Merge branch 'develop'

README.md

@@ -1,90 +1,96 @@
-# PyLoT
+# PyLoT
-
+
-version: 0.1a
+version: 0.2
-
+
-The Python picking and Localisation Tool
+The Python picking and Localisation Tool
-
+
-This python library contains a graphical user interfaces for picking
+This python library contains a graphical user interfaces for picking
-seismic phases. This software needs [ObsPy][ObsPy]
+seismic phases. This software needs [ObsPy][ObsPy]
-and the PySide Qt4 bindings for python to be installed first.
+and the PySide Qt4 bindings for python to be installed first.
-
+
-PILOT has originally been developed in Mathworks' MatLab. In order to
+PILOT has originally been developed in Mathworks' MatLab. In order to
-distribute PILOT without facing portability problems, it has been decided
+distribute PILOT without facing portability problems, it has been decided
-to redevelop the software package in Python. The great work of the ObsPy
+to redevelop the software package in Python. The great work of the ObsPy
-group allows easy handling of a bunch of seismic data and PyLoT will
+group allows easy handling of a bunch of seismic data and PyLoT will
-benefit a lot compared to the former MatLab version.
+benefit a lot compared to the former MatLab version.
-
+
-The development of PyLoT is part of the joint research project MAGS2.
+The development of PyLoT is part of the joint research project MAGS2 and AlpArray.
-
+
-## Installation
+## Installation
-
+
-At the moment there is no automatic installation procedure available for PyLoT.
+At the moment there is no automatic installation procedure available for PyLoT.
-Best way to install is to clone the repository and add the path to your Python path.
+Best way to install is to clone the repository and add the path to your Python path.
-
+
-#### Prerequisites:
+#### Prerequisites:
-
+
-In order to run PyLoT you need to install:
+In order to run PyLoT you need to install:
-
+
-- python
+- python 2 or 3
-- scipy
+- scipy
-- numpy
+- numpy
-- matplotlib
+- matplotlib
-- obspy
+- obspy
-- pyside
+- pyside
-
+
-#### Some handwork:
+#### Some handwork:
-
+
-PyLoT needs a properties folder on your system to work. It should be situated in your home directory:
+PyLoT needs a properties folder on your system to work. It should be situated in your home directory 
-
+(on Windows usually C:/Users/*username*):
-    mkdir ~/.pylot
+
-
+    mkdir ~/.pylot
-In the next step you have to copy some files to this directory:
+
-
+In the next step you have to copy some files to this directory:
-    cp path-to-pylot/inputs/pylot.in ~/.pylot/
+
-
+*for local distance seismicity*
-for local distance seismicity
+
-
+    cp path-to-pylot/inputs/pylot_local.in ~/.pylot/pylot.in
-    cp path-to-pylot/inputs/autoPyLoT_local.in ~/.pylot/autoPyLoT.in
+
-
+*for regional distance seismicity*
-for regional distance seismicity
+
-
+    cp path-to-pylot/inputs/pylot_regional.in ~/.pylot/pylot.in
-    cp path-to-pylot/inputs/autoPyLoT_regional.in ~/.pylot/autoPyLoT.in
+
-
+*for global distance seismicity*
-and some extra information on filtering, error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling relation
+
-
+    cp path-to-pylot/inputs/pylot_global.in ~/.pylot/pylot.in
-    cp path-to-pylot/inputs/filter.in path-to-pylot/inputs/PILOT_TimeErrors.in path-to-pylot/inputs/richter_scaling.data ~/.pylot/
+
-
+and some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling relation
-You may need to do some modifications to these files. Especially folder names should be reviewed.
+
-
+    cp path-to-pylot/inputs/PILOT_TimeErrors.in path-to-pylot/inputs/richter_scaling.data ~/.pylot/
-PyLoT has been tested on Mac OSX (10.11) and Debian Linux 8.
+
-
+You may need to do some modifications to these files. Especially folder names should be reviewed.
-
+
-## Release notes
+PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
-
+
-#### Features:
+
-
+## Release notes
-- consistent manual phase picking through predefined SNR dependant zoom level
+
-- uniform uncertainty estimation from waveform's properties for automatic and manual picks
+#### Features:
-- pdf representation and comparison of picks taking the uncertainty intrinsically into account 
+
-- Richter and moment magnitude estimation
+- event organisation in project files and waveform visualisation
-- location determination with external installation of [NonLinLoc](http://alomax.free.fr/nlloc/index.html)
+- consistent manual phase picking through predefined SNR dependant zoom level
-
+- consistent automatic phase picking routines using Higher Order Statistics, AIC and Autoregression
-#### Known issues:
+- interactive tuning of auto-pick parameters
-
+- uniform uncertainty estimation from waveform's properties for automatic and manual picks
-- Magnitude estimation from manual PyLoT takes some time (instrument correction)
+- pdf representation and comparison of picks taking the uncertainty intrinsically into account 
-
+- Richter and moment magnitude estimation
-We hope to solve these with the next release.
+- location determination with external installation of [NonLinLoc](http://alomax.free.fr/nlloc/index.html)
-
+
-## Staff
+#### Known issues:
-
+
-Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
+- Sometimes an error might occur when using Qt
-
+
-Developer(s): S. Wehling-Benatelli, L. Kueperkoch, K. Olbert, M. Bischoff,
+We hope to solve these with the next release.
-              C. Wollin, M. Rische, M. Paffrath
+
-
+## Staff
-Others: A. Bruestle, T. Meier, W. Friederich
+
-
+Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
-
+
-[ObsPy]: http://github.com/obspy/obspy/wiki
+Developer(s): S. Wehling-Benatelli, L. Kueperkoch, K. Olbert, M. Bischoff,
-
+              C. Wollin, M. Rische, M. Paffrath
-October 2016
+
+Others: A. Bruestle, T. Meier, W. Friederich
+
+
+[ObsPy]: http://github.com/obspy/obspy/wiki
+
+September 2017

autoPyLoT.py

@@ -4,31 +4,37 @@
 from __future__ import print_function
 
 import argparse
+import datetime
 import glob
 import os
-import datetime
+
-from obspy import read_events
-import pylot.core.loc.hyposat as hyposat
-import pylot.core.loc.hypo71 as hypo71
-import pylot.core.loc.velest as velest
-import pylot.core.loc.hypodd as hypodd
 import pylot.core.loc.focmec as focmec
 import pylot.core.loc.hash as hash
+import pylot.core.loc.hypo71 as hypo71
+import pylot.core.loc.hypodd as hypodd
+import pylot.core.loc.hyposat as hyposat
 import pylot.core.loc.nll as nll
-#from PySide.QtGui import QWidget, QInputDialog
+import pylot.core.loc.velest as velest
+from obspy import read_events
+from obspy.core.event import ResourceIdentifier
+# from PySide.QtGui import QWidget, QInputDialog
 from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import PylotParameter
 from pylot.core.pick.autopick import autopickevent, iteratepicker
-from pylot.core.util.dataprocessing import restitute_data, read_metadata, \
+from pylot.core.util.dataprocessing import restitute_data, read_metadata
-    remove_underscores
+from pylot.core.util.defaults import SEPARATOR
+from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
+from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps, check4doubled, \
+    check4rotated
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
 
-def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None, station='all', iplot=0):
+def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None,
+              savexml=True, station='all', iplot=0, ncores=0):
     """
     Determine phase onsets automatically utilizing the automatic picking
     algorithms by Kueperkoch et al. 2010/2012.
@@ -42,40 +48,68 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
     .. rubric:: Example
 
     """
+
+    if ncores == 1:
+        sp_info = 'autoPyLoT is running serial on 1 cores.'
+    else:
+        if ncores == 0:
+            ncores_readable = 'all available'
+        else:
+            ncores_readable = ncores
+        sp_info = 'autoPyLoT is running in parallel on {} cores.'.format(ncores_readable)
+
     splash = '''************************************\n
                 *********autoPyLoT starting*********\n
                 The Python picking and Location Tool\n
-                Version {version} 2015\n
+                Version {version} 2017\n
                 \n
                 Authors:\n
-                S. Wehling-Benatelli (Ruhr-Universitaet Bochum)\n
                 L. Kueperkoch (BESTEC GmbH, Landau i. d. Pfalz)\n
-                K. Olbert (Christian-Albrechts Universitaet zu Kiel)\n
+                M. Paffrath (Ruhr-Universitaet Bochum)\n
-                ***********************************'''.format(version=_getVersionString())
+                S. Wehling-Benatelli (Ruhr-Universitaet Bochum)\n
+                
+                {sp}
+                ***********************************'''.format(version=_getVersionString(),
+                                                              sp=sp_info)
     print(splash)
 
+
+    parameter = real_None(parameter)
+    inputfile = real_None(inputfile)
+    eventid = real_None(eventid)
+
+    fig_dict = None
+    fig_dict_wadatijack = None
+
     locflag = 1
     if input_dict and isinstance(input_dict, dict):
-        if input_dict.has_key('parameter'):
+        if 'parameter' in input_dict:
             parameter = input_dict['parameter']
-        if input_dict.has_key('fig_dict'):
+        if 'fig_dict' in input_dict:
             fig_dict = input_dict['fig_dict']
-        if input_dict.has_key('station'):
+        if 'fig_dict_wadatijack' in input_dict:
+            fig_dict_wadatijack = input_dict['fig_dict_wadatijack']
+        if 'station' in input_dict:
             station = input_dict['station']
-        if input_dict.has_key('fnames'):
+        if 'fnames' in input_dict:
             fnames = input_dict['fnames']
-        if input_dict.has_key('iplot'):
+        if 'eventid' in input_dict:
+            eventid = input_dict['eventid']
+        if 'iplot' in input_dict:
             iplot = input_dict['iplot']
-        if input_dict.has_key('locflag'):
+        if 'locflag' in input_dict:
             locflag = input_dict['locflag']
+        if 'savexml' in input_dict:
+            savexml = input_dict['savexml']
 
     if not parameter:
         if inputfile:
             parameter = PylotParameter(inputfile)
-            iplot = parameter['iplot']
+            #iplot = parameter['iplot']
         else:
-            print('No parameters set and no input file given. Choose either of both.')
+            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            return
+            print('Using default input file {}'.format(infile))
+            parameter = PylotParameter(infile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -83,8 +117,6 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         if inputfile:
             print('Parameters set and input file given. Choose either of both.')
             return
-            
-    data = Data()
 
     evt = None
 
@@ -97,7 +129,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                     'dbase': parameter.get('database')}
 
         exf = ['root', 'dpath', 'dbase']
-        
+
         if parameter['eventID'] is not '*' and fnames == 'None':
             dsfields['eventID'] = parameter['eventID']
             exf.append('eventID')
@@ -106,7 +138,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         datastructure.setExpandFields(exf)
 
         # check if default location routine NLLoc is available
-        if parameter['nllocbin'] and locflag:
+        if real_None(parameter['nllocbin']) and locflag:
             # get NLLoc-root path
             nllocroot = parameter.get('nllocroot')
             # get path to NLLoc executable
@@ -137,9 +169,14 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 # multiple event processing
                 # read each event in database
                 events = [events for events in glob.glob(os.path.join(datapath, '*')) if os.path.isdir(events)]
-            elif fnames == 'None' and parameter['eventID'] is not '*':
+            elif fnames == 'None' and parameter['eventID'] is not '*' and not type(parameter['eventID']) == list:
                 # single event processing
                 events = glob.glob(os.path.join(datapath, parameter['eventID']))
+            elif fnames == 'None' and type(parameter['eventID']) == list:
+                # multiple event processing
+                events = []
+                for eventID in parameter['eventID']:
+                    events.append(os.path.join(datapath, eventID))
             else:
                 # autoPyLoT was initialized from GUI
                 events = []
@@ -147,22 +184,41 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 evID = os.path.split(eventid)[-1]
                 locflag = 2
         else:
-            # started in tune mode
+            # started in tune or interactive mode
             datapath = os.path.join(parameter['rootpath'],
                                     parameter['datapath'])
             events = []
-            events.append(os.path.join(datapath,
+            for eventID in eventid:
-                                       parameter['database'],
+                events.append(os.path.join(datapath,
-                                       parameter['eventID']))
+                                           parameter['database'],
+                                           eventID))
 
         if not events:
             print('autoPyLoT: No events given. Return!')
             return
-        
+
-        for event in events:
+        # transform system path separator to '/'
+        for index, eventpath in enumerate(events):
+            eventpath = eventpath.replace(SEPARATOR, '/')
+            events[index] = eventpath
+
+        allpicks = {}
+        glocflag = locflag
+        for eventpath in events:
+            evID = os.path.split(eventpath)[-1]
+            fext = '.xml'
+            filename = os.path.join(eventpath, 'PyLoT_' + evID + fext)
+            try:
+                data = Data(evtdata=filename)
+                data.get_evt_data().path = eventpath
+                print('Reading event data from filename {}...'.format(filename))
+            except Exception as e:
+                print('Could not read event from file {}: {}'.format(filename, e))
+                data = Data()
+                pylot_event = Event(eventpath)  # event should be path to event directory
+                data.setEvtData(pylot_event)
             if fnames == 'None':
-                data.setWFData(glob.glob(os.path.join(datapath, event, '*')))
+                data.setWFData(glob.glob(os.path.join(datapath, eventpath, '*')))
-                evID = os.path.split(event)[-1]
                 # the following is necessary because within
                 # multiple event processing no event ID is provided
                 # in autopylot.in
@@ -178,10 +234,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                     parameter.setParam(eventID=eventID)
             else:
                 data.setWFData(fnames)
-                
+
-                event = events[0]
+                eventpath = events[0]
-                #now = datetime.datetime.now()
+                # now = datetime.datetime.now()
-                #evID = '%d%02d%02d%02d%02d' % (now.year,
+                # evID = '%d%02d%02d%02d%02d' % (now.year,
                 #                               now.month,
                 #                               now.day,
                 #                               now.hour,
@@ -192,22 +248,31 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 wfdat = wfdat.select(station=station)
                 if not wfdat:
                     print('Could not find station {}. STOP!'.format(station))
-                    return                      
+                    return
             wfdat = remove_underscores(wfdat)
-            metadata =  read_metadata(parameter.get('invdir'))
+            # trim components for each station to avoid problems with different trace starttimes for one station
-            print("Restitute data ...")
+            wfdat = check4gaps(wfdat)
-            corr_dat = restitute_data(wfdat.copy(), *metadata)
+            wfdat = check4doubled(wfdat)
-               
+            wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
-            print('Working on event %s. Stations: %s' % (event, station))
+            metadata = read_metadata(parameter.get('invdir'))
+            # rotate stations to ZNE
+            wfdat = check4rotated(wfdat, metadata)
+            corr_dat = None
+            if locflag:
+                print("Restitute data ...")
+                corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores)
+            if not corr_dat and locflag:
+                locflag = 2
+            print('Working on event %s. Stations: %s' % (eventpath, station))
             print(wfdat)
             ##########################################################
             # !automated picking starts here!
-            if input_dict:
+            fdwj = None
-                if input_dict.has_key('fig_dict'):
+            if fig_dict_wadatijack:
-                    fig_dict = input_dict['fig_dict']
+                fdwj = fig_dict_wadatijack[evID]
-                    picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict)
+            picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict,
-            else:
+                                  fig_dict_wadatijack=fdwj,
-                picks = autopickevent(wfdat, parameter, iplot=iplot)
+                                  ncores=ncores, metadata=metadata, origin=data.get_evt_data().origins)
             ##########################################################
             # locating
             if locflag > 0:
@@ -246,11 +311,11 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                         # calculate seismic moment Mo and moment magnitude Mw
                         moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
                                                      parameter.get('Qp'),
-                                                     parameter.get('rho'), True, \
+                                                     parameter.get('rho'), True,
                                                      iplot)
                         # update pick with moment property values (w0, fc, Mo)
-                        for station, props in moment_mag.moment_props.items():
+                        for stats, props in moment_mag.moment_props.items():
-                            picks[station]['P'].update(props)
+                            picks[stats]['P'].update(props)
                         evt = moment_mag.updated_event()
                         net_mw = moment_mag.net_magnitude()
                         print("Network moment magnitude: %4.1f" % net_mw.mag)
@@ -258,12 +323,12 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                         WAscaling = parameter.get('WAscaling')
                         magscaling = parameter.get('magscaling')
                         local_mag = LocalMagnitude(corr_dat, evt,
-                                                   parameter.get('sstop'), 
+                                                   parameter.get('sstop'),
                                                    WAscaling, True, iplot)
-                        for station, amplitude in local_mag.amplitudes.items():
+                        for stats, amplitude in local_mag.amplitudes.items():
-                            picks[station]['S']['Ao'] = amplitude.generic_amplitude
+                            picks[stats]['S']['Ao'] = amplitude.generic_amplitude
                         print("Local station magnitudes scaled with:")
-                        print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0], 
+                        print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0],
                                                                        WAscaling[1],
                                                                        WAscaling[2]))
                         evt = local_mag.updated_event(magscaling)
@@ -289,9 +354,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                 break
                             print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
                             if input_dict:
-                                if input_dict.has_key('fig_dict'):
+                                if 'fig_dict' in input_dict:
                                     fig_dict = input_dict['fig_dict']
-                                    picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter, fig_dict=fig_dict)
+                                    picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter,
+                                                          fig_dict=fig_dict)
                             else:
                                 picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
                             # write phases to NLLoc-phase file
@@ -308,7 +374,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                             for key in picks:
                                 if picks[key]['P']['weight'] >= 4 or picks[key]['S']['weight'] >= 4:
                                     badpicks.append([key, picks[key]['P']['mpp']])
-                            print("autoPyLoT: After iteration No. %d: %d bad onsets found ..." % (nlloccounter, \
+                            print("autoPyLoT: After iteration No. %d: %d bad onsets found ..." % (nlloccounter,
                                                                                                   len(badpicks)))
                             if len(badpicks) == 0:
                                 print("autoPyLoT: No more bad onsets found, stop iterative picking!")
@@ -318,11 +384,12 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                             # calculate seismic moment Mo and moment magnitude Mw
                             moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
                                                          parameter.get('Qp'),
-                                                         parameter.get('rho'), True, \
+                                                         parameter.get('rho'), True,
                                                          iplot)
                             # update pick with moment property values (w0, fc, Mo)
-                            for station, props in moment_mag.moment_props.items():
+                            for stats, props in moment_mag.moment_props.items():
-                                picks[station]['P'].update(props)
+                                if picks.has_key(stats):
+                                    picks[stats]['P'].update(props)
                             evt = moment_mag.updated_event()
                             net_mw = moment_mag.net_magnitude()
                             print("Network moment magnitude: %4.1f" % net_mw.mag)
@@ -330,12 +397,13 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                             WAscaling = parameter.get('WAscaling')
                             magscaling = parameter.get('magscaling')
                             local_mag = LocalMagnitude(corr_dat, evt,
-                                                       parameter.get('sstop'), 
+                                                       parameter.get('sstop'),
                                                        WAscaling, True, iplot)
-                            for station, amplitude in local_mag.amplitudes.items():
+                            for stats, amplitude in local_mag.amplitudes.items():
-                                picks[station]['S']['Ao'] = amplitude.generic_amplitude
+                                if picks.has_key(stats):
+                                    picks[stats]['S']['Ao'] = amplitude.generic_amplitude
                             print("Local station magnitudes scaled with:")
-                            print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0], 
+                            print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0],
                                                                            WAscaling[1],
                                                                            WAscaling[2]))
                             evt = local_mag.updated_event(magscaling)
@@ -350,46 +418,57 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             # write phase files for various location 
             # and fault mechanism calculation routines
             # ObsPy event object
-            data.applyEVTData(picks)
             if evt is not None:
+                event_id = eventpath.split('/')[-1]
+                evt.resource_id = ResourceIdentifier('smi:local/' + event_id)
                 data.applyEVTData(evt, 'event')
-            fnqml = '%s/PyLoT_%s' % (event, evID)
+            data.applyEVTData(picks)
-            data.exportEvent(fnqml, fnext='.xml', fcheck='manual')
+            if savexml:
+                if savepath == 'None' or savepath == None:
+                    saveEvtPath = eventpath
+                else:
+                    saveEvtPath = savepath
+                fnqml = '%s/PyLoT_%s' % (saveEvtPath, evID)
+                data.exportEvent(fnqml, fnext='.xml', fcheck=['auto', 'magnitude', 'origin'])
             if locflag == 1:
                 # HYPO71
-                hypo71file = '%s/PyLoT_%s_HYPO71_phases' % (event, evID)
+                hypo71file = '%s/PyLoT_%s_HYPO71_phases' % (eventpath, evID)
                 hypo71.export(picks, hypo71file, parameter)
                 # HYPOSAT
-                hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (event, evID)
+                hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (eventpath, evID)
                 hyposat.export(picks, hyposatfile, parameter)
-            	# VELEST
+                # VELEST
-            	velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (event, evID)
+                velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (eventpath, evID)
-            	velest.export(picks, velestfile, parameter, evt)
+                velest.export(picks, velestfile, evt, parameter)
-            	# hypoDD
+                # hypoDD
-            	hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (event, evID)
+                hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (eventpath, evID)
-            	hypodd.export(picks, hypoddfile, parameter, evt)
+                hypodd.export(picks, hypoddfile, parameter, evt)
-            	# FOCMEC
+                # FOCMEC
-            	focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (event, evID)
+                focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (eventpath, evID)
-            	focmec.export(picks, focmecfile, parameter, evt)
+                focmec.export(picks, focmecfile, parameter, evt)
-            	# HASH
+                # HASH
-            	hashfile = '%s/PyLoT_%s_HASH' % (event, evID)
+                hashfile = '%s/PyLoT_%s_HASH' % (eventpath, evID)
-            	hash.export(picks, hashfile, parameter, evt)
+                hash.export(picks, hashfile, parameter, evt)
 
             endsplash = '''------------------------------------------\n'
                            -----Finished event %s!-----\n'
                            ------------------------------------------'''.format \
                             (version=_getVersionString()) % evID
             print(endsplash)
+            locflag = glocflag
             if locflag == 0:
                 print("autoPyLoT was running in non-location mode!")
 
+            # save picks for current event ID to dictionary with ALL picks
+            allpicks[evID] = picks
+
     endsp = '''####################################\n
                ************************************\n
                *********autoPyLoT terminates*******\n
                The Python picking and Location Tool\n
                ************************************'''.format(version=_getVersionString())
     print(endsp)
-    return picks
+    return allpicks
 
 
 if __name__ == "__main__":
@@ -399,30 +478,28 @@ if __name__ == "__main__":
                        autoregressive prediction and AIC followed by locating the seismic events using 
                        NLLoc''')
 
-    #parser.add_argument('-d', '-D', '--input_dict', type=str,
-    #                    action='store',
-    #                    help='''optional, dictionary containing processing parameters''')
-    #parser.add_argument('-p', '-P', '--parameter', type=str,
-    #                    action='store',
-    #                    help='''parameter file, default=None''')
     parser.add_argument('-i', '-I', '--inputfile', type=str,
                         action='store',
                         help='''full path to the file containing the input
-                        parameters for autoPyLoT''') 
+                        parameters for autoPyLoT''')
+    parser.add_argument('-p', '-P', '--iplot', type=int, 
+                        action='store',
+                        help='''optional, logical variable for plotting: 0=none, 1=partial, 2=all''') 
     parser.add_argument('-f', '-F', '--fnames', type=str,
                         action='store',
                         help='''optional, list of data file names''')
-    parser.add_argument('-e', '-E', '--eventid', type=str,
+    parser.add_argument('-e', '--eventid', type=str,
                         action='store',
                         help='''optional, event path incl. event ID''')
     parser.add_argument('-s', '-S', '--spath', type=str,
                         action='store',
                         help='''optional, save path for autoPyLoT output''')
-    #parser.add_argument('-v', '-V', '--version', action='version',
+    parser.add_argument('-c', '-C', '--ncores', type=int,
-    #                    version='autoPyLoT ' + __version__,
+                        action='store', default=0,
-    #                    help='show version information and exit')
+                        help='''optional, number of CPU cores used for parallel processing (default: all available(=0))''')
 
     cla = parser.parse_args()
-    
+
-    picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames), 
+    picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames),
-                      eventid=str(cla.eventid), savepath=str(cla.spath))
+                      eventid=str(cla.eventid), savepath=str(cla.spath),
+                      ncores=cla.ncores, iplot=int(cla.iplot))

git_out

@@ -1,8 +0,0 @@
-git pull
-Entferne qrc_resources.py
-KONFLIKT (ändern/löschen): pylot/core/pick/getSNR.py gelöscht in HEAD und geändert in 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324. Stand 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324 von pylot/core/pick/getSNR.py wurde im Arbeitsbereich gelassen.
-KONFLIKT (ändern/löschen): pylot/core/pick/fmpicker.py gelöscht in HEAD und geändert in 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324. Stand 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324 von pylot/core/pick/fmpicker.py wurde im Arbeitsbereich gelassen.
-KONFLIKT (ändern/löschen): pylot/core/pick/earllatepicker.py gelöscht in HEAD und geändert in 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324. Stand 67dd66535a213ba5c7cfe2be52aa6d5a7e8b7324 von pylot/core/pick/earllatepicker.py wurde im Arbeitsbereich gelassen.
-Automatisches Zusammenfügen von icons.qrc
-Automatischer Merge fehlgeschlagen; beheben Sie die Konflikte und committen Sie dann das Ergebnis.
-

help/index.html

@@ -1,17 +1,19 @@
-<html><head><title>PyLoT - the Python picking and Localisation Tool</title></head>
+<html>
+<head><title>PyLoT - the Python picking and Localisation Tool</title></head>
 <body>
 <p><b>PyLoT</b> is a program which is capable of picking seismic phases,
-exporting these as numerous standard phase format and localize the corresponding
+    exporting these as numerous standard phase format and localize the corresponding
-seismic event with external software as, e.g.:</p>
+    seismic event with external software as, e.g.:</p>
 <ul type="circle">
-<li><a href="http://alomax.free.fr/nlloc/index.html">NonLinLoc</a></li>
+    <li><a href="http://alomax.free.fr/nlloc/index.html">NonLinLoc</a></li>
-<li>HypoInvers</li>
+    <li>HypoInvers</li>
-<li>HypoSat</li>
+    <li>HypoSat</li>
-<li>whatever you want ...</li>
+    <li>whatever you want ...</li>
 </ul>
 <p>Read more on the
-<a href="https://ariadne.geophysik.rub.de/trac/PyLoT/wiki/">PyLoT WikiPage</a>.</p>
+    <a href="https://ariadne.geophysik.rub.de/trac/PyLoT/wiki/">PyLoT WikiPage</a>.</p>
 <p>Bug reports are very much appreciated and can also be delivered on our
-<a href="https://ariadne.geophysik.rub.de/trac/PyLoT">PyLoT TracPage</a> after
+    <a href="https://ariadne.geophysik.rub.de/trac/PyLoT">PyLoT TracPage</a> after
-successful registration.</p>
+    successful registration.</p>
-</body></html>
+</body>
+</html>

icons.qrc

@@ -2,6 +2,8 @@
     <qresource>
         <file>icons/pylot.ico</file>
         <file>icons/pylot.png</file>
+        <file>icons/back.png</file>
+        <file>icons/home.png</file>
         <file>icons/newfile.png</file>
         <file>icons/open.png</file>
         <file>icons/openproject.png</file>
@@ -23,6 +25,8 @@
         <file>icons/savepicks.png</file>
         <file>icons/preferences.png</file>
         <file>icons/parameter.png</file>
+        <file>icons/inventory.png</file>
+        <file>icons/map.png</file>
         <file>icons/openloc.png</file>
         <file>icons/compare_button.png</file>
         <file>icons/locate_button.png</file>

inputs/autoPyLoT.in

@@ -1,100 +0,0 @@
-%This is a parameter input file for autoPyLoT.
-%All main and special settings regarding data handling
-%and picking are to be set here!
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-#main settings#
-/DATA/Insheim                       #rootpath#     %project path
-EVENT_DATA/LOCAL		    #datapath#     %data path
-2013.02_Insheim                     #database#     %name of data base
-e0019.048.13                        #eventID#      %certain evnt ID for processing
-True                                #apverbose#
-PILOT				    #datastructure#  %choose data structure
-0                                   #iplot#        %flag for plotting: 0 none, 1, partly, >1 everything
-AUTOPHASES_AIC_HOS4_ARH             #phasefile#    %name of autoPILOT output phase file 
-AUTOLOC_AIC_HOS4_ARH                #locfile#      %name of autoPILOT output location file 
-AUTOFOCMEC_AIC_HOS4_ARH.in          #focmecin#     %name of focmec input file containing polarities
-HYPOSAT                             #locrt#        %location routine used ("HYPOINVERSE" or "HYPOSAT")
-6                                   #pmin#         %minimum required P picks for location
-4                                   #p0min#        %minimum required P picks for location if at least
-                                                   %3 excellent P picks are found
-2                                   #smin#         %minimum required S picks for location
-/home/ludger/bin/run_HYPOSAT4autoPILOT.csh #cshellp# %path and name of c-shell script to run location routine
-7.6 8.5                             #blon#         %longitude bounding for location map
-49 49.4                             #blat#         %lattitude bounding for location map
-#parameters for moment magnitude estimation#
-5000                                #vp#           %average P-wave velocity
-2800                                #vs#           %average S-wave velocity
-2200                                #rho#          %rock density [kg/m^3]
-300                                 #Qp#           %quality factor for P waves
-100                                 #Qs#           %quality factor for S waves
-#common settings picker#
-15                                  #pstart#       %start time [s] for calculating CF for P-picking
-40                                  #pstop#        %end time [s] for calculating CF for P-picking
--1.0                                #sstart#       %start time [s] after or before(-) P-onset for calculating CF for S-picking
-7                                   #sstop#        %end time [s] after P-onset for calculating CF for S-picking
-2 20                                #bpz1#         %lower/upper corner freq. of first band pass filter Z-comp. [Hz]
-2 30                                #bpz2#         %lower/upper corner freq. of second band pass filter Z-comp. [Hz]
-2 15                                #bph1#         %lower/upper corner freq. of first band pass filter H-comp. [Hz]
-2 20                                #bph2#         %lower/upper corner freq. of second band pass filter z-comp. [Hz]
-#special settings for calculating CF#
-%!!Be careful when editing the following!!
-#Z-component#
-HOS                                 #algoP#        %choose algorithm for P-onset determination (HOS, ARZ, or AR3)
-7                                   #tlta#         %for HOS-/AR-AIC-picker, length of LTA window [s] 
-4                                   #hosorder#     %for HOS-picker, order of Higher Order Statistics
-2                                   #Parorder#     %for AR-picker, order of AR process of Z-component
-1.2                                 #tdet1z#       %for AR-picker, length of AR determination window [s] for Z-component, 1st pick
-0.4                                 #tpred1z#      %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick
-0.6                                 #tdet2z#       %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick
-0.2                                 #tpred2z#      %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick
-0.001                               #addnoise#     %add noise to seismogram for stable AR prediction
-3 0.1 0.5 0.1                       #tsnrz#        %for HOS/AR, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-3                                   #pickwinP#     %for initial AIC pick, length of P-pick window [s]
-8                                   #Precalcwin#   %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)
-0                                   #peps4aic#     %for HOS/AR, artificial uplift of samples of AIC-function (P)
-0.2                                 #aictsmooth#   %for HOS/AR, take average of samples for smoothing of AIC-function [s]
-0.1                                 #tsmoothP#     %for HOS/AR, take average of samples for smoothing CF [s]
-0.001                               #ausP#         %for HOS/AR, artificial uplift of samples (aus) of CF (P)
-1.3                                 #nfacP#        %for HOS/AR, noise factor for noise level determination (P)
-#H-components#
-ARH                                 #algoS#        %choose algorithm for S-onset determination (ARH or AR3)
-0.8                                 #tdet1h#       %for HOS/AR, length of AR-determination window [s], H-components, 1st pick
-0.4                                 #tpred1h#      %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick
-0.6                                 #tdet2h#       %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick
-0.3                                 #tpred2h#      %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick
-4                                   #Sarorder#     %for AR-picker, order of AR process of H-components
-6                                   #Srecalcwin#   %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)
-3                                   #pickwinS#     %for initial AIC pick, length of S-pick window [s]
-2 0.2 1.5 0.5                       #tsnrh#        %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-0.05                                #aictsmoothS#  %for AIC-picker, take average of samples for smoothing of AIC-function [s]
-0.02                                #tsmoothS#     %for AR-picker, take average of samples for smoothing CF [s] (S)
-0.2                                 #pepsS#        %for AR-picker, artificial uplift of samples of CF (S) 
-0.4                                 #ausS#         %for HOS/AR, artificial uplift of samples (aus) of CF (S)
-1.5                                 #nfacS#        %for AR-picker, noise factor for noise level determination (S)
-%first-motion picker%
-1                                   #minfmweight#  %minimum required p weight for first-motion determination
-2                                   #minFMSNR#     %miniumum required SNR for first-motion determination
-0.2                                 #fmpickwin#    %pick window around P onset for calculating zero crossings
-%quality assessment%
-#inital AIC onset#
-0.01 0.02 0.04 0.08                 #timeerrorsP#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P
-0.04 0.08 0.16 0.32                 #timeerrorsS#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S
-80                                  #minAICPslope#  %below this slope [counts/s] the initial P pick is rejected
-1.2                                 #minAICPSNR#    %below this SNR the initial P pick is rejected
-50                                  #minAICSslope#  %below this slope [counts/s] the initial S pick is rejected
-1.5                                 #minAICSSNR#    %below this SNR the initial S pick is rejected
-#check duration of signal using envelope function#
-1.5                                 #prepickwin#   %pre-signal window length [s] for noise level estimation 
-0.7                                 #minsiglength# %minimum required length of signal [s]
-0.2                                 #sgap#         %safety gap between noise and signal window [s]
-2                                   #noisefactor#  %noiselevel*noisefactor=threshold
-60                                  #minpercent#   %per cent of samples required higher than threshold
-#check for spuriously picked S-onsets#
-3.0                                 #zfac#         %P-amplitude must exceed zfac times RMS-S amplitude 
-#jackknife-processing for P-picks#
-3                                   #thresholdweight#%minimum required weight of picks
-3                                   #dttolerance#  %maximum allowed deviation of P picks from median [s]
-4                                   #minstats#     %minimum number of stations with reliable P picks
-3                                   #Sdttolerance# %maximum allowed deviation from Wadati-diagram
-

inputs/autoPyLoT_local.in

@@ -1,99 +0,0 @@
-%This is a parameter input file for autoPyLoT.
-%All main and special settings regarding data handling
-%and picking are to be set here!
-%Parameters are optimized for local data sets!
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#main settings#
-/DATA/Insheim                       #rootpath#     %project path
-EVENT_DATA/LOCAL		    #datapath#     %data path
-2016.08_Insheim                     #database#     %name of data base
-e0007.224.16                        #eventID#      %event ID for single event processing
-/DATA/Insheim/STAT_INFO             #invdir#       %full path to inventory or dataless-seed file
-PILOT				    #datastructure#%choose data structure
-0                                   #iplot#        %flag for plotting: 0 none, 1 partly, >1 everything
-True                                #apverbose#    %choose 'True' or 'False' for terminal output
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#NLLoc settings#
-/home/ludger/NLLOC                  #nllocbin#     %path to NLLoc executable
-/home/ludger/NLLOC/Insheim          #nllocroot#    %root of NLLoc-processing directory
-AUTOPHASES.obs                      #phasefile#    %name of autoPyLoT-output phase file for NLLoc
-                                                   %(in nllocroot/obs)
-Insheim_min1d032016_auto.in         #ctrfile#      %name of autoPyLoT-output control file for NLLoc
-                                                   %(in nllocroot/run)
-ttime                               #ttpatter#     %pattern of NLLoc ttimes from grid
-                                                   %(in nllocroot/times)
-AUTOLOC_nlloc                       #outpatter#    %pattern of NLLoc-output file
-                                                   %(returns 'eventID_outpatter')
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#parameters for seismic moment estimation#
-3530                                #vp#           %average P-wave velocity
-2500                                #rho#          %average rock density [kg/m^3]
-300 0.8                             #Qp#           %quality factor for P waves ([Qp, ap], Qp*f^a)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-AUTOFOCMEC_AIC_HOS4_ARH.in          #focmecin#     %name of focmec input file containing derived polarities
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#common settings picker#
-15.0                                #pstart#       %start time [s] for calculating CF for P-picking
-60.0                                #pstop#        %end time [s] for calculating CF for P-picking
--1.0                                #sstart#       %start time [s] relative to P-onset for calculating CF for S-picking
-10.0                                #sstop#        %end time [s] after P-onset for calculating CF for S-picking
-2 20                                #bpz1#         %lower/upper corner freq. of first band pass filter Z-comp. [Hz]
-2 30                                #bpz2#         %lower/upper corner freq. of second band pass filter Z-comp. [Hz]
-2 15                                #bph1#         %lower/upper corner freq. of first band pass filter H-comp. [Hz]
-2 20                                #bph2#         %lower/upper corner freq. of second band pass filter z-comp. [Hz]
-#special settings for calculating CF#
-%!!Edit the following only if you know what you are doing!!%
-#Z-component#
-HOS                                 #algoP#        %choose algorithm for P-onset determination (HOS, ARZ, or AR3)
-7.0                                 #tlta#         %for HOS-/AR-AIC-picker, length of LTA window [s] 
-4                                   #hosorder#     %for HOS-picker, order of Higher Order Statistics
-2                                   #Parorder#     %for AR-picker, order of AR process of Z-component
-1.2                                 #tdet1z#       %for AR-picker, length of AR determination window [s] for Z-component, 1st pick
-0.4                                 #tpred1z#      %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick
-0.6                                 #tdet2z#       %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick
-0.2                                 #tpred2z#      %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick
-0.001                               #addnoise#     %add noise to seismogram for stable AR prediction
-3 0.1 0.5 0.5                       #tsnrz#        %for HOS/AR, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-3.0                                 #pickwinP#     %for initial AIC pick, length of P-pick window [s]
-6.0                                 #Precalcwin#   %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)
-0.2                                 #aictsmooth#   %for HOS/AR, take average of samples for smoothing of AIC-function [s]
-0.1                                 #tsmoothP#     %for HOS/AR, take average of samples for smoothing CF [s]
-0.001                               #ausP#         %for HOS/AR, artificial uplift of samples (aus) of CF (P)
-1.3                                 #nfacP#        %for HOS/AR, noise factor for noise level determination (P)
-#H-components#
-ARH                                 #algoS#        %choose algorithm for S-onset determination (ARH or AR3)
-0.8                                 #tdet1h#       %for HOS/AR, length of AR-determination window [s], H-components, 1st pick
-0.4                                 #tpred1h#      %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick
-0.6                                 #tdet2h#       %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick
-0.3                                 #tpred2h#      %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick
-4                                   #Sarorder#     %for AR-picker, order of AR process of H-components
-5.0                                 #Srecalcwin#   %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)
-3.0                                 #pickwinS#     %for initial AIC pick, length of S-pick window [s]
-2 0.2 1.5 0.5                       #tsnrh#        %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-0.5                                 #aictsmoothS#  %for AIC-picker, take average of samples for smoothing of AIC-function [s]
-0.7                                 #tsmoothS#     %for AR-picker, take average of samples for smoothing CF [s] (S)
-0.9                                 #ausS#         %for HOS/AR, artificial uplift of samples (aus) of CF (S)
-1.5                                 #nfacS#        %for AR-picker, noise factor for noise level determination (S)
-%first-motion picker%
-1                                   #minfmweight#  %minimum required P weight for first-motion determination
-2                                   #minFMSNR#     %miniumum required SNR for first-motion determination
-0.2                                 #fmpickwin#    %pick window around P onset for calculating zero crossings
-%quality assessment%
-#inital AIC onset#
-0.01 0.02 0.04 0.08                 #timeerrorsP#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P
-0.04 0.08 0.16 0.32                 #timeerrorsS#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S
-4                                   #minAICPslope#  %below this slope [counts/s] the initial P pick is rejected
-1.2                                 #minAICPSNR#    %below this SNR the initial P pick is rejected
-2                                   #minAICSslope#  %below this slope [counts/s] the initial S pick is rejected
-1.5                                 #minAICSSNR#    %below this SNR the initial S pick is rejected
-#check duration of signal using envelope function#
-3                                   #minsiglength# %minimum required length of signal [s]
-1.0                                 #noisefactor#  %noiselevel*noisefactor=threshold
-40                                  #minpercent#   %required percentage of samples higher than threshold
-#check for spuriously picked S-onsets#
-2.0                                 #zfac#         %P-amplitude must exceed at least zfac times RMS-S amplitude 
-#check statistics of P onsets#
-2.5                                 #mdttolerance#  %maximum allowed deviation of P picks from median [s]
-#wadati check#
-1.0                                 #wdttolerance# %maximum allowed deviation from Wadati-diagram
-

inputs/autoPyLoT_regional.in

@@ -1,100 +0,0 @@
-%This is a parameter input file for autoPyLoT.
-%All main and special settings regarding data handling
-%and picking are to be set here!
-%Parameters are optimized for regional data sets!
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-#main settings#
-/DATA/Egelados                      #rootpath#     %project path
-EVENT_DATA/LOCAL		    #datapath#     %data path
-2006.01_Nisyros                     #database#     %name of data base
-e1412.008.06                        #eventID#      %event ID for single event processing
-/DATA/Egelados/STAT_INFO            #invdir#       %full path to inventory or dataless-seed file
-PILOT				    #datastructure#  %choose data structure
-0                                   #iplot#        %flag for plotting: 0 none, 1, partly, >1 everything
-True                                #apverbose#    %choose 'True' or 'False' for terminal output
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#NLLoc settings#
-/home/ludger/NLLOC                  #nllocbin#     %path to NLLoc executable
-/home/ludger/NLLOC/Insheim          #nllocroot#    %root of NLLoc-processing directory
-AUTOPHASES.obs                      #phasefile#    %name of autoPyLoT-output phase file for NLLoc
-                                                   %(in nllocroot/obs)
-Insheim_min1d2015_auto.in           #ctrfile#      %name of autoPyLoT-output control file for NLLoc
-                                                   %(in nllocroot/run)
-ttime                               #ttpatter#     %pattern of NLLoc ttimes from grid
-                                                   %(in nllocroot/times)
-AUTOLOC_nlloc                       #outpatter#    %pattern of NLLoc-output file
-                                                   %(returns 'eventID_outpatter')
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#parameters for seismic moment estimation#
-3530                                #vp#           %average P-wave velocity
-2700                                #rho#          %average rock density [kg/m^3]
-1000f**0.8                          #Qp#           %quality factor for P waves (Qp*f^a)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-AUTOFOCMEC_AIC_HOS4_ARH.in          #focmecin#     %name of focmec input file containing derived polarities
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#common settings picker#
-20                                  #pstart#       %start time [s] for calculating CF for P-picking
-100                                 #pstop#        %end time [s] for calculating CF for P-picking
-1.0                                 #sstart#       %start time [s] after or before(-) P-onset for calculating CF for S-picking
-100                                 #sstop#        %end time [s] after P-onset for calculating CF for S-picking
-3 10                                #bpz1#         %lower/upper corner freq. of first band pass filter Z-comp. [Hz]
-3 12                                #bpz2#         %lower/upper corner freq. of second band pass filter Z-comp. [Hz]
-3 8                                 #bph1#         %lower/upper corner freq. of first band pass filter H-comp. [Hz]
-3 6                                 #bph2#         %lower/upper corner freq. of second band pass filter H-comp. [Hz]
-#special settings for calculating CF#
-%!!Be careful when editing the following!!
-#Z-component#
-HOS                                 #algoP#        %choose algorithm for P-onset determination (HOS, ARZ, or AR3)
-7                                   #tlta#         %for HOS-/AR-AIC-picker, length of LTA window [s] 
-4                                   #hosorder#     %for HOS-picker, order of Higher Order Statistics
-2                                   #Parorder#     %for AR-picker, order of AR process of Z-component
-1.2                                 #tdet1z#       %for AR-picker, length of AR determination window [s] for Z-component, 1st pick
-0.4                                 #tpred1z#      %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick
-0.6                                 #tdet2z#       %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick
-0.2                                 #tpred2z#      %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick
-0.001                               #addnoise#     %add noise to seismogram for stable AR prediction
-5 0.2 3.0 1.5                       #tsnrz#        %for HOS/AR, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-3                                   #pickwinP#     %for initial AIC and refined pick, length of P-pick window [s]
-8                                   #Precalcwin#   %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)
-1.0                                 #aictsmooth#   %for HOS/AR, take average of samples for smoothing of AIC-function [s]
-0.3                                 #tsmoothP#     %for HOS/AR, take average of samples for smoothing CF [s]
-0.3                                 #ausP#         %for HOS/AR, artificial uplift of samples (aus) of CF (P)
-1.3                                 #nfacP#        %for HOS/AR, noise factor for noise level determination (P)
-#H-components#
-ARH                                 #algoS#        %choose algorithm for S-onset determination (ARH or AR3)
-0.8                                 #tdet1h#       %for HOS/AR, length of AR-determination window [s], H-components, 1st pick
-0.4                                 #tpred1h#      %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick
-0.6                                 #tdet2h#       %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick
-0.3                                 #tpred2h#      %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick
-4                                   #Sarorder#     %for AR-picker, order of AR process of H-components
-10                                  #Srecalcwin#   %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)
-25                                  #pickwinS#     %for initial AIC and refined pick, length of S-pick window [s]
-5 0.2 3.0 3.0                       #tsnrh#        %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-3.5                                 #aictsmoothS#  %for AIC-picker, take average of samples for smoothing of AIC-function [s]
-1.0                                 #tsmoothS#     %for AR-picker, take average of samples for smoothing CF [s] (S)
-0.2                                 #ausS#         %for HOS/AR, artificial uplift of samples (aus) of CF (S)
-1.5                                 #nfacS#        %for AR-picker, noise factor for noise level determination (S)
-%first-motion picker%
-1                                   #minfmweight#  %minimum required p weight for first-motion determination
-2                                   #minFMSNR#     %miniumum required SNR for first-motion determination
-6.0                                 #fmpickwin#    %pick window around P onset for calculating zero crossings
-%quality assessment%
-#inital AIC onset#
-0.04 0.08 0.16 0.32                 #timeerrorsP#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P
-0.04 0.08 0.16 0.32                 #timeerrorsS#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S
-3                                   #minAICPslope#  %below this slope [counts/s] the initial P pick is rejected
-1.2                                 #minAICPSNR#    %below this SNR the initial P pick is rejected
-5                                   #minAICSslope#  %below this slope [counts/s] the initial S pick is rejected
-2.5                                 #minAICSSNR#    %below this SNR the initial S pick is rejected
-#check duration of signal using envelope function#
-30                                  #minsiglength# %minimum required length of signal [s]
-2.5                                 #noisefactor#  %noiselevel*noisefactor=threshold
-60                                  #minpercent#   %required percentage of samples higher than threshold
-#check for spuriously picked S-onsets#
-0.5                                 #zfac#         %P-amplitude must exceed at least zfac times RMS-S amplitude 
-#check statistics of P onsets#
-45                                  #mdttolerance#  %maximum allowed deviation of P picks from median [s]
-#wadati check#
-3.0                                 #wdttolerance# %maximum allowed deviation from Wadati-diagram
-

