949 lines
28 KiB
Python
949 lines
28 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import hashlib
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import os
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import platform
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import re
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import subprocess
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import numpy as np
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from obspy import UTCDateTime, read
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from obspy.core import AttribDict
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from obspy.signal.rotate import rotate2zne
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from obspy.io.xseed.utils import SEEDParserException
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from pylot.core.io.inputs import PylotParameter
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from scipy.interpolate import splrep, splev
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from PySide import QtCore, QtGui
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try:
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import pyqtgraph as pg
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except Exception as e:
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print('QtPyLoT: Could not import pyqtgraph. {}'.format(e))
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pg = None
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def _pickle_method(m):
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if m.im_self is None:
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return getattr, (m.im_class, m.im_func.func_name)
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else:
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return getattr, (m.im_self, m.im_func.func_name)
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def readDefaultFilterInformation(fname):
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pparam = PylotParameter(fname)
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return readFilterInformation(pparam)
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def readFilterInformation(pylot_parameter):
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p_filter = {'filtertype': pylot_parameter['filter_type'][0],
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'freq': [pylot_parameter['minfreq'][0], pylot_parameter['maxfreq'][0]],
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'order': int(pylot_parameter['filter_order'][0])}
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s_filter = {'filtertype': pylot_parameter['filter_type'][1],
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'freq': [pylot_parameter['minfreq'][1], pylot_parameter['maxfreq'][1]],
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'order': int(pylot_parameter['filter_order'][1])}
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filter_information = {'P': p_filter,
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'S': s_filter}
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return filter_information
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def fit_curve(x, y):
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return splev, splrep(x, y)
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def getindexbounds(f, eta):
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mi = f.argmax()
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m = max(f)
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b = m * eta
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l = find_nearest(f[:mi], b)
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u = find_nearest(f[mi:], b) + mi
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return mi, l, u
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def gen_Pool(ncores=0):
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'''
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:param ncores: number of CPU cores for multiprocessing.Pool, if ncores == 0 use all available
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:return: multiprocessing.Pool object
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'''
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import multiprocessing
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if ncores == 0:
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ncores = multiprocessing.cpu_count()
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pool = multiprocessing.Pool(ncores)
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return pool
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def excludeQualityClasses(picks, qClasses, timeerrorsP, timeerrorsS):
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'''
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takes PyLoT picks dictionary and returns a new dictionary with certain classes excluded.
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:param picks: PyLoT picks dictionary
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:param qClasses: list (or int) of quality classes (0-4) to exclude
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:param timeerrorsP: time errors for classes (0-4) for P
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:param timeerrorsS: time errors for classes (0-4) for S
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:return: new picks dictionary
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'''
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from pylot.core.pick.utils import getQualityFromUncertainty
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if type(qClasses) in [int, float]:
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qClasses = [qClasses]
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picksdict_new = {}
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phaseError = {'P': timeerrorsP,
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'S': timeerrorsS}
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for station, phases in picks.items():
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for phase, pick in phases.items():
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if not type(pick) in [AttribDict, dict]:
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continue
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pickerror = phaseError[identifyPhaseID(phase)]
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quality = getQualityFromUncertainty(pick['spe'], pickerror)
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if not quality in qClasses:
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if not station in picksdict_new:
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picksdict_new[station] = {}
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picksdict_new[station][phase] = pick
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return picksdict_new
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def clims(lim1, lim2):
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"""
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takes two pairs of limits and returns one pair of common limts
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:param lim1:
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:param lim2:
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:return:
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>>> clims([0, 4], [1, 3])
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[0, 4]
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>>> clims([1, 4], [0, 3])
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[0, 4]
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>>> clims([1, 3], [0, 4])
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[0, 4]
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>>> clims([0, 3], [1, 4])
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[0, 4]
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>>> clims([0, 3], [0, 4])
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[0, 4]
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>>> clims([1, 4], [0, 4])
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[0, 4]
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>>> clims([0, 4], [0, 4])
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[0, 4]
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>>> clims([0, 4], [1, 4])
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[0, 4]
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>>> clims([0, 4], [0, 3])
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[0, 4]
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"""
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lim = [None, None]
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if lim1[0] < lim2[0]:
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lim[0] = lim1[0]
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else:
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lim[0] = lim2[0]
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if lim1[1] > lim2[1]:
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lim[1] = lim1[1]
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else:
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lim[1] = lim2[1]
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return lim
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def demeanTrace(trace, window):
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"""
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takes a trace object and returns the same trace object but with data
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demeaned within a certain time window
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:param trace: waveform trace object
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:type trace: `~obspy.core.stream.Trace`
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:param window:
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:type window: tuple
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:return: trace
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:rtype: `~obspy.core.stream.Trace`
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"""
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trace.data -= trace.data[window].mean()
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return trace
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def findComboBoxIndex(combo_box, val):
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"""
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Function findComboBoxIndex takes a QComboBox object and a string and
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returns either 0 or the index throughout all QComboBox items.
