/
test_spectral_estimation.py
902 lines (822 loc) · 38.7 KB
/
test_spectral_estimation.py
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
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
The psd test suite.
"""
import gzip
import io
import os
import re
import warnings
from copy import deepcopy
import numpy as np
from obspy import Stream, Trace, UTCDateTime, read, read_inventory, Inventory
from obspy.core import Stats
from obspy.core.inventory import Response
from obspy.core.util import NUMPY_VERSION, AttribDict
from obspy.core.util.base import NamedTemporaryFile, MATPLOTLIB_VERSION
from obspy.core.util.obspy_types import ObsPyException
from obspy.io.xseed import Parser
from obspy.signal.spectral_estimation import (PPSD, welch_taper, welch_window)
from obspy.signal.spectral_estimation import earthquake_models
from obspy.signal.spectral_estimation import get_idc_infra_low_noise
from obspy.signal.spectral_estimation import get_idc_infra_hi_noise
import pytest
PATH = os.path.join(os.path.dirname(__file__), 'data')
def _internal_get_sample_data():
"""
Returns some real data (trace and poles and zeroes) for PPSD testing.
Data was downsampled to 100Hz so the PPSD is a bit distorted which does
not matter for the purpose of testing.
"""
# load test file
file_data = os.path.join(
PATH, 'BW.KW1._.EHZ.D.2011.090_downsampled.asc.gz')
# parameters for the test
with gzip.open(file_data) as f:
data = np.loadtxt(f)
stats = {'_format': 'MSEED',
'calib': 1.0,
'channel': 'EHZ',
'delta': 0.01,
'endtime': UTCDateTime(2011, 3, 31, 2, 36, 0, 180000),
'location': '',
'mseed': {'dataquality': 'D', 'record_length': 512,
'encoding': 'STEIM2', 'byteorder': '>'},
'network': 'BW',
'npts': 936001,
'sampling_rate': 100.0,
'starttime': UTCDateTime(2011, 3, 31, 0, 0, 0, 180000),
'station': 'KW1'}
tr = Trace(data, stats)
paz = {'gain': 60077000.0,
'poles': [(-0.037004 + 0.037016j), (-0.037004 - 0.037016j),
(-251.33 + 0j), (-131.04 - 467.29j),
(-131.04 + 467.29j)],
'sensitivity': 2516778400.0,
'zeros': [0j, 0j]}
return tr, paz
_sample_data = _internal_get_sample_data()
def _get_sample_data():
tr, paz = _sample_data
return tr.copy(), deepcopy(paz)
def _internal_get_ppsd():
"""
Returns ready computed ppsd for testing purposes.
"""
tr, paz = _get_sample_data()
st = Stream([tr])
ppsd = PPSD(tr.stats, paz, db_bins=(-200, -50, 0.5))
ppsd.add(st)
ppsd.calculate_histogram()
return ppsd
_ppsd = _internal_get_ppsd()
def _get_ppsd():
return deepcopy(_ppsd)
# XXX get rid of if/else again when bumping minimal numpy to 1.10
if NUMPY_VERSION >= [1, 10]:
allow_pickle = {'allow_pickle': True}
allow_pickle_false = {'allow_pickle': False}
else:
allow_pickle = {}
allow_pickle_false = {}
@pytest.mark.usefixtures('ignore_numpy_errors')
class TestPsd:
"""
Test cases for psd.
"""
@pytest.fixture()
def state(self):
# directory where the test files are located
out = AttribDict()
out.path = PATH
out.path_images = os.path.join(PATH, os.pardir, "images")
# some pre-computed ppsd used for plotting tests:
# (ppsd._psd_periods was downcast to np.float16 to save space)
out.example_ppsd_npz = os.path.join(PATH, "ppsd_kw1_ehz.npz")
# ignore some "RuntimeWarning: underflow encountered in multiply"
return out
def test_obspy_psd_vs_pitsa(self, state):
"""
Test to compare results of PITSA's psd routine to the
:func:`matplotlib.mlab.psd` routine wrapped in
:func:`obspy.signal.spectral_estimation.psd`.
The test works on 8192 samples long Gaussian noise with a standard
deviation of 0.1 generated with PITSA, sampling rate for processing in
PITSA was 100.0 Hz, length of nfft 512 samples. The overlap in PITSA
cannot be controlled directly, instead only the number of overlapping
segments can be specified. Therefore the test works with zero overlap
to have full control over the data segments used in the psd.
It seems that PITSA has one frequency entry more, i.e. the psd is one
point longer. I dont know were this can come from, for now this last
sample in the psd is ignored.
