utils.py 36.7 KB
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# @author lucasmiranda42
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import cv2
import matplotlib.pyplot as plt
import multiprocessing
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import networkx as nx
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import numpy as np
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import os
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import pandas as pd
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import regex as re
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import scipy
import seaborn as sns
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from copy import deepcopy
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from itertools import cycle, combinations, product
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from joblib import Parallel, delayed
from scipy import spatial
from sklearn import mixture
from tqdm import tqdm_notebook as tqdm


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# QUALITY CONTROL AND PREPROCESSING #
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def likelihood_qc(dframe: pd.DataFrame, threshold: float = 0.9) -> np.array:
    """Returns a DataFrame filtered dataframe, keeping only the rows entirely above the threshold.

        Parameters:
            - dframe (pandas.DataFrame): DeepLabCut output, with positions over time and associated likelihhod
            - threshold (float): minimum acceptable confidence

        Returns:
            - filt_mask (np.array): mask on the rows of dframe"""

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    Likes = np.array([dframe[i]["likelihood"] for i in list(dframe.columns.levels[0])])
    Likes = np.nan_to_num(Likes, nan=1.0)
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    filt_mask = np.all(Likes > threshold, axis=0)

    return filt_mask
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def bp2polar(tab: pd.DataFrame) -> pd.DataFrame:
    """Returns the DataFrame in polar coordinates.

        Parameters:
            - tab (pandas.DataFrame):Table with cartesian coordinates

        Returns:
            - polar (pandas.DataFrame): Equivalent to input, but with values in polar coordinates"""

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    tab_ = np.array(tab)
    complex_ = tab_[:, 0] + 1j * tab_[:, 1]
    polar = pd.DataFrame(np.array([abs(complex_), np.angle(complex_)]).T)
    polar.rename(columns={0: "rho", 1: "phi"}, inplace=True)
    return polar


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def tab2polar(cartesian_df: pd.DataFrame) -> pd.DataFrame:
    """Returns a pandas.DataFrame in which all the coordinates are polar.

        Parameters:
            - cartesian_df (pandas.DataFrame):DataFrame containing tables with cartesian coordinates

        Returns:
            - result (pandas.DataFrame): Equivalent to input, but with values in polar coordinates"""

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    result = []
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    for df in list(cartesian_df.columns.levels[0]):
        result.append(bp2polar(cartesian_df[df]))
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    result = pd.concat(result, axis=1)
    idx = pd.MultiIndex.from_product(
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        [list(cartesian_df.columns.levels[0]), ["rho", "phi"]],
        names=["bodyparts", "coords"],
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    )
    result.columns = idx
    return result


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def compute_dist(
    pair_array: np.array, arena_abs: int = 1, arena_rel: int = 1
) -> pd.DataFrame:
    """Returns a pandas.DataFrame with the scaled distances between a pair of body parts.

        Parameters:
            - pair_array (numpy.array): np.array of shape N * 4 containing X,y positions
            over time for a given pair of body parts
            - arena_abs (int): diameter of the real arena in cm
            - arena_rel (int): diameter of the captured arena in pixels

        Returns:
            - result (pd.DataFrame): pandas.DataFrame with the
            absolute distances between a pair of body parts"""

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    lim = 2 if pair_array.shape[1] == 4 else 1
    a, b = pair_array[:, :lim], pair_array[:, lim:]
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    ab = a - b
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    dist = np.sqrt(np.einsum("...i,...i", ab, ab))
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    return pd.DataFrame(dist * arena_abs / arena_rel)


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def bpart_distance(
    dataframe: pd.DataFrame, arena_abs: int = 1, arena_rel: int = 1
) -> pd.DataFrame:
    """Returns a pandas.DataFrame with the scaled distances between all pairs of body parts.

        Parameters:
            - dataframe (pandas.DataFrame): pd.DataFrame of shape N*(2*bp) containing X,y positions
        over time for a given set of bp body parts
            - arena_abs (int): diameter of the real arena in cm
            - arena_rel (int): diameter of the captured arena in pixels
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        Returns:
            - result (pd.DataFrame): pandas.DataFrame with the
            absolute distances between all pairs of body parts"""

    indexes = combinations(dataframe.columns.levels[0], 2)
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    dists = []
    for idx in indexes:
        dist = compute_dist(np.array(dataframe.loc[:, list(idx)]), arena_abs, arena_rel)
        dist.columns = [idx]
        dists.append(dist)

    return pd.concat(dists, axis=1)
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def angle(a: np.array, b: np.array, c: np.array) -> np.array:
    """Returns a numpy.array with the angles between the provided instances.

