Merged feature/NLL4QtPylLoT into develop
This commit is contained in:
commit
bcff0b74fe
62
QtPyLoT.py
62
QtPyLoT.py
@ -35,8 +35,9 @@ from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
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from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
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QWidget, QHBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
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QDialog, QErrorMessage, QApplication, QPixmap, QMessageBox, QSplashScreen, \
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QActionGroup, QListWidget, QDockWidget
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QActionGroup, QListWidget, QDockWidget, QLineEdit
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import numpy as np
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import subprocess
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from obspy import UTCDateTime
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from pylot.core.io.data import Data
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@ -44,7 +45,7 @@ from pylot.core.io.inputs import FilterOptions, AutoPickParameter
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from pylot.core.pick.autopick import autopickevent
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from pylot.core.pick.compare import Comparison
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from pylot.core.io.phases import picksdict_from_picks
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from pylot.core.loc.nll import locate as locateNll
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import pylot.core.loc.nll as nll
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from pylot.core.util.defaults import FILTERDEFAULTS, COMPNAME_MAP, \
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AUTOMATIC_DEFAULTS
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from pylot.core.util.errors import FormatError, DatastructureError, \
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@ -61,7 +62,7 @@ from pylot.core.util.thread import AutoPickThread
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from pylot.core.util.version import get_git_version as _getVersionString
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import icons_rc
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locateTool = dict(nll=locateNll)
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locateTool = dict(nll=nll)
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class MainWindow(QMainWindow):
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@ -630,6 +631,8 @@ class MainWindow(QMainWindow):
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ans = self.data.setWFData(self.fnames)
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elif self.fnames is None and self.okToContinue():
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ans = self.data.setWFData(self.getWFFnames())
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else:
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ans = False
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self._stime = getGlobalTimes(self.getData().getWFData())[0]
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if ans:
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self.plotWaveformData()
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@ -889,12 +892,59 @@ class MainWindow(QMainWindow):
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raise TypeError('Unknow picktype {0}'.format(picktype))
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def locateEvent(self):
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"""
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locate event using the manually picked phases
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:return:
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"""
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if not self.okToContinue():
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return
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settings = QSettings()
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# get location tool hook
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loctool = settings.value("loc/tool", "nll")
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extlocpath = settings.value("%s/binPath".format(loctool), None)
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locroot = settings.value("%s/rootPath".format(loctool), None)
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if extlocpath is None or locroot is None:
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lt = locateTool[loctool]
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# get working directory
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locroot = settings.value("{0}/rootPath".format(loctool), None)
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if locroot is None:
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self.PyLoTprefs()
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self.locateEvent()
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infile = settings.value("{0}/inputFile".format(loctool), None)
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if not infile:
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caption = 'Select {0} input file'.format(loctool)
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filt = "Supported file formats" \
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" (*.in *.ini *.conf *.cfg)"
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ans = QFileDialog().getOpenFileName(self, caption=caption,
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filter=filt, dir=locroot)
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infile = ans[0]
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settings.setValue("{0}/inputFile".format(loctool), infile)
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settings.sync()
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if loctool == 'nll':
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ttt = settings.value("{0}/travelTimeTables", None)
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ok = False
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if ttt is None:
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while not ok:
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text, ok = QInputDialog.getText(self, 'Pattern for travel time tables',
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'Base name of travel time tables',
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echo=QLineEdit.Normal,
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text="ttime")
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ttt = text
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outfile = settings.value("{0}/outputFile".format(loctool),
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os.path.split(os.tempnam())[-1])
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phasefile = os.path.split(os.tempnam())[-1]
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phasepath = os.path.join(locroot, 'obs', phasefile)
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locpath = os.path.join(locroot, 'loc', outfile)
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lt.export(self.getPicks(), phasepath)
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lt.modify_inputs(infile, locroot, outfile, phasefile, ttt)
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try:
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lt.locate(infile)
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except RuntimeError as e:
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print(e.message)
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finally:
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os.remove(phasepath)
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self.getData().applyEVTData(lt.read_location(locpath), type='event')
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def check4Loc(self):
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return self.picksNum() > 4
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45
autoPyLoT.py
45
autoPyLoT.py
@ -6,13 +6,15 @@ from __future__ import print_function
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import argparse
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import glob
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import string
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import os
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import numpy as np
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from pylot.core.analysis.magnitude import M0Mw
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from pylot.core.io.data import Data
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from pylot.core.io.inputs import AutoPickParameter
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from pylot.core.loc.nll import *
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import pylot.core.loc.nll as nll
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import pylot.core.loc.hsat as hsat
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from pylot.core.pick.autopick import autopickevent, iteratepicker
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from pylot.core.util.structure import DATASTRUCTURE
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from pylot.core.util.version import get_git_version as _getVersionString
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@ -112,16 +114,17 @@ def autoPyLoT(inputfile):
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# locating
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if locflag == 1:
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# write phases to NLLoc-phase file
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picksExport(picks, 'NLLoc', phasefile)
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nll.export(picks, phasefile)
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# For locating the event the NLLoc-control file has to be modified!
