Source code for pyrocko.util

# http://pyrocko.org - GPLv3
#
# The Pyrocko Developers, 21st Century
# ---|P------/S----------~Lg----------
'''Utility functions for Pyrocko.'''
from __future__ import division, print_function
from past.builtins import zip, long
from builtins import range
from builtins import object

import time
import logging
import os
import sys
import re
import calendar
import math
import fnmatch
import fcntl
import shlex
import optparse
import os.path as op
import platform
import errno

import numpy as num
from scipy import signal
from pyrocko import dummy_progressbar


force_dummy_progressbar = False


if platform.system() != 'Darwin':
    from pyrocko import util_ext
else:
    util_ext = None


logger = logging.getLogger('pyrocko.util')

try:
    import progressbar as progressbar_mod
except ImportError:
    from pyrocko import dummy_progressbar as progressbar_mod


try:
    num_full = num.full
except AttributeError:
    def num_full(shape, fill_value, dtype=None, order='C'):
        a = num.empty(shape, dtype=dtype, order=order)
        a.fill(fill_value)
        return a

try:
    num_full_like = num.full_like
except AttributeError:
    def num_full_like(arr, fill_value, dtype=None, order='K', subok=True):
        a = num.empty_like(arr, dtype=dtype, order=order, subok=subok)
        a.fill(fill_value)
        return a


[docs]def progressbar_module(): return progressbar_mod
[docs]def setup_logging(programname='pyrocko', levelname='warning'): ''' Initialize logging. :param programname: program name to be written in log :param levelname: string indicating the logging level ('debug', 'info', 'warning', 'error', 'critical') This function is called at startup by most pyrocko programs to set up a consistent logging format. This is simply a shortcut to a call to :py:func:`logging.basicConfig()`. ''' levels = {'debug': logging.DEBUG, 'info': logging.INFO, 'warning': logging.WARNING, 'error': logging.ERROR, 'critical': logging.CRITICAL} logging.basicConfig( level=levels[levelname], format=programname+':%(name)-20s - %(levelname)-8s - %(message)s')
[docs]def data_file(fn): return os.path.join(os.path.split(__file__)[0], 'data', fn)
[docs]class DownloadError(Exception): pass
[docs]class PathExists(DownloadError): pass
def _download(url, fpath, username=None, password=None, force=False, method='download', stats=None, status_callback=None, entries_wanted=None, recursive=False, header=None): import requests from requests.auth import HTTPBasicAuth from requests.exceptions import HTTPError requests.adapters.DEFAULT_RETRIES = 5 urljoin = requests.compat.urljoin session = requests.Session() session.header = header session.auth = None if username is None\ else HTTPBasicAuth(username, password) try: url_to_size = {} status = dict( ntotal_files=0, nread_files=0, ntotal_bytes_all_files=0, nread_bytes_all_files=0, ntotal_bytes_current_file=0, nread_bytes_current_file=0) if callable(status_callback): status_callback(status) if not recursive and url.endswith('/'): raise DownloadError( 'URL: %s appears to be a directory' ' but recurvise download is False' % url) if recursive and not url.endswith('/'): url += '/' def parse_directory_tree(url, subdir=''): r = session.get(urljoin(url, subdir)) r.raise_for_status() entries = re.findall(r'href="([a-zA-Z0-9_.-]+/?)"', r.text) files = sorted(set(subdir + fn for fn in entries if not fn.endswith('/'))) if entries_wanted is not None: files = [fn for fn in files if (fn in wanted for wanted in entries_wanted)] status['ntotal_files'] += len(files) dirs = sorted(set(subdir + dn for dn in entries if dn.endswith('/') and dn not in ('./', '../'))) for dn in dirs: files.extend(parse_directory_tree( url, subdir=dn)) return files def get_content_length(url): if url not in url_to_size: r = session.head(url, headers={'Accept-Encoding': ''}) content_length = r.headers.get('content-length', None) if content_length is None: logger.debug('Could not get HTTP header ' 'Content-Length for %s' % url) content_length = None else: content_length = int(content_length) status['ntotal_bytes_all_files'] += content_length if callable(status_callback): status_callback(status) url_to_size[url] = content_length return url_to_size[url] def download_file(url, fn): logger.info('starting download of %s...' % url) ensuredirs(fn) fsize = get_content_length(url) status['ntotal_bytes_current_file'] = fsize status['nread_bytes_current_file'] = 0 if callable(status_callback): status_callback(status) r = session.get(url, stream=True, timeout=5) r.raise_for_status() frx = 0 fn_tmp = fn + '.%i.temp' % os.getpid() with open(fn_tmp, 'wb') as f: for d in r.iter_content(chunk_size=1024): f.write(d) frx += len(d) status['nread_bytes_all_files'] += len(d) status['nread_bytes_current_file'] += len(d) if callable(status_callback): status_callback(status) os.rename(fn_tmp, fn) if fsize is not None and frx != fsize: logger.warning( 'HTTP header Content-Length: %i bytes does not match ' 'download size %i bytes' % (fsize, frx)) logger.info('finished download of %s' % url) status['nread_files'] += 1 if callable(status_callback): status_callback(status) if recursive: if op.exists(fpath) and not force: raise PathExists('path %s already exists' % fpath) files = parse_directory_tree(url) dsize = 0 for fn in files: file_url = urljoin(url, fn) dsize += get_content_length(file_url) or 0 if method == 'calcsize': return dsize else: for fn in files: file_url = urljoin(url, fn) download_file(file_url, op.join(fpath, fn)) else: status['ntotal_files'] += 1 if callable(status_callback): status_callback(status) fsize = get_content_length(url) if method == 'calcsize': return fsize else: download_file(url, fpath) except HTTPError as e: logging.warn("http error: %s" % e) raise DownloadError('could not download file(s) from: %s' % url) finally: session.close()
[docs]def download_file( url, fpath, username=None, password=None, status_callback=None, **kwargs): return _download( url, fpath, username, password, recursive=False, status_callback=status_callback, **kwargs)
[docs]def download_dir( url, fpath, username=None, password=None, status_callback=None, **kwargs): return _download( url, fpath, username, password, recursive=True, status_callback=status_callback, **kwargs)
if hasattr(num, 'float128'): hpfloat = num.float128 elif hasattr(num, 'float96'): hpfloat = num.float96 else: def hpfloat(x): raise Exception( 'NumPy lacks support for float128 or float96 data type on this ' 'platform.')
