polyTEM.tomography.alignment

Tomography Alignment using fiduciary markers

Uses the alignment procedure developed by Zhongqi Jing and Frederick Sachs, 1990 https://www-sciencedirect-com.stanford.idm.oclc.org/science/article/pii/0304399191900425?via%3Dihub by solving linear equations

Functions

chain_affine_transformation_mats(M0, M1)	Chaining affine transformations given by M0 and M1 matrices to use with OpenCV2 warpAffine.
find_alignment_error(x_coords, y_coords, ...)	Finds the rotation angle and image displacement by aligning markers
find_markers(imgarray, num_markers[, ...])	Find gold fiduciary markers in image
proj_tilt_mat(alpha)	Matrix representing projection of tilted image
shift_markers(x_coords, y_coords, ...)	Use approximate solution from find_alignment_errors to align markers
sort_marker_labels(coo_list)	used to sort the outputs from find_markers so that the labels match for each marker
tilt_mat(alpha[, inverse])	Creates Tilt matrix for angle alpha, in radians

Classes

AlignmentResult([beta_history, dx_history, ...])

AlignmentResult object contains the parameters and results of aligning a stack of tilt images based on fiduciary marker locations