From 39d6e682e615638c02c03e363d6bb92a5edb3bbf Mon Sep 17 00:00:00 2001 From: Valentin Boettcher Date: Wed, 8 May 2024 14:47:05 -0400 Subject: [PATCH] init --- .envrc | 3 + .gitignore | 11 + __pycache__/main.cpython-311.pyc | Bin 0 -> 646 bytes devenv.lock | 156 ++++ devenv.nix | 17 + devenv.yaml | 14 + fitting_ringdown.org | 4 + main.py | 11 + poetry.lock | 809 +++++++++++++++++++ pyproject.toml | 20 + ringfit/__init__.py | 0 ringfit/__pycache__/__init__.cpython-311.pyc | Bin 0 -> 180 bytes ringfit/__pycache__/data.cpython-311.pyc | Bin 0 -> 3824 bytes ringfit/__pycache__/plotting.cpython-311.pyc | Bin 0 -> 5145 bytes ringfit/__pycache__/utils.cpython-311.pyc | Bin 0 -> 1651 bytes ringfit/data.py | 97 +++ ringfit/fit.py | 3 + ringfit/plotting.py | 116 +++ ringfit/utils.py | 33 + scripts/first_test.py | 12 + scripts/startup.ipy | 2 + 21 files changed, 1308 insertions(+) create mode 100644 .envrc create mode 100644 .gitignore create mode 100644 __pycache__/main.cpython-311.pyc create 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enable = true; + activate.enable = true; + }; + }; +} diff --git a/devenv.yaml b/devenv.yaml new file mode 100644 index 0000000..2457af5 --- /dev/null +++ b/devenv.yaml @@ -0,0 +1,14 @@ +inputs: + nixpkgs: + url: github:cachix/devenv-nixpkgs/rolling + +# If you're using non-OSS software, you can set allowUnfree to true. +# allowUnfree: true + +# If you're willing to use a package that's vulnerable +# permittedInsecurePackages: +# - "openssl-1.1.1w" + +# If you have more than one devenv you can merge them +#imports: +# - ./backend diff --git a/fitting_ringdown.org b/fitting_ringdown.org new file mode 100644 index 0000000..a986624 --- /dev/null +++ b/fitting_ringdown.org @@ -0,0 +1,4 @@ +:PROPERTIES: +:ID: d7630955-6ca9-4de7-9770-2d50d4847bcd +:END: +#+title: Fitting Ringdown diff --git a/main.py b/main.py new file mode 100644 index 0000000..f8797eb --- /dev/null +++ b/main.py @@ -0,0 +1,11 @@ +import argparse +import ringfit.data as data +import click + +if __name__ == "main": + parser 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patch literal 1651 zcmb7EO>7%Q6rSDn{=~7}B&6G*g0xAhO3uMn4^0mQA|c43KuT4_!54e+%-Y-TuFcGv z5No3v1QL}vSSV6`Oa%%->7l)aTaFw!*pd&{N|lgM4-uDCA(x(bv(B0rsRy2S-^_da zzV~M4edC|g=_CUAacaf-HG$Bd+=xXzo1AK=hzn)MWQ2wnHXydPQM9O8_U)P%DwOyQ>XpT~ER1{!61*pEfiK(#9ZP_A!P*~r z0-*`WEin+W&;%S7?{OreGI*qBnt$^n&oD!P0&y1*`=feWk}t>E5xP5y4J4ch#7Xq6 z`1(s7^aJIFuO?%;A)hKIX1SvieY|1s97PoDB_6I zgmQJnDYqUb2(A!ddBUw>QW>7zAFEk0RI0?TRQ*uHHuFudOtNYy!7?asStxq-P^z0a zl+4dqD7ogBloKYaQOJ`>^>U1qIjB%d;}I z>kyX9<+%^O=NrE5uv~pJoQ>}LsEtKlpV2pqO zwSk&$3tu(cx4*vMxQ7tEXS@>(^Vip3UmpYXj|4N9$befbMJa zJ8OI9qYs|w2iKln?k>K4xOOaw7nK(X)ZbjSJ~~y9KDYfThbbMkqxLmpXL;}Tqqm+Y z2lG!Sy9+Ca%K*|jNarA3X|11XXl8a>@1*xKy}9My^o{=Xjn>UUBGX=anEN5un_1}3 zEc6l!t((tNdb_!|c%XDstG(1}Kec)&^i%J)-XBa(wLUz7?V_we`K8NFgtFIg>zi~M ztT4sOc6~E9 1: + raise ValueError("end_fraction must be between 0 and 1.") + + window = int(step_size * end_fraction) + + return np.array([self._output[step - window : step].mean() for step in steps]) + + +def load_scan(directory: str | Path): + """Load and parse the oscilloscope data from the ``directory``. + + The directory should contain ``signal_laser.npy``, ``signal_outp.npy``, and ``time.npy``. + """ + + directory = Path(directory) + laser = np.load(directory / "signal_laser.npy") + output = np.load(directory / "signal_outp.npy") + time = np.load(directory / "time.npy") + + return ScanData(laser, output, time) diff --git a/ringfit/fit.py b/ringfit/fit.py new file mode 100644 index 0000000..0e496ef --- /dev/null +++ b/ringfit/fit.py @@ -0,0 +1,3 @@ +############################################################################### +# Fitting Routine # +############################################################################### diff --git a/ringfit/plotting.py b/ringfit/plotting.py new file mode 100644 index 0000000..a093ae5 --- /dev/null +++ b/ringfit/plotting.py @@ -0,0 +1,116 @@ +from . import data +import matplotlib.pyplot as plt +from scipy.ndimage import uniform_filter1d +from scipy.interpolate import make_interp_spline, BSpline +import numpy as np + + +def wrap_plot(f): + def wrapped(*args, ax=None, setup_function=plt.subplots, **kwargs): + fig = None + if not ax: + fig, ax = setup_function() + + ret_val = f(*args, ax=ax, **kwargs) + return (fig, ax, ret_val) if ret_val else (fig, ax) + + return wrapped + + +def lighten_color(color, amount=0.5): + """ + Lightens the given color by multiplying (1-luminosity) by the given amount. + Input can be matplotlib color string, hex string, or RGB tuple. + + Examples: + >> lighten_color('g', 0.3) + >> lighten_color('#F034A3', 0.6) + >> lighten_color((.3,.55,.1), 0.5) + """ + import matplotlib.colors as mc + import colorsys + + try: + c = mc.cnames[color] + except: + c = color + c = colorsys.rgb_to_hls(*mc.to_rgb(c)) + return colorsys.hls_to_rgb(c[0], 1 - amount * (1 - c[1]), c[2]) + + +def fancy_error(x, y, err, ax, **kwargs): + line = ax.plot( + x, + y, + **kwargs, + ) + + err = ax.fill_between( + x, + y + err, + y - err, + color=lighten_color(line[0].get_color(), 0.5), + alpha=0.5, + ) + + return line, err + + +@wrap_plot +def plot_scan( + data: data.ScanData, + laser=False, + output=True, + steps=False, + normalize=False, + smoothe_output=False, + ax=None, + **kwargs, +): + if not (laser or output): + raise ValueError("At least one of 'laser' or 'output' must be True.") + + if laser: + laser = data.laser + if normalize: + laser = (laser - laser.min()) / (laser.max() - laser.min()) + + lines = ax.plot(data.time, laser, **kwargs) + + if output: + output = data.output + if normalize: + output = (output - output.min()) / (output.max() - output.min()) + + if smoothe_output: + if not isinstance(smoothe_output, int): + smoothe_output = 60 + + window = len(output) // smoothe_output + output = uniform_filter1d(output, window) + + lines = ax.plot(data.time, output, **kwargs) + + if steps: + peaks = data.laser_steps() + for peak in peaks: + ax.axvline( + data.time[peak], + color=lighten_color(lines[0].get_color()), + linestyle="--", + zorder=-10, + ) + + +@wrap_plot +def plot_transmission(data: data.ScanData, timepoints=1000, ax=None, **kwargs): + amplitude = data.output_end_averages() + times = data.laser_step_times() + + smoothed = make_interp_spline(times, amplitude, k=3) + smooth_times = np.linspace(times.min(), times.max(), timepoints) + + lines = ax.plot(smooth_times, smoothed(smooth_times), **kwargs) + plt.plot( + times, amplitude, "o", color=lighten_color(lines[0].get_color()), alpha=0.5 + ) diff --git a/ringfit/utils.py b/ringfit/utils.py new file mode 100644 index 0000000..95b584b --- /dev/null +++ b/ringfit/utils.py @@ -0,0 +1,33 @@ +############################################################################### +# Utilities # +############################################################################### + +import numpy as np +from scipy.signal import find_peaks +from scipy.ndimage import uniform_filter1d + + +def find_frequency_steps(laser: np.ndarray, window_fraction: int = 60) -> np.ndarray: + """Find the indices of the laser signal ``laser`` where the + frequency of the laser changes. The parameter ``window_fraction`` + is the fraction of the signal length that is used as the window + size for the sliding average. + """ + + window = len(laser) // window_fraction + if window % 2 != 0: + window += 1 + + sliding_average = uniform_filter1d(laser, window) + left_averages = np.pad( + sliding_average[:-window], (window // 2, window // 2), mode="edge" + ) + right_averages = np.pad( + sliding_average[window:], (window // 2, window // 2), mode="edge" + ) + + step_diffs = np.abs(left_averages - right_averages) + step_diffs /= step_diffs.max() + + peaks = find_peaks(step_diffs, height=0.5, distance=window)[0] + return peaks diff --git a/scripts/first_test.py b/scripts/first_test.py new file mode 100644 index 0000000..354c563 --- /dev/null +++ b/scripts/first_test.py @@ -0,0 +1,12 @@ +import sys + +sys.path.append("../") +from ringfit import data +import matplotlib.pyplot as plt +from ringfit.data import * +from ringfit.plotting import * + +path = "/home/hiro/Documents/org/roam/code/fitting_ringdown/data/24_05_24/characterization_first" +scan = data.load_scan(path) + +plot_scan(scan, steps=True) diff --git a/scripts/startup.ipy b/scripts/startup.ipy new file mode 100644 index 0000000..a969d8a --- /dev/null +++ b/scripts/startup.ipy @@ -0,0 +1,2 @@ +%matplotlib tk +plt.ion()