cellects 0.1.0.dev1__py3-none-any.whl

cellects/image_analysis/shape_descriptors.py

@@ -0,0 +1,981 @@
+"""
+    Shape descriptors: The following names, lists and computes all the variables describing a shape in a binary image. 
+    If you want to allow the software to compute another variable:
+    1) In the following dicts and list, you need to:
+            add the variable name and whether to compute it (True/False) by default
+    2) In the ShapeDescriptors class:
+            add a method to compute that variable 
+    3) In the init method of the ShapeDescriptors class
+        attribute a None value to the variable that store it
+        add a if condition in the for loop to compute that variable when its name appear in the wanted_descriptors_list
+"""
+import cv2
+import numpy as np
+from copy import deepcopy
+from cellects.utils.utilitarian import translate_dict
+from cellects.utils.formulas import get_inertia_axes, get_standard_deviations, get_skewness, get_kurtosis
+from cellects.image_analysis.morphological_operations import cc
+
+descriptors_categories = {'area': True, 'perimeter': False, 'circularity': False, 'rectangularity': False,
+                          'total_hole_area': False, 'solidity': False, 'convexity': False, 'eccentricity': False,
+                          'euler_number': False, 'standard_deviation_xy': False, 'skewness_xy': False,
+                          'kurtosis_xy': False, 'major_axes_len_and_angle': True, 'iso_digi_analysis': False,
+                          'oscilacyto_analysis': False, 'network_analysis': False, 'graph_extraction': False,
+                          'fractal_analysis': False
+                          }
+
+descriptors_names_to_display = ['Area', 'Perimeter', 'Circularity', 'Rectangularity', 'Total hole area',
+                                'Solidity', 'Convexity', 'Eccentricity', 'Euler number', 'Standard deviation xy',
+                                'Skewness xy', 'Kurtosis xy', 'Major axes lengths and angle',
+                                'Growth transitions', 'Oscillations', 'Network', 'Graph',
+                                'Fractals'
+                                ]#, 'Oscillating cluster nb and size'
+
+from_shape_descriptors_class = {'area': True, 'perimeter': False, 'circularity': False, 'rectangularity': False,
+               'total_hole_area': False, 'solidity': False, 'convexity': False, 'eccentricity': False,
+               'euler_number': False, 'standard_deviation_y': False, 'standard_deviation_x': False,
+               'skewness_y': False, 'skewness_x': False, 'kurtosis_y': False, 'kurtosis_x': False,
+               'major_axis_len': True, 'minor_axis_len': True, 'axes_orientation': True
+                               }
+
+descriptors = deepcopy(from_shape_descriptors_class)
+descriptors.update({'cluster_number': False, 'mean_cluster_area': False, 'minkowski_dimension': False,
+                    'vertices_number': False, 'edges_number': False})
+
+
+
+class ShapeDescriptors:
+    """
+        This class takes :
+        - a binary image of 0 and 1 drawing one shape
+        - a list of descriptors to calculate from that image
+        ["area", "perimeter", "circularity", "rectangularity", "total_hole_area", "solidity", "convexity",
+         "eccentricity", "euler_number",
+
+        "standard_deviation_y", "standard_deviation_x", "skewness_y", "skewness_x", "kurtosis_y", "kurtosis_x",
+        "major_axis_len", "minor_axis_len", "axes_orientation",
+
+        "mo", "contours", "min_bounding_rectangle", "convex_hull"]
+
+        Be careful! mo, contours, min_bounding_rectangle, convex_hull,
+        standard_deviations, skewness and kurtosis are not atomics
+    https://www.researchgate.net/publication/27343879_Estimators_for_Orientation_and_Anisotropy_in_Digitized_Images
+    """
+
+    def __init__(self, binary_image, wanted_descriptors_list):
+        """
+        Class to compute various descriptors for a binary image.
+
+        Parameters
+        ----------
+        binary_image : ndarray
+            Binary image used to compute the descriptors.
