PyPlaque_phenotypes_plaque

PyPlaque.phenotypes.plaque

Plaque(object)

Plaque Class The Plaque class is designed to hold a single virological plaque phenotype as an object. It encapsulates the properties and behaviors related to a specific plaque, including its mask, centroid coordinates, bounding box, and usage preference for pick measurements.

Args: mask (2D numpy array, required): A binary mask representing a single virological plaque object.

centroid (float tuple, optional): A tuple containing the x and y coordinates of the centroid 
of the plaque.

bbox (float tuple, optional): A tuple containing the minr, minc, maxr, maxc limits of the 
bounding box surrounding the plaque.

use_picks (bool, optional): A boolean flag indicating whether to use pick measurements or not. 
Defaults to False.

Raises: TypeError: If the mask is not a 2D numpy array, if centroid is not a tuple of coordinates, or if bbox is not a tuple of limits.

.eccentricity(self)

eccentricity Method Calculates and returns the eccentricity of an individual plaque object. The eccentricity is determined by fitting an ellipse to the plaque's boundary contour and using the formula sqrt(1 - (b^2 / a^2)), where b represents the length of the semi-minor axis, and a represents the length of the semi-major axis.

Args: None: The method operates directly on the instance's attributes (self.mask).

Returns: float: The calculated eccentricity value of the plaque.

.measure(self)

measure Method Computes and returns the bounding box area (in pixels) of a plaque object, as well as an approximation of its actual area based on the proportion of white pixels in the mask. The method uses either the pre-computed self.area if available or calculates it from the binary mask (self.mask) if not.

Args: None: The method operates directly on the instance's attributes (self.bbox, self.use_picks, self.mask, self.area).

Returns: tuple: A tuple containing two elements, the first is the area of the bounding box surrounding the plaque (in pixels), and the second is an approximation of the actual area based on the mask (also in pixels).

.roundness(self)

roundness Method Calculates and returns the roundness of an individual plaque object. The roundness is calculated using the formula 4 * pi * Area / (Perimeter^2), where Area is estimated as pi * radius^2, and Perimeter is calculated as 2 * pi * radius. This method uses either Pick's measured area and perimeter or estimates them based on bounding box coordinates if not already computed.

Args: None: The method operates directly on the instance's attributes (self.use_picks, self.perimeter, self.bbox).

Returns: float: The calculated roundness value of the plaque.