inputs/filter.in

@@ -1,2 +0,0 @@
-P bandpass 4 2.0 20.0
-S bandpass 4 2.0 15.0

inputs/pylot.in

@@ -1,98 +0,0 @@
-%This is a example parameter input file for PyLoT.
-%All main and special settings regarding data handling
-%and picking are to be set here!
-%Parameters shown here are optimized for local data sets!
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#main settings#
-/data/Geothermie/Insheim            #rootpath#      %project path
-EVENT_DATA/LOCAL                    #datapath#      %data path
-2013.02_Insheim                     #database#      %name of data base
-e0019.048.13                        #eventID#       %event ID for single event processing
-/data/Geothermie/Insheim/STAT_INFO  #invdir#        %full path to  inventory or dataless-seed file
-PILOT                               #datastructure# %choose data structure
-0                                   #iplot#         %flag for plotting: 0 none, 1 partly, >1 everything
-True                                #apverbose#     %choose 'True' or 'False' for terminal output
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#NLLoc settings#
-/progs/bin                          #nllocbin#      %path to NLLoc executable
-/data/Geothermie/Insheim/LOCALISATION/NLLoc          #nllocroot#     %root of NLLoc-processing directory
-AUTOPHASES.obs                      #phasefile#     %name of autoPyLoT-output phase file for NLLoc
-                                                    %(in nllocroot/obs)
-Insheim_min1d2015.in           #ctrfile#       %name of PyLoT-output control file for NLLoc
-                                                    %(in nllocroot/run)
-ttime                               #ttpatter#      %pattern of NLLoc ttimes from grid
-                                                    %(in nllocroot/times)
-AUTOLOC_nlloc                       #outpatter#     %pattern of NLLoc-output file
-                                                    %(returns 'eventID_outpatter')
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#parameters for seismic moment estimation#
-3530                                #vp#            %average P-wave velocity
-2500                                #rho#           %average rock density [kg/m^3]
-300 0.8                           #Qp#            %quality factor for P waves (Qp*f^a); list(Qp, a)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-AUTOFOCMEC_AIC_HOS4_ARH.in          #focmecin#      %name of focmec input file containing derived polarities
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#common settings picker#
-15.0                                #pstart#        %start time [s] for calculating CF for P-picking
-60.0                                #pstop#         %end time [s] for calculating CF for P-picking
--1.0                                #sstart#        %start time [s] relative to P-onset for calculating CF for S-picking
-10.0                                #sstop#         %end time [s] after P-onset for calculating CF for S-picking
-2 20                                #bpz1#          %lower/upper corner freq. of first band pass filter Z-comp. [Hz]
-2 30                                #bpz2#          %lower/upper corner freq. of second band pass filter Z-comp. [Hz]
-2 15                                #bph1#          %lower/upper corner freq. of first band pass filter H-comp. [Hz]
-2 20                                #bph2#          %lower/upper corner freq. of second band pass filter z-comp. [Hz]
-#special settings for calculating CF#
-%!!Edit the following only if you know what you are doing!!%
-#Z-component#
-HOS                                 #algoP#         %choose algorithm for P-onset determination (HOS, ARZ, or AR3)
-7.0                                 #tlta#          %for HOS-/AR-AIC-picker, length of LTA window [s]
-4                                   #hosorder#      %for HOS-picker, order of Higher Order Statistics
-2                                   #Parorder#      %for AR-picker, order of AR process of Z-component
-1.2                                 #tdet1z#        %for AR-picker, length of AR determination window [s] for Z-component, 1st pick
-0.4                                 #tpred1z#       %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick
-0.6                                 #tdet2z#        %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick
-0.2                                 #tpred2z#       %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick
-0.001                               #addnoise#      %add noise to seismogram for stable AR prediction
-3 0.1 0.5 0.5                       #tsnrz#         %for HOS/AR, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-3.0                                 #pickwinP#      %for initial AIC pick, length of P-pick window [s]
-6.0                                 #Precalcwin#    %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)
-0.2                                 #aictsmooth#    %for HOS/AR, take average of samples for smoothing of AIC-function [s]
-0.1                                 #tsmoothP#      %for HOS/AR, take average of samples for smoothing CF [s]
-0.001                               #ausP#          %for HOS/AR, artificial uplift of samples (aus) of CF (P)
-1.3                                 #nfacP#         %for HOS/AR, noise factor for noise level determination (P)
-#H-components#
-ARH                                 #algoS#         %choose algorithm for S-onset determination (ARH or AR3)
-0.8                                 #tdet1h#        %for HOS/AR, length of AR-determination window [s], H-components, 1st pick
-0.4                                 #tpred1h#       %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick
-0.6                                 #tdet2h#        %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick
-0.3                                 #tpred2h#       %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick
-4                                   #Sarorder#      %for AR-picker, order of AR process of H-components
-5.0                                 #Srecalcwin#    %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)
-3.0                                 #pickwinS#      %for initial AIC pick, length of S-pick window [s]
-2 0.2 1.5 0.5                       #tsnrh#         %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise,tsafetey,tsignal,tslope] [s]
-0.5                                 #aictsmoothS#   %for AIC-picker, take average of samples for smoothing of AIC-function [s]
-0.7                                 #tsmoothS#      %for AR-picker, take average of samples for smoothing CF [s] (S)
-0.9                                 #ausS#          %for HOS/AR, artificial uplift of samples (aus) of CF (S)
-1.5                                 #nfacS#         %for AR-picker, noise factor for noise level determination (S)
-%first-motion picker%
-1                                   #minfmweight#   %minimum required P weight for first-motion determination
-2                                   #minFMSNR#      %miniumum required SNR for first-motion determination
-0.2                                 #fmpickwin#     %pick window around P onset for calculating zero crossings
-%quality assessment%
-#inital AIC onset#
-0.01 0.02 0.04 0.08                 #timeerrorsP#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P
-0.04 0.08 0.16 0.32                 #timeerrorsS#   %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S
-4                                   #minAICPslope#  %below this slope [counts/s] the initial P pick is rejected
-1.2                                 #minAICPSNR#    %below this SNR the initial P pick is rejected
-2                                   #minAICSslope#  %below this slope [counts/s] the initial S pick is rejected
-1.5                                 #minAICSSNR#    %below this SNR the initial S pick is rejected
-#check duration of signal using envelope function#
-3                                   #minsiglength#  %minimum required length of signal [s]
-1.0                                 #noisefactor#   %noiselevel*noisefactor=threshold
-40                                  #minpercent#    %required percentage of samples higher than threshold
-#check for spuriously picked S-onsets#
-2.0                                 #zfac#          %P-amplitude must exceed at least zfac times RMS-S amplitude
-#check statistics of P onsets#
-2.5                                 #mdttolerance#  %maximum allowed deviation of P picks from median [s]
-#wadati check#
-1.0                                 #wdttolerance#  %maximum allowed deviation from Wadati-diagram

inputs/pylot_global.in

@@ -0,0 +1,100 @@
+%This is a parameter input file for PyLoT/autoPyLoT.
+%All main and special settings regarding data handling
+%and picking are to be set here!
+%Parameters are optimized for %extent data sets!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#main settings#
+                                                   #rootpath#       %project path                                                                                        
+                                                   #datapath#       %data path                                                                                           
+                                                   #database#       %name of data base                                                                                   
+                                                   #eventID#        %event ID for single event processing (* for all events found in database)                           
+                                                   #invdir#         %full path to  inventory or dataless-seed file                                                       
+PILOT                                              #datastructure#  %choose data structure                                                                               
+True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#NLLoc settings#
+None                                               #nllocbin#       %path to NLLoc executable                                                                            
+None                                               #nllocroot#      %root of NLLoc-processing directory                                                                  
+None                                               #phasefile#      %name of autoPyLoT-output phase file for NLLoc                                                       
+None                                               #ctrfile#        %name of autoPyLoT-output control file for NLLoc                                                     
+ttime                                              #ttpatter#       %pattern of NLLoc ttimes from grid                                                                   
+AUTOLOC_nlloc                                      #outpatter#      %pattern of NLLoc-output file                                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#parameters for seismic moment estimation#
+3530.0                                             #vp#             %average P-wave velocity                                                                             
+2500.0                                             #rho#            %average rock density [kg/m^3]                                                                       
+300.0 0.8                                          #Qp#             %quality factor for P waves (Qp*f^a); list(Qp, a)                                                    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#settings local magnitude#
+1.0 1.0 1.0                                        #WAscaling#      %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]                           If zeros are set, original Richter magnitude is calculated!
+1.0 1.0                                            #magscaling#     %Scaling relation for derived local magnitude [a*Ml+b].                            If zeros are set, no scaling of network magnitude is applied!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#filter settings#
+0.01 0.01                                          #minfreq#        %Lower filter frequency [P, S]                                                                       
+0.3 0.3                                            #maxfreq#        %Upper filter frequency [P, S]                                                                       
+3 3                                                #filter_order#   %filter order [P, S]                                                                                 
+bandpass bandpass                                  #filter_type#    %filter type (bandpass, bandstop, lowpass, highpass) [P, S]                                          
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#common settings picker#
+global                                             #extent#         %extent of array ("local", "regional" or "global")                                                   
+-150.0                                             #pstart#         %start time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)     
+600.0                                              #pstop#          %end time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)       
+200.0                                              #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
+1150.0                                             #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
+True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+0.05 0.5                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
+0.001 0.5                                          #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
+0.05 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     
+0.001 0.5                                          #bph2#           %lower/upper corner freq. of second band pass filter z-comp. [Hz]                                    
+#special settings for calculating CF#
+%!!Edit the following only if you know what you are doing!!%
+#Z-component#
+HOS                                                #algoP#          %choose algorithm for P-onset determination (HOS, ARZ, or AR3)                                       
+150.0                                              #tlta#           %for HOS-/AR-AIC-picker, length of LTA window [s]                                                    
+4                                                  #hosorder#       %for HOS-picker, order of Higher Order Statistics                                                    
+2                                                  #Parorder#       %for AR-picker, order of AR process of Z-component                                                   
+16.0                                               #tdet1z#         %for AR-picker, length of AR determination window [s] for Z-component, 1st pick                      
+10.0                                               #tpred1z#        %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick                         
+12.0                                               #tdet2z#         %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick                      
+6.0                                                #tpred2z#        %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick                         
+0.001                                              #addnoise#       %add noise to seismogram for stable AR prediction                                                    
+60.0 10.0 40.0 10.0                                #tsnrz#          %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]     
+150.0                                              #pickwinP#       %for initial AIC pick, length of P-pick window [s]                                                   
+35.0                                               #Precalcwin#     %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)                        
+6.0                                                #aictsmooth#     %for HOS/AR, take average of samples for smoothing of AIC-function [s]                               
+4.0                                                #tsmoothP#       %for HOS/AR, take average of samples for smoothing CF [s]                                            
+0.001                                              #ausP#           %for HOS/AR, artificial uplift of samples (aus) of CF (P)                                            
+1.1                                                #nfacP#          %for HOS/AR, noise factor for noise level determination (P)                                          
+#H-components#
+ARH                                                #algoS#          %choose algorithm for S-onset determination (ARH or AR3)                                             
+12.0                                               #tdet1h#         %for HOS/AR, length of AR-determination window [s], H-components, 1st pick                           
+6.0                                                #tpred1h#        %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick                              
+8.0                                                #tdet2h#         %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick                            
+4.0                                                #tpred2h#        %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick                              
+4                                                  #Sarorder#       %for AR-picker, order of AR process of H-components                                                  
+30.0                                               #Srecalcwin#     %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)                             
+195.0                                              #pickwinS#       %for initial AIC pick, length of S-pick window [s]                                                   
+100.0 10.0 45.0 10.0                               #tsnrh#          %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]    
+22.0                                               #aictsmoothS#    %for AIC-picker, take average of samples for smoothing of AIC-function [s]                           
+10.0                                               #tsmoothS#       %for AR-picker, take average of samples for smoothing CF [s] (S)                                     
+0.001                                              #ausS#           %for HOS/AR, artificial uplift of samples (aus) of CF (S)                                            
+1.2                                                #nfacS#          %for AR-picker, noise factor for noise level determination (S)                                       
+#first-motion picker#
+1                                                  #minfmweight#    %minimum required P weight for first-motion determination                                            
+3.0                                                #minFMSNR#       %miniumum required SNR for first-motion determination                                                
+10.0                                               #fmpickwin#      %pick window around P onset for calculating zero crossings                                           
+#quality assessment#
+1.0 2.0 4.0 8.0                                    #timeerrorsP#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P                           
+4.0 8.0 16.0 32.0                                  #timeerrorsS#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S                           
+0.5                                                #minAICPslope#   %below this slope [counts/s] the initial P pick is rejected                                          
+1.1                                                #minAICPSNR#     %below this SNR the initial P pick is rejected                                                       
+1.0                                                #minAICSslope#   %below this slope [counts/s] the initial S pick is rejected                                          
+1.3                                                #minAICSSNR#     %below this SNR the initial S pick is rejected                                                       
+5.0                                                #minsiglength#   %length of signal part for which amplitudes must exceed noiselevel [s]                               
+1.0                                                #noisefactor#    %noiselevel*noisefactor=threshold                                                                    
+10.0                                               #minpercent#     %required percentage of amplitudes exceeding threshold                                               
+1.2                                                #zfac#           %P-amplitude must exceed at least zfac times RMS-S amplitude                                         
+25.0                                               #mdttolerance#   %maximum allowed deviation of P picks from median [s]                                                
+50.0                                               #wdttolerance#   %maximum allowed deviation from Wadati-diagram                                                       
+5.0                                                #jackfactor#     %pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor

inputs/pylot_local.in

@@ -0,0 +1,100 @@
+%This is a parameter input file for PyLoT/autoPyLoT.
+%All main and special settings regarding data handling
+%and picking are to be set here!
+%Parameters are optimized for %extent data sets!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#main settings#
+                                                   #rootpath#       %project path                                                                                        
+                                                   #datapath#       %data path                                                                                           
+                                                   #database#       %name of data base                                                                                   
+                                                   #eventID#        %event ID for single event processing (* for all events found in database)                           
+                                                   #invdir#         %full path to  inventory or dataless-seed file                                                       
+PILOT                                              #datastructure#  %choose data structure                                                                               
+True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#NLLoc settings#
+None                                               #nllocbin#       %path to NLLoc executable                                                                            
+None                                               #nllocroot#      %root of NLLoc-processing directory                                                                  
+None                                               #phasefile#      %name of autoPyLoT-output phase file for NLLoc                                                       
+None                                               #ctrfile#        %name of autoPyLoT-output control file for NLLoc                                                     
+ttime                                              #ttpatter#       %pattern of NLLoc ttimes from grid                                                                   
+AUTOLOC_nlloc                                      #outpatter#      %pattern of NLLoc-output file                                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#parameters for seismic moment estimation#
+3530.0                                             #vp#             %average P-wave velocity                                                                             
+2500.0                                             #rho#            %average rock density [kg/m^3]                                                                       
+300.0 0.8                                          #Qp#             %quality factor for P waves (Qp*f^a); list(Qp, a)                                                    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#settings local magnitude#
+1.11 0.0009 -2.0                                   #WAscaling#      %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]                           If zeros are set, original Richter magnitude is calculated!
+1.0382 -0.447                                      #magscaling#     %Scaling relation for derived local magnitude [a*Ml+b].                            If zeros are set, no scaling of network magnitude is applied!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#filter settings#
+1.0 1.0                                            #minfreq#        %Lower filter frequency [P, S]                                                                       
+10.0 10.0                                          #maxfreq#        %Upper filter frequency [P, S]                                                                       
+2 2                                                #filter_order#   %filter order [P, S]                                                                                 
+bandpass bandpass                                  #filter_type#    %filter type (bandpass, bandstop, lowpass, highpass) [P, S]                                          
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#common settings picker#
+local                                              #extent#         %extent of array ("local", "regional" or "global")                                                   
+15.0                                               #pstart#         %start time [s] for calculating CF for P-picking                                                     
+60.0                                               #pstop#          %end time [s] for calculating CF for P-picking                                                       
+-1.0                                               #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
+10.0                                               #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
+True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation                                                        
+2.0 10.0                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
+2.0 12.0                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
+2.0 8.0                                            #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     
+2.0 10.0                                           #bph2#           %lower/upper corner freq. of second band pass filter z-comp. [Hz]                                    
+#special settings for calculating CF#
+%!!Edit the following only if you know what you are doing!!%
+#Z-component#
+HOS                                                #algoP#          %choose algorithm for P-onset determination (HOS, ARZ, or AR3)                                       
+7.0                                                #tlta#           %for HOS-/AR-AIC-picker, length of LTA window [s]                                                    
+4                                                  #hosorder#       %for HOS-picker, order of Higher Order Statistics                                                    
+2                                                  #Parorder#       %for AR-picker, order of AR process of Z-component                                                   
+1.2                                                #tdet1z#         %for AR-picker, length of AR determination window [s] for Z-component, 1st pick                      
+0.4                                                #tpred1z#        %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick                         
+0.6                                                #tdet2z#         %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick                      
+0.2                                                #tpred2z#        %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick                         
+0.001                                              #addnoise#       %add noise to seismogram for stable AR prediction                                                    
+3.0 0.1 0.5 1.0                                    #tsnrz#          %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]     
+3.0                                                #pickwinP#       %for initial AIC pick, length of P-pick window [s]                                                   
+6.0                                                #Precalcwin#     %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)                        
+0.2                                                #aictsmooth#     %for HOS/AR, take average of samples for smoothing of AIC-function [s]                               
+0.1                                                #tsmoothP#       %for HOS/AR, take average of samples for smoothing CF [s]                                            
+0.001                                              #ausP#           %for HOS/AR, artificial uplift of samples (aus) of CF (P)                                            
+1.3                                                #nfacP#          %for HOS/AR, noise factor for noise level determination (P)                                          
+#H-components#
+ARH                                                #algoS#          %choose algorithm for S-onset determination (ARH or AR3)                                             
+0.8                                                #tdet1h#         %for HOS/AR, length of AR-determination window [s], H-components, 1st pick                           
+0.4                                                #tpred1h#        %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick                              
+0.6                                                #tdet2h#         %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick                            
+0.3                                                #tpred2h#        %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick                              
+4                                                  #Sarorder#       %for AR-picker, order of AR process of H-components                                                  
+5.0                                                #Srecalcwin#     %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)                             
+4.0                                                #pickwinS#       %for initial AIC pick, length of S-pick window [s]                                                   
+2.0 0.3 1.5 1.0                                    #tsnrh#          %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]    
+1.0                                                #aictsmoothS#    %for AIC-picker, take average of samples for smoothing of AIC-function [s]                           
+0.7                                                #tsmoothS#       %for AR-picker, take average of samples for smoothing CF [s] (S)                                     
+0.9                                                #ausS#           %for HOS/AR, artificial uplift of samples (aus) of CF (S)                                            
+1.5                                                #nfacS#          %for AR-picker, noise factor for noise level determination (S)                                       
+#first-motion picker#
+1                                                  #minfmweight#    %minimum required P weight for first-motion determination                                            
+2.0                                                #minFMSNR#       %miniumum required SNR for first-motion determination                                                
+0.2                                                #fmpickwin#      %pick window around P onset for calculating zero crossings                                           
+#quality assessment#
+0.02 0.04 0.08 0.16                                #timeerrorsP#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P                           
+0.04 0.08 0.16 0.32                                #timeerrorsS#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S                           
+0.8                                                #minAICPslope#   %below this slope [counts/s] the initial P pick is rejected                                          
+1.1                                                #minAICPSNR#     %below this SNR the initial P pick is rejected                                                       
+1.0                                                #minAICSslope#   %below this slope [counts/s] the initial S pick is rejected                                          
+1.5                                                #minAICSSNR#     %below this SNR the initial S pick is rejected                                                       
+1.0                                                #minsiglength#   %length of signal part for which amplitudes must exceed noiselevel [s]                               
+1.0                                                #noisefactor#    %noiselevel*noisefactor=threshold                                                                    
+10.0                                               #minpercent#     %required percentage of amplitudes exceeding threshold                                               
+1.5                                                #zfac#           %P-amplitude must exceed at least zfac times RMS-S amplitude                                         
+6.0                                                #mdttolerance#   %maximum allowed deviation of P picks from median [s]                                                
+1.0                                                #wdttolerance#   %maximum allowed deviation from Wadati-diagram                                                       
+5.0                                                #jackfactor#     %pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor

inputs/pylot_regional.in

@@ -0,0 +1,100 @@
+%This is a parameter input file for PyLoT/autoPyLoT.
+%All main and special settings regarding data handling
+%and picking are to be set here!
+%Parameters are optimized for %extent data sets!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#main settings#
+                                                   #rootpath#       %project path                                                                                        
+                                                   #datapath#       %data path                                                                                           
+                                                   #database#       %name of data base                                                                                   
+                                                   #eventID#        %event ID for single event processing (* for all events found in database)                           
+                                                   #invdir#         %full path to  inventory or dataless-seed file                                                       
+PILOT                                              #datastructure#  %choose data structure                                                                               
+True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#NLLoc settings#
+None                                               #nllocbin#       %path to NLLoc executable                                                                            
+None                                               #nllocroot#      %root of NLLoc-processing directory                                                                  
+None                                               #phasefile#      %name of autoPyLoT-output phase file for NLLoc                                                       
+None                                               #ctrfile#        %name of autoPyLoT-output control file for NLLoc                                                     
+ttime                                              #ttpatter#       %pattern of NLLoc ttimes from grid                                                                   
+AUTOLOC_nlloc                                      #outpatter#      %pattern of NLLoc-output file                                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#parameters for seismic moment estimation#
+3530.0                                             #vp#             %average P-wave velocity                                                                             
+2500.0                                             #rho#            %average rock density [kg/m^3]                                                                       
+300.0 0.8                                          #Qp#             %quality factor for P waves (Qp*f^a); list(Qp, a)                                                    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#settings local magnitude#
+1.11 0.0009 -2.0                                   #WAscaling#      %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]                           If zeros are set, original Richter magnitude is calculated!
+1.0382 -0.447                                      #magscaling#     %Scaling relation for derived local magnitude [a*Ml+b].                            If zeros are set, no scaling of network magnitude is applied!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#filter settings#
+1.0 1.0                                            #minfreq#        %Lower filter frequency [P, S]                                                                       
+10.0 10.0                                          #maxfreq#        %Upper filter frequency [P, S]                                                                       
+2 2                                                #filter_order#   %filter order [P, S]                                                                                 
+bandpass bandpass                                  #filter_type#    %filter type (bandpass, bandstop, lowpass, highpass) [P, S]                                          
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#common settings picker#
+local                                              #extent#         %extent of array ("local", "regional" or "global")                                                   
+15.0                                               #pstart#         %start time [s] for calculating CF for P-picking                                                     
+60.0                                               #pstop#          %end time [s] for calculating CF for P-picking                                                       
+-1.0                                               #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
+10.0                                               #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
+True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation                                                        
+2.0 10.0                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
+2.0 12.0                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
+2.0 8.0                                            #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     
+2.0 10.0                                           #bph2#           %lower/upper corner freq. of second band pass filter z-comp. [Hz]                                    
+#special settings for calculating CF#
+%!!Edit the following only if you know what you are doing!!%
+#Z-component#
+HOS                                                #algoP#          %choose algorithm for P-onset determination (HOS, ARZ, or AR3)                                       
+7.0                                                #tlta#           %for HOS-/AR-AIC-picker, length of LTA window [s]                                                    
+4                                                  #hosorder#       %for HOS-picker, order of Higher Order Statistics                                                    
+2                                                  #Parorder#       %for AR-picker, order of AR process of Z-component                                                   
+1.2                                                #tdet1z#         %for AR-picker, length of AR determination window [s] for Z-component, 1st pick                      
+0.4                                                #tpred1z#        %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick                         
+0.6                                                #tdet2z#         %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick                      
+0.2                                                #tpred2z#        %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick                         
+0.001                                              #addnoise#       %add noise to seismogram for stable AR prediction                                                    
+3.0 0.1 0.5 1.0                                    #tsnrz#          %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]     
+3.0                                                #pickwinP#       %for initial AIC pick, length of P-pick window [s]                                                   
+6.0                                                #Precalcwin#     %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)                        
+0.2                                                #aictsmooth#     %for HOS/AR, take average of samples for smoothing of AIC-function [s]                               
+0.1                                                #tsmoothP#       %for HOS/AR, take average of samples for smoothing CF [s]                                            
+0.001                                              #ausP#           %for HOS/AR, artificial uplift of samples (aus) of CF (P)                                            
+1.3                                                #nfacP#          %for HOS/AR, noise factor for noise level determination (P)                                          
+#H-components#
+ARH                                                #algoS#          %choose algorithm for S-onset determination (ARH or AR3)                                             
+0.8                                                #tdet1h#         %for HOS/AR, length of AR-determination window [s], H-components, 1st pick                           
+0.4                                                #tpred1h#        %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick                              
+0.6                                                #tdet2h#         %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick                            
+0.3                                                #tpred2h#        %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick                              
+4                                                  #Sarorder#       %for AR-picker, order of AR process of H-components                                                  
+5.0                                                #Srecalcwin#     %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)                             
+4.0                                                #pickwinS#       %for initial AIC pick, length of S-pick window [s]                                                   
+2.0 0.3 1.5 1.0                                    #tsnrh#          %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]    
+1.0                                                #aictsmoothS#    %for AIC-picker, take average of samples for smoothing of AIC-function [s]                           
+0.7                                                #tsmoothS#       %for AR-picker, take average of samples for smoothing CF [s] (S)                                     
+0.9                                                #ausS#           %for HOS/AR, artificial uplift of samples (aus) of CF (S)                                            
+1.5                                                #nfacS#          %for AR-picker, noise factor for noise level determination (S)                                       
+#first-motion picker#
+1                                                  #minfmweight#    %minimum required P weight for first-motion determination                                            
+2.0                                                #minFMSNR#       %miniumum required SNR for first-motion determination                                                
+0.2                                                #fmpickwin#      %pick window around P onset for calculating zero crossings                                           
+#quality assessment#
+0.02 0.04 0.08 0.16                                #timeerrorsP#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P                           
+0.04 0.08 0.16 0.32                                #timeerrorsS#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S                           
+0.8                                                #minAICPslope#   %below this slope [counts/s] the initial P pick is rejected                                          
+1.1                                                #minAICPSNR#     %below this SNR the initial P pick is rejected                                                       
+1.0                                                #minAICSslope#   %below this slope [counts/s] the initial S pick is rejected                                          
+1.5                                                #minAICSSNR#     %below this SNR the initial S pick is rejected                                                       
+1.0                                                #minsiglength#   %length of signal part for which amplitudes must exceed noiselevel [s]                               
+1.0                                                #noisefactor#    %noiselevel*noisefactor=threshold                                                                    
+10.0                                               #minpercent#     %required percentage of amplitudes exceeding threshold                                               
+1.5                                                #zfac#           %P-amplitude must exceed at least zfac times RMS-S amplitude                                         
+6.0                                                #mdttolerance#   %maximum allowed deviation of P picks from median [s]                                                
+1.0                                                #wdttolerance#   %maximum allowed deviation from Wadati-diagram                                                       
+5.0                                                #jackfactor#     %pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor

makePyLoT.py

@@ -158,24 +158,29 @@ def buildPyLoT(verbosity=None):
 
 
 def installPyLoT(verbosity=None):
-    files_to_copy = {'autoPyLoT_local.in':['~', '.pylot'],
+    files_to_copy = {'pylot_local.in': ['~', '.pylot'],
-                     'autoPyLoT_regional.in':['~', '.pylot'],
+                     'pylot_regional.in': ['~', '.pylot'],
-                     'filter.in':['~', '.pylot']}
+                     'pylot_global.in': ['~', '.pylot']}
     if verbosity > 0:
-        print ('starting installation of PyLoT ...')
+        print('starting installation of PyLoT ...')
     if verbosity > 1:
-        print ('copying input files into destination folder ...')
+        print('copying input files into destination folder ...')
     ans = input('please specify scope of interest '
-                '([0]=local, 1=regional) :') or 0
+                '([0]=local, 1=regional, 2=global) :') or 0
     if not isinstance(ans, int):
         ans = int(ans)
-    ans = 'local' if ans is 0 else 'regional'
+    if ans == 0:
+        ans = 'local'
+    elif ans == 1:
+        ans = 'regional'
+    elif ans == 2:
+        ans = 'global'
     link_dest = []
     for file, destination in files_to_copy.items():
         link_file = ans in file
         if link_file:
             link_dest = copy.deepcopy(destination)
-            link_dest.append('autoPyLoT.in')
+            link_dest.append('pylot.in')
             link_dest = os.path.join(*link_dest)
         destination.append(file)
         destination = os.path.join(*destination)
@@ -183,7 +188,7 @@ def installPyLoT(verbosity=None):
         assert not os.path.isabs(srcfile), 'source files seem to be ' \
                                            'corrupted ...'
         if verbosity > 1:
-            print ('copying file {file} to folder {dest}'.format(file=file, dest=destination))
+            print('copying file {file} to folder {dest}'.format(file=file, dest=destination))
         shutil.copyfile(srcfile, destination)
         if link_file:
             if verbosity:
@@ -191,8 +196,6 @@ def installPyLoT(verbosity=None):
             os.symlink(destination, link_dest)
 
 
-
-
 def cleanUp(verbosity=None):
     if verbosity >= 1:
         print('cleaning up build files...')

pylot/core/analysis/magnitude.py

@@ -6,27 +6,27 @@ Revised/extended summer 2017.
 
 :author: Ludger Küperkoch / MAGS2 EP3 working group
 """
-import os
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy.core.event as ope
 from obspy.geodetics import degrees2kilometers
-from scipy import integrate, signal
-from scipy.optimize import curve_fit
 from pylot.core.pick.utils import getsignalwin, crossings_nonzero_all, \
     select_for_phase
 from pylot.core.util.utils import common_range, fit_curve
+from scipy import integrate, signal
+from scipy.optimize import curve_fit
+
 
 def richter_magnitude_scaling(delta):
-    distance = np.array([0, 10, 20, 25, 30, 35,40, 45, 50, 60, 70, 75, 85, 90, 100, 110,
+    distance = np.array([0, 10, 20, 25, 30, 35, 40, 45, 50, 60, 70, 75, 85, 90, 100, 110,
                          120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 230, 240, 250,
                          260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380,
                          390, 400, 430, 470, 510, 560, 600, 700, 800, 900, 1000])
-    richter_scaling = np.array([1.4, 1.5, 1.7, 1.9, 2.1, 2.3, 2.4, 2.5, 2.6, 2.8, 2.8, 2.9, 
+    richter_scaling = np.array([1.4, 1.5, 1.7, 1.9, 2.1, 2.3, 2.4, 2.5, 2.6, 2.8, 2.8, 2.9,
-                     2.9, 3.0, 3.1, 3.1, 3.2, 3.2, 3.3, 3.3, 3.4, 3.4, 3.5, 3.5, 
+                                2.9, 3.0, 3.1, 3.1, 3.2, 3.2, 3.3, 3.3, 3.4, 3.4, 3.5, 3.5,
-                     3.6, 3.7, 3.7, 3.8, 3.8, 3.9, 3.9, 4.0, 4.0, 4.1, 4.2, 4.2,
+                                3.6, 3.7, 3.7, 3.8, 3.8, 3.9, 3.9, 4.0, 4.0, 4.1, 4.2, 4.2,
-                     4.2, 4.2, 4.3, 4.3, 4.3, 4.4, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 
+                                4.2, 4.2, 4.3, 4.3, 4.3, 4.4, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9,
-                     5.1, 5.2, 5.4, 5.5, 5.7])
+                                5.1, 5.2, 5.4, 5.5, 5.7])
     # prepare spline interpolation to calculate return value
     func, params = fit_curve(distance, richter_scaling)
     return func(delta, params)
@@ -47,7 +47,7 @@ class Magnitude(object):
 
     def __str__(self):
         print(
-        'number of stations used: {0}\n'.format(len(self.magnitudes.values())))
+            'number of stations used: {0}\n'.format(len(self.magnitudes.values())))
         print('\tstation\tmagnitude')
         for s, m in self.magnitudes.items(): print('\t{0}\t{1}'.format(s, m))
 
@@ -126,8 +126,8 @@ class Magnitude(object):
                 # scaling necessary
                 print("Scaling network magnitude ...")
                 mag = ope.Magnitude(
-                    mag=np.median([M.mag for M in self.magnitudes.values()]) *\
+                    mag=np.median([M.mag for M in self.magnitudes.values()]) * \
-                                   magscaling[0] + magscaling[1],
+                        magscaling[0] + magscaling[1],
                     magnitude_type=self.type,
                     origin_id=self.origin_id,
                     station_count=len(self.magnitudes),
@@ -192,6 +192,14 @@ class LocalMagnitude(Magnitude):
 
     def peak_to_peak(self, st, t0):
 
+        try:
+            iplot = int(self.plot_flag)
+        except:
+            if self.plot_flag == True or self.plot_flag == 'True':
+                iplot = 2
+            else:
+                iplot = 0
+
         # simulate Wood-Anderson response
         st.simulate(paz_remove=None, paz_simulate=self._paz)
 
@@ -215,7 +223,7 @@ class LocalMagnitude(Magnitude):
         th = np.arange(0, len(sqH) * dt, dt)
         # get maximum peak within pick window
         iwin = getsignalwin(th, t0 - stime, self.calc_win)
-        ii = min([iwin[len(iwin)-1], len(th)])
+        ii = min([iwin[len(iwin) - 1], len(th)])
         iwin = iwin[0:ii]
         wapp = np.max(sqH[iwin])
         if self.verbose:
@@ -224,7 +232,7 @@ class LocalMagnitude(Magnitude):
 
         # check for plot flag (for debugging only)
         fig = None
-        if self.plot_flag > 1:
+        if iplot > 1:
             st.plot()
             fig = plt.figure()
             ax = fig.add_subplot(111)
@@ -250,8 +258,8 @@ class LocalMagnitude(Magnitude):
             if not wf:
                 if self.verbose:
                     print(
-                    'WARNING: no waveform data found for station {0}'.format(
+                        'WARNING: no waveform data found for station {0}'.format(
-                        station))
+                            station))
                 continue
             delta = degrees2kilometers(a.distance)
             onset = pick.time
@@ -270,13 +278,14 @@ class LocalMagnitude(Magnitude):
             if str(self.wascaling) == '[0.0, 0.0, 0.0]':
                 print("Calculating original Richter magnitude ...")
                 magnitude = ope.StationMagnitude(mag=np.log10(a0) \
-                            + richter_magnitude_scaling(delta))
+                                                     + richter_magnitude_scaling(delta))
             else:
                 print("Calculating scaled local magnitude ...")
-                a0 = a0 * 1e03 # mm to nm (see Havskov & Ottemöller, 2010)
+                a0 = a0 * 1e03  # mm to nm (see Havskov & Ottemöller, 2010)
                 magnitude = ope.StationMagnitude(mag=np.log10(a0) \
-                            + self.wascaling[0] * np.log10(delta) + self.wascaling[1] 
+                                                     + self.wascaling[0] * np.log10(delta) + self.wascaling[1]
-                            * delta + self.wascaling[2])
+                                                                                             * delta + self.wascaling[
+                                                         2])
             magnitude.origin_id = self.origin_id
             magnitude.waveform_id = pick.waveform_id
             magnitude.amplitude_id = amplitude.resource_id
@@ -397,8 +406,8 @@ def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):
 
     if verbosity:
         print(
-        "calcMoMw: Calculating seismic moment Mo and moment magnitude Mw for station {0} ...".format(
+            "calcMoMw: Calculating seismic moment Mo and moment magnitude Mw for station {0} ...".format(
-            tr.stats.station))
+                tr.stats.station))
 
     # additional common parameters for calculating Mo
     rP = 2 / np.sqrt(
@@ -412,8 +421,8 @@ def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):
 
     if verbosity:
         print(
-        "calcMoMw: Calculated seismic moment Mo = {0} Nm => Mw = {1:3.1f} ".format(
+            "calcMoMw: Calculated seismic moment Mo = {0} Nm => Mw = {1:3.1f} ".format(
-            Mo, Mw))
+                Mo, Mw))
 
     return Mo, Mw
 
@@ -452,7 +461,15 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
     :type:  integer
     '''
     if verbosity:
-        print ("Calculating source spectrum for station %s ...." % wfstream[0].stats.station)
+        print("Calculating source spectrum for station %s ...." % wfstream[0].stats.station)
+
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+            iplot = 2
+        else:
+            iplot = 0
 
     # get Q value
     Q, A = qp
@@ -509,9 +526,9 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
     zc = crossings_nonzero_all(wfzc)
     if np.size(zc) == 0 or len(zc) <= 3:
         if verbosity:
-            print ("calcsourcespec: Something is wrong with the waveform, "
+            print("calcsourcespec: Something is wrong with the waveform, "
-                   "no zero crossings derived!\n")
+                  "no zero crossings derived!\n")
-            print ("No calculation of source spectrum possible!")
+            print("No calculation of source spectrum possible!")
         plotflag = 0
     else:
         plotflag = 1
@@ -558,22 +575,22 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
         [optspecfit, _] = curve_fit(synthsourcespec, F, YYcor, [w0in, Fcin])
         w0 = optspecfit[0]
         fc = optspecfit[1]
-        #w01 = optspecfit[0]
+        # w01 = optspecfit[0]
-        #fc1 = optspecfit[1]
+        # fc1 = optspecfit[1]
         if verbosity:
-            print ("calcsourcespec: Determined w0-value: %e m/Hz, \n"
+            print("calcsourcespec: Determined w0-value: %e m/Hz, \n"
-                   "calcsourcespec: Determined corner frequency: %f Hz" % (w0, fc))
+                  "calcsourcespec: Determined corner frequency: %f Hz" % (w0, fc))
 
-        # use of conventional fitting
+            # use of conventional fitting
-        # [w02, fc2] = fitSourceModel(F, YYcor, Fcin, iplot, verbosity)
+            # [w02, fc2] = fitSourceModel(F, YYcor, Fcin, iplot, verbosity)
 
-        # get w0 and fc as median of both
+            # get w0 and fc as median of both
-        # source spectrum fits
+            # source spectrum fits
-        #w0 = np.median([w01, w02])
+            # w0 = np.median([w01, w02])
-        #fc = np.median([fc1, fc2])
+            # fc = np.median([fc1, fc2])
-        #if verbosity:
+            # if verbosity:
-        #    print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
+            #    print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
-        #    w0, fc))
+            #    w0, fc))
 
     if iplot > 1:
         f1 = plt.figure()
@@ -600,9 +617,9 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
             p3, = plt.loglog(F, YYcor, 'r')
             p4, = plt.loglog(F, fit, 'g')
             plt.loglog([fc, fc], [w0 / 100, w0], 'g')
-            plt.legend([p1, p2, p3, p4], ['Raw Spectrum', \
+            plt.legend([p1, p2, p3, p4], ['Raw Spectrum',
-                                          'Used Raw Spectrum', \
+                                          'Used Raw Spectrum',
-                                          'Q-Corrected Spectrum', \
+                                          'Q-Corrected Spectrum',
                                           'Fit to Spectrum'])
             plt.title('Source Spectrum from P Pulse, w0=%e m/Hz, fc=%6.2f Hz' \
                       % (w0, fc))
@@ -650,6 +667,14 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
     :type:   float
     '''
 
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+            iplot = 2
+        else:
+            iplot = 0
+
     w0 = []
     stdw0 = []
     fc = []
@@ -659,9 +684,9 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
     # left side of initial corner frequency
     fcstopl = max(f[0], fc0 - max(1, fc0 / 2))
     il = np.where(f <= fcstopl)
-    il = il[0][np.size(il) - 1] 
+    il = il[0][np.size(il) - 1]
     # right side of initial corner frequency
-    fcstopr = min(fc0 + (fc0 / 2), f[len(f) - 1]) 
+    fcstopr = min(fc0 + (fc0 / 2), f[len(f) - 1])
     ir = np.where(f >= fcstopr)
     # check, if fcstopr is available
     if np.size(ir) == 0:
@@ -672,16 +697,16 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
 