+        wanted_descriptors_list : list
+            List of strings with the names of the wanted descriptors.
+
+        Attributes
+        ----------
+        binary_image : ndarray
+            The binary image.
+        descriptors : dict
+            Dictionary containing the computed descriptors.
+        mo : float or None, optional
+            Moment of inertia (default is `None`).
+        area : int or None, optional
+            Area of the object (default is `None`).
+        contours : ndarray or None, optional
+            Contours of the object (default is `None`).
+        min_bounding_rectangle : tuple or None, optional
+            Minimum bounding rectangle of the object (default is `None`).
+        convex_hull : ndarray or None, optional
+            Convex hull of the object (default is `None`).
+        major_axis_len : float or None, optional
+            Major axis length of the object (default is `None`).
+        minor_axis_len : float or None, optional
+            Minor axis length of the object (default is `None`).
+        axes_orientation : float or None, optional
+            Orientation of the axes (default is `None`).
+        sx : float or None, optional
+            Standard deviation in x-axis (default is `None`).
+        kx : float or None, optional
+            Kurtosis in x-axis (default is `None`).
+        skx : float or None, optional
+            Skewness in x-axis (default is `None`).
+        perimeter : float or None, optional
+            Perimeter of the object (default is `None`).
+        convexity : float or None, optional
+            Convexity of the object (default is `None`).
+
+        Examples
+        --------
+        >>> binary_image = np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8)
+        >>> wanted_descriptors_list = ["area", "perimeter"]
+        >>> SD = ShapeDescriptors(binary_image, wanted_descriptors_list)
+        >>> SD.descriptors
+        {'area': np.uint64(9), 'perimeter': 8.0}
+        """
+        # Give a None value to each parameters whose presence is assessed before calculation (less calculus for speed)
+        self.mo = None
+        self.area = None
+        self.contours = None
+        self.min_bounding_rectangle = None
+        self.convex_hull = None
+        self.major_axis_len = None
+        self.minor_axis_len = None
+        self.axes_orientation = None
+        self.sx = None
+        self.kx = None
+        self.skx = None
+        self.perimeter = None
+        self.convexity = None
+
+        self.binary_image = binary_image
+        if self.binary_image.dtype == 'bool':
+            self.binary_image = self.binary_image.astype(np.uint8)
+
+        self.descriptors = {i: np.empty(0, dtype=np.float64) for i in wanted_descriptors_list}
+
+        self.get_area()
+
+        for name in self.descriptors.keys():
+            if self.area == 0:
+                self.descriptors[name] = 0
+            else:
+                if name == "mo":
+                    self.get_mo()
+                    self.descriptors[name] = self.mo
+                elif name == "area":
+                    self.descriptors[name] = self.area
+                elif name == "contours":
+                    self.get_contours()
+                    self.descriptors[name] = self.contours
+                elif name == "min_bounding_rectangle":
+                    self.get_min_bounding_rectangle()
+                    self.descriptors[name] = self.min_bounding_rectangle
+                elif name == "major_axis_len":
+                    self.get_major_axis_len()
+                    self.descriptors[name] = self.major_axis_len
+                elif name == "minor_axis_len":
+                    self.get_minor_axis_len()
+                    self.descriptors[name] = self.minor_axis_len
+                elif name == "axes_orientation":
+                    self.get_inertia_axes()
+                    self.descriptors[name] = self.axes_orientation
+                elif name == "standard_deviation_y":
+                    self.get_standard_deviations()
+                    self.descriptors[name] = self.sy
+                elif name == "standard_deviation_x":
+                    self.get_standard_deviations()
+                    self.descriptors[name] = self.sx
+                elif name == "skewness_y":
+                    self.get_skewness()
+                    self.descriptors[name] = self.sky
+                elif name == "skewness_x":
+                    self.get_skewness()
+                    self.descriptors[name] = self.skx
+                elif name == "kurtosis_y":
+                    self.get_kurtosis()
+                    self.descriptors[name] = self.ky
+                elif name == "kurtosis_x":
+                    self.get_kurtosis()
+                    self.descriptors[name] = self.kx
+                elif name == "convex_hull":
+                    self.get_convex_hull()
