File: test_quantity_array_methods.py

package info (click to toggle)
python-astropy 1.3-8~bpo8%2B2
  • links: PTS, VCS
  • area: main
  • in suites: jessie-backports
  • size: 44,292 kB
  • sloc: ansic: 160,360; python: 137,322; sh: 11,493; lex: 7,638; yacc: 4,956; xml: 1,796; makefile: 474; cpp: 364
file content (552 lines) | stat: -rw-r--r-- 18,487 bytes parent folder | download | duplicates (2)
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
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
# The purpose of these tests are to ensure that calling quantities using
# array methods returns quantities with the right units, or raises exceptions.

import numpy as np

from ... import units as u
from ...tests.helper import pytest
from ...utils.compat import (NUMPY_LT_1_8, NUMPY_LT_1_9_1,
                             NUMPY_LT_1_10, NUMPY_LT_1_10_4)


class TestQuantityArrayCopy(object):
    """
    Test whether arrays are properly copied/used in place
    """

    def test_copy_on_creation(self):
        v = np.arange(1000.)
        q_nocopy = u.Quantity(v, "km/s", copy=False)
        q_copy = u.Quantity(v, "km/s", copy=True)
        v[0] = -1.
        assert q_nocopy[0].value == v[0]
        assert q_copy[0].value != v[0]

    def test_to_copies(self):
        q = u.Quantity(np.arange(1.,100.), "km/s")
        q2 = q.to(u.m/u.s)
        assert np.all(q.value != q2.value)
        q3 = q.to(u.km/u.s)
        assert np.all(q.value == q3.value)
        q[0] = -1.*u.km/u.s
        assert q[0].value != q3[0].value

    def test_si_copies(self):
        q = u.Quantity(np.arange(100.), "m/s")
        q2 = q.si
        assert np.all(q.value == q2.value)
        q[0] = -1.*u.m/u.s
        assert q[0].value != q2[0].value

    def test_getitem_is_view(self):
        """Check that [keys] work, and that, like ndarray, it returns
        a view, so that changing one changes the other.

        Also test that one can add axes (closes #1422)
        """
        q = u.Quantity(np.arange(100.), "m/s")
        q_sel = q[10:20]
        q_sel[0] = -1.*u.m/u.s
        assert q_sel[0] == q[10]
        # also check that getitem can do new axes
        q2 = q[:, np.newaxis]
        q2[10,0] = -9*u.m/u.s
        assert np.all(q2.flatten() == q)

    def test_flat(self):
        q = u.Quantity(np.arange(9.).reshape(3, 3), "m/s")
        q_flat = q.flat
        # check that a single item is a quantity (with the right value)
        assert q_flat[8] == 8. * u.m / u.s
        # and that getting a range works as well
        assert np.all(q_flat[0:2] == np.arange(2.) * u.m / u.s)
        # as well as getting items via iteration
        q_flat_list = [_q for _q in q.flat]
        assert np.all(u.Quantity(q_flat_list) ==
                      u.Quantity([_a for _a in q.value.flat], q.unit))
        # check that flat works like a view of the real array
        q_flat[8] = -1. * u.km / u.s
        assert q_flat[8] == -1. * u.km / u.s
        assert q[2,2] == -1. * u.km / u.s
        # while if one goes by an iterated item, a copy is made
        q_flat_list[8] = -2 * u.km / u.s
        assert q_flat_list[8] == -2. * u.km / u.s
        assert q_flat[8] == -1. * u.km / u.s
        assert q[2,2] == -1. * u.km / u.s


class TestQuantityReshapeFuncs(object):
    """Test different ndarray methods that alter the array shape

    tests: reshape, squeeze, ravel, flatten, transpose, swapaxes
    """
    def test_reshape(self):
        q = np.arange(6.) * u.m
        q_reshape = q.reshape(3, 2)
        assert isinstance(q_reshape, u.Quantity)
        assert q_reshape.unit == q.unit
        assert np.all(q_reshape.value == q.value.reshape(3, 2))

    def test_squeeze(self):
        q = np.arange(6.).reshape(6, 1) * u.m
        q_squeeze = q.squeeze()
        assert isinstance(q_squeeze, u.Quantity)
        assert q_squeeze.unit == q.unit
        assert np.all(q_squeeze.value == q.value.squeeze())