        Parameters:
            - a (2D np.array): positions over time for a bodypart
            - b (2D np.array): positions over time for a bodypart
            - c (2D np.array): positions over time for a bodypart
        Returns:
            - ang (1D np.array): angles between the three-point-instances"""

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    ba = a - b
    bc = c - b

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    cosine_angle = np.einsum("...i,...i", ba, bc) / (
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        np.linalg.norm(ba, axis=1) * np.linalg.norm(bc, axis=1)
    )
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    ang = np.arccos(cosine_angle)

    return ang


def angle_trio(bpart_array: np.array) -> np.array:
    """Returns a numpy.array with all three possible angles between the provided instances.
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        Parameters:
            - bpart_array (2D numpy.array): positions over time for a bodypart
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        Returns:
            - ang_trio (2D numpy.array): all-three angles between the three-point-instances"""
    a, b, c = bpart_array
    ang_trio = np.array([angle(a, b, c), angle(a, c, b), angle(b, a, c)])
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    return ang_trio
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def rotate(
    p: np.array, angles: np.array, origin: np.array = np.array([0, 0])
) -> np.array:
    """Returns a numpy.array with the initial values rotated by angles radians
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        Parameters:
            - p (2D numpy.array): array containing positions of bodyparts over time
            - angles (2D numpy.array): set of angles (in radians) to rotate p with
            - origin (2D numpy.array): rotation axis (zero vector by default)

        Returns:
            - rotated (2D numpy.array): rotated positions over time"""
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    R = np.array([[np.cos(angles), -np.sin(angles)], [np.sin(angles), np.cos(angles)]])

    o = np.atleast_2d(origin)
    p = np.atleast_2d(p)

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    rotated = np.squeeze((R @ (p.T - o.T) + o.T).T)

    return rotated

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def align_trajectories(data: np.array, mode: str = "all") -> np.array:
    """Returns a numpy.array with the positions rotated in a way that the center (0 vector)
    and the body part in the first column of data are aligned with the y axis.
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        Parameters:
            - data (3D numpy.array): array containing positions of body parts over time, where
            shape is N (sliding window instances) * m (sliding window size) * l (features)
            - mode (string): specifies if *all* instances of each sliding window get
            aligned, or only the *center*
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        Returns:
            - aligned_trajs (2D np.array): aligned positions over time"""
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    angles = np.zeros(data.shape[0])
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    data = deepcopy(data)
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    dshape = data.shape
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    if mode == "center":
        center_time = (data.shape[1] - 1) // 2
        angles = np.arctan2(data[:, center_time, 0], data[:, center_time, 1])
    elif mode == "all":
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        data = data.reshape(-1, dshape[-1], order="C")
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        angles = np.arctan2(data[:, 0], data[:, 1])
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    elif mode == "none":
        data = data.reshape(-1, dshape[-1], order="C")
        angles = np.zeros(data.shape[0])
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    aligned_trajs = np.zeros(data.shape)

    for frame in range(data.shape[0]):
        aligned_trajs[frame] = rotate(
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            data[frame].reshape([-1, 2], order="C"), angles[frame],
        ).reshape(data.shape[1:], order="C")
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    if mode == "all" or mode == "none":
        aligned_trajs = aligned_trajs.reshape(dshape, order="C")
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    return aligned_trajs


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def smooth_boolean_array(a: np.array) -> np.array:
    """Returns a boolean array in which isolated appearances of a feature are smoothened

        Parameters:
            - a (1D numpy.array): boolean instances

        Returns:
            - a (1D numpy.array): smoothened boolean instances"""

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    for i in range(1, len(a) - 1):
        if a[i - 1] == a[i + 1]:
            a[i] = a[i - 1]
    return a == 1


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def rolling_window(a: np.array, window_size: int, window_step: int) -> np.array:
    """Returns a 3D numpy.array with a sliding-window extra dimension

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        Parameters:
            - a (2D np.array): N (instances) * m (features) shape
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        Returns:
            - rolled_a (3D np.array):
            N (sliding window instances) * l (sliding window size) * m (features)"""
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    shape = (a.shape[0] - window_size + 1, window_size) + a.shape[1:]
    strides = (a.strides[0],) + a.strides
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    rolled_a = np.lib.stride_tricks.as_strided(
        a, shape=shape, strides=strides, writeable=True
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    )[::window_step]
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    return rolled_a
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def smooth_mult_trajectory(series: np.array, alpha: float = 0.15) -> np.array:
    """Returns a smooths a trajectory using exponentially weighted averages

