.gitignore

@@ -1,4 +1,3 @@
 *.pyc
 *~
-.idea
 pylot/RELEASE-VERSION

PyLoT.py

@@ -91,8 +91,6 @@ from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
 from pylot.core.util.version import get_git_version as _getVersionString
-from pylot.core.io.getEventListFromXML import geteventlistfromxml 
-from pylot.core.io.getQualitiesfromxml import getQualitiesfromxml
 
 from pylot.styles import style_settings
 
@@ -348,9 +346,6 @@ class MainWindow(QMainWindow):
         compare_icon.addPixmap(QPixmap(':/icons/compare_button.png'))
         qualities_icon = QIcon()
         qualities_icon.addPixmap(QPixmap(':/icons/pick_qualities_button.png'))
-        eventlist_xml_icon = QIcon()
-        eventlist_xml_icon.addPixmap(QPixmap(':/icons/eventlist_xml_button.png'))
-
         self.newProjectAction = self.createAction(self, "&New project ...",
                                                   self.createNewProject,
                                                   QKeySequence.New, newIcon,
@@ -491,11 +486,6 @@ class MainWindow(QMainWindow):
         # LK will be implemented soon, basic script has already (03/2021) been finished
         self.qualities_action.setVisible(True)
 
-        self.eventlist_xml_action = self.createAction(parent=self, text='Create Eventlist from XML',
-                                                  slot=self.eventlistXml, shortcut='Alt+X',
-                                                  icon=eventlist_xml_icon, tip='Create an Eventlist from a XML File')
-        self.eventlist_xml_action.setEnabled(False)
-
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -564,7 +554,7 @@ class MainWindow(QMainWindow):
                                                                                   ' the complete project on grid engine.')
         self.auto_pick_sge.setEnabled(False)
 
-        pickActions = (self.auto_tune, self.auto_pick, self.compare_action, self.qualities_action, self.eventlist_xml_action)
+        pickActions = (self.auto_tune, self.auto_pick, self.compare_action, self.qualities_action)
 
         # pickToolBar = self.addToolBar("PickTools")
         # pickToolActions = (selectStation, )
@@ -1658,14 +1648,6 @@ class MainWindow(QMainWindow):
         self.cmpw.show()
 
     def pickQualities(self):
-        path = self._inputs['rootpath'] + '/'  + self._inputs['datapath'] + '/' + self._inputs['database']
-        getQualitiesfromxml(path)
-        return
-
-    def eventlistXml(self):
-        path = self._inputs['rootpath'] + '/'  + self._inputs['datapath'] + '/' + self._inputs['database']
-        outpath = self.project.location[:self.project.location.rfind('/')]
-        geteventlistfromxml(path, outpath) 
         return
 
     def compareMulti(self):
@@ -2109,7 +2091,6 @@ class MainWindow(QMainWindow):
         if event.pylot_picks or event.pylot_autopicks:
             self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
-            self.eventlist_xml_action.setEnabled(True)
         if True in self.comparable.values():
             self.compare_action.setEnabled(True)
         self.draw()
@@ -2182,7 +2163,6 @@ class MainWindow(QMainWindow):
         self.loadpilotevent.setEnabled(False)
         self.compare_action.setEnabled(False)
         self.qualities_action.setEnabled(False)
-        self.eventlist_xml_action.setEnabled(False)
         self.locateEventAction.setEnabled(False)
         if not refresh_plot:
             self.wf_scroll_area.setVisible(False)
@@ -2563,13 +2543,7 @@ class MainWindow(QMainWindow):
                 self.drawPicks(station)
                 self.draw()
             if self.nextStation:
-                if not self.get_loc_flag() and self.check4Loc():
-                    self.locateEventAction.setEnabled(True)
-                    self.set_loc_flag(True)
-                elif self.get_loc_flag() and not self.check4Loc():
-                    self.set_loc_flag(False)
                 self.pickDialog(wfID - 1)
-
         else:
             self.update_status('picks discarded ({0})'.format(station))
         if not self.get_loc_flag() and self.check4Loc():

icons.qrc

@@ -30,7 +30,6 @@
         <file>icons/openloc.png</file>
         <file>icons/compare_button.png</file>
         <file>icons/pick_qualities_button.png</file>
-        <file>icons/eventlist_xml_button.png</file>
         <file>icons/locate_button.png</file>
         <file>icons/Matlab_PILOT_icon.png</file>
         <file>icons/printer.png</file>

