File: test_column.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 (549 lines) | stat: -rw-r--r-- 20,637 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
# Licensed under a 3-clause BSD style license - see LICENSE.rst

# TEST_UNICODE_LITERALS

import operator

import numpy as np

from ...tests.helper import pytest, assert_follows_unicode_guidelines
from ... import table
from ... import units as u
from ...extern import six
from ...utils.compat import NUMPY_LT_1_8


class TestColumn():

    def test_subclass(self, Column):
        c = Column(name='a')
        assert isinstance(c, np.ndarray)
        c2 = c * 2
        assert isinstance(c2, Column)
        assert isinstance(c2, np.ndarray)

    def test_numpy_ops(self, Column):
        """Show that basic numpy operations with Column behave sensibly"""

        arr = np.array([1, 2, 3])
        c = Column(arr, name='a')

        for op, test_equal in ((operator.eq, True),
                               (operator.ne, False),
                               (operator.ge, True),
                               (operator.gt, False),
                               (operator.le, True),
                               (operator.lt, False)):
            for eq in (op(c, arr), op(arr, c)):

                assert np.all(eq) if test_equal else not np.any(eq)
                assert len(eq) == 3
                if Column is table.Column:
                    assert type(eq) == np.ndarray
                else:
                    assert type(eq) == np.ma.core.MaskedArray
                assert eq.dtype.str == '|b1'

        lt = c - 1 < arr
        assert np.all(lt)

    def test_numpy_boolean_ufuncs(self, Column):
        """Show that basic numpy operations with Column behave sensibly"""

        arr = np.array([1, 2, 3])
        c = Column(arr, name='a')

        for ufunc, test_true in ((np.isfinite, True),
                                 (np.isinf, False),
                                 (np.isnan, False),
                                 (np.sign, True),
                                 (np.signbit, False)):
            result = ufunc(c)
            assert len(result) == len(c)
            assert np.all(result) if test_true else not np.any(result)
            if Column is table.Column:
                assert type(result) == np.ndarray
            else:
                assert type(result) == np.ma.core.MaskedArray
                if ufunc is not np.sign:
                    assert result.dtype.str == '|b1'

    def test_view(self, Column):
        c = np.array([1, 2, 3], dtype=np.int64).view(Column)
        assert repr(c) == "<{0} dtype='int64' length=3>\n1\n2\n3".format(Column.__name__)

    def test_format(self, Column):
        """Show that the formatted output from str() works"""
        from ... import conf
        with conf.set_temp('max_lines', 8):
            c1 = Column(np.arange(2000), name='a', dtype=float,
                        format='%6.2f')
            assert str(c1).splitlines() == ['   a   ',
                                            '-------',
                                            '   0.00',
                                            '   1.00',
                                            '    ...',
                                            '1998.00',
                                            '1999.00',
                                            'Length = 2000 rows']

    def test_convert_numpy_array(self, Column):
        d = Column([1, 2, 3], name='a', dtype='i8')

        np_data = np.array(d)
        assert np.all(np_data == d)
        np_data = np.array(d, copy=False)
        assert np.all(np_data == d)
        np_data = np.array(d, dtype='i4')
        assert np.all(np_data == d)

    def test_convert_unit(self, Column):
        d = Column([1, 2, 3], name='a', dtype="f8", unit="m")
        d.convert_unit_to("km")
        assert np.all(d.data == [0.001, 0.002, 0.003])

    def test_array_wrap(self):
        """Test that the __array_wrap__ method converts a reduction ufunc
        output that has a different shape into an ndarray view.  Without this a
        method call like c.mean() returns a Column array object with length=1."""
        # Mean and sum for a 1-d float column
        c = table.Column(name='a', data=[1., 2., 3.])
        assert np.allclose(c.mean(), 2.0)
        assert isinstance(c.mean(), (np.floating, float))
        assert np.allclose(c.sum(), 6.)
        assert isinstance(c.sum(), (np.floating, float))

        # Non-reduction ufunc preserves Column class
        assert isinstance(np.cos(c), table.Column)

        # Sum for a 1-d int column
        c = table.Column(name='a', data=[1, 2, 3])
        assert np.allclose(c.sum(), 6)
        assert isinstance(c.sum(), (np.integer, int))

        # Sum for a 2-d int column
        c = table.Column(name='a', data=[[1, 2, 3],
                                         [4, 5, 6]])
        assert c.sum() == 21
        assert isinstance(c.sum(), (np.integer, int))
        assert np.all(c.sum(axis=0) == [5, 7, 9])
        assert c.sum(axis=0).shape == (3,)
        assert isinstance(c.sum(axis=0), np.ndarray)

