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# http://pyrocko.org - GPLv3 

# 

# The Pyrocko Developers, 21st Century 

# ---|P------/S----------~Lg---------- 

'''Utility functions for Pyrocko.''' 

from __future__ import division, print_function 

 

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 

 

try: 

from urllib.parse import urlencode, quote, unquote # noqa 

from urllib.request import ( 

Request, build_opener, HTTPDigestAuthHandler, urlopen) # noqa 

from urllib.error import HTTPError, URLError # noqa 

 

except ImportError: 

from urllib import urlencode, quote, unquote # noqa 

from urllib2 import (Request, build_opener, HTTPDigestAuthHandler, # noqa 

HTTPError, URLError, urlopen) # noqa 

 

 

class URLErrorSSL(URLError): 

 

def __init__(self, urlerror): 

self.__dict__ = urlerror.__dict__.copy() 

 

def __str__(self): 

return ( 

'Requesting web resource failed and the problem could be ' 

'related to SSL. Python standard libraries on some older ' 

'systems (like Ubuntu 14.04) are known to have trouble ' 

'with some SSL setups of today\'s servers: %s' 

% URLError.__str__(self)) 

 

 

def urlopen_ssl_check(*args, **kwargs): 

try: 

return urlopen(*args, **kwargs) 

except URLError as e: 

if str(e).find('SSL') != -1: 

raise URLErrorSSL(e) 

else: 

raise 

 

 

try: 

long 

except NameError: 

long = int 

 

 

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 

 

 

def progressbar_module(): 

return progressbar_mod 

 

 

g_setup_logging_args = 'pyrocko', 'warning' 

 

 

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()`. 

''' 

 

global g_setup_logging_args 

g_setup_logging_args = (programname, levelname) 

 

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') 

 

 

def subprocess_setup_logging_args(): 

''' 

Get arguments from previous call to setup_logging. 

 

These can be sent down to a worker process so it can setup its logging 

in the same way as the main process. 

''' 

return g_setup_logging_args 

 

 

def data_file(fn): 

return os.path.join(os.path.split(__file__)[0], 'data', fn) 

 

 

class DownloadError(Exception): 

pass 

 

 

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 as req_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) 

 

status = { 

'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, 

'finished': False 

} 

 

try: 

url_to_size = {} 

 

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 req_HTTPError as e: 

logging.warn("http error: %s" % e) 

raise DownloadError('could not download file(s) from: %s' % url) 

 

finally: 

status['finished'] = True 

if callable(status_callback): 

status_callback(status) 

session.close() 

 

 

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) 

 

 

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.') 

 

 

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 

 

 

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 

 

 

class BetterHelpFormatter(optparse.IndentedHelpFormatter): 

 

def __init__(self, *args, **kwargs): 

optparse.IndentedHelpFormatter.__init__(self, *args, **kwargs) 

 

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) 

 

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]) 

 

 

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 

 

 

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() 

 

 

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() 

 

 

class ArangeError(Exception): 

pass 

 

 

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 

 

 

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 

 

 

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):]) 

 

 

def diff_fd_1d_4o(dt, data): 

''' 

Approximate first derivative of an array (forth order, central FD). 

 

:param dt: sampling interval 

:param data: NumPy array with data samples 

 

:returns: NumPy array with same shape as input 

 

Interior points are approximated to fourth order, edge points to first 

order right- or left-sided respectively, points next to edge to second 

order central. 

''' 

import scipy.signal 

 

ddata = num.empty_like(data, dtype=num.float) 

 

if data.size >= 5: 

ddata[2:-2] = scipy.signal.lfilter( 

[-1., +8., 0., -8., 1.], [1.], data)[4:] / (12.*dt) 

 

if data.size >= 3: 

ddata[1] = (data[2] - data[0]) / (2. * dt) 

ddata[-2] = (data[-1] - data[-3]) / (2. * dt) 

 

if data.size >= 2: 

ddata[0] = (data[1] - data[0]) / dt 

ddata[-1] = (data[-1] - data[-2]) / dt 

 

if data.size == 1: 

ddata[0] = 0.0 

 

return ddata 

 

 

def diff_fd_1d_2o(dt, data): 

''' 

Approximate first derivative of an array (second order, central FD). 

 

:param dt: sampling interval 

:param data: NumPy array with data samples 

 

:returns: NumPy array with same shape as input 

 

Interior points are approximated to second order, edge points to first 

order right- or left-sided respectively. 

