release version 0.2

release notes:
==============
Features:
- centralize all functionalities of PyLoT and control them from within the main GUI
- handling multiple events inside GUI with project files (save and load work progress)
- GUI based adjustments of pick parameters and I/O
- interactive tuning of parameters from within the GUI
- call automatic picking algorithm from within the GUI
- comparison of automatic with manual picks for multiple events using clear differentiation of manual picks into 'tune' and 'test-set' (beta)
- manual picking of different (user defined) phase types
- phase onset estimation with ObsPy TauPy

- interactive zoom/scale functionalities in all plots (mousewheel, pan, pan-zoom)
- array map to visualize stations and control onsets (beta feature, switch to manual picks not implemented)

Platform support:
- python 3 support
- Windows support

Performance:
- multiprocessing for automatic picking and restitution of multiple stations
- use pyqtgraph library for better performance on main waveform plot

Visualization:
- pick uncertainty (quality classes) visualization with gradients
- pick color unification for all plots
- new icons and stylesheets

Known Issues:

README.md

@@ -1,2 +1,110 @@
-# PyLoT
-Python picking and Location Tool
+# PyLoT
+
+version: 0.2
+
+The Python picking and Localisation Tool
+
+This python library contains a graphical user interfaces for picking
+seismic phases. This software needs [ObsPy][ObsPy]
+and the PySide Qt4 bindings for python to be installed first.
+
+PILOT has originally been developed in Mathworks' MatLab. In order to
+distribute PILOT without facing portability problems, it has been decided
+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
+benefit a lot compared to the former MatLab version.
+
+The development of PyLoT is part of the joint research project MAGS2 and AlpArray.
+
+## Installation
+
+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.
+
+#### Prerequisites:
+
+In order to run PyLoT you need to install:
+
+- python 2 or 3
+- scipy
+- numpy
+- matplotlib
+- obspy
+- pyside
+
+#### Some handwork:
+
+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
+
+In the next step you have to copy some files to this directory:
+
+*for local distance seismicity*
+
+    cp path-to-pylot/inputs/pylot_local.in ~/.pylot/pylot.in
+
+*for regional distance seismicity*
+
+    cp path-to-pylot/inputs/pylot_regional.in ~/.pylot/pylot.in
+
+*for global distance seismicity*
+
+    cp path-to-pylot/inputs/pylot_global.in ~/.pylot/pylot.in
+
+and some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling relation
+
+    cp path-to-pylot/inputs/PILOT_TimeErrors.in path-to-pylot/inputs/richter_scaling.data ~/.pylot/
+
+You may need to do some modifications to these files. Especially folder names should be reviewed.
+
+PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
+
+
+## Release notes
+
+#### Features:
+
+- centralize all functionalities of PyLoT and control them from within the main GUI
+- handling multiple events inside GUI with project files (save and load work progress)
+- GUI based adjustments of pick parameters and I/O
+- interactive tuning of parameters from within the GUI
+- call automatic picking algorithm from within the GUI
+- comparison of automatic with manual picks for multiple events using clear differentiation of manual picks into 'tune' and 'test-set' (beta)
+- manual picking of different (user defined) phase types
+- phase onset estimation with ObsPy TauPy
+- interactive zoom/scale functionalities in all plots (mousewheel, pan, pan-zoom)
+- array map to visualize stations and control onsets (beta feature, switch to manual picks not implemented)
+
+##### Platform support:
+- Python 3 support
+- Windows support
+
+##### Performance:
+- multiprocessing for automatic picking and restitution of multiple stations
+- use pyqtgraph library for better performance on main waveform plot
+
+##### Visualization:
+- pick uncertainty (quality classes) visualization with gradients
+- pick color unification for all plots
+- new icons and stylesheets
+
+#### Known Issues:
+- some Qt related errors might occur at runtime
+- filter toggle not working in pickDlg
+- PyLoT data structure requires at least three parent directories for waveform data directory
+
+## Staff
+
+Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
+
+Developer(s): S. Wehling-Benatelli, L. Kueperkoch, M. Paffrath, K. Olbert,
+M. Bischoff, C. Wollin, M. Rische
+
+Others: A. Bruestle, T. Meier, W. Friederich
+
+
+[ObsPy]: http://github.com/obspy/obspy/wiki
+
+September 2017

autoPyLoT.py

@@ -0,0 +1,505 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import glob
+import os
+
+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
+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.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,
+              savexml=True, station='all', iplot=0, ncores=0):
+    """
+    Determine phase onsets automatically utilizing the automatic picking
+    algorithms by Kueperkoch et al. 2010/2012.
+
+    :param inputfile: path to the input file containing all parameter
+    information for automatic picking (for formatting details, see.
+    `~pylot.core.io.inputs.PylotParameter`
+    :type inputfile: str
+    :return:
+
+    .. 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} 2017\n
+                \n
+                Authors:\n
+                L. Kueperkoch (BESTEC GmbH, Landau i. d. Pfalz)\n
+                M. Paffrath (Ruhr-Universitaet Bochum)\n
+                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 'parameter' in input_dict:
+            parameter = input_dict['parameter']
+        if 'fig_dict' in input_dict:
+            fig_dict = input_dict['fig_dict']
+        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 'fnames' in input_dict:
+            fnames = input_dict['fnames']
+        if 'eventid' in input_dict:
+            eventid = input_dict['eventid']
+        if 'iplot' in input_dict:
+            iplot = input_dict['iplot']
+        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']
+        else:
+            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+            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)))
+            return
+        if inputfile:
+            print('Parameters set and input file given. Choose either of both.')
+            return
+
+    evt = None
+
+    # reading parameter file
+    if parameter.hasParam('datastructure'):
+        # getting information on data structure
+        datastructure = DATASTRUCTURE[parameter.get('datastructure')]()
+        dsfields = {'root': parameter.get('rootpath'),
+                    'dpath': parameter.get('datapath'),
+                    'dbase': parameter.get('database')}
+
+        exf = ['root', 'dpath', 'dbase']
+
+        if parameter['eventID'] is not '*' and fnames == 'None':
+            dsfields['eventID'] = parameter['eventID']
+            exf.append('eventID')
+
+        datastructure.modifyFields(**dsfields)
+        datastructure.setExpandFields(exf)
+
+        # check if default location routine NLLoc is available
+        if real_None(parameter['nllocbin']) and locflag:
+            # get NLLoc-root path
+            nllocroot = parameter.get('nllocroot')
+            # get path to NLLoc executable
+            nllocbin = parameter.get('nllocbin')
+            nlloccall = '%s/NLLoc' % nllocbin
+            # get name of phase file
+            phasef = parameter.get('phasefile')
+            phasefile = '%s/obs/%s' % (nllocroot, phasef)
+            # get name of NLLoc-control file
+            ctrf = parameter.get('ctrfile')
+            ctrfile = '%s/run/%s' % (nllocroot, ctrf)
+            # pattern of NLLoc ttimes from location grid
+            ttpat = parameter.get('ttpatter')
+            # pattern of NLLoc-output file
+            nllocoutpatter = parameter.get('outpatter')
+            maxnumit = 3  # maximum number of iterations for re-picking
+        else:
+            locflag = 0
+            print("                 !!!              ")
+            print("!!No location routine available, autoPyLoT is running in non-location mode!!")
+            print("!!No source parameter estimation possible!!")
+            print("                 !!!              ")
+
+        if not input_dict:
+            # started in production mode
+            datapath = datastructure.expandDataPath()
+            if fnames == 'None' and parameter['eventID'] is '*':
+                # 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 '*' 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 = []
+                events.append(eventid)
+                evID = os.path.split(eventid)[-1]
+                locflag = 2
+        else:
+            # started in tune or interactive mode
+            datapath = os.path.join(parameter['rootpath'],
+                                    parameter['datapath'])
+            events = []
+            for eventID in eventid:
+                events.append(os.path.join(datapath,
+                                           parameter['database'],
+                                           eventID))
+
+        if not events:
+            print('autoPyLoT: No events given. Return!')
+            return
+
+        # 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, eventpath, '*')))
+                # the following is necessary because within
+                # multiple event processing no event ID is provided
+                # in autopylot.in
+                try:
+                    parameter.get('eventID')
+                except:
+                    now = datetime.datetime.now()
+                    eventID = '%d%02d%02d%02d%02d' % (now.year,
+                                                      now.month,
+                                                      now.day,
+                                                      now.hour,
+                                                      now.minute)
+                    parameter.setParam(eventID=eventID)
+            else:
+                data.setWFData(fnames)
+
+                eventpath = events[0]
+                # now = datetime.datetime.now()
+                # evID = '%d%02d%02d%02d%02d' % (now.year,
+                #                               now.month,
+                #                               now.day,
+                #                               now.hour,
+                #                               now.minute)
+                parameter.setParam(eventID=eventid)
+            wfdat = data.getWFData()  # all available streams
+            if not station == 'all':
+                wfdat = wfdat.select(station=station)
+                if not wfdat:
+                    print('Could not find station {}. STOP!'.format(station))
+                    return
+            wfdat = remove_underscores(wfdat)
+            # trim components for each station to avoid problems with different trace starttimes for one station
+            wfdat = check4gaps(wfdat)
+            wfdat = check4doubled(wfdat)
+            wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
+            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!
+            fdwj = None
+            if fig_dict_wadatijack:
+                fdwj = fig_dict_wadatijack[evID]
+            picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict,
+                                  fig_dict_wadatijack=fdwj,
+                                  ncores=ncores, metadata=metadata, origin=data.get_evt_data().origins)
+            ##########################################################
+            # locating
+            if locflag > 0:
+                # write phases to NLLoc-phase file
+                nll.export(picks, phasefile, parameter)
+
+                # For locating the event the NLLoc-control file has to be modified!
+                nllocout = '%s_%s' % (evID, nllocoutpatter)
+                # create comment line for NLLoc-control file
+                nll.modify_inputs(ctrf, nllocroot, nllocout, phasef,
+                                  ttpat)
+
+                # locate the event
+                nll.locate(ctrfile, inputfile)
+
+                # !iterative picking if traces remained unpicked or occupied with bad picks!
+                # get theoretical onset times for picks with weights >= 4
+                # in order to reprocess them using smaller time windows around theoretical onset
+                # get stations with bad onsets
+                badpicks = []
+                for key in picks:
+                    if picks[key]['P']['weight'] >= 4 or picks[key]['S']['weight'] >= 4:
+                        badpicks.append([key, picks[key]['P']['mpp']])
+
+                # TODO keep code DRY (Don't Repeat Yourself) the following part is written twice
+                # suggestion: delete block and modify the later similar block to work properly
+
+                if len(badpicks) == 0:
+                    print("autoPyLoT: No bad onsets found, thus no iterative picking necessary!")
+                    # get NLLoc-location file
+                    locsearch = '%s/loc/%s.????????.??????.grid?.loc.hyp' % (nllocroot, nllocout)
+                    if len(glob.glob(locsearch)) > 0:
+                        # get latest NLLoc-location file if several are available
+                        nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
+                        evt = read_events(nllocfile)[0]
+                        # calculate seismic moment Mo and moment magnitude Mw
+                        moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
+                                                     parameter.get('Qp'),
+                                                     parameter.get('rho'), True,
+                                                     iplot)
+                        # update pick with moment property values (w0, fc, Mo)
+                        for stats, props in moment_mag.moment_props.items():
+                            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)
+                        # calculate local (Richter) magntiude
+                        WAscaling = parameter.get('WAscaling')
+                        magscaling = parameter.get('magscaling')
+                        local_mag = LocalMagnitude(corr_dat, evt,
+                                                   parameter.get('sstop'),
+                                                   WAscaling, True, iplot)
+                        for stats, amplitude in local_mag.amplitudes.items():
+                            picks[stats]['S']['Ao'] = amplitude.generic_amplitude
+                        print("Local station magnitudes scaled with:")
+                        print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0],
+                                                                       WAscaling[1],
+                                                                       WAscaling[2]))
+                        evt = local_mag.updated_event(magscaling)
+                        net_ml = local_mag.net_magnitude(magscaling)
+                        print("Network local magnitude: %4.1f" % net_ml.mag)
+                        print("Network local magnitude scaled with:")
+                        print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
+                    else:
+                        print("autoPyLoT: No NLLoc-location file available!")
+                        print("No source parameter estimation possible!")
+                        locflag = 9
+                else:
+                    # get theoretical P-onset times from NLLoc-location file
+                    locsearch = '%s/loc/%s.????????.??????.grid?.loc.hyp' % (nllocroot, nllocout)
+                    if len(glob.glob(locsearch)) > 0:
+                        # get latest file if several are available
+                        nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
+                        nlloccounter = 0
+                        while len(badpicks) > 0 and nlloccounter <= maxnumit:
+                            nlloccounter += 1
+                            if nlloccounter > maxnumit:
+                                print("autoPyLoT: Number of maximum iterations reached, stop iterative picking!")
+                                break
+                            print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
+                            if input_dict:
+                                if 'fig_dict' in input_dict:
+                                    fig_dict = input_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
+                            nll.export(picks, phasefile, parameter)
+                            # remove actual NLLoc-location file to keep only the last
+                            os.remove(nllocfile)
+                            # locate the event
+                            nll.locate(ctrfile, inputfile)
+                            print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
+                            # get updated NLLoc-location file
+                            nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
+                            # check for bad picks
+                            badpicks = []
+                            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,
+                                                                                                  len(badpicks)))
+                            if len(badpicks) == 0:
+                                print("autoPyLoT: No more bad onsets found, stop iterative picking!")
+                                nlloccounter = maxnumit
+                        evt = read_events(nllocfile)[0]
+                        if locflag < 2:
+                            # calculate seismic moment Mo and moment magnitude Mw
+                            moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
+                                                         parameter.get('Qp'),
+                                                         parameter.get('rho'), True,
+                                                         iplot)
+                            # update pick with moment property values (w0, fc, Mo)
+                            for stats, props in moment_mag.moment_props.items():
+                                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)
+                            # calculate local (Richter) magntiude
+                            WAscaling = parameter.get('WAscaling')
+                            magscaling = parameter.get('magscaling')
+                            local_mag = LocalMagnitude(corr_dat, evt,
+                                                       parameter.get('sstop'),
+                                                       WAscaling, True, iplot)
+                            for stats, amplitude in local_mag.amplitudes.items():
+                                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],
+                                                                           WAscaling[1],
+                                                                           WAscaling[2]))
+                            evt = local_mag.updated_event(magscaling)
+                            net_ml = local_mag.net_magnitude(magscaling)
+                            print("Network local magnitude: %4.1f" % net_ml.mag)
+                            print("Network local magnitude scaled with:")
+                            print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
+                    else:
+                        print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
+                        locflag = 9
+            ##########################################################
+            # write phase files for various location 
+            # and fault mechanism calculation routines
+            # ObsPy event object
+            if evt is not None:
+                event_id = eventpath.split('/')[-1]
+                evt.resource_id = ResourceIdentifier('smi:local/' + event_id)
+                data.applyEVTData(evt, 'event')
+            data.applyEVTData(picks)
+            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' % (eventpath, evID)
+                hypo71.export(picks, hypo71file, parameter)
+                # HYPOSAT
+                hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (eventpath, evID)
+                hyposat.export(picks, hyposatfile, parameter)
+                # VELEST
+                velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (eventpath, evID)
+                velest.export(picks, velestfile, evt, parameter)
+                # hypoDD
+                hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (eventpath, evID)
+                hypodd.export(picks, hypoddfile, parameter, evt)
+                # FOCMEC
+                focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (eventpath, evID)
+                focmec.export(picks, focmecfile, parameter, evt)
+                # HASH
+                hashfile = '%s/PyLoT_%s_HASH' % (eventpath, evID)
+                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 allpicks
+
+
+if __name__ == "__main__":
+    # parse arguments
+    parser = argparse.ArgumentParser(
+        description='''autoPyLoT automatically picks phase onset times using higher order statistics,
+                       autoregressive prediction and AIC followed by locating the seismic events using 
+                       NLLoc''')
+
+    parser.add_argument('-i', '-I', '--inputfile', type=str,
+                        action='store',
+                        help='''full path to the file containing the input
+                        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', '--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('-c', '-C', '--ncores', type=int,
+                        action='store', default=0,
+                        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),
+                      eventid=str(cla.eventid), savepath=str(cla.spath),
+                      ncores=cla.ncores, iplot=int(cla.iplot))

help/index.html

@@ -0,0 +1,19 @@
+<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
+    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>HypoInvers</li>
+    <li>HypoSat</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>
+<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
+    successful registration.</p>
+</body>
+</html>

icons.qrc

@@ -0,0 +1,57 @@
+<RCC>
+    <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>
+        <file>icons/add.png</file>
+        <file>icons/save.png</file>
+        <file>icons/saveas.png</file>
+        <file>icons/saveproject.png</file>
+        <file>icons/saveprojectas.png</file>
+        <file>icons/manupicksicon_small.png</file>
+        <file>icons/autopicksicon_small.png</file>
+        <file>icons/tune.png</file>
+        <file>icons/autopylot_button.png</file>
+        <file>icons/pick.png</file>
+        <file>icons/waveform.png</file>
+        <file>icons/openpick.png</file>
+        <file>icons/openpicks.png</file>
+        <file>icons/openpick.png</file>
+        <file>icons/openpicks.png</file>
+        <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>
+        <file>icons/Matlab_PILOT_icon.png</file>
+        <file>icons/printer.png</file>
+        <file>icons/delete.png</file>
+        <file>icons/key_E.png</file>
+        <file>icons/key_N.png</file>
+        <file>icons/key_P.png</file>
+        <file>icons/key_Q.png</file>
+        <file>icons/key_R.png</file>
+        <file>icons/key_S.png</file>
+        <file>icons/key_T.png</file>
+        <file>icons/key_U.png</file>
+        <file>icons/key_V.png</file>
+        <file>icons/key_W.png</file>
+        <file>icons/key_Z.png</file>
+        <file>icons/filter.png</file>
+        <file>icons/sync.png</file>
+        <file>icons/zoom_0.png</file>
+        <file>icons/zoom_in.png</file>
+        <file>icons/zoom_out.png</file>
+        <file>splash/splash.png</file>
+    </qresource>
+    <qresource prefix="/help">
+        <file>help/index.html</file>
+    </qresource>
+</RCC>

inputs/PILOT_TimeErrors.in

@@ -0,0 +1,3 @@
+## default time errors for old PILOT phases
+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

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

inputs/richter_scaling.data

@@ -0,0 +1,53 @@
+ 0 1.4
+ 10 1.5
+ 20 1.7
+ 25 1.9
+ 30 2.1
+ 35 2.3
+ 40 2.4
+ 45 2.5
+ 50 2.6
+ 60 2.8
+ 70 2.8
+ 75 2.9
+ 85 2.9
+ 90 3.0
+100 3.0
+110 3.1
+120 3.1
+130 3.2
+140 3.2
+150 3.3
+160 3.3
+170 3.4
+180 3.4
+190 3.5
+200 3.5
+210 3.6
+230 3.7
+240 3.7
+250 3.8
+260 3.8
+270 3.9
+280 3.9
+290 4.0
+300 4.0
+310 4.1
+320 4.2
+330 4.2
+340 4.2
+350 4.3
+360 4.3
+370 4.3
+380 4.4
+390 4.4
+400 4.5
+430 4.6
+470 4.7
+510 4.8
+560 4.9
+600 5.1
+700 5.2
+800 5.4
+900 5.5
+1000 5.7

makePyLoT.py

@@ -0,0 +1,226 @@
+#!/usr/bin/env python
+# encoding: utf-8
+from __future__ import print_function
+
+"""
+makePyLoT -- build and install PyLoT
+
+makePyLoT is a python make file in order to establish the folder structure and
+meet requisites
+
+It defines
+:class CLIError:
+:method main:
+
+:author:     Sebastian Wehling-Benatelli
+
+:copyright:  2014 MAGS2 EP3 Working Group. All rights reserved.
+
+:license:    GNU Lesser General Public License, Version 3
+    (http://www.gnu.org/copyleft/lesser.html)
+
+:contact:    sebastian.wehling@rub.de
+
+updated: Updated
+"""
+
+import glob
+import os
+import sys
+import shutil
+import copy
+
+from argparse import ArgumentParser
+from argparse import RawDescriptionHelpFormatter
+
+__all__ = []
+__version__ = 0.1
+__date__ = '2014-11-26'
+__updated__ = '2016-04-28'
+
+DEBUG = 0
+TESTRUN = 0
+PROFILE = 0
+
+
+class CLIError(Exception):
+    """Generic exception to raise and log different fatal errors."""
+
+    def __init__(self, msg):
+        super(CLIError).__init__(type(self))
+        self.msg = "E: %s" % msg
+
+    def __str__(self):
+        return self.msg
+
+    def __unicode__(self):
+        return self.msg
+
+
+def main(argv=None):  # IGNORE:C0111
+    '''Command line options.'''
+
+    if argv is None:
+        argv = sys.argv
+    else:
+        sys.argv.extend(argv)
+
+    program_name = os.path.basename(sys.argv[0])
+    program_version = "v%s" % __version__
+    program_build_date = str(__updated__)
+    program_version_message = 'makePyLoT %s (%s)' % (
+        program_version, program_build_date)
+    program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
+    program_license = '''{0:s}
+
+    Created by Sebastian Wehling-Benatelli on {1:s}.
+    Copyright 2014 MAGS2 EP3 Working Group. All rights reserved.
+
+    GNU Lesser General Public License, Version 3
+    (http://www.gnu.org/copyleft/lesser.html)
+
+    Distributed on an "AS IS" basis without warranties
+    or conditions of any kind, either express or implied.
+
+    USAGE
+    '''.format(program_shortdesc, str(__date__))
+
+    try:
+        # Setup argument parser
+        parser = ArgumentParser(description=program_license,
+                                formatter_class=RawDescriptionHelpFormatter)
+        parser.add_argument("-b", "--build", dest="build", action="store_true",
+                            help="build PyLoT")
+        parser.add_argument("-v", "--verbose", dest="verbose", action="count",
+                            help="set verbosity level")
+        parser.add_argument("-i", "--install", dest="install",
+                            action="store_true",
+                            help="install PyLoT on the system")
+        parser.add_argument("-d", "--directory", dest="directory",
+                            help="installation directory", metavar="RE")
+        parser.add_argument('-V', '--version', action='version',
+                            version=program_version_message)
+
+        # Process arguments
+        args = parser.parse_args()
+
+        verbose = args.verbose
+        build = args.build
+        install = args.install
+        directory = args.directory
+
+        if verbose > 0:
+            print("Verbose mode on")
+        if install and not directory:
+            raise CLIError("""Trying to install without appropriate
+                           destination; please specify an installation
+                           directory!""")
+        if build and install:
+            print("Building and installing PyLoT ...\n")
+            buildPyLoT(verbose)
+            installPyLoT(verbose)
+        elif build and not install:
+            print("Building PyLoT without installing! Please wait ...\n")
+            buildPyLoT(verbose)
+        cleanUp()
+        return 0
+    except KeyboardInterrupt:
+        cleanUp(1)
+        return 0
+    except Exception as e:
+        if DEBUG or TESTRUN:
+            raise e
+        indent = len(program_name) * " "
+        sys.stderr.write(program_name + ": " + repr(e) + "\n")
+        sys.stderr.write(indent + "  for help use --help")
+        return 2
+
+
+def buildPyLoT(verbosity=None):
+    system = sys.platform
+    if verbosity > 1:
+        msg = ("... on system: {0}\n"
+               "\n"
+               "              Current working directory: {1}\n"
+               ).format(system, os.getcwd())
+        print(msg)
+    if system.startswith(('win', 'microsoft')):
+        raise CLIError(
+            "building on Windows system not tested yet; implementation pending")
+    elif system == 'darwin':
+        # create a symbolic link to the desired python interpreter in order to
+        # display the right application name
+        for path in os.getenv('PATH').split(':'):
+            found = glob.glob(os.path.join(path, 'python'))
+            if found:
+                os.symlink(found, './PyLoT')
+                break
+
+
+def installPyLoT(verbosity=None):
+    files_to_copy = {'pylot_local.in': ['~', '.pylot'],
+                     'pylot_regional.in': ['~', '.pylot'],
+                     'pylot_global.in': ['~', '.pylot']}
+    if verbosity > 0:
+        print('starting installation of PyLoT ...')
+    if verbosity > 1:
+        print('copying input files into destination folder ...')
+    ans = input('please specify scope of interest '
+                '([0]=local, 1=regional, 2=global) :') or 0
+    if not isinstance(ans, int):
+        ans = int(ans)
+    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('pylot.in')
+            link_dest = os.path.join(*link_dest)
+        destination.append(file)
+        destination = os.path.join(*destination)
+        srcfile = os.path.join('input', file)
+        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))
+        shutil.copyfile(srcfile, destination)
+        if link_file:
+            if verbosity:
+                print('linking input file for autoPyLoT ...')
+            os.symlink(destination, link_dest)
+
+
+def cleanUp(verbosity=None):
+    if verbosity >= 1:
+        print('cleaning up build files...')
+    if sys.platform == 'darwin':
+        os.remove('./PyLoT')
+
+
+if __name__ == "__main__":
+    if DEBUG:
+        sys.argv.append("-h")
+        sys.argv.append("-v")
+    if TESTRUN:
+        import doctest
+
+        doctest.testmod()
+    if PROFILE:
+        import cProfile
+        import pstats
+
+        profile_filename = 'makePyLoT_profile.txt'
+        cProfile.run('main()', profile_filename)
+        statsfile = open("profile_stats.txt", "wb")
+        p = pstats.Stats(profile_filename, stream=statsfile)
+        stats = p.strip_dirs().sort_stats('cumulative')
+        stats.print_stats()
+        statsfile.close()
+        sys.exit(0)
+    sys.exit(main())