"""
from matplotlib.mlab import psd
sampling_rate = 100.0
nfft = 512
noverlap = 0
file_noise = os.path.join(state.path, "pitsa_noise.npy")
fn_psd_pitsa = "pitsa_noise_psd_samprate_100_nfft_512_noverlap_0.npy"
file_psd_pitsa = os.path.join(state.path, fn_psd_pitsa)
noise = np.load(file_noise, **allow_pickle)
# in principle to mimic PITSA's results detrend should be specified as
# some linear detrending (e.g. from matplotlib.mlab.detrend_linear)
psd_obspy, _ = psd(noise, NFFT=nfft, Fs=sampling_rate,
window=welch_taper, noverlap=noverlap,
sides="onesided", scale_by_freq=True)
psd_pitsa = np.load(file_psd_pitsa)
# mlab's psd routine returns Nyquist frequency as last entry, PITSA
# seems to omit it and returns a psd one frequency sample shorter.
psd_obspy = psd_obspy[:-1]
# test results. first couple of frequencies match not as exactly as all
# the rest, test them separately with a little more allowance..
np.testing.assert_array_almost_equal(psd_obspy[:3], psd_pitsa[:3],
decimal=4)
np.testing.assert_array_almost_equal(psd_obspy[1:5], psd_pitsa[1:5],
decimal=5)
np.testing.assert_array_almost_equal(psd_obspy[5:], psd_pitsa[5:],
decimal=6)
def test_welch_window_vs_pitsa(self, state):
"""
Test that the helper function to generate the welch window delivers the
same results as PITSA's routine.
Testing both even and odd values for length of window.
Not testing strange cases like length <5, though.
"""
welch_even = os.path.join(state.path, "pitsa_welch_window_512.npy")
welch_odd = os.path.join(state.path, "pitsa_welch_window_513.npy")
for file, n in zip((welch_even, welch_odd), (512, 513)):
window_pitsa = np.load(file)
window_obspy = welch_window(n)
np.testing.assert_array_almost_equal(window_pitsa, window_obspy)
def test_ppsd(self, state):
"""
Test PPSD routine with some real data.
"""
# paths of the expected result data
file_histogram = os.path.join(
state.path,
'BW.KW1._.EHZ.D.2011.090_downsampled__ppsd_hist_stack.npy')
file_binning = os.path.join(
state.path, 'BW.KW1._.EHZ.D.2011.090_downsampled__ppsd_mixed.npz')
file_mode_mean = os.path.join(
state.path,
'BW.KW1._.EHZ.D.2011.090_downsampled__ppsd_mode_mean.npz')
tr, _paz = _get_sample_data()
st = Stream([tr])
ppsd = _get_ppsd()
# read results and compare
result_hist = np.load(file_histogram)
assert len(ppsd.times_processed) == 4
assert ppsd.nfft == 65536
assert ppsd.nlap == 49152
np.testing.assert_array_equal(ppsd.current_histogram, result_hist)
# add the same data a second time (which should do nothing at all) and
# test again - but it will raise UserWarnings, which we omit for now
with warnings.catch_warnings(record=True):
warnings.simplefilter('ignore', UserWarning)
ppsd.add(st)
np.testing.assert_array_equal(ppsd.current_histogram, result_hist)
# test the binning arrays
binning = np.load(file_binning)
np.testing.assert_array_equal(ppsd.db_bin_edges, binning['spec_bins'])
np.testing.assert_array_equal(ppsd.period_bin_centers,
binning['period_bins'])
# test the mode/mean getter functions
per_mode, mode = ppsd.get_mode()
per_mean, mean = ppsd.get_mean()
result_mode_mean = np.load(file_mode_mean)
np.testing.assert_array_equal(per_mode, result_mode_mean['per_mode'])
np.testing.assert_array_equal(mode, result_mode_mean['mode'])
np.testing.assert_array_equal(per_mean, result_mode_mean['per_mean'])
np.testing.assert_array_equal(mean, result_mode_mean['mean'])
# test saving and loading of the PPSD (using a temporary file)
with NamedTemporaryFile(suffix=".npz") as tf:
filename = tf.name
# test saving and loading to npz
ppsd.save_npz(filename)
ppsd_loaded = PPSD.load_npz(filename)
ppsd_loaded.calculate_histogram()
assert len(ppsd_loaded.times_processed) == 4
assert ppsd_loaded.nfft == 65536
assert ppsd_loaded.nlap == 49152
np.testing.assert_array_equal(ppsd_loaded.current_histogram,
result_hist)
np.testing.assert_array_equal(ppsd_loaded.db_bin_edges,
binning['spec_bins'])
np.testing.assert_array_equal(ppsd_loaded.period_bin_centers,
binning['period_bins'])
def test_ppsd_warnings(self):
"""
Test some warning messages shown by PPSD routine
"""
ppsd = _get_ppsd()
# test warning message if SEED ID is mismatched
for key in ('network', 'station', 'location', 'channel'):
tr, _ = _get_sample_data()
# change starttime, data could then be added if ID and sampling
# rate match
tr.stats.starttime += 24 * 3600
tr.stats[key] = 'XX'
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', UserWarning)
assert not ppsd.add(tr)
assert len(w) == 1
assert str(w[0].message) == \
'No traces with matching SEED ID in provided stream object.'
