ruby_fit_improved.py

"""Fitting the ruby luminescence spectrum."""

import glob
import numpy as np
import matplotlib.pyplot as plt
from pandas import read_csv
from scipy.optimize import curve_fit


def lorentz(x, wL):
    # Lorentz with max=1 and w=FWHM:
    gamma = wL
    return 1 / (1 + np.square(x / gma))


def gauss(x, wG):
    # Gauss with max=1 and w=FWHM
    sigma = wG / np.sqrt(2 * np.log(2))
    return np.exp(-(x**2) / (2 * sigma**2))


def pseudo_voigt(x, x0, w, n, a):
    # pseudo-voigt with max=1 and w=FWHM:
    return a * (n * gauss((x - x0), w) + (1 - n) * lorentz((x - x0), w))


def background(x, b0, b1, b2):
    return b0 + b1 * x + b2 * x**2


def ruby(x, x1, w1, n1, a1, x2, w2, n2, a2, b0, b1, b2):
    return (
        background(x, b0, b1, b2)
        + pseudo_voigt(x, x1, w1, n1, a1)
        + pseudo_voigt(x, x2, w2, n2, a2)
    )


def pressure(wl):
    A = 1904.0
    B = 7.665
    wl0 = 693.29427
    return A / B * (((wl - wl0) / wl0 + 1) ** B - 1)


# Genral figure preperation
plt.close("all")
plt.rc("font", **{"family": "sans-serif", "sans-serif": ["DejaVu Sans"]})
plt.rc("text", usetex=False)
plt.rc("xtick", labelsize=14)
plt.rc("ytick", labelsize=14)

# read data from csv file
files = glob.glob("./*.txt")
for file in sorted(files):
    data = read_csv(file, skiprows=5, header=None, sep="\t", lineterminator="\n")
    x = data.iloc[:, 0]
    y = data.iloc[:, 1]

    guess = data.loc[data[1].idxmax()]
    h_guess2 = guess[1]
    h_guess1 = h_guess2 * 0.6
    wl_guess2 = guess[0]
    wl_guess1 = wl_guess2 - 1.58

    popt, pcov = curve_fit(
        ruby,
        x,
        y,
        p0=(wl_guess1, 0.62, 0.5, h_guess1, wl_guess2, 0.696, 0.5, h_guess2, 0, 0, 0),
        bounds=(
            (650, 0.01, 0.01, 0.01, 650, 0.01, 0.01, 0.01, -np.inf, -np.inf, -np.inf),
            (720, 30, 1, +np.inf, 720, 30, 1, +np.inf, +np.inf, +np.inf, +np.inf),
        ),
    )
    perr = np.sqrt(np.diag(pcov))
    #    print(popt)
    #    print(pcov)

    yfit = ruby(x, *popt)
    ydif = yfit - y

    # create figure
    title = "Pressure measurement by ruby luminescence"
    lamb = "%s" % float("%.8g" % popt[4])
    press = "%s" % float("%.4g" % pressure(popt[4]))
    subtitle = "$ \\lambda $ = " + lamb + " nm  ,  P = " + press + " GPa"

    plt.figure(figsize=(11.7, 8.3), dpi=144)

    plt.suptitle(title, y=0.97, fontsize=20)
    plt.title(subtitle, y=1.01, fontsize=18)

    plt.plot(
        x,
        y - background(x, *popt[8:11]),
        "o",
        markersize=5,
        alpha=0.7,
        fillstyle="none",
        label="experiment",
    )
    plt.plot(
        x,
        yfit - background(x, *popt[8:11]),
        linestyle="-",
        alpha=0.7,
        linewidth=2,
        label="fit",
    )
    #    plt.plot(x, background(x, *popt[8:11]),
    #             label='background')
    #    plt.plot(x, background(x, *popt[8:11]) + pseudo_voigt(x, *popt[0:4]),
    #             label='peak 1')
    #    plt.plot(x, background(x, *popt[8:11]) + pseudo_voigt(x, *popt[4:8]),
    #             label='peak 2')
    plt.plot(x, ydif, linestyle="-", alpha=0.7, linewidth=2, label="residual")

    # plt.grid(True,
    #          which='major',
    #          axis='both',
    #          color='grey',
    #          linestyle='-',
    #          linewidth=0.5)
    # plt.grid(True,
    #          which='minor',
    #          axis='both',
    #          color='grey',
    #          linestyle='-',
    #          linewidth=0.25)
    plt.tick_params(
        which="major",
        axis="both",
        right=True,
        top=True,
        direction="in",
        length=8,
        width=1,
    )
    plt.minorticks_on()
    plt.tick_params(
        which="minor",
        axis="both",
        right=True,
        top=True,
        direction="in",
        length=4,
        width=0.5,
    )
    plt.legend(loc="best")
    plt.xlabel("wavelength (nm)", fontsize=18)
    plt.ylabel("intesity (arb.)", fontsize=18)

    plt.figtext(0.15, 0.90, file, ha="left", va="center")

    plt.savefig(file.strip(".\\").strip("/").strip(".txt"))
    plt.show()