Merge branch 'refs/heads/develop' into correlation_picker

Certain tests fail on snrdb calculation which has to be examined (WIP)

.gitignore

@@ -2,3 +2,4 @@
 *~
 .idea
 pylot/RELEASE-VERSION
+/tests/test_autopicker/dmt_database_test/

.mailmap

@@ -0,0 +1,39 @@
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <Darius_A@web.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <darius.arnold@rub.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <darius.arnold@ruhr-uni-bochum.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <mail@dariusarnold.de>
+
+Dennis Wlecklik <dennisw@minos02.geophysik.ruhr-uni-bochum.de>
+
+Jeldrik Gaal <jeldrikgaal@gmail.com>
+
+Kaan Coekerim <kaan.coekerim@ruhr-uni-bochum.de>
+Kaan Coekerim <kaan.coekerim@ruhr-uni-bochum.de> <kaan.coekerim@rub.de>
+
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <kueperkoch@bestec-for-nature.com>
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <ludger@quake2.(none)>
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <ludger@sauron.bestec-for-nature>
+
+Marc S. Boxberg <marc.boxberg@rub.de>
+
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel.paffrath@rub.de> 
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos01.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos02.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos25.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@email.com>
+
+Sally Zimmermann <sally.zimmermann@ruhr-uni-bochum.de>
+
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos01.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos02.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos22.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling-benatelli@scisys.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling@rub.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling@rub.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <DarkBeQst@users.noreply.github.com>
+
+Thomas Moeller <thomas.moeller@rub.de>
+
+Ann-Christin Koch <ann-christin.koch@ruhr-uni-bochum.de> <Ann-Christin.Koch@ruhr-uni-bochum.de>
+
+Sebastian Priebe <sebastian.priebe@rub.de>

PyLoT.py

@@ -83,7 +83,7 @@ from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
 from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
-    ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
+    ComparisonWidget, TuneAutopicker, PylotParameterWidget, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
     SpectrogramTab, SearchFileByExtensionDialog
 from pylot.core.util.array_map import Array_map
@@ -136,7 +136,7 @@ class MainWindow(QMainWindow):
         self.project.parameter = self._inputs
         self.tap = None
         self.apw = None
-        self.paraBox = None
+        self.parameterWidget = None
         self.array_map = None
         self._metadata = Metadata(verbosity=0)
         self._eventChanged = [False, False]
@@ -188,7 +188,6 @@ class MainWindow(QMainWindow):
         self.table_headers = ['', 'Event', 'Time', 'Lat', 'Lon', 'Depth', 'Ml', 'Mw', '[N] MP', '[N] AP', 'Tuning Set',
                               'Test Set', 'Notes']
 
-        # TODO: refactor rootpath to datapath
         while True:
             try:
                 if settings.value("user/FullName", None) is None:
@@ -686,10 +685,9 @@ class MainWindow(QMainWindow):
         # add scroll area used in case number of traces gets too high
         self.wf_scroll_area = QtWidgets.QScrollArea(self)
         self.wf_scroll_area.setVisible(False)
-        self.no_data_label = QLabel('No Data')
+        self.no_data_label = QLabel('No Data. If data were already loaded, try to select the event again in the eventbox.')
         self.no_data_label.setStyleSheet('color: red')
         self.no_data_label.setAlignment(Qt.AlignCenter)
-
         # create central matplotlib figure canvas widget
         self.init_wfWidget()
 
@@ -1032,8 +1030,24 @@ class MainWindow(QMainWindow):
                 fname = self.filename_from_action(action)
                 if not fname:
                     return
+
         if not event:
             event = self.get_current_event()
+
+        if event.picks:
+            qmb = QMessageBox(self, icon=QMessageBox.Question,
+                              text='Do you want to overwrite the data?',)
+            overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
+            merge_button = qmb.addButton('Merge', QMessageBox.NoRole)
+            qmb.exec_()
+
+            if qmb.clickedButton() == overwrite_button:
+                merge_strategy = 'Overwrite'
+            elif qmb.clickedButton() == merge_button:
+                merge_strategy = 'Merge'
+            else:
+                return
+
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
@@ -1196,7 +1210,7 @@ class MainWindow(QMainWindow):
                 with open(eventlist_file, 'r') as infile:
                     eventlist_subset = [os.path.join(basepath, filename.split('\n')[0]) for filename in
                                         infile.readlines()]
-                    msg = 'Found file "eventlist.txt" in database path. WILL ONLY USE SELECTED EVENTS out of {} events ' \
+                    msg = 'Found file "eventlist.txt" in datapath. WILL ONLY USE SELECTED EVENTS out of {} events ' \
                           'contained in this subset'
                     print(msg.format(len(eventlist_subset)))
                     eventlist = [eventname for eventname in eventlist if eventname in eventlist_subset]
@@ -1221,49 +1235,34 @@ class MainWindow(QMainWindow):
         # get path from first event in list and split them
         path = eventlist[0]
         try:
-            system_name = platform.system()
-            if system_name in ["Linux", "Darwin"]:
-                dirs = {
-                    'database': path.split('/')[-2],
-                    'datapath': os.path.split(path)[0],  # path.split('/')[-3],
-                    'rootpath': '/' + os.path.join(*path.split('/')[:-3])
-                }
-            elif system_name == "Windows":
-                rootpath = path.split('/')[:-3]
-                rootpath[0] += '/'
-                dirs = {
-                    # TODO: Arrange path to meet Win standards
-                    'database': path.split('/')[-2],
-                    'datapath': path.split('/')[-3],
-                    'rootpath': os.path.join(*rootpath)
-                }
+            datapath = os.path.split(path)[0]
+            dirs = {
+                'datapath': datapath,
+            }
         except Exception as e:
             dirs = {
-                'database': '',
                 'datapath': '',
-                'rootpath': ''
             }
             print('Warning: Could not automatically init folder structure. ({})'.format(e))
 