     # vary corner frequency around initial point
     print("fitSourceModel: Varying corner frequency "
-           "around initial corner frequency ...")
+          "around initial corner frequency ...")
     # check difference of il and ir in order to
     # keep calculation time acceptable
     idiff = ir - il
     if idiff > 10000:
-       increment = 100
+        increment = 100
     elif idiff <= 20:
-       increment = 1
+        increment = 1
     else:
-       increment = 10 
+        increment = 10
 
     for i in range(il, ir, increment):
         FC = f[i]
@@ -707,10 +732,10 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
         w0 = max(S)
     if verbosity:
         print(
-        "fitSourceModel: best fc: {0} Hz, best w0: {1} m/Hz".format(fc, w0))
+            "fitSourceModel: best fc: {0} Hz, best w0: {1} m/Hz".format(fc, w0))
 
     if iplot > 1:
-        plt.figure()#iplot)
+        plt.figure()  # iplot)
         plt.loglog(f, S, 'k')
         plt.loglog([f[0], fc], [w0, w0], 'g')
         plt.loglog([fc, fc], [w0 / 100, w0], 'g')
@@ -719,7 +744,7 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
         plt.xlabel('Frequency [Hz]')
         plt.ylabel('Amplitude [m/Hz]')
         plt.grid()
-        plt.figure()#iplot + 1)
+        plt.figure()  # iplot + 1)
         plt.subplot(311)
         plt.plot(f[il:ir], STD, '*')
         plt.title('Common Standard Deviations')

pylot/core/analysis/magnitude.py.orig

@@ -1,242 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""
-Created August/September 2015.
-
-:author: Ludger Küperkoch / MAGS2 EP3 working group
-"""
-
-import matplotlib.pyplot as plt
-import numpy as np
-from obspy.core import Stream
-from pylot.core.pick.utils import getsignalwin
-from scipy.optimize import curve_fit
-
-class Magnitude(object):
-    '''
-    Superclass for calculating Wood-Anderson peak-to-peak
-    amplitudes, local magnitudes and moment magnitudes.
-    '''
-
-    def __init__(self, wfstream, To, pwin, iplot):
-        '''
-        :param: wfstream
-        :type: `~obspy.core.stream.Stream
-
-        :param: To, onset time, P- or S phase
-        :type:  float
-
-        :param: pwin, pick window [To To+pwin] to get maximum
-                peak-to-peak amplitude (WApp) or to calculate
-                source spectrum (DCfc)
-        :type:  float
-
-        :param: iplot, no. of figure window for plotting interims results
-        :type: integer
-
-        '''
-
-        assert isinstance(wfstream, Stream), "%s is not a stream object" % str(wfstream)
-
-        self.setwfstream(wfstream)
-        self.setTo(To)
-        self.setpwin(pwin)
-        self.setiplot(iplot)
-        self.calcwapp()
-        self.calcsourcespec()
-
-
-    def getwfstream(self):
-        return self.wfstream
-
-    def setwfstream(self, wfstream):
-        self.wfstream = wfstream
-
-    def getTo(self):
-        return self.To
-
-    def setTo(self, To):
-        self.To = To
-
-    def getpwin(self):
-        return self.pwin
-
-    def setpwin(self, pwin):
-        self.pwin = pwin
-
-    def getiplot(self):
-        return self.iplot
-
-    def setiplot(self, iplot):
-        self.iplot = iplot
-
-    def getwapp(self):
-        return self.wapp
-
-    def getw0(self):
-        return self.w0
-
-    def getfc(self):
-        return self.fc
-
-    def calcwapp(self):
-        self.wapp = None
-
-    def calcsourcespec(self):
-        self.sourcespek = None
-
-class WApp(Magnitude):
-    '''
-    Method to derive peak-to-peak amplitude as seen on a Wood-Anderson-
-    seismograph. Has to be derived from instrument corrected traces!
-    '''
-
-    def calcwapp(self):
-        print ("Getting Wood-Anderson peak-to-peak amplitude ...")
-        print ("Simulating Wood-Anderson seismograph ...")
-
-        self.wapp = None
-        stream = self.getwfstream()
-
-        # poles, zeros and sensitivity of WA seismograph
-        # (see Uhrhammer & Collins, 1990, BSSA, pp. 702-716)
-        paz_wa = {
-            'poles': [5.6089 - 5.4978j, -5.6089 - 5.4978j],
-            'zeros': [0j, 0j],
-            'gain': 2080,
-            'sensitivity': 1}
-
-        stream.simulate(paz_remove=None, paz_simulate=paz_wa)
-
-        trH1 = stream[0].data
-        trH2 = stream[1].data
-        ilen = min([len(trH1), len(trH2)])
-        # get RMS of both horizontal components
-        sqH = np.sqrt(np.power(trH1[0:ilen], 2) + np.power(trH2[0:ilen], 2))
-        # get time array
-        th = np.arange(0, len(sqH) * stream[0].stats.delta, stream[0].stats.delta)
-        # get maximum peak within pick window
-        iwin = getsignalwin(th, self.getTo(), self.getpwin())
-        self.wapp = np.max(sqH[iwin])
-        print ("Determined Wood-Anderson peak-to-peak amplitude: %f mm") % self.wapp
-
-        if self.getiplot() > 1:
-            stream.plot()
-            f = plt.figure(2)
-            plt.plot(th, sqH)
-            plt.plot(th[iwin], sqH[iwin], 'g')
-            plt.plot([self.getTo(), self.getTo()], [0, max(sqH)], 'r', linewidth=2)
-            plt.title('Station %s, RMS Horizontal Traces, WA-peak-to-peak=%4.1f mm' \
-                      % (stream[0].stats.station, self.wapp))
-            plt.xlabel('Time [s]')
-            plt.ylabel('Displacement [mm]')
-            plt.show()
-            raw_input()
-            plt.close(f)
-
-
-class DCfc(Magnitude):
-    '''
-    Method to calculate the source spectrum and to derive from that the plateau
-    (so-called DC-value) and the corner frequency assuming Aki's omega-square
-    source model. Has to be derived from instrument corrected displacement traces!
-    '''
-
-    def calcsourcespec(self):
-        print ("Calculating source spectrum ....")
-
-        self.w0 = None # DC-value
-        self.fc = None # corner frequency
-
-        stream = self.getwfstream()
-        tr = stream[0]
-
-        # get time array
-        t = np.arange(0, len(tr) * tr.stats.delta, tr.stats.delta)
-        iwin = getsignalwin(t, self.getTo(), self.getpwin())
-        xdat = tr.data[iwin]
-
-        # fft
-        fny = tr.stats.sampling_rate / 2
-        l = len(xdat) / tr.stats.sampling_rate
-        n = tr.stats.sampling_rate * l # number of fft bins after Bath
-        # find next power of 2 of data length
-        m = pow(2, np.ceil(np.log(len(xdat)) / np.log(2)))
-        N = int(np.power(m, 2))
-        y = tr.stats.delta * np.fft.fft(xdat, N)
-        Y = abs(y[: N/2])
-        L = (N - 1) / tr.stats.sampling_rate
-        f = np.arange(0, fny, 1/L)
-
-        # remove zero-frequency and frequencies above
-        # corner frequency of seismometer (assumed
-        # to be 100 Hz)
-        fi = np.where((f >= 1) & (f < 100))
-        F = f[fi]
-        YY = Y[fi]
-        # get plateau (DC value) and corner frequency
-        # initial guess of plateau
-        DCin = np.mean(YY[0:100])
-        # initial guess of corner frequency
-        # where spectral level reached 50% of flat level
-        iin = np.where(YY >= 0.5 * DCin)
-        Fcin = F[iin[0][np.size(iin) - 1]]
-        fit = synthsourcespec(F, DCin, Fcin)
-        [optspecfit, pcov] = curve_fit(synthsourcespec, F, YY.real, [DCin, Fcin])
-        self.w0 = optspecfit[0]
-        self.fc = optspecfit[1]
-        print ("DCfc: Determined DC-value: %e m/Hz, \n" \
-               "Determined corner frequency: %f Hz" % (self.w0, self.fc)) 
-        
-        
-        #if self.getiplot() > 1:
-        iplot=2
-        if iplot > 1:
-            print ("DCfc: Determined DC-value: %e m/Hz, \n"
-                   "Determined corner frequency: %f Hz" % (self.w0, self.fc))
-
-
-        if self.getiplot() > 1:
-            f1 = plt.figure()
-            plt.subplot(2,1,1)
-            # show displacement in mm
-            plt.plot(t, np.multiply(tr, 1000), 'k')
-            plt.plot(t[iwin], np.multiply(xdat, 1000), 'g')
-            plt.title('Seismogram and P pulse, station %s' % tr.stats.station)
-            plt.xlabel('Time since %s' % tr.stats.starttime)
-            plt.ylabel('Displacement [mm]')
-
-            plt.subplot(2,1,2)
-            plt.loglog(f, Y.real, 'k')
-            plt.loglog(F, YY.real)
-            plt.loglog(F, fit, 'g')
-            plt.title('Source Spectrum from P Pulse, DC=%e m/Hz, fc=%4.1f Hz' \
-                       % (self.w0, self.fc))
-            plt.xlabel('Frequency [Hz]')
-            plt.ylabel('Amplitude [m/Hz]')
-            plt.grid()
-            plt.show()
-            raw_input()
-            plt.close(f1)
-
-
-def synthsourcespec(f, omega0, fcorner):
-    '''
-    Calculates synthetic source spectrum from given plateau and corner
-    frequency assuming Akis omega-square model.
-
-    :param: f, frequencies
-    :type:  array
-
-    :param: omega0, DC-value (plateau) of source spectrum
-    :type:  float
-
-    :param: fcorner, corner frequency of source spectrum
-    :type:  float
-    '''
-
-    #ssp = omega0 / (pow(2, (1 + f / fcorner)))
-    ssp = omega0 / (1 + pow(2, (f / fcorner)))
-
-    return ssp
-

pylot/core/io/data.py

@@ -3,15 +3,18 @@
 
 import copy
 import os
+
 from obspy import read_events
 from obspy.core import read, Stream, UTCDateTime
-from obspy.io.sac import SacIOError
 from obspy.core.event import Event as ObsPyEvent
+from obspy.io.sac import SacIOError
 from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
     picksdict_from_pilot, merge_picks
 from pylot.core.util.errors import FormatError, OverwriteError
-from pylot.core.util.utils import fnConstructor, full_range
 from pylot.core.util.event import Event
+from pylot.core.util.utils import fnConstructor, full_range
+import pylot.core.loc.velest as velest
+
 
 class Data(object):
     """
@@ -39,7 +42,7 @@ class Data(object):
         elif isinstance(evtdata, dict):
             evt = readPILOTEvent(**evtdata)
             evtdata = evt
-        elif isinstance(evtdata, basestring):
+        elif isinstance(evtdata, str):
             try:
                 cat = read_events(evtdata)
                 if len(cat) is not 1:
@@ -75,7 +78,7 @@ class Data(object):
     def __add__(self, other):
         assert isinstance(other, Data), "operands must be of same type 'Data'"
         rs_id = self.get_evt_data().get('resource_id')
-        rs_id_other = other.get_evt_data().get('resource_id')        
+        rs_id_other = other.get_evt_data().get('resource_id')
         if other.isNew() and not self.isNew():
             picks_to_add = other.get_evt_data().picks
             old_picks = self.get_evt_data().picks
@@ -98,7 +101,7 @@ class Data(object):
     def getPicksStr(self):
         picks_str = ''
         for pick in self.get_evt_data().picks:
-            picks_str += str(PyLoT) + '\n'
+            picks_str += str(pick) + '\n'
         return picks_str
 
     def getParent(self):
@@ -147,89 +150,158 @@ class Data(object):
         # handle forbidden filenames especially on windows systems
         return fnConstructor(str(ID))
 
-    def exportEvent(self, fnout, fnext='.xml', fcheck='auto'):
+    def checkEvent(self, event, fcheck, forceOverwrite=False):
+        if 'origin' in fcheck:
+            self.replaceOrigin(event, forceOverwrite)
+        if 'magnitude' in fcheck:
+            self.replaceMagnitude(event, forceOverwrite)
+        if 'auto' in fcheck:
+            self.replacePicks(event, 'auto')
+        if 'manual' in fcheck:
+            self.replacePicks(event, 'manual')
+
+    def replaceOrigin(self, event, forceOverwrite=False):
+        if self.get_evt_data().origins or forceOverwrite:
+            if event.origins:
+                print("Found origin, replace it by new origin.")
+            event.origins = self.get_evt_data().origins
+
+    def replaceMagnitude(self, event, forceOverwrite=False):
+        if self.get_evt_data().magnitudes or forceOverwrite:
+            if event.magnitudes:
+                print("Found magnitude, replace it by new magnitude")
+            event.magnitudes = self.get_evt_data().magnitudes
+
+    def replacePicks(self, event, picktype):
+        checkflag = 0
+        picks = event.picks
+        # remove existing picks
+        for j, pick in reversed(list(enumerate(picks))):
+            if picktype in str(pick.method_id.id):
+                picks.pop(j)
+                checkflag = 1
+        if checkflag:
+            print("Found %s pick(s), remove them and append new picks to catalog." % picktype)
+
+        # append new picks
+        for pick in self.get_evt_data().picks:
+            if picktype in str(pick.method_id.id):
+                picks.append(pick)
+
+    def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
 
         """
-
+        :param fnout: basename of file
-        :param fnout:
+        :param fnext: file extension
-        :param fnext:
+        :param fcheck: check and delete existing information
-        :param fcheck:
+        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
-        :raise KeyError:
         """
         from pylot.core.util.defaults import OUTPUTFORMATS
 
+        if not type(fcheck) == list:
+            fcheck = [fcheck]
+
         try:
             evtformat = OUTPUTFORMATS[fnext]
         except KeyError as e:
             errmsg = '{0}; selected file extension {1} not ' \
                      'supported'.format(e, fnext)
             raise FormatError(errmsg)
-   
+
         # check for already existing xml-file
         if fnext == '.xml':
             if os.path.isfile(fnout + fnext):
                 print("xml-file already exists! Check content ...")
-                cat_old = read_events(fnout + fnext)
+                cat = read_events(fnout + fnext)
-                checkflag = 0
+                if len(cat) > 1:
-                for j in range(len(cat_old.events[0].picks)):
+                    raise IOError('Ambigious event information in file {}'.format(fnout + fnext))
-                   if cat_old.events[0].picks[j].method_id.id.split('/')[1] == fcheck:
+                if len(cat) < 1:
-                      print("Found %s pick(s), append to new catalog." % fcheck)
+                    raise IOError('No event information in file {}'.format(fnout + fnext))
-                      checkflag = 1
+                event = cat[0]
-                      break
+                if not event.resource_id == self.get_evt_data().resource_id:
-                if checkflag == 1:
+                    raise IOError("Missmatching event resource id's: {} and {}".format(event.resource_id,
-                    self.get_evt_data().write(fnout + fnext, format=evtformat)
+                                                                                       self.get_evt_data().resource_id))
-                    cat_new = read_events(fnout + fnext)
+                self.checkEvent(event, fcheck)
-                    cat_new.append(cat_old.events[0])
+                self.setEvtData(event)
-                    cat_new.write(fnout + fnext, format=evtformat)
+            self.get_evt_data().write(fnout + fnext, format=evtformat)
-                else:
+        # try exporting event  
-                    self.get_evt_data().write(fnout + fnext, format=evtformat)
-            else:
-                self.get_evt_data().write(fnout + fnext, format=evtformat)
-
-        # try exporting event via ObsPy
         else:
+            evtdata_org = self.get_evt_data()
+            picks = evtdata_org.picks
+            eventpath = evtdata_org.path
+            picks_copy = copy.deepcopy(picks)
+            evtdata_copy = Event(eventpath)
+            evtdata_copy.picks = picks_copy
+
             # check for stations picked automatically as well as manually
             # Prefer manual picks!
-            evtdata_copy = self.get_evt_data().copy()
+            for i in range(len(picks)):
-            evtdata_org = self.get_evt_data()
+                if picks[i].method_id == 'manual':
-            for i in range(len(evtdata_org.picks)):
+                    mstation = picks[i].waveform_id.station_code
-                if evtdata_org.picks[i].method_id == 'manual':
+                    mstation_ext = mstation + '_'
-                   mstation = evtdata_org.picks[i].waveform_id.station_code
+                    for k in range(len(picks_copy)):
-                   mstation_ext = mstation + '_'
+                        if ((picks_copy[k].waveform_id.station_code == mstation) or
-                   for k in range(len(evtdata_copy.picks)):
+                                (picks_copy[k].waveform_id.station_code == mstation_ext)) and \
-                       if evtdata_copy.picks[k].waveform_id.station_code == mstation  or \
+                                (picks_copy[k].method_id == 'auto'):
-                          evtdata_copy.picks[k].waveform_id.station_code == mstation_ext and \
+                            del picks_copy[k]
-                          evtdata_copy.picks[k].method_id == 'auto':
+                            break
-                          del evtdata_copy.picks[k]
+            lendiff = len(picks) - len(picks_copy)
-                          break
-            lendiff = len(evtdata_org.picks) - len(evtdata_copy.picks)
             if lendiff is not 0:
-               print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
+                print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
+
+            if upperErrors:
+                # check for pick uncertainties exceeding adjusted upper errors
+                # Picks with larger uncertainties will not be saved in output file!
+                for j in range(len(picks)):
+                    for i in range(len(picks_copy)):
+                        if picks_copy[i].phase_hint[0] == 'P':
+                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
+                                    (picks_copy[i].time_errors['uncertainty'] == None):
+                                print("Uncertainty exceeds or equal adjusted upper time error!")
+                                print("Adjusted uncertainty: {}".format(upperErrors[0]))
+                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
+                                print("{1} P-Pick of station {0} will not be saved in outputfile".format(
+                                    picks_copy[i].waveform_id.station_code,
+                                    picks_copy[i].method_id))
+                                print("#")
+                                del picks_copy[i]
+                                break
+                        if picks_copy[i].phase_hint[0] == 'S':
+                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
+                                    (picks_copy[i].time_errors['uncertainty'] == None):
+                                print("Uncertainty exceeds or equal adjusted upper time error!")
+                                print("Adjusted uncertainty: {}".format(upperErrors[1]))
+                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
+                                print("{1} S-Pick of station {0} will not be saved in outputfile".format(
+                                    picks_copy[i].waveform_id.station_code,
+                                    picks_copy[i].method_id))
+                                print("#")
+                                del picks_copy[i]
+                                break
 
             if fnext == '.obs':
-               try:
+                try:
-                   evtdata_copy.write(fnout + fnext, format=evtformat)
+                    evtdata_copy.write(fnout + fnext, format=evtformat)
-                   # write header afterwards
+                    # write header afterwards
-                   evid = str(evtdata_org.resource_id).split('/')[1]
+                    evid = str(evtdata_org.resource_id).split('/')[1]
-                   header = '# EQEVENT:  Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' % evid
+                    header = '# EQEVENT:  Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' % evid
-                   nllocfile = open(fnout + fnext)
+                    nllocfile = open(fnout + fnext)
-                   l = nllocfile.readlines()
+                    l = nllocfile.readlines()
-                   nllocfile.close()
+                    nllocfile.close()
-                   l.insert(0, header)
+                    l.insert(0, header)
-                   nllocfile = open(fnout + fnext, 'w')
+                    nllocfile = open(fnout + fnext, 'w')
-                   nllocfile.write("".join(l))
+                    nllocfile.write("".join(l))
-                   nllocfile.close()
+                    nllocfile.close()
-               except KeyError as e:
+                except KeyError as e:
-                   raise KeyError('''{0} export format
+                    raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.cnv':
-               try:
+                try:
-                   evtdata_org.write(fnout + fnext, format=evtformat)
+                    velest.export(picks_copy, fnout + fnext, eventinfo=self.get_evt_data())
-               except KeyError as e:
+                except KeyError as e:
-                   raise KeyError('''{0} export format
+                    raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
 
-
     def getComp(self):
         """
 
@@ -294,7 +366,7 @@ class Data(object):
                 except Exception as e:
                     warnmsg += '{0}\n{1}\n'.format(fname, e)
             except SacIOError as se:
-                    warnmsg += '{0}\n{1}\n'.format(fname, se)
+                warnmsg += '{0}\n{1}\n'.format(fname, se)
         if warnmsg:
             warnmsg = 'WARNING: unable to read\n' + warnmsg
             print(warnmsg)
@@ -359,21 +431,20 @@ class Data(object):
             :raise OverwriteError: raises an OverwriteError if the picks list is
              not empty. The GUI will then ask for a decision.
             """
-            #firstonset = find_firstonset(picks)
+            # firstonset = find_firstonset(picks)
             # check for automatic picks
             print("Writing phases to ObsPy-quakeml file")
             for key in picks:
                 if picks[key]['P']['picker'] == 'auto':
-                   print("Existing picks will be overwritten!")
+                    print("Existing picks will be overwritten!")
-                   picks = picks_from_picksdict(picks)
+                    picks = picks_from_picksdict(picks)
-                   break
+                    break
                 else:
-                   if self.get_evt_data().picks:
+                    if self.get_evt_data().picks:
-                       raise OverwriteError('Existing picks would be overwritten!')
+                        raise OverwriteError('Existing picks would be overwritten!')
-                       break
+                    else:
-                   else:
+                        picks = picks_from_picksdict(picks)
-                       picks = picks_from_picksdict(picks)
+                        break
-                       break
             self.get_evt_data().picks = picks
             # if 'smi:local' in self.getID() and firstonset:
             #     fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
@@ -381,7 +452,6 @@ class Data(object):
             #     ID.convertIDToQuakeMLURI(authority_id=authority_id)
             #     self.get_evt_data().resource_id = ID
 
-
         def applyEvent(event):
             """
             takes an `obspy.core.event.Event` object and applies all new
@@ -393,13 +463,13 @@ class Data(object):
             else:
                 # prevent overwriting original pick information
                 event_old = self.get_evt_data()
-                print(event_old.resource_id, event.resource_id)
                 if not event_old.resource_id == event.resource_id:
                     print("WARNING: Missmatch in event resource id's: {} and {}".format(
                         event_old.resource_id,
                         event.resource_id))
-                picks = copy.deepcopy(event_old.picks)
+                else:
-                event = merge_picks(event, picks)
+                    picks = copy.deepcopy(event_old.picks)
+                    event = merge_picks(event, picks)
                 # apply event information from location
                 event_old.update(event)
 
@@ -408,7 +478,6 @@ class Data(object):
 
         applydata[typ](data)
         self._new = False
-        
 
 
 class GenericDataStructure(object):

pylot/core/io/default_parameters.py

@@ -3,293 +3,401 @@
 
 defaults = {'rootpath': {'type': str,
                          'tooltip': 'project path',
-                         'value': ''},
+                         'value': '',
-            
+                         'namestring': 'Root path'},
+
             'datapath': {'type': str,
                          'tooltip': 'data path',
-                         'value': ''},
+                         'value': '',
-            
+                         'namestring': 'Data path'},
+
             'database': {'type': str,
                          'tooltip': 'name of data base',
-                         'value': ''},
+                         'value': '',
-            
+                         'namestring': 'Database path'},
+
             'eventID': {'type': str,
                         'tooltip': 'event ID for single event processing (* for all events found in database)',
-                        'value': ''},
+                        'value': '',
-            
+                        'namestring': 'Event ID'},
+
             'extent': {'type': str,
                        'tooltip': 'extent of array ("local", "regional" or "global")',
-                       'value': 'local'},
+                       'value': 'local',
-            
+                       'namestring': 'Array extent'},
+
             'invdir': {'type': str,
                        'tooltip': 'full path to  inventory or dataless-seed file',
-                       'value': ''},
+                       'value': '',
-            
+                       'namestring': 'Inversion dir'},
+
             'datastructure': {'type': str,
                               'tooltip': 'choose data structure',
-                              'value': 'PILOT'},
+                              'value': 'PILOT',
-            
+                              'namestring': 'Datastructure'},
+
             'apverbose': {'type': bool,
                           'tooltip': "choose 'True' or 'False' for terminal output",
-                          'value':  True},
+                          'value': True,
-            
+                          'namestring': 'App. verbosity'},
+
             'nllocbin': {'type': str,
                          'tooltip': 'path to NLLoc executable',
-                         'value': ''},
+                         'value': '',
-            
+                         'namestring': 'NLLoc bin path'},
+
             'nllocroot': {'type': str,
                           'tooltip': 'root of NLLoc-processing directory',
-                          'value': ''},
+                          'value': '',
-            
+                          'namestring': 'NLLoc root path'},
+
             'phasefile': {'type': str,
                           'tooltip': 'name of autoPyLoT-output phase file for NLLoc',
-                          'value': 'AUTOPHASES.obs'},
+                          'value': 'AUTOPHASES.obs',
-            
+                          'namestring': 'Phase filename'},
+
             'ctrfile': {'type': str,
                         'tooltip': 'name of autoPyLoT-output control file for NLLoc',
-                        'value': 'Insheim_min1d2015_auto.in'},
+                        'value': 'Insheim_min1d2015_auto.in',
-            
+                        'namestring': 'Control filename'},
+
             'ttpatter': {'type': str,
                          'tooltip': 'pattern of NLLoc ttimes from grid',
-                         'value': 'ttime'},
+                         'value': 'ttime',
-            
+                         'namestring': 'Traveltime pattern'},
+
             'outpatter': {'type': str,
                           'tooltip': 'pattern of NLLoc-output file',
-                          'value': 'AUTOLOC_nlloc'},
+                          'value': 'AUTOLOC_nlloc',
-            
+                          'namestring': 'NLLoc output pattern'},
+
             'vp': {'type': float,
                    'tooltip': 'average P-wave velocity',
-                   'value': 3530.},
+                   'value': 3530.,
-            
+                   'namestring': 'P-velocity'},
+
             'rho': {'type': float,
                     'tooltip': 'average rock density [kg/m^3]',
-                    'value': 2500.},
+                    'value': 2500.,
-            
+                    'namestring': 'Density'},
+
             'Qp': {'type': (float, float),
                    'tooltip': 'quality factor for P waves (Qp*f^a); list(Qp, a)',
-                   'value': (300., 0.8)},
+                   'value': (300., 0.8),
-            
+                   'namestring': ('Quality factor', 'Qp1', 'Qp2')},
+
             'pstart': {'type': float,
-                       'tooltip': 'start time [s] for calculating CF for P-picking',
+                       'tooltip': 'start time [s] for calculating CF for P-picking (if TauPy:'
-                       'value': 15.0},
+                                  ' seconds relative to estimated onset)',
-            
+                       'value': 15.0,
+                       'namestring': 'P start'},
+
             'pstop': {'type': float,
-                      'tooltip': 'end time [s] for calculating CF for P-picking',
+                      'tooltip': 'end time [s] for calculating CF for P-picking (if TauPy:'
-                      'value': 60.0},
+                                 ' seconds relative to estimated onset)',
-            
+                      'value': 60.0,
+                      'namestring': 'P stop'},
+
             'sstart': {'type': float,
                        'tooltip': 'start time [s] relative to P-onset for calculating CF for S-picking',
-                       'value': -1.0},
+                       'value': -1.0,
-            
+                       'namestring': 'S start'},
+
             'sstop': {'type': float,
                       'tooltip': 'end time [s] after P-onset for calculating CF for S-picking',
-                      'value': 10.0},
+                      'value': 10.0,
-            
+                      'namestring': 'S stop'},
+
             'bpz1': {'type': (float, float),
                      'tooltip': 'lower/upper corner freq. of first band pass filter Z-comp. [Hz]',
-                     'value': (2, 20)},
+                     'value': (2, 20),
-            
+                     'namestring': ('Z-bandpass 1', 'Lower', 'Upper')},
+
             'bpz2': {'type': (float, float),
                      'tooltip': 'lower/upper corner freq. of second band pass filter Z-comp. [Hz]',
-                     'value': (2, 30)},
+                     'value': (2, 30),
-            
+                     'namestring': ('Z-bandpass 2', 'Lower', 'Upper')},
+
             'bph1': {'type': (float, float),
                      'tooltip': 'lower/upper corner freq. of first band pass filter H-comp. [Hz]',
-                     'value': (2, 15)},
+                     'value': (2, 15),
-            
+                     'namestring': ('H-bandpass 1', 'Lower', 'Upper')},
+
             'bph2': {'type': (float, float),
                      'tooltip': 'lower/upper corner freq. of second band pass filter z-comp. [Hz]',
-                     'value': (2, 20)},
+                     'value': (2, 20),
-            
+                     'namestring': ('H-bandpass 2', 'Lower', 'Upper')},
+
             'algoP': {'type': str,
                       'tooltip': 'choose algorithm for P-onset determination (HOS, ARZ, or AR3)',
-                      'value': 'HOS'},
+                      'value': 'HOS',
-            
+                      'namestring': 'P algorithm'},
+
             'tlta': {'type': float,
                      'tooltip': 'for HOS-/AR-AIC-picker, length of LTA window [s]',
-                     'value': 7.0},
+                     'value': 7.0,
-            
+                     'namestring': 'LTA window'},
+
             'hosorder': {'type': int,
                          'tooltip': 'for HOS-picker, order of Higher Order Statistics',
-                         'value': 4},
+                         'value': 4,
-            
+                         'namestring': 'HOS order'},
+
             'Parorder': {'type': int,
                          'tooltip': 'for AR-picker, order of AR process of Z-component',
-                         'value': 2},
+                         'value': 2,
-            
+                         'namestring': 'AR order P'},
+
             'tdet1z': {'type': float,
                        'tooltip': 'for AR-picker, length of AR determination window [s] for Z-component, 1st pick',
-                       'value': 1.2},
+                       'value': 1.2,
-            
+                       'namestring': 'AR det. window Z 1'},
+
             'tpred1z': {'type': float,
                         'tooltip': 'for AR-picker, length of AR prediction window [s] for Z-component, 1st pick',
-                        'value': 0.4},
+                        'value': 0.4,
-            
+                        'namestring': 'AR pred. window Z 1'},
+
             'tdet2z': {'type': float,
                        'tooltip': 'for AR-picker, length of AR determination window [s] for Z-component, 2nd pick',
-                       'value': 0.6},
+                       'value': 0.6,
-            
+                       'namestring': 'AR det. window Z 2'},
+
             'tpred2z': {'type': float,
                         'tooltip': 'for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick',
-                        'value': 0.2},
+                        'value': 0.2,
-            
+                        'namestring': 'AR pred. window Z 2'},
+
             'addnoise': {'type': float,
                          'tooltip': 'add noise to seismogram for stable AR prediction',
-                         'value': 0.001},
+                         'value': 0.001,
-            
+                         'namestring': 'Add noise'},
+
             'tsnrz': {'type': (float, float, float, float),
                       'tooltip': 'for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]',
-                      'value': (3, 0.1, 0.5, 1.0)},
+                      'value': (3, 0.1, 0.5, 1.0),
-            
+                      'namestring': ('SNR windows P', 'Noise', 'Safety', 'Signal', 'Slope')},
+
             'pickwinP': {'type': float,
                          'tooltip': 'for initial AIC pick, length of P-pick window [s]',
-                         'value': 3.0},
+                         'value': 3.0,
-            
+                         'namestring': 'AIC window P'},
+
             'Precalcwin': {'type': float,
                            'tooltip': 'for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)',
-                           'value': 6.0},
+                           'value': 6.0,
-            
+                           'namestring': 'Recal. window P'},
+
             'aictsmooth': {'type': float,
                            'tooltip': 'for HOS/AR, take average of samples for smoothing of AIC-function [s]',
-                           'value': 0.2},
+                           'value': 0.2,
-            
+                           'namestring': 'AIC smooth P'},
+
             'tsmoothP': {'type': float,
                          'tooltip': 'for HOS/AR, take average of samples for smoothing CF [s]',
-                         'value': 0.1},
+                         'value': 0.1,
-            
+                         'namestring': 'CF smooth P'},
+
             'ausP': {'type': float,
                      'tooltip': 'for HOS/AR, artificial uplift of samples (aus) of CF (P)',
-                     'value': 0.001},
+                     'value': 0.001,
-            
+                     'namestring': 'Artificial uplift P'},
+
             'nfacP': {'type': float,
                       'tooltip': 'for HOS/AR, noise factor for noise level determination (P)',
-                      'value': 1.3},
+                      'value': 1.3,
-            
+                      'namestring': 'Noise factor P'},
+
             'algoS': {'type': str,
                       'tooltip': 'choose algorithm for S-onset determination (ARH or AR3)',
-                      'value': 'ARH'},
+                      'value': 'ARH',
-            
+                      'namestring': 'S algorithm'},
+
             'tdet1h': {'type': float,
                        'tooltip': 'for HOS/AR, length of AR-determination window [s], H-components, 1st pick',
-                       'value': 0.8},
+                       'value': 0.8,
-            
+                       'namestring': 'AR det. window H 1'},
+
             'tpred1h': {'type': float,
                         'tooltip': 'for HOS/AR, length of AR-prediction window [s], H-components, 1st pick',
-                        'value': 0.4},
+                        'value': 0.4,
-            
+                        'namestring': 'AR pred. window H 1'},
+
             'tdet2h': {'type': float,
                        'tooltip': 'for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick',
-                       'value': 0.6},
+                       'value': 0.6,
-            
+                       'namestring': 'AR det. window H 2'},
+
             'tpred2h': {'type': float,
                         'tooltip': 'for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick',
-                        'value': 0.3},
+                        'value': 0.3,
-            
+                        'namestring': 'AR pred. window H 2'},
+
             'Sarorder': {'type': int,
                          'tooltip': 'for AR-picker, order of AR process of H-components',
-                         'value': 4},
+                         'value': 4,
-            
+                         'namestring': 'AR order S'},
+
             'Srecalcwin': {'type': float,
                            'tooltip': 'for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)',
-                           'value': 5.0},
+                           'value': 5.0,
-            
+                           'namestring': 'Recal. window S'},
+
             'pickwinS': {'type': float,
                          'tooltip': 'for initial AIC pick, length of S-pick window [s]',
-                         'value': 3.0},
+                         'value': 3.0,
-            
+                         'namestring': 'AIC window S'},
+
             'tsnrh': {'type': (float, float, float, float),
                       'tooltip': 'for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]',
-                      'value': (2, 0.2, 1.5, 0.5)},
+                      'value': (2, 0.2, 1.5, 0.5),
-            
+                      'namestring': ('SNR windows S', 'Noise', 'Safety', 'Signal', 'Slope')},
+
             'aictsmoothS': {'type': float,
                             'tooltip': 'for AIC-picker, take average of samples for smoothing of AIC-function [s]',
-                            'value': 0.5},
+                            'value': 0.5,
-            
+                            'namestring': 'AIC smooth S'},
+
             'tsmoothS': {'type': float,
                          'tooltip': 'for AR-picker, take average of samples for smoothing CF [s] (S)',
-                         'value': 0.7},
+                         'value': 0.7,
-            
+                         'namestring': 'CF smooth S'},
+
             'ausS': {'type': float,
                      'tooltip': 'for HOS/AR, artificial uplift of samples (aus) of CF (S)',
-                     'value': 0.9},
+                     'value': 0.9,
-            
+                     'namestring': 'Artificial uplift S'},
+
             'nfacS': {'type': float,
                       'tooltip': 'for AR-picker, noise factor for noise level determination (S)',
-                      'value': 1.5},
+                      'value': 1.5,
-            
+                      'namestring': 'Noise factor S'},
+
             'minfmweight': {'type': int,
                             'tooltip': 'minimum required P weight for first-motion determination',
-                            'value': 1},
+                            'value': 1,
-            
+                            'namestring': 'Min. P weight'},
+
             'minFMSNR': {'type': float,
                          'tooltip': 'miniumum required SNR for first-motion determination',
-                         'value': 2.},
+                         'value': 2.,
-            
+                         'namestring': 'Min SNR'},
+
             'fmpickwin': {'type': float,
                           'tooltip': 'pick window around P onset for calculating zero crossings',
-                          'value': 0.2},
+                          'value': 0.2,
-            
+                          'namestring': 'Zero crossings window'},
+
             'timeerrorsP': {'type': (float, float, float, float),
                             'tooltip': 'discrete time errors [s] corresponding to picking weights [0 1 2 3] for P',
-                            'value': (0.01, 0.02, 0.04, 0.08)},
+                            'value': (0.01, 0.02, 0.04, 0.08),
-            
+                            'namestring': ('Time errors P', '0', '1', '2', '3')},
+
             'timeerrorsS': {'type': (float, float, float, float),
                             'tooltip': 'discrete time errors [s] corresponding to picking weights [0 1 2 3] for S',
-                            'value': (0.04, 0.08, 0.16, 0.32)},
+                            'value': (0.04, 0.08, 0.16, 0.32),
-            
+                            'namestring': ('Time errors S', '0', '1', '2', '3')},
+
             'minAICPslope': {'type': float,
                              'tooltip': 'below this slope [counts/s] the initial P pick is rejected',
-                             'value': 0.8},
+                             'value': 0.8,
-            
+                             'namestring': 'Min. slope P'},
+
             'minAICPSNR': {'type': float,
                            'tooltip': 'below this SNR the initial P pick is rejected',
-                           'value': 1.1},
+                           'value': 1.1,
-            
+                           'namestring': 'Min. SNR P'},
+
             'minAICSslope': {'type': float,
                              'tooltip': 'below this slope [counts/s] the initial S pick is rejected',
-                             'value': 1.},
+                             'value': 1.,
-            
+                             'namestring': 'Min. slope S'},
+
             'minAICSSNR': {'type': float,
                            'tooltip': 'below this SNR the initial S pick is rejected',
-                           'value': 1.5},
+                           'value': 1.5,
-            
+                           'namestring': 'Min. SNR S'},
+
             'minsiglength': {'type': float,
                              'tooltip': 'length of signal part for which amplitudes must exceed noiselevel [s]',
-                             'value': 1.},
+                             'value': 1.,
-            
+                             'namestring': 'Min. signal length'},
+
             'noisefactor': {'type': float,
                             'tooltip': 'noiselevel*noisefactor=threshold',
-                            'value': 1.0},
+                            'value': 1.0,
-            
+                            'namestring': 'Noise factor'},
+
             'minpercent': {'type': float,
                            'tooltip': 'required percentage of amplitudes exceeding threshold',
-                           'value': 10.},
+                           'value': 10.,
-            
+                           'namestring': 'Min amplitude [%]'},
+
             'zfac': {'type': float,
                      'tooltip': 'P-amplitude must exceed at least zfac times RMS-S amplitude',
-                     'value': 1.5},
+                     'value': 1.5,
-            
+                     'namestring': 'Z factor'},
+
             'mdttolerance': {'type': float,
                              'tooltip': 'maximum allowed deviation of P picks from median [s]',
-                             'value': 6.0},
+                             'value': 6.0,
-            
+                             'namestring': 'Median tolerance'},
+
             'wdttolerance': {'type': float,
                              'tooltip': 'maximum allowed deviation from Wadati-diagram',
-                             'value': 1.0},
+                             'value': 1.0,
-            
+                             'namestring': 'Wadati tolerance'},
+
+            'jackfactor': {'type': float,
+                             'tooltip': 'pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor',
+                             'value': 5.0,
+                             'namestring': 'Jackknife safety factor'},
+
             'WAscaling': {'type': (float, float, float),
-                         'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] \
+                          'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] \
-                                     If zeros are set, original Richter magnitude is calculated!',
+                          If zeros are set, original Richter magnitude is calculated!',
-                         'value': (0., 0., 0.)},
+                          'value': (0., 0., 0.),
+                          'namestring': ('Wood-Anderson scaling', '', '', '')},
 
             'magscaling': {'type': (float, float),
-                         'tooltip': 'Scaling relation for derived local magnitude [a*Ml+b]. \
+                           'tooltip': 'Scaling relation for derived local magnitude [a*Ml+b]. \
-                                     If zeros are set, no scaling of network magnitude is applied!',
+                           If zeros are set, no scaling of network magnitude is applied!',
-                         'value': (0., 0.)}
+                           'value': (0., 0.),
-}
+                           'namestring': ('Local mag. scaling', '', '')},
 
-settings_main={
+            'minfreq': {'type': (float, float),
-    'dirs':[
+                        'tooltip': 'Lower filter frequency [P, S]',
+                        'value': (1.0, 1.0),
+                        'namestring': ('Lower freq.', 'P', 'S')},
+
+            'maxfreq': {'type': (float, float),
+                        'tooltip': 'Upper filter frequency [P, S]',
+                        'value': (10.0, 10.0),
+                        'namestring': ('Upper freq.', 'P', 'S')},
+
+            'filter_order': {'type': (int, int),
+                             'tooltip': 'filter order [P, S]',
+                             'value': (2, 2),
+                             'namestring': ('Order', 'P', 'S')},
+
+            'filter_type': {'type': (str, str),
+                            'tooltip': 'filter type (bandpass, bandstop, lowpass, highpass) [P, S]',
+                            'value': ('bandpass', 'bandpass'),
+                            'namestring': ('Type', 'P', 'S')},
+
+            'use_taup': {'type': bool,
+                         'tooltip': 'use estimated traveltimes from TauPy for calculating windows for CF',
+                         'value': True,
+                         'namestring': 'Use TauPy'},
+
+            'taup_model': {'type': str,
+                           'tooltip': 'define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
+                           'value': 'iasp91',
+                           'namestring': 'TauPy model'}
+            }
+
+settings_main = {
+    'dirs': [
         'rootpath',
         'datapath',
         'database',
@@ -297,34 +405,41 @@ settings_main={
         'invdir',
         'datastructure',
         'apverbose'],
-    'nlloc':[
+    'nlloc': [
         'nllocbin',
         'nllocroot',
         'phasefile',
         'ctrfile',
         'ttpatter',
         'outpatter'],
-    'smoment':[
+    'smoment': [
         'vp',
         'rho',
         'Qp'],
-    'localmag':[
+    'localmag': [
         'WAscaling',
         'magscaling'],
-    'pick':[
+    'filter': [
+        'minfreq',
+        'maxfreq',
+        'filter_order',
+        'filter_type'],
+    'pick': [
         'extent',
         'pstart',
         'pstop',
         'sstart',
         'sstop',
+        'use_taup',
+        'taup_model',
         'bpz1',
         'bpz2',
         'bph1',
         'bph2']
 }
 
-settings_special_pick={
+settings_special_pick = {
-    'z':[
+    'z': [
         'algoP',
         'tlta',
         'hosorder',
@@ -341,7 +456,7 @@ settings_special_pick={
         'tsmoothP',
         'ausP',
         'nfacP'],
-    'h':[
+    'h': [
         'algoS',
         'tdet1h',
         'tpred1h',
@@ -355,11 +470,11 @@ settings_special_pick={
         'tsmoothS',
         'ausS',
         'nfacS'],
-    'fm':[
+    'fm': [
         'minfmweight',
         'minFMSNR',
         'fmpickwin'],
-    'quality':[
+    'quality': [
         'timeerrorsP',
         'timeerrorsS',
         'minAICPslope',
@@ -371,5 +486,6 @@ settings_special_pick={
         'minpercent',
         'zfac',
         'mdttolerance',
-        'wdttolerance']
+        'wdttolerance',
+        'jackfactor'],
 }

pylot/core/io/inputs.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+from pylot.core.io import default_parameters
 from pylot.core.util.errors import ParameterError
-import default_parameters
+
 
 class PylotParameter(object):
     '''
@@ -69,13 +70,13 @@ class PylotParameter(object):
 
     # Set default values of parameter names
     def __init_default_paras(self):
-        parameters=default_parameters.defaults
+        parameters = default_parameters.defaults
         self.__defaults = parameters
 
     def __init_subsettings(self):
-        self._settings_main=default_parameters.settings_main
+        self._settings_main = default_parameters.settings_main
-        self._settings_special_pick=default_parameters.settings_special_pick
+        self._settings_special_pick = default_parameters.settings_special_pick
-        
+
     # String representation of the object
     def __repr__(self):
         return "PylotParameter('%s')" % self.__filename
@@ -107,7 +108,7 @@ class PylotParameter(object):
             yield key, value
 
     def hasParam(self, parameter):
-        if self.__parameter.has_key(parameter):
+        if parameter in self.__parameter.keys():
             return True
         return False
 
@@ -136,12 +137,13 @@ class PylotParameter(object):
         return self._settings_special_pick
 
     def get_all_para_names(self):
-        all_names=[]
+        all_names = []
         all_names += self.get_main_para_names()['dirs']
         all_names += self.get_main_para_names()['nlloc']
         all_names += self.get_main_para_names()['smoment']
         all_names += self.get_main_para_names()['localmag']
-        all_names += self.get_main_para_names()['pick']        
+        all_names += self.get_main_para_names()['pick']
+        all_names += self.get_main_para_names()['filter']
         all_names += self.get_special_para_names()['z']
         all_names += self.get_special_para_names()['h']
         all_names += self.get_special_para_names()['fm']
@@ -155,14 +157,14 @@ class PylotParameter(object):
             message = 'Type check failed for param: {}, is type: {}, expected type:{}'
             message = message.format(param, is_type, expect_type)
             print(Warning(message))
-        
+
     def setParamKV(self, param, value):
         self.__setitem__(param, value)
 
     def setParam(self, **kwargs):
         for key in kwargs:
             self.__setitem__(key, kwargs[key])
-        
+
     @staticmethod
     def _printParameterError(errmsg):
         print('ParameterError:\n non-existent parameter %s' % errmsg)
@@ -171,7 +173,7 @@ class PylotParameter(object):
         defaults = self.get_defaults()
         for param in defaults:
             self.setParamKV(param, defaults[param]['value'])
-        
+
     def from_file(self, fnin=None):
         if not fnin:
             if self.__filename is not None:
@@ -208,7 +210,10 @@ class PylotParameter(object):
                         vallist = value.strip().split(' ')
                         val = []
                         for val0 in vallist:
-                            val0 = float(val0)
+                            try:
+                                val0 = float(val0)
+                            except:
+                                pass
                             val.append(val0)
                     else:
                         val = str(value.strip())
@@ -221,9 +226,9 @@ class PylotParameter(object):
         # for key, value in self.iteritems():
         #     lines.append('{key}\t{value}\n'.format(key=key, value=value))
         # fid_out.writelines(lines)
-        header = ('%This is a parameter input file for PyLoT/autoPyLoT.\n'+
+        header = ('%This is a parameter input file for PyLoT/autoPyLoT.\n' +
-                  '%All main and special settings regarding data handling\n'+
+                  '%All main and special settings regarding data handling\n' +
-                  '%and picking are to be set here!\n'+
+                  '%and picking are to be set here!\n' +
                   '%Parameters are optimized for %{} data sets!\n'.format(self.get_main_para_names()['pick'][0]))
         separator = '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n'
 
@@ -236,16 +241,18 @@ class PylotParameter(object):
                            'parameters for seismic moment estimation', separator)
         self.write_section(fid_out, self.get_main_para_names()['localmag'],
                            'settings local magnitude', separator)
+        self.write_section(fid_out, self.get_main_para_names()['filter'],
+                           'filter settings', separator)
         self.write_section(fid_out, self.get_main_para_names()['pick'],
                            'common settings picker', separator)
-        fid_out.write(('#special settings for calculating CF#\n'+
+        fid_out.write(('#special settings for calculating CF#\n' +
                        '%!!Edit the following only if you know what you are doing!!%\n'))
         self.write_section(fid_out, self.get_special_para_names()['z'],
                            'Z-component', None)
         self.write_section(fid_out, self.get_special_para_names()['h'],
                            'H-components', None)
         self.write_section(fid_out, self.get_special_para_names()['fm'],
-                           'first-motion picker', None)                           
+                           'first-motion picker', None)
         self.write_section(fid_out, self.get_special_para_names()['quality'],
                            'quality assessment', None)
 
@@ -261,7 +268,7 @@ class PylotParameter(object):
             if type(value) == list or type(value) == tuple:
                 value_tmp = ''
                 for vl in value:
-                    value_tmp+= '{} '.format(vl)
+                    value_tmp += '{} '.format(vl)
                 value = value_tmp
             tooltip = self.get_defaults()[name]['tooltip']
             if not len(str(value)) > l_val:
@@ -277,7 +284,7 @@ class PylotParameter(object):
                 ttip = '%{:<{}}\n'.format(tooltip, l_ttip)
             else:
                 ttip = '%{}\n'.format(tooltip)
-            line = value+name+ttip
+            line = value + name + ttip
             fid.write(line)
 
 
@@ -335,12 +342,13 @@ class FilterOptions(object):
     def parseFilterOptions(self):
         if self:
             robject = {'type': self.getFilterType(), 'corners': self.getOrder()}
-            if len(self.getFreq()) > 1:
+            if not self.getFilterType() in ['highpass', 'lowpass']:
                 robject['freqmin'] = self.getFreq()[0]
                 robject['freqmax'] = self.getFreq()[1]
-            else:
+            elif self.getFilterType() == 'highpass':
-                robject['freq'] = self.getFreq() if type(self.getFreq()) is \
+                robject['freq'] = self.getFreq()[0]
-                                                    float else self.getFreq()[0]
+            elif self.getFilterType() == 'lowpass':
+                robject['freq'] = self.getFreq()[1]
             return robject
         return None
 

pylot/core/io/phases.py

@@ -2,19 +2,23 @@
 # -*- coding: utf-8 -*-
 
 import glob
-import obspy.core.event as ope
 import os
-import scipy.io as sio
 import warnings
-from obspy.core import UTCDateTime
-from obspy.core.util import AttribDict
 
+import matplotlib.pyplot as plt
+import numpy as np
+import obspy.core.event as ope
+import scipy.io as sio
+from obspy.core import UTCDateTime
+from obspy.core.event import read_events
+from obspy.core.util import AttribDict
 from pylot.core.io.inputs import PylotParameter
-from pylot.core.io.location import create_arrival, create_event, \
+from pylot.core.io.location import create_event, \
-    create_magnitude, create_origin, create_pick
+    create_magnitude
 from pylot.core.pick.utils import select_for_phase
 from pylot.core.util.utils import getOwner, full_range, four_digits
 
+
 def add_amplitudes(event, amplitudes):
     amplitude_list = []
     for pick in event.picks:
@@ -33,6 +37,7 @@ def add_amplitudes(event, amplitudes):
     event.amplitudes = amplitude_list
     return event
 
+
 def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     """
     readPILOTEvent - function
@@ -189,26 +194,35 @@ def picksdict_from_picks(evt):
     PyLoT
     :param evt: Event object contain all available information
     :type evt: `~obspy.core.event.Event`
-    :return: pick dictionary
+    :return: pick dictionary (auto and manual)
     """
-    picks = {}
+    picksdict = {
+        'manual': {},
+        'auto': {}
+    }
     for pick in evt.picks:
         phase = {}
         station = pick.waveform_id.station_code
         channel = pick.waveform_id.channel_code
         network = pick.waveform_id.network_code
-        try:
-            onsets = picks[station]
-        except KeyError as e:
-            #print(e)
-            onsets = {}
         mpp = pick.time
         spe = pick.time_errors.uncertainty
+        try:
+            picker = str(pick.method_id)
+            if picker.startswith('smi:local/'):
+                picker = picker.split('smi:local/')[1]
+        except IndexError:
+            picker = 'manual' # MP MP TODO maybe improve statement
+        try:
+            onsets = picksdict[picker][station]
+        except KeyError as e:
+            # print(e)
+            onsets = {}
         try:
             lpp = mpp + pick.time_errors.upper_uncertainty
             epp = mpp - pick.time_errors.lower_uncertainty
         except TypeError as e:
-            msg = e.message + ',\n falling back to symmetric uncertainties'
+            msg = e + ',\n falling back to symmetric uncertainties'
             warnings.warn(msg)
             lpp = mpp + spe
             epp = mpp - spe
@@ -218,17 +232,12 @@ def picksdict_from_picks(evt):
         phase['spe'] = spe
         phase['channel'] = channel
         phase['network'] = network
-        try:
+        phase['picker'] = picker
-            picker = str(pick.method_id)
-            if picker.startswith('smi:local/'):
-                picker = picker.split('smi:local/')[1]
-            phase['picker'] = picker
-        except IndexError:
-            pass
 
         onsets[pick.phase_hint] = phase.copy()
-        picks[station] = onsets.copy()
+        picksdict[picker][station] = onsets.copy()
-    return picks
+    return picksdict
+
 
 def picks_from_picksdict(picks, creation_info=None):
     picks_list = list()
@@ -238,8 +247,8 @@ def picks_from_picksdict(picks, creation_info=None):
                 continue
             onset = phase['mpp']
             try:
-            	ccode = phase['channel']
+                ccode = phase['channel']
-            	ncode = phase['network']
+                ncode = phase['network']
             except:
                 continue
             pick = ope.Pick()
@@ -253,8 +262,8 @@ def picks_from_picksdict(picks, creation_info=None):
                 lpp = phase['lpp']
                 pick.time_errors.lower_uncertainty = onset - epp
                 pick.time_errors.upper_uncertainty = lpp - onset
-            except KeyError as e:
+            except (KeyError, TypeError) as e:
-                warnings.warn(e.message, RuntimeWarning)
+                warnings.warn(str(e), RuntimeWarning)
             try:
                 picker = phase['picker']
             except KeyError as e:
@@ -263,8 +272,8 @@ def picks_from_picksdict(picks, creation_info=None):
             pick.phase_hint = label
             pick.method_id = ope.ResourceIdentifier(id=picker)
             pick.waveform_id = ope.WaveformStreamID(station_code=station,
-                                                      channel_code=ccode,
+                                                    channel_code=ccode,
-                                                      network_code=ncode)
+                                                    network_code=ncode)
             try:
                 polarity = phase['fm']
                 if polarity == 'U' or '+':
@@ -274,7 +283,7 @@ def picks_from_picksdict(picks, creation_info=None):
                 else:
                     pick.polarity = 'undecidable'
             except KeyError as e:
-                if 'fm' in e.message: # no polarity information found for this phase
+                if 'fm' in str(e):  # no polarity information found for this phase
                     pass
                 else:
                     raise e
@@ -286,7 +295,7 @@ def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0
     import glob
 
     db_root = os.path.join(root_dir, db_dir)
-    evt_list = glob.glob1(db_root,'e????.???.??')
+    evt_list = glob.glob1(db_root, 'e????.???.??')
 
     for evt in evt_list:
         if verbosity > 0:
@@ -294,7 +303,6 @@ def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0
         reassess_pilot_event(root_dir, db_dir, evt, out_dir, fn_param, verbosity)
 
 
-
 def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
     from obspy import read
 
@@ -302,7 +310,6 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
     from pylot.core.pick.utils import earllatepicker
 
     if fn_param is None:
-        import pylot.core.util.defaults as defaults
         fn_param = defaults.AUTOMATIC_DEFAULTS
 
     default = PylotParameter(fn_param, verbosity)
@@ -336,7 +343,8 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
                 except Exception as e:
                     if 'No file matching file pattern:' in e.message:
                         if verbosity > 0:
-                            warnings.warn('no waveform data found for station {station}'.format(station=station), RuntimeWarning)
+                            warnings.warn('no waveform data found for station {station}'.format(station=station),
+                                          RuntimeWarning)
                         datacheck.append(fn_pattern + ' (no data)\n')
                         continue
                     else:
@@ -360,7 +368,7 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
                                            default.get('nfac{0}'.format(phase)),
                                            default.get('tsnrz' if phase == 'P' else 'tsnrh'),
                                            Pick1=rel_pick,
-                                           iplot=None,
+                                           iplot=0,
                                            verbosity=0)
             if epp is None or lpp is None:
                 continue
@@ -392,10 +400,10 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
             os.makedirs(out_dir)
         fnout_prefix = os.path.join(out_dir, 'PyLoT_{0}.'.format(event_id))
     evt.write(fnout_prefix + 'xml', format='QUAKEML')
-    #evt.write(fnout_prefix + 'cnv', format='VELEST')
+    # evt.write(fnout_prefix + 'cnv', format='VELEST')
 
 
-def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
+def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
     """
     Function of methods to write phases to the following standard file
     formats used for locating earthquakes:
@@ -421,10 +429,10 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
     :param: eventinfo, optional, needed for VELEST-cnv file 
             and FOCMEC- and HASH-input files 
     :type:  `obspy.core.event.Event` object
-    """ 
+    """
 
     if fformat == 'NLLoc':
-        print ("Writing phases to %s for NLLoc" % filename)
+        print("Writing phases to %s for NLLoc" % filename)
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
@@ -448,7 +456,7 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                 ss = onset.second
                 ms = onset.microsecond
                 ss_ms = ss + ms / 1000000.0
-                pweight = 1 # use pick
+                pweight = 1  # use pick
                 try:
                     if arrivals[key]['P']['weight'] >= 4:
                         pweight = 0  # do not use pick
@@ -475,7 +483,7 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                 ss = onset.second
                 ms = onset.microsecond
                 ss_ms = ss + ms / 1000000.0
-                sweight = 1 # use pick
+                sweight = 1  # use pick
                 try:
                     if arrivals[key]['S']['weight'] >= 4:
                         sweight = 0  # do not use pick
@@ -493,15 +501,15 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
 
         fid.close()
     elif fformat == 'HYPO71':
-        print ("Writing phases to %s for HYPO71" % filename)
+        print("Writing phases to %s for HYPO71" % filename)
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('                                                                %s\n' %
-                                                                            parameter.get('eventID'))
+                  parameter.get('eventID'))
         for key in arrivals:
             if arrivals[key]['P']['weight'] < 4:
                 stat = key
-                if len(stat) > 4: # HYPO71 handles only 4-string station IDs
+                if len(stat) > 4:  # HYPO71 handles only 4-string station IDs
                     stat = stat[1:5]
                 Ponset = arrivals[key]['P']['mpp']
                 Sonset = arrivals[key]['S']['mpp']
@@ -541,41 +549,39 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                     elif sweight >= 2:
                         sstr = 'E'
                     fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f       %s%sS %d   %s\n' % (stat,
-                                                                                             pstr,
+                                                                                               pstr,
-                                                                                             fm,
+                                                                                               fm,
-                                                                                             pweight,
+                                                                                               pweight,
-                                                                                             year,
+                                                                                               year,
-                                                                                             month,
+                                                                                               month,
-                                                                                             day,
+                                                                                               day,
-                                                                                             hh,
+                                                                                               hh,
-                                                                                             mm,
+                                                                                               mm,
-                                                                                             ss_ms,
+                                                                                               ss_ms,
-                                                                                             Sss_ms,
+                                                                                               Sss_ms,
-                                                                                             sstr,
+                                                                                               sstr,
-                                                                                             sweight,
+                                                                                               sweight,
-                                                                                             Ao))
+                                                                                               Ao))
                 else:
                     fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f                  %s\n' % (stat,
-                                                                                             pstr,
+                                                                                               pstr,
-                                                                                             fm,
+                                                                                               fm,
-                                                                                             pweight,
+                                                                                               pweight,
-                                                                                             year,
+                                                                                               year,
-                                                                                             month,
+                                                                                               month,
-                                                                                             day,
+                                                                                               day,
-                                                                                             hh,
+                                                                                               hh,
-                                                                                             mm,
+                                                                                               mm,
-                                                                                             ss_ms,
+                                                                                               ss_ms,
-                                                                                             Ao))
+                                                                                               Ao))
 
         fid.close()
 
     elif fformat == 'HYPOSAT':
-        print ("Writing phases to %s for HYPOSAT" % filename)
+        print("Writing phases to %s for HYPOSAT" % filename)
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
-        errP = parameter.get('timeerrorsP')
-        errS = parameter.get('timeerrorsS')
         for key in arrivals:
             # P onsets
             if arrivals[key].has_key('P'):
@@ -592,7 +598,7 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                     # use symmetrized picking error as std
                     # (read the HYPOSAT manual)
                     pstd = arrivals[key]['P']['spe']
-                    fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n' 
+                    fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
                               % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
             # S onsets
             if arrivals[key].has_key('S') and arrivals[key]['S']:
@@ -607,16 +613,20 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                     sms = Sonset.microsecond
                     Sss = sss + sms / 1000000.0
                     sstd = arrivals[key]['S']['spe']
-                    fid.write('%-5s S1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n' 
+                    fid.write('%-5s S1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
                               % (key, syear, smonth, sday, shh, smm, Sss, sstd))
         fid.close()
 
     elif fformat == 'VELEST':
-        print ("Writing phases to %s for VELEST" % filename)
+        print("Writing phases to %s for VELEST" % filename)
         fid = open("%s" % filename, 'w')
         # get informations needed in cnv-file
         # check, whether latitude is N or S and longitude is E or W
-        eventsource = eventinfo.origins[0]
+        try:
+            eventsource = eventinfo.origins[0]
+        except:
+            print("No source origin calculated yet, thus no cnv-file creation possible!")
+            return
         if eventsource['latitude'] < 0:
             cns = 'S'
         else:
@@ -628,14 +638,14 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
         # get last two integers of origin year
         stime = eventsource['time']
         if stime.year - 2000 >= 0:
-           syear = stime.year - 2000
+            syear = stime.year - 2000
         else:
-           syear = stime.year - 1900
+            syear = stime.year - 1900
-        ifx = 0 # default value, see VELEST manual, pp. 22-23
+        ifx = 0  # default value, see VELEST manual, pp. 22-23
         # write header
         fid.write('%s%02d%02d %02d%02d %05.2f %7.4f%c %8.4f%c %7.2f %6.2f     %02.0f  0.0 0.03  1.0  1.0\n' % (
-                   syear, stime.month, stime.day, stime.hour, stime.minute, stime.second, eventsource['latitude'],
+            syear, stime.month, stime.day, stime.hour, stime.minute, stime.second, eventsource['latitude'],
-                   cns, eventsource['longitude'], cew, eventsource['depth'],eventinfo.magnitudes[0]['mag'], ifx))
+            cns, eventsource['longitude'], cew, eventsource['depth'], eventinfo.magnitudes[0]['mag'], ifx))
         n = 0
         for key in arrivals:
             # P onsets
@@ -643,33 +653,33 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                 if arrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
-                    if len(stat) > 4: # VELEST handles only 4-string station IDs
+                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
                     Ponset = arrivals[key]['P']['mpp']
                     Pweight = arrivals[key]['P']['weight']
-                    Prt = Ponset - stime # onset time relative to source time
+                    Prt = Ponset - stime  # onset time relative to source time
                     if n % 6 is not 0:
-                        fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))  
+                        fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))
                     else:
-                        fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))  
+                        fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
-            # S onsets
+                        # S onsets
             if arrivals[key].has_key('S'):
                 if arrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
-                    if len(stat) > 4: # VELEST handles only 4-string station IDs
+                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
                     Sonset = arrivals[key]['S']['mpp']
                     Sweight = arrivals[key]['S']['weight']
-                    Srt = Ponset - stime # onset time relative to source time
+                    Srt = Ponset - stime  # onset time relative to source time
                     if n % 6 is not 0:
-                        fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))  
+                        fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))
                     else:
-                        fid.write('%-4sS%d%6.2f\n' % (stat, Sweight, Srt))  
+                        fid.write('%-4sS%d%6.2f\n' % (stat, Sweight, Srt))
         fid.close()
 
     elif fformat == 'hypoDD':
-        print ("Writing phases to %s for hypoDD" % filename)
+        print("Writing phases to %s for hypoDD" % filename)
         fid = open("%s" % filename, 'w')
         # get event information needed for hypoDD-phase file
         eventsource = eventinfo.origins[0]
@@ -678,59 +688,62 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
         hddID = event.split('.')[0][1:5]
         # write header
         fid.write('# %d  %d %d %d %d %5.2f %7.4f +%6.4f %7.4f %4.2f 0.1 0.5 %4.2f      %s\n' % (
-                      stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second, 
+            stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
-                      eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
+            eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
-                      eventinfo.magnitudes[0]['mag'], eventsource['quality']['standard_error'], hddID))
+            eventinfo.magnitudes[0]['mag'], eventsource['quality']['standard_error'], hddID))
         for key in arrivals:
             if arrivals[key].has_key('P'):
                 # P onsets
                 if arrivals[key]['P']['weight'] < 4:
                     Ponset = arrivals[key]['P']['mpp']
-                    Prt = Ponset - stime # onset time relative to source time
+                    Prt = Ponset - stime  # onset time relative to source time
-                    fid.write('%s    %6.3f  1  P\n' % (key, Prt)) 
+                    fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-                # S onsets
+                    # S onsets
                 if arrivals[key]['S']['weight'] < 4:
                     Sonset = arrivals[key]['S']['mpp']
-                    Srt = Sonset - stime # onset time relative to source time
+                    Srt = Sonset - stime  # onset time relative to source time
-                    fid.write('%-5s    %6.3f  1  S\n' % (key, Srt)) 
+                    fid.write('%-5s    %6.3f  1  S\n' % (key, Srt))
 
         fid.close()
 
     elif fformat == 'FOCMEC':
-        print ("Writing phases to %s for FOCMEC" % filename)
+        print("Writing phases to %s for FOCMEC" % filename)
         fid = open("%s" % filename, 'w')
         # get event information needed for FOCMEC-input file
         eventsource = eventinfo.origins[0]
         stime = eventsource['time']
         # write header line including event information
         fid.write('%s %d%02d%02d%02d%02d%02.0f %7.4f %6.4f %3.1f %3.1f\n' % (parameter.get('eventID'),
-                   stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
+                                                                             stime.year, stime.month, stime.day,
-                   eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
+                                                                             stime.hour, stime.minute, stime.second,
-                   eventinfo.magnitudes[0]['mag']))
+                                                                             eventsource['latitude'],
+                                                                             eventsource['longitude'],
+                                                                             eventsource['depth'] / 1000,
+                                                                             eventinfo.magnitudes[0]['mag']))
         picks = eventinfo.picks
         for key in arrivals:
             if arrivals[key].has_key('P'):
                 if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
                     stat = key
                     for i in range(len(picks)):
-                         station = picks[i].waveform_id.station_code
+                        station = picks[i].waveform_id.station_code
-                         if station == stat:
+                        if station == stat:
-                             # get resource ID
+                            # get resource ID
-                             resid_picks = picks[i].get('resource_id')
+                            resid_picks = picks[i].get('resource_id')
-                             # find same ID in eventinfo
+                            # find same ID in eventinfo
-                             # there it is the pick_id!!
+                            # there it is the pick_id!!
-                             for j in range(len(eventinfo.origins[0].arrivals)):
+                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                 resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
+                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                 if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
+                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                     if len(stat) > 4: # FOCMEC handles only 4-string station IDs
+                                    if len(stat) > 4:  # FOCMEC handles only 4-string station IDs
-                                         stat = stat[1:5]
+                                        stat = stat[1:5]
-                                     az = eventinfo.origins[0].arrivals[j].get('azimuth')
+                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                     inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
+                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                     fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
+                                    fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
-                                                                        az,
+                                                                           az,
-                                                                        inz,
+                                                                           inz,
-                                                    arrivals[key]['P']['fm']))
+                                                                           arrivals[key]['P']['fm']))
-                                     break
+                                    break
 
         fid.close()
 
@@ -739,9 +752,9 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
         # HASH-driver 1 and 2 (see HASH manual!)
         filename1 = filename + 'drv1' + '.phase'
         filename2 = filename + 'drv2' + '.phase'
-        print ("Writing phases to %s for HASH for HASH-driver 1" % filename1)
+        print("Writing phases to %s for HASH for HASH-driver 1" % filename1)
         fid1 = open("%s" % filename1, 'w')
-        print ("Writing phases to %s for HASH for HASH-driver 2" % filename2)
+        print("Writing phases to %s for HASH for HASH-driver 2" % filename2)
         fid2 = open("%s" % filename2, 'w')
         # get event information needed for HASH-input file
         eventsource = eventinfo.origins[0]
@@ -756,26 +769,32 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
         erz = eventsource.depth_errors['uncertainty']
         stime = eventsource['time']
         if stime.year - 2000 >= 0:
-           syear = stime.year - 2000
+            syear = stime.year - 2000
         else:
-           syear = stime.year - 1900
+            syear = stime.year - 1900
         picks = eventinfo.picks
         # write header line including event information
         # for HASH-driver 1
         fid1.write('%s%02d%02d%02d%02d%5.2f%2dN%5.2f%3dE%5.2f%6.3f%4.2f%5.2f%5.2f%s\n' % (syear,
-                             stime.month, stime.day, stime.hour, stime.minute, stime.second, 
+                                                                                          stime.month, stime.day,
-                                       latdeg, latmin, londeg, lonmin, eventsource['depth'], 
+                                                                                          stime.hour, stime.minute,
-                                                   eventinfo.magnitudes[0]['mag'], erh, erz, 
+                                                                                          stime.second,
-                                                                                    hashID))
+                                                                                          latdeg, latmin, londeg,
+                                                                                          lonmin, eventsource['depth'],
+                                                                                          eventinfo.magnitudes[0][
+                                                                                              'mag'], erh, erz,
+                                                                                          hashID))
         # write header line including event information
         # for HASH-driver 2
-        fid2.write('%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f    %d                                          %5.2f %5.2f                                        %4.2f      %s \n' % (syear, stime.month, stime.day, 
+        fid2.write(
-                                               stime.hour, stime.minute, stime.second, 
+            '%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f    %d                                          %5.2f %5.2f                                        %4.2f      %s \n' % (
-                                                         latdeg,latmin,londeg, lonmin, 
+                syear, stime.month, stime.day,
-                                                                 eventsource['depth'], 
+                stime.hour, stime.minute, stime.second,
-                                           eventsource['quality']['used_phase_count'],
+                latdeg, latmin, londeg, lonmin,
-                                               erh, erz, eventinfo.magnitudes[0]['mag'],
+                eventsource['depth'],
-                                                                                hashID))
+                eventsource['quality']['used_phase_count'],
+                erh, erz, eventinfo.magnitudes[0]['mag'],
+                hashID))
 
         # write phase lines
         for key in arrivals:
@@ -786,36 +805,38 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
                     ncode = arrivals[key]['P']['network']
 
                     if arrivals[key]['P']['weight'] < 2:
-                        Pqual='I'
+                        Pqual = 'I'
                     else:
-                        Pqual='E'
+                        Pqual = 'E'
-                    
+
                     for i in range(len(picks)):
-                         station = picks[i].waveform_id.station_code
+                        station = picks[i].waveform_id.station_code
-                         if station == stat:
+                        if station == stat:
-                             # get resource ID
+                            # get resource ID
-                             resid_picks = picks[i].get('resource_id')
+                            resid_picks = picks[i].get('resource_id')
-                             # find same ID in eventinfo
+                            # find same ID in eventinfo
-                             # there it is the pick_id!!
+                            # there it is the pick_id!!
-                             for j in range(len(eventinfo.origins[0].arrivals)):
+                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                 resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
+                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                 if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
+                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                     if len(stat) > 4: # HASH handles only 4-string station IDs
+                                    if len(stat) > 4:  # HASH handles only 4-string station IDs
-                                         stat = stat[1:5]
+                                        stat = stat[1:5]
-                                     az = eventinfo.origins[0].arrivals[j].get('azimuth')
+                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                     inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
+                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                     dist = eventinfo.origins[0].arrivals[j].get('distance') 
+                                    dist = eventinfo.origins[0].arrivals[j].get('distance')
-                                     # write phase line for HASH-driver 1
+                                    # write phase line for HASH-driver 1
-                                     fid1.write('%-4s%sP%s%d                   0                                   %3.1f          %03d %03d   2     1   %s\n' % (stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'], 
+                                    fid1.write(
-                                                                               dist, inz, az, ccode))
+                                        '%-4s%sP%s%d                   0                                   %3.1f          %03d %03d   2     1   %s\n' % (
-                                     # write phase line for HASH-driver 2
+                                            stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'],
-                                     fid2.write('%-4s %s   %s %s %s                    \n' % (
+                                            dist, inz, az, ccode))
-                                                                                           stat,
+                                    # write phase line for HASH-driver 2
-                                                                                          ncode,
+                                    fid2.write('%-4s %s   %s %s %s                    \n' % (
-                                                                                          ccode,
+                                        stat,
-                                                                                          Pqual,
+                                        ncode,
-                                                                       arrivals[key]['P']['fm']))
+                                        ccode,
-                                     break
+                                        Pqual,
+                                        arrivals[key]['P']['fm']))
+                                    break
 
         fid1.write('                                    %s' % hashID)
         fid1.close()
@@ -841,7 +862,155 @@ def merge_picks(event, picks):
         network = pick.waveform_id.network_code
         method = pick.method_id
         for p in event.picks:
-            if p.waveform_id.station_code == station and p.phase_hint == phase:
+            if p.waveform_id.station_code == station\
+                    and p.waveform_id.network_code == network\
+                    and p.phase_hint == phase\
+                    and (str(p.method_id) in str(method)
+                         or str(method) in str(p.method_id)):
                 p.time, p.time_errors, p.waveform_id.network_code, p.method_id = time, err, network, method
         del time, err, phase, station, network, method
     return event
+
+
+def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
+    """
+   Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
+   Uncertainties are tranformed into quality classes and visualized via histogram if desired.
+   Ludger Küperkoch, BESTEC GmbH, 07/2017
+   """
+
+    from pylot.core.pick.utils import getQualityFromUncertainty
+    from pylot.core.util.utils import loopIdentifyPhase, identifyPhase
+
+    # read all onset weights
+    Pw0 = []
+    Pw1 = []
+    Pw2 = []
+    Pw3 = []
+    Pw4 = []
+    Sw0 = []
+    Sw1 = []
+    Sw2 = []
+    Sw3 = []
+    Sw4 = []
+    for names in xmlnames:
+        print("Getting onset weights from {}".format(names))
+        cat = read_events(names)
+        cat_copy = cat.copy()
+        arrivals = cat.events[0].picks
+        arrivals_copy = cat_copy.events[0].picks
+        # Prefere manual picks if qualities are sufficient!
+        for Pick in arrivals:
+            if (Pick.method_id.id).split('/')[1] == 'manual':
+                mstation = Pick.waveform_id.station_code
+                mstation_ext = mstation + '_'
+                for mpick in arrivals_copy:
+                    phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
+                    if phase == 'P':
+                        if ((mpick.waveform_id.station_code == mstation) or
+                                (mpick.waveform_id.station_code == mstation_ext)) and \
+                                ((mpick.method_id).split('/')[1] == 'auto') and \
+                                (mpick.time_errors['uncertainty'] <= ErrorsP[3]):
+                            del mpick
+                            break
+                    elif phase == 'S':
+                        if ((mpick.waveform_id.station_code == mstation) or
+                                (mpick.waveform_id.station_code == mstation_ext)) and \
+                                ((mpick.method_id).split('/')[1] == 'auto') and \
+                                (mpick.time_errors['uncertainty'] <= ErrorsS[3]):
+                            del mpick
+                            break
+        lendiff = len(arrivals) - len(arrivals_copy)
+        if lendiff is not 0:
+            print("Found manual as well as automatic picks, prefered the {} manual ones!".format(lendiff))
+
+        for Pick in arrivals_copy:
+            phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
+            if phase == 'P':
+                Pqual = getQualityFromUncertainty(Pick.time_errors.uncertainty, ErrorsP)
+                if Pqual == 0:
+                    Pw0.append(Pick.time_errors.uncertainty)
+                elif Pqual == 1:
+                    Pw1.append(Pick.time_errors.uncertainty)
+                elif Pqual == 2:
+                    Pw2.append(Pick.time_errors.uncertainty)
+                elif Pqual == 3:
+                    Pw3.append(Pick.time_errors.uncertainty)
+                elif Pqual == 4:
+                    Pw4.append(Pick.time_errors.uncertainty)
+            elif phase == 'S':
+                Squal = getQualityFromUncertainty(Pick.time_errors.uncertainty, ErrorsS)
+                if Squal == 0:
+                    Sw0.append(Pick.time_errors.uncertainty)
+                elif Squal == 1:
+                    Sw1.append(Pick.time_errors.uncertainty)
+                elif Squal == 2:
+                    Sw2.append(Pick.time_errors.uncertainty)
+                elif Squal == 3:
+                    Sw3.append(Pick.time_errors.uncertainty)
+                elif Squal == 4:
+                    Sw4.append(Pick.time_errors.uncertainty)
+            else:
+                print("Phase hint not defined for picking!")
+                pass
+
+    if plotflag == 0:
+        Punc = [Pw0, Pw1, Pw2, Pw3, Pw4]
+        Sunc = [Sw0, Sw1, Sw2, Sw3, Sw4]
+        return Punc, Sunc
+    else:
+        # get percentage of weights
+        numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
+        numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
+        if len(Pw0) > 0:
+            P0perc = 100 / numPweights * len(Pw0)
+        else:
+            P0perc = 0
+        if len(Pw1) > 0:
+            P1perc = 100 / numPweights * len(Pw1)
+        else:  
+            P1perc = 0
+        if len(Pw2) > 0:
+            P2perc = 100 / numPweights * len(Pw2)
+        else:  
+            P2perc = 0
+        if len(Pw3) > 0:
+            P3perc = 100 / numPweights * len(Pw3)
+        else:  
+            P3perc = 0
+        if len(Pw4) > 0:
+            P4perc = 100 / numPweights * len(Pw4)
+        else:  
+            P4perc = 0
+        if len(Sw0) > 0:
+            S0perc = 100 / numSweights * len(Sw0)
+        else:
+            S0perc = 0
+        if len(Sw1) > 0:
+            S1perc = 100 / numSweights * len(Sw1)
+        else:  
+            S1perc = 0
+        if len(Sw2) > 0:
+            S2perc = 100 / numSweights * len(Sw2)
+        else:  
+            S2perc = 0
+        if len(Sw3) > 0:
+            S3perc = 100 / numSweights * len(Sw3)
+        else:  
+            S3perc = 0
+        if len(Sw4) > 0:
+            S4perc = 100 / numSweights * len(Sw4)
+        else:  
+            S4perc = 0
+
+        weights = ('0', '1', '2', '3', '4')
+        y_pos = np.arange(len(weights))
+        width = 0.34
+        plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
+        plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
+        plt.ylabel('%')
+        plt.xticks(y_pos, weights)
+        plt.xlim([-0.5, 4.5])
+        plt.xlabel('Qualities')
+        plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
+        plt.show()

pylot/core/loc/focmec.py

@@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 def export(picks, fnout, parameter, eventinfo):
     '''
     Take <picks> dictionary and exports picking data to a focmec

pylot/core/loc/hash.py

@@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 def export(picks, fnout, parameter, eventinfo):
     '''
     Take <picks> dictionary and exports picking data to a HASH

pylot/core/loc/hypo71.py

@@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 def export(picks, fnout, parameter):
     '''
     Take <picks> dictionary and exports picking data to a HYPO71

pylot/core/loc/hypodd.py

@@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 def export(picks, fnout, parameter, eventinfo):
     '''
     Take <picks> dictionary and exports picking data to a hypoDD

pylot/core/loc/hyposat.py

@@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 def export(picks, fnout, parameter):
     '''
     Take <picks> dictionary and exports picking data to a HYPOSAT

pylot/core/loc/nll.py

@@ -1,9 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import subprocess
-import os
 import glob
+import os
+import subprocess
+
 from obspy import read_events
 from pylot.core.io.phases import writephases
 from pylot.core.util.utils import getPatternLine, runProgram, which
@@ -11,9 +12,11 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
+
 class NLLocError(EnvironmentError):
     pass
 
+
 def export(picks, fnout, parameter):
     '''
     Take <picks> dictionary and exports picking data to a NLLOC-obs
@@ -58,7 +61,7 @@ def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
     locfiles = 'LOCFILES %s NLLOC_OBS %s %s 0\n' % (phasefile, tttable, nllocout)
 
     # modification of NLLoc-control file
-    print ("Modifying  NLLoc-control file %s ..." % ctrfile)
+    print("Modifying  NLLoc-control file %s ..." % ctrfile)
     curlocfiles = getPatternLine(ctrfile, 'LOCFILES')
     nllfile = open(ctrfile, 'r')
     filedata = nllfile.read()
@@ -94,7 +97,7 @@ def locate(fnin, infile=None):
 
 def read_location(fn):
     path, file = os.path.split(fn)
-    file = glob.glob1(path, file +  '.[0-9]*.grid0.loc.hyp')
+    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])

pylot/core/loc/velest.py

@@ -6,7 +6,8 @@ from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 
-def export(picks, fnout, parameter, eventinfo):
+
+def export(picks, fnout, eventinfo, parameter=None):
     '''
     Take <picks> dictionary and exports picking data to a VELEST-cnv
     <phasefile> without creating an ObsPy event object.
@@ -17,11 +18,11 @@ def export(picks, fnout, parameter, eventinfo):
     :param fnout: complete path to the exporting obs file
     :type fnout: str
     
-    :param: parameter, all input information
-    :type:  object
-
     :param: eventinfo, source time needed for VELEST-cnv format
     :type:  list object
+
+    :param: parameter, all input information
+    :type:  object
     '''
     # write phases to VELEST-phase file
     writephases(picks, 'VELEST', fnout, parameter, eventinfo)

pylot/core/pick/autopick.py

@@ -11,25 +11,37 @@ function conglomerate utils.
 
 import matplotlib.pyplot as plt
 import numpy as np
+from pylot.core.io.data import Data
 from pylot.core.io.inputs import PylotParameter
-from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.charfuns import CharacteristicFunction
 from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
+from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     getSNR, fmpicker, checkPonsets, wadaticheck
-from pylot.core.util.utils import getPatternLine, gen_Pool
+from pylot.core.util.utils import getPatternLine, gen_Pool,\
-from pylot.core.io.data import Data
+    real_Bool, identifyPhaseID
+
+from obspy.taup import TauPyModel
 
 
-def autopickevent(data, param, iplot=0, fig_dict=None):
+def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
     stations = []
     all_onsets = {}
     input_tuples = []
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+           iplot = 2
+        else:
+           iplot = 0
+
 
     # get some parameters for quality control from
-    # parameter input file (usually autoPyLoT.in).
+    # parameter input file (usually pylot.in).
     wdttolerance = param.get('wdttolerance')
     mdttolerance = param.get('mdttolerance')
+    jackfactor = param.get('jackfactor')
     apverbose = param.get('apverbose')
     for n in range(len(data)):
         station = data[n].stats.station
@@ -41,46 +53,67 @@ def autopickevent(data, param, iplot=0, fig_dict=None):
     for station in stations:
         topick = data.select(station=station)
 
-        if not iplot:
+        if iplot == None or iplot == 'None' or iplot == 0:
-            input_tuples.append((topick, param, apverbose))
+            input_tuples.append((topick, param, apverbose, metadata, origin))
-        if iplot>0:
+        if iplot > 0:
-            all_onsets[station] = autopickstation(topick, param, verbose=apverbose, iplot=iplot, fig_dict=fig_dict)
+            all_onsets[station] = autopickstation(topick, param, verbose=apverbose,
+                                                  iplot=iplot, fig_dict=fig_dict,
+                                                  metadata=metadata, origin=origin)
 
-    if iplot>0:
+    if iplot > 0:
         print('iPlot Flag active: NO MULTIPROCESSING possible.')
         return all_onsets
 
-    pool = gen_Pool()
+    # rename str for ncores in case ncores == 0 (use all cores)
+    ncores_str = ncores if ncores != 0 else 'all available'
+
+    print('Autopickstation: Distribute autopicking for {} '
+          'stations on {} cores.'.format(len(input_tuples), ncores_str))
+
+    pool = gen_Pool(ncores)
     result = pool.map(call_autopickstation, input_tuples)
     pool.close()
 
     for pick in result:
-        station = pick['station']
+        if pick:
-        pick.pop('station')
+            station = pick['station']
-        all_onsets[station] = pick
+            pick.pop('station')
+            all_onsets[station] = pick
 
-    return all_onsets
+    #return all_onsets
 
     # quality control
     # median check and jackknife on P-onset times
-    jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, iplot)
+    jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, 1, fig_dict_wadatijack)
+    #return jk_checked_onsets
     # check S-P times (Wadati)
-    return wadaticheck(jk_checked_onsets, wdttolerance, iplot)
+    wadationsets = wadaticheck(jk_checked_onsets, wdttolerance, 1, fig_dict_wadatijack)
+    return wadationsets
 
 
 def call_autopickstation(input_tuple):
-    wfstream, pickparam, verbose = input_tuple
+    wfstream, pickparam, verbose, metadata, origin = input_tuple
-    #multiprocessing not possible with interactive plotting
+    # multiprocessing not possible with interactive plotting
-    return autopickstation(wfstream, pickparam, verbose, iplot=0)
+    return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin)
 
 
-def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
+def get_source_coords(parser, station_id):
+    station_coords = None
+    try:
+        station_coords = parser.get_coordinates(station_id)
+    except Exception as e:
+        print('Could not get source coordinates for station {}: {}'.format(station_id, e))
+    return station_coords
+
+
+def autopickstation(wfstream, pickparam, verbose=False,
+                    iplot=0, fig_dict=None, metadata=None, origin=None):
     """
     :param wfstream: `~obspy.core.stream.Stream`  containing waveform
     :type wfstream: obspy.core.stream.Stream
 
     :param pickparam: container of picking parameters from input file,
-           usually autoPyLoT.in
+           usually pylot.in
     :type pickparam: PylotParameter
     :param verbose:
     :type verbose: bool
@@ -88,11 +121,10 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
     """
 
     # declaring pickparam variables (only for convenience)
-    # read your autoPyLoT.in for details!
+    # read your pylot.in for details!
+    plt_flag = 0
 
     # special parameters for P picking
-    iplot = iplot
-    
     algoP = pickparam.get('algoP')
     pstart = pickparam.get('pstart')
     pstop = pickparam.get('pstop')
@@ -102,6 +134,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
     bpz1 = pickparam.get('bpz1')
     bpz2 = pickparam.get('bpz2')
     pickwinP = pickparam.get('pickwinP')
+    aictsmoothP = pickparam.get('aictsmooth')
     tsmoothP = pickparam.get('tsmoothP')
     ausP = pickparam.get('ausP')
     nfacP = pickparam.get('nfacP')
@@ -117,6 +150,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
     algoS = pickparam.get('algoS')
     sstart = pickparam.get('sstart')
     sstop = pickparam.get('sstop')
+    use_taup = real_Bool(pickparam.get('use_taup'))
+    taup_model = pickparam.get('taup_model')
     bph1 = pickparam.get('bph1')
     bph2 = pickparam.get('bph2')
     tsnrh = pickparam.get('tsnrh')
@@ -182,25 +217,82 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
     if len(ndat) == 0:  # check for other components
         ndat = wfstream.select(component="1")
 
+    if not zdat:
+        print('No z-component found for station {}. STOP'.format(wfstream[0].stats.station))
+        return
+
     if algoP == 'HOS' or algoP == 'ARZ' and zdat is not None:
         msg = '##################################################\nautopickstation:' \
               ' Working on P onset of station {station}\nFiltering vertical ' \
-              'trace ...\n{data}'.format(station=zdat[0].stats.station,
+              'trace ...\n{data}'.format(station=wfstream[0].stats.station,
                                          data=str(zdat))
         if verbose: print(msg)
         z_copy = zdat.copy()
-        # filter and taper data
         tr_filt = zdat[0].copy()
+        #remove constant offset from data to avoid unwanted filter response
+        tr_filt.detrend(type='demean')
+        # filter and taper data
         tr_filt.filter('bandpass', freqmin=bpz1[0], freqmax=bpz1[1],
                        zerophase=False)
         tr_filt.taper(max_percentage=0.05, type='hann')
         z_copy[0].data = tr_filt.data
         ##############################################################
         # check length of waveform and compare with cut times
-        Lc = pstop - pstart
+
+        # for global seismology: use tau-p method for estimating travel times (needs source and station coords.)
+        # if not given: sets Lc to infinity to use full stream
+        if use_taup == True:
+            Lc = np.inf
+            print('autopickstation: use_taup flag active.')
+            if not metadata[1]:
+                print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
+            else:
+                station_id = wfstream[0].get_id()
+                parser = metadata[1]
+                station_coords = get_source_coords(parser, station_id)
+                if station_coords and origin:
+                    source_origin = origin[0]
+                    model = TauPyModel(taup_model)
+                    arrivals = model.get_travel_times_geo(
+                        source_origin.depth,
+                        source_origin.latitude,
+                        source_origin.longitude,
+                        station_coords['latitude'],
+                        station_coords['longitude']
+                    )
+                    phases = {'P': [],
+                              'S': []}
+                    for arr in arrivals:
+                        phases[identifyPhaseID(arr.phase.name)].append(arr)
+
+                    # get first P and S onsets from arrivals list
+                    arrP, estFirstP = min([(arr, arr.time) for arr in phases['P']], key = lambda t: t[1])
+                    arrS, estFirstS = min([(arr, arr.time) for arr in phases['S']], key = lambda t: t[1])
+                    print('autopick: estimated first arrivals for P: {} s, S:{} s after event'
+                          ' origin time using TauPy'.format(estFirstP, estFirstS))
+
+                    # modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
+                    pstart += (source_origin.time + estFirstP) - zdat[0].stats.starttime
+                    pstop += (source_origin.time + estFirstP) - zdat[0].stats.starttime
+                    print('autopick: CF calculation times respectively:'
+                          ' pstart: {} s, pstop: {} s'.format(pstart, pstop))
+                elif not origin:
+                    print('No source origins given!')
+
+        # make sure pstart and pstop are inside zdat[0]
+        pstart = max(pstart, 0)
+        pstop = min(pstop, len(zdat[0])*zdat[0].stats.delta)
+
+        if not use_taup == True or origin:
+            Lc = pstop - pstart
+
         Lwf = zdat[0].stats.endtime - zdat[0].stats.starttime
-        Ldiff = Lwf - Lc
+        if not Lwf > 0:
-        if Ldiff < 0:
+            print('autopickstation: empty trace! Return!')
+            return
+
+        Ldiff = Lwf - abs(Lc)
+        if Ldiff < 0 or pstop <= pstart:
             msg = 'autopickstation: Cutting times are too large for actual ' \
                   'waveform!\nUsing entire waveform instead!'
             if verbose: print(msg)
@@ -235,9 +327,17 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
         key = 'aicFig'
         if fig_dict:
             fig = fig_dict[key]
+            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
         else:
             fig = None
-        aicpick = AICPicker(aiccf, tsnrz, pickwinP, iplot, None, tsmoothP, fig=fig)
+            linecolor = 'k'
+        aicpick = AICPicker(aiccf, tsnrz, pickwinP, iplot, None, aictsmoothP, fig=fig, linecolor=linecolor)
+        # add pstart and pstop to aic plot
+        if fig:
+            for ax in fig.axes:
+                ax.vlines(pstart, ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P start')
+                ax.vlines(pstop, ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P stop')
+                ax.legend(loc=1)
         ##############################################################
         if aicpick.getpick() is not None:
             # check signal length to detect spuriously picked noise peaks
@@ -254,16 +354,21 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 key = 'slength'
                 if fig_dict:
                     fig = fig_dict[key]
+                    linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                 else:
                     fig = None
+                    linecolor = 'k'
                 Pflag = checksignallength(zne, aicpick.getpick(), tsnrz,
                                           minsiglength / 2,
                                           nfacsl, minpercent, iplot,
-                                          fig)
+                                          fig, linecolor)
             else:
                 # filter and taper horizontal traces
                 trH1_filt = edat.copy()
                 trH2_filt = ndat.copy()
+                # remove constant offset from data to avoid unwanted filter response
+                trH1_filt.detrend(type='demean')
+                trH2_filt.detrend(type='demean')
                 trH1_filt.filter('bandpass', freqmin=bph1[0],
                                  freqmax=bph1[1],
                                  zerophase=False)
@@ -276,12 +381,14 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 zne += trH2_filt
                 if fig_dict:
                     fig = fig_dict['slength']
+                    linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                 else:
                     fig = None
+                    linecolor = 'k'
                 Pflag = checksignallength(zne, aicpick.getpick(), tsnrz,
                                           minsiglength,
                                           nfacsl, minpercent, iplot,
-                                          fig)
+                                          fig, linecolor)
 
             if Pflag == 1:
                 # check for spuriously picked S onset
@@ -291,13 +398,15 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                           'Skipping control function checkZ4S.'
                     if verbose: print(msg)
                 else:
-                    if iplot>1:
+                    if iplot > 1:
                         if fig_dict:
                             fig = fig_dict['checkZ4s']
+                            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                         else:
                             fig = None
+                            linecolor = 'k'
                     Pflag = checkZ4S(zne, aicpick.getpick(), zfac,
-                                     tsnrz[3], iplot, fig)
+                                     tsnrz[2], iplot, fig, linecolor)
                     if Pflag == 0:
                         Pmarker = 'SinsteadP'
                         Pweight = 9
@@ -306,8 +415,11 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 Pweight = 9
         ##############################################################
         # go on with processing if AIC onset passes quality control
-        if (aicpick.getSlope() >= minAICPslope and
+        slope = aicpick.getSlope()
-                    aicpick.getSNR() >= minAICPSNR and Pflag == 1):
+        if not slope:
+            slope = 0
+        if (slope >= minAICPslope and
+            aicpick.getSNR() >= minAICPSNR and Pflag == 1):
             aicPflag = 1
             msg = 'AIC P-pick passes quality control: Slope: {0} counts/s, ' \
                   'SNR: {1}\nGo on with refined picking ...\n' \
@@ -317,6 +429,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             # re-filter waveform with larger bandpass
             z_copy = zdat.copy()
             tr_filt = zdat[0].copy()
+            tr_filt.detrend(type='demean')
             tr_filt.filter('bandpass', freqmin=bpz2[0], freqmax=bpz2[1],
                            zerophase=False)
             tr_filt.taper(max_percentage=0.05, type='hann')
@@ -346,10 +459,12 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 algoP=algoP)
             if fig_dict:
                 fig = fig_dict['refPpick']
+                linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
             else:
                 fig = None
+                linecolor = 'k'
             refPpick = PragPicker(cf2, tsnrz, pickwinP, iplot, ausP, tsmoothP,
-                                  aicpick.getpick(), fig)
+                                  aicpick.getpick(), fig, linecolor)
             mpickP = refPpick.getpick()
             #############################################################
             if mpickP is not None:
@@ -358,28 +473,34 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 if iplot:
                     if fig_dict:
                         fig = fig_dict['el_Ppick']
+                        linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                     else:
                         fig = None
+                        linecolor = 'k'
                     epickP, lpickP, Perror = earllatepicker(z_copy, nfacP, tsnrz,
-                                                            mpickP, iplot, fig=fig)
+                                                            mpickP, iplot, fig=fig,
+                                                            linecolor=linecolor)
                 else:
                     epickP, lpickP, Perror = earllatepicker(z_copy, nfacP, tsnrz,
-                                                              mpickP, iplot)
+                                                            mpickP, iplot)
 
                 # get SNR
                 [SNRP, SNRPdB, Pnoiselevel] = getSNR(z_copy, tsnrz, mpickP)
 
                 # weight P-onset using symmetric error
-                if Perror <= timeerrorsP[0]:
+                if Perror == None:
-                    Pweight = 0
-                elif timeerrorsP[0] < Perror <= timeerrorsP[1]:
-                    Pweight = 1
-                elif timeerrorsP[1] < Perror <= timeerrorsP[2]:
-                    Pweight = 2
-                elif timeerrorsP[2] < Perror <= timeerrorsP[3]:
-                    Pweight = 3
-                elif Perror > timeerrorsP[3]:
                     Pweight = 4
+                else:
+                    if Perror <= timeerrorsP[0]:
+                        Pweight = 0
+                    elif timeerrorsP[0] < Perror <= timeerrorsP[1]:
+                        Pweight = 1
+                    elif timeerrorsP[1] < Perror <= timeerrorsP[2]:
+                        Pweight = 2
+                    elif timeerrorsP[2] < Perror <= timeerrorsP[3]:
+                        Pweight = 3
+                    elif Perror > timeerrorsP[3]:
+                        Pweight = 4
 
                 ##############################################################
                 # get first motion of P onset
@@ -388,11 +509,12 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                     if iplot:
                         if fig_dict:
                             fig = fig_dict['fm_picker']
+                            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                         else:
                             fig = None
-                        FM = fmpicker(zdat, z_copy, fmpickwin, mpickP, iplot, fig)
+                        FM = fmpicker(zdat, z_copy, fmpickwin, mpickP, iplot, fig, linecolor)
                     else:
-                        FM = fmpicker(zdat, z_copy, fmpickwin, mpickP, iplot)                        
+                        FM = fmpicker(zdat, z_copy, fmpickwin, mpickP, iplot)
                 else:
                     FM = 'N'
 
@@ -402,6 +524,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                                                                      SNRPdB,
                                                                      FM)
                 print(msg)
+                msg = 'autopickstation: Refined P-Pick: {} s | P-Error: {} s'.format(mpickP, Perror)
+                print(msg)
                 Sflag = 1
 
         else:
@@ -419,16 +543,46 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
         print('autopickstation: No vertical component data available!, '
               'Skipping station!')
 
-    if edat is not None and ndat is not None and len(edat) > 0 and len(
+    if ((len(edat) > 0 and len(ndat) == 0) or (
-            ndat) > 0 and Pweight < 4:
+        len(ndat) > 0 and len(edat) == 0)) and Pweight < 4:
+        msg = 'Go on picking S onset ...\n' \
+              '##################################################\n' \
+              'Only one horizontal component available!\n' \
+              'ARH prediction requires at least 2 components!\n' \
+              'Copying existing horizontal component ...'
+        if verbose: print(msg)
+
+        # check which component is missing
+        if len(edat) == 0:
+            edat = ndat
+        else:
+            ndat = edat
+
+    pickSonset = (edat is not None and ndat is not None and len(edat) > 0 and len(
+                  ndat) > 0 and Pweight < 4)
+
+    if pickSonset:
+        # determine time window for calculating CF after P onset
+        cuttimesh = [
+            round(max([mpickP + sstart, 0])), # MP MP relative time axis
+            round(min([
+                mpickP + sstop,
+                edat[0].stats.endtime-edat[0].stats.starttime,
+                ndat[0].stats.endtime-ndat[0].stats.starttime
+            ]))
+        ]
+
+        if not cuttimesh[1] >= cuttimesh[0]:
+            print('Cut window for horizontal phases too small! Will not pick S onsets.')
+            pickSonset = False
+
+    if pickSonset:
         msg = 'Go on picking S onset ...\n' \
               '##################################################\n' \
               'Working on S onset of station {0}\nFiltering horizontal ' \
               'traces ...'.format(edat[0].stats.station)
         if verbose: print(msg)
-        # determine time window for calculating CF after P onset
+
-        cuttimesh = [round(max([mpickP + sstart, 0])),
-                     round(min([mpickP + sstop, Lwf]))]
 
         if algoS == 'ARH':
             # re-create stream object including both horizontal components
@@ -438,6 +592,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             # filter and taper data
             trH1_filt = hdat[0].copy()
             trH2_filt = hdat[1].copy()
+            trH1_filt.detrend(type='demean')
+            trH2_filt.detrend(type='demean')
             trH1_filt.filter('bandpass', freqmin=bph1[0], freqmax=bph1[1],
                              zerophase=False)
             trH2_filt.filter('bandpass', freqmin=bph1[0], freqmax=bph1[1],
@@ -456,6 +612,9 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             trH1_filt = hdat[0].copy()
             trH2_filt = hdat[1].copy()
             trH3_filt = hdat[2].copy()
+            trH1_filt.detrend(type='demean')
+            trH2_filt.detrend(type='demean')
+            trH3_filt.detrend(type='demean')
             trH1_filt.filter('bandpass', freqmin=bph1[0], freqmax=bph1[1],
                              zerophase=False)
             trH2_filt.filter('bandpass', freqmin=bph1[0], freqmax=bph1[1],
@@ -493,15 +652,20 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
         # of class AutoPicking
         if fig_dict:
             fig = fig_dict['aicARHfig']
+            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
         else:
             fig = None
+            linecolor = 'k'
         aicarhpick = AICPicker(haiccf, tsnrh, pickwinS, iplot, None,
-                               aictsmoothS, fig=fig)
+                               aictsmoothS, fig=fig, linecolor=linecolor)
         ###############################################################
         # go on with processing if AIC onset passes quality control
-        if (aicarhpick.getSlope() >= minAICSslope and
+        slope = aicarhpick.getSlope()
-                    aicarhpick.getSNR() >= minAICSSNR and
+        if not slope:
-                    aicarhpick.getpick() is not None):
+            slope = 0
+        if (slope >= minAICSslope and
+            aicarhpick.getSNR() >= minAICSSNR and
+            aicarhpick.getpick() is not None):
             aicSflag = 1
             msg = 'AIC S-pick passes quality control: Slope: {0} counts/s, ' \
                   'SNR: {1}\nGo on with refined picking ...\n' \
@@ -518,6 +682,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             if algoS == 'ARH':
                 trH1_filt = hdat[0].copy()
                 trH2_filt = hdat[1].copy()
+                trH1_filt.detrend(type='demean')
+                trH2_filt.detrend(type='demean')
                 trH1_filt.filter('bandpass', freqmin=bph2[0], freqmax=bph2[1],
                                  zerophase=False)
                 trH2_filt.filter('bandpass', freqmin=bph2[0], freqmax=bph2[1],
@@ -533,6 +699,9 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 trH1_filt = hdat[0].copy()
                 trH2_filt = hdat[1].copy()
                 trH3_filt = hdat[2].copy()
+                trH1_filt.detrend(type='demean')
+                trH2_filt.detrend(type='demean')
+                trH3_filt.detrend(type='demean')
                 trH1_filt.filter('bandpass', freqmin=bph2[0], freqmax=bph2[1],
                                  zerophase=False)
                 trH2_filt.filter('bandpass', freqmin=bph2[0], freqmax=bph2[1],
@@ -552,10 +721,12 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             # get refined onset time from CF2 using class Picker
             if fig_dict:
                 fig = fig_dict['refSpick']
+                linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
             else:
                 fig = None
+                linecolor = 'k'
             refSpick = PragPicker(arhcf2, tsnrh, pickwinS, iplot, ausS,
-                                  tsmoothS, aicarhpick.getpick(), fig)
+                                  tsmoothS, aicarhpick.getpick(), fig, linecolor)
             mpickS = refSpick.getpick()
             #############################################################
             if mpickS is not None:
@@ -565,27 +736,33 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 if iplot:
                     if fig_dict:
                         fig = fig_dict['el_S1pick']
+                        linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                     else:
                         fig = None
-                    epickS1, lpickS1, Serror1  = earllatepicker(h_copy, nfacS,
+                        linecolor = 'k'
-                                                                tsnrh,
+                    epickS1, lpickS1, Serror1 = earllatepicker(h_copy, nfacS,
-                                                                mpickS, iplot,
+                                                               tsnrh,
-                                                                fig=fig)
+                                                               mpickS, iplot,
+                                                               fig=fig,
+                                                               linecolor=linecolor)
                 else:
                     epickS1, lpickS1, Serror1 = earllatepicker(h_copy, nfacS,
                                                                tsnrh,
                                                                mpickS, iplot)
-                    
+
                 h_copy[0].data = trH2_filt.data
                 if iplot:
                     if fig_dict:
                         fig = fig_dict['el_S2pick']
+                        linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
                     else:
                         fig = None
+                        linecolor = ''
                     epickS2, lpickS2, Serror2 = earllatepicker(h_copy, nfacS,
                                                                tsnrh,
                                                                mpickS, iplot,
-                                                               fig=fig)
+                                                               fig=fig,
+                                                               linecolor=linecolor)
                 else:
                     epickS2, lpickS2, Serror2 = earllatepicker(h_copy, nfacS,
                                                                tsnrh,
@@ -629,6 +806,9 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                     lpickS = lpick[ipick]
                     Serror = pickerr[ipick]
 
+                    msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(mpickS, Serror)
+                    print(msg)
+
                     # get SNR
                     [SNRS, SNRSdB, Snoiselevel] = getSNR(h_copy, tsnrh, mpickS)
 
@@ -651,7 +831,6 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 ################################################################
                 # get Wood-Anderson peak-to-peak amplitude
                 # initialize Data object
-                data = Data()
                 # re-create stream object including both horizontal components
                 hdat = edat.copy()
                 hdat += ndat
@@ -670,21 +849,33 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             ############################################################
             # get Wood-Anderson peak-to-peak amplitude
             # initialize Data object
-            data = Data()
             # re-create stream object including both horizontal components
             hdat = edat.copy()
             hdat += ndat
+ 
     else:
-        print('autopickstation: No horizontal component data available or ' \
+        print('autopickstation: No horizontal component data available or '
               'bad P onset, skipping S picking!')
 
     ##############################################################
+    try:
+       iplot = int(iplot)
+    except:
+       if iplot == True or iplot == 'True':
+           iplot = 2
+       else:
+           iplot = 0
+
     if iplot > 0:
         # plot vertical trace
-        if not fig_dict:
+        if fig_dict == None or fig_dict == 'None':
             fig = plt.figure()
+            plt_flag = 1
+            linecolor = 'k'
         else:
             fig = fig_dict['mainFig']
+            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
+        fig._tight = True
         ax1 = fig.add_subplot(311)
         tdata = np.arange(0, zdat[0].stats.npts / tr_filt.stats.sampling_rate,
                           tr_filt.stats.delta)
@@ -692,7 +883,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
         wfldiff = len(tr_filt.data) - len(tdata)
         if wfldiff < 0:
             tdata = tdata[0:len(tdata) - abs(wfldiff)]
-        ax1.plot(tdata, tr_filt.data / max(tr_filt.data), 'k', label='Data')
+        ax1.plot(tdata, tr_filt.data / max(tr_filt.data), color=linecolor, linewidth=0.7, label='Data')
         if Pweight < 4:
             ax1.plot(cf1.getTimeArray(), cf1.getCF() / max(cf1.getCF()),
                      'b', label='CF1')
@@ -706,7 +897,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 ax1.plot([aicpick.getpick() - 0.5, aicpick.getpick() + 0.5],
                          [-1, -1], 'r')
                 ax1.plot([refPpick.getpick(), refPpick.getpick()],
-                             [-1.3, 1.3], 'r', linewidth=2, label='Final P Pick')
+                         [-1.3, 1.3], 'r', linewidth=2, label='Final P Pick')
                 ax1.plot([refPpick.getpick() - 0.5, refPpick.getpick() + 0.5],
                          [1.3, 1.3], 'r', linewidth=2)
                 ax1.plot([refPpick.getpick() - 0.5, refPpick.getpick() + 0.5],
@@ -714,28 +905,35 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 ax1.plot([lpickP, lpickP], [-1.1, 1.1], 'r--', label='lpp')
                 ax1.plot([epickP, epickP], [-1.1, 1.1], 'r--', label='epp')
                 ax1.set_title('%s, %s, P Weight=%d, SNR=%7.2f, SNR[dB]=%7.2f '
-                             'Polarity: %s' % (tr_filt.stats.station,
+                              'Polarity: %s' % (tr_filt.stats.station,
-                                               tr_filt.stats.channel,
+                                                tr_filt.stats.channel,
-                                               Pweight,
+                                                Pweight,
-                                               SNRP,
+                                                SNRP,
-                                               SNRPdB,
+                                                SNRPdB,
-                                               FM))
+                                                FM))
             else:
                 ax1.set_title('%s, P Weight=%d, SNR=None, '
-                             'SNRdB=None' % (tr_filt.stats.channel, Pweight))
+                              'SNRdB=None' % (tr_filt.stats.channel, Pweight))
         else:
             ax1.set_title('%s, %s, P Weight=%d' % (tr_filt.stats.station,
-                                               tr_filt.stats.channel,
+                                                   tr_filt.stats.channel,
-                                               Pweight))
+                                                   Pweight))
-        ax1.legend()
+        ax1.legend(loc=1)
         ax1.set_yticks([])
         ax1.set_ylim([-1.5, 1.5])
         ax1.set_ylabel('Normalized Counts')
-        #fig.suptitle(tr_filt.stats.starttime)
+        # fig.suptitle(tr_filt.stats.starttime)
-
+        try:
+            len(edat[0])
+        except:
+            edat = ndat
+        try:
+            len(ndat[0])
+        except:
+            ndat = edat
         if len(edat[0]) > 1 and len(ndat[0]) > 1 and Sflag == 1:
             # plot horizontal traces
-            ax2 = fig.add_subplot(3,1,2,sharex=ax1)
+            ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
             th1data = np.arange(0,
                                 trH1_filt.stats.npts /
                                 trH1_filt.stats.sampling_rate,
@@ -744,13 +942,13 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             wfldiff = len(trH1_filt.data) - len(th1data)
             if wfldiff < 0:
                 th1data = th1data[0:len(th1data) - abs(wfldiff)]
-            ax2.plot(th1data, trH1_filt.data / max(trH1_filt.data), 'k', label='Data')
+            ax2.plot(th1data, trH1_filt.data / max(trH1_filt.data), color=linecolor, linewidth=0.7, label='Data')
             if Pweight < 4:
                 ax2.plot(arhcf1.getTimeArray(),
                          arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1')
-                if aicSflag == 1:
+                if aicSflag == 1 and Sweight < 4:
                     ax2.plot(arhcf2.getTimeArray(),
-                                 arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2')
+                             arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2')
                     ax2.plot(
                         [aicarhpick.getpick(), aicarhpick.getpick()],
                         [-1, 1], 'g', label='Initial S Onset')
@@ -778,13 +976,13 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                 else:
                     ax2.set_title('%s, S Weight=%d, SNR=None, SNRdB=None' % (
                         trH1_filt.stats.channel, Sweight))
-            ax2.legend()
+            ax2.legend(loc=1)
             ax2.set_yticks([])
             ax2.set_ylim([-1.5, 1.5])
             ax2.set_ylabel('Normalized Counts')
-            #fig.suptitle(trH1_filt.stats.starttime)
+            # fig.suptitle(trH1_filt.stats.starttime)
 
-            ax3 = fig.add_subplot(3,1,3, sharex=ax1)
+            ax3 = fig.add_subplot(3, 1, 3, sharex=ax1)
             th2data = np.arange(0,
                                 trH2_filt.stats.npts /
                                 trH2_filt.stats.sampling_rate,
@@ -793,7 +991,7 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
             wfldiff = len(trH2_filt.data) - len(th2data)
             if wfldiff < 0:
                 th2data = th2data[0:len(th2data) - abs(wfldiff)]
-            ax3.plot(th2data, trH2_filt.data / max(trH2_filt.data), 'k', label='Data')
+            ax3.plot(th2data, trH2_filt.data / max(trH2_filt.data), color=linecolor, linewidth=0.7, label='Data')
             if Pweight < 4:
                 p22, = ax3.plot(arhcf1.getTimeArray(),
                                 arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1')
@@ -821,18 +1019,23 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                         [-1.3, -1.3], 'g', linewidth=2)
                     ax3.plot([lpickS, lpickS], [-1.1, 1.1], 'g--', label='lpp')
                     ax3.plot([epickS, epickS], [-1.1, 1.1], 'g--', label='epp')
-            ax3.legend()
+            ax3.legend(loc=1)
             ax3.set_yticks([])
             ax3.set_ylim([-1.5, 1.5])
             ax3.set_xlabel('Time [s] after %s' % tr_filt.stats.starttime)
             ax3.set_ylabel('Normalized Counts')
             ax3.set_title(trH2_filt.stats.channel)
+            if plt_flag == 1:
+                fig.show()
+                try: input()
+                except SyntaxError: pass
+                plt.close(fig)
     ##########################################################################
     # calculate "real" onset times
     if lpickP is not None and lpickP == mpickP:
-        lpickP += timeerrorsP[0]
+        lpickP += zdat[0].stats.delta
     if epickP is not None and epickP == mpickP:
-        epickP -= timeerrorsP[0]
+        epickP -= zdat[0].stats.delta
     if mpickP is not None and epickP is not None and lpickP is not None:
         lpickP = zdat[0].stats.starttime + lpickP
         epickP = zdat[0].stats.starttime + epickP
@@ -844,20 +1047,27 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
         epickP = zdat[0].stats.starttime - timeerrorsP[3]
         mpickP = zdat[0].stats.starttime
 
+    if edat:
+        hdat = edat[0]
+    elif ndat:
+        hdat = ndat[0]
+    else:
+        return
+
     if lpickS is not None and lpickS == mpickS:
-        lpickS += timeerrorsS[0]
+        lpickS += hdat.stats.delta
     if epickS is not None and epickS == mpickS:
-        epickS -= timeerrorsS[0]
+        epickS -= hdat.stats.delta
     if mpickS is not None and epickS is not None and lpickS is not None:
-        lpickS = edat[0].stats.starttime + lpickS
+        lpickS = hdat.stats.starttime + lpickS
-        epickS = edat[0].stats.starttime + epickS
+        epickS = hdat.stats.starttime + epickS
-        mpickS = edat[0].stats.starttime + mpickS
+        mpickS = hdat.stats.starttime + mpickS
     else:
         # dummy values (start of seismic trace) in order to derive
         # theoretical onset times for iteratve picking
-        lpickS = edat[0].stats.starttime + timeerrorsS[3]
+        lpickS = hdat.stats.starttime + timeerrorsS[3]
-        epickS = edat[0].stats.starttime - timeerrorsS[3]
+        epickS = hdat.stats.starttime - timeerrorsS[3]
-        mpickS = edat[0].stats.starttime
+        mpickS = hdat.stats.starttime
 
     # create dictionary
     # for P phase
@@ -867,8 +1077,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
                  snrdb=SNRPdB, weight=Pweight, fm=FM, w0=None, fc=None, Mo=None,
                  Mw=None, picker=picker, marked=Pmarker)
     # add S phase
-    ccode = edat[0].stats.channel
+    ccode = hdat.stats.channel
-    ncode = edat[0].stats.network
+    ncode = hdat.stats.network
     spick = dict(channel=ccode, network=ncode, lpp=lpickS, epp=epickS, mpp=mpickS, spe=Serror, snr=SNRS,
                  snrdb=SNRSdB, weight=Sweight, fm=None, picker=picker, Ao=Ao)
     # merge picks into returning dictionary
@@ -923,17 +1133,21 @@ def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None):
         Precalcwin_old = pickparameter.get('Precalcwin')
         noisefactor_old = pickparameter.get('noisefactor')
         zfac_old = pickparameter.get('zfac')
-        pickparameter.setParam(
+        twindows = pickparameter.get('tsnrz')
-            pstart=max([0, badpicks[i][1] - wf2pick[0].stats.starttime \
+        tsafety = twindows[1]
-                        - pickparameter.get('tlta')]))
+        pstart = max([0, badpicks[i][1] - wf2pick[0].stats.starttime - pickparameter.get('tlta')])
-        pickparameter.setParam(pstop=pickparameter.get('pstart') + \
+        if abs(float(res)) <= tsafety / 2 or pstart == 0:
-                                     (3 * pickparameter.get('tlta')))
+            print("iteratepicker: Small residuum, leave parameters unchanged for this phase!")
-        pickparameter.setParam(sstop=pickparameter.get('sstop') / 2)
+        else:
-        pickparameter.setParam(pickwinP=pickparameter.get('pickwinP') / 2)
+            pickparameter.setParam(pstart=pstart)
-        pickparameter.setParam(
+            pickparameter.setParam(pstop=pickparameter.get('pstart') + \
-            Precalcwin=pickparameter.get('Precalcwin') / 2)
+                                         (pickparameter.get('Precalcwin')))
-        pickparameter.setParam(noisefactor=1.0)
+            pickparameter.setParam(sstop=pickparameter.get('sstop') / 2)
-        pickparameter.setParam(zfac=1.0)
+            pickparameter.setParam(pickwinP=pickparameter.get('pickwinP') / 2)
+            pickparameter.setParam(Precalcwin=pickparameter.get('Precalcwin') / 2)
+            pickparameter.setParam(noisefactor=1.0)
+            pickparameter.setParam(zfac=1.0)
+
         print(
             "iteratepicker: The following picking parameters have been modified for iterative picking:")
         print(

pylot/core/pick/charfuns.py

@@ -17,7 +17,6 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 :author: MAGS2 EP3 working group
 """
 
-import matplotlib.pyplot as plt
 import numpy as np
 from obspy.core import Stream
 
@@ -27,7 +26,7 @@ class CharacteristicFunction(object):
     SuperClass for different types of characteristic functions.
     '''
 
-    def __init__(self, data, cut, t2=None, order=None, t1=None, fnoise=None, stealthMode=False):
+    def __init__(self, data, cut, t2=None, order=None, t1=None, fnoise=None):
         '''
         Initialize data type object with information from the original
         Seismogram.
@@ -64,7 +63,6 @@ class CharacteristicFunction(object):
         self.calcCF(self.getDataArray())
         self.arpara = np.array([])
         self.xpred = np.array([])
-        self._stealthMode = stealthMode
 
     def __str__(self):
         return '''\n\t{name} object:\n
@@ -138,9 +136,6 @@ class CharacteristicFunction(object):
     def getXCF(self):
         return self.xcf
 
-    def _getStealthMode(self):
-        return self._stealthMode()
-
     def getDataArray(self, cut=None):
         '''
         If cut times are given, time series is cut from cut[0] (start time)
@@ -225,13 +220,11 @@ class AICcf(CharacteristicFunction):
 
     def calcCF(self, data):
 
-        # if self._getStealthMode() is False:
-        #    print 'Calculating AIC ...'
         x = self.getDataArray()
         xnp = x[0].data
-        nn = np.isnan(xnp)
+        ind = np.where(~np.isnan(xnp))[0]
-        if len(nn) > 1:
+        if ind.size:
-            xnp[nn] = 0
+            xnp[:ind[0]] = xnp[ind[0]]
         datlen = len(xnp)
         k = np.arange(1, datlen)
         cf = np.zeros(datlen)
@@ -265,13 +258,9 @@ class HOScf(CharacteristicFunction):
         if len(nn) > 1:
             xnp[nn] = 0
         if self.getOrder() == 3:  # this is skewness
-            # if self._getStealthMode() is False:
-            #    print 'Calculating skewness ...'
             y = np.power(xnp, 3)
             y1 = np.power(xnp, 2)
         elif self.getOrder() == 4:  # this is kurtosis
-            # if self._getStealthMode() is False:
-            #    print 'Calculating kurtosis ...'
             y = np.power(xnp, 4)
             y1 = np.power(xnp, 2)
 
@@ -297,9 +286,12 @@ class HOScf(CharacteristicFunction):
             elif self.getOrder() == 4:
                 LTA[j] = lta / np.power(lta1, 2)
 
-        nn = np.isnan(LTA)
+        # remove NaN's with first not-NaN-value,
-        if len(nn) > 1:
+        # so autopicker doesnt pick discontinuity at start of the trace
-            LTA[nn] = 0
+        ind = np.where(~np.isnan(LTA))[0]
+        if ind.size:
+            first = ind[0]
+            LTA[:first] = LTA[first]
         self.cf = LTA
         self.xcf = x
 
@@ -307,7 +299,7 @@ class HOScf(CharacteristicFunction):
 class ARZcf(CharacteristicFunction):
     def calcCF(self, data):
 
-        print 'Calculating AR-prediction error from single trace ...'
+        print('Calculating AR-prediction error from single trace ...')
         x = self.getDataArray(self.getCut())
         xnp = x[0].data
         nn = np.isnan(xnp)
@@ -343,7 +335,8 @@ class ARZcf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
-        cf[io] = cf[ino[0][0]]
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
 
         self.cf = cf
         self.xcf = x
@@ -430,7 +423,7 @@ class ARZcf(CharacteristicFunction):
 class ARHcf(CharacteristicFunction):
     def calcCF(self, data):
 
-        print 'Calculating AR-prediction error from both horizontal traces ...'
+        print('Calculating AR-prediction error from both horizontal traces ...')
 
         xnp = self.getDataArray(self.getCut())
         n0 = np.isnan(xnp[0].data)
@@ -466,7 +459,7 @@ class ARHcf(CharacteristicFunction):
             # prediction error = CF
             cf[i + lpred] = np.sqrt(np.sum(np.power(self.xpred[0][i:i + lpred] - xnp[0][i:i + lpred], 2) \
                                            + np.power(self.xpred[1][i:i + lpred] - xnp[1][i:i + lpred], 2)) / (
-                                    2 * lpred))
+                                        2 * lpred))
         nn = np.isnan(cf)
         if len(nn) > 1:
             cf[nn] = 0
@@ -475,7 +468,8 @@ class ARHcf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
-        cf[io] = cf[ino[0][0]]
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
 
         self.cf = cf
         self.xcf = xnp
@@ -567,7 +561,7 @@ class ARHcf(CharacteristicFunction):
 class AR3Ccf(CharacteristicFunction):
     def calcCF(self, data):
 
-        print 'Calculating AR-prediction error from all 3 components ...'
+        print('Calculating AR-prediction error from all 3 components ...')
 
         xnp = self.getDataArray(self.getCut())
         n0 = np.isnan(xnp[0].data)
@@ -608,7 +602,7 @@ class AR3Ccf(CharacteristicFunction):
             cf[i + lpred] = np.sqrt(np.sum(np.power(self.xpred[0][i:i + lpred] - xnp[0][i:i + lpred], 2) \
                                            + np.power(self.xpred[1][i:i + lpred] - xnp[1][i:i + lpred], 2) \
                                            + np.power(self.xpred[2][i:i + lpred] - xnp[2][i:i + lpred], 2)) / (
-                                    3 * lpred))
+                                        3 * lpred))
         nn = np.isnan(cf)
         if len(nn) > 1:
             cf[nn] = 0
@@ -617,7 +611,8 @@ class AR3Ccf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
-        cf[io] = cf[ino[0][0]]
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
 
         self.cf = cf
         self.xcf = xnp

pylot/core/pick/compare.py

@@ -4,11 +4,11 @@
 import copy
 import operator
 import os
-import numpy as np
-import glob
-import matplotlib.pyplot as plt
-from obspy import read_events
 
+import matplotlib.pyplot as plt
+import numpy as np
+from obspy import read_events
+from obspy.core import AttribDict
 from pylot.core.io.phases import picksdict_from_picks
 from pylot.core.util.pdf import ProbabilityDensityFunction
 from pylot.core.util.utils import find_in_list
@@ -27,16 +27,8 @@ class Comparison(object):
     """
 
     def __init__(self, **kwargs):
-        names = list()
         self._pdfs = dict()
-        for name, fn in kwargs.items():
+        names = self.iter_kwargs(kwargs)
-            if isinstance(fn, PDFDictionary):
-                self._pdfs[name] = fn
-            elif isinstance(fn, dict):
-                self._pdfs[name] = PDFDictionary(fn)
-            else:
-                self._pdfs[name] = PDFDictionary.from_quakeml(fn)
-            names.append(name)
         if len(names) > 2:
             raise ValueError('Comparison is only defined for two '
                              'arguments!')
@@ -48,6 +40,40 @@ class Comparison(object):
             return False
         return True
 
+    def iter_kwargs(self, kwargs):
+        names = list()
+        for name, fn in kwargs.items():
+            if name == 'eventlist':
+                names = self.init_by_eventlist(fn)
+                break
+            if isinstance(fn, PDFDictionary):
+                self._pdfs[name] = fn
+            elif isinstance(fn, dict) or isinstance(fn, AttribDict):
+                self._pdfs[name] = PDFDictionary(fn)
+            else:
+                self._pdfs[name] = PDFDictionary.from_quakeml(fn)
+            names.append(name)
+        return names
+
+    def init_by_eventlist(self, eventlist):
+        # create one dictionary containing all picks for all events (therefore modify station key)
+        global_picksdict = {}
+        for event in eventlist:
+            automanu = {'manu': event.pylot_picks,
+                        'auto': event.pylot_autopicks}
+            for method, picksdict in automanu.items():
+                if not method in global_picksdict.keys():
+                    global_picksdict[method] = {}
+                for station, picks in picksdict.items():
+                    new_picksdict = global_picksdict[method]
+                    # new id combining event and station in one dictionary for all events
+                    id = '{}_{}'.format(event.pylot_id, station)
+                    new_picksdict[id] = picks
+        for method, picksdict in global_picksdict.items():
+            self._pdfs[method] = PDFDictionary(picksdict)
+        names = list(global_picksdict.keys())
+        return names
+
     def get(self, name):
         return self._pdfs[name]
 
@@ -92,8 +118,8 @@ class Comparison(object):
         """
         compare_pdfs = dict()
 
-        pdf_a = self.get(self.names[0]).generate_pdf_data(type)
+        pdf_a = self.get('auto').generate_pdf_data(type)
-        pdf_b = self.get(self.names[1]).generate_pdf_data(type)
+        pdf_b = self.get('manu').generate_pdf_data(type)
 
         for station, phases in pdf_a.items():
             if station in pdf_b.keys():
@@ -154,7 +180,7 @@ class Comparison(object):
     def get_array(self, phase, method_name):
         method = operator.methodcaller(method_name)
         pdf_list = self.get_all(phase)
-        rarray = map(method, pdf_list)
+        rarray = list(map(method, pdf_list))
         return np.array(rarray)
 
     def get_expectation_array(self, phase):
@@ -252,11 +278,7 @@ class PDFDictionary(object):
 
     @classmethod
     def from_quakeml(self, fn):
-        cat = read_events(fn)
+        return PDFDictionary(fn)
-        if len(cat) > 1:
-            raise NotImplementedError('reading more than one event at the same '
-                                      'time is not implemented yet! Sorry!')
-        return PDFDictionary(picksdict_from_picks(cat[0]))
 
     def get_all(self, phase):
         rlist = list()
@@ -334,7 +356,7 @@ class PDFDictionary(object):
                     axarr[l].set_title(phase)
                     if l is 0:
                         axann = axarr[l].annotate(station, xy=(.05, .5),
-                                                     xycoords='axes fraction')
+                                                  xycoords='axes fraction')
                         bbox_props = dict(boxstyle='round', facecolor='lightgrey',
                                           alpha=.7)
                         axann.set_bbox(bbox_props)
@@ -352,7 +374,6 @@ class PDFstatistics(object):
     Takes a path as argument.
     """
 
-
     def __init__(self, directory):
         """Initiates some values needed when dealing with pdfs later"""
         self._rootdir = directory
@@ -449,7 +470,7 @@ class PDFstatistics(object):
         else:
             raise ValueError("for call to method {0} value has to be "
                              "defined but is 'None' ".format(method_options[
-                                                             property.upper()]))
+                                                                 property.upper()]))
 
         for pdf_dict in self:
             # create worklist
@@ -459,7 +480,7 @@ class PDFstatistics(object):
 
         return rlist
 
-    def writeThetaToFile(self,array,out_dir):
+    def writeThetaToFile(self, array, out_dir):
         """
         Method to write array like data to file. Useful since acquiring can take
         serious amount of time when dealing with large databases.
@@ -471,16 +492,16 @@ class PDFstatistics(object):
         """
         fid = open(os.path.join(out_dir), 'w')
         for val in array:
-            fid.write(str(val)+'\n')
+            fid.write(str(val) + '\n')
         fid.close()
 
 
 def main():
-    root_dir ='/home/sebastianp/Codetesting/xmls/'
+    root_dir = '/home/sebastianp/Codetesting/xmls/'
     Insheim = PDFstatistics(root_dir)
     Insheim.curphase = 'p'
     qdlist = Insheim.get('qdf', 0.2)
-    print qdlist
+    print(qdlist)
 
 
 if __name__ == "__main__":

pylot/core/pick/picker.py

@@ -19,12 +19,14 @@ calculated after Diehl & Kissling (2009).
 :author: MAGS2 EP3 working group / Ludger Kueperkoch
 """
 
-import numpy as np
-import matplotlib.pyplot as plt
-from pylot.core.pick.utils import getnoisewin, getsignalwin
-from pylot.core.pick.charfuns import CharacteristicFunction
 import warnings
 
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy.signal import argrelmax
+from pylot.core.pick.charfuns import CharacteristicFunction
+from pylot.core.pick.utils import getnoisewin, getsignalwin
+
 
 class AutoPicker(object):
     '''
@@ -34,7 +36,7 @@ class AutoPicker(object):
 
     warnings.simplefilter('ignore')
 
-    def __init__(self, cf, TSNR, PickWindow, iplot=None, aus=None, Tsmooth=None, Pick1=None, fig=None):
+    def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None, linecolor='k'):
         '''
         :param: cf, characteristic function, on which the picking algorithm is applied
         :type: `~pylot.core.pick.CharFuns.CharacteristicFunction` object
@@ -61,7 +63,8 @@ class AutoPicker(object):
         '''
 
         assert isinstance(cf, CharacteristicFunction), "%s is not a CharacteristicFunction object" % str(cf)
-
+        self._linecolor = linecolor
+        self._pickcolor_p = 'b'
         self.cf = cf.getCF()
         self.Tcf = cf.getTimeArray()
         self.Data = cf.getXCF()
@@ -153,6 +156,15 @@ class AICPicker(AutoPicker):
         self.Pick = None
         self.slope = None
         self.SNR = None
+        plt_flag = 0
+        try:
+            iplot = int(self.iplot)
+        except:
+            if self.iplot == True or self.iplot == 'True':
+               iplot = 2
+            else:
+               iplot = 0
+
         # find NaN's
         nn = np.isnan(self.cf)
         if len(nn) > 1:
@@ -208,106 +220,146 @@ class AICPicker(AutoPicker):
             inoise = getnoisewin(self.Tcf, self.Pick, self.TSNR[0], self.TSNR[1])
             # check, if these are counts or m/s, important for slope estimation!
             # this is quick and dirty, better solution?
-            if max(self.Data[0].data < 1e-3):
+            if max(self.Data[0].data < 1e-3) and max(self.Data[0].data >= 1e-6):
-                self.Data[0].data = self.Data[0].data * 1000000
+                self.Data[0].data = self.Data[0].data * 1000000.
+            elif max(self.Data[0].data < 1e-6):
+                self.Data[0].data = self.Data[0].data * 1e13
             # get signal window
             isignal = getsignalwin(self.Tcf, self.Pick, self.TSNR[2])
-            ii = min([isignal[len(isignal)-1], len(self.Tcf)])
+            if len(isignal) == 0:
+                return
+            ii = min([isignal[len(isignal) - 1], len(self.Tcf)])
             isignal = isignal[0:ii]
             try:
-               aic[isignal]
+                self.Data[0].data[isignal]
             except IndexError as e:
-               msg = "Time series out of bounds! {}".format(e)
+                msg = "Time series out of bounds! {}".format(e)
-               print(msg)
+                print(msg)
-               return
+                return
             # calculate SNR from CF
-            self.SNR = max(abs(aic[isignal] - np.mean(aic[isignal]))) / \
+            self.SNR = max(abs(self.Data[0].data[isignal] - np.mean(self.Data[0].data[isignal]))) / \
-                       max(abs(aic[inoise] - np.mean(aic[inoise])))
+                       max(abs(self.Data[0].data[inoise] - np.mean(self.Data[0].data[inoise])))
             # calculate slope from CF after initial pick
             # get slope window
             tslope = self.TSNR[3]  # slope determination window
-            islope = np.where((self.Tcf <= min([self.Pick + tslope, len(self.Data[0].data)])) \
+            islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \
-                              & (self.Tcf >= self.Pick))
+                              & (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
             # find maximum within slope determination window
             # 'cause slope should be calculated up to first local minimum only!
-            imax = np.argmax(self.Data[0].data[islope])
+            try:
-            iislope = islope[0][0:imax]
+                dataslope = self.Data[0].data[islope[0][0:-1]]
-            if len(iislope) <= 2:
+            except IndexError:
+                print("Slope Calculation: empty array islope, check signal window")
+                return
+            if len(dataslope) < 1:
+                print('No data in slope window found!')
+                return
+            imaxs, = argrelmax(dataslope)
+            if imaxs.size:
+                imax = imaxs[0]
+            else:
+                imax = np.argmax(dataslope)
+            iislope = islope[0][0:imax + 1]
+            if len(iislope) < 2:
                 # calculate slope from initial onset to maximum of AIC function
                 print("AICPicker: Not enough data samples left for slope calculation!")
                 print("Calculating slope from initial onset to maximum of AIC function ...")
-                imax = np.argmax(aicsmooth[islope])
+                imax = np.argmax(aicsmooth[islope[0][0:-1]])
                 if imax == 0:
                     print("AICPicker: Maximum for slope determination right at the beginning of the window!")
                     print("Choose longer slope determination window!")
                     if self.iplot > 1:
-                        if not self.fig:
+                        if self.fig == None or self.fig == 'None':
-                            fig = plt.figure() #self.iplot) ### WHY? MP MP
+                            fig = plt.figure()
+                            plt_flag = 1
                         else:
                             fig = self.fig
                         ax = fig.add_subplot(111)
                         x = self.Data[0].data
-                        ax.plot(self.Tcf, x / max(x), 'k', label='(HOS-/AR-) Data')
+                        ax.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
                         ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
-                        ax.legend()
+                        ax.legend(loc=1)
                         ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
                         ax.set_yticks([])
                         ax.set_title(self.Data[0].stats.station)
+                        if plt_flag == 1:
+                            fig.show()
+                            try: input()
+                            except SyntaxError: pass
+                            plt.close(fig)
                     return
-                iislope = islope[0][0:imax]
+                iislope = islope[0][0:imax+1]
             dataslope = self.Data[0].data[iislope]
             # calculate slope as polynomal fit of order 1
             xslope = np.arange(0, len(dataslope), 1)
             P = np.polyfit(xslope, dataslope, 1)
             datafit = np.polyval(P, xslope)
-            if datafit[0] >= datafit[len(datafit) - 1]:
+            if datafit[0] >= datafit[-1]:
                 print('AICPicker: Negative slope, bad onset skipped!')
                 return
-            self.slope = 1 / tslope * (datafit[len(dataslope) - 1] - datafit[0])
+            self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
 
         else:
             self.SNR = None
             self.slope = None
 
-        if self.iplot > 1:
+        if iplot > 1:
-            if not self.fig:
+            if self.fig == None or self.fig == 'None':
-                fig = plt.figure()#self.iplot)
+                fig = plt.figure()  # self.iplot)
+                plt_flag = 1
             else:
                 fig = self.fig
+            fig._tight = True
             ax1 = fig.add_subplot(211)
             x = self.Data[0].data
-            ax1.plot(self.Tcf, x / max(x), 'k', label='(HOS-/AR-) Data')
+            if len(self.Tcf) > len(self.Data[0].data): # why? LK
+                self.Tcf = self.Tcf[0:len(self.Tcf)-1]
+            ax1.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
             ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
             if self.Pick is not None:
                 ax1.plot([self.Pick, self.Pick], [-0.1, 0.5], 'b', linewidth=2, label='AIC-Pick')
             ax1.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
             ax1.set_yticks([])
-            ax1.legend()
+            ax1.legend(loc=1)
-            
+
             if self.Pick is not None:
-                ax2 = fig.add_subplot(2,1,2, sharex=ax1)
+                ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
-                ax2.plot(self.Tcf, x, 'k', label='Data')
+                ax2.plot(self.Tcf, x, color=self._linecolor, linewidth=0.7, label='Data')
-                ax1.axvspan(self.Tcf[inoise[0]],self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
+                ax1.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
-                ax1.axvspan(self.Tcf[isignal[0]],self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
+                ax1.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
-                ax1.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')
+                            label='Signal Window')
-                
+                ax1.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
-                ax2.axvspan(self.Tcf[inoise[0]],self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
+                            label='Slope Window')
-                ax2.axvspan(self.Tcf[isignal[0]],self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
+
-                ax2.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')                
+                ax2.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
+                ax2.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
+                            label='Signal Window')
+                ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
+                            label='Slope Window')
                 ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope')
-                
+
                 ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station,
-                                                                                self.SNR, self.slope))
+                                                                                 self.SNR, self.slope))
                 ax2.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
                 ax2.set_ylabel('Counts')
                 ax2.set_yticks([])
-                ax2.legend()
+                ax2.legend(loc=1)
+                if plt_flag == 1:
+                    fig.show()
+                    try: input()
+                    except SyntaxError: pass
+                    plt.close(fig)
             else:
                 ax1.set_title(self.Data[0].stats.station)
+                if plt_flag == 1:
+                    fig.show()
+                    try: input()
+                    except SyntaxError: pass
+                    plt.close(fig)
 
         if self.Pick == None:
             print('AICPicker: Could not find minimum, picking window too short?')
-            
+
         return
 
 
@@ -317,7 +369,15 @@ class PragPicker(AutoPicker):
     '''
 
     def calcPick(self):
-        
+
+        try:
+            iplot = int(self.getiplot())
+        except:
+            if self.getiplot() == True or self.getiplot() == 'True':
+               iplot = 2
+            else:
+               iplot = 0
+
         if self.getpick1() is not None:
             print('PragPicker: Get most likely pick from HOS- or AR-CF using pragmatic picking algorithm ...')
 
@@ -325,6 +385,7 @@ class PragPicker(AutoPicker):
             self.SNR = None
             self.slope = None
             pickflag = 0
+            plt_flag = 0
             # smooth CF
             ismooth = int(round(self.Tsmooth / self.dt))
             cfsmooth = np.zeros(len(self.cf))
@@ -349,12 +410,19 @@ class PragPicker(AutoPicker):
             ipick1 = np.argmin(abs(self.Tcf - self.getpick1()))
             cfpick1 = 2 * self.cf[ipick1]
 
-            # check trend of CF, i.e. differences of CF and adjust aus regarding this trend
+            # check trend of CF, i.e. differences of CF and adjust aus ("artificial uplift 
+            # of picks") regarding this trend
             # prominent trend: decrease aus
             # flat: use given aus
             cfdiff = np.diff(cfipick)
+            if len(cfdiff)<20:
+                print('PragPicker: Very few samples for CF. Check LTA window dimensions!')
             i0diff = np.where(cfdiff > 0)
             cfdiff = cfdiff[i0diff]
+            if len(cfdiff)<1:
+                print('PragPicker: Negative slope for CF. Check LTA window dimensions! STOP')
+                self.Pick = None
+                return
             minaus = min(cfdiff * (1 + self.aus))
             aus1 = max([minaus, self.aus])
 
@@ -375,15 +443,20 @@ class PragPicker(AutoPicker):
                             break
 
             # now we look to the left
-            for i in range(ipick1, max([ipick1 - lpickwindow + 1, 2]), -1):
+            if len(self.cf) > ipick1 +1:
-                if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]:
+                for i in range(ipick1, max([ipick1 - lpickwindow + 1, 2]), -1):
-                    if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
+                    if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]:
-                        if cfpick1 >= self.cf[i]:
+                        if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
-                            pick_l = self.Tcf[i]
+                            if cfpick1 >= self.cf[i]:
-                            self.Pick = pick_l
+                                pick_l = self.Tcf[i]
-                            flagpick_r = 1
+                                self.Pick = pick_l
-                            cfpick_l = self.cf[i]
+                                flagpick_r = 1
-                            break
+                                cfpick_l = self.cf[i]
+                                break
+            else:
+                msg ='PragPicker: Initial onset too close to start of CF! \
+                      Stop finalizing pick to the left.'
+                print(msg)
 
             # now decide which pick: left or right?
             if flagpick_l > 0 and flagpick_r > 0 and cfpick_l <= 3 * cfpick_r:
@@ -396,27 +469,34 @@ class PragPicker(AutoPicker):
                 self.Pick = pick_l
                 pickflag = 1
             else:
-                print('PragPicker: Could not find reliable onset!')
+                print("PragPicker: Could not find reliable onset!")
                 self.Pick = None
                 pickflag = 0
 
-            if self.getiplot() > 1:
+            if iplot > 1:
-                if not self.fig:
+                if self.fig == None or self.fig == 'None':
-                    fig = plt.figure()#self.getiplot())
+                    fig = plt.figure()  # self.getiplot())
+                    plt_flag = 1
                 else:
                     fig = self.fig
+                fig._tight = True
                 ax = fig.add_subplot(111)
-                ax.plot(Tcfpick, cfipick, 'k', label='CF')
+                ax.plot(Tcfpick, cfipick, color=self._linecolor, linewidth=0.7, label='CF')
                 ax.plot(Tcfpick, cfsmoothipick, 'r', label='Smoothed CF')
                 if pickflag > 0:
-                    ax.plot([self.Pick, self.Pick], [min(cfipick), max(cfipick)], 'b', linewidth=2, label='Pick')
+                    ax.plot([self.Pick, self.Pick], [min(cfipick), max(cfipick)], self._pickcolor_p, linewidth=2, label='Pick')
                 ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
                 ax.set_yticks([])
                 ax.set_title(self.Data[0].stats.station)
-                ax.legend()
+                ax.legend(loc=1)
+                if plt_flag == 1:
+                    fig.show()
+                    try: input()
+                    except SyntaxError: pass
+                    plt.close(fig)
                 return
 
         else:
-            print('PragPicker: No initial onset time given! Check input!')
+            print("PragPicker: No initial onset time given! Check input!")
             self.Pick = None
             return

pylot/core/pick/utils.py

@@ -9,12 +9,13 @@
 """
 
 import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
 from obspy.core import Stream, UTCDateTime
 
 
-def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
+def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
     '''
     Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
     as reasonable uncertainties. Latest possible pick is based on noise level,
@@ -41,14 +42,23 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
     if verbosity == 2:
-        print('earllatepicker:')        
+        print('earllatepicker:')
         print('nfac:', nfac)
         print('Init pick:', Pick1)
         print('TSNR (T_noise, T_gap, T_signal):', TSNR)
-        
+
     LPick = None
     EPick = None
     PickError = None
+    plt_flag = 0
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+           iplot = 2
+        else:
+           iplot = 0
+
     if verbosity:
         print('earllatepicker: Get earliest and latest possible pick'
               ' relative to most likely pick ...')
@@ -69,14 +79,14 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
         print('x_inoise:', x[inoise])
         print('x_isignal:', x[isignal])
         print('nlevel:', nlevel)
-    
+
     # get time where signal exceeds nlevel
     ilup, = np.where(x[isignal] > nlevel)
     ildown, = np.where(x[isignal] < -nlevel)
     if not ilup.size and not ildown.size:
         if verbosity:
-            print ("earllatepicker: Signal lower than noise level!\n"
+            print("earllatepicker: Signal lower than noise level!\n"
-                   "Skip this trace!")
+                  "Skip this trace!")
         return LPick, EPick, PickError
     il = min(np.min(ilup) if ilup.size else float('inf'),
              np.min(ildown) if ildown.size else float('inf'))
@@ -84,7 +94,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
 
     # get earliest possible pick
 
-    EPick = np.nan;
+    EPick = np.nan
     count = 0
     pis = isignal
 
@@ -117,34 +127,41 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
     PickError = symmetrize_error(diffti_te, diffti_tl)
 
     if iplot > 1:
-        if not fig:
+        if fig == None or fig == 'None':
-            fig = plt.figure()#iplot)
+            fig = plt.figure()  # iplot)
+            plt_flag = 1
+        fig._tight = True
         ax = fig.add_subplot(111)
-        ax.plot(t, x, 'k', label='Data')
+        ax.plot(t, x, color=linecolor, linewidth=0.7, label='Data')
         ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
         ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
-        ax.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k', label='Noise Level')
+        ax.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], color=linecolor, linewidth=0.7, linestyle='dashed', label='Noise Level')
-        ax.plot(t[isignal[zc]], np.zeros(len(zc)), '*g',
+        ax.plot(t[pis[zc]], np.zeros(len(zc)), '*g',
                 markersize=14, label='Zero Crossings')
-        ax.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], '--k')
+        ax.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], color=linecolor, linewidth=0.7, linestyle='dashed')
         ax.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2, label='mpp')
-        ax.plot([LPick, LPick], [max(x) / 2, -max(x) / 2], '--k', label='lpp')
+        ax.plot([LPick, LPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed', label='lpp')
-        ax.plot([EPick, EPick], [max(x) / 2, -max(x) / 2], '--k', label='epp')
+        ax.plot([EPick, EPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed', label='epp')
         ax.plot([Pick1 + PickError, Pick1 + PickError],
-                 [max(x) / 2, -max(x) / 2], 'r--', label='spe')
+                [max(x) / 2, -max(x) / 2], 'r--', label='spe')
         ax.plot([Pick1 - PickError, Pick1 - PickError],
-                 [max(x) / 2, -max(x) / 2], 'r--')
+                [max(x) / 2, -max(x) / 2], 'r--')
         ax.set_xlabel('Time [s] since %s' % X[0].stats.starttime)
         ax.set_yticks([])
         ax.set_title(
             'Earliest-/Latest Possible/Most Likely Pick & Symmetric Pick Error, %s' %
             X[0].stats.station)
-        ax.legend()
+        ax.legend(loc=1)
+        if plt_flag == 1:
+            fig.show()
+            try: input()
+            except SyntaxError: pass
+            plt.close(fig)
 
     return EPick, LPick, PickError
 
 
-def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
+def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
     '''
     Function to derive first motion (polarity) of given phase onset Pick.
     Calculation is based on zero crossings determined within time window pickwin
@@ -166,6 +183,15 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
     :type: int
     '''
 
+    plt_flag = 0
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+           iplot = 2
+        else:
+           iplot = 0
+
     warnings.simplefilter('ignore', np.RankWarning)
 
     assert isinstance(Xraw, Stream), "%s is not a stream object" % str(Xraw)
@@ -173,15 +199,17 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
 
     FM = None
     if Pick is not None:
-        print ("fmpicker: Get first motion (polarity) of onset using unfiltered seismogram...")
+        print("fmpicker: Get first motion (polarity) of onset using unfiltered seismogram...")
 
         xraw = Xraw[0].data
         xfilt = Xfilt[0].data
         t = np.arange(0, Xraw[0].stats.npts / Xraw[0].stats.sampling_rate,
                       Xraw[0].stats.delta)
         # get pick window
-        ipick = np.where(
+        ipick = np.where((t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
-            (t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
+        if len(ipick[0]) <= 1:
+            print('fmpicker: Zero crossings window to short!')
+            return
         # remove mean
         xraw[ipick] = xraw[ipick] - np.mean(xraw[ipick])
         xfilt[ipick] = xfilt[ipick] - np.mean(xfilt[ipick])
@@ -204,6 +232,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
             if len(zc1) == 3:
                 break
 
+        if len(zc1) < 3:
+            print('fmpicker: Could not determine zero crossings!')
+            return
+
         # if time difference betweeen 1st and 2cnd zero crossing
         # is too short, get time difference between 1st and 3rd
         # to derive maximum
@@ -211,16 +243,16 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
             li1 = index1[1]
         else:
             li1 = index1[0]
-        if np.size(xraw[ipick[0][1]:ipick[0][li1]]) == 0:
+        if np.size(xraw[ipick[0][1]:ipick[0][li1]]) == 0 or len(index1) <= 1:
-            print ("fmpicker: Onset on unfiltered trace too emergent for first motion determination!")
+            print("fmpicker: Onset on unfiltered trace too emergent for first motion determination!")
             P1 = None
         else:
             imax1 = np.argmax(abs(xraw[ipick[0][1]:ipick[0][li1]]))
             if imax1 == 0:
                 imax1 = np.argmax(abs(xraw[ipick[0][1]:ipick[0][index1[1]]]))
                 if imax1 == 0:
-                    print ("fmpicker: Zero crossings too close!")
+                    print("fmpicker: Zero crossings too close!")
-                    print ("Skip first motion determination!")
+                    print("Skip first motion determination!")
                     return FM
 
             islope1 = np.where((t >= Pick) & (t <= Pick + t[imax1]))
@@ -253,16 +285,16 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
             li2 = index2[1]
         else:
             li2 = index2[0]
-        if np.size(xfilt[ipick[0][1]:ipick[0][li2]]) == 0:
+        if np.size(xfilt[ipick[0][1]:ipick[0][li2]]) == 0 or len(index2) <= 1:
-            print ("fmpicker: Onset on filtered trace too emergent for first motion determination!")
+            print("fmpicker: Onset on filtered trace too emergent for first motion determination!")
             P2 = None
         else:
             imax2 = np.argmax(abs(xfilt[ipick[0][1]:ipick[0][li2]]))
             if imax2 == 0:
                 imax2 = np.argmax(abs(xfilt[ipick[0][1]:ipick[0][index2[1]]]))
                 if imax2 == 0:
-                    print ("fmpicker: Zero crossings too close!")
+                    print("fmpicker: Zero crossings too close!")
-                    print ("Skip first motion determination!")
+                    print("Skip first motion determination!")
                     return FM
 
             islope2 = np.where((t >= Pick) & (t <= Pick + t[imax2]))
@@ -286,29 +318,31 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
             elif P1[0] > 0 >= P2[0]:
                 FM = '+'
 
-        print ("fmpicker: Found polarity %s" % FM)
+        print("fmpicker: Found polarity %s" % FM)
 
     if iplot > 1:
-        if not fig:
+        if fig == None or fig == 'None':
-            fig = plt.figure()#iplot)
+            fig = plt.figure()  # iplot)
+            plt_flag = 1
+        fig._tight = True
         ax1 = fig.add_subplot(211)
-        ax1.plot(t, xraw, 'k')
+        ax1.plot(t, xraw, color=linecolor, linewidth=0.7)
         ax1.plot([Pick, Pick], [max(xraw), -max(xraw)], 'b', linewidth=2, label='Pick')
         if P1 is not None:
             ax1.plot(t[islope1], xraw[islope1], label='Slope Window')
             ax1.plot(zc1, np.zeros(len(zc1)), '*g', markersize=14, label='Zero Crossings')
             ax1.plot(t[islope1], datafit1, '--g', linewidth=2)
-            ax1.legend()
+            ax1.legend(loc=1)
             ax1.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
         ax1.set_yticks([])
         ax1.set_title('First-Motion Determination, %s, Unfiltered Data' % Xraw[
             0].stats.station)
 
-        ax2=fig.add_subplot(2,1,2, sharex=ax1)
+        ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
         ax2.set_title('First-Motion Determination, Filtered Data')
-        ax2.plot(t, xfilt, 'k')
+        ax2.plot(t, xfilt, color=linecolor, linewidth=0.7)
         ax2.plot([Pick, Pick], [max(xfilt), -max(xfilt)], 'b',
-                       linewidth=2)
+                 linewidth=2)
         if P2 is not None:
             ax2.plot(t[islope2], xfilt[islope2])
             ax2.plot(zc2, np.zeros(len(zc2)), '*g', markersize=14)
@@ -316,6 +350,11 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
             ax2.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
         ax2.set_xlabel('Time [s] since %s' % Xraw[0].stats.starttime)
         ax2.set_yticks([])
+        if plt_flag == 1:
+            fig.show()
+            try: input()
+            except SyntaxError: pass
+            plt.close(fig)
 
     return FM
 
@@ -357,9 +396,9 @@ def getSNR(X, TSNR, t1, tracenum=0):
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
     SNR = None
-    SNRdb = None
+    SNRdB = None
     noiselevel = None
-    
+
     x = X[tracenum].data
     npts = X[tracenum].stats.npts
     sr = X[tracenum].stats.sampling_rate
@@ -372,7 +411,7 @@ def getSNR(X, TSNR, t1, tracenum=0):
     # get signal window
     isignal = getsignalwin(t, t1, TSNR[2])
     if np.size(inoise) < 1:
-        print ("getSNR: Empty array inoise, check noise window!")
+        print("getSNR: Empty array inoise, check noise window!")
         return SNR, SNRdB, noiselevel
 
     # demean over entire waveform
@@ -380,13 +419,13 @@ def getSNR(X, TSNR, t1, tracenum=0):
 
     # calculate ratios
     noiselevel = np.sqrt(np.mean(np.square(x[inoise])))
-    #signallevel = np.sqrt(np.mean(np.square(x[isignal])))
+    # signallevel = np.sqrt(np.mean(np.square(x[isignal])))
 
     if np.size(isignal) < 1:
-        print ("getSNR: Empty array isignal, check signal window!")
+        print("getSNR: Empty array isignal, check signal window!")
         return SNR, SNRdB, noiselevel
-    
+
-    #noiselevel = np.abs(x[inoise]).max()
+    # noiselevel = np.abs(x[inoise]).max()
     signallevel = np.abs(x[isignal]).max()
 
     SNR = signallevel / noiselevel
@@ -418,9 +457,9 @@ def getnoisewin(t, t1, tnoise, tgap):
     inoise, = np.where((t <= max([t1 - tgap, 0])) \
                        & (t >= max([t1 - tnoise - tgap, 0])))
     if np.size(inoise) < 1:
-        inoise, = np.where((t>=t[0]) & (t<=t1))
+        inoise, = np.where((t >= t[0]) & (t <= t1))
         if np.size(inoise) < 1:
-            print ("getnoisewin: Empty array inoise, check noise window!")
+            print("getnoisewin: Empty array inoise, check noise window!")
 
     return inoise
 
@@ -441,10 +480,10 @@ def getsignalwin(t, t1, tsignal):
     '''
 
     # get signal window
-    isignal, = np.where((t <= min([t1 + tsignal, len(t)])) \
+    isignal, = np.where((t <= min([t1 + tsignal, t[-1]])) \
                         & (t >= t1))
     if np.size(isignal) < 1:
-        print ("getsignalwin: Empty array isignal, check signal window!")
+        print("getsignalwin: Empty array isignal, check signal window!")
 
     return isignal
 
@@ -473,24 +512,25 @@ def getResolutionWindow(snr, extent):
     >>> getResolutionWindow(2)
     2.5
     """
-    
+
     res_wins = {
         'regional': {'HRW': 2., 'MRW': 5., 'LRW': 10., 'VLRW': 15.},
         'local': {'HRW': 2., 'MRW': 5., 'LRW': 10., 'VLRW': 15.},
         'global': {'HRW': 40., 'MRW': 100., 'LRW': 200., 'VLRW': 300.}
     }
 
-    if snr < 1.5:
+    if snr:
-        time_resolution = res_wins[extent]['VLRW']
+        if snr < 1.5:
-    elif snr < 2.:
+            time_resolution = res_wins[extent]['VLRW']
-        time_resolution = res_wins[extent]['LRW']
+        elif snr < 2.:
-    elif snr < 3.:
+            time_resolution = res_wins[extent]['LRW']
-        time_resolution = res_wins[extent]['MRW']
+        elif snr < 3.:
-    elif snr >3.:
+            time_resolution = res_wins[extent]['MRW']
-        time_resolution = res_wins[extent]['HRW']
+        elif snr > 3.:
+            time_resolution = res_wins[extent]['HRW']
     else:
         time_resolution = res_wins[extent]['VLRW']
-        
+
     return time_resolution / 2
 
 
@@ -528,7 +568,7 @@ def select_for_phase(st, phase):
     return sel_st
 
 
-def wadaticheck(pickdic, dttolerance, iplot):
+def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
     '''
     Function to calculate Wadati-diagram from given P and S onsets in order
     to detect S pick outliers. If a certain S-P time deviates by dttolerance
@@ -551,7 +591,10 @@ def wadaticheck(pickdic, dttolerance, iplot):
     Ppicks = []
     Spicks = []
     SPtimes = []
-    for key in pickdic:
+    stations = []
+    ibad = 0
+
+    for key in list(pickdic.keys()):
         if pickdic[key]['P']['weight'] < 4 and pickdic[key]['S']['weight'] < 4:
             # calculate S-P time
             spt = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp']
@@ -572,25 +615,29 @@ def wadaticheck(pickdic, dttolerance, iplot):
 
         # calculate vp/vs ratio before check
         vpvsr = p1[0] + 1
-        print ("###############################################")
+        print("###############################################")
-        print ("wadaticheck: Average Vp/Vs ratio before check: %f" % vpvsr)
+        print("wadaticheck: Average Vp/Vs ratio before check: %f" % vpvsr)
 
         checkedPpicks = []
         checkedSpicks = []
         checkedSPtimes = []
+        badstations = []
         # calculate deviations from Wadati regression
         ii = 0
-        ibad = 0
+        for key in list(pickdic.keys()):
-        for key in pickdic:
+            if 'SPt' in pickdic[key]:
-            if pickdic[key].has_key('SPt'):
+                stations.append(key)
                 wddiff = abs(pickdic[key]['SPt'] - wdfit[ii])
                 ii += 1
                 # check, if deviation is larger than adjusted
                 if wddiff > dttolerance:
-                    # mark onset and downgrade S-weight to 9
+                    # remove pick from dictionary
-                    # (not used anymore)
+                    pickdic.pop(key)
-                    marker = 'badWadatiCheck'
+                    # # mark onset and downgrade S-weight to 9
-                    pickdic[key]['S']['weight'] = 9
+                    # # (not used anymore)
+                    # marker = 'badWadatiCheck'
+                    # pickdic[key]['S']['weight'] = 9
+                    badstations.append(key)
                     ibad += 1
                 else:
                     marker = 'goodWadatiCheck'
@@ -601,7 +648,10 @@ def wadaticheck(pickdic, dttolerance, iplot):
                     checkedSPtime = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp']
                     checkedSPtimes.append(checkedSPtime)
 
-                pickdic[key]['S']['marked'] = marker
+                    pickdic[key]['S']['marked'] = marker
+                #pickdic[key]['S']['marked'] = marker
+        print("wadaticheck: the following stations failed the check:")
+        print(badstations)
 
         if len(checkedPpicks) >= 3:
             # calculate new slope
@@ -610,42 +660,67 @@ def wadaticheck(pickdic, dttolerance, iplot):
 
             # calculate vp/vs ratio after check
             cvpvsr = p2[0] + 1
-            print ("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
+            print("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
-            print ("wadatacheck: Skipped %d S pick(s)" % ibad)
+            print("wadatacheck: Skipped %d S pick(s)" % ibad)
         else:
-            print ("###############################################")
+            print("###############################################")
-            print ("wadatacheck: Not enough checked S-P times available!")
+            print("wadaticheck: Not enough checked S-P times available!")
-            print ("Skip Wadati check!")
+            print("Skip Wadati check!")
+            wfitflag = 1
+            wdfit2 = None
 
         checkedonsets = pickdic
 
     else:
-        print ("wadaticheck: Not enough S-P times available for reliable regression!")
+        print("wadaticheck: Not enough S-P times available for reliable regression!")
-        print ("Skip wadati check!")
+        print("Skip wadati check!")
         wfitflag = 1
 
     # plot results
     if iplot > 0:
-        plt.figure()#iplot)
+        if fig_dict:
-        f1, = plt.plot(Ppicks, SPtimes, 'ro')
+            fig = fig_dict['wadati']
-        if wfitflag == 0:
+            linecolor = fig_dict['plot_style']['linecolor']['rgba_mpl']
-            f2, = plt.plot(Ppicks, wdfit, 'k')
+            plt_flag = 0
-            f3, = plt.plot(checkedPpicks, checkedSPtimes, 'ko')
-            f4, = plt.plot(checkedPpicks, wdfit2, 'g')
-            plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
-                      'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
-            plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1',
-                                          'Reliable S-Picks', 'Wadati 2'], loc='best')
         else:
-            plt.title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
+            fig = plt.figure()
+            linecolor = 'k'
+            plt_flag = 1
+        ax = fig.add_subplot(111)
+        if ibad > 0:
+            ax.plot(Ppicks, SPtimes, 'ro', label='Skipped S-Picks')
+        if wfitflag == 0:
+            ax.plot(Ppicks, wdfit, color=linecolor, linewidth=0.7, label='Wadati 1')
+            ax.plot(Ppicks, wdfit+dttolerance, color='0.9', linewidth=0.5, label='Wadati 1 Tolerance')
+            ax.plot(Ppicks, wdfit-dttolerance, color='0.9', linewidth=0.5)
+            ax.plot(checkedPpicks, wdfit2, 'g', label='Wadati 2')
+            ax.plot(checkedPpicks, checkedSPtimes, color=linecolor,
+                    linewidth=0, marker='o', label='Reliable S-Picks')
+            for Ppick, SPtime, station in zip(Ppicks, SPtimes, stations):
+                ax.text(Ppick, SPtime + 0.01, '{0}'.format(station), color='0.25')
 
-        plt.ylabel('S-P Times [s]')
+            ax.set_title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
-        plt.xlabel('P Times [s]')
+                      'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
+            ax.legend(loc=1, numpoints=1)
+        else:
+            ax.set_title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
+
+        ax.set_ylabel('S-P Times [s]')
+        ax.set_xlabel('P Times [s]')
+        if plt_flag:
+            fig.show()
 
     return checkedonsets
 
 
-def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fig=None):
+def RMS(X):
+    '''
+    Function returns root mean square of a given array X
+    '''
+    return np.sqrt(np.sum(np.power(X, 2)) / len(X))
+
+
+def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fig=None, linecolor='k'):
     '''
     Function to detect spuriously picked noise peaks.
     Uses RMS trace of all 3 components (if available) to determine,
@@ -676,9 +751,18 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
     : type:  int
     '''
 
+    plt_flag = 0
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+           iplot = 2
+        else:
+           iplot = 0
+
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
-    print ("Checking signal length ...")
+    print("Checking signal length ...")
 
     if len(X) > 1:
         # all three components available
@@ -691,51 +775,59 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
         rms = np.sqrt((np.power(x1, 2) + np.power(x2, 2) + np.power(x3, 2)) / 3)
     else:
         x1 = X[0].data
-        rms = np.sqrt(np.power(2, x1))
+        ilen = len(x1)
+        rms = abs(x1)
 
     t = np.arange(0, ilen / X[0].stats.sampling_rate,
                   X[0].stats.delta)
 
     # get noise window in front of pick plus saftey gap
-    inoise = getnoisewin(t, pick - 0.5, TSNR[0], TSNR[1])
+    inoise = getnoisewin(t, pick, TSNR[0], TSNR[1])
     # get signal window
     isignal = getsignalwin(t, pick, minsiglength)
     # calculate minimum adjusted signal level
-    minsiglevel = max(rms[inoise]) * nfac
+    minsiglevel = np.mean(rms[inoise]) * nfac
     # minimum adjusted number of samples over minimum signal level
     minnum = len(isignal) * minpercent / 100
     # get number of samples above minimum adjusted signal level
     numoverthr = len(np.where(rms[isignal] >= minsiglevel)[0])
 
     if numoverthr >= minnum:
-        print ("checksignallength: Signal reached required length.")
+        print("checksignallength: Signal reached required length.")
         returnflag = 1
     else:
-        print ("checksignallength: Signal shorter than required minimum signal length!")
+        print("checksignallength: Signal shorter than required minimum signal length!")
-        print ("Presumably picked noise peak, pick is rejected!")
+        print("Presumably picked noise peak, pick is rejected!")
-        print ("(min. signal length required: %s s)" % minsiglength)
+        print("(min. signal length required: %s s)" % minsiglength)
         returnflag = 0
 
-    if iplot == 2:
+    if iplot > 1:
-        if not fig:
+        if fig == None or fig == 'None':
-            fig = plt.figure()#iplot)
+            fig = plt.figure()  # iplot)
+            plt_flag = 1
+        fig._tight = True
         ax = fig.add_subplot(111)
-        ax.plot(t, rms, 'k', label='RMS Data')
+        ax.plot(t, rms, color=linecolor, linewidth=0.7, label='RMS Data')
-        ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')        
+        ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
-        ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')        
+        ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
         ax.plot([t[isignal[0]], t[isignal[len(isignal) - 1]]],
                 [minsiglevel, minsiglevel], 'g', linewidth=2, label='Minimum Signal Level')
         ax.plot([pick, pick], [min(rms), max(rms)], 'b', linewidth=2, label='Onset')
-        ax.legend()
+        ax.legend(loc=1)
         ax.set_xlabel('Time [s] since %s' % X[0].stats.starttime)
         ax.set_ylabel('Counts')
         ax.set_title('Check for Signal Length, Station %s' % X[0].stats.station)
         ax.set_yticks([])
+        if plt_flag == 1:
+            fig.show()
+            try: input()
+            except SyntaxError: pass
+            plt.close(fig)
 
     return returnflag
 
 
-def checkPonsets(pickdic, dttolerance, iplot):
+def checkPonsets(pickdic, dttolerance, jackfactor=5, iplot=0, fig_dict=None):
     '''
     Function to check statistics of P-onset times: Control deviation from
     median (maximum adjusted deviation = dttolerance) and apply pseudo-
@@ -757,24 +849,26 @@ def checkPonsets(pickdic, dttolerance, iplot):
     # search for good quality P picks
     Ppicks = []
     stations = []
-    for key in pickdic:
+    for station in pickdic:
-        if pickdic[key]['P']['weight'] < 4:
+        if pickdic[station]['P']['weight'] < 4:
             # add P onsets to list
-            UTCPpick = UTCDateTime(pickdic[key]['P']['mpp'])
+            UTCPpick = UTCDateTime(pickdic[station]['P']['mpp'])
             Ppicks.append(UTCPpick.timestamp)
-            stations.append(key)
+            stations.append(station)
 
     # apply jackknife bootstrapping on variance of P onsets
-    print ("###############################################")
+    print("###############################################")
-    print ("checkPonsets: Apply jackknife bootstrapping on P-onset times ...")
+    print("checkPonsets: Apply jackknife bootstrapping on P-onset times ...")
     [xjack, PHI_pseudo, PHI_sub] = jackknife(Ppicks, 'VAR', 1)
+    if not xjack:
+        return
     # get pseudo variances smaller than average variances
     # (times safety factor), these picks passed jackknife test
-    ij = np.where(PHI_pseudo <= 5 * xjack)
+    ij = np.where(PHI_pseudo <= jackfactor * xjack)
     # these picks did not pass jackknife test
-    badjk = np.where(PHI_pseudo > 5 * xjack)
+    badjk = np.where(PHI_pseudo > jackfactor * xjack)
     badjkstations = np.array(stations)[badjk]
-    print ("checkPonsets: %d pick(s) did not pass jackknife test!" % len(badjkstations))
+    print("checkPonsets: %d pick(s) did not pass jackknife test!" % len(badjkstations))
     print(badjkstations)
 
     # calculate median from these picks
@@ -787,9 +881,10 @@ def checkPonsets(pickdic, dttolerance, iplot):
     goodstations = np.array(stations)[igood]
     badstations = np.array(stations)[ibad]
 
-    print ("checkPonsets: %d pick(s) deviate too much from median!" % len(ibad))
+    print("checkPonsets: %d pick(s) deviate too much from median!" % len(ibad))
-    print ("checkPonsets: Skipped %d P pick(s) out of %d" % (len(badstations) \
+    print(badstations)
-                                                             + len(badjkstations), len(stations)))
+    print("checkPonsets: Skipped %d P pick(s) out of %d" % (len(badstations) \
+                                                            + len(badjkstations), len(stations)))
 
     goodmarker = 'goodPonsetcheck'
     badmarker = 'badPonsetcheck'
@@ -798,34 +893,52 @@ def checkPonsets(pickdic, dttolerance, iplot):
         # mark P onset as checked and keep P weight
         pickdic[goodstations[i]]['P']['marked'] = goodmarker
     for i in range(0, len(badstations)):
-        # mark P onset and downgrade P weight to 9
+        # remove pick from dictionary
-        # (not used anymore)
+        pickdic.pop(badstations[i])
-        pickdic[badstations[i]]['P']['marked'] = badmarker
-        pickdic[badstations[i]]['P']['weight'] = 9
     for i in range(0, len(badjkstations)):
-        # mark P onset and downgrade P weight to 9
+        # remove pick from dictionary
-        # (not used anymore)
+        pickdic.pop(badjkstations[i])
-        pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
+    # for i in range(0, len(badstations)):
-        pickdic[badjkstations[i]]['P']['weight'] = 9
+    #     # mark P onset and downgrade P weight to 9
+    #     # (not used anymore)
+    #     pickdic[badstations[i]]['P']['marked'] = badmarker
+    #     pickdic[badstations[i]]['P']['weight'] = 9
+    # for i in range(0, len(badjkstations)):
+    #     # mark P onset and downgrade P weight to 9
+    #     # (not used anymore)
+    #     pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
+    #     pickdic[badjkstations[i]]['P']['weight'] = 9
 
     checkedonsets = pickdic
 
     if iplot > 0:
-        p1, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'ro', markersize=14)
+        if fig_dict:
-        if len(badstations) < 1 and len(badjkstations) < 1:
+            fig = fig_dict['jackknife']
-            p2, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'go', markersize=14)
+            plt_flag = 0
         else:
-            p2, = plt.plot(igood, np.array(Ppicks)[igood], 'go', markersize=14)
+            fig = plt.figure()
-        p3, = plt.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g',
+            plt_flag = 1
-                       linewidth=2)
+        ax = fig.add_subplot(111)
-        for i in range(0, len(Ppicks)):
-            plt.text(i, Ppicks[i] + 0.01, '{0}'.format(stations[i]))
 
-        plt.xlabel('Number of P Picks')
+        if len(badstations) > 0:
-        plt.ylabel('Onset Time [s] from 1.1.1970')
+            ax.plot(ibad, np.array(Ppicks)[ibad], marker ='o', markerfacecolor='orange', markersize=14,
-        plt.legend([p1, p2, p3], ['Skipped P Picks', 'Good P Picks', 'Median'],
+                    linestyle='None', label='Median Skipped P Picks')
-                   loc='best')
+        if len(badjkstations) > 0:
-        plt.title('Jackknifing and Median Tests on P Onsets')
+            ax.plot(badjk[0], np.array(Ppicks)[badjk], 'ro', markersize=14, label='Jackknife Skipped P Picks')
+        ax.plot(igood, np.array(Ppicks)[igood], 'go', markersize=14, label='Good P Picks')
+        ax.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g', linewidth=2, label='Median')
+        ax.plot([0, len(Ppicks) - 1], [pmedian + dttolerance, pmedian + dttolerance], 'g--', linewidth=1.2,
+                dashes=[25, 25], label='Median Tolerance')
+        ax.plot([0, len(Ppicks) - 1], [pmedian - dttolerance, pmedian - dttolerance], 'g--', linewidth=1.2,
+                dashes=[25, 25])
+        for index, pick in enumerate(Ppicks):
+            ax.text(index, pick + 0.01, '{0}'.format(stations[index]), color='0.25')
+        ax.set_xlabel('Number of P Picks')
+        ax.set_ylabel('Onset Time [s] from 1.1.1970') # MP MP Improve this?
+        ax.legend(loc=1, numpoints=1)
+        ax.set_title('Jackknifing and Median Tests on P Onsets')
+        if plt_flag:
+            fig.show()
 
     return checkedonsets
 
@@ -854,13 +967,13 @@ def jackknife(X, phi, h):
     PHI_sub = None
 
     # determine number of subgroups
-    g = len(X) / h
 
-    if type(g) is not int:
+    if len(X) % h:
-        print ("jackknife: Cannot divide quantity X in equal sized subgroups!")
+        print("jackknife: Cannot divide quantity X in equal sized subgroups!")
-        print ("Choose another size for subgroups!")
+        print("Choose another size for subgroups!")
         return PHI_jack, PHI_pseudo, PHI_sub
     else:
+        g = int(len(X) / h)
         # estimator of undisturbed spot check
         if phi == 'MEA':
             phi_sc = np.mean(X)
@@ -894,7 +1007,7 @@ def jackknife(X, phi, h):
     return PHI_jack, PHI_pseudo, PHI_sub
 
 
-def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None):
+def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None, linecolor='k'):
     '''
     Function to compare energy content of vertical trace with
     energy content of horizontal traces to detect spuriously
@@ -923,10 +1036,20 @@ def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None):
              are shown
     : type:  int
     '''
+    
+    plt_flag = 0
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+           iplot = 2
+        else:
+           iplot = 0
+
 
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
-    print ("Check for spuriously picked S onset instead of P onset ...")
+    print("Check for spuriously picked S onset instead of P onset ...")
 
     returnflag = 0
 
@@ -941,74 +1064,122 @@ def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None):
     if len(ndat) == 0:  # check for other components
         ndat = X.select(component="1")
 
-    z = zdat[0].data
+    # get earliest time of all 3 traces
+    min_t = min(zdat[0].stats.starttime, edat[0].stats.starttime, ndat[0].stats.starttime)
+
+    # generate time arrays for all 3 traces
     tz = np.arange(0, zdat[0].stats.npts / zdat[0].stats.sampling_rate,
                    zdat[0].stats.delta)
+    tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
+                   ndat[0].stats.delta)
+    te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
+                   edat[0].stats.delta)
 
-    # calculate RMS trace from vertical component
+    zdiff = (zdat[0].stats.starttime - min_t)
-    absz = np.sqrt(np.power(z, 2))
+    ndiff = (ndat[0].stats.starttime - min_t)
-    # calculate RMS trace from both horizontal traces
+    ediff = (edat[0].stats.starttime - min_t)
-    # make sure, both traces have equal lengths
-    lene = len(edat[0].data)
-    lenn = len(ndat[0].data)
-    minlen = min([lene, lenn])
-    absen = np.sqrt(np.power(edat[0].data[0:minlen - 1], 2) \
-                    + np.power(ndat[0].data[0:minlen - 1], 2))
 
-    # get signal window
+    # get signal windows
-    isignal = getsignalwin(tz, pick, checkwin)
+    isignalz = getsignalwin(tz, pick - zdiff, checkwin)
+    isignaln = getsignalwin(tn, pick - ndiff, checkwin)
+    isignale = getsignalwin(te, pick - ediff, checkwin)
 
-    # calculate energy levels
+    # calculate RMS of traces
-    try:
+    rmsz = RMS(zdat[0].data[isignalz])
-       zcodalevel = max(absz[isignal])
+    rmsn = RMS(ndat[0].data[isignaln])
-    except:
+    rmse = RMS(edat[0].data[isignale])
-       ii = np.where(isignal <= len(absz))
-       isignal = isignal[ii]
-       zcodalevel = max(absz[isignal - 1])
-    try:
-       encodalevel = max(absen[isignal])
-    except:
-       ii = np.where(isignal <= len(absen))
-       isignal = isignal[ii]
-       encodalevel = max(absen[isignal - 1])
 
     # calculate threshold
-    minsiglevel = encodalevel * zfac
+    minsiglevel = (rmsn + rmse) / 2 * zfac
 
     # vertical P-coda level must exceed horizontal P-coda level
     # zfac times encodalevel
-    if zcodalevel < minsiglevel:
+    if rmsz < minsiglevel:
-        print ("checkZ4S: Maybe S onset? Skip this P pick!")
+        print("checkZ4S: Maybe S onset? Skip this P pick!")
     else:
-        print ("checkZ4S: P onset passes checkZ4S test!")
+        print("checkZ4S: P onset passes checkZ4S test!")
         returnflag = 1
 
     if iplot > 1:
-        te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
+        rms_dict = {'Z': rmsz,
-                       edat[0].stats.delta)
+                    'N': rmsn,
-        tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
+                    'E': rmse}
-                       ndat[0].stats.delta)
-        if not fig:
-            fig = plt.figure()
-        ax = fig.add_subplot(111)
-        ax.plot(tz, z / max(z), 'k')
-        ax.axvspan(tz[isignal[0]], tz[isignal[-1]], color='b', alpha=0.2,
-                   lw=0, label='Signal Window')
-        ax.plot(te, edat[0].data / max(edat[0].data) + 1, 'k')
-        ax.plot(tn, ndat[0].data / max(ndat[0].data) + 2, 'k')
-        ax.plot([tz[isignal[0]], tz[isignal[len(isignal) - 1]]],
-                [minsiglevel / max(z), minsiglevel / max(z)], 'g',
-                linewidth=2, label='Minimum Signal Level')
-        ax.set_xlabel('Time [s] since %s' % zdat[0].stats.starttime)
-        ax.set_ylabel('Normalized Counts')
-        ax.set_yticks([0, 1, 2], [zdat[0].stats.channel, edat[0].stats.channel,
-                                  ndat[0].stats.channel])
-        ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
-        ax.legend()
 
+        traces_dict = {'Z': zdat[0],
+                       'N': ndat[0],
+                       'E': edat[0]}
+
+        diff_dict = {'Z': zdiff,
+                     'N': ndiff,
+                     'E': ediff}
+
+        signal_dict = {'Z': isignalz,
+                       'N': isignaln,
+                       'E': isignale}
+
+        for i, key in enumerate(['Z', 'N', 'E']):
+            rms = rms_dict[key]
+            trace = traces_dict[key]
+            t = np.arange(diff_dict[key], trace.stats.npts / trace.stats.sampling_rate + diff_dict[key],
+                          trace.stats.delta)
+            if i == 0:
+                if fig == None or fig == 'None':
+                    fig = plt.figure()  # self.iplot) ### WHY? MP MP
+                    plt_flag = 1
+                ax1 = fig.add_subplot(3, 1, i + 1)
+                ax = ax1
+                ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
+            else:
+                if fig == None or fig == 'None':
+                    fig = plt.figure()  # self.iplot) ### WHY? MP MP
+                    plt_flag = 1
+                ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
+            fig._tight = True
+            ax.plot(t, abs(trace.data), color='b', label='abs')
+            ax.plot(t, trace.data, color=linecolor, linewidth=0.7)
+            name = str(trace.stats.channel) + ': {}'.format(rms)
+            ax.plot([pick, pick + checkwin], [rms, rms], 'r', label='RMS {}'.format(name))
+            ax.plot([pick, pick], ax.get_ylim(), 'm', label='Pick')
+            ax.set_ylabel('Normalized Counts')
+            ax.axvspan(pick, pick + checkwin, color='c', alpha=0.2,
+                       lw=0)
+            ax.legend(loc=1)
+        ax.set_xlabel('Time [s] since %s' % zdat[0].stats.starttime)
+        if plt_flag == 1:
+            fig.show()
+            try: input()
+            except SyntaxError: pass
+            plt.close(fig)
     return returnflag
 
 
+def getQualityFromUncertainty(uncertainty, Errors):
+    '''Script to transform uncertainty into quality classes 0-4
+       regarding adjusted time errors Errors.
+    '''
+
+    # set initial quality to 4 (worst) and change only if one condition is hit
+    quality = 4
+
+    if uncertainty == None or uncertainty == 'None':
+        return quality
+
+    if uncertainty <= Errors[0]:
+        quality = 0
+    elif (uncertainty > Errors[0]) and \
+         (uncertainty < Errors[1]):
+        quality = 1
+    elif (uncertainty > Errors[1]) and \
+         (uncertainty < Errors[2]):
+        quality = 2
+    elif (uncertainty > Errors[2]) and \
+         (uncertainty < Errors[3]):
+        quality = 3
+    elif uncertainty > Errors[3]:
+        quality = 4
+
+    return quality
+
 if __name__ == '__main__':
     import doctest
 

pylot/core/util/connection.py

@@ -1,13 +1,16 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import urllib2
+try:
+    from urllib2 import urlopen
+except:
+    from urllib.request import urlopen
 
 
-def checkurl(url='https://ariadne.geophysik.rub.de/trac/PyLoT'):
+def checkurl(url='https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/'):
     try:
-        urllib2.urlopen(url, timeout=1)
+        urlopen(url, timeout=1)
         return True
-    except urllib2.URLError:
+    except:
         pass
     return False

pylot/core/util/dataprocessing.py

@@ -1,13 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import os
 import glob
+import os
 import sys
-from obspy.io.xseed import Parser
 
 import numpy as np
-
 from obspy import UTCDateTime, read_inventory, read
 from obspy.io.xseed import Parser
 from pylot.core.util.utils import key_for_set_value, find_in_list, \
@@ -117,7 +115,7 @@ def make_time_line(line, datetime):
     return newline
 
 
-def evt_head_check(root_dir, out_dir = None):
+def evt_head_check(root_dir, out_dir=None):
     """
     A function to make sure that an arbitrary number of .gse files have correct values in their header.
     :param root_dir: a directory leading to the .gse files.
@@ -170,7 +168,7 @@ def read_metadata(path_to_inventory):
     invfile = list()
     respfile = list()
     # possible file extensions specified here:
-    inv = dict(dless=dlfile, xml=invfile, resp=respfile, dseed=dlfile)
+    inv = dict(dless=dlfile, xml=invfile, resp=respfile, dseed=dlfile[:])
     if os.path.isfile(path_to_inventory):
         ext = os.path.splitext(path_to_inventory)[1].split('.')[1]
         inv[ext] += [path_to_inventory]
@@ -184,7 +182,7 @@ def read_metadata(path_to_inventory):
         print("Neither dataless-SEED file, inventory-xml file nor "
               "RESP-file found!")
         print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
-        robj = None, 
+        robj = None,
     elif invtype == 'dless':  # prevent multiple read of large dlsv
         print("Reading metadata information from dataless-SEED file ...")
         if len(inv[invtype]) == 1:
@@ -202,7 +200,7 @@ def restitute_trace(input_tuple):
     tr, invtype, inobj, unit, force = input_tuple
 
     remove_trace = False
-    
+
     seed_id = tr.get_id()
     # check, whether this trace has already been corrected
     if 'processing' in tr.stats.keys() \
@@ -245,14 +243,14 @@ def restitute_trace(input_tuple):
         remove_trace = True
     # apply restitution to data
     print("Correcting instrument at station %s, channel %s" \
-            % (tr.stats.station, tr.stats.channel))
+          % (tr.stats.station, tr.stats.channel))
     try:
         if invtype in ['resp', 'dless']:
             try:
-               tr.simulate(**kwargs)
+                tr.simulate(**kwargs)
             except ValueError as e:
-               vmsg = '{0}'.format(e)
+                vmsg = '{0}'.format(e)
-               print(vmsg)
+                print(vmsg)
 
         else:
             tr.attach_response(inventory)
@@ -271,7 +269,7 @@ def restitute_trace(input_tuple):
     return tr, remove_trace
 
 
-def restitute_data(data, invtype, inobj, unit='VEL', force=False):
+def restitute_data(data, invtype, inobj, unit='VEL', force=False, ncores=0):
     """
     takes a data stream and a path_to_inventory and returns the corrected
     waveform data stream
@@ -294,15 +292,15 @@ def restitute_data(data, invtype, inobj, unit='VEL', force=False):
     for tr in data:
         input_tuples.append((tr, invtype, inobj, unit, force))
         data.remove(tr)
-        
+
-    pool = gen_Pool()
+    pool = gen_Pool(ncores)
     result = pool.map(restitute_trace, input_tuples)
     pool.close()
-    
+
     for tr, remove_trace in result:
         if not remove_trace:
             data.traces.append(tr)
-        
+
     # check if ALL traces could be restituted, take care of large datasets
     # better try restitution for smaller subsets of data (e.g. station by
     # station)
@@ -344,8 +342,8 @@ def get_prefilt(trace, tlow=(0.5, 0.9), thi=(5., 2.), verbosity=0):
             trace.stats.station, trace.stats.channel))
     # get corner frequencies for pre-filtering
     fny = trace.stats.sampling_rate / 2
-    fc21 = fny - (fny * thi[0]/100.)
+    fc21 = fny - (fny * thi[0] / 100.)
-    fc22 = fny - (fny * thi[1]/100.)
+    fc22 = fny - (fny * thi[1] / 100.)
     return (tlow[0], tlow[1], fc21, fc22)
 
 

pylot/core/util/defaults.py

@@ -7,43 +7,29 @@ Created on Wed Feb 26 12:31:25 2014
 """
 
 import os
-from pylot.core.loc import nll
+import platform
-from pylot.core.loc import hyposat
+
+from pylot.core.util.utils import readDefaultFilterInformation
 from pylot.core.loc import hypo71
 from pylot.core.loc import hypodd
+from pylot.core.loc import hyposat
+from pylot.core.loc import nll
 from pylot.core.loc import velest
 
 
-def readFilterInformation(fname):
+# determine system dependent path separator
-    def convert2FreqRange(*args):
+system_name = platform.system()
-        if len(args) > 1:
+if system_name in ["Linux", "Darwin"]:
-            return [float(arg) for arg in args]
+    SEPARATOR = '/'
-        elif len(args) == 1:
+elif system_name == "Windows":
-            return float(args[0])
+    SEPARATOR = '\\'
-        return None
 
-    filter_file = open(fname, 'r')
+# suffix for phase name if not phase identified by last letter (P, p, etc.)
-    filter_information = dict()
+ALTSUFFIX = ['diff', 'n', 'g', '1', '2', '3']
-    for filter_line in filter_file.readlines():
-        filter_line = filter_line.split(' ')
-        for n, pos in enumerate(filter_line):
-            if pos == '\n':
-                filter_line[n] = ''
-        filter_information[filter_line[0]] = {'filtertype': filter_line[1]
-        if filter_line[1]
-        else None,
-                                              'order': int(filter_line[2])
-                                              if filter_line[1]
-                                              else None,
-                                              'freq': convert2FreqRange(*filter_line[3:])
-                                              if filter_line[1]
-                                              else None}
-    return filter_information
 
-
+FILTERDEFAULTS = readDefaultFilterInformation(os.path.join(os.path.expanduser('~'),
-FILTERDEFAULTS = readFilterInformation(os.path.join(os.path.expanduser('~'),
+                                                           '.pylot',
-                                                    '.pylot',
+                                                           'pylot.in'))
-                                                    'filter.in'))
 
 TIMEERROR_DEFAULTS = os.path.join(os.path.expanduser('~'),
                                   '.pylot',
@@ -59,14 +45,14 @@ LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=h
 class SetChannelComponents(object):
     def __init__(self):
         self.setDefaultCompPosition()
-        
+
     def setDefaultCompPosition(self):
         # default component order
         self.compPosition_Map = dict(Z=2, N=1, E=0)
         self.compName_Map = {'3': 'Z',
                              '1': 'N',
                              '2': 'E'}
-        
+
     def _getCurrentPosition(self, component):
         for key, value in self.compName_Map.items():
             if value == component:
@@ -85,10 +71,10 @@ class SetChannelComponents(object):
     def setCompPosition(self, component_alter, component, switch=True):
         component_alter = str(component_alter)
         if not component_alter in self.compName_Map.keys():
-            errMsg='setCompPosition: Unrecognized alternative component {}. Expecting one of {}.'
+            errMsg = 'setCompPosition: Unrecognized alternative component {}. Expecting one of {}.'
             raise ValueError(errMsg.format(component_alter, self.compName_Map.keys()))
         if not component in self.compPosition_Map.keys():
-            errMsg='setCompPosition: Unrecognized target component {}. Expecting one of {}.'
+            errMsg = 'setCompPosition: Unrecognized target component {}. Expecting one of {}.'
             raise ValueError(errMsg.format(component, self.compPosition_Map.keys()))
         print('setCompPosition: set component {} to {}'.format(component_alter, component))
         if switch:
@@ -97,7 +83,7 @@ class SetChannelComponents(object):
 
     def getCompPosition(self, component):
         return self._getCurrentPosition(component)[0]
-        
+
     def getPlotPosition(self, component):
         component = str(component)
         if component in self.compPosition_Map.keys():
@@ -105,6 +91,5 @@ class SetChannelComponents(object):
         elif component in self.compName_Map.keys():
             return self.compPosition_Map[self.compName_Map[component]]
         else:
-            errMsg='getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
+            errMsg = 'getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
             raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))
-   

pylot/core/util/errors.py

@@ -25,5 +25,6 @@ class OverwriteError(IOError):
 class ParameterError(Exception):
     pass
 
+
 class ProcessingError(RuntimeError):
     pass

pylot/core/util/event.py

@@ -5,8 +5,7 @@ import os
 
 from obspy import UTCDateTime
 from obspy.core.event import Event as ObsPyEvent
-from obspy.core.event import Origin, Magnitude, ResourceIdentifier
+from obspy.core.event import Origin, ResourceIdentifier
-
 from pylot.core.io.phases import picks_from_picksdict
 