[docs]class Stopwatch(object): ''' Simple stopwatch to measure elapsed wall clock time. Usage:: s = Stopwatch() time.sleep(1) print s() time.sleep(1) print s() ''' def __init__(self): self.start = time.time() def __call__(self): return time.time() - self.start
[docs]def wrap(text, line_length=80): ''' Paragraph and list-aware wrapping of text. ''' text = text.strip('\n') at_lineend = re.compile(r' *\n') at_para = re.compile(r'((^|(\n\s*)?\n)(\s+[*] )|\n\s*\n)') paragraphs = at_para.split(text)[::5] listindents = at_para.split(text)[4::5] newlist = at_para.split(text)[3::5] listindents[0:0] = [None] listindents.append(True) newlist.append(None) det_indent = re.compile(r'^ *') outlines = [] for ip, p in enumerate(paragraphs): if not p: continue if listindents[ip] is None: _indent = det_indent.findall(p)[0] findent = _indent else: findent = listindents[ip] _indent = ' ' * len(findent) ll = line_length - len(_indent) llf = ll oldlines = [s.strip() for s in at_lineend.split(p.rstrip())] p1 = ' '.join(oldlines) possible = re.compile(r'(^.{1,%i}|.{1,%i})( |$)' % (llf, ll)) for imatch, match in enumerate(possible.finditer(p1)): parout = match.group(1) if imatch == 0: outlines.append(findent + parout) else: outlines.append(_indent + parout) if ip != len(paragraphs)-1 and ( listindents[ip] is None or newlist[ip] is not None or listindents[ip+1] is None): outlines.append('') return outlines
[docs]class BetterHelpFormatter(optparse.IndentedHelpFormatter): def __init__(self, *args, **kwargs): optparse.IndentedHelpFormatter.__init__(self, *args, **kwargs)
[docs] def format_option(self, option): ''' From IndentedHelpFormatter but using a different wrap method. ''' help_text_position = 4 + self.current_indent help_text_width = self.width - help_text_position opts = self.option_strings[option] opts = "%*s%s" % (self.current_indent, "", opts) if option.help: help_text = self.expand_default(option) if self.help_position + len(help_text) + 1 <= self.width: lines = [ '', '%-*s %s' % (self.help_position, opts, help_text), ''] else: lines = [''] lines.append(opts) lines.append('') if option.help: help_lines = wrap(help_text, help_text_width) lines.extend(["%*s%s" % (help_text_position, "", line) for line in help_lines]) lines.append('') return "\n".join(lines)
[docs] def format_description(self, description): if not description: return '' if self.current_indent == 0: lines = [] else: lines = [''] lines.extend(wrap(description, self.width - self.current_indent)) if self.current_indent == 0: lines.append('\n') return '\n'.join( ['%*s%s' % (self.current_indent, '', line) for line in lines])
[docs]def progressbar(label, maxval): progressbar_mod = progressbar_module() if force_dummy_progressbar: progressbar_mod = dummy_progressbar widgets = [ label, ' ', progressbar_mod.Bar(marker='-', left='[', right=']'), ' ', progressbar_mod.Percentage(), ' ', progressbar_mod.ETA()] pbar = progressbar_mod.ProgressBar(widgets=widgets, maxval=maxval).start() return pbar
[docs]def progress_beg(label): ''' Notify user that an operation has started. :param label: name of the operation To be used in conjuction with :py:func:`progress_end`. ''' sys.stderr.write(label) sys.stderr.flush()
[docs]def progress_end(label=''): ''' Notify user that an operation has ended. :param label: name of the operation To be used in conjuction with :py:func:`progress_beg`. ''' sys.stderr.write(' done. %s\n' % label) sys.stderr.flush()
[docs]class ArangeError(Exception): pass
[docs]def arange2(start, stop, step, dtype=num.float, epsilon=1e-6, error='raise'): ''' Return evenly spaced numbers over a specified interval. Like :py:func:`numpy.arange` but returning floating point numbers by default and with defined behaviour when stepsize is inconsistent with interval bounds. It is considered inconsistent if the difference between the closest multiple of ``step`` and ``stop`` is larger than ``epsilon * step``. Inconsistencies are handled according to the ``error`` parameter. If it is set to ``'raise'`` an exception of type :py:exc:`ArangeError` is raised. If it is set to ``'round'``, ``'floor'``, or ``'ceil'``, ``stop`` is silently changed to the closest, the next smaller, or next larger multiple of ``step``, respectively. ''' assert error in ('raise', 'round', 'floor', 'ceil') start = dtype(start) stop = dtype(stop) step = dtype(step) rnd = {'floor': math.floor, 'ceil': math.ceil}.get(error, round) n = int(rnd((stop - start) / step)) + 1 stop_check = start + (n-1) * step if error == 'raise' and abs(stop_check - stop) > step * epsilon: raise ArangeError( 'inconsistent range specification: start=%g, stop=%g, step=%g' % (start, stop, step)) x = num.arange(n, dtype=dtype) x *= step x += start return x