         settings = QSettings()
-        settings.setValue("data/dataRoot", dirs['datapath'])  # d irs['rootpath'])
+        settings.setValue("data/dataRoot", dirs['datapath'])
         settings.sync()
 
         if not self.project.eventlist:
             # init parameter object
             self.setParameter(show=False)
             # hide all parameter (show all needed parameter later)
-            self.paraBox.hide_parameter()
+            self.parameterWidget.hide_parameter()
             for directory in dirs.keys():
                 # set parameter
-                box = self.paraBox.boxes[directory]
-                self.paraBox.setValue(box, dirs[directory])
+                box = self.parameterWidget.boxes[directory]
+                self.parameterWidget.setValue(box, dirs[directory])
                 # show needed parameter in box
-                self.paraBox.show_parameter(directory)
-            dirs_box = self.paraBox.get_groupbox_dialog('Directories')
+                self.parameterWidget.show_parameter(directory)
+            dirs_box = self.parameterWidget.get_groupbox_dialog('Directories')
             if not dirs_box.exec_():
                 return
-            self.project.rootpath = dirs['rootpath']
             self.project.datapath = dirs['datapath']
         else:
             if hasattr(self.project, 'datapath'):
@@ -1272,7 +1271,6 @@ class MainWindow(QMainWindow):
                                         'Datapath missmatch to current project!')
                     return
             else:
-                self.project.rootpath = dirs['rootpath']
                 self.project.datapath = dirs['datapath']
 
         self.project.add_eventlist(eventlist)
@@ -1360,11 +1358,10 @@ class MainWindow(QMainWindow):
             return True
 
     def modify_project_path(self, new_rootpath):
-        # TODO: change root to datapath
-        self.project.rootpath = new_rootpath
+        self.project.datapath = new_rootpath
         for event in self.project.eventlist:
-            event.rootpath = new_rootpath
-            event.path = os.path.join(event.rootpath, event.datapath, event.database, event.pylot_id)
+            event.datapath = new_rootpath
+            event.path = os.path.join(event.datapath, event.pylot_id)
             event.path = event.path.replace('\\', '/')
             event.path = event.path.replace('//', '/')
 
@@ -1558,7 +1555,7 @@ class MainWindow(QMainWindow):
             self.set_fname(self.get_data().getEventFileName(), type)
         return self.get_fnames(type)
 
-    def saveData(self, event=None, directory=None, outformats=['.xml', '.cnv', '.obs', '_focmec.in', '.pha']):
+    def saveData(self, event=None, directory=None, outformats=None):
         '''
         Save event data to directory with specified output formats.
         :param event: PyLoT Event, if not set current event will be used
@@ -1566,6 +1563,8 @@ class MainWindow(QMainWindow):
         :param outformats: str/list of output formats
         :return:
         '''
+        if outformats is None:
+            outformats = ['.xml', '.cnv', '.obs', '_focmec.in', '.pha']
         if not event:
             event = self.get_current_event()
         if not type(outformats) == list:
@@ -1701,7 +1700,7 @@ class MainWindow(QMainWindow):
 
