Automatic spectral acquisition

Python command line interface for the automatic data acquisition of spectral data. Connects to an Arduino running a custom program and to an oscilloscope.

Experimental setup

An Arduino running the code on arduino_code.ino (GitHub repository) is connected to a stepper motor controller (using a DVR8825 breakout board driver). The stepper motor is connected to a manual monochromator with a timing belt and two gears. For the detection, a PMT is connected to an oscilloscope or an ADC (MCP3421). All components can then be controlled using this CLI.

Experimental setup when using the oscilloscope:

Experimental setup when using the ADC:

The diagram for the stepper motor controller is shown next.

The diagram for the ADC board is:

Installation

Install using

pip install automatic-spectral-acquisition

Calibration process

An initial calibration is necessary for setting the DEFAULT_POSITION (default=0) and CALIBRATION_POSITIONS in automatic_spectral_acquisition\constants.py. This calibration has to be done manually for now, and requires the user to choose a set of points that will be used for further calibrations:

1. Define a default position and a default wavelength. Ideally DEFAULT_POSITION=0 and a wavelength in the middle of the available range, e.g., 650 nm.
2. Select a set of wavelengths (e.g.: [350, 500, 650, 800, 950] nm)
3. Manually set the monochromator to the default wavelength and start the Arduino code.
4. Find the associated position by trial and error with spectral moveto <position>. Use these values to populate CALIBRATION_POSITIONS.

As long as the following measurements conclude successfully, redefining these constants won't be necessary. Even if there is some problem and the motor doesn't return to the default position, if DEFAULT_POSITION=0, the monochromator can be manually set to the default wavelength associated with the default position to return to normal functionality.

After that, the calibration process can be performed using, e.g., spectral config calibrate. The motor will be moved to the set positions and the user will be asked to input the current wavelength value.

At the end of a measurement, the motor will return to the default position to guarantee the correct behaviour of further measurements.

The calibration parameters are saved to a file and can be reused for every measurement. However, it is recommended to recalibrate the system every session.

Options

The options for the program are contained in the file automatic_spectral_acquisition\constants.py and should be edited when necessary. You can select whether you are using an oscilloscope or the ADC.

How to use

To call the program, use the command spectral. To get help using the CLI, use the command spectral --help or spectral <subcommand> --help.

To create a configuration file, use

spectal config create

You will be asked to select the serial ports for the Arduino and oscilloscope, as well as, to calibrate the stepper motor.

If a configuration file already exists, you can choose to just re-calibrate the stepper motor using

spectral config calibrate

You can see the current configuration using

spectral config show

Or delete it using

spectral config delete

To record a spectrum use

spectral spectrum <start> <end> <step> [options]

• <start> is the wavelength of the start of the spectrum
• <end> is the wavelength of the end of the spectrum
• <step> is the space between measurements

[options] can contain:

• -n <number of measurements> is used to select how many measurements are taken and averaged for each wavelength
• -f <name of output file> is used to change the name of the output file
• -p if this options is present, the spectrum will be plotted at the end of acquisition

You can also take a single measurement using

spectral single <wavelength> [options]

[options] can contain:

• -n <number of measurements> is used to select how many measurements are taken and averaged for each wavelength
• -f <name of output file> is used to change the name of the output file
• -p if this options is present, the values measured will be printed on the terminal

Use

spectral live <wavelength> [options]

To perform continuous measurements that are printed on the screen.

[options] can contain:

• -d <delay> changes the delay (in seconds) between measurements.