.. _plotting_saving:

*******************
Plotting and Saving
*******************

One of the main benefits of ParticleSpy is the ability to plot particle properties natively.
The main method for plotting particle properties is :py:meth:`~.particle_list.plot`.
This method plots either a histogram of any specified property or a scatter plot of two properties, as long as you have added these properties to each particle (either automatically or manually).

An example of plotting a histogram of particle areas in shown here:

.. code-block:: python

    >>> particles = ps.particle_analysis(data, params, mask=generated_mask)
    >>> particles.plot('area', bins = 20)

.. image:: _static/area_dist.png
    :align: center

In the above code it is possible to plot particle area because this is automatically calculated in the particle_analysis function.

To plot a scatter plot of two properties you simply need to specify two properties in the arguments:

.. code-block:: python

    >>> particles.plot(['area','circularity'])
    
.. image:: _static/area_circ_scatter.png
    :align: center

It is also possible to plot a 3D scatter plot of three properties by specifying three properties in the argument.
    
Plotting of more than one particle_list can be done using the top level :py:meth:`~.api.plot` function:

.. code-block:: python

    >>> ps.plot([particles1,particles2],['area','circularity'])

All keyword arguments in matplotlib are available by passing them as arguments to the corresponding plotting function.


Plotting Radial Profiles
-----------------------

ParticleSpy provides the ability to plot a radial profile (that is an intensity profile from particle centre to edge) of image intensity or EDS signal intensity.
A radial profile can be very useful for illustrating distributions in particles.

The following code shows how to plot a radial profile of image intensity.

.. code-block:: python

    >>> rp = ps.radial_profile(particle,['Image'],plot=True)

.. image:: _static/radial_profile_adf.png
    :align: center
    
It is also possible to plot the intensity of certain elements from an EDS signal.

.. code-block:: python

    >>> rp = ps.radial_profile(particle,['Pt','Ni'],plot=True)

.. image:: _static/radial_profile_eds.png
    :align: center

Saving Particle Images and Maps
-------------------------------

In order to save images and maps of particles it is necessary to use Hyperspy's save function.

.. code-block:: python

    >>> particles.list[0].image.save(filename)