1# http://pyrocko.org - GPLv3
3#
4# The Pyrocko Developers, 21st Century
5# ---|P------/S----------~Lg----------
6'''
7Utility functions for Pyrocko.
9.. _time-handling-mode:
11High precision time handling mode
12.................................
14Pyrocko can treat timestamps either as standard double precision (64 bit)
15floating point values, or as high precision float (:py:class:`numpy.float128`
16or :py:class:`numpy.float96`, whichever is available), aliased here as
17:py:class:`pyrocko.util.hpfloat`. High precision time stamps are required when
18handling data with sub-millisecond precision, i.e. kHz/MHz data streams and
19event catalogs derived from such data.
21Not all functions in Pyrocko and in programs depending on Pyrocko may work
22correctly with high precision times. Therefore, Pyrocko's high precision time
23handling mode has to be actively activated by user config, command line option
24or enforced within a certain script/program.
26The default high precision time handling mode can be configured globally with
27the user config variable
28:py:gattr:`~pyrocko.config.Config.use_high_precision_time`. Calling the
29function :py:func:`use_high_precision_time` overrides the default from the
30config file. This function may be called at startup of a program/script
31requiring a specific time handling mode.
33To create a valid time stamp for use in Pyrocko (e.g. in
34:py:class:`~pyrocko.model.Event` or :py:class:`~pyrocko.trace.Trace` objects),
35use:
37.. code-block :: python
39 import time
40 from pyrocko import util
42 # By default using mode selected in user config, override with:
43 # util.use_high_precision_time(True) # force high precision mode
44 # util.use_high_precision_time(False) # force low precision mode
46 t1 = util.str_to_time('2020-08-27 10:22:00')
47 t2 = util.str_to_time('2020-08-27 10:22:00.111222')
48 t3 = util.to_time_float(time.time())
50 # To get the appropriate float class, use:
52 time_float = util.get_time_float()
53 # -> float, numpy.float128 or numpy.float96
54 [isinstance(t, time_float) for t in [t1, t2, t3]]
55 # -> [True, True, True]
57 # Shortcut:
58 util.check_time_class(t1)
60Module content
61..............
62'''
64from __future__ import division, print_function
66import time
67import logging
68import os
69import sys
70import re
71import calendar
72import math
73import fnmatch
74try:
75 import fcntl
76except ImportError:
77 fcntl = None
78import optparse
79import os.path as op
80import errno
82import numpy as num
83from scipy import signal
84import pyrocko
85from pyrocko import dummy_progressbar
88try:
89 from urllib.parse import urlencode, quote, unquote # noqa
90 from urllib.request import (
91 Request, build_opener, HTTPDigestAuthHandler, urlopen as _urlopen) # noqa
92 from urllib.error import HTTPError, URLError # noqa
94except ImportError:
95 from urllib import urlencode, quote, unquote # noqa
96 from urllib2 import (Request, build_opener, HTTPDigestAuthHandler, # noqa
97 HTTPError, URLError, urlopen as _urlopen) # noqa
99try:
100 import certifi
101 import ssl
102 g_ssl_context = ssl.create_default_context(cafile=certifi.where())
103except ImportError:
104 g_ssl_context = None
107class URLErrorSSL(URLError):
109 def __init__(self, urlerror):
110 self.__dict__ = urlerror.__dict__.copy()
112 def __str__(self):
113 return (
114 'Requesting web resource failed and the problem could be '
115 'related to SSL. Python standard libraries on some older '
116 'systems (like Ubuntu 14.04) are known to have trouble '
117 'with some SSL setups of today\'s servers: %s'
118 % URLError.__str__(self))
121def urlopen_ssl_check(*args, **kwargs):
122 try:
123 return urlopen(*args, **kwargs)
124 except URLError as e:
125 if str(e).find('SSL') != -1:
126 raise URLErrorSSL(e)
127 else:
128 raise
131def urlopen(*args, **kwargs):
133 if 'context' not in kwargs and g_ssl_context is not None:
134 kwargs['context'] = g_ssl_context
136 return _urlopen(*args, **kwargs)
139try:
140 long
141except NameError:
142 long = int
145force_dummy_progressbar = False
148try:
149 from pyrocko import util_ext
150except ImportError:
151 util_ext = None
154logger = logging.getLogger('pyrocko.util')
156try:
157 import progressbar as progressbar_mod
158except ImportError:
159 from pyrocko import dummy_progressbar as progressbar_mod
162try:
163 num_full = num.full
164except AttributeError:
165 def num_full(shape, fill_value, dtype=None, order='C'):
166 a = num.empty(shape, dtype=dtype, order=order)
167 a.fill(fill_value)
168 return a
170try:
171 num_full_like = num.full_like
172except AttributeError:
173 def num_full_like(arr, fill_value, dtype=None, order='K', subok=True):
174 a = num.empty_like(arr, dtype=dtype, order=order, subok=subok)
175 a.fill(fill_value)
176 return a
179def progressbar_module():
180 return progressbar_mod
183g_setup_logging_args = 'pyrocko', 'warning'
186def setup_logging(programname='pyrocko', levelname='warning'):
187 '''
188 Initialize logging.
190 :param programname: program name to be written in log
191 :param levelname: string indicating the logging level ('debug', 'info',
192 'warning', 'error', 'critical')
194 This function is called at startup by most pyrocko programs to set up a
195 consistent logging format. This is simply a shortcut to a call to
196 :py:func:`logging.basicConfig()`.
197 '''
199 global g_setup_logging_args
200 g_setup_logging_args = (programname, levelname)
202 levels = {'debug': logging.DEBUG,
203 'info': logging.INFO,
204 'warning': logging.WARNING,
205 'error': logging.ERROR,
206 'critical': logging.CRITICAL}
208 logging.basicConfig(
209 level=levels[levelname],
210 format=programname+':%(name)-25s - %(levelname)-8s - %(message)s')
213def subprocess_setup_logging_args():
214 '''
215 Get arguments from previous call to setup_logging.
217 These can be sent down to a worker process so it can setup its logging
218 in the same way as the main process.
219 '''
220 return g_setup_logging_args
223def data_file(fn):
224 return os.path.join(os.path.split(__file__)[0], 'data', fn)
227class DownloadError(Exception):
228 pass
231class PathExists(DownloadError):
232 pass
235def _download(url, fpath, username=None, password=None,
236 force=False, method='download', stats=None,
237 status_callback=None, entries_wanted=None,
238 recursive=False, header=None):
240 import requests
241 from requests.auth import HTTPBasicAuth
242 from requests.exceptions import HTTPError as req_HTTPError
244 requests.adapters.DEFAULT_RETRIES = 5
245 urljoin = requests.compat.urljoin
247 session = requests.Session()
248 session.header = header
249 session.auth = None if username is None\
250 else HTTPBasicAuth(username, password)
252 status = {
253 'ntotal_files': 0,
254 'nread_files': 0,
255 'ntotal_bytes_all_files': 0,
256 'nread_bytes_all_files': 0,
257 'ntotal_bytes_current_file': 0,
258 'nread_bytes_current_file': 0,
259 'finished': False
260 }
262 try:
263 url_to_size = {}
265 if callable(status_callback):
266 status_callback(status)
268 if not recursive and url.endswith('/'):
269 raise DownloadError(
270 'URL: %s appears to be a directory'
271 ' but recurvise download is False' % url)
273 if recursive and not url.endswith('/'):
274 url += '/'
276 def parse_directory_tree(url, subdir=''):
277 r = session.get(urljoin(url, subdir))
278 r.raise_for_status()
280 entries = re.findall(r'href="([a-zA-Z0-9_.-]+/?)"', r.text)
282 files = sorted(set(subdir + fn for fn in entries
283 if not fn.endswith('/')))
285 if entries_wanted is not None:
286 files = [fn for fn in files
287 if (fn in wanted for wanted in entries_wanted)]
289 status['ntotal_files'] += len(files)
291 dirs = sorted(set(subdir + dn for dn in entries
292 if dn.endswith('/')
293 and dn not in ('./', '../')))
295 for dn in dirs:
296 files.extend(parse_directory_tree(
297 url, subdir=dn))
299 return files
301 def get_content_length(url):
302 if url not in url_to_size:
303 r = session.head(url, headers={'Accept-Encoding': ''})
305 content_length = r.headers.get('content-length', None)
306 if content_length is None:
307 logger.debug('Could not get HTTP header '
308 'Content-Length for %s' % url)
310 content_length = None
312 else:
313 content_length = int(content_length)
314 status['ntotal_bytes_all_files'] += content_length
315 if callable(status_callback):
316 status_callback(status)
318 url_to_size[url] = content_length
320 return url_to_size[url]
322 def download_file(url, fn):
323 logger.info('starting download of %s...' % url)
324 ensuredirs(fn)
326 fsize = get_content_length(url)
327 status['ntotal_bytes_current_file'] = fsize
328 status['nread_bytes_current_file'] = 0
329 if callable(status_callback):
330 status_callback(status)
332 r = session.get(url, stream=True, timeout=5)
333 r.raise_for_status()
335 frx = 0
336 fn_tmp = fn + '.%i.temp' % os.getpid()
337 with open(fn_tmp, 'wb') as f:
338 for d in r.iter_content(chunk_size=1024):
339 f.write(d)
340 frx += len(d)
342 status['nread_bytes_all_files'] += len(d)
343 status['nread_bytes_current_file'] += len(d)
344 if callable(status_callback):
345 status_callback(status)
347 os.rename(fn_tmp, fn)
349 if fsize is not None and frx != fsize:
350 logger.warning(
351 'HTTP header Content-Length: %i bytes does not match '
352 'download size %i bytes' % (fsize, frx))
354 logger.info('finished download of %s' % url)
356 status['nread_files'] += 1
357 if callable(status_callback):
358 status_callback(status)
360 if recursive:
361 if op.exists(fpath) and not force:
362 raise PathExists('path %s already exists' % fpath)
364 files = parse_directory_tree(url)
366 dsize = 0
367 for fn in files:
368 file_url = urljoin(url, fn)
369 dsize += get_content_length(file_url) or 0
371 if method == 'calcsize':
372 return dsize
374 else:
375 for fn in files:
376 file_url = urljoin(url, fn)
377 download_file(file_url, op.join(fpath, fn))
379 else:
380 status['ntotal_files'] += 1
381 if callable(status_callback):
382 status_callback(status)
384 fsize = get_content_length(url)
385 if method == 'calcsize':
386 return fsize
387 else:
388 download_file(url, fpath)
390 except req_HTTPError as e:
391 logging.warning("http error: %s" % e)
392 raise DownloadError('could not download file(s) from: %s' % url)
394 finally:
395 status['finished'] = True
396 if callable(status_callback):
397 status_callback(status)
398 session.close()
401def download_file(
402 url, fpath, username=None, password=None, status_callback=None,
403 **kwargs):
404 return _download(
405 url, fpath, username, password,
406 recursive=False,
407 status_callback=status_callback,
408 **kwargs)
411def download_dir(
412 url, fpath, username=None, password=None, status_callback=None,
413 **kwargs):
415 return _download(
416 url, fpath, username, password,
417 recursive=True,
418 status_callback=status_callback,
419 **kwargs)
422class HPFloatUnavailable(Exception):
423 pass
426class dummy_hpfloat(object):
427 def __init__(self, *args, **kwargs):
428 raise HPFloatUnavailable(
429 'NumPy lacks support for float128 or float96 data type on this '
430 'platform.')
