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
|
#!/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.
#
"""
Test for MRC file format imagess.
"""
import unittest
import os
import logging
logger = logging.getLogger(__name__)
import fabio
from ...mrcimage import MrcImage
from ...openimage import openimage
from ..utilstest import UtilsTest
class TestMrc(unittest.TestCase):
"""basic test"""
mrcfilename = ('EMD-3001.map', "0p67_5s_0000.mrc")
npyfilename = ('EMD-3001.npy', "0p67_5s_0000.npy")
results = """EMD-3001.map 73 43 -0.36814222 0.678705 0.0062340125 0.16349247
0p67_5s_0000.mrc 2048 2048 -344.0 33553.0 82.653259 243.213061"""
def setUp(self):
"""Download files"""
self.fn = {}
for i in self.mrcfilename + self.npyfilename:
self.fn[i] = UtilsTest.getimage(i + ".bz2")[:-4]
for i in self.fn:
assert os.path.exists(self.fn[i])
def test_read(self):
""" check we can read mrc images"""
for results in self.results.split("\n"):
vals = results.split()
dim1, dim2 = [int(x) for x in vals[1:3]]
shape = dim2, dim1
mini, maxi, mean, stddev = [float(x) for x in vals[3:]]
for ext in ["", ".gz", ".bz2"]:
filename = self.fn[vals[0]] + ext
try:
obj = openimage(filename)
except Exception as err:
logger.error("unable to read: %s", filename)
raise err
self.assertAlmostEqual(mini, obj.getmin(), 4, f"{filename} getmin")
self.assertAlmostEqual(maxi, obj.getmax(), 4, f"{filename} getmax")
self.assertAlmostEqual(mean, obj.getmean(), 4, f"{filename} getmean")
self.assertAlmostEqual(stddev, obj.getstddev(), 4, f"{filename} getstddev")
self.assertEqual(shape, obj.shape, f"{filename} shape")
def test_same(self):
""" see if we can read mrc images and if they are the same as the numpy dump"""
for mrcfilename, npyfilename in zip(self.mrcfilename, self.npyfilename):
logger.info("Comparing files %s and %s", mrcfilename, npyfilename)
mrc = MrcImage()
mrc.read(self.fn[mrcfilename])
npy = fabio.open(self.fn[npyfilename])
diff = (mrc.data - npy.data)
self.assertAlmostEqual(abs(diff).sum(), 0, 4, msg=mrcfilename)
def suite():
loadTests = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite = unittest.TestSuite()
testsuite.addTest(loadTests(TestMrc))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
|