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evID = event[string.rfind(event, "/") + 1: len(events) - 1]
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nllocout = '%s_%s' % (evID, nllocoutpatter)
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# create comment line for NLLoc-control file
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modifyInputFile(ctrf, nllocroot, nllocout, phasef, ttpat)
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nll.modify_inputs(ctrf, nllocroot, nllocout, phasef,
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ttpat)
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# locate the event
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locate(nlloccall, ctrfile)
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nll.locate(ctrfile)
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# !iterative picking if traces remained unpicked or occupied with bad picks!
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# get theoretical onset times for picks with weights >= 4
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@ -162,11 +165,11 @@ def autoPyLoT(inputfile):
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print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
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picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
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# write phases to NLLoc-phase file
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picksExport(picks, 'NLLoc', phasefile)
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nll.export(picks, phasefile)
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# remove actual NLLoc-location file to keep only the last
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os.remove(nllocfile)
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# locate the event
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locate(nlloccall, ctrfile)
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nll.locate(ctrfile)
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print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
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# get updated NLLoc-location file
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nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
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@ -199,15 +202,11 @@ def autoPyLoT(inputfile):
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# write phase files for various location routines
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# HYPO71
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hypo71file = '%s/autoPyLoT_HYPO71.pha' % event
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if hasattr(finalpicks, 'getpicdic'):
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if finalpicks.getpicdic() is not None:
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writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
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if hasattr(finalpicks, 'getpicdic') and finalpicks.getpicdic() is not None:
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hsat.export(finalpicks.getpicdic(), hypo71file)
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data.applyEVTData(finalpicks.getpicdic())
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else:
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writephases(picks, 'HYPO71', hypo71file)
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data.applyEVTData(picks)
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else:
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writephases(picks, 'HYPO71', hypo71file)
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hsat.export(picks, hypo71file)
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data.applyEVTData(picks)
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fnqml = '%s/autoPyLoT' % event
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data.exportEvent(fnqml)
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@ -235,15 +234,15 @@ def autoPyLoT(inputfile):
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# locating
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if locflag == 1:
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# write phases to NLLoc-phase file
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picksExport(picks, 'NLLoc', phasefile)
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nll.export(picks, phasefile)
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# For locating the event the NLLoc-control file has to be modified!
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nllocout = '%s_%s' % (parameter.get('eventID'), nllocoutpatter)
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# create comment line for NLLoc-control file
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modifyInputFile(ctrf, nllocroot, nllocout, phasef, ttpat)
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nll.modify_inputs(ctrf, nllocroot, nllocout, phasef, ttpat)
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# locate the event
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locate(nlloccall, ctrfile)
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nll.locate(ctrfile)
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# !iterative picking if traces remained unpicked or occupied with bad picks!
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# get theoretical onset times for picks with weights >= 4
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# in order to reprocess them using smaller time windows around theoretical onset
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@ -283,11 +282,11 @@ def autoPyLoT(inputfile):
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print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
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picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
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# write phases to NLLoc-phase file
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picksExport(picks, 'NLLoc', phasefile)
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nll.export(picks, phasefile)
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# remove actual NLLoc-location file to keep only the last
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os.remove(nllocfile)
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# locate the event
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locate(nlloccall, ctrfile)
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nll.locate(ctrfile)
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print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
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# get updated NLLoc-location file
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nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
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@ -320,15 +319,11 @@ def autoPyLoT(inputfile):
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# write phase files for various location routines
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# HYPO71
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hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.get('eventID'))
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if hasattr(finalpicks, 'getpicdic'):
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if finalpicks.getpicdic() is not None:
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writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
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if hasattr(finalpicks, 'getpicdic') and finalpicks.getpicdic() is not None:
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hsat.export(finalpicks.getpicdic(), hypo71file)
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data.applyEVTData(finalpicks.getpicdic())
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else:
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writephases(picks, 'HYPO71', hypo71file)
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data.applyEVTData(picks)
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else:
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writephases(picks, 'HYPO71', hypo71file)
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hsat.export(picks, hypo71file)
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data.applyEVTData(picks)
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fnqml = '%s/%s/autoPyLoT' % (datapath, parameter.get('eventID'))
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data.exportEvent(fnqml)
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@ -1,6 +1,7 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import copy
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import glob
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import os
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from obspy import read_events, read_inventory
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@ -434,6 +435,7 @@ class Data(object):
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#firstonset = find_firstonset(picks)
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if self.getEvtData().picks:
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raise OverwriteError('Actual picks would be overwritten!')
