"""

Alignment functions for the ST Analysis packages.

Aligment refers to the matrix that transforms

spots in array coordinates to image pixel coordinates.

"""

import numpy as np

import os

def parseAlignmentMatrix(alignment_file):

"""

Takes a file as input that contains

the values of a 3x3 affine matrix in one line

as :

a11 a12 a13 a21 a22 a23 a31 a32 a33

and returns a 3x3 matrix with the parsed elements

:param alignment_file: a file containing the 9 elements of a 3x3 matrix

:return: a 3x3 matrix (default identify if error happens)

"""

alignment_matrix = np.zeros((3,3), dtype=np.float)

alignment_matrix[0,0] = 1

alignment_matrix[0,1] = 0

alignment_matrix[0,2] = 0

alignment_matrix[1,0] = 0

alignment_matrix[1,1] = 1

alignment_matrix[1,2] = 0

alignment_matrix[2,0] = 0

alignment_matrix[2,1] = 0

alignment_matrix[2,2] = 1

if alignment_file is None or not os.path.isfile(alignment_file):

return alignment_matrix

with open(alignment_file, "r") as filehandler:

line = filehandler.readline()

tokens = line.split()

assert(len(tokens) == 9)

alignment_matrix[0,0] = float(tokens[0])

alignment_matrix[0,1] = float(tokens[1])

alignment_matrix[0,2] = float(tokens[2])

alignment_matrix[1,0] = float(tokens[3])

alignment_matrix[1,1] = float(tokens[4])

alignment_matrix[1,2] = float(tokens[5])

alignment_matrix[2,0] = float(tokens[6])

alignment_matrix[2,1] = float(tokens[7])

alignment_matrix[2,2] = float(tokens[8])

return alignment_matrix