From d1449db695f263f5015a6faed4726bd461da131a Mon Sep 17 00:00:00 2001 From: pc494 Date: Tue, 28 Jan 2020 11:23:03 +0000 Subject: [PATCH 1/2] Change as discussed in #56 --- diffsims/utils/sim_utils.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/diffsims/utils/sim_utils.py b/diffsims/utils/sim_utils.py index 5adbd837..6ce09b22 100644 --- a/diffsims/utils/sim_utils.py +++ b/diffsims/utils/sim_utils.py @@ -372,7 +372,7 @@ def simulate_rotated_structure(diffraction_generator, structure, rotation_matrix stdbase = structure.lattice.stdbase stdbase_inverse = np.linalg.inv(stdbase) rotation_matrix_diffpy = stdbase_inverse @ rotation_matrix @ stdbase - + lattice_rotated = diffpy.structure.lattice.Lattice( *structure.lattice.abcABG(), baserot=rotation_matrix_diffpy) @@ -407,7 +407,8 @@ def get_points_in_sphere(reciprocal_lattice, reciprocal_radius): spot_distances : numpy.array Distance of reciprocal lattice points in sphere from the origin. """ - a, b, c = reciprocal_lattice.a, reciprocal_lattice.b, reciprocal_lattice.c + standard_base = diffpy.structure.lattice.Lattice(base=reciprocal_lattice.stdbase) + a, b, c = standard_base.a, standard_base.b, standard_base.c h_max = np.floor(reciprocal_radius / a) k_max = np.floor(reciprocal_radius / b) l_max = np.floor(reciprocal_radius / c) @@ -416,7 +417,7 @@ def get_points_in_sphere(reciprocal_lattice, reciprocal_radius): k_list = np.arange(-k_max, k_max + 1) l_list = np.arange(-l_max, l_max + 1) potential_points = np.asarray(list(product(h_list, k_list, l_list))) - in_sphere = np.abs(reciprocal_lattice.dist(potential_points, [0, 0, 0])) < reciprocal_radius + in_sphere = np.abs(standard_base.dist(potential_points, [0, 0, 0])) < reciprocal_radius spot_indicies = potential_points[in_sphere] spot_coords = reciprocal_lattice.cartesian(spot_indicies) spot_distances = reciprocal_lattice.dist(spot_indicies, [0, 0, 0]) From 133e2d2852a1cc0afcb97456c00933c1428e8227 Mon Sep 17 00:00:00 2001 From: pc494 Date: Tue, 28 Jan 2020 11:23:43 +0000 Subject: [PATCH 2/2] Makes a local import global --- diffsims/utils/sim_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/diffsims/utils/sim_utils.py b/diffsims/utils/sim_utils.py index 6ce09b22..3841080a 100644 --- a/diffsims/utils/sim_utils.py +++ b/diffsims/utils/sim_utils.py @@ -22,6 +22,7 @@ from scipy.constants import h, m_e, e, c, pi import collections import diffpy.structure +from itertools import product from transforms3d.axangles import axangle2mat from transforms3d.euler import mat2euler @@ -412,7 +413,6 @@ def get_points_in_sphere(reciprocal_lattice, reciprocal_radius): h_max = np.floor(reciprocal_radius / a) k_max = np.floor(reciprocal_radius / b) l_max = np.floor(reciprocal_radius / c) - from itertools import product h_list = np.arange(-h_max, h_max + 1) #arange has a non-inclusive endpoint k_list = np.arange(-k_max, k_max + 1) l_list = np.arange(-l_max, l_max + 1)