waveforms 2.0.1__tar.gz → 2.0.2__tar.gz

{waveforms-2.0.1 → waveforms-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: waveforms
-Version: 2.0.1
+Version: 2.0.2
 Summary: Edit waveforms used in experiment
 Author-email: feihoo87 <feihoo87@gmail.com>
 Maintainer-email: feihoo87 <feihoo87@gmail.com>
@@ -38,6 +38,7 @@ Provides-Extra: docs
 Requires-Dist: Sphinx; extra == "docs"
 Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
 Requires-Dist: sphinxcontrib-zopeext; extra == "docs"
+Dynamic: license-file
 
 # waveforms
 [![View build status](https://github.com/feihoo87/waveforms/actions/workflows/workflow.yml/badge.svg)](https://github.com/feihoo87/waveforms/)

waveforms-2.0.2/waveforms/distortion.py

@@ -0,0 +1,376 @@
+import warnings
+from itertools import repeat, zip_longest
+from typing import Sequence
+
+import numpy as np
+from scipy.fftpack import fft, fftfreq, ifft, ifftshift
+from scipy.optimize import curve_fit
+from scipy.signal import fftconvolve, lfilter, lfiltic, tf2zpk, zpk2sos, zpk2tf
+
+
+def shift(signal: np.ndarray, delay: float, dt: float) -> np.ndarray:
+    """
+    delay a signal
+
+    Args:
+        signal (np.ndarray): input signal
+        delay (float): delayed time
+        dt (float): time step of signal samples
+
+    Returns:
+        np.ndarray: delayed signal
+    """
+    points = int(delay // dt)
+    delta = delay / dt - points
+
+    if delta > 0:
+        ker = np.array([0, 1 - delta, delta])
+        signal = np.convolve(signal, ker, mode='same')
+
+    if points == 0:
+        return signal
+
+    ret = np.zeros_like(signal)
+    if points < 0:
+        ret[:points] = signal[-points:]
+    else:
+        ret[points:] = signal[:-points]
+    return ret
+
+
+def extractKernel(sig_in, sig_out, sample_rate, bw=None, skip=0):
+    corr = fft(sig_in) / fft(sig_out)
+    ker = np.real(ifftshift(ifft(corr)))
+    if bw is not None and bw < 0.5 * sample_rate:
+        k = np.exp(-0.5 * np.linspace(-3.0, 3.0, int(2 * sample_rate / bw))**2)
+        ker = np.convolve(ker, k / k.sum(), mode='same')
+    return ker[int(skip):len(ker) - int(skip)]
+
+
+def zDistortKernel(dt: float, params: Sequence[tuple]) -> np.ndarray:
+    t = 3 * np.asarray(params)[:, 0].max()
+    omega = 2 * np.pi * fftfreq(int(t / dt) + 1, dt)
+
+    H = 1
+    for tau, A in params:
+        H += (1j * A * omega * tau) / (1j * omega * tau + 1)
+
+    ker = ifftshift(ifft(1 / H)).real
+    return ker
+
+
+def high_pass_filter(tau, sample_rate):
+    """
+    high pass filter
+    """
+    k = 2.0 * tau * sample_rate
+    a = [1.0, (1 - k) / (1 + k)]
+    b = [k / (1 + k), -k / (1 + k)]
+    return b, a
+
+
+def exp_decay_filter_old(amp, tau, sample_rate):
+    """
+    exp decay filter
+
+                    A
+    H(w) = --------------------
+            1 - 1j / (w * tau)
+
+    Args:
+        amp (float): amplitude of the filter
+        tau (float): decay time
+        sample_rate (float): sampling rate
+    """
+
+    alpha = 1 - np.exp(-1 / (abs(sample_rate * tau) * (1 + amp)))
+
+    if amp >= 0:
+        k = amp / (1 + amp - alpha)
+        a = [(1 - k + k * alpha), -(1 - k) * (1 - alpha)]
+    else:
+        k = -amp / (1 + amp) / (1 - alpha)
+        a = [(1 + k - k * alpha), -(1 + k) * (1 - alpha)]
+
+    b = [1 / a[0], -(1 - alpha) / a[0]]
+    a = [1, a[1] / a[0]]
+
+    return b, a
+
+
+def exp_decay_filter(amp: float | Sequence[float],
+                     tau: float | Sequence[float],
+                     sample_rate: float,
+                     inv: bool = False,
+                     output='ba') -> tuple[np.ndarray, np.ndarray]:
+    """
+    exp decay filter
+
+    Infinite impulse response as multiexponential decay. When input signal
+    is the Heaviside theta function u(t), the output signal is:
+    out(t) = u(t) * (1 - A_1 * exp(-t / tau_1) - A_2 * exp(-t / tau_2) ...)
+    where A_i and tau_i are the amplitude and decay time of the i-th
+    exponential decay.
+
+    The transfer function of the filter is:
+
+    H(w) = 1 - H_1(w) - H_2(w) - ... - H_n(w)
+
+    where
+                       A_i
+    H_i(w) = --------------------------
+              1 - 1 / (1j * w * tau_i)
+
+    Args:
+        amp (float): amplitude of the filter
+        tau (float): decay time
+        sample_rate (float): sampling rate
+        inv (bool): if True, the filter is inverted
+        output (str): output type, 'ba' for numerator (b) and denominator (a)
+            polynomials, 'sos' for second-order sections, 'zpk' for zeros (z),
+            poles (p) and gain (k). See scipy.signal.lfilter for more.
+
+    Returns:
+        tuple: (b, a) array like, numerator (b) and denominator (a)
+        polynomials of the IIR filter. See scipy.signal.lfilter for more.
+    """
+
+    if isinstance(amp, (int, float, complex)):
+        amp = [amp]
+        tau = [tau]
+    numerator, denominator = np.poly1d([0.0]), np.poly1d([1.0])
+    for i, (A, t) in enumerate(zip(amp, tau)):
+        denominator = denominator * np.poly1d([1, -1 / t])
+        n = np.poly1d([-A, 0.0])
+        for j, t_ in enumerate(tau):
+            if j != i:
+                n = n * np.poly1d([1, -1 / t_])
+        numerator = numerator + n
+    numerator = numerator + denominator
+
+    z = np.exp(-numerator.roots / sample_rate)
+    p = np.exp(-denominator.roots / sample_rate)
+    if inv:
+        z, p = p, z
+    k = numerator(0) / denominator(0) * np.prod(1 - p) / np.prod(1 - z)
+
+    if output == 'sos':
+        return zpk2sos(z, p, k)
+    elif output == 'ba':
+        return zpk2tf(z, p, k)
+    elif output == 'zpk':
+        return z, p, k
+
+
+def reflection_filter(f, A, tau):
+    """
+    reflection filter
+
+    Infinite impulse response as reflection. When input signal
+    is in(t), the output signal is:
+    out(t) = in(t) + A * in(t - tau) + A^2 * in(t - 2 * tau) + ...
+
+    The transfer function of the filter is:
+                      1 - A
+    H(w) = ----------------------------
