/
core.py
726 lines (653 loc) · 30.1 KB
/
core.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
# -*- coding: utf-8 -*-
"""
SEG Y bindings to ObsPy core module.
:copyright:
The ObsPy Development Team (devs@obspy.org)
:license:
GNU Lesser General Public License, Version 3
(https://www.gnu.org/copyleft/lesser.html)
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from future.builtins import * # NOQA
import warnings
from copy import deepcopy
from struct import unpack
import numpy as np
from obspy import Stream, Trace, UTCDateTime
from obspy.core import AttribDict
from .header import (BINARY_FILE_HEADER_FORMAT, DATA_SAMPLE_FORMAT_CODE_DTYPE,
ENDIAN, TRACE_HEADER_FORMAT, TRACE_HEADER_KEYS)
from .segy import _read_segy as _read_segyrev1
from .segy import _read_su as _read_su_file
from .segy import (SEGYBinaryFileHeader, SEGYError, SEGYFile, SEGYTrace,
SEGYTraceHeader, SUFile,
autodetect_endian_and_sanity_check_su)
from .util import unpack_header_value
# Valid data format codes as specified in the SEGY rev1 manual.
VALID_FORMATS = [1, 2, 3, 4, 5, 8]
# This is the maximum possible interval between two samples due to the nature
# of the SEG Y format.
MAX_INTERVAL_IN_SECONDS = 0.065535
# largest number possible with int16
MAX_NUMBER_OF_SAMPLES = 32767
class SEGYCoreWritingError(SEGYError):
"""
Raised if the writing of the Stream object fails due to some reason.
"""
pass
class SEGYSampleIntervalError(SEGYError):
"""
Raised if the interval between two samples is too large.
"""
pass
def _is_segy(filename):
"""
Checks whether or not the given file is a SEG Y file.
:type filename: str
:param filename: SEG Y file to be checked.
:rtype: bool
:return: ``True`` if a SEG Y file.
"""
# This is a very weak test. It tests two things: First if the data sample
# format code is valid. This is also used to determine the endianness. This
# is then used to check if the sampling interval is set to any sane number
# greater than 0 and that the number of samples per trace is greater than
# 0.
try:
with open(filename, 'rb') as fp:
fp.seek(3212)
_number_of_data_traces = fp.read(2)
_number_of_auxiliary_traces = fp.read(2)
_sample_interval = fp.read(2)
fp.seek(2, 1)
_samples_per_trace = fp.read(2)
fp.seek(2, 1)
data_format_code = fp.read(2)
fp.seek(3500, 0)
_format_number = fp.read(2)
_fixed_length = fp.read(2)
_extended_number = fp.read(2)
except Exception:
return False
# Unpack using big endian first and check if it is valid.
try:
format = unpack(b'>h', data_format_code)[0]
except Exception:
return False
if format in VALID_FORMATS:
_endian = '>'
# It can only every be one. It is impossible for little and big endian to
# both yield a valid data sample format code because they are restricted to
# be between 1 and 8.
else:
format = unpack(b'<h', data_format_code)[0]
if format in VALID_FORMATS:
_endian = '<'
else:
return False
# Check if the sample interval and samples per Trace make sense.
fmt = ('%sh' % _endian).encode('ascii', 'strict')
_sample_interval = unpack(fmt, _sample_interval)[0]
_samples_per_trace = unpack(fmt, _samples_per_trace)[0]
_number_of_data_traces = unpack(fmt, _number_of_data_traces)[0]
_number_of_auxiliary_traces = unpack(fmt,
_number_of_auxiliary_traces)[0]
_format_number = unpack(fmt, _format_number)[0]
# Test the version number. The only really supported version number in
# ObsPy is 1.0 which is encoded as 0100_16. Many file have version
# number zero which is used to indicate "traditional SEG-Y" conforming
# to the 1975 standard.
# Also allow 0010_16 and 0001_16 as the definition is honestly awkward
# and I image many writers get it wrong.
if _format_number not in (0x0000, 0x0100, 0x0010, 0x0001):
return False
_fixed_length = unpack(fmt, _fixed_length)[0]
_extended_number = unpack(fmt, _extended_number)[0]
# Make some sanity checks and return False if they fail.
if _sample_interval <= 0 or _samples_per_trace <= 0 \
or _number_of_data_traces < 0 or _number_of_auxiliary_traces < 0 \
or _fixed_length < 0 or _extended_number < 0:
return False
return True
def _read_segy(filename, headonly=False, byteorder=None,
textual_header_encoding=None, unpack_trace_headers=False,
**kwargs): # @UnusedVariable
"""
Reads a SEG Y file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: SEG Y rev1 file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the header and omit the waveform
data.