433if hasattr(num, 'float128'):
434 hpfloat = num.float128
436elif hasattr(num, 'float96'):
437 hpfloat = num.float96
439else:
440 hpfloat = dummy_hpfloat
443g_time_float = None
444g_time_dtype = None
447class TimeFloatSettingError(Exception):
448 pass
451def use_high_precision_time(enabled):
452 '''
453 Globally force a specific time handling mode.
455 See :ref:`High precision time handling mode <time-handling-mode>`.
457 :param enabled: enable/disable use of high precision time type
458 :type enabled: bool
460 This function should be called before handling/reading any time data.
461 It can only be called once.
463 Special attention is required when using multiprocessing on a platform
464 which does not use fork under the hood. In such cases, the desired setting
465 must be set also in the subprocess.
466 '''
467 _setup_high_precision_time_mode(enabled_app=enabled)
470def _setup_high_precision_time_mode(enabled_app=False):
471 global g_time_float
472 global g_time_dtype
474 if not (g_time_float is None and g_time_dtype is None):
475 raise TimeFloatSettingError(
476 'Cannot set time handling mode: too late, it has already been '
477 'fixed by an earlier call.')
479 from pyrocko import config
481 conf = config.config()
482 enabled_config = conf.use_high_precision_time
484 enabled_env = os.environ.get('PYROCKO_USE_HIGH_PRECISION_TIME', None)
485 if enabled_env is not None:
486 try:
487 enabled_env = int(enabled_env) == 1
488 except ValueError:
489 raise TimeFloatSettingError(
490 'Environment variable PYROCKO_USE_HIGH_PRECISION_TIME '
491 'should be set to 0 or 1.')
493 enabled = enabled_config
494 mode_from = 'config variable `use_high_precision_time`'
495 notify = enabled
497 if enabled_env is not None:
498 if enabled_env != enabled:
499 notify = True
500 enabled = enabled_env
501 mode_from = 'environment variable `PYROCKO_USE_HIGH_PRECISION_TIME`'
503 if enabled_app is not None:
504 if enabled_app != enabled:
505 notify = True
506 enabled = enabled_app
507 mode_from = 'application override'
509 logger.debug('''
510Pyrocko high precision time mode selection (latter override earlier):
511 config: %s
512 env: %s
513 app: %s
514 -> enabled: %s'''.lstrip() % (
515 enabled_config, enabled_env, enabled_app, enabled))
517 if notify:
518 logger.info('Pyrocko high precision time mode %s by %s.' % (
519 'activated' if enabled else 'deactivated',
520 mode_from))
522 if enabled:
523 g_time_float = hpfloat
524 g_time_dtype = hpfloat
525 else:
526 g_time_float = float
527 g_time_dtype = num.float64
530def get_time_float():
531 '''
532 Get the effective float class for timestamps.
534 See :ref:`High precision time handling mode <time-handling-mode>`.
536 :returns: :py:class:`float` or :py:class:`hpfloat`, depending on the
537 current time handling mode
538 '''
539 global g_time_float
541 if g_time_float is None:
542 _setup_high_precision_time_mode()
544 return g_time_float
547def get_time_dtype():
548 '''
549 Get effective NumPy float class to handle timestamps.
551 See :ref:`High precision time handling mode <time-handling-mode>`.
552 '''
554 global g_time_dtype
556 if g_time_dtype is None:
557 _setup_high_precision_time_mode()
559 return g_time_dtype
562def to_time_float(t):
563 '''
564 Convert float to valid time stamp in the current time handling mode.
566 See :ref:`High precision time handling mode <time-handling-mode>`.
567 '''
568 return get_time_float()(t)
571class TimestampTypeError(ValueError):
572 pass
575def check_time_class(t, error='raise'):
576 '''
577 Type-check variable against current time handling mode.
579 See :ref:`High precision time handling mode <time-handling-mode>`.
580 '''
582 if t == 0.0:
583 return
585 if not isinstance(t, get_time_float()):
586 message = (
587 'Timestamp %g is of type %s but should be of type %s with '
588 'Pyrocko\'s currently selected time handling mode.\n\n'
589 'See https://pyrocko.org/docs/current/library/reference/util.html'
590 '#high-precision-time-handling-mode' % (
591 t, type(t), get_time_float()))
593 if error == 'raise':
594 raise TimestampTypeError(message)
595 elif error == 'warn':
596 logger.warning(message)
597 else:
598 assert False
601class Stopwatch(object):
602 '''
603 Simple stopwatch to measure elapsed wall clock time.
605 Usage::
607 s = Stopwatch()
608 time.sleep(1)
609 print s()
610 time.sleep(1)
611 print s()
612 '''
614 def __init__(self):
615 self.start = time.time()
617 def __call__(self):
618 return time.time() - self.start
621def wrap(text, line_length=80):
622 '''
623 Paragraph and list-aware wrapping of text.
624 '''
626 text = text.strip('\n')
627 at_lineend = re.compile(r' *\n')
628 at_para = re.compile(r'((^|(\n\s*)?\n)(\s+[*] )|\n\s*\n)')
630 paragraphs = at_para.split(text)[::5]
631 listindents = at_para.split(text)[4::5]
632 newlist = at_para.split(text)[3::5]
634 listindents[0:0] = [None]
635 listindents.append(True)
636 newlist.append(None)
638 det_indent = re.compile(r'^ *')
640 outlines = []
641 for ip, p in enumerate(paragraphs):
642 if not p:
643 continue
645 if listindents[ip] is None:
646 _indent = det_indent.findall(p)[0]
647 findent = _indent
648 else:
649 findent = listindents[ip]
650 _indent = ' ' * len(findent)
652 ll = line_length - len(_indent)
653 llf = ll
655 oldlines = [s.strip() for s in at_lineend.split(p.rstrip())]
656 p1 = ' '.join(oldlines)
657 possible = re.compile(r'(^.{1,%i}|.{1,%i})( |$)' % (llf, ll))
658 for imatch, match in enumerate(possible.finditer(p1)):
659 parout = match.group(1)
660 if imatch == 0:
661 outlines.append(findent + parout)
662 else:
663 outlines.append(_indent + parout)
665 if ip != len(paragraphs)-1 and (
666 listindents[ip] is None
667 or newlist[ip] is not None
668 or listindents[ip+1] is None):
670 outlines.append('')
672 return outlines
675def ewrap(lines, width=80, indent=''):
676 lines = list(lines)
677 if not lines:
678 return ''
679 fwidth = max(len(s) for s in lines)
680 nx = max(1, (80-len(indent)) // (fwidth+1))
681 i = 0
682 rows = []
683 while i < len(lines):
684 rows.append(indent + ' '.join(x.ljust(fwidth) for x in lines[i:i+nx]))
685 i += nx
687 return '\n'.join(rows)
690class BetterHelpFormatter(optparse.IndentedHelpFormatter):
692 def __init__(self, *args, **kwargs):
693 optparse.IndentedHelpFormatter.__init__(self, *args, **kwargs)
695 def format_option(self, option):
696 '''
697 From IndentedHelpFormatter but using a different wrap method.
698 '''
700 help_text_position = 4 + self.current_indent
701 help_text_width = self.width - help_text_position
703 opts = self.option_strings[option]
704 opts = "%*s%s" % (self.current_indent, "", opts)
705 if option.help:
706 help_text = self.expand_default(option)
708 if self.help_position + len(help_text) + 1 <= self.width:
709 lines = [
710 '',
711 '%-*s %s' % (self.help_position, opts, help_text),
712 '']
713 else:
714 lines = ['']
715 lines.append(opts)
716 lines.append('')
717 if option.help:
718 help_lines = wrap(help_text, help_text_width)
719 lines.extend(["%*s%s" % (help_text_position, "", line)
720 for line in help_lines])
721 lines.append('')
723 return "\n".join(lines)
725 def format_description(self, description):
726 if not description:
727 return ''
729 if self.current_indent == 0:
730 lines = []
731 else:
732 lines = ['']
734 lines.extend(wrap(description, self.width - self.current_indent))
735 if self.current_indent == 0:
736 lines.append('\n')
738 return '\n'.join(
739 ['%*s%s' % (self.current_indent, '', line) for line in lines])
742def progressbar(label, maxval):
743 progressbar_mod = progressbar_module()
744 if force_dummy_progressbar:
745 progressbar_mod = dummy_progressbar
747 widgets = [
748 label, ' ',
749 progressbar_mod.Bar(marker='-', left='[', right=']'), ' ',
750 progressbar_mod.Percentage(), ' ',
751 progressbar_mod.ETA()]
753 pbar = progressbar_mod.ProgressBar(widgets=widgets, maxval=maxval).start()
754 return pbar
757def progress_beg(label):
758 '''
759 Notify user that an operation has started.
761 :param label: name of the operation
763 To be used in conjuction with :py:func:`progress_end`.
764 '''
766 sys.stderr.write(label)
767 sys.stderr.flush()
770def progress_end(label=''):
771 '''
772 Notify user that an operation has ended.
774 :param label: name of the operation
776 To be used in conjuction with :py:func:`progress_beg`.
777 '''
779 sys.stderr.write(' done. %s\n' % label)
780 sys.stderr.flush()
783class ArangeError(Exception):
784 pass
787def arange2(start, stop, step, dtype=float, epsilon=1e-6, error='raise'):
788 '''
789 Return evenly spaced numbers over a specified interval.
791 Like :py:func:`numpy.arange` but returning floating point numbers by
792 default and with defined behaviour when stepsize is inconsistent with
793 interval bounds. It is considered inconsistent if the difference between
794 the closest multiple of ``step`` and ``stop`` is larger than ``epsilon *
795 step``. Inconsistencies are handled according to the ``error`` parameter.
