:py:mod:`neurorosettes.utilities`
=================================

.. py:module:: neurorosettes.utilities


Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   neurorosettes.utilities.Tissue
   neurorosettes.utilities.RectangularTissue
   neurorosettes.utilities.HexagonalTissue
   neurorosettes.utilities.Animator



Functions
~~~~~~~~~

.. autoapisummary::

   neurorosettes.utilities.get_random_position
   neurorosettes.utilities.get_random_unit_vector



.. py:class:: Tissue(use_2d = True)

   Bases: :py:obj:`abc.ABC`

   Class to represent a multicellular tissue through the cell cooridnates.

   :param use_2d: If the cells are placed in a single plane or if
                  the tissue is a 3D tissue.

   .. py:method:: get_coordinates()
      :abstractmethod:

      Returns the initial cell coordinates according to the tissue geometry



.. py:class:: RectangularTissue(size, spacing = 16.0, use_2d = True)

   Bases: :py:obj:`Tissue`

   Class to represent a tissue that is a rectangular grid.

   :param size: The domain bounds of the tissue.
   :param spacing: The distance between cell centres.
   :param use_2d: If the cells are placed in a single plane or if
                  the tissue is a 3D tissue.

   .. py:method:: get_coordinates()

      Returns the initial cell coordinates according to the tissue geometry



.. py:class:: HexagonalTissue(size, spacing = 20.0, use_2d = True)

   Bases: :py:obj:`Tissue`

   Class to represent a tissue that is a hexagonal grid.

   :param size: The domain bounds of the tissue.
   :param spacing: The distance between cell centres.
   :param use_2d: If the cells are placed in a single plane or if
                  the tissue is a 3D tissue.

   .. py:method:: get_coordinates()

      Returns the initial cell coordinates according to the tissue geometry



.. py:function:: get_random_position(scaling_factor)

   Returns the coordinates for a random position between -scaling_factor and scaling factor.

   :param scaling_factor: The range of the interval where coorinates will be
                          sampled from.


.. py:function:: get_random_unit_vector(two_dimensions=False)

   Returns a vector for a random point in a unit sphere.


.. py:class:: Animator

   Class to render the simulaiton results through vedo.

   .. py:method:: show(interactive = False)

      Shows the simulation results in a display window.

      :param interactive: If the plot should support user interaction.


   .. py:method:: update_clock(time_point)

      Updates the simulation clock string with the new time point.

      :param time_point: The new time point to be shown on the clock string.


   .. py:method:: add_grid(x_grid, y_grid)

      Adds a 2D grid object to the middle plane of the domain.

      :param x_grid: The x coordinates of the cells of the grid.
      :param y_grid: The y coordinates of the cell of the grid.


   .. py:method:: set_camera(height)

      Places the plotter camera at a given height.

      :param height: The height to place the camera at.


   .. py:method:: draw_spring(base_point, top_point, radius)

      Plots a spring and a sphere to represent a cylinder object.

      The spring connects the two points passed as coordinates,
      and a sphere is placed centred on the top point.

      :param base_point: The coordinates for the base of the spring.
      :param top_point: The coordinates for the top of the spring.
      :param radius: The radius of the cylinder object.


   .. py:method:: draw_sphere(center, radius, **kwargs)

      Plots a sphere to represent a sphere object.

      :param center: The coordinates for the sphere center.
      :param radius: The radius of the sphere.


   .. py:method:: save_screenshot(file_name)

      Saves the current rendering to a PNG file.

      :param file_name: The name of the PNG file to be created.