     # WIP JG
     def eventlistXml(self):
-        path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
+        path = self._inputs['datapath']
         outpath = self.project.location[:self.project.location.rfind('/')]
         geteventlistfromxml(path, outpath)
         return
@@ -2428,7 +2427,7 @@ class MainWindow(QMainWindow):
         filterS = filteroptions['S']
         minP, maxP = filterP.getFreq()
         minS, maxS = filterS.getFreq()
-        self.paraBox.params_to_gui()
+        self.parameterWidget.params_to_gui()
 
     def getFilterOptions(self):
         return self.filteroptions
@@ -3176,8 +3175,8 @@ class MainWindow(QMainWindow):
         ttt = parameter['ttpatter']
         outfile = parameter['outpatter']
         eventname = self.get_current_event_name()
-        obsdir = os.path.join(self._inputs['rootpath'], self._inputs['datapath'], self._inputs['database'], eventname)
-        self.saveData(event=self.get_current_event(), directory=obsdir, outformats='.obs')
+        obsdir = os.path.join(self._inputs['datapath'], eventname)
+        self.saveData(event=self.get_current_event(), directory=obsdir, outformats=['.obs'])
         filename = 'PyLoT_' + eventname
         locpath = os.path.join(locroot, 'loc', filename)
         phasefile = os.path.join(obsdir, filename + '.obs')
@@ -3734,6 +3733,7 @@ class MainWindow(QMainWindow):
                 if self.project.parameter:
                     # do this step to update default parameter on older PyLoT projects
                     self.project.parameter.reinit_default_parameters()
+                    PylotParameter.check_deprecated_parameters(self.project.parameter)
 
                     self._inputs = self.project.parameter
                     self.updateFilteroptions()
@@ -3851,13 +3851,13 @@ class MainWindow(QMainWindow):
 
     def setParameter(self, checked=0, show=True):
         if checked: pass  # dummy argument to receive trigger signal (checked) if called by QAction
-        if not self.paraBox:
-            self.paraBox = PylotParaBox(self._inputs, parent=self, windowflag=Qt.Window)
-            self.paraBox.accepted.connect(self._setDirty)
-            self.paraBox.accepted.connect(self.filterOptionsFromParameter)
+        if not self.parameterWidget:
+            self.parameterWidget = PylotParameterWidget(self._inputs, parent=self, windowflag=Qt.Window)
+            self.parameterWidget.accepted.connect(self._setDirty)
+            self.parameterWidget.accepted.connect(self.filterOptionsFromParameter)
         if show:
-            self.paraBox.params_to_gui()
-            self.paraBox.show()
+            self.parameterWidget.params_to_gui()
+            self.parameterWidget.show()
 
     def deleteAllAutopicks(self):
         qmb = QMessageBox(self, icon=QMessageBox.Question,
@@ -3904,16 +3904,18 @@ class Project(object):
     Pickable class containing information of a PyLoT project, like event lists and file locations.
     '''
 
-    # TODO: remove rootpath
     def __init__(self):
         self.eventlist = []
         self.location = None
-        self.rootpath = None
         self.datapath = None
         self.dirty = False
         self.parameter = None
         self._table = None
 
+    @property
+    def rootpath(self):
+        return self.datapath
+
     def add_eventlist(self, eventlist):
         '''
         Add events from an eventlist containing paths to event directories.
@@ -3923,8 +3925,6 @@ class Project(object):
             return
         for item in eventlist:
             event = Event(item)
-            event.rootpath = self.parameter['rootpath']
-            event.database = self.parameter['database']
             event.datapath = self.parameter['datapath']
             if not event.path in self.getPaths():
                 self.eventlist.append(event)

autoPyLoT.py

@@ -136,11 +136,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
     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')}
+        dsfields = {'dpath': parameter.get('datapath'),}
 
-        exf = ['root', 'dpath', 'dbase']
+        exf = ['dpath']
 
         if parameter['eventID'] != '*' and fnames == 'None':
             dsfields['eventID'] = parameter['eventID']
@@ -186,15 +184,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         if not input_dict:
             # started in production mode
             datapath = datastructure.expandDataPath()
-            if fnames == 'None' and parameter['eventID'] == '*':
+            if fnames in [None, 'None'] and parameter['eventID'] == '*':
                 # multiple event processing
                 # read each event in database
                 events = [event for event in glob.glob(os.path.join(datapath, '*')) if
                           (os.path.isdir(event) and not event.endswith('EVENTS-INFO'))]
-            elif fnames == 'None' and parameter['eventID'] != '*' and not type(parameter['eventID']) == list:
+            elif fnames in [None, 'None'] and parameter['eventID'] != '*' 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:
+            elif fnames in [None, 'None'] and type(parameter['eventID']) == list:
                 # multiple event processing
                 events = []
                 for eventID in parameter['eventID']:
@@ -206,12 +204,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 locflag = 2
         else:
             # started in tune or interactive mode
-            datapath = os.path.join(parameter['rootpath'],
-                                    parameter['datapath'])
+            datapath = parameter['datapath']
             events = []
             for eventID in eventid:
                 events.append(os.path.join(datapath,
-                                           parameter['database'],
                                            eventID))
 
         if not events:
@@ -238,12 +234,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 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))
+                if type(e) == FileNotFoundError:
+                    print('Creating new event file.')
+                else:
+                    print('Could not read event from file {}: {}'.format(filename, e))
                 data = Data()
                 pylot_event = Event(eventpath)  # event should be path to event directory
                 data.setEvtData(pylot_event)
-            if fnames == 'None':
-                data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
+            if fnames in [None, 'None']:
+                data.setWFData(glob.glob(os.path.join(event_datapath, '*')))
                 # the following is necessary because within
                 # multiple event processing no event ID is provided
                 # in autopylot.in

docs/gui.md

@@ -203,8 +203,6 @@ The meaning of the header entries is:
 PyLoT GUI starts with an empty project. To add events, use the add event data button. Select one or multiple folders
 containing events.
 