:type byteorder: str or ``None``
:param byteorder: Determines the endianness of the file. Either ``'>'`` for
big endian or ``'<'`` for little endian. If it is ``None``, it will try
to autodetect the endianness. The endianness is always valid for the
whole file. Defaults to ``None``.
:type textual_header_encoding: str or ``None``
:param textual_header_encoding: The encoding of the textual header. Can be
``'EBCDIC'``, ``'ASCII'`` or ``None``. If it is ``None``, autodetection
will be attempted. Defaults to ``None``.
:type unpack_trace_headers: bool, optional
:param unpack_trace_headers: Determines whether or not all trace header
values will be unpacked during reading. If ``False`` it will greatly
enhance performance and especially memory usage with large files. The
header values can still be accessed and will be calculated on the fly
but tab completion will no longer work. Look in the headers.py for a
list of all possible trace header values. Defaults to ``False``.
:returns: A ObsPy :class:`~obspy.core.stream.Stream` object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/00001034.sgy_first_trace")
>>> st # doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) # doctest: +ELLIPSIS
1 Trace(s) in Stream:
Seq. No. in line: 1 | 2009-06-22T14:47:37.000000Z - ... 2001 samples
"""
# Read file to the internal segy representation.
segy_object = _read_segyrev1(
filename, endian=byteorder,
textual_header_encoding=textual_header_encoding,
unpack_headers=unpack_trace_headers)
# Create the stream object.
stream = Stream()
# SEGY has several file headers that apply to all traces. They will be
# stored in Stream.stats.
stream.stats = AttribDict()
# Get the textual file header.
textual_file_header = segy_object.textual_file_header
# The binary file header will be a new AttribDict
binary_file_header = AttribDict()
for key, value in segy_object.binary_file_header.__dict__.items():
setattr(binary_file_header, key, value)
# Get the data encoding and the endianness from the first trace.
data_encoding = segy_object.traces[0].data_encoding
endian = segy_object.traces[0].endian
textual_file_header_encoding = segy_object.textual_header_encoding.upper()
# Add the file wide headers.
stream.stats.textual_file_header = textual_file_header
stream.stats.binary_file_header = binary_file_header
# Also set the data encoding, endianness and the encoding of the
# textual_file_header.
stream.stats.data_encoding = data_encoding
stream.stats.endian = endian
stream.stats.textual_file_header_encoding = \
textual_file_header_encoding
# Convert traces to ObsPy Trace objects.
for tr in segy_object.traces:
stream.append(tr.to_obspy_trace(
headonly=headonly,
unpack_trace_headers=unpack_trace_headers))
return stream
def _write_segy(stream, filename, data_encoding=None, byteorder=None,
textual_header_encoding=None, **kwargs): # @UnusedVariable
"""
Writes a SEG Y file from given ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
the :meth:`~obspy.core.stream.Stream.write` method of an
ObsPy :class:`~obspy.core.stream.Stream` object, call this instead.
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: The ObsPy Stream object to write.
:type filename: str
:param filename: Name of file to write.
:type data_encoding: int
:param data_encoding: The data encoding is an integer with the following
currently supported meaning:
``1``
4 byte IBM floating points (float32)
``2``
4 byte Integers (int32)
``3``
2 byte Integer (int16)
``5``
4 byte IEEE floating points (float32)
The value in the brackets is the necessary dtype of the data. ObsPy
will now automatically convert the data because data might change/loose
precision during the conversion so the user has to take care of the
correct dtype.
If it is ``None``, the value of the first Trace will be used for all
consecutive Traces. If it is None for the first Trace, 1 (IBM floating
point numbers) will be used. Different data encodings for different
traces are currently not supported because these will most likely not
be readable by other software.
:type byteorder: str or ``None``
:param byteorder: Determines the endianness of the file. Either ``'>'`` for
big endian or ``'<'`` for little endian. If is ``None``, it will either
be the endianness of the first Trace or if that is also not set, it
will be big endian. A mix between little and big endian for the headers
and traces is currently not supported.
