grainstats.py

"""Contains class for calculating the statistics of grains - 2d raster images."""

from __future__ import annotations

import logging
from pathlib import Path
from random import randint

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.ndimage
import skimage.feature as skimage_feature
import skimage.measure as skimage_measure
import skimage.morphology as skimage_morphology

from topostats.logs.logs import LOGGER_NAME
from topostats.utils import create_empty_dataframe

# pylint: disable=too-many-lines
# pylint: disable=too-many-instance-attributes
# pylint: disable=too-many-arguments
# pylint: disable=too-many-branches
# pylint: disable=line-too-long
# pylint: disable=fixme
# FIXME : The calculate_stats() and calculate_aspect_ratio() raise this error when linting, could consider putting
#         variables into dictionar, see example of breaking code out to staticmethod extremes() and returning a
#         dictionary of x_min/x_max/y_min/y_max
# pylint: disable=too-many-locals
# FIXME : calculate_aspect_ratio raises this error when linting it has 65 statements, recommended not to exceed 50.
#         Could break some out to small functions such as the lines that calculate the samllest bounding rectangle
# pylint: disable=too-many-statements

LOGGER = logging.getLogger(LOGGER_NAME)


GRAIN_STATS_COLUMNS = [
    "molecule_number",
    "centre_x",
    "centre_y",
    "radius_min",
    "radius_max",
    "radius_mean",
    "radius_median",
    "height_min",
    "height_max",
    "height_median",
    "height_mean",
    "volume",
    "area",
    "area_cartesian_bbox",
    "smallest_bounding_width",
    "smallest_bounding_length",
    "smallest_bounding_area",
    "aspect_ratio",
]


class GrainStats:
    """Class for calculating grain stats."""

    def __init__(
        self,
        data: np.ndarray,
        labelled_data: np.ndarray,
        pixel_to_nanometre_scaling: float,
        direction: str,
        base_output_dir: str | Path,
        image_name: str = None,
        edge_detection_method: str = "binary_erosion",
        cropped_size: float = -1,
        plot_opts: dict = None,
        metre_scaling_factor: float = 1e-9,
    ):
        """Initialise the class.

        Parameters
        ----------
        data : np.ndarray
            2D Numpy array containing the flattened afm image. Data in this 2D array is floating point.
        labelled_data : np.ndarray
            2D Numpy array containing all the grain masks in the image. Data in this 2D array is boolean.
        pixel_to_nanometre_scaling : float
            Floating point value that defines the scaling factor between nanometres and pixels.
        direction: str
            Direction for which grains have been detected ("above" or "below").
        base_output_dir : Path
            Path to the folder that will store the grain stats output images and data.
        image_name : str
            The name of the file being processed.
        edge_detection_method : str
            Method used for detecting the edges of grain masks before calculating statistics on them.
            Do not change unless you know exactly what this is doing. Options: "binary_erosion", "canny".
        cropped_size : float
            Length of square side (in nm) to crop grains to.
        plot_opts : dict
            Plotting options dictionary for the cropped grains
        metre_scaling_factor : float
            Multiplier to convert the current length scale to metres. Default: 1e-9 for the
            usual AFM length scale of nanometres.
        """
        self.data = data
        self.labelled_data = labelled_data
        self.pixel_to_nanometre_scaling = pixel_to_nanometre_scaling
        self.direction = direction
        self.base_output_dir = Path(base_output_dir)
        self.start_point = None
        self.image_name = image_name
        self.edge_detection_method = edge_detection_method
        self.cropped_size = cropped_size
        self.plot_opts = plot_opts
        self.metre_scaling_factor = metre_scaling_factor

    @staticmethod
    def get_angle(point_1: tuple, point_2: tuple) -> float:
        """Calculate the angle in radians between two points.

        Parameters
        ----------
        point1: tuple
            Coordinate vectors for the first point to find the angle between.
        point2: tuple
            Coordinate vectors for the second point to find the angle between.

        Returns
        -------
        angle : float
            The angle in radians between the two input vectors.
        """
        return np.arctan2(point_1[1] - point_2[1], point_1[0] - point_2[0])

    @staticmethod
    def is_clockwise(p_1: tuple, p_2: tuple, p_3: tuple) -> bool:
        """Determine if three points make a clockwise or counter-clockwise turn.

        Parameters
        ----------
        p_1: tuple
            First point to be used to calculate turn.
        p_2: tuple
            Second point to be used to calculate turn.
        p_3: tuple
            Third point to be used to calculate turn.

        Returns
        -------
        boolean
            Indicator of whether turn is clockwise.
        """
        # Determine if three points form a clockwise or counter-clockwise turn.
        # I use the method of calculating the determinant of the following rotation matrix here. If the determinant
        # is > 0 then the rotation is counter-clockwise.
        rotation_matrix = np.array(((p_1[0], p_1[1], 1), (p_2[0], p_2[1], 1), (p_3[0], p_3[1], 1)))
        return not np.linalg.det(rotation_matrix) > 0

    def calculate_stats(self) -> dict:
        """Calculate the stats of grains in the labelled image.