    def test_ravel(self):
        q = np.arange(6.).reshape(3, 2) * u.m
        q_ravel = q.ravel()
        assert isinstance(q_ravel, u.Quantity)
        assert q_ravel.unit == q.unit
        assert np.all(q_ravel.value == q.value.ravel())

    def test_flatten(self):
        q = np.arange(6.).reshape(3, 2) * u.m
        q_flatten = q.flatten()
        assert isinstance(q_flatten, u.Quantity)
        assert q_flatten.unit == q.unit
        assert np.all(q_flatten.value == q.value.flatten())

    def test_transpose(self):
        q = np.arange(6.).reshape(3, 2) * u.m
        q_transpose = q.transpose()
        assert isinstance(q_transpose, u.Quantity)
        assert q_transpose.unit == q.unit
        assert np.all(q_transpose.value == q.value.transpose())

    def test_swapaxes(self):
        q = np.arange(6.).reshape(3, 1, 2) * u.m
        q_swapaxes = q.swapaxes(0, 2)
        assert isinstance(q_swapaxes, u.Quantity)
        assert q_swapaxes.unit == q.unit
        assert np.all(q_swapaxes.value == q.value.swapaxes(0, 2))


class TestQuantityStatsFuncs(object):
    """
    Test statistical functions
    """

    def test_mean(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        assert np.mean(q1) == 3.6 * u.m

    def test_mean_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        qi = 1.5 * u.s
        qi2 = np.mean(q1, out=qi)
        assert qi2 is qi
        assert qi == 3.6 * u.m

    def test_std(self):
        q1 = np.array([1., 2.]) * u.m
        assert np.std(q1) == 0.5 * u.m

    # For 1.7 <= Numpy < 1.9.1, inplace causes the variance to be stored instead
    # of the standard deviation; https://github.com/numpy/numpy/issues/5240
    @pytest.mark.xfail(NUMPY_LT_1_9_1, reason="Numpy 1.9.1 or later is required")
    def test_std_inplace(self):
        q1 = np.array([1., 2.]) * u.m
        qi = 1.5 * u.s
        np.std(q1, out=qi)
        assert qi == 0.5 * u.m

    def test_var(self):
        q1 = np.array([1., 2.]) * u.m
        assert np.var(q1) == 0.25 * u.m ** 2

    def test_var_inplace(self):
        q1 = np.array([1., 2.]) * u.m
        qi = 1.5 * u.s
        np.var(q1, out=qi)
        assert qi == 0.25 * u.m ** 2

    def test_median(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        assert np.median(q1) == 4. * u.m

    def test_median_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        qi = 1.5 * u.s
        np.median(q1, out=qi)
        assert qi == 4 * u.m

    def test_min(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        assert np.min(q1) == 1. * u.m

    def test_min_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        qi = 1.5 * u.s
        np.min(q1, out=qi)
        assert qi == 1. * u.m

    def test_argmin(self):
        q1 = np.array([6., 2., 4., 5., 6.]) * u.m
        assert np.argmin(q1) == 1

    def test_max(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        assert np.max(q1) == 6. * u.m

    def test_max_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        qi = 1.5 * u.s
        np.max(q1, out=qi)
        assert qi == 6. * u.m

    def test_argmax(self):
        q1 = np.array([5., 2., 4., 5., 6.]) * u.m
        assert np.argmax(q1) == 4

    def test_clip(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.km / u.m
        c1 = q1.clip(1500, 5.5 * u.Mm / u.km)
        assert np.all(c1 == np.array([1.5, 2., 4., 5., 5.5]) * u.km / u.m)

    def test_clip_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.km / u.m
        c1 = q1.clip(1500, 5.5 * u.Mm / u.km, out=q1)
        assert np.all(q1 == np.array([1.5, 2., 4., 5., 5.5]) * u.km / u.m)
        c1[0] = 10 * u.Mm/u.mm
        assert np.all(c1.value == q1.value)

    def test_conj(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.km / u.m
        assert np.all(q1.conj() == q1)

    def test_ptp(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        assert np.ptp(q1) == 5. * u.m

    def test_ptp_inplace(self):
        q1 = np.array([1., 2., 4., 5., 6.]) * u.m
        qi = 1.5 * u.s
        np.ptp(q1, out=qi)
        assert qi == 5. * u.m

