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
|
import gc
from pathlib import Path
import numpy as np
import numpy.testing as npt
import pytest
from rsciio.ripple import _api as ripple
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
exspy = pytest.importorskip("exspy", reason="exspy not installed")
# Tuple of tuples (data shape, signal_dimensions)
SHAPES_SDIM = (
((3,), (1,)),
((2, 3), (1, 2)),
((2, 3, 4), (1, 2)),
)
TEST_DATA_PATH = Path(__file__).parent / "data" / "ripple"
def test_write_unsupported_data_shape():
data = np.arange(5 * 10 * 15 * 20).reshape((5, 10, 15, 20))
s = hs.signals.Signal1D(data)
with pytest.raises(TypeError):
s.save("test_write_unsupported_data_shape.rpl")
def test_write_unsupported_data_type():
data = np.arange(5 * 10 * 15).reshape((5, 10, 15)).astype(np.float16)
s = hs.signals.Signal1D(data)
with pytest.raises(IOError):
s.save("test_write_unsupported_data_type.rpl")
# Test failing
# def test_write_scalar():
# data = np.array([2])
# with tempfile.TemporaryDirectory() as tmpdir:
# s = hs.signals.BaseSignal(data)
# fname = os.path.join(tmpdir, 'test_write_scalar_data.rpl')
# s.save(fname)
# s2 = hs.load(fname)
# np.testing.assert_allclose(s.data, s2.data)
def test_write_without_metadata(tmp_path):
data = np.arange(5 * 10 * 15).reshape((5, 10, 15))
s = hs.signals.Signal1D(data)
fname = tmp_path / "test_write_without_metadata.rpl"
s.save(fname)
s2 = hs.load(fname)
np.testing.assert_allclose(s.data, s2.data)
# for windows
del s2
gc.collect()
def test_write_with_metadata(tmp_path):
data = np.arange(5 * 10).reshape((5, 10))
s = hs.signals.Signal1D(data)
s.metadata.set_item("General.date", "2016-08-06")
s.metadata.set_item("General.time", "10:55:00")
s.metadata.set_item("General.title", "Test title")
fname = tmp_path / "test_write_with_metadata.rpl"
s.save(fname)
s2 = hs.load(fname)
np.testing.assert_allclose(s.data, s2.data)
assert s.metadata.General.date == s2.metadata.General.date
assert s.metadata.General.title == s2.metadata.General.title
assert s.metadata.General.time == s2.metadata.General.time
del s2
gc.collect()
def generate_parameters():
parameters = []
for dtype in ripple.dtype2keys.keys():
for shape, dims in SHAPES_SDIM:
for dim in dims:
for metadata in [True, False]:
parameters.append(
{
"dtype": dtype,
"shape": shape,
"dim": dim,
"metadata": metadata,
}
)
return parameters
def _get_filename(s, metadata):
filename = "test_ripple_sdim-%i_ndim-%i_%s%s.rpl" % (
s.axes_manager.signal_dimension,
s.axes_manager.navigation_dimension,
s.data.dtype.name,
"_meta" if metadata else "",
)
return filename
def _create_signal(shape, dim, dtype, metadata):
data = np.arange(np.prod(shape)).reshape(shape).astype(dtype)
if dim == 1:
if len(shape) > 2:
s = exspy.signals.EELSSpectrum(data)
if metadata:
s.set_microscope_parameters(
beam_energy=100.0, convergence_angle=1.0, collection_angle=10.0
)
else:
s = exspy.signals.EDSTEMSpectrum(data)
if metadata:
s.set_microscope_parameters(
beam_energy=100.0,
live_time=1.0,
tilt_stage=2.0,
azimuth_angle=3.0,
elevation_angle=4.0,
energy_resolution_MnKa=5.0,
)
else:
s = hs.signals.BaseSignal(data).transpose(signal_axes=dim)
if metadata:
s.metadata.General.date = "2016-08-06"
s.metadata.General.time = "10:55:00"
s.metadata.General.title = "Test title"
for i, axis in enumerate(s.axes_manager._axes):
i += 1
axis.offset = i * 0.5
axis.scale = i * 100
axis.name = "%i" % i
if axis.navigate:
axis.units = "m"
else:
axis.units = "eV"
return s
@pytest.mark.parametrize("pdict", generate_parameters())
def test_data(pdict, tmp_path):
dtype, shape, dim, metadata = (
pdict["dtype"],
pdict["shape"],
pdict["dim"],
pdict["metadata"],
)
s = _create_signal(shape=shape, dim=dim, dtype=dtype, metadata=metadata)
filename = _get_filename(s, metadata)
s.save(tmp_path / filename)
s_just_saved = hs.load(tmp_path / filename)
s_ref = hs.load(TEST_DATA_PATH / filename)
try:
for stest in (s_just_saved, s_ref):
npt.assert_array_equal(s.data, stest.data)
assert s.data.dtype == stest.data.dtype
assert s.axes_manager.signal_shape == stest.axes_manager.signal_shape
assert (
s.axes_manager.navigation_shape == stest.axes_manager.navigation_shape
)
assert s.metadata.General.title == stest.metadata.General.title
mdpaths = ("Signal.signal_type",)
if s.metadata.Signal.signal_type == "EELS" and metadata:
mdpaths += (
"Acquisition_instrument.TEM.convergence_angle",
"Acquisition_instrument.TEM.beam_energy",
"Acquisition_instrument.TEM.Detector.EELS.collection_angle",
)
elif "EDS" in s.metadata.Signal.signal_type and metadata:
mdpaths += (
"Acquisition_instrument.TEM.Stage.tilt_alpha",
"Acquisition_instrument.TEM.Detector.EDS.azimuth_angle",
"Acquisition_instrument.TEM.Detector.EDS.elevation_angle",
"Acquisition_instrument.TEM.Detector." "EDS.energy_resolution_MnKa",
"Acquisition_instrument.TEM.Detector.EDS.live_time",
)
if metadata:
mdpaths = (
"General.date",
"General.time",
"General.title",
)
for mdpath in mdpaths:
assert s.metadata.get_item(mdpath) == stest.metadata.get_item(mdpath)
for saxis, taxis in zip(s.axes_manager._axes, stest.axes_manager._axes):
taxis.convert_to_units()
assert saxis.scale == taxis.scale
assert saxis.offset == taxis.offset
assert saxis.units == taxis.units
assert saxis.name == taxis.name
except Exception:
raise
finally:
# As of v0.8.5 the data in the ripple files are loaded as memmaps
# instead of array. In Windows the garbage collector doesn't close
# the file before attempting to delete it making the test fail.
# The following lines simply make sure that the memmap is closed.
# del s_just_saved.data
# del s_ref.data
del s_just_saved
del s_ref
gc.collect()
def generate_files():
"""Generate the test files that are distributed with HyperSpy.
Unless new features are introduced there shouldn't be any need to recreate
the files.
"""
for dtype in ripple.dtype2keys.keys():
for shape, dims in SHAPES_SDIM:
for dim in dims:
for metadata in [True, False]:
s = _create_signal(
shape=shape, dim=dim, dtype=dtype, metadata=metadata
)
filename = _get_filename(s, metadata)
s.save(TEST_DATA_PATH / filename, overwrite=True)
|