        # Sum and mean for a 1-d masked column
        c = table.MaskedColumn(name='a', data=[1., 2., 3.], mask=[0, 0, 1])
        assert np.allclose(c.mean(), 1.5)
        assert isinstance(c.mean(), (np.floating, float))
        assert np.allclose(c.sum(), 3.)
        assert isinstance(c.sum(), (np.floating, float))

    def test_name_none(self, Column):
        """Can create a column without supplying name, which defaults to None"""
        c = Column([1, 2])
        assert c.name is None
        assert np.all(c == np.array([1, 2]))

    def test_quantity_init(self, Column):

        c = Column(data=np.array([1, 2, 3]) * u.m)
        assert np.all(c.data == np.array([1, 2, 3]))
        assert np.all(c.unit == u.m)

        c = Column(data=np.array([1, 2, 3]) * u.m, unit=u.cm)
        assert np.all(c.data == np.array([100, 200, 300]))
        assert np.all(c.unit == u.cm)

    def test_attrs_survive_getitem_after_change(self, Column):
        """
        Test for issue #3023: when calling getitem with a MaskedArray subclass
        the original object attributes are not copied.
        """
        c1 = Column([1, 2, 3], name='a', unit='m', format='i',
                    description='aa', meta={'a': 1})
        c1.name = 'b'
        c1.unit = 'km'
        c1.format = 'i2'
        c1.description = 'bb'
        c1.meta = {'bbb': 2}

        for item in (slice(None, None), slice(None, 1), np.array([0, 2]),
                     np.array([False, True, False])):
            c2 = c1[item]
            assert c2.name == 'b'
            assert c2.unit is u.km
            assert c2.format == 'i2'
            assert c2.description == 'bb'
            assert c2.meta == {'bbb': 2}

        # Make sure that calling getitem resulting in a scalar does
        # not copy attributes.
        val = c1[1]
        for attr in ('name', 'unit', 'format', 'description', 'meta'):
            assert not hasattr(val, attr)

    def test_to_quantity(self, Column):
        d = Column([1, 2, 3], name='a', dtype="f8", unit="m")

        assert np.all(d.quantity == ([1, 2, 3.] * u.m))
        assert np.all(d.quantity.value == ([1, 2, 3.] * u.m).value)
        assert np.all(d.quantity == d.to('m'))
        assert np.all(d.quantity.value == d.to('m').value)

        np.testing.assert_allclose(d.to(u.km).value, ([.001, .002, .003] * u.km).value)
        np.testing.assert_allclose(d.to('km').value, ([.001, .002, .003] * u.km).value)

        np.testing.assert_allclose(d.to(u.MHz,u.equivalencies.spectral()).value,
                                   [299.792458, 149.896229,  99.93081933])

        d_nounit = Column([1, 2, 3], name='a', dtype="f8", unit=None)
        with pytest.raises(u.UnitsError):
            d_nounit.to(u.km)
        assert np.all(d_nounit.to(u.dimensionless_unscaled) == np.array([1, 2, 3]))

        #make sure the correct copy/no copy behavior is happening
        q = [1, 3, 5]*u.km

        # to should always make a copy
        d.to(u.km)[:] = q
        np.testing.assert_allclose(d, [1, 2, 3])

        # explcit copying of the quantity should not change the column
        d.quantity.copy()[:] = q
        np.testing.assert_allclose(d, [1, 2, 3])

        # but quantity directly is a "view", accessing the underlying column
        d.quantity[:] = q
        np.testing.assert_allclose(d, [1000, 3000, 5000])

        #view should also work for integers
        d2 = Column([1, 2, 3], name='a', dtype=int, unit="m")
        d2.quantity[:] = q
        np.testing.assert_allclose(d2, [1000, 3000, 5000])

        #but it should fail for strings or other non-numeric tables
        d3 = Column(['arg', 'name', 'stuff'], name='a', unit="m")
        with pytest.raises(TypeError):
            d3.quantity

    def test_item_access_type(self, Column):
        """
        Tests for #3095, which forces integer item access to always return a plain
        ndarray or MaskedArray, even in the case of a multi-dim column.
        """
        integer_types = (int, long, np.int) if six.PY2 else (int, np.int)

        for int_type in integer_types:
            c = Column([[1, 2], [3, 4]])
            i0 = int_type(0)
            i1 = int_type(1)
            assert np.all(c[i0] == [1, 2])
            assert type(c[i0]) == (np.ma.MaskedArray if hasattr(Column, 'mask') else np.ndarray)
            assert c[i0].shape == (2,)

            c01 = c[i0:i1]
            assert np.all(c01 == [[1, 2]])
            assert isinstance(c01, Column)
            assert c01.shape == (1, 2)

            c = Column([1, 2])
            assert np.all(c[i0] == 1)
            assert isinstance(c[i0], np.integer)
            assert c[i0].shape == ()

            c01 = c[i0:i1]
            assert np.all(c01 == [1])
            assert isinstance(c01, Column)
            assert c01.shape == (1,)

    def test_insert_basic(self, Column):
        c = Column([0, 1, 2], name='a', dtype=int, unit='mJy', format='%i',
                   description='test column', meta={'c': 8, 'd': 12})