    def test_round(self):
        q1 = np.array([1.253, 2.253, 3.253]) * u.kg
        assert np.all(np.round(q1) == np.array([1, 2, 3]) * u.kg)
        assert np.all(np.round(q1, decimals=2) ==
                      np.round(q1.value, decimals=2) * u.kg)
        assert np.all(q1.round(decimals=2) ==
                      q1.value.round(decimals=2) * u.kg)

    def test_round_inplace(self):
        q1 = np.array([1.253, 2.253, 3.253]) * u.kg
        qi = np.zeros(3) * u.s
        a = q1.round(decimals=2, out=qi)
        assert a is qi
        assert np.all(q1.round(decimals=2) == qi)

    def test_sum(self):

        q1 = np.array([1., 2., 6.]) * u.m
        assert np.all(q1.sum() == 9. * u.m)
        assert np.all(np.sum(q1) == 9. * u.m)

        q2 = np.array([[4., 5., 9.], [1., 1., 1.]]) * u.s
        assert np.all(q2.sum(0) == np.array([5., 6., 10.]) * u.s)
        assert np.all(np.sum(q2, 0) == np.array([5., 6., 10.]) * u.s)

    def test_sum_inplace(self):
        q1 = np.array([1., 2., 6.]) * u.m
        qi = 1.5 * u.s
        np.sum(q1, out=qi)
        assert qi == 9. * u.m

    def test_cumsum(self):

        q1 = np.array([1, 2, 6]) * u.m
        assert np.all(q1.cumsum() == np.array([1, 3, 9]) * u.m)
        assert np.all(np.cumsum(q1) == np.array([1, 3, 9]) * u.m)

        q2 = np.array([4, 5, 9]) * u.s
        assert np.all(q2.cumsum() == np.array([4, 9, 18]) * u.s)
        assert np.all(np.cumsum(q2) == np.array([4, 9, 18]) * u.s)

    def test_cumsum_inplace(self):
        q1 = np.array([1, 2, 6]) * u.m
        qi = np.ones(3) * u.s
        np.cumsum(q1, out=qi)
        assert np.all(qi == np.array([1, 3, 9]) * u.m)
        q2 = q1
        q1.cumsum(out=q1)
        assert np.all(q2 == qi)

    def test_nansum(self):

        q1 = np.array([1., 2., np.nan]) * u.m
        assert np.all(q1.nansum() == 3. * u.m)
        assert np.all(np.nansum(q1) == 3. * u.m)

        q2 = np.array([[np.nan, 5., 9.], [1., np.nan, 1.]]) * u.s
        assert np.all(q2.nansum(0) == np.array([1., 5., 10.]) * u.s)
        assert np.all(np.nansum(q2, 0) == np.array([1., 5., 10.]) * u.s)

    @pytest.mark.xfail(NUMPY_LT_1_8, reason="Numpy 1.8 or later is required")
    def test_nansum_inplace(self):

        q1 = np.array([1., 2., np.nan]) * u.m
        qi = 1.5 * u.s
        qout = q1.nansum(out=qi)
        assert qout is qi
        assert qi == np.nansum(q1.value) * q1.unit

        qi2 = 1.5 * u.s
        qout2 = np.nansum(q1, out=qi2)
        assert qout2 is qi2
        assert qi2 == np.nansum(q1.value) * q1.unit

    def test_prod(self):

        q1 = np.array([1, 2, 6]) * u.m
        with pytest.raises(ValueError) as exc:
            q1.prod()
        assert 'cannot use prod' in exc.value.args[0]

        with pytest.raises(ValueError) as exc:
            np.prod(q1)
        assert 'cannot use prod' in exc.value.args[0]

        q2 = np.array([3., 4., 5.]) * u.Unit(1)
        assert q2.prod() == 60. * u.Unit(1)
        assert np.prod(q2) == 60. * u.Unit(1)

    def test_cumprod(self):

        q1 = np.array([1, 2, 6]) * u.m
        with pytest.raises(ValueError) as exc:
            q1.cumprod()
        assert 'cannot use cumprod' in exc.value.args[0]

        with pytest.raises(ValueError) as exc:
            np.cumprod(q1)
        assert 'cannot use cumprod' in exc.value.args[0]

        q2 = np.array([3, 4, 5]) * u.Unit(1)
        assert np.all(q2.cumprod() == np.array([3, 12, 60]) * u.Unit(1))
        assert np.all(np.cumprod(q2) == np.array([3, 12, 60]) * u.Unit(1))

    def test_diff(self):

        q1 = np.array([1., 2., 4., 10.]) * u.m
        assert np.all(q1.diff() == np.array([1., 2., 6.]) * u.m)
        assert np.all(np.diff(q1) == np.array([1., 2., 6.]) * u.m)

    def test_ediff1d(self):

        q1 = np.array([1., 2., 4., 10.]) * u.m
        assert np.all(q1.ediff1d() == np.array([1., 2., 6.]) * u.m)
        assert np.all(np.ediff1d(q1) == np.array([1., 2., 6.]) * u.m)