# test warning message if sampling rate is mismatched
tr, _ = _get_sample_data()
# change starttime, data could then be added if ID and sampling
# rate match
tr.stats.starttime += 24 * 3600
tr.stats.sampling_rate = 123
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', UserWarning)
assert not ppsd.add(tr)
expected = ('No traces with matching sampling rate in provided '
'stream object.')
assert len(w) == 1
assert str(w[0].message) == expected
def test_ppsd_w_iris(self, state):
# Bands to be used this is the upper and lower frequency band pairs
fres = zip([0.1, 0.05], [0.2, 0.1])
file_data_anmo = os.path.join(state.path, 'IUANMO.seed')
# Read in ANMO data for one day
st = read(file_data_anmo)
# Use a canned ANMO response which will stay static
paz = {'gain': 86298.5, 'zeros': [0, 0],
'poles': [-59.4313, -22.7121 + 27.1065j, -22.7121 + 27.1065j,
-0.0048004, -0.073199],
'sensitivity': 3.3554 * 10 ** 9}
# Make an empty PPSD and add the data
# use highest frequency given by IRIS Mustang noise-pdf web service
# (0.475683 Hz == 2.10224036 s) as center of first bin, so that we
# end up with the same bins.
ppsd = PPSD(st[0].stats, paz, period_limits=(2.10224036, 1400))
ppsd.add(st)
ppsd.calculate_histogram()
# Get the 50th percentile from the PPSD
(per, perval) = ppsd.get_percentile(percentile=50)
perinv = 1 / per
# Read in the results obtained from a Mustang flat file
file_data_iris = os.path.join(state.path, 'IRISpdfExample')
data = np.genfromtxt(
file_data_iris, comments='#', delimiter=',',
dtype=[("freq", np.float64),
("power", np.int32),
("hits", np.int32)])
freq = data["freq"]
power = data["power"]
hits = data["hits"]
# cut data to same period range as in the ppsd we computed
# (Mustang returns more long periods, probably due to some zero padding
# or longer nfft in psd)
num_periods = len(ppsd.period_bin_centers)
freqdistinct = np.array(sorted(set(freq), reverse=True)[:num_periods])
# just make sure that we compare the same periods in the following
# (as we access both frequency arrays by indices from now on)
np.testing.assert_allclose(freqdistinct, 1 / ppsd.period_bin_centers,
rtol=1e-4)
# For each frequency pair we want to compare the mean of the bands
for fre in fres:
# determine which bins we want to compare
mask = (fre[0] < perinv) & (perinv < fre[1])
# Get the values for the bands from the PPSD
per_val_good_obspy = perval[mask]
percenlist = []
# Now we sort out all of the data from the IRIS flat file
# We will loop through the frequency values and compute a
# 50th percentile
for curfreq in freqdistinct[mask]:
mask_ = curfreq == freq
tempvalslist = np.repeat(power[mask_], hits[mask_])
percenlist.append(np.percentile(tempvalslist, 50))
# Here is the actual test
np.testing.assert_allclose(np.mean(per_val_good_obspy),
np.mean(percenlist), rtol=0.0, atol=1.2)
def test_ppsd_w_iris_against_obspy_results(self, state):
"""
Test against results obtained after merging of #1108.
