m-thesis-introduction/simulations/11_pulsed_timing.py

#!/usr/bin/env python3


from lib import util
from scipy import signal, interpolate
import matplotlib.pyplot as plt
import numpy as np

try:
    from tqdm import tqdm
except:
    tqdm = lambda x: x

rng = np.random.default_rng()

class Waveform:
    name = None
    signal = None
    dt = None

    _t = None

    def __init__(self,signal=None, dt=None, t=None, name=None):
        self.signal = signal
        self.name = name

        if t is not None:
            assert len(t) == len(signal)

            self._t = t
            self.dt = t[1] - t[0]
        elif dt is not None:
            self.dt = dt

    # Lazy evaluation of time
    @property
    def t(self):
        if self._t is None:
            return self.dt * np.arange(0, len(self.signal))
        return self._t

    @t.setter
    def t(self, value):
        self._t = value

    @t.deleter
    def t(self):
        del self._t

    def __len__():
        return len(self.signal)

def white_noise_realisation(N_samples, noise_sigma=1, rng=rng):
    return rng.normal(0, noise_sigma or 0, size=N_samples)

def antenna_bp(trace, low_bp, high_bp, dt, order=3):
    fs = 1/dt

    bp_filter = signal.butter(order, [low_bp, high_bp], 'band', fs=fs, output='sos')
    bandpassed = signal.sosfilt(bp_filter, trace)

    return bandpassed

def my_correlation(in1, template, lags=None):
    template_length = len(template)
    in1_length = len(in1)

    if lags is None:
        lags = np.arange(-template_length+1, in1_length + 1)

    # do the correlation jig
    corrs = np.zeros_like(lags, dtype=float)
    for i, l in enumerate(lags):
        if l <= 0: # shorten template at the front
            in1_start = 0
            template_end = template_length

            template_start = -template_length - l
            in1_end = max(0, min(in1_length, -template_start)) # 0 =< l + template_length =< in1_lengt

        elif l > in1_length - template_length:
            # shorten template from the back
            in1_end = in1_length
            template_start = 0

            in1_start = min(l, in1_length)
            template_end = max(0,  in1_length - l)

        else:
            in1_start = min(l, in1_length)
            in1_end   = min(in1_start + template_length, in1_length)

            # full template
            template_start = 0
            template_end   = template_length

        # Slice in1 and template
        in1_slice = in1[in1_start:in1_end]
        template_slice = template[template_start:template_end]

        corrs[i] = np.dot(in1_slice, template_slice)

    return corrs, (in1, template, lags)

def trace_upsampler(trace, template_t, trace_t):
    template_dt = template.t[1] - template.t[0]
    trace_dt = trace_t[1] - trace_t[0]

    upsample_factor = trace_dt/template_dt
    upsampled_trace_N = np.ceil(len(trace) * upsample_factor)

    upsample_factor = int(upsample_factor)
    upsampled_trace_N = int(upsampled_trace_N)

    # upsample trace
    upsampled_trace = np.zeros(upsampled_trace_N)
    upsampled_trace[::upsample_factor] = trace

    #upsampled_t = np.arange(trace_t[0], trace_t[-1], template_dt)
    upsampled_t = template_dt * np.arange(len(upsampled_trace)) + trace_t[0]

    return upsampled_trace, upsampled_t

def trace_downsampler(trace, template_t, trace_t, offset):
    pass


if __name__ == "__main__":
    import os
    import matplotlib
    import sys
    if os.name == 'posix' and "DISPLAY" not in os.environ:
        matplotlib.use('Agg')

    bp_freq = (30e-3, 80e-3) # GHz
    template_dt = 5e-2 # ns
    template_length = 500 # ns
    noise_sigma_factor = 1e-1 # amplitude factor