pylot/__init__.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+# --------------------------------------------------------
+# Purpose: Convience imports for PyLoT
+#
+'''
+================================================
+PyLoT - the Python picking and Localization Tool
+================================================
+
+This python library contains a graphical user interfaces for picking
+seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
+and the Qt4 libraries to be installed first.
+
+PILOT has been developed in Mathworks' MatLab. In order to distribute
+PILOT without facing portability problems, it has been decided to re-
+develop the software package in Python. The great work of the ObsPy
+group allows easy handling of a bunch of seismic data and PyLoT will
+benefit a lot compared to the former MatLab version.
+
+The development of PyLoT is part of the joint research project MAGS2.
+
+:copyright:
+    The PyLoT Development Team
+:license:
+    GNU Lesser General Public License, Version 3
+    (http://www.gnu.org/copyleft/lesser.html)
+'''

pylot/core/__init__.py

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

pylot/core/analysis/__init__.py

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

pylot/core/analysis/magnitude.py

@@ -0,0 +1,761 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Created autumn/winter 2015.
+Revised/extended summer 2017.
+
+:author: Ludger Küperkoch / MAGS2 EP3 working group
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+import obspy.core.event as ope
+from obspy.geodetics import degrees2kilometers
+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,
+                         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,
+                                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,
+                                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])
+    # prepare spline interpolation to calculate return value
+    func, params = fit_curve(distance, richter_scaling)
+    return func(delta, params)
+
+
+class Magnitude(object):
+    """
+    Base class object for Magnitude calculation within PyLoT.
+    """
+
+    def __init__(self, stream, event, verbosity=False, iplot=0):
+        self._type = "M"
+        self._stream = stream
+        self._plot_flag = iplot
+        self._verbosity = verbosity
+        self._event = event
+        self._magnitudes = dict()
+
+    def __str__(self):
+        print(
+            '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))
+
+    def __nonzero__(self):
+        return bool(self.magnitudes)
+
+    @property
+    def type(self):
+        return self._type
+
+    @property
+    def plot_flag(self):
+        return self._plot_flag
+
+    @plot_flag.setter
+    def plot_flag(self, value):
+        self._plot_flag = value
+
+    @property
+    def verbose(self):
+        return self._verbosity
+
+    @verbose.setter
+    def verbose(self, value):
+        if not isinstance(value, bool):
+            print('WARNING: only boolean values accepted...\n')
+            value = bool(value)
+        self._verbosity = value
+
+    @property
+    def stream(self):
+        return self._stream
+
+    @stream.setter
+    def stream(self, value):
+        self._stream = value
+
+    @property
+    def event(self):
+        return self._event
+
+    @property
+    def origin_id(self):
+        return self._event.origins[0].resource_id
+
+    @property
+    def arrivals(self):
+        return self._event.origins[0].arrivals
+
+    @property
+    def magnitudes(self):
+        return self._magnitudes
+
+    @magnitudes.setter
+    def magnitudes(self, value):
+        """
+        takes a tuple and saves the key value pair to private
+        attribute _magnitudes
+        :param value: station, magnitude value pair
+        :type value: tuple or list
+        :return:
+        """
+        station, magnitude = value
+        self._magnitudes[station] = magnitude
+
+    def calc(self):
+        pass
+
+    def updated_event(self, magscaling=None):
+        self.event.magnitudes.append(self.net_magnitude(magscaling))
+        return self.event
+
+    def net_magnitude(self, magscaling=None):
+        if self:
+            if magscaling is not None and str(magscaling) is not '[0.0, 0.0]':
+                # scaling necessary
+                print("Scaling network magnitude ...")
+                mag = ope.Magnitude(
+                    mag=np.median([M.mag for M in self.magnitudes.values()]) * \
+                        magscaling[0] + magscaling[1],
+                    magnitude_type=self.type,
+                    origin_id=self.origin_id,
+                    station_count=len(self.magnitudes),
+                    azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
+            else:
+                # no saling necessary
+                mag = ope.Magnitude(
+                    mag=np.median([M.mag for M in self.magnitudes.values()]),
+                    magnitude_type=self.type,
+                    origin_id=self.origin_id,
+                    station_count=len(self.magnitudes),
+                    azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
+            return mag
+        return None
+
+
+class LocalMagnitude(Magnitude):
+    """
+    Method to derive peak-to-peak amplitude as seen on a Wood-Anderson-
+    seismograph. Has to be derived from instrument corrected traces!
+    """
+
+    # poles, zeros and sensitivity of WA seismograph
+    # (see Uhrhammer & Collins, 1990, BSSA, pp. 702-716)
+    _paz = {
+        'poles': [5.6089 - 5.4978j, -5.6089 - 5.4978j],
+        'zeros': [0j, 0j],
+        'gain': 2080,
+        'sensitivity': 1
+    }
+
+    _amplitudes = dict()
+
+    def __init__(self, stream, event, calc_win, wascaling, verbosity=False, iplot=0):
+        super(LocalMagnitude, self).__init__(stream, event, verbosity, iplot)
+
+        self._calc_win = calc_win
+        self._wascaling = wascaling
+        self._type = 'ML'
+        self.calc()
+
+    @property
+    def calc_win(self):
+        return self._calc_win
+
+    @calc_win.setter
+    def calc_win(self, value):
+        self._calc_win = value
+
+    @property
+    def wascaling(self):
+        return self._wascaling
+
+    @property
+    def amplitudes(self):
+        return self._amplitudes
+
+    @amplitudes.setter
+    def amplitudes(self, value):
+        station, a0 = value
+        self._amplitudes[station] = a0
+
+    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)
+
+        # trim waveform to common range
+        stime, etime = common_range(st)
+        st.trim(stime, etime)
+
+        # get time delta from waveform data
+        dt = st[0].stats.delta
+
+        power = [np.power(tr.data, 2) for tr in st if tr.stats.channel[-1] not
+                 in 'Z3']
+        if len(power) != 2:
+            raise ValueError('Wood-Anderson amplitude defintion only valid for '
+                             'two horizontals: {0} given'.format(len(power)))
+        power_sum = power[0] + power[1]
+        #
+        sqH = np.sqrt(power_sum)
+
+        # get time array
+        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)])
+        iwin = iwin[0:ii]
+        wapp = np.max(sqH[iwin])
+        if self.verbose:
+            print("Determined Wood-Anderson peak-to-peak amplitude for station {0}: {1} "
+                  "mm".format(st[0].stats.station, wapp))
+
+        # check for plot flag (for debugging only)
+        fig = None
+        if iplot > 1:
+            st.plot()
+            fig = plt.figure()
+            ax = fig.add_subplot(111)
+            ax.plot(th, sqH)
+            ax.plot(th[iwin], sqH[iwin], 'g')
+            ax.plot([t0, t0], [0, max(sqH)], 'r', linewidth=2)
+            ax.title(
+                'Station %s, RMS Horizontal Traces, WA-peak-to-peak=%4.1f mm' \
+                % (st[0].stats.station, wapp))
+            ax.set_xlabel('Time [s]')
+            ax.set_ylabel('Displacement [mm]')
+
+        return wapp, fig
+
+    def calc(self):
+        for a in self.arrivals:
+            if a.phase not in 'sS':
+                continue
+            pick = a.pick_id.get_referred_object()
+            station = pick.waveform_id.station_code
+            wf = select_for_phase(self.stream.select(
+                station=station), a.phase)
+            if not wf:
+                if self.verbose:
+                    print(
+                        'WARNING: no waveform data found for station {0}'.format(
+                            station))
+                continue
+            delta = degrees2kilometers(a.distance)
+            onset = pick.time
+            a0, self.p2p_fig = self.peak_to_peak(wf, onset)
+            amplitude = ope.Amplitude(generic_amplitude=a0 * 1e-3)
+            amplitude.unit = 'm'
+            amplitude.category = 'point'
+            amplitude.waveform_id = pick.waveform_id
+            amplitude.magnitude_hint = self.type
+            amplitude.pick_id = pick.resource_id
+            amplitude.type = 'AML'
+            self.event.amplitudes.append(amplitude)
+            self.amplitudes = (station, amplitude)
+            # using standard Gutenberg-Richter relation
+            # or scale WA amplitude with given scaling relation
+            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))
+            else:
+                print("Calculating scaled local magnitude ...")
+                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]
+                                                                                             * delta + self.wascaling[
+                                                         2])
+            magnitude.origin_id = self.origin_id
+            magnitude.waveform_id = pick.waveform_id
+            magnitude.amplitude_id = amplitude.resource_id
+            magnitude.station_magnitude_type = self.type
+            self.event.station_magnitudes.append(magnitude)
+            self.magnitudes = (station, magnitude)
+
+
+class MomentMagnitude(Magnitude):
+    '''
+    Method to calculate seismic moment Mo and moment magnitude Mw.
+    Requires results of class calcsourcespec for calculating plateau w0
+    and corner frequency fc of source spectrum, respectively. Uses
+    subfunction calcMoMw.py. Returns modified dictionary of picks including
+    Dc-value, corner frequency fc, seismic moment Mo and
+    corresponding moment magntiude Mw.
+    '''
+
+    _props = dict()
+
+    def __init__(self, stream, event, vp, Qp, density, verbosity=False,
+                 iplot=False):
+        super(MomentMagnitude, self).__init__(stream, event, verbosity, iplot)
+
+        self._vp = vp
+        self._Qp = Qp
+        self._density = density
+        self._type = 'Mw'
+        self.calc()
+
+    @property
+    def p_velocity(self):
+        return self._vp
+
+    @property
+    def p_attenuation(self):
+        return self._Qp
+
+    @property
+    def rock_density(self):
+        return self._density
+
+    @property
+    def moment_props(self):
+        return self._props
+
+    @moment_props.setter
+    def moment_props(self, value):
+        station, props = value
+        self._props[station] = props
+
+    @property
+    def seismic_moment(self):
+        return self._m0
+
+    @seismic_moment.setter
+    def seismic_moment(self, value):
+        self._m0 = value
+
+    def calc(self):
+        for a in self.arrivals:
+            if a.phase not in 'pP':
+                continue
+            pick = a.pick_id.get_referred_object()
+            station = pick.waveform_id.station_code
+            scopy = self.stream.copy()
+            wf = scopy.select(station=station)
+            if not wf:
+                continue
+            onset = pick.time
+            distance = degrees2kilometers(a.distance)
+            azimuth = a.azimuth
+            incidence = a.takeoff_angle
+            w0, fc = calcsourcespec(wf, onset, self.p_velocity, distance,
+                                    azimuth, incidence, self.p_attenuation,
+                                    self.plot_flag, self.verbose)
+            if w0 is None or fc is None:
+                if self.verbose:
+                    print("WARNING: insufficient frequency information")
+                continue
+            WF = select_for_phase(self.stream.select(
+                station=station), a.phase)
+            WF = select_for_phase(WF, "P")
+            m0, mw = calcMoMw(WF, w0, self.rock_density, self.p_velocity,
+                              distance, self.verbose)
+            self.moment_props = (station, dict(w0=w0, fc=fc, Mo=m0))
+            magnitude = ope.StationMagnitude(mag=mw)
+            magnitude.origin_id = self.origin_id
+            magnitude.waveform_id = pick.waveform_id
+            magnitude.station_magnitude_type = self.type
+            self.event.station_magnitudes.append(magnitude)
+            self.magnitudes = (station, magnitude)
+
+
+def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):
+    '''
+    Subfunction of run_calcMoMw to calculate individual
+    seismic moments and corresponding moment magnitudes.
+
+    :param: wfstream
+    :type:  `~obspy.core.stream.Stream`
+
+    :param: w0, height of plateau of source spectrum
+    :type:  float
+
+    :param: rho, rock density [kg/m³]
+    :type:  integer
+
+    :param: delta, hypocentral distance [km]
+    :type:  integer
+
+    :param: inv, name/path of inventory or dataless-SEED file
+    :type:  string
+    '''
+
+    tr = wfstream[0]
+    delta = delta * 1000  # hypocentral distance in [m]
+
+    if verbosity:
+        print(
+            "calcMoMw: Calculating seismic moment Mo and moment magnitude Mw for station {0} ...".format(
+                tr.stats.station))
+
+    # additional common parameters for calculating Mo
+    rP = 2 / np.sqrt(
+        15)  # average radiation pattern of P waves (Aki & Richards, 1980)
+    freesurf = 2.0  # free surface correction, assuming vertical incidence
+
+    Mo = w0 * 4 * np.pi * rho * np.power(vp, 3) * delta / (rP * freesurf)
+
+    # Mw = np.log10(Mo * 1e07) * 2 / 3 - 10.7 # after Hanks & Kanamori (1979), defined for [dyn*cm]!
+    Mw = np.log10(Mo) * 2 / 3 - 6.7  # for metric units
+
+    if verbosity:
+        print(
+            "calcMoMw: Calculated seismic moment Mo = {0} Nm => Mw = {1:3.1f} ".format(
+                Mo, Mw))
+
+    return Mo, Mw
+
+
+def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
+                   qp, iplot=0, verbosity=False):
+    '''
+    Subfunction to calculate the source spectrum and to derive from that the plateau
+    (usually called omega0) and the corner frequency assuming Aki's omega-square
+    source model. Has to be derived from instrument corrected displacement traces,
+    thus restitution and integration necessary! Integrated traces are rotated
+    into ray-coordinate system ZNE => LQT using Obspy's rotate modul!
+
+    :param: wfstream (corrected for instrument)
+    :type:  `~obspy.core.stream.Stream`
+
+    :param: onset, P-phase onset time
+    :type: float
+
+    :param: vp, Vp-wave velocity
+    :type:  float
+
+    :param: delta, hypocentral distance [km]
+    :type:  integer
+
+    :param: azimuth
+    :type:  integer
+
+    :param: incidence
+    :type:  integer
+
+    :param: Qp, quality factor for P-waves
+    :type:  integer
+
+    :param: iplot, show results (iplot>1) or not (iplot<1)
+    :type:  integer
+    '''
+    if verbosity:
+        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
+
+    dist = delta * 1000  # hypocentral distance in [m]
+
+    fc = None
+    w0 = None
+
+    zdat = select_for_phase(wfstream, "P")
+
+    dt = zdat[0].stats.delta
+
+    freq = zdat[0].stats.sampling_rate
+
+    # trim traces to common range (for rotation)
+    trstart, trend = common_range(wfstream)
+    wfstream.trim(trstart, trend)
+
+    # rotate into LQT (ray-coordindate-) system using Obspy's rotate
+    # L: P-wave direction
+    # Q: SV-wave direction
+    # T: SH-wave direction
+    LQT = wfstream.rotate('ZNE->LQT', azimuth, incidence)
+    ldat = LQT.select(component="L")
+    if len(ldat) == 0:
+        # if horizontal channels are 1 and 2
+        # no azimuth information is available and thus no
+        # rotation is possible!
+        if verbosity:
+            print("calcsourcespec: Azimuth information is missing, "
+                  "no rotation of components possible!")
+        # instead, use component 3
+        ldat = LQT.select(component="3")
+        if len(ldat) == 0:
+            # maybe component z available
+            ldat = LQT.select(component="Z")
+
+    # integrate to displacement
+    # unrotated vertical component (for comparison)
+    inttrz = signal.detrend(integrate.cumtrapz(zdat[0].data, None, dt))
+    # rotated component Z => L
+    Ldat = signal.detrend(integrate.cumtrapz(ldat[0].data, None, dt))
+
+    # get window after P pulse for
+    # calculating source spectrum
+    rel_onset = onset - trstart
+    impickP = int(rel_onset * freq)
+    wfzc = Ldat[impickP: len(Ldat) - 1]
+    # get time array
+    t = np.arange(0, len(inttrz) * dt, dt)
+    # calculate spectrum using only first cycles of
+    # waveform after P onset!
+    zc = crossings_nonzero_all(wfzc)
+    if np.size(zc) == 0 or len(zc) <= 3:
+        if verbosity:
+            print("calcsourcespec: Something is wrong with the waveform, "
+                  "no zero crossings derived!\n")
+            print("No calculation of source spectrum possible!")
+        plotflag = 0
+    else:
+        plotflag = 1
+        index = min([3, len(zc) - 1])
+        calcwin = (zc[index] - zc[0]) * dt
+        iwin = getsignalwin(t, rel_onset, calcwin)
+        xdat = Ldat[iwin]
+
+        # fft
+        fny = freq / 2
+        l = len(xdat) / freq
+        # number of fft bins after Bath
+        n = freq * l
+        # 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 = dt * np.fft.fft(xdat, N)
+        Y = abs(y[: N / 2])
+        L = (N - 1) / freq
+        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]
+
+        # correction for attenuation
+        wa = 2 * np.pi * F  # angular frequency
+        D = np.exp((wa * dist) / (2 * vp * Q * F ** A))
+        YYcor = YY.real * D
+
+        # get plateau (DC value) and corner frequency
+        # initial guess of plateau
+        w0in = np.mean(YYcor[0:100])
+        # initial guess of corner frequency
+        # where spectral level reached 50% of flat level
+        iin = np.where(YYcor >= 0.5 * w0in)
+        Fcin = F[iin[0][np.size(iin) - 1]]
+
+        # use of implicit scipy otimization function
+        fit = synthsourcespec(F, w0in, Fcin)
+        [optspecfit, _] = curve_fit(synthsourcespec, F, YYcor, [w0in, Fcin])
+        w0 = optspecfit[0]
+        fc = optspecfit[1]
+        # w01 = optspecfit[0]
+        # fc1 = optspecfit[1]
+        if verbosity:
+            print("calcsourcespec: Determined w0-value: %e m/Hz, \n"
+                  "calcsourcespec: Determined corner frequency: %f Hz" % (w0, fc))
+
+            # use of conventional fitting
+            # [w02, fc2] = fitSourceModel(F, YYcor, Fcin, iplot, verbosity)
+
+            # get w0 and fc as median of both
+            # source spectrum fits
+            # w0 = np.median([w01, w02])
+            # fc = np.median([fc1, fc2])
+            # if verbosity:
+            #    print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
+            #    w0, fc))
+
+    if iplot > 1:
+        f1 = plt.figure()
+        tLdat = np.arange(0, len(Ldat) * dt, dt)
+        plt.subplot(2, 1, 1)
+        # show displacement in mm
+        p1, = plt.plot(t, np.multiply(inttrz, 1000), 'k')
+        p2, = plt.plot(tLdat, np.multiply(Ldat, 1000))
+        plt.legend([p1, p2], ['Displacement', 'Rotated Displacement'])
+        if plotflag == 1:
+            plt.plot(t[iwin], np.multiply(xdat, 1000), 'g')
+            plt.title('Seismogram and P Pulse, Station %s-%s' \
+                      % (zdat[0].stats.station, zdat[0].stats.channel))
+        else:
+            plt.title('Seismogram, Station %s-%s' \
+                      % (zdat[0].stats.station, zdat[0].stats.channel))
+        plt.xlabel('Time since %s' % zdat[0].stats.starttime)
+        plt.ylabel('Displacement [mm]')
+
+        if plotflag == 1:
+            plt.subplot(2, 1, 2)
+            p1, = plt.loglog(f, Y.real, 'k')
+            p2, = plt.loglog(F, YY.real)
+            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',
+                                          'Used Raw Spectrum',
+                                          'Q-Corrected Spectrum',
+                                          'Fit to Spectrum'])
+            plt.title('Source Spectrum from P Pulse, w0=%e m/Hz, fc=%6.2f Hz' \
+                      % (w0, fc))
+            plt.xlabel('Frequency [Hz]')
+            plt.ylabel('Amplitude [m/Hz]')
+            plt.grid()
+
+    return w0, fc
+
+
+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
+
+
+def fitSourceModel(f, S, fc0, iplot, verbosity=False):
+    '''
+    Calculates synthetic source spectrum by varying corner frequency fc.
+    Returns best approximated plateau omega0 and corner frequency, i.e. with least
+    common standard deviations.
+
+    :param:  f, frequencies
+    :type:   array
+
+    :param:  S, observed source spectrum
+    :type:   array
+
+    :param:  fc0, initial corner frequency
+    :type:   float
+    '''
+
+    try:
+        iplot = int(iplot)
+    except:
+        if iplot == True or iplot == 'True':
+            iplot = 2
+        else:
+            iplot = 0
+
+    w0 = []
+    stdw0 = []
+    fc = []
+    stdfc = []
+    STD = []
+    # get window around initial corner frequency for trials
+    # 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]
+    # right side of initial corner frequency
+    fcstopr = min(fc0 + (fc0 / 2), f[len(f) - 1])
+    ir = np.where(f >= fcstopr)
+    # check, if fcstopr is available
+    if np.size(ir) == 0:
+        fcstopr = fc0
+        ir = len(f) - 1
+    else:
+        ir = ir[0][0]
+
+    # vary corner frequency around initial point
+    print("fitSourceModel: Varying 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
+    elif idiff <= 20:
+        increment = 1
+    else:
+        increment = 10
+
+    for i in range(il, ir, increment):
+        FC = f[i]
+        indexdc = np.where((f > 0) & (f <= FC))
+        dc = np.mean(S[indexdc])
+        stddc = np.std(dc - S[indexdc])
+        w0.append(dc)
+        stdw0.append(stddc)
+        fc.append(FC)
+        # slope
+        indexfc = np.where((f >= FC) & (f <= fcstopr))
+        yi = dc / (1 + (f[indexfc] / FC) ** 2)
+        stdFC = np.std(yi - S[indexfc])
+        stdfc.append(stdFC)
+        STD.append(stddc + stdFC)
+
+    # get best found w0 anf fc from minimum
+    if len(STD) > 0:
+        fc = fc[np.argmin(STD)]
+        w0 = w0[np.argmin(STD)]
+    elif len(STD) == 0:
+        fc = fc0
+        w0 = max(S)
+    if verbosity:
+        print(
+            "fitSourceModel: best fc: {0} Hz, best w0: {1} m/Hz".format(fc, w0))
+
+    if iplot > 1:
+        plt.figure()  # iplot)
+        plt.loglog(f, S, 'k')
+        plt.loglog([f[0], fc], [w0, w0], 'g')
+        plt.loglog([fc, fc], [w0 / 100, w0], 'g')
+        plt.title('Calculated Source Spectrum, Omega0=%e m/Hz, fc=%6.2f Hz' \
+                  % (w0, fc))
+        plt.xlabel('Frequency [Hz]')
+        plt.ylabel('Amplitude [m/Hz]')
+        plt.grid()
+        plt.figure()  # iplot + 1)
+        plt.subplot(311)
+        plt.plot(f[il:ir], STD, '*')
+        plt.title('Common Standard Deviations')
+        plt.xticks([])
+        plt.subplot(312)
+        plt.plot(f[il:ir], stdw0, '*')
+        plt.title('Standard Deviations of w0-Values')
+        plt.xticks([])
+        plt.subplot(313)
+        plt.plot(f[il:ir], stdfc, '*')
+        plt.title('Standard Deviations of Corner Frequencies')
+        plt.xlabel('Corner Frequencies [Hz]')
+
+    return w0, fc