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        Parameters:
            - series (numpy.array): 1D trajectory array with N (instances) - alpha (float): 0 <= alpha <= 1;
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            indicates the inverse weight assigned to previous observations. Higher (alpha~1) indicates less smoothing;
            lower indicates more (alpha~0)
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        Returns:
            - smoothed_series (np.array): smoothed version of the input, with equal shape"""
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    result = [series[0]]
    for n in range(len(series)):
        result.append(alpha * series[n] + (1 - alpha) * result[n - 1])

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    smoothed_series = np.array(result)

    return smoothed_series
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# BEHAVIOUR RECOGNITION FUNCTIONS #
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def close_single_contact(
    pos_dframe: pd.DataFrame, left: str, right: str, tol: float
) -> np.array:
    """Returns a boolean array that's True if the specified body parts are closer than tol.
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        Parameters:
            - pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
            to two-animal experiments.
            - left (string): First member of the potential contact
            - right (string): Second member of the potential contact
            - tol (float)
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        Returns:
            - contact_array (np.array): True if the distance between the two specified points
            is less than tol, False otherwise"""
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    close_contact = np.linalg.norm(pos_dframe[left] - pos_dframe[right], axis=1) < tol
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    return close_contact
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def close_double_contact(
    pos_dframe: pd.DataFrame,
    left1: str,
    left2: str,
    right1: str,
    right2: str,
    tol: float,
    rev: bool = False,
) -> np.array:
    """Returns a boolean array that's True if the specified body parts are closer than tol.

        Parameters:
            - pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
            to two-animal experiments.
            - left1 (string): First contact point of animal 1
            - left2 (string): Second contact point of animal 1
            - right1 (string): First contact point of animal 2
            - right2 (string): Second contact point of animal 2
            - tol (float)

        Returns:
            - double_contact (np.array): True if the distance between the two specified points
            is less than tol, False otherwise"""

    if rev:
        double_contact = (
            np.linalg.norm(pos_dframe[right1] - pos_dframe[left2], axis=1) < tol
        ) & (np.linalg.norm(pos_dframe[right2] - pos_dframe[left1], axis=1) < tol)

    else:
        double_contact = (
            np.linalg.norm(pos_dframe[right1] - pos_dframe[left1], axis=1) < tol
        ) & (np.linalg.norm(pos_dframe[right2] - pos_dframe[left2], axis=1) < tol)

    return double_contact
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def recognize_arena(
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    videos: list,
    vid_index: int,
    path: str = ".",
    recoglimit: int = 1,
    arena_type: str = "circular",
) -> np.array:
    """Returns numpy.array with information about the arena recognised from the first frames
    of the video. WARNING: estimates won't be reliable if the camera moves along the video.

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        Parameters:
            - videos (list): relative paths of the videos to analise
            - vid_index (int): element of videos to use
            - path (string): full path of the directory where the videos are
            - recoglimit (int): number of frames to use for position estimates
            - arena_type (string): arena type; must be one of ['circular']
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        Returns:
            - arena (np.array): 1D-array containing information about the arena.
                "circular" (3-element-array) -> x-y position of the center and the radius"""
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    cap = cv2.VideoCapture(os.path.join(path, videos[vid_index]))
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    # Loop over the first frames in the video to get resolution and center of the arena
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    arena, fnum, h, w = False, 0, None, None
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    while cap.isOpened() and fnum < recoglimit:
        ret, frame = cap.read()
        # if frame is read correctly ret is True
        if not ret:
            print("Can't receive frame (stream end?). Exiting ...")
            break

        if arena_type == "circular":

            # Detect arena and extract positions
            arena = circular_arena_recognition(frame)[0]
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            if h is not None and w is not None:
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                h, w = frame.shape[0], frame.shape[1]

        fnum += 1

    return arena


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def circular_arena_recognition(frame: np.array) -> np.array:
    """Returns x,y position of the center and the radius of the recognised arena
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        Parameters:
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            - frame (np.array): numpy.array representing an individual frame of a video
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        Returns:
            - circles (np.array): 3-element-array containing x,y positions of the center
            of the arena, and a third value indicating the radius"""
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    # Convert image to greyscale, threshold it, blur it and detect the biggest best fitting circle
    # using the Hough algorithm
    gray_image = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
    ret, thresh = cv2.threshold(gray_image, 50, 255, 0)
    frame = cv2.medianBlur(thresh, 9)
    circle = cv2.HoughCircles(
        frame,
        cv2.HOUGH_GRADIENT,
        1,
        300,
        param1=50,
        param2=10,
        minRadius=0,
        maxRadius=0,
    )

    circles = []

    if circle is not None:
        circle = np.uint16(np.around(circle[0]))
        circles.append(circle)

    return circles[0]


