Register stack spatially.

Options are phase correlation (PC) maximization, StackReg, center of mass (‘COM’), or combined center of mass and common line methods. See docstring for etspy.align.align_stack() for details.

Parameters:¶

method: AlignmentMethod | 'PC' | 'COM' | 'COM-CL' | 'StackReg' = AlignmentMethod.PC¶

Algorithm to use for registration calculation. Must be one of the values specified by the etspy.AlignmentMethod enum.

start: int | None = None¶

Position in tilt series to use as starting point for the alignment. If None, the central projection is used.

show_progressbar: bool = False¶

Enable/disable progress bar

cuda: bool | None = False¶

Whether or not to use CUDA-accelerated reconstruction algorithms.

crop: bool = False¶

If True, crop aligned stack to eliminate border pixels. Default is False.

shift_type: 'interp' | 'fourier' = 'fourier'¶

Calculated image shifts can be applied using either interpolation via scipy.ndimage.shift or via Fourier shift as implemented in scipy.ndimage.fourier_shift. Must be either ‘interp’ or ‘fourier’.

**kwargs

Remaining keyword arguments are passed to the underlying alignment functions.

include : Keyword arguments that may be used

xrange

(Only used when method ==COM) The range for performing alignment. See calculate_shifts_com() for more details.

p

(Only used when method ==COM) Padding element. See calculate_shifts_com() for more details.

nslices

(Only used when method ==COM) Number of slices to return. See calculate_shifts_com() for more details.

com_ref_index

(Only used when method ==COM_CL) Reference slice for center of mass alignment. All other slices will be aligned to this reference. If not provided, the midpoint of the stack will be chosen. See calc_shifts_com_cl() for more details.

cl_ref_index

(Only used when method ==COM_CL) Reference slice for common line alignment. All other slices will be aligned to this reference. If not provided, the midpoint of the stack will be chosen.

cl_resolution

(Only used when method ==COM_CL) Resolution for subpixel common line alignment. Default is 0.05. Should be less than 0.5. See calc_shifts_com_cl() for more details.

cl_div_factor

(Only used when method ==COM_CL) Factor which determines the number of iterations of common line alignment to perform. Default is 8. See calc_shifts_com_cl() for more details.

Returns:¶

out – Spatially registered copy of the input stack

Return type:¶

TomoStack

Examples¶

Registration with phase correlation algorithm (PC)

>>> import etspy.datasets as ds
>>> stack = ds.get_needle_data()
>>> regPC = stack.stack_register('PC')

Registration with center of mass tracking (COM)

>>> import etspy.datasets as ds
>>> stack = ds.get_needle_data()
>>> regCOM = stack.stack_register('COM')

Registration with StackReg

>>> import etspy.datasets as ds
>>> stack = ds.get_needle_data()
>>> regSR = stack.stack_register('StackReg')

Registration with center of mass and common line (COM-CL)

>>> import etspy.datasets as ds
>>> stack = ds.get_needle_data()
>>> regCOMCL = stack.stack_register('COM-CL')