-[//]: <> (TODO: explain _Directories: Root path, Data path, Database path_)
-
 ### Saving projects
 
 Save the current project from the menu with File->Save project or File->Save project as. PyLoT uses ``.plp`` files to

inputs/pylot_global.in

@@ -4,10 +4,8 @@
 %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)                           
+                                                   #datapath#       %data path
+                                                   #eventID#        %event ID for single event processing (* for all events found in datapath)
                                                    #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 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
+P,Pdiff                                            #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 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]                                     

inputs/pylot_local.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/DATA/Insheim                                      #rootpath#       %project path                                                                                        
-EVENT_DATA/LOCAL                                   #datapath#       %data path                                                                                           
-2018.02_Insheim                                    #database#       %name of data base                                                                                   
-e0006.038.18                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/DATA/Insheim/EVENT_DATA/LOCAL/2018.02_Insheim     #datapath#       %data path
+e0006.038.18                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /DATA/Insheim/STAT_INFO                            #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -42,7 +40,8 @@ local                                              #extent#         %extent of a
 -0.5                                               #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                                         
 False                                              #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
-iasp91                                             #taup_model#     %define TauPy model for traveltime estimation                                                        
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation
+P                                                  #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 2.0 20.0                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 2.0 30.0                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 2.0 10.0                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

inputs/pylot_regional.in

@@ -4,10 +4,8 @@
 %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)                           
+                                                   #datapath#       %data path
+                                                   #eventID#        %event ID for single event processing (* for all events found in datapath)
                                                    #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -42,7 +40,8 @@ local                                              #extent#         %extent of a
 -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                                                        
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation
+P                                                  #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 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]                                     

pylot/core/io/default_parameters.py

@@ -6,24 +6,14 @@ import numpy as np
 Default parameters used for picking
 """
 
-defaults = {'rootpath': {'type': str,
-                         'tooltip': 'project path',
-                         'value': '',
-                         'namestring': 'Root path'},
-
-            'datapath': {'type': str,
-                         'tooltip': 'data path',
+defaults = {'datapath': {'type': str,
+                         'tooltip': 'path to eventfolders',
                          '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': '',
+                        'tooltip': 'event ID for single event processing (* for all events found in datapath)',
+                        'value': '*',
                         'namestring': 'Event ID'},
 
             'extent': {'type': str,
@@ -522,9 +512,7 @@ defaults = {'rootpath': {'type': str,
 
 settings_main = {
     'dirs': [
-        'rootpath',
         'datapath',
-        'database',
         'eventID',
         'invdir',
         'datastructure',

pylot/core/io/inputs.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+import logging
+import os
 
 from pylot.core.io import default_parameters
 from pylot.core.util.errors import ParameterError
@@ -88,10 +90,10 @@ class PylotParameter(object):
         return bool(self.__parameter)
 
     def __getitem__(self, key):
-        try:
+        if key in self.__parameter:
             return self.__parameter[key]
-        except:
-            return None
+        else:
+            logging.warning(f'{key} not found in PylotParameter')
 
     def __setitem__(self, key, value):
         try:
@@ -418,6 +420,28 @@ class PylotParameter(object):
             line = value + name + ttip
             fid.write(line)
 
+    @staticmethod
+    def check_deprecated_parameters(parameters):
+        if parameters.hasParam('database') and parameters.hasParam('rootpath'):
+            parameters['datapath'] = os.path.join(parameters['rootpath'], parameters['datapath'],
+                                                  parameters['database'])
+            logging.warning(
+                f'Parameters database and rootpath are deprecated. '
+                f'Tried to merge them to now path: {parameters["datapath"]}.'
+            )
+
+        remove_keys = []
+        for key in parameters:
+            if not key in default_parameters.defaults.keys():
+                remove_keys.append(key)
+                logging.warning(f'Removing deprecated parameter: {key}')
+
+        for key in remove_keys:
+            del parameters[key]
+
+        parameters._settings_main = default_parameters.settings_main
+        parameters._settings_special_pick = default_parameters.settings_special_pick
+
 
 class FilterOptions(object):
     '''

pylot/core/io/phases.py

@@ -512,7 +512,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         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')))
+                  (parameter.get('datapath'), parameter.get('eventID')))
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
@@ -665,7 +665,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         print("Writing phases to %s for HYPOSAT" % filename)
         fid = open("%s" % filename, 'w')
         # write header
-        fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
+        fid.write('%s, event %s \n' % (parameter.get('datapath'), parameter.get('eventID')))
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets

pylot/core/pick/autopick.py

@@ -262,6 +262,10 @@ class AutopickStation(object):
         self.metadata = metadata
         self.origin = origin
 