pylot/core/io/__init__.py

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

pylot/core/io/data.py

@@ -0,0 +1,750 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import copy
+import os
+
+from obspy import read_events
+from obspy.core import read, Stream, UTCDateTime
+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.event import Event
+from pylot.core.util.utils import fnConstructor, full_range
+import pylot.core.loc.velest as velest
+
+
+class Data(object):
+    """
+    Data container with attributes wfdata holding ~obspy.core.stream.
+
+    :type parent: PySide.QtGui.QWidget object, optional
+    :param parent: A PySide.QtGui.QWidget object utilized when
+    called by a GUI to display a PySide.QtGui.QMessageBox instead of printing
+    to standard out.
+    :type evtdata: ~obspy.core.event.Event object, optional
+    :param evtdata ~obspy.core.event.Event object containing all derived or
+    loaded event. Container object holding, e.g. phase arrivals, etc.
+    """
+
+    def __init__(self, parent=None, evtdata=None):
+        self._parent = parent
+        if self.getParent():
+            self.comp = parent.getComponent()
+        else:
+            self.comp = 'Z'
+            self.wfdata = Stream()
+        self._new = False
+        if isinstance(evtdata, ObsPyEvent) or isinstance(evtdata, Event):
+            pass
+        elif isinstance(evtdata, dict):
+            evt = readPILOTEvent(**evtdata)
+            evtdata = evt
+        elif isinstance(evtdata, str):
+            try:
+                cat = read_events(evtdata)
+                if len(cat) is not 1:
+                    raise ValueError('ambiguous event information for file: '
+                                     '{file}'.format(file=evtdata))
+                evtdata = cat[0]
+            except TypeError as e:
+                if 'Unknown format for file' in e.message:
+                    if 'PHASES' in evtdata:
+                        picks = picksdict_from_pilot(evtdata)
+                        evtdata = ObsPyEvent()
+                        evtdata.picks = picks_from_picksdict(picks)
+                    elif 'LOC' in evtdata:
+                        raise NotImplementedError('PILOT location information '
+                                                  'read support not yet '
+                                                  'implemeted.')
+                    else:
+                        raise e
+                else:
+                    raise e
+        else:  # create an empty Event object
+            self.setNew()
+            evtdata = ObsPyEvent()
+            evtdata.picks = []
+        self.evtdata = evtdata
+        self.wforiginal = None
+        self.cuttimes = None
+        self.dirty = False
+
+    def __str__(self):
+        return str(self.wfdata)
+
+    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')
+        if other.isNew() and not self.isNew():
+            picks_to_add = other.get_evt_data().picks
+            old_picks = self.get_evt_data().picks
+            for pick in picks_to_add:
+                if pick not in old_picks:
+                    old_picks.append(pick)
+        elif not other.isNew() and self.isNew():
+            new = other + self
+            self.evtdata = new.get_evt_data()
+        elif self.isNew() and other.isNew():
+            pass
+        elif rs_id == rs_id_other:
+            other.setNew()
+            return self + other
+        else:
+            raise ValueError("both Data objects have differing "
+                             "unique Event identifiers")
+        return self
+
+    def getPicksStr(self):
+        picks_str = ''
+        for pick in self.get_evt_data().picks:
+            picks_str += str(pick) + '\n'
+        return picks_str
+
+    def getParent(self):
+        """
+
+
+        :return:
+        """
+        return self._parent
+
+    def isNew(self):
+        """
+
+
+        :return:
+        """
+        return self._new
+
+    def setNew(self):
+        self._new = True
+
+    def getCutTimes(self):
+        """
+
+
+        :return:
+        """
+        if self.cuttimes is None:
+            self.updateCutTimes()
+        return self.cuttimes
+
+    def updateCutTimes(self):
+        """
+
+
+        """
+        self.cuttimes = full_range(self.getWFData())
+
+    def getEventFileName(self):
+        """
+
+
+        :return:
+        """
+        ID = self.getID()
+        # handle forbidden filenames especially on windows systems
+        return fnConstructor(str(ID))
+
+    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 fnext: file extension
+        :param fcheck: check and delete existing information
+        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
+        """
+        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 = read_events(fnout + fnext)
+                if len(cat) > 1:
+                    raise IOError('Ambigious event information in file {}'.format(fnout + fnext))
+                if len(cat) < 1:
+                    raise IOError('No event information in file {}'.format(fnout + fnext))
+                event = cat[0]
+                if not event.resource_id == self.get_evt_data().resource_id:
+                    raise IOError("Missmatching event resource id's: {} and {}".format(event.resource_id,
+                                                                                       self.get_evt_data().resource_id))
+                self.checkEvent(event, fcheck)
+                self.setEvtData(event)
+            self.get_evt_data().write(fnout + fnext, format=evtformat)
+        # try exporting event  
+        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!
+            for i in range(len(picks)):
+                if picks[i].method_id == 'manual':
+                    mstation = picks[i].waveform_id.station_code
+                    mstation_ext = mstation + '_'
+                    for k in range(len(picks_copy)):
+                        if ((picks_copy[k].waveform_id.station_code == mstation) or
+                                (picks_copy[k].waveform_id.station_code == mstation_ext)) and \
+                                (picks_copy[k].method_id == 'auto'):
+                            del picks_copy[k]
+                            break
+            lendiff = len(picks) - len(picks_copy)
+            if lendiff is not 0:
+                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:
+                    evtdata_copy.write(fnout + fnext, format=evtformat)
+                    # write header afterwards
+                    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
+                    nllocfile = open(fnout + fnext)
+                    l = nllocfile.readlines()
+                    nllocfile.close()
+                    l.insert(0, header)
+                    nllocfile = open(fnout + fnext, 'w')
+                    nllocfile.write("".join(l))
+                    nllocfile.close()
+                except KeyError as e:
+                    raise KeyError('''{0} export format
+                                     not implemented: {1}'''.format(evtformat, e))
+            if fnext == '.cnv':
+                try:
+                    velest.export(picks_copy, fnout + fnext, eventinfo=self.get_evt_data())
+                except KeyError as e:
+                    raise KeyError('''{0} export format
+                                     not implemented: {1}'''.format(evtformat, e))
+
+    def getComp(self):
+        """
+
+
+        :return:
+        """
+        return self.comp
+
+    def getID(self):
+        """
+
+
+        :return:
+        """
+        try:
+            return self.evtdata.get('resource_id').id
+        except:
+            return None
+
+    def filterWFData(self, kwargs):
+        """
+
+        :param kwargs:
+        """
+        self.getWFData().filter(**kwargs)
+        self.dirty = True
+
+    def setWFData(self, fnames):
+        """
+
+        :param fnames:
+        """
+        self.wfdata = Stream()
+        self.wforiginal = None
+        if fnames is not None:
+            self.appendWFData(fnames)
+        else:
+            return False
+        self.wforiginal = self.getWFData().copy()
+        self.dirty = False
+        return True
+
+    def appendWFData(self, fnames):
+        """
+
+        :param fnames:
+        """
+        assert isinstance(fnames, list), "input parameter 'fnames' is " \
+                                         "supposed to be of type 'list' " \
+                                         "but is actually" \
+                                         " {0}".format(type(fnames))
+        if self.dirty:
+            self.resetWFData()
+
+        warnmsg = ''
+        for fname in fnames:
+            try:
+                self.wfdata += read(fname)
+            except TypeError:
+                try:
+                    self.wfdata += read(fname, format='GSE2')
+                except Exception as e:
+                    warnmsg += '{0}\n{1}\n'.format(fname, e)
+            except SacIOError as se:
+                warnmsg += '{0}\n{1}\n'.format(fname, se)
+        if warnmsg:
+            warnmsg = 'WARNING: unable to read\n' + warnmsg
+            print(warnmsg)
+
+    def getWFData(self):
+        """
+
+
+        :return:
+        """
+        return self.wfdata
+
+    def getOriginalWFData(self):
+        """
+
+
+        :return:
+        """
+        return self.wforiginal
+
+    def resetWFData(self):
+        """
+
+
+        """
+        self.wfdata = self.getOriginalWFData().copy()
+        self.dirty = False
+
+    def resetPicks(self):
+        """
+
+
+        """
+        self.get_evt_data().picks = []
+
+    def get_evt_data(self):
+        """
+
+
+        :return:
+        """
+        return self.evtdata
+
+    def setEvtData(self, event):
+        self.evtdata = event
+
+    def applyEVTData(self, data, typ='pick', authority_id='rub'):
+
+        """
+
+        :param data:
+        :param typ:
+        :param authority_id:
+        :raise OverwriteError:
+        """
+
+        def applyPicks(picks):
+            """
+            Creates ObsPy pick objects and append it to the picks list from the
+            PyLoT dictionary contain all picks.
+            :param picks:
+            :raise OverwriteError: raises an OverwriteError if the picks list is
+             not empty. The GUI will then ask for a decision.
+            """
+            # 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!")
+                    picks = picks_from_picksdict(picks)
+                    break
+                else:
+                    if self.get_evt_data().picks:
+                        raise OverwriteError('Existing picks would be overwritten!')
+                    else:
+                        picks = picks_from_picksdict(picks)
+                        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')
+            #     ID = ResourceIdentifier('event/' + fonset_str)
+            #     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
+            information on the event to the actual data
+            :param event:
+            """
+            if self.isNew():
+                self.setEvtData(event)
+            else:
+                # prevent overwriting original pick information
+                event_old = self.get_evt_data()
+                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))
+                else:
+                    picks = copy.deepcopy(event_old.picks)
+                    event = merge_picks(event, picks)
+                # apply event information from location
+                event_old.update(event)
+
+        applydata = {'pick': applyPicks,
+                     'event': applyEvent}
+
+        applydata[typ](data)
+        self._new = False
+
+
+class GenericDataStructure(object):
+    """
+    GenericDataBase type holds all information about the current data-
+    base working on.
+    """
+
+    def __init__(self, **kwargs):
+
+        self.allowedFields = []
+        self.expandFields = ['root']
+        self.dsFields = {}
+
+        self.modifyFields(**kwargs)
+
+    def modifyFields(self, **kwargs):
+
+        """
+
+        :param kwargs:
+        """
+        assert isinstance(kwargs, dict), 'dictionary type object expected'
+
+        if not self.extraAllowed():
+            kwargs = self.updateNotAllowed(kwargs)
+
+        for key, value in kwargs.items():
+            key = str(key).lower()
+            if value is not None:
+                if type(value) not in (str, int, float):
+                    for n, val in enumerate(value):
+                        value[n] = str(val)
+                else:
+                    value = str(value)
+            try:
+                self.setFieldValue(key, value)
+            except KeyError as e:
+                errmsg = ''
+                errmsg += 'WARNING:\n'
+                errmsg += 'unable to set values for datastructure fields\n'
+                errmsg += '%s; desired value was: %s\n' % (e, value)
+                print(errmsg)
+
+    def isField(self, key):
+        """
+
+        :param key:
+        :return:
+        """
+        return key in self.getFields().keys()
+
+    def getFieldValue(self, key):
+        """
+
+        :param key:
+        :return:
+        """
+        if self.isField(key):
+            return self.getFields()[key]
+        else:
+            return
+
+    def setFieldValue(self, key, value):
+        """
+
+        :param key:
+        :param value:
+        :raise KeyError:
+        """
+        if not self.extraAllowed() and key not in self.getAllowed():
+            raise KeyError
+        else:
+            if not self.isField(key):
+                print('creating new field "%s"' % key)
+            self.getFields()[key] = value
+
+    def getFields(self):
+        """
+
+
+        :return:
+        """
+        return self.dsFields
+
+    def getExpandFields(self):
+        """
+
+
+        :return:
+        """
+        return self.expandFields
+
+    def setExpandFields(self, keys):
+        """
+
+        :param keys:
+        """
+        expandFields = []
+        for key in keys:
+            if self.isField(key):
+                expandFields.append(key)
+        self.expandFields = expandFields
+
+    def getAllowed(self):
+        """
+
+
+        :return:
+        """
+        return self.allowedFields
+
+    def extraAllowed(self):
+        """
+
+
+        :return:
+        """
+        return not self.allowedFields
+
+    def updateNotAllowed(self, kwargs):
+        """
+
+        :param kwargs:
+        :return:
+        """
+        for key in kwargs:
+            if key not in self.getAllowed():
+                kwargs.__delitem__(key)
+        return kwargs
+
+    def hasSuffix(self):
+        """
+
+
+        :return:
+        """
+        try:
+            self.getFieldValue('suffix')
+        except KeyError:
+            return False
+        else:
+            if self.getFieldValue('suffix'):
+                return True
+        return False
+
+    def expandDataPath(self):
+        """
+
+
+        :return:
+        """
+        expandList = []
+        for item in self.getExpandFields():
+            expandList.append(self.getFieldValue(item))
+        if self.hasSuffix():
+            expandList.append('*%s' % self.getFieldValue('suffix'))
+        return os.path.join(*expandList)
+
+    def getCatalogName(self):
+        """
+
+
+        :return:
+        """
+        return os.path.join(self.getFieldValue('root'), 'catalog.qml')
+
+
+class PilotDataStructure(GenericDataStructure):
+    """
+    Object containing the data access information for the old PILOT data
+    structure.
+    """
+
+    def __init__(self, **fields):
+        if not fields:
+            fields = {'database': '2006.01',
+                      'root': '/data/Egelados/EVENT_DATA/LOCAL'}
+
+        GenericDataStructure.__init__(self, **fields)
+
+        self.setExpandFields(['root', 'database'])
+
+
+class SeiscompDataStructure(GenericDataStructure):
+    """
+    Dictionary containing the data access information for an SDS data archive:
+
+    :param str dataType: Desired data type. Default: ``'waveform'``
+    :param sdate, edate: Either date string or an instance of
+         :class:`obspy.core.utcdatetime.UTCDateTime. Default: ``None``
+    :type sdate, edate: str or UTCDateTime or None
+    """
+
+    def __init__(self, rootpath='/data/SDS', dataformat='MSEED',
+                 filesuffix=None, **kwargs):
+        super(GenericDataStructure, self).__init__()
+
+        edate = UTCDateTime()
+        halfyear = UTCDateTime('1970-07-01')
+        sdate = UTCDateTime(edate - halfyear)
+        del halfyear
+
+        year = ''
+        if not edate.year == sdate.year:
+            nyears = edate.year - sdate.year
+            for yr in range(nyears):
+                year += '{0:04d},'.format(sdate.year + yr)
+            year = '{' + year[:-1] + '}'
+        else:
+            year = '{0:04d}'.format(sdate.year)
+
+        # SDS fields' default values
+        # definitions from
+        # http://www.seiscomp3.org/wiki/doc/applications/slarchive/SDS
+
+        self.dsFields = {'root': '/data/SDS', 'YEAR': year, 'NET': '??',
+                         'STA': '????', 'CHAN': 'HH?', 'TYPE': 'D', 'LOC': '',
+                         'DAY': '{0:03d}'.format(sdate.julday)
+                         }
+        self.modifiyFields(**kwargs)
+
+    def modifiyFields(self, **kwargs):
+        """
+
+        :param kwargs:
+        """
+        if kwargs and isinstance(kwargs, dict):
+            for key, value in kwargs.iteritems():
+                key = str(key)
+                if type(value) not in (str, int, float):
+                    for n, val in enumerate(value):
+                        value[n] = str(val)
+                else:
+                    value = str(value)
+                try:
+                    self.setFieldValue(key, value)
+                except KeyError as e:
+                    errmsg = ''
+                    errmsg += 'WARNING:\n'
+                    errmsg += 'unable to set values for SDS fields\n'
+                    errmsg += '%s; desired value was: %s\n' % (e, value)
+                    print(errmsg)
+
+    def setFieldValue(self, key, value):
+        """
+
+        :param key:
+        :param value:
+        """
+        if self.isField(key):
+            self.getFields()[key] = value
+        else:
+            print('Warning: trying to set value of non-existent field '
+                  '{field}'.format(field=key))
+
+    def expandDataPath(self):
+        """
+
+
+        :return:
+        """
+        fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType())
+        dataPath = os.path.join(self.getFields()['SDSdir'],
+                                self.getFields()['YEAR'],
+                                self.getFields()['NET'],
+                                self.getFields()['STA'],
+                                fullChan,
+                                '*{0}'.format(self.getFields()['DAY']))
+        return dataPath

pylot/core/io/default_parameters.py

@@ -0,0 +1,491 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+defaults = {'rootpath': {'type': str,
+                         'tooltip': 'project path',
+                         'value': '',
+                         'namestring': 'Root path'},
+
+            'datapath': {'type': str,
+                         'tooltip': 'data path',
+                         'value': '',
+                         'namestring': 'Data path'},
+
+            'database': {'type': str,
+                         'tooltip': 'name of data base',
+                         'value': '',
+                         'namestring': 'Database path'},
+
+            'eventID': {'type': str,
+                        'tooltip': 'event ID for single event processing (* for all events found in database)',
+                        'value': '',
+                        'namestring': 'Event ID'},
+
+            'extent': {'type': str,
+                       'tooltip': 'extent of array ("local", "regional" or "global")',
+                       'value': 'local',
+                       'namestring': 'Array extent'},
+
+            'invdir': {'type': str,
+                       'tooltip': 'full path to  inventory or dataless-seed file',
+                       'value': '',
+                       'namestring': 'Inversion dir'},
+
+            'datastructure': {'type': str,
+                              'tooltip': 'choose data structure',
+                              'value': 'PILOT',
+                              'namestring': 'Datastructure'},
+
+            'apverbose': {'type': bool,
+                          'tooltip': "choose 'True' or 'False' for terminal output",
+                          'value': True,
+                          'namestring': 'App. verbosity'},
+
+            'nllocbin': {'type': str,
+                         'tooltip': 'path to NLLoc executable',
+                         'value': '',
+                         'namestring': 'NLLoc bin path'},
+
+            'nllocroot': {'type': str,
+                          'tooltip': 'root of NLLoc-processing directory',
+                          'value': '',
+                          'namestring': 'NLLoc root path'},
+
+            'phasefile': {'type': str,
+                          'tooltip': 'name of autoPyLoT-output phase file for NLLoc',
+                          'value': 'AUTOPHASES.obs',
+                          'namestring': 'Phase filename'},
+
+            'ctrfile': {'type': str,
+                        'tooltip': 'name of autoPyLoT-output control file for NLLoc',
+                        'value': 'Insheim_min1d2015_auto.in',
+                        'namestring': 'Control filename'},
+
+            'ttpatter': {'type': str,
+                         'tooltip': 'pattern of NLLoc ttimes from grid',
+                         'value': 'ttime',
+                         'namestring': 'Traveltime pattern'},
+
+            'outpatter': {'type': str,
+                          'tooltip': 'pattern of NLLoc-output file',
+                          'value': 'AUTOLOC_nlloc',
+                          'namestring': 'NLLoc output pattern'},
+
+            'vp': {'type': float,
+                   'tooltip': 'average P-wave velocity',
+                   'value': 3530.,
+                   'namestring': 'P-velocity'},
+
+            'rho': {'type': float,
+                    'tooltip': 'average rock density [kg/m^3]',
+                    'value': 2500.,
+                    'namestring': 'Density'},
+
+            'Qp': {'type': (float, float),
+                   'tooltip': 'quality factor for P waves (Qp*f^a); list(Qp, a)',
+                   'value': (300., 0.8),
+                   'namestring': ('Quality factor', 'Qp1', 'Qp2')},
+
+            'pstart': {'type': float,
+                       'tooltip': 'start time [s] for calculating CF for P-picking (if TauPy:'
+                                  ' seconds relative to estimated onset)',
+                       'value': 15.0,
+                       'namestring': 'P start'},
+
+            'pstop': {'type': float,
+                      'tooltip': 'end time [s] for calculating CF for P-picking (if TauPy:'
+                                 ' 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,
+                       'namestring': 'S start'},
+
+            'sstop': {'type': float,
+                      'tooltip': 'end time [s] after P-onset for calculating CF for S-picking',
+                      '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),
+                     '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),
+                     '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),
+                     '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),
+                     'namestring': ('H-bandpass 2', 'Lower', 'Upper')},
+
+            'algoP': {'type': str,
+                      'tooltip': 'choose algorithm for P-onset determination (HOS, ARZ, or AR3)',
+                      'value': 'HOS',
+                      'namestring': 'P algorithm'},
+
+            'tlta': {'type': float,
+                     'tooltip': 'for HOS-/AR-AIC-picker, length of LTA window [s]',
+                     'value': 7.0,
+                     'namestring': 'LTA window'},
+
+            'hosorder': {'type': int,
+                         'tooltip': 'for HOS-picker, order of Higher Order Statistics',
+                         'value': 4,
+                         'namestring': 'HOS order'},
+
+            'Parorder': {'type': int,
+                         'tooltip': 'for AR-picker, order of AR process of Z-component',
+                         '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,
+                       '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,
+                        '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,
+                       '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,
+                        'namestring': 'AR pred. window Z 2'},
+
+            'addnoise': {'type': float,
+                         'tooltip': 'add noise to seismogram for stable AR prediction',
+                         '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),
+                      '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,
+                         '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,
+                           'namestring': 'Recal. window P'},
+
+            'aictsmooth': {'type': float,
+                           'tooltip': 'for HOS/AR, take average of samples for smoothing of AIC-function [s]',
+                           '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,
+                         'namestring': 'CF smooth P'},
+
+            'ausP': {'type': float,
+                     'tooltip': 'for HOS/AR, artificial uplift of samples (aus) of CF (P)',
+                     'value': 0.001,
+                     'namestring': 'Artificial uplift P'},
+
+            'nfacP': {'type': float,
+                      'tooltip': 'for HOS/AR, noise factor for noise level determination (P)',
+                      'value': 1.3,
+                      'namestring': 'Noise factor P'},
+
+            'algoS': {'type': str,
+                      'tooltip': 'choose algorithm for S-onset determination (ARH or AR3)',
+                      '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,
+                       '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,
+                        '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,
+                       '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,
+                        'namestring': 'AR pred. window H 2'},
+
+            'Sarorder': {'type': int,
+                         'tooltip': 'for AR-picker, order of AR process of H-components',
+                         '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,
+                           'namestring': 'Recal. window S'},
+
+            'pickwinS': {'type': float,
+                         'tooltip': 'for initial AIC pick, length of S-pick window [s]',
+                         '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),
+                      '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,
+                            'namestring': 'AIC smooth S'},
+
+            'tsmoothS': {'type': float,
+                         'tooltip': 'for AR-picker, take average of samples for smoothing CF [s] (S)',
+                         '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,
+                     'namestring': 'Artificial uplift S'},
+
+            'nfacS': {'type': float,
+                      'tooltip': 'for AR-picker, noise factor for noise level determination (S)',
+                      'value': 1.5,
+                      'namestring': 'Noise factor S'},
+
+            'minfmweight': {'type': int,
+                            'tooltip': 'minimum required P weight for first-motion determination',
+                            'value': 1,
+                            'namestring': 'Min. P weight'},
+
+            'minFMSNR': {'type': float,
+                         'tooltip': 'miniumum required SNR for first-motion determination',
+                         'value': 2.,
+                         'namestring': 'Min SNR'},
+
+            'fmpickwin': {'type': float,
+                          'tooltip': 'pick window around P onset for calculating zero crossings',
+                          '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),
+                            '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),
+                            '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,
+                             'namestring': 'Min. slope P'},
+
+            'minAICPSNR': {'type': float,
+                           'tooltip': 'below this SNR the initial P pick is rejected',
+                           'value': 1.1,
+                           'namestring': 'Min. SNR P'},
+
+            'minAICSslope': {'type': float,
+                             'tooltip': 'below this slope [counts/s] the initial S pick is rejected',
+                             'value': 1.,
+                             'namestring': 'Min. slope S'},
+
+            'minAICSSNR': {'type': float,
+                           'tooltip': 'below this SNR the initial S pick is rejected',
+                           'value': 1.5,
+                           'namestring': 'Min. SNR S'},
+
+            'minsiglength': {'type': float,
+                             'tooltip': 'length of signal part for which amplitudes must exceed noiselevel [s]',
+                             'value': 1.,
+                             'namestring': 'Min. signal length'},
+
+            'noisefactor': {'type': float,
+                            'tooltip': 'noiselevel*noisefactor=threshold',
+                            'value': 1.0,
+                            'namestring': 'Noise factor'},
+
+            'minpercent': {'type': float,
+                           'tooltip': 'required percentage of amplitudes exceeding threshold',
+                           'value': 10.,
+                           'namestring': 'Min amplitude [%]'},
+
+            'zfac': {'type': float,
+                     'tooltip': 'P-amplitude must exceed at least zfac times RMS-S amplitude',
+                     'value': 1.5,
+                     'namestring': 'Z factor'},
+
+            'mdttolerance': {'type': float,
+                             'tooltip': 'maximum allowed deviation of P picks from median [s]',
+                             'value': 6.0,
+                             'namestring': 'Median tolerance'},
+
+            'wdttolerance': {'type': float,
+                             'tooltip': 'maximum allowed deviation from Wadati-diagram',
+                             '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] \
+                          If zeros are set, original Richter magnitude is calculated!',
+                          'value': (0., 0., 0.),
+                          'namestring': ('Wood-Anderson scaling', '', '', '')},
+
+            'magscaling': {'type': (float, float),
+                           'tooltip': 'Scaling relation for derived local magnitude [a*Ml+b]. \
+                           If zeros are set, no scaling of network magnitude is applied!',
+                           'value': (0., 0.),
+                           'namestring': ('Local mag. scaling', '', '')},
+
+            'minfreq': {'type': (float, float),
+                        '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',
+        'eventID',
+        'invdir',
+        'datastructure',
+        'apverbose'],
+    'nlloc': [
+        'nllocbin',
+        'nllocroot',
+        'phasefile',
+        'ctrfile',
+        'ttpatter',
+        'outpatter'],
+    'smoment': [
+        'vp',
+        'rho',
+        'Qp'],
+    'localmag': [
+        'WAscaling',
+        'magscaling'],
+    'filter': [
+        'minfreq',
+        'maxfreq',
+        'filter_order',
+        'filter_type'],
+    'pick': [
+        'extent',
+        'pstart',
+        'pstop',
+        'sstart',
+        'sstop',
+        'use_taup',
+        'taup_model',
+        'bpz1',
+        'bpz2',
+        'bph1',
+        'bph2']
+}
+
+settings_special_pick = {
+    'z': [
+        'algoP',
+        'tlta',
+        'hosorder',
+        'Parorder',
+        'tdet1z',
+        'tpred1z',
+        'tdet2z',
+        'tpred2z',
+        'addnoise',
+        'tsnrz',
+        'pickwinP',
+        'Precalcwin',
+        'aictsmooth',
+        'tsmoothP',
+        'ausP',
+        'nfacP'],
+    'h': [
+        'algoS',
+        'tdet1h',
+        'tpred1h',
+        'tdet2h',
+        'tpred2h',
+        'Sarorder',
+        'Srecalcwin',
+        'pickwinS',
+        'tsnrh',
+        'aictsmoothS',
+        'tsmoothS',
+        'ausS',
+        'nfacS'],
+    'fm': [
+        'minfmweight',
+        'minFMSNR',
+        'fmpickwin'],
+    'quality': [
+        'timeerrorsP',
+        'timeerrorsS',
+        'minAICPslope',
+        'minAICPSNR',
+        'minAICSslope',
+        'minAICSSNR',
+        'minsiglength',
+        'noisefactor',
+        'minpercent',
+        'zfac',
+        'mdttolerance',
+        'wdttolerance',
+        'jackfactor'],
+}