:type textual_header_encoding: str or ``None``
:param textual_header_encoding: The encoding of the textual header. Can be
``'EBCDIC'``, ``'ASCII'`` or ``None``. If it is ``None``, the
textual_file_header_encoding attribute in the stats.segy dictionary of
the first Trace is used and if that is not set, ASCII will be used.
This function will automatically set the data encoding field of the binary
file header so the user does not need to worry about it.
The starttime of every trace is not a required field in the SEG Y
specification. If the starttime of a trace is UTCDateTime(0) it will be
interpreted as a not-set starttime and no time is written to the trace
header. Every other time will be written.
SEG Y supports a sample interval from 1 to 65535 microseconds in steps of 1
microsecond. Larger intervals cannot be supported due to the definition of
the SEG Y format. Therefore the smallest possible sampling rate is ~ 15.26
Hz. Please keep that in mind.
"""
for i, tr in enumerate(stream):
if len(tr) > MAX_NUMBER_OF_SAMPLES:
msg = ('Can not write traces with more than {:d} samples (trace '
'at index {:d}):\n{!s}')
raise ValueError(msg.format(MAX_NUMBER_OF_SAMPLES, i, tr))
# Some sanity checks to catch invalid arguments/keyword arguments.
if data_encoding is not None and data_encoding not in VALID_FORMATS:
msg = "Invalid data encoding."
raise SEGYCoreWritingError(msg)
# Figure out the data encoding if it is not set.
if data_encoding is None:
if hasattr(stream, 'stats') and hasattr(stream.stats, 'data_encoding'):
data_encoding = stream.stats.data_encoding
if hasattr(stream, 'stats') and hasattr(stream.stats,
'binary_file_header'):
data_encoding = \
stream.stats.binary_file_header.data_sample_format_code
# Set it to float if it in not given.
else:
data_encoding = 1
# Create empty file wide headers if they do not exist.
if not hasattr(stream, 'stats'):
stream.stats = AttribDict()
if not hasattr(stream.stats, 'textual_file_header'):
stream.stats.textual_file_header = b""
if not hasattr(stream.stats, 'binary_file_header'):
stream.stats.binary_file_header = SEGYBinaryFileHeader()
# Valid dtype for the data encoding.
valid_dtype = DATA_SAMPLE_FORMAT_CODE_DTYPE[data_encoding]
# Makes sure that the dtype is for every Trace is correct.
for trace in stream:
# Check the dtype.
if trace.data.dtype != valid_dtype:
msg = """
The dtype of the data and the chosen data_encoding do not match.
You need to manually convert the dtype if you want to use that
data_encoding. Please refer to the obspy.io.segy manual for more
details.
""".strip()
raise SEGYCoreWritingError(msg)
# Check the sample interval.
if trace.stats.delta > MAX_INTERVAL_IN_SECONDS:
msg = """
SEG Y supports a maximum interval of %s seconds in between two
samples (trace.stats.delta value).
""".strip()
msg = msg % MAX_INTERVAL_IN_SECONDS
raise SEGYSampleIntervalError(msg)
# Figure out endianness and the encoding of the textual file header.
if byteorder is None:
if hasattr(stream, 'stats') and hasattr(stream.stats, 'endian'):
byteorder = stream.stats.endian
else:
byteorder = '>'
# Map the byte order.
byteorder = ENDIAN[byteorder]
if textual_header_encoding is None:
if hasattr(stream, 'stats') and hasattr(
stream.stats, 'textual_file_header_encoding'):
textual_header_encoding = \
stream.stats.textual_file_header_encoding
else:
textual_header_encoding = 'ASCII'
# Loop over all Traces and create a SEGY File object.
segy_file = SEGYFile()
# Set the file wide headers.
segy_file.textual_file_header = stream.stats.textual_file_header
segy_file.textual_header_encoding = \
textual_header_encoding
binary_header = SEGYBinaryFileHeader()
this_binary_header = stream.stats.binary_file_header
# Loop over all items and if they exists set them. Ignore all other
# attributes.
for _, item, _ in BINARY_FILE_HEADER_FORMAT:
if hasattr(this_binary_header, item):
setattr(binary_header, item, getattr(this_binary_header, item))
# Set the data encoding.
binary_header.data_sample_format_code = data_encoding
segy_file.binary_file_header = binary_header
# Add all traces.
for trace in stream:
new_trace = SEGYTrace()
