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https://gitlab.science.ru.nl/mthesis-edeboone/m-thesis-introduction.git
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Simple Pulse finding using Template Correlation
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465b78c535
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1 changed files with 224 additions and 144 deletions
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@ -10,16 +10,40 @@ rng = np.random.default_rng()
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class Waveform:
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name = None
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time = None
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signal = None
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dt = None
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def __init__(signal, time=None, name=None, dt=None):
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_t = None
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def __init__(self,signal=None, dt=None, t=None, name=None):
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self.signal = signal
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self.time = time
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self.name = name
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if self.time is None and dt is not None:
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self.time = dt * len(signal)
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if t is not None:
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assert len(t) == len(signal)
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self._t = t
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self.dt = t[1] - t[0]
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elif dt is not None:
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self.dt = dt
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# Lazy evaluation of time
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@property
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def t(self):
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if self._t is None:
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return self.dt * np.arange(0, len(self.signal))
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return self._t
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@t.setter
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def t(self, value):
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self._t = value
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@t.deleter
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def t(self):
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del self._t
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def __len__():
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return len(self.signal)
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def white_noise_realisation(N_samples, noise_sigma=1, rng=rng):
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return rng.normal(0, noise_sigma or 0, size=N_samples)
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@ -56,7 +80,7 @@ def my_correlation(in1, template):
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return corrs, (in1_long, template_long, lags)
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def trace_upsampler(template_signal, trace, template_t, trace_t):
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template_dt = template_t[1] - template_t[0]
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template_dt = template.t[1] - template.t[0]
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trace_dt = trace_t[1] - trace_t[0]
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upsample_factor = trace_dt/template_dt
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@ -89,56 +113,81 @@ if __name__ == "__main__":
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template_length = 100 # ns
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noise_sigma_factor = 1e1 # keep between 10 and 0.1
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N_residuals = 50*3
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antenna_dt = 2 # ns
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antenna_timelength = 2048 # ns
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_deltapeak = util.deltapeak(timelength=template_length, samplerate=1/template_dt, offset=10/template_dt)
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template_t = util.sampled_time(1/template_dt, start=0, end=template_length)
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template_signal = antenna_bp(_deltapeak[0], *bp_freq, (np.sqrt(antenna_dt/template_dt))*template_dt) # TODO: fix sqrt constant
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template_peak_time = template_t[_deltapeak[1]]
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#
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# Create the template
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#
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template = Waveform(None, dt=template_dt, name='Template')
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_deltapeak = util.deltapeak(timelength=template_length, samplerate=1/template.dt, offset=10/template.dt)
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template.signal = antenna_bp(_deltapeak[0], *bp_freq, (np.sqrt(antenna_dt/template_dt))*template_dt) # TODO: fix sqrt constant
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template.peak_sample = _deltapeak[1]
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template.peak_time = template.dt * template.peak_sample
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if False: # show template
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if True: # show template
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fig, ax = plt.subplots()
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ax.set_title("Deltapeak and Bandpassed Template")
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ax.set_xlabel("Time [ns]")
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ax.set_ylabel("Amplitude")
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ax.plot(template_t, max(template_signal)*_deltapeak[0])
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ax.plot(template_t, template_signal)
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ax.plot(template.t, max(template.signal)*_deltapeak[0])
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ax.plot(template.t, template.signal)
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fig.savefig('figures/11_template_deltapeak.pdf')
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if True:
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plt.close(fig)
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#
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# Find difference between true and templated times
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#
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time_residuals = np.zeros(N_residuals)
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for j in range(N_residuals):
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do_plots = j==0
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# receive at antenna
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antenna_t = util.sampled_time(1/antenna_dt, start=0, end=antenna_timelength)
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antenna_samplelength = len(antenna_t)
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## place the deltapeak signal at a random location
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antenna_true_signal, antenna_peak_location = util.deltapeak(timelength=antenna_timelength, samplerate=1/antenna_dt, offset=[0.2, 0.8], rng=rng)