pylot/core/io/inputs.py

@@ -0,0 +1,371 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io import default_parameters
+from pylot.core.util.errors import ParameterError
+
+
+class PylotParameter(object):
+    '''
+    PylotParameter is a parameter type object capable to read and/or write
+    parameter ASCII.
+
+    :param fn str: Filename of the input file
+
+    Parameters are given for example as follows:
+    ==========  ==========  =======================================
+    Name        Value       Comment
+    ==========  ==========  =======================================
+    phl         S           # phaselabel
+    ff1         0.1         # freqmin
+    ff2         0.5         # freqmax
+    tdet        6.875       # det-window_(s)_for_ar
+    tpred       2.5         # pred-window_(s)_for_ar
+    order       4           # order_of_ar
+    fnoise      0           # noise_level_for_ar
+    suppp       7           # envelopecoeff
+    tolt        300         # (s)time around arrival time
+    f1tpwt      4           # propfact_minfreq_secondtaper
+    pickwindow  9           # length_of_pick_window
+    w1          1           # length_of_smoothing_window
+    w2          0.37        # cf(i-1)*(1+peps)_for_local_min
+    w3          0.25        # cf(i-1)*(1+peps)_for_local_min
+    tslope      0.8;2       # slope_det_window_loc_glob
+    aerr        30;60       # adjusted_error_slope_fitting_loc_glob
+    tsn         20;5;20;10  # length_signal_window_S/N
+    proPh       Sn          # nextprominentphase
+    ==========  ==========  =======================================
+    '''
+
+    def __init__(self, fnin=None, fnout=None, verbosity=0, **kwargs):
+        '''
+        Initialize parameter object:
+
+        io content of an ASCII file an form a type consistent dictionary
+        contain all parameters.
+        '''
+
+        self.__init_default_paras()
+        self.__init_subsettings()
+        self.__filename = fnin
+        self._verbosity = verbosity
+        self._parFileCont = {}
+        # io from parsed arguments alternatively
+        for key, val in kwargs.items():
+            self._parFileCont[key] = val
+        self.from_file()
+        if fnout:
+            self.export2File(fnout)
+
+    # Human-readable string representation of the object
+    def __str__(self):
+        string = ''
+        string += 'Automated picking parameter:\n\n'
+        if self.__parameter:
+            for key, value in self.iteritems():
+                string += '%s:\t\t%s\n' % (key, value)
+        else:
+            string += 'Empty parameter dictionary.'
+        return string
+
+    # Set default values of parameter names
+    def __init_default_paras(self):
+        parameters = default_parameters.defaults
+        self.__defaults = parameters
+
+    def __init_subsettings(self):
+        self._settings_main = default_parameters.settings_main
+        self._settings_special_pick = default_parameters.settings_special_pick
+
+    # String representation of the object
+    def __repr__(self):
+        return "PylotParameter('%s')" % self.__filename
+
+    # Boolean test
+    def __nonzero__(self):
+        return bool(self.__parameter)
+
+    def __getitem__(self, key):
+        try:
+            return self.__parameter[key]
+        except:
+            return None
+
+    def __setitem__(self, key, value):
+        self.__parameter[key] = value
+
+    def __delitem__(self, key):
+        del self.__parameter[key]
+
+    def __iter__(self):
+        return iter(self.__parameter)
+
+    def __len__(self):
+        return len(self.__parameter.keys())
+
+    def iteritems(self):
+        for key, value in self.__parameter.items():
+            yield key, value
+
+    def hasParam(self, parameter):
+        if parameter in self.__parameter.keys():
+            return True
+        return False
+
+    def get(self, *args):
+        try:
+            for param in args:
+                try:
+                    return self.__getitem__(param)
+                except KeyError as e:
+                    self._printParameterError(e)
+                    raise ParameterError(e)
+        except TypeError:
+            try:
+                return self.__getitem__(args)
+            except KeyError as e:
+                self._printParameterError(e)
+                raise ParameterError(e)
+
+    def get_defaults(self):
+        return self.__defaults
+
+    def get_main_para_names(self):
+        return self._settings_main
+
+    def get_special_para_names(self):
+        return self._settings_special_pick
+
+    def get_all_para_names(self):
+        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()['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']
+        all_names += self.get_special_para_names()['quality']
+        return all_names
+
+    def checkValue(self, param, value):
+        is_type = type(value)
+        expect_type = self.get_defaults()[param]['type']
+        if not is_type == expect_type and not is_type == tuple:
+            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)
+
+    def reset_defaults(self):
+        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:
+                fnin = self.__filename
+            else:
+                return
+
+        if isinstance(fnin, (list, tuple)):
+            fnin = fnin[0]
+
+        inputFile = open(fnin, 'r')
+        try:
+            lines = inputFile.readlines()
+            for line in lines:
+                parspl = line.split('\t')[:2]
+                self._parFileCont[parspl[0].strip()] = parspl[1]
+        except IndexError as e:
+            if self._verbosity > 0:
+                self._printParameterError(e)
+            inputFile.seek(0)
+            lines = inputFile.readlines()
+            for line in lines:
+                if not line.startswith(('#', '%', '\n', ' ')):
+                    parspl = line.split('#')[:2]
+                    self._parFileCont[parspl[1].strip()] = parspl[0].strip()
+        for key, value in self._parFileCont.items():
+            try:
+                val = int(value)
+            except:
+                try:
+                    val = float(value)
+                except:
+                    if len(value.split(' ')) > 1:
+                        vallist = value.strip().split(' ')
+                        val = []
+                        for val0 in vallist:
+                            try:
+                                val0 = float(val0)
+                            except:
+                                pass
+                            val.append(val0)
+                    else:
+                        val = str(value.strip())
+            self._parFileCont[key] = val
+        self.__parameter = self._parFileCont
+
+    def export2File(self, fnout):
+        fid_out = open(fnout, 'w')
+        lines = []
+        # 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' +
+                  '%All main and special settings regarding data handling\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'
+
+        fid_out.write(header)
+        self.write_section(fid_out, self.get_main_para_names()['dirs'],
+                           'main settings', separator)
+        self.write_section(fid_out, self.get_main_para_names()['nlloc'],
+                           'NLLoc settings', separator)
+        self.write_section(fid_out, self.get_main_para_names()['smoment'],
+                           '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' +
+                       '%!!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)
+        self.write_section(fid_out, self.get_special_para_names()['quality'],
+                           'quality assessment', None)
+
+    def write_section(self, fid, names, title, separator):
+        if separator:
+            fid.write(separator)
+        fid.write('#{}#\n'.format(title))
+        l_val = 50
+        l_name = 15
+        l_ttip = 100
+        for name in names:
+            value = self[name]
+            if type(value) == list or type(value) == tuple:
+                value_tmp = ''
+                for vl in value:
+                    value_tmp += '{} '.format(vl)
+                value = value_tmp
+            tooltip = self.get_defaults()[name]['tooltip']
+            if not len(str(value)) > l_val:
+                value = '{:<{}} '.format(str(value), l_val)
+            else:
+                value = '{} '.format(str(value))
+            name += '#'
+            if not len(name) > l_name:
+                name = '#{:<{}} '.format(name, l_name)
+            else:
+                name = '#{} '.format(name)
+            if not len(tooltip) > l_ttip:
+                ttip = '%{:<{}}\n'.format(tooltip, l_ttip)
+            else:
+                ttip = '%{}\n'.format(tooltip)
+            line = value + name + ttip
+            fid.write(line)
+
+
+class FilterOptions(object):
+    '''
+    FilterOptions is a parameter object type providing Butterworth filter
+    option parameter for PyLoT. Its easy to access properties helps to manage
+    file based as well as parameter manipulation within the GUI.
+
+    :type filtertype: str, optional
+    :param filtertype: String containing the desired filtertype For information
+    about the supported filter types see _`Supported Filter` section .
+
+    :type freq: list, optional
+    :param freq: list of float(s) describing the cutoff limits of the filter
+
+    :type order: int, optional
+    :param order: Integer value describing the order of the desired Butterworth
+    filter.
+
+    .. rubric:: _`Supported Filter`
+
+        ``'bandpass'``
+            Butterworth-Bandpass
+
+        ``'bandstop'``
+            Butterworth-Bandstop
+
+        ``'lowpass'``
+            Butterworth-Lowpass
+
+        ``'highpass'``
+            Butterworth-Highpass
+    '''
+
+    def __init__(self, filtertype='bandpass', freq=[2., 5.], order=3,
+                 **kwargs):
+        self._order = order
+        self._filtertype = filtertype
+        self._freq = freq
+
+    def __str__(self):
+        hrs = '''\n\tFilter parameter:\n
+        Type:\t\t{ftype}\n
+        Frequencies:\t{freq}\n
+        Order:\t\t{order}\n
+        '''.format(ftype=self.getFilterType(),
+                   freq=self.getFreq(),
+                   order=self.getOrder())
+        return hrs
+
+    def __nonzero__(self):
+        return bool(self.getFilterType())
+
+    def parseFilterOptions(self):
+        if self:
+            robject = {'type': self.getFilterType(), 'corners': self.getOrder()}
+            if not self.getFilterType() in ['highpass', 'lowpass']:
+                robject['freqmin'] = self.getFreq()[0]
+                robject['freqmax'] = self.getFreq()[1]
+            elif self.getFilterType() == 'highpass':
+                robject['freq'] = self.getFreq()[0]
+            elif self.getFilterType() == 'lowpass':
+                robject['freq'] = self.getFreq()[1]
+            return robject
+        return None
+
+    def getFreq(self):
+        return self.__getattribute__('_freq')
+
+    def setFreq(self, freq):
+        self.__setattr__('_freq', freq)
+
+    def getOrder(self):
+        return self.__getattribute__('_order')
+
+    def setOrder(self, order):
+        self.__setattr__('_order', order)
+
+    def getFilterType(self):
+        return self.__getattribute__('_filtertype')
+
+    def setFilterType(self, filtertype):
+        self.__setattr__('_filtertype', filtertype)

pylot/core/io/location.py

@@ -0,0 +1,220 @@
+from obspy import UTCDateTime
+from obspy.core import event as ope
+
+from pylot.core.util.utils import getLogin, getHash
+
+
+def create_amplitude(pickID, amp, unit, category, cinfo):
+    '''
+
+    :param pickID:
+    :param amp:
+    :param unit:
+    :param category:
+    :param cinfo:
+    :return:
+    '''
+    amplitude = ope.Amplitude()
+    amplitude.creation_info = cinfo
+    amplitude.generic_amplitude = amp
+    amplitude.unit = ope.AmplitudeUnit(unit)
+    amplitude.type = ope.AmplitudeCategory(category)
+    amplitude.pick_id = pickID
+    return amplitude
+
+
+def create_arrival(pickresID, cinfo, phase, azimuth=None, dist=None):
+    '''
+    create_arrival - function to create an Obspy Arrival
+
+    :param pickresID: Resource identifier of the created pick
+    :type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
+    :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
+    holding information on the creation of the returned object
+    :type cinfo: :class: `~obspy.core.event.CreationInfo` object
+    :param phase: name of the arrivals seismic phase
+    :type phase: str
+    :param azimuth: azimuth between source and receiver
+    :type azimuth: float or int, optional
+    :param dist: distance between source and receiver
+    :type dist: float or int, optional
+    :return: An ObsPy :class: `~obspy.core.event.Arrival` object
+    '''
+    arrival = ope.Arrival()
+    arrival.creation_info = cinfo
+    arrival.pick_id = pickresID
+    arrival.phase = phase
+    if azimuth is not None:
+        arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
+    else:
+        arrival.azimuth = azimuth
+    arrival.distance = dist
+    return arrival
+
+
+def create_creation_info(agency_id=None, creation_time=None, author=None):
+    '''
+
+    :param agency_id:
+    :param creation_time:
+    :param author:
+    :return:
+    '''
+    if author is None:
+        author = getLogin()
+    if creation_time is None:
+        creation_time = UTCDateTime()
+    return ope.CreationInfo(agency_id=agency_id, author=author,
+                            creation_time=creation_time)
+
+
+def create_event(origintime, cinfo, originloc=None, etype='earthquake',
+                 resID=None, authority_id=None):
+    '''
+    create_event - funtion to create an ObsPy Event
+
+    :param origintime: the events origintime
+    :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
+        holding information on the creation of the returned object
+    :type cinfo: :class: `~obspy.core.event.CreationInfo` object
+    :param originloc: tuple containing the location of the origin
+        (LAT, LON, DEP) affiliated with the event which is created
+    :type originloc: tuple, list
+    :param etype: Event type str object. converted via ObsPy to a valid event
+        type string.
+    :type etype: str
+    :param resID: Resource identifier of the created event
+    :type resID: :class: `~obspy.core.event.ResourceIdentifier` object, str
+    :param authority_id: name of the institution carrying out the processing
+    :type authority_id: str
+    :return: An ObsPy :class: `~obspy.core.event.Event` object
+    '''
+
+    if originloc is not None:
+        o = create_origin(origintime, cinfo,
+                          originloc[0], originloc[1], originloc[2])
+    else:
+        o = None
+    if not resID:
+        resID = create_resourceID(origintime, etype, authority_id)
+    elif isinstance(resID, str):
+        resID = create_resourceID(origintime, etype, authority_id, resID)
+    elif not isinstance(resID, ope.ResourceIdentifier):
+        raise TypeError("unsupported type(resID) for resource identifier "
+                        "generation: %s" % type(resID))
+    event = ope.Event(resource_id=resID)
+    event.creation_info = cinfo
+    event.event_type = etype
+    if o:
+        event.origins = [o]
+    return event
+
+
+def create_magnitude(originID, cinfo):
+    '''
+    create_magnitude - function to create an ObsPy Magnitude object
+    :param originID:
+    :type originID:
+    :param cinfo:
+    :type cinfo:
+    :return:
+    '''
+    magnitude = ope.Magnitude()
+    magnitude.creation_info = cinfo
+    magnitude.origin_id = originID
+    return magnitude
+
+
+def create_origin(origintime, cinfo, latitude, longitude, depth):
+    '''
+    create_origin - function to create an ObsPy Origin
+    :param origintime: the origins time of occurence
+    :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :param cinfo:
+    :type cinfo:
+    :param latitude: latitude in decimal degree of the origins location
+    :type latitude: float
+    :param longitude: longitude in decimal degree of the origins location
+    :type longitude: float
+    :param depth: hypocentral depth of the origin
+    :type depth: float
+    :return: An ObsPy :class: `~obspy.core.event.Origin` object
+    '''
+
+    assert isinstance(origintime, UTCDateTime), "origintime has to be " \
+                                                "a UTCDateTime object, but " \
+                                                "actually is of type " \
+                                                "'%s'" % type(origintime)
+
+    origin = ope.Origin()
+    origin.time = origintime
+    origin.creation_info = cinfo
+    origin.latitude = latitude
+    origin.longitude = longitude
+    origin.depth = depth
+    return origin
+
+
+def create_pick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
+                wfseedstr, authority_id):
+    '''
+    create_pick - function to create an ObsPy Pick
+
+    :param origintime:
+    :type origintime:
+    :param picknum: number of the created pick
+    :type picknum: int
+    :param picktime:
+    :type picktime:
+    :param eventnum: human-readable event identifier
+    :type eventnum: str
+    :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
+        holding information on the creation of the returned object
+    :type cinfo: :class: `~obspy.core.event.CreationInfo` object
+    :param phase: name of the arrivals seismic phase
+    :type phase: str
+    :param station: name of the station at which the seismic phase has been
+        picked
+    :type station: str
+    :param wfseedstr: A SEED formatted string of the form
+        network.station.location.channel in order to set a referenced waveform
+    :type wfseedstr: str, SEED formatted
+    :param authority_id: name of the institution carrying out the processing
+    :type authority_id: str
+    :return: An ObsPy :class: `~obspy.core.event.Pick` object
+    '''
+    pickID = eventnum + '_' + station.strip() + '/{0:03d}'.format(picknum)
+    pickresID = create_resourceID(origintime, 'pick', authority_id, pickID)
+    pick = ope.Pick()
+    pick.resource_id = pickresID
+    pick.time = picktime
+    pick.creation_info = cinfo
+    pick.phase_hint = phase
+    pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
+    return pick
+
+
+def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
+    '''
+
+    :param timetohash:
+    :type timetohash
+    :param restype: type of the resource, e.g. 'orig', 'earthquake' ...
+    :type restype: str
+    :param authority_id: name of the institution carrying out the processing
+    :type authority_id: str, optional
+    :param hrstr:
+    :type hrstr:
+    :return:
+    '''
+    assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
+                                                "UTCDateTime object"
+    hid = getHash(timetohash)
+    if hrstr is None:
+        resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
+    else:
+        resID = ope.ResourceIdentifier(restype + '/' + hrstr)
+    if authority_id is not None:
+        resID.convertIDToQuakeMLURI(authority_id=authority_id)
+    return resID

pylot/core/loc/__init__.py

@@ -0,0 +1,2 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-

pylot/core/loc/focmec.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, parameter, eventinfo):
+    '''
+    Take <picks> dictionary and exports picking data to a focmec
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    
+    :param: parameter, all input information
+    :type:  object
+
+    :param: eventinfo, source information needed for focmec format
+    :type:  list object
+    '''
+    # write phases to FOCMEC-phase file
+    writephases(picks, 'FOCMEC', fnout, parameter, eventinfo)

pylot/core/loc/hash.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, parameter, eventinfo):
+    '''
+    Take <picks> dictionary and exports picking data to a HASH
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    
+    :param: parameter, all input information
+    :type:  object
+
+    :param: eventinfo, source information needed for HASH format
+    :type:  list object
+    '''
+    # write phases to HASH-phase file
+    writephases(picks, 'HASH', fnout, parameter, eventinfo)

pylot/core/loc/hypo71.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, parameter):
+    '''
+    Take <picks> dictionary and exports picking data to a HYPO71
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+
+    :param: parameter, all input information
+    :type:  object
+    '''
+    # write phases to HYPO71-phase file
+    writephases(picks, 'HYPO71', fnout, parameter)

pylot/core/loc/hypodd.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, parameter, eventinfo):
+    '''
+    Take <picks> dictionary and exports picking data to a hypoDD
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    
+    :param: parameter, all input information
+    :type:  object
+
+    :param: eventinfo, source information needed for hypoDD format
+    :type:  list object
+    '''
+    # write phases to hypoDD-phase file
+    writephases(picks, 'hypoDD', fnout, parameter, eventinfo)

pylot/core/loc/hyposat.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, parameter):
+    '''
+    Take <picks> dictionary and exports picking data to a HYPOSAT
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    
+    :param: parameter, all input information
+    :type:  object
+    '''
+    # write phases to HYPOSAT-phase file
+    writephases(picks, 'HYPOSAT', fnout, parameter)

pylot/core/loc/nll.py

@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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
+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
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+ 
+    :param: parameter, all input information
+    :type:  object
+    '''
+    # write phases to NLLoc-phase file
+    writephases(picks, 'NLLoc', fnout, parameter)
+
+
+def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
+    '''
+    :param ctrfn: name of NLLoc-control file
+    :type: str
+
+    :param root: root path to NLLoc working directory
+    :type: str
+
+    :param nllocoutn: name of NLLoc-location output file
+    :type: str
+
+    :param phasefn: name of NLLoc-input phase file
+    :type: str
+
+    :param tttn: pattern of precalculated NLLoc traveltime tables
+    :type: str
+    '''
+    # For locating the event the NLLoc-control file has to be modified!
+    # create comment line for NLLoc-control file NLLoc-output file
+    ctrfile = os.path.join(root, 'run', ctrfn)
+    nllocout = os.path.join(root, 'loc', nllocoutn)
+    phasefile = os.path.join(root, 'obs', phasefn)
+    tttable = os.path.join(root, 'time', 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)
+    curlocfiles = getPatternLine(ctrfile, 'LOCFILES')
+    nllfile = open(ctrfile, 'r')
+    filedata = nllfile.read()
+    if filedata.find(locfiles) < 0:
+        # replace old command
+        filedata = filedata.replace(curlocfiles, locfiles)
+        nllfile = open(ctrfile, 'w')
+        nllfile.write(filedata)
+    nllfile.close()
+
+
+def locate(fnin, infile=None):
+    """
+    takes an external program name
+    :param fnin:
+    :return:
+    """
+
+    if infile is None:
+        exe_path = which('NLLoc')
+    else:
+        exe_path = which('NLLoc', infile)
+    if exe_path is None:
+        raise NLLocError('NonLinLoc executable not found; check your '
+                         'environment variables')
+
+    # locate the event utilizing external NonLinLoc installation
+    try:
+        runProgram(exe_path, fnin)
+    except subprocess.CalledProcessError as e:
+        raise RuntimeError(e.output)
+
+
+def read_location(fn):
+    path, file = os.path.split(fn)
+    file = glob.glob1(path, file + '.[0-9]*.grid0.loc.hyp')
+    if len(file) > 1:
+        raise IOError('ambiguous location name {0}'.format(file))
+    fn = os.path.join(path, file[0])
+    return read_events(fn)[0]
+
+
+if __name__ == '__main__':
+    pass

pylot/core/loc/velest.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylot.core.io.phases import writephases
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+
+
+def export(picks, fnout, eventinfo, parameter=None):
+    '''
+    Take <picks> dictionary and exports picking data to a VELEST-cnv
+    <phasefile> without creating an ObsPy event object.
+
+    :param picks: picking data dictionary
+    :type picks: dict
+
+    :param fnout: complete path to the exporting obs file
+    :type fnout: str
+    
+    :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/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+#