796 If it is set to ``'raise'`` an exception of type :py:exc:`ArangeError` is
797 raised. If it is set to ``'round'``, ``'floor'``, or ``'ceil'``, ``stop``
798 is silently changed to the closest, the next smaller, or next larger
799 multiple of ``step``, respectively.
800 '''
802 assert error in ('raise', 'round', 'floor', 'ceil')
804 start = dtype(start)
805 stop = dtype(stop)
806 step = dtype(step)
808 rnd = {'floor': math.floor, 'ceil': math.ceil}.get(error, round)
810 n = int(rnd((stop - start) / step)) + 1
811 stop_check = start + (n-1) * step
813 if error == 'raise' and abs(stop_check - stop) > step * epsilon:
814 raise ArangeError(
815 'inconsistent range specification: start=%g, stop=%g, step=%g'
816 % (start, stop, step))
818 x = num.arange(n, dtype=dtype)
819 x *= step
820 x += start
821 return x
824def polylinefit(x, y, n_or_xnodes):
825 '''
826 Fit piece-wise linear function to data.
828 :param x,y: arrays with coordinates of data
829 :param n_or_xnodes: int, number of segments or x coordinates of polyline
831 :returns: `(xnodes, ynodes, rms_error)` arrays with coordinates of
832 polyline, root-mean-square error
833 '''
835 x = num.asarray(x)
836 y = num.asarray(y)
838 if isinstance(n_or_xnodes, int):
839 n = n_or_xnodes
840 xmin = x.min()
841 xmax = x.max()
842 xnodes = num.linspace(xmin, xmax, n+1)
843 else:
844 xnodes = num.asarray(n_or_xnodes)
845 n = xnodes.size - 1
847 assert len(x) == len(y)
848 assert n > 0
850 ndata = len(x)
851 a = num.zeros((ndata+(n-1), n*2))
852 for i in range(n):
853 xmin_block = xnodes[i]
854 xmax_block = xnodes[i+1]
855 if i == n-1: # don't loose last point
856 indices = num.where(
857 num.logical_and(xmin_block <= x, x <= xmax_block))[0]
858 else:
859 indices = num.where(
860 num.logical_and(xmin_block <= x, x < xmax_block))[0]
862 a[indices, i*2] = x[indices]
863 a[indices, i*2+1] = 1.0
865 w = float(ndata)*100.
866 if i < n-1:
867 a[ndata+i, i*2] = xmax_block*w
868 a[ndata+i, i*2+1] = 1.0*w
869 a[ndata+i, i*2+2] = -xmax_block*w
870 a[ndata+i, i*2+3] = -1.0*w
872 d = num.concatenate((y, num.zeros(n-1)))
873 model = num.linalg.lstsq(a, d, rcond=-1)[0].reshape((n, 2))
875 ynodes = num.zeros(n+1)
876 ynodes[:n] = model[:, 0]*xnodes[:n] + model[:, 1]
877 ynodes[1:] += model[:, 0]*xnodes[1:] + model[:, 1]
878 ynodes[1:n] *= 0.5
880 rms_error = num.sqrt(num.mean((num.interp(x, xnodes, ynodes) - y)**2))
882 return xnodes, ynodes, rms_error
885def plf_integrate_piecewise(x_edges, x, y):
886 '''
887 Calculate definite integral of piece-wise linear function on intervals.
889 Use trapezoidal rule to calculate definite integral of a piece-wise linear
890 function for a series of consecutive intervals. ``x_edges`` and ``x`` must
891 be sorted.
893 :param x_edges: array with edges of the intervals
894 :param x,y: arrays with coordinates of piece-wise linear function's
895 control points
896 '''
898 x_all = num.concatenate((x, x_edges))
899 ii = num.argsort(x_all)
900 y_edges = num.interp(x_edges, x, y)
901 y_all = num.concatenate((y, y_edges))
902 xs = x_all[ii]
903 ys = y_all[ii]
904 y_all[ii[1:]] = num.cumsum((xs[1:] - xs[:-1]) * 0.5 * (ys[1:] + ys[:-1]))
905 return num.diff(y_all[-len(y_edges):])
908def diff_fd_1d_4o(dt, data):
909 '''
910 Approximate first derivative of an array (forth order, central FD).
912 :param dt: sampling interval
913 :param data: NumPy array with data samples
915 :returns: NumPy array with same shape as input
917 Interior points are approximated to fourth order, edge points to first
918 order right- or left-sided respectively, points next to edge to second
919 order central.
920 '''
921 import scipy.signal
923 ddata = num.empty_like(data, dtype=float)
925 if data.size >= 5:
926 ddata[2:-2] = scipy.signal.lfilter(
927 [-1., +8., 0., -8., 1.], [1.], data)[4:] / (12.*dt)
929 if data.size >= 3:
930 ddata[1] = (data[2] - data[0]) / (2. * dt)
931 ddata[-2] = (data[-1] - data[-3]) / (2. * dt)
933 if data.size >= 2:
934 ddata[0] = (data[1] - data[0]) / dt
935 ddata[-1] = (data[-1] - data[-2]) / dt
937 if data.size == 1:
938 ddata[0] = 0.0
940 return ddata
943def diff_fd_1d_2o(dt, data):
944 '''
945 Approximate first derivative of an array (second order, central FD).
947 :param dt: sampling interval
948 :param data: NumPy array with data samples
950 :returns: NumPy array with same shape as input
952 Interior points are approximated to second order, edge points to first
953 order right- or left-sided respectively.
955 Uses :py:func:`numpy.gradient`.
956 '''
958 return num.gradient(data, dt)
961def diff_fd_2d_4o(dt, data):
962 '''
963 Approximate second derivative of an array (forth order, central FD).
965 :param dt: sampling interval
966 :param data: NumPy array with data samples
968 :returns: NumPy array with same shape as input
970 Interior points are approximated to fourth order, next-to-edge points to
971 second order, edge points repeated.
972 '''
973 import scipy.signal
975 ddata = num.empty_like(data, dtype=float)
977 if data.size >= 5:
978 ddata[2:-2] = scipy.signal.lfilter(
979 [-1., +16., -30., +16., -1.], [1.], data)[4:] / (12.*dt**2)
981 if data.size >= 3:
982 ddata[:2] = (data[2] - 2.0 * data[1] + data[0]) / dt**2
983 ddata[-2:] = (data[-1] - 2.0 * data[-2] + data[-3]) / dt**2
985 if data.size < 3:
986 ddata[:] = 0.0
988 return ddata
991def diff_fd_2d_2o(dt, data):
992 '''
993 Approximate second derivative of an array (second order, central FD).
995 :param dt: sampling interval
996 :param data: NumPy array with data samples
998 :returns: NumPy array with same shape as input
1000 Interior points are approximated to second order, edge points repeated.
1001 '''
1002 import scipy.signal
1004 ddata = num.empty_like(data, dtype=float)
1006 if data.size >= 3:
1007 ddata[1:-1] = scipy.signal.lfilter(
1008 [1., -2., 1.], [1.], data)[2:] / (dt**2)
1010 ddata[0] = ddata[1]
1011 ddata[-1] = ddata[-2]
1013 if data.size < 3:
1014 ddata[:] = 0.0
1016 return ddata
1019def diff_fd(n, order, dt, data):
1020 '''
1021 Approximate 1st or 2nd derivative of an array.
1023 :param n: 1 for first derivative, 2 for second
1024 :param order: order of the approximation 2 and 4 are supported
1025 :param dt: sampling interval
1026 :param data: NumPy array with data samples
1028 :returns: NumPy array with same shape as input
1030 This is a frontend to the functions :py:func:`diff_fd_1d_2o`,
1031 :py:func:`diff_fd_1d_4o`, :py:func:`diff_fd_2d_2o`, and
1032 :py:func:`diff_fd_2d_4o`.
1034 Raises :py:exc:`ValueError` for unsupported `n` or `order`.
1035 '''
1037 funcs = {
1038 1: {2: diff_fd_1d_2o, 4: diff_fd_1d_4o},
1039 2: {2: diff_fd_2d_2o, 4: diff_fd_2d_4o}}
1041 try:
1042 funcs_n = funcs[n]
1043 except KeyError:
1044 raise ValueError(
1045 'pyrocko.util.diff_fd: '
1046 'Only 1st and 2sd derivatives are supported.')
1048 try:
1049 func = funcs_n[order]
1050 except KeyError:
1051 raise ValueError(
1052 'pyrocko.util.diff_fd: '
1053 'Order %i is not supported for %s derivative. Supported: %s' % (
1054 order, ['', '1st', '2nd'][n],
1055 ', '.join('%i' % order for order in sorted(funcs_n.keys()))))
1057 return func(dt, data)
1060class GlobalVars(object):
1061 reuse_store = dict()
1062 decitab_nmax = 0
1063 decitab = {}
1064 decimate_fir_coeffs = {}
1065 decimate_fir_remez_coeffs = {}
1066 decimate_iir_coeffs = {}
1067 re_frac = None
1070def decimate_coeffs(q, n=None, ftype='iir'):
1072 q = int(q)
1074 if n is None:
1075 if ftype == 'fir':
1076 n = 30
1077 elif ftype == 'fir-remez':
1078 n = 40*q
1079 else:
1080 n = 8
1082 if ftype == 'fir':
1083 coeffs = GlobalVars.decimate_fir_coeffs
1084 if (n, 1./q) not in coeffs:
1085 coeffs[n, 1./q] = signal.firwin(n+1, .75/q, window='hamming')
1087 b = coeffs[n, 1./q]
1088 return b, [1.], n
1090 elif ftype == 'fir-remez':
1091 coeffs = GlobalVars.decimate_fir_remez_coeffs
1092 if (n, 1./q) not in coeffs:
1093 coeffs[n, 1./q] = signal.remez(
1094 n+1, (0., .75/q, 1./q, 1.),
1095 (1., 0.), Hz=2, weight=(1, 50))
1096 b = coeffs[n, 1./q]
1097 return b, [1.], n
1099 else:
1100 coeffs = GlobalVars.decimate_iir_coeffs
1101 if (n, 0.05, 0.8/q) not in coeffs:
1102 coeffs[n, 0.05, 0.8/q] = signal.cheby1(n, 0.05, 0.8/q)
1104 b, a = coeffs[n, 0.05, 0.8/q]
1105 return b, a, n
1108def decimate(x, q, n=None, ftype='iir', zi=None, ioff=0):
1109 '''
1110 Downsample the signal x by an integer factor q, using an order n filter
1112 By default, an order 8 Chebyshev type I filter is used or a 30 point FIR
1113 filter with hamming window if ftype is 'fir'.