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def climb_wall(
    arena_type: str, arena: np.array, pos_dict: pd.DataFrame, tol: float, nose: str
) -> np.array:
    """Returns True if the specified mouse is climbing the wall
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        Parameters:
            - arena_type (str): arena type; must be one of ['circular']
            - arena (np.array): contains arena location and shape details
            - pos_dict (table_dict): position over time for all videos in a project
            - tol (float): minimum tolerance to report a hit
            - nose (str): indicates the name of the body part representing the nose of
            the selected animal

        Returns:
            - climbing (np.array): boolean array. True if selected animal
            is climbing the walls of the arena"""

    nose = pos_dict[nose]
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    if arena_type == "circular":
        center = np.array(arena[:2])
        climbing = np.linalg.norm(nose - center, axis=1) > (arena[2] + tol)

    else:
        raise NotImplementedError("Supported values for arena_type are ['circular']")
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    return climbing
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def rolling_speed(
    dframe: pd.DatetimeIndex, window: int = 10, rounds: int = 10, deriv: int = 1
) -> pd.DataFrame:
    """Returns the average speed over n frames in pixels per frame
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        Parameters:
            - dframe (pandas.DataFrame): position over time dataframe
            - pause (int):  frame-length of the averaging window
            - rounds (int): float rounding decimals
            - deriv (int): position derivative order; 1 for speed,
            2 for acceleration, 3 for jerk, etc
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        Returns:
            - speeds (pd.DataFrame): containing 2D speeds for each body part
            in the original data or their consequent derivatives"""

    original_shape = dframe.shape
    body_parts = dframe.columns.levels[0]
    speeds = pd.DataFrame

    for der in range(deriv):
        distances = np.concatenate(
            [
                np.array(dframe).reshape([-1, (2 if der == 0 else 1)], order="F"),
                np.array(dframe.shift()).reshape(
                    [-1, (2 if der == 0 else 1)], order="F"
                ),
            ],
            axis=1,
        )
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        distances = np.array(compute_dist(distances))
        distances = distances.reshape(
            [original_shape[0], original_shape[1] // 2], order="F"
        )
        distances = pd.DataFrame(distances, index=dframe.index)
        speeds = np.round(distances.rolling(window).mean(), rounds)
        speeds[np.isnan(speeds)] = 0.0
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        dframe = speeds
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    speeds.columns = body_parts
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    return speeds


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def huddle(pos_dframe: pd.DataFrame, tol_forward: float, tol_spine: float) -> np.array:
    """Returns true when the mouse is huddling using simple rules. (!!!) Designed to
    work with deepof's default DLC mice models; not guaranteed to work otherwise.
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        Parameters:
            - pos_dframe (pandas.DataFrame):
            - tol_forward (float): Maximum tolerated distance between ears and
            forward limbs
            - tol_rear (float): Maximum tolerated average distance between spine
            body parts
        Returns:
            hudd (np.array): True if the animal is huddling, False otherwise
        """

    forward = (
        np.linalg.norm(pos_dframe["Left_ear"] - pos_dframe["Left_fhip"], axis=1)
        < tol_forward
    ) & (
        np.linalg.norm(pos_dframe["Right_ear"] - pos_dframe["Right_fhip"], axis=1)
        < tol_forward
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    )

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    spine = ["Spine1", "Center", "Spine2", "Tail_base"]
    spine_dists = []
    for comb in range(2):
        spine_dists.append(
            np.linalg.norm(
                pos_dframe[spine[comb]] - pos_dframe[spine[comb + 1]], axis=1
            )
        )
    spine = np.mean(spine_dists) < tol_spine

    hudd = forward & spine

    return hudd

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def following_path(distancedf, dframe, follower="B", followed="W", frames=20, tol=0):
    """Returns true if follower is closer than tol to the path that followed has walked over
    the last specified number of frames"""

    # Check that follower is close enough to the path that followed has passed though in the last frames
    shift_dict = {i: dframe[followed + "_Tail_base"].shift(i) for i in range(frames)}
    dist_df = pd.DataFrame(
        {
            i: np.linalg.norm(dframe[follower + "_Nose"] - shift_dict[i], axis=1)
            for i in range(frames)
        }
    )

    # Check that the animals are oriented follower's nose -> followed's tail
    right_orient1 = (
        distancedf[tuple(sorted([follower + "_Nose", followed + "_Tail_base"]))]
        < distancedf[tuple(sorted([follower + "_Tail_base", followed + "_Tail_base"]))]
    )

    right_orient2 = (
        distancedf[tuple(sorted([follower + "_Nose", followed + "_Tail_base"]))]
        < distancedf[tuple(sorted([follower + "_Nose", followed + "_Nose"]))]
    )

    return pd.Series(
        np.all(
            np.array([(dist_df.min(axis=1) < tol), right_orient1, right_orient2]),
            axis=0,
        ),
        index=dframe.index,
    )