    @pytest.mark.xfail
    def test_dot_func(self):

        q1 = np.array([1., 2., 4., 10.]) * u.m
        q2 = np.array([3., 4., 5., 6.]) * u.s
        q3 = np.dot(q1, q2)
        assert q3.value == np.dot(q1.value, q2.value)
        assert q3.unit == u.m * u.s

    def test_dot_meth(self):

        q1 = np.array([1., 2., 4., 10.]) * u.m
        q2 = np.array([3., 4., 5., 6.]) * u.s
        q3 = q1.dot(q2)
        assert q3.value == np.dot(q1.value, q2.value)
        assert q3.unit == u.m * u.s

    @pytest.mark.xfail(NUMPY_LT_1_10_4,
                       reason="Numpy 1.10.4 or later is required")
    def test_trace_func(self):

        q = np.array([[1.,2.],[3.,4.]]) * u.m
        assert np.trace(q) == 5. * u.m

    def test_trace_meth(self):

        q1 = np.array([[1.,2.],[3.,4.]]) * u.m
        assert q1.trace() == 5. * u.m

        cont = u.Quantity(4., u.s)

        q2 = np.array([[3.,4.],[5.,6.]]) * u.m
        q2.trace(out=cont)
        assert cont == 9. * u.m

    def test_clip_func(self):

        q = np.arange(10) * u.m
        assert np.all(np.clip(q, 3 * u.m, 6 * u.m) == np.array([3., 3.,3.,3.,4.,5.,6.,6.,6.,6.]) * u.m)

    def test_clip_meth(self):

        expected = np.array([3.,3.,3.,3.,4.,5.,6.,6.,6.,6.]) * u.m

        q1 = np.arange(10) * u.m
        q3 = q1.clip(3 * u.m, 6 * u.m)
        assert np.all(q1.clip(3 * u.m, 6 * u.m) == expected)

        cont = np.zeros(10) * u.s

        q1.clip(3 * u.m, 6 * u.m, out=cont)

        assert np.all(cont == expected)


class TestArrayConversion(object):
    """
    Test array conversion methods
    """

    def test_item(self):
        q1 = u.Quantity(np.array([1, 2, 3]), u.m / u.km, dtype=int)
        assert q1.item(1) == 2 * q1.unit
        q1.itemset(1, 1)
        assert q1.item(1) == 1000 * u.m / u.km
        q1.itemset(1, 100 * u.cm / u.km)
        assert q1.item(1) == 1 * u.m / u.km
        with pytest.raises(TypeError):
            q1.itemset(1, 1.5 * u.m / u.km)
        with pytest.raises(ValueError):
            q1.itemset()

        q1[1] = 1
        assert q1[1] == 1000 * u.m / u.km
        q1[1] = 100 * u.cm / u.km
        assert q1[1] == 1 * u.m / u.km
        with pytest.raises(TypeError):
            q1[1] = 1.5 * u.m / u.km

        q1 = np.array([1, 2, 3]) * u.m / u.km
        assert all(q1.take((0, 2)) == np.array([1, 3]) * u.m / u.km)
        q1.put((1, 2), (3, 4))
        assert np.all(q1.take((1, 2)) == np.array([3000, 4000]) * q1.unit)
        q1.put(0, 500 * u.cm / u.km)
        assert q1.item(0) == 5 * u.m / u.km

