#!/usr/bin/python
# -*- coding: utf-8 -*-

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"""Vertex-based object-model of morphologies.

"""
doc = """

In this scheme, each *node* has a position :math:`$(x,y,z)$`, and a radius denoted by the green line.
Each node, except one, has a single parent.


.. image:: /img_srcs/morphology_overview_simpledetails.svg
    :align: center
"""

import numpy as np
from morphforge.morphology.core.base import MorphologyBase


[docs]class MorphologyArray(MorphologyBase):

    def to_array(self):
        return self

    def to_tree(self, **kwargs):
        from morphforge.morphology.conversion import MorphologyConverter
        return MorphologyConverter.array_to_tree(self, **kwargs)

[docs]    def __init__(self, vertices, connectivity, dummy_vertex_index=0, section_types=None, region_number_to_name_bidict=None, name=None, metadata=None):
        #MorphologyBase.__init__(self, region_number_to_name_bidict=region_number_to_name_bidict, name=name, metadata=metadata)
        super(MorphologyArray, self).__init__(region_number_to_name_bidict=region_number_to_name_bidict, name=name, metadata=metadata)
        
        # Save the data in the correct formats:
        self._connectivity = np.array(connectivity).reshape(-1, 2)
        N = self._connectivity.shape[0]
        self._vertices = np.array(vertices).reshape(-1, 4)
        M = self._vertices.shape[0]

        self._section_types = (np.array(section_types) if section_types else np.zeros(len(connectivity)))

        self._dummy_vertex_index = dummy_vertex_index

        # Some Error Checking:

        assert N == M - 1, 'N != M-1 (N:%d, M:%d)' % (N, M)

        if self.is_directed():
            # Lets check connectivity forms a tree:
            pass

        # If we store the data in arrays, then we no longer store which
        # is our dummy vertex, which we will need for generating trees

[docs]    def get_leaf_vertices_indices(self):
        vertex_connections = np.zeros(len(self._vertices))
        for (i, j) in self._connectivity:
            vertex_connections[i] = vertex_connections[i] + 1
            vertex_connections[j] = vertex_connections[j] + 1
        leaf_vertices = np.where(vertex_connections == 1)[0]
        return leaf_vertices

[docs]    def is_directed(self):
        return self._dummy_vertex_index is not None

[docs]    def get_vertex_by_index(self, i):
        return self._vertices[i, :]

[docs]    def get_connection_by_index(self, i):
        return self._connectivity[i, :]

[docs]    def __len__(self):
        """ Returns the number of cylinders in the morphology
        (Chosen over the number for vertices, in order to maintain compatibility with MorphologyTree,
        """

        return self._connectivity.size / 2

[docs]    def connections_to_index(self, pid):
        return [i for (i, j) in self._connectivity if j == pid] + [j for (i, j) in self._connectivity if i == pid]

[docs]    def index_of_connection(self, _id, pid):
        for (index, (i, j)) in enumerate(self._connectivity):
            if i == _id and j == pid:
                return index
            if i == pid and j == _id:
                return index
        assert False, ' Connection not found'