.. _making_nice_figures:

=========================
Plotting for publications
=========================

Please consider citing `Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting <https://ascimaging.springeropen.com/articles/10.1186/s40679-017-0042-5>`_ if you publish work where you have used Atomap as a tool.

Figures for publications are often customized, and here are a few tips on how to extract the data you wish to plot in a fancy plot.

Saving specific data
--------------------

When making advanced figures containing specific data for publication, it can be a good idea to save this data for example in separate numpy files.
This makes it quick to load the data when using for example matplotlib to make figures.

.. code-block:: python

    >>> import numpy as np
    >>> np.savez("datafile.npz", x=sublattice_A.x_position, y=sublattice_A.y_position, e=sublattice_A.ellipticity) # doctest: +SKIP

Alternatively, the data can be saved in comma-separated values (CSV) file, which can be opened in spreadsheet software:

.. code-block:: python

    >>> np.savetxt("datafile.csv", (sublattice_A.x_position, sublattice_A.y_position, sublattice_A.sigma_x, sublattice_A.sigma_y, sublattice_A.ellipticity), delimiter=',') # doctest: +SKIP


Signals can be saved by using the inbuilt `save` function.

.. code-block:: python

    >>> s_monolayer.save("monolayer_distances.hdf5", overwrite=True) # doctest: +SKIP

Here, we will first save analysis data for the fantasite dummy data atom lattice.
It can be a good idea to save analysis results as numpy, csv or hyperspy signals, as the runtime of the analysis can sometimes be lengthy.
Making nice figures often require a lot of tweaking, trial and error, so it is nice to have the data readily available without having to re-run the full analysis.
First, the analysis results are generated, and then saved.

.. literalinclude:: images/make_nice_figures_generate_data.py


Matplotlib
----------

The saved results can then be loaded into the script that is making nice figures.
The below code block will create this figure.

.. image:: images/make_nice_figures/Atom_lattice.png

.. literalinclude:: images/make_nice_figures_plotting.py