[docs]def polylinefit(x, y, n_or_xnodes): ''' Fit piece-wise linear function to data. :param x,y: arrays with coordinates of data :param n_or_xnodes: int, number of segments or x coordinates of polyline :returns: `(xnodes, ynodes, rms_error)` arrays with coordinates of polyline, root-mean-square error ''' x = num.asarray(x) y = num.asarray(y) if isinstance(n_or_xnodes, int): n = n_or_xnodes xmin = x.min() xmax = x.max() xnodes = num.linspace(xmin, xmax, n+1) else: xnodes = num.asarray(n_or_xnodes) n = xnodes.size - 1 assert len(x) == len(y) assert n > 0 ndata = len(x) a = num.zeros((ndata+(n-1), n*2)) for i in range(n): xmin_block = xnodes[i] xmax_block = xnodes[i+1] if i == n-1: # don't loose last point indices = num.where( num.logical_and(xmin_block <= x, x <= xmax_block))[0] else: indices = num.where( num.logical_and(xmin_block <= x, x < xmax_block))[0] a[indices, i*2] = x[indices] a[indices, i*2+1] = 1.0 w = float(ndata)*100. if i < n-1: a[ndata+i, i*2] = xmax_block*w a[ndata+i, i*2+1] = 1.0*w a[ndata+i, i*2+2] = -xmax_block*w a[ndata+i, i*2+3] = -1.0*w d = num.concatenate((y, num.zeros(n-1))) model = num.linalg.lstsq(a, d, rcond=-1)[0].reshape((n, 2)) ynodes = num.zeros(n+1) ynodes[:n] = model[:, 0]*xnodes[:n] + model[:, 1] ynodes[1:] += model[:, 0]*xnodes[1:] + model[:, 1] ynodes[1:n] *= 0.5 rms_error = num.sqrt(num.mean((num.interp(x, xnodes, ynodes) - y)**2)) return xnodes, ynodes, rms_error
[docs]def plf_integrate_piecewise(x_edges, x, y): ''' Calculate definite integral of piece-wise linear function on intervals. Use trapezoidal rule to calculate definite integral of a piece-wise linear function for a series of consecutive intervals. ``x_edges`` and ``x`` must be sorted. :param x_edges: array with edges of the intervals :param x,y: arrays with coordinates of piece-wise linear function's control points ''' x_all = num.concatenate((x, x_edges)) ii = num.argsort(x_all) y_edges = num.interp(x_edges, x, y) y_all = num.concatenate((y, y_edges)) xs = x_all[ii] ys = y_all[ii] y_all[ii[1:]] = num.cumsum((xs[1:] - xs[:-1]) * 0.5 * (ys[1:] + ys[:-1])) return num.diff(y_all[-len(y_edges):])
[docs]class GlobalVars(object): reuse_store = dict() decitab_nmax = 0 decitab = {} decimate_fir_coeffs = {} decimate_iir_coeffs = {} re_frac = None
[docs]def decimate_coeffs(q, n=None, ftype='iir'): q = int(q) if n is None: if ftype == 'fir': n = 30 else: n = 8 if ftype == 'fir': coeffs = GlobalVars.decimate_fir_coeffs if (n, 1./q) not in coeffs: coeffs[n, 1./q] = signal.firwin(n+1, 1./q, window='hamming') b = coeffs[n, 1./q] return b, [1.], n else: coeffs = GlobalVars.decimate_iir_coeffs if (n, 0.05, 0.8/q) not in coeffs: coeffs[n, 0.05, 0.8/q] = signal.cheby1(n, 0.05, 0.8/q) b, a = coeffs[n, 0.05, 0.8/q] return b, a, n
[docs]def decimate(x, q, n=None, ftype='iir', zi=None, ioff=0): ''' Downsample the signal x by an integer factor q, using an order n filter By default, an order 8 Chebyshev type I filter is used or a 30 point FIR filter with hamming window if ftype is 'fir'. :param x: the signal to be downsampled (1D NumPy array) :param q: the downsampling factor :param n: order of the filter (1 less than the length of the filter for a 'fir' filter) :param ftype: type of the filter; can be 'iir' or 'fir' :returns: the downsampled signal (1D NumPy array) ''' b, a, n = decimate_coeffs(q, n, ftype) if zi is None or zi is True: zi_ = num.zeros(max(len(a), len(b))-1, dtype=num.float) else: zi_ = zi y, zf = signal.lfilter(b, a, x, zi=zi_) if zi is not None: return y[n//2+ioff::q].copy(), zf else: return y[n//2+ioff::q].copy()
[docs]class UnavailableDecimation(Exception): ''' Exception raised by :py:func:`decitab` for unavailable decimation factors. ''' pass
[docs]def gcd(a, b, epsilon=1e-7): ''' Greatest common divisor. ''' while b > epsilon*a: a, b = b, a % b return a
[docs]def lcm(a, b): ''' Least common multiple. ''' return a*b // gcd(a, b)
[docs]def mk_decitab(nmax=100): ''' Make table with decimation sequences. Decimation from one sampling rate to a lower one is achieved by a successive application of :py:func:`decimation` with small integer downsampling factors (because using large downampling factors can make the decimation unstable or slow). This function sets up a table with downsample sequences for factors up to ``nmax``. ''' tab = GlobalVars.decitab for i in range(1, 10): for j in range(1, i+1): for k in range(1, j+1): for l in range(1, k+1): for m in range(1, l+1): p = i*j*k*l*m if p > nmax: break if p not in tab: tab[p] = (i, j, k, l, m) if i*j*k*l > nmax: break if i*j*k > nmax: break if i*j > nmax: break if i > nmax: break GlobalVars.decitab_nmax = nmax
[docs]def zfmt(n): return '%%0%ii' % (int(math.log10(n - 1)) + 1)
[docs]def julian_day_of_year(timestamp): ''' Get the day number after the 1st of January of year in ``timestamp``. :returns: day number as int ''' return time.gmtime(int(timestamp)).tm_yday
[docs]def day_start(timestamp): ''' Get beginning of day for any point in time. :param timestamp: time instant as system timestamp (in seconds) :returns: instant of day start as system timestamp ''' tt = time.gmtime(int(timestamp)) tts = tt[0:3] + (0, 0, 0) + tt[6:9] return calendar.timegm(tts)
[docs]def month_start(timestamp): ''' Get beginning of month for any point in time. :param timestamp: time instant as system timestamp (in seconds) :returns: instant of month start as system timestamp ''' tt = time.gmtime(int(timestamp)) tts = tt[0:2] + (1, 0, 0, 0) + tt[6:9] return calendar.timegm(tts)
[docs]def year_start(timestamp): ''' Get beginning of year for any point in time. :param timestamp: time instant as system timestamp (in seconds) :returns: instant of year start as system timestamp ''' tt = time.gmtime(int(timestamp)) tts = tt[0:1] + (1, 1, 0, 0, 0) + tt[6:9] return calendar.timegm(tts)
[docs]def iter_days(tmin, tmax): ''' Yields begin and end of days until given time span is covered. :param tmin,tmax: input time span :yields: tuples with (begin, end) of days as system timestamps ''' t = day_start(tmin) while t < tmax: tend = day_start(t + 26*60*60) yield t, tend t = tend