        Returns
        -------
        grainstats: pd.DataFrame
            A DataFrame containing all the grain stats that have been calculated for the labelled image.
        grains_plot_data:
            A list of dictionaries containing grain data to be plotted.
        """
        grains_plot_data = []
        if self.labelled_data is None:
            LOGGER.info(
                f"[{self.image_name}] : No labelled regions for this image, grain statistics can not be calculated."
            )
            return pd.DataFrame(columns=GRAIN_STATS_COLUMNS), grains_plot_data

        # Calculate region properties
        region_properties = skimage_measure.regionprops(self.labelled_data)

        # Iterate over all the grains in the image
        stats_array = []
        # List to hold all the plot data for all the grains. Each entry is a dictionary of plotting data.
        # There are multiple entries for each grain.
        for index, region in enumerate(region_properties):
            LOGGER.info(f"[{self.image_name}] : Processing grain: {index}")

            # Skip grain if too small to calculate stats for
            LOGGER.debug(f"[{self.image_name}] : Grain size: {region.image.size}")
            if min(region.image.shape) < 5:
                LOGGER.info(
                    f"[{self.image_name}] : Skipping grain due to being too small (size: {region.image.shape}) to calculate stats for."
                )
                continue

            # Create directory for each grain's plots
            output_grain = self.base_output_dir / self.direction
            # Obtain cropped grain mask and image
            minr, minc, maxr, maxc = region.bbox
            grain_mask = np.array(region.image)
            grain_image = self.data[minr:maxr, minc:maxc]
            grain_mask_image = np.ma.masked_array(grain_image, mask=np.invert(grain_mask), fill_value=np.nan).filled()

            if self.cropped_size == -1:
                for name, image in {
                    "grain_image": grain_image,
                    "grain_mask": grain_mask,
                    "grain_mask_image": grain_mask_image,
                }.items():
                    grains_plot_data.append(
                        {
                            "data": image,
                            "output_dir": output_grain,
                            "filename": f"{self.image_name}_{name}_{index}",
                            "name": name,
                        }
                    )

            else:
                # Get cropped image and mask
                grain_centre = int((minr + maxr) / 2), int((minc + maxc) / 2)
                length = int(self.cropped_size / (2 * self.pixel_to_nanometre_scaling))
                solo_mask = self.labelled_data.copy()
                solo_mask[solo_mask != index + 1] = 0
                solo_mask[solo_mask == index + 1] = 1
                cropped_grain_image = self.get_cropped_region(self.data, length, np.asarray(grain_centre))
                cropped_grain_mask = self.get_cropped_region(solo_mask, length, np.asarray(grain_centre)).astype(bool)
                cropped_grain_mask_image = np.ma.masked_array(
                    grain_image, mask=np.invert(grain_mask), fill_value=np.nan
                ).filled()
                for name, image in {
                    "grain_image": cropped_grain_image,
                    "grain_mask": cropped_grain_mask,
                    "grain_mask_image": cropped_grain_mask_image,
                }.items():
                    grains_plot_data.append(
                        {
                            "data": image,
                            "output_dir": output_grain,
                            "filename": f"{self.image_name}_{name}_{index}",
                            "name": name,
                        }
                    )

            points = self.calculate_points(grain_mask)
            edges = self.calculate_edges(grain_mask, edge_detection_method=self.edge_detection_method)
            radius_stats = self.calculate_radius_stats(edges, points)
            # hull, hull_indices, hull_simplexes = self.convex_hull(edges, output_grain)
            _, _, hull_simplexes = self.convex_hull(edges, output_grain)
            centroid = self._calculate_centroid(points)
            # Centroids for the grains (minc and minr added because centroid returns values local to the cropped grain images)
            centre_x = centroid[0] + minc
            centre_y = centroid[1] + minr
            (
                smallest_bounding_width,
                smallest_bounding_length,
                aspect_ratio,
            ) = self.calculate_aspect_ratio(
                edges=edges,
                hull_simplices=hull_simplexes,
                path=output_grain,
            )

            # Calculate minimum and maximum feret diameters
            min_feret, max_feret = self.get_max_min_ferets(edge_points=edges)

