Source code for neurom.check.structural_checks

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"""Module with consistency/validity checks for raw data  blocks."""
import numpy as np
from neurom.check import CheckResult
from neurom.core.dataformat import COLS
from neurom.core.dataformat import POINT_TYPE
from neurom.core import make_soma
from neurom.fst._core import make_neurites
from neurom.exceptions import SomaError


[docs]def has_sequential_ids(data_wrapper):
    """Check that IDs are increasing and consecutive.

    returns tuple (bool, list of IDs that are not consecutive
    with their predecessor)
    """
    db = data_wrapper.data_block
    ids = db[:, COLS.ID]
    steps = ids[np.where(np.diff(ids) != 1)[0] + 1].astype(int)
    return CheckResult(len(steps) == 0, steps)


[docs]def no_missing_parents(data_wrapper):
    """Check that all points have existing parents.

    Point's parent ID must exist and parent must be declared
    before child.

    Returns:
        CheckResult with result and list of IDs that have no parent
    """
    db = data_wrapper.data_block
    ids = np.setdiff1d(db[:, COLS.P], db[:, COLS.ID])[1:]
    return CheckResult(len(ids) == 0, ids.astype(np.int) + 1)


[docs]def is_single_tree(data_wrapper):
    """Check that data forms a single tree.

    Only the first point has ID of -1.

    Returns:
        CheckResult with result and list of IDs

    Note:
        This assumes no_missing_parents passed.
    """
    db = data_wrapper.data_block
    bad_ids = db[db[:, COLS.P] == -1][1:, COLS.ID]
    return CheckResult(len(bad_ids) == 0, bad_ids.tolist())


[docs]def has_increasing_ids(data_wrapper):
    """Check that IDs are increasing.

    Returns:
        CheckResult with result and list of IDs that are inconsistent
        with their predecessor
    """
    db = data_wrapper.data_block
    ids = db[:, COLS.ID]
    steps = ids[np.where(np.diff(ids) <= 0)[0] + 1].astype(int)
    return CheckResult(len(steps) == 0, steps)


[docs]def has_soma_points(data_wrapper):
    """Checks if the TYPE column of raw data block has an element of type soma.

    Returns:
        CheckResult with result
    """
    db = data_wrapper.data_block
    return CheckResult(POINT_TYPE.SOMA in db[:, COLS.TYPE], None)


[docs]def has_all_finite_radius_neurites(data_wrapper, threshold=0.0):
    """Check that all points with neurite type have a finite radius.

    Returns:
        CheckResult with result and list of IDs of neurite points with zero radius
    """
    db = data_wrapper.data_block
    neurite_ids = np.in1d(db[:, COLS.TYPE], POINT_TYPE.NEURITES)
    zero_radius_ids = db[:, COLS.R] <= threshold
    bad_pts = np.array(db[neurite_ids & zero_radius_ids][:, COLS.ID],
                       dtype=int).tolist()
    return CheckResult(len(bad_pts) == 0, bad_pts)


[docs]def has_valid_soma(data_wrapper):
    """Check if a data block has a valid soma.

    Returns:
        CheckResult with result
    """
    try:
        make_soma(data_wrapper.soma_points())
        return CheckResult(True)
    except SomaError:
        return CheckResult(False)


[docs]def has_valid_neurites(data_wrapper):
    """Check if any neurites can be reconstructed from data block.

    Returns:
        CheckResult with result
    """
    n, _ = make_neurites(data_wrapper)
    return CheckResult(len(n) > 0)