[docs]def iter_months(tmin, tmax): ''' Yields begin and end of months until given time span is covered. :param tmin,tmax: input time span :yields: tuples with (begin, end) of months as system timestamps ''' t = month_start(tmin) while t < tmax: tend = month_start(t + 24*60*60*33) yield t, tend t = tend
[docs]def iter_years(tmin, tmax): ''' Yields begin and end of years until given time span is covered. :param tmin,tmax: input time span :yields: tuples with (begin, end) of years as system timestamps ''' t = year_start(tmin) while t < tmax: tend = year_start(t + 24*60*60*369) yield t, tend t = tend
[docs]def decitab(n): ''' Get integer decimation sequence for given downampling factor. :param n: target decimation factor :returns: tuple with downsampling sequence ''' if n > GlobalVars.decitab_nmax: mk_decitab(n*2) if n not in GlobalVars.decitab: raise UnavailableDecimation('ratio = %g' % n) return GlobalVars.decitab[n]
[docs]def ctimegm(s, format="%Y-%m-%d %H:%M:%S"): ''' Convert string representing UTC time to system time. :param s: string to be interpreted :param format: format string passed to :py:func:`strptime` :returns: system time stamp Interpretes string with format ``'%Y-%m-%d %H:%M:%S'``, using strptime. .. note:: This function is to be replaced by :py:func:`str_to_time`. ''' return calendar.timegm(time.strptime(s, format))
[docs]def gmctime(t, format="%Y-%m-%d %H:%M:%S"): ''' Get string representation from system time, UTC. Produces string with format ``'%Y-%m-%d %H:%M:%S'``, using strftime. .. note:: This function is to be repaced by :py:func:`time_to_str`. ''' return time.strftime(format, time.gmtime(t))
[docs]def gmctime_v(t, format="%a, %d %b %Y %H:%M:%S"): ''' Get string representation from system time, UTC. Same as :py:func:`gmctime` but with a more verbose default format. .. note:: This function is to be replaced by :py:func:`time_to_str`. ''' return time.strftime(format, time.gmtime(t))
[docs]def gmctime_fn(t, format="%Y-%m-%d_%H-%M-%S"): ''' Get string representation from system time, UTC. Same as :py:func:`gmctime` but with a default usable in filenames. .. note:: This function is to be replaced by :py:func:`time_to_str`. ''' return time.strftime(format, time.gmtime(t))
[docs]class TimeStrError(Exception): pass
[docs]class FractionalSecondsMissing(TimeStrError): ''' Exception raised by :py:func:`str_to_time` when the given string lacks fractional seconds. ''' pass
[docs]class FractionalSecondsWrongNumberOfDigits(TimeStrError): ''' Exception raised by :py:func:`str_to_time` when the given string has an incorrect number of digits in the fractional seconds part. ''' pass
def _endswith_n(s, endings): for ix, x in enumerate(endings): if s.endswith(x): return ix return -1
[docs]def str_to_time(s, format='%Y-%m-%d %H:%M:%S.OPTFRAC'): ''' Convert string representing UTC time to floating point system time. :param s: string representing UTC time :param format: time string format :returns: system time stamp as floating point value Uses the semantics of :py:func:`time.strptime` but allows for fractional seconds. If the format ends with ``'.FRAC'``, anything after a dot is interpreted as fractional seconds. If the format ends with ``'.OPTFRAC'``, the fractional part, including the dot is made optional. The latter has the consequence, that the time strings and the format may not contain any other dots. If the format ends with ``'.xFRAC'`` where x is 1, 2, or 3, it is ensured, that exactly that number of digits are present in the fractional seconds. ''' if util_ext is not None: try: t, tfrac = util_ext.stt(s, format) except util_ext.UtilExtError as e: raise TimeStrError( '%s, string=%s, format=%s' % (str(e), s, format)) return t+tfrac fracsec = 0. fixed_endings = '.FRAC', '.1FRAC', '.2FRAC', '.3FRAC' iend = _endswith_n(format, fixed_endings) if iend != -1: dotpos = s.rfind('.') if dotpos == -1: raise FractionalSecondsMissing( 'string=%s, format=%s' % (s, format)) if iend > 0 and iend != (len(s)-dotpos-1): raise FractionalSecondsWrongNumberOfDigits( 'string=%s, format=%s' % (s, format)) format = format[:-len(fixed_endings[iend])] fracsec = float(s[dotpos:]) s = s[:dotpos] elif format.endswith('.OPTFRAC'): dotpos = s.rfind('.') format = format[:-8] if dotpos != -1 and len(s[dotpos:]) > 1: fracsec = float(s[dotpos:]) if dotpos != -1: s = s[:dotpos] try: return calendar.timegm(time.strptime(s, format)) + fracsec except ValueError as e: raise TimeStrError('%s, string=%s, format=%s' % (str(e), s, format))
stt = str_to_time
[docs]def time_to_str(t, format='%Y-%m-%d %H:%M:%S.3FRAC'): ''' Get string representation for floating point system time. :param t: floating point system time :param format: time string format :returns: string representing UTC time Uses the semantics of :py:func:`time.strftime` but additionally allows for fractional seconds. If ``format`` contains ``'.xFRAC'``, where ``x`` is a digit between 1 and 9, this is replaced with the fractional part of ``t`` with ``x`` digits precision. ''' if isinstance(format, int): if format > 0: format = '%Y-%m-%d %H:%M:%S.' + '%iFRAC' % format else: format = '%Y-%m-%d %H:%M:%S' if util_ext is not None: t0 = math.floor(t) try: return util_ext.tts(int(t0), t - t0, format) except util_ext.UtilExtError as e: raise TimeStrError( '%s, timestamp=%f, format=%s' % (str(e), t, format)) if not GlobalVars.re_frac: GlobalVars.re_frac = re.compile(r'\.[1-9]FRAC') GlobalVars.frac_formats = dict( [('.%sFRAC' % x, '%.'+x+'f') for x in '123456789']) ts = float(num.floor(t)) tfrac = t-ts m = GlobalVars.re_frac.search(format) if m: sfrac = (GlobalVars.frac_formats[m.group(0)] % tfrac) if sfrac[0] == '1': ts += 1. format, nsub = GlobalVars.re_frac.subn(sfrac[1:], format, 1) return time.strftime(format, time.gmtime(ts))