new_trace.data = trace.data
# Create empty trace header if none is there.
if not hasattr(trace.stats, 'segy'):
warnings.warn("CREATING TRACE HEADER")
trace.stats.segy = {}
trace.stats.segy.trace_header = SEGYTraceHeader(endian=byteorder)
elif not hasattr(trace.stats.segy, 'trace_header'):
warnings.warn("CREATING TRACE HEADER")
trace.stats.segy.trace_header = SEGYTraceHeader()
this_trace_header = trace.stats.segy.trace_header
new_trace_header = new_trace.header
# Again loop over all field of the trace header and if they exists, set
# them. Ignore all additional attributes.
for _, item, _, _ in TRACE_HEADER_FORMAT:
if hasattr(this_trace_header, item):
setattr(new_trace_header, item,
getattr(this_trace_header, item))
starttime = trace.stats.starttime
# Set the date of the Trace if it is not UTCDateTime(0).
if starttime == UTCDateTime(0):
new_trace.header.year_data_recorded = 0
new_trace.header.day_of_year = 0
new_trace.header.hour_of_day = 0
new_trace.header.minute_of_hour = 0
new_trace.header.second_of_minute = 0
else:
new_trace.header.year_data_recorded = starttime.year
new_trace.header.day_of_year = starttime.julday
new_trace.header.hour_of_day = starttime.hour
new_trace.header.minute_of_hour = starttime.minute
new_trace.header.second_of_minute = starttime.second
# Set the sampling rate.
new_trace.header.sample_interval_in_ms_for_this_trace = \
int(trace.stats.delta * 1E6)
# Set the data encoding and the endianness.
new_trace.data_encoding = data_encoding
new_trace.endian = byteorder
# Add the trace to the SEGYFile object.
segy_file.traces.append(new_trace)
# Write the file
segy_file.write(filename, data_encoding=data_encoding, endian=byteorder)
def _is_su(filename):
"""
Checks whether or not the given file is a Seismic Unix (SU) file.
:type filename: str
:param filename: Seismic Unix file to be checked.
:rtype: bool
:return: ``True`` if a Seismic Unix file.
.. note::
This test is rather shaky because there is no reliable identifier in a
Seismic Unix file.
"""
with open(filename, 'rb') as f:
stat = autodetect_endian_and_sanity_check_su(f)
if stat is False:
return False
else:
return True
def _read_su(filename, headonly=False, byteorder=None,
unpack_trace_headers=False, **kwargs): # @UnusedVariable
"""
Reads a Seismic Unix (SU) file and returns an ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
ObsPy :func:`~obspy.core.stream.read` function, call this instead.
:type filename: str
:param filename: SU file to be read.
:type headonly: bool, optional
:param headonly: If set to True, read only the header and omit the waveform
data.
:type byteorder: str or ``None``
:param byteorder: Determines the endianness of the file. Either ``'>'`` for
big endian or ``'<'`` for little endian. If it is ``None``, it will try
to autodetect the endianness. The endianness is always valid for the
whole file. Defaults to ``None``.
:type unpack_trace_headers: bool, optional
:param unpack_trace_headers: Determines whether or not all trace header
values will be unpacked during reading. If ``False`` it will greatly
enhance performance and especially memory usage with large files. The
header values can still be accessed and will be calculated on the fly
but tab completion will no longer work. Look in the headers.py for a
list of all possible trace header values. Defaults to ``False``.
:returns: A ObsPy :class:`~obspy.core.stream.Stream` object.
.. rubric:: Example
>>> from obspy import read
>>> st = read("/path/to/1.su_first_trace")
>>> st #doctest: +ELLIPSIS
<obspy.core.stream.Stream object at 0x...>
>>> print(st) #doctest: +ELLIPSIS
1 Trace(s) in Stream:
... | 2005-12-19T15:07:54.000000Z - ... | 4000.0 Hz, 8000 samples
"""
# Read file to the internal segy representation.
su_object = _read_su_file(filename, endian=byteorder,
unpack_headers=unpack_trace_headers)
# Create the stream object.
stream = Stream()
# Get the endianness from the first trace.
endian = su_object.traces[0].endian
# Loop over all traces.
for tr in su_object.traces:
# Create new Trace object for every segy trace and append to the Stream
# object.
trace = Trace()
stream.append(trace)
# skip data if headonly is set
if headonly:
trace.stats.npts = tr.npts
else:
trace.data = tr.data
trace.stats.su = AttribDict()