    N_residuals = 50*3 if len(sys.argv) < 2 else int(sys.argv[1])

    antenna_dt = 2 # ns
    antenna_timelength = 2048 # ns

    #
    # Create the template
    #
    template = Waveform(None, dt=template_dt, name='Template')
    _deltapeak = util.deltapeak(timelength=template_length, samplerate=1/template.dt, offset=0)
    template.signal = antenna_bp(_deltapeak[0], *bp_freq, template_dt)
    template.peak_sample = _deltapeak[1]
    template.peak_time = template.dt * template.peak_sample
    interp1d_template = interpolate.interp1d(template.t, template.signal, assume_sorted=True, fill_value=0, bounds_error=False)

    if True: # show template
        fig, ax = plt.subplots()
        ax.set_title("Deltapeak and Bandpassed Template")
        ax.set_xlabel("Time [ns]")
        ax.set_ylabel("Amplitude")
        ax.plot(template.t, max(template.signal)*_deltapeak[0], label='Impulse Template')
        ax.plot(template.t, template.signal, label='Filtered Template')
        fig.savefig('figures/11_template_deltapeak.pdf')

        if True: # show filtering equivalence samplerates
            _deltapeak = util.deltapeak(timelength=template_length, samplerate=1/antenna_dt, offset=0)
            _time = util.sampled_time(end=template_length, sample_rate=1/antenna_dt)
            _bandpassed = antenna_bp(_deltapeak[0], *bp_freq, antenna_dt)

            ax.plot(_time, max(_bandpassed)*_deltapeak[0], label='Impulse Antenna')
            ax.plot(_time, _bandpassed, label='Filtered Antenna')

            ax.legend()
            fig.savefig('figures/11_template_deltapeak+antenna.pdf')

        if True:
            plt.close(fig)

    #
    # Find difference between true and templated times
    #
    time_residuals = np.zeros(N_residuals)
    for j in tqdm(range(N_residuals)):
        do_plots = j==0

        # receive at antenna
        ## place the deltapeak signal at a random location
        antenna = Waveform(None, dt=antenna_dt, name='Signal')

        if not True: # Create antenna trace without template
            antenna_true_signal, antenna_peak_sample = util.deltapeak(timelength=antenna_timelength, samplerate=1/antenna.dt, offset=[0.2, 0.8], rng=rng)

            antenna.peak_sample = antenna_peak_sample
            antenna.peak_time = antenna.dt * antenna.peak_sample
            antenna.signal = antenna_bp(antenna.signal, *bp_freq, antenna.dt)

        else: # Sample the template at some offset
            antenna.peak_time = antenna_timelength * ((0.8 - 0.2) *rng.random(1) + 0.2)
            sampling_offset = rng.random(1)*antenna.dt

            antenna.t = util.sampled_time(1/antenna.dt, start=0, end=antenna_timelength)

            antenna.signal = interp1d_template(antenna.t - antenna.peak_time)

            antenna.peak_sample = antenna.peak_time/antenna.dt
            antenna_true_signal = antenna.signal


        true_time_offset = antenna.peak_time - template.peak_time

        if do_plots:
            print(f"Antenna Peak Time: {antenna.peak_time}")
            print(f"Antenna Peak Sample: {antenna.peak_sample}")

        if False: # flip polarisation
            antenna.signal *= -1

        ## Add noise
        noise_amplitude = max(template.signal) * noise_sigma_factor
        noise_realisation = noise_amplitude * white_noise_realisation(len(antenna.signal))
        filtered_noise = antenna_bp(noise_realisation, *bp_freq, antenna.dt)

        antenna.signal += filtered_noise

        if do_plots: # show signals
            fig, axs = plt.subplots(2, sharex=True)
            axs[0].set_title("Antenna Waveform")
            axs[-1].set_xlabel("Time [ns]")
            axs[0].set_ylabel("Amplitude")
            axs[0].plot(antenna.t, antenna.signal, label='bandpassed w/ noise', alpha=0.9)
            axs[0].plot(antenna.t, antenna.signal - filtered_noise, label='bandpassed w/o noise', alpha=0.9)
            axs[0].legend()

            axs[1].set_title("Template")
            axs[1].set_ylabel("Amplitude")
            axs[1].plot(template.t, template.signal, label='orig')
            axs[1].plot(template.t + true_time_offset, template.signal, label='true moved orig')
            axs[1].legend()

            axs[0].grid()
            axs[1].grid()

            fig.savefig('figures/11_antenna_signals.pdf')

            if True: # zoom
                wx = 100
                x0 = true_time_offset

                old_xlims = axs[0].get_xlim()
                axs[0].set_xlim( x0-wx, x0+wx)
                fig.savefig('figures/11_antenna_signals_zoom.pdf')

