1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
|
# -*- coding: utf-8 -*-
# Copyright 2007-2023 The HyperSpy developers
#
# This file is part of RosettaSciIO.
#
# RosettaSciIO is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RosettaSciIO is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with RosettaSciIO. If not, see <https://www.gnu.org/licenses/#GPL>.
from pathlib import Path
import numpy as np
import pytest
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
t = pytest.importorskip("traits.api", reason="traits not installed")
TEST_DATA_PATH = Path(__file__).parent / "data" / "emd"
def test_all_but_4D():
filename = TEST_DATA_PATH / "Si100_2D_3D_DPC_potential_2slices.emd"
s = hs.load(filename)
assert len(s) == 4
# DPC: navigation dimension are DPC and depth
assert s[0].data.shape == (2, 2, 22, 22)
# annular detectors: navigation dimension is depth
assert s[1].data.shape == (2, 22, 22)
# virtual detectors: navigation dimension are depth and scattering angle
assert s[2].data.shape == (4, 16, 16)
# projected potential: navigation dimension is number of slices
assert s[3].data.shape == (2, 18, 22, 22)
def check_depth_axis(axis):
assert "depth" in axis.name
assert axis.units == "Å"
np.testing.assert_allclose(axis.scale, 2.715)
np.testing.assert_allclose(axis.offset, 2.715)
np.testing.assert_allclose(axis.size, 2)
def check_signal_axes(signal_axes):
assert signal_axes[0].name == "R_x"
assert signal_axes[1].name == "R_y"
for axis in signal_axes:
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 0.25)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 22)
for i in [0, 1, 3]:
# signal axis
check_signal_axes(s[i].axes_manager.signal_axes)
# depth axis
check_depth_axis(s[i].axes_manager.navigation_axes[-1])
# DPC axis
axis = s[0].axes_manager[0]
assert axis.name == t.Undefined
assert axis.units == t.Undefined
np.testing.assert_allclose(axis.scale, 1)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 2)
axis = s[2].axes_manager[0]
assert axis.name == "R_z"
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 1.3575)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 4)
# signal axes
signal_axes = s[2].axes_manager.signal_axes
assert signal_axes[0].name == "R_x"
assert signal_axes[1].name == "R_y"
for axis in signal_axes:
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 0.339375)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 16)
def test_depth_axis_zStart():
filename = TEST_DATA_PATH / "Si100_1x1x3-zStart5.43.emd"
s = hs.load(filename)
axis = s.axes_manager[1]
assert "depth" in axis.name
assert axis.units == "Å"
np.testing.assert_allclose(axis.scale, 5.43)
np.testing.assert_allclose(axis.offset, 5.43)
np.testing.assert_allclose(axis.size, 3)
# non-uniform depth axis, not supported yet
# only the depth of the last image differ from others
filename = TEST_DATA_PATH / "Si100_1x1x3-zStart6.7875.emd"
s = hs.load(filename)
axis = s.axes_manager[1]
assert "depth" in axis.name
assert axis.units == t.Undefined
np.testing.assert_allclose(axis.scale, 1)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 2)
def test_all_but_4D_no_stack():
filename = TEST_DATA_PATH / "Si100_2D_3D_DPC_potential_2slices.emd"
s = hs.load(filename, stack_group=False)
assert len(s) == 7
s2 = hs.load(filename, stack_group=True)
np.testing.assert_allclose(np.stack([s[0].data, s[1].data]), s2[0].data)
@pytest.mark.parametrize(
"dataset_path",
[
"4DSTEM_simulation/data/realslices/annular_detector_depth0000/realslice",
"4DSTEM_simulation/data/realslices/virtual_detector_depth0000/realslice",
"4DSTEM_simulation/data/realslices/DPC_CoM_depth0000/realslice",
"4DSTEM_simulation/data/realslices/ppotential/realslice",
],
)
def test_load_single_dataset(dataset_path):
filename = TEST_DATA_PATH / "Si100_2D_3D_DPC_potential_2slices.emd"
s = hs.load(filename, dataset_path=dataset_path)
assert isinstance(s, hs.signals.Signal2D)
def test_load_specific_datasets():
filename = TEST_DATA_PATH / "Si100_2D_3D_DPC_potential_2slices.emd"
dataset_path = [
"4DSTEM_simulation/data/realslices/annular_detector_depth0000/realslice",
"4DSTEM_simulation/data/realslices/virtual_detector_depth0000/realslice",
]
s = hs.load(filename, dataset_path=dataset_path)
assert len(s) == 2
@pytest.mark.parametrize("lazy", (True, False))
def test_3D_only(lazy):
filename = TEST_DATA_PATH / "Si100_3D.emd"
s = hs.load(filename, lazy=lazy)
if lazy:
s.compute(close_file=True)
assert s.data.shape == (37, 22, 22)
# scattering angle axis
axis = s.axes_manager[0]
assert axis.name == "bin_outer_angle"
assert axis.units == "mrad"
np.testing.assert_allclose(axis.scale, 0.001, rtol=1e-6)
np.testing.assert_allclose(axis.offset, 0.0005)
np.testing.assert_allclose(axis.size, 37)
# signal axes
signal_axes = s.axes_manager.signal_axes
assert signal_axes[0].name == "R_x"
assert signal_axes[1].name == "R_y"
for axis in signal_axes:
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 0.25)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 22)
def test_non_square_3D():
filename = TEST_DATA_PATH / "Si100_2x1x1_3D.emd"
s = hs.load(filename)
assert s.data.shape == (22, 44)
# signal axes
signal_axes = s.axes_manager.signal_axes
assert signal_axes[0].name == "R_x"
assert signal_axes[1].name == "R_y"
assert signal_axes[0].size == 44
assert signal_axes[1].size == 22
for axis in signal_axes:
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 0.25)
np.testing.assert_allclose(axis.offset, 0)
@pytest.mark.parametrize("lazy", (True, False))
def test_4D(lazy):
filename = TEST_DATA_PATH / "Si100_4D.emd"
s = hs.load(filename, lazy=lazy)
if lazy:
s.compute(close_file=True)
assert s.data.shape == (2, 11, 11, 8, 8)
# navigation x, y axes
navigation_axes = s.axes_manager.navigation_axes
assert navigation_axes[0].name == "R_y"
assert navigation_axes[1].name == "R_x"
for axis in navigation_axes[:2]:
assert axis.units == "nm"
np.testing.assert_allclose(axis.scale, 0.5)
np.testing.assert_allclose(axis.offset, 0)
np.testing.assert_allclose(axis.size, 11)
axis = s.axes_manager[2]
assert axis.name == "CBED_array_depth"
assert axis.units == "Å"
# Needs metadata to know these values?
np.testing.assert_allclose(axis.scale, 2.715)
np.testing.assert_allclose(axis.offset, 2.715)
np.testing.assert_allclose(axis.size, 2)
# signal axes
signal_axes = s.axes_manager.signal_axes
assert signal_axes[0].name == "Q_y"
assert signal_axes[1].name == "Q_x"
assert signal_axes[0].size == 8
assert signal_axes[1].size == 8
for axis in signal_axes:
assert axis.units == "1 / nm"
np.testing.assert_allclose(axis.scale, 0.18416205)
np.testing.assert_allclose(axis.offset, -0.73664826)
|
