Filter Fabry-Pérot resonance from luminescence spectra shown in Plotcommander

F-P-resonance-filter

fw=int(len(xs[0])/30) # filter width
fl=int(len(xs[0])/20) # filter limit: minimum position of the Fabry-Pérot peak in correlation function
skippoints = 0 # sometimes the first point is some header

def nGaN(energies):
    ## returns index of refraction in GaN according to [Tisch et al., JAP 89 (2001)]
    eV = [1.503,      1.655,      1.918,      2.300, 2.668, 2.757, 2.872, 3.006, 3.136, 3.229, 3.315,     3.395,      3.422] 
    n  = [2.359+0.08, 2.366+0.04, 2.383+0.02, 2.419, 2.470, 2.486, 2.511, 2.549, 2.596, 2.643, 2.711-.01, 2.818-.045, 2.893-.100]     
    return np.interp(energies, eV, n)

xs = [xx[skippoints:] for xx in xs]; ys = [yy[skippoints:] for yy in ys]
result_data = [xs[0]]
for x, y, param, label, xlabel, ylabel, color in         zip(xs, ys, params, labels, xlabels, ylabels, colors):
    ## initially, x is free space wavelength (in nanometers)
    ax.plot(x, y, label="%s" % (label), color='k', lw=.5)
    ## convert x1 to wavenumber in GaN
    x1 = 2*np.pi*nGaN(1239.8/x)/(x*1e-9)   # (1 eV photon has wavelength of 1239.8 nm in vacuum)

    ## interpolate so that the x-axis is in increasing order and equidistant
    x2 = np.linspace(np.min(x1), np.max(x1), len(x1)*4)  ## finer resample to keep all spectral details
    y2 = np.interp(x2, x1[~np.isnan(y)][::-1], y[~np.isnan(y)][::-1])
    ax.plot(x2, y2, label="%s" % (label), color='b', lw=.5)

    ## using FFT, x2 is transformed roughly into "thicknesses of virtual Fabry-Perot resonators"
    print(color)
    xf = np.fft.fftfreq(len(x2), x2[1]-x2[0])
    yf = np.fft.fft(y2)
    ax.plot(np.fft.fftshift(xf)*1e6, np.fft.fftshift(np.abs(yf)), label="%s" % (label), color=color, lw=1)
    print(color, len(xf), yf)
    
    ## now find and remove the spectral peak
    findmax = np.argmax(np.abs(yf[fl:-fl])) + fl
    yf[findmax-fw:findmax+fw] = (yf[findmax-fw] + yf[findmax+fw])/2
    yf[len(yf)-findmax-fw:len(yf)-findmax+fw] = (yf[findmax-fw] + yf[findmax+5])/2
    ax.plot(np.fft.fftshift(xf)*1e6, np.fft.fftshift(np.abs(yf)), label="%s" % (label), color=color, lw=1)

    # invert FFT of spectra and re-interpolate wavenumber in GaN back to wavelength
    y3 = np.interp(2*np.pi*nGaN(1239.8/x)/(x*1e-9), x2, (np.abs(np.fft.ifft(yf))))  ## np.fft.fftshift(xf)
    #ax.plot(x, y3, label="%s" % (label), color=color, lw=1.5)
    result_data.append(y3)
ax.set_xlabel('free-space wavelength (nm)')
ax.set_ylabel('thin-film luminescence spectra (A. U.)')
ax.set_ylim(ymin=.3e-1)
ax.set_title('')
np.savetxt('filtered_output.dat', np.vstack(result_data).T, fmt='%6f')

An example follows, color lines are photoluminescence spectra automatically filtered for Fabry-Pérot resonance artifacts: