Source code for neurom.core.types

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"""Type enumerations."""

from enum import unique

from neurom.utils import OrderedEnum


[docs]@unique
class NeuriteIter(OrderedEnum):
    """Neurite iteration orders."""
    FileOrder = 1  # Order in which neurites appear in the file

    # NRN simulator order: soma -> axon -> basal -> apical
    # Coming from:
    # https://github.com/neuronsimulator/nrn/blob/2dbf2ebf95f1f8e5a9f0565272c18b1c87b2e54c/share/lib/hoc/import3d/import3d_gui.hoc#L874
    NRN = 2


[docs]@unique
class NeuriteType(OrderedEnum):
    """Enum representing valid tree types."""
    undefined = 0
    soma = 1
    axon = 2
    basal_dendrite = 3
    apical_dendrite = 4
    custom = 5
    all = 32


NEURITES = (NeuriteType.all,
            NeuriteType.axon,
            NeuriteType.basal_dendrite,
            NeuriteType.apical_dendrite)

ROOT_ID = -1


[docs]def tree_type_checker(*ref):
    """Tree type checker functor.

    Returns:
        Functor that takes a tree, and returns true if that tree matches any of
        NeuriteTypes in ref

    Ex:
        >>> from neurom.core.types import NeuriteType, tree_type_checker
        >>> tree_filter = tree_type_checker(NeuriteType.axon, NeuriteType.basal_dendrite)
        >>> nrn.i_neurites(tree.isegment, tree_filter=tree_filter)
    """
    ref = tuple(ref)
    if NeuriteType.all in ref:
        def check_tree_type(_):
            """Always returns true."""
            return True
    else:
        def check_tree_type(tree):
            """Check whether tree has the same type as ref.

            Returns:
                True if ref in the same type as tree.type or ref is NeuriteType.all
            """
            return tree.type in ref

    return check_tree_type


[docs]def dendrite_filter(n):
    """Select only dendrites."""
    return n.type == NeuriteType.basal_dendrite or n.type == NeuriteType.apical_dendrite


[docs]def axon_filter(n):
    """Select only axons."""
    return n.type == NeuriteType.axon