"""
# Read in ANMO data for one day
st = read(os.path.join(state.path, 'IUANMO.seed'))
# Read in metadata in various different formats
paz = {'gain': 86298.5, 'zeros': [0, 0],
'poles': [-59.4313, -22.7121 + 27.1065j, -22.7121 + 27.1065j,
-0.0048004, -0.073199],
'sensitivity': 3.3554 * 10 ** 9}
resp = os.path.join(state.path, 'IUANMO.resp')
parser = Parser(os.path.join(state.path, 'IUANMO.dataless'))
inv = read_inventory(os.path.join(state.path, 'IUANMO.xml'))
# load expected results, for both only PAZ and full response
filename_paz = os.path.join(state.path, 'IUANMO_ppsd_paz.npz')
results_paz = PPSD.load_npz(filename_paz, metadata=None,
allow_pickle=True)
filename_full = os.path.join(state.path,
'IUANMO_ppsd_fullresponse.npz')
results_full = PPSD.load_npz(filename_full, metadata=None,
allow_pickle=True)
# Calculate the PPSDs and test against expected results
# first: only PAZ
ppsd = PPSD(st[0].stats, paz)
ppsd.add(st)
# commented code to generate the test data:
# ## np.savez(filename_paz,
# ## **dict([(k, getattr(ppsd, k))
# ## for k in PPSD.NPZ_STORE_KEYS]))
for key in PPSD.NPZ_STORE_KEYS_ARRAY_TYPES:
np.testing.assert_allclose(
getattr(ppsd, key), getattr(results_paz, key), rtol=1e-5)
for key in PPSD.NPZ_STORE_KEYS_LIST_TYPES:
for got, expected in zip(getattr(ppsd, key),
getattr(results_paz, key)):
np.testing.assert_allclose(got, expected, rtol=1e-5)
for key in PPSD.NPZ_STORE_KEYS_SIMPLE_TYPES:
if key in ["obspy_version", "numpy_version", "matplotlib_version"]:
continue
assert getattr(ppsd, key) == getattr(results_paz, key)
# second: various methods for full response
for metadata in [parser, inv, resp]:
ppsd = PPSD(st[0].stats, metadata)
ppsd.add(st)
# commented code to generate the test data:
# ## np.savez(filename_full,
# ## **dict([(k, getattr(ppsd, k))
# ## for k in PPSD.NPZ_STORE_KEYS]))
for key in PPSD.NPZ_STORE_KEYS_ARRAY_TYPES:
np.testing.assert_allclose(
getattr(ppsd, key), getattr(results_full, key), rtol=1e-5)
for key in PPSD.NPZ_STORE_KEYS_LIST_TYPES:
for got, expected in zip(getattr(ppsd, key),
getattr(results_full, key)):
np.testing.assert_allclose(got, expected, rtol=1e-5)
for key in PPSD.NPZ_STORE_KEYS_SIMPLE_TYPES:
if key in ["obspy_version", "numpy_version",
"matplotlib_version"]:
continue
assert getattr(ppsd, key) == getattr(results_full, key)
def test_ppsd_save_and_load_npz(self):
"""
Test PPSD.load_npz() and PPSD.save_npz()
"""
_, paz = _get_sample_data()
ppsd = _get_ppsd()
# save results to npz file
with NamedTemporaryFile(suffix=".npz") as tf:
filename = tf.name
# test saving and loading an uncompressed file
ppsd.save_npz(filename)
ppsd_loaded = PPSD.load_npz(filename, metadata=paz)
for key in PPSD.NPZ_STORE_KEYS:
if isinstance(getattr(ppsd, key), np.ndarray) or \
key == '_binned_psds':
np.testing.assert_equal(getattr(ppsd, key),
getattr(ppsd_loaded, key))
else:
assert getattr(ppsd, key) == getattr(ppsd_loaded, key)
def test_ppsd_restricted_stacks(self, state, image_path):
"""
Test PPSD.calculate_histogram() with restrictions to what data should
be stacked. Also includes image tests.
"""
# set up a bogus PPSD, with fixed random psds but with real start times
# of psd pieces, to facilitate testing the stack selection.
ppsd = PPSD(stats=Stats(dict(sampling_rate=150)), metadata=None,
db_bins=(-200, -50, 20.), period_step_octaves=1.4)
# change data to nowadays used nanoseconds POSIX timestamp
ppsd._times_processed = [
UTCDateTime(t)._ns for t in np.load(
os.path.join(state.path, "ppsd_times_processed.npy")).tolist()]
np.random.seed(1234)
ppsd._binned_psds = [
arr for arr in np.random.uniform(
-200, -50,
(len(ppsd._times_processed), len(ppsd.period_bin_centers)))]