# If all values will be unpacked create a normal dictionary.
if unpack_trace_headers:
# Add the trace header as a new attrib dictionary.
header = AttribDict()
for key, value in tr.header.__dict__.items():
setattr(header, key, value)
# Otherwise use the LazyTraceHeaderAttribDict.
else:
# Add the trace header as a new lazy attrib dictionary.
header = LazyTraceHeaderAttribDict(tr.header.unpacked_header,
tr.header.endian)
trace.stats.su.trace_header = header
# Also set the endianness.
trace.stats.su.endian = endian
# The sampling rate should be set for every trace. It is a sample
# interval in microseconds. The only sanity check is that is should be
# larger than 0.
tr_header = trace.stats.su.trace_header
if tr_header.sample_interval_in_ms_for_this_trace > 0:
trace.stats.delta = \
float(tr.header.sample_interval_in_ms_for_this_trace) / \
1E6
# If the year is not zero, calculate the start time. The end time is
# then calculated from the start time and the sampling rate.
# 99 is often used as a placeholder.
if tr_header.year_data_recorded > 0:
year = tr_header.year_data_recorded
# The SEG Y rev 0 standard specifies the year to be a 4 digit
# number. Before that it was unclear if it should be a 2 or 4
# digit number. Old or wrong software might still write 2 digit
# years. Every number <30 will be mapped to 2000-2029 and every
# number between 30 and 99 will be mapped to 1930-1999.
if year < 100:
if year < 30:
year += 2000
else:
year += 1900
julday = tr_header.day_of_year
julday = tr_header.day_of_year
hour = tr_header.hour_of_day
minute = tr_header.minute_of_hour
second = tr_header.second_of_minute
trace.stats.starttime = UTCDateTime(
year=year, julday=julday, hour=hour, minute=minute,
second=second)
return stream
def _write_su(stream, filename, byteorder=None, **kwargs): # @UnusedVariable
"""
Writes a Seismic Unix (SU) file from given ObsPy Stream object.
.. warning::
This function should NOT be called directly, it registers via the
the :meth:`~obspy.core.stream.Stream.write` method of an
ObsPy :class:`~obspy.core.stream.Stream` object, call this instead.
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: The ObsPy Stream object to write.
:type filename: str
:param filename: Name of file to write.
:type byteorder: str or ``None``
:param byteorder: Determines the endianness of the file. Either ``'>'`` for
big endian or ``'<'`` for little endian. If is ``None``, it will either
be the endianness of the first Trace or if that is also not set, it
will be big endian. A mix between little and big endian for the headers
and traces is currently not supported.
This function will automatically set the data encoding field of the binary
file header so the user does not need to worry about it.
"""
# Check that the dtype for every Trace is correct.
for trace in stream:
# Check the dtype.
if trace.data.dtype != np.float32:
msg = """
The dtype of the data is not float32. You need to manually convert
the dtype. Please refer to the obspy.io.segy manual for more
details.
""".strip()
raise SEGYCoreWritingError(msg)
# Check the sample interval.
if trace.stats.delta > MAX_INTERVAL_IN_SECONDS:
msg = """
Seismic Unix supports a maximum interval of %s seconds in between
two samples (trace.stats.delta value).
""".strip()
msg = msg % MAX_INTERVAL_IN_SECONDS
raise SEGYSampleIntervalError(msg)
# Figure out endianness and the encoding of the textual file header.
if byteorder is None:
if hasattr(stream[0].stats, 'su') and hasattr(stream[0].stats.su,
'endian'):
byteorder = stream[0].stats.su.endian
else:
byteorder = '>'
# Loop over all Traces and create a SEGY File object.
su_file = SUFile()
# Add all traces.
for trace in stream:
new_trace = SEGYTrace()
new_trace.data = trace.data
# Use header saved in stats if one exists.
if hasattr(trace.stats, 'su') and \
hasattr(trace.stats.su, 'trace_header'):
this_trace_header = trace.stats.su.trace_header
else:
this_trace_header = AttribDict()
new_trace_header = new_trace.header
# Again loop over all field of the trace header and if they exists, set
# them. Ignore all additional attributes.
for _, item, _, _ in TRACE_HEADER_FORMAT:
if hasattr(this_trace_header, item):
setattr(new_trace_header, item,
getattr(this_trace_header, item))