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def single_behaviour_analysis(
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    behaviour_name,
    treatment_dict,
    behavioural_dict,
    plot=False,
    stats=False,
    save=False,
    ylim=False,
):
    """Given the name of the behaviour, a dictionary with the names of the groups to compare, and a dictionary
       with the actual taggings, outputs a box plot and a series of significance tests amongst the groups"""

    beh_dict = {condition: [] for condition in treatment_dict.keys()}

    for condition in beh_dict.keys():
        for ind in treatment_dict[condition]:
            beh_dict[condition].append(
                np.sum(behavioural_dict[ind][behaviour_name])
                / len(behavioural_dict[ind][behaviour_name])
            )

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    if plot:
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        sns.boxplot(list(beh_dict.keys()), list(beh_dict.values()), orient="vertical")

        plt.title("{} across groups".format(behaviour_name))
        plt.ylabel("Proportion of frames")

        if ylim != False:
            plt.ylim(*ylim)

        plt.tight_layout()
        plt.savefig("Exploration_heatmaps.pdf")

        if save != False:
            plt.savefig(save)

        plt.show()

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    if stats:
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        for i in combinations(treatment_dict.keys(), 2):
            print(i)
            print(scipy.stats.mannwhitneyu(beh_dict[i[0]], beh_dict[i[1]]))

    return beh_dict

    ##### MAIN BEHAVIOUR TAGGING FUNCTION #####


def Tag_video(
    Tracks,
    Videos,
    Track_dict,
    Distance_dict,
    Like_QC_dict,
    vid_index,
    show=False,
    save=False,
    fps=25.0,
    speedpause=50,
    framelimit=np.inf,
    recoglimit=1,
    path="./",
    classifiers={},
):
    """Outputs a dataframe with the motives registered per frame. If mp4==True, outputs a video in mp4 format"""

    vid_name = re.findall("(.*?)_", Tracks[vid_index])[0]

    cap = cv2.VideoCapture(path + Videos[vid_index])
    dframe = Track_dict[vid_name]
    h, w = None, None
    bspeed, wspeed = None, None

    # Disctionary with motives per frame
    tagdict = {
        func: np.zeros(dframe.shape[0])
        for func in [
            "nose2nose",
            "bnose2tail",
            "wnose2tail",
            "sidebyside",
            "sidereside",
            "bclimbwall",
            "wclimbwall",
            "bspeed",
            "wspeed",
            "bhuddle",
            "whuddle",
            "bfollowing",
            "wfollowing",
        ]
    }

    # Keep track of the frame number, to align with the tracking data
    fnum = 0
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    if save:
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        writer = None

    # Loop over the first frames in the video to get resolution and center of the arena
    while cap.isOpened() and fnum < recoglimit:
        ret, frame = cap.read()
        # if frame is read correctly ret is True
        if not ret:
            print("Can't receive frame (stream end?). Exiting ...")
            break

        # Detect arena and extract positions
        arena = circular_arena_recognition(frame)[0]
        if h == None and w == None:
            h, w = frame.shape[0], frame.shape[1]

        fnum += 1

    # Define behaviours that can be computed on the fly from the distance matrix
    tagdict["nose2nose"] = smooth_boolean_array(
        Distance_dict[vid_name][("B_Nose", "W_Nose")] < 15
    )
    tagdict["bnose2tail"] = smooth_boolean_array(
        Distance_dict[vid_name][("B_Nose", "W_Tail_base")] < 15
    )
    tagdict["wnose2tail"] = smooth_boolean_array(
        Distance_dict[vid_name][("B_Tail_base", "W_Nose")] < 15
    )
    tagdict["sidebyside"] = smooth_boolean_array(
        (Distance_dict[vid_name][("B_Nose", "W_Nose")] < 40)
        & (Distance_dict[vid_name][("B_Tail_base", "W_Tail_base")] < 40)
    )
    tagdict["sidereside"] = smooth_boolean_array(
        (Distance_dict[vid_name][("B_Nose", "W_Tail_base")] < 40)
        & (Distance_dict[vid_name][("B_Tail_base", "W_Nose")] < 40)
    )