                # restore
                axs[0].set_xlim(*old_xlims)

            if False:
                plt.close(fig)

        axs2 = None
        if True: # upsampled trace
            upsampled_trace, upsampled_t = trace_upsampler(antenna.signal, template.t, antenna.t)

            if do_plots: # Show upsampled traces
                fig2, axs2 = plt.subplots(1, sharex=True)
                if not hasattr(axs2, '__len__'):
                    axs2 = [axs2]

                axs2[-1].set_xlabel("Time [ns]")
                axs2[0].set_ylabel("Amplitude")
                axs2[0].plot(antenna.t, antenna.signal, marker='o', label='orig')
                axs2[0].plot(upsampled_t, upsampled_trace, label='upsampled')
                axs2[0].legend(loc='upper right')

                fig2.savefig('figures/11_upsampled.pdf')

                wx = 1e2
                x0 = upsampled_t[0] + wx - 5
                axs2[0].set_xlim(x0-wx, x0+wx)
                fig2.savefig('figures/11_upsampled_zoom.pdf')

                if True:
                    plt.close(fig2)

            # determine correlations with arguments
            lag_dt = upsampled_t[1] - upsampled_t[0]
            corrs, (out1_signal, out2_template, lags) = my_correlation(upsampled_trace, template.signal)

        else: # downsampled template
            raise NotImplementedError

            corrs, (out1_signal, out2_template, lags) = my_downsampling_correlation(template.signal, antenna.signal, template.t, antenna.t)
            lag_dt = upsampled_t[1] - upsampled_t[0]

        # Determine best correlation time
        idx = np.argmax(abs(corrs))
        best_sample_lag = lags[idx]
        best_time_lag = best_sample_lag * lag_dt
        time_residuals[j] = best_time_lag - true_time_offset

        if do_plots and axs2:
            axs2[-1].axvline(best_time_lag, color='r', alpha=0.5, linewidth=2)
            axs2[-1].axvline(true_time_offset, color='g', alpha=0.5, linewidth=2)

        # Show the final signals correlated
        if do_plots:
            # amplitude scaling required for single axis plotting
            template_amp_scaler = max(abs(template.signal)) / max(abs(antenna.signal))

            # start the figure
            fig, axs = plt.subplots(2, sharex=True)
            ylabel_kwargs = dict(
                                #rotation=0,
                                ha='right',
                                va='center'
                            )
            axs[-1].set_xlabel("Time [ns]")

            offset_list = [
                    [best_time_lag, dict(label=template.name, color='orange')],
                    [true_time_offset, dict(label='True offset', color='green')],
                    ]

            # Signal
            i=0
            axs[i].set_ylabel("Amplitude", **ylabel_kwargs)
            axs[i].plot(antenna.t, antenna.signal, label=antenna.name)

            # Plot the template
            for offset_args in offset_list:
                this_kwargs = offset_args[1]
                offset = offset_args[0]

                l = axs[i].plot(offset + template.t, template_amp_scaler * template.signal, **this_kwargs)

            axs[i].legend()

            # Correlation
            i=1
            axs[i].set_ylabel("Correlation", **ylabel_kwargs)
            axs[i].plot(lags * lag_dt, corrs)

            # Lines across both axes
            for offset_args in offset_list:
                this_kwargs = offset_args[1]
                offset = offset_args[0]

                for i in [0,1]:
                    axs[i].axvline(offset, ls='--', color=this_kwargs['color'], alpha=0.7)

                axs[0].axvline(offset + len(template.signal) * (template.t[1] - template.t[0]), color=this_kwargs['color'], alpha=0.7)


            if True: # zoom
                wx = len(template.signal) * (template.dt)/2
                t0 = best_time_lag

                old_xlims = axs[0].get_xlim()
                axs[i].set_xlim( x0-wx, x0+3*wx)
                fig.savefig('figures/11_corrs_zoom.pdf')

                # restore
                axs[i].set_xlim(*old_xlims)

            fig.tight_layout()
            fig.savefig('figures/11_corrs.pdf')

            if False:
                plt.close(fig)

    # Make a plot of the time residuals
    if len(time_residuals) > 1:
        fig, ax = plt.subplots()
        ax.set_title("Template Correlation Lag finding")
        ax.set_xlabel("Time Residual [ns]")
        ax.set_ylabel("#")
        ax.hist(time_residuals, bins='sqrt', density=False)

        ax.legend(title=f"template dt: {template.dt: .1e}ns\nantenna dt: {antenna.dt: .1e}ns")

        fig.savefig("figures/11_time_residual_hist.pdf")

    plt.show()