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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Fable Input Output
# https://github.com/silx-kit/fabio
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""
2011: Jerome Kieffer for ESRF.
Unit tests for CBF images based on references images taken from:
http://pilatus.web.psi.ch/DATA/DATASETS/insulin_0.2/
19/01/2015
"""
import unittest
import os
import time
import logging
logger = logging.getLogger(__name__)
import numpy
import fabio
from fabio.cbfimage import CbfImage
from fabio.compression import decByteOffset_numpy, decByteOffset_cython
from ..utilstest import UtilsTest
class TestCbfReader(unittest.TestCase):
""" test cbf image reader """
def setUp(self):
"""Download images"""
self.edf_filename = "run2_1_00148.edf.bz2"
self.edf_filename = UtilsTest.getimage(self.edf_filename)[:-4]
self.cbf_filename = "run2_1_00148.cbf.bz2"
self.cbf_filename = UtilsTest.getimage(self.cbf_filename)[:-4]
def test_read(self):
""" check whole reader"""
times = []
times.append(time.time())
cbf = fabio.open(self.cbf_filename)
times.append(time.time())
edf = fabio.open(self.edf_filename)
times.append(time.time())
self.assertAlmostEqual(0, abs(cbf.data - edf.data).max())
logger.info("Reading CBF took %.3fs whereas the same EDF took %.3fs" % (times[1] - times[0], times[2] - times[1]))
def test_write(self):
"Rest writing with self consistency at the fabio level"
name = os.path.basename(self.cbf_filename)
obj = CbfImage()
obj.read(self.cbf_filename)
obj.write(os.path.join(UtilsTest.tempdir, name))
other = CbfImage()
other.read(os.path.join(UtilsTest.tempdir, name))
self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same")
for key in obj.header:
if key in["filename", "X-Binary-Size-Padding"]:
continue
self.assertTrue(key in other.header, "Key %s is in header" % key)
self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s" % key)
# By destroying the object, one actually closes the file, which is needed under windows.
del obj
del other
if os.path.exists(os.path.join(UtilsTest.tempdir, name)):
os.unlink(os.path.join(UtilsTest.tempdir, name))
def test_byte_offset(self):
""" check byte offset algorithm"""
cbf = fabio.open(self.cbf_filename)
starter = b"\x0c\x1a\x04\xd5"
cbs = cbf.cbs
startPos = cbs.find(starter) + 4
data = cbs[startPos: startPos + int(cbf.header["X-Binary-Size"])]
startTime = time.time()
size = cbf.shape[0] * cbf.shape[1]
numpyRes = decByteOffset_numpy(data, size=size)
tNumpy = time.time() - startTime
logger.info("Timing for Numpy method : %.3fs" % tNumpy)
startTime = time.time()
cythonRes = decByteOffset_cython(stream=data, size=size)
tCython = time.time() - startTime
delta = abs(numpyRes - cythonRes).max()
self.assertAlmostEqual(0, delta)
logger.info("Timing for Cython method : %.3fs, max delta= %s" % (tCython, delta))
def test_consitency_manual(self):
"""
Test if an image can be read and saved and the results are "similar"
"""
name = os.path.basename(self.cbf_filename)
obj = fabio.open(self.cbf_filename)
new = CbfImage(data=obj.data, header=obj.header)
new.write(os.path.join(UtilsTest.tempdir, name))
other = fabio.open(os.path.join(UtilsTest.tempdir, name))
self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same")
for key in obj.header:
if key in["filename", "X-Binary-Size-Padding"]:
continue
self.assertTrue(key in other.header, "Key %s is in header" % key)
self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key]))
def test_consitency_convert(self):
"""
Test if an image can be read and saved and the results are "similar"
"""
name = os.path.basename(self.cbf_filename)
obj = fabio.open(self.cbf_filename)
new = obj.convert("cbf")
new.write(os.path.join(UtilsTest.tempdir, name))
other = fabio.open(os.path.join(UtilsTest.tempdir, name))
self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same")
for key in obj.header:
if key in["filename", "X-Binary-Size-Padding"]:
continue
self.assertTrue(key in other.header, "Key %s is in header" % key)
self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key]))
def test_unicode(self):
"""
Test if an image can be read and saved to an unicode named
"""
name = u"%s" % os.path.basename(self.cbf_filename)
obj = fabio.open(self.cbf_filename)
obj.write(os.path.join(UtilsTest.tempdir, name))
other = fabio.open(os.path.join(UtilsTest.tempdir, name))
self.assertEqual(abs(obj.data - other.data).max(), 0, "data are the same")
for key in obj.header:
if key in["filename", "X-Binary-Size-Padding"]:
continue
self.assertTrue(key in other.header, "Key %s is in header" % key)
self.assertEqual(obj.header[key], other.header[key], "value are the same for key %s [%s|%s]" % (key, obj.header[key], other.header[key]))
def test_bug_388(self):
data = numpy.random.randint(0, 100, size=(27, 31)).astype(numpy.int32)
im = CbfImage(data=data, header={})
filename = os.path.join(UtilsTest.tempdir, "bad_name.edf")
im.write(filename)
res = fabio.open(filename)
self.assertEqual(abs(data-res.data).max(), 0, "Data are the same despite the wrong name")
def test_bug_408(self):
"Bug when reading files generated by XDS"
xds_filename = UtilsTest.getimage("XDS.cbf.bz2")[:-4]
f = fabio.open(xds_filename)
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestCbfReader))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
|