    B_mouse_X = np.array(
        Distance_dict[vid_name][
            [j for j in Distance_dict[vid_name].keys() if "B_" in j[0] and "B_" in j[1]]
        ]
    )
    W_mouse_X = np.array(
        Distance_dict[vid_name][
            [j for j in Distance_dict[vid_name].keys() if "W_" in j[0] and "W_" in j[1]]
        ]
    )

    tagdict["bhuddle"] = smooth_boolean_array(classifiers["huddle"].predict(B_mouse_X))
    tagdict["whuddle"] = smooth_boolean_array(classifiers["huddle"].predict(W_mouse_X))

    tagdict["bclimbwall"] = smooth_boolean_array(
        pd.Series(
            (
                spatial.distance.cdist(
                    np.array(dframe["B_Nose"]), np.array([arena[:2]])
                )
                > (w / 200 + arena[2])
            ).reshape(dframe.shape[0]),
            index=dframe.index,
        )
    )
    tagdict["wclimbwall"] = smooth_boolean_array(
        pd.Series(
            (
                spatial.distance.cdist(
                    np.array(dframe["W_Nose"]), np.array([arena[:2]])
                )
                > (w / 200 + arena[2])
            ).reshape(dframe.shape[0]),
            index=dframe.index,
        )
    )
    tagdict["bfollowing"] = smooth_boolean_array(
        following_path(
            Distance_dict[vid_name],
            dframe,
            follower="B",
            followed="W",
            frames=20,
            tol=20,
        )
    )
    tagdict["wfollowing"] = smooth_boolean_array(
        following_path(
            Distance_dict[vid_name],
            dframe,
            follower="W",
            followed="B",
            frames=20,
            tol=20,
        )
    )

    # Compute speed on a rolling window
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    tagdict["bspeed"] = rolling_speed(dframe["B_Center"], window=speedpause)
    tagdict["wspeed"] = rolling_speed(dframe["W_Center"], window=speedpause)
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    if any([show, save]):
        # Loop over the frames in the video
        pbar = tqdm(total=min(dframe.shape[0] - recoglimit, framelimit))
        while cap.isOpened() and fnum < framelimit:

            ret, frame = cap.read()
            # if frame is read correctly ret is True
            if not ret:
                print("Can't receive frame (stream end?). Exiting ...")
                break

            font = cv2.FONT_HERSHEY_COMPLEX_SMALL

            if Like_QC_dict[vid_name][fnum]:

                # Extract positions
                pos_dict = {
                    i: np.array([dframe[i]["x"][fnum], dframe[i]["y"][fnum]])
                    for i in dframe.columns.levels[0]
                    if i != "Like_QC"
                }

                if h == None and w == None:
                    h, w = frame.shape[0], frame.shape[1]

                # Label positions
                downleft = (int(w * 0.3 / 10), int(h / 1.05))
                downright = (int(w * 6.5 / 10), int(h / 1.05))
                upleft = (int(w * 0.3 / 10), int(h / 20))
                upright = (int(w * 6.3 / 10), int(h / 20))

                # Display all annotations in the output video
                if tagdict["nose2nose"][fnum] and not tagdict["sidebyside"][fnum]:
                    cv2.putText(
                        frame,
                        "Nose-Nose",
                        (downleft if bspeed > wspeed else downright),
                        font,
                        1,
                        (255, 255, 255),
                        2,
                    )
                if tagdict["bnose2tail"][fnum] and not tagdict["sidereside"][fnum]:
                    cv2.putText(
                        frame, "Nose-Tail", downleft, font, 1, (255, 255, 255), 2
                    )
                if tagdict["wnose2tail"][fnum] and not tagdict["sidereside"][fnum]:
                    cv2.putText(
                        frame, "Nose-Tail", downright, font, 1, (255, 255, 255), 2
                    )
                if tagdict["sidebyside"][fnum]:
                    cv2.putText(
                        frame,
                        "Side-side",
                        (downleft if bspeed > wspeed else downright),
                        font,
                        1,
                        (255, 255, 255),
                        2,
                    )
                if tagdict["sidereside"][fnum]:
                    cv2.putText(
                        frame,
                        "Side-Rside",
                        (downleft if bspeed > wspeed else downright),
                        font,
                        1,
                        (255, 255, 255),
                        2,
                    )
                if tagdict["bclimbwall"][fnum]:
                    cv2.putText(
                        frame, "Climbing", downleft, font, 1, (255, 255, 255), 2
                    )
                if tagdict["wclimbwall"][fnum]:
                    cv2.putText(
                        frame, "Climbing", downright, font, 1, (255, 255, 255), 2
                    )
                if tagdict["bhuddle"][fnum] and not tagdict["bclimbwall"][fnum]:
                    cv2.putText(frame, "huddle", downleft, font, 1, (255, 255, 255), 2)
                if tagdict["whuddle"][fnum] and not tagdict["wclimbwall"][fnum]:
                    cv2.putText(frame, "huddle", downright, font, 1, (255, 255, 255), 2)
                if tagdict["bfollowing"][fnum] and not tagdict["bclimbwall"][fnum]:
                    cv2.putText(
                        frame,
                        "*f",
                        (int(w * 0.3 / 10), int(h / 10)),
                        font,
                        1,
                        ((150, 150, 255) if wspeed > bspeed else (150, 255, 150)),
                        2,
                    )
                if tagdict["wfollowing"][fnum] and not tagdict["wclimbwall"][fnum]:
                    cv2.putText(
                        frame,
                        "*f",
                        (int(w * 6.3 / 10), int(h / 10)),
                        font,
                        1,
                        ((150, 150, 255) if wspeed < bspeed else (150, 255, 150)),
                        2,
                    )