1115 :param x: the signal to be downsampled (1D :class:`numpy.ndarray`)
1116 :param q: the downsampling factor
1117 :param n: order of the filter (1 less than the length of the filter for a
1118 `fir` filter)
1119 :param ftype: type of the filter; can be `iir`, `fir` or `fir-remez`
1121 :returns: the downsampled signal (1D :class:`numpy.ndarray`)
1123 '''
1125 b, a, n = decimate_coeffs(q, n, ftype)
1127 if zi is None or zi is True:
1128 zi_ = num.zeros(max(len(a), len(b))-1, dtype=float)
1129 else:
1130 zi_ = zi
1132 y, zf = signal.lfilter(b, a, x, zi=zi_)
1134 if zi is not None:
1135 return y[n//2+ioff::q].copy(), zf
1136 else:
1137 return y[n//2+ioff::q].copy()
1140class UnavailableDecimation(Exception):
1141 '''
1142 Exception raised by :py:func:`decitab` for unavailable decimation factors.
1143 '''
1145 pass
1148def gcd(a, b, epsilon=1e-7):
1149 '''
1150 Greatest common divisor.
1151 '''
1153 while b > epsilon*a:
1154 a, b = b, a % b
1156 return a
1159def lcm(a, b):
1160 '''
1161 Least common multiple.
1162 '''
1164 return a*b // gcd(a, b)
1167def mk_decitab(nmax=100):
1168 '''
1169 Make table with decimation sequences.
1171 Decimation from one sampling rate to a lower one is achieved by a
1172 successive application of :py:func:`decimation` with small integer
1173 downsampling factors (because using large downampling factors can make the
1174 decimation unstable or slow). This function sets up a table with downsample
1175 sequences for factors up to ``nmax``.
1176 '''
1178 tab = GlobalVars.decitab
1179 for i in range(1, 10):
1180 for j in range(1, i+1):
1181 for k in range(1, j+1):
1182 for l_ in range(1, k+1):
1183 for m in range(1, l_+1):
1184 p = i*j*k*l_*m
1185 if p > nmax:
1186 break
1187 if p not in tab:
1188 tab[p] = (i, j, k, l_, m)
1189 if i*j*k*l_ > nmax:
1190 break
1191 if i*j*k > nmax:
1192 break
1193 if i*j > nmax:
1194 break
1195 if i > nmax:
1196 break
1198 GlobalVars.decitab_nmax = nmax
1201def zfmt(n):
1202 return '%%0%ii' % (int(math.log10(n - 1)) + 1)
1205def _year_to_time(year):
1206 tt = (year, 1, 1, 0, 0, 0)
1207 return to_time_float(calendar.timegm(tt))
1210def _working_year(year):
1211 try:
1212 tt = (year, 1, 1, 0, 0, 0)
1213 t = calendar.timegm(tt)
1214 tt2_ = time.gmtime(t)
1215 tt2 = tuple(tt2_)[:6]
1216 if tt != tt2:
1217 return False
1219 s = '%i-01-01 00:00:00' % year
1220 s2 = time.strftime('%Y-%m-%d %H:%M:%S', tt2_)
1221 if s != s2:
1222 return False
1224 t3 = str_to_time(s2, format='%Y-%m-%d %H:%M:%S')
1225 s3 = time_to_str(t3, format='%Y-%m-%d %H:%M:%S')
1226 if s3 != s2:
1227 return False
1229 except Exception:
1230 return False
1232 return True
1235def working_system_time_range(year_min_lim=None, year_max_lim=None):
1236 '''
1237 Check time range supported by the systems's time conversion functions.
1239 Returns system time stamps of start of year of first/last fully supported
1240 year span. If this is before 1900 or after 2100, return first/last century
1241 which is fully supported.
1243 :returns: ``(tmin, tmax, year_min, year_max)``
1244 '''
1246 year0 = 2000
1247 year_min = year0
1248 year_max = year0
1250 itests = list(range(101))
1251 for i in range(19):
1252 itests.append(200 + i*100)
1254 for i in itests:
1255 year = year0 - i
1256 if year_min_lim is not None and year < year_min_lim:
1257 year_min = year_min_lim
1258 break
1259 elif not _working_year(year):
1260 break
1261 else:
1262 year_min = year
1264 for i in itests:
1265 year = year0 + i
1266 if year_max_lim is not None and year > year_max_lim:
1267 year_max = year_max_lim
1268 break
1269 elif not _working_year(year + 1):
1270 break
1271 else:
1272 year_max = year
1274 return (
1275 _year_to_time(year_min),
1276 _year_to_time(year_max),
1277 year_min, year_max)
1280g_working_system_time_range = None
1283def get_working_system_time_range():
1284 '''
1285 Caching variant of :py:func:`working_system_time_range`.
1286 '''
1288 global g_working_system_time_range
1289 if g_working_system_time_range is None:
1290 g_working_system_time_range = working_system_time_range()
1292 return g_working_system_time_range
1295def is_working_time(t):
1296 tmin, tmax, _, _ = get_working_system_time_range()
1297 return tmin <= t <= tmax
1300def julian_day_of_year(timestamp):
1301 '''
1302 Get the day number after the 1st of January of year in ``timestamp``.
1304 :returns: day number as int
1305 '''
1307 return time.gmtime(int(timestamp)).tm_yday
1310def hour_start(timestamp):
1311 '''
1312 Get beginning of hour for any point in time.
1314 :param timestamp: time instant as system timestamp (in seconds)
1316 :returns: instant of hour start as system timestamp
1317 '''
1319 tt = time.gmtime(int(timestamp))
1320 tts = tt[0:4] + (0, 0)
1321 return to_time_float(calendar.timegm(tts))
1324def day_start(timestamp):
1325 '''
1326 Get beginning of day for any point in time.
1328 :param timestamp: time instant as system timestamp (in seconds)
1330 :returns: instant of day start as system timestamp
1331 '''
1333 tt = time.gmtime(int(timestamp))
1334 tts = tt[0:3] + (0, 0, 0)
1335 return to_time_float(calendar.timegm(tts))
1338def month_start(timestamp):
1339 '''
1340 Get beginning of month for any point in time.
1342 :param timestamp: time instant as system timestamp (in seconds)
1344 :returns: instant of month start as system timestamp
1345 '''
1347 tt = time.gmtime(int(timestamp))
1348 tts = tt[0:2] + (1, 0, 0, 0)
1349 return to_time_float(calendar.timegm(tts))
1352def year_start(timestamp):
1353 '''
1354 Get beginning of year for any point in time.
1356 :param timestamp: time instant as system timestamp (in seconds)
1358 :returns: instant of year start as system timestamp
1359 '''
1361 tt = time.gmtime(int(timestamp))
1362 tts = tt[0:1] + (1, 1, 0, 0, 0)
1363 return to_time_float(calendar.timegm(tts))
1366def iter_days(tmin, tmax):
1367 '''
1368 Yields begin and end of days until given time span is covered.
1370 :param tmin,tmax: input time span
1372 :yields: tuples with (begin, end) of days as system timestamps
1373 '''
1375 t = day_start(tmin)
1376 while t < tmax:
1377 tend = day_start(t + 26*60*60)
1378 yield t, tend
1379 t = tend
1382def iter_months(tmin, tmax):
1383 '''
1384 Yields begin and end of months until given time span is covered.
1386 :param tmin,tmax: input time span
1388 :yields: tuples with (begin, end) of months as system timestamps
1389 '''
1391 t = month_start(tmin)
1392 while t < tmax:
1393 tend = month_start(t + 24*60*60*33)
1394 yield t, tend
1395 t = tend
1398def iter_years(tmin, tmax):
1399 '''
1400 Yields begin and end of years until given time span is covered.
1402 :param tmin,tmax: input time span
1404 :yields: tuples with (begin, end) of years as system timestamps
1405 '''
1407 t = year_start(tmin)
1408 while t < tmax:
1409 tend = year_start(t + 24*60*60*369)
1410 yield t, tend
1411 t = tend
1414def today():
1415 return day_start(time.time())
1418def tomorrow():
1419 return day_start(time.time() + 24*60*60)
1422def decitab(n):
1423 '''
1424 Get integer decimation sequence for given downampling factor.
1426 :param n: target decimation factor
1428 :returns: tuple with downsampling sequence
1429 '''
1431 if n > GlobalVars.decitab_nmax:
1432 mk_decitab(n*2)
1433 if n not in GlobalVars.decitab:
1434 raise UnavailableDecimation('ratio = %g' % n)
1435 return GlobalVars.decitab[n]
1438def ctimegm(s, format="%Y-%m-%d %H:%M:%S"):
1439 '''
1440 Convert string representing UTC time to system time.
1442 :param s: string to be interpreted
1443 :param format: format string passed to :py:func:`strptime`
1445 :returns: system time stamp
1447 Interpretes string with format ``'%Y-%m-%d %H:%M:%S'``, using strptime.
1449 .. note::
1450 This function is to be replaced by :py:func:`str_to_time`.
1451 '''
1453 return calendar.timegm(time.strptime(s, format))
1456def gmctime(t, format="%Y-%m-%d %H:%M:%S"):
1457 '''
1458 Get string representation from system time, UTC.
1460 Produces string with format ``'%Y-%m-%d %H:%M:%S'``, using strftime.
1462 .. note::
1463 This function is to be repaced by :py:func:`time_to_str`.
1464 '''
1466 return time.strftime(format, time.gmtime(t))
1469def gmctime_v(t, format="%a, %d %b %Y %H:%M:%S"):
1470 '''
1471 Get string representation from system time, UTC. Same as
1472 :py:func:`gmctime` but with a more verbose default format.