            # Save the stats to dictionary. Note that many of the stats are multiplied by a scaling factor to convert
            # from pixel units to nanometres.
            # Removed formatting, better to keep accurate until the end, including in CSV, then shorten display
            length_scaling_factor = self.pixel_to_nanometre_scaling * self.metre_scaling_factor
            area_scaling_factor = length_scaling_factor**2
            stats = {
                "centre_x": centre_x * length_scaling_factor,
                "centre_y": centre_y * length_scaling_factor,
                "radius_min": radius_stats["min"] * length_scaling_factor,
                "radius_max": radius_stats["max"] * length_scaling_factor,
                "radius_mean": radius_stats["mean"] * length_scaling_factor,
                "radius_median": radius_stats["median"] * length_scaling_factor,
                "height_min": np.nanmin(grain_mask_image) * self.metre_scaling_factor,
                "height_max": np.nanmax(grain_mask_image) * self.metre_scaling_factor,
                "height_median": np.nanmedian(grain_mask_image) * self.metre_scaling_factor,
                "height_mean": np.nanmean(grain_mask_image) * self.metre_scaling_factor,
                # [volume] = [pixel] * [pixel] * [height] = px * px * nm.
                # To turn into m^3, multiply by pixel_to_nanometre_scaling^2 and metre_scaling_factor^3.
                "volume": np.nansum(grain_mask_image)
                * self.pixel_to_nanometre_scaling**2
                * (self.metre_scaling_factor**3),
                "area": region.area * area_scaling_factor,
                "area_cartesian_bbox": region.area_bbox * area_scaling_factor,
                "smallest_bounding_width": smallest_bounding_width * length_scaling_factor,
                "smallest_bounding_length": smallest_bounding_length * length_scaling_factor,
                "smallest_bounding_area": smallest_bounding_length * smallest_bounding_width * area_scaling_factor,
                "aspect_ratio": aspect_ratio,
                "threshold": self.direction,
                "max_feret": max_feret * length_scaling_factor,
                "min_feret": min_feret * length_scaling_factor,
            }
            stats_array.append(stats)
        if len(stats_array) > 0:
            grainstats_df = pd.DataFrame(data=stats_array)
        else:
            grainstats_df = create_empty_dataframe()
        grainstats_df.index.name = "molecule_number"
        grainstats_df["image"] = self.image_name

        return grainstats_df, grains_plot_data

    @staticmethod
    def calculate_points(grain_mask: np.ndarray):
        """Convert a 2D boolean array to a list of coordinates.

        Parameters
        ----------
        grain_mask : np.ndarray
            A 2D numpy array image of a grain. Data in the array must be boolean.

        Returns
        -------
        points : list
        A python list containing the coordinates of the pixels in the grain.
        """
        nonzero_coordinates = grain_mask.nonzero()
        points = []
        for point in np.transpose(nonzero_coordinates):
            points.append(list(point))

        return points

    @staticmethod
    def calculate_edges(grain_mask: np.ndarray, edge_detection_method: str):
        """Convert 2D boolean array to list of the coordinates of the edges of the grain.

        Parameters
        ----------
        grain_mask : np.ndarray
            A 2D numpy array image of a grain. Data in the array must be boolean.
        edge_detection_method : str
            Method used for detecting the edges of grain masks before calculating statistics on them.
            Do not change unless you know exactly what this is doing. Options: "binary_erosion", "canny".

        Returns
        -------
        edges : list
            List containing the coordinates of the edges of the grain.
        """
        # Fill any holes
        filled_grain_mask = scipy.ndimage.binary_fill_holes(grain_mask)

        if edge_detection_method == "binary_erosion":
            # Add padding (needed for erosion)
            padded = np.pad(filled_grain_mask, 1)
            # Erode by 1 pixel
            eroded = skimage_morphology.binary_erosion(padded)
            # Remove padding
            eroded = eroded[1:-1, 1:-1]

            # Edges is equal to the difference between the
            # original image and the eroded image.
            edges = filled_grain_mask.astype(int) - eroded.astype(int)
        else:
            # Get outer edge using canny filtering
            edges = skimage_feature.canny(filled_grain_mask, sigma=3)

        nonzero_coordinates = edges.nonzero()
        # Get vector representation of the points
        # FIXME : Switched to list comprehension but should be unnecessary to create this as a list as we can use
        # np.stack() to combine the arrays and use that...
        # return np.stack(nonzero_coordinates, axis=1)
        # edges = []
        # for vector in np.transpose(nonzero_coordinates):
        #     edges.append(list(vector))
        # return edges
        return [list(vector) for vector in np.transpose(nonzero_coordinates)]

    def calculate_radius_stats(self, edges: list, points: list) -> tuple:
        """Calculate the radius of grains.

        The radius in this context is the distance from the centroid to points on the edge of the grain.

        Parameters
        ----------
        edges: list
            A 2D python list containing the coordinates of the edges of a grain.
        points: list
            A 2D python list containing the coordinates of the points in a grain.

        Returns
        -------
        Tuple[float]
            A tuple of the minimum, maximum, mean and median radius of the grain
        """
        # Calculate the centroid of the grain
        centroid = self._calculate_centroid(points)
        # Calculate the displacement
        displacements = self._calculate_displacement(edges, centroid)
        # Calculate the radius of each point
        radii = self._calculate_radius(displacements)
        return {
            "min": np.min(radii),
            "max": np.max(radii),
            "mean": np.mean(radii),
            "median": np.median(radii),
        }

    @staticmethod
    def _calculate_centroid(points: np.array) -> tuple:
        """Calculate the centroid of a bounding box.

        Parameters
        ----------
        points: list
            A 2D python list containing the coordinates of the points in a grain.

        Returns
        -------
        tuple
            The coordinates of the centroid.
        """
        # FIXME : Remove once we have a numpy array returned by calculate_edges
        points = np.array(points)
        return (np.mean(points[:, 0]), np.mean(points[:, 1]))

    @staticmethod
    def _calculate_displacement(edges: np.array, centroid: tuple) -> np.array:
        """Calculate the displacement between the centroid and edges."""
        # FIXME : Remove once we have a numpy array returned by calculate_edges
        return np.array(edges) - centroid

    @staticmethod
    def _calculate_radius(displacements) -> np.array:
        """Calculate the radius of each point from the centroid.

