atomize-py 0.3.2

A modular software for working with scientific devices and combining them into unified multifunctional setup

Atomize - Split your spectrometer apart!

Atomize is a modular software designed to control a wide range of scientific and industrial instruments, integrate them into a unified multifunctional setup, and automate routine experimental work.
The general idea is close to FSC2 software developed by Jens Thomas Törring.
Remote control of spectrometers is usually carried out using home-written programs, which are often restricted to doing a certain experiment with a specific set of devices. In contrast, the programs like FSC2 and Atomize are much more flexible, since they are based on a modular approach for communication with device and scripting language (EDL in FSC2; Python in Atomize) for data measuring.

Atomize[^1] uses liveplot library based on pyqtgraph as a main graphics library. Liveplot was originally developed by Phil Reinhold. Since then, several improvements have been made to use it in Atomize, and it has been directly embedded into Atomize.

Python Programming Language is used inside experimental scripts, which opens up almost unlimited possibilities for raw experimental data treatment. In addition, with PyQt, one can create experimental scripts with a simple graphical interface, allowing users not familiar with Python to use it. Several examples of scripts (with dummy data) are provided in the /atomize/tests/ directory, including a GUI script with extended comments inside. Also a variant of the Atomize with GUI Control Window extension can be found here.

Currently there are more than 200 device specific and general functions available for over 27 different devices, including 6 series of devices. If you would like to write a module for the device that is not currently available, please, read this short instruction.

Documentation and Available Instruments

Detailed documentation
Available instruments

Status

At the moment, Atomize has been tested and is currently used for controlling several EPR spectrometers using a broad range of different devices. The program has been tested on Ubuntu 18.04 LTS, 20.04 LTS, and 22.04 LTS.

Requirements

• Python >= 3.9
• Numpy >= 1.25
• PyQt6 >= 6.2
• pyqtgraph >= 0.12
• PyVisa >= 1.11
• PyVisa-py >= 0.5
• platformdirs >= 4.5
• hatchling >= 1.9
  Optional:
• PySerial; for serial instruments
• Minimalmodbus; for Modbus instruments
• SciPy; for mathematical modules
• GPIB driver; for GPIB devices
• Telegram bot API; for Telegram bot messages
• SpinAPI; for Pulse Blaster ESR 500 Pro
• Spcm driver; for Spectrum M4I 6631 X8; M4I 4450 X8

Usage

1. Installation

Install from PyPi:

pip3 install atomize-py

Run GUI from terminal:

atomize

2. General Configuration

In the terminal where you launched Atomize, the paths to the configuration files and some other details are displayed as follows:

SYSTEM: Linux
DATA DIRECTORY: /path/to/experimental/data/to/open/
SCRIPTS DIRECTORY: /path/to/atomize/scripts/
MAIN CONFIG PATH: ~/.config/atomize-py/
DEVICE CONFIG DIRECTORY: ~/.config/atomize-py/device_config/
EDITOR: text editor used for editing scripts

The "MAIN CONFIG PATH" shows a path to a general configuration file with the name main_config.ini. It should be changed at will according to the description below:

[DEFAULT]
# configure the text editor that will opened when the Edit  button is pressed.
# "EDITOR":
editor = subl # Linux
editorW = /path/to/text_editor/on/Windows/  # Windows

# configure the directory that will opened when Open 1D Data or Open 2D Data
# feature is used in the Liveplot tab. 
# "DATA DIRECTORY":
open_dir = /path/to/experimental/data/to/open/

# configure the directory that will be opened when the Open Script button is pressed:
# "SCRIPTS DIRECTORY":
script_dir = /path/to/atomize/scripts/

# configure Telegram bot
telegram_bot_token = 
message_id = 

3. Using Instrument Modules

To communicate with a device one should:

1. Modify the config file located in "DEVICE CONFIG DIRECTORY" of the desired device accordingly. Choose the desired protocol (rs-232, gpib, ethernet, etc.) and correct the settings of the specified protocol in accordance with device settings. A little bit more detailed information about protocol settings can be found here.
2. Import the module or modules in your script and initialize the appropriate class. A class always has the same name as the module file. Initialization connect the desired device, if the settings are correct.

# importing of the instruments
import atomize.device_modules.Keysight_3000_Xseries as keys
import atomize.device_modules.Lakeshore331 as tc

# initialization of the instruments
dsox3034t = keys.Keysight_3000_Xseries()
lakeshore331 = tc.Lakeshore331()

# using the instruments
name_oscilloscope = dsox3034t.oscilloscope_name()
temperature = lakeshore331.tc_temperature('CH A')

The same idea is valid for plotting and file handling modules.

# importing of the general purpose modules
import atomize.general_modules.general_functions as general
import atomize.general_modules.csv_opener_saver_tk_kinter as openfile

# initialization
file_handler = openfile.Saver_Opener()
head, data = file_handler.open_1D_dialog(header = 0)

# using
general.plot_1d('1D Plot', data[0], data[1], label = 'test_data', yname = 'Y axis', yscale = 'V')

4. Experimental Scripts

Python is used to write an experimental script. Examples (with dummy data) can be found in the "SCRIPTS DIRECTORY".

Screenshots

[^1]: Atomize = A + TOM + ize; A stands for Anatoly, main developer; TOMo stands for the International TOMography center, our organization