+        # initialize TauPy pick estimates
+        self.estFirstP = None
+        self.estFirstS = None
+
         # initialize picking results
         self.p_results = PickingResults()
         self.s_results = PickingResults()
@@ -443,15 +447,15 @@ class AutopickStation(object):
             for arr in arrivals:
                 phases[identifyPhaseID(arr.phase.name)].append(arr)
             # get first P and S onsets from arrivals list
-            estFirstP = 0
-            estFirstS = 0
+            arrival_time_p = 0
+            arrival_time_s = 0
             if len(phases['P']) > 0:
-                arrP, estFirstP = min([(arr, arr.time) for arr in phases['P']], key=lambda t: t[1])
+                arrP, arrival_time_p = min([(arr, arr.time) for arr in phases['P']], key=lambda t: t[1])
             if len(phases['S']) > 0:
-                arrS, estFirstS = min([(arr, arr.time) for arr in phases['S']], key=lambda t: t[1])
+                arrS, arrival_time_s = min([(arr, arr.time) for arr in phases['S']], key=lambda t: t[1])
             print('autopick: estimated first arrivals for P: {} s, S:{} s after event'
-                  ' origin time using TauPy'.format(estFirstP, estFirstS))
-            return estFirstP, estFirstS
+                  ' origin time using TauPy'.format(arrival_time_p, arrival_time_s))
+            return arrival_time_p, arrival_time_s
 
         def exit_taupy():
             """If taupy failed to calculate theoretical starttimes, picking continues.
@@ -477,10 +481,13 @@ class AutopickStation(object):
             raise AttributeError('No source origins given!')
 
         arrivals = create_arrivals(self.metadata, self.origin, self.pickparams["taup_model"])
-        estFirstP, estFirstS = first_PS_onsets(arrivals)
+        arrival_P, arrival_S = first_PS_onsets(arrivals)
+
+        self.estFirstP = (self.origin[0].time + arrival_P) - self.ztrace.stats.starttime
+
         # modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
-        self.pickparams["pstart"] += (self.origin[0].time + estFirstP) - self.ztrace.stats.starttime
-        self.pickparams["pstop"] += (self.origin[0].time + estFirstP) - self.ztrace.stats.starttime
+        self.pickparams["pstart"] += self.estFirstP
+        self.pickparams["pstop"] += self.estFirstP
         print('autopick: CF calculation times respectively:'
               ' pstart: {} s, pstop: {} s'.format(self.pickparams["pstart"], self.pickparams["pstop"]))
         # make sure pstart and pstop are inside the starttime/endtime of vertical trace
@@ -491,9 +498,10 @@ class AutopickStation(object):
             # for the two horizontal components take earliest and latest time to make sure that the s onset is not clipped
             # if start and endtime of horizontal traces differ, the s windowsize will automatically increase
             trace_s_start = min([self.etrace.stats.starttime, self.ntrace.stats.starttime])
+            self.estFirstS = (self.origin[0].time + arrival_S) - trace_s_start
             # modifiy sstart and sstop relative to estimated first S arrival (relative to station time axis)
-            self.pickparams["sstart"] += (self.origin[0].time + estFirstS) - trace_s_start
-            self.pickparams["sstop"] += (self.origin[0].time + estFirstS) - trace_s_start
+            self.pickparams["sstart"] += self.estFirstS
+            self.pickparams["sstop"] += self.estFirstS
             print('autopick: CF calculation times respectively:'
                   ' sstart: {} s, sstop: {} s'.format(self.pickparams["sstart"], self.pickparams["sstop"]))
             # make sure pstart and pstop are inside the starttime/endtime of horizontal traces
@@ -609,6 +617,12 @@ class AutopickStation(object):
             # plot tapered trace filtered with bpz2 filter settings
             ax1.plot(tdata, self.tr_filt_z_bpz2.data / max(self.tr_filt_z_bpz2.data), color=linecolor, linewidth=0.7,
                      label='Data')
+            # plot pickwindows for P
+            pstart, pstop = self.pickparams['pstart'], self.pickparams['pstop']
+            if pstart is not None and pstop is not None:
+                ax1.axvspan(pstart, pstop, color='r', alpha=0.1, zorder=0, label='P window')
+            if self.estFirstP is not None:
+                ax1.axvline(self.estFirstP, ls='dashed', color='r', alpha=0.4, label='TauPy estimate')
             if self.p_results.weight < 4:
                 # plot CF of initial onset (HOScf or ARZcf)
                 ax1.plot(self.cf1.getTimeArray(), self.cf1.getCF() / max(self.cf1.getCF()), 'b', label='CF1')
@@ -713,6 +727,15 @@ class AutopickStation(object):
                         ax3.plot([refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [-1.3, -1.3], 'g', linewidth=2)
                         ax3.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
                         ax3.plot([self.s_results.epp, self.s_results.epp], [-1.1, 1.1], 'g--', label='epp')
+
+                # plot pickwindows for S
+                sstart, sstop = self.pickparams['sstart'], self.pickparams['sstop']
+                if sstart is not None and sstop is not None:
+                    for axis in [ax2, ax3]:
+                        axis.axvspan(sstart, sstop, color='b', alpha=0.1, zorder=0, label='S window')
+                        if self.estFirstS is not None:
+                            axis.axvline(self.estFirstS, ls='dashed', color='b', alpha=0.4, label='TauPy estimate')
+
                 ax3.legend(loc=1)
                 ax3.set_yticks([])
                 ax3.set_ylim([-1.5, 1.5])
@@ -835,14 +858,21 @@ class AutopickStation(object):
             self.cf1 = None
         assert isinstance(self.cf1, CharacteristicFunction), 'cf1 is not set correctly: maybe the algorithm name ({})' \
                                                              ' is corrupted'.format(self.pickparams["algoP"])
+        # get the original waveform stream from first CF class cut to identical length as CF for plotting
+        cut_ogstream = self.cf1.getDataArray(self.cf1.getCut())
+
+        # MP: Rename to cf_stream for further use of z_copy and to prevent chaos when z_copy suddenly becomes a cf
+        # stream and later again a waveform stream
+        cf_stream = z_copy.copy()
+        cf_stream[0].data = self.cf1.getCF()
+
         # calculate AIC cf from first cf (either HOS or ARZ)
-        z_copy[0].data = self.cf1.getCF()
-        aiccf = AICcf(z_copy, cuttimes)
+        aiccf = AICcf(cf_stream, cuttimes)
         # get preliminary onset time from AIC-CF
         self.set_current_figure('aicFig')
         aicpick = AICPicker(aiccf, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
                             Tsmooth=self.pickparams["aictsmooth"], fig=self.current_figure,
-                            linecolor=self.current_linecolor)
+                            linecolor=self.current_linecolor, ogstream=cut_ogstream)
         # save aicpick for plotting later
         self.p_data.aicpick = aicpick
         # add pstart and pstop to aic plot
@@ -855,7 +885,7 @@ class AutopickStation(object):
                           label='P stop')
                 ax.legend(loc=1)
 
