.. _various_tools:

=============
Various tools
=============

.. _rotate_images_points:

Rotating image and points
=========================

.. code-block:: python

    >>> from scipy.ndimage import rotate
    >>> import atomap.api as am
    >>> from atomap.tools import rotate_points_around_signal_centre
    >>> import matplotlib.pyplot as plt

    >>> sublattice = am.dummy_data.get_distorted_cubic_sublattice()
    >>> s = sublattice.get_atom_list_on_image()
    >>> s_orig = s.deepcopy()
    >>> rotation = 30
    >>> s.map(rotate, angle=rotation, reshape=False)
    >>> x, y = sublattice.x_position, sublattice.y_position
    >>> x_rot, y_rot = rotate_points_around_signal_centre(s, x, y, rotation)

    >>> fig, (ax0, ax1) = plt.subplots(1, 2, figsize=(8, 4))
    >>> cax0 = ax0.imshow(s_orig.data, origin='lower', extent=s_orig.axes_manager.signal_extent)
    >>> cax01 = ax0.scatter(x, y, s=0.2, color='red')
    >>> cax1 = ax1.imshow(s.data, origin='lower', extent=s.axes_manager.signal_extent)
    >>> cax11 = ax1.scatter(x_rot, y_rot, s=0.2, color='red')

    >>> a = ax1.set_xlim(s.axes_manager[0].low_value, s.axes_manager[0].high_value)
    >>> b = ax1.set_ylim(s.axes_manager[1].low_value, s.axes_manager[1].high_value)

    >>> fig.tight_layout()
    >>> fig.savefig("rotate_image_and_points.png", dpi=200)

.. image:: images/makevarioustools/rotate_image_and_points.png
    :align: center
    :scale: 70 %


.. _single_atom_sublattice:


Working with single atom sublattices
====================================

Normally refining the atom positions requires using knowing the distances to the
atom's nearest neighbors, to avoid fitting overlap.
However, with sublattices consisting of a single atom, this clearly does not work.
The ``mask_radius`` argument in :py:meth:`~atomap.sublattice.Sublattice.refine_atom_positions_using_center_of_mass`
and :py:meth:`~atomap.sublattice.Sublattice.refine_atom_positions_using_2d_gaussian` can be used in this case.

.. code-block:: python

    >>> sublattice = am.dummy_data.get_single_atom_sublattice()
    >>> sublattice.refine_atom_positions_using_center_of_mass(mask_radius=9)
    >>> sublattice.refine_atom_positions_using_2d_gaussian(mask_radius=9)
    >>> sublattice.plot()

.. image:: images/makevarioustools/single_atom_sublattice.png
    :align: center
    :scale: 70 %