+                    self.descriptors[name] = self.convex_hull
+                elif name == "perimeter":
+                    self.get_perimeter()
+                    self.descriptors[name] = self.perimeter
+                elif name == "circularity":
+                    self.get_circularity()
+                    self.descriptors[name] = self.circularity
+                elif name == "rectangularity":
+                    self.get_rectangularity()
+                    self.descriptors[name] = self.rectangularity
+                elif name == "total_hole_area":
+                    self.get_total_hole_area()
+                    self.descriptors[name] = self.total_hole_area
+                elif name == "solidity":
+                    self.get_solidity()
+                    self.descriptors[name] = self.solidity
+                elif name == "convexity":
+                    self.get_convexity()
+                    self.descriptors[name] = self.convexity
+                elif name == "eccentricity":
+                    self.get_eccentricity()
+                    self.descriptors[name] = self.eccentricity
+                elif name == "euler_number":
+                    self.get_euler_number()
+                    self.descriptors[name] = self.euler_number
+
+    """
+        The following methods can be called to compute parameters for descriptors requiring it
+    """
+
+    def get_mo(self):
+        """
+        Get moments of a binary image.
+
+        Calculate the image moments for a given binary image using OpenCV's
+        `cv2.moments` function and then translate these moments into a formatted
+        dictionary.
+
+        Parameters
+        ----------
+        self : object
+            The instance of the class containing this method.
+        binary_image : numpy.ndarray
+            A binary image (2D array) where pixels are 0 or 255.
+
+        Other Parameters
+        ----------------
+        None
+
+        Returns
+        -------
+        dict
+            A dictionary containing the translated moments of the binary image.
+
+        Raises
+        ------
+        TypeError
+            If `binary_image` is not a NumPy array.
+
+        Notes
+        -----
+        This function assumes the binary image has already been processed and is in a
+        suitable format for moment calculation.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["mo"])
+        >>> print(SD.mo["m00"])
+        9.0
+        """
+        self.mo = translate_dict(cv2.moments(self.binary_image))
+
+    def get_area(self):
+        """
+        Calculate the area of a binary image by summing its pixel values.
+
+        This function computes the area covered by white pixels (value 1) in a binary image,
+        which is equivalent to counting the number of 'on' pixels.
+
+        Parameters
+        ----------
+        self : object
+            The instance of a class containing the binary_image attribute.
+
+        Returns
+        -------
+        int
+            The total number of white pixels in the binary image, representing its area.
+
+        Notes
+        -----
+        This function assumes the binary_image attribute is a NumPy array containing only 0s and 1s.
+        If the image contains other values, this function might not produce accurate results.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["area"])
+        >>> print(SD.area)
+        9.0
+        """
+        self.area = self.binary_image.sum()
+
+    def get_contours(self):
+        """
+        Find and process the largest contour in a binary image.
+
+        Retrieves contours from a binary image, calculates the Euler number,
+        and identifies the largest contour based on its length.
+
+        Parameters
+        ----------
+        self : ImageProcessingObject
+            The image processing object containing the binary image.
+
+        Other Parameters
+        ----------------
+        None
+
+        Returns
+        -------
+        None
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        This function modifies the internal state of the `self` object to store
+        the largest contour and Euler number.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["euler_number"])
+        >>> print(len(SD.contours))
+        8
+        """
+        contours, hierarchy = cv2.findContours(self.binary_image, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
+        nb, shapes = cv2.connectedComponents(self.binary_image, ltype=cv2.CV_16U)
+        self.euler_number = (nb - 1) - len(contours)
+        self.contours = contours[0]
+        if len(contours) > 1:
+            all_lengths = np.zeros(len(contours))
+            for i, contour in enumerate(contours):
+                all_lengths[i] = len(contour)
+            self.contours = contours[np.argmax(all_lengths)]
+
+    def get_min_bounding_rectangle(self):
+        """
+        Retrieve the minimum bounding rectangle from the contours of an image.
