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
|
# -*- 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>.
import importlib
import os
import tempfile
from datetime import datetime
from time import perf_counter, sleep
import numpy as np
import numpy.testing as npt
import pytest
from rsciio.utils.tests import assert_deep_almost_equal
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
mrcz = pytest.importorskip("mrcz", reason="mrcz not installed")
# ==============================================================================
# MRCZ Test
#
# Internal python-only test. Build a random image and save and re-load it.
# ==============================================================================
tmpDir = tempfile.gettempdir()
MAX_ASYNC_TIME = 10.0
dtype_list = ["float32", "int8", "int16", "uint16", "complex64"]
def _generate_parameters():
parameters = []
for dtype in dtype_list:
for compressor in [None, "zstd", "lz4"]:
for clevel in [1, 9]:
for lazy in [True, False]:
parameters.append([dtype, compressor, clevel, lazy])
return parameters
class TestPythonMrcz:
def setup_method(self, method):
pass
def compareSaveLoad(
self,
testShape,
dtype="int8",
compressor=None,
clevel=1,
lazy=False,
do_async=False,
**kwargs,
):
# This is the main function which reads and writes from disk.
mrcName = os.path.join(tmpDir, "testMage_{}_lazy_{}.mrcz".format(dtype, lazy))
dtype = np.dtype(dtype)
if dtype == "float32" or dtype == "float64":
testData = np.random.normal(size=testShape).astype(dtype)
elif dtype == "complex64" or dtype == "complex128":
testData = np.random.normal(size=testShape).astype(
dtype
) + 1.0j * np.random.normal(size=testShape).astype(dtype)
else: # integers
testData = np.random.randint(10, size=testShape).astype(dtype)
testSignal = hs.signals.Signal2D(testData)
if lazy:
testSignal = testSignal.as_lazy()
# Add "File" metadata to testSignal
testSignal.metadata.General.add_dictionary(
{
"FileIO": {
"0": {
"operation": "load",
"hyperspy_version": hs.__version__,
"io_plugin": "rsciio.mrcz",
"timestamp": datetime.now().astimezone().isoformat(),
}
}
}
)
# Unfortunately one cannot iterate over axes_manager in a Pythonic way
# for axis in testSignal.axes_manager:
testSignal.axes_manager[0].name = "z"
testSignal.axes_manager[0].scale = np.random.uniform(low=0.0, high=1.0)
testSignal.axes_manager[0].units = "nm"
testSignal.axes_manager[1].name = "x"
testSignal.axes_manager[1].scale = np.random.uniform(low=0.0, high=1.0)
testSignal.axes_manager[1].units = "nm"
testSignal.axes_manager[2].name = "y"
testSignal.axes_manager[2].scale = np.random.uniform(low=0.0, high=1.0)
testSignal.axes_manager[2].units = "nm"
# Meta-data that goes into MRC fixed header
testSignal.metadata.set_item("Acquisition_instrument.TEM.beam_energy", 300.0)
# Meta-data that goes into JSON extended header
testSignal.metadata.set_item("Acquisition_instrument.TEM.magnification", 25000)
testSignal.metadata.set_item(
"Signal.Noise_properties.Variance_linear_model.gain_factor", 1.0
)
testSignal.save(
mrcName, compressor=compressor, clevel=clevel, do_async=do_async, **kwargs
)
if do_async:
# Poll file on disk since we don't return the
# concurrent.futures.Future
t_stop = perf_counter() + MAX_ASYNC_TIME
sleep(0.005)
while perf_counter() < t_stop:
try:
fh = open(mrcName, "a")
fh.close()
break
except IOError:
sleep(0.001)
print(
"Time to save file: {} s".format(
perf_counter() - (t_stop - MAX_ASYNC_TIME)
)
)
sleep(0.1)
reSignal = hs.load(mrcName)
try:
os.remove(mrcName)
except IOError:
print("Warning: file {} left on disk".format(mrcName))
# change file timestamp to make the metadata of both signals equal
testSignal.metadata.General.FileIO.Number_0.timestamp = (
reSignal.metadata.General.FileIO.Number_0.timestamp
)
npt.assert_array_almost_equal(testSignal.data.shape, reSignal.data.shape)
npt.assert_array_almost_equal(testSignal.data, reSignal.data)
npt.assert_almost_equal(
testSignal.metadata.Acquisition_instrument.TEM.beam_energy,
reSignal.metadata.Acquisition_instrument.TEM.beam_energy,
)
npt.assert_almost_equal(
testSignal.metadata.Acquisition_instrument.TEM.magnification,
reSignal.metadata.Acquisition_instrument.TEM.magnification,
)
for aName in ["x", "y", "z"]:
npt.assert_equal(
testSignal.axes_manager[aName].size, reSignal.axes_manager[aName].size
)
npt.assert_almost_equal(
testSignal.axes_manager[aName].scale, reSignal.axes_manager[aName].scale
)
if dtype == "complex64":
assert isinstance(reSignal, hs.signals.ComplexSignal2D)
else:
assert isinstance(reSignal, hs.signals.Signal2D)
# delete last load operation from reSignal metadata so we can compare
del reSignal.metadata.General.FileIO.Number_2
assert_deep_almost_equal(
testSignal.axes_manager.as_dictionary(),
reSignal.axes_manager.as_dictionary(),
)
assert_deep_almost_equal(
testSignal.metadata.as_dictionary(), reSignal.metadata.as_dictionary()
)
return reSignal
@pytest.mark.parametrize(
("dtype", "compressor", "clevel", "lazy"), _generate_parameters()
)
def test_MRC(self, dtype, compressor, clevel, lazy):
blosc = importlib.util.find_spec("blosc")
if blosc is None and compressor is not None:
with pytest.raises(ImportError):
self.compareSaveLoad(
[2, 64, 32],
dtype=dtype,
compressor=compressor,
clevel=clevel,
lazy=lazy,
)
else:
self.compareSaveLoad(
[2, 64, 32],
dtype=dtype,
compressor=compressor,
clevel=clevel,
lazy=lazy,
)
@pytest.mark.parametrize("dtype", dtype_list)
def test_Async(self, dtype):
_ = pytest.importorskip("blosc", reason="skipping test_async, requires blosc")
t_start = perf_counter()
self.compareSaveLoad(
[2, 64, 32], dtype=dtype, compressor="zstd", clevel=1, do_async=True
)
print("MRCZ Asychronous test finished in {} s".format(perf_counter() - t_start))
|
