Usage


Installation


Atomize can be installed from PyPi:

pip3 install atomize-py

Run GUI from terminal:

atomize

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 =

Instrument Modules


To communicate with a device one should:

  • 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.
  • 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. For more detailed information, see documentation.
# 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 as openfile

# initialization
file_handler = openfile.Saver_Opener()
file_data = file_handler.open_file_dialog()
header, data = file_handler.open_1d(file_data, header = 0)

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

Experimental Scripts


Python is used to write an experimental script. Examples can be found in the “SCRIPTS DIRECTORY”.

Additional Interactivity


The Main tab has the following additional features in the Output dock:

  • clear all text from the dock;
  • open the local directory with the device configuration files;
  • print in the terminal all available instruments connected to your computer using pyvisa.

These features are available in the menu that can be opened by a right-click in the Output dock area.

  • keyboard shortcuts for pressing buttons on the Main tab. The format is ‘Alt + [O, E, U, T, S, Q, H]’.

The Script Editor dock has the following features:

  • press ‘Ctrl + G’ to jump to specified line;
  • press ‘Ctrl + F’ to search for the specified text; press ‘Ctrl + N’ to show the next occurrence;
  • hidden characters can be displayed by selecting any part of text;

The Queue dock is used to create an execution queue by pressing ‘Add to Queue’ button. All scripts will be tested before being added to the queue. The execution oreder is from top to bottom. If there are items in the queue, pressing the ‘Stop Experiment’ button will stop the execution of the current script and clear the queue. Additional features:

  • delete the selected file from the queue;
  • clear the queue;
  • drag and drop files to change the execution order;

The removal features are available in the menu that can be opened by a right-click in the Queue dock area.

The Liveplot tab the following additional features in the Current Plots dock:

  • delete a selected dock with graphs;
  • open 1d data in csv multi-column format and plot it in a new graph dock;
  • open 2d data in csv format and plot it in a new graph dock.

These features are available in the menu that can be opened by a right-click in the Current Plots dock area.

The graph docks have the following additional features:

  • delete the selected curve from the graph dock;
  • vertically shift the selected curve from the graph dock;
  • open 1d data in csv multi-column format and plot it in this graph dock;
  • save 2d data from the displayed contour plot.

These features are available in the Plot Options menu of pyqtgraph that can be opened by a right-click in the graph dock area.

  • double-click the left mouse button to display / hide the cross-hair widget (for 1D plots) or the cross-section widget (for 2D plots);
  • click the middle mouse button to lock the cross-hair or cross-section widget in its current position.