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
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
|
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2019-2022 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF.
#
# 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.
#
#############################################################################*/
__author__ = "Wout De Nolf"
__contact__ = "wout.de_nolf@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import unittest
import tempfile
import shutil
import os
import sys
import numpy
import itertools
from contextlib import contextmanager
try:
from PyMca5.PyMcaCore import McaStackView
except ImportError:
McaStackView = None
try:
import h5py
except ImportError:
h5py = None
class testMcaStackView(unittest.TestCase):
def setUp(self):
self.path = tempfile.mkdtemp(prefix='pymca')
def tearDown(self):
shutil.rmtree(self.path)
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
def testViewUtils(self):
n = 20
slices = [slice(None), slice(1, -2),
slice(8, 2, -1), slice(0, n, 3),
slice(0, n, -2), slice(n-2, 2, -3),
slice(n-1, None, -1), slice(None, -2, 3)]
lst = list(range(n))
for idx in slices:
idxn = McaStackView.sliceNormalize(idx, n)
self.assertEqual(lst[idx], lst[idxn])
for idx in slices:
self.assertEqual(McaStackView.sliceLen(idx, n), len(lst[idx]))
for idx in slices:
idxi = McaStackView.sliceReverse(idx, n)
self.assertEqual(lst[idx][::-1], lst[idxi])
for idx in slices:
idxc = McaStackView.sliceComplement(idx, n)
self.assertEqual(list(sorted(lst[idx]+idxc)), lst)
for idx in slices:
start, stop, step = idx.indices(n)
lst1 = list(range(start, stop, int(numpy.sign(step))))
it = McaStackView.chunkIndexGen(start, stop, step)
self.assertEqual(len(lst1), sum(ns for it, ns in it))
it = McaStackView.chunkIndexGen(start, stop, step)
lst2 = [i for idxc, ns in it for i in lst[idxc]]
self.assertEqual(lst1, lst2)
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
def testfullChunkIndex(self):
for ndim in [2, 3, 4]:
shape = tuple(range(3, 3+ndim))
data = numpy.zeros(shape, dtype=int)
for chunkAxes, axesOrder, nChunksTot in self._chunkIndexAxes(shape, ndim):
for nChunksMax in range(nChunksTot+2):
data[()] = 0
result = McaStackView.fullChunkIndex(shape, nChunksMax,
chunkAxes=chunkAxes,
axesOrder=axesOrder)
chunkIndex, chunkAxes, axesOrder, nChunksMax2 = result
self.assertTrue(nChunksMax2 <= max(nChunksMax, 1))
for i, (idxChunk, idxShape, nChunks) in enumerate(chunkIndex, 1):
data[idxChunk] += i
self.assertEqual(data[idxChunk].shape, idxShape)
self.assertTrue(nChunks <= nChunksMax2)
# Verify data coverage:
self.assertFalse((data == 0).any())
# Verify single element access and chunk access order:
arr = data.transpose(axesOrder[::-1]+chunkAxes).flatten()
lst1 = [k for k, g in itertools.groupby(arr)]
lst2 = list(range(1, i+1))
self.assertEqual(lst1, lst2)
def _chunkIndexAxes(self, shape, ndim):
axes = set(range(ndim))
for ndimChunk in range(ndim+1):
nOther = ndim-ndimChunk
for chunkAxes in itertools.permutations(axes, ndimChunk):
nChunksTot = numpy.prod([shape[i] for i in axes])
yield chunkAxes, None, nChunksTot
other = axes-set(chunkAxes)
if other:
nChunksTot = numpy.prod([shape[i] for i in other])
else:
nChunksTot = 1
for axesOrder in itertools.permutations(other, nOther):