        Parameters
        ----------
        displacements: List[list]

        Retrurns
        --------
        np.array
        """
        return np.array([np.sqrt(radius[0] ** 2 + radius[1] ** 2) for radius in displacements])

    def convex_hull(self, edges: list, base_output_dir: Path, debug: bool = False):
        """Calculate a grain's convex hull.

        Based off of the Graham Scan algorithm and should ideally scale in time with O(nlog(n)).

        Parameters
        ----------
        edges : list
            A python list containing the coordinates of the edges of the grain.
        base_output_dir : Union[str, Path]
            Directory to save output to.
        debug : bool
            Default false. If true, debug information will be displayed to the terminal and plots for the convex hulls and edges will be saved.

        Returns
        -------
        hull : list
            Coordinates of the points in the hull.
        hull_indices : list
            The hull points indices inside the edges list. In other words, this provides a way to find the points from the hull inside the edges list that was passed.
        simplices : list
            List of tuples, each tuple representing a simplex of the convex hull. These simplices are sorted such that they follow each other in counterclockwise order.
        """
        hull, hull_indices, simplexes = self.graham_scan(edges)

        # Debug information
        if debug:
            base_output_dir.mkdir(parents=True, exist_ok=True)
            self.plot(edges, hull, base_output_dir / "_points_hull.png")
            LOGGER.info(f"points: {edges}")
            LOGGER.info(f"hull: {hull}")
            LOGGER.info(f"hull indexes: {hull_indices}")
            LOGGER.info(f"simplexes: {simplexes}")

        return hull, hull_indices, simplexes

    def calculate_squared_distance(self, point_2: tuple, point_1: tuple = None) -> float:
        """Calculate the squared distance between two points.

        Used for distance sorting purposes and therefore does not perform a square root in the interests of efficiency.

        Parameters
        ----------
        point_2 : tuple
            The point to find the squared distance to.
        point_1 : tuple
            Optional - defaults to the starting point defined in the graham_scan() function. The point to find the
        squared distance from.

        Returns
        -------
        distance_squared : float
            The squared distance between the two points.
        """
        # Get the distance squared between two points. If the second point is not provided, use the starting point.
        point_1 = self.start_point if point_1 is None else point_1
        delta_x = point_2[0] - point_1[0]
        delta_y = point_2[1] - point_1[1]
        # Don't need the sqrt since just sorting for dist
        return float(delta_x**2 + delta_y**2)

    def sort_points(self, points: list) -> list:
        #    def sort_points(self, points: np.array) -> List:
        """Sort points in counter-clockwise order of angle made with the starting point.

        Parameters
        ----------
        points: list
            A python list of the coordinates to sort.

        Returns
        -------
        sorted_points : list
            A python list of sorted points.
        """
        # Return if the list is length 1 or 0 (i.e. a single point).
        if len(points) <= 1:
            return points
        # Lists that allow sorting of points relative to a current comparison point
        smaller, equal, larger = [], [], []
        # Get a random point in the array to calculate the pivot angle from. This sorts the points relative to this point.
        pivot_angle = self.get_angle(points[randint(0, len(points) - 1)], self.start_point)  # noqa: S311
        for point in points:
            point_angle = self.get_angle(point, self.start_point)
            # If the
            if point_angle < pivot_angle:
                smaller.append(point)
            elif point_angle == pivot_angle:
                equal.append(point)
            else:
                larger.append(point)
        # Lets take a different approach and use arrays, we have a start point lets work out the angle of each point
        # relative to that and _then_ sort it.
        # pivot_angles = self.get_angle(points, self.start_point)
        # Recursively sort the arrays until each point is sorted
        return self.sort_points(smaller) + sorted(equal, key=self.calculate_squared_distance) + self.sort_points(larger)
        # Return sorted array where equal angle points are sorted by distance

    def get_start_point(self, edges) -> None:
        """Determine the index of the bottom most point of the hull when sorted by x-position.

        Parameters
        ----------
        edges: np.array

        """
        min_y_index = np.argmin(edges[:, 1])
        self.start_point = edges[min_y_index]

    def graham_scan(self, edges: list):
        """Construct the convex hull using the  Graham Scan algorithm.

        Ideally this algorithm will take O( n * log(n) ) time.

        Parameters
        ----------
        edges : list
            A python list of coordinates that make up the edges of the grain.