+
+        This method calculates the smallest area rectangle that can enclose
+        the object outlines present in the image, which is useful for
+        object detection and analysis tasks.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        tuple
+            A tuple containing the following elements:
+                - (cx, cy): The center point of the rectangle.
+                - (width, height): Width and height of the bounding rectangle.
+                - angle: Angle in degrees describing how much the ellipse is rotated.
+
+        Raises
+        ------
+        RuntimeError
+            If the contours are not available and cannot be retrieved,
+            indicating a problem with the image or preprocessing steps.
+
+        Notes
+        -----
+        - The bounding rectangle is calculated only if contours are available.
+          If not, they will be retrieved first before calculating the rectangle.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["rectangularity"])
+        >>> print(len(SD.min_bounding_rectangle))
+        3
+        """
+        if self.contours is None:
+            self.get_contours()
+        self.min_bounding_rectangle = cv2.minAreaRect(self.contours)  # ((cx, cy), (width, height), angle)
+
+    def get_inertia_axes(self):
+        """
+        Calculate and set the moments of inertia properties of an object.
+
+        This function computes the centroid, major axis length,
+        minor axis length, and axes orientation for an object. It
+        first ensures that the moments of inertia (`mo`) attribute is available,
+        computing them if necessary, before using the `get_inertia_axes` function.
+
+        Returns
+        -------
+        None
+
+            This method sets the following attributes:
+            - `cx` : float
+                The x-coordinate of the centroid.
+            - `cy` : float
+                The y-coordinate of the centroid.
+            - `major_axis_len` : float
+                The length of the major axis.
+            - `minor_axis_len` : float
+                The length of the minor axis.
+            - `axes_orientation` : float
+                The orientation angle of the axes.
+
+        Raises
+        ------
+        ValueError
+            If there is an issue with the moments of inertia computation.
+
+        Notes
+        -----
+        This function modifies in-place the object's attributes related to its geometry.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["major_axis_len"])
+        >>> print(SD.axes_orientation)
+        0.0
+        """
+        if self.mo is None:
+            self.get_mo()
+
+        self.cx, self.cy, self.major_axis_len, self.minor_axis_len, self.axes_orientation = get_inertia_axes(self.mo)
+
+    def get_standard_deviations(self):
+        """
+        Calculate the standard deviations along x and y.
+
+        Parameters
+        ----------
+        moment_order : int
+            The order of moments to consider in calculations.
+        binary_image : numpy.ndarray
+            A 2D binary image where the shape corresponds to `[height, width]`.
+        center_x : float
+            The x-coordinate of the centroid of the object in the image.
+        center_y : float
+            The y-coordinate of the centroid of the object in the image.
+
+        Returns
+        -------
+        tuple[float, float]
+            A tuple containing the standard deviations along x and y (sx, sy).
+
+        Notes
+        -----
+        The function calculates the standard deviations of a binary image about its centroid.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["standard_deviation_x", "standard_deviation_y"])
+        >>> print(SD.sx, SD.sy)
+        0.816496580927726 0.816496580927726
+        """
+        if self.sx is None:
+            if self.axes_orientation is None:
+                self.get_inertia_axes()
+            self.sx, self.sy = get_standard_deviations(self.mo, self.binary_image, self.cx, self.cy)
+
+    def get_skewness(self):
+        """
+        Calculate the skewness of an image.
+
+        This function computes the skewness about the x-axis and y-axis of
+        an image. Skewness is a measure of the asymmetry of the probability
+        distribution of values in an image.
+
+        Parameters
+        ----------
+        binary_image : numpy.ndarray
+            A binary image represented as a 2D array of integers, where 0 represents
+            background and other values represent foreground.
+        mo : dict
+            Moments of the image.
+        cx, cy : float
+            The x and y coordinates of the centroid of the object in the image.
