Calculate shifts using combined center of mass and common line methods.

Center of mass aligns stack perpendicular to the tilt axis and common line is used to align the stack parallel to the tilt axis.

Parameters:¶

stack: TomoStack¶

Tilt series to be aligned

com_ref_index: int¶

Reference slice for center of mass alignment. All other slices will be aligned to this reference.

cl_ref_index: int | None = None¶

Reference slice for common line alignment. All other slices will be aligned to this reference. If not provided the projection closest to the middle of the stack will be chosen.

cl_resolution: float = 0.05¶

Resolution for subpixel common line alignment. Default is 0.05. Should be less than 0.5.

cl_div_factor: int = 8¶

Factor which determines the number of iterations of common line alignment to perform. Default is 8.

Returns:¶

reg – The X- and Y-shifts to be applied to each image

Return type:¶

ndarray