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Script for SNR determination: somethings up here
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426
fourier/signal_to_noise.py
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426
fourier/signal_to_noise.py
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#!/usr/bin/env python3
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__doc__ = \
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"""
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Show
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"""
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from collections import namedtuple
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import matplotlib.pyplot as plt
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import matplotlib.gridspec as gridspec
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import numpy as np
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import scipy.fftpack as ft
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rng = np.random.default_rng()
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passband = namedtuple("Band", ['low', 'high'], defaults=[0, np.inf])
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def get_freq_spec(val,dt):
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"""From earsim/tools.py"""
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fval = np.abs(np.fft.fft(val))[:len(val)//2]
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freq = np.fft.fftfreq(len(val),dt)[:len(val)//2]
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return fval, freq
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def ft_spectrum( signal, sample_rate=1, ftfunc=None, freqfunc=None, mask_bias=False, normalise_amplitude=False):
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"""Return a FT of $signal$, with corresponding frequencies"""
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if True:
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return get_freq_spec(signal, 1/sample_rate)
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n_samples = len(signal)
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if ftfunc is None:
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real_signal = np.isrealobj(signal)
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if False and real_signal:
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ftfunc = ft.rfft
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freqfunc = ft.rfftfreq
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else:
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ftfunc = ft.fft
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freqfunc = ft.fftfreq
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if freqfunc is None:
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freqfunc = ft.fftfreq
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normalisation = 2/len(signal) if normalise_amplitude else 1
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spectrum = normalisation * ftfunc(signal)
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freqs = freqfunc(n_samples, 1/sample_rate)
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if not mask_bias:
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return spectrum, freqs
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else:
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return spectrum[1:], freqs[1:]
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def plot_spectrum( spectrum, freqs, plot_complex=False, plot_power=False, plot_amplitude=None, ax=None, freq_unit="Hz", freq_scaler=1):
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""" Plot a signal's spectrum on an Axis object"""
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plot_amplitude = plot_amplitude or (not plot_power and not plot_complex)
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alpha = 1
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if ax is None:
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ax = plt.gca()
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ax.set_title("Spectrum")
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ax.set_xlabel("f" + (" ["+freq_unit+"]" if freq_unit else "" ))
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ylabel = ""
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if plot_amplitude or plot_complex:
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ylabel = "Amplitude"
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if plot_power:
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if ylabel:
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ylabel += "|"
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ylabel += "Power"
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ax.set_ylabel(ylabel)
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if plot_complex:
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alpha = 0.5
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ax.plot(freqs/freq_scaler, np.real(spectrum), '.-', label='Real', alpha=alpha)
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ax.plot(freqs/freq_scaler, np.imag(spectrum), '.-', label='Imag', alpha=alpha)
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if plot_power:
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ax.plot(freqs/freq_scaler, np.abs(spectrum)**2, '.-', label='Power', alpha=alpha)
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if plot_amplitude:
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ax.plot(freqs/freq_scaler, np.abs(spectrum), '.-', label='Abs', alpha=alpha)
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ax.legend()
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return ax
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def plot_phase( spectrum, freqs, ylim_epsilon=0.5, ax=None, freq_unit="Hz", freq_scaler=1):
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if ax is None:
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ax = plt.gca()
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ax.set_ylabel("Phase")
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ax.set_xlabel("f" + (" ["+freq_unit+"]" if freq_unit else "" ))
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ax.plot(freqs/freq_scaler, np.angle(spectrum), '.-')
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ax.set_ylim(-1*np.pi - ylim_epsilon, np.pi + ylim_epsilon)
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return ax
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def plot_signal( signal, sample_rate = 1, ax=None, time=None, time_unit="s", **kwargs):
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if ax is None:
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ax = plt.gca()
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if time is None:
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time = np.arange(len(signal))/sample_rate
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ax.set_title("Signal")
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ax.set_xlabel("t" + (" ["+time_unit+"]" if time_unit else "" ))
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ax.set_ylabel("A(t)")
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ax.plot(time, signal, **kwargs)
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return ax
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def plot_combined_spectrum(spectrum, freqs,
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spectrum_kwargs={}, fig=None, gs=None, freq_scaler=1, freq_unit="Hz"):
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"""Plot both the frequencies and phase in one figure."""
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# configure plotting layout
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if fig is None:
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fig = plt.figure(figsize=(8, 16))
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if gs is None:
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gs = gridspec.GridSpec(2, 1, figure=fig, height_ratios=[3,1], hspace=0)
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ax1 = fig.add_subplot(gs[:-1, -1])
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ax2 = fig.add_subplot(gs[-1, -1], sharex=ax1)
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axes = np.array([ax1, ax2])
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# plot the spectrum
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plot_spectrum(spectrum, freqs, ax=ax1, freq_scaler=freq_scaler, freq_unit=freq_unit, **spectrum_kwargs)
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# plot the phase
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plot_phase(spectrum, freqs, ax=ax2, freq_scaler=freq_scaler, freq_unit=freq_unit)
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ax1.xaxis.tick_top()
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[label.set_visible(False) for label in ax1.get_xticklabels()]
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return fig, axes
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def phasemod(phase, low=np.pi):
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"""
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Modulo phase such that it falls within the
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interval $[-low, 2\pi - low)$.