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else:
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picks = picks_from_picksdict(picks)
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self.getEvtData().picks = picks
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# if 'smi:local' in self.getID() and firstonset:
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@ -443,25 +445,22 @@ class Data(object):
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# self.getEvtData().resource_id = ID
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def applyArrivals(arrivals):
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"""
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:param arrivals:
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"""
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pass
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def applyEvent(event):
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"""
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takes an `obspy.core.event.Event` object and applies all new
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information on the event to the actual data
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:param event:
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"""
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if not self.isNew():
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self.setEvtData(event)
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else:
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raise OverwriteError('Acutal event would be overwritten!')
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# prevent overwriting uncertainty information
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picks = copy.deepcopy(self.getEvtData().picks)
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event.picks = picks
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# apply event information from location
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self.getEvtData().update(event)
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applydata = {'pick': applyPicks,
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'arrival': applyArrivals,
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'event': applyEvent}
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applydata[type](data)
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@ -117,7 +117,7 @@ def picksdict_from_pilot(fn):
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except IndexError as e:
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print(e.message + '\ntake two times the largest default error value')
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spe = timeerrors[onset_name][-1] * 2
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phases[onset_name] = dict(mpp=pick, spe=spe)
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phases[onset_name] = dict(mpp=pick, spe=spe, weight=ierror)
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picks[station] = phases
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return picks
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@ -395,7 +395,11 @@ def writephases(arrivals, fformat, filename):
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for key in arrivals:
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# P onsets
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if arrivals[key]['P']:
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try:
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fm = arrivals[key]['P']['fm']
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except KeyError as e:
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print(e)
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fm = None
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if fm == None:
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fm = '?'
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onset = arrivals[key]['P']['mpp']
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@ -407,10 +411,12 @@ def writephases(arrivals, fformat, filename):
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ss = onset.second
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ms = onset.microsecond
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ss_ms = ss + ms / 1000000.0
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if arrivals[key]['P']['weight'] < 4:
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pweight = 1 # use pick
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else:
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try:
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if arrivals[key]['P']['weight'] >= 4:
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pweight = 0 # do not use pick
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except KeyError as e:
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print(e.message + '; no weight set during processing')
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fid.write('%s ? ? ? P %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
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fm,
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year,
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@ -421,7 +427,7 @@ def writephases(arrivals, fformat, filename):
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ss_ms,
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pweight))
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# S onsets
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if arrivals[key]['S']:
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if arrivals[key].has_key('S') and arrivals[key]['S']:
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fm = '?'
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onset = arrivals[key]['S']['mpp']
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year = onset.year
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@ -432,10 +438,12 @@ def writephases(arrivals, fformat, filename):
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ss = onset.second
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ms = onset.microsecond
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ss_ms = ss + ms / 1000000.0
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if arrivals[key]['S']['weight'] < 4:
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sweight = 1 # use pick
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else:
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try:
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if arrivals[key]['S']['weight'] >= 4:
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sweight = 0 # do not use pick
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except KeyError as e:
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print(str(e) + '; no weight set during processing')
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fid.write('%s ? ? ? S %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
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fm,
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year,
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|
@ -1,2 +1,21 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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from pylot.core.io.phases import writephases
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from pylot.core.util.version import get_git_version as _getVersionString
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__version__ = _getVersionString()
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def export(picks, fnout):
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'''
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Take <picks> dictionary and exports picking data to a NLLOC-obs
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<phasefile> without creating an ObsPy event object.
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:param picks: picking data dictionary
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:type picks: dict
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:param fnout: complete path to the exporting obs file
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:type fnout: str
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'''
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# write phases to NLLoc-phase file
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writephases(picks, 'HYPO71', fnout)
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|
@ -3,14 +3,18 @@
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import subprocess
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import os
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import glob
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from obspy import read_events
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from pylot.core.io.phases import writephases
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from pylot.core.util.utils import getPatternLine, runProgram
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from pylot.core.util.utils import getPatternLine, runProgram, which
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from pylot.core.util.version import get_git_version as _getVersionString
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__version__ = _getVersionString()
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class NLLocError(EnvironmentError):
|
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pass
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def picksExport(picks, locrt, phasefile):
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def export(picks, fnout):
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'''
|
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Take <picks> dictionary and exports picking data to a NLLOC-obs
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<phasefile> without creating an ObsPy event object.