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antenna_peak_time = antenna_t[antenna_peak_location]
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antenna = Waveform(None, dt=antenna_dt, name='Signal')
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antenna_true_signal, antenna_peak_sample = util.deltapeak(timelength=antenna_timelength, samplerate=1/antenna.dt, offset=[0.2, 0.8], rng=rng)
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antenna.signal = antenna_true_signal
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antenna.peak_sample = antenna_peak_sample
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antenna.peak_time = antenna.dt * antenna.peak_sample
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if not True: # flip polarisation
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antenna_true_signal *= -1
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if do_plots:
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print(f"Antenna Peak Time: {antenna.peak_time}")
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print(f"Antenna Peak Sample: {antenna.peak_sample}")
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if False: # bandpass when emitting the signal
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antenna.signal = antenna_bp(antenna.signal, *bp_freq, antenna.dt)
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if False: # flip polarisation
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antenna.signal *= -1
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## Add noise
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noise_amplitude = max(template_signal) * noise_sigma_factor
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noise_realisation = noise_amplitude * white_noise_realisation(len(antenna_true_signal))
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antenna_unfiltered_signal = antenna_true_signal + noise_realisation
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antenna_signal = antenna_bp(antenna_unfiltered_signal, *bp_freq, antenna_dt)
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noise_amplitude = max(template.signal) * noise_sigma_factor
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noise_realisation = noise_amplitude * white_noise_realisation(len(antenna.signal))
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true_time_offset = antenna_peak_time - template_peak_time
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antenna_unfiltered_signal = antenna.signal + noise_realisation
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antenna.signal = antenna_bp(antenna_unfiltered_signal, *bp_freq, antenna.dt)
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if True: # show signals
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true_time_offset = antenna.peak_time - template.peak_time
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if do_plots: # show signals
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fig, axs = plt.subplots(2, sharex=True)
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axs[0].set_title("Antenna Waveform")
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axs[-1].set_xlabel("Time [ns]")
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axs[0].set_ylabel("Amplitude")
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axs[0].plot(antenna_t, antenna_signal, label='bandpassed w/ noise')
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axs[0].plot(antenna_t, antenna_unfiltered_signal, label='true signal w/ noise')
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axs[0].plot(antenna_t, antenna_true_signal, label='true signal w/o noise')
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axs[0].plot(antenna.t, antenna.signal, label='bandpassed w/ noise', alpha=0.9)
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axs[0].plot(antenna.t, antenna_unfiltered_signal, label='true signal w/ noise', alpha=0.9)
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axs[0].plot(antenna.t, antenna_true_signal, label='true signal w/o noise', alpha=0.9)
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axs[0].legend()
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axs[1].set_title("Template")
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axs[1].set_ylabel("Amplitude")
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axs[1].plot(template_t, template_signal, label='orig')
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axs[1].plot(template_t + true_time_offset, template_signal, label='moved orig')
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axs[1].plot(template.t, template.signal, label='orig')
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axs[1].plot(template.t + true_time_offset, template.signal, label='true moved orig')
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axs[1].legend()
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fig.savefig('figures/11_antenna_signals.pdf')
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@ -154,17 +203,21 @@ if __name__ == "__main__":
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# restore
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axs[0].set_xlim(*old_xlims)
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if True: # upsampled trace
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upsampled_trace, upsampled_t = trace_upsampler(template_signal, antenna_signal, template_t, antenna_t)
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if False:
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plt.close(fig)
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if True: # Show upsampled traces
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axs2 = None
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if True: # upsampled trace
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upsampled_trace, upsampled_t = trace_upsampler(template.signal, antenna.signal, template.t, antenna.t)
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if do_plots: # Show upsampled traces
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fig2, axs2 = plt.subplots(1, sharex=True)
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if not hasattr(axs2, '__len__'):
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axs2 = [axs2]
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axs2[-1].set_xlabel("Time [ns]")
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axs2[0].set_ylabel("Amplitude")
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axs2[0].plot(antenna_t, antenna_signal, marker='o', label='orig')
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axs2[0].plot(antenna.t, antenna.signal, marker='o', label='orig')
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axs2[0].plot(upsampled_t, upsampled_trace, label='upsampled')
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axs2[0].legend(loc='upper right')
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@ -175,68 +228,95 @@ if __name__ == "__main__":
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axs2[0].set_xlim(x0-wx, x0+wx)
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fig2.savefig('figures/11_upsampled_zoom.pdf')
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if True:
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plt.close(fig2)
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# determine correlations with arguments
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lag_dt = upsampled_t[1] - upsampled_t[0]
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corrs, (out1_signal, out2_template, lags) = my_correlation(upsampled_trace, template_signal)
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corrs, (out1_signal, out2_template, lags) = my_correlation(upsampled_trace, template.signal)