-        Pflag = self._pick_p_quality_control(aicpick, z_copy, tr_filt)
+        Pflag = self._pick_p_quality_control(aicpick, cf_stream, tr_filt)
         # go on with processing if AIC onset passes quality control
         slope = aicpick.getSlope()
         if not slope: slope = 0
@@ -894,7 +924,7 @@ class AutopickStation(object):
         refPpick = PragPicker(self.cf2, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
                               self.pickparams["ausP"],
                               self.pickparams["tsmoothP"], aicpick.getpick(), self.current_figure,
-                              self.current_linecolor)
+                              self.current_linecolor, ogstream=cut_ogstream)
         # save PragPicker result for plotting
         self.p_data.refPpick = refPpick
         self.p_results.mpp = refPpick.getpick()
@@ -1146,11 +1176,14 @@ class AutopickStation(object):
         # calculate AIC cf
         haiccf = self._calculate_aic_cf_s_pick(cuttimesh)
 
+        # get the original waveform stream cut to identical length as CF for plotting
+        ogstream = haiccf.getDataArray(haiccf.getCut())
+
         # get preliminary onset time from AIC cf
         self.set_current_figure('aicARHfig')
         aicarhpick = AICPicker(haiccf, self.pickparams["tsnrh"], self.pickparams["pickwinS"], self.iplot,
                                Tsmooth=self.pickparams["aictsmoothS"], fig=self.current_figure,
-                               linecolor=self.current_linecolor)
+                               linecolor=self.current_linecolor, ogstream=ogstream)
         # save pick for later plotting
         self.aicarhpick = aicarhpick
 

pylot/core/pick/charfuns.py

@@ -17,7 +17,11 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 :author: MAGS2 EP3 working group
 """
 import numpy as np
-from scipy import signal
+try:
+    from scipy.signal import tukey
+except ImportError:
+    from scipy.signal.windows import tukey
+
 from obspy.core import Stream
 
 from pylot.core.pick.utils import PickingFailedException
@@ -56,7 +60,7 @@ class CharacteristicFunction(object):
         self.setOrder(order)
         self.setFnoise(fnoise)
         self.setARdetStep(t2)
-        self.calcCF(self.getDataArray())
+        self.calcCF()
         self.arpara = np.array([])
         self.xpred = np.array([])
 
