Microspectrometer Manual

Introduction

This manual provides guidance on using the provided Python code to control a UV-Vis spectrometer using the SeaBreeze library. The code is designed to connect to a UV-Vis spectrometer, measure spectra, and perform various operations such as saving, plotting, and continuous monitoring of absorption or transmission spectra.

Requirements

Before using the code, ensure the following requirements are met:

• Python 3.x installed.
• SeaBreeze library installed (pip install seabreeze).
• pyseabreeze installed (pip install pyseabreeze). (if this command doesn't work try pip install seabreeze[pyseabreeze])
• Matplotlib library installed (pip install matplotlib).
• pip install libusb

Code Overview

Spectrum Class

The Spectrum class represents a spectrum and has the following attributes:

• scan_number: Scan number identifier.
• integration_time: Integration time in microseconds.
• measurement_time_stamp: Timestamp of the measurement.
• wavelengths: Array of wavelengths.
• counts: Array of counts corresponding to the wavelengths.
• spectrum_type: Type of spectrum (current_spectrum, reference, dark).
• comments: Comments associated with the spectrum.

Microspectrometer Class

The Microspectrometer class manages the UV-Vis spectrometer and provides various methods to control and monitor the spectrometer.

Methods:

• connect(): Connects to the first available UV-Vis spectrometer.
• disconnect(): Disconnects the connected spectrometer.
• change_integration_time(integration_time): Sets the integration time of the device in microseconds.
• measure(spectrum_type, number_of_scans, save, filename, comments, store): Measures the current spectrum for the attached spectrometer.
• datetime_stamp(): Updates the object's datetime stamp for the current datetime.
• start_new_experiment(directory): Creates a new directory for storing data.
• plot_absorbance(save): Plots the log10 absorbance of the current spectrum.
• save_transmission(spectrum_type, filename, comments): Saves the transmission spectrum.
• save_absorbance(filename, comments): Saves the current absorbance spectrum.
• load_spectrum(spectrum_type, filename): Loads an ASCII .xy spectrum to overwrite dark or reference.
• save_all_spectra(): Dumps all spectra in memory to files.
• describe_all_spectra(): Prints information about all stored spectra.
• set_spectrum(spectrum_type, index): Sets a spectrum in memory to a dark or reference.
• continuous_measurements(update_time, ref_spec_index): Continuously measures and displays the absorbance spectrum.
• continuous_transmission(update_time, ref_spec_index): Continuously measures and displays the transmission spectrum.

Getting Started

1. Import the required libraries.

   import seabreeze
   import os
   from datetime import date, datetime
   from seabreeze.spectrometers import list_devices, Spectrometer
   import matplotlib.pyplot as plt
   import numpy as np
   from IPython import display
   import time
   # explicitly request pyseabreeze
   seabreeze.use('pyseabreeze')

2. Create an instance of the Microspectrometer class.

   spectrometer = Microspectrometer()
   

3. Connect to the spectrometer.

   spectrometer.connect()
   

4. Perform measurements using the measure method, and save or analyze the spectra as needed.

Example Code

### Example Usage with New Experiment
from Microspectrometer import Microspectrometer
spectrometer = Microspectrometer()

### Connect to the spectrometer
spectrometer.connect()

### Start a new experiment with a custom directory name
experiment_directory = 'my_experiment'
spectrometer.start_new_experiment(directory=experiment_directory)

### Perform a measurement
spectrometer.measure(spectrum_type='current_spectrum', number_of_scans=10, save=True)

### Plot absorbance
spectrometer.plot_absorbance(save=False)

### Save transmission spectrum
spectrometer.save_transmission(spectrum_type='current_spectrum')

### Disconnect from the spectrometer
spectrometer.disconnect()