                if (bspeed == None and wspeed == None) or fnum % speedpause == 0:
                    bspeed = tagdict["bspeed"][fnum]
                    wspeed = tagdict["wspeed"][fnum]

                cv2.putText(
                    frame,
                    "W: " + str(np.round(wspeed, 2)) + " mmpf",
                    (upright[0] - 20, upright[1]),
                    font,
                    1,
                    ((150, 150, 255) if wspeed < bspeed else (150, 255, 150)),
                    2,
                )
                cv2.putText(
                    frame,
                    "B: " + str(np.round(bspeed, 2)) + " mmpf",
                    upleft,
                    font,
                    1,
                    ((150, 150, 255) if bspeed < wspeed else (150, 255, 150)),
                    2,
                )

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                if show:
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                    cv2.imshow("frame", frame)

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                if save:
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                    if writer is None:
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                        # Define the codec and create VideoWriter object.The output is stored in 'outpy.avi' file.
                        # Define the FPS. Also frame size is passed.
                        writer = cv2.VideoWriter()
                        writer.open(
                            re.findall("(.*?)_", Tracks[vid_index])[0] + "_tagged.avi",
                            cv2.VideoWriter_fourcc(*"MJPG"),
                            fps,
                            (frame.shape[1], frame.shape[0]),
                            True,
                        )
                    writer.write(frame)

            if cv2.waitKey(1) == ord("q"):
                break

            pbar.update(1)
            fnum += 1

    cap.release()
    cv2.destroyAllWindows()

    tagdf = pd.DataFrame(tagdict)

    return tagdf, arena


def max_behaviour(array, window_size=50):
    """Returns the most frequent behaviour in a window of window_size frames"""
    array = array.drop(["bspeed", "wspeed"], axis=1).astype("float")
    win_array = array.rolling(window_size, center=True).sum()[::50]
    max_array = win_array[1:].idxmax(axis=1)
    return list(max_array)

    ##### MACHINE LEARNING FUNCTIONS #####


def gmm_compute(x, n_components, cv_type):
    gmm = mixture.GaussianMixture(
        n_components=n_components,
        covariance_type=cv_type,
        max_iter=100000,
        init_params="kmeans",
    )
    gmm.fit(x)
    return [gmm, gmm.bic(x)]


def GMM_Model_Selection(
    X,
    n_components_range,
    n_runs=100,
    part_size=10000,
    n_cores=False,
    cv_types=["spherical", "tied", "diag", "full"],
):
    """Runs GMM clustering model selection on the specified X dataframe, outputs the bic distribution per model,
       a vector with the median BICs and an object with the overall best model"""

    # Set the default of n_cores to the most efficient value
    if not n_cores:
        n_cores = min(multiprocessing.cpu_count(), n_runs)

    bic = []
    m_bic = []
    lowest_bic = np.inf

    pbar = tqdm(total=len(cv_types) * len(n_components_range))

    for cv_type in cv_types:

        for n_components in n_components_range:

            res = Parallel(n_jobs=n_cores, prefer="threads")(
                delayed(gmm_compute)(X.sample(part_size), n_components, cv_type)
                for i in range(n_runs)
            )
            bic.append([i[1] for i in res])

            pbar.update(1)
            m_bic.append(np.median([i[1] for i in res]))
            if m_bic[-1] < lowest_bic:
                lowest_bic = m_bic[-1]
                best_bic_gmm = res[0][0]

    return bic, m_bic, best_bic_gmm

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    ##### RESULT ANALYSIS FUNCTIONS #####


def cluster_transition_matrix(
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):
    """
    Computes the transition matrix between clusters and the autocorrelation in the sequence.
    """

    # Stores all possible transitions between clusters
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    clusters = [str(i) for i in range(nclusts)]
    cluster_sequence = cluster_sequence.astype(str)

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    trans = {t: 0 for t in product(clusters, clusters)}
    k = len(clusters)

    # Stores the cluster sequence as a string
    transtr = "".join(list(cluster_sequence))

    # Assigns to each transition the number of times it occurs in the sequence
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    for t in trans.keys():
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        trans[t] = len(re.findall("".join(t), transtr, overlapped=True))

    # Normalizes the counts to add up to 1 for each departing cluster
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    trans_normed = np.zeros([k, k]) + 1e-5
    for t in trans.keys():
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        trans_normed[int(t[0]), int(t[1])] = np.round(
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            / (sum({i: j for i, j in trans.items() if i[0] == t[0]}.values()) + 1e-5),
            3,
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        )

    # If specified, returns the transition matrix as an nx.Graph object
    if return_graph:
        trans_normed = nx.Graph(trans_normed)

    if autocorrelation:
        cluster_sequence = list(map(int, cluster_sequence))
        return trans_normed, np.corrcoef(cluster_sequence[:-1], cluster_sequence[1:])

    return trans_normed

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    ##### PLOTTING FUNCTIONS #####


def plot_speed(Behaviour_dict, Treatments):
    """Plots a histogram with the speed of the specified mouse.
       Treatments is expected to be a list of lists with mice keys per treatment"""

    fig, [ax1, ax2] = plt.subplots(1, 2, figsize=(20, 10))

    for Treatment, Mice_list in Treatments.items():
        hist = pd.concat([Behaviour_dict[mouse] for mouse in Mice_list])
        sns.kdeplot(hist["bspeed"], shade=True, label=Treatment, ax=ax1)
        sns.kdeplot(hist["wspeed"], shade=True, label=Treatment, ax=ax2)

    ax1.set_xlim(0, 7)
    ax2.set_xlim(0, 7)
    ax1.set_title("Average speed density for black mouse")
    ax2.set_title("Average speed density for white mouse")
    plt.xlabel("Average speed")
    plt.ylabel("Density")
    plt.show()


def plot_heatmap(dframe, bodyparts, xlim, ylim, save=False):
    """Returns a heatmap of the movement of a specific bodypart in the arena.
       If more than one bodypart is passed, it returns one subplot for each"""

    fig, ax = plt.subplots(1, len(bodyparts), sharex=True, sharey=True)

    for i, bpart in enumerate(bodyparts):
        heatmap = dframe[bpart]
        if len(bodyparts) > 1:
            sns.kdeplot(heatmap.x, heatmap.y, cmap="jet", shade=True, alpha=1, ax=ax[i])
        else:
            sns.kdeplot(heatmap.x, heatmap.y, cmap="jet", shade=True, alpha=1, ax=ax)
            ax = np.array([ax])

    [x.set_xlim(xlim) for x in ax]
    [x.set_ylim(ylim) for x in ax]
    [x.set_title(bp) for x, bp in zip(ax, bodyparts)]

    if save != False:
        plt.savefig(save)

    plt.show()


def model_comparison_plot(
    bic,
    m_bic,
    best_bic_gmm,
    n_components_range,
    cov_plot,
    save,
    cv_types=["spherical", "tied", "diag", "full"],
):
    """Plots model comparison statistics over all tests"""

    m_bic = np.array(m_bic)
    color_iter = cycle(["navy", "turquoise", "cornflowerblue", "darkorange"])
    clf = best_bic_gmm
    bars = []

    # Plot the BIC scores
    plt.figure(figsize=(12, 8))
    spl = plt.subplot(2, 1, 1)
    covplot = np.repeat(cv_types, len(m_bic) / 4)

    for i, (cv_type, color) in enumerate(zip(cv_types, color_iter)):
        xpos = np.array(n_components_range) + 0.2 * (i - 2)
        bars.append(
            spl.bar(
                xpos,
                m_bic[i * len(n_components_range) : (i + 1) * len(n_components_range)],
                color=color,
                width=0.2,
            )
        )

    spl.set_xticks(n_components_range)
    plt.title("BIC score per model")
    xpos = (
        np.mod(m_bic.argmin(), len(n_components_range))
        + 0.5
        + 0.2 * np.floor(m_bic.argmin() / len(n_components_range))
    )
    spl.text(xpos, m_bic.min() * 0.97 + 0.1 * m_bic.max(), "*", fontsize=14)
    spl.legend([b[0] for b in bars], cv_types)
    spl.set_ylabel("BIC value")

    spl2 = plt.subplot(2, 1, 2, sharex=spl)
    spl2.boxplot(list(np.array(bic)[covplot == cov_plot]), positions=n_components_range)
    spl2.set_xlabel("Number of components")
    spl2.set_ylabel("BIC value")

    plt.tight_layout()

    if save:
        plt.savefig(save)

    plt.show()