Merge branch 'develop' into feature/port-to-py3

.gitignore

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

PyLoT.py

@@ -91,6 +91,8 @@ 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
 
@@ -346,6 +348,9 @@ 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,
@@ -486,6 +491,11 @@ 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,
@@ -554,7 +564,7 @@ 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)
+        pickActions = (self.auto_tune, self.auto_pick, self.compare_action, self.qualities_action, self.eventlist_xml_action)
 
         # pickToolBar = self.addToolBar("PickTools")
         # pickToolActions = (selectStation, )
@@ -1648,6 +1658,14 @@ 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):
@@ -2091,6 +2109,7 @@ 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()
@@ -2163,6 +2182,7 @@ 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)
@@ -2543,7 +2563,13 @@ 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

@@ -30,6 +30,7 @@
         <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

@@ -0,0 +1,79 @@
+#!/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

@@ -0,0 +1,139 @@
+#!/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'):
@@ -573,6 +573,8 @@ 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,
@@ -592,6 +594,7 @@ 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
@@ -668,6 +671,7 @@ 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:
@@ -763,30 +767,33 @@ 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)
-        for key in arrivals:
+        # check for automatic and manual picks
+        # prefer manual picks
+        usedarrivals = chooseArrival(arrivals) 
+        for key in usedarrivals:
             # P onsets
-            if arrivals[key].has_key('P'):
+            if usedarrivals[key].has_key('P'):
-                if arrivals[key]['P']['weight'] < 4:
+                if usedarrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
                     if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
-                    Ponset = arrivals[key]['P']['mpp']
+                    Ponset = usedarrivals[key]['P']['mpp']
-                    Pweight = arrivals[key]['P']['weight']
+                    Pweight = usedarrivals[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 arrivals[key].has_key('S'):
+            if usedarrivals[key].has_key('S'):
-                if arrivals[key]['S']['weight'] < 4:
+                if usedarrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
                     if len(stat) > 4:  # VELEST handles only 4-string station IDs
                         stat = stat[1:5]
-                    Sonset = arrivals[key]['S']['mpp']
+                    Sonset = usedarrivals[key]['S']['mpp']
-                    Sweight = arrivals[key]['S']['weight']
+                    Sweight = usedarrivals[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))
@@ -804,8 +811,12 @@ 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']
-        event = parameter.get('eventID')
+        try:
-        hddID = event.split('.')[0][1:5]        
+            event = eventinfo['pylot_id']
+            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,
@@ -817,17 +828,20 @@ 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)
-        for key in arrivals:
+        # check for automatic and manual picks
-            if arrivals[key].has_key('P'):
+        # prefer manual picks
+        usedarrivals = chooseArrival(arrivals)
+        for key in usedarrivals:
+            if usedarrivals[key].has_key('P'):
                 # P onsets
-                if arrivals[key]['P']['weight'] < 4:
+                if usedarrivals[key]['P']['weight'] < 4:
-                    Ponset = arrivals[key]['P']['mpp']
+                    Ponset = usedarrivals[key]['P']['mpp']
                     Prt = Ponset - stime  # onset time relative to source time
                     fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if arrivals[key].has_key('S'):
+            if usedarrivals[key].has_key('S'):
                 # S onsets
-                if arrivals[key]['S']['weight'] < 4:
+                if usedarrivals[key]['S']['weight'] < 4:
-                    Sonset = arrivals[key]['S']['mpp']
+                    Sonset = usedarrivals[key]['S']['mpp']
                     Srt = Sonset - stime  # onset time relative to source time
                     fid.write('%-5s    %6.3f  1  S\n' % (key, Srt))
 
@@ -865,9 +879,12 @@ 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)
-        for key in arrivals:
+        # check for automatic and manual picks
-            if arrivals[key].has_key('P'):
+        # prefer manual picks
-                if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
+        usedarrivals = chooseArrival(arrivals)
+        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
@@ -886,7 +903,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                     fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
                                                                            az,
                                                                            inz,
-                                                                           arrivals[key]['P']['fm']))
+                                                                           usedarrivals[key]['P']['fm']))
                                     break
 
         fid.close()
@@ -944,7 +961,8 @@ 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'):
@@ -991,6 +1009,25 @@ 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):
     """