Use MorphIO specification for definitions doc page

doc/source/definitions.rst

@@ -32,121 +32,5 @@
 NeuroM morphology definitions
 =============================
 
-``NeuroM`` specific working definitions of various components of neuron morphologies.
-
-
-.. _point-label:
-
-Point
------
-
-A point is a ``numpy`` array of numbers **[X, Y, Z, R]** where the components are
-
-* X, Y, Z: Cartesian coordinates of position
-* R: Radius
-
-.. _segment-label:
-
-Segment
--------
-
-A segment consists of two consecutive :ref:`points<point-label>` belonging to
-the same :ref:`neurite<neurite-label>` and :ref:`section<section-label>`.
-
-In ``NeuroM`` a segment is represented as a tuple or a ``numpy`` array of two `points<point-label>`.
-
-
-.. _section-label:
-
-Section
--------
-
-A section is a node of morphology tree containing a series of two or more :ref:`points<point-label>`
-whose first and last element are any of the following combinations:
-
-* root node, forking point
-* forking point, forking point
-* forking point, end point
-* root node, end point
-
-The first point of a section is a duplicate of the last point of its parent section,
-unless the latter is a soma section.
-
-In ``NeuroM``, a section is represented by class :class:`Section<neurom.core.neuron.Section>`.
-
-.. _soma-label:
-
-Soma
-----
-
-A soma can be represented by one or more :ref:`points<point-label>`.
-The soma is classified solely based on the number of points it contains thus:
-
-* Type A: 1 point defining the center and radius.
-* Type B: 3 points. Only the centers of the points are considered.
-  The first point defines the center. The radius is estimated from
-  the mean distance between the center and the two remaining points.
-* Type C: More than three points. The center is defined as the mean position
-  of all points. The radius is defined as the mean distance of all points to
-  the center.
-
-.. todo::
-    Expand list if and when specifications require new types of soma.
-
-The soma is represented by classes derived from :py:class:`Soma<neurom.core.soma.Soma>`.
-The interface exports a center and radius. These can be calculated in different
-ways, but the default is to use the center and radius for type A and the mean center
-and radius for types B and C.
-
-.. todo::
-    In the future, type B may be interpreted as 3 points on an ellipse.
-    In this case, the points would have to be non-collinear.
-    Currently there is no such restriction.
-
-See also
-
-.. seealso:: The :py:mod:`soma implementation module<neurom.core.soma>`
-
-
-.. _neurite-label:
-
-Neurite tree
-------------
-
-A neurite is essentially a tree of :ref:`sections<section-label>`. The tree structure
-implies the following:
-
-* A node can only have one parent.
-* A node can have an arbitrary number of children.
-* No loops are present in the structure.
-
-Neurites are represented by the class :py:class:`Neurite<neurom.core.Neurite>`, which contains
-the root node of the aforementioned tree as well as some helper functions to aid iteration
-over sections and collection of points.
-
-In :py:mod:`NeuroM<neurom>` neurite trees are implemented using the recursive structure
-:py:class:`neurom.core.Section`, :ref:`described above<section-label>`.
-
-
-Neuron
-------
-
-A neuron structure consists of a single :ref:`soma<soma-label>` and a collection of
-:ref:`neurites<neurite-label>`.
-
-The trees that are expected to be present depend on the type of cell:
-
-* Interneuron (IN): basal dendrite, axon
-* Pyramidal cell (PC): basal dendrite, apical dendrite, axon
-
-Neurons are represented by the class :py:class:`Neuron<neurom.core.Neuron>`. This is more
-or less what it looks like:
-
-.. code-block:: python
-
-    neuron = {
-        soma,
-        neurites,
-        points,
-        name
-    }
+``NeuroM`` uses ``MorphIO`` for reading hence ``NeuroM`` uses ``MorphIO`` definitions and follows
+`<https://morphio.readthedocs.io/en/latest/specification.html>`__.