:py:mod:`neurorosettes.neurons`
===============================

.. py:module:: neurorosettes.neurons

.. autoapi-nested-parse::

   This module deals with the neuron structure and functions



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

Classes
~~~~~~~

.. autoapisummary::

   neurorosettes.neurons.Neuron
   neurorosettes.neurons.NeuronFactory




.. py:class:: Neuron(position, outgrowth_axis, factory, clocks, max_number_of_neurites = 4, differentiation_grade = 0)

   Class to represent a neuron as a combination of a cell body and neurites.

   :param position: The center position of the neuron's cell body.
   :param outgrowth_axis: The direction of growth of the neuron's neurites.
   :param factory: The factory object to be used to create new neuron components.
   :param clocks: The rates of the neuron's biological processes.
   :param max_number_of_neurites: The total number of neurites a neuron can have before
                                  proliferation is blocked.
   :param differentiation_grade: The starting differentiation stage of the neurite, represented
                                 by the initial number of neurites.

   .. py:property:: cell_radius

      The radius of the neuron's cell body.

   .. py:property:: ready_for_division

      If the neuron is ready to proliferate.

   .. py:property:: ready_for_differentiation

      If the neuron is ready to differentiate.

   .. py:property:: ready_to_die

      If the neuron is ready to die.

   .. py:method:: set_outgrowth_axis(coordinates)

      Sets the axis that neurites will follow when new neurites are created.

      Prameters
      ----------
      outgrowth_axis
          The direction of growth of the neuron's neurites.


   .. py:method:: get_neurite_position_on_cell_surface()

      Returns the coordinates on the cell surface where the first neurite should be placed


   .. py:method:: place_neurite_on_cell_surface(neurite)

      Places the neurite base on the cell surface according to the cell-distal vector.

      :param neurite: The neurite to be placed on the cell body's surface.


   .. py:method:: create_first_neurite(factory)

      Creates a neurite attached to the soma cell

      :param factory: The factory object to be used to create new neuron components.


   .. py:method:: create_secondary_neurite(factory)

      Creates a neurite attached to the most recent neurite.

      :param factory: The factory object to be used to create new neuron components.



.. py:class:: NeuronFactory

   Helper class to create instances of neurons based on defined properties.

   .. py:attribute:: max_number_of_neurites
      :annotation: :int

      The maximum number of neurites that a neuron can have.

   .. py:attribute:: objects_factory
      :annotation: :neurorosettes.subcellular.ObjectFactory

      The ObjectFactory used to create new object instances.

   .. py:attribute:: clocks_factory
      :annotation: :neurorosettes.clocks.ClocksFactory

      The ClocksFactory used to create new clock instances.

   .. py:method:: create_neuron(coordinates, outgrowth_axis)

      Returns a Neuron object placed in the given coordinates.