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||||
@ -18,17 +22,14 @@ def picksExport(picks, locrt, phasefile):
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:param picks: picking data dictionary
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:type picks: dict
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:param locrt: choose location routine
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:type locrt: str
|
||||
|
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:param phasefile: complete path to the exporting obs file
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:type phasefile: str
|
||||
:param fnout: complete path to the exporting obs file
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:type fnout: str
|
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'''
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# write phases to NLLoc-phase file
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writephases(picks, locrt, phasefile)
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writephases(picks, 'NLLoc', fnout)
|
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|
||||
|
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def modifyInputFile(ctrfn, root, nllocoutn, phasefn, tttn):
|
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def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
|
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'''
|
||||
:param ctrfn: name of NLLoc-control file
|
||||
:type: str
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@ -66,24 +67,32 @@ def modifyInputFile(ctrfn, root, nllocoutn, phasefn, tttn):
|
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nllfile.close()
|
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|
||||
|
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def locate(call, fnin):
|
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'''
|
||||
Takes paths to NLLoc executable <call> and input parameter file <fnin>
|
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and starts the location calculation.
|
||||
def locate(fnin):
|
||||
"""
|
||||
takes an external program name
|
||||
:param fnin:
|
||||
:return:
|
||||
"""
|
||||
|
||||
:param call: full path to NLLoc executable
|
||||
:type call: str
|
||||
exe_path = which('NLLoc')
|
||||
if exe_path is None:
|
||||
raise NLLocError('NonLinLoc executable not found; check your '
|
||||
'environment variables')
|
||||
|
||||
:param fnin: full path to input parameter file
|
||||
:type fnin: str
|
||||
'''
|
||||
|
||||
# locate the event
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||||
runProgram(call, fnin)
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||||
# locate the event utilizing external NonLinLoc installation
|
||||
try:
|
||||
runProgram(exe_path, fnin)
|
||||
except subprocess.CalledProcessError as e:
|
||||
raise RuntimeError(e.output)
|
||||
|
||||
|
||||
def readLocation(fn):
|
||||
pass
|
||||
def read_location(fn):
|
||||
path, file = os.path.split(fn)
|
||||
file = glob.glob1(path, file + '.[0-9]*.grid0.loc.hyp')
|
||||
if len(file) > 1:
|
||||
raise IOError('ambiguous location name {0}'.format(file))
|
||||
fn = os.path.join(path, file[0])
|
||||
return read_events(fn)[0]
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
@ -277,6 +277,15 @@ def getPatternLine(fn, pattern):
|
||||
|
||||
return None
|
||||
|
||||
def is_executable(fn):
|
||||
"""
|
||||
takes a filename and returns True if the file is executable on the system
|
||||
and False otherwise
|
||||
:param fn: path to the file to be tested
|
||||
:return: True or False
|
||||
"""
|
||||
return os.path.isfile(fn) and os.access(fn, os.X_OK)
|
||||
|
||||
|
||||
def isSorted(iterable):
|
||||
'''
|
||||
@ -393,9 +402,44 @@ def runProgram(cmd, parameter=None):
|
||||
cmd.strip()
|
||||
cmd += ' %s 2>&1' % parameter
|
||||
|
||||
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
|
||||
shell=True)
|
||||
subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
|
||||
|
||||
def which(program):
|
||||
"""
|
||||
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))
|
||||
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
|
||||
|
||||
if __name__ == "__main__":
|
||||
import doctest
|
||||
|
@ -1337,8 +1337,8 @@ class LocalisationTab(PropTab):
|
||||
|
||||
self.locToolComboBox.setCurrentIndex(toolind)
|
||||
|
||||
curroot = settings.value("%s/rootPath".format(curtool), None)
|
||||
curbin = settings.value("%s/binPath".format(curtool), None)
|
||||
curroot = settings.value("{0}/rootPath".format(curtool), None)
|
||||
curbin = settings.value("{0}/binPath".format(curtool), None)
|
||||
|
||||
self.rootlabel = QLabel("root directory")
|
||||
self.binlabel = QLabel("bin directory")
|
||||
@ -1385,8 +1385,8 @@ class LocalisationTab(PropTab):
|
||||
|
||||
def getValues(self):
|
||||
loctool = self.locToolComboBox.currentText()
|
||||
values = {"%s/rootPath".format(loctool): self.rootedit.text(),
|
||||
"%s/binPath".format(loctool): self.binedit.text(),
|
||||
values = {"{0}/rootPath".format(loctool): self.rootedit.text(),
|
||||
"{0}/binPath".format(loctool): self.binedit.text(),
|
||||
"loc/tool": loctool}
|
||||
return values
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user