tts = time_to_str
[docs]def mystrftime(fmt=None, tt=None, milliseconds=0): if fmt is None: fmt = '%Y-%m-%d %H:%M:%S .%r' if tt is None: tt = time.time() fmt = fmt.replace('%r', '%03i' % int(round(milliseconds))) fmt = fmt.replace('%u', '%06i' % int(round(milliseconds*1000))) fmt = fmt.replace('%n', '%09i' % int(round(milliseconds*1000000))) return time.strftime(fmt, tt)
[docs]def gmtime_x(timestamp): etimestamp = float(num.floor(timestamp)) tt = time.gmtime(etimestamp) ms = (timestamp-etimestamp)*1000 return tt, ms
[docs]def plural_s(n): if n == 1: return '' else: return 's'
[docs]def ensuredirs(dst): ''' Create all intermediate path components for a target path. :param dst: target path The leaf part of the target path is not created (use :py:func:`ensuredir` if a the target path is a directory to be created). ''' d, x = os.path.split(dst.rstrip(os.sep)) dirs = [] while d and not os.path.exists(d): dirs.append(d) d, x = os.path.split(d) dirs.reverse() for d in dirs: try: os.mkdir(d) except OSError as e: if not e.errno == errno.EEXIST: raise
[docs]def ensuredir(dst): ''' Create directory and all intermediate path components to it as needed. :param dst: directory name Nothing is done if the given target already exists. ''' if os.path.exists(dst): return dst.rstrip(os.sep) ensuredirs(dst) try: os.mkdir(dst) except OSError as e: if not e.errno == errno.EEXIST: raise
[docs]def reuse(x): ''' Get unique instance of an object. :param x: hashable object :returns: reference to x or an equivalent object Cache object ``x`` in a global dict for reuse, or if x already is in that dict, return a reference to it. ''' grs = GlobalVars.reuse_store if x not in grs: grs[x] = x return grs[x]
[docs]def deuse(x): grs = GlobalVars.reuse_store if x in grs: del grs[x]
[docs]class Anon(object): ''' Dict-to-object utility. Any given arguments are stored as attributes. Example:: a = Anon(x=1, y=2) print a.x, a.y ''' def __init__(self, **dict): for k in dict: self.__dict__[k] = dict[k]
[docs]def select_files(paths, selector=None, regex=None, show_progress=True): ''' Recursively select files. :param paths: entry path names :param selector: callback for conditional inclusion :param regex: pattern for conditional inclusion :param show_progress: if True, indicate start and stop of processing :returns: list of path names Recursively finds all files under given entry points ``paths``. If parameter ``regex`` is a regular expression, only files with matching path names are included. If additionally parameter ``selector`` is given a callback function, only files for which the callback returns ``True`` are included. The callback should take a single argument. The callback is called with a single argument, an object, having as attributes, any named groups given in ``regex``. Examples To find all files ending in ``'.mseed'`` or ``'.msd'``:: select_files(paths, regex=r'\.(mseed|msd)$') To find all files ending with ``'$Year.$DayOfYear'``, having set 2009 for the year:: select_files(paths, regex=r'(?P<year>\d\d\d\d)\.(?P<doy>\d\d\d)$', selector=(lambda x: int(x.year) == 2009)) ''' if show_progress: progress_beg('selecting files...') if logger.isEnabledFor(logging.DEBUG): sys.stderr.write('\n') good = [] if regex: rselector = re.compile(regex) def addfile(path): if regex: logger.debug("looking at filename: '%s'" % path) m = rselector.search(path) if m: infos = Anon(**m.groupdict()) logger.debug(" regex '%s' matches." % regex) for k, v in m.groupdict().items(): logger.debug( " attribute '%s' has value '%s'" % (k, v)) if selector is None or selector(infos): good.append(os.path.abspath(path)) else: logger.debug(" regex '%s' does not match." % regex) else: good.append(os.path.abspath(path)) if isinstance(paths, str): paths = [paths] for path in paths: if os.path.isdir(path): for (dirpath, dirnames, filenames) in os.walk(path): for filename in filenames: addfile(op.join(dirpath, filename)) else: addfile(path) if show_progress: progress_end('%i file%s selected.' % (len(good), plural_s(len(good)))) return good
[docs]def base36encode(number, alphabet='0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ'): ''' Convert positive integer to a base36 string. ''' if not isinstance(number, (int, long)): raise TypeError('number must be an integer') if number < 0: raise ValueError('number must be positive') # Special case for small numbers if number < 36: return alphabet[number] base36 = '' while number != 0: number, i = divmod(number, 36) base36 = alphabet[i] + base36 return base36
[docs]def base36decode(number): ''' Decode base36 endcoded positive integer. ''' return int(number, 36)
[docs]class UnpackError(Exception): ''' Exception raised when :py:func:`unpack_fixed` encounters an error. ''' pass
ruler = ''.join(['%-10i' % i for i in range(8)]) \ + '\n' + '0123456789' * 8 + '\n'