+            1 - A * exp(- i * w * tau)
+    Args:
+        f (float): frequency
+        A (float): amplitude of the reflection
+        tau (float): delay time
+    """
+    return (1 - A) / (1 - A * np.exp(-2j * np.pi * f * tau))
+
+
+def reflection(sig, A, tau, sample_rate):
+    freq = np.fft.fftfreq(len(sig), 1 / sample_rate)
+    return np.fft.ifft(np.fft.fft(sig) * reflection_filter(freq, A, tau)).real
+
+
+def correct_reflection(sig, A, tau, sample_rate=None):
+    from waveforms.waveform import Waveform
+
+    if isinstance(sig, Waveform):
+        return 1 / (1 - A) * sig - A / (1 - A) * (sig >> tau)
+    if sample_rate is not None:
+        freq = np.fft.fftfreq(len(sig), 1 / sample_rate)
+        return np.fft.ifft(np.fft.fft(sig) /
+                           reflection_filter(freq, A, tau)).real
+    else:
+        raise ValueError('sample_rate is not given')
+
+
+def combine_filters(
+    filters: list[tuple[np.ndarray,
+                        np.ndarray]]) -> tuple[np.ndarray, np.ndarray]:
+    """
+    combine filters
+
+    Args:
+        filters (list): list of (b, a) array like, numerator (b) and denominator
+        (a) polynomials of the IIR filter. See scipy.signal.lfilter for more.
+
+    Returns:
+        tuple: (b, a) array like, numerator (b) and denominator (a)
+        polynomials of the combined filter. See scipy.signal.lfilter for more.
+    """
+    b, a = np.poly1d([1.0]), np.poly1d([1.0])
+    for b_, a_ in filters:
+        b = b * np.poly1d(b_)
+        a = a * np.poly1d(a_)
+    return b.coeffs, a.coeffs
+
+
+def factor_filter(b, a):
+    """
+    factor filter
+
+    Args:
+        b (array_like): numerator polynomial of the IIR filter.
+        a (array_like): denominator polynomial of the IIR filter.
+
+    Returns:
+        list: list of (b, a) array like, numerator (b) and denominator
+    """
+    b, a = np.poly1d(b), np.poly1d(a)
+    p = a.roots
+    q = b.roots
+    b_amp = (b[0] / a[0])**(1 / max(len(q), len(p)))
+    filters = []
+    for a_, b_ in zip_longest(p, q, fillvalue=0):
+        filters.append(([b_amp, -b_amp * b_], [1, -a_]))
+    return filters
+
+
+def stable_filter(exp_decay_filters: list, sample_rate: float):
+    """
+    check if the filter is stable
+
+    Args:
+        exp_decay_filters (list): list of (amp, tau) pairs
+    """
+    filters = []
+    for amp, tau in exp_decay_filters:
+        a, b = exp_decay_filter(amp, tau, sample_rate)
+        filters.append((b, a))
+
+    b, a = combine_filters(filters)
+    z, p, k = tf2zpk(b, a)
+    if np.all(np.abs(p) < 1):
+        return True
+    else:
+        return False
+
+
+def predistort(sig: np.ndarray,
+               filters: list = None,
+               ker: np.ndarray = None,
+               initial: float = 0.0,
+               initial_x: np.ndarray | None = None,
+               initial_y: np.ndarray | None = None,
+               zi: np.ndarray | None = None,
+               return_zf: bool = False) -> np.ndarray:
+    if filters is not None:
+        b, a = combine_filters(filters)
+        z, p, k = tf2zpk(b, a)
+        if np.all(np.abs(p) < 1):
+            pass
+        else:
+            warnings.warn('Warning: filter is unstable')
+
+        if zi is None:
+            if initial_x is None:
+                initial_x = np.full((len(b) - 1, ), initial)
+            else:
+                initial_x = np.asarray(initial_x)[:len(b) - 1]
+            if initial_y is None:
+                initial_y = np.full((len(a) - 1, ), initial)
+            else:
+                initial_y = np.asarray(initial_y)[:len(a) - 1]
+            zi = lfiltic(
+                b,
+                a,
+                initial_y,
+                initial_x,
+            )
+        sig, zf = lfilter(b, a, sig, zi=zi)
+
+    if ker is None:
+        if return_zf:
+            return sig, zf
+        else:
+            return sig
+
+    size = len(sig)
+    sig = np.hstack((np.zeros_like(sig), sig, np.zeros_like(sig)))
+    start = size + len(ker) // 2
+    stop = start + size
+    points = fftconvolve(sig, ker, mode='full')[start:stop]
+    if return_zf:
+        return points, zf
+    else:
+        return points
+
+
+def distort(points, params, sample_rate, initial=0.0):
+    filters = []
+    for amp, tau in np.asarray(params).reshape(-1, 2):
+        b, a = exp_decay_filter(amp, abs(tau), sample_rate)
+        filters.append((b, a))
+    return predistort(points, filters, initial=initial)
+
+
+def phase_curve(t, params, df_dphi, pulse_width, start, wav, sample_rate):
+    lim = max(np.max(np.abs(t)), 20e-6)
+    num = round(2 * lim * sample_rate)
+    tlist = np.arange(num) / sample_rate - lim
+    points = wav(tlist)
+
+    pulse_points = round(pulse_width * sample_rate)
+    start_points = round((start + pulse_width) * sample_rate) - 1
+
+    ker = np.hstack(
+        [np.ones(pulse_points) / sample_rate,
+         np.zeros(start_points)])
+
+    points = np.convolve(2 * np.pi * df_dphi *
+                         distort(points, params, sample_rate),
+                         ker,
+                         mode='same')
+    return np.interp(t, tlist, points)
+
+
+if __name__ == '__main__':
+    import matplotlib.pyplot as plt
+    from waveforms import square
+
+    data = np.load('Z_distortion.npz')
+
+    x = data['time'] * 1e-6
+    y = data['phase']
+    df_dphi = 4343.313e6
+
+    sample_rate = 2e9
+    wav = 0.1 * (square(2e-6) << 1e-6)
+
+    def f(t, *params):
+        return phase_curve(t, params, df_dphi, 10e-9, 25e-9)
+
+    params = [-0.03, 0.1e-6, 0.02, 0.3e-6]
+    popt, pcov = curve_fit(f, x, y, p0=params)
+
+    plt.plot(x / 1e-6, y, 'o')
+    plt.semilogx(
+        x / 1e-6,
+        phase_curve(x,
+                    params,
+                    df_dphi,
+                    10e-9,
+                    0,
+                    wav=wav,
+                    sample_rate=sample_rate))
+    plt.plot(x / 1e-6, f(x, *popt))
+
+    plt.xlabel('delay [us]')
+    plt.ylabel('phase')
+    plt.show()