+        sx, sy : float
+            The standard deviations along the x and y axes.
+
+        Other Parameters
+        ----------------
+        None
+
+        Returns
+        -------
+        skx, sky : tuple of float
+            The skewness about the x-axis and y-axis.
+
+        Notes
+        -----
+        This method internally calls `get_standard_deviations` if the standard deviation
+        values are not already computed.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["skewness_x", "skewness_y"])
+        >>> print(SD.skx, SD.sky)
+        0.0 0.0
+        """
+        if self.skx is None:
+            if self.sx is None:
+                self.get_standard_deviations()
+
+            self.skx, self.sky = get_skewness(self.mo, self.binary_image, self.cx, self.cy, self.sx, self.sy)
+
+    def get_kurtosis(self):
+        """
+        Calculates the kurtosis of the image moments.
+
+        Kurtosis is a statistical measure that describes the shape of
+        a distribution's tails in relation to its overall shape. It is
+        used here in the context of image moments analysis.
+
+        Notes
+        -----
+        This function first checks if the kurtosis values have already been calculated.
+        If not, it calculates them using the `get_kurtosis` function.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["kurtosis_x", "kurtosis_y"])
+        >>> print(SD.kx, SD.ky)
+        1.5 1.5
+        """
+        if self.kx is None:
+            if self.sx is None:
+                self.get_standard_deviations()
+
+            self.kx, self.ky = get_kurtosis(self.mo, self.binary_image, self.cx, self.cy, self.sx, self.sy)
+
+    def get_convex_hull(self):
+        """
+        Compute the convex hull of an object's contours.
+
+        This method calculates the convex hull for the object represented by its
+        contours. If the contours are not already computed, it will first compute them.
+
+        Parameters
+        ----------
+        self : Object
+            The object containing the contours and convex hull attributes.
+
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        This method modifies the object in place by setting its `convex_hull`
+        attribute to the result of the convex hull computation.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["solidity"])
+        >>> print(len(SD.convex_hull))
+        4
+        """
+        if self.contours is None:
+            self.get_contours()
+        self.convex_hull = cv2.convexHull(self.contours)
+
+    def get_perimeter(self):
+        """
+        Get the perimeter of a contour.
+
+        Calculates the perimeter length of the contours present in
+        the image after determining them if they are not already available.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        float
+            The perimeter length of the contours in the image.
+
+        Notes
+        -----
+        This function retrieves the contours if they have not been determined
+        yet using `self.get_contours()`. This is crucial for accurate perimeter
+        measurement.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["perimeter"])
+        >>> print(SD.perimeter)
+        8.0
+        """
+        if self.contours is None:
+            self.get_contours()
+        self.perimeter = cv2.arcLength(self.contours, True)
+
+    def get_circularity(self):
+        """
+        Calculate and set the circularity of a binary image object.
+
+        Circularity is defined as (4 * pi * area) / perimeter^2.
+        If the perimeter has not been calculated yet, it will be computed first.
+
+        Parameters
+        ----------
+        self : ShapeObject
+            The object which contains the binary image and its properties.
+
+        Attributes
+        ----------
+        circularity : float
+            The calculated circularity value, set as an attribute of the object.
+
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        Circularity is a measure of how closely the shape of an object approximates a circle.
+        A perfect circle has a circularity of 1.0.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["circularity"])
+        >>> print(SD.circularity)
+        1.7671458676442586
+        """
+        if self.perimeter is None:
+            self.get_perimeter()
+        self.circularity = (4 * np.pi * self.binary_image.sum()) / np.square(self.perimeter)
+
+    def get_rectangularity(self):
+        """
+        Calculates the rectangularity of a binary image.
+
+        Rectangularity is defined as the ratio of the number of pixels in
+        the shape to the area of its bounding rectangle. This function
+        computes this value by considering the binary image stored in
+        `self.binary_image`.