[docs]def unpack_fixed(format, line, *callargs): ''' Unpack fixed format string, as produced by many fortran codes. :param format: format specification :param line: string to be processed :param callargs: callbacks for callback fields in the format The format is described by a string of comma-separated fields. Each field is defined by a character for the field type followed by the field width. A questionmark may be appended to the field description to allow the argument to be optional (The data string is then allowed to be filled with blanks and ``None`` is returned in this case). The following field types are available: ==== ================================================================ Type Description ==== ================================================================ A string (full field width is extracted) a string (whitespace at the beginning and the end is removed) i integer value f floating point value @ special type, a callback must be given for the conversion x special field type to skip parts of the string ==== ================================================================ ''' ipos = 0 values = [] icall = 0 for form in format.split(','): form = form.strip() optional = form[-1] == '?' form = form.rstrip('?') typ = form[0] ln = int(form[1:]) s = line[ipos:ipos+ln] cast = { 'x': None, 'A': str, 'a': lambda x: x.strip(), 'i': int, 'f': float, '@': 'extra'}[typ] if cast == 'extra': cast = callargs[icall] icall += 1 if cast is not None: if optional and s.strip() == '': values.append(None) else: try: values.append(cast(s)) except Exception: mark = [' '] * 80 mark[ipos:ipos+ln] = ['^'] * ln mark = ''.join(mark) raise UnpackError( 'Invalid cast to type "%s" at position [%i:%i] of ' 'line: \n%s%s\n%s' % ( typ, ipos, ipos+ln, ruler, line.rstrip(), mark)) ipos += ln return values
_pattern_cache = {} def _nslc_pattern(pattern): if pattern not in _pattern_cache: rpattern = re.compile(fnmatch.translate(pattern), re.I) _pattern_cache[pattern] = rpattern else: rpattern = _pattern_cache[pattern] return rpattern
[docs]def match_nslc(patterns, nslc): ''' Match network-station-location-channel code against pattern or list of patterns. :param patterns: pattern or list of patterns :param nslc: tuple with (network, station, location, channel) as strings :returns: ``True`` if the pattern matches or if any of the given patterns match; or ``False``. The patterns may contain shell-style wildcards: \*, ?, [seq], [!seq]. Example:: match_nslc('*.HAM3.*.BH?', ('GR', 'HAM3', '', 'BHZ')) # -> True ''' if isinstance(patterns, str): patterns = [patterns] if not isinstance(nslc, str): s = '.'.join(nslc) else: s = nslc for pattern in patterns: if _nslc_pattern(pattern).match(s): return True return False
[docs]def match_nslcs(patterns, nslcs): ''' Get network-station-location-channel codes that match given pattern or any of several given patterns. :param patterns: pattern or list of patterns :param nslcs: list of (network, station, location, channel) tuples See also :py:func:`match_nslc` ''' matching = [] for nslc in nslcs: if match_nslc(patterns, nslc): matching.append(nslc) return matching
[docs]class SoleError(Exception): ''' Exception raised by objects of type :py:class:`Sole`, when an concurrent instance is running. ''' pass
[docs]class Sole(object): ''' Use POSIX advisory file locking to ensure that only a single instance of a program is running. :param pid_path: path to lockfile to be used Usage:: from pyrocko.util import Sole, SoleError, setup_logging import os setup_logging('my_program') pid_path = os.path.join(os.environ['HOME'], '.my_program_lock') try: sole = Sole(pid_path) except SoleError, e: logger.fatal( str(e) ) sys.exit(1) ''' def __init__(self, pid_path): self._pid_path = pid_path self._other_running = False ensuredirs(self._pid_path) self._lockfile = None try: self._lockfile = os.open(self._pid_path, os.O_CREAT | os.O_WRONLY) except Exception: raise SoleError( 'Cannot open lockfile (path = %s)' % self._pid_path) try: fcntl.lockf(self._lockfile, fcntl.LOCK_EX | fcntl.LOCK_NB) except IOError: self._other_running = True try: f = open(self._pid_path, 'r') pid = f.read().strip() f.close() except Exception: pid = '?' raise SoleError('Other instance is running (pid = %s)' % pid) try: os.ftruncate(self._lockfile, 0) os.write(self._lockfile, '%i\n' % os.getpid()) os.fsync(self._lockfile) except Exception: # the pid is only stored for user information, so this is allowed # to fail pass def __del__(self): if not self._other_running: import os import fcntl if self._lockfile is not None: fcntl.lockf(self._lockfile, fcntl.LOCK_UN) os.close(self._lockfile) try: os.unlink(self._pid_path) except Exception: pass
re_escapequotes = re.compile(r"(['\\])")
[docs]def escapequotes(s): return re_escapequotes.sub(r"\\\1", s)
[docs]class TableWriter(object): ''' Write table of space separated values to a file. :param f: file like object Strings containing spaces are quoted on output. ''' def __init__(self, f): self._f = f