 
@@ -14,10 +13,11 @@ class Event(ObsPyEvent):
     '''
     Pickable class derived from ~obspy.core.event.Event containing information on a single event.
     '''
+
     def __init__(self, path):
         self.pylot_id = path.split('/')[-1]
         # initialize super class
-        super(Event, self).__init__(resource_id=ResourceIdentifier('smi:local/'+self.pylot_id))
+        super(Event, self).__init__(resource_id=ResourceIdentifier('smi:local/' + self.pylot_id))
         self.path = path
         self.database = path.split('/')[-2]
         self.datapath = path.split('/')[-3]
@@ -32,13 +32,13 @@ class Event(ObsPyEvent):
     def get_notes_path(self):
         notesfile = os.path.join(self.path, 'notes.txt')
         return notesfile
-    
+
     def get_notes(self):
         notesfile = self.get_notes_path()
         if os.path.isfile(notesfile):
             with open(notesfile) as infile:
                 path = str(infile.readlines()[0].split('\n')[0])
-                text = '[eventInfo: '+path+']'
+                text = '[eventInfo: ' + path + ']'
                 self.addNotes(text)
                 try:
                     datetime = UTCDateTime(path.split('/')[-1])
@@ -67,31 +67,47 @@ class Event(ObsPyEvent):
         self._testEvent = bool
         if bool: self._refEvent = False
 
+    def clearObsPyPicks(self, picktype):
+        for index, pick in reversed(list(enumerate(self.picks))):
+            if picktype in str(pick.method_id):
+                self.picks.pop(index)
+
     def addPicks(self, picks):
         '''
-        add pylot picks and overwrite existing
+        add pylot picks and overwrite existing ones
         '''
         for station in picks:
             self.pylot_picks[station] = picks[station]
-        #add ObsPy picks
+        # add ObsPy picks (clear old manual and copy all new manual from pylot)
-        self.picks = picks_from_picksdict(self.pylot_picks)
+        self.clearObsPyPicks('manual')
-        
+        self.picks += picks_from_picksdict(self.pylot_picks)
+
     def addAutopicks(self, autopicks):
         for station in autopicks:
             self.pylot_autopicks[station] = autopicks[station]
-        
+        # add ObsPy picks (clear old auto and copy all new auto from pylot)
+        self.clearObsPyPicks('auto')
+        self.picks += picks_from_picksdict(self.pylot_autopicks)
+
     def setPick(self, station, pick):
         if pick:
             self.pylot_picks[station] = pick
-        self.picks = picks_from_picksdict(self.pylot_picks)
+        else:
-        
+            try:
+                self.pylot_picks.pop(station)
+            except Exception as e:
+                print('Could not remove pick {} from station {}: {}'.format(pick, station, e))
+        self.clearObsPyPicks('manual')
+        self.picks += picks_from_picksdict(self.pylot_picks)
+
     def setPicks(self, picks):
         '''
         set pylot picks and delete and overwrite all existing
         '''
         self.pylot_picks = picks
-        self.picks = picks_from_picksdict(self.pylot_picks)
+        self.clearObsPyPicks('manual')
-                
+        self.picks += picks_from_picksdict(self.pylot_picks)
+
     def getPick(self, station):
         if station in self.pylot_picks.keys():
             return self.pylot_picks[station]
@@ -99,13 +115,25 @@ class Event(ObsPyEvent):
     def getPicks(self):
         return self.pylot_picks
 
-    def setAutopick(self, station, autopick):
+    def setAutopick(self, station, pick):
-        if autopick:
+        if pick:
-            self.pylot_autopicks[station] = autopick
+            self.pylot_autopicks[station] = pick
+        else:
+            try:
+                self.pylot_autopicks.pop(station)
+            except Exception as e:
+                print('Could not remove pick {} from station {}: {}'.format(pick, station, e))
+        self.clearObsPyPicks('auto')
+        self.picks += picks_from_picksdict(self.pylot_autopicks)
+
+    def setAutopicks(self, picks):
+        '''
+        set pylot picks and delete and overwrite all existing
+        '''
+        self.pylot_autopicks = picks
+        self.clearObsPyPicks('auto')
+        self.picks += picks_from_picksdict(self.pylot_autopicks)
 
-    def setAutopicks(self, autopicks):
-        self.pylot_autopicks = autopicks
-        
     def getAutopick(self, station):
         if station in self.pylot_autopicks.keys():
             return self.pylot_autopicks[station]

pylot/core/util/map_projection.py

@@ -1,24 +1,28 @@
-from mpl_toolkits.basemap import Basemap
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy
-from matplotlib import cm
+from PySide import QtGui
-from scipy.interpolate import griddata
 from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
-from PySide import QtCore, QtGui
+from mpl_toolkits.basemap import Basemap
-
 from pylot.core.util.widgets import PickDlg
+from scipy.interpolate import griddata
 
 plt.interactive(False)
 
+
 class map_projection(QtGui.QWidget):
     def __init__(self, parent, figure=None):
         '''
+
         :param: picked, can be False, auto, manual
         :value: str
         '''
         QtGui.QWidget.__init__(self)
         self._parent = parent
+        self.metadata = parent.metadata
         self.parser = parent.metadata[1]
         self.picks = None
         self.picks_dict = None
@@ -28,7 +32,7 @@ class map_projection(QtGui.QWidget):
         self.init_stations()
         self.init_basemap(resolution='l')
         self.init_map()
-        #self.show()
+        # self.show()
 
     def init_map(self):
         self.init_lat_lon_dimensions()
@@ -36,7 +40,7 @@ class map_projection(QtGui.QWidget):
         self.init_x_y_dimensions()
         self.connectSignals()
         self.draw_everything()
-        
+
     def onpick(self, event):
         ind = event.ind
         button = event.mouseevent.button
@@ -44,7 +48,7 @@ class map_projection(QtGui.QWidget):
             return
         data = self._parent.get_data().getWFData()
         for index in ind:
-            station=str(self.station_names[index].split('.')[-1])
+            station = str(self.station_names[index].split('.')[-1])
             try:
                 pickDlg = PickDlg(self, parameter=self._parent._inputs,
                                   data=data.select(station=station),
@@ -89,7 +93,7 @@ class map_projection(QtGui.QWidget):
             else:
                 self.figure = self._parent.am_figure
                 self.toolbar = self._parent.am_toolbar
-                
+
         self.main_ax = self.figure.add_subplot(111)
         self.canvas = self.figure.canvas
 
@@ -105,29 +109,29 @@ class map_projection(QtGui.QWidget):
 
         self.comboBox_am = QtGui.QComboBox()
         self.comboBox_am.insertItem(0, 'auto')
-        self.comboBox_am.insertItem(1, 'manual')        
+        self.comboBox_am.insertItem(1, 'manual')
-        
+
         self.top_row.addWidget(QtGui.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
-        self.top_row.setStretch(1,1) #set stretch of item 1 to 1        
+        self.top_row.setStretch(1, 1)  # set stretch of item 1 to 1
 
         self.main_box.addWidget(self.canvas)
         self.main_box.addWidget(self.toolbar)
-        
+
     def init_stations(self):
         def get_station_names_lat_lon(parser):
-            station_names=[]
+            station_names = []
-            lat=[]
+            lat = []
-            lon=[]
+            lon = []
             for station in parser.stations:
-                station_name=station[0].station_call_letters
+                station_name = station[0].station_call_letters
-                network=station[0].network_code
+                network = station[0].network_code
                 if not station_name in station_names:
-                    station_names.append(network+'.'+station_name)
+                    station_names.append(network + '.' + station_name)
                     lat.append(station[0].latitude)
                     lon.append(station[0].longitude)
             return station_names, lat, lon
-        
+
         station_names, lat, lon = get_station_names_lat_lon(self.parser)
         self.station_names = station_names
         self.lat = lat
@@ -135,52 +139,53 @@ class map_projection(QtGui.QWidget):
 
     def init_picks(self):
         phase = self.comboBox_phase.currentText()
+
         def get_picks(station_names):
-            picks=[]
+            picks = []
             for station in station_names:
                 try:
-                    station=station.split('.')[-1]
+                    station = station.split('.')[-1]
                     picks.append(self.picks_dict[station][phase]['mpp'])
                 except:
                     picks.append(np.nan)
             return picks
 
         def get_picks_rel(picks):
-            picks_rel=[]
+            picks_rel = []
             picks_utc = []
             for pick in picks:
                 if type(pick) is obspy.core.utcdatetime.UTCDateTime:
                     picks_utc.append(pick)
             minp = min(picks_utc)
             for pick in picks:
-                if type(pick) is obspy.core.utcdatetime.UTCDateTime:                
+                if type(pick) is obspy.core.utcdatetime.UTCDateTime:
                     pick -= minp
                 picks_rel.append(pick)
             return picks_rel
-        
+
         self.picks = get_picks(self.station_names)
         self.picks_rel = get_picks_rel(self.picks)
 
     def init_picks_active(self):
         def remove_nan_picks(picks):
-            picks_no_nan=[]
+            picks_no_nan = []
             for pick in picks:
                 if not np.isnan(pick):
                     picks_no_nan.append(pick)
             return picks_no_nan
-        
+
         self.picks_no_nan = remove_nan_picks(self.picks_rel)
 
     def init_stations_active(self):
         def remove_nan_lat_lon(picks, lat, lon):
-            lat_no_nan=[]
+            lat_no_nan = []
-            lon_no_nan=[]
+            lon_no_nan = []
             for index, pick in enumerate(picks):
                 if not np.isnan(pick):
                     lat_no_nan.append(lat[index])
                     lon_no_nan.append(lon[index])
             return lat_no_nan, lon_no_nan
-        
+
         self.lat_no_nan, self.lon_no_nan = remove_nan_lat_lon(self.picks_rel, self.lat, self.lon)
 
     def init_lat_lon_dimensions(self):
@@ -188,7 +193,7 @@ class map_projection(QtGui.QWidget):
             londim = max(lon) - min(lon)
             latdim = max(lat) - min(lat)
             return londim, latdim
-        
+
         self.londim, self.latdim = get_lon_lat_dim(self.lon, self.lat)
 
     def init_x_y_dimensions(self):
@@ -196,30 +201,30 @@ class map_projection(QtGui.QWidget):
             xdim = max(x) - min(x)
             ydim = max(y) - min(y)
             return xdim, ydim
-        
+
         self.x, self.y = self.basemap(self.lon, self.lat)
         self.xdim, self.ydim = get_x_y_dim(self.x, self.y)
 
     def init_basemap(self, resolution='l'):
-        #basemap = Basemap(projection=projection, resolution = resolution, ax=self.main_ax)
+        # basemap = Basemap(projection=projection, resolution = resolution, ax=self.main_ax)
-        basemap = Basemap(projection='lcc', resolution = resolution, ax=self.main_ax,
+        basemap = Basemap(projection='lcc', resolution=resolution, ax=self.main_ax,
                           width=5e6, height=2e6,
-                          lat_0=(min(self.lat)+max(self.lat))/2.,
+                          lat_0=(min(self.lat) + max(self.lat)) / 2.,
-                          lon_0=(min(self.lon)+max(self.lon))/2.)
+                          lon_0=(min(self.lon) + max(self.lon)) / 2.)
-            
+
-        #basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
+        # basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
-        basemap.drawmapboundary(zorder=2)#fill_color='darkblue')
+        basemap.drawmapboundary(zorder=2)  # fill_color='darkblue')
         basemap.shadedrelief(zorder=3)
         basemap.drawcountries(zorder=4)
         basemap.drawstates(zorder=5)
         basemap.drawcoastlines(zorder=6)
         self.basemap = basemap
         self.figure.tight_layout()
-        
+
     def init_lat_lon_grid(self):
         def get_lat_lon_axis(lat, lon):
-            steplat = (max(lat)-min(lat))/250
+            steplat = (max(lat) - min(lat)) / 250
-            steplon = (max(lon)-min(lon))/250
+            steplon = (max(lon) - min(lon)) / 250
 
             lataxis = np.arange(min(lat), max(lat), steplat)
             lonaxis = np.arange(min(lon), max(lon), steplon)
@@ -234,7 +239,8 @@ class map_projection(QtGui.QWidget):
 
     def init_picksgrid(self):
         self.picksgrid_no_nan = griddata((self.lat_no_nan, self.lon_no_nan),
-                                         self.picks_no_nan, (self.latgrid, self.longrid), method='linear') ##################
+                                         self.picks_no_nan, (self.latgrid, self.longrid),
+                                         method='linear')  ##################
 
     def draw_contour_filled(self, nlevel='50'):
         levels = np.linspace(min(self.picks_no_nan), max(self.picks_no_nan), nlevel)
@@ -243,7 +249,7 @@ class map_projection(QtGui.QWidget):
 
     def scatter_all_stations(self):
         self.sc = self.basemap.scatter(self.lon, self.lat, s=50, facecolor='none', latlon=True,
-                                  zorder=10, picker=True, edgecolor='m', label='Not Picked')
+                                       zorder=10, picker=True, edgecolor='m', label='Not Picked')
         self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
         if self.eventLoc:
             lat, lon = self.eventLoc
@@ -254,11 +260,11 @@ class map_projection(QtGui.QWidget):
         lon = self.lon_no_nan
         lat = self.lat_no_nan
 
-        #workaround because of an issue with latlon transformation of arrays with len <3
+        # workaround because of an issue with latlon transformation of arrays with len <3
         if len(lon) <= 2 and len(lat) <= 2:
             self.sc_picked = self.basemap.scatter(lon[0], lat[0], s=50, facecolor='white',
                                                   c=self.picks_no_nan[0], latlon=True, zorder=11, label='Picked')
-        if len(lon) == 2 and len(lat) == 2:            
+        if len(lon) == 2 and len(lat) == 2:
             self.sc_picked = self.basemap.scatter(lon[1], lat[1], s=50, facecolor='white',
                                                   c=self.picks_no_nan[1], latlon=True, zorder=11)
         else:
@@ -266,11 +272,11 @@ class map_projection(QtGui.QWidget):
                                                   c=self.picks_no_nan, latlon=True, zorder=11, label='Picked')
 
     def annotate_ax(self):
-        self.annotations=[]
+        self.annotations = []
         for index, name in enumerate(self.station_names):
             self.annotations.append(self.main_ax.annotate(' %s' % name, xy=(self.x[index], self.y[index]),
                                                           fontsize='x-small', color='white', zorder=12))
-        self.legend=self.main_ax.legend()
+        self.legend = self.main_ax.legend(loc=1)
 
     def add_cbar(self, label):
         cbar = self.main_ax.figure.colorbar(self.sc_picked, fraction=0.025)
@@ -306,19 +312,19 @@ class map_projection(QtGui.QWidget):
     def remove_drawings(self):
         if hasattr(self, 'sc_picked'):
             self.sc_picked.remove()
-            del(self.sc_picked)
+            del (self.sc_picked)
         if hasattr(self, 'sc_event'):
             self.sc_event.remove()
-            del(self.sc_event)
+            del (self.sc_event)
         if hasattr(self, 'cbar'):
             self.cbar.remove()
-            del(self.cbar)
+            del (self.cbar)
         if hasattr(self, 'contourf'):
             self.remove_contourf()
-            del(self.contourf)
+            del (self.contourf)
         if hasattr(self, 'cid'):
             self.canvas.mpl_disconnect(self.cid)
-            del(self.cid)
+            del (self.cid)
         try:
             self.sc.remove()
         except Exception as e:
@@ -342,18 +348,18 @@ class map_projection(QtGui.QWidget):
         xlim = map.ax.get_xlim()
         ylim = map.ax.get_ylim()
         x, y = event.xdata, event.ydata
-        zoom = {'up': 1./2.,
+        zoom = {'up': 1. / 2.,
                 'down': 2.}
-        
+
         if not event.xdata or not event.ydata:
             return
-        
+
         if event.button in zoom:
             factor = zoom[event.button]
-            xdiff = (xlim[1]-xlim[0])*factor
+            xdiff = (xlim[1] - xlim[0]) * factor
             xl = x - 0.5 * xdiff
             xr = x + 0.5 * xdiff
-            ydiff = (ylim[1]-ylim[0])*factor
+            ydiff = (ylim[1] - ylim[0]) * factor
             yb = y - 0.5 * ydiff
             yt = y + 0.5 * ydiff
 
@@ -363,10 +369,8 @@ class map_projection(QtGui.QWidget):
             map.ax.set_xlim(xl, xr)
             map.ax.set_ylim(yb, yt)
             map.ax.figure.canvas.draw()
-            
+
     def _warn(self, message):
         self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
                                      'Warning', message)
-        self.qmb.show()        
+        self.qmb.show()
-            
-    

pylot/core/util/pdf.py

@@ -2,20 +2,23 @@
 # -*- coding: utf-8 -*-
 
 import warnings
+
 import numpy as np
 from obspy import UTCDateTime
-from pylot.core.util.utils import fit_curve, find_nearest, clims
+from pylot.core.util.utils import fit_curve, clims
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 __author__ = 'sebastianw'
 
+
 def create_axis(x0, incr, npts):
     ax = np.zeros(npts)
     for i in range(npts):
         ax[i] = x0 + incr * i
     return ax
 
+
 def gauss_parameter(te, tm, tl, eta):
     '''
     takes three onset times and returns the parameters sig1, sig2, a1 and a2
@@ -59,7 +62,7 @@ def exp_parameter(te, tm, tl, eta):
     return tm, sig1, sig2, a
 
 
-def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
+def gauss_branches(k, param_tuple):
     '''
     function gauss_branches takes an axes x, a center value mu, two sigma
     values sig1 and sig2 and two scaling factors a1 and a2 and return a
@@ -79,6 +82,9 @@ def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
     :returns fun_vals: list with function values along axes x
     '''
 
+    # python 3 workaround
+    mu, sig1, sig2, a1, a2 = param_tuple
+
     def _func(k, mu, sig1, sig2, a1, a2):
         if k < mu:
             rval = a1 * 1 / (np.sqrt(2 * np.pi) * sig1) * np.exp(-((k - mu) / sig1) ** 2 / 2)
@@ -93,7 +99,7 @@ def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
         return _func(k, mu, sig1, sig2, a1, a2)
 
 
-def exp_branches(k, (mu, sig1, sig2, a)):
+def exp_branches(k, param_tuple):
     '''
     function exp_branches takes an axes x, a center value mu, two sigma
     values sig1 and sig2 and a scaling factor a and return a
@@ -107,6 +113,9 @@ def exp_branches(k, (mu, sig1, sig2, a)):
     :returns fun_vals: list with function values along axes x:
     '''
 
+    # python 3 workaround
+    mu, sig1, sig2, a = param_tuple
+
     def _func(k, mu, sig1, sig2, a):
         mu = float(mu)
         if k < mu:
@@ -239,7 +248,7 @@ class ProbabilityDensityFunction(object):
         self._x = np.array(x)
 
     @classmethod
-    def from_pick(self, lbound, barycentre, rbound, incr=0.001, decfact=0.01,
+    def from_pick(self, lbound, barycentre, rbound, incr=0.1, decfact=0.01,
                   type='exp'):
         '''
         Initialize a new ProbabilityDensityFunction object.
@@ -307,14 +316,14 @@ class ProbabilityDensityFunction(object):
         :return float: rval
         '''
 
-        #rval = 0
+        # rval = 0
-        #for x in self.axis:
+        # for x in self.axis:
         #    rval += x * self.data(x)
         rval = self.mu
         # Not sure about this! That might not be the barycentre.
         # However, for std calculation (next function)
         # self.mu is also used!! (LK, 02/2017) 
-        return rval 
+        return rval
 
     def standard_deviation(self):
         mu = self.mu
@@ -388,7 +397,6 @@ class ProbabilityDensityFunction(object):
         qu = self.quantile(1 - prob_value)
         return qu - ql
 
-
     def quantile_dist_frac(self, x):
         """
         takes a probability value and returns the fraction of two
@@ -405,8 +413,7 @@ class ProbabilityDensityFunction(object):
         """
         if x <= 0 or x >= 0.25:
             raise ValueError('Value out of range.')
-        return self.quantile_distance(0.5-x)/self.quantile_distance(x)
+        return self.quantile_distance(0.5 - x) / self.quantile_distance(x)
-
 
     def plot(self, label=None):
         import matplotlib.pyplot as plt
@@ -480,4 +487,3 @@ class ProbabilityDensityFunction(object):
         x0, npts = self.commonlimits(incr, other)
 
         return x0, incr, npts
-

pylot/core/util/plotting.py

@@ -3,6 +3,7 @@
 
 import matplotlib.pyplot as plt
 
+
 def create_bin_list(l_boundary, u_boundary, nbins=100):
     """
     takes two boundaries and a number of bins and creates a list of bins for
@@ -54,4 +55,4 @@ def histplot(array, binlist, xlab='Values',
     if fnout:
         plt.savefig(fnout)
     else:
-        plt.show()
+        plt.show()

pylot/core/util/thread.py

@@ -1,82 +1,167 @@
 # -*- coding: utf-8 -*-
-import sys, os
+import sys, os, traceback
-from PySide.QtCore import QThread, Signal, Qt
+import multiprocessing
-from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout
+from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
-
+from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
-
-class AutoPickThread(QThread):
-    message = Signal(str)
-    finished = Signal()
-
-    def __init__(self, parent, func, infile, fnames, eventid, savepath):
-        super(AutoPickThread, self).__init__()
-        self.setParent(parent)
-        self.func = func
-        self.infile = infile
-        self.fnames = fnames
-        self.eventid = eventid
-        self.savepath = savepath
-
-    def run(self):
-        sys.stdout = self
-
-        picks = self.func(None, None, self.infile, self.fnames, self.eventid, self.savepath)
-
-        print("Autopicking finished!\n")
-
-        try:
-            for station in picks:
-                self.parent().addPicks(station, picks[station], type='auto')
-        except AttributeError:
-            print(picks)
-        sys.stdout = sys.__stdout__
-        self.finished.emit()
-
-    def write(self, text):
-        self.message.emit(text)
-
-    def flush(self):
-        pass
 
 
 class Thread(QThread):
     message = Signal(str)
-    
+
-    def __init__(self, parent, func, arg=None, progressText=None, pb_widget=None, redirect_stdout=False):
+    def __init__(self, parent, func, arg=None, progressText=None,
+                 pb_widget=None, redirect_stdout=False, abortButton=False):
         QThread.__init__(self, parent)
         self.func = func
         self.arg = arg
         self.progressText = progressText
         self.pb_widget = pb_widget
         self.redirect_stdout = redirect_stdout
+        self.abortButton = abortButton
         self.finished.connect(self.hideProgressbar)
         self.showProgressbar()
 
     def run(self):
         if self.redirect_stdout:
-            sys.stdout = self        
+            sys.stdout = self
         try:
             if self.arg:
                 self.data = self.func(self.arg)
             else:
                 self.data = self.func()
             self._executed = True
+        except Exception as e:
+            self._executed = False
+            self._executedError = e
+            traceback.print_exc()
+            exctype, value = sys.exc_info ()[:2]
+            self._executedErrorInfo = '{} {} {}'.\
+                format(exctype, value, traceback.format_exc())
+        sys.stdout = sys.__stdout__
+
+    def showProgressbar(self):
+        if self.progressText:
+
+            # generate widget if not given in init
+            if not self.pb_widget:
+                self.pb_widget = QDialog(self.parent())
+                self.pb_widget.setWindowFlags(Qt.SplashScreen)
+                self.pb_widget.setModal(True)
+
+            # add button
+            delete_button = QPushButton('X')
+            delete_button.clicked.connect(self.exit)
+            hl = QHBoxLayout()
+            pb = QProgressBar()
+            pb.setRange(0, 0)
+            hl.addWidget(pb)
+            hl.addWidget(QLabel(self.progressText))
+            if self.abortButton:
+                hl.addWidget(delete_button)
+            self.pb_widget.setLayout(hl)
+            self.pb_widget.show()
+
+    def hideProgressbar(self):
+        if self.pb_widget:
+            self.pb_widget.hide()
+
+    def write(self, text):
+        self.message.emit(text)
+
+    def flush(self):
+        pass
+
+
+class Worker(QRunnable):
+    '''
+    Worker class to be run by MultiThread(QThread).
+    '''
+    def __init__(self, fun, args,
+                 progressText=None,
+                 pb_widget=None,
+                 redirect_stdout=False):
+        super(Worker, self).__init__()
+        self.fun = fun
+        self.args = args
+        #self.kwargs = kwargs
+        self.signals = WorkerSignals()
+        self.progressText = progressText
+        self.pb_widget = pb_widget
+        self.redirect_stdout = redirect_stdout
+
+    @Slot()
+    def run(self):
+        if self.redirect_stdout:
+            sys.stdout = self
+
+        try:
+            result = self.fun(self.args)
+        except:
+            exctype, value = sys.exc_info ()[:2]
+            print(exctype, value, traceback.format_exc())
+            self.signals.error.emit ((exctype, value, traceback.format_exc ()))
+        else:
+            self.signals.result.emit(result)
+        finally:
+            self.signals.finished.emit('Done')
+        sys.stdout = sys.__stdout__
+
+    def write(self, text):
+        self.signals.message.emit(text)
+
+    def flush(self):
+        pass
+
+
+class WorkerSignals(QObject):
+    '''
+    Class to provide signals for Worker Class
+    '''
+    finished = Signal(str)
+    message = Signal(str)
+    error = Signal(tuple)
+    result = Signal(object)
+
+
+class MultiThread(QThread):
+    finished = Signal(str)
+    message = Signal(str)
+
+    def __init__(self, parent, func, args, ncores=1,
+                 progressText=None, pb_widget=None, redirect_stdout=False):
+        QThread.__init__(self, parent)
+        self.func = func
+        self.args = args
+        self.ncores = ncores
+        self.progressText = progressText
+        self.pb_widget = pb_widget
+        self.redirect_stdout = redirect_stdout
+        self.finished.connect(self.hideProgressbar)
+        self.showProgressbar()
+
+    def run(self):
+        if self.redirect_stdout:
+             sys.stdout = self
+        try:
+            if not self.ncores:
+                self.ncores = multiprocessing.cpu_count()
+            pool = multiprocessing.Pool(self.ncores)
+            self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
+            #self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
+            pool.close()
+            self._executed = True
         except Exception as e:
             self._executed = False
             self._executedError = e
             exc_type, exc_obj, exc_tb = sys.exc_info()
             fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
             print('Exception: {}, file: {}, line: {}'.format(exc_type, fname, exc_tb.tb_lineno))
-        sys.stdout = sys.__stdout__        
+        sys.stdout = sys.__stdout__
-
-    def __del__(self):
-        self.wait()
 
     def showProgressbar(self):
         if self.progressText:
             if not self.pb_widget:
                 self.pb_widget = QDialog(self.parent())
-                self.pb_widget.setWindowFlags(Qt.SplashScreen)                
+                self.pb_widget.setWindowFlags(Qt.SplashScreen)
                 self.pb_widget.setModal(True)
             hl = QHBoxLayout()
             pb = QProgressBar()
@@ -95,4 +180,8 @@ class Thread(QThread):
 
     def flush(self):
         pass
-    
+
+    def emitDone(self, result):
+        print('emitDone!')
+        self.finished.emit('Done thread!')
+        self.hideProgressbar()

pylot/core/util/utils.py

@@ -2,26 +2,57 @@
 # -*- coding: utf-8 -*-
 
 import hashlib
-import numpy as np
-from scipy.interpolate import splrep, splev
 import os
-import pwd
+import platform
 import re
-import warnings
 import subprocess
-from obspy import UTCDateTime, read
-from pylot.core.io.inputs import PylotParameter
 
-    
+import numpy as np
+from obspy import UTCDateTime, read
+from obspy.core import AttribDict
+from obspy.signal.rotate import rotate2zne
+from obspy.io.xseed.utils import SEEDParserException
+
+from pylot.core.io.inputs import PylotParameter
+from pylot.styles import style_settings
+
+from scipy.interpolate import splrep, splev
+from PySide import QtCore, QtGui
+
+try:
+    import pyqtgraph as pg
+except Exception as e:
+    print('PyLoT: Could not import pyqtgraph. {}'.format(e))
+    pg = None
+
 def _pickle_method(m):
     if m.im_self is None:
         return getattr, (m.im_class, m.im_func.func_name)
     else:
         return getattr, (m.im_self, m.im_func.func_name)
 
+
+def readDefaultFilterInformation(fname):
+    pparam = PylotParameter(fname)
+    return readFilterInformation(pparam)
+
+
+def readFilterInformation(pylot_parameter):
+    p_filter = {'filtertype': pylot_parameter['filter_type'][0],
+                'freq': [pylot_parameter['minfreq'][0], pylot_parameter['maxfreq'][0]],
+                'order': int(pylot_parameter['filter_order'][0])}
+    s_filter = {'filtertype': pylot_parameter['filter_type'][1],
+                'freq': [pylot_parameter['minfreq'][1], pylot_parameter['maxfreq'][1]],
+                'order': int(pylot_parameter['filter_order'][1])}
+    filter_information = {'P': p_filter,
+                          'S': s_filter}
+    return filter_information
+
+
 def fit_curve(x, y):
     return splev, splrep(x, y)
 
+
 def getindexbounds(f, eta):
     mi = f.argmax()
     m = max(f)
@@ -31,16 +62,55 @@ def getindexbounds(f, eta):
     return mi, l, u
 
 
-def gen_Pool(ncores='max'):
+def gen_Pool(ncores=0):
+    '''
+    :param ncores: number of CPU cores for multiprocessing.Pool, if ncores == 0 use all available
+    :return: multiprocessing.Pool object
+    '''
     import multiprocessing
 
-    if ncores=='max':
+    if ncores == 0:
-        ncores=multiprocessing.cpu_count()
+        ncores = multiprocessing.cpu_count()
-        
+
+    print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
+
     pool = multiprocessing.Pool(ncores)
     return pool
 
 
+def excludeQualityClasses(picks, qClasses, timeerrorsP, timeerrorsS):
+    '''
+    takes PyLoT picks dictionary and returns a new dictionary with certain classes excluded.
+    :param picks: PyLoT picks dictionary
+    :param qClasses: list (or int) of quality classes (0-4) to exclude
+    :param timeerrorsP: time errors for classes (0-4) for P
+    :param timeerrorsS: time errors for classes (0-4) for S
+    :return: new picks dictionary
+    '''
+    from pylot.core.pick.utils import getQualityFromUncertainty
+
+    if type(qClasses) in [int, float]:
+        qClasses = [qClasses]
+
+    picksdict_new = {}
+
+    phaseError = {'P': timeerrorsP,
+                  'S': timeerrorsS}
+
+    for station, phases in picks.items():
+        for phase, pick in phases.items():
+            if not type(pick) in [AttribDict, dict]:
+                continue
+            pickerror = phaseError[identifyPhaseID(phase)]
+            quality = getQualityFromUncertainty(pick['spe'], pickerror)
+            if not quality in qClasses:
+                if not station in picksdict_new:
+                    picksdict_new[station] = {}
+                picksdict_new[station][phase] = pick
+
+    return picksdict_new
+
+
 def clims(lim1, lim2):
     """
     takes two pairs of limits and returns one pair of common limts
@@ -106,6 +176,7 @@ def findComboBoxIndex(combo_box, val):
     """
     return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
 
+
 def find_in_list(list, str):
     """
     takes a list of strings and a string and returns the first list item
@@ -135,6 +206,7 @@ def find_in_list(list, str):
         return rlist[0]
     return None
 
+
 def find_nearest(array, value):
     '''
     function find_nearest takes an array and a value and returns the
@@ -182,6 +254,22 @@ def fnConstructor(s):
     return fn
 
 
+def real_None(value):
+    if value == 'None':
+        return None
+    else:
+        return value
+
+
+def real_Bool(value):
+    if value == 'True':
+        return True
+    elif value == 'False':
+        return False
+    else:
+        return value
+
+
 def four_digits(year):
     """
     takes a two digit year integer and returns the correct four digit equivalent
@@ -258,7 +346,7 @@ def getLogin():
     returns the actual user's login ID
     :return: login ID
     '''
-    return pwd.getpwuid(os.getuid())[0]
+    return os.getlogin()
 
 
 def getOwner(fn):
@@ -268,7 +356,15 @@ def getOwner(fn):
     :type fn: str
     :return: login ID of the file's owner
     '''
-    return pwd.getpwuid(os.stat(fn).st_uid).pw_name
+    system_name = platform.system()
+    if system_name in ["Linux", "Darwin"]:
+        import pwd
+        return pwd.getpwuid(os.stat(fn).st_uid).pw_name
+    elif system_name == "Windows":
+        import win32security
+        f = win32security.GetFileSecurity(fn, win32security.OWNER_SECURITY_INFORMATION)
+        (username, domain, sid_name_use) = win32security.LookupAccountSid(None, f.GetSecurityDescriptorOwner())
+        return username
 
 
 def getPatternLine(fn, pattern):
@@ -294,6 +390,7 @@ def getPatternLine(fn, pattern):
 
     return None
 
+
 def is_executable(fn):
     """
     takes a filename and returns True if the file is executable on the system
@@ -362,7 +459,7 @@ def key_for_set_value(d):
     return r
 
 
-def prepTimeAxis(stime, trace):
+def prepTimeAxis(stime, trace, verbosity=0):
     '''
     takes a starttime and a trace object and returns a valid time axis for
     plotting
@@ -376,16 +473,18 @@ def prepTimeAxis(stime, trace):
     etime = stime + nsamp / srate
     time_ax = np.arange(stime, etime, tincr)
     if len(time_ax) < nsamp:
-        print('elongate time axes by one datum')
+        if verbosity:
+            print('elongate time axes by one datum')
         time_ax = np.arange(stime, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
-        print('shorten time axes by one datum')
+        if verbosity:
+            print('shorten time axes by one datum')
         time_ax = np.arange(stime, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
-                      '{2} length of time vector \n'
+              '{2} length of time vector \n'
-                      'delta: {3}'.format(trace.stats.station,
+              'delta: {3}'.format(trace.stats.station,
-                                   nsamp, len(time_ax), tincr))
+                                  nsamp, len(time_ax), tincr))
         time_ax = None
     return time_ax
 
@@ -413,6 +512,91 @@ def find_horizontals(data):
     return rval
 
 
+def make_pen(picktype, phase, key, quality):
+    if pg:
+        rgba = pick_color(picktype, phase, quality)
+        linestyle, width = pick_linestyle_pg(picktype, key)
+        pen = pg.mkPen(rgba, width=width, style=linestyle)
+        return pen
+
+
+def pick_color(picktype, phase, quality=0):
+    min_quality = 3
+    bpc = base_phase_colors(picktype, phase)
+    rgba = bpc['rgba']
+    modifier = bpc['modifier']
+    intensity = 255.*quality/min_quality
+    rgba = modify_rgba(rgba, modifier, intensity)
+    return rgba
+
+
+def pick_color_plt(picktype, phase, quality=0):
+    rgba = list(pick_color(picktype, phase, quality))
+    for index, val in enumerate(rgba):
+        rgba[index] /= 255.
+    return rgba
+
+
+def pick_linestyle_plt(picktype, key):
+    linestyles_manu = {'mpp': ('solid', 2.),
+                       'epp': ('dashed', 1.),
+                       'lpp': ('dashed', 1.),
+                       'spe': ('dashed', 1.)}
+    linestyles_auto = {'mpp': ('dotted', 2.),
+                       'epp': ('dashdot', 1.),
+                       'lpp': ('dashdot', 1.),
+                       '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):
+    phasecolors = style_settings.phasecolors
+    return phasecolors[picktype][phase]
+
+def transform_colors_mpl_str(colors, no_alpha=False):
+    colors = list(colors)
+    colors_mpl = tuple([color / 255. for color in colors])
+    if no_alpha:
+        colors_mpl = '({}, {}, {})'.format(*colors_mpl)
+    else:
+        colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
+    return colors_mpl
+
+def transform_colors_mpl(colors):
+    colors = list(colors)
+    colors_mpl = tuple([color / 255. for color in colors])
+    return colors_mpl
+
 def remove_underscores(data):
     """
     takes a `obspy.core.stream.Stream` object and removes all underscores
@@ -427,6 +611,176 @@ def remove_underscores(data):
     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, verbosity=1):
+
+    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:
+            if verbosity:
+                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,))
+            if verbosity:
+                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,
@@ -477,6 +831,7 @@ def runProgram(cmd, parameter=None):
 
     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
@@ -495,7 +850,7 @@ def which(program, infile=None):
             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
@@ -523,6 +878,61 @@ def which(program, infile=None):
 
     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
 

pylot/styles/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

pylot/styles/bright.qss

@@ -0,0 +1,259 @@
+QMainWindow{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(255, 255, 255, 255));
+color: rgba(0, 0, 0, 255);
+}
+
+QWidget{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(235, 235, 235, 255), stop:1 rgba(230, 230, 230, 255));
+color: rgba(0, 0, 0, 255);
+}
+
+QToolBar QWidget:checked{
+background-color: transparent;
+border-color: rgba(230, 230, 230, 255);
+border-width: 2px;
+border-style:inset;
+}
+
+QComboBox{
+background-color: rgba(255, 255, 255, 255);
+color: rgba(0, 0, 0, 255);
+min-height: 1.5em;
+
+selection-background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 55, 140, 150), stop:1 rgba(0, 70, 180, 150));
+}
+
+QComboBox *{
+background-color: rgba(255, 255, 255, 255);
+color: rgba(0, 0, 0, 255);
+
+selection-background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 55, 140, 150), stop:1 rgba(0, 70, 180, 150));
+selection-color: rgba(255, 255, 255, 255);
+}
+
+QMenuBar{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:2, stop:0 rgba(240, 240, 240, 255), stop:1 rgba(230, 230, 230, 255));
+padding:1px;
+}
+
+QMenuBar::item{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:2, stop:0 rgba(240, 240, 240, 255), stop:1 rgba(230, 230, 230, 255));
+color: rgba(0, 0, 0, 255);
+padding:3px;
+padding-left:5px;
+padding-right:5px;
+}
+
+QMenu{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(230, 230, 230 255));
+color: rgba(0, 0, 0, 255);
+padding:0;
+}
+
+*::item:selected{
+color: rgba(0, 0, 0, 255);
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 55, 140, 150), stop:1 rgba(0, 70, 180, 150));
+}
+
+QToolBar{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(255, 255, 255, 255));
+border-style:solid;
+border-color:rgba(200, 200, 200, 150);
+border-width:1px;
+}
+
+QToolBar *{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(255, 255, 255, 255));
+}
+
+QMessageBox{
+background-color: rgba(255, 255, 255, 255);
+color: rgba(0, 0, 0, 255);
+}
+
+QTableWidget{
+background-color: rgba(255, 255, 255, 255);
+color:rgba(0, 0, 0, 255);
+border-color:rgba(0, 0, 0, 255);
+selection-background-color: rgba(200, 210, 230, 255);
+}
+
+QTableCornerButton::section{
+border: none;
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(255, 255, 255, 255), stop:1 rgba(230, 230, 230, 255));
+}
+
+QHeaderView::section{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(255, 255, 255, 255), stop:1 rgba(230, 230, 230, 255));
+border:none;
+border-top-style:solid;
+border-width:1px;
+border-top-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(255, 255, 255, 255), stop:1 rgba(230, 230, 230, 255));
+color:rgba(0, 0, 0, 255);
+padding:5px;
+}
+
+QHeaderView::section:checked{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 55, 140, 150), stop:1 rgba(0, 70, 180, 150));
+border-top-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 55, 140, 150), stop:1 rgba(0, 70, 180, 150));
+}
+
+QHeaderView{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(255, 255, 255, 255), stop:1 rgba(230, 230, 230, 255));
+
+border:none;
+border-top-style:solid;
+border-width:1px;
+border-top-color:rgba(230, 230, 230, 255);
+color:rgba(0, 0, 0, 255);
+}
+
+QListWidget{
+background-color:rgba(230, 230, 230, 255);
+color:rgba(0, 0, 0, 255);
+}
+
+QStatusBar{
+background-color:rgba(255, 255, 255, 255);
+color:rgba(0, 0, 0, 255);
+}
+
+QPushButton{
+background-color:qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(245, 245, 245, 255));
+color:rgba(0, 0, 0, 255);
+border-style: outset;
+border-width: 1px;
+border-color: rgba(100, 100, 120, 255);
+min-width: 6em;
+padding: 4px;
+padding-left:5px;
+padding-right:5px;
+border-radius: 2px;
+}
+
+QPushButton:pressed{
+background-color: rgba(230, 230, 230, 255);
+border-style: inset;
+}
+
+QPushButton:checked{
+background-color: rgba(230, 230, 230, 255);
+border-style: inset;
+}
+
+*:disabled{
+color:rgba(100, 100, 120, 255);
+}
+
+QTabBar{
+background-color:transparent;
+}
+
+QTabBar::tab{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(210, 210, 210, 255));
+color: rgba(0, 0, 0, 255);
+border-style:solid;
+border-color:rgba(210, 210, 210 255);
+border-bottom-color: transparent;
+border-width:1px;
+padding:5px;
+}
+
+QTabBar::tab:selected{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(255, 255, 255, 255), stop:1 rgba(245, 245, 245, 255));
+color: rgba(0, 0, 0, 255);
+border-style:solid;
+border-color:rgba(245, 245, 245, 255);
+border-bottom-color: transparent;
+border-width:1px;
+padding:5px;
+}
+
+QTabBar::tab:disabled{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(230, 230, 230, 255), stop:1 rgba(210, 210, 210, 255));
+color: rgba(100, 100, 120, 255);
+}
+
+QTabWidget{
+background-color:transparent;
+}
+
+QTabWidget::pane{
+background-color:rgba(0, 0, 0, 255);
+border-style:solid;
+border-color:rgba(245, 245, 245, 255);
+border-width:1px;
+}
+
+QTabWidget::tab{
+background-color:rgba(255, 255, 255, 255);
+}
+
+QTabWidget > QWidget{
+background-color: rgba(245, 245, 245, 255);
+color: rgba(0, 0, 0, 255);
+}
+
+QScrollArea{
+background: transparent;
+}
+
+QScrollArea>QWidget>QWidget{
+background: transparent;
+}
+
+QLabel{
+color: rgba(0, 0, 0, 255);
+background-color: transparent;
+}
+
+QTextEdit{
+color: rgba(0, 0, 0, 255);
+background-color: rgba(255, 255, 255, 255);
+}
+
+QSpinBox{
+color: rgba(0, 0, 0, 255);
+background-color: rgba(255, 255, 255, 255);
+}
+
+QDoubleSpinBox{
+color: rgba(0, 0, 0, 255);
+background-color: rgba(255, 255, 255, 255);
+}
+
+QCheckBox{
+background-color:transparent;
+border:none;
+}
+
+QLineEdit{
+background-color: rgba(255, 255, 255, 255);
+border: 1px inset;
+border-radius:0;
+border-color: rgba(100, 100, 120, 255);
+}
+
+QLineEdit:disabled{
+background-color: rgba(255, 255, 255, 255);
+border: 1px inset;
+border-radius:0;
+border-color: rgba(200, 200, 200, 255);
+}
+
+QListWidget{
+background-color:rgba(255, 255, 255, 255)
+}
+
+QProgressBar{
+background-color:rgba(230, 230, 230, 255);
+}
+
+QProgressBar::chunk{
+background-color:qlineargradient(spread:reflect, x1:0, y1:0, x2:0.5, y2:0, stop:0 transparent, stop:1 rgba(0, 70, 180, 150));
+}
+
+QStatusBar{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(235, 235, 235, 255), stop:1 rgba(230, 230, 230, 255));
+color: rgba(0, 0, 0, 255);
+}

