Source code for replay_trajectory_classification.likelihoods.diffusion

"""Calculate diffusion distances by simulating diffusion at
each position bin. This can be used for more accurate 2D kernel density
estimates with boundaries."""
from __future__ import annotations
import numpy as np
from replay_trajectory_classification.environments import diffuse_each_bin, get_bin_ind

from typing import Optional




def estimate_diffusion_position_distance(
    positions: np.ndarray,
    edges: np.ndarray,
    is_track_interior: Optional[np.ndarray] = None,
    is_track_boundary: Optional[np.ndarray] = None,
    position_std: float = 3.0,
    bin_distances: Optional[np.ndarray] = None,
) -> np.ndarray:
    """Estimates a distance between a given position and all position bins
    using a diffusion.

    Parameters
    ----------
    positions : np.ndarray, shape (n_time, n_position_dims)
    position_std : float

    Returns
    -------
    position_distance : np.ndarray, shape (n_time, n_position_bins)

    """
    if bin_distances is None:
        n_time = positions.shape[0]

        dx = edges[0][1] - edges[0][0]
        dy = edges[1][1] - edges[1][0]

        bin_distances = diffuse_each_bin(
            is_track_interior,
            is_track_boundary,
            dx,
            dy,
            std=position_std,
        ).reshape((n_time, -1), order="F")

    bin_ind = get_bin_ind(positions, [edge[1:-1] for edge in edges])
    linear_ind = np.ravel_multi_index(
        bin_ind, [len(edge) - 1 for edge in edges], order="F"
    )
    return bin_distances[linear_ind]





def estimate_diffusion_position_density(
    positions: np.ndarray,
    edges: np.ndarray,
    is_track_interior: Optional[np.ndarray] = None,
    is_track_boundary: Optional[np.ndarray] = None,
    position_std: float = 3.0,
    bin_distances: Optional[np.ndarray] = None,
    block_size: Optional[int] = 100,
) -> np.ndarray:
    """Kernel density estimate over all position bins using diffusion.

    Parameters
    ----------
    place_bin_centers : np.ndarray, shape (n_position_bins, n_position_dims)
    positions : np.ndarray, shape (n_time, n_position_dims)
    position_std : float

    Returns
    -------
    position_density : np.ndarray, shape (n_position_bins,)

    """
    n_time = positions.shape[0]

    if block_size is None:
        block_size = n_time

    return np.mean(
        estimate_diffusion_position_distance(
            positions,
            edges,
            is_track_interior=is_track_interior,
            is_track_boundary=is_track_boundary,
            position_std=position_std,
            bin_distances=bin_distances,
        ),
        axis=0,
    )