pylot/core/pick/charfuns.py

@@ -0,0 +1,705 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Created Oct/Nov 2014
+
+Implementation of the Characteristic Functions (CF) published and described in:
+
+Kueperkoch, L., Meier, T., Lee, J., Friederich, W., & EGELADOS Working Group, 2010:
+Automated determination of P-phase arrival times at regional and local distances
+using higher order statistics, Geophys. J. Int., 181, 1159-1170
+
+Kueperkoch, L., Meier, T., Bruestle, A., Lee, J., Friederich, W., & EGELADOS
+Working Group, 2012: Automated determination of S-phase arrival times using
+autoregressive prediction: application ot local and regional distances, Geophys. J. Int.,
+188, 687-702.
+
+:author: MAGS2 EP3 working group
+"""
+
+import numpy as np
+from obspy.core import Stream
+
+
+class CharacteristicFunction(object):
+    '''
+    SuperClass for different types of characteristic functions.
+    '''
+
+    def __init__(self, data, cut, t2=None, order=None, t1=None, fnoise=None):
+        '''
+        Initialize data type object with information from the original
+        Seismogram.
+
+        :param: data
+        :type: `~obspy.core.stream.Stream`
+
+        :param: cut
+        :type: tuple
+
+        :param: t2
+        :type: float
+
+        :param: order
+        :type: int
+
+        :param: t1
+        :type: float (optional, only for AR)
+
+        :param: fnoise
+        :type: float (optional, only for AR)
+        '''
+
+        assert isinstance(data, Stream), "%s is not a stream object" % str(data)
+
+        self.orig_data = data
+        self.dt = self.orig_data[0].stats.delta
+        self.setCut(cut)
+        self.setTime1(t1)
+        self.setTime2(t2)
+        self.setOrder(order)
+        self.setFnoise(fnoise)
+        self.setARdetStep(t2)
+        self.calcCF(self.getDataArray())
+        self.arpara = np.array([])
+        self.xpred = np.array([])
+
+    def __str__(self):
+        return '''\n\t{name} object:\n
+        Cut:\t\t{cut}\n
+        t1:\t{t1}\n
+        t2:\t{t2}\n
+        Order:\t\t{order}\n
+        Fnoise:\t{fnoise}\n
+        ARdetStep:\t{ardetstep}\n
+        '''.format(name=type(self).__name__,
+                   cut=self.getCut(),
+                   t1=self.getTime1(),
+                   t2=self.getTime2(),
+                   order=self.getOrder(),
+                   fnoise=self.getFnoise(),
+                   ardetstep=self.getARdetStep[0]())
+
+    def getCut(self):
+        return self.cut
+
+    def setCut(self, cut):
+        self.cut = cut
+
+    def getTime1(self):
+        return self.t1
+
+    def setTime1(self, t1):
+        self.t1 = t1
+
+    def getTime2(self):
+        return self.t2
+
+    def setTime2(self, t2):
+        self.t2 = t2
+
+    def getARdetStep(self):
+        return self.ARdetStep
+
+    def setARdetStep(self, t1):
+        if t1:
+            self.ARdetStep = []
+            self.ARdetStep.append(t1 / 4)
+            self.ARdetStep.append(int(np.ceil(self.getTime2() / self.getIncrement()) / 4))
+
+    def getOrder(self):
+        return self.order
+
+    def setOrder(self, order):
+        self.order = order
+
+    def getIncrement(self):
+        """
+        :rtype : int
+        """
+        return self.dt
+
+    def getTimeArray(self):
+        incr = self.getIncrement()
+        self.TimeArray = np.arange(0, len(self.getCF()) * incr, incr) + self.getCut()[0]
+        return self.TimeArray
+
+    def getFnoise(self):
+        return self.fnoise
+
+    def setFnoise(self, fnoise):
+        self.fnoise = fnoise
+
+    def getCF(self):
+        return self.cf
+
+    def getXCF(self):
+        return self.xcf
+
+    def getDataArray(self, cut=None):
+        '''
+        If cut times are given, time series is cut from cut[0] (start time)
+        till cut[1] (stop time) in order to calculate CF for certain part
+        only where you expect the signal!
+        input: cut (tuple) ()
+        cutting window
+        '''
+        if cut is not None:
+            if len(self.orig_data) == 1:
+                if self.cut[0] == 0 and self.cut[1] == 0:
+                    start = 0
+                    stop = len(self.orig_data[0])
+                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                    start = 0
+                    stop = self.cut[1] / self.dt
+                else:
+                    start = self.cut[0] / self.dt
+                    stop = self.cut[1] / self.dt
+                zz = self.orig_data.copy()
+                z1 = zz[0].copy()
+                zz[0].data = z1.data[int(start):int(stop)]
+                data = zz
+                return data
+            elif len(self.orig_data) == 2:
+                if self.cut[0] == 0 and self.cut[1] == 0:
+                    start = 0
+                    stop = min([len(self.orig_data[0]), len(self.orig_data[1])])
+                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                    start = 0
+                    stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
+                                len(self.orig_data[1])])
+                else:
+                    start = max([0, self.cut[0] / self.dt])
+                    stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
+                                len(self.orig_data[1])])
+                hh = self.orig_data.copy()
+                h1 = hh[0].copy()
+                h2 = hh[1].copy()
+                hh[0].data = h1.data[int(start):int(stop)]
+                hh[1].data = h2.data[int(start):int(stop)]
+                data = hh
+                return data
+            elif len(self.orig_data) == 3:
+                if self.cut[0] == 0 and self.cut[1] == 0:
+                    start = 0
+                    stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
+                                len(self.orig_data[1]), len(self.orig_data[2])])
+                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                    start = 0
+                    stop = self.cut[1] / self.dt
+                else:
+                    start = max([0, self.cut[0] / self.dt])
+                    stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
+                                len(self.orig_data[1]), len(self.orig_data[2])])
+                hh = self.orig_data.copy()
+                h1 = hh[0].copy()
+                h2 = hh[1].copy()
+                h3 = hh[2].copy()
+                hh[0].data = h1.data[int(start):int(stop)]
+                hh[1].data = h2.data[int(start):int(stop)]
+                hh[2].data = h3.data[int(start):int(stop)]
+                data = hh
+                return data
+        else:
+            data = self.orig_data.copy()
+            return data
+
+    def calcCF(self, data=None):
+        self.cf = data
+
+
+class AICcf(CharacteristicFunction):
+    '''
+    Function to calculate the Akaike Information Criterion (AIC) after
+    Maeda (1985).
+    :param: data, time series (whether seismogram or CF)
+    :type: tuple
+
+    Output: AIC function
+    '''
+
+    def calcCF(self, data):
+
+        x = self.getDataArray()
+        xnp = x[0].data
+        ind = np.where(~np.isnan(xnp))[0]
+        if ind.size:
+            xnp[:ind[0]] = xnp[ind[0]]
+        datlen = len(xnp)
+        k = np.arange(1, datlen)
+        cf = np.zeros(datlen)
+        cumsumcf = np.cumsum(np.power(xnp, 2))
+        i = np.where(cumsumcf == 0)
+        cumsumcf[i] = np.finfo(np.float64).eps
+        cf[k] = ((k - 1) * np.log(cumsumcf[k] / k) + (datlen - k + 1) *
+                 np.log((cumsumcf[datlen - 1] - cumsumcf[k - 1]) / (datlen - k + 1)))
+        cf[0] = cf[1]
+        inf = np.isinf(cf)
+        ff = np.where(inf == True)
+        if len(ff) >= 1:
+            cf[ff] = 0
+
+        self.cf = cf - np.mean(cf)
+        self.xcf = x
+
+
+class HOScf(CharacteristicFunction):
+    '''
+    Function to calculate skewness (statistics of order 3) or kurtosis
+    (statistics of order 4), using one long moving window, as published
+    in Kueperkoch et al. (2010).
+    '''
+
+    def calcCF(self, data):
+
+        x = self.getDataArray(self.getCut())
+        xnp = x[0].data
+        nn = np.isnan(xnp)
+        if len(nn) > 1:
+            xnp[nn] = 0
+        if self.getOrder() == 3:  # this is skewness
+            y = np.power(xnp, 3)
+            y1 = np.power(xnp, 2)
+        elif self.getOrder() == 4:  # this is kurtosis
+            y = np.power(xnp, 4)
+            y1 = np.power(xnp, 2)
+
+        # Initialisation
+        # t2: long term moving window
+        ilta = int(round(self.getTime2() / self.getIncrement()))
+        lta = y[0]
+        lta1 = y1[0]
+        # moving windows
+        LTA = np.zeros(len(xnp))
+        for j in range(0, len(xnp)):
+            if j < 4:
+                LTA[j] = 0
+            elif j <= ilta:
+                lta = (y[j] + lta * (j - 1)) / j
+                lta1 = (y1[j] + lta1 * (j - 1)) / j
+            else:
+                lta = (y[j] - y[j - ilta]) / ilta + lta
+                lta1 = (y1[j] - y1[j - ilta]) / ilta + lta1
+            # define LTA
+            if self.getOrder() == 3:
+                LTA[j] = lta / np.power(lta1, 1.5)
+            elif self.getOrder() == 4:
+                LTA[j] = lta / np.power(lta1, 2)
+
+        # remove NaN's with first not-NaN-value,
+        # so autopicker doesnt pick discontinuity at start of the trace
+        ind = np.where(~np.isnan(LTA))[0]
+        if ind.size:
+            first = ind[0]
+            LTA[:first] = LTA[first]
+        self.cf = LTA
+        self.xcf = x
+
+
+class ARZcf(CharacteristicFunction):
+    def calcCF(self, data):
+
+        print('Calculating AR-prediction error from single trace ...')
+        x = self.getDataArray(self.getCut())
+        xnp = x[0].data
+        nn = np.isnan(xnp)
+        if len(nn) > 1:
+            xnp[nn] = 0
+        # some parameters needed
+        # add noise to time series
+        xnoise = xnp + np.random.normal(0.0, 1.0, len(xnp)) * self.getFnoise() * max(abs(xnp))
+        tend = len(xnp)
+        # Time1: length of AR-determination window [sec]
+        # Time2: length of AR-prediction window [sec]
+        ldet = int(round(self.getTime1() / self.getIncrement()))  # length of AR-determination window [samples]
+        lpred = int(np.ceil(self.getTime2() / self.getIncrement()))  # length of AR-prediction window [samples]
+
+        cf = np.zeros(len(xnp))
+        loopstep = self.getARdetStep()
+        arcalci = ldet + self.getOrder()  # AR-calculation index
+        for i in range(ldet + self.getOrder(), tend - lpred - 1):
+            if i == arcalci:
+                # determination of AR coefficients
+                # to speed up calculation, AR-coefficients are calculated only every i+loopstep[1]!
+                self.arDetZ(xnoise, self.getOrder(), i - ldet, i)
+                arcalci = arcalci + loopstep[1]
+            # AR prediction of waveform using calculated AR coefficients
+            self.arPredZ(xnp, self.arpara, i + 1, lpred)
+            # prediction error = CF
+            cf[i + lpred - 1] = np.sqrt(np.sum(np.power(self.xpred[i:i + lpred - 1] - xnp[i:i + lpred - 1], 2)) / lpred)
+        nn = np.isnan(cf)
+        if len(nn) > 1:
+            cf[nn] = 0
+        # remove zeros and artefacts
+        tap = np.hanning(len(cf))
+        cf = tap * cf
+        io = np.where(cf == 0)
+        ino = np.where(cf > 0)
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
+
+        self.cf = cf
+        self.xcf = x
+
+    def arDetZ(self, data, order, rind, ldet):
+        '''
+        Function to calculate AR parameters arpara after Thomas Meier (CAU), published
+        in  Kueperkoch et al. (2012). This function solves SLE using the Moore-
+        Penrose inverse, i.e. the least-squares approach.
+        :param: data, time series to calculate AR parameters from
+        :type: array
+
+        :param: order, order of AR process
+        :type: int
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: ldet, length of AR-determination window (=end of summation index)
+        :type: int
+
+        Output: AR parameters arpara
+        '''
+
+        # recursive calculation of data vector (right part of eq. 6.5 in Kueperkoch et al. (2012)
+        rhs = np.zeros(self.getOrder())
+        for k in range(0, self.getOrder()):
+            for i in range(rind, ldet + 1):
+                ki = k + 1
+                rhs[k] = rhs[k] + data[i] * data[i - ki]
+
+        # recursive calculation of data array (second sum at left part of eq. 6.5 in Kueperkoch et al. 2012)
+        A = np.zeros((self.getOrder(), self.getOrder()))
+        for k in range(1, self.getOrder() + 1):
+            for j in range(1, k + 1):
+                for i in range(rind, ldet + 1):
+                    ki = k - 1
+                    ji = j - 1
+                    A[ki, ji] = A[ki, ji] + data[i - j] * data[i - k]
+
+                A[ji, ki] = A[ki, ji]
+
+        # apply Moore-Penrose inverse for SVD yielding the AR-parameters
+        self.arpara = np.dot(np.linalg.pinv(A), rhs)
+
+    def arPredZ(self, data, arpara, rind, lpred):
+        '''
+        Function to predict waveform, assuming an autoregressive process of order
+        p (=size(arpara)), with AR parameters arpara calculated in arDet. After
+        Thomas Meier (CAU), published in Kueperkoch et al. (2012).
+        :param: data, time series to be predicted
+        :type: array
+
+        :param: arpara, AR parameters
+        :type: float
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: lpred, length of prediction window (=end of summation index)
+        :type: int
+
+        Output: predicted waveform z
+        '''
+        # be sure of the summation indeces
+        if rind < len(arpara):
+            rind = len(arpara)
+        if rind > len(data) - lpred:
+            rind = len(data) - lpred
+        if lpred < 1:
+            lpred = 1
+        if lpred > len(data) - 2:
+            lpred = len(data) - 2
+
+        z = np.append(data[0:rind], np.zeros(lpred))
+        for i in range(rind, rind + lpred):
+            for j in range(1, len(arpara) + 1):
+                ji = j - 1
+                z[i] = z[i] + arpara[ji] * z[i - j]
+
+        self.xpred = z
+
+
+class ARHcf(CharacteristicFunction):
+    def calcCF(self, data):
+
+        print('Calculating AR-prediction error from both horizontal traces ...')
+
+        xnp = self.getDataArray(self.getCut())
+        n0 = np.isnan(xnp[0].data)
+        if len(n0) > 1:
+            xnp[0].data[n0] = 0
+        n1 = np.isnan(xnp[1].data)
+        if len(n1) > 1:
+            xnp[1].data[n1] = 0
+
+        # some parameters needed
+        # add noise to time series
+        xenoise = xnp[0].data + np.random.normal(0.0, 1.0, len(xnp[0].data)) * self.getFnoise() * max(abs(xnp[0].data))
+        xnnoise = xnp[1].data + np.random.normal(0.0, 1.0, len(xnp[1].data)) * self.getFnoise() * max(abs(xnp[1].data))
+        Xnoise = np.array([xenoise.tolist(), xnnoise.tolist()])
+        tend = len(xnp[0].data)
+        # Time1: length of AR-determination window [sec]
+        # Time2: length of AR-prediction window [sec]
+        ldet = int(round(self.getTime1() / self.getIncrement()))  # length of AR-determination window [samples]
+        lpred = int(np.ceil(self.getTime2() / self.getIncrement()))  # length of AR-prediction window [samples]
+
+        cf = np.zeros(len(xenoise))
+        loopstep = self.getARdetStep()
+        arcalci = lpred + self.getOrder() - 1  # AR-calculation index
+        # arcalci = ldet + self.getOrder() - 1 #AR-calculation index
+        for i in range(lpred + self.getOrder() - 1, tend - 2 * lpred + 1):
+            if i == arcalci:
+                # determination of AR coefficients
+                # to speed up calculation, AR-coefficients are calculated only every i+loopstep[1]!
+                self.arDetH(Xnoise, self.getOrder(), i - ldet, i)
+                arcalci = arcalci + loopstep[1]
+            # AR prediction of waveform using calculated AR coefficients
+            self.arPredH(xnp, self.arpara, i + 1, lpred)
+            # 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))
+        nn = np.isnan(cf)
+        if len(nn) > 1:
+            cf[nn] = 0
+        # remove zeros and artefacts
+        tap = np.hanning(len(cf))
+        cf = tap * cf
+        io = np.where(cf == 0)
+        ino = np.where(cf > 0)
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
+
+        self.cf = cf
+        self.xcf = xnp
+
+    def arDetH(self, data, order, rind, ldet):
+        '''
+        Function to calculate AR parameters arpara after Thomas Meier (CAU), published
+        in  Kueperkoch et al. (2012). This function solves SLE using the Moore-
+        Penrose inverse, i.e. the least-squares approach. "data" is a structured array.
+        AR parameters are calculated based on both horizontal components in order
+        to account for polarization.
+        :param: data, horizontal component seismograms to calculate AR parameters from
+        :type: structured array
+
+        :param: order, order of AR process
+        :type: int
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: ldet, length of AR-determination window (=end of summation index)
+        :type: int
+
+        Output: AR parameters arpara
+        '''
+
+        # recursive calculation of data vector (right part of eq. 6.5 in Kueperkoch et al. (2012)
+        rhs = np.zeros(self.getOrder())
+        for k in range(0, self.getOrder()):
+            for i in range(rind, ldet):
+                rhs[k] = rhs[k] + data[0, i] * data[0, i - k] + data[1, i] * data[1, i - k]
+
+        # recursive calculation of data array (second sum at left part of eq. 6.5 in Kueperkoch et al. 2012)
+        A = np.zeros((4, 4))
+        for k in range(1, self.getOrder() + 1):
+            for j in range(1, k + 1):
+                for i in range(rind, ldet):
+                    ki = k - 1
+                    ji = j - 1
+                    A[ki, ji] = A[ki, ji] + data[0, i - ji] * data[0, i - ki] + data[1, i - ji] * data[1, i - ki]
+
+                A[ji, ki] = A[ki, ji]
+
+        # apply Moore-Penrose inverse for SVD yielding the AR-parameters
+        self.arpara = np.dot(np.linalg.pinv(A), rhs)
+
+    def arPredH(self, data, arpara, rind, lpred):
+        '''
+        Function to predict waveform, assuming an autoregressive process of order
+        p (=size(arpara)), with AR parameters arpara calculated in arDet. After
+        Thomas Meier (CAU), published in Kueperkoch et al. (2012).
+        :param: data, horizontal component seismograms to be predicted
+        :type: structured array
+
+        :param: arpara, AR parameters
+        :type: float
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: lpred, length of prediction window (=end of summation index)
+        :type: int
+
+        Output: predicted waveform z
+        :type: structured array
+        '''
+        # be sure of the summation indeces
+        if rind < len(arpara) + 1:
+            rind = len(arpara) + 1
+        if rind > len(data[0]) - lpred + 1:
+            rind = len(data[0]) - lpred + 1
+        if lpred < 1:
+            lpred = 1
+        if lpred > len(data[0]) - 1:
+            lpred = len(data[0]) - 1
+
+        z1 = np.append(data[0][0:rind], np.zeros(lpred))
+        z2 = np.append(data[1][0:rind], np.zeros(lpred))
+        for i in range(rind, rind + lpred):
+            for j in range(1, len(arpara) + 1):
+                ji = j - 1
+                z1[i] = z1[i] + arpara[ji] * z1[i - ji]
+                z2[i] = z2[i] + arpara[ji] * z2[i - ji]
+
+        z = np.array([z1.tolist(), z2.tolist()])
+        self.xpred = z
+
+
+class AR3Ccf(CharacteristicFunction):
+    def calcCF(self, data):
+
+        print('Calculating AR-prediction error from all 3 components ...')
+
+        xnp = self.getDataArray(self.getCut())
+        n0 = np.isnan(xnp[0].data)
+        if len(n0) > 1:
+            xnp[0].data[n0] = 0
+        n1 = np.isnan(xnp[1].data)
+        if len(n1) > 1:
+            xnp[1].data[n1] = 0
+        n2 = np.isnan(xnp[2].data)
+        if len(n2) > 1:
+            xnp[2].data[n2] = 0
+
+        # some parameters needed
+        # add noise to time series
+        xenoise = xnp[0].data + np.random.normal(0.0, 1.0, len(xnp[0].data)) * self.getFnoise() * max(abs(xnp[0].data))
+        xnnoise = xnp[1].data + np.random.normal(0.0, 1.0, len(xnp[1].data)) * self.getFnoise() * max(abs(xnp[1].data))
+        xznoise = xnp[2].data + np.random.normal(0.0, 1.0, len(xnp[2].data)) * self.getFnoise() * max(abs(xnp[2].data))
+        Xnoise = np.array([xenoise.tolist(), xnnoise.tolist(), xznoise.tolist()])
+        tend = len(xnp[0].data)
+        # Time1: length of AR-determination window [sec]
+        # Time2: length of AR-prediction window [sec]
+        ldet = int(round(self.getTime1() / self.getIncrement()))  # length of AR-determination window [samples]
+        lpred = int(np.ceil(self.getTime2() / self.getIncrement()))  # length of AR-prediction window [samples]
+
+        cf = np.zeros(len(xenoise))
+        loopstep = self.getARdetStep()
+        arcalci = ldet + self.getOrder() - 1  # AR-calculation index
+        for i in range(ldet + self.getOrder() - 1, tend - 2 * lpred + 1):
+            if i == arcalci:
+                # determination of AR coefficients
+                # to speed up calculation, AR-coefficients are calculated only every i+loopstep[1]!
+                self.arDet3C(Xnoise, self.getOrder(), i - ldet, i)
+                arcalci = arcalci + loopstep[1]
+
+            # AR prediction of waveform using calculated AR coefficients
+            self.arPred3C(xnp, self.arpara, i + 1, lpred)
+            # 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) \
+                                           + np.power(self.xpred[2][i:i + lpred] - xnp[2][i:i + lpred], 2)) / (
+                                        3 * lpred))
+        nn = np.isnan(cf)
+        if len(nn) > 1:
+            cf[nn] = 0
+        # remove zeros and artefacts
+        tap = np.hanning(len(cf))
+        cf = tap * cf
+        io = np.where(cf == 0)
+        ino = np.where(cf > 0)
+        if np.size(ino):
+            cf[io] = cf[ino[0][0]]
+
+        self.cf = cf
+        self.xcf = xnp
+
+    def arDet3C(self, data, order, rind, ldet):
+        '''
+        Function to calculate AR parameters arpara after Thomas Meier (CAU), published
+        in  Kueperkoch et al. (2012). This function solves SLE using the Moore-
+        Penrose inverse, i.e. the least-squares approach. "data" is a structured array.
+        AR parameters are calculated based on both horizontal components and vertical
+        componant.
+        :param: data, horizontal component seismograms to calculate AR parameters from
+        :type: structured array
+
+        :param: order, order of AR process
+        :type: int
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: ldet, length of AR-determination window (=end of summation index)
+        :type: int
+
+        Output: AR parameters arpara
+        '''
+
+        # recursive calculation of data vector (right part of eq. 6.5 in Kueperkoch et al. (2012)
+        rhs = np.zeros(self.getOrder())
+        for k in range(0, self.getOrder()):
+            for i in range(rind, ldet):
+                rhs[k] = rhs[k] + data[0, i] * data[0, i - k] + data[1, i] * data[1, i - k] \
+                         + data[2, i] * data[2, i - k]
+
+        # recursive calculation of data array (second sum at left part of eq. 6.5 in Kueperkoch et al. 2012)
+        A = np.zeros((4, 4))
+        for k in range(1, self.getOrder() + 1):
+            for j in range(1, k + 1):
+                for i in range(rind, ldet):
+                    ki = k - 1
+                    ji = j - 1
+                    A[ki, ji] = A[ki, ji] + data[0, i - ji] * data[0, i - ki] + data[1, i - ji] * data[1, i - ki] \
+                                + data[2, i - ji] * data[2, i - ki]
+
+                A[ji, ki] = A[ki, ji]
+
+        # apply Moore-Penrose inverse for SVD yielding the AR-parameters
+        self.arpara = np.dot(np.linalg.pinv(A), rhs)
+
+    def arPred3C(self, data, arpara, rind, lpred):
+        '''
+        Function to predict waveform, assuming an autoregressive process of order
+        p (=size(arpara)), with AR parameters arpara calculated in arDet3C. After
+        Thomas Meier (CAU), published in Kueperkoch et al. (2012).
+        :param: data, horizontal and vertical component seismograms to be predicted
+        :type: structured array
+
+        :param: arpara, AR parameters
+        :type: float
+
+        :param: rind, first running summation index
+        :type: int
+
+        :param: lpred, length of prediction window (=end of summation index)
+        :type: int
+
+        Output: predicted waveform z
+        :type: structured array
+        '''
+        # be sure of the summation indeces
+        if rind < len(arpara) + 1:
+            rind = len(arpara) + 1
+        if rind > len(data[0]) - lpred + 1:
+            rind = len(data[0]) - lpred + 1
+        if lpred < 1:
+            lpred = 1
+        if lpred > len(data[0]) - 1:
+            lpred = len(data[0]) - 1
+
+        z1 = np.append(data[0][0:rind], np.zeros(lpred))
+        z2 = np.append(data[1][0:rind], np.zeros(lpred))
+        z3 = np.append(data[2][0:rind], np.zeros(lpred))
+        for i in range(rind, rind + lpred):
+            for j in range(1, len(arpara) + 1):
+                ji = j - 1
+                z1[i] = z1[i] + arpara[ji] * z1[i - ji]
+                z2[i] = z2[i] + arpara[ji] * z2[i - ji]
+                z3[i] = z3[i] + arpara[ji] * z3[i - ji]
+
+        z = np.array([z1.tolist(), z2.tolist(), z3.tolist()])
+        self.xpred = z