starttime = trace.stats.starttime
# Set some special attributes, e.g. the sample count and other stuff.
new_trace_header.number_of_samples_in_this_trace = trace.stats.npts
new_trace_header.sample_interval_in_ms_for_this_trace = \
int(round((trace.stats.delta * 1E6)))
# Set the date of the Trace if it is not UTCDateTime(0).
if starttime == UTCDateTime(0):
new_trace.header.year_data_recorded = 0
new_trace.header.day_of_year = 0
new_trace.header.hour_of_day = 0
new_trace.header.minute_of_hour = 0
new_trace.header.second_of_minute = 0
else:
new_trace.header.year_data_recorded = starttime.year
new_trace.header.day_of_year = starttime.julday
new_trace.header.hour_of_day = starttime.hour
new_trace.header.minute_of_hour = starttime.minute
new_trace.header.second_of_minute = starttime.second
# Set the data encoding and the endianness.
new_trace.endian = byteorder
# Add the trace to the SEGYFile object.
su_file.traces.append(new_trace)
# Write the file
su_file.write(filename, endian=byteorder)
def _segy_trace_str_(self, *args, **kwargs):
"""
Monkey patch for the __str__ method of the Trace object. SEGY object do not
have network, station, channel codes. It just prints the trace sequence
number within the line.
"""
try:
out = "%s" % (
'Seq. No. in line: %4i' %
self.stats.segy.trace_header.trace_sequence_number_within_line)
except (KeyError, AttributeError):
# fall back if for some reason the segy attribute does not exists
return getattr(Trace, '__original_str__')(self, *args, **kwargs)
# output depending on delta or sampling rate bigger than one
if self.stats.sampling_rate < 0.1:
if hasattr(self.stats, 'preview') and self.stats.preview:
out = out + ' | '\
"%(starttime)s - %(endtime)s | " + \
"%(delta).1f s, %(npts)d samples [preview]"
else:
out = out + ' | '\
"%(starttime)s - %(endtime)s | " + \
"%(delta).1f s, %(npts)d samples"
else:
if hasattr(self.stats, 'preview') and self.stats.preview:
out = out + ' | '\
"%(starttime)s - %(endtime)s | " + \
"%(sampling_rate).1f Hz, %(npts)d samples [preview]"
else:
out = out + ' | '\
"%(starttime)s - %(endtime)s | " + \
"%(sampling_rate).1f Hz, %(npts)d samples"
# check for masked array
if np.ma.count_masked(self.data):
out += ' (masked)'
return out % (self.stats)
class LazyTraceHeaderAttribDict(AttribDict):
"""
This version of AttribDict will unpack header values only if needed.
This saves a huge amount of memory. The disadvantage is that it is no
longer possible to use tab completion in e.g. ipython.
This version is used for the SEGY/SU trace headers.
"""
readonly = ["unpacked_header", "endian"]
def __init__(self, unpacked_header, unpacked_header_endian, data={}):
dict.__init__(data)
self.update(data)
self.__dict__['unpacked_header'] = unpacked_header
self.__dict__['endian'] = unpacked_header_endian
def __getitem__(self, name):
# Return if already set.
if name in self.__dict__:
return self.__dict__[name]
# Otherwise try to unpack them.
try:
index = TRACE_HEADER_KEYS.index(name)
# If not found raise an attribute error.
except ValueError:
msg = "'%s' object has no attribute '%s'" % \
(self.__class__.__name__, name)
raise AttributeError(msg)
# Unpack the one value and set the class attribute so it will does not
# have to unpacked again if accessed in the future.
length, name, special_format, start = TRACE_HEADER_FORMAT[index]
string = self.__dict__['unpacked_header'][start: start + length]
attribute = unpack_header_value(self.__dict__['endian'], string,
length, special_format)
setattr(self, name, attribute)
return attribute
__getattr__ = __getitem__
def __deepcopy__(self, *args, **kwargs): # @UnusedVariable, see #689
ad = self.__class__(
unpacked_header=deepcopy(self.__dict__['unpacked_header']),
unpacked_header_endian=deepcopy(self.__dict__['endian']),
data=dict((k, deepcopy(v)) for k, v in self.__dict__.items()
if k not in self.readonly))
return ad
if __name__ == '__main__':
import doctest
doctest.testmod(exclude_empty=True)
# Monkey patch the __str__ method for the all Trace instances used in the
# following.
# XXX: Check if this is not messing anything up. Patching every single
# instance did not reliably work.
setattr(Trace, '__original_str__', Trace.__str__)
setattr(Trace, '__str__', _segy_trace_str_)