pylot/core/io/getEventListFromXML.py

@@ -1,79 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to get event parameters from PyLoT-xml file to write
-   them into eventlist.
-   LK, igem, 03/2021
-   Edited for use in PyLoT
-   JG, igem, 01/2022
-"""
-import pdb
-import os
-import argparse
-import numpy as np
-import matplotlib.pyplot as plt
-from obspy.core.event import read_events
-from pyproj import Proj
-import glob
-
-"""
-Creates an eventlist file summarizing all events found in a certain folder. Only called by pressing UI Button eventlis_xml_action
-
-:rtype:
-:param path: Path to root folder where single Event folder are to found
-"""
-
-def geteventlistfromxml(path, outpath):
-    p = Proj(proj='utm', zone=32, ellps='WGS84')
-
-
-    # open eventlist file and write header
-    evlist = outpath + '/eventlist'
-    evlistobj = open(evlist, 'w')
-    evlistobj.write('EventID      Date      To    Lat    Lon     EAST    NORTH  Dep  Ml  NoP  NoS RMS  errH  errZ  Gap \n')
-
-    # data path
-    dp = path + "/e*/*.xml"
-    # list of all available xml-files
-    xmlnames = glob.glob(dp)
-
-    # read all onset weights
-    for names in xmlnames:
-        print("Getting location parameters from {}".format(names))
-        cat = read_events(names)
-        try:
-            st = cat.events[0].origins[0].time
-            Lat = cat.events[0].origins[0].latitude
-            Lon = cat.events[0].origins[0].longitude
-            EAST, NORTH = p(Lon, Lat)
-            Dep = cat.events[0].origins[0].depth / 1000
-            Ml = cat.events[0].magnitudes[1].mag
-            NoP = []
-            NoS = []
-        except IndexError:
-            print ('Insufficient data found for event (not localised): ' + names.split('/')[-1].split('_')[-1][:-4] + ' Skipping event for eventlist.' )
-            continue
- 
-        for i in range(len(cat.events[0].origins[0].arrivals)):
-            if cat.events[0].origins[0].arrivals[i].phase == 'P':
-                NoP.append(cat.events[0].origins[0].arrivals[i].phase)
-            elif cat.events[0].origins[0].arrivals[i].phase == 'S':
-                NoS.append(cat.events[0].origins[0].arrivals[i].phase)
-        #NoP = cat.events[0].origins[0].quality.used_station_count
-        errH = cat.events[0].origins[0].origin_uncertainty.max_horizontal_uncertainty
-        errZ = cat.events[0].origins[0].depth_errors.uncertainty
-        Gap = cat.events[0].origins[0].quality.azimuthal_gap
-        #evID = names.split('/')[6]
-        evID = names.split('/')[-1].split('_')[-1][:-4]
-        Date = str(st.year) + str('%02d' % st.month) + str('%02d' % st.day)
-        To = str('%02d' % st.hour) + str('%02d' % st.minute) + str('%02d' % st.second) + \
-                  '.' + str('%06d' % st.microsecond)
-
-        # write into eventlist
-        evlistobj.write('%s %s %s %9.6f %9.6f %13.6f %13.6f %8.6f %3.1f %d %d NaN %d %d %d\n' %(evID, \
-                         Date, To, Lat, Lon, EAST, NORTH, Dep, Ml, len(NoP), len(NoS), errH, errZ, Gap))
-        print ('Adding Event ' + names.split('/')[-1].split('_')[-1][:-4]  + ' to eventlist')
-    print('Eventlist created and saved in: ' + outpath)
-    evlistobj.close()
-

