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
|
# -*- 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")
TEST_DATA_DIR = Path(__file__).parent / "data" / "mrc"
def test_single_image():
# Acquired from Velox
s = hs.load(TEST_DATA_DIR / "HAADFscan.mrc")
assert s.data.shape == (16, 16)
assert s.axes_manager.signal_shape == (16, 16)
assert s.axes_manager.navigation_shape == ()
for axis in s.axes_manager.signal_axes:
assert axis.scale == 5.679131317138672
assert axis.offset == 0
assert axis.units == "nm"
def test_4DSTEM_image():
# Acquired from Velox
s = hs.load(TEST_DATA_DIR / "4DSTEMscan.mrc")
assert s.data.shape == (256, 256, 256)
assert s.axes_manager.signal_shape == (256, 256)
assert s.axes_manager.navigation_shape == (256,)
def test_4DSTEM_image_navigation_shape_16_16():
# Acquired from Velox
s = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
navigation_shape=(16, 16),
)
assert s.data.shape == (16, 16, 256, 256)
assert s.axes_manager.signal_shape == (256, 256)
assert s.axes_manager.navigation_shape == (16, 16)
@pytest.mark.parametrize("distributed", [True, False])
def test_4DSTEM_image_navigation_shape_8_32(distributed):
s = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
navigation_shape=(8, 32),
distributed=distributed,
)
assert s.data.shape == (32, 8, 256, 256)
assert s.axes_manager.signal_shape == (256, 256)
assert s.axes_manager.navigation_shape == (8, 32)
def test_mrc_distributed_equal():
s = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
navigation_shape=(8, 32),
distributed=False,
)
s2 = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
navigation_shape=(8, 32),
distributed=True,
)
np.testing.assert_array_equal(s.data, s2.data)
@pytest.mark.parametrize("distributed", [True, False])
def test_mrc_chunks_equal(distributed):
s = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
navigation_shape=(8, 32),
distributed=distributed,
chunks=(16, 4, 256, 256),
lazy=True,
)
assert s.data.chunks == (
(
16,
16,
),
(
4,
4,
),
(256,),
(256,),
)
@pytest.mark.parametrize("navigation_shape", [None, (256,), (8, 32), (8, 16, 2)])
def test_mrc_metadata(navigation_shape):
s = hs.load(
TEST_DATA_DIR / "4DSTEMscan.mrc",
metadata_file=TEST_DATA_DIR / "info.txt",
navigation_shape=navigation_shape,
)
if navigation_shape is None:
navigation_shape = (8, 32)
shape = navigation_shape[::-1] + (256, 256)
assert s.data.shape == shape
assert s.axes_manager.signal_shape == (256, 256)
assert s.axes_manager.navigation_shape == navigation_shape
assert s.metadata.Acquisition_instrument.TEM.detector == "CeleritasXS"
assert s.metadata.Acquisition_instrument.TEM.magnification == "1000"
assert s.metadata.Acquisition_instrument.TEM.frames_per_second == "40000"
def test_mrc_metadata_auto():
s = hs.load(TEST_DATA_DIR / "20241021_00405_movie.mrc", lazy=True)
navigation_shape = (8, 4)
shape = navigation_shape[::-1] + (4, 8)
assert s.data.shape == shape
assert s.axes_manager.signal_shape == (8, 4)
assert s.axes_manager.navigation_shape == navigation_shape
assert s.metadata.Acquisition_instrument.TEM.detector == "DESim"
assert s.metadata.Acquisition_instrument.TEM.magnification == "1000"
assert s.metadata.Acquisition_instrument.TEM.frames_per_second == "700"
assert len(s.metadata.General.virtual_images) == 2
assert len(s.metadata.General.external_detectors) == 1
assert s.metadata._HyperSpy.navigator is not None
shape = (
s.axes_manager._navigation_shape_in_array
+ s.axes_manager._signal_shape_in_array
)
assert s.data.shape == shape
@pytest.mark.parametrize(
"metadata_file",
[
TEST_DATA_DIR / "3DSTEM_scan_info.txt",
TEST_DATA_DIR / "3DTEM_scan_info.txt",
TEST_DATA_DIR / "3DTEMDiffracting_scan_info.txt",
],
)
def test_mrc_metadata_modes(metadata_file):
s = hs.load(TEST_DATA_DIR / "20241021_00405_movie.mrc", metadata_file=metadata_file)
diffracting = "STEM" in metadata_file.name or "Diffracting" in metadata_file.name
s.axes_manager.navigation_axes[0].units = "sec"
if diffracting:
s.axes_manager.signal_axes[0].units = "nm^-1"
s.axes_manager.signal_axes[1].units = "nm^-1"
else:
s.axes_manager.signal_axes[0].units = "nm"
s.axes_manager.signal_axes[1].units = "nm"
|