 

Uses :py:func:`numpy.gradient`. 

''' 

 

return num.gradient(data, dt) 

 

 

def diff_fd_2d_4o(dt, data): 

''' 

Approximate second derivative of an array (forth order, central FD). 

 

:param dt: sampling interval 

:param data: NumPy array with data samples 

 

:returns: NumPy array with same shape as input 

 

Interior points are approximated to fourth order, next-to-edge points to 

second order, edge points repeated. 

''' 

import scipy.signal 

 

ddata = num.empty_like(data, dtype=num.float) 

 

if data.size >= 5: 

ddata[2:-2] = scipy.signal.lfilter( 

[-1., +16., -30., +16., -1.], [1.], data)[4:] / (12.*dt**2) 

 

if data.size >= 3: 

ddata[:2] = (data[2] - 2.0 * data[1] + data[0]) / dt**2 

ddata[-2:] = (data[-1] - 2.0 * data[-2] + data[-3]) / dt**2 

 

if data.size < 3: 

ddata[:] = 0.0 

 

return ddata 

 

 

def diff_fd_2d_2o(dt, data): 

''' 

Approximate second derivative of an array (second order, central FD). 

 

:param dt: sampling interval 

:param data: NumPy array with data samples 

 

:returns: NumPy array with same shape as input 

 

Interior points are approximated to second order, edge points repeated. 

''' 

import scipy.signal 

 

ddata = num.empty_like(data, dtype=num.float) 

 

if data.size >= 3: 

ddata[1:-1] = scipy.signal.lfilter( 

[1., -2., 1.], [1.], data)[2:] / (dt**2) 

 

ddata[0] = ddata[1] 

ddata[-1] = ddata[-2] 

 

if data.size < 3: 

ddata[:] = 0.0 

 

return ddata 

 

 

def diff_fd(n, order, dt, data): 

''' 

Approximate 1st or 2nd derivative of an array. 

 

:param n: 1 for first derivative, 2 for second 

:param order: order of the approximation 2 and 4 are supported 

:param dt: sampling interval 

:param data: NumPy array with data samples 

 

:returns: NumPy array with same shape as input 

 

This is a frontend to the functions :py:func:`diff_fd_1d_2o`, 

:py:func:`diff_fd_1d_4o`, :py:func:`diff_fd_2d_2o`, and 

:py:func:`diff_fd_2d_4o`. 

 

Raises :py:exc:`ValueError` for unsupported `n` or `order`. 

''' 

 

funcs = { 

1: {2: diff_fd_1d_2o, 4: diff_fd_1d_4o}, 

2: {2: diff_fd_2d_2o, 4: diff_fd_2d_4o}} 

 

try: 

funcs_n = funcs[n] 

except KeyError: 

raise ValueError( 

'pyrocko.util.diff_fd: ' 

'Only 1st and 2sd derivatives are supported.') 

 

try: 

func = funcs_n[order] 

except KeyError: 

raise ValueError( 

'pyrocko.util.diff_fd: ' 

'Order %i is not supported for %s derivative. Supported: %s' % ( 

order, ['', '1st', '2nd'][n], 

', '.join('%i' % order for order in sorted(funcs_n.keys())))) 

 

return func(dt, data) 

 

 

class GlobalVars(object): 

reuse_store = dict() 

decitab_nmax = 0 

decitab = {} 

decimate_fir_coeffs = {} 

decimate_iir_coeffs = {} 

re_frac = None 

 

 

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 

 

 

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() 

 

 

class UnavailableDecimation(Exception): 

''' 

Exception raised by :py:func:`decitab` for unavailable decimation factors. 

''' 

 

pass 

 

 

def gcd(a, b, epsilon=1e-7): 

''' 

Greatest common divisor. 

''' 

 

while b > epsilon*a: 

a, b = b, a % b 

 

return a 

 

 

def lcm(a, b): 

''' 

Least common multiple. 

''' 

 

return a*b // gcd(a, b) 

 

 

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 

 

 

def zfmt(n): 

return '%%0%ii' % (int(math.log10(n - 1)) + 1) 

 

 

def _year_to_time(year): 

tt = (year, 1, 1, 0, 0, 0) 

return calendar.timegm(tt) 

 

 

def _working_year(year): 

try: 

tt = (year, 1, 1, 0, 0, 0) 

t = calendar.timegm(tt) 

tt2_ = time.gmtime(t) 

tt2 = tuple(tt2_)[:6] 

if tt != tt2: 

return False 

 

s = '%i-01-01 00:00:00' % year 

s2 = time.strftime('%Y-%m-%d %H:%M:%S', tt2_) 

if s != s2: 

return False 

 

except Exception: 

return False 

 

return True 

 

 

g_working_system_time_range = None 

 

 

def get_working_system_time_range(): 

''' 

Check time range supported by the systems's time conversion functions. 

 

Returns system time stamps of start of year of first/last fully supported 

year span. If this is before 1900 or after 2100, return first/last century 

which is fully supported. 

 

:returns: ``(tmin, tmax, year_min, year_max)`` 

''' 

 

global g_working_system_time_range 

 

if g_working_system_time_range is None: 

year0 = 2000 

year_min = year0 

year_max = year0 

 

itests = list(range(101)) 

for i in range(19): 

itests.append(200 + i*100) 

 

for i in itests: 

if not _working_year(year0 - i): 

break 

else: 

year_min = year0 - i 

 

for i in itests: 

if not _working_year(year0 + i + 1): 

break 

else: 

year_max = year0 + i 

 

g_working_system_time_range = ( 

_year_to_time(year_min), 

_year_to_time(year_max), 

year_min, year_max) 

 

return g_working_system_time_range 

 

 

def is_working_time(t): 

tmin, tmax, _, _ = get_working_system_time_range() 

return tmin <= t <= tmax 

 

 

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 

 

 

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) 

 

 

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) 

 

 

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) 

 

 

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 

 

 

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 

 

 

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 

 

 

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] 

 

 

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)) 

 

 

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)) 

 

 

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)) 

 

 

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)) 

 

 

class TimeStrError(Exception): 

pass 

 

 

class FractionalSecondsMissing(TimeStrError): 

''' 

Exception raised by :py:func:`str_to_time` when the given string lacks 

fractional seconds. 

''' 

 

pass 

 

 

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 

 

 

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 

 

 

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 

 

 

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) 

 

 

def gmtime_x(timestamp): 

etimestamp = float(num.floor(timestamp)) 

tt = time.gmtime(etimestamp) 

ms = (timestamp-etimestamp)*1000 

return tt, ms 

 

 

def plural_s(n): 

if n == 1: 

return '' 

else: 

return 's' 

 

 

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 

 

 

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 

 

 

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] 

 

 

def deuse(x): 

grs = GlobalVars.reuse_store 

if x in grs: 

del grs[x] 

 

 

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] 

 

 

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 

 

 

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 

 

 

def base36decode(number): 

''' 

Decode base36 endcoded positive integer. 

''' 

 

return int(number, 36) 

 

 

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' 

 

 

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 

 

 

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 

 

 

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 

 

 

class SoleError(Exception): 

''' 

Exception raised by objects of type :py:class:`Sole`, when an concurrent 

instance is running. 

''' 

 

pass 

 

 

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 

self._os = os 

self._fcntl = fcntl 

 

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: 

if self._lockfile is not None: 

self._fcntl.lockf(self._lockfile, self._fcntl.LOCK_UN) 

self._os.close(self._lockfile) 

try: 

self._os.unlink(self._pid_path) 

except Exception: 

pass 

 

 

re_escapequotes = re.compile(r"(['\\])") 

 

 

def escapequotes(s): 

return re_escapequotes.sub(r"\\\1", s) 

 

 

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 

 

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') 

 

 

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 

 

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 

 

 

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 

 

 

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))\.' 

) 

 

 

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 

 

 

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 

 

 

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 

 

 

class LeapSecondsError(Exception): 

pass 

 

 

class LeapSecondsOutdated(LeapSecondsError): 

pass 

 

 

class InvalidLeapSecondsFile(LeapSecondsOutdated): 

pass 

 

 

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 

 

 

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.') 

 

 

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 

 

 

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) 

 

 

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 

 

 

class Inconsistency(Exception): 

pass 

 

 

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)) 

 

 

class defaultzerodict(dict): 

def __missing__(self, k): 

return 0 

 

 

def mostfrequent(x): 

c = defaultzerodict() 

for e in x: 

c[e] += 1 

 

return sorted(list(c.keys()), key=lambda k: c[k])[-1] 

 

 

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 list(zip(*list_of_tuples))[1:]]) 

 

 

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 

 

 

def mpl_show(plt): 

import matplotlib 

if matplotlib.get_backend().lower() == 'agg': 

logger.warning('Cannot show() when using matplotlib "agg" backend') 

else: 

plt.show()