pylot/core/io/getQualitiesfromxml.py

@@ -1,139 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
-   Uncertainties are tranformed into quality classes and visualized via histogram if desired.
-   Ludger Küperkoch, BESTEC GmbH, 07/2017
-   rev.: Ludger Küperkoch, igem, 10/2020
-   Edited for usage in PyLoT: Jeldrik Gaal, igem, 01/2022
-"""
-
-import argparse
-import numpy as np
-import matplotlib.pyplot as plt
-from obspy.core.event import read_events
-import glob
-
-def getQualitiesfromxml(path):
-
-    # uncertainties 
-    ErrorsP = [0.02, 0.04, 0.08, 0.16]
-    ErrorsS = [0.04, 0.08, 0.16, 0.32]
-
-    Pw0 = []
-    Pw1 = []
-    Pw2 = []
-    Pw3 = []
-    Pw4 = []
-    Sw0 = []
-    Sw1 = []
-    Sw2 = []
-    Sw3 = []
-    Sw4 = []
-    
-    # data path
-    dp = path + '/e*/*.xml'
-    # list of all available xml-files
-    xmlnames = glob.glob(dp)
-
-    # read all onset weights
-    for names in xmlnames: 
-        print("Getting onset weights from {}".format(names))
-        cat = read_events(names)
-        arrivals = cat.events[0].picks
-        for Pick in arrivals:
-            if Pick.phase_hint[0] == 'P':
-                if Pick.time_errors.uncertainty <= ErrorsP[0]:     
-                    Pw0.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsP[0] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[1]:
-                     Pw1.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsP[1] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[2]:
-                     Pw2.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsP[2] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[3]:
-                     Pw3.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsP[3]:
-                     Pw4.append(Pick.time_errors.uncertainty)      
-                else:
-                    pass
-            elif Pick.phase_hint[0] == 'S':
-                if Pick.time_errors.uncertainty <= ErrorsS[0]:     
-                     Sw0.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsS[0] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[1]:
-                     Sw1.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsS[1] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[2]:
-                     Sw2.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsS[2] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[3]:
-                     Sw3.append(Pick.time_errors.uncertainty)      
-                elif Pick.time_errors.uncertainty > ErrorsS[3]:
-                     Sw4.append(Pick.time_errors.uncertainty)      
-                else:
-                    pass
-            else:
-                print("Phase hint not defined for picking!")
-                pass
-    # get percentage of weights
-    numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
-    numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
-    try:
-        P0perc = 100.0 / numPweights * len(Pw0)
-    except:
-        P0perc = 0
-    try:
-        P1perc = 100.0 / numPweights * len(Pw1)
-    except:
-        P1perc = 0
-    try:
-        P2perc = 100.0 / numPweights * len(Pw2)
-    except:
-        P2perc = 0
-    try:
-        P3perc = 100.0 / numPweights * len(Pw3)
-    except:
-        P3perc = 0
-    try:
-        P4perc = 100.0 / numPweights * len(Pw4)
-    except:
-        P4perc = 0
-    try:
-        S0perc = 100.0 / numSweights * len(Sw0)
-    except:
-        Soperc = 0
-    try:
-        S1perc = 100.0 / numSweights * len(Sw1)
-    except:
-        S1perc = 0
-    try:
-        S2perc = 100.0 / numSweights * len(Sw2)
-    except:
-        S2perc = 0
-    try:
-        S3perc = 100.0 / numSweights * len(Sw3)
-    except:
-        S3perc = 0
-    try:
-        S4perc = 100.0 / numSweights * len(Sw4)
-    except:
-        S4perc = 0
-
-    weights = ('0', '1', '2', '3', '4')
-    y_pos = np.arange(len(weights))
-    width = 0.34
-    p1, = plt.bar(0 - width, P0perc, width, color='black')
-    p2, = plt.bar(0, S0perc, width, color='red')
-    plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
-    plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
-    plt.ylabel('%')
-    plt.xticks(y_pos, weights)
-    plt.xlim([-0.5, 4.5])
-    plt.xlabel('Qualities')
-    plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights)) 
-    plt.legend([p1, p2], ['P-Weights', 'S-Weights'])
-    plt.show()
-