        # Basic insert
        c1 = c.insert(1, 100)
        assert np.all(c1 == [0, 100, 1, 2])
        assert c1.attrs_equal(c)
        assert type(c) is type(c1)
        if hasattr(c1, 'mask'):
            assert c1.data.shape == c1.mask.shape

        c1 = c.insert(-1, 100)
        assert np.all(c1 == [0, 1, 100, 2])

        c1 = c.insert(3, 100)
        assert np.all(c1 == [0, 1, 2, 100])

        c1 = c.insert(-3, 100)
        assert np.all(c1 == [100, 0, 1, 2])

        c1 = c.insert(1, [100, 200, 300])
        if hasattr(c1, 'mask'):
            assert c1.data.shape == c1.mask.shape

        # Out of bounds index
        with pytest.raises((ValueError, IndexError)):
            c1 = c.insert(-4, 100)
        with pytest.raises((ValueError,IndexError)):
            c1 = c.insert(4, 100)

    def test_insert_multidim(self, Column):
        c = Column([[1, 2],
                    [3, 4]], name='a', dtype=int)

        # Basic insert
        c1 = c.insert(1, [100, 200])
        assert np.all(c1 == [[1, 2], [100, 200], [3, 4]])

        # Broadcast
        c1 = c.insert(1, 100)
        assert np.all(c1 == [[1, 2], [100, 100], [3, 4]])

        # Wrong shape
        with pytest.raises(ValueError):
            c1 = c.insert(1, [100, 200, 300])

    def test_insert_object(self, Column):
        c = Column(['a', 1, None], name='a', dtype=object)

        # Basic insert
        c1 = c.insert(1, [100, 200])
        assert np.all(c1 == ['a', [100, 200], 1, None])

    def test_insert_masked(self):
        c = table.MaskedColumn([0, 1, 2], name='a', mask=[False, True, False])

        # Basic insert
        c1 = c.insert(1, 100)
        assert np.all(c1.data.data == [0, 100, 1, 2])
        assert np.all(c1.data.mask == [False, False, True, False])
        assert type(c) is type(c1)

        for mask in (False, True):
            c1 = c.insert(1, 100, mask=mask)
            assert np.all(c1.data.data == [0, 100, 1, 2])
            assert np.all(c1.data.mask == [False, mask, True, False])

    def test_insert_masked_multidim(self):
        c = table.MaskedColumn([[1, 2],
                                [3, 4]], name='a', dtype=int)

        c1 = c.insert(1, [100, 200], mask=True)
        assert np.all(c1.data.data == [[1, 2], [100, 200], [3, 4]])
        assert np.all(c1.data.mask == [[False, False], [True, True], [False, False]])

        c1 = c.insert(1, [100, 200], mask=[True, False])
        assert np.all(c1.data.data == [[1, 2], [100, 200], [3, 4]])
        assert np.all(c1.data.mask == [[False, False], [True, False], [False, False]])

        with pytest.raises(ValueError):
            c1 = c.insert(1, [100, 200], mask=[True, False, True])

    def test_mask_on_non_masked_table(self):
        """
        When table is not masked and trying to set mask on column then
        it's Raise AttributeError.
        """

        t = table.Table([[1, 2], [3, 4]], names=('a', 'b'), dtype=('i4', 'f8'))

        with pytest.raises(AttributeError):
            t['a'].mask = [True, False]


class TestAttrEqual():
    """Bunch of tests originally from ATpy that test the attrs_equal method."""

    def test_5(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy')
        c2 = Column(name='a', dtype=int, unit='mJy')
        assert c1.attrs_equal(c2)

    def test_6(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        assert c1.attrs_equal(c2)

    def test_7(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='b', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_8(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=float, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_9(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='erg.cm-2.s-1.Hz-1', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_10(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='mJy', format='%g',
                    description='test column', meta={'c': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_11(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='another test column', meta={'c': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_12(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'e': 8, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_13(self, Column):
        c1 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 8, 'd': 12})
        c2 = Column(name='a', dtype=int, unit='mJy', format='%i',
                    description='test column', meta={'c': 9, 'd': 12})
        assert not c1.attrs_equal(c2)

    def test_col_and_masked_col(self):
        c1 = table.Column(name='a', dtype=int, unit='mJy', format='%i',
                          description='test column', meta={'c': 8, 'd': 12})
        c2 = table.MaskedColumn(name='a', dtype=int, unit='mJy', format='%i',
                                description='test column', meta={'c': 8, 'd': 12})
        assert c1.attrs_equal(c2)
        assert c2.attrs_equal(c1)

