Start Atomap

Starting Python

The first step is starting an interactive Python environment (IPython).


Open a terminal and start ipython3:

$ ipython3 --matplotlib qt

If ipython3 is not available, try ipython:

$ ipython --matplotlib qt


This depends on the installation method.

If the HyperSpy bundle was installed, go to the “HyperSpy WinPython Bundle” in the start-menu and start “Jupyter QtConsole”.

If Anaconda was used, there should be an Anaconda3 folder in the start menu. Start the interactive Python environment, it should be called either IPython or Jupyter QtConsole.

This will open a command line prompt, which will referred to as the IPython terminal. In this terminal, run:

>>> %matplotlib qt 


To get you started with using Atomap, and getting and overview and understanding of how Atomap works there are tutorials available. The first tutorial Finding the atom lattice aims at showing how atom positions are found, while Analysing atom lattices shows how this information can be visualized. There is also a tutorial showing how you can make your analysis semi-automatic, Automation of the analysis.

The >>> used in the tutorials and documentation means the comment should be typed inside some kind of Python prompt, and can be copy-pasted directly into both the QtConsole, and Jupyter Notebooks.

Jupyter Notebook

In addition to the tutorials on this webpage, interactive tutorials in the form of a Jupyter Notebook are available: