Merged feature/NLL4QtPylLoT into develop

QtPyLoT.py

@@ -35,8 +35,9 @@ from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
 from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
     QWidget, QHBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
     QDialog, QErrorMessage, QApplication, QPixmap, QMessageBox, QSplashScreen, \
-    QActionGroup, QListWidget, QDockWidget
+    QActionGroup, QListWidget, QDockWidget, QLineEdit
 import numpy as np
+import subprocess
 from obspy import UTCDateTime
 
 from pylot.core.io.data import Data
@@ -44,7 +45,7 @@ from pylot.core.io.inputs import FilterOptions, AutoPickParameter
 from pylot.core.pick.autopick import autopickevent
 from pylot.core.pick.compare import Comparison
 from pylot.core.io.phases import picksdict_from_picks
-from pylot.core.loc.nll import locate as locateNll
+import pylot.core.loc.nll as nll
 from pylot.core.util.defaults import FILTERDEFAULTS, COMPNAME_MAP, \
     AUTOMATIC_DEFAULTS
 from pylot.core.util.errors import FormatError, DatastructureError, \
@@ -61,7 +62,7 @@ from pylot.core.util.thread import AutoPickThread
 from pylot.core.util.version import get_git_version as _getVersionString
 import icons_rc
 
-locateTool = dict(nll=locateNll)
+locateTool = dict(nll=nll)
 
 
 class MainWindow(QMainWindow):
@@ -630,6 +631,8 @@ class MainWindow(QMainWindow):
             ans = self.data.setWFData(self.fnames)
         elif self.fnames is None and self.okToContinue():
             ans = self.data.setWFData(self.getWFFnames())
+        else:
+            ans = False
         self._stime = getGlobalTimes(self.getData().getWFData())[0]
         if ans:
             self.plotWaveformData()
@@ -889,12 +892,59 @@ class MainWindow(QMainWindow):
                 raise TypeError('Unknow picktype {0}'.format(picktype))
 
     def locateEvent(self):
+        """
+        locate event using the manually picked phases
+        :return:
+        """
+        if not self.okToContinue():
+            return
         settings = QSettings()
+        # get location tool hook
         loctool = settings.value("loc/tool", "nll")
-        extlocpath = settings.value("%s/binPath".format(loctool), None)
+        lt = locateTool[loctool]
-        locroot = settings.value("%s/rootPath".format(loctool), None)
+        # get working directory
-        if extlocpath is None or locroot is None:
+        locroot = settings.value("{0}/rootPath".format(loctool), None)
+        if locroot is None:
             self.PyLoTprefs()
+            self.locateEvent()
+
+        infile = settings.value("{0}/inputFile".format(loctool), None)
+
+        if not infile:
+            caption = 'Select {0} input file'.format(loctool)
+            filt = "Supported file formats" \
+                   " (*.in *.ini *.conf *.cfg)"
+            ans = QFileDialog().getOpenFileName(self, caption=caption,
+                                                filter=filt, dir=locroot)
+            infile = ans[0]
+            settings.setValue("{0}/inputFile".format(loctool), infile)
+            settings.sync()
+        if loctool == 'nll':
+            ttt = settings.value("{0}/travelTimeTables", None)
+            ok = False
+            if ttt is None:
+                while not ok:
+                    text, ok = QInputDialog.getText(self, 'Pattern for travel time tables',
+                                                    'Base name of travel time tables',
+                                                    echo=QLineEdit.Normal,
+                                                    text="ttime")
+                ttt = text
+
+        outfile = settings.value("{0}/outputFile".format(loctool),
+                                 os.path.split(os.tempnam())[-1])
+        phasefile = os.path.split(os.tempnam())[-1]
+        phasepath = os.path.join(locroot, 'obs', phasefile)
+        locpath = os.path.join(locroot, 'loc', outfile)
+        lt.export(self.getPicks(), phasepath)
+        lt.modify_inputs(infile, locroot, outfile, phasefile, ttt)
+        try:
+            lt.locate(infile)
+        except RuntimeError as e:
+            print(e.message)
+        finally:
+            os.remove(phasepath)
+
+        self.getData().applyEVTData(lt.read_location(locpath), type='event')
 
     def check4Loc(self):
         return self.picksNum() > 4

autoPyLoT.py

@@ -6,13 +6,15 @@ from __future__ import print_function
 import argparse
 import glob
 import string
+import os
 
 import numpy as np
 
 from pylot.core.analysis.magnitude import M0Mw
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import AutoPickParameter
-from pylot.core.loc.nll import *
+import pylot.core.loc.nll as nll
+import pylot.core.loc.hsat as hsat
 from pylot.core.pick.autopick import autopickevent, iteratepicker
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.version import get_git_version as _getVersionString
@@ -112,16 +114,17 @@ def autoPyLoT(inputfile):
                 # locating
                 if locflag == 1:
                     # write phases to NLLoc-phase file
-                    picksExport(picks, 'NLLoc', phasefile)
+                    nll.export(picks, phasefile)
 
                     # For locating the event the NLLoc-control file has to be modified!
                     evID = event[string.rfind(event, "/") + 1: len(events) - 1]
                     nllocout = '%s_%s' % (evID, nllocoutpatter)
                     # create comment line for NLLoc-control file
-                    modifyInputFile(ctrf, nllocroot, nllocout, phasef, ttpat)
+                    nll.modify_inputs(ctrf, nllocroot, nllocout, phasef,
+                                      ttpat)
 
                     # locate the event
-                    locate(nlloccall, ctrfile)
+                    nll.locate(ctrfile)
 
                     # !iterative picking if traces remained unpicked or occupied with bad picks!
                     # get theoretical onset times for picks with weights >= 4
@@ -162,11 +165,11 @@ def autoPyLoT(inputfile):
                                 print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
                                 picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
                                 # write phases to NLLoc-phase file
-                                picksExport(picks, 'NLLoc', phasefile)
+                                nll.export(picks, phasefile)
                                 # remove actual NLLoc-location file to keep only the last
                                 os.remove(nllocfile)
                                 # locate the event
-                                locate(nlloccall, ctrfile)
+                                nll.locate(ctrfile)
                                 print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
                                 # get updated NLLoc-location file
                                 nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
@@ -199,15 +202,11 @@ def autoPyLoT(inputfile):
                 # write phase files for various location routines
                 # HYPO71
                 hypo71file = '%s/autoPyLoT_HYPO71.pha' % event
-                if hasattr(finalpicks, 'getpicdic'):
+                if hasattr(finalpicks, 'getpicdic') and finalpicks.getpicdic() is not None:
-                    if finalpicks.getpicdic() is not None:
+                    hsat.export(finalpicks.getpicdic(), hypo71file)
-                        writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
                     data.applyEVTData(finalpicks.getpicdic())
                 else:
-                        writephases(picks, 'HYPO71', hypo71file)
+                    hsat.export(picks, hypo71file)
-                        data.applyEVTData(picks)
-                else:
-                    writephases(picks, 'HYPO71', hypo71file)
                     data.applyEVTData(picks)
                 fnqml = '%s/autoPyLoT' % event
                 data.exportEvent(fnqml)
@@ -235,15 +234,15 @@ def autoPyLoT(inputfile):
             # locating
             if locflag == 1:
                 # write phases to NLLoc-phase file
-                picksExport(picks, 'NLLoc', phasefile)
+                nll.export(picks, phasefile)
 
                 # For locating the event the NLLoc-control file has to be modified!
                 nllocout = '%s_%s' % (parameter.get('eventID'), nllocoutpatter)
                 # create comment line for NLLoc-control file
-                modifyInputFile(ctrf, nllocroot, nllocout, phasef, ttpat)
+                nll.modify_inputs(ctrf, nllocroot, nllocout, phasef, ttpat)
 
                 # locate the event
-                locate(nlloccall, ctrfile)
+                nll.locate(ctrfile)
                 # !iterative picking if traces remained unpicked or occupied with bad picks!
                 # get theoretical onset times for picks with weights >= 4
                 # in order to reprocess them using smaller time windows around theoretical onset
@@ -283,11 +282,11 @@ def autoPyLoT(inputfile):
                             print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
                             picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
                             # write phases to NLLoc-phase file
-                            picksExport(picks, 'NLLoc', phasefile)
+                            nll.export(picks, phasefile)
                             # remove actual NLLoc-location file to keep only the last
                             os.remove(nllocfile)
                             # locate the event
-                            locate(nlloccall, ctrfile)
+                            nll.locate(ctrfile)
                             print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
                             # get updated NLLoc-location file
                             nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
@@ -320,15 +319,11 @@ def autoPyLoT(inputfile):
             # write phase files for various location routines
             # HYPO71
             hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.get('eventID'))
-            if hasattr(finalpicks, 'getpicdic'):
+            if hasattr(finalpicks, 'getpicdic') and finalpicks.getpicdic() is not None:
-                if finalpicks.getpicdic() is not None:
+                hsat.export(finalpicks.getpicdic(), hypo71file)
-                    writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
                 data.applyEVTData(finalpicks.getpicdic())
             else:
-                    writephases(picks, 'HYPO71', hypo71file)
+                hsat.export(picks, hypo71file)
-                    data.applyEVTData(picks)
-            else:
-                writephases(picks, 'HYPO71', hypo71file)
                 data.applyEVTData(picks)
             fnqml =  '%s/%s/autoPyLoT' % (datapath, parameter.get('eventID'))
             data.exportEvent(fnqml)

pylot/core/io/data.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import copy
 import glob
 import os
 from obspy import read_events, read_inventory
@@ -434,6 +435,7 @@ class Data(object):
             #firstonset = find_firstonset(picks)
             if self.getEvtData().picks:
                 raise OverwriteError('Actual picks would be overwritten!')
+            else:
                 picks = picks_from_picksdict(picks)
             self.getEvtData().picks = picks
             # if 'smi:local' in self.getID() and firstonset:
@@ -443,25 +445,22 @@ class Data(object):
             #     self.getEvtData().resource_id = ID
 
 
-        def applyArrivals(arrivals):
-            """
-
-            :param arrivals:
-            """
-            pass
-
         def applyEvent(event):
             """
-
+            takes an `obspy.core.event.Event` object and applies all new
+            information on the event to the actual data
             :param event:
             """
             if not self.isNew():
                 self.setEvtData(event)
             else:
-                raise OverwriteError('Acutal event would be overwritten!')
+                # prevent overwriting uncertainty information
+                picks =  copy.deepcopy(self.getEvtData().picks)
+                event.picks = picks
+                # apply event information from location
+                self.getEvtData().update(event)
 
         applydata = {'pick': applyPicks,
-                     'arrival': applyArrivals,
                      'event': applyEvent}
 
         applydata[type](data)

pylot/core/io/phases.py

@@ -117,7 +117,7 @@ def picksdict_from_pilot(fn):
             except IndexError as e:
                 print(e.message + '\ntake two times the largest default error value')
                 spe = timeerrors[onset_name][-1] * 2
-            phases[onset_name] = dict(mpp=pick, spe=spe)
+            phases[onset_name] = dict(mpp=pick, spe=spe, weight=ierror)
         picks[station] = phases
 
     return picks
@@ -395,7 +395,11 @@ def writephases(arrivals, fformat, filename):
         for key in arrivals:
             # P onsets
             if arrivals[key]['P']:
+                try:
                     fm = arrivals[key]['P']['fm']
+                except KeyError as e:
+                    print(e)
+                    fm = None
                 if fm == None:
                     fm = '?'
                 onset = arrivals[key]['P']['mpp']
@@ -407,10 +411,12 @@ def writephases(arrivals, fformat, filename):
                 ss = onset.second
                 ms = onset.microsecond
                 ss_ms = ss + ms / 1000000.0
-                if arrivals[key]['P']['weight'] < 4:
                 pweight = 1 # use pick
-                else:
+                try:
+                    if arrivals[key]['P']['weight'] >= 4:
                         pweight = 0  # do not use pick
+                except KeyError as e:
+                    print(e.message + '; no weight set during processing')
                 fid.write('%s ? ? ? P   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
                                                                                            fm,
                                                                                            year,
@@ -421,7 +427,7 @@ def writephases(arrivals, fformat, filename):
                                                                                            ss_ms,
                                                                                            pweight))
             # S onsets
-            if arrivals[key]['S']:
+            if arrivals[key].has_key('S') and arrivals[key]['S']:
                 fm = '?'
                 onset = arrivals[key]['S']['mpp']
                 year = onset.year
@@ -432,10 +438,12 @@ def writephases(arrivals, fformat, filename):
                 ss = onset.second
                 ms = onset.microsecond
                 ss_ms = ss + ms / 1000000.0
-                if arrivals[key]['S']['weight'] < 4:
                 sweight = 1 # use pick
-                else:
+                try:
+                    if arrivals[key]['S']['weight'] >= 4:
                         sweight = 0  # do not use pick
+                except KeyError as e:
+                    print(str(e) + '; no weight set during processing')
                 fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
                                                                                            fm,
                                                                                            year,

pylot/core/loc/hsat.py

@@ -1,2 +1,21 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+def export(picks, fnout):
+    '''
+    Take <picks> dictionary and exports picking data to a NLLOC-obs
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    '''
+    # write phases to NLLoc-phase file
+    writephases(picks, 'HYPO71', fnout)

pylot/core/loc/nll.py

@@ -3,14 +3,18 @@
 
 import subprocess
 import os
+import glob
+from obspy import read_events
 from pylot.core.io.phases import writephases
-from pylot.core.util.utils import getPatternLine, runProgram
+from pylot.core.util.utils import getPatternLine, runProgram, which
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+class NLLocError(EnvironmentError):
+    pass
 
-def picksExport(picks, locrt, phasefile):
+def export(picks, fnout):
     '''
     Take <picks> dictionary and exports picking data to a NLLOC-obs
     <phasefile> without creating an ObsPy event object.
@@ -18,17 +22,14 @@ def picksExport(picks, locrt, phasefile):
     :param picks: picking data dictionary
     :type picks: dict
 
-    :param locrt: choose location routine
+    :param fnout: complete path to the exporting obs file
-    :type locrt: str
+    :type fnout: str
-
-    :param phasefile: complete path to the exporting obs file
-    :type phasefile: str
     '''
     # write phases to NLLoc-phase file
-    writephases(picks, locrt, phasefile)
+    writephases(picks, 'NLLoc', fnout)
 
 
-def modifyInputFile(ctrfn, root, nllocoutn, phasefn, tttn):
+def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
     '''
     :param ctrfn: name of NLLoc-control file
     :type: str
@@ -66,24 +67,32 @@ def modifyInputFile(ctrfn, root, nllocoutn, phasefn, tttn):
     nllfile.close()
 
 
-def locate(call, fnin):
+def locate(fnin):
-    '''
+    """
-    Takes paths to NLLoc executable <call> and input parameter file <fnin>
+    takes an external program name
-    and starts the location calculation.
+    :param fnin:
+    :return:
+    """
 
-    :param call: full path to NLLoc executable
+    exe_path = which('NLLoc')
-    :type call: str
+    if exe_path is None:
+        raise NLLocError('NonLinLoc executable not found; check your '
+                         'environment variables')
 
-    :param fnin: full path to input parameter file
+    # locate the event utilizing external NonLinLoc installation
-    :type fnin: str
+    try:
-    '''
+        runProgram(exe_path, fnin)
-
+    except subprocess.CalledProcessError as e:
-    # locate the event
+        raise RuntimeError(e.output)
-    runProgram(call, fnin)
 
 
-def readLocation(fn):
+def read_location(fn):
-    pass
+    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__':

pylot/core/util/utils.py

@@ -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),
+    subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
-                                     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

pylot/core/util/widgets.py

@@ -1337,8 +1337,8 @@ class LocalisationTab(PropTab):
 
         self.locToolComboBox.setCurrentIndex(toolind)
 
-        curroot = settings.value("%s/rootPath".format(curtool), None)
+        curroot = settings.value("{0}/rootPath".format(curtool), None)
-        curbin = settings.value("%s/binPath".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(),
+        values = {"{0}/rootPath".format(loctool): self.rootedit.text(),
-                  "%s/binPath".format(loctool): self.binedit.text(),
+                  "{0}/binPath".format(loctool): self.binedit.text(),
                   "loc/tool": loctool}
         return values