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"""
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return (phase + low) % (2*np.pi) - low
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def save_all_figs_to_path(fnames, figs=None, default_basename=__file__, default_extensions=['.pdf', '.png']):
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if figs is None:
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figs = [plt.figure(i) for i in plt.get_fignums()]
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default_basename = path.basename(default_basename)
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# singular value
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if isinstance(fnames, (str, True)):
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fnames = [fnames]
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if len(fnames) == len(figs):
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fnames_list = zip(figs, fnames, False)
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elif len(fnames) == 1:
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fnames_list = ( (fig, fnames[0], len(figs) > 1) for fig in figs)
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else:
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# outer product magic
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fnames_list = ( (fig,fname, False) for fname in fnames for fig in figs )
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del fnames
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# format fnames
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pad_width = max(2, int(np.floor(np.log10(len(figs))+1)))
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fig_fnames = []
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for fig, fnames, append_num in fnames_list:
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if not hasattr(fnames, '__len__') or isinstance(fnames, str):
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# single name
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fnames = [fnames]
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new_fnames = []
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for fname in fnames:
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if path.isdir(fname):
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fname = path.join(fname, path.splitext(default_basename)[0]) # leave off extension
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if append_num is True:
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fname += ("_fig{:0"+str(pad_width)+"d}").format(fig.number)
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if not path.splitext(fname)[1]: # no extension
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for ext in default_extensions:
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new_fnames.append(fname+ext)
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else:
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new_fnames.append(fname)
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fig_fnames.append(new_fnames)
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# save files
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for fnames, fig in zip(fig_fnames, figs):
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for fname in fnames:
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fig.savefig(fname, transparent=True)
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def sine_fitfunc(t, amp=1, freq=1, phase=0, off=0):
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"""Simple sine wave for fitting purposes"""
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return amp*np.sin( 2*np.pi*freq*t + phase) + off
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def sampled_time(sample_rate=1, start=0, end=1, offset=0):
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return offset + np.arange(start, end, 1/sample_rate)
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def bandpass_mask(freqs, band=passband()):
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low_pass = abs(freqs) <= band[1]
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high_pass = abs(freqs) >= band[0]
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return low_pass & high_pass
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def bandsize(band = passband()):
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return band[1] - band[0]
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def bandlevel(samples, samplerate=1, band=passband(), normalise_bandsize=True, **ft_kwargs):
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fft, freqs = ft_spectrum(samples, samplerate, **ft_kwargs)
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bandmask = bandpass_mask(freqs, band=band)
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if normalise_bandsize:
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bins = np.count_nonzero(bandmask, axis=-1)
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else:
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bins = 1
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level = np.sum(np.abs(fft[bandmask]))
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return level/bins
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def noisy_sine_sampling(time, init_params, noise_sigma=1, rng=rng):
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if init_params[2] is None:
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init_params[2] = phasemod(2*np.pi*rng.random())
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samples = sine_fitfunc(time, *init_params)
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noise = rng.normal(0, noise_sigma, size=len(samples))
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return samples, noise
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def main(
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N = 1,
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f_sample = 250e6, # Hz
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t_length = 1e4 * 1e-9, # s
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noise_band = passband(30e6, 80e6),
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noise_sigma = 1,
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# signal properties
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f_sine = 50e6,
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signal_band = passband(50e6 - 1e6, 50e6 + 1e6),
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sine_amp = 0.2,
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sine_offset = 0,
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return_ranges_plot = False,
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cut_signal_band_from_noise_band = False
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):
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N = int(N)
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init_params = np.array([sine_amp, f_sine, None, sine_offset])
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axs = None
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snrs = np.zeros( N )
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time = sampled_time(f_sample, end=t_length)
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for j in range(N):
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samples, noise = noisy_sine_sampling(time, init_params, noise_sigma)
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# determine signal to noise
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noise_level = bandlevel(noise, f_sample, noise_band)
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if cut_signal_band_from_noise_band:
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lower_noise_band = passband(noise_band[0], signal_band[0])
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upper_noise_band = passband(signal_band[1], noise_band[1])
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noise_level = bandlevel(noise, f_sample, lower_noise_band)
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noise_level += bandlevel(noise, f_sample, upper_noise_band)
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signal_level = bandlevel(samples, f_sample, signal_band)
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snrs[j] = signal_level/noise_level
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# make a nice plot showing what ranges were taken
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# and the bandlevels associated with them
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if return_ranges_plot and j == 0:
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combined_fft, freqs = ft_spectrum(samples+noise, f_sample)
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# plot the original signal
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if False:
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_, ax = plt.subplots()
