m-thesis-introduction/fourier/06_direct_fourier.py

#!/usr/bin/env python3
# vim: fdm=indent ts=4

__doc__ = \
"""
Show how the fourier transform can be calculated
in a continuous fashion
"""

if __name__ == "__main__":
    import numpy as np
    import matplotlib.pyplot as plt
    from mpl_toolkits.mplot3d import Axes3D

    from mylib.fft import direct_fourier_transform

    n_samples = 1000
    nphi = 100
    f_beacon = 2.3434
    noise_A = 5

    t = np.linspace(0, 100, n_samples+1)

    phi_in = np.linspace(0, 2*np.pi, nphi)
    test_freqs = f_beacon + 0.1 * np.linspace(-1, 1, 100+1)


    phi_out = np.zeros( (len(phi_in), len(test_freqs)) )
    amp_out = np.zeros( (len(phi_in), len(test_freqs)) )

    if not True:
        # Same length samples
        # means we can precalculate the c_k and s_k terms
        c_k, s_k = ft_corr_vectors(test_freqs, t)

        for i, phi in enumerate(phi_in):
            s = np.sin(2*np.pi*t*f_beacon + phi) + noise_A * np.random.normal(size=len(t))

            real = np.dot(c_k, s)
            imag = np.dot(s_k, s)

            phi_out[i] = (np.arctan2(real, imag))
            amp_out[i] = (2/len(t) * (real**2 + imag**2)**0.5)
    else:
        sampleset_gen = ( np.sin(2*np.pi*t*f_beacon + phi) + noise_A*np.random.normal(size=len(t)) for phi in phi_in )
        ft_amp_gen = direct_fourier_transform(test_freqs, t, sampleset_gen)

        for i, ft_amp in enumerate(ft_amp_gen):
            real = ft_amp[0]
            imag = ft_amp[1]

            phi_out[i] = np.arctan2(real, imag)
            amp_out[i] = 2/len(t) * (real**2 + imag**2)**0.5

    ######
    # Figures
    ######
    import matplotlib.colors as colors
    cmap = plt.cm.plasma
    freq_norm = colors.Normalize(vmin=np.amin(test_freqs), vmax=np.amax(test_freqs))
    freq_cmap = cmap(freq_norm(test_freqs))
    try:
        # Amplitudes Histogram
        if True:
            fig = plt.figure()
            ax = fig.add_subplot(projection='3d')
            ax.set_xlabel("Amplitude")
            ax.set_ylabel("Frequency")
            ax.set_zlabel("Count")

            for j, amp in enumerate(amp_out.T):
                # per test_freq
                counts, edges = np.histogram(amp, bins='auto', )
                l = ax.plot(edges[:-1], counts, zs=test_freqs[j], zdir='y', color=freq_cmap[j])

                ax.add_collection3d(plt.fill_between(edges[:-1], 0, counts, color=l[0].get_color(), alpha=0.3), zs=test_freqs[j], zdir='y')


            ax.view_init(elev=20., azim=-35)
        elif False:
            fig, ax = plt.subplots()
            ax.set_xlabel("Amplitude")
            ax.set_ylabel("Count")
            # 
            for j, amp in enumerate(amp_out.T):
                # per test_freq
                ax.hist(amp, histtype='step', bins='auto', color=freq_cmap[j])

        # Single Amplitude / Frequency plot showing frequency fitting
        freq_out = None
        if True:
            from numpy.polynomial import Polynomial as P
        
            freq_out = np.zeros(len(phi_in))
            amp_cut = 0.5

            fig, ax = plt.subplots()
            ax.set_title("Frequency estimation by parabola fitting.\nStars are used for the parabola fit, vertical line is where $\\partial_f = 0 $")
            ax.set_xlabel("Frequency")
            ax.set_ylabel("Amplitude")

            ax.axvline(f_beacon, lw=5, ls=(0,(5,5)))
        
            for j, amp in enumerate(amp_out):

                if j > 2:
                    continue

                max_amp_idx = np.argmax(amp)
                max_amp = amp[max_amp_idx]
                # filter amplitudes below amp_cut*max_amp
                valid_mask = amp >= amp_cut*max_amp

                if True:
                    # make sure not to use other peaks
                    lower_mask = valid_mask[0:max_amp_idx]
                    upper_mask = valid_mask[max_amp_idx:]

                    lower_end = np.argmin(lower_mask[::-1])
                    upper_end = np.argmin(upper_mask)

                    valid_mask[0:(max_amp_idx - lower_end)] = False
                    valid_mask[(max_amp_idx + upper_end):] = False

                p_fit = P.fit(test_freqs[valid_mask], amp[valid_mask], 2)
                func  = p_fit.convert()

                # Find frequency of derivative == 0
                deriv = func.deriv(1)
                freq = deriv.roots()[0]
                freq_out[j] = freq


                l = ax.plot(test_freqs, amp, marker='.')
                ax.plot(test_freqs[valid_mask], amp[valid_mask], marker='*', color=l[0].get_color())
                ax.axvline(freq_out[j], color=l[0].get_color())

                if True: # plot the fit
                    tmp_test_freqs = test_freqs[max_amp_idx] + 0.05*np.linspace(-1,1,101, endpoint=True)
                    func_amps = func(tmp_test_freqs)

                    func_amps_idx = func_amps > 0
                    func_amps = func_amps[func_amps_idx]
                    tmp_test_freqs = tmp_test_freqs[func_amps_idx]

                    ax.plot(tmp_test_freqs, func_amps, ls='dotted', color=l[0].get_color())

        # Amplitudes figure
        if True:
            fig, ax = plt.subplots()
            ax.set_ylabel("Amplitude")
            ax.set_xlabel("Frequency")
            if True:
                for j, amp in enumerate(amp_out.T):
                    #per test_freq
                    ax.plot(np.tile(test_freqs[j], len(amp)), amp, marker='.', color=freq_cmap[j], alpha=max(0.05, 0))


            ax.errorbar(test_freqs, np.mean(amp_out, axis=0), yerr=np.std(amp_out, axis=0))
            ax.plot(test_freqs, np.mean(amp_out, axis=0), marker='*', color='red', zorder=6)

        # Phase in vs. Phase out figure
        if True:
            fig, ax = plt.subplots()
            amp_cut = 0.8

            ax.set_title(f"Measured phases passing amplitude > {amp_cut}")
            ax.set_xlabel("Phase in")
            ax.set_ylabel("Phase out")

            for j, phi in enumerate(phi_out.T):
                if np.mean(amp_out[:,j]) < amp_cut:
                    # ignore when the amplitudes are not close to 1
                    continue

                # per test_freq
                ax.plot(phi_in, np.unwrap(phi), label='f-test_f:{:.2e}'.format(f_beacon-test_freqs[j]))#, color=freq_cmap[j])

            ax.legend()
    finally:
        plt.show()