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:param combo_box: Combo box object.
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:type combo_box: `~QComboBox`
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:param val: Name of a combo box to search for.
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:type val: basestring
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:return: index value of item with name val or 0
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"""
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return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
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def find_in_list(list, str):
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"""
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takes a list of strings and a string and returns the first list item
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matching the string pattern
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:param list: list to search in
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:param str: pattern to search for
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:return: first list item containing pattern
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.. example::
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>>> l = ['/dir/e1234.123.12', '/dir/e2345.123.12', 'abc123', 'def456']
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>>> find_in_list(l, 'dir')
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'/dir/e1234.123.12'
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>>> find_in_list(l, 'e1234')
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'/dir/e1234.123.12'
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>>> find_in_list(l, 'e2')
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'/dir/e2345.123.12'
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>>> find_in_list(l, 'ABC')
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'abc123'
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>>> find_in_list(l, 'f456')
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'def456'
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>>> find_in_list(l, 'gurke')
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"""
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rlist = [s for s in list if str.lower() in s.lower()]
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if rlist:
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return rlist[0]
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return None
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def find_nearest(array, value):
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'''
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function find_nearest takes an array and a value and returns the
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index of the nearest value found in the array
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:param array: array containing values
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:type array: `~numpy.ndarray`
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:param value: number searched for
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:return: index of the array item being nearest to the value
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>>> a = np.array([ 1.80339578, -0.72546654, 0.95769195, -0.98320759, 0.85922623])
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>>> find_nearest(a, 1.3)
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2
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>>> find_nearest(a, 0)
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1
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>>> find_nearest(a, 2)
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0
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>>> find_nearest(a, -1)
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3
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>>> a = np.array([ 1.1, -0.7, 0.9, -0.9, 0.8])
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>>> find_nearest(a, 0.849)
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4
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'''
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return (np.abs(array - value)).argmin()
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def fnConstructor(s):
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'''
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takes a string and returns a valid filename (especially on windows machines)
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:param s: desired filename
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:type s: str
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:return: valid filename
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'''
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if type(s) is str:
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s = s.split(':')[-1]
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else:
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s = getHash(UTCDateTime())
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badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
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badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
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fn = badchars.sub('_', s)
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if badsuffix.match(fn):
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fn = '_' + fn
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return fn
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def real_None(value):
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if value == 'None':
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return None
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else:
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return value
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def real_Bool(value):
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if value == 'True':
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return True
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elif value == 'False':
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return False
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else:
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return value
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def four_digits(year):
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"""
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takes a two digit year integer and returns the correct four digit equivalent
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from the last 100 years
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:param year: two digit year
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:type year: int
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:return: four digit year correspondant
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>>> four_digits(20)
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1920
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>>> four_digits(16)
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2016
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>>> four_digits(00)
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2000
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"""
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if year + 2000 <= UTCDateTime.utcnow().year:
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year += 2000
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else:
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year += 1900
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return year
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def common_range(stream):
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'''
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takes a stream object and returns the earliest end and the latest start
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time of all contained trace objects
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:param stream: seismological data stream
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:type stream: `~obspy.core.stream.Stream`
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:return: maximum start time and minimum end time
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'''
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max_start = None
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min_end = None
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for trace in stream:
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if max_start is None or trace.stats.starttime > max_start:
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max_start = trace.stats.starttime
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if min_end is None or trace.stats.endtime < min_end:
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min_end = trace.stats.endtime
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return max_start, min_end
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def full_range(stream):
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'''
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takes a stream object and returns the latest end and the earliest start
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time of all contained trace objects
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:param stream: seismological data stream
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:type stream: `~obspy.core.stream.Stream`
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:return: minimum start time and maximum end time
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'''
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min_start = UTCDateTime()
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max_end = None
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for trace in stream:
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if trace.stats.starttime < min_start:
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min_start = trace.stats.starttime
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if max_end is None or trace.stats.endtime > max_end:
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max_end = trace.stats.endtime
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return min_start, max_end
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def getHash(time):
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'''
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takes a time object and returns the corresponding SHA1 hash of the
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formatted date string
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:param time: time object for which a hash should be calculated
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:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
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:return: str
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'''
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hg = hashlib.sha1()
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hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
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return hg.hexdigest()
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def getLogin():
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'''
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returns the actual user's login ID
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:return: login ID
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'''
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return os.getlogin()
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def getOwner(fn):
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'''
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takes a filename and return the login ID of the actual owner of the file
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:param fn: filename of the file tested
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:type fn: str
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:return: login ID of the file's owner
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'''
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system_name = platform.system()
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if system_name in ["Linux", "Darwin"]:
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import pwd
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return pwd.getpwuid(os.stat(fn).st_uid).pw_name
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elif system_name == "Windows":
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import win32security
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f = win32security.GetFileSecurity(fn, win32security.OWNER_SECURITY_INFORMATION)
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(username, domain, sid_name_use) = win32security.LookupAccountSid(None, f.GetSecurityDescriptorOwner())
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return username
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def getPatternLine(fn, pattern):
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"""
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takes a file name and a pattern string to search for in the file and
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returns the first line which contains the pattern string otherwise 'None'
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:param fn: file name
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:type fn: str
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:param pattern: pattern string to search for
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:type pattern: str
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:return: the complete line containing the pattern string or None
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>>> getPatternLine('utils.py', 'python')
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'#!/usr/bin/env python\\n'
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>>> print(getPatternLine('version.py', 'palindrome'))
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None
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"""
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fobj = open(fn, 'r')
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for line in fobj.readlines():
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if pattern in line:
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fobj.close()
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return line
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return None
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def is_executable(fn):
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"""
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takes a filename and returns True if the file is executable on the system
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and False otherwise
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:param fn: path to the file to be tested
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:return: True or False
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"""
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return os.path.isfile(fn) and os.access(fn, os.X_OK)
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def isSorted(iterable):
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'''
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takes an iterable and returns 'True' if the items are in order otherwise
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'False'
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:param iterable: an iterable object
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:type iterable:
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:return: Boolean
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>>> isSorted(1)
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Traceback (most recent call last):
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...
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AssertionError: object is not iterable; object: 1
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>>> isSorted([1,2,3,4])
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True
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>>> isSorted('abcd')
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True
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>>> isSorted('bcad')
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False
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>>> isSorted([2,3,1,4])
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False
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'''
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assert isIterable(iterable), 'object is not iterable; object: {' \
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'0}'.format(iterable)
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if type(iterable) is str:
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iterable = [s for s in iterable]
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return sorted(iterable) == iterable
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def isIterable(obj):
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"""
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takes a python object and returns 'True' is the object is iterable and
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'False' otherwise
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:param obj: a python object
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:return: True of False
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"""
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try:
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iterator = iter(obj)
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except TypeError as te:
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return False
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return True
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def key_for_set_value(d):
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"""
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takes a dictionary and returns the first key for which's value the
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boolean is True
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:param d: dictionary containing values
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:type d: dict
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:return: key to the first non-False value found; None if no value's
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boolean equals True
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"""
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r = None
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for k, v in d.items():
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if v:
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return k
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return r
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def prepTimeAxis(stime, trace, verbosity=0):
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'''
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takes a starttime and a trace object and returns a valid time axis for
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plotting
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:param stime: start time of the actual seismogram as UTCDateTime
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:param trace: seismic trace object
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:return: valid numpy array with time stamps for plotting
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'''
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nsamp = trace.stats.npts
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srate = trace.stats.sampling_rate
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tincr = trace.stats.delta
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etime = stime + nsamp / srate
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time_ax = np.arange(stime, etime, tincr)
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if len(time_ax) < nsamp:
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if verbosity:
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print('elongate time axes by one datum')
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time_ax = np.arange(stime, etime + tincr, tincr)
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elif len(time_ax) > nsamp:
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if verbosity:
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print('shorten time axes by one datum')
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time_ax = np.arange(stime, etime - tincr, tincr)
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if len(time_ax) != nsamp:
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print('Station {0}, {1} samples of data \n '
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'{2} length of time vector \n'
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'delta: {3}'.format(trace.stats.station,
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nsamp, len(time_ax), tincr))
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time_ax = None
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return time_ax
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def find_horizontals(data):
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"""
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takes `obspy.core.stream.Stream` object and returns a list containing the component labels of the horizontal components available
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:param data: waveform data
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:type data: `obspy.core.stream.Stream`
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:return: components list
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:rtype: list
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..example::
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>>> st = read()
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>>> find_horizontals(st)
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[u'N', u'E']
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"""
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rval = []
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for tr in data:
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if tr.stats.channel[-1].upper() in ['Z', '3']:
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continue
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else:
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rval.append(tr.stats.channel[-1].upper())
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return rval
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def make_pen(picktype, phase, key, quality):
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if pg:
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rgba = pick_color(picktype, phase, quality)
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linestyle, width = pick_linestyle_pg(picktype, key)
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pen = pg.mkPen(rgba, width=width, style=linestyle)
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return pen
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def pick_color(picktype, phase, quality=0):
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min_quality = 3
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bpc = base_phase_colors(picktype, phase)
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rgba = bpc['rgba']
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modifier = bpc['modifier']
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intensity = 255.*quality/min_quality
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rgba = modify_rgba(rgba, modifier, intensity)
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return rgba
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def pick_color_plt(picktype, phase, quality=0):
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rgba = list(pick_color(picktype, phase, quality))
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for index, val in enumerate(rgba):
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rgba[index] /= 255.
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return rgba
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def pick_linestyle_plt(picktype, key):
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linestyles_manu = {'mpp': ('solid', 2.),
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'epp': ('dashed', 1.),
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'lpp': ('dashed', 1.),
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'spe': ('dashed', 1.)}
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linestyles_auto = {'mpp': ('dotted', 2.),
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'epp': ('dashdot', 1.),
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'lpp': ('dashdot', 1.),
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|
'spe': ('dashdot', 1.)}
|
|
linestyles = {'manual': linestyles_manu,
|
|
'auto': linestyles_auto}
|
|
return linestyles[picktype][key]
|
|
|
|
|
|
def pick_linestyle_pg(picktype, key):
|
|
linestyles_manu = {'mpp': (QtCore.Qt.SolidLine, 2.),
|
|
'epp': (QtCore.Qt.DashLine, 1.),
|
|
'lpp': (QtCore.Qt.DashLine, 1.),
|
|
'spe': (QtCore.Qt.DashLine, 1.)}
|
|
linestyles_auto = {'mpp': (QtCore.Qt.DotLine, 2.),
|
|
'epp': (QtCore.Qt.DashDotLine, 1.),
|
|
'lpp': (QtCore.Qt.DashDotLine, 1.),
|
|
'spe': (QtCore.Qt.DashDotLine, 1.)}
|
|
linestyles = {'manual': linestyles_manu,
|
|
'auto': linestyles_auto}
|
|
return linestyles[picktype][key]
|
|
|
|
|
|
def modify_rgba(rgba, modifier, intensity):
|
|
rgba = list(rgba)
|
|
index = {'r': 0,
|
|
'g': 1,
|
|
'b': 2}
|
|
val = rgba[index[modifier]] + intensity
|
|
if val > 255.:
|
|
val = 255.
|
|
elif val < 0.:
|
|
val = 0
|
|
rgba[index[modifier]] = val
|
|
return tuple(rgba)
|
|
|
|
|
|
def base_phase_colors(picktype, phase):
|
|
phases = {
|
|
'manual':
|
|
{
|
|
'P':
|
|
{
|
|
'rgba': (0, 0, 255, 255),
|
|
'modifier': 'g'
|
|
},
|
|
'S':
|
|
{
|
|
'rgba': (255, 0, 0, 255),
|
|
'modifier': 'b'
|
|
}
|
|
},
|
|
'auto':
|
|
{
|
|
'P':
|
|
{
|
|
'rgba': (140, 0, 255, 255),
|
|
'modifier': 'g'
|
|
},
|
|
'S':
|
|
{
|
|
'rgba': (255, 140, 0, 255),
|
|
'modifier': 'b'
|
|
}
|
|
}
|
|
}
|
|
return phases[picktype][phase]
|
|
|
|
|
|
def remove_underscores(data):
|
|
"""
|
|
takes a `obspy.core.stream.Stream` object and removes all underscores
|
|
from stationnames
|
|
:param data: stream of seismic data
|
|
:type data: `obspy.core.stream.Stream`
|
|
:return: data stream
|
|
"""
|
|
for tr in data:
|
|
# remove underscores
|
|
tr.stats.station = tr.stats.station.strip('_')
|
|
return data
|
|
|
|
|
|
def trim_station_components(data, trim_start=True, trim_end=True):
|
|
'''
|
|
cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
|
|
:param data: stream of seismic data
|
|
:type data: `obspy.core.stream.Stream`
|
|
:param trim_start: trim start of stream
|
|
:type trim_start: bool
|
|
:param trim_end: trim end of stream
|
|
:type trim_end: bool
|
|
:return: data stream
|
|
'''
|
|
starttime = {False: None}
|
|
endtime = {False: None}
|
|
|
|
stations = get_stations(data)
|
|
|
|
print('trim_station_components: Will trim stream for trim_start: {} and for '
|
|
'trim_end: {}.'.format(trim_start, trim_end))
|
|
for station in stations:
|
|
wf_station = data.select(station=station)
|
|
starttime[True] = max([trace.stats.starttime for trace in wf_station])
|
|
endtime[True] = min([trace.stats.endtime for trace in wf_station])
|
|
wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
|
|
|
|
return data
|
|
|
|
|
|
def check4gaps(data):
|
|
'''
|
|
check for gaps in Stream and remove them
|
|
:param data: stream of seismic data
|
|
:return: data stream
|
|
'''
|
|
stations = get_stations(data)
|
|
|
|
for station in stations:
|
|
wf_station = data.select(station=station)
|
|
if wf_station.get_gaps():
|
|
for trace in wf_station:
|
|
data.remove(trace)
|
|
print('check4gaps: Found gaps and removed station {} from waveform data.'.format(station))
|
|
|
|
return data
|
|
|
|
|
|
def check4doubled(data):
|
|
'''
|
|
check for doubled stations for same channel in Stream and take only the first one
|
|
:param data: stream of seismic data
|
|
:return: data stream
|
|
'''
|
|
stations = get_stations(data)
|
|
|
|
for station in stations:
|
|
wf_station = data.select(station=station)
|
|
# create list of all possible channels
|
|
channels = []
|
|
for trace in wf_station:
|
|
channel = trace.stats.channel
|
|
if not channel in channels:
|
|
channels.append(channel)
|
|
else:
|
|
print('check4doubled: removed the following trace for station {}, as there is'
|
|
' already a trace with the same channel given:\n{}'.format(
|
|
station, trace
|
|
))
|
|
data.remove(trace)
|
|
return data
|
|
|
|
|
|
def get_stations(data):
|
|
stations = []
|
|
for tr in data:
|
|
station = tr.stats.station
|
|
if not station in stations:
|
|
stations.append(station)
|
|
|
|
return stations
|
|
|
|
|
|
def check4rotated(data, metadata=None):
|
|
|
|
def rotate_components(wfstream, metadata=None):
|
|
"""rotates components if orientation code is numeric.
|
|
azimut and dip are fetched from metadata"""
|
|
try:
|
|
# indexing fails if metadata is None
|
|
metadata[0]
|
|
except:
|
|
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
|
|
print(msg)
|
|
return wfstream
|
|
if metadata[0] is None:
|
|
# sometimes metadata is (None, (None,))
|
|
msg = 'Warning: could not rotate traces since no metadata was given\nCheck inventory directory!'
|
|
print(msg)
|
|
return wfstream
|
|
else:
|
|
parser = metadata[1]
|
|
|
|
def get_dip_azimut(parser, trace_id):
|
|
"""gets azimut and dip for a trace out of the metadata parser"""
|
|
dip = None
|
|
azimut = None
|
|
try:
|
|
blockettes = parser._select(trace_id)
|
|
except SEEDParserException as e:
|
|
print(e)
|
|
raise ValueError
|
|
for blockette_ in blockettes:
|
|
if blockette_.id != 52:
|
|
continue
|
|
dip = blockette_.dip
|
|
azimut = blockette_.azimuth
|
|
break
|
|
if dip is None or azimut is None:
|
|
error_msg = 'Dip and azimuth not available for trace_id {}'.format(trace_id)
|
|
raise ValueError(error_msg)
|
|
return dip, azimut
|
|
|
|
trace_ids = [trace.id for trace in wfstream]
|
|
for trace_id in trace_ids:
|
|
orientation = trace_id[-1]
|
|
if orientation.isnumeric():
|
|
# misaligned channels have a number as orientation
|
|
azimuts = []
|
|
dips = []
|
|
for trace_id in trace_ids:
|
|
try:
|
|
dip, azimut = get_dip_azimut(parser, trace_id)
|
|
except ValueError as e:
|
|
print(e)
|
|
print('Failed to rotate station {}, no azimuth or dip available in metadata'.format(trace_id))
|
|
return wfstream
|
|
azimuts.append(azimut)
|
|
dips.append(dip)
|
|
# to rotate all traces must have same length
|
|
wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
|
|
z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
|
|
wfstream[1], azimuts[1], dips[1],
|
|
wfstream[2], azimuts[2], dips[2])
|
|
print('check4rotated: rotated station {} to ZNE'.format(trace_id))
|
|
z_index = dips.index(min(dips)) # get z-trace index (dip is measured from 0 to -90
|
|
wfstream[z_index].data = z
|
|
wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
|
|
del trace_ids[z_index]
|
|
for trace_id in trace_ids:
|
|
dip, az = get_dip_azimut(parser, trace_id)
|
|
trace = wfstream.select(id=trace_id)[0]
|
|
if az > 315 and az <= 45 or az > 135 and az <= 225:
|
|
trace.data = n
|
|
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
|
|
elif az > 45 and az <= 135 or az > 225 and az <= 315:
|
|
trace.data = e
|
|
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
|
|
break
|
|
else:
|
|
continue
|
|
return wfstream
|
|
|
|
stations = get_stations(data)
|
|
|
|
for station in stations:
|
|
wf_station = data.select(station=station)
|
|
wf_station = rotate_components(wf_station, metadata)
|
|
return data
|
|
|
|
|
|
def scaleWFData(data, factor=None, components='all'):
|
|
"""
|
|
produce scaled waveforms from given waveform data and a scaling factor,
|
|
waveform may be selected by their components name
|
|
:param data: waveform data to be scaled
|
|
:type data: `~obspy.core.stream.Stream` object
|
|
:param factor: scaling factor
|
|
:type factor: float
|
|
:param components: components labels for the traces in data to be scaled by
|
|
the scaling factor (optional, default: 'all')
|
|
:type components: tuple
|
|
:return: scaled waveform data
|
|
:rtype: `~obspy.core.stream.Stream` object
|
|
"""
|
|
if components is not 'all':
|
|
for comp in components:
|
|
if factor is None:
|
|
max_val = np.max(np.abs(data.select(component=comp)[0].data))
|
|
data.select(component=comp)[0].data /= 2 * max_val
|
|
else:
|
|
data.select(component=comp)[0].data /= 2 * factor
|
|
else:
|
|
for tr in data:
|
|
if factor is None:
|
|
max_val = float(np.max(np.abs(tr.data)))
|
|
tr.data /= 2 * max_val
|
|
else:
|
|
tr.data /= 2 * factor
|
|
|
|
return data
|
|
|
|
|
|
def runProgram(cmd, parameter=None):
|
|
"""
|
|
run an external program specified by cmd with parameters input returning the
|
|
stdout output
|
|
:param cmd: name of the command to run
|
|
:type cmd: str
|
|
:param parameter: filename of parameter file or parameter string
|
|
:type parameter: str
|
|
:return: stdout output
|
|
:rtype: str
|
|
"""
|
|
|
|
if parameter:
|
|
cmd.strip()
|
|
cmd += ' %s 2>&1' % parameter
|
|
|
|
subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
|
|
|
|
|
|
def which(program, infile=None):
|
|
"""
|
|
takes a program name and returns the full path to the executable or None
|
|
modified after: http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
|
|
:param program: name of the desired external program
|
|
:return: full path of the executable file
|
|
"""
|
|
try:
|
|
from PySide.QtCore import QSettings
|
|
settings = QSettings()
|
|
for key in settings.allKeys():
|
|
if 'binPath' in key:
|
|
os.environ['PATH'] += ':{0}'.format(settings.value(key))
|
|
if infile is None:
|
|
# use default parameter-file name
|
|
bpath = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
|
|
else:
|
|
bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
|
|
|
|
if os.path.exists(bpath):
|
|
nllocpath = ":" + PylotParameter(bpath).get('nllocbin')
|
|
os.environ['PATH'] += nllocpath
|
|
except ImportError as e:
|
|
print(e.message)
|
|
|
|
def is_exe(fpath):
|
|
return os.path.exists(fpath) and os.access(fpath, os.X_OK)
|
|
|
|
def ext_candidates(fpath):
|
|
yield fpath
|
|
for ext in os.environ.get("PATHEXT", "").split(os.pathsep):
|
|
yield fpath + ext
|
|
|
|
fpath, fname = os.path.split(program)
|
|
if fpath:
|
|
if is_exe(program):
|
|
return program
|
|
else:
|
|
for path in os.environ["PATH"].split(os.pathsep):
|
|
exe_file = os.path.join(path, program)
|
|
for candidate in ext_candidates(exe_file):
|
|
if is_exe(candidate):
|
|
return candidate
|
|
|
|
return None
|
|
|
|
|
|
def loopIdentifyPhase(phase):
|
|
'''
|
|
Loop through phase string and try to recognize its type (P or S wave).
|
|
Global variable ALTSUFFIX gives alternative suffix for phases if they do not end with P, p or S, s.
|
|
If ALTSUFFIX is not given, the function will cut the last letter of the phase string until string ends
|
|
with P or S.
|
|
:param phase: phase name (str)
|
|
:return:
|
|
'''
|
|
from pylot.core.util.defaults import ALTSUFFIX
|
|
|
|
phase_copy = phase
|
|
while not identifyPhase(phase_copy):
|
|
identified = False
|
|
for alt_suf in ALTSUFFIX:
|
|
if phase_copy.endswith(alt_suf):
|
|
phase_copy = phase_copy.split(alt_suf)[0]
|
|
identified = True
|
|
if not identified:
|
|
phase_copy = phase_copy[:-1]
|
|
if len(phase_copy) < 1:
|
|
print('Warning: Could not identify phase {}!'.format(phase))
|
|
return
|
|
return phase_copy
|
|
|
|
|
|
def identifyPhase(phase):
|
|
'''
|
|
Returns capital P or S if phase string is identified by last letter. Else returns False.
|
|
:param phase: phase name (str)
|
|
:return: 'P', 'S' or False
|
|
'''
|
|
# common phase suffix for P and S
|
|
common_P = ['P', 'p']
|
|
common_S = ['S', 's']
|
|
if phase[-1] in common_P:
|
|
return 'P'
|
|
if phase[-1] in common_S:
|
|
return 'S'
|
|
else:
|
|
return False
|
|
|
|
|
|
def identifyPhaseID(phase):
|
|
return identifyPhase(loopIdentifyPhase(phase))
|
|
|
|
|
|
def has_spe(pick):
|
|
if not 'spe' in pick.keys():
|
|
return None
|
|
else:
|
|
return pick['spe']
|
|
|
|
|
|
if __name__ == "__main__":
|
|
import doctest
|
|
|
|
doctest.testmod()
|