neuron_morphology.features.statistics.overlap

Module Contents

Functions

calculate_coordinate_overlap_from_min_max(coordinates: np.ndarray, minv: float, maxv: float, dimension: int = 1)	Return the % of coordinates that are above the max,
calculate_coordinate_overlap(coordinates_a, coordinates_b, dimension: int = 1)	Return the % of coordinates_a that are above, overlaping, and below
overlap(data: Data, node_types: Optional[List[int]] = None, node_types_to_compare: Optional[List[int]] = None, coord_type: COORD_TYPE = COORD_TYPE.NODE, dimension: int = 1)	Compares the locations of node_types to node_types_to_compare

neuron_morphology.features.statistics.overlap.calculate_coordinate_overlap_from_min_max(coordinates: np.ndarray, minv: float, maxv: float, dimension: int = 1)

Return the % of coordinates that are above the max, between, or below the min

Parameters:

coordinates: np.ndarray with x, y, z columns

minv: min to check against

maxv: max to check against

dimension: dimension to compare (0, 1, 2 for x, y, z), default 1 (y)

neuron_morphology.features.statistics.overlap.calculate_coordinate_overlap(coordinates_a, coordinates_b, dimension: int = 1)

Return the % of coordinates_a that are above, overlaping, and below coordinates_b, and the same for b over a

Parameters:

coordinates_a: 2d array-like with x, y, z cols

coordinates_b: 2d array-like with x, y, z cols

dimension: dimension to compare (0, 1, 2 for x, y, z), default 1 (y)

Returns:

dict: a_above_b, a_overlap_b, a_below_b, or

-1’s if coordinates_b is empty

neuron_morphology.features.statistics.overlap.overlap(data: Data, node_types: Optional[List[int]] = None, node_types_to_compare: Optional[List[int]] = None, coord_type: COORD_TYPE = COORD_TYPE.NODE, dimension: int = 1)

Compares the locations of node_types to node_types_to_compare Calculate % of coordinates of node_types that are above, overlapping, and below the coordinates of node_types_to_compare

Example: calculate_overlap(

morphology, node_types=[AXON], node_types_to_compare=[APICAL_DENDRITE, BASAL_DENDRITE])

will return the percentage of AXON nodes that are above, overlapping, and below DENDRITE nodes

Parameters:

data: Data Object containing a morphology

node_types: a list of node types (see neuron_morphology constants)

node_types_to_compare: a list of node types (see neuron_morphology constants)

coord_type: Restrict analysis to specific coordinate type

(see neuron_morphology.features.statistics.coordinates for options)

dimension: dimension to compare (0, 1, 2 for x, y, z), default 1 (y)