+
+        Parameters
+        ----------
+        None
+
+        Other Parameters
+        ----------------
+        None
+
+        Returns
+        -------
+        float
+            The rectangularity of the binary image.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        This function uses `self.binary_image` to determine the number of pixels in
+        the shape and `self.min_bounding_rectangle` to determine the bounding rectangle area.
+        If the minimum bounding rectangle has not been computed yet, it will be calculated
+        through `self.get_min_bounding_rectangle()`.
+
+        Attributes
+        ----------
+        None
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["rectangularity"])
+        >>> print(SD.rectangularity)
+        2.25
+        """
+        if self.min_bounding_rectangle is None:
+            self.get_min_bounding_rectangle()
+        bounding_rectangle_area = self.min_bounding_rectangle[1][0] * self.min_bounding_rectangle[1][1]
+        if bounding_rectangle_area != 0:
+            self.rectangularity = self.binary_image.sum() / bounding_rectangle_area
+        else:
+            self.rectangularity = 1
+
+    def get_total_hole_area(self):
+        """
+        Calculate the total area of holes in a binary image.
+
+        This function uses connected component labeling to detect and
+        measure the area of holes in a binary image.
+
+        Returns
+        -------
+        float
+            The total area of all detected holes in the binary image.
+
+        Notes
+        -----
+        This function assumes that the binary image has been pre-processed
+        and that holes are represented as connected components of zero
+        pixels within the foreground
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["total_hole_area"])
+        >>> print(SD.total_hole_area)
+        0
+        """
+        new_order, stats, centers = cc(1 - self.binary_image)
+        self.total_hole_area = np.sum(stats[2:, 4])
+
+    def get_solidity(self):
+        """
+        Calculate the solidity of a contour, which is the ratio of the area
+        of the contour to the area of its convex hull.
+
+        Extended Summary
+        ----------------
+        The solidity is a dimensionless measure that compares the area of a shape to
+        its convex hull. A solidity of 1 means the contour is fully convex, while a
+        value less than 1 indicates concavities.
+
+        Parameters
+        ----------
+        None
+
+        Other Parameters
+        -----------------
+        None
+
+        Returns
+        -------
+        float
+            The solidity of the contour.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        The solidity is computed by dividing the area of the contour by the area of its
+        convex hull. If the convex hull is empty, solidity defaults to 1.
+
+        Attributes
+        ----------
+            self.convex_hull : array-like or None
+                The convex hull of the contour.
+            self.solidity : float
+                The calculated solidity value of the contour.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["solidity"])
+        >>> print(SD.solidity)
+        1.0
+        """
+        if self.convex_hull is None:
+            self.get_convex_hull()
+        conv_h_cont_area = cv2.contourArea(self.convex_hull)
+        if conv_h_cont_area != 0:
+            self.solidity = cv2.contourArea(self.contours) / cv2.contourArea(self.convex_hull)
+        else:
+            self.solidity = 1
+
+    def get_convexity(self):
+        """
+        Calculate the convexity of a shape.
+
+        Convexity is defined as the ratio of the length of
+        the contour to the perimeter of the convex hull.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        float
+            The convexity ratio of the shape.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        This method requires that both `perimeter` and `convex_hull`
+        attributes are computed before calling this method.
+        Convexity is a dimensionless quantity and should always be in the range [0, 1].
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["convexity"])
+        >>> print(SD.convexity)
+        1.0
+        """
+        if self.perimeter is None:
+            self.get_perimeter()
+        if self.convex_hull is None:
+            self.get_convex_hull()
+        self.convexity = cv2.arcLength(self.convex_hull, True) / self.perimeter
+
+    def get_eccentricity(self):
+        """
+        Calculate the eccentricity of an ellipsoid based on its major and minor axis lengths.
+
+        This function computes the eccentricity of an ellipsoid using its major
+        and minor axis lengths. The eccentricity is a measure of how much the
+        ellipsoid deviates from being circular.
+
+        Parameters
+        ----------
+        self : Ellipsoid
+            The ellipsoid object containing the major and minor axis lengths.
+            These values are assumed to be already set.