@@ -208,17 +212,15 @@ class CharacteristicFunction(object):
             data = self.orig_data.copy()
             return data
 
-    def calcCF(self, data=None):
-        self.cf = data
+    def calcCF(self):
+        pass
 
 
 class AICcf(CharacteristicFunction):
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate the Akaike Information Criterion (AIC) after Maeda (1985).
-        :param data: data, time series (whether seismogram or CF)
-        :type data: tuple
         :return: AIC function
         :rtype:
         """
@@ -227,7 +229,7 @@ class AICcf(CharacteristicFunction):
         ind = np.where(~np.isnan(xnp))[0]
         if ind.size:
             xnp[:ind[0]] = xnp[ind[0]]
-        xnp = signal.tukey(len(xnp), alpha=0.05) * xnp
+        xnp = tukey(len(xnp), alpha=0.05) * xnp
         xnp = xnp - np.mean(xnp)
         datlen = len(xnp)
         k = np.arange(1, datlen)
@@ -256,13 +258,11 @@ class HOScf(CharacteristicFunction):
         """
         super(HOScf, self).__init__(data, cut, pickparams["tlta"], pickparams["hosorder"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         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), or order 2, i.e. STA/LTA.
-        :param data: data, time series (whether seismogram or CF)
-        :type data: tuple
         :return: HOS cf
         :rtype:
         """
@@ -277,47 +277,28 @@ class HOScf(CharacteristicFunction):
         elif self.getOrder() == 4:  # this is kurtosis
             y = np.power(xnp, 4)
             y1 = np.power(xnp, 2)
-        elif self.getOrder() == 2:  # this is variance, used for STA/LTA processing
-            y = np.power(xnp, 2)
-            y1 = np.power(xnp, 2)
 
         # Initialisation
         # t2: long term moving window
         ilta = int(round(self.getTime2() / self.getIncrement()))
-        ista = int(round((self.getTime2() / 10) / self.getIncrement()))  # TODO: still hard coded!!
         lta = y[0]
         lta1 = y1[0]
-        sta = y[0]
         # moving windows
         LTA = np.zeros(len(xnp))
-        STA = np.zeros(len(xnp))
         for j in range(0, len(xnp)):
             if j < 4:
                 LTA[j] = 0
-                STA[j] = 0
-            elif j <= ista and self.getOrder() == 2:
-                lta = (y[j] + lta * (j - 1)) / j
-                if self.getOrder() == 2:
-                    sta = (y[j] + sta * (j - 1)) / j
-            # elif j < 4:
             elif j <= ilta:
                 lta = (y[j] + lta * (j - 1)) / j
                 lta1 = (y1[j] + lta1 * (j - 1)) / j
-                if self.getOrder() == 2:
-                    sta = (y[j] - y[j - ista]) / ista + sta
             else:
                 lta = (y[j] - y[j - ilta]) / ilta + lta
                 lta1 = (y1[j] - y1[j - ilta]) / ilta + lta1
-                if self.getOrder() == 2:
-                    sta = (y[j] - y[j - ista]) / ista + sta
             # 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)
-            else:
-                LTA[j] = lta
-                STA[j] = sta
 
         # remove NaN's with first not-NaN-value,
         # so autopicker doesnt pick discontinuity at start of the trace
@@ -326,10 +307,7 @@ class HOScf(CharacteristicFunction):
             first = ind[0]
             LTA[:first] = LTA[first]
 
-        if self.getOrder() > 2:
-            self.cf = LTA
-        else:  # order 2 means STA/LTA!
-            self.cf = STA / LTA
+        self.cf = LTA
         self.xcf = x
 
 
@@ -339,12 +317,10 @@ class ARZcf(CharacteristicFunction):
         super(ARZcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Parorder"],
                                     fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         function used to calculate the AR prediction error from a single vertical trace. Can be used to pick
         P onsets.
-        :param data:
-        :type data: ~obspy.core.stream.Stream
         :return: ARZ cf
         :rtype:
         """
@@ -475,14 +451,12 @@ class ARHcf(CharacteristicFunction):
         super(ARHcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
                                     fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate a characteristic function using autoregressive modelling of the waveform of
         both horizontal traces.
         The waveform is predicted in a moving time window using the calculated AR parameters. The difference
         between the predicted and the actual waveform servers as a characteristic function.
-        :param data: wavefor stream
-        :type data: ~obspy.core.stream.Stream
         :return: ARH cf
         :rtype:
         """
@@ -631,14 +605,12 @@ class AR3Ccf(CharacteristicFunction):
         super(AR3Ccf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
                                      fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate a characteristic function using autoregressive modelling of the waveform of
         all three traces.
         The waveform is predicted in a moving time window using the calculated AR parameters. The difference
         between the predicted and the actual waveform servers as a characteristic function
-        :param data: stream holding all three traces
-        :type data: ~obspy.core.stream.Stream
         :return: AR3C cf
         :rtype:
         """

pylot/core/pick/picker.py

@@ -37,7 +37,8 @@ class AutoPicker(object):
 
     warnings.simplefilter('ignore')
 