# Test callback function that selects a fixed random set of the
# timestamps. Also checks that we get passed the type we expect,
# which is 1D numpy ndarray of int type.
def callback(t_array):
assert isinstance(t_array, np.ndarray)
assert t_array.shape == (len(ppsd._times_processed),)
assert np.issubdtype(t_array.dtype, np.integer)
np.random.seed(1234)
res = np.random.randint(0, 2, len(t_array)).astype(bool)
return res
# test several different sets of stack criteria, should cover
# everything, even with lots of combined criteria
stack_criteria_list = [
dict(starttime=UTCDateTime(2015, 3, 8), month=[2, 3, 5, 7, 8]),
dict(endtime=UTCDateTime(2015, 6, 7), year=[2015],
time_of_weekday=[(1, 0, 24), (2, 0, 24), (-1, 0, 11)]),
dict(year=[2013, 2014, 2016, 2017], month=[2, 3, 4]),
dict(month=[1, 2, 5, 6, 8], year=2015),
dict(isoweek=[4, 5, 6, 13, 22, 23, 24, 44, 45]),
dict(time_of_weekday=[(5, 22, 24), (6, 0, 2), (6, 22, 24)]),
dict(callback=callback, month=[1, 3, 5, 7]),
dict(callback=callback)]
expected_selections = np.load(
os.path.join(state.path, "ppsd_stack_selections.npy"))
# test every set of criteria
for stack_criteria, expected_selection in zip(
stack_criteria_list, expected_selections):
selection_got = ppsd._stack_selection(**stack_criteria)
np.testing.assert_array_equal(selection_got, expected_selection)
plot_kwargs = dict(max_percentage=15, xaxis_frequency=True,
period_lim=(0.01, 50))
ppsd.calculate_histogram(**stack_criteria_list[1])
fig = ppsd.plot(show=False, **plot_kwargs)
fig.axes[1].set_xlim(left=fig.axes[1].get_xlim()[0] - 2)
image_path_1 = image_path.parent / 'test_ppsd_restricted_stacks_1.png'
with np.errstate(under='ignore'):
fig.savefig(image_path_1)
# test it again, checking that updating an existing plot with different
# stack selection works..
# a) we start with the stack for the expected image and test that it
# matches (like above):
ppsd.calculate_histogram(**stack_criteria_list[1])
image_path_2 = image_path.parent / 'test_ppsd_restricted_stacks_2.png'
with np.errstate(under='ignore'):
fig.savefig(image_path_2)
ppsd.calculate_histogram(**stack_criteria_list[1])
image_path_3 = image_path.parent / 'test_ppsd_restricted_stacks_3.png'
ppsd._plot_histogram(fig=fig, draw=True)
with np.errstate(under='ignore'):
fig.savefig(image_path_3)
def test_earthquake_models(self):
"""
Test earthquake models
"""
ppsd = _get_ppsd()
test_magnitudes = [3.5, 2.5, 1.5]
distance = 10
for magnitude in test_magnitudes:
key = (magnitude, distance)
fig = ppsd.plot(
show_earthquakes=(magnitude - 0.5, magnitude + 0.5, 5, 15),
show_noise_models=False, show=False)
ax = fig.axes[0]
line = ax.lines[0]
frequencies, accelerations = earthquake_models[key]
accelerations = np.array(accelerations)
periods = 1 / np.array(frequencies)
power = accelerations / (periods ** (-.5))
power = 20 * np.log10(power / 2)
assert list(line.get_ydata()) == list(power)
assert list(line.get_xdata()) == list(periods)
caption = 'M%.1f\n%dkm' % (magnitude, distance)
assert ax.texts[0].get_text() == caption
def test_ppsd_infrasound(self):
"""
Test plotting psds on infrasound data
"""
wf = os.path.join(
PATH, 'IM.I59H1..BDF_2020_10_31.mseed')
md = os.path.join(
PATH, 'IM.I59H1..BDF_2020_10_31.xml')
st = read(wf)
inv = read_inventory(md)
tr = st[0]
ppsd = PPSD(tr.stats, metadata=inv, special_handling='infrasound',
db_bins=(-100, 40, 1.), ppsd_length=300, overlap=0.5)
ppsd.add(st)
fig = ppsd.plot(xaxis_frequency=True, period_lim=(0.01, 10),
show=False)
models = (get_idc_infra_hi_noise(), get_idc_infra_low_noise())
lines = fig.axes[0].lines
freq1 = lines[0].get_xdata()
per1 = 1 / freq1
hn = lines[0].get_ydata()
freq2 = lines[1].get_xdata()
per2 = 1 / freq2
ln = lines[1].get_ydata()
per1_m, hn_m = models[0]
per2_m, ln_m = models[1]
np.testing.assert_array_equal(hn, hn_m)
np.testing.assert_array_equal(ln, ln_m)
np.testing.assert_array_equal(per1, per1_m)
np.testing.assert_array_equal(per2, per2_m)
# test calculated psd values
psd = ppsd.psd_values[0]
assert len(psd) == 73
psd = psd[:20]
expected = np.array([
-63.424206, -64.07918, -64.47593, -64.77374, -65.09937,
-67.17343, -66.36576, -65.75002, -65.34155, -64.58012,
-63.72327, -62.615784, -61.612656, -61.085754, -60.09534,
-58.949272, -57.600315, -56.43776, -55.448067, -54.242218],
dtype=np.float32)
np.testing.assert_array_almost_equal(psd, expected, decimal=2)
def test_ppsd_add_npz(self, state):
"""
Test PPSD.add_npz().