        Returns
        -------
        hull : list
            A list containing coordinates of the points in the hull.
        hull_indices : list
            A list containing the hull points indices inside the edges list. In other words, this provides a way to find
            the points from the hull inside the edges list that was passed.
        simplices : list
            A  list of tuples, each tuple representing a simplex of the convex hull. These simplices are sorted such
            that they follow each other in counterclockwise order.
        """
        # FIXME : Make this an isolated method
        # Find a point guaranteed to be on the hull. I find the bottom most point(s) and sort by x-position.
        min_y_index = None
        for index, point in enumerate(edges):
            if min_y_index is None or point[1] < edges[min_y_index][1]:
                min_y_index = index
            if point[1] == edges[min_y_index][1] and point[0] < edges[min_y_index][0]:
                min_y_index = index
        self.start_point = edges[min_y_index]
        # This does the same thing, but as a separate method and with Numpy Array rather than a list
        # self.get_start_point(edges)
        # Sort the points
        points_sorted_by_angle = self.sort_points(edges)

        # Remove starting point from the list so it's not added more than once to the hull
        start_point_index = points_sorted_by_angle.index(self.start_point)
        del points_sorted_by_angle[start_point_index]
        # Add start point and the first point sorted by angle. Both of these points will always be on the hull.
        hull = [self.start_point, points_sorted_by_angle[0]]

        # Iterate through each point, checking if this point would cause a clockwise rotation if added to the hull, and
        # if so, backtracking.
        for _, point in enumerate(points_sorted_by_angle[1:]):
            # Determine if the proposed point demands a clockwise rotation
            while self.is_clockwise(hull[-2], hull[-1], point) is True:
                # Delete the failed point
                del hull[-1]
                if len(hull) < 2:
                    break
            # The point does not immediately cause a clockwise rotation.
            hull.append(point)

        # Get hull indices from original points array
        hull_indices = []
        for point in hull:
            hull_indices.append(edges.index(point))

        # Create simplices from the hull points
        simplices = []
        for index, value in enumerate(hull_indices):
            simplices.append((hull_indices[index - 1], value))

        return hull, hull_indices, simplices

    @staticmethod
    def plot(edges: list, convex_hull: list = None, file_path: Path = None) -> None:
        """Plot and save the coordinates of the edges in the grain and optionally the hull.

        Parameters
        ----------
        coordinates : list
            A list of points to be plotted.
        convex_hull : list
            Optional argument. A list of points that form the convex hull. Will be plotted with the coordinates if
            provided.
        file_path : Path
            Path of the file to save the plot as.
        """
        _, ax = plt.subplots(1, 1, figsize=(8, 8))
        x_s, y_s = zip(*edges)
        ax.scatter(x_s, y_s)
        if convex_hull is not None:
            for index in range(1, len(convex_hull) + 1):
                # Loop on the final simplex of the hull to join the last and first points together.
                if len(convex_hull) == index:
                    index = 0
                point2 = convex_hull[index]
                point1 = convex_hull[index - 1]
                # Plot a line between the two points
                plt.plot((point1[0], point2[0]), (point1[1], point2[1]), "#994400")
        plt.savefig(file_path)
        plt.close()

    def calculate_aspect_ratio(self, edges: list, hull_simplices: np.ndarray, path: Path, debug: bool = False) -> tuple:
        """Calculate the width, length and aspect ratio of the smallest bounding rectangle of a grain.

        Parameters
        ----------
        edges : list
            A python list of coordinates of the edge of the grain.
        hull_simplices : np.ndarray
            A 2D numpy array of simplices that the hull is comprised of.
        path : Path
            Path to the save folder for the grain.
        debug : bool
            If true, various plots will be saved for diagnostic purposes.

        Returns
        -------
        smallest_bounding_width : float
            The width in pixels (not nanometres), of the smallest bounding rectangle for the grain.
        smallest_bounding_length : float
            The length in pixels (not nanometres), of the smallest bounding rectangle for the grain.
        aspect_ratio : float
            The width divided by the length of the smallest bounding rectangle for the grain. It will always be greater
            or equal to 1.
        """
        # Ensure the edges are in the form of a numpy array.
        edges = np.array(edges)

        # Create a variable to store the smallest area in - this is to be able to compare whilst iterating
        smallest_bounding_area = None
        # FIXME : pylint complains that this is unused which looks like a false positive to me as it is used.
        #         Probably does not need initiating here though (and code runs fine when doing so)
        # smallest_bounding_rectangle = None

        # Iterate through the simplices
        for simplex_index, simplex in enumerate(hull_simplices):
            p_1 = edges[simplex[0]]
            p_2 = edges[simplex[1]]
            delta = p_1 - p_2
            angle = np.arctan2(delta[0], delta[1])

            # Find the centroid of the points
            centroid = (sum(edges[:, 0]) / len(edges), sum(edges[:, 1] / len(edges)))

            # Map the coordinates such that the centroid is now centered on the origin. This is needed for the
            # matrix rotation step coming up.
            remapped_points = edges - centroid

            # Rotate the coordinates using a rotation matrix
            rotated_coordinates = np.array(((np.cos(angle), -np.sin(angle)), (np.sin(angle), np.cos(angle))))

            # For each point in the set, rotate it using the above rotation matrix.
            rotated_points = []
            for _, point in enumerate(remapped_points):
                newpoint = rotated_coordinates @ point
                # FIXME : Can probably use np.append() here to append arrays directly, something like
                # np.append(rotated_points, newpoint, axis=0) but doing so requires other areas to be modified
                rotated_points.append(newpoint)
            rotated_points = np.array(rotated_points)
            # Find the cartesian extremities
            extremes = self.find_cartesian_extremes(rotated_points)

            if debug:
                # Ensure directory is there
                path.mkdir(parents=True, exist_ok=True)