1474 .. note::
1475 This function is to be replaced by :py:func:`time_to_str`.
1476 '''
1478 return time.strftime(format, time.gmtime(t))
1481def gmctime_fn(t, format="%Y-%m-%d_%H-%M-%S"):
1482 '''
1483 Get string representation from system time, UTC. Same as
1484 :py:func:`gmctime` but with a default usable in filenames.
1486 .. note::
1487 This function is to be replaced by :py:func:`time_to_str`.
1488 '''
1490 return time.strftime(format, time.gmtime(t))
1493class TimeStrError(Exception):
1494 pass
1497class FractionalSecondsMissing(TimeStrError):
1498 '''
1499 Exception raised by :py:func:`str_to_time` when the given string lacks
1500 fractional seconds.
1501 '''
1503 pass
1506class FractionalSecondsWrongNumberOfDigits(TimeStrError):
1507 '''
1508 Exception raised by :py:func:`str_to_time` when the given string has an
1509 incorrect number of digits in the fractional seconds part.
1510 '''
1512 pass
1515def _endswith_n(s, endings):
1516 for ix, x in enumerate(endings):
1517 if s.endswith(x):
1518 return ix
1519 return -1
1522def str_to_time(s, format='%Y-%m-%d %H:%M:%S.OPTFRAC'):
1523 '''
1524 Convert string representing UTC time to floating point system time.
1526 :param s: string representing UTC time
1527 :param format: time string format
1528 :returns: system time stamp as floating point value
1530 Uses the semantics of :py:func:`time.strptime` but allows for fractional
1531 seconds. If the format ends with ``'.FRAC'``, anything after a dot is
1532 interpreted as fractional seconds. If the format ends with ``'.OPTFRAC'``,
1533 the fractional part, including the dot is made optional. The latter has the
1534 consequence, that the time strings and the format may not contain any other
1535 dots. If the format ends with ``'.xFRAC'`` where x is 1, 2, or 3, it is
1536 ensured, that exactly that number of digits are present in the fractional
1537 seconds.
1538 '''
1540 time_float = get_time_float()
1542 if util_ext is not None:
1543 try:
1544 t, tfrac = util_ext.stt(s, format)
1545 except util_ext.UtilExtError as e:
1546 raise TimeStrError(
1547 '%s, string=%s, format=%s' % (str(e), s, format))
1549 return time_float(t)+tfrac
1551 fracsec = 0.
1552 fixed_endings = '.FRAC', '.1FRAC', '.2FRAC', '.3FRAC'
1554 iend = _endswith_n(format, fixed_endings)
1555 if iend != -1:
1556 dotpos = s.rfind('.')
1557 if dotpos == -1:
1558 raise FractionalSecondsMissing(
1559 'string=%s, format=%s' % (s, format))
1561 if iend > 0 and iend != (len(s)-dotpos-1):
1562 raise FractionalSecondsWrongNumberOfDigits(
1563 'string=%s, format=%s' % (s, format))
1565 format = format[:-len(fixed_endings[iend])]
1566 fracsec = float(s[dotpos:])
1567 s = s[:dotpos]
1569 elif format.endswith('.OPTFRAC'):
1570 dotpos = s.rfind('.')
1571 format = format[:-8]
1572 if dotpos != -1 and len(s[dotpos:]) > 1:
1573 fracsec = float(s[dotpos:])
1575 if dotpos != -1:
1576 s = s[:dotpos]
1578 try:
1579 return time_float(calendar.timegm(time.strptime(s, format))) \
1580 + fracsec
1581 except ValueError as e:
1582 raise TimeStrError('%s, string=%s, format=%s' % (str(e), s, format))
1585stt = str_to_time
1588def str_to_time_fillup(s):
1589 '''
1590 Default :py:func:`str_to_time` with filling in of missing values.
1592 Allows e.g. `'2010-01-01 00:00:00'` as `'2010-01-01 00:00'`,
1593 `'2010-01-01 00'`, ..., or `'2010'`.
1594 '''
1596 if len(s) in (4, 7, 10, 13, 16):
1597 s += '0000-01-01 00:00:00'[len(s):]
1599 return str_to_time(s)
1602def time_to_str(t, format='%Y-%m-%d %H:%M:%S.3FRAC'):
1603 '''
1604 Get string representation for floating point system time.
1606 :param t: floating point system time
1607 :param format: time string format
1608 :returns: string representing UTC time
1610 Uses the semantics of :py:func:`time.strftime` but additionally allows for
1611 fractional seconds. If ``format`` contains ``'.xFRAC'``, where ``x`` is a
1612 digit between 1 and 9, this is replaced with the fractional part of ``t``
1613 with ``x`` digits precision.
1614 '''
1616 if pyrocko.grumpy > 0:
1617 check_time_class(t, 'warn' if pyrocko.grumpy == 1 else 'raise')
1619 if isinstance(format, int):
1620 if format > 0:
1621 format = '%Y-%m-%d %H:%M:%S.' + '%iFRAC' % format
1622 else:
1623 format = '%Y-%m-%d %H:%M:%S'
1625 if util_ext is not None:
1626 t0 = num.floor(t)
1627 try:
1628 return util_ext.tts(int(t0), float(t - t0), format)
1629 except util_ext.UtilExtError as e:
1630 raise TimeStrError(
1631 '%s, timestamp=%f, format=%s' % (str(e), t, format))
1633 if not GlobalVars.re_frac:
1634 GlobalVars.re_frac = re.compile(r'\.[1-9]FRAC')
1635 GlobalVars.frac_formats = dict(
1636 [('.%sFRAC' % x, '%.'+x+'f') for x in '123456789'])
1638 ts = float(num.floor(t))
1639 tfrac = t-ts
1641 m = GlobalVars.re_frac.search(format)
1642 if m:
1643 sfrac = (GlobalVars.frac_formats[m.group(0)] % tfrac)
1644 if sfrac[0] == '1':
1645 ts += 1.
1647 format, nsub = GlobalVars.re_frac.subn(sfrac[1:], format, 1)
1649 return time.strftime(format, time.gmtime(ts))
1652tts = time_to_str
1655def mystrftime(fmt=None, tt=None, milliseconds=0):
1657 if fmt is None:
1658 fmt = '%Y-%m-%d %H:%M:%S .%r'
1660 if tt is None:
1661 tt = time.time()
1663 fmt = fmt.replace('%r', '%03i' % int(round(milliseconds)))
1664 fmt = fmt.replace('%u', '%06i' % int(round(milliseconds*1000)))
1665 fmt = fmt.replace('%n', '%09i' % int(round(milliseconds*1000000)))
1666 return time.strftime(fmt, tt)
1669def gmtime_x(timestamp):
1670 etimestamp = float(num.floor(timestamp))
1671 tt = time.gmtime(etimestamp)
1672 ms = (timestamp-etimestamp)*1000
1673 return tt, ms
1676def plural_s(n):
1677 if not isinstance(n, int):
1678 n = len(n)
1680 return 's' if n != 1 else ''
1683def ensuredirs(dst):
1684 '''
1685 Create all intermediate path components for a target path.
1687 :param dst: target path
1689 The leaf part of the target path is not created (use :py:func:`ensuredir`
1690 if a the target path is a directory to be created).
1691 '''
1693 d, x = os.path.split(dst.rstrip(os.sep))
1694 dirs = []
1695 while d and not os.path.exists(d):
1696 dirs.append(d)
1697 d, x = os.path.split(d)
1699 dirs.reverse()
1701 for d in dirs:
1702 try:
1703 os.mkdir(d)
1704 except OSError as e:
1705 if not e.errno == errno.EEXIST:
1706 raise
1709def ensuredir(dst):
1710 '''
1711 Create directory and all intermediate path components to it as needed.
1713 :param dst: directory name
1715 Nothing is done if the given target already exists.
1716 '''
1718 if os.path.exists(dst):
1719 return
1721 dst.rstrip(os.sep)
1723 ensuredirs(dst)
1724 try:
1725 os.mkdir(dst)
1726 except OSError as e:
1727 if not e.errno == errno.EEXIST:
1728 raise
1731def reuse(x):
1732 '''
1733 Get unique instance of an object.
1735 :param x: hashable object
1736 :returns: reference to x or an equivalent object
1738 Cache object ``x`` in a global dict for reuse, or if x already
1739 is in that dict, return a reference to it.
1740 '''
1742 grs = GlobalVars.reuse_store
1743 if x not in grs:
1744 grs[x] = x
1745 return grs[x]
1748def deuse(x):
1749 grs = GlobalVars.reuse_store
1750 if x in grs:
1751 del grs[x]
1754class Anon(object):
1755 '''
1756 Dict-to-object utility.
1758 Any given arguments are stored as attributes.
1760 Example::
1762 a = Anon(x=1, y=2)
1763 print a.x, a.y
1764 '''
1766 def __init__(self, **dict):
1767 for k in dict:
1768 self.__dict__[k] = dict[k]
1771def iter_select_files(
1772 paths,
1773 include=None,
1774 exclude=None,
1775 selector=None,
1776 show_progress=True,
1777 pass_through=None):
1779 '''
1780 Recursively select files (generator variant).
1782 See :py:func:`select_files`.
1783 '''
1785 if show_progress:
1786 progress_beg('selecting files...')
