How do I fit a sine curve to my data with pylab and numpy?

You can use the least-square optimization function in scipy to fit any arbitrary function to another. In case of fitting a sin function, the 3 parameters to fit are the offset ('a'), amplitude ('b') and the phase ('c').

As long as you provide a reasonable first guess of the parameters, the optimization should converge well.Fortunately for a sine function, first estimates of 2 of these are easy: the offset can be estimated by taking the mean of the data and the amplitude via the RMS (3*standard deviation/sqrt(2)).

Note: as a later edit, frequency fitting has also been added. This does not work very well (can lead to extremely poor fits). Thus, use at your discretion, my advise would be to not use frequency fitting unless frequency error is smaller than a few percent.

This leads to the following code:

import numpy as np
from scipy.optimize import leastsq
import pylab as plt

N = 1000 # number of data points
t = np.linspace(0, 4*np.pi, N)
f = 1.15247 # Optional!! Advised not to use
data = 3.0*np.sin(f*t+0.001) + 0.5 + np.random.randn(N) # create artificial data with noise

guess_mean = np.mean(data)
guess_std = 3*np.std(data)/(2**0.5)/(2**0.5)
guess_phase = 0
guess_freq = 1
guess_amp = 1

# we'll use this to plot our first estimate. This might already be good enough for you
data_first_guess = guess_std*np.sin(t+guess_phase) + guess_mean

# Define the function to optimize, in this case, we want to minimize the difference
# between the actual data and our "guessed" parameters
optimize_func = lambda x: x[0]*np.sin(x[1]*t+x[2]) + x[3] - data
est_amp, est_freq, est_phase, est_mean = leastsq(optimize_func, [guess_amp, guess_freq, guess_phase, guess_mean])[0]

# recreate the fitted curve using the optimized parameters
data_fit = est_amp*np.sin(est_freq*t+est_phase) + est_mean

# recreate the fitted curve using the optimized parameters

fine_t = np.arange(0,max(t),0.1)
data_fit=est_amp*np.sin(est_freq*fine_t+est_phase)+est_mean

plt.plot(t, data, '.')
plt.plot(t, data_first_guess, label='first guess')
plt.plot(fine_t, data_fit, label='after fitting')
plt.legend()
plt.show()

Edit: I assumed that you know the number of periods in the sine-wave. If you don't, it's somewhat trickier to fit. You can try and guess the number of periods by manual plotting and try and optimize it as your 6th parameter.

Here is a parameter-free fitting function fit_sin() that does not require manual guess of frequency:

import numpy, scipy.optimize

def fit_sin(tt, yy):
    '''Fit sin to the input time sequence, and return fitting parameters "amp", "omega", "phase", "offset", "freq", "period" and "fitfunc"'''
    tt = numpy.array(tt)
    yy = numpy.array(yy)
    ff = numpy.fft.fftfreq(len(tt), (tt[1]-tt[0]))   # assume uniform spacing
    Fyy = abs(numpy.fft.fft(yy))
    guess_freq = abs(ff[numpy.argmax(Fyy[1:])+1])   # excluding the zero frequency "peak", which is related to offset
    guess_amp = numpy.std(yy) * 2.**0.5
    guess_offset = numpy.mean(yy)
    guess = numpy.array([guess_amp, 2.*numpy.pi*guess_freq, 0., guess_offset])

    def sinfunc(t, A, w, p, c):  return A * numpy.sin(w*t + p) + c
    popt, pcov = scipy.optimize.curve_fit(sinfunc, tt, yy, p0=guess)
    A, w, p, c = popt
    f = w/(2.*numpy.pi)
    fitfunc = lambda t: A * numpy.sin(w*t + p) + c
    return {"amp": A, "omega": w, "phase": p, "offset": c, "freq": f, "period": 1./f, "fitfunc": fitfunc, "maxcov": numpy.max(pcov), "rawres": (guess,popt,pcov)}

The initial frequency guess is given by the peak frequency in the frequency domain using FFT. The fitting result is almost perfect assuming there is only one dominant frequency (other than the zero frequency peak).

import pylab as plt

N, amp, omega, phase, offset, noise = 500, 1., 2., .5, 4., 3
#N, amp, omega, phase, offset, noise = 50, 1., .4, .5, 4., .2
#N, amp, omega, phase, offset, noise = 200, 1., 20, .5, 4., 1
tt = numpy.linspace(0, 10, N)
tt2 = numpy.linspace(0, 10, 10*N)
yy = amp*numpy.sin(omega*tt + phase) + offset
yynoise = yy + noise*(numpy.random.random(len(tt))-0.5)

res = fit_sin(tt, yynoise)
print( "Amplitude=%(amp)s, Angular freq.=%(omega)s, phase=%(phase)s, offset=%(offset)s, Max. Cov.=%(maxcov)s" % res )

plt.plot(tt, yy, "-k", label="y", linewidth=2)
plt.plot(tt, yynoise, "ok", label="y with noise")
plt.plot(tt2, res["fitfunc"](tt2), "r-", label="y fit curve", linewidth=2)
plt.legend(loc="best")
plt.show()

The result is good even with high noise:

Amplitude=1.00660540618, Angular freq.=2.03370472482, phase=0.360276844224, offset=3.95747467506, Max. Cov.=0.0122923578658

More userfriendly to us is the function curvefit. Here an example:

import numpy as np
from scipy.optimize import curve_fit
import pylab as plt

N = 1000 # number of data points
t = np.linspace(0, 4*np.pi, N)
data = 3.0*np.sin(t+0.001) + 0.5 + np.random.randn(N) # create artificial data with noise

guess_freq = 1
guess_amplitude = 3*np.std(data)/(2**0.5)
guess_phase = 0
guess_offset = np.mean(data)

p0=[guess_freq, guess_amplitude,
    guess_phase, guess_offset]

# create the function we want to fit
def my_sin(x, freq, amplitude, phase, offset):
    return np.sin(x * freq + phase) * amplitude + offset

# now do the fit
fit = curve_fit(my_sin, t, data, p0=p0)

# we'll use this to plot our first estimate. This might already be good enough for you
data_first_guess = my_sin(t, *p0)

# recreate the fitted curve using the optimized parameters
data_fit = my_sin(t, *fit[0])

plt.plot(data, '.')
plt.plot(data_fit, label='after fitting')
plt.plot(data_first_guess, label='first guess')
plt.legend()
plt.show()

The current methods to fit a sin curve to a given data set require a first guess of the parameters, followed by an interative process. This is a non-linear regression problem.

A different method consists in transforming the non-linear regression to a linear regression thanks to a convenient integral equation. Then, there is no need for initial guess and no need for iterative process : the fitting is directly obtained.

In case of the function y = a + r*sin(w*x+phi) or y=a+b*sin(w*x)+c*cos(w*x), see pages 35-36 of the paper "Régression sinusoidale" published on Scribd

In case of the function y = a + p*x + r*sin(w*x+phi) : pages 49-51 of the chapter "Mixed linear and sinusoidal regressions".

In case of more complicated functions, the general process is explained in the chapter "Generalized sinusoidal regression" pages 54-61, followed by a numerical example y = r*sin(w*x+phi)+(b/x)+c*ln(x), pages 62-63