derotation.analysis.fit_ellipse#

This module contains functions to fit an ellipse to the largest blob centers in each image of an image stack. The fit_ellipse_to_points function uses the least squares optimization to fit an ellipse to the points. The plot_ellipse_fit_and_centers function plots the fitted ellipse on the largest blob centers. The derive_angles_from_ellipse_fits function derives the rotation plane angle and orientation from the ellipse fits.

Functions

derive_angles_from_ellipse_fits(ellipse_fits)

Derive the rotation plane angle and orientation from the ellipse fits.

fit_ellipse_to_points(centers[, pixels_in_row])

Fit an ellipse to the points using least squares optimization.

plot_ellipse_fit_and_centers(centers, ...[, ...])

Plot the fitted ellipse on the largest blob centers.
derotation.analysis.fit_ellipse.fit_ellipse_to_points(centers, pixels_in_row=256)[source]#

Fit an ellipse to the points using least squares optimization.

Parameters:

centers (np.ndarray) – The centers of the largest blob in each image.

Returns:

The center of the ellipse (center_x, center_y), the semi-major axis (a), the semi-minor axis (b), and the rotation angle (theta).

Return type:

Tuple[int, int, int, int, int]

derotation.analysis.fit_ellipse.plot_ellipse_fit_and_centers(centers, center_x, center_y, a, b, theta, image_stack, debug_plots_folder, saving_name='ellipse_fit.png')[source]#

Plot the fitted ellipse on the largest blob centers.

Parameters:

  • centers (np.ndarray) – The centers of the largest blob in each image.

  • center_x (int) – The x-coordinate of the center of the ellipse

  • center_y (int) – The y-coordinate of the center of the ellipse

  • a (int) – The semi-major axis of the ellipse

  • b (int) – The semi-minor axis of the ellipse

  • theta (int) – The rotation angle of the ellipse

  • image_stack (np.ndarray) – The image stack to plot the ellipse on.

  • debug_plots_folder (Path) – The folder to save the debug plot to.

  • saving_name (str, optional) – The name of the file to save the plot to, by default “ellipse_fit.png”.

derotation.analysis.fit_ellipse.derive_angles_from_ellipse_fits(ellipse_fits)[source]#

Derive the rotation plane angle and orientation from the ellipse fits.

Parameters:

ellipse_fits (np.ndarray) – The fitted ellipse parameters

Returns:

The rotation plane (in degrees) angle and orientation

Return type:

Tuple[int, int]