# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
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"""Morphology classes and functions."""

from collections import deque
import warnings

import morphio
import numpy as np
from neurom import morphmath
from neurom.core.soma import make_soma
from neurom.core.dataformat import COLS
from neurom.core.types import NeuriteIter, NeuriteType
from neurom.core.population import Population
from neurom.utils import flatten, warn_deprecated


class Section:
    """Simple recursive tree class."""

    def __init__(self, morphio_section):
        """The section constructor."""
        self.morphio_section = morphio_section

    @property
    def id(self):
        """Returns the section ID."""
        return self.morphio_section.id

    @property
    def parent(self):
        """Returns the parent section if non root section else None."""
        if self.morphio_section.is_root:
            return None
        return Section(self.morphio_section.parent)

    @property
    def children(self):
        """Returns a list of child section."""
        return [Section(child) for child in self.morphio_section.children]

    def append_section(self, section):
        """Appends a section to the current section object.

        Args:
            section (morphio.Section|morphio.mut.Section|Section|morphio.PointLevel): a section
        """
        if isinstance(section, Section):
            return self.morphio_section.append_section(section.morphio_section)
        return self.morphio_section.append_section(section)

    def is_forking_point(self):
        """Is this section a forking point?"""
        return len(self.children) > 1

    def is_bifurcation_point(self):
        """Is tree a bifurcation point?"""
        return len(self.children) == 2

    def is_leaf(self):
        """Is tree a leaf?"""
        return len(self.children) == 0

    def is_root(self):
        """Is tree the root node?"""
        return self.parent is None

    def ipreorder(self):
        """Depth-first pre-order iteration of tree nodes."""
        children = deque((self, ))
        while children:
            cur_node = children.pop()
            children.extend(reversed(cur_node.children))
            yield cur_node

    def ipostorder(self):
        """Depth-first post-order iteration of tree nodes."""
        children = [self, ]
        seen = set()
        while children:
            cur_node = children[-1]
            if cur_node not in seen:
                seen.add(cur_node)
                children.extend(reversed(cur_node.children))
            else:
                children.pop()
                yield cur_node

    def iupstream(self):
        """Iterate from a tree node to the root nodes."""
        t = self
        while t is not None:
            yield t
            t = t.parent

    def ileaf(self):
        """Iterator to all leaves of a tree."""
        return filter(Section.is_leaf, self.ipreorder())

    def iforking_point(self, iter_mode=ipreorder):
        """Iterator to forking points.

        Args:
            iter_mode: iteration mode. Default: ipreorder.
        """
        return filter(Section.is_forking_point, iter_mode(self))

    def ibifurcation_point(self, iter_mode=ipreorder):
        """Iterator to bifurcation points.

        Args:
            iter_mode: iteration mode. Default: ipreorder.
        """
        return filter(Section.is_bifurcation_point, iter_mode(self))

    def __eq__(self, other):
        """Equal when its morphio section is equal."""
        return self.morphio_section == other.morphio_section

    def __hash__(self):
        """Hash of its id."""
        return self.id

    def __nonzero__(self):
        """If has children."""
        return self.morphio_section is not None

    __bool__ = __nonzero__

    @property
    def points(self):
        """Returns the section list of points the NeuroM way (points + radius)."""
        return np.concatenate((self.morphio_section.points,
                               self.morphio_section.diameters[:, np.newaxis] / 2.),
                              axis=1)

    @points.setter
    def points(self, value):
        """Set the points."""
        self.morphio_section.points = np.copy(value[:, COLS.XYZ])
        self.morphio_section.diameters = np.copy(value[:, COLS.R]) * 2

    @property
    def type(self):
        """Returns the section type."""
        return NeuriteType(int(self.morphio_section.type))

    @property
    def length(self):
        """Return the path length of this section."""
        return morphmath.section_length(self.points)

    @property
    def area(self):
        """Return the surface area of this section.

        The area is calculated from the segments, as defined by this
        section's points
        """
        return sum(morphmath.segment_area(s) for s in iter_segments(self))

    @property
    def volume(self):
        """Return the volume of this section.

        The volume is calculated from the segments, as defined by this
        section's points
        """
        return sum(morphmath.segment_volume(s) for s in iter_segments(self))

    def __repr__(self):
        """Text representation."""
        parent_id = None if self.parent is None else self.parent.id
        return (f'Section(id={self.id}, type={self.type}, n_points={len(self.points)})'
                f'<parent: Section(id={parent_id}), nchildren: {len(self.children)}>')


# NRN simulator iteration order
# See:
# https://github.com/neuronsimulator/nrn/blob/2dbf2ebf95f1f8e5a9f0565272c18b1c87b2e54c/share/lib/hoc/import3d/import3d_gui.hoc#L874
NRN_ORDER = {NeuriteType.soma: 0,
             NeuriteType.axon: 1,
             NeuriteType.basal_dendrite: 2,
             NeuriteType.apical_dendrite: 3,
             NeuriteType.undefined: 4}


def iter_neurites(obj, mapfun=None, filt=None, neurite_order=NeuriteIter.FileOrder):
    """Iterator to a neurite, morphology or morphology population.