{waveforms-2.0.1 → waveforms-2.0.2}/waveforms/version.py

@@ -1,2 +1,2 @@
 """Define version number here and read it from setup.py automatically"""
-__version__ = "2.0.1"
+__version__ = "2.0.2"

{waveforms-2.0.1 → waveforms-2.0.2}/waveforms.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: waveforms
-Version: 2.0.1
+Version: 2.0.2
 Summary: Edit waveforms used in experiment
 Author-email: feihoo87 <feihoo87@gmail.com>
 Maintainer-email: feihoo87 <feihoo87@gmail.com>
@@ -38,6 +38,7 @@ Provides-Extra: docs
 Requires-Dist: Sphinx; extra == "docs"
 Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
 Requires-Dist: sphinxcontrib-zopeext; extra == "docs"
+Dynamic: license-file
 
 # waveforms
 [![View build status](https://github.com/feihoo87/waveforms/actions/workflows/workflow.yml/badge.svg)](https://github.com/feihoo87/waveforms/)

{waveforms-2.0.1 → waveforms-2.0.2}/waveforms.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ waveforms/__init__.py
 waveforms/__main__.py
 waveforms/_waveform.pyi
 waveforms/_waveform.pyx
+waveforms/distortion.py
 waveforms/multy_drag.py
 waveforms/utils.py
 waveforms/version.py