"""
# set up a bogus PPSD, with fixed random psds but with real start times
# of psd pieces, to facilitate testing the stack selection.
ppsd = PPSD(stats=Stats(dict(sampling_rate=150)), metadata=None,
db_bins=(-200, -50, 20.), period_step_octaves=1.4)
_times_processed = np.load(
os.path.join(state.path, "ppsd_times_processed.npy")).tolist()
# change data to nowadays used nanoseconds POSIX timestamp
_times_processed = [UTCDateTime(t)._ns for t in _times_processed]
np.random.seed(1234)
_binned_psds = [
arr for arr in np.random.uniform(
-200, -50,
(len(_times_processed), len(ppsd.period_bin_centers)))]
with NamedTemporaryFile(suffix=".npz") as tf1, \
NamedTemporaryFile(suffix=".npz") as tf2, \
NamedTemporaryFile(suffix=".npz") as tf3:
# save data split up over three separate temporary files
ppsd._times_processed = _times_processed[:200]
ppsd._binned_psds = _binned_psds[:200]
ppsd.save_npz(tf1.name)
ppsd._times_processed = _times_processed[200:400]
ppsd._binned_psds = _binned_psds[200:400]
ppsd.save_npz(tf2.name)
ppsd._times_processed = _times_processed[400:]
ppsd._binned_psds = _binned_psds[400:]
ppsd.matplotlib_version = "X.X.X"
ppsd.save_npz(tf3.name)
# now load these saved npz files and check if all data is present
ppsd = PPSD.load_npz(tf1.name, metadata=None)
ppsd.add_npz(tf2.name)
# we changed a version number so this should emit a warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ppsd.add_npz(tf3.name)
assert len(w) == 1
np.testing.assert_array_equal(_binned_psds, ppsd._binned_psds)
np.testing.assert_array_equal(_times_processed,
ppsd._times_processed)
# adding data already present should also emit a warning and the
# PPSD should not be changed
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ppsd.add_npz(tf2.name)
assert len(w) == 1
np.testing.assert_array_equal(_binned_psds, ppsd._binned_psds)
np.testing.assert_array_equal(_times_processed,
ppsd._times_processed)
def test_ppsd_time_checks(self):
"""
Some tests that make sure checking if a new PSD slice to be addded to
existing PPSD has an invalid overlap or not works as expected.
"""
ppsd = PPSD(Stats(), Response())
one_second = 1000000000
t0 = 946684800000000000 # 2000-01-01T00:00:00
time_diffs = [
0, one_second, one_second * 2, one_second * 3,
one_second * 8, one_second * 9, one_second * 10]
ppsd._times_processed = [t0 + td for td in time_diffs]
ppsd.ppsd_length = 2
ppsd.overlap = 0.5
# valid time stamps to insert data for (i.e. data that overlaps with
# existing data at most "overlap" times "ppsd_length")
ns_ok = [
t0 - 3 * one_second,
t0 - 1.01 * one_second,
t0 - one_second,
t0 + 4 * one_second,
t0 + 4.01 * one_second,
t0 + 6 * one_second,
t0 + 7 * one_second,
t0 + 6.99 * one_second,
t0 + 11 * one_second,
t0 + 11.01 * one_second,
t0 + 15 * one_second,
]
for ns in ns_ok:
t = UTCDateTime(ns=int(ns))
# getting False means time is not present yet and a PSD slice would
# be added to the PPSD data
assert not ppsd._PPSD__check_time_present(t)
# invalid time stamps to insert data for (i.e. data that overlaps with
# existing data more than "overlap" times "ppsd_length")
ns_bad = [
t0 - 0.99 * one_second,
t0 - 0.5 * one_second,
t0,
t0 + 1.1 * one_second,
t0 + 3.99 * one_second,
t0 + 7.01 * one_second,
t0 + 7.5 * one_second,
t0 + 8 * one_second,
t0 + 8.8 * one_second,
t0 + 10 * one_second,
t0 + 10.99 * one_second,
]
for ns in ns_bad:
t = UTCDateTime(ns=int(ns))
# getting False means time is not present yet and a PSD slice would
# be added to the PPSD data
assert ppsd._PPSD__check_time_present(t)
def test_issue1216(self):
tr, paz = _get_sample_data()
st = Stream([tr])
ppsd = PPSD(tr.stats, paz, db_bins=(-200, -50, 0.5))
