diff --git a/tomotools/align.py b/tomotools/align.py index 1dc31418..c4479d24 100644 --- a/tomotools/align.py +++ b/tomotools/align.py @@ -249,12 +249,10 @@ def calculate_shifts_conservation_of_mass(stack, xrange=None, p=20): xrange = [round(xrange[0]) + p, round(xrange[1]) - p] xshifts = np.zeros([ntilts, 1]) - # total_mass = np.zeros([ntilts, xrange[1] - xrange[0] + 2 * p]) total_mass = np.zeros([ntilts, xrange[1] - xrange[0] + 2 * p + 1]) + for i in range(0, ntilts): - total_mass[i, :] = np.sum( - stack.data[i, :, xrange[0] - p - 1: xrange[1] + p], 0 - ) + total_mass[i, :] = np.sum(stack.data[i, :, xrange[0] - p - 1: xrange[1] + p], 0) mean_mass = np.mean(total_mass[:, p:-p], 0) @@ -383,7 +381,7 @@ def calculate_shifts_stackreg(stack, start, show_progressbar): return shifts -def calc_com_cl_shifts(stack, com_ref_index, cl_ref_index, cl_resolution, cl_div_factor): +def calc_shifts_com_cl(stack, com_ref_index, cl_ref_index, cl_resolution, cl_div_factor): """ Align stack using combined center of mass and common line methods. @@ -520,7 +518,7 @@ def align_stack(stack, method, start, show_progressbar, **kwargs): cl_ref_index = kwargs.get('cl_ref_index', stack.data.shape[0] // 2) cl_resolution = kwargs.get('cl_resolution', 0.05) cl_div_factor = kwargs.get('cl_div_factor', 8) - shifts = calc_com_cl_shifts(stack, com_ref_index, cl_ref_index, cl_resolution, cl_div_factor) + shifts = calc_shifts_com_cl(stack, com_ref_index, cl_ref_index, cl_resolution, cl_div_factor) else: raise ValueError('Invalid alignment method %s' % method) aligned = apply_shifts(stack, shifts)