pylot/core/pick/compare.py

@@ -0,0 +1,515 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import copy
+import operator
+import os
+
+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
+from pylot.core.util.version import get_git_version as _getVersionString
+
+__version__ = _getVersionString()
+__author__ = 'sebastianw'
+
+
+class Comparison(object):
+    """
+    A Comparison object contains information on the evaluated picks' probability
+    density function and compares these in terms of building the difference of
+    compared pick sets. The results can be displayed as histograms showing its
+    properties.
+    """
+
+    def __init__(self, **kwargs):
+        self._pdfs = dict()
+        names = self.iter_kwargs(kwargs)
+        if len(names) > 2:
+            raise ValueError('Comparison is only defined for two '
+                             'arguments!')
+        self._names = names
+        self._compare = self.compare_picksets()
+
+    def __nonzero__(self):
+        if not len(self.names) == 2 or not self._pdfs:
+            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]
+
+    @property
+    def names(self):
+        return self._names
+
+    @names.setter
+    def names(self, names):
+        assert isinstance(names, list) and len(names) == 2, 'variable "names"' \
+                                                            ' is either not a' \
+                                                            ' list or its ' \
+                                                            'length is not 2:' \
+                                                            'names : {names}'.format(
+            names=names)
+        self._names = names
+
+    @property
+    def comparison(self):
+        return self._compare
+
+    @property
+    def stations(self):
+        return self.comparison.keys()
+
+    @property
+    def nstations(self):
+        return len(self.stations)
+
+    def compare_picksets(self, type='exp'):
+        """
+        Compare two picksets A and B and return a dictionary compiling the results.
+        Comparison is carried out with the help of pdf representation of the picks
+        and a probabilistic approach to the time difference of two onset
+        measurements.
+        :param a: filename for pickset A
+        :type a: str
+        :param b: filename for pickset B
+        :type b: str
+        :return: dictionary containing the resulting comparison pdfs for all picks
+        :rtype: dict
+        """
+        compare_pdfs = dict()
+
+        pdf_a = self.get('auto').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():
+                compare_pdf = dict()
+                for phase in phases:
+                    if phase in pdf_b[station].keys():
+                        compare_pdf[phase] = phases[phase] - pdf_b[station][
+                            phase]
+                if compare_pdf is not None:
+                    compare_pdfs[station] = compare_pdf
+
+        return compare_pdfs
+
+    def plot(self, stations=None):
+        if stations is None:
+            nstations = self.nstations
+            stations = self.stations
+        else:
+            nstations = len(stations)
+        istations = range(nstations)
+        fig, axarr = plt.subplots(nstations, 2, sharex='col', sharey='row')
+
+        for n in istations:
+            station = stations[n]
+            if station not in self.comparison.keys():
+                continue
+            compare_pdf = self.comparison[station]
+            for l, phase in enumerate(compare_pdf.keys()):
+                axarr[n, l].plot(compare_pdf[phase].axis,
+                                 compare_pdf[phase].data)
+                if n is 0:
+                    axarr[n, l].set_title(phase)
+                if l is 0:
+                    axann = axarr[n, l].annotate(station, xy=(.05, .5),
+                                                 xycoords='axes fraction')
+                    bbox_props = dict(boxstyle='round', facecolor='lightgrey',
+                                      alpha=.7)
+                    axann.set_bbox(bbox_props)
+                if n == int(np.median(istations)) and l is 0:
+                    label = 'probability density (qualitative)'
+                    axarr[n, l].set_ylabel(label)
+        plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False)
+        plt.setp([a.get_yticklabels() for a in axarr[:, 1]], visible=False)
+        plt.setp([a.get_yticklabels() for a in axarr[:, 0]], visible=False)
+
+        plt.show()
+
+    def get_all(self, phasename):
+        pdf_dict = self.comparison
+        rlist = list()
+        for phases in pdf_dict.values():
+            try:
+                rlist.append(phases[phasename])
+            except KeyError:
+                continue
+        return rlist
+
+    def get_array(self, phase, method_name):
+        method = operator.methodcaller(method_name)
+        pdf_list = self.get_all(phase)
+        rarray = list(map(method, pdf_list))
+        return np.array(rarray)
+
+    def get_expectation_array(self, phase):
+        return self.get_array(phase, 'expectation')
+
+    def get_std_array(self, phase):
+        return self.get_array(phase, 'standard_deviation')
+
+    def hist_expectation(self, phases='all', bins=20, normed=False):
+        phases.strip()
+        if phases.find('all') is 0:
+            phases = 'ps'
+        phases = phases.upper()
+        nsp = len(phases)
+        fig, axarray = plt.subplots(1, nsp, sharey=True)
+        for n, phase in enumerate(phases):
+            ax = axarray[n]
+            data = self.get_expectation_array(phase)
+            xlims = [min(data), max(data)]
+            ax.hist(data, range=xlims, bins=bins, normed=normed)
+            title_str = 'phase: {0}, samples: {1}'.format(phase, len(data))
+            ax.set_title(title_str)
+            ax.set_xlabel('expectation [s]')
+            if n is 0:
+                ax.set_ylabel('abundance [-]')
+        plt.setp([a.get_yticklabels() for a in axarray[1:]], visible=False)
+        plt.show()
+
+    def hist_standard_deviation(self, phases='all', bins=20, normed=False):
+        phases.strip()
+        if phases.find('all') == 0:
+            phases = 'ps'
+        phases = phases.upper()
+        nsp = len(phases)
+        fig, axarray = plt.subplots(1, nsp, sharey=True)
+        for n, phase in enumerate(phases):
+            ax = axarray[n]
+            data = self.get_std_array(phase)
+            xlims = [min(data), max(data)]
+            ax.hist(data, range=xlims, bins=bins, normed=normed)
+            title_str = 'phase: {0}, samples: {1}'.format(phase, len(data))
+            ax.set_title(title_str)
+            ax.set_xlabel('standard deviation [s]')
+            if n is 0:
+                ax.set_ylabel('abundance [-]')
+        plt.setp([a.get_yticklabels() for a in axarray[1:]], visible=False)
+        plt.show()
+
+    def hist(self, type='std'):
+        pass
+
+
+class PDFDictionary(object):
+    """
+    A PDFDictionary is a dictionary like object containing structured data on
+    the probability density function of seismic phase onsets.
+    """
+
+    def __init__(self, data):
+        self._pickdata = data
+        self._pdfdata = self.generate_pdf_data()
+
+    def __nonzero__(self):
+        if len(self.pick_data) < 1:
+            return False
+        else:
+            return True
+
+    def __getitem__(self, item):
+        return self.pdf_data[item]
+
+    @property
+    def pdf_data(self):
+        return self._pdfdata
+
+    @pdf_data.setter
+    def pdf_data(self, data):
+        self._pdfdata = data
+
+    @property
+    def pick_data(self):
+        return self._pickdata
+
+    @pick_data.setter
+    def pick_data(self, data):
+        self._pickdata = data
+
+    @property
+    def stations(self):
+        return self.pick_data.keys()
+
+    @property
+    def nstations(self):
+        return len(self.stations)
+
+    @classmethod
+    def from_quakeml(self, fn):
+        return PDFDictionary(fn)
+
+    def get_all(self, phase):
+        rlist = list()
+        for phases in self.pdf_data.values():
+            try:
+                rlist.append(phases[phase])
+            except KeyError:
+                continue
+        return rlist
+
+    def generate_pdf_data(self, type='exp'):
+        """
+        Returns probabiliy density function dictionary containing the
+        representation of the actual pick_data.
+        :param type: type of the returned
+         `~pylot.core.util.pdf.ProbabilityDensityFunction` object
+        :type type: str
+        :return: a dictionary containing the picks represented as pdfs
+        """
+
+        pdf_picks = copy.deepcopy(self.pick_data)
+
+        for station, phases in pdf_picks.items():
+            for phase, values in phases.items():
+                if phase not in 'PS':
+                    continue
+                phases[phase] = ProbabilityDensityFunction.from_pick(
+                    values['epp'],
+                    values['mpp'],
+                    values['lpp'],
+                    type=type)
+        return pdf_picks
+
+    def plot(self, stations=None):
+        '''
+        plots the all probability density function for either desired STATIONS
+        or all available date
+        :param stations: list of stations to be plotted
+        :type stations: list
+        :return: matplotlib figure object containing the plot
+        '''
+        assert stations is not None or not isinstance(stations, list), \
+            'parameter stations should be a list not {0}'.format(type(stations))
+        if not stations:
+            nstations = self.nstations
+            stations = self.stations
+        else:
+            nstations = len(stations)
+
+        istations = range(nstations)
+        fig, axarr = plt.subplots(nstations, 2, sharex='col', sharey='row')
+        hide_labels = True
+
+        for n in istations:
+            station = stations[n]
+            pdfs = self.pdf_data[station]
+            for l, phase in enumerate(pdfs.keys()):
+                try:
+                    axarr[n, l].plot(pdfs[phase].axis, pdfs[phase].data())
+                    if n is 0:
+                        axarr[n, l].set_title(phase)
+                    if l is 0:
+                        axann = axarr[n, l].annotate(station, xy=(.05, .5),
+                                                     xycoords='axes fraction')
+                        bbox_props = dict(boxstyle='round', facecolor='lightgrey',
+                                          alpha=.7)
+                        axann.set_bbox(bbox_props)
+                    if n == int(np.median(istations)) and l is 0:
+                        label = 'probability density (qualitative)'
+                        axarr[n, l].set_ylabel(label)
+                except IndexError as e:
+                    print('trying aligned plotting\n{0}'.format(e))
+                    hide_labels = False
+                    axarr[l].plot(pdfs[phase].axis, pdfs[phase].data())
+                    axarr[l].set_title(phase)
+                    if l is 0:
+                        axann = axarr[l].annotate(station, xy=(.05, .5),
+                                                  xycoords='axes fraction')
+                        bbox_props = dict(boxstyle='round', facecolor='lightgrey',
+                                          alpha=.7)
+                        axann.set_bbox(bbox_props)
+        if hide_labels:
+            plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False)
+            plt.setp([a.get_yticklabels() for a in axarr[:, 1]], visible=False)
+            plt.setp([a.get_yticklabels() for a in axarr[:, 0]], visible=False)
+
+        return fig
+
+
+class PDFstatistics(object):
+    """
+    This object can be used to get various statistic values from probabillity density functions.
+    Takes a path as argument.
+    """
+
+    def __init__(self, directory):
+        """Initiates some values needed when dealing with pdfs later"""
+        self._rootdir = directory
+        self._evtlist = list()
+        self._rphase = None
+        self.make_fnlist()
+
+    def make_fnlist(self, fn_pattern='*.xml'):
+        """
+        Takes a file pattern and searches for that recursively in the set path for the object.
+        :param fn_pattern: A pattern that can identify all datafiles. Default Value = '*.xml'
+        :type  fn_pattern: string
+        :return: creates a list of events saved in the PDFstatistics object.
+        """
+        evtlist = list()
+        for root, _, files in os.walk(self.root):
+            for file in files:
+                if file.endswith(fn_pattern[1:]):
+                    evtlist.append(os.path.join(root, file))
+        self._evtlist = evtlist
+
+    def __iter__(self):
+        for evt in self._evtlist:
+            yield PDFDictionary.from_quakeml(evt)
+
+    def __getitem__(self, item):
+        evt = find_in_list(self._evtlist, item)
+        if evt:
+            return PDFDictionary.from_quakeml(evt)
+        return None
+
+    @property
+    def root(self):
+        return self._rootdir
+
+    @root.setter
+    def root(self, value):
+        if os.path.exists(value):
+            self._rootdir = value
+        else:
+            raise ValueError("path doesn't exist: %s" % value)
+
+    @property
+    def curphase(self):
+        """
+        return the current phase type of interest
+        :return: current phase
+        """
+        return self._rphase
+
+    @curphase.setter
+    def curphase(self, type):
+        """
+        setter method for property curphase
+        :param type: specify the phase type of interest
+        :type  type: string ('p' or 's')
+        :return: -
+        """
+        if type.upper() not in 'PS':
+            raise ValueError("phase type must be either 'P' or 'S'!")
+        else:
+            self._rphase = type.upper()
+
+    def get(self, property='std', value=None):
+        """
+        takes a property str and a probability value and returns all
+        property's values for the current phase of interest
+        :func:`self.curphase`
+
+        :param property: property name (default: 'std')
+        :type property: str
+        :param value: probability value :math:\alpha
+        :type  value: float
+        :return: list containing all property's values
+        """
+        assert isinstance(self.curphase,
+                          str), 'phase has to be set before being ' \
+                                'able to iterate over items...'
+        rlist = []
+        method_options = dict(STD='standard_deviation',
+                              Q='quantile',
+                              QD='quantile_distance',
+                              QDF='quantile_dist_frac')
+
+        # create method caller for easy mapping
+        if property.upper() == 'STD':
+            method = operator.methodcaller(method_options[property.upper()])
+        elif value is not None:
+            try:
+                method = operator.methodcaller(method_options[property.upper()],
+                                               value)
+            except KeyError:
+                raise KeyError('unknwon property: {0}'.format(property.upper()))
+        else:
+            raise ValueError("for call to method {0} value has to be "
+                             "defined but is 'None' ".format(method_options[
+                                                                 property.upper()]))
+
+        for pdf_dict in self:
+            # create worklist
+            wlist = pdf_dict.get_all(self.curphase)
+            # map method calls to object in worklist
+            rlist += map(method, wlist)
+
+        return rlist
+
+    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.
+        :param array: List of values.
+        :type  array: list
+        :param out_dir: Path to save file to including file name.
+        :type  out_dir: str
+        :return: Saves a file at given output directory.
+        """
+        fid = open(os.path.join(out_dir), 'w')
+        for val in array:
+            fid.write(str(val) + '\n')
+        fid.close()
+
+
+def main():
+    root_dir = '/home/sebastianp/Codetesting/xmls/'
+    Insheim = PDFstatistics(root_dir)
+    Insheim.curphase = 'p'
+    qdlist = Insheim.get('qdf', 0.2)
+    print(qdlist)
+
+
+if __name__ == "__main__":
+    import cProfile
+
+    pr = cProfile.Profile()
+    pr.enable()
+    main()
+    pr.disable()
+    # after your program ends
+    pr.print_stats(sort="calls")

pylot/core/pick/picker.py

@@ -0,0 +1,502 @@
+# -*- coding: utf-8 -*-
+"""
+Created Dec 2014 to Feb 2015
+Implementation of the automated picking algorithms published and described in:
+
+Kueperkoch, L., Meier, T., Lee, J., Friederich, W., & Egelados Working Group, 2010:
+Automated determination of P-phase arrival times at regional and local distances
+using higher order statistics, Geophys. J. Int., 181, 1159-1170
+
+Kueperkoch, L., Meier, T., Bruestle, A., Lee, J., Friederich, W., & Egelados
+Working Group, 2012: Automated determination of S-phase arrival times using
+autoregressive prediction: application ot local and regional distances, Geophys. J. Int.,
+188, 687-702.
+
+The picks with the above described algorithms are assumed to be the most likely picks.
+For each most likely pick the corresponding earliest and latest possible picks are
+calculated after Diehl & Kissling (2009).
+
+:author: MAGS2 EP3 working group / Ludger Kueperkoch
+"""
+
+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):
+    '''
+    Superclass of different, automated picking algorithms applied on a CF determined
+    using AIC, HOS, or AR prediction.
+    '''
+
+    warnings.simplefilter('ignore')
+
+    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
+
+        :param: TSNR, length of time windows around pick used to determine SNR [s]
+        :type: tuple (T_noise, T_gap, T_signal)
+
+        :param: PickWindow, length of pick window [s]
+        :type: float
+
+        :param: iplot, no. of figure window for plotting interims results
+        :type: integer
+
+        :param: aus ("artificial uplift of samples"), find local minimum at i if aic(i-1)*(1+aus) >= aic(i)
+        :type: float
+
+        :param: Tsmooth, length of moving smoothing window to calculate smoothed CF [s]
+        :type: float
+
+        :param: Pick1, initial (prelimenary) onset time, starting point for PragPicker and
+         EarlLatePicker
+        :type: float
+
+        '''
+
+        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()
+        self.dt = cf.getIncrement()
+        self.setTSNR(TSNR)
+        self.setPickWindow(PickWindow)
+        self.setiplot(iplot)
+        self.setaus(aus)
+        self.setTsmooth(Tsmooth)
+        self.setpick1(Pick1)
+        self.fig = fig
+        self.calcPick()
+
+    def __str__(self):
+        return '''\n\t{name} object:\n
+        TSNR:\t\t\t{TSNR}\n
+        PickWindow:\t{PickWindow}\n
+        aus:\t{aus}\n
+        Tsmooth:\t{Tsmooth}\n
+        Pick1:\t{Pick1}\n
+        '''.format(name=type(self).__name__,
+                   TSNR=self.getTSNR(),
+                   PickWindow=self.getPickWindow(),
+                   aus=self.getaus(),
+                   Tsmooth=self.getTsmooth(),
+                   Pick1=self.getpick1())
+
+    def getTSNR(self):
+        return self.TSNR
+
+    def setTSNR(self, TSNR):
+        self.TSNR = TSNR
+
+    def getPickWindow(self):
+        return self.PickWindow
+
+    def setPickWindow(self, PickWindow):
+        self.PickWindow = PickWindow
+
+    def getaus(self):
+        return self.aus
+
+    def setaus(self, aus):
+        self.aus = aus
+
+    def setTsmooth(self, Tsmooth):
+        self.Tsmooth = Tsmooth
+
+    def getTsmooth(self):
+        return self.Tsmooth
+
+    def getpick(self):
+        return self.Pick
+
+    def getSNR(self):
+        return self.SNR
+
+    def getSlope(self):
+        return self.slope
+
+    def getiplot(self):
+        return self.iplot
+
+    def setiplot(self, iplot):
+        self.iplot = iplot
+
+    def getpick1(self):
+        return self.Pick1
+
+    def setpick1(self, Pick1):
+        self.Pick1 = Pick1
+
+    def calcPick(self):
+        self.Pick = None
+
+
+class AICPicker(AutoPicker):
+    '''
+    Method to derive the onset time of an arriving phase based on CF
+    derived from AIC. In order to get an impression of the quality of this inital pick,
+    a quality assessment is applied based on SNR and slope determination derived from the CF,
+    from which the AIC has been calculated.
+    '''
+
+    def calcPick(self):
+
+        print('AICPicker: Get initial onset time (pick) from AIC-CF ...')
+
+        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:
+            self.cf[nn] = 0
+        # taper AIC-CF to get rid off side maxima
+        tap = np.hanning(len(self.cf))
+        aic = tap * self.cf + max(abs(self.cf))
+        # smooth AIC-CF
+        ismooth = int(round(self.Tsmooth / self.dt))
+        aicsmooth = np.zeros(len(aic))
+        if len(aic) < ismooth:
+            print('AICPicker: Tsmooth larger than CF!')
+            return
+        else:
+            for i in range(1, len(aic)):
+                if i > ismooth:
+                    ii1 = i - ismooth
+                    aicsmooth[i] = aicsmooth[i - 1] + (aic[i] - aic[ii1]) / ismooth
+                else:
+                    aicsmooth[i] = np.mean(aic[1: i])
+        # remove offset in AIC function
+        offset = abs(min(aic) - min(aicsmooth))
+        aicsmooth = aicsmooth - offset
+        # get maximum of HOS/AR-CF as startimg point for searching
+        # minimum in AIC function 
+        icfmax = np.argmax(self.Data[0].data)
+
+        # find minimum in AIC-CF front of maximum of HOS/AR-CF
+        lpickwindow = int(round(self.PickWindow / self.dt))
+        for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
+            if aicsmooth[i - 1] >= aicsmooth[i]:
+                self.Pick = self.Tcf[i]
+                break
+        # if no minimum could be found:
+        # search in 1st derivative of AIC-CF
+        if self.Pick is None:
+            diffcf = np.diff(aicsmooth)
+            # find NaN's
+            nn = np.isnan(diffcf)
+            if len(nn) > 1:
+                diffcf[nn] = 0
+            # taper CF to get rid off side maxima
+            tap = np.hanning(len(diffcf))
+            diffcf = tap * diffcf * max(abs(aicsmooth))
+            for i in range(icfmax - 1, max([icfmax - lpickwindow, 2]), -1):
+                if diffcf[i - 1] >= diffcf[i]:
+                    self.Pick = self.Tcf[i]
+                    break
+
+        # quality assessment using SNR and slope from CF
+        if self.Pick is not None:
+            # get noise window
+            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) and max(self.Data[0].data >= 1e-6):
+                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])
+            if len(isignal) == 0:
+                return
+            ii = min([isignal[len(isignal) - 1], len(self.Tcf)])
+            isignal = isignal[0:ii]
+            try:
+                self.Data[0].data[isignal]
+            except IndexError as e:
+                msg = "Time series out of bounds! {}".format(e)
+                print(msg)
+                return
+            # calculate SNR from CF
+            self.SNR = max(abs(self.Data[0].data[isignal] - np.mean(self.Data[0].data[isignal]))) / \
+                       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, self.Tcf[-1]])) \
+                              & (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!
+            try:
+                dataslope = self.Data[0].data[islope[0][0:-1]]
+            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[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 self.fig == None or self.fig == 'None':
+                            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), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
+                        ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
+                        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+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[-1]:
+                print('AICPicker: Negative slope, bad onset skipped!')
+                return
+            self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
+
+        else:
+            self.SNR = None
+            self.slope = None
+
+        if iplot > 1:
+            if self.fig == None or self.fig == 'None':
+                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
+            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(loc=1)
+
+            if self.Pick is not None:
+                ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
+                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[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
+                            label='Signal Window')
+                ax1.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))
+                ax2.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
+                ax2.set_ylabel('Counts')
+                ax2.set_yticks([])
+                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
+
+
+class PragPicker(AutoPicker):
+    '''
+    Method of pragmatic picking exploiting information given by CF.
+    '''
+
+    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 ...')
+
+            self.Pick = None
+            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))
+            if len(self.cf) < ismooth:
+                print('PragPicker: Tsmooth larger than CF!')
+                return
+            else:
+                for i in range(1, len(self.cf)):
+                    if i > ismooth:
+                        ii1 = i - ismooth
+                        cfsmooth[i] = cfsmooth[i - 1] + (self.cf[i] - self.cf[ii1]) / ismooth
+                    else:
+                        cfsmooth[i] = np.mean(self.cf[1: i])
+
+            # select picking window
+            # which is centered around tpick1
+            ipick = np.where((self.Tcf >= self.getpick1() - self.PickWindow / 2) \
+                             & (self.Tcf <= self.getpick1() + self.PickWindow / 2))
+            cfipick = self.cf[ipick] - np.mean(self.cf[ipick])
+            Tcfpick = self.Tcf[ipick]
+            cfsmoothipick = cfsmooth[ipick] - np.mean(self.cf[ipick])
+            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 ("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])
+
+            # at first we look to the right until the end of the pick window is reached
+            flagpick_r = 0
+            flagpick_l = 0
+            cfpick_r = 0
+            cfpick_l = 0
+            lpickwindow = int(round(self.PickWindow / self.dt))
+            for i in range(max(np.insert(ipick, 0, 2)), min([ipick1 + lpickwindow + 1, len(self.cf) - 1])):
+                if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]:
+                    if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
+                        if cfpick1 >= self.cf[i]:
+                            pick_r = self.Tcf[i]
+                            self.Pick = pick_r
+                            flagpick_l = 1
+                            cfpick_r = self.cf[i]
+                            break
+
+            # now we look to the left
+            if len(self.cf) > ipick1 +1:
+                for i in range(ipick1, max([ipick1 - lpickwindow + 1, 2]), -1):
+                    if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]:
+                        if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
+                            if cfpick1 >= self.cf[i]:
+                                pick_l = self.Tcf[i]
+                                self.Pick = pick_l
+                                flagpick_r = 1
+                                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:
+                self.Pick = pick_l
+                pickflag = 1
+            elif flagpick_l > 0 and flagpick_r > 0 and cfpick_l >= cfpick_r:
+                self.Pick = pick_r
+                pickflag = 1
+            elif flagpick_l == 0 and flagpick_r > 0 and cfpick_l >= cfpick_r:
+                self.Pick = pick_l
+                pickflag = 1
+            else:
+                print("PragPicker: Could not find reliable onset!")
+                self.Pick = None
+                pickflag = 0
+
+            if iplot > 1:
+                if self.fig == None or self.fig == 'None':
+                    fig = plt.figure()  # self.getiplot())
+                    plt_flag = 1
+                else:
+                    fig = self.fig
+                fig._tight = True
+                ax = fig.add_subplot(111)
+                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)], 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(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!")
+            self.Pick = None
+            return

pylot/core/util/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+from pylot.core.util.version import get_git_version as _getVersionString

pylot/core/util/connection.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+    from urllib2 import urlopen
+except:
+    from urllib.request import urlopen
+
+
+def checkurl(url='https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/'):
+    try:
+        urlopen(url, timeout=1)
+        return True
+    except:
+        pass
+    return False

pylot/core/util/dataprocessing.py

@@ -0,0 +1,353 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import glob
+import os
+import sys
+
+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, \
+    remove_underscores, gen_Pool
+
+
+def time_from_header(header):
+    """
+    Function takes in the second line from a .gse file and takes out the date and time from that line.
+    :param header: second line from .gse file
+    :type header: string
+    :return: a list of integers of form [year, month, day, hour, minute, second, microsecond]
+    """
+    timeline = header.split(' ')
+    time = timeline[1].split('/') + timeline[2].split(':')
+    time = time[:-1] + time[-1].split('.')
+    return [int(t) for t in time]
+
+
+def check_time(datetime):
+    """
+    Function takes in date and time as list and validates it's values by trying to make an UTCDateTime object from it
+    :param datetime: list of integers [year, month, day, hour, minute, second, microsecond]
+    :type datetime: list
+    :return: returns True if Values are in supposed range, returns False otherwise
+
+    >>> check_time([1999, 01, 01, 23, 59, 59, 999000])
+    True
+    >>> check_time([1999, 01, 01, 23, 59, 60, 999000])
+    False
+    >>> check_time([1999, 01, 01, 23, 59, 59, 1000000])
+    False
+    >>> check_time([1999, 01, 01, 23, 60, 59, 999000])
+    False
+    >>> check_time([1999, 01, 01, 23, 60, 59, 999000])
+    False
+    >>> check_time([1999, 01, 01, 24, 59, 59, 999000])
+    False
+    >>> check_time([1999, 01, 31, 23, 59, 59, 999000])
+    True
+    >>> check_time([1999, 02, 30, 23, 59, 59, 999000])
+    False
+    >>> check_time([1999, 02, 29, 23, 59, 59, 999000])
+    False
+    >>> check_time([2000, 02, 29, 23, 59, 59, 999000])
+    True
+    >>> check_time([2000, 13, 29, 23, 59, 59, 999000])
+    False
+    """
+    try:
+        UTCDateTime(*datetime)
+        return True
+    except ValueError:
+        return False
+
+
+def get_file_list(root_dir):
+    """
+    Function uses a directorie to get all the *.gse files from it.
+    :param root_dir: a directorie leading to the .gse files
+    :type root_dir: string
+    :return: returns a list of filenames (without path to them)
+    """
+    file_list = glob.glob1(root_dir, '*.gse')
+    return file_list
+
+
+def checks_station_second(datetime, file):
+    """
+    Function uses the given list to check if the parameter 'second' is set to 60 by mistake
+     and sets the time correctly if so. Can only correct time if no date change would be necessary.
+    :param datetime: [year, month, day, hour, minute, second, microsecond]
+    :return: returns the input with the correct value for second
+    """
+    if datetime[5] == 60:
+        if datetime[4] == 59:
+            if datetime[3] == 23:
+                err_msg = 'Date should be next day. ' \
+                          'File not changed: {0}'.format(file)
+                raise ValueError(err_msg)
+            else:
+                datetime[3] += 1
+                datetime[4] = 0
+                datetime[5] = 0
+        else:
+            datetime[4] += 1
+            datetime[5] = 0
+    return datetime
+
+
+def make_time_line(line, datetime):
+    """
+    Function takes in the original line from a .gse file and a list of date and
+    time values to make a new line with corrected date and time.
+    :param line: second line from .gse file.
+    :type line: string
+    :param datetime: list of integers [year, month, day, hour, minute, second, microsecond]
+    :type datetime: list
+    :return: returns a string to write it into a file.
+    """
+    ins_form = '{0:02d}:{1:02d}:{2:02d}.{3:03d}'
+    insertion = ins_form.format(int(datetime[3]),
+                                int(datetime[4]),
+                                int(datetime[5]),
+                                int(datetime[6] * 1e-3))
+    newline = line[:16] + insertion + line[28:]
+    return newline
+
+
+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.
+    :type root_dir: string
+    :param out_dir: a directory to store the new files somwhere els.
+    :return: returns nothing
+    """
+    if not out_dir:
+        print('WARNING files are going to be overwritten!')
+        inp = str(raw_input('Continue? [y/N]'))
+        if not inp == 'y':
+            sys.exit()
+    filelist = get_file_list(root_dir)
+    nfiles = 0
+    for file in filelist:
+        infile = open(os.path.join(root_dir, file), 'r')
+        lines = infile.readlines()
+        infile.close()
+        datetime = time_from_header(lines[1])
+        if check_time(datetime):
+            continue
+        else:
+            nfiles += 1
+            datetime = checks_station_second(datetime, file)
+            print('writing ' + file)
+            # write File
+            lines[1] = make_time_line(lines[1], datetime)
+            if not out_dir:
+                out = open(os.path.join(root_dir, file), 'w')
+                out.writelines(lines)
+                out.close()
+            else:
+                out = open(os.path.join(out_dir, file), 'w')
+                out.writelines(lines)
+                out.close()
+    print(nfiles)
+
+
+def read_metadata(path_to_inventory):
+    """
+    take path_to_inventory and return either the corresponding list of files
+    found or the Parser object for a network dataless seed volume to prevent
+    read overhead for large dataless seed volumes
+    :param path_to_inventory:
+    :return: tuple containing a either list of files or `obspy.io.xseed.Parser`
+    object and the inventory type found
+    :rtype: tuple
+    """
+    dlfile = list()
+    invfile = list()
+    respfile = list()
+    # possible file extensions specified here:
+    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]
+    else:
+        for ext in inv.keys():
+            inv[ext] += glob.glob1(path_to_inventory, '*.{0}'.format(ext))
+
+    invtype = key_for_set_value(inv)
+
+    if invtype is None:
+        print("Neither dataless-SEED file, inventory-xml file nor "
+              "RESP-file found!")
+        print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
+        robj = None,
+    elif invtype == 'dless':  # prevent multiple read of large dlsv
+        print("Reading metadata information from dataless-SEED file ...")
+        if len(inv[invtype]) == 1:
+            fullpath_inv = os.path.join(path_to_inventory, inv[invtype][0])
+            robj = Parser(fullpath_inv)
+        else:
+            robj = inv[invtype]
+    else:
+        print("Reading metadata information from inventory-xml file ...")
+        robj = inv[invtype]
+    return invtype, robj
+
+
+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() \
+            and np.any(['remove' in p for p in tr.stats.processing]) \
+            and not force:
+        print("Trace {0} has already been corrected!".format(seed_id))
+        return tr, False
+    stime = tr.stats.starttime
+    prefilt = get_prefilt(tr)
+    if invtype == 'resp':
+        fresp = find_in_list(inobj, seed_id)
+        if not fresp:
+            raise IOError('no response file found '
+                          'for trace {0}'.format(seed_id))
+        fname = fresp
+        seedresp = dict(filename=fname,
+                        date=stime,
+                        units=unit)
+        kwargs = dict(paz_remove=None, pre_filt=prefilt, seedresp=seedresp)
+    elif invtype == 'dless':
+        if type(inobj) is list:
+            fname = Parser(find_in_list(inobj, seed_id))
+        else:
+            fname = inobj
+        seedresp = dict(filename=fname,
+                        date=stime,
+                        units=unit)
+        kwargs = dict(pre_filt=prefilt, seedresp=seedresp)
+    elif invtype == 'xml':
+        invlist = inobj
+        if len(invlist) > 1:
+            finv = find_in_list(invlist, seed_id)
+        else:
+            finv = invlist[0]
+        inventory = read_inventory(finv, format='STATIONXML')
+    elif invtype == None:
+        print("No restitution possible, as there are no station-meta data available!")
+        return tr, True
+    else:
+        remove_trace = True
+    # apply restitution to data
+    print("Correcting instrument at station %s, channel %s" \
+          % (tr.stats.station, tr.stats.channel))
+    try:
+        if invtype in ['resp', 'dless']:
+            try:
+                tr.simulate(**kwargs)
+            except ValueError as e:
+                vmsg = '{0}'.format(e)
+                print(vmsg)
+
+        else:
+            tr.attach_response(inventory)
+            tr.remove_response(output=unit,
+                               pre_filt=prefilt)
+    except ValueError as e:
+        msg0 = 'Response for {0} not found in Parser'.format(seed_id)
+        msg1 = 'evalresp failed to calculate response'
+        if msg0 not in e.message or msg1 not in e.message:
+            raise
+        else:
+            # restitution done to copies of data thus deleting traces
+            # that failed should not be a problem
+            remove_trace = True
+
+    return tr, remove_trace
+
+
+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
+    :param data: seismic data stream
+    :param invtype: type of found metadata
+    :param inobj: either list of metadata files or `obspy.io.xseed.Parser`
+    object
+    :param unit: unit to correct for (default: 'VEL')
+    :param force: force restitution for already corrected traces (default:
+    False)
+    :return: corrected data stream
+    """
+
+    restflag = list()
+
+    data = remove_underscores(data)
+
+    # loop over traces
+    input_tuples = []
+    for tr in data:
+        input_tuples.append((tr, invtype, inobj, unit, force))
+        data.remove(tr)
+
+    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)
+
+    # if len(restflag) > 0:
+    #     restflag = bool(np.all(restflag))
+    # else:
+    #     restflag = False
+    return data
+
+
+def get_prefilt(trace, tlow=(0.5, 0.9), thi=(5., 2.), verbosity=0):
+    """
+    takes a `obspy.core.stream.Trace` object, taper parameters tlow and thi and
+    returns the pre-filtering corner frequencies for the cosine taper for
+    further processing
+    :param trace: seismic data trace
+    :type trace: `obspy.core.stream.Trace`
+    :param tlow: tuple or list containing the desired lower corner
+    frequenices for a cosine taper
+    :type tlow: tuple or list
+    :param thi: tuple or list containing the percentage values of the
+    Nyquist frequency for the desired upper corner frequencies of the cosine
+    taper
+    :type thi: tuple or list
+    :param verbosity: verbosity level
+    :type verbosity: int
+    :return: pre-filt cosine taper corner frequencies
+    :rtype: tuple
+
+    ..example::
+
+    >>> st = read()
+    >>> get_prefilt(st[0])
+    (0.5, 0.9, 47.5, 49.0)
+    """
+    if verbosity:
+        print("Calculating pre-filter values for %s, %s ..." % (
+            trace.stats.station, trace.stats.channel))
+    # get corner frequencies for pre-filtering
+    fny = trace.stats.sampling_rate / 2
+    fc21 = fny - (fny * thi[0] / 100.)
+    fc22 = fny - (fny * thi[1] / 100.)
+    return (tlow[0], tlow[1], fc21, fc22)
+
+
+if __name__ == "__main__":
+    import doctest
+
+    doctest.testmod()

pylot/core/util/defaults.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Feb 26 12:31:25 2014
+
+@author: sebastianw
+"""
+
+import os
+import platform
+
+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
+
+
+# determine system dependent path separator
+system_name = platform.system()
+if system_name in ["Linux", "Darwin"]:
+    SEPARATOR = '/'
+elif system_name == "Windows":
+    SEPARATOR = '\\'
+
+# suffix for phase name if not phase identified by last letter (P, p, etc.)
+ALTSUFFIX = ['diff', 'n', 'g', '1', '2', '3']
+
+FILTERDEFAULTS = readDefaultFilterInformation(os.path.join(os.path.expanduser('~'),
+                                                           '.pylot',
+                                                           'pylot.in'))
+
+TIMEERROR_DEFAULTS = os.path.join(os.path.expanduser('~'),
+                                  '.pylot',
+                                  'PILOT_TimeErrors.in')
+
+OUTPUTFORMATS = {'.xml': 'QUAKEML',
+                 '.cnv': 'CNV',
+                 '.obs': 'NLLOC_OBS'}
+
+LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=hypodd)
+
+
+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:
+                return key, value
+        errMsg = 'getCurrentPosition: Could not find former position of component {}.'.format(component)
+        raise ValueError(errMsg)
+
+    def _switch(self, component, component_alter):
+        # Without switching, multiple definitions of the same alter_comp are possible
+        old_alter_comp, _ = self._getCurrentPosition(component)
+        old_comp = self.compName_Map[component_alter]
+        if not old_alter_comp == component_alter and not old_comp == component:
+            self.compName_Map[old_alter_comp] = old_comp
+            print('switch: Automatically switched component {} to {}'.format(old_alter_comp, old_comp))
+
+    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 {}.'
+            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 {}.'
+            raise ValueError(errMsg.format(component, self.compPosition_Map.keys()))
+        print('setCompPosition: set component {} to {}'.format(component_alter, component))
+        if switch:
+            self._switch(component, component_alter)
+        self.compName_Map[component_alter] = component
+
+    def getCompPosition(self, component):
+        return self._getCurrentPosition(component)[0]
+
+    def getPlotPosition(self, component):
+        component = str(component)
+        if component in self.compPosition_Map.keys():
+            return self.compPosition_Map[component]
+        elif component in self.compName_Map.keys():
+            return self.compPosition_Map[self.compName_Map[component]]
+        else:
+            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

@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Mar 20 09:47:04 2014
+
+@author: sebastianw
+"""
+
+
+class OptionsError(Exception):
+    pass
+
+
+class FormatError(Exception):
+    pass
+
+
+class DatastructureError(Exception):
+    pass
+
+
+class OverwriteError(IOError):
+    pass
+
+
+class ParameterError(Exception):
+    pass
+
+
+class ProcessingError(RuntimeError):
+    pass

pylot/core/util/event.py

@@ -0,0 +1,172 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+
+from obspy import UTCDateTime
+from obspy.core.event import Event as ObsPyEvent
+from obspy.core.event import Origin, ResourceIdentifier
+from pylot.core.io.phases import picks_from_picksdict
+
+
+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))
+        self.path = path
+        self.database = path.split('/')[-2]
+        self.datapath = path.split('/')[-3]
+        self.rootpath = '/' + os.path.join(*path.split('/')[:-3])
+        self.pylot_autopicks = {}
+        self.pylot_picks = {}
+        self.notes = ''
+        self._testEvent = False
+        self._refEvent = False
+        self.get_notes()
+
+    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 + ']'
+                self.addNotes(text)
+                try:
+                    datetime = UTCDateTime(path.split('/')[-1])
+                    origin = Origin(resource_id=self.resource_id, time=datetime, latitude=0, longitude=0, depth=0)
+                    self.origins.append(origin)
+                except:
+                    pass
+
+    def addNotes(self, notes):
+        self.notes = str(notes)
+
+    def clearNotes(self):
+        self.notes = None
+
+    def isRefEvent(self):
+        return self._refEvent
+
+    def isTestEvent(self):
+        return self._testEvent
+
+    def setRefEvent(self, bool):
+        self._refEvent = bool
+        if bool: self._testEvent = False
+
+    def setTestEvent(self, bool):
+        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 ones
+        '''
+        for station in picks:
+            self.pylot_picks[station] = picks[station]
+        # add ObsPy picks (clear old manual and copy all new manual from pylot)
+        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
+        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.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]
+
+    def getPicks(self):
+        return self.pylot_picks
+
+    def setAutopick(self, station, pick):
+        if pick:
+            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 getAutopick(self, station):
+        if station in self.pylot_autopicks.keys():
+            return self.pylot_autopicks[station]
+
+    def getAutopicks(self):
+        return self.pylot_autopicks
+
+    def save(self, filename):
+        '''
+        Save PyLoT Event to a file. 
+        Can be loaded by using event.load(filename).
+        '''
+        try:
+            import cPickle
+        except ImportError:
+            import _pickle as cPickle
+
+        try:
+            outfile = open(filename, 'wb')
+            cPickle.dump(self, outfile, -1)
+        except Exception as e:
+            print('Could not pickle PyLoT event. Reason: {}'.format(e))
+
+    @staticmethod
+    def load(filename):
+        '''
+        Load project from filename.
+        '''
+        try:
+            import cPickle
+        except ImportError:
+            import _pickle as cPickle
+        infile = open(filename, 'rb')
+        event = cPickle.load(infile)
+        print('Loaded %s' % filename)
+        return event

pylot/core/util/map_projection.py

@@ -0,0 +1,376 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import matplotlib.pyplot as plt
+import numpy as np
+import obspy
+from PySide import QtGui
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
+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
+        self.eventLoc = None
+        self.figure = figure
+        self.init_graphics()
+        self.init_stations()
+        self.init_basemap(resolution='l')
+        self.init_map()
+        # self.show()
+
+    def init_map(self):
+        self.init_lat_lon_dimensions()
+        self.init_lat_lon_grid()
+        self.init_x_y_dimensions()
+        self.connectSignals()
+        self.draw_everything()
+
+    def onpick(self, event):
+        ind = event.ind
+        button = event.mouseevent.button
+        if ind == [] or not button == 1:
+            return
+        data = self._parent.get_data().getWFData()
+        for index in ind:
+            station = str(self.station_names[index].split('.')[-1])
+            try:
+                pickDlg = PickDlg(self, parameter=self._parent._inputs,
+                                  data=data.select(station=station),
+                                  station=station,
+                                  picks=self._parent.get_current_event().getPick(station),
+                                  autopicks=self._parent.get_current_event().getAutopick(station))
+            except Exception as e:
+                message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+                return
+            pyl_mw = self._parent
+            try:
+                if pickDlg.exec_():
+                    pyl_mw.setDirty(True)
+                    pyl_mw.update_status('picks accepted ({0})'.format(station))
+                    replot = pyl_mw.get_current_event().setPick(station, pickDlg.getPicks())
+                    self._refresh_drawings()
+                    if replot:
+                        pyl_mw.plotWaveformData()
+                        pyl_mw.drawPicks()
+                        pyl_mw.draw()
+                    else:
+                        pyl_mw.drawPicks(station)
+                        pyl_mw.draw()
+                else:
+                    pyl_mw.update_status('picks discarded ({0})'.format(station))
+            except Exception as e:
+                message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+
+    def connectSignals(self):
+        self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
+        self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
+
+    def init_graphics(self):
+        if not self.figure:
+            if not hasattr(self._parent, 'am_figure'):
+                self.figure = plt.figure()
+                self.toolbar = NavigationToolbar(self.figure.canvas, self)
+            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
+
+        self.main_box = QtGui.QVBoxLayout()
+        self.setLayout(self.main_box)
+
+        self.top_row = QtGui.QHBoxLayout()
+        self.main_box.addLayout(self.top_row)
+
+        self.comboBox_phase = QtGui.QComboBox()
+        self.comboBox_phase.insertItem(0, 'P')
+        self.comboBox_phase.insertItem(1, 'S')
+
+        self.comboBox_am = QtGui.QComboBox()
+        self.comboBox_am.insertItem(0, 'auto')
+        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.main_box.addWidget(self.canvas)
+        self.main_box.addWidget(self.toolbar)
+
+    def init_stations(self):
+        def get_station_names_lat_lon(parser):
+            station_names = []
+            lat = []
+            lon = []
+            for station in parser.stations:
+                station_name = station[0].station_call_letters
+                network = station[0].network_code
+                if not station_name in station_names:
+                    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
+        self.lon = lon
+
+    def init_picks(self):
+        phase = self.comboBox_phase.currentText()
+
+        def get_picks(station_names):
+            picks = []
+            for station in station_names:
+                try:
+                    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_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:
+                    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 = []
+            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 = []
+            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):
+        def get_lon_lat_dim(lon, lat):
+            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):
+        def get_x_y_dim(x, y):
+            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='lcc', resolution=resolution, ax=self.main_ax,
+                          width=5e6, height=2e6,
+                          lat_0=(min(self.lat) + max(self.lat)) / 2.,
+                          lon_0=(min(self.lon) + max(self.lon)) / 2.)
+
+        # basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
+        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
+            steplon = (max(lon) - min(lon)) / 250
+
+            lataxis = np.arange(min(lat), max(lat), steplat)
+            lonaxis = np.arange(min(lon), max(lon), steplon)
+            return lataxis, lonaxis
+
+        def get_lat_lon_grid(lataxis, lonaxis):
+            longrid, latgrid = np.meshgrid(lonaxis, lataxis)
+            return latgrid, longrid
+
+        self.lataxis, self.lonaxis = get_lat_lon_axis(self.lat, self.lon)
+        self.latgrid, self.longrid = get_lat_lon_grid(self.lataxis, self.lonaxis)
+
+    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')  ##################
+
+    def draw_contour_filled(self, nlevel='50'):
+        levels = np.linspace(min(self.picks_no_nan), max(self.picks_no_nan), nlevel)
+        self.contourf = self.basemap.contourf(self.longrid, self.latgrid, self.picksgrid_no_nan,
+                                              levels, latlon=True, zorder=9, alpha=0.5)
+
+    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')
+        self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
+        if self.eventLoc:
+            lat, lon = self.eventLoc
+            self.sc_event = self.basemap.scatter(lon, lat, s=100, facecolor='red',
+                                                 latlon=True, zorder=11, label='Event (might be outside map region)')
+
+    def scatter_picked_stations(self):
+        lon = self.lon_no_nan
+        lat = self.lat_no_nan
+
+        # 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:
+            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:
+            self.sc_picked = self.basemap.scatter(lon, lat, s=50, facecolor='white',
+                                                  c=self.picks_no_nan, latlon=True, zorder=11, label='Picked')
+
+    def annotate_ax(self):
+        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(loc=1)
+
+    def add_cbar(self, label):
+        cbar = self.main_ax.figure.colorbar(self.sc_picked, fraction=0.025)
+        cbar.set_label(label)
+        return cbar
+
+    def refresh_drawings(self, picks=None):
+        self.picks_dict = picks
+        self._refresh_drawings()
+
+    def _refresh_drawings(self):
+        self.remove_drawings()
+        self.draw_everything()
+
+    def draw_everything(self):
+        if self.picks_dict:
+            self.init_picks()
+            self.init_picks_active()
+            self.init_stations_active()
+            if len(self.picks_no_nan) >= 3:
+                self.init_picksgrid()
+                self.draw_contour_filled()
+        self.scatter_all_stations()
+        if self.picks_dict:
+            self.scatter_picked_stations()
+            self.cbar = self.add_cbar(label='Time relative to first onset [s]')
+            self.comboBox_phase.setEnabled(True)
+        else:
+            self.comboBox_phase.setEnabled(False)
+        self.annotate_ax()
+        self.canvas.draw()
+
+    def remove_drawings(self):
+        if hasattr(self, 'sc_picked'):
+            self.sc_picked.remove()
+            del (self.sc_picked)
+        if hasattr(self, 'sc_event'):
+            self.sc_event.remove()
+            del (self.sc_event)
+        if hasattr(self, 'cbar'):
+            self.cbar.remove()
+            del (self.cbar)
+        if hasattr(self, 'contourf'):
+            self.remove_contourf()
+            del (self.contourf)
+        if hasattr(self, 'cid'):
+            self.canvas.mpl_disconnect(self.cid)
+            del (self.cid)
+        try:
+            self.sc.remove()
+        except Exception as e:
+            print('Warning: could not remove station scatter plot.\nReason: {}'.format(e))
+        try:
+            self.legend.remove()
+        except Exception as e:
+            print('Warning: could not remove legend. Reason: {}'.format(e))
+        self.canvas.draw()
+
+    def remove_contourf(self):
+        for item in self.contourf.collections:
+            item.remove()
+
+    def remove_annotations(self):
+        for annotation in self.annotations:
+            annotation.remove()
+
+    def zoom(self, event):
+        map = self.basemap
+        xlim = map.ax.get_xlim()
+        ylim = map.ax.get_ylim()
+        x, y = event.xdata, event.ydata
+        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
+            xl = x - 0.5 * xdiff
+            xr = x + 0.5 * xdiff
+            ydiff = (ylim[1] - ylim[0]) * factor
+            yb = y - 0.5 * ydiff
+            yt = y + 0.5 * ydiff
+
+            if xl < map.xmin or yb < map.ymin or xr > map.xmax or yt > map.ymax:
+                xl, xr = map.xmin, map.xmax
+                yb, yt = map.ymin, map.ymax
+            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()

pylot/core/util/pdf.py

@@ -0,0 +1,489 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import warnings
+
+import numpy as np
+from obspy import UTCDateTime
+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
+    to represent the pick as a probability density funtion (PDF) with two
+    Gauss branches
+    :param te:
+    :param tm:
+    :param tl:
+    :param eta:
+    :return:
+    '''
+
+    sig1 = (tm - te) / np.sqrt(2 * np.log(1 / eta))
+    sig2 = (tl - tm) / np.sqrt(2 * np.log(1 / eta))
+
+    a1 = 2 / (1 + sig2 / sig1)
+    a2 = 2 / (1 + sig1 / sig2)
+
+    return tm, sig1, sig2, a1, a2
+
+
+def exp_parameter(te, tm, tl, eta):
+    '''
+    takes three onset times te, tm and tl and returns the parameters sig1,
+    sig2 and a to represent the pick as a probability density function (PDF)
+    with two exponential decay branches
+    :param te:
+    :param tm:
+    :param tl:
+    :param eta:
+    :return:
+    '''
+
+    sig1 = np.log(eta) / (te - tm)
+    sig2 = np.log(eta) / (tm - tl)
+    if np.isinf(sig1) == True:
+        sig1 = np.log(eta) / (tm - tl)
+    if np.isinf(sig2) == True:
+        sig2 = np.log(eta) / (te - tm)
+    a = 1 / (1 / sig1 + 1 / sig2)
+    return tm, sig1, sig2, a
+
+
+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
+    list containing the values of a probability density function (PDF)
+    consisting of gauss branches
+    :param x:
+    :type x:
+    :param mu:
+    :type mu:
+    :param sig1:
+    :type sig1:
+    :param sig2:
+    :type sig2:
+    :param a1:
+    :type a1:
+    :param 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)
+        else:
+            rval = a2 * 1 / (np.sqrt(2 * np.pi) * sig2) * np.exp(-((k - mu) /
+                                                                   sig2) ** 2 / 2)
+        return rval
+
+    try:
+        return [_func(x, mu, sig1, sig2, a1, a2) for x in iter(k)]
+    except TypeError:
+        return _func(k, mu, sig1, sig2, a1, a2)
+
+
+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
+    list containing the values of a probability density function (PDF)
+    consisting of exponential decay branches
+    :param x:
+    :param mu:
+    :param sig1:
+    :param sig2:
+    :param 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:
+            rval = a * np.exp(sig1 * (k - mu))
+        else:
+            rval = a * np.exp(-sig2 * (k - mu))
+        return rval
+
+    try:
+        return [_func(x, mu, sig1, sig2, a) for x in iter(k)]
+    except TypeError:
+        return _func(k, mu, sig1, sig2, a)
+
+
+# define container dictionaries for different types of pdfs
+parameter = dict(gauss=gauss_parameter, exp=exp_parameter)
+branches = dict(gauss=gauss_branches, exp=exp_branches)
+
+
+class ProbabilityDensityFunction(object):
+    '''
+    A probability density function toolkit.
+    '''
+
+    version = __version__
+
+    def __init__(self, x0, incr, npts, pdf, mu, params, eta=0.01):
+        self.x0 = x0
+        self.incr = incr
+        self.npts = npts
+        self.axis = create_axis(x0, incr, npts)
+        self.mu = mu
+        self.eta = eta
+        self._pdf = pdf
+        self.params = params
+
+    def __add__(self, other):
+
+        assert self.eta == other.eta, 'decline factors differ please use equally defined pdfs for comparison'
+
+        eta = self.eta
+
+        x0, incr, npts = self.commonparameter(other)
+
+        axis = create_axis(x0, incr, npts)
+        pdf_self = np.array(self.data(axis))
+        pdf_other = np.array(other.data(axis))
+
+        pdf = np.convolve(pdf_self, pdf_other, 'full') * incr
+
+        # shift axis values for correct plotting
+        npts = pdf.size
+        x0 *= 2
+        axis = create_axis(x0, incr, npts)
+        mu = axis[np.where(pdf == max(pdf))][0]
+
+        func, params = fit_curve(axis, pdf)
+
+        return ProbabilityDensityFunction(x0, incr, npts, func, mu,
+                                          params, eta)
+
+    def __sub__(self, other):
+
+        assert self.eta == other.eta, 'decline factors differ please use equally defined pdfs for comparison'
+
+        eta = self.eta
+
+        x0, incr, npts = self.commonparameter(other)
+
+        axis = create_axis(x0, incr, npts)
+        pdf_self = np.array(self.data(axis))
+        pdf_other = np.array(other.data(axis))
+
+        pdf = np.correlate(pdf_self, pdf_other, 'full') * incr
+
+        # shift axis values for correct plotting
+        npts = len(pdf)
+        midpoint = npts / 2
+        x0 = -incr * midpoint
+        axis = create_axis(x0, incr, npts)
+        mu = axis[np.where(pdf == max(pdf))][0]
+
+        func, params = fit_curve(axis, pdf)
+
+        return ProbabilityDensityFunction(x0, incr, npts, func, mu,
+                                          params, eta)
+
+    def __nonzero__(self):
+        prec = self.precision(self.incr)
+        data = np.array(self.data())
+        gtzero = np.all(data >= 0)
+        probone = bool(np.round(self.prob_gt_val(self.axis[0]), prec) == 1.)
+        return bool(gtzero and probone)
+
+    def __str__(self):
+        return str([self.data()])
+
+    @staticmethod
+    def precision(incr):
+        prec = int(np.ceil(np.abs(np.log10(incr)))) - 2
+        return prec if prec >= 0 else 0
+
+    def data(self, value=None):
+        if value is None:
+            return self._pdf(self.axis, self.params)
+        return self._pdf(value, self.params)
+
+    @property
+    def eta(self):
+        return self._eta
+
+    @eta.setter
+    def eta(self, value):
+        self._eta = value
+
+    @property
+    def mu(self):
+        return self._mu
+
+    @mu.setter
+    def mu(self, mu):
+        self._mu = mu
+
+    @property
+    def axis(self):
+        return self._x
+
+    @axis.setter
+    def axis(self, x):
+        self._x = np.array(x)
+
+    @classmethod
+    def from_pick(self, lbound, barycentre, rbound, incr=0.1, decfact=0.01,
+                  type='exp'):
+        '''
+        Initialize a new ProbabilityDensityFunction object.
+        Takes incr, lbound, barycentre and rbound to derive x0 and the number
+        of points npts for the axis vector.
+        Maximum density
+        is given at the barycentre and on the boundaries the function has
+        declined to decfact times the maximum value. Integration of the
+        function over a particular interval gives the probability for the
+        variable value to be in that interval.
+        '''
+
+        # derive adequate window of definition
+        margin = 2. * np.max([barycentre - lbound, rbound - barycentre])
+
+        # find midpoint accounting also for `~obspy.UTCDateTime` object usage
+        try:
+            midpoint = (rbound + lbound) / 2
+        except TypeError:
+            try:
+                midpoint = (rbound + float(lbound)) / 2
+            except TypeError:
+                midpoint = float(rbound + float(lbound)) / 2
+
+        # find x0 on a grid point and sufficient npts
+        was_datetime = None
+        if isinstance(barycentre, UTCDateTime):
+            barycentre = float(barycentre)
+            was_datetime = True
+        n = int(np.ceil((barycentre - midpoint) / incr))
+        m = int(np.ceil((margin / incr)))
+        midpoint = barycentre - n * incr
+        margin = m * incr
+        x0 = midpoint - margin
+        npts = 2 * m
+
+        if was_datetime:
+            barycentre = UTCDateTime(barycentre)
+
+        # calculate parameter for pdf representing function
+        params = parameter[type](lbound, barycentre, rbound, decfact)
+
+        # select pdf type
+        pdf = branches[type]
+
+        # return the object
+        return ProbabilityDensityFunction(x0, incr, npts, pdf, barycentre,
+                                          params, decfact)
+
+    def broadcast(self, pdf, si, ei, data):
+        try:
+            pdf[si:ei] = data
+        except ValueError as e:
+            warnings.warn(str(e), Warning)
+            return self.broadcast(pdf, si, ei, data[:-1])
+        return pdf
+
+    def expectation(self):
+        '''
+        returns the expectation value of the actual pdf object
+
+        ..formula::
+                mu_{\Delta t} = \int\limits_{-\infty}^\infty x \cdot f(x)dx
+
+        :return float: rval
+        '''
+
+        # rval = 0
+        # 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
+
+    def standard_deviation(self):
+        mu = self.mu
+        rval = 0
+        for x in self.axis:
+            rval += (x - float(mu)) ** 2 * self.data(x)
+        return rval * self.incr
+
+    def prob_lt_val(self, value):
+        if value <= self.axis[0] or value > self.axis[-1]:
+            raise ValueError('value out of bounds: {0}'.format(value))
+        return self.prob_limits((self.axis[0], value))
+
+    def prob_gt_val(self, value):
+        if value < self.axis[0] or value >= self.axis[-1]:
+            raise ValueError('value out of bounds: {0}'.format(value))
+        return self.prob_limits((value, self.axis[-1]))
+
+    def prob_limits(self, limits, oversampling=1.):
+        sampling = self.incr / oversampling
+        lim = np.arange(limits[0], limits[1], sampling)
+        data = self.data(lim)
+        min_est, max_est = 0., 0.
+        for n in range(len(data) - 1):
+            min_est += min(data[n], data[n + 1])
+            max_est += max(data[n], data[n + 1])
+        return (min_est + max_est) / 2. * sampling
+
+    def prob_val(self, value):
+        if not (self.axis[0] <= value <= self.axis[-1]):
+            Warning('{0} not on axis'.format(value))
+            return None
+        return self.data(value) * self.incr
+
+    def quantile(self, prob_value, eps=0.01):
+        '''
+
+        :param prob_value:
+        :param eps:
+        :return:
+        '''
+        l = self.axis[0]
+        r = self.axis[-1]
+        m = (r + l) / 2
+        diff = prob_value - self.prob_lt_val(m)
+        while abs(diff) > eps and ((r - l) > self.incr):
+            if diff > 0:
+                l = m
+            else:
+                r = m
+            m = (r + l) / 2
+            diff = prob_value - self.prob_lt_val(m)
+        return m
+
+    def quantile_distance(self, prob_value):
+        """
+        takes a probability value and and returns the distance
+        between two complementary quantiles
+
+        .. math::
+
+            QA_\alpha = Q(1 - \alpha) - Q(\alpha)
+
+        :param value: probability value :math:\alpha
+        :type  value: float
+        :return: quantile distance
+        """
+        if 0 >= prob_value or prob_value >= 0.5:
+            raise ValueError('Value out of range.')
+        ql = self.quantile(prob_value)
+        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
+        corresponding quantile distances (
+        :func:`pylot.core.util.pdf.ProbabilityDensityFunction
+        #quantile_distance`)
+
+        .. math::
+
+            Q\Theta_\alpha = \frac{QA(0.5 - \alpha)}{QA(\alpha)}
+
+        :param value: probability value :math:\alpha
+        :return: quantile distance fraction
+        """
+        if x <= 0 or x >= 0.25:
+            raise ValueError('Value out of range.')
+        return self.quantile_distance(0.5 - x) / self.quantile_distance(x)
+
+    def plot(self, label=None):
+        import matplotlib.pyplot as plt
+
+        plt.plot(self.axis, self.data())
+        plt.xlabel('x')
+        plt.ylabel('f(x)')
+        plt.autoscale(axis='x', tight=True)
+        if self:
+            title_str = 'Probability density function '
+            if label:
+                title_str += label
+            title_str.strip()
+        else:
+            title_str = 'Function not suitable as probability density function'
+        plt.title(title_str)
+        plt.show()
+
+    def limits(self):
+        l1 = self.x0
+        r1 = l1 + self.incr * self.npts
+
+        return l1, r1
+
+    def cincr(self, other):
+        if not self.incr == other.incr:
+            raise NotImplementedError(
+                'Upsampling of the lower sampled PDF not implemented yet!')
+        else:
+            return self.incr
+
+    def commonlimits(self, incr, other, max_npts=1e5):
+        '''
+        Takes an increment incr and two left and two right limits and returns
+        the left most limit and the minimum number of points needed to cover
+        the whole given interval.
+        :param incr:
+        :param l1:
+        :param l2:
+        :param r1:
+        :param r2:
+        :param max_npts:
+        :return:
+        '''
+
+        x0, r = clims(self.limits(), other.limits())
+
+        # calculate index for rounding
+        ri = self.precision(incr)
+
+        npts = int(round(r - x0, ri) // incr)
+
+        if npts > max_npts:
+            raise ValueError('Maximum number of points exceeded:\n'
+                             'max_npts - %d\n'
+                             'npts - %d\n' % (max_npts, npts))
+
+        npts = np.max([npts, self.npts, other.npts])
+
+        if npts < self.npts or npts < other.npts:
+            raise ValueError('new npts is to small')
+
+        return x0, npts
+
+    def commonparameter(self, other):
+        assert isinstance(other, ProbabilityDensityFunction), \
+            'both operands must be of type ProbabilityDensityFunction'
+
+        incr = self.cincr(other)
+
+        x0, npts = self.commonlimits(incr, other)
+
+        return x0, incr, npts

pylot/core/util/plotting.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+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
+    histogram plotting
+    :param l_boundary: Any number.
+    :type  l_boundary: float
+    :param u_boundary: Any number that is greater than l_boundary.
+    :type  u_boundary: float
+    :param nbins: Any positive integer.
+    :type  nbins: int
+    :return: A list of equidistant bins.
+    """
+    if u_boundary <= l_boundary:
+        raise ValueError('Upper boundary must be greather than lower!')
+    elif nbins <= 0:
+        raise ValueError('Number of bins is not valid.')
+    binlist = []
+    for i in range(nbins):
+        binlist.append(l_boundary + i * (u_boundary - l_boundary) / nbins)
+    return binlist
+
+
+def histplot(array, binlist, xlab='Values',
+             ylab='Frequency', title=None, fnout=None):
+    """
+    function to quickly show some distribution of data. Takes array like data,
+    and a list of bins. Editing detail and inserting a legend is not possible.
+    :param array: List of values.
+    :type  array: Array like
+    :param binlist: List of bins.
+    :type  binlist: list
+    :param xlab: A label for the x-axes.
+    :type  xlab: str
+    :param ylab: A label for the y-axes.
+    :type  ylab: str
+    :param title: A title for the Plot.
+    :type  title: str
+    :param fnout: A path to save the plot instead of showing.
+                  Has to contain filename and type. Like: 'path/to/file.png'
+    :type  fnout. str
+    :return: -
+    """
+
+    plt.hist(array, bins=binlist)
+    plt.xlabel(xlab)
+    plt.ylabel(ylab)
+    if title:
+        plt.title(title)
+    if fnout:
+        plt.savefig(fnout)
+    else:
+        plt.show()

pylot/core/util/structure.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jan 26 17:47:25 2015
+
+@author: sebastianw
+"""
+
+from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure
+
+DATASTRUCTURE = {'PILOT': PilotDataStructure, 'SeisComP': SeiscompDataStructure,
+                 None: None}

pylot/core/util/thread.py

@@ -0,0 +1,187 @@
+# -*- coding: utf-8 -*-
+import sys, os, traceback
+import multiprocessing
+from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
+from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
+
+
+class Thread(QThread):
+    message = Signal(str)
+
+    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
+        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__
+
+    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.setModal(True)
+            hl = QHBoxLayout()
+            pb = QProgressBar()
+            pb.setRange(0, 0)
+            hl.addWidget(pb)
+            hl.addWidget(QLabel(self.progressText))
+            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
+
+    def emitDone(self, result):
+        print('emitDone!')
+        self.finished.emit('Done thread!')
+        self.hideProgressbar()

pylot/core/util/utils.py

@@ -0,0 +1,939 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import hashlib
+import os
+import platform
+import re
+import subprocess
+
+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)
+    b = m * eta
+    l = find_nearest(f[:mi], b)
+    u = find_nearest(f[mi:], b) + mi
+    return mi, l, u
+
+
+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 == 0:
+        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
+    :param lim1:
+    :param lim2:
+    :return:
+
+    >>> clims([0, 4], [1, 3])
+    [0, 4]
+    >>> clims([1, 4], [0, 3])
+    [0, 4]
+    >>> clims([1, 3], [0, 4])
+    [0, 4]
+    >>> clims([0, 3], [1, 4])
+    [0, 4]
+    >>> clims([0, 3], [0, 4])
+    [0, 4]
+    >>> clims([1, 4], [0, 4])
+    [0, 4]
+    >>> clims([0, 4], [0, 4])
+    [0, 4]
+    >>> clims([0, 4], [1, 4])
+    [0, 4]
+    >>> clims([0, 4], [0, 3])
+    [0, 4]
+    """
+    lim = [None, None]
+    if lim1[0] < lim2[0]:
+        lim[0] = lim1[0]
+    else:
+        lim[0] = lim2[0]
+    if lim1[1] > lim2[1]:
+        lim[1] = lim1[1]
+    else:
+        lim[1] = lim2[1]
+    return lim
+
+
+def demeanTrace(trace, window):
+    """
+    takes a trace object and returns the same trace object but with data
+    demeaned within a certain time window
+    :param trace: waveform trace object
+    :type trace: `~obspy.core.stream.Trace`
+    :param window:
+    :type window: tuple
+    :return: trace
+    :rtype: `~obspy.core.stream.Trace`
+    """
+    trace.data -= trace.data[window].mean()
+    return trace
+
+
+def findComboBoxIndex(combo_box, val):
+    """
+    Function findComboBoxIndex takes a QComboBox object and a string and
+    returns either 0 or the index throughout all QComboBox items.
+    :param combo_box: Combo box object.
+    :type combo_box: `~QComboBox`
+    :param val: Name of a combo box to search for.
+    :type val: basestring
+    :return: index value of item with name val or 0
+    """
+    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
+    matching the string pattern
+    :param list: list to search in
+    :param str: pattern to search for
+    :return: first list item containing pattern
+
+    .. example::
+
+    >>> l = ['/dir/e1234.123.12', '/dir/e2345.123.12', 'abc123', 'def456']
+    >>> find_in_list(l, 'dir')
+    '/dir/e1234.123.12'
+    >>> find_in_list(l, 'e1234')
+    '/dir/e1234.123.12'
+    >>> find_in_list(l, 'e2')
+    '/dir/e2345.123.12'
+    >>> find_in_list(l, 'ABC')
+    'abc123'
+    >>> find_in_list(l, 'f456')
+    'def456'
+    >>> find_in_list(l, 'gurke')
+
+    """
+    rlist = [s for s in list if str.lower() in s.lower()]
+    if rlist:
+        return rlist[0]
+    return None
+
+
+def find_nearest(array, value):
+    '''
+    function find_nearest takes an array and a value and returns the
+    index of the nearest value found in the array
+    :param array: array containing values
+    :type array: `~numpy.ndarray`
+    :param value: number searched for
+    :return: index of the array item being nearest to the value
+
+    >>> a = np.array([ 1.80339578, -0.72546654,  0.95769195, -0.98320759, 0.85922623])
+    >>> find_nearest(a, 1.3)
+    2
+    >>> find_nearest(a, 0)
+    1
+    >>> find_nearest(a, 2)
+    0
+    >>> find_nearest(a, -1)
+    3
+    >>> a = np.array([ 1.1, -0.7,  0.9, -0.9, 0.8])
+    >>> find_nearest(a, 0.849)
+    4
+    '''
+    return (np.abs(array - value)).argmin()
+
+
+def fnConstructor(s):
+    '''
+    takes a string and returns a valid filename (especially on windows machines)
+    :param s: desired filename
+    :type s: str
+    :return: valid filename
+    '''
+    if type(s) is str:
+        s = s.split(':')[-1]
+    else:
+        s = getHash(UTCDateTime())
+
+    badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
+    badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
+
+    fn = badchars.sub('_', s)
+
+    if badsuffix.match(fn):
+        fn = '_' + fn
+    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
+    from the last 100 years
+    :param year: two digit year
+    :type year: int
+    :return: four digit year correspondant
+
+    >>> four_digits(20)
+    1920
+    >>> four_digits(16)
+    2016
+    >>> four_digits(00)
+    2000
+    """
+    if year + 2000 <= UTCDateTime.utcnow().year:
+        year += 2000
+    else:
+        year += 1900
+    return year
+
+
+def common_range(stream):
+    '''
+    takes a stream object and returns the earliest end and the latest start
+    time of all contained trace objects
+    :param stream: seismological data stream
+    :type stream: `~obspy.core.stream.Stream`
+    :return: maximum start time and minimum end time
+    '''
+    max_start = None
+    min_end = None
+    for trace in stream:
+        if max_start is None or trace.stats.starttime > max_start:
+            max_start = trace.stats.starttime
+        if min_end is None or trace.stats.endtime < min_end:
+            min_end = trace.stats.endtime
+    return max_start, min_end
+
+
+def full_range(stream):
+    '''
+    takes a stream object and returns the latest end and the earliest start
+    time of all contained trace objects
+    :param stream: seismological data stream
+    :type stream: `~obspy.core.stream.Stream`
+    :return: minimum start time and maximum end time
+    '''
+    min_start = UTCDateTime()
+    max_end = None
+    for trace in stream:
+        if trace.stats.starttime < min_start:
+            min_start = trace.stats.starttime
+        if max_end is None or trace.stats.endtime > max_end:
+            max_end = trace.stats.endtime
+    return min_start, max_end
+
+
+def getHash(time):
+    '''
+    takes a time object and returns the corresponding SHA1 hash of the
+    formatted date string
+    :param time: time object for which a hash should be calculated
+    :type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :return: str
+    '''
+    hg = hashlib.sha1()
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    return hg.hexdigest()
+
+
+def getLogin():
+    '''
+    returns the actual user's login ID
+    :return: login ID
+    '''
+    return os.getlogin()
+
+
+def getOwner(fn):
+    '''
+    takes a filename and return the login ID of the actual owner of the file
+    :param fn: filename of the file tested
+    :type fn: str
+    :return: login ID of the file's owner
+    '''
+    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):
+    """
+    takes a file name and a pattern string to search for in the file and
+    returns the first line which contains the pattern string otherwise 'None'
+    :param fn: file name
+    :type fn: str
+    :param pattern: pattern string to search for
+    :type pattern: str
+    :return: the complete line containing the pattern string or None
+
+    >>> getPatternLine('utils.py', 'python')
+    '#!/usr/bin/env python\\n'
+    >>> print(getPatternLine('version.py', 'palindrome'))
+    None
+    """
+    fobj = open(fn, 'r')
+    for line in fobj.readlines():
+        if pattern in line:
+            fobj.close()
+            return line
+
+    return None
+
+
+def is_executable(fn):
+    """
+    takes a filename and returns True if the file is executable on the system
+    and False otherwise
+    :param fn: path to the file to be tested
+    :return: True or False
+    """
+    return os.path.isfile(fn) and os.access(fn, os.X_OK)
+
+
+def isSorted(iterable):
+    '''
+    takes an iterable and returns 'True' if the items are in order otherwise
+    'False'
+    :param iterable: an iterable object
+    :type iterable:
+    :return: Boolean
+
+    >>> isSorted(1)
+    Traceback (most recent call last):
+    ...
+    AssertionError: object is not iterable; object: 1
+    >>> isSorted([1,2,3,4])
+    True
+    >>> isSorted('abcd')
+    True
+    >>> isSorted('bcad')
+    False
+    >>> isSorted([2,3,1,4])
+    False
+    '''
+    assert isIterable(iterable), 'object is not iterable; object: {' \
+                                 '0}'.format(iterable)
+    if type(iterable) is str:
+        iterable = [s for s in iterable]
+    return sorted(iterable) == iterable
+
+
+def isIterable(obj):
+    """
+    takes a python object and returns 'True' is the object is iterable and
+    'False' otherwise
+    :param obj: a python object
+    :return: True of False
+    """
+    try:
+        iterator = iter(obj)
+    except TypeError as te:
+        return False
+    return True
+
+
+def key_for_set_value(d):
+    """
+    takes a dictionary and returns the first key for which's value the
+    boolean is True
+    :param d: dictionary containing values
+    :type d: dict
+    :return: key to the first non-False value found; None if no value's
+    boolean equals True
+    """
+    r = None
+    for k, v in d.items():
+        if v:
+            return k
+    return r
+
+
+def prepTimeAxis(stime, trace, verbosity=0):
+    '''
+    takes a starttime and a trace object and returns a valid time axis for
+    plotting
+    :param stime: start time of the actual seismogram as UTCDateTime
+    :param trace: seismic trace object
+    :return: valid numpy array with time stamps for plotting
+    '''
+    nsamp = trace.stats.npts
+    srate = trace.stats.sampling_rate
+    tincr = trace.stats.delta
+    etime = stime + nsamp / srate
+    time_ax = np.arange(stime, etime, tincr)
+    if len(time_ax) < nsamp:
+        if verbosity:
+            print('elongate time axes by one datum')
+        time_ax = np.arange(stime, etime + tincr, tincr)
+    elif len(time_ax) > nsamp:
+        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'
+              'delta: {3}'.format(trace.stats.station,
+                                  nsamp, len(time_ax), tincr))
+        time_ax = None
+    return time_ax
+
+
+def find_horizontals(data):
+    """
+    takes `obspy.core.stream.Stream` object and returns a list containing the component labels of the horizontal components available
+    :param data: waveform data
+    :type data: `obspy.core.stream.Stream`
+    :return: components list
+    :rtype: list
+
+    ..example::
+
+    >>> st = read()
+    >>> find_horizontals(st)
+    [u'N', u'E']
+    """
+    rval = []
+    for tr in data:
+        if tr.stats.channel[-1].upper() in ['Z', '3']:
+            continue
+        else:
+            rval.append(tr.stats.channel[-1].upper())
+    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
+    from stationnames
+    :param data: stream of seismic data
+    :type data: `obspy.core.stream.Stream`
+    :return: data stream
+    """
+    for tr in data:
+        # remove underscores
+        tr.stats.station = tr.stats.station.strip('_')
+    return data
+
+
+def trim_station_components(data, trim_start=True, trim_end=True):
+    '''
+    cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
+    :param data: stream of seismic data
+    :type data: `obspy.core.stream.Stream`
+    :param trim_start: trim start of stream
+    :type trim_start: bool
+    :param trim_end: trim end of stream
+    :type trim_end: bool
+    :return: data stream
+    '''
+    starttime = {False: None}
+    endtime = {False: None}
+
+    stations = get_stations(data)
+
+    print('trim_station_components: Will trim stream for trim_start: {} and for '
+          'trim_end: {}.'.format(trim_start, trim_end))
+    for station in stations:
+        wf_station = data.select(station=station)
+        starttime[True] = max([trace.stats.starttime for trace in wf_station])
+        endtime[True] = min([trace.stats.endtime for trace in wf_station])
+        wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
+
+    return data
+
+
+def check4gaps(data):
+    '''
+    check for gaps in Stream and remove them
+    :param data: stream of seismic data
+    :return: data stream
+    '''
+    stations = get_stations(data)
+
+    for station in stations:
+        wf_station = data.select(station=station)
+        if wf_station.get_gaps():
+            for trace in wf_station:
+                data.remove(trace)
+            print('check4gaps: Found gaps and removed station {} from waveform data.'.format(station))
+
+    return data
+
+
+def check4doubled(data):
+    '''
+    check for doubled stations for same channel in Stream and take only the first one
+    :param data: stream of seismic data
+    :return: data stream
+    '''
+    stations = get_stations(data)
+
+    for station in stations:
+        wf_station = data.select(station=station)
+        # create list of all possible channels
+        channels = []
+        for trace in wf_station:
+            channel = trace.stats.channel
+            if not channel in channels:
+                channels.append(channel)
+            else:
+                print('check4doubled: removed the following trace for station {}, as there is'
+                      ' already a trace with the same channel given:\n{}'.format(
+                    station, trace
+                ))
+                data.remove(trace)
+    return data
+
+
+def get_stations(data):
+    stations = []
+    for tr in data:
+        station = tr.stats.station
+        if not station in stations:
+            stations.append(station)
+
+    return stations
+
+
+def check4rotated(data, metadata=None, 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,
+    waveform may be selected by their components name
+    :param data: waveform data to be scaled
+    :type data: `~obspy.core.stream.Stream` object
+    :param factor: scaling factor
+    :type factor: float
+    :param components: components labels for the traces in data to be scaled by
+     the scaling factor (optional, default: 'all')
+    :type components: tuple
+    :return:  scaled waveform data
+    :rtype: `~obspy.core.stream.Stream` object
+    """
+    if components is not 'all':
+        for comp in components:
+            if factor is None:
+                max_val = np.max(np.abs(data.select(component=comp)[0].data))
+                data.select(component=comp)[0].data /= 2 * max_val
+            else:
+                data.select(component=comp)[0].data /= 2 * factor
+    else:
+        for tr in data:
+            if factor is None:
+                max_val = float(np.max(np.abs(tr.data)))
+                tr.data /= 2 * max_val
+            else:
+                tr.data /= 2 * factor
+
+    return data
+
+
+def runProgram(cmd, parameter=None):
+    """
+    run an external program specified by cmd with parameters input returning the
+    stdout output
+    :param cmd: name of the command to run
+    :type cmd: str
+    :param parameter: filename of parameter file  or parameter string
+    :type parameter: str
+    :return: stdout output
+    :rtype: str
+    """
+
+    if parameter:
+        cmd.strip()
+        cmd += ' %s 2>&1' % parameter
+
+    subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
+
+
+def which(program, infile=None):
+    """
+    takes a program name and returns the full path to the executable or None
+    modified after: http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
+    :param program: name of the desired external program
+    :return: full path of the executable file
+    """
+    try:
+        from PySide.QtCore import QSettings
+        settings = QSettings()
+        for key in settings.allKeys():
+            if 'binPath' in key:
+                os.environ['PATH'] += ':{0}'.format(settings.value(key))
+        if infile is None:
+            # use default parameter-file name
+            bpath = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+        else:
+            bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
+
+        if os.path.exists(bpath):
+            nllocpath = ":" + PylotParameter(bpath).get('nllocbin')
+            os.environ['PATH'] += nllocpath
+    except ImportError as e:
+        print(e.message)
+
+    def is_exe(fpath):
+        return os.path.exists(fpath) and os.access(fpath, os.X_OK)
+
+    def ext_candidates(fpath):
+        yield fpath
+        for ext in os.environ.get("PATHEXT", "").split(os.pathsep):
+            yield fpath + ext
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            exe_file = os.path.join(path, program)
+            for candidate in ext_candidates(exe_file):
+                if is_exe(candidate):
+                    return candidate
+
+    return None
+
+
+def loopIdentifyPhase(phase):
+    '''
+    Loop through phase string and try to recognize its type (P or S wave).
+    Global variable ALTSUFFIX gives alternative suffix for phases if they do not end with P, p or S, s.
+    If ALTSUFFIX is not given, the function will cut the last letter of the phase string until string ends
+    with P or S.
+    :param phase: phase name (str)
+    :return:
+    '''
+    from pylot.core.util.defaults import ALTSUFFIX
+
+    phase_copy = phase
+    while not identifyPhase(phase_copy):
+        identified = False
+        for alt_suf in ALTSUFFIX:
+            if phase_copy.endswith(alt_suf):
+                phase_copy = phase_copy.split(alt_suf)[0]
+                identified = True
+        if not identified:
+            phase_copy = phase_copy[:-1]
+        if len(phase_copy) < 1:
+            print('Warning: Could not identify phase {}!'.format(phase))
+            return
+    return phase_copy
+
+
+def identifyPhase(phase):
+    '''
+    Returns capital P or S if phase string is identified by last letter. Else returns False.
+    :param phase: phase name (str)
+    :return: 'P', 'S' or False
+    '''
+    # common phase suffix for P and S
+    common_P = ['P', 'p']
+    common_S = ['S', 's']
+    if phase[-1] in common_P:
+        return 'P'
+    if phase[-1] in common_S:
+        return 'S'
+    else:
+        return False
+
+
+def identifyPhaseID(phase):
+    return identifyPhase(loopIdentifyPhase(phase))
+
+
+def has_spe(pick):
+    if not 'spe' in pick.keys():
+        return None
+    else:
+        return pick['spe']
+
+
+if __name__ == "__main__":
+    import doctest
+
+    doctest.testmod()

pylot/core/util/version.py

@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+# Author: Douglas Creager <dcreager@dcreager.net>
+# This file is placed into the public domain.
+
+# Calculates the current version number.  If possible, this is the
+# output of “git describe”, modified to conform to the versioning
+# scheme that setuptools uses.  If “git describe” returns an error
+# (most likely because we're in an unpacked copy of a release tarball,
+# rather than in a git working copy), then we fall back on reading the
+# contents of the RELEASE-VERSION file.
+#
+# To use this script, simply import it your setup.py file, and use the
+# results of get_git_version() as your package version:
+#
+# from version import *
+#
+# setup(
+#     version=get_git_version(),
+#     .
+#     .
+#     .
+# )
+#
+# This will automatically update the RELEASE-VERSION file, if
+# necessary.  Note that the RELEASE-VERSION file should *not* be
+# checked into git; please add it to your top-level .gitignore file.
+#
+# You'll probably want to distribute the RELEASE-VERSION file in your
+# sdist tarballs; to do this, just create a MANIFEST.in file that
+# contains the following line:
+#
+#   include RELEASE-VERSION
+
+from __future__ import print_function
+
+__all__ = "get_git_version"
+
+# NO IMPORTS FROM PYLOT IN THIS FILE! (file gets used at installation time)
+import os
+import inspect
+from subprocess import Popen, PIPE
+
+# NO IMPORTS FROM PYLOT IN THIS FILE! (file gets used at installation time)
+
+script_dir = os.path.abspath(os.path.dirname(inspect.getfile(
+    inspect.currentframe())))
+PYLOT_ROOT = os.path.abspath(os.path.join(script_dir, os.pardir,
+                                          os.pardir, os.pardir))
+VERSION_FILE = os.path.join(PYLOT_ROOT, "pylot", "RELEASE-VERSION")
+
+
+def call_git_describe(abbrev=4):
+    try:
+        p = Popen(['git', 'rev-parse', '--show-toplevel'],
+                  cwd=PYLOT_ROOT, stdout=PIPE, stderr=PIPE)
+        p.stderr.close()
+        path = p.stdout.readlines()[0].strip()
+    except:
+        return None
+    if os.path.normpath(path) != PYLOT_ROOT:
+        return None
+    try:
+        p = Popen(['git', 'describe', '--dirty', '--abbrev=%d' % abbrev,
+                   '--always'],
+                  cwd=PYLOT_ROOT, stdout=PIPE, stderr=PIPE)
+        p.stderr.close()
+        line = p.stdout.readlines()[0]
+        # (this line prevents official releases)
+        if "-" not in line and "." not in line:
+            line = "0.0.0-g%s" % line
+        return line.strip()
+    except:
+        return None
+
+
+def read_release_version():
+    try:
+        version = open(VERSION_FILE, "r").readlines()[0]
+        return version.strip()
+    except:
+        return None
+
+
+def write_release_version(version):
+    open(VERSION_FILE, "w").write("%s\n" % version)
+
+
+def get_git_version(abbrev=4):
+    # Read in the version that's currently in RELEASE-VERSION.
+    release_version = read_release_version()
+
+    # First try to get the current version using “git describe”.
+    version = call_git_describe(abbrev)
+
+    # If that doesn't work, fall back on the value that's in
+    # RELEASE-VERSION.
+    if version is None:
+        version = release_version
+
+    # If we still don't have anything, that's an error.
+    if version is None:
+        return '0.0.0-tar/zipball'
+
+    # If the current version is different from what's in the
+    # RELEASE-VERSION file, update the file to be current.
+    if version != release_version:
+        write_release_version(version)
+
+    # Finally, return the current version.
+    return version
+
+
+if __name__ == "__main__":
+    print(get_git_version())