    Applies optional neurite filter and mapping functions.

    Arguments:
        obj: a neurite, morphology or morphology population.
        mapfun: optional neurite mapping function.
        filt: optional neurite filter function.
        neurite_order (NeuriteIter): order upon which neurites should be iterated
            - NeuriteIter.FileOrder: order of appearance in the file
            - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

    Examples:
        Get the number of points in each neurite in a morphology population

        >>> from neurom.core.morphology import iter_neurites
        >>> from neurom import load_morphologies
        >>> pop = load_morphologies('path/to/morphologies')
        >>> n_points = [n for n in iter_neurites(pop, lambda x : len(x.points))]

        Get the number of points in each axon in a morphology population

        >>> import neurom as nm
        >>> from neurom.core.morphology import iter_neurites
        >>> filter = lambda n : n.type == nm.AXON
        >>> mapping = lambda n : len(n.points)
        >>> n_points = [n for n in iter_neurites(pop, mapping, filter)]
    """
    neurites = ((obj,) if isinstance(obj, Neurite) else
                obj.neurites if hasattr(obj, 'neurites') else obj)
    if neurite_order == NeuriteIter.NRN:
        if isinstance(obj, Population):
            warnings.warn('`iter_neurites` with `neurite_order` over Population orders neurites'
                          'within the whole population, not within each morphology separately.')
        last_position = max(NRN_ORDER.values()) + 1
        neurites = sorted(neurites, key=lambda neurite: NRN_ORDER.get(neurite.type, last_position))

    neurite_iter = iter(neurites) if filt is None else filter(filt, neurites)
    return neurite_iter if mapfun is None else map(mapfun, neurite_iter)


def iter_sections(neurites,
                  iterator_type=Section.ipreorder,
                  neurite_filter=None,
                  neurite_order=NeuriteIter.FileOrder):
    """Iterator to the sections in a neurite, morphology or morphology population.

    Arguments:
        neurites: morphology, population, neurite, or iterable containing neurite objects
        iterator_type: section iteration order within a given neurite. Must be one of:
            Section.ipreorder: Depth-first pre-order iteration of tree nodes
            Section.ipostorder: Depth-first post-order iteration of tree nodes
            Section.iupstream: Iterate from a tree node to the root nodes
            Section.ibifurcation_point: Iterator to bifurcation points
            Section.ileaf: Iterator to all leaves of a tree

        neurite_filter: optional top level filter on properties of neurite neurite objects.
        neurite_order (NeuriteIter): order upon which neurites should be iterated
            - NeuriteIter.FileOrder: order of appearance in the file
            - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical


    Examples:
        Get the number of points in each section of all the axons in a morphology population

        >>> import neurom as nm
        >>> from neurom.core.morphology import iter_sections
        >>> filter = lambda n : n.type == nm.AXON
        >>> n_points = [len(s.points) for s in iter_sections(pop,  neurite_filter=filter)]
    """
    return flatten(
        iterator_type(neurite.root_node)
        for neurite in iter_neurites(neurites, filt=neurite_filter, neurite_order=neurite_order)
    )


def iter_segments(obj, neurite_filter=None, neurite_order=NeuriteIter.FileOrder):
    """Return an iterator to the segments in a collection of neurites.

    Arguments:
        obj: morphology, population, neurite, section, or iterable containing neurite objects
        neurite_filter: optional top level filter on properties of neurite neurite objects
        neurite_order: order upon which neurite should be iterated. Values:
            - NeuriteIter.FileOrder: order of appearance in the file
            - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

    Note:
        This is a convenience function provided for generic access to
        morphology segments. It may have a performance overhead WRT custom-made
        segment analysis functions that leverage numpy and section-wise iteration.
    """
    sections = iter((obj,) if isinstance(obj, Section) else
                    iter_sections(obj,
                                  neurite_filter=neurite_filter,
                                  neurite_order=neurite_order))

    return flatten(
        zip(section.points[:-1], section.points[1:])
        for section in sections
    )


def graft_morphology(section):
    """Returns a morphology starting at section."""
    assert isinstance(section, Section)
    m = morphio.mut.Morphology()
    m.append_root_section(section.morphio_section)
    return Morphology(m)


def graft_neuron(section):
    """Deprecated in favor of ``graft_morphology``."""
    warn_deprecated('`neurom.core.neuron.graft_neuron` is deprecated in favor of '
                    '`neurom.core.morphology.graft_morphology`')  # pragma: no cover
    return graft_morphology(section)  # pragma: no cover


class Neurite:
    """Class representing a neurite tree."""

    def __init__(self, root_node):
        """Constructor.

        Args:
            root_node (morphio.Section): root section
        """
        self.morphio_root_node = root_node

    @property
    def root_node(self):
        """The first section of the neurite."""
        return Section(self.morphio_root_node)

    @property
    def type(self):
        """The type of the root node."""
        return self.root_node.type

    @property
    def points(self):
        """Array with all the points in this neurite.

        Note: Duplicate points at section bifurcations are removed
        """
        # Neurite first point must be added manually
        _ptr = [self.root_node.points[0][COLS.XYZR]]
        for s in iter_sections(self):
            _ptr.append(s.points[1:, COLS.XYZR])
        return np.vstack(_ptr)

    @property
    def length(self):
        """Returns the total length of this neurite.

        The length is defined as the sum of lengths of the sections.
        """
        return sum(s.length for s in self.iter_sections())

    @property
    def area(self):
        """Return the surface area of this neurite.

        The area is defined as the sum of area of the sections.
        """
        return sum(s.area for s in self.iter_sections())

    @property
    def volume(self):
        """Return the volume of this neurite.

        The volume is defined as the sum of volumes of the sections.
        """
        return sum(s.volume for s in self.iter_sections())

    def iter_sections(self, order=Section.ipreorder, neurite_order=NeuriteIter.FileOrder):
        """Iteration over section nodes.

        Arguments:
            order: section iteration order within a given neurite. Must be one of:
                Section.ipreorder: Depth-first pre-order iteration of tree nodes
                Section.ipostorder: Depth-first post-order iteration of tree nodes
                Section.iupstream: Iterate from a tree node to the root nodes
                Section.ibifurcation_point: Iterator to bifurcation points
                Section.ileaf: Iterator to all leaves of a tree

            neurite_order: order upon which neurites should be iterated. Values:
                - NeuriteIter.FileOrder: order of appearance in the file
                - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical
        """
        return iter_sections(self, iterator_type=order, neurite_order=neurite_order)

    def __nonzero__(self):
        """If has root node."""
        return bool(self.morphio_root_node)

    def __eq__(self, other):
        """If root node ids and types are equal."""
        return self.type == other.type and self.morphio_root_node.id == other.morphio_root_node.id

    def __hash__(self):
        """Hash is made of tuple of type and root_node."""
        return hash((self.type, self.root_node))

    __bool__ = __nonzero__

    def __repr__(self):
        """Return a string representation."""
        return 'Neurite <type: %s>' % self.type


class Morphology(morphio.mut.Morphology):
    """Class representing a simple morphology."""

    def __init__(self, filename, name=None):
        """Morphology constructor.

        Args:
            filename (str|Path): a filename
            name (str): a option morphology name
        """
        super().__init__(filename)
        self.name = name if name else 'Morphology'
        self.morphio_soma = super().soma
        self.neurom_soma = make_soma(self.morphio_soma)

    @property
    def soma(self):
        """Corresponding soma."""
        return self.neurom_soma

    @property
    def neurites(self):
        """The list of neurites."""
        return [Neurite(root_section) for root_section in self.root_sections]

    @property
    def sections(self):
        """The array of all sections, excluding the soma."""
        return list(iter_sections(self))

    @property
    def points(self):
        """Returns the list of points."""
        return np.concatenate(
            [section.points for section in iter_sections(self)])

    def transform(self, trans):
        """Return a copy of this morphology with a 3D transformation applied."""
        obj = Morphology(self)
        obj.morphio_soma.points = trans(obj.morphio_soma.points)

        for section in obj.sections:
            section.morphio_section.points = trans(section.morphio_section.points)
        return obj

    def __copy__(self):
        """Creates a deep copy of Morphology instance."""
        return Morphology(self, self.name)

    def __deepcopy__(self, memodict={}):
        """Creates a deep copy of Morphology instance."""
        # pylint: disable=dangerous-default-value
        return Morphology(self, self.name)

    def __repr__(self):
        """Return a string representation."""
        return 'Morphology <soma: %s, n_neurites: %d>' % \
            (self.soma, len(self.neurites))


class Neuron(Morphology):
    """Deprecated ``Neuron`` class. Use ``Morphology`` instead."""
    def __init__(self, filename, name=None):
        """Dont use me."""
        super().__init__(filename, name)  # pragma: no cover
        warn_deprecated('`neurom.core.neuron.Neuron` is deprecated in favor of '
                        '`neurom.core.morphology.Morphology`')  # pragma: no cover