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else: # downsampled template
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raise NotImplementedError
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corrs, (out1_signal, out2_signal, lags) = my_downsampling_correlation(template_signal, antenna_signal, template_t, antenna_t)
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corrs, (out1_signal, out2_template, lags) = my_downsampling_correlation(template.signal, antenna.signal, template.t, antenna.t)
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lag_dt = upsampled_t[1] - upsampled_t[0]
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# Determine best correlation time
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idx = np.argmax(abs(corrs))
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best_sample_lag = lags[idx]
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best_time_lag = best_sample_lag * lag_dt
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if axs2:
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time_residuals[j] = best_time_lag - true_time_offset
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if do_plots and axs2:
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axs2[-1].axvline(best_time_lag, color='r', alpha=0.5, linewidth=2)
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# Show the final signals correlated
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if True:
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fig, axs = plt.subplots(3, sharex=True)
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if do_plots:
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fig, axs = plt.subplots(2, sharex=True)
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ylabel_kwargs = dict(
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rotation=0,
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#rotation=0,
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ha='right',
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va='center'
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)
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axs[-1].set_xlabel("Time [ns]")
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offset_list = [
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[best_time_lag, dict(label=template.name, color='orange')],
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[true_time_offset, dict(label='True offset', color='green')],
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]
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# Signal
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i=0
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axs[i].set_ylabel("Signal\nAmplitude", **ylabel_kwargs)
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axs[i].plot(antenna_t, antenna_signal)
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axs[i].set_ylabel("Amplitude", **ylabel_kwargs)
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axs[i].plot(antenna.t, antenna.signal, label=antenna.name)
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# Template
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i=1
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axs[i].set_ylabel("Template\nAmplitude", **ylabel_kwargs)
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for offset in [0, best_time_lag]:
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axs[i].axvline(offset + len(template_signal) * (template_t[1] - template_t[0]), color='g')
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axs[i].axvline(offset, color='g')
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axs[i].plot(offset + template_t, template_signal)
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# Put template on an twinned axis (magnitudes are different)
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ax2 = axs[i].twinx()
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for i, offset_args in enumerate(offset_list):
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this_kwargs = offset_args[1]
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offset = offset_args[0]
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ax2.axvline(offset + len(template.signal) * (template.t[1] - template.t[0]), color=this_kwargs['color'], alpha=0.7)
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ax2.axvline(offset, color=this_kwargs['color'], alpha=0.7)
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ax2.plot(offset + template.t, template.signal, **this_kwargs)
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# Correlation
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i=2
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i=1
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axs[i].set_ylabel("Correlation", **ylabel_kwargs)
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axs[i].plot(lags * lag_dt, corrs)
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axs[i].axvline(best_time_lag, color='r', ls='--')
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for i, offset_args in enumerate(offset_list):
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this_kwargs = offset_args[1]
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offset = offset_args[0]
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axs[i].axvline(offset, ls='--', **this_kwargs)
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if True: # zoom
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wx = len(template_signal) * (template_t[1] - template_t[0])/2
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wx = len(template.signal) * (template.t[1] - template.t[0])/2
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t0 = best_time_lag
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for t in [t0-wx, t0+wx]:
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axs[2].axvline(t, color='g')
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old_xlims = axs[0].get_xlim()
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axs[i].set_xlim( x0-wx, x0+3*wx)
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fig.savefig('figures/11_corrs_zoom.pdf')
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# restore
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axs[i].set_xlim(*old_xlims)
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fig.tight_layout()
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fig.legend()
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fig.savefig('figures/11_corrs.pdf')
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#
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time_residual = best_time_lag - true_time_offset
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if False:
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plt.close(fig)
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print(time_residual, template_dt, antenna_dt)
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# Make a plot of the time residuals
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fig, ax = plt.subplots()
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ax.set_title("Template Correlation Lag finding")
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ax.set_xlabel("Time Residual [ns]")
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ax.set_ylabel("#")
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ax.hist(time_residuals, bins='sqrt', density=False)
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ax.legend(title=f"template dt: {template.dt: .1e}ns\nantenna dt: {antenna.dt: .1e}ns")
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fig.savefig("figures/11_time_residual_hist.pdf")
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plt.show()
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