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”.