1788 ngood = 0
1789 check_include = None
1790 if include is not None:
1791 rinclude = re.compile(include)
1793 def check_include(path):
1794 m = rinclude.search(path)
1795 if not m:
1796 return False
1798 if selector is None:
1799 return True
1801 infos = Anon(**m.groupdict())
1802 return selector(infos)
1804 check_exclude = None
1805 if exclude is not None:
1806 rexclude = re.compile(exclude)
1808 def check_exclude(path):
1809 return not bool(rexclude.search(path))
1811 if check_include and check_exclude:
1813 def check(path):
1814 return check_include(path) and check_exclude(path)
1816 elif check_include:
1817 check = check_include
1819 elif check_exclude:
1820 check = check_exclude
1822 else:
1823 check = None
1825 if isinstance(paths, str):
1826 paths = [paths]
1828 for path in paths:
1829 if pass_through and pass_through(path):
1830 if check is None or check(path):
1831 yield path
1833 elif os.path.isdir(path):
1834 for (dirpath, dirnames, filenames) in os.walk(path):
1835 dirnames.sort()
1836 filenames.sort()
1837 for filename in filenames:
1838 path = op.join(dirpath, filename)
1839 if check is None or check(path):
1840 yield os.path.abspath(path)
1841 ngood += 1
1842 else:
1843 if check is None or check(path):
1844 yield os.path.abspath(path)
1845 ngood += 1
1847 if show_progress:
1848 progress_end('%i file%s selected.' % (ngood, plural_s(ngood)))
1851def select_files(
1852 paths, include=None, exclude=None, selector=None, show_progress=True,
1853 regex=None):
1855 '''
1856 Recursively select files.
1858 :param paths: entry path names
1859 :param include: pattern for conditional inclusion
1860 :param exclude: pattern for conditional exclusion
1861 :param selector: callback for conditional inclusion
1862 :param show_progress: if True, indicate start and stop of processing
1863 :param regex: alias for ``include`` (backwards compatibility)
1864 :returns: list of path names
1866 Recursively finds all files under given entry points ``paths``. If
1867 parameter ``include`` is a regular expression, only files with matching
1868 path names are included. If additionally parameter ``selector`` is given a
1869 callback function, only files for which the callback returns ``True`` are
1870 included. The callback should take a single argument. The callback is
1871 called with a single argument, an object, having as attributes, any named
1872 groups given in ``include``.
1874 Examples
1876 To find all files ending in ``'.mseed'`` or ``'.msd'``::
1878 select_files(paths,
1879 include=r'\\.(mseed|msd)$')
1881 To find all files ending with ``'$Year.$DayOfYear'``, having set 2009 for
1882 the year::
1884 select_files(paths,
1885 include=r'(?P<year>\\d\\d\\d\\d)\\.(?P<doy>\\d\\d\\d)$',
1886 selector=(lambda x: int(x.year) == 2009))
1887 '''
1888 if regex is not None:
1889 assert include is None
1890 include = regex
1892 return list(iter_select_files(
1893 paths, include, exclude, selector, show_progress))
1896def base36encode(number, alphabet='0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ'):
1897 '''
1898 Convert positive integer to a base36 string.
1899 '''
1901 if not isinstance(number, (int, long)):
1902 raise TypeError('number must be an integer')
1903 if number < 0:
1904 raise ValueError('number must be positive')
1906 # Special case for small numbers
1907 if number < 36:
1908 return alphabet[number]
1910 base36 = ''
1911 while number != 0:
1912 number, i = divmod(number, 36)
1913 base36 = alphabet[i] + base36
1915 return base36
1918def base36decode(number):
1919 '''
1920 Decode base36 endcoded positive integer.
1921 '''
1923 return int(number, 36)
1926class UnpackError(Exception):
1927 '''
1928 Exception raised when :py:func:`unpack_fixed` encounters an error.
1929 '''
1931 pass
1934ruler = ''.join(['%-10i' % i for i in range(8)]) \
1935 + '\n' + '0123456789' * 8 + '\n'
1938def unpack_fixed(format, line, *callargs):
1939 '''
1940 Unpack fixed format string, as produced by many fortran codes.
1942 :param format: format specification
1943 :param line: string to be processed
1944 :param callargs: callbacks for callback fields in the format
1946 The format is described by a string of comma-separated fields. Each field
1947 is defined by a character for the field type followed by the field width. A
1948 questionmark may be appended to the field description to allow the argument
1949 to be optional (The data string is then allowed to be filled with blanks
1950 and ``None`` is returned in this case).
1952 The following field types are available:
1954 ==== ================================================================
1955 Type Description
1956 ==== ================================================================
1957 A string (full field width is extracted)
1958 a string (whitespace at the beginning and the end is removed)
1959 i integer value
1960 f floating point value
1961 @ special type, a callback must be given for the conversion
1962 x special field type to skip parts of the string
1963 ==== ================================================================
1964 '''
1966 ipos = 0
1967 values = []
1968 icall = 0
1969 for form in format.split(','):
1970 form = form.strip()
1971 optional = form[-1] == '?'
1972 form = form.rstrip('?')
1973 typ = form[0]
1974 ln = int(form[1:])
1975 s = line[ipos:ipos+ln]
1976 cast = {
1977 'x': None,
1978 'A': str,
1979 'a': lambda x: x.strip(),
1980 'i': int,
1981 'f': float,
1982 '@': 'extra'}[typ]
1984 if cast == 'extra':
1985 cast = callargs[icall]
1986 icall += 1
1988 if cast is not None:
1989 if optional and s.strip() == '':
1990 values.append(None)
1991 else:
1992 try:
1993 values.append(cast(s))
1994 except Exception:
1995 mark = [' '] * 80
1996 mark[ipos:ipos+ln] = ['^'] * ln
1997 mark = ''.join(mark)
1998 raise UnpackError(
1999 'Invalid cast to type "%s" at position [%i:%i] of '
2000 'line: \n%s%s\n%s' % (
2001 typ, ipos, ipos+ln, ruler, line.rstrip(), mark))
2003 ipos += ln
2005 return values
2008_pattern_cache = {}
2011def _nslc_pattern(pattern):
2012 if pattern not in _pattern_cache:
2013 rpattern = re.compile(fnmatch.translate(pattern), re.I)
2014 _pattern_cache[pattern] = rpattern
2015 else:
2016 rpattern = _pattern_cache[pattern]
2018 return rpattern
2021def match_nslc(patterns, nslc):
2022 '''
2023 Match network-station-location-channel code against pattern or list of
2024 patterns.
2026 :param patterns: pattern or list of patterns
2027 :param nslc: tuple with (network, station, location, channel) as strings
2029 :returns: ``True`` if the pattern matches or if any of the given patterns
2030 match; or ``False``.
2032 The patterns may contain shell-style wildcards: \\*, ?, [seq], [!seq].
2034 Example::
2036 match_nslc('*.HAM3.*.BH?', ('GR', 'HAM3', '', 'BHZ')) # -> True
2037 '''
2039 if isinstance(patterns, str):
2040 patterns = [patterns]
2042 if not isinstance(nslc, str):
2043 s = '.'.join(nslc)
2044 else:
2045 s = nslc
2047 for pattern in patterns:
2048 if _nslc_pattern(pattern).match(s):
2049 return True
2051 return False
2054def match_nslcs(patterns, nslcs):
2055 '''
2056 Get network-station-location-channel codes that match given pattern or any
2057 of several given patterns.
2059 :param patterns: pattern or list of patterns
2060 :param nslcs: list of (network, station, location, channel) tuples
2062 See also :py:func:`match_nslc`
2063 '''
2065 matching = []
2066 for nslc in nslcs:
2067 if match_nslc(patterns, nslc):
2068 matching.append(nslc)
2070 return matching
2073class Timeout(Exception):
2074 pass
2077def create_lockfile(fn, timeout=None, timewarn=10.):
2078 t0 = time.time()
2080 while True:
2081 try:
2082 f = os.open(fn, os.O_CREAT | os.O_WRONLY | os.O_EXCL)
2083 os.close(f)
2084 return
2086 except OSError as e:
2087 if e.errno == errno.EEXIST:
2088 tnow = time.time()
2090 if timeout is not None and tnow - t0 > timeout:
2091 raise Timeout(
2092 'Timeout (%gs) occured while waiting to get exclusive '
2093 'access to: %s' % (timeout, fn))
2095 if timewarn is not None and tnow - t0 > timewarn:
2096 logger.warning(
2097 'Waiting since %gs to get exclusive access to: %s' % (
2098 timewarn, fn))
2100 timewarn *= 2
2102 time.sleep(0.01)
2103 else:
2104 raise
2107def delete_lockfile(fn):
2108 os.unlink(fn)
2111class Lockfile(Exception):
2113 def __init__(self, path, timeout=5, timewarn=10.):
2114 self._path = path
2115 self._timeout = timeout
2116 self._timewarn = timewarn
2118 def __enter__(self):
2119 create_lockfile(
2120 self._path, timeout=self._timeout, timewarn=self._timewarn)
2121 return None
2123 def __exit__(self, type, value, traceback):
2124 delete_lockfile(self._path)
2127class SoleError(Exception):
2128 '''
2129 Exception raised by objects of type :py:class:`Sole`, when an concurrent
2130 instance is running.
2131 '''
2133 pass
2136class Sole(object):
2137 '''
2138 Use POSIX advisory file locking to ensure that only a single instance of a
2139 program is running.
2141 :param pid_path: path to lockfile to be used
2143 Usage::
2145 from pyrocko.util import Sole, SoleError, setup_logging
2146 import os
2148 setup_logging('my_program')
2150 pid_path = os.path.join(os.environ['HOME'], '.my_program_lock')
2151 try:
2152 sole = Sole(pid_path)
2154 except SoleError, e:
2155 logger.fatal( str(e) )
2156 sys.exit(1)
2157 '''
2159 def __init__(self, pid_path):
2160 self._pid_path = pid_path
2161 self._other_running = False
2162 ensuredirs(self._pid_path)
2163 self._lockfile = None
2164 self._os = os
2166 if not fcntl:
2167 raise SoleError(
2168 'Python standard library module "fcntl" not available on '
2169 'this platform.')
2171 self._fcntl = fcntl
2173 try:
2174 self._lockfile = os.open(self._pid_path, os.O_CREAT | os.O_WRONLY)
2175 except Exception:
2176 raise SoleError(
2177 'Cannot open lockfile (path = %s)' % self._pid_path)
2179 try:
2180 fcntl.lockf(self._lockfile, fcntl.LOCK_EX | fcntl.LOCK_NB)
2182 except IOError:
2183 self._other_running = True
2184 try:
2185 f = open(self._pid_path, 'r')
2186 pid = f.read().strip()
2187 f.close()
2188 except Exception:
2189 pid = '?'