                # Create plot
                # FIXME : Make this a method
                fig = plt.figure(figsize=(8, 8))
                ax = fig.add_subplot(111)

                # Draw the points and the current simplex that is being tested
                plt.scatter(x=remapped_points[:, 0], y=remapped_points[:, 1])
                plt.plot(
                    remapped_points[simplex, 0],
                    remapped_points[simplex, 1],
                    "#444444",
                    linewidth=4,
                )
                plt.scatter(x=rotated_points[:, 0], y=rotated_points[:, 1])
                plt.plot(
                    rotated_points[simplex, 0],
                    rotated_points[simplex, 1],
                    "k-",
                    linewidth=5,
                )
                LOGGER.info(rotated_points[simplex, 0], rotated_points[simplex, 1])

                # Draw the convex hulls
                for _simplex in hull_simplices:
                    plt.plot(
                        remapped_points[_simplex, 0],
                        remapped_points[_simplex, 1],
                        "#888888",
                    )
                    plt.plot(
                        rotated_points[_simplex, 0],
                        rotated_points[_simplex, 1],
                        "#555555",
                    )

                # Draw bounding box
                plt.plot(
                    [
                        extremes["x_min"],
                        extremes["x_min"],
                        extremes["x_max"],
                        extremes["x_max"],
                        extremes["x_min"],
                    ],
                    [
                        extremes["y_min"],
                        extremes["y_max"],
                        extremes["y_max"],
                        extremes["y_min"],
                        extremes["y_min"],
                    ],
                    "#994400",
                )
                plt.savefig(path / ("bounding_rectangle_construction_simplex_" + str(simplex_index) + ".png"))

            # Calculate the area of the proposed bounding rectangle
            bounding_area = (extremes["x_max"] - extremes["x_min"]) * (extremes["y_max"] - extremes["y_min"])

            # If current bounding rectangle is the smallest so far
            if smallest_bounding_area is None or bounding_area < smallest_bounding_area:
                smallest_bounding_area = bounding_area
                # smallest_bounding_rectangle = (
                #     extremes["x_min"],
                #     extremes["x_max"],
                #     extremes["y_min"],
                #     extremes["y_max"],
                # )
                aspect_ratio = (extremes["x_max"] - extremes["x_min"]) / (extremes["y_max"] - extremes["y_min"])
                smallest_bounding_width = min(
                    (extremes["x_max"] - extremes["x_min"]),
                    (extremes["y_max"] - extremes["y_min"]),
                )
                smallest_bounding_length = max(
                    (extremes["x_max"] - extremes["x_min"]),
                    (extremes["y_max"] - extremes["y_min"]),
                )
                # Enforce >= 1 aspect ratio
                if aspect_ratio < 1.0:
                    aspect_ratio = 1 / aspect_ratio

        # Unrotate the bounding box vertices
        r_inverse = rotated_coordinates.T
        translated_rotated_bounding_rectangle_vertices = np.array(
            (
                [extremes["x_min"], extremes["y_min"]],
                [extremes["x_max"], extremes["y_min"]],
                [extremes["x_max"], extremes["y_max"]],
                [extremes["x_min"], extremes["y_max"]],
            )
        )
        translated_bounding_rectangle_vertices = []
        for _, point in enumerate(translated_rotated_bounding_rectangle_vertices):
            newpoint = r_inverse @ point
            # FIXME : As above can likely use np.append(, axis=0) here
            translated_bounding_rectangle_vertices.append(newpoint)
        translated_bounding_rectangle_vertices = np.array(translated_bounding_rectangle_vertices)

        if debug:
            # Create plot
            # FIXME : Make this a private method
            fig = plt.figure(figsize=(8, 8))
            ax = fig.add_subplot(111)
            plt.scatter(x=edges[:, 0], y=edges[:, 1])
            ax.plot(
                np.append(
                    translated_rotated_bounding_rectangle_vertices[:, 0],
                    translated_rotated_bounding_rectangle_vertices[0, 0],
                ),
                np.append(
                    translated_rotated_bounding_rectangle_vertices[:, 1],
                    translated_rotated_bounding_rectangle_vertices[0, 1],
                ),
                "#994400",
                label="rotated",
            )
            ax.plot(
                np.append(
                    translated_bounding_rectangle_vertices[:, 0],
                    translated_bounding_rectangle_vertices[0, 0],
                ),
                np.append(
                    translated_bounding_rectangle_vertices[:, 1],
                    translated_bounding_rectangle_vertices[0, 1],
                ),
                "#004499",
                label="unrotated",
            )
            ax.scatter(
                x=remapped_points[:, 0],
                y=remapped_points[:, 1],
                color="#004499",
                label="translated",
            )
            ax.scatter(x=rotated_points[:, 0], y=rotated_points[:, 1], label="rotated")
            ax.legend()
            plt.savefig(path / "hull_bounding_rectangle_extra")

