Align the tilt axis of a TomoStack.

Uses either a center-of-mass approach or a maximum image approach

Available methods are 'CoM' and 'MaxImage':

CoM: Track the center of mass (CoM) of the projections at three locations. Fit the motion of the CoM as a function of tilt to that expected for an ideal cylinder to calculate an X-shift at each location. Perform a linear fit of the three X-shifts to calculate an ideal rotation.

MaxImage: Perform automated determination of the tilt axis of a TomoStack by analyzing features in the projected maximum image. A combination of edge detection and Hough transform analysis is used to determine the global rotation of the stack. Optionally, the global shift of the tilt axis can also be calculated by minimization of the sum of the reconstruction.

Parameters:¶

method: 'CoM' | 'MaxImage'¶

Algorithm to use for registration alignment. Must be either 'CoM' or 'MaxImage'.

slices: ndarray | None = None¶

(Only used when method == "CoM") Locations at which to perform the Center of Mass analysis. If not provided, an appropriate list of slices will be automatically determined.

nslices: int | None = None¶

(Only used when method == "CoM") Nubmer of slices to use for the center of mass analysis (only used if the slices parameter is not specified). If None, a value of 10% of the x-axis size will be used, clamped to the range [3, 50], as calculated in the tilt_com() function.

limit: float = 10¶

(Only used when method == "MaxImage") Maximum rotation angle for MaxImage calculation

delta: float = 0.1¶

(Only used when method == "MaxImage") Angular increment in degrees for MaxImage calculation

plot_results: bool = False¶

(Only used when method == "MaxImage") If True, plot the maximum image along with the lines determined by Hough analysis

also_shift: bool = False¶

(Only used when method == "MaxImage") If True, also calculate and apply the global shift perpendicular to the tilt by minimizing the sum of the reconstruction

shift_limit: int = 20¶

(Only used when method == "MaxImage") The limit of shifts applied if also_shift is set to True

Returns:¶

out – Copy of the input stack rotated by calculated angle

Return type:¶

TomoStack

Examples¶

Align tilt axis using the center of mass (CoM) method:

>>> import etspy.datasets as ds
>>> import numpy as np
>>> stack = ds.get_needle_data()
>>> reg = stack.stack_register('PC', show_progressbar=False)
>>> method = 'CoM'
>>> ali = reg.tilt_align(method, slices=np.array([50,100,160]))

Align tilt axis using the maximum image method:

>>> import etspy.datasets as ds
>>> stack = ds.get_needle_data()
>>> reg = stack.stack_register('PC', show_progressbar=False)
>>> method = 'MaxImage'
>>> ali = reg.tilt_align(method)