable starting vector. To do this, I start from the estimated mean and standard deviation of your dataset
#estimate mean and standard deviation
meam = sum(x * y)
sigma = sum(y * (x - m)**2)
#do the fit!
popt, pcov = curve_fit(gauss_function, x, y, p0 = [1, mean, sigma])
#plot the fit results
plot(x,gauss_function(x, *popt))
#confront with the given data
plot(x,y,'ok')
This will perfectly approximate your results. Remember that curve fitting in general cannot work unless you start from a good point (inside the convergence basin, to be clear), and this doesn't depend on the implementation. Never do blind fit when you can use your knowledge!
Álvaro
Updated on July 09, 2022Comments
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Álvaro almost 2 years
I am having some trouble to fit a gaussian to data. I think the problem is that most of the elements are close to zero, and there not many points to actually be fitted. But in any case, I think they make a good dataset to fit, and I don't get what is confussing python. Here is the program, I have also added a line to plot the data so you can see what I am trying to fit
#Gaussian function def gauss_function(x, a, x0, sigma): return a*np.exp(-(x-x0)**2/(2*sigma**2)) # program from scipy.optimize import curve_fit x = np.arange(0,21.,0.2) # sorry about these data! y = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.2888599818864958e-275, 1.0099964933708256e-225, 4.9869496866403137e-184, 4.4182929795060327e-149, 7.2953754336628778e-120, 1.6214815763354974e-95, 2.5845990267696154e-75, 1.2195550372375896e-58, 5.6756631456872126e-45, 7.2520963306599953e-34, 6.0926453402093181e-25, 7.1075523112494745e-18, 2.1895584709541657e-12, 3.1040093615952226e-08, 3.2818874974043519e-05, 0.0039462011337049593, 0.077653596114448178, 0.33645159419151383, 0.40139213808285212, 0.15616093582013874, 0.0228751827752081, 0.0014423440677009125, 4.4400754532288282e-05, 7.4939123408714068e-07, 7.698340466102054e-09, 5.2805658851032628e-11, 2.6233358880470556e-13, 1.0131613609937094e-15, 3.234727006243684e-18, 9.0031014316344088e-21, 2.2867065482392331e-23, 5.5126221075296919e-26, 1.3045106781768978e-28, 3.1185031969890313e-31, 7.7170036365830092e-34, 2.0179753504732056e-36, 5.6739187799428708e-39, 1.7403776988666581e-41, 5.8939645426573027e-44, 2.2255784749636281e-46, 9.4448944519959299e-49, 4.5331936383388069e-51, 2.4727435506007072e-53, 1.5385048936078214e-55, 1.094651071873419e-57, 8.9211199390945735e-60, 8.3347561634783632e-62, 8.928140776588251e-64, 1.0960564546383266e-65, 1.5406342485015278e-67, 2.4760905399114866e-69, 4.5423744881977258e-71, 9.4921949220625905e-73, 2.2543765002199549e-74, 6.0698995872666723e-76, 1.8478996852922248e-77, 6.3431644488676084e-79, 0.0, 0.0, 0.0, 0.0] plot(x,y) #Plot the curve, the gaussian is quite clear plot(x,y,'ok') #Overplot the dots # Try to fit the result popt, pcov = curve_fit(gauss_function, x, y)
The problem is that the results for popt is
print popt array([ 7.39717176e-10, 1.00000000e+00, 1.00000000e+00])
Any hint on why this could be happening?
Thanks!
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Ciprian Tomoiagă almost 7 yearsIt works, but why ? Why do you start with
mean = sum(x * y)
?