2191 raise SoleError('Other instance is running (pid = %s)' % pid)
2193 try:
2194 os.ftruncate(self._lockfile, 0)
2195 os.write(self._lockfile, '%i\n' % os.getpid())
2196 os.fsync(self._lockfile)
2198 except Exception:
2199 # the pid is only stored for user information, so this is allowed
2200 # to fail
2201 pass
2203 def __del__(self):
2204 if not self._other_running:
2205 if self._lockfile is not None:
2206 self._fcntl.lockf(self._lockfile, self._fcntl.LOCK_UN)
2207 self._os.close(self._lockfile)
2208 try:
2209 self._os.unlink(self._pid_path)
2210 except Exception:
2211 pass
2214re_escapequotes = re.compile(r"(['\\])")
2217def escapequotes(s):
2218 return re_escapequotes.sub(r"\\\1", s)
2221class TableWriter(object):
2222 '''
2223 Write table of space separated values to a file.
2225 :param f: file like object
2227 Strings containing spaces are quoted on output.
2228 '''
2230 def __init__(self, f):
2231 self._f = f
2233 def writerow(self, row, minfieldwidths=None):
2235 '''
2236 Write one row of values to underlying file.
2238 :param row: iterable of values
2239 :param minfieldwidths: minimum field widths for the values
2241 Each value in in ``row`` is converted to a string and optionally padded
2242 with blanks. The resulting strings are output separated with blanks. If
2243 any values given are strings and if they contain whitespace, they are
2244 quoted with single quotes, and any internal single quotes are
2245 backslash-escaped.
2246 '''
2248 out = []
2250 for i, x in enumerate(row):
2251 w = 0
2252 if minfieldwidths and i < len(minfieldwidths):
2253 w = minfieldwidths[i]
2255 if isinstance(x, str):
2256 if re.search(r"\s|'", x):
2257 x = "'%s'" % escapequotes(x)
2259 x = x.ljust(w)
2260 else:
2261 x = str(x).rjust(w)
2263 out.append(x)
2265 self._f.write(' '.join(out).rstrip() + '\n')
2268class TableReader(object):
2270 '''
2271 Read table of space separated values from a file.
2273 :param f: file-like object
2275 This uses Pythons shlex module to tokenize lines. Should deal correctly
2276 with quoted strings.
2277 '''
2279 def __init__(self, f):
2280 self._f = f
2281 self.eof = False
2283 def readrow(self):
2284 '''
2285 Read one row from the underlying file, tokenize it with shlex.
2287 :returns: tokenized line as a list of strings.
2288 '''
2290 line = self._f.readline()
2291 if not line:
2292 self.eof = True
2293 return []
2294 line.strip()
2295 if line.startswith('#'):
2296 return []
2298 return qsplit(line)
2301def gform(number, significant_digits=3):
2302 '''
2303 Pretty print floating point numbers.
2305 Align floating point numbers at the decimal dot.
2307 ::
2309 | -d.dde+xxx|
2310 | -d.dde+xx |
2311 |-ddd. |
2312 | -dd.d |
2313 | -d.dd |
2314 | -0.ddd |
2315 | -0.0ddd |
2316 | -0.00ddd |
2317 | -d.dde-xx |
2318 | -d.dde-xxx|
2319 | nan|
2322 The formatted string has length ``significant_digits * 2 + 6``.
2323 '''
2325 no_exp_range = (pow(10., -1),
2326 pow(10., significant_digits))
2327 width = significant_digits+significant_digits-1+1+1+5
2329 if (no_exp_range[0] <= abs(number) < no_exp_range[1]) or number == 0.:
2330 s = ('%#.*g' % (significant_digits, number)).rstrip('0')
2331 else:
2332 s = '%.*E' % (significant_digits-1, number)
2333 s = (' '*(-s.find('.')+(significant_digits+1))+s).ljust(width)
2334 if s.strip().lower() == 'nan':
2335 s = 'nan'.rjust(width)
2336 return s
2339def human_bytesize(value):
2341 exts = 'Bytes kB MB GB TB PB EB ZB YB'.split()
2343 if value == 1:
2344 return '1 Byte'
2346 for i, ext in enumerate(exts):
2347 x = float(value) / 1000**i
2348 if round(x) < 10. and not value < 1000:
2349 return '%.1f %s' % (x, ext)
2350 if round(x) < 1000.:
2351 return '%.0f %s' % (x, ext)
2353 return '%i Bytes' % value
2356re_compatibility = re.compile(
2357 r'!pyrocko\.(trace|gf\.(meta|seismosizer)|fomosto\.' +
2358 r'(dummy|poel|qseis|qssp))\.'
2359)
2362def pf_is_old(fn):
2363 oldstyle = False
2364 with open(fn, 'r') as f:
2365 for line in f:
2366 if re_compatibility.search(line):
2367 oldstyle = True
2369 return oldstyle
2372def pf_upgrade(fn):
2373 need = pf_is_old(fn)
2374 if need:
2375 fn_temp = fn + '.temp'
2377 with open(fn, 'r') as fin:
2378 with open(fn_temp, 'w') as fout:
2379 for line in fin:
2380 line = re_compatibility.sub('!pf.', line)
2381 fout.write(line)
2383 os.rename(fn_temp, fn)
2385 return need
2388def read_leap_seconds(tzfile='/usr/share/zoneinfo/right/UTC'):
2389 '''
2390 Extract leap second information from tzdata.
2392 Based on example at http://stackoverflow.com/questions/19332902/\
2393 extract-historic-leap-seconds-from-tzdata
2395 See also 'man 5 tzfile'.
2396 '''
2398 from struct import unpack, calcsize
2399 out = []
2400 with open(tzfile, 'rb') as f:
2401 # read header
2402 fmt = '>4s c 15x 6l'
2403 (magic, format, ttisgmtcnt, ttisstdcnt, leapcnt, timecnt,
2404 typecnt, charcnt) = unpack(fmt, f.read(calcsize(fmt)))
2405 assert magic == 'TZif'.encode('US-ASCII'), 'Not a timezone file'
2407 # skip over some uninteresting data
2408 fmt = '>%(timecnt)dl %(timecnt)dB %(ttinfo)s %(charcnt)ds' % dict(
2409 timecnt=timecnt, ttinfo='lBB'*typecnt, charcnt=charcnt)
2410 f.read(calcsize(fmt))
2412 # read leap-seconds
2413 fmt = '>2l'
2414 for i in range(leapcnt):
2415 tleap, nleap = unpack(fmt, f.read(calcsize(fmt)))
2416 out.append((tleap-nleap+1, nleap))
2418 return out
2421class LeapSecondsError(Exception):
2422 pass
2425class LeapSecondsOutdated(LeapSecondsError):
2426 pass
2429class InvalidLeapSecondsFile(LeapSecondsOutdated):
2430 pass
2433def parse_leap_seconds_list(fn):
2434 data = []
2435 texpires = None
2436 try:
2437 t0 = int(round(str_to_time('1900-01-01 00:00:00')))
2438 except TimeStrError:
2439 t0 = int(round(str_to_time('1970-01-01 00:00:00'))) - 2208988800
2441 tnow = int(round(time.time()))
2443 if not op.exists(fn):
2444 raise LeapSecondsOutdated('no leap seconds file found')
2446 try:
2447 with open(fn, 'rb') as f:
2448 for line in f:
2449 if line.strip().startswith(b'<!DOCTYPE'):
2450 raise InvalidLeapSecondsFile('invalid leap seconds file')
2452 if line.startswith(b'#@'):
2453 texpires = int(line.split()[1]) + t0
2454 elif line.startswith(b'#') or len(line) < 5:
2455 pass
2456 else:
2457 toks = line.split()
2458 t = int(toks[0]) + t0
2459 nleap = int(toks[1]) - 10
2460 data.append((t, nleap))
2462 except IOError:
2463 raise LeapSecondsError('cannot read leap seconds file %s' % fn)
2465 if texpires is None or tnow > texpires:
2466 raise LeapSecondsOutdated('leap seconds list is outdated')
2468 return data
2471def read_leap_seconds2():
2472 from pyrocko import config
2473 conf = config.config()
2474 fn = conf.leapseconds_path
2475 url = conf.leapseconds_url
2476 # check for outdated default URL
2477 if url == 'http://www.ietf.org/timezones/data/leap-seconds.list':
2478 url = 'https://www.ietf.org/timezones/data/leap-seconds.list'
2479 logger.info(
2480 'Leap seconds default URL is now: %s\nUsing new default.' % url)
2482 for i in range(3):
2483 try:
2484 return parse_leap_seconds_list(fn)
2486 except LeapSecondsOutdated:
2487 try:
2488 logger.info('updating leap seconds list...')
2489 download_file(url, fn)
2491 except Exception as e:
2492 raise LeapSecondsError(
2493 'cannot download leap seconds list from %s to %s (%s)'
2494 % (url, fn, e))
2496 raise LeapSecondsError('Could not retrieve/read leap seconds file.')
2499def gps_utc_offset(t_utc):
2500 '''
2501 Time offset t_gps - t_utc for a given t_utc.
2502 '''
2503 ls = read_leap_seconds2()
2504 i = 0
2505 if t_utc < ls[0][0]:
2506 return ls[0][1] - 1 - 9
2508 while i < len(ls) - 1:
2509 if ls[i][0] <= t_utc and t_utc < ls[i+1][0]:
2510 return ls[i][1] - 9
2511 i += 1
2513 return ls[-1][1] - 9
2516def utc_gps_offset(t_gps):
2517 '''