# Check that the meta descriptor is working as expected. The MetaBaseTest class
# takes care of defining all the tests, and we simply have to define the class
# and any minimal set of args to pass.

from ...utils.tests.test_metadata import MetaBaseTest


class TestMetaColumn(MetaBaseTest):
    test_class = table.Column
    args = ()


class TestMetaMaskedColumn(MetaBaseTest):
    test_class = table.MaskedColumn
    args = ()


def test_getitem_metadata_regression():
    """
    Regression test for #1471: MaskedArray does not call __array_finalize__ so
    the meta-data was not getting copied over. By overloading _update_from we
    are able to work around this bug.
    """

    # Make sure that meta-data gets propagated with __getitem__

    c = table.Column(data=[1,2], name='a', description='b', unit='m', format="%i", meta={'c': 8})
    assert c[1:2].name == 'a'
    assert c[1:2].description == 'b'
    assert c[1:2].unit == 'm'
    assert c[1:2].format == '%i'
    assert c[1:2].meta['c'] == 8

    c = table.MaskedColumn(data=[1,2], name='a', description='b', unit='m', format="%i", meta={'c': 8})
    assert c[1:2].name == 'a'
    assert c[1:2].description == 'b'
    assert c[1:2].unit == 'm'
    assert c[1:2].format == '%i'
    assert c[1:2].meta['c'] == 8

    # As above, but with take() - check the method and the function

    c = table.Column(data=[1,2,3], name='a', description='b', unit='m', format="%i", meta={'c': 8})
    for subset in [c.take([0, 1]), np.take(c, [0, 1])]:
        assert subset.name == 'a'
        assert subset.description == 'b'
        assert subset.unit == 'm'
        assert subset.format == '%i'
        assert subset.meta['c'] == 8

    # Metadata isn't copied for scalar values
    if NUMPY_LT_1_8:
        with pytest.raises(ValueError):
            c.take(0)
        with pytest.raises(ValueError):
            np.take(c, 0)
    else:
        for subset in [c.take(0), np.take(c, 0)]:
            assert subset == 1
            assert subset.shape == ()
            assert not isinstance(subset, table.Column)

    c = table.MaskedColumn(data=[1,2,3], name='a', description='b', unit='m', format="%i", meta={'c': 8})
    for subset in [c.take([0, 1]), np.take(c, [0, 1])]:
        assert subset.name == 'a'
        assert subset.description == 'b'
        assert subset.unit == 'm'
        assert subset.format == '%i'
        assert subset.meta['c'] == 8

    # Metadata isn't copied for scalar values
    if NUMPY_LT_1_8:
        with pytest.raises(ValueError):
            c.take(0)
        with pytest.raises(ValueError):
            np.take(c, 0)
    else:
        for subset in [c.take(0), np.take(c, 0)]:
            assert subset == 1
            assert subset.shape == ()
            assert not isinstance(subset, table.MaskedColumn)


def test_unicode_guidelines():
    arr = np.array([1, 2, 3])
    c = table.Column(arr, name='a')

    assert_follows_unicode_guidelines(c)


def test_scalar_column():
    """
    Column is not designed to hold scalars, but for numpy 1.6 this can happen:

      >> type(np.std(table.Column([1, 2])))
      astropy.table.column.Column
    """
    c = table.Column(1.5)
    assert repr(c) == '1.5'
    assert str(c) == '1.5'


def test_qtable_column_conversion():
    """
    Ensures that a QTable that gets assigned a unit switches to be Quantity-y
    """
    qtab = table.QTable([[1, 2], [3, 4.2]], names=['i', 'f'])

    assert isinstance(qtab['i'], table.column.Column)
    assert isinstance(qtab['f'], table.column.Column)

    qtab['i'].unit = 'km/s'
    assert isinstance(qtab['i'], u.Quantity)
    assert isinstance(qtab['f'], table.column.Column)

    # should follow from the above, but good to make sure as a #4497 regression test
    assert isinstance(qtab['i'][0], u.Quantity)
    assert isinstance(qtab[0]['i'], u.Quantity)
    assert not isinstance(qtab['f'][0], u.Quantity)
    assert not isinstance(qtab[0]['f'], u.Quantity)

    # Regression test for #5342: if a function unit is assigned, the column
    # should become the appropriate FunctionQuantity subclass.
    qtab['f'].unit = u.dex(u.cm/u.s**2)
    assert isinstance(qtab['f'], u.Dex)