Start Atomap

Starting Python

The first step is starting an interactive Jupyter Notebook environment.

Linux

Open a terminal and start ipython3:

$ ipython3 notebook

If ipython3 is not available, try ipython:

$ ipython notebook

This will open a browser window (or a new browser tab). Press the “New” button (top right), and start a Python 3 Notebook. In the first cell, run the following commands (paste them, and press Shift + Enter). If you are unfamiliar with the Jupyter Notebook interface, see the Jupyter Notebook guide.

%matplotlib nbagg
import atomap.api as am

If this works, continue to the Tutorials. If you get some kind of error, please report it as a New issue on the Atomap GitLab.

Windows

This depends on the installation method:

  • If the HyperSpy bundle was installed, go to the “HyperSpy Bundle” in the start-menu and start “Jupyter Notebook”.
  • If Anaconda was used, go to “Anaconda3” in the start menu, and start “Jupyter Notebook”.

This will open a browser window (or a new browser tab). Press the “New” button (top right), and start a Python 3 Notebook. In the first cell, run the following commands (paste them, and press Shift + Enter). If you are unfamiliar with the Jupyter Notebook interface, see the Jupyter Notebook guide.

%matplotlib nbagg
import atomap.api as am

If this works, continue to the Tutorials. If you get some kind of error, please report it as a New issue on the Atomap GitLab.

MacOS

Open the Terminal, and write:

$ jupyter notebook

This will open a browser window (or a new browser tab). Press the “New” button (top right), and start a Python 3 Notebook. In the first cell, run the following commands (paste them, and press Shift + Enter). If you are unfamiliar with the Jupyter Notebook interface, see the Jupyter Notebook guide.

%matplotlib nbagg
import atomap.api as am

If this works, continue to the Tutorials. If you get some kind of error, please report it as a New issue on the Atomap GitLab.

Tutorials

To get you started on using Atomap 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 the Jupyter Notebooks.

Atomap demos

In addition to the guides on this webpage, another good resource is the Atomap demos, which are pre-filled Jupyter Notebooks showing various aspects of Atomap’s functionality. For beginners, the Introduction to Atomap notebook is a good place to start.