        fig = plt.figure(figsize=(8, 8))
        ax = fig.add_subplot(111)
        bounding_rectangle_vertices = translated_bounding_rectangle_vertices + centroid
        ax.plot(
            np.append(bounding_rectangle_vertices[:, 0], bounding_rectangle_vertices[0, 0]),
            np.append(bounding_rectangle_vertices[:, 1], bounding_rectangle_vertices[0, 1]),
            "#994400",
            label="unrotated",
        )
        ax.scatter(x=edges[:, 0], y=edges[:, 1], label="original points")
        ax.set_aspect(1)
        ax.legend()
        plt.xlabel("Grain Length (nm)")
        plt.ylabel("Grain Width (nm)")
        # plt.savefig(path / "minimum_bbox.png")
        plt.close()

        return smallest_bounding_width, smallest_bounding_length, aspect_ratio

    @staticmethod
    def find_cartesian_extremes(rotated_points: np.ndarray) -> dict:
        """Find the limits of x and y of rotated points.

        Parameters
        ----------
        rotated_points: np.ndarray
            2-D array of rotated points.

        Returns
        -------
        Dict
            Dictionary of the x and y min and max.__annotations__
        """
        extremes = {}
        extremes["x_min"] = np.min(rotated_points[:, 0])
        extremes["x_max"] = np.max(rotated_points[:, 0])
        extremes["y_min"] = np.min(rotated_points[:, 1])
        extremes["y_max"] = np.max(rotated_points[:, 1])
        return extremes

    @staticmethod
    def get_shift(coords: np.ndarray, shape: np.ndarray) -> int:
        """Obtain the coordinate shift to reflect the cropped image box for molecules near the edges of the image.

        Parameters
        ----------
        coords: np.ndarray
            Value representing integer coordinates which may be outside of the image.
        shape: np.ndarray
            Array of the shape of an image.

        Returns
        -------
        np.int64
            Max value of the shift to reflect the croped region so it stays within the image.
        """
        shift = shape - coords[np.where(coords > shape)]
        shift = np.hstack((shift, -coords[np.where(coords < 0)]))
        if len(shift) == 0:
            return 0
        max_index = np.argmax(abs(shift))
        return shift[max_index]

    def get_cropped_region(self, image: np.ndarray, length: int, centre: np.ndarray) -> np.ndarray:
        """Crops the image with respect to a given pixel length around the centre coordinates.

        Parameters
        ----------
        image: np.ndarray
            The image array.
        length: int
            The length (in pixels) of the resultant cropped image.
        centre: np.ndarray
            The centre of the object to crop.

        Returns
        -------
        np.ndarray
            Cropped array of the image.
        """
        shape = image.shape
        xy1 = shape - (centre + length + 1)
        xy2 = shape - (centre - length)
        xy = np.stack((xy1, xy2))
        shiftx = self.get_shift(xy[:, 0], shape[0])
        shifty = self.get_shift(xy[:, 1], shape[1])
        return image.copy()[
            centre[0] - length - shiftx : centre[0] + length + 1 - shiftx,  # noqa: E203
            centre[1] - length - shifty : centre[1] + length + 1 - shifty,  # noqa: E203
        ]

    @staticmethod
    def get_triangle_height(base_point_1: np.array, base_point_2: np.array, top_point: np.array) -> float:
        """Return the height of a triangle defined by the input point vectors.

        Parameters
        ----------
        base_point_1: np.ndarray
            a base point of the triangle, eg: [5, 3].

        base_point_2: np.ndarray
            a base point of the triangle, eg: [8, 3].

        top_point: np.ndarray
            the top point of the triangle, defining the height from the line between the two base points, eg: [6,10].

        Returns
        -------
        Float
            The height of the triangle - ie the shortest distance between the top point and the line between the two
        base points.
        """
        # Height of triangle = A/b = ||AB X AC|| / ||AB||
        a_b = base_point_1 - base_point_2
        a_c = base_point_1 - top_point
        return np.linalg.norm(np.cross(a_b, a_c)) / np.linalg.norm(a_b)

    @staticmethod
    def get_max_min_ferets(edge_points: list):  # noqa: C901
        """Return the minimum and maximum feret diameters for a grain.

        These are defined as the smallest and greatest distances between a pair of callipers that are rotating around a
        2d object, maintaining contact at all times.

        Parameters
        ----------
        edge_points: list
            a list of the vector positions of the pixels comprising the edge of the
            grain. Eg: [[0, 0], [1, 0], [2, 1]]

        Returns
        -------
        min_feret: float
            the minimum feret diameter of the grain
        max_feret: float
            the maximum feret diameter of the grain

        Notes
        -----
        The method starts out by calculating the upper and lower convex hulls using  an algorithm based on the Graham
        Scan Algorithm [1]. Using these upper and lower hulls, the callipers are simulated as rotating clockwise around
        the grain. We determine the order in which vertices are encountered by comparing the gradients of the slopes
        between vertices. An array of pairs of points that are in contact with either calliper at a given time is
        created in order to be able to calculate the maximum feret diameter. The minimum diameter is a little tricky,
        since it won't simply be the shortest distance between two contact points, but it will occur somewhere during
        the rotation around a pair of contact points. It turns out that the point will always be such that two points
        are in contact with one calliper while the other calliper is in contact with another point. We can use this fact
        to be sure of finding the smallest feret diameter, simply by testing each triangle of 3 contact points as we
        iterate, finding the height of the triangle that is formed between the three aforementioned points, as this will
        be the perpendicular distance between the callipers.