pylot/styles/dark.qss

@@ -0,0 +1,258 @@
+QMainWindow{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+}
+
+QWidget{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+}
+
+QToolBar QWidget:checked{
+background-color: transparent;
+border-color: rgba(100, 100, 120, 255);
+border-width: 2px;
+border-style:inset;
+}
+
+QComboBox{
+background-color: rgba(90, 90, 100, 255);
+color: rgba(255, 255, 255, 255);
+min-height: 1.5em;
+
+selection-background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 144, 180, 255), stop:1 rgba(0, 150, 190, 255));
+}
+
+QComboBox *{
+background-color: rgba(90, 90, 100, 255);
+color: rgba(255, 255, 255, 255);
+
+selection-background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 144, 180, 255), stop:1 rgba(0, 150, 190, 255));
+selection-color: rgba(255, 255, 255, 255);
+}
+
+QMenuBar{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+padding:1px;
+}
+
+QMenuBar::item{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+padding:3px;
+padding-left:5px;
+padding-right:5px;
+}
+QMenu{
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+padding:0;
+}
+
+*::item:selected{
+color: rgba(255, 255, 255, 255);
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 144, 180, 255), stop:1 rgba(0, 150, 190, 255));
+}
+
+QToolBar{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+border-style:solid;
+border-color:rgba(80, 80, 90, 255);
+border-width:1px;
+}
+
+QToolBar *{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+}
+
+QMessageBox{
+background-color: rgba(60, 60, 70, 255);
+color: rgba(255, 255, 255, 255);
+}
+
+QTableWidget{
+background-color: rgba(80, 80, 90, 255);
+color:rgba(255, 255, 255, 255);
+border-color:rgba(255, 255, 255, 255);
+selection-background-color: rgba(200, 210, 230, 255);
+}
+
+QTableCornerButton::section{
+border: none;
+background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(60, 60, 70, 255), stop:1 rgba(70, 70, 80, 255));
+}
+
+QHeaderView::section{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(60, 60, 70, 255), stop:1 rgba(70, 70, 80, 255));
+border:none;
+border-top-style:solid;
+border-width:1px;
+border-top-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(60, 60, 70, 255), stop:1 rgba(70, 70, 80, 255));
+color:rgba(255, 255, 255, 255);
+padding:5px;
+}
+
+QHeaderView::section:checked{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 120, 150, 255), stop:1 rgba(0, 150, 190, 255));
+border-top-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 120, 150, 255), stop:1 rgba(0, 150, 190, 255));
+}
+
+QHeaderView{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(60, 60, 70, 255), stop:1 rgba(70, 70, 80, 255));
+
+border:none;
+border-top-style:solid;
+border-width:1px;
+border-top-color:rgba(70, 70, 80, 255);
+color:rgba(255, 255, 255, 255);
+}
+
+QListWidget{
+background-color:rgba(200, 200, 200, 255);
+color:rgba(255, 255, 255, 255);
+}
+
+QStatusBar{
+background-color:rgba(60, 60, 70, 255);
+color:rgba(255, 255, 255, 255);
+}
+
+QPushButton{
+background-color:qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color:rgba(255, 255, 255, 255);
+border-style: outset;
+border-width: 2px;
+border-color: rgba(50, 50, 60, 255);
+min-width: 6em;
+padding: 4px;
+padding-left:5px;
+padding-right:5px;
+border-radius: 2px;
+}
+
+QPushButton:pressed{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(80, 80, 90, 255), stop:1 rgba(70, 70, 80, 255));
+border-style: inset;
+}
+
+QPushButton:checked{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(80, 80, 90, 255), stop:1 rgba(70, 70, 80, 255));
+border-style: inset;
+}
+
+*:disabled{
+color: rgba(130, 130, 130, 255);
+}
+
+QTabBar{
+background-color:transparent;
+}
+
+QTabBar::tab{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+border-style:solid;
+border-color:rgba(70, 70, 80, 255);
+border-bottom-color: transparent;
+border-width:1px;
+padding:5px;
+}
+
+QTabBar::tab:selected{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(80, 80, 90, 255), stop:1 rgba(70, 70, 80, 255));
+color: rgba(255, 255, 255, 255);
+border-style:solid;
+border-color:rgba(70, 70, 80, 255);
+border-bottom-color: transparent;
+border-width:1px;
+padding:5px;
+}
+
+QTabBar::tab:disabled{
+background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(100, 100, 120, 255);
+}
+
+QTabWidget{
+background-color:transparent;
+}
+
+QTabWidget::pane{
+background-color:rgba(70, 70, 80, 255);
+border-style:solid;
+border-color:rgba(70, 70, 80, 255);
+border-width:1px;
+}
+
+QTabWidget::tab{
+background-color:rgba(70, 70, 80, 255);
+}
+
+QTabWidget > QWidget{
+background-color: rgba(70, 70, 80, 255);
+color: rgba(255, 255, 255, 255);
+}
+
+QScrollArea{
+background: transparent;
+}
+
+QScrollArea>QWidget>QWidget{
+background: transparent;
+}
+
+QLabel{
+color: rgba(255, 255, 255, 255);
+background-color: transparent;
+}
+
+QTextEdit{
+color: rgba(255, 255, 255, 255);
+background-color: rgba(90, 90, 100, 255);
+}
+
+QSpinBox{
+color: rgba(255, 255, 255, 255);
+background-color: rgba(90, 90, 100, 255);
+}
+
+QDoubleSpinBox{
+color: rgba(255, 255, 255, 255);
+background-color: rgba(90, 90, 100, 255);
+}
+
+QCheckBox{
+background-color:transparent;
+border:none;
+}
+
+QLineEdit{
+background-color: rgba(90, 90, 100, 255);
+border: 1px inset;
+border-radius:0;
+border-color: rgba(100, 100, 120, 255);
+}
+
+QLineEdit:disabled{
+background-color: rgba(90, 90, 100, 255);
+border: 1px inset;
+border-radius:0;
+border-color: rgba(200, 200, 200, 255);
+}
+
+QListWidget{
+background-color:rgba(60, 60, 70, 255)
+}
+
+QProgressBar{
+background-color:rgba(60, 60, 70, 255);
+}
+
+QProgressBar::chunk{
+background-color:qlineargradient(spread:reflect, x1:0, y1:0, x2:0.5, y2:0, stop:0 transparent, stop:1 rgba(0, 150, 190, 255));
+}
+
+QStatusBar{
+background-color: qlineargradient(spread:reflect, x1:0, y1:0, x2:0, y2:0.5, stop:0 rgba(70, 70, 80, 255), stop:1 rgba(60, 60, 70, 255));
+color: rgba(255, 255, 255, 255);
+}

pylot/styles/style_settings.py

@@ -0,0 +1,70 @@
+# -*- coding: utf-8 -*-
+
+# Set base phase colors for manual and automatic picks
+# together with a modifier (r, g, or b) used to alternate
+# the base color
+phasecolors = {
+    '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'}
+    }
+}
+
+# Set plot colors and stylesheet for each style
+stylecolors = {
+    'default':{
+        'linecolor':{
+            'rgba': (0, 0, 0, 255)},
+        'background': {
+            'rgba': (255, 255, 255, 255)},
+        'multicursor': {
+            'rgba': (255, 190, 0, 255)},
+        'ref': {
+            'rgba': (200, 210, 230, 255)},
+        'test': {
+            'rgba': (200, 230, 200, 255)},
+        'stylesheet': {
+            'filename': None}
+    },
+    'dark': {
+        'linecolor': {
+            'rgba': (230, 230, 230, 255)},
+        'background': {
+            'rgba': (50, 50, 60, 255)},
+        'multicursor': {
+            'rgba': (0, 150, 190, 255)},
+        'ref': {
+            'rgba': (80, 110, 170, 255)},
+        'test': {
+            'rgba': (130, 190, 100, 255)},
+        'stylesheet': {
+            'filename': 'dark.qss'}
+    },
+    'bright': {
+        'linecolor': {
+            'rgba': (0, 0, 0, 255)},
+        'background': {
+            'rgba': (255, 255, 255, 255)},
+        'multicursor': {
+            'rgba': (100, 100, 190, 255)},
+        'ref': {
+            'rgba': (200, 210, 230, 255)},
+        'test': {
+            'rgba': (200, 230, 200, 255)},
+        'stylesheet': {
+            'filename': 'bright.qss'}
+    }
+}
+

pylot/testing/testHelpForm.py

@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys, time
-from PySide.QtGui import QApplication
-from pylot.core.util.widgets import HelpForm
-
-app = QApplication(sys.argv)
-
-win = HelpForm()
-win.show()
-app.exec_()

pylot/testing/testPickDlg.py

@@ -1,20 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-import matplotlib
-
-matplotlib.use('Qt4Agg')
-matplotlib.rcParams['backend.qt4'] = 'PySide'
-
-from PySide.QtGui import QApplication
-from obspy.core import read
-from pylot.core.util.widgets import PickDlg
-import icons_rc
-
-app = QApplication(sys.argv)
-
-data = read()
-win = PickDlg(data=data)
-win.show()
-app.exec_()

pylot/testing/testPropDlg.py

@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys, time
-from PySide.QtGui import QApplication
-from pylot.core.util.widgets import PropertiesDlg
-
-app = QApplication(sys.argv)
-
-win = PropertiesDlg()
-win.show()
-app.exec_()

pylot/testing/testUIcomponents.py

@@ -1,17 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-
-import sys, time
-from PySide.QtGui import QApplication
-from pylot.core.util.widgets import FilterOptionsDialog, PropertiesDlg, HelpForm
-
-dialogs = [FilterOptionsDialog, PropertiesDlg, HelpForm]
-
-app = QApplication(sys.argv)
-
-for dlg in dialogs:
-    win = dlg()
-    win.show()
-    time.sleep(1)
-    win.destroy()

pylot/testing/testUtils.py

@@ -1,27 +0,0 @@
-# -*- coding: utf-8 -*-
-'''
-Created on 10.11.2014
-
-@author: sebastianw
-'''
-import unittest
-
-
-class Test(unittest.TestCase):
-
-
-    def setUp(self):
-        pass
-
-
-    def tearDown(self):
-        pass
-
-
-    def testName(self):
-        pass
-
-
-if __name__ == "__main__":
-    #import sys;sys.argv = ['', 'Test.testName']
-    unittest.main()

pylot/testing/testWidgets.py

@@ -1,19 +0,0 @@
-# -*- coding: utf-8 -*-
-'''
-Created on 10.11.2014
-
-@author: sebastianw
-'''
-import unittest
-
-
-class Test(unittest.TestCase):
-
-
-    def testName(self):
-        pass
-
-
-if __name__ == "__main__":
-    #import sys;sys.argv = ['', 'Test.testName']
-    unittest.main()

pylot/testing/test_autopick.py

@@ -1,303 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to run autoPyLoT-script "makeCF.py".
-   Only for test purposes!
-"""
-
-from obspy.core import read
-import matplotlib.pyplot as plt
-import numpy as np
-from pylot.core.pick.charfuns import *
-from pylot.core.pick.picker import *
-import glob
-import argparse
-
-def run_makeCF(project, database, event, iplot, station=None):
-    #parameters for CF calculation
-    t2 = 7                   #length of moving window for HOS calculation [sec]
-    p = 4                    #order of HOS
-    cuttimes = [10, 50]      #start and end time for CF calculation
-    bpz = [2, 30]            #corner frequencies of bandpass filter, vertical component
-    bph = [2, 15]            #corner frequencies of bandpass filter, horizontal components
-    tdetz= 1.2               #length of AR-determination window [sec], vertical component
-    tdeth= 0.8               #length of AR-determination window [sec], horizontal components
-    tpredz = 0.4             #length of AR-prediction window [sec], vertical component
-    tpredh = 0.4             #length of AR-prediction window [sec], horizontal components
-    addnoise = 0.001         #add noise to seismogram for stable AR prediction
-    arzorder = 2             #chosen order of AR process, vertical component
-    arhorder = 4             #chosen order of AR process, horizontal components
-    TSNRhos = [5, 0.5, 1, 0.1] #window lengths [s] for calculating SNR for earliest/latest pick and quality assessment
-                             #from HOS-CF [noise window, safety gap, signal window, slope determination window]
-    TSNRarz = [5, 0.5, 1, 0.5] #window lengths [s] for calculating SNR for earliest/lates pick and quality assessment
-                             #from ARZ-CF
-    #get waveform data
-    if station:
-       dpz = '/data/%s/EVENT_DATA/LOCAL/%s/%s/%s*HZ.msd' % (project, database, event, station)
-       dpe = '/data/%s/EVENT_DATA/LOCAL/%s/%s/%s*HE.msd' % (project, database, event, station)
-       dpn = '/data/%s/EVENT_DATA/LOCAL/%s/%s/%s*HN.msd' % (project, database, event, station)
-       #dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_z.gse' % (project, database, event, station)
-       #dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_e.gse' % (project, database, event, station)
-       #dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_n.gse' % (project, database, event, station)
-    else:
-        # dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*_z.gse' % (project, database, event)
-        # dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*_e.gse' % (project, database, event)
-        # dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*_n.gse' % (project, database, event)
-        dpz = '/data/%s/EVENT_DATA/LOCAL/%s/%s/*HZ.msd' % (project, database, event)
-        dpe = '/data/%s/EVENT_DATA/LOCAL/%s/%s/*HE.msd' % (project, database, event)
-        dpn = '/data/%s/EVENT_DATA/LOCAL/%s/%s/*HN.msd' % (project, database, event)
-    wfzfiles = glob.glob(dpz)
-    wfefiles = glob.glob(dpe)
-    wfnfiles = glob.glob(dpn)
-    if wfzfiles:
-       for i in range(len(wfzfiles)):
-          print 'Vertical component data found ...'
-          print wfzfiles[i]
-          st = read('%s' % wfzfiles[i])
-          st_copy = st.copy()
-          #filter and taper data
-          tr_filt = st[0].copy()
-          tr_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
-          tr_filt.taper(max_percentage=0.05, type='hann')
-          st_copy[0].data = tr_filt.data
-          ##############################################################
-          #calculate HOS-CF using subclass HOScf of class CharacteristicFunction
-          hoscf = HOScf(st_copy, cuttimes, t2, p) #instance of HOScf
-          ##############################################################
-          #calculate AIC-HOS-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_aic = tr_filt.copy()
-          tr_aic.data = hoscf.getCF()
-          st_copy[0].data = tr_aic.data
-          aiccf = AICcf(st_copy, cuttimes) #instance of AICcf
-          ##############################################################
-          #get prelimenary onset time from AIC-HOS-CF using subclass AICPicker of class AutoPicking
-          aicpick = AICPicker(aiccf, None, TSNRhos, 3, 10, None, 0.1)
-          ##############################################################
-          #get refined onset time from HOS-CF using class Picker
-          hospick = PragPicker(hoscf, None, TSNRhos, 2, 10, 0.001, 0.2, aicpick.getpick())
-          #get earliest and latest possible picks
-          hosELpick = EarlLatePicker(hoscf, 1.5, TSNRhos, None, 10, None, None, hospick.getpick())
-          ##############################################################
-          #calculate ARZ-CF using subclass ARZcf of class CharcteristicFunction
-          #get stream object of filtered data
-          st_copy[0].data = tr_filt.data
-          arzcf = ARZcf(st_copy, cuttimes, tpredz, arzorder, tdetz, addnoise) #instance of ARZcf
-          ##############################################################
-          #calculate AIC-ARZ-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_arzaic = tr_filt.copy()
-          tr_arzaic.data = arzcf.getCF()
-          st_copy[0].data = tr_arzaic.data
-          araiccf = AICcf(st_copy, cuttimes, tpredz, 0, tdetz) #instance of AICcf
-          ##############################################################
-          #get onset time from AIC-ARZ-CF using subclass AICPicker of class AutoPicking
-          aicarzpick = AICPicker(araiccf, 1.5, TSNRarz, 2, 10, None, 0.1)
-          ##############################################################
-          #get refined onset time from ARZ-CF using class Picker
-          arzpick = PragPicker(arzcf, 1.5, TSNRarz, 2.0, 10, 0.1, 0.05, aicarzpick.getpick())
-          #get earliest and latest possible picks
-          arzELpick = EarlLatePicker(arzcf, 1.5, TSNRarz, None, 10, None, None, arzpick.getpick())
-    elif not wfzfiles:
-       print 'No vertical component data found!'
-
-    if wfefiles and wfnfiles:
-       for i in range(len(wfefiles)):
-          print 'Horizontal component data found ...'
-          print wfefiles[i]
-          print wfnfiles[i]
-          #merge streams
-          H = read('%s' % wfefiles[i])
-          H += read('%s' % wfnfiles[i])
-          H_copy = H.copy()
-          #filter and taper data
-          trH1_filt = H[0].copy()
-          trH2_filt = H[1].copy()
-          trH1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          trH2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          trH1_filt.taper(max_percentage=0.05, type='hann')
-          trH2_filt.taper(max_percentage=0.05, type='hann')
-          H_copy[0].data = trH1_filt.data
-          H_copy[1].data = trH2_filt.data
-
-          ##############################################################
-          #calculate ARH-CF using subclass ARHcf of class CharcteristicFunction
-          arhcf = ARHcf(H_copy, cuttimes, tpredh, arhorder, tdeth, addnoise) #instance of ARHcf
-          ##############################################################
-          #calculate AIC-ARH-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_arhaic = trH1_filt.copy()
-          tr_arhaic.data = arhcf.getCF()
-          H_copy[0].data = tr_arhaic.data
-          #calculate ARH-AIC-CF
-          arhaiccf = AICcf(H_copy, cuttimes, tpredh, 0, tdeth) #instance of AICcf
-          ##############################################################
-          #get onset time from AIC-ARH-CF using subclass AICPicker of class AutoPicking
-          aicarhpick = AICPicker(arhaiccf, 1.5, TSNRarz, 4, 10, None, 0.1)
-          ###############################################################
-          #get refined onset time from ARH-CF using class Picker
-          arhpick = PragPicker(arhcf, 1.5, TSNRarz, 2.5, 10, 0.1, 0.05, aicarhpick.getpick())
-          #get earliest and latest possible picks
-          arhELpick = EarlLatePicker(arhcf, 1.5, TSNRarz, None, 10, None, None, arhpick.getpick())
-
-          #create stream with 3 traces
-          #merge streams
-          AllC = read('%s' % wfefiles[i])
-          AllC += read('%s' % wfnfiles[i])
-          AllC += read('%s' % wfzfiles[i])
-          #filter and taper data
-          All1_filt = AllC[0].copy()
-          All2_filt = AllC[1].copy()
-          All3_filt = AllC[2].copy()
-          All1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All3_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
-          All1_filt.taper(max_percentage=0.05, type='hann')
-          All2_filt.taper(max_percentage=0.05, type='hann')
-          All3_filt.taper(max_percentage=0.05, type='hann')
-          AllC[0].data = All1_filt.data
-          AllC[1].data = All2_filt.data
-          AllC[2].data = All3_filt.data
-          #calculate AR3C-CF using subclass AR3Ccf of class CharacteristicFunction
-          ar3ccf = AR3Ccf(AllC, cuttimes, tpredz, arhorder, tdetz, addnoise) #instance of AR3Ccf
-          #get earliest and latest possible pick from initial ARH-pick
-          ar3cELpick = EarlLatePicker(ar3ccf, 1.5, TSNRarz, None, 10, None, None, arhpick.getpick())
-          ##############################################################
-          if iplot:
-             #plot vertical trace
-             plt.figure()
-             tr = st[0]
-             tdata = np.arange(0, tr.stats.npts / tr.stats.sampling_rate, tr.stats.delta)
-             p1, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
-             p2, = plt.plot(hoscf.getTimeArray(), hoscf.getCF() / max(hoscf.getCF()), 'r')
-             p3, = plt.plot(aiccf.getTimeArray(), aiccf.getCF()/max(aiccf.getCF()), 'b')
-             p4, = plt.plot(arzcf.getTimeArray(), arzcf.getCF()/max(arzcf.getCF()), 'g')
-             p5, = plt.plot(araiccf.getTimeArray(), araiccf.getCF()/max(araiccf.getCF()), 'y')
-             plt.plot([aicpick.getpick(), aicpick.getpick()], [-1, 1], 'b--')
-             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([hospick.getpick(), hospick.getpick()], [-1.3, 1.3], 'r', linewidth=2)
-             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [1.3, 1.3], 'r')
-             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [-1.3, -1.3], 'r')
-             plt.plot([hosELpick.getLpick(), hosELpick.getLpick()], [-1.1, 1.1], 'r--')
-             plt.plot([hosELpick.getEpick(), hosELpick.getEpick()], [-1.1, 1.1], 'r--')
-             plt.plot([aicarzpick.getpick(), aicarzpick.getpick()], [-1.2, 1.2], 'y', linewidth=2)
-             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [1.2, 1.2], 'y')
-             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [-1.2, -1.2], 'y')
-             plt.plot([arzpick.getpick(), arzpick.getpick()], [-1.4, 1.4], 'g', linewidth=2)
-             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [1.4, 1.4], 'g')
-             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [-1.4, -1.4], 'g')
-             plt.plot([arzELpick.getLpick(), arzELpick.getLpick()], [-1.2, 1.2], 'g--')
-             plt.plot([arzELpick.getEpick(), arzELpick.getEpick()], [-1.2, 1.2], 'g--')
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.xlabel('Time [s]')
-             plt.ylabel('Normalized Counts')
-             plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station, \
-                        tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
-             plt.suptitle(tr.stats.starttime)
-             plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
-             #plot horizontal traces
-             plt.figure(2)
-             plt.subplot(2,1,1)
-             tsteph = tpredh / 4
-             th1data = np.arange(0, trH1_filt.stats.npts / trH1_filt.stats.sampling_rate, trH1_filt.stats.delta)
-             th2data = np.arange(0, trH2_filt.stats.npts / trH2_filt.stats.sampling_rate, trH2_filt.stats.delta)
-             tarhcf = np.arange(0, len(arhcf.getCF()) * tsteph, tsteph) + cuttimes[0] + tdeth +tpredh
-             p21, = plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
-             p22, = plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
-             p23, = plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
-             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
-             plt.plot([arhELpick.getLpick(), arhELpick.getLpick()], [-0.8, 0.8], 'r--')
-             plt.plot([arhELpick.getEpick(), arhELpick.getEpick()], [-0.8, 0.8], 'r--')
-             plt.plot([arhpick.getpick() + arhELpick.getPickError(), arhpick.getpick() + arhELpick.getPickError()], \
-                       [-0.2, 0.2], 'r--')
-             plt.plot([arhpick.getpick() - arhELpick.getPickError(), arhpick.getpick() - arhELpick.getPickError()], \
-                       [-0.2, 0.2], 'r--')
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
-             plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p21, p22, p23], ['Data', 'ARH-CF', 'ARHAIC-CF'])
-             plt.subplot(2,1,2)
-             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
-             plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
-             plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
-             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
-             plt.plot([arhELpick.getLpick(), arhELpick.getLpick()], [-0.8, 0.8], 'r--')
-             plt.plot([arhELpick.getEpick(), arhELpick.getEpick()], [-0.8, 0.8], 'r--')
-             plt.plot([arhpick.getpick() + arhELpick.getPickError(), arhpick.getpick() + arhELpick.getPickError()], \
-                       [-0.2, 0.2], 'r--')
-             plt.plot([arhpick.getpick() - arhELpick.getPickError(), arhpick.getpick() - arhELpick.getPickError()], \
-                       [-0.2, 0.2], 'r--')
-             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.xlabel('Time [s]')
-             plt.ylabel('Normalized Counts')
-             #plot 3-component window
-             plt.figure(3)
-             plt.subplot(3,1,1)
-             p31, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
-             p32, = plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([ar3cELpick.getLpick(), ar3cELpick.getLpick()], [-0.8, 0.8], 'b--')
-             plt.plot([ar3cELpick.getEpick(), ar3cELpick.getEpick()], [-0.8, 0.8], 'b--')
-             plt.yticks([])
-             plt.xticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([tr.stats.station, tr.stats.channel])
-             plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p31, p32], ['Data', 'AR3C-CF'])
-             plt.subplot(3,1,2)
-             plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
-             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([ar3cELpick.getLpick(), ar3cELpick.getLpick()], [-0.8, 0.8], 'b--')
-             plt.plot([ar3cELpick.getEpick(), ar3cELpick.getEpick()], [-0.8, 0.8], 'b--')
-             plt.yticks([])
-             plt.xticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
-             plt.subplot(3,1,3)
-             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
-             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([ar3cELpick.getLpick(), ar3cELpick.getLpick()], [-0.8, 0.8], 'b--')
-             plt.plot([ar3cELpick.getEpick(), ar3cELpick.getEpick()], [-0.8, 0.8], 'b--')
-             plt.yticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
-             plt.xlabel('Time [s]')
-             plt.show()
-             raw_input()
-             plt.close()
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--project', type=str, help='project name (e.g. Insheim)')
-    parser.add_argument('--database', type=str, help='event data base (e.g. 2014.09_Insheim)')
-    parser.add_argument('--event', type=str, help='event ID (e.g. e0010.015.14)')
-    parser.add_argument('--iplot', help='anything, if set, figure occurs')
-    parser.add_argument('--station', type=str, help='Station ID (e.g. INS3) (optional)')
-    args = parser.parse_args()
-
-    run_makeCF(args.project, args.database, args.event, args.iplot, args.station)

pylot/testing/test_pdf.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from pylot.core.util.pdf import ProbabilityDensityFunction
-pdf = ProbabilityDensityFunction.from_pick(0.34, 0.5, 0.54, type='exp')
-pdf2 = ProbabilityDensityFunction.from_pick(0.34, 0.5, 0.54, type='exp')
-diff = pdf - pdf2

scripts/pylot-noisewindow.py

@@ -1,15 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-import numpy
-from pylot.core.pick.utils import getnoisewin
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--t', type=numpy.array, help='numpy array of time stamps')
-    parser.add_argument('--t1', type=float, help='time from which relativ to it noise window is extracted')
-    parser.add_argument('--tnoise', type=float, help='length of time window [s] for noise part extraction')
-    parser.add_argument('--tgap', type=float, help='safety gap between signal (t1=onset) and noise')
-    args = parser.parse_args()
-    getnoisewin(args.t, args.t1, args.tnoise, args.tgap)

scripts/pylot-pick-earliest-latest.py

@@ -1,28 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-"""
-   Created Mar 2015
-   Transcription of the rezipe of Diehl et al. (2009) for consistent phase
-   picking. For a given inital (the most likely) pick, the corresponding earliest
-   and latest possible pick is calculated based on noise measurements in front of
-   the most likely pick and signal wavelength derived from zero crossings.
-
-   :author: Ludger Kueperkoch / MAGS2 EP3 working group
-"""
-
-import argparse
-import obspy
-from pylot.core.pick.utils import earllatepicker
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--X', type=~obspy.core.stream.Stream,
-                        help='time series (seismogram) read with obspy module read')
-    parser.add_argument('--nfac', type=int,
-                        help='(noise factor), nfac times noise level to calculate latest possible pick')
-    parser.add_argument('--TSNR', type=tuple, help='length of time windows around pick used to determine SNR \
-                        [s] (Tnoise, Tgap, Tsignal)')
-    parser.add_argument('--Pick1', type=float, help='Onset time of most likely pick')
-    parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
-    args = parser.parse_args()
-    earllatepicker(args.X, args.nfac, args.TSNR, args.Pick1, args.iplot)

scripts/pylot-pick-firstmotion.py

@@ -1,24 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-"""
-   Created Mar 2015
-   Function to derive first motion (polarity) for given phase onset based on zero crossings.
-
-   :author: MAGS2 EP3 working group / Ludger Kueperkoch
-"""
-
-import argparse
-import obspy
-from pylot.core.pick.utils import fmpicker
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--Xraw', type=obspy.core.stream.Stream,
-                        help='unfiltered time series (seismogram) read with obspy module read')
-    parser.add_argument('--Xfilt', type=obspy.core.stream.Stream,
-                        help='filtered time series (seismogram) read with obspy module read')
-    parser.add_argument('--pickwin', type=float, help='length of pick window [s] for first motion determination')
-    parser.add_argument('--Pick', type=float, help='Onset time of most likely pick')
-    parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
-    args = parser.parse_args()
-    fmpicker(args.Xraw, args.Xfilt, args.pickwin, args.Pick, args.iplot)

scripts/pylot-reasses-pilot-db.py

@@ -1,41 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-
-from pylot.core.util.version import get_git_version as _getVersionString
-from pylot.core.io.phases import reassess_pilot_db
-
-__version__ = _getVersionString()
-__author__ = 'S. Wehling-Benatelli'
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(
-        description='reassess old PILOT event data base in terms of consistent '
-                    'automatic uncertainty estimation',
-        epilog='Script written by {author} belonging to PyLoT version'
-               ' {version}\n'.format(author=__author__,
-                                     version=__version__)
-    )
-
-    parser.add_argument(
-        'root', type=str, help='specifies the root directory'
-    )
-    parser.add_argument(
-        'db', type=str, help='specifies the database name'
-    )
-    parser.add_argument(
-        '--output', '-o', type=str, help='path to the output directory',
-        dest='output'
-    )
-    parser.add_argument(
-        '--parameterfile', '-p', type=str,
-        help='full path to the parameterfile', dest='parfile'
-    )
-    parser.add_argument(
-        '--verbosity', '-v', action='count', help='increase output verbosity',
-        default=0, dest='verbosity'
-    )
-
-    args = parser.parse_args()
-    reassess_pilot_db(args.root, args.db, args.output, args.parfile, args.verbosity)

scripts/pylot-reasses-pilot-event.py

@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-
-from pylot.core.util.version import get_git_version as _getVersionString
-from pylot.core.io.phases import reassess_pilot_event
-
-__version__ = _getVersionString()
-__author__ = 'S. Wehling-Benatelli'
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(
-        description='reassess old PILOT event data in terms of consistent '
-                    'automatic uncertainty estimation',
-        epilog='Script written by {author} belonging to PyLoT version'
-               ' {version}\n'.format(author=__author__,
-                                     version=__version__)
-    )
-
-    parser.add_argument(
-        'root', type=str, help='specifies the root directory'
-    )
-    parser.add_argument(
-        'db', type=str, help='specifies the database name'
-    )
-    parser.add_argument(
-        'id', type=str, help='PILOT event identifier'
-    )
-    parser.add_argument(
-        '--output', '-o', type=str, help='path to the output directory', dest='output'
-    )
-    parser.add_argument(
-        '--parameterfile', '-p', type=str, help='full path to the parameterfile', dest='parfile'
-    )
-
-    args = parser.parse_args()
-    reassess_pilot_event(args.root, args.db, args.id, args.output, args.parfile)

scripts/pylot-signalwindow.py

@@ -1,14 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-import numpy
-from pylot.core.pick.utils import getsignalwin
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--t', type=numpy.array, help='numpy array of time stamps')
-    parser.add_argument('--t1', type=float, help='time from which relativ to it signal window is extracted')
-    parser.add_argument('--tsignal', type=float, help='length of time window [s] for signal part extraction')
-    args = parser.parse_args()
-    getsignalwin(args.t, args.t1, args.tsignal)

scripts/pylot-snr.py

@@ -1,30 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-"""
-   Created Mar/Apr 2015
-   Function to calculate SNR of certain part of seismogram relative
-   to given time. Returns SNR and SNR [dB].
-
-   :author: Ludger Kueperkoch /MAGS EP3 working group
-"""
-
-import argparse
-import obspy
-from pylot.core.pick.utils import getSNR
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--data', '-d', type=obspy.core.stream.Stream,
-                        help='time series (seismogram) read with obspy module '
-                             'read',
-                        dest='data')
-    parser.add_argument('--tsnr', '-s', type=tuple,
-                        help='length of time windows around pick used to '
-                             'determine SNR [s] (Tnoise, Tgap, Tsignal)',
-                        dest='tsnr')
-    parser.add_argument('--time', '-t', type=float,
-                        help='initial time from which noise and signal windows '
-                             'are calculated',
-                        dest='time')
-    args = parser.parse_args()
-    print getSNR(args.data, args.tsnr, args.time)

scripts/run_makeCF.py

@@ -1,307 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to run autoPyLoT-script "run_makeCF.py".
-   Only for test purposes!
-"""
-
-from obspy.core import read
-import matplotlib.pyplot as plt
-import numpy as np
-from pylot.core.pick.charfuns import CharacteristicFunction
-from pylot.core.pick.picker import AutoPicker
-from pylot.core.pick.utils import *
-import glob
-import argparse
-
-def run_makeCF(project, database, event, iplot, station=None):
-    #parameters for CF calculation
-    t2 = 7                   #length of moving window for HOS calculation [sec]
-    p = 4                    #order of HOS
-    cuttimes = [10, 50]      #start and end time for CF calculation
-    bpz = [2, 30]            #corner frequencies of bandpass filter, vertical component
-    bph = [2, 15]            #corner frequencies of bandpass filter, horizontal components
-    tdetz= 1.2               #length of AR-determination window [sec], vertical component
-    tdeth= 0.8               #length of AR-determination window [sec], horizontal components
-    tpredz = 0.4             #length of AR-prediction window [sec], vertical component
-    tpredh = 0.4             #length of AR-prediction window [sec], horizontal components
-    addnoise = 0.001         #add noise to seismogram for stable AR prediction
-    arzorder = 2             #chosen order of AR process, vertical component
-    arhorder = 4             #chosen order of AR process, horizontal components
-    TSNRhos = [5, 0.5, 1, .6] #window lengths [s] for calculating SNR for earliest/latest pick and quality assessment
-                             #from HOS-CF [noise window, safety gap, signal window, slope determination window]
-    TSNRarz = [5, 0.5, 1, 1.0] #window lengths [s] for calculating SNR for earliest/lates pick and quality assessment
-                             #from ARZ-CF
-    #get waveform data
-    if station:
-       dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HZ.msd' % (project, database, event, station)
-       dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HE.msd' % (project, database, event, station)
-       dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*HN.msd' % (project, database, event, station)
-       #dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_z.gse' % (project, database, event, station)
-       #dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_e.gse' % (project, database, event, station)
-       #dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/%s*_n.gse' % (project, database, event, station)
-    else:
-       dpz = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HZ.msd' % (project, database, event)
-       dpe = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HE.msd' % (project, database, event)
-       dpn = '/DATA/%s/EVENT_DATA/LOCAL/%s/%s/*HN.msd' % (project, database, event)
-    wfzfiles = glob.glob(dpz)
-    wfefiles = glob.glob(dpe)
-    wfnfiles = glob.glob(dpn)
-    if wfzfiles:
-       for i in range(len(wfzfiles)):
-          print 'Vertical component data found ...'
-          print wfzfiles[i]
-          st = read('%s' % wfzfiles[i])
-          st_copy = st.copy()
-          #filter and taper data
-          tr_filt = st[0].copy()
-          tr_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
-          tr_filt.taper(max_percentage=0.05, type='hann')
-          st_copy[0].data = tr_filt.data
-          ##############################################################
-          #calculate HOS-CF using subclass HOScf of class CharacteristicFunction
-          hoscf = HOScf(st_copy, cuttimes, t2, p) #instance of HOScf
-          ##############################################################
-          #calculate AIC-HOS-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_aic = tr_filt.copy()
-          tr_aic.data = hoscf.getCF()
-          st_copy[0].data = tr_aic.data
-          aiccf = AICcf(st_copy, cuttimes) #instance of AICcf
-          ##############################################################
-          #get prelimenary onset time from AIC-HOS-CF using subclass AICPicker of class AutoPicking
-          aicpick = AICPicker(aiccf, TSNRhos, 3, 10, None, 0.1)
-          ##############################################################
-          #get refined onset time from HOS-CF using class Picker
-          hospick = PragPicker(hoscf, TSNRhos, 2, 10, 0.001, 0.2, aicpick.getpick())
-          #############################################################
-          #get earliest and latest possible picks
-          st_copy[0].data = tr_filt.data
-          [lpickhos, epickhos, pickerrhos] = earllatepicker(st_copy, 1.5, TSNRhos, hospick.getpick(), 10)
-          #############################################################
-          #get SNR
-          [SNR, SNRdB] = getSNR(st_copy, TSNRhos, hospick.getpick())
-          print 'SNR:', SNR, 'SNR[dB]:', SNRdB
-          ##########################################################
-          #get first motion of onset
-          hosfm = fmpicker(st, st_copy, 0.2, hospick.getpick(), 11)
-          ##############################################################
-          #calculate ARZ-CF using subclass ARZcf of class CharcteristicFunction
-          arzcf = ARZcf(st, cuttimes, tpredz, arzorder, tdetz, addnoise) #instance of ARZcf
-          ##############################################################
-          #calculate AIC-ARZ-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_arzaic = tr_filt.copy()
-          tr_arzaic.data = arzcf.getCF()
-          st_copy[0].data = tr_arzaic.data
-          araiccf = AICcf(st_copy, cuttimes, tpredz, 0, tdetz) #instance of AICcf
-          ##############################################################
-          #get onset time from AIC-ARZ-CF using subclass AICPicker of class AutoPicking
-          aicarzpick = AICPicker(araiccf, TSNRarz, 2, 10, None, 0.1)
-          ##############################################################
-          #get refined onset time from ARZ-CF using class Picker
-          arzpick = PragPicker(arzcf, TSNRarz, 2.0, 10, 0.1, 0.05, aicarzpick.getpick())
-          #get earliest and latest possible picks
-          st_copy[0].data = tr_filt.data
-          [lpickarz, epickarz, pickerrarz] = earllatepicker(st_copy, 1.5, TSNRarz, arzpick.getpick(), 10)
-    elif not wfzfiles:
-       print 'No vertical component data found!'
-
-    if wfefiles and wfnfiles:
-       for i in range(len(wfefiles)):
-          print 'Horizontal component data found ...'
-          print wfefiles[i]
-          print wfnfiles[i]
-          #merge streams
-          H = read('%s' % wfefiles[i])
-          H += read('%s' % wfnfiles[i])
-          H_copy = H.copy()
-          #filter and taper data
-          trH1_filt = H[0].copy()
-          trH2_filt = H[1].copy()
-          trH1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          trH2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          trH1_filt.taper(max_percentage=0.05, type='hann')
-          trH2_filt.taper(max_percentage=0.05, type='hann')
-          H_copy[0].data = trH1_filt.data
-          H_copy[1].data = trH2_filt.data
-
-          ##############################################################
-          #calculate ARH-CF using subclass ARHcf of class CharcteristicFunction
-          arhcf = ARHcf(H_copy, cuttimes, tpredh, arhorder, tdeth, addnoise) #instance of ARHcf
-          ##############################################################
-          #calculate AIC-ARH-CF using subclass AICcf of class CharacteristicFunction
-          #class needs stream object => build it
-          tr_arhaic = trH1_filt.copy()
-          tr_arhaic.data = arhcf.getCF()
-          H_copy[0].data = tr_arhaic.data
-          #calculate ARH-AIC-CF
-          arhaiccf = AICcf(H_copy, cuttimes, tpredh, 0, tdeth) #instance of AICcf
-          ##############################################################
-          #get onset time from AIC-ARH-CF using subclass AICPicker of class AutoPicking
-          aicarhpick = AICPicker(arhaiccf, TSNRarz, 4, 10, None, 0.1)
-          ###############################################################
-          #get refined onset time from ARH-CF using class Picker
-          arhpick = PragPicker(arhcf, TSNRarz, 2.5, 10, 0.1, 0.05, aicarhpick.getpick())
-          #get earliest and latest possible picks
-          H_copy[0].data = trH1_filt.data
-          [lpickarh1, epickarh1, pickerrarh1] = earllatepicker(H_copy, 1.5, TSNRarz, arhpick.getpick(), 10)
-          H_copy[0].data = trH2_filt.data
-          [lpickarh2, epickarh2, pickerrarh2] = earllatepicker(H_copy, 1.5, TSNRarz, arhpick.getpick(), 10)
-          #get earliest pick of both earliest possible picks
-          epick = [epickarh1, epickarh2]
-          lpick = [lpickarh1, lpickarh2]
-          pickerr = [pickerrarh1, pickerrarh2]
-          ipick =np.argmin([epickarh1, epickarh2])
-          epickarh = epick[ipick]
-          lpickarh = lpick[ipick]
-          pickerrarh = pickerr[ipick]
-
-          #create stream with 3 traces
-          #merge streams
-          AllC = read('%s' % wfefiles[i])
-          AllC += read('%s' % wfnfiles[i])
-          AllC += read('%s' % wfzfiles[i])
-          #filter and taper data
-          All1_filt = AllC[0].copy()
-          All2_filt = AllC[1].copy()
-          All3_filt = AllC[2].copy()
-          All1_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All2_filt.filter('bandpass', freqmin=bph[0], freqmax=bph[1], zerophase=False)
-          All3_filt.filter('bandpass', freqmin=bpz[0], freqmax=bpz[1], zerophase=False)
-          All1_filt.taper(max_percentage=0.05, type='hann')
-          All2_filt.taper(max_percentage=0.05, type='hann')
-          All3_filt.taper(max_percentage=0.05, type='hann')
-          AllC[0].data = All1_filt.data
-          AllC[1].data = All2_filt.data
-          AllC[2].data = All3_filt.data
-          #calculate AR3C-CF using subclass AR3Ccf of class CharacteristicFunction
-          ar3ccf = AR3Ccf(AllC, cuttimes, tpredz, arhorder, tdetz, addnoise) #instance of AR3Ccf
-          ##############################################################
-          if iplot:
-             #plot vertical trace
-             plt.figure()
-             tr = st[0]
-             tdata = np.arange(0, tr.stats.npts / tr.stats.sampling_rate, tr.stats.delta)
-             p1, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
-             p2, = plt.plot(hoscf.getTimeArray(), hoscf.getCF() / max(hoscf.getCF()), 'r')
-             p3, = plt.plot(aiccf.getTimeArray(), aiccf.getCF()/max(aiccf.getCF()), 'b')
-             p4, = plt.plot(arzcf.getTimeArray(), arzcf.getCF()/max(arzcf.getCF()), 'g')
-             p5, = plt.plot(araiccf.getTimeArray(), araiccf.getCF()/max(araiccf.getCF()), 'y')
-             plt.plot([aicpick.getpick(), aicpick.getpick()], [-1, 1], 'b--')
-             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicpick.getpick()-0.5, aicpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([hospick.getpick(), hospick.getpick()], [-1.3, 1.3], 'r', linewidth=2)
-             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [1.3, 1.3], 'r')
-             plt.plot([hospick.getpick()-0.5, hospick.getpick()+0.5], [-1.3, -1.3], 'r')
-             plt.plot([lpickhos, lpickhos], [-1.1, 1.1], 'r--')
-             plt.plot([epickhos, epickhos], [-1.1, 1.1], 'r--')
-             plt.plot([aicarzpick.getpick(), aicarzpick.getpick()], [-1.2, 1.2], 'y', linewidth=2)
-             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [1.2, 1.2], 'y')
-             plt.plot([aicarzpick.getpick()-0.5, aicarzpick.getpick()+0.5], [-1.2, -1.2], 'y')
-             plt.plot([arzpick.getpick(), arzpick.getpick()], [-1.4, 1.4], 'g', linewidth=2)
-             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [1.4, 1.4], 'g')
-             plt.plot([arzpick.getpick()-0.5, arzpick.getpick()+0.5], [-1.4, -1.4], 'g')
-             plt.plot([lpickarz, lpickarz], [-1.2, 1.2], 'g--')
-             plt.plot([epickarz, epickarz], [-1.2, 1.2], 'g--')
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.xlabel('Time [s]')
-             plt.ylabel('Normalized Counts')
-             plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station,
-                                                                  tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
-             plt.suptitle(tr.stats.starttime)
-             plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
-             #plot horizontal traces
-             plt.figure(2)
-             plt.subplot(2,1,1)
-             tsteph = tpredh / 4
-             th1data = np.arange(0, trH1_filt.stats.npts / trH1_filt.stats.sampling_rate, trH1_filt.stats.delta)
-             th2data = np.arange(0, trH2_filt.stats.npts / trH2_filt.stats.sampling_rate, trH2_filt.stats.delta)
-             tarhcf = np.arange(0, len(arhcf.getCF()) * tsteph, tsteph) + cuttimes[0] + tdeth +tpredh
-             p21, = plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
-             p22, = plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
-             p23, = plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
-             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
-             plt.plot([lpickarh, lpickarh], [-0.8, 0.8], 'r--')
-             plt.plot([epickarh, epickarh], [-0.8, 0.8], 'r--')
-             plt.plot([arhpick.getpick() + pickerrarh, arhpick.getpick() + pickerrarh], [-0.2, 0.2], 'r--')
-             plt.plot([arhpick.getpick() - pickerrarh, arhpick.getpick() - pickerrarh], [-0.2, 0.2], 'r--')
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
-             plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p21, p22, p23], ['Data', 'ARH-CF', 'ARHAIC-CF'])
-             plt.subplot(2,1,2)
-             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
-             plt.plot(arhcf.getTimeArray(), arhcf.getCF()/max(arhcf.getCF()), 'r')
-             plt.plot(arhaiccf.getTimeArray(), arhaiccf.getCF()/max(arhaiccf.getCF()))
-             plt.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [1, 1], 'b')
-             plt.plot([aicarhpick.getpick()-0.5, aicarhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'r')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'r')
-             plt.plot([lpickarh, lpickarh], [-0.8, 0.8], 'r--')
-             plt.plot([epickarh, epickarh], [-0.8, 0.8], 'r--')
-             plt.plot([arhpick.getpick() + pickerrarh, arhpick.getpick() + pickerrarh], [-0.2, 0.2], 'r--')
-             plt.plot([arhpick.getpick() - pickerrarh, arhpick.getpick() - pickerrarh], [-0.2, 0.2], 'r--')
-             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
-             plt.yticks([])
-             plt.ylim([-1.5, 1.5])
-             plt.xlabel('Time [s]')
-             plt.ylabel('Normalized Counts')
-             #plot 3-component window
-             plt.figure(3)
-             plt.subplot(3,1,1)
-             p31, = plt.plot(tdata, tr_filt.data/max(tr_filt.data), 'k')
-             p32, = plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.yticks([])
-             plt.xticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([tr.stats.station, tr.stats.channel])
-             plt.suptitle(trH1_filt.stats.starttime)
-             plt.legend([p31, p32], ['Data', 'AR3C-CF'])
-             plt.subplot(3,1,2)
-             plt.plot(th1data, trH1_filt.data/max(trH1_filt.data), 'k')
-             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.yticks([])
-             plt.xticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH1_filt.stats.station, trH1_filt.stats.channel])
-             plt.subplot(3,1,3)
-             plt.plot(th2data, trH2_filt.data/max(trH2_filt.data), 'k')
-             plt.plot(ar3ccf.getTimeArray(), ar3ccf.getCF()/max(ar3ccf.getCF()), 'r')
-             plt.plot([arhpick.getpick(), arhpick.getpick()], [-1, 1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [-1, -1], 'b')
-             plt.plot([arhpick.getpick()-0.5, arhpick.getpick()+0.5], [1, 1], 'b')
-             plt.yticks([])
-             plt.ylabel('Normalized Counts')
-             plt.title([trH2_filt.stats.station, trH2_filt.stats.channel])
-             plt.xlabel('Time [s]')
-             plt.show()
-             raw_input()
-             plt.close()
-
-parser = argparse.ArgumentParser()
-parser.add_argument('--project', type=str, help='project name (e.g. Insheim)')
-parser.add_argument('--database', type=str, help='event data base (e.g. 2014.09_Insheim)')
-parser.add_argument('--event', type=str, help='event ID (e.g. e0010.015.14)')
-parser.add_argument('--iplot', help='anything, if set, figure occurs')
-parser.add_argument('--station', type=str, help='Station ID (e.g. INS3) (optional)')
-args = parser.parse_args()
-
-run_makeCF(args.project, args.database, args.event, args.iplot, args.station)

setup.py

@@ -4,11 +4,11 @@ from distutils.core import setup
 
 setup(
     name='PyLoT',
-    version='0.1a1',
+    version='0.2',
     packages=['pylot', 'pylot.core', 'pylot.core.loc', 'pylot.core.pick',
               'pylot.core.io', 'pylot.core.util', 'pylot.core.active',
               'pylot.core.analysis', 'pylot.testing'],
-    requires=['obspy', 'PySide'],
+    requires=['obspy', 'PySide', 'matplotlib', 'numpy'],
     url='dummy',
     license='LGPLv3',
     author='Sebastian Wehling-Benatelli',