plot seabreeze

sbplot.py

#!/usr/bin/env python3

# a live plotter for oceanoptics spectrometers
# needs https://github.com/ap--/python-seabreeze

# written by [email protected]
# python3 <(curl -sL https://gist.github.com/greyltc/7bc7d916976e48b3d2fa991444b9cc1e/raw)

from seabreeze import spectrometers
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import time
import os


class SBLivePlot(object):
    correct_nonlinearity = True
    correct_dark_counts = True
    _integration_time_ms = 17
    plot_update_ms = 200
    spec = None
    wls = np.array([])
    ax = None
    ani = None
    l = None
    fig = None
    export_raw_data_to_disk = False
    clip_first = True  # ignore the first spectral point


    def __init__(self, spec_num=0):
        devs = spectrometers.list_devices()
        try:
            self.spec = spectrometers.Spectrometer(devs[spec_num])
        except Exception as e:
            raise ValueError(f"Initial spectrometer setup failed. Is the spectrometer connected and powered on? Error: {e}")
        self.integration_time_ms = self._integration_time_ms
        self.update_wls()

    def update_wls(self):
        if self.clip_first:
            self.wls = self.spec.wavelengths()[1::]
        else:
            self.wls = self.spec.wavelengths()
        if self.export_raw_data_to_disk:
            np.savetxt(f"wls_{time.time()}.csv", self.wls, delimiter=",")
        return self.wls

    @property
    def integration_time_ms(self):
        return self._integration_time_ms

    @integration_time_ms.setter
    def integration_time_ms(self, value):
        try:
            self.spec.integration_time_micros(value * 1000)
            # trash 2 measurements, one to flush the buffer, one to disard what's in process
            self.get_counts()
            self.get_counts()
            self._integration_time_ms = value
        except Exception as e:
            raise ValueError(f"Error setting integration time to {value}ms: {e}")

    def get_counts(self):
        counts = self.spec.intensities(correct_dark_counts=self.correct_dark_counts, correct_nonlinearity=self.correct_nonlinearity)
        if self.clip_first:
            retcounts = counts[1::]
        else:
            retcounts = counts
        return retcounts

    def prep_plot(self):
        self.fig, self.ax = plt.subplots()
        self.ax.autoscale(enable=True, tight=True)
        plt.subplots_adjust(bottom=0.2)
        (self.l,) = plt.plot(self.wls, np.zeros(len(self.wls)))
        self.ax.set(xlabel="Wavelength [nm]", ylabel="Intensity [arbitrary units]")
        self.ax.grid()

        self.pause_btn = matplotlib.widgets.Button( plt.axes([0.65, 0.05, 0.1, 0.075]), "Pause")
        self.resume_btn = matplotlib.widgets.Button(plt.axes([0.80, 0.05, 0.1, 0.075]), "Resume")
        self.once_btn = matplotlib.widgets.Button(  plt.axes([0.10, 0.05, 0.1, 0.075]), "Once")
        self.export_btn = matplotlib.widgets.Button(plt.axes([0.25, 0.05, 0.1, 0.075]), "Export")

    def update_data(self, event=None):
        # print(event)
        y = self.get_counts()
        if self.export_raw_data_to_disk:
            np.savetxt(f"counts_{time.time()}.csv", y, delimiter=",")
        i_ymax = np.argmax(y)
        self.l.set_ydata(y)
        self.ax.set(title=f"Some Spectrum.\nMax = {y[i_ymax]:0.3f} @ {self.wls[i_ymax]:0.1f} nm; {self.integration_time_ms:0.1f}ms exposure time")
        self.ax.relim()
        self.ax.autoscale_view(True, True, True)
        plt.draw()
        # fig.savefig("spectrum.png")

    def run(self):
        self.prep_plot()
        self.ani = animation.FuncAnimation(self.fig, self.update_data, interval=self.plot_update_ms)
        self.pause_btn.on_clicked(self.pause)
        self.resume_btn.on_clicked(self.resume)
        self.once_btn.on_clicked(self.update_data)
        self.export_btn.on_clicked(self.export)

    def export(self, event=None):
        x = self.l.get_xdata()
        y = self.l.get_ydata()
        xy = np.column_stack((x, y))
        filename = f"spectrum_{time.time()}.csv"
        np.savetxt(filename, xy, delimiter=",", header="Wavelength [nm], Counts", comments='# ')
        print(f"Saved file://{os.getcwd() + os.sep + filename}")

    def pause(self, event=None):
        self.ani.pause()

    def resume(self, event=None):
        self.ani.resume()


def main(plot_example=True):
    sblp = SBLivePlot()
    if plot_example == True:
        sblp.run()
        plt.show()
    else:  # non-plotting example
        wls = sblp.wls
        print(f"{wls=}")

        counts = sblp.get_counts()
        print(f"{counts=}")

        sblp.integration_time_ms = 300
        counts = sblp.get_counts()
        print(f"{counts=}")

        sblp.integration_time_ms = 50
        counts = sblp.get_counts()
        print(f"{counts=}")

        sblp.integration_time_ms = 5000
        counts = sblp.get_counts()
        print(f"{counts=}")

        sblp.integration_time_ms = 30
        counts = sblp.get_counts()
        print(f"{counts=}")

        print("Done!")


if __name__ == "__main__":
    main()