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ax = plot_signal(samples+noise, sample_rate=f_sample/1e6, time_unit='us', ax=ax)
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# plot the spectrum
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if True:
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freq_scaler=1e6
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_, axs = plot_combined_spectrum(combined_fft, freqs, freq_scaler=freq_scaler, freq_unit='MHz')
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# indicate band ranges and frequency
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for ax in axs:
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ax.axvline(f_sine/freq_scaler, color='r', alpha=0.4)
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ax.axvspan(noise_band[0]/freq_scaler, noise_band[1]/freq_scaler, color='purple', alpha=0.3, label='noiseband')
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ax.axvspan(signal_band[0]/freq_scaler, signal_band[1]/freq_scaler, color='orange', alpha=0.3, label='signalband')
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# indicate initial phase
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axs[1].axhline(init_params[2], color='r', alpha=0.4)
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# plot the band levels
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levelax = axs[0].twinx()
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levelax.set_ylabel("Bandlevel")
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levelax.hlines(signal_level, noise_band[0]/freq_scaler, signal_band[1]/freq_scaler, colors=['orange'])
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levelax.hlines(noise_level, noise_band[0]/freq_scaler, noise_band[1]/freq_scaler, colors=['purple'])
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levelax.set_ylim(bottom=0)
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axs[0].legend()
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# plot signal_band pass signal
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if False:
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freqs = np.fft.fftfreq(len(samples), 1/f_sample)
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bandmask = bandpass_mask(freqs, band=signal_band)
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fft = np.fft.fft(samples)
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fft[ ~bandmask ] = 0
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bandpassed_samples = np.fft.ifft(fft)
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_, ax3 = plt.subplots()
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ax3 = plot_signal(bandpassed_samples, sample_rate=f_sample/1e6, time_unit='us', ax=ax3)
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ax3.set_title("Bandpassed Signal")
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return snrs, axs
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if __name__ == "__main__":
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from argparse import ArgumentParser
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import os.path as path
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rng = np.random.default_rng(1)
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parser = ArgumentParser(description=__doc__)
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parser.add_argument("fname", metavar="path/to/figure[/]", nargs="?", help="Location for generated figure, will append __file__ if a directory. If not supplied, figure is shown.")
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args = parser.parse_args()
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default_extensions = ['.pdf', '.png']
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if args.fname == 'none':
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args.fname = None
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###
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t_lengths = np.linspace(1e3, 5e4)* 1e-9 # s
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N = 10e1
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f_sine = 53e6 # Hz
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f_sample = 250e6 # Hz
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if True:
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N = 2 # Note: keep this low, N figures will be displayed!
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N_t_length = 2
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for t_length in t_lengths[-N_t_length-1:-1]:
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snrs = np.zeros( int(N))
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for i in range(int(N)):
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delta_f = 1/t_length
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snrs[i], axs = main(
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N=1,
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t_length=t_length,
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f_sample=f_sample,
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# signal properties
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f_sine = f_sine,
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sine_amp = 1,
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noise_sigma = 1,
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noise_band = passband(30e6, 80e6),
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signal_band = passband(f_sine- 3*delta_f, f_sine + 3*delta_f),
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return_ranges_plot=True
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)
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axs[0].set_title("SNR: {}, N:{}".format(snrs[i], t_length*f_sample))
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axs[0].set_xlim(
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(f_sine - 20*delta_f)/1e6,
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(f_sine + 20*delta_f)/1e6
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)
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print(snrs, "M:",np.mean(snrs))
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plt.show(block=True)
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else:
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#original code
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my_snrs = np.zeros( (len(t_lengths), int(N)) )
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for j, t_length in enumerate(t_lengths):
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return_ranges_plot = ((j==0) and True) or ( (j==(len(t_lengths)-1)) and True)
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delta_f = 1/t_length
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my_snrs[j], axs = main(
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N=N,
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t_length=t_length,
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f_sample = f_sample,
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# signal properties
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f_sine = f_sine,
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sine_amp = 1,
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noise_sigma = 1,
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noise_band = passband(30e6, 80e6),
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signal_band = passband(f_sine- 3*delta_f, f_sine + 3*delta_f),
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return_ranges_plot=return_ranges_plot,
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)
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if return_ranges_plot:
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ranges_axs = axs
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fig, axs2 = plt.subplots()
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axs2.set_xlabel("N = T*$f_s$")
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axs2.set_ylabel("SNR")
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for j, t_length in enumerate(t_lengths):
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t_length = t_length * f_sample
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axs2.plot(np.repeat(t_length, my_snrs.shape[1]), my_snrs[j], ls='none', color='blue', marker='o', alpha=max(0.01, 1/my_snrs.shape[1]))
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axs2.plot(t_length, np.mean(my_snrs[j]), color='green', marker='*', ls='none')
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### Save or show figures
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if not args.fname:
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# empty list, False, None
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plt.show()
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else:
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save_all_figs_to_path(args.fname, default_basename=__file__)
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