yield chunkAxes, axesOrder, nChunksTot
def assert_array_equal(self, *var):
if sys.maxsize > 2**32:
# 64-bit interpreter
return numpy.testing.assert_array_equal(*var)
else:
# 32-bit interpreter
return numpy.testing.assert_allclose(*var)
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
def testMaskedChunkIndex(self):
for ndim in [2, 3, 4]:
shape = tuple(range(3, 3+ndim))
data = numpy.zeros(shape, dtype=int)
for chunkAxes, axesOrder, nChunksTot in self._chunkIndexAxes(shape, ndim):
# Create Mask
mask, indices, nmask = self._randomMask(shape, chunkAxes, axesOrder)
# Mask entire array
maskFull = numpy.zeros(shape, dtype=bool)
if mask is None:
maskFull[()] = False
nmask = 0
else:
indicesFull = [slice(None)]*ndim
if axesOrder:
for i, ind in zip(axesOrder, indices):
indicesFull[i] = ind
elif chunkAxes:
tmp = tuple(i for i in range(ndim)
if i not in chunkAxes)
for i, ind in zip(tmp, indices):
indicesFull[i] = ind
else:
indicesFull = indices
indicesFull = tuple(indicesFull)
maskFull[indicesFull] = True
for nChunksMax in [2, nmask//3, nmask-1, nmask+1]:
for usedmask in [mask, None]:
data[()] = 0
self.assertFalse((data != 0).any())
chunkIndex, chunkAxes2, axesOrder, nChunksMax2 =\
McaStackView.maskedChunkIndex(shape, nChunksMax,
mask=usedmask,
chunkAxes=chunkAxes,
axesOrder=axesOrder)
for i, (idxChunk, idxShape, nChunks) in enumerate(chunkIndex, 1):
data[idxChunk] += i
self.assertEqual(data[idxChunk].shape, idxShape)
self.assertTrue(nChunks <= nChunksMax2)
# Verify data coverage:
if usedmask is None:
self.assertFalse((data == 0).any())
else:
self.assertFalse((data[maskFull] == 0).any())
self.assertTrue((data[~maskFull] == 0).all())
# Verify single element access:
lst1 = numpy.unique(data).tolist()
lst2 = list(range(int(usedmask is None), i+1))
self.assertEqual(lst1, lst2)
def _randomMask(self, shape, chunkAxes, axesOrder):
if axesOrder:
mshape = tuple(shape[i] for i in axesOrder)
elif chunkAxes:
mshape = tuple(shape[i] for i in range(len(shape))
if i not in chunkAxes)
else:
mshape = shape
if mshape:
mask = numpy.zeros(mshape, dtype=bool)
indices = numpy.arange(mask.size)
numpy.random.shuffle(indices)
indices = indices[:mask.size//2]
nmask = indices.size
indices = numpy.unravel_index(indices, mshape)
mask[indices] = True
else:
mask = None
indices = None
nmask = 0
return mask, indices, nmask
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
def testFullViewNumpy(self):
for ndim in [2, 3, 4]:
shape = range(6, 6+ndim)
data = numpy.random.uniform(size=shape)
self._assertFullView(data)
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
@unittest.skipIf(h5py is None,
'h5py cannot be imported')
def testFullViewH5py(self):
for ndim in [2, 3]:
shape = range(6, 6+ndim)
data = numpy.random.uniform(size=shape)
with self.h5Open('testFullView') as f:
name = 'data{}'.format(ndim)
f.create_dataset(name, data=data, chunks=(1,)*ndim)
self._assertFullView(f[name])
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
def testMaskedViewNumpy(self):
for ndim in [2, 3, 4]:
shape = range(6, 6+ndim)
data = numpy.random.uniform(size=shape)
self._assertMaskedView(data)
@unittest.skipIf(McaStackView is None,
'PyMca5.PyMcaCore.McaStackView cannot be imported')
@unittest.skipIf(h5py is None,
'h5py cannot be imported')