    def test_slice(self):
        """Test that setitem changes the unit if needed (or ignores it for
        values where that is allowed; viz., #2695)"""
        q2 = np.array([[1., 2., 3.], [4., 5., 6.]]) * u.km / u.m
        q1 = q2.copy()
        q2[0, 0] = 10000.
        assert q2.unit == q1.unit
        assert q2[0, 0].value == 10.
        q2[0] = 9. * u.Mm / u.km
        assert all(q2.flatten()[:3].value == np.array([9., 9., 9.]))
        q2[0, :-1] = 8000.
        assert all(q2.flatten()[:3].value == np.array([8., 8., 9.]))
        with pytest.raises(u.UnitsError):
            q2[1, 1] = 10 * u.s
        # just to be sure, repeat with a dimensionfull unit
        q3 = u.Quantity(np.arange(10.), "m/s")
        q3[5] = 100. * u.cm / u.s
        assert q3[5].value == 1.
        # and check unit is ignored for 0, inf, nan, where that is reasonable
        q3[5] = 0.
        assert q3[5] == 0.
        q3[5] = np.inf
        assert np.isinf(q3[5])
        q3[5] = np.nan
        assert np.isnan(q3[5])

    def test_fill(self):
        q1 = np.array([1, 2, 3]) * u.m / u.km
        q1.fill(2)
        assert np.all(q1 == 2000 * u.m / u.km)

    def test_repeat_compress_diagonal(self):
        q1 = np.array([1, 2, 3]) * u.m / u.km
        q2 = q1.repeat(2)
        assert q2.unit == q1.unit
        assert all(q2.value == q1.value.repeat(2))
        q2.sort()
        assert q2.unit == q1.unit
        q2 = q1.compress(np.array([True, True, False, False]))
        assert q2.unit == q1.unit
        assert all(q2.value == q1.value.compress(np.array([True, True,
                                                           False, False])))
        q1 = np.array([[1, 2], [3, 4]]) * u.m / u.km
        q2 = q1.diagonal()
        assert q2.unit == q1.unit
        assert all(q2.value == q1.value.diagonal())

    def test_view(self):
        q1 = np.array([1, 2, 3], dtype=np.int64) * u.m / u.km
        q2 = q1.view(np.ndarray)
        assert not hasattr(q2, 'unit')
        q3 = q2.view(u.Quantity)
        assert q3._unit is None
        # MaskedArray copies and properties assigned in __dict__
        q4 = np.ma.MaskedArray(q1)
        assert q4._unit is q1._unit
        q5 = q4.view(u.Quantity)
        assert q5.unit is q1.unit

    def test_slice_to_quantity(self):
        """
        Regression test for https://github.com/astropy/astropy/issues/2003
        """

        a = np.random.uniform(size=(10, 8))
        x, y, z = a[:,1:4].T * u.km/u.s
        total = np.sum(a[:, 1] * u.km / u.s - x)

        assert isinstance(total, u.Quantity)
        assert total == (0.0 * u.km / u.s)

    def test_byte_type_view_field_changes(self):
        q1 = np.array([1, 2, 3], dtype=np.int64) * u.m / u.km
        q2 = q1.byteswap()
        assert q2.unit == q1.unit
        assert all(q2.value == q1.value.byteswap())
        q2 = q1.astype(np.float64)
        assert all(q2 == q1)
        assert q2.dtype == np.float64
        q2a = q1.getfield(np.int32, offset=0)
        q2b = q1.byteswap().getfield(np.int32, offset=4)
        assert q2a.unit == q1.unit
        assert all(q2b.byteswap() == q2a)

    def test_sort(self):
        q1 = np.array([1., 5., 2., 4.]) * u.km / u.m
        i = q1.argsort()
        assert not hasattr(i, 'unit')
        q1.sort()
        i = q1.searchsorted([1500, 2500])
        assert not hasattr(i, 'unit')
        assert all(i == q1.to(
            u.dimensionless_unscaled).value.searchsorted([1500, 2500]))

    def test_not_implemented(self):
        q1 = np.array([1, 2, 3]) * u.m / u.km

        with pytest.raises(NotImplementedError):
            q1.choose([0, 0, 1])

        with pytest.raises(NotImplementedError):
            q1.tolist()
        with pytest.raises(NotImplementedError):
            q1.tostring()
        with pytest.raises(NotImplementedError):
            q1.tofile(0)
        with pytest.raises(NotImplementedError):
            q1.dump('a.a')
        with pytest.raises(NotImplementedError):
            q1.dumps()


class TestRecArray(object):
    """Record arrays are not specifically supported, but we should not
    prevent their use unnecessarily"""
    def test_creation(self):
        ra = (np.array(np.arange(12.).reshape(4,3))
              .view(dtype=('f8,f8,f8')).squeeze())
        qra = u.Quantity(ra, u.m)
        assert np.all(qra[:2].value == ra[:2])
        qra[1] = qra[2]
        assert qra[1] == qra[2]