2518 Time offset t_utc - t_gps for a given t_gps.
2519 '''
2520 ls = read_leap_seconds2()
2522 if t_gps < ls[0][0] + ls[0][1] - 9:
2523 return - (ls[0][1] - 1 - 9)
2525 i = 0
2526 while i < len(ls) - 1:
2527 if ls[i][0] + ls[i][1] - 9 <= t_gps \
2528 and t_gps < ls[i+1][0] + ls[i+1][1] - 9:
2529 return - (ls[i][1] - 9)
2530 i += 1
2532 return - (ls[-1][1] - 9)
2535def make_iload_family(iload_fh, doc_fmt='FMT', doc_yielded_objects='FMT'):
2536 import itertools
2537 import glob
2538 from pyrocko.io.io_common import FileLoadError
2540 def iload_filename(filename, **kwargs):
2541 try:
2542 with open(filename, 'rb') as f:
2543 for cr in iload_fh(f, **kwargs):
2544 yield cr
2546 except FileLoadError as e:
2547 e.set_context('filename', filename)
2548 raise
2550 def iload_dirname(dirname, **kwargs):
2551 for entry in os.listdir(dirname):
2552 fpath = op.join(dirname, entry)
2553 if op.isfile(fpath):
2554 for cr in iload_filename(fpath, **kwargs):
2555 yield cr
2557 def iload_glob(pattern, **kwargs):
2559 for fn in glob.iglob(pattern):
2560 for cr in iload_filename(fn, **kwargs):
2561 yield cr
2563 def iload(source, **kwargs):
2564 if isinstance(source, str):
2565 if op.isdir(source):
2566 return iload_dirname(source, **kwargs)
2567 elif op.isfile(source):
2568 return iload_filename(source, **kwargs)
2569 else:
2570 return iload_glob(source, **kwargs)
2572 elif hasattr(source, 'read'):
2573 return iload_fh(source, **kwargs)
2574 else:
2575 return itertools.chain.from_iterable(
2576 iload(subsource, **kwargs) for subsource in source)
2578 iload_filename.__doc__ = '''
2579 Read %s information from named file.
2580 ''' % doc_fmt
2582 iload_dirname.__doc__ = '''
2583 Read %s information from directory of %s files.
2584 ''' % (doc_fmt, doc_fmt)
2586 iload_glob.__doc__ = '''
2587 Read %s information from files matching a glob pattern.
2588 ''' % doc_fmt
2590 iload.__doc__ = '''
2591 Load %s information from given source(s)
2593 The ``source`` can be specified as the name of a %s file, the name of a
2594 directory containing %s files, a glob pattern of %s files, an open
2595 filehandle or an iterator yielding any of the forementioned sources.
2597 This function behaves as a generator yielding %s objects.
2598 ''' % (doc_fmt, doc_fmt, doc_fmt, doc_fmt, doc_yielded_objects)
2600 for f in iload_filename, iload_dirname, iload_glob, iload:
2601 f.__module__ = iload_fh.__module__
2603 return iload_filename, iload_dirname, iload_glob, iload
2606class Inconsistency(Exception):
2607 pass
2610def consistency_check(list_of_tuples, message='values differ:'):
2611 '''
2612 Check for inconsistencies.
2614 Given a list of tuples, check that all tuple elements except for first one
2615 match. E.g. ``[('STA.N', 55.3, 103.2), ('STA.E', 55.3, 103.2)]`` would be
2616 valid because the coordinates at the two channels are the same.
2617 '''
2619 if len(list_of_tuples) >= 2:
2620 if any(t[1:] != list_of_tuples[0][1:] for t in list_of_tuples[1:]):
2621 raise Inconsistency('%s\n' % message + '\n'.join(
2622 ' %s: %s' % (t[0], ', '.join(str(x) for x in t[1:]))
2623 for t in list_of_tuples))
2626class defaultzerodict(dict):
2627 def __missing__(self, k):
2628 return 0
2631def mostfrequent(x):
2632 c = defaultzerodict()
2633 for e in x:
2634 c[e] += 1
2636 return sorted(list(c.keys()), key=lambda k: c[k])[-1]
2639def consistency_merge(list_of_tuples,
2640 message='values differ:',
2641 error='raise',
2642 merge=mostfrequent):
2644 assert error in ('raise', 'warn', 'ignore')
2646 if len(list_of_tuples) == 0:
2647 raise Exception('cannot merge empty sequence')
2649 try:
2650 consistency_check(list_of_tuples, message)
2651 return list_of_tuples[0][1:]
2652 except Inconsistency as e:
2653 if error == 'raise':
2654 raise
2656 elif error == 'warn':
2657 logger.warning(str(e))
2659 return tuple([merge(x) for x in list(zip(*list_of_tuples))[1:]])
2662def short_to_list(nmax, it):
2663 import itertools
2665 if isinstance(it, list):
2666 return it
2668 li = []
2669 for i in range(nmax+1):
2670 try:
2671 li.append(next(it))
2672 except StopIteration:
2673 return li
2675 return itertools.chain(li, it)
2678def parse_md(f):
2679 try:
2680 with open(op.join(
2681 op.dirname(op.abspath(f)),
2682 'README.md'), 'r') as readme:
2683 mdstr = readme.read()
2684 except IOError as e:
2685 return 'Failed to get README.md: %s' % e
2687 # Remve the title
2688 mdstr = re.sub(r'^# .*\n?', '', mdstr)
2689 # Append sphinx reference to `pyrocko.` modules
2690 mdstr = re.sub(r'`pyrocko\.(.*)`', r':py:mod:`pyrocko.\1`', mdstr)
2691 # Convert Subsections to toc-less rubrics
2692 mdstr = re.sub(r'## (.*)\n', r'.. rubric:: \1\n', mdstr)
2693 return mdstr
2696def mpl_show(plt):
2697 import matplotlib
2698 if matplotlib.get_backend().lower() == 'agg':
2699 logger.warning('Cannot show() when using matplotlib "agg" backend')
2700 else:
2701 plt.show()
2704g_re_qsplit = re.compile(
2705 r'"([^"\\]*(?:\\.[^"\\]*)*)"|\'([^\'\\]*(?:\\.[^\'\\]*)*)\'|(\S+)')
2706g_re_qsplit_sep = {}
2709def get_re_qsplit(sep):
2710 if sep is None:
2711 return g_re_qsplit
2712 else:
2713 if sep not in g_re_qsplit_sep:
2714 assert len(sep) == 1
2715 assert sep not in '\'"'
2716 esep = re.escape(sep)
2717 g_re_qsplit_sep[sep] = re.compile(
2718 r'"([^"\\]*(?:\\.[^"\\]*)*)"|\'([^\'\\]*(?:\\.[^\'\\]*)*)\'|'
2719 + r'([^' + esep + r']+|(?<=' + esep + r')(?=' + esep + r')|^(?=' + esep + r')|(?<=' + esep + r')$)') # noqa
2720 return g_re_qsplit_sep[sep]
2723g_re_trivial = re.compile(r'\A[^\'"\s]+\Z')
2724g_re_trivial_sep = {}
2727def get_re_trivial(sep):
2728 if sep is None:
2729 return g_re_trivial
2730 else:
2731 if sep not in g_re_qsplit_sep:
2732 assert len(sep) == 1
2733 assert sep not in '\'"'
2734 esep = re.escape(sep)
2735 g_re_trivial_sep[sep] = re.compile(r'\A[^\'"' + esep + r']+\Z')
2737 return g_re_trivial_sep[sep]
2740g_re_escape_s = re.compile(r'([\\\'])')
2741g_re_unescape_s = re.compile(r'\\([\\\'])')
2742g_re_escape_d = re.compile(r'([\\"])')
2743g_re_unescape_d = re.compile(r'\\([\\"])')
2746def escape_s(s):
2747 '''
2748 Backslash-escape single-quotes and backslashes.
2750 Example: ``Jack's`` => ``Jack\\'s``
2752 '''
2753 return g_re_escape_s.sub(r'\\\1', s)
2756def unescape_s(s):
2757 '''
2758 Unescape backslash-escaped single-quotes and backslashes.
2760 Example: ``Jack\\'s`` => ``Jack's``
2761 '''
2762 return g_re_unescape_s.sub(r'\1', s)
2765def escape_d(s):
2766 '''
2767 Backslash-escape double-quotes and backslashes.
2769 Example: ``"Hello \\O/"`` => ``\\"Hello \\\\O/\\"``
2770 '''
2771 return g_re_escape_d.sub(r'\\\1', s)
2774def unescape_d(s):
2775 '''
2776 Unescape backslash-escaped double-quotes and backslashes.
2778 Example: ``\\"Hello \\\\O/\\"`` => ``"Hello \\O/"``
2779 '''
2780 return g_re_unescape_d.sub(r'\1', s)
2783def qjoin_s(it, sep=None):
2784 '''
2785 Join sequence of strings into a line, single-quoting non-trivial strings.
2787 Example: ``["55", "Sparrow's Island"]`` => ``"55 'Sparrow\\\\'s Island'"``
2788 '''
2789 re_trivial = get_re_trivial(sep)
2791 if sep is None:
2792 sep = ' '
2794 return sep.join(
2795 w if re_trivial.search(w) else "'%s'" % escape_s(w) for w in it)
2798def qjoin_d(it, sep=None):
2799 '''
2800 Join sequence of strings into a line, double-quoting non-trivial strings.
2802 Example: ``['55', 'Pete "The Robot" Smith']`` =>
2803 ``'55' "Pete \\\\"The Robot\\\\" Smith"'``
2804 '''
2805 re_trivial = get_re_trivial(sep)
2806 if sep is None:
2807 sep = ' '
2809 return sep.join(
2810 w if re_trivial.search(w) else '"%s"' % escape_d(w) for w in it)
2813def qsplit(s, sep=None):
2814 '''
2815 Split line into list of strings, allowing for quoted strings.
2817 Example: ``"55 'Sparrow\\\\'s Island'"`` =>
2818 ``["55", "Sparrow's Island"]``,
2819 ``'55' "Pete \\\\"The Robot\\\\" Smith"'`` =>
2820 ``['55', 'Pete "The Robot" Smith']``
2821 '''
2822 re_qsplit = get_re_qsplit(sep)
2823 return [
2824 (unescape_d(x[0]) or unescape_s(x[1]) or x[2])
2825 for x in re_qsplit.findall(s)]
2828g_have_warned_threadpoolctl = False
2831class threadpool_limits_dummy(object):
2833 def __init__(self, *args, **kwargs):
2834 pass
2836 def __enter__(self):
2837 global g_have_warned_threadpoolctl
2839 if not g_have_warned_threadpoolctl:
2840 logger.warning(
2841 'Cannot control number of BLAS threads because '
2842 '`threadpoolctl` module is not available. You may want to '
2843 'install `threadpoolctl`.')
2845 g_have_warned_threadpoolctl = True
2847 return self
2849 def __exit__(self, type, value, traceback):
2850 pass
2853def get_threadpool_limits():
2854 '''
2855 Try to import threadpoolctl.threadpool_limits, provide dummy if not avail.
2856 '''
2858 try:
2859 from threadpoolctl import threadpool_limits
2860 return threadpool_limits
2862 except ImportError:
2863 return threadpool_limits_dummy