[docs] def writerow(self, row, minfieldwidths=None): ''' Write one row of values to underlying file. :param row: iterable of values :param minfieldwidths: minimum field widths for the values Each value in in ``row`` is converted to a string and optionally padded with blanks. The resulting strings are output separated with blanks. If any values given are strings and if they contain whitespace, they are quoted with single quotes, and any internal single quotes are backslash-escaped. ''' out = [] for i, x in enumerate(row): w = 0 if minfieldwidths and i < len(minfieldwidths): w = minfieldwidths[i] if isinstance(x, str): if re.search(r"\s|'", x): x = "'%s'" % escapequotes(x) x = x.ljust(w) else: x = str(x).rjust(w) out.append(x) self._f.write(' '.join(out).rstrip() + '\n')
[docs]class TableReader(object): ''' Read table of space separated values from a file. :param f: file-like object This uses Pythons shlex module to tokenize lines. Should deal correctly with quoted strings. ''' def __init__(self, f): self._f = f self.eof = False
[docs] def readrow(self): ''' Read one row from the underlying file, tokenize it with shlex. :returns: tokenized line as a list of strings. ''' line = self._f.readline() if not line: self.eof = True return [] s = shlex.shlex(line, posix=True) s.whitespace_split = True s.whitespace = ' \t\n\r\f\v' # compatible with re's \s row = [] while True: x = s.get_token() if x is None: break row.append(x) return row
[docs]def gform(number, significant_digits=3): ''' Pretty print floating point numbers. Align floating point numbers at the decimal dot. :: | -d.dde+xxx| | -d.dde+xx | |-ddd. | | -dd.d | | -d.dd | | -0.ddd | | -0.0ddd | | -0.00ddd | | -d.dde-xx | | -d.dde-xxx| | nan| The formatted string has length ``significant_digits * 2 + 6``. ''' no_exp_range = (pow(10., -1), pow(10., significant_digits)) width = significant_digits+significant_digits-1+1+1+5 if (no_exp_range[0] <= abs(number) < no_exp_range[1]) or number == 0.: s = ('%#.*g' % (significant_digits, number)).rstrip('0') else: s = '%.*E' % (significant_digits-1, number) s = (' '*(-s.find('.')+(significant_digits+1))+s).ljust(width) if s.strip().lower() == 'nan': s = 'nan'.rjust(width) return s
[docs]def human_bytesize(value): exts = 'Bytes kB MB GB TB PB EB ZB YB'.split() if value == 1: return '1 Byte' for i, ext in enumerate(exts): x = float(value) / 1000**i if round(x) < 10. and not value < 1000: return '%.1f %s' % (x, ext) if round(x) < 1000.: return '%.0f %s' % (x, ext) return '%i Bytes' % value
re_compatibility = re.compile( r'!pyrocko\.(trace|gf\.(meta|seismosizer)|fomosto\.' + r'(dummy|poel|qseis|qssp))\.' )
[docs]def pf_is_old(fn): oldstyle = False with open(fn, 'r') as f: for line in f: if re_compatibility.search(line): oldstyle = True return oldstyle
[docs]def pf_upgrade(fn): need = pf_is_old(fn) if need: fn_temp = fn + '.temp' with open(fn, 'r') as fin: with open(fn_temp, 'w') as fout: for line in fin: line = re_compatibility.sub('!pf.', line) fout.write(line) os.rename(fn_temp, fn) return need
[docs]def read_leap_seconds(tzfile='/usr/share/zoneinfo/right/UTC'): ''' Extract leap second information from tzdata. Based on example at http://stackoverflow.com/questions/19332902/\ extract-historic-leap-seconds-from-tzdata See also 'man 5 tzfile'. ''' from struct import unpack, calcsize out = [] with open(tzfile, 'rb') as f: # read header fmt = '>4s c 15x 6l' (magic, format, ttisgmtcnt, ttisstdcnt, leapcnt, timecnt, typecnt, charcnt) = unpack(fmt, f.read(calcsize(fmt))) assert magic == 'TZif'.encode('US-ASCII'), 'Not a timezone file' # skip over some uninteresting data fmt = '>%(timecnt)dl %(timecnt)dB %(ttinfo)s %(charcnt)ds' % dict( timecnt=timecnt, ttinfo='lBB'*typecnt, charcnt=charcnt) f.read(calcsize(fmt)) # read leap-seconds fmt = '>2l' for i in range(leapcnt): tleap, nleap = unpack(fmt, f.read(calcsize(fmt))) out.append((tleap-nleap+1, nleap)) return out
[docs]class LeapSecondsError(Exception): pass
[docs]class LeapSecondsOutdated(LeapSecondsError): pass
[docs]class InvalidLeapSecondsFile(LeapSecondsOutdated): pass
[docs]def parse_leap_seconds_list(fn): data = [] texpires = None try: t0 = int(round(str_to_time('1900-01-01 00:00:00'))) except TimeStrError: t0 = int(round(str_to_time('1970-01-01 00:00:00'))) - 2208988800 tnow = int(round(time.time())) if not op.exists(fn): raise LeapSecondsOutdated('no leap seconds file found') try: with open(fn, 'rb') as f: for line in f: if line.strip().startswith(b'<!DOCTYPE'): raise InvalidLeapSecondsFile('invalid leap seconds file') if line.startswith(b'#@'): texpires = int(line.split()[1]) + t0 elif line.startswith(b'#') or len(line) < 5: pass else: toks = line.split() t = int(toks[0]) + t0 nleap = int(toks[1]) - 10 data.append((t, nleap)) except IOError: raise LeapSecondsError('cannot read leap seconds file %s' % fn) if texpires is None or tnow > texpires: raise LeapSecondsOutdated('leap seconds list is outdated') return data
[docs]def read_leap_seconds2(): from pyrocko import config conf = config.config() fn = conf.leapseconds_path url = conf.leapseconds_url # check for outdated default URL if url == 'http://www.ietf.org/timezones/data/leap-seconds.list': url = 'https://www.ietf.org/timezones/data/leap-seconds.list' logger.info( 'Leap seconds default URL is now: %s\nUsing new default.' % url) for i in range(3): try: return parse_leap_seconds_list(fn) except LeapSecondsOutdated: try: logger.info('updating leap seconds list...') download_file(url, fn) except Exception as e: raise LeapSecondsError( 'cannot download leap seconds list from %s to %s (%s)' % (url, fn, e)) raise LeapSecondsError('Could not retrieve/read leap seconds file.')