ppsd.add(st)
# After adding data internal representation of hist stack is None
assert ppsd._current_hist_stack is None
# Accessing the current_histogram property calculates the default stack
assert ppsd.current_histogram is not None
assert ppsd._current_hist_stack is not None
# Adding the same data again does not invalidate the internal stack
# but raises "UserWarning: Already covered time spans detected"
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', UserWarning)
ppsd.add(st)
assert len(w) == 4
for w_ in w:
assert str(w_.message).startswith(
"Already covered time spans detected")
assert ppsd._current_hist_stack is not None
# Adding new data invalidates the internal stack
tr.stats.starttime += 3600
st2 = Stream([tr])
# raises "UserWarning: Already covered time spans detected"
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', UserWarning)
ppsd.add(st2)
assert len(w) == 2
for w_ in w:
assert str(w_.message).startswith(
"Already covered time spans detected")
assert ppsd._current_hist_stack is None
# Accessing current_histogram again calculates the stack
assert ppsd.current_histogram is not None
assert ppsd._current_hist_stack is not None
def test_wrong_trace_id_message(self, state):
"""
Test that we get the expected warning message on waveform/metadata
mismatch.
"""
tr, _paz = _get_sample_data()
inv = read_inventory(os.path.join(state.path, 'IUANMO.xml'))
st = Stream([tr])
ppsd = PPSD(tr.stats, inv)
# metadata doesn't fit the trace ID specified via stats
# should show a warning..
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ret = ppsd.add(st)
# the trace is sliced into four segments, so we get the warning
# message four times..
assert len(w) == 4
for w_ in w:
assert str(w_.message).startswith(
"Error getting response from provided metadata")
# should not add the data to the ppsd
assert not ret
def test_ppsd_psd_values(self):
"""
Test property psd values
"""
ppsd = _get_ppsd()
# just test against existing low level data access
assert ppsd.psd_values == ppsd._binned_psds
np.testing.assert_array_equal(ppsd.psd_values, ppsd._binned_psds)
# property can't be set
with pytest.raises(AttributeError):
ppsd.psd_values = 123
def test_ppsd_temporal_plot(self, state, image_path):
"""
Test plot of several period bins over time
"""
ppsd = PPSD.load_npz(state.example_ppsd_npz, allow_pickle=True)
restrictions = {'starttime': UTCDateTime(2011, 2, 6, 1, 1),
'endtime': UTCDateTime(2011, 2, 7, 21, 12),
'year': [2011],
'time_of_weekday': [(-1, 2, 23)]}
# add some gaps in the middle
for i in sorted(list(range(30, 40)) + list(range(8, 18)) + [4])[::-1]:
ppsd._times_processed.pop(i)
ppsd._binned_psds.pop(i)
fig = ppsd.plot_temporal([0.1, 1, 10], filename=None, show=False,
**restrictions)
fig.savefig(image_path)
def test_exclude_last_sample(self):
start = UTCDateTime("2017-01-01T00:00:00")
header = {
"starttime": start,
"network": "GR",
"station": "FUR",
"channel": "BHZ"
}
# 49 segments of 30 minutes to allow 30 minutes overlap in next day
tr = Trace(data=np.arange(30 * 60 * 4, dtype=np.int32), header=header)
ppsd = PPSD(tr.stats, read_inventory())
ppsd.add(tr)
assert 3 == len(ppsd._times_processed)
assert 3600 == ppsd.len
for i, time in enumerate(ppsd._times_processed):
current = start.ns + (i * 30 * 60) * 1e9
assert time == current
@pytest.mark.skipif(MATPLOTLIB_VERSION[0] >= 3,
reason='matplotlib >= 3 shifts labels')
def test_ppsd_spectrogram_plot(self, state, image_path):
"""
Test spectrogram type plot of PPSD
Matplotlib version 3 shifts the x-axis labels but everything else looks
the same. Skipping test for matplotlib >= 3 on 05/12/2018.
