:py:mod:`neurorosettes.subcellular`
===================================

.. py:module:: neurorosettes.subcellular

.. autoapi-nested-parse::

   This module deals with the two components of the neurons: soma cells and neurites



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

Classes
~~~~~~~

.. autoapisummary::

   neurorosettes.subcellular.CellBody
   neurorosettes.subcellular.Neurite
   neurorosettes.subcellular.ObjectFactory




.. py:class:: CellBody(position, mechanics)

   Class to represent a cell body with physical properties.

   :param position: The coordinates of the cell body centre.
   :param mechanics: The physical properties of the sphere that defines
                     the cell body object.

   .. py:method:: set_center_position(coordinates)

      Sets the cell position based on the given coordinates.

      :param coordinates: The cocordinates of the cell body centre.


   .. py:method:: set_force_from_daughter(force)

      Sets the force transmitted by the cell's daughter, if it exists.

      :param force: The force components of the force transmitted by the
                    daughter object.


   .. py:method:: set_mechanics(mechanics)

      Sets the physical properties of the cell


   .. py:method:: set_sphere_representation(animator, color='red')

      Creates and sets the sphere representation of the cell


   .. py:method:: update_representation()

      Updates the sphere representation of the cell


   .. py:method:: get_neighbor_force(neighbor, interaction)

      Returns the interaction force between two cells



.. py:class:: Neurite(proximal_point, axis, cylinder_mechanics)

   Class to represent a neurite with physical properties.

   :param proximal_point: The coordinates of the neurite's proximal point.
   :param axis: The axis of growth used to calculate the neurite's distal point.
   :param cylinder_mechanics: The physical properties of the sphere that defines
                              the cell body object.

   .. py:property:: tension
      :type: float

      Returns the tension of the spring.

   .. py:property:: spring_axis
      :type: numpy.ndarray

      Returns the vector that defines the spring.

   .. py:property:: current_length
      :type: float

      Returns the current length of the spring.

   .. py:method:: set_force_from_daughter(force)

      Sets the force transmitted by the cell's daughter, if it exists.

      :param force: The force components of the force transmitted by the
                    daughter object.


   .. py:method:: create_neurite_representation(animator)

      Creates a spring+sphere representation of the neurite.


   .. py:method:: update_representation()

      Updates the Animator representation of the neurite.


   .. py:method:: move_distal_point(coordinates)

      Moves the distal point of the spring to the given position.


   .. py:method:: move_proximal_point(coordinates)

      Moves the proximal point of the spring to the given position.


   .. py:method:: get_growth_force(magnitude)

      Returns the force created by neurite growth


   .. py:method:: get_spring_force()

      Returns the force created by spring tension


   .. py:method:: get_cell_neighbor_force(neighbor, interaction)

      Returns the interaction force between the neurite and a CellBody.

      :param neighbor: The CellBody with which the object is interacting.
      :param interactions: The contact force to be used to calculate the interaction force.

      :returns: * *np.ndarray* -- The components of the interaction force between the two objects.
                * *float* -- The fraction of the force to be applied to the distal point.


   .. py:method:: get_neurite_neighbor_force(neighbor, interaction)

      Returns the interaction force between the neurite and another Neurite.

      :param neighbor: The other Neurite with which the object is interacting.
      :param interactions: The contact force to be used to calculate the interaction force.

      :returns: * *np.ndarray* -- The components of the interaction force between the two objects.
                * *float* -- The fraction of the force to be applied to the distal point.



.. py:class:: ObjectFactory

   Helper class to create instances of cell bodies and neurties based on defined properties.

   .. py:attribute:: cell_radius
      :type: float

      The cell radius.

   .. py:attribute:: cell_interaction_factor
      :type: float

      The factor used to calculate the cell's interaction radius.

   .. py:attribute:: neurite_radius
      :type: float

      The neurite radius.

   .. py:attribute:: neurite_interaction_factor
      :type: float

      The factor used to calculate the neurite's interaction radius.

   .. py:attribute:: neurite_spring_constant
      :type: float

      The neurite's spring constant.

   .. py:attribute:: neurite_default_length
      :type: float

      The initial default length of a new neuritte.

   .. py:method:: get_cell_body(center_position)

      Returns a CellBody object centred on the given position.

      :param center_position: The coordinates of the cell body's centre.

      :rtype: A CellBody with the given coordinates and the chosen properties.


   .. py:method:: get_neurite(proximal_position, axis, restriction_factor = 0.9)

      Returns a Neurite object placed on the given position, pointing towards the axis.

      :param proximal_position: The coordinates of the neurite's proximal point.
      :param axis: The axis of growth of the new neurite.
      :param restriction_factor: The restriction factor used to compute the direction of a new neurite
                                 (the neurite will follow the axis with a given degree of freedom, defined
                                 by the restriction factor). Should be between 0 and 1.

      :rtype: A Neurite with the given coordinates and the chosen properties.