pylot/core/io/phases.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import pdb
+
 import glob
 import matplotlib.pyplot as plt
 import numpy as np
@@ -512,13 +512,13 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             and FOCMEC- and HASH-input files 
     :type eventinfo: `obspy.core.event.Event` object
     """
+
     if fformat == 'NLLoc':
         print("Writing phases to %s for NLLoc" % filename)
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
                   (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)
         for key in arrivals:
             # P onsets
             if arrivals[key].has_key('P'):
@@ -573,8 +573,6 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                 except KeyError as e:
                     print(str(e) + '; no weight set during processing')
                 Ao = arrivals[key]['S']['Ao'] # peak-to-peak amplitude
-                if Ao == None:
-                    Ao = 0.0
                 #fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
                 fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 %9.2f 0 0 %d \n' % (key,
                                                                                            fm,
@@ -594,7 +592,6 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # write header
         fid.write('                                                                %s\n' %
                   parameter.get('eventID'))
-        arrivals = chooseArrivals(arrivals)
         for key in arrivals:
             if arrivals[key]['P']['weight'] < 4:
                 stat = key
@@ -671,7 +668,6 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)
         for key in arrivals:
             # P onsets
             if arrivals[key].has_key('P') and arrivals[key]['P']['mpp'] is not None:
@@ -767,33 +763,30 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
             arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
+        for key in arrivals:
-        # prefer manual picks
-        usedarrivals = chooseArrival(arrivals) 
-        for key in usedarrivals:
             # P onsets
-            if usedarrivals[key].has_key('P'):
+            if arrivals[key].has_key('P'):
-                if usedarrivals[key]['P']['weight'] < 4:
+                if arrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
                     if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
-                    Ponset = usedarrivals[key]['P']['mpp']
+                    Ponset = arrivals[key]['P']['mpp']
-                    Pweight = usedarrivals[key]['P']['weight']
+                    Pweight = arrivals[key]['P']['weight']
                     Prt = Ponset - stime  # onset time relative to source time
                     if n % 6 != 0:
                         fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))
                     else:
                         fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
                         # S onsets
-            if usedarrivals[key].has_key('S'):
+            if arrivals[key].has_key('S'):
-                if usedarrivals[key]['S']['weight'] < 4:
+                if arrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
                     if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
-                    Sonset = usedarrivals[key]['S']['mpp']
+                    Sonset = arrivals[key]['S']['mpp']
-                    Sweight = usedarrivals[key]['S']['weight']
+                    Sweight = arrivals[key]['S']['weight']
                     Srt = Ponset - stime  # onset time relative to source time
                     if n % 6 != 0:
                         fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))
@@ -811,12 +804,8 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             print("No source origin calculated yet, thus no hypoDD-infile creation possible!")
             return
         stime = eventsource['time']
-        try:
+        event = parameter.get('eventID')
-            event = eventinfo['pylot_id']
+        hddID = event.split('.')[0][1:5]        
-            hddID = event.split('.')[0][1:5]
-        except:
-            print ("Error 1111111!")
-            hddID = "00000"       
         # write header
         fid.write('# %d  %d %d %d %d %5.2f %7.4f +%6.4f %7.4f %4.2f 0.1 0.5 %4.2f      %s\n' % (
             stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
@@ -828,20 +817,17 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
             arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
+        for key in arrivals:
-        # prefer manual picks
+            if arrivals[key].has_key('P'):
-        usedarrivals = chooseArrival(arrivals)
-        for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
                 # P onsets
-                if usedarrivals[key]['P']['weight'] < 4:
+                if arrivals[key]['P']['weight'] < 4:
-                    Ponset = usedarrivals[key]['P']['mpp']
+                    Ponset = arrivals[key]['P']['mpp']
                     Prt = Ponset - stime  # onset time relative to source time
                     fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if usedarrivals[key].has_key('S'):
+            if arrivals[key].has_key('S'):
                 # S onsets
-                if usedarrivals[key]['S']['weight'] < 4:
+                if arrivals[key]['S']['weight'] < 4:
-                    Sonset = usedarrivals[key]['S']['mpp']
+                    Sonset = arrivals[key]['S']['mpp']
                     Srt = Sonset - stime  # onset time relative to source time
                     fid.write('%-5s    %6.3f  1  S\n' % (key, Srt))
 
@@ -879,12 +865,9 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
             arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
+        for key in arrivals:
-        # prefer manual picks
+            if arrivals[key].has_key('P'):
-        usedarrivals = chooseArrival(arrivals)
+                if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
-        for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
-                if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
                     stat = key
                     for i in range(len(picks)):
                         station = picks[i].waveform_id.station_code
@@ -903,7 +886,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                     fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
                                                                            az,
                                                                            inz,
-                                                                           usedarrivals[key]['P']['fm']))
+                                                                           arrivals[key]['P']['fm']))
                                     break
 
         fid.close()
@@ -961,8 +944,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                 eventsource['quality']['used_phase_count'],
                 erh, erz, eventinfo.magnitudes[0]['mag'],
                 hashID))
-        # Prefer Manual Picks over automatic ones if possible
+
-        arrivals = chooseArrivals(arrivals)
         # write phase lines
         for key in arrivals:
             if arrivals[key].has_key('P'):
@@ -1009,25 +991,6 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid1.close()
         fid2.close()
 
-def chooseArrival(arrivals):
-    """
-    takes arrivals and returns the manual picks if manual and automatic ones are there
-    returns automatic picks if only automatic picks are there
-    :param arrivals: 'dictionary' with automatic and or manual arrivals
-    :return: arrivals but with the manual picks prefered if possible
-    """
-    # If len of arrivals is greater than 2 it comes from autopicking so only autopicks are available
-    print("=== CHOOSE ===")
-    if len(arrivals) > 2:
-        return arrivals
-    if arrivals['auto'] and arrivals['manual']:
-        usedarrivals = arrivals['manual']
-    elif arrivals['auto']:
-        usedarrivals = arrivals['auto']
-    elif arrivals['manual']:
-        usedarrivals = arrivals['manual']
-    return usedarrivals
-
 
 def merge_picks(event, picks):
     """