"""
ppsd = PPSD.load_npz(state.example_ppsd_npz, allow_pickle=True)
# add some gaps in the middle
for i in sorted(list(range(30, 40)) + list(range(8, 18)) + [4])[::-1]:
ppsd._times_processed.pop(i)
ppsd._binned_psds.pop(i)
ppsd.plot_spectrogram(filename=image_path, show=False)
def test_exception_reading_newer_npz(self, state):
"""
Checks that an exception is properly raised when trying to read a npz
that was written on a more recent ObsPy version (specifically that has
a higher 'ppsd_version' number which is used to keep track of changes
in PPSD and the npz file used for serialization).
"""
msg = ("Trying to read/add a PPSD npz with 'ppsd_version=100'. This "
"file was written on a more recent ObsPy version that very "
"likely has incompatible changes in PPSD internal structure "
"and npz serialization. It can not safely be read with this "
"ObsPy version (current 'ppsd_version' is {!s}). Please "
"consider updating your ObsPy installation.".format(
PPSD(stats=Stats(), metadata=None).ppsd_version))
# 1 - loading a npz
data = np.load(state.example_ppsd_npz, **allow_pickle)
# we have to load, modify 'ppsd_version' and save the npz file for the
# test..
items = {key: data[key] for key in data.files}
# deliberately set a higher ppsd_version number
items['ppsd_version'] = items['ppsd_version'].copy()
items['ppsd_version'].fill(100)
with NamedTemporaryFile() as tf:
filename = tf.name
with open(filename, 'wb') as fh:
np.savez(fh, **items)
with pytest.raises(ObsPyException, match=re.escape(msg)):
PPSD.load_npz(filename)
# 2 - adding a npz
ppsd = PPSD.load_npz(state.example_ppsd_npz, allow_pickle=True)
for method in (ppsd.add_npz, ppsd._add_npz):
with NamedTemporaryFile() as tf:
filename = tf.name
with open(filename, 'wb') as fh:
np.savez(fh, **items)
with pytest.raises(ObsPyException, match=re.escape(msg)):
method(filename)
def test_nice_ringlaser_metadata_error_msg(self):
expected = ("When using `special_handling='ringlaser'`, `metadata` "
"must be a plain dictionary with key 'sensitivity' "
"stating the overall sensitivity`.")
with pytest.raises(TypeError, match=re.escape(expected)):
PPSD(stats=Stats(), metadata=Inventory(networks=[], source=""),
special_handling='ringlaser')
def test_can_read_npz_without_pickle(self, state):
"""
Ensures that a default PPSD can be written and read without having to
allow np.load the use of pickle, or that a helpful error message is
raised if allow_pickle is required. See #2409.
"""
# Init a test PPSD and empty byte stream.
ppsd = PPSD.load_npz(state.example_ppsd_npz, allow_pickle=True)
byte_me = io.BytesIO()
# Save PPSD to byte stream and rewind to 0.
ppsd.save_npz(byte_me)
byte_me.seek(0)
# Load dict, will raise an exception if pickle is needed.
loaded_dict = dict(np.load(byte_me, **allow_pickle_false))
assert isinstance(loaded_dict, dict)
# the rest of the test is only relevant on numpy versions that have
# allow_pickle kwarg (starting with version 1.10.0), older versions
# will always allow pickle and thus reading works
if NUMPY_VERSION < [1, 10]:
return
# A helpful error message is issued when allow_pickle is needed.
with pytest.raises(ValueError, match='Loading PPSD results'):
PPSD.load_npz(state.example_ppsd_npz)
def test_can_add_npz_without_pickle(self):
"""
Ensure PPSD can be added without using the pickle protocol, or
that a helpful error message is raised if allow_pickle is required.
See #2409.
"""
def _save_nps_require_pickle(filename, ppsd):
""" Save npz in such a way that requires pickle to load"""
out = {}
for key in PPSD.NPZ_STORE_KEYS:
out[key] = getattr(ppsd, key)
np.savez_compressed(filename, **out)
ppsd = _internal_get_ppsd()
# save PPSD in such a way to mock old versions.
with NamedTemporaryFile(suffix='.npz') as ntemp:
temp_path = ntemp.name
_save_nps_require_pickle(temp_path, ppsd)
# We should be able to load the files when allowing pickle.
ppsd.add_npz(temp_path, allow_pickle=True)
# the rest of the test is only relevant on numpy versions that have
# allow_pickle kwarg (starting with version 1.10.0), older versions
# will always allow pickle and thus reading works
if NUMPY_VERSION < [1, 10]:
return
# If not allow_pickle, a helpful error msg should be raised.
with pytest.raises(ValueError, match='Loading PPSD results'):
ppsd.add_npz(temp_path)