+
+        Other Parameters
+        ----------------
+        None
+
+        Returns
+        -------
+        float
+            The calculated eccentricity of the ellipsoid.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        - This function assumes that the major and minor axis lengths are already set.
+          If not, you must call `self.get_inertia_axes()` to update these values before
+          calling this function.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8), ["eccentricity"])
+        >>> print(SD.eccentricity)
+        0.0
+        """
+        self.get_inertia_axes()
+        self.eccentricity = np.sqrt(1 - np.square(self.minor_axis_len / self.major_axis_len))
+
+    def get_euler_number(self):
+        """
+        Get Euler number from the contour data.
+
+        Calculate and return the Euler characteristic of the current contour or
+        contours, which is a topological invariant that describes the shape.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        int or None
+            The Euler number of the contour(s). Returns `None` if no contours exist.
+
+        Raises
+        ------
+        ValueError
+            If the Euler number cannot be calculated due to invalid contour data.
+
+        Notes
+        -----
+        The Euler characteristic is computed as: ``vertices - edges + faces``.
+        This method handles both single contour and multiple contours cases.
+
+        Examples
+        --------
+        >>> contour_object.get_euler_number()
+        1
+
+        >>> no_contours = Contour()  # Object with no contours
+        >>> no_contours.get_euler_number()
+        None
+        """
+        if self.contours is None:
+            self.get_contours()
+
+    def get_major_axis_len(self):
+        """
+        Get the length of the major axis.
+
+        Calculate or retrieve the length of the major axis, ensuring it is
+        computed if not already available.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        float or None
+            The length of the major axis. If the major_axis_len could not be
+            computed, returns `None`.
+
+        Raises
+        ------
+        AttributeError
+           If the major axis length is not available and cannot be computed.
+
+        Notes
+        -----
+        - This method may trigger computation of inertia axes if they haven't been
+          precomputed to determine the major axis length.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[0, 1, 0], [0, 1, 0], [0, 1, 0]], dtype=np.uint8), ["major_axis_len"])
+        >>> print(SD.major_axis_len)
+        2.8284271247461907
+        """
+        if self.major_axis_len is None:
+            self.get_inertia_axes()
+
+    def get_minor_axis_len(self):
+        """
+        Get the length of the minor axis.
+
+        This method returns the calculated length of the minor axis. If
+        `self.minor_axis_len` is `None`, it will first compute the inertia axes.
+
+        Parameters
+        ----------
+        none
+
+        Returns
+        -------
+        float:
+            The length of the minor axis.
+
+        Raises
+        ------
+        RuntimeError:
+            If the minor axis cannot be calculated. This might happen if there are not enough data points
+            to determine the inertia axes.
+
+        Notes
+        -----
+        This method will compute the inertia axes if `self.minor_axis_len` is not cached.
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[0, 1, 0], [0, 1, 0], [0, 1, 0]], dtype=np.uint8), ["minor_axis_len"])
+        >>> print(SD.minor_axis_len)
+        0.0
+        """
+        if self.minor_axis_len is None:
+            self.get_inertia_axes()
+
+    def get_axes_orientation(self):
+        """
+
+        Get the orientation of the axes.
+
+        Extended summary
+        ----------------
+
+        This method retrieves the current orientation of the axes. If the orientation is not already computed, it will compute and store it by calling `get_inertia_axes()`.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        `np.ndarray`
+            A 3x3 matrix representing the orientation of the axes.
+
+        Raises
+        ------
+        None
+
+        Notes
+        -----
+        This method may trigger a computation of inertia axes if they haven't been computed yet.
+
+        Examples
+        --------
+
+        Examples
+        --------
+        >>> SD = ShapeDescriptors(np.array([[0, 1, 0], [0, 1, 0], [0, 1, 0]], dtype=np.uint8), ["axes_orientation"])
+        >>> print(SD.axes_orientation)
+        1.5707963267948966
+        """
+        if self.axes_orientation is None:
+            self.get_inertia_axes()
+