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
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
|
#!/usr/bin/env python
# coding: utf-8
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2015-2018 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 suite for masked arrays"
from __future__ import absolute_import, division, print_function
__author__ = "Jérôme Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "12/01/2018"
import tempfile
import contextlib
import os
import unittest
import numpy.testing
import fabio
import logging
from .utilstest import UtilsTest
logger = logging.getLogger(__name__)
from ..azimuthalIntegrator import AzimuthalIntegrator
from ..containers import Integrate1dResult
from ..containers import Integrate2dResult
from ..io import DefaultAiWriter
from ..detectors import Pilatus1M
from ..utils import mathutil
@contextlib.contextmanager
def resulttempfile():
fd, path = tempfile.mkstemp(prefix="pyfai_", suffix=".out")
os.close(fd)
os.remove(path)
yield path
os.remove(path)
class TestIntegrate1D(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.npt = 1000
self.img = UtilsTest.getimage("Pilatus1M.edf")
self.data = fabio.open(self.img).data
self.ai = AzimuthalIntegrator(1.58323111834, 0.0334170169115, 0.0412277798782, 0.00648735642526, 0.00755810191106, 0.0, detector=Pilatus1M())
self.ai.wavelength = 1e-10
self.Rmax = 3
self.methods = ["numpy", "cython", "BBox", "splitpixel", "lut"]
if UtilsTest.opencl:
self.methods.append("lut_ocl")
def tearDown(self):
unittest.TestCase.tearDown(self)
self.npt = self.img = self.data = self.ai = self.Rmax = None
def testQ(self):
res = {}
for m in self.methods:
res[m] = self.ai.integrate1d(self.data, self.npt, method=m, radial_range=(0.5, 5.8))
for a in res:
for b in res:
R = mathutil.rwp(res[a], res[b])
mesg = "testQ: %s vs %s measured R=%s<%s" % (a, b, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(R <= self.Rmax, mesg)
def testR(self):
res = {}
for m in self.methods:
res[m] = self.ai.integrate1d(self.data, self.npt, method=m, unit="r_mm", radial_range=(20, 150))
for a in res:
for b in res:
R = mathutil.rwp(res[a], res[b])
mesg = "testR: %s vs %s measured R=%s<%s" % (a, b, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(R <= self.Rmax, mesg)
def test2th(self):
res = {}
for m in self.methods:
res[m] = self.ai.integrate1d(self.data, self.npt, method=m, unit="2th_deg", radial_range=(0.5, 5.5))
for a in res:
for b in res:
R = mathutil.rwp(res[a], res[b])
mesg = "test2th: %s vs %s measured R=%s<%s" % (a, b, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(R <= self.Rmax, mesg)
def test_filename(self):
with resulttempfile() as filename:
self.ai.integrate1d(self.data, self.npt, filename=filename)
self.assertGreater(os.path.getsize(filename), 40)
def test_defaultwriter(self):
with resulttempfile() as filename:
result = self.ai.integrate1d(self.data, self.npt)
writer = DefaultAiWriter(filename, self.ai)
writer.write(result)
writer.close()
self.assertGreater(os.path.getsize(filename), 40)
class TestIntegrate2D(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.npt = 500
cls.img = UtilsTest.getimage("Pilatus1M.edf")
cls.data = fabio.open(cls.img).data
cls.ai = AzimuthalIntegrator(1.58323111834, 0.0334170169115, 0.0412277798782, 0.00648735642526, 0.00755810191106, 0.0, detector=Pilatus1M())
cls.ai.wavelength = 1e-10
cls.Rmax = 20
cls.delta_pos_azim_max = 0.28
@classmethod
def tearDownClass(cls):
cls.npt = None
cls.img = None
cls.data = None
cls.ai = None
cls.Rmax = None
cls.delta_pos_azim_max = None
def testQ(self):
res = {}
for m in ("numpy", "cython", "BBox", "splitpixel"):
res[m] = self.ai.integrate2d(self.data, self.npt, method=m)
mask = (res["numpy"][0] != 0)
self.assertTrue(mask.sum() > 36 * self.npt, "10%% of the pixels are valid at least")
for a in res:
for b in res:
delta_pos_rad = abs(res[a][1] - res[b][1]).max()
delta_pos_azim = abs(res[a][2] - res[b][2]).max()
R = abs((res[a][0][mask] - res[b][0][mask]) / numpy.maximum(1, res[a][0][mask])).mean() * 100
mesg = "testQ 2D: %s vs %s measured delta rad=%s azim=%s R=%s<%s" % (a, b, delta_pos_rad, delta_pos_azim, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(delta_pos_rad <= 0.01, mesg)
self.assertTrue(delta_pos_azim <= self.delta_pos_azim_max, mesg)
self.assertTrue(R <= self.Rmax, mesg)
def testR(self):
res = {}
for m in ("numpy", "cython", "BBox", "splitpixel"):
res[m] = self.ai.integrate2d(self.data, self.npt, method=m, unit="r_mm")
mask = (res["numpy"][0] != 0)
self.assertTrue(mask.sum() > 36 * self.npt, "10%% of the pixels are valid at least")
for a in res:
for b in res:
delta_pos_rad = abs(res[a][1] - res[b][1]).max()
delta_pos_azim = abs(res[a][2] - res[b][2]).max()
R = abs((res[a][0][mask] - res[b][0][mask]) / numpy.maximum(1, res[a][0][mask])).mean() * 100
mesg = "testR 2D: %s vs %s measured delta rad=%s azim=%s R=%s<%s" % (a, b, delta_pos_rad, delta_pos_azim, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(delta_pos_rad <= 0.28, mesg)
self.assertTrue(delta_pos_azim <= self.delta_pos_azim_max, mesg)
self.assertTrue(R <= self.Rmax, mesg)
def test2th(self):
res = {}
for m in ("numpy", "cython", "BBox", "splitpixel"):
res[m] = self.ai.integrate2d(self.data, self.npt, method=m, unit="2th_deg")
mask = (res["numpy"][0] != 0)
self.assertTrue(mask.sum() > 36 * self.npt, "10%% of the pixels are valid at least")
for a in res:
for b in res:
if a == b:
continue
delta_pos_rad = abs(res[a][1] - res[b][1]).max()
delta_pos_azim = abs(res[a][2] - res[b][2]).max()
R = abs((res[a][0][mask] - res[b][0][mask]) / numpy.maximum(1, res[a][0][mask])).mean() * 100
mesg = "test2th 2D: %s vs %s measured delta rad=%s azim=%s R=%s<%s" % (a, b, delta_pos_rad, delta_pos_azim, R, self.Rmax)
if R > self.Rmax:
logger.error(mesg)
else:
logger.info(mesg)
self.assertTrue(delta_pos_rad <= 0.01, mesg)
self.assertTrue(R <= self.Rmax, mesg)
def test_filename(self):
with resulttempfile() as filename:
self.ai.integrate2d(self.data, self.npt, filename=filename)
self.assertGreater(os.path.getsize(filename), 40)
def test_defaultwriter(self):
with resulttempfile() as filename:
result = self.ai.integrate2d(self.data, self.npt)
writer = DefaultAiWriter(filename, self.ai)
writer.write(result)
writer.close()
self.assertGreater(os.path.getsize(filename), 40)
class TestIntegrateResult(unittest.TestCase):
def setUp(self):
self.I = numpy.array([[1, 2], [3, 4]])
self.radial = numpy.array([[3, 2], [3, 4]])
self.azimuthal = numpy.array([[2, 2], [3, 4]])
self.sigma = numpy.array([[4, 2], [3, 4]])
def tearDown(self):
self.I = self.radial = self.azimuthal = self.sigma = None
def test_result_1d(self):
result = Integrate1dResult(self.radial, self.I)
# as tuple
radial, I = result
numpy.testing.assert_equal((self.I, self.radial), (I, radial))
# as attributes
numpy.testing.assert_array_equal(self.I, result.intensity)
numpy.testing.assert_array_equal(self.radial, result.radial)
self.assertIsNone(result.sigma)
def test_result_2d(self):
result = Integrate2dResult(self.I, self.radial, self.azimuthal)
# as tuple
I, radial, azimuthal = result
numpy.testing.assert_equal((self.I, self.radial, self.azimuthal), (I, radial, azimuthal))
# as attributes
numpy.testing.assert_array_equal(self.I, result.intensity)
numpy.testing.assert_array_equal(self.radial, result.radial)
numpy.testing.assert_array_equal(self.azimuthal, result.azimuthal)
self.assertIsNone(result.sigma)
def test_result_1d_with_sigma(self):
result = Integrate1dResult(self.radial, self.I, self.sigma)
# as tuple
radial, I, sigma = result
numpy.testing.assert_equal((self.radial, self.I, self.sigma), (radial, I, sigma))
# as attributes
numpy.testing.assert_array_equal(self.I, result.intensity)
numpy.testing.assert_array_equal(self.radial, result.radial)
numpy.testing.assert_array_equal(self.sigma, result.sigma)
def test_result_2d_with_sigma(self):
result = Integrate2dResult(self.I, self.radial, self.azimuthal, self.sigma)
# as tuple
I, radial, azimuthal, sigma = result
numpy.testing.assert_equal((self.I, self.radial, self.azimuthal, self.sigma), (I, radial, azimuthal, sigma))
# as attributes
numpy.testing.assert_array_equal(self.I, result.intensity)
numpy.testing.assert_array_equal(self.radial, result.radial)
numpy.testing.assert_array_equal(self.azimuthal, result.azimuthal)
numpy.testing.assert_array_equal(self.sigma, result.sigma)
def test_result_1d_unit(self):
result = Integrate1dResult(self.radial, self.I, self.sigma)
result._set_unit("foobar")
numpy.testing.assert_array_equal("foobar", result.unit)
def test_result_1d_count(self):
result = Integrate1dResult(self.radial, self.I, self.sigma)
result._set_count(self.sigma)
numpy.testing.assert_array_equal(self.sigma, result.count)
def test_result_2d_sum(self):
result = Integrate2dResult(self.I, self.radial, self.azimuthal, self.sigma)
result._set_sum(self.sigma)
numpy.testing.assert_array_equal(self.sigma, result.sum)
def suite():
testsuite = unittest.TestSuite()
loader = unittest.defaultTestLoader.loadTestsFromTestCase
testsuite.addTest(loader(TestIntegrate1D))
testsuite.addTest(loader(TestIntegrate2D))
testsuite.addTest(loader(TestIntegrateResult))
return testsuite
if __name__ == '__main__':
runner = unittest.TextTestRunner()
runner.run(suite())
|