def testMaskedViewH5py(self):
for ndim in [2, 3]:
shape = range(6, 6+ndim)
data = numpy.random.uniform(size=shape)
with self.h5Open('testMaskedView') as f:
name = 'data{}'.format(ndim)
f.create_dataset(name, data=data, chunks=(1,)*ndim)
self._assertMaskedView(f[name])
def _assertFullView(self, data):
mcaSlice = slice(2, -1)
for nMca in range(numpy.prod(data.shape[1:])+2):
for mcaAxis in range(data.ndim):
dataView = McaStackView.FullView(data,
readonly=False,
mcaAxis=mcaAxis,
mcaSlice=mcaSlice,
nMca=nMca)
npAdd = numpy.arange(data.size).reshape(data.shape)
addView = McaStackView.FullView(npAdd,
readonly=True,
mcaAxis=mcaAxis,
mcaSlice=mcaSlice,
nMca=nMca)
idxFull = dataView.idxFull
for readonly in [True, False]:
dataView.readonly = readonly
dataOrg = numpy.copy(data)
iters = dataView.items(), addView.items()
chunks = McaStackView.izipChunkItems(*iters)
for (key, chunk), (addKey, add) in chunks:
chunk += add
for idxFullComplement in dataView.idxFullComplement:
numpy.testing.assert_allclose(data[idxFullComplement],
dataOrg[idxFullComplement])
if readonly:
numpy.testing.assert_allclose(data[idxFull],
dataOrg[idxFull])
else:
numpy.testing.assert_allclose(data[idxFull],
dataOrg[idxFull]+npAdd[idxFull])
def _assertMaskedView(self, data):
mcaSlice = slice(2, -1)
isH5py = isinstance(data, h5py.Dataset)
for mcaAxis in range(data.ndim):
mask, indices, nmask = self._randomMask(data.shape, (mcaAxis,), None)
it = itertools.product([2, nmask//3, nmask-1, nmask+1], [mask, None])
for nMca, usedmask in it:
dataView = McaStackView.MaskedView(data,
mask=usedmask,
readonly=False,
mcaAxis=mcaAxis,
mcaSlice=mcaSlice,
nMca=nMca)
npAdd = numpy.arange(data.size).reshape(data.shape)
addView = McaStackView.MaskedView(npAdd,
mask=usedmask,
readonly=True,
mcaAxis=mcaAxis,
mcaSlice=mcaSlice,
nMca=nMca)
idxFull = dataView.idxFull
for readonly in [True, False]:
dataView.readonly = readonly
dataOrg = numpy.copy(data)
iters = dataView.items(), addView.items()
chunks = McaStackView.izipChunkItems(*iters)
for (key, chunk), (addKey, add) in chunks:
chunk += add
if isH5py:
_data = data[()]
else:
_data = data
for idxFullComplement in dataView.idxFullComplement:
numpy.testing.assert_allclose(_data[idxFullComplement],
dataOrg[idxFullComplement])
if readonly:
numpy.testing.assert_allclose(_data[idxFull],
dataOrg[idxFull])
else:
numpy.testing.assert_allclose(_data[idxFull],
dataOrg[idxFull]+npAdd[idxFull])
@contextmanager
def h5Open(self, name):
filename = os.path.join(self.path, name+'.h5')
with h5py.File(filename, mode='a') as f:
yield f
def getSuite(auto=True):
testSuite = unittest.TestSuite()
if auto:
testSuite.addTest(
unittest.TestLoader().loadTestsFromTestCase(testMcaStackView))
else:
# use a predefined order
testSuite.addTest(testMcaStackView('testViewUtils'))
testSuite.addTest(testMcaStackView('testfullChunkIndex'))
testSuite.addTest(testMcaStackView('testFullViewNumpy'))
testSuite.addTest(testMcaStackView('testFullViewH5py'))
testSuite.addTest(testMcaStackView('testMaskedChunkIndex'))
testSuite.addTest(testMcaStackView('testMaskedViewNumpy'))
testSuite.addTest(testMcaStackView('testMaskedViewH5py'))
return testSuite
def test(auto=False):
unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto))
if __name__ == '__main__':
test()
|