[docs]def gps_utc_offset(t_utc): '''Time offset t_gps - t_utc for a given t_utc.''' ls = read_leap_seconds2() i = 0 if t_utc < ls[0][0]: return ls[0][1] - 1 - 9 while i < len(ls) - 1: if ls[i][0] <= t_utc and t_utc < ls[i+1][0]: return ls[i][1] - 9 i += 1 return ls[-1][1] - 9
[docs]def utc_gps_offset(t_gps): '''Time offset t_utc - t_gps for a given t_gps.''' ls = read_leap_seconds2() if t_gps < ls[0][0] + ls[0][1] - 9: return - (ls[0][1] - 1 - 9) i = 0 while i < len(ls) - 1: if ls[i][0] + ls[i][1] - 9 <= t_gps \ and t_gps < ls[i+1][0] + ls[i+1][1] - 9: return - (ls[i][1] - 9) i += 1 return - (ls[-1][1] - 9)
[docs]def make_iload_family(iload_fh, doc_fmt='FMT', doc_yielded_objects='FMT'): import itertools import glob from pyrocko.io.io_common import FileLoadError def iload_filename(filename, **kwargs): try: with open(filename, 'rb') as f: for cr in iload_fh(f, **kwargs): yield cr except FileLoadError as e: e.set_context('filename', filename) raise def iload_dirname(dirname, **kwargs): for entry in os.listdir(dirname): fpath = op.join(dirname, entry) if op.isfile(fpath): for cr in iload_filename(fpath, **kwargs): yield cr def iload_glob(pattern, **kwargs): fns = glob.glob(pattern) for fn in fns: for cr in iload_filename(fn, **kwargs): yield cr def iload(source, **kwargs): if isinstance(source, str): if op.isdir(source): return iload_dirname(source, **kwargs) elif op.isfile(source): return iload_filename(source, **kwargs) else: return iload_glob(source, **kwargs) elif hasattr(source, 'read'): return iload_fh(source, **kwargs) else: return itertools.chain.from_iterable( iload(subsource, **kwargs) for subsource in source) iload_filename.__doc__ = ''' Read %s information from named file. ''' % doc_fmt iload_dirname.__doc__ = ''' Read %s information from directory of %s files. ''' % (doc_fmt, doc_fmt) iload_glob.__doc__ = ''' Read %s information from files matching a glob pattern. ''' % doc_fmt iload.__doc__ = ''' Load %s information from given source(s) The ``source`` can be specified as the name of a %s file, the name of a directory containing %s files, a glob pattern of %s files, an open filehandle or an iterator yielding any of the forementioned sources. This function behaves as a generator yielding %s objects. ''' % (doc_fmt, doc_fmt, doc_fmt, doc_fmt, doc_yielded_objects) for f in iload_filename, iload_dirname, iload_glob, iload: f.__module__ = iload_fh.__module__ return iload_filename, iload_dirname, iload_glob, iload
[docs]class Inconsistency(Exception): pass
[docs]def consistency_check(list_of_tuples, message='values differ:'): ''' Check for inconsistencies. Given a list of tuples, check that all tuple elements except for first one match. E.g. ``[('STA.N', 55.3, 103.2), ('STA.E', 55.3, 103.2)]`` would be valid because the coordinates at the two channels are the same. ''' if len(list_of_tuples) >= 2: if any(t[1:] != list_of_tuples[0][1:] for t in list_of_tuples[1:]): raise Inconsistency('%s\n' % message + '\n'.join( ' %s: %s' % (t[0], ', '.join('%g' % x for x in t[1:])) for t in list_of_tuples))
[docs]class defaultzerodict(dict): def __missing__(self, k): return 0
[docs]def mostfrequent(x): c = defaultzerodict() for e in x: c[e] += 1 return sorted(list(c.keys()), key=lambda k: c[k])[-1]
[docs]def consistency_merge(list_of_tuples, message='values differ:', error='raise', merge=mostfrequent): assert error in ('raise', 'warn', 'ignore') if len(list_of_tuples) == 0: raise Exception('cannot merge empty sequence') try: consistency_check(list_of_tuples, message) return list_of_tuples[0][1:] except Inconsistency as e: if error == 'raise': raise elif error == 'warn': logger.warning(str(e)) return tuple([merge(x) for x in zip(*list_of_tuples)[1:]])
[docs]def parse_md(f): try: with open(op.join( op.dirname(op.abspath(f)), 'README.md'), 'r') as readme: mdstr = readme.read() except IOError as e: return 'Failed to get README.md: %s' % e # Remve the title mdstr = re.sub(r'^# .*\n?', '', mdstr) # Append sphinx reference to `pyrocko.` modules mdstr = re.sub(r'`pyrocko\.(.*)`', r':py:mod:`pyrocko.\1`', mdstr) # Convert Subsections to toc-less rubrics mdstr = re.sub(r'## (.*)\n', r'.. rubric:: \1\n', mdstr) return mdstr