        References
        ----------
        [1] Graham, R.L. (1972).
            "An Efficient Algorithm for Determining the Convex Hull of a Finite Planar Set".
            Information Processing Letters. 1 (4): 132-133.
            doi:10.1016/0020-0190(72)90045-2.
        """
        # Sort the vectors by their x coordinate and then by their y coordinate.
        # The conversion between list and numpy array can be removed, though it would be harder
        # to read.
        edge_points.sort()
        edge_points = np.array(edge_points)

        # Construct upper and lower hulls for the edge points. Sadly we can't just use the standard hull
        # that graham_scan() returns, since we need to separate the upper and lower hulls. I might streamline
        # these two into one method later.
        upper_hull = []
        lower_hull = []
        for point in edge_points:
            while len(lower_hull) > 1 and GrainStats.is_clockwise(lower_hull[-2], lower_hull[-1], point):
                lower_hull.pop()
            lower_hull.append(point)
            while len(upper_hull) > 1 and not GrainStats.is_clockwise(upper_hull[-2], upper_hull[-1], point):
                upper_hull.pop()
            upper_hull.append(point)

        upper_hull = np.array(upper_hull)
        lower_hull = np.array(lower_hull)

        # Create list of contact vertices for calipers on the antipodal hulls
        contact_points = []
        upper_index = 0
        lower_index = len(lower_hull) - 1
        min_feret = None
        while upper_index < len(upper_hull) - 1 or lower_index > 0:
            contact_points.append([lower_hull[lower_index, :], upper_hull[upper_index, :]])
            # If we have reached the end of the upper hull, continue iterating over the lower hull
            if upper_index == len(upper_hull) - 1:
                lower_index -= 1
                small_feret = GrainStats.get_triangle_height(
                    np.array(lower_hull[lower_index + 1, :]),
                    np.array(lower_hull[lower_index, :]),
                    np.array(upper_hull[upper_index, :]),
                )
                if min_feret is None or small_feret < min_feret:
                    min_feret = small_feret
            # If we have reached the end of the lower hull, continue iterating over the upper hull
            elif lower_index == 0:
                upper_index += 1
                small_feret = GrainStats.get_triangle_height(
                    np.array(upper_hull[upper_index - 1, :]),
                    np.array(upper_hull[upper_index, :]),
                    np.array(lower_hull[lower_index, :]),
                )
                if min_feret is None or small_feret < min_feret:
                    min_feret = small_feret
            # Check if the gradient of the last point and the proposed next point in the upper hull is greater than the gradient
            # of the two corresponding points in the lower hull, if so, this means that the next point in the upper hull
            # will be encountered before the next point in the lower hull and vice versa.
            # Note that the calculation here for gradients is the simple delta upper_y / delta upper_x > delta lower_y / delta lower_x
            # however I have multiplied through the denominators such that there are no instances of division by zero. The
            # inequality still holds and provides what is needed.
            elif (upper_hull[upper_index + 1, 1] - upper_hull[upper_index, 1]) * (
                lower_hull[lower_index, 0] - lower_hull[lower_index - 1, 0]
            ) > (lower_hull[lower_index, 1] - lower_hull[lower_index - 1, 1]) * (
                upper_hull[upper_index + 1, 0] - upper_hull[upper_index, 0]
            ):
                # If the upper hull is encountered first, increment the iteration index for the upper hull
                # Also consider the triangle that is made as the two upper hull vertices are colinear with the caliper
                upper_index += 1
                small_feret = GrainStats.get_triangle_height(
                    np.array(upper_hull[upper_index - 1, :]),
                    np.array(upper_hull[upper_index, :]),
                    np.array(lower_hull[lower_index, :]),
                )
                if min_feret is None or small_feret < min_feret:
                    min_feret = small_feret
            else:
                # The next point in the lower hull will be encountered first, so increment the lower hull iteration index.
                lower_index -= 1
                small_feret = GrainStats.get_triangle_height(
                    np.array(lower_hull[lower_index + 1, :]),
                    np.array(lower_hull[lower_index, :]),
                    np.array(upper_hull[upper_index, :]),
                )

                if min_feret is None or small_feret < min_feret:
                    min_feret = small_feret

        contact_points = np.array(contact_points)

        # Find the minimum and maximum distance in the contact points
        max_feret = None
        for point_pair in contact_points:
            dist = np.sqrt((point_pair[0, 0] - point_pair[1, 0]) ** 2 + (point_pair[0, 1] - point_pair[1, 1]) ** 2)
            if max_feret is None or max_feret < dist:
                max_feret = dist

        return min_feret, max_feret