-    def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None, linecolor='k'):
+    def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None,
+                 fig=None, linecolor='k', ogstream=None):
         """
         Create AutoPicker object
         :param cf: characteristic function, on which the picking algorithm is applied
@@ -59,12 +60,15 @@ class AutoPicker(object):
         :type fig: `~matplotlib.figure.Figure`
         :param linecolor: matplotlib line color string
         :type linecolor: str
+        :param ogstream: original stream (waveform), e.g. for plotting purposes
+        :type ogstream: `~obspy.core.stream.Stream`
         """
 
         assert isinstance(cf, CharacteristicFunction), "%s is not a CharacteristicFunction object" % str(cf)
         self._linecolor = linecolor
         self._pickcolor_p = 'b'
         self.cf = cf.getCF()
+        self.ogstream = ogstream
         self.Tcf = cf.getTimeArray()
         self.Data = cf.getXCF()
         self.dt = cf.getIncrement()
@@ -173,7 +177,7 @@ class AICPicker(AutoPicker):
         nn = np.isnan(self.cf)
         if len(nn) > 1:
             self.cf[nn] = 0
-        # taper AIC-CF to get rid off side maxima
+        # taper AIC-CF to get rid of side maxima
         tap = np.hanning(len(self.cf))
         aic = tap * self.cf + max(abs(self.cf))
         # smooth AIC-CF
@@ -316,16 +320,7 @@ class AICPicker(AutoPicker):
                             plt.close(fig)
                     return
                 iislope = islope[0][0:imax + 1]
-            # MP MP change slope calculation
-            # get all maxima of aicsmooth
-            iaicmaxima = argrelmax(aicsmooth)[0]
-            # get first index of maximum after pickindex (indices saved in iaicmaxima)
-            aicmax = iaicmaxima[np.where(iaicmaxima > pickindex)[0]]
-            if len(aicmax) > 0:
-                iaicmax = aicmax[0]
-            else:
-                iaicmax = -1
-            dataslope = aicsmooth[pickindex: iaicmax]
+            dataslope = self.Data[0].data[iislope]
             # calculate slope as polynomal fit of order 1
             xslope = np.arange(0, len(dataslope), 1)
             try:
@@ -336,7 +331,7 @@ class AICPicker(AutoPicker):
                 else:
                     self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
                     # normalize slope to maximum of cf to make it unit independent
-                    self.slope /= aicsmooth[iaicmax]
+                    self.slope /= self.Data[0].data[icfmax]
             except Exception as e:
                 print("AICPicker: Problems with data fitting! {}".format(e))
 
@@ -356,6 +351,12 @@ class AICPicker(AutoPicker):
                 self.Tcf = self.Tcf[0:len(self.Tcf) - 1]
             ax1.plot(self.Tcf, cf / max(cf), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
             ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
+            # plot the original waveform also for evaluation of the CF and pick
+            if self.ogstream:
+                data = self.ogstream[0].data
+                if len(data) == len(self.Tcf):
+                    ax1.plot(self.Tcf, 0.5 * data / max(data), 'k', label='Seismogram', alpha=0.3, zorder=0,
+                             lw=0.5)
             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)
@@ -376,7 +377,7 @@ class AICPicker(AutoPicker):
                             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[pickindex: iaicmax], datafit, 'g', linewidth=2,
+                ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2,
                          label='Slope')  # MP MP changed temporarily!
 
                 if self.slope is not None:

pylot/core/pick/utils.py

@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents, common_range
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -828,14 +828,22 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
     if len(X) > 1:
         # all three components available
         # make sure, all components have equal lengths
-        ilen = min([len(X[0].data), len(X[1].data), len(X[2].data)])
-        x1 = X[0][0:ilen]
-        x2 = X[1][0:ilen]
-        x3 = X[2][0:ilen]
+        earliest_starttime = min(tr.stats.starttime for tr in X)
+        cuttimes = common_range(X)
+        X = X.slice(cuttimes[0], cuttimes[1])
+        x1, x2, x3 = X[:3]
+
+        if not (len(x1) == len(x2) == len(x3)):
+            raise PickingFailedException('checksignallength: unequal lengths of components!')
+
         # get RMS trace
         rms = np.sqrt((np.power(x1, 2) + np.power(x2, 2) + np.power(x3, 2)) / 3)
+        ilen = len(rms)
+        dt = earliest_starttime - X[0].stats.starttime
+        pick -= dt
     else:
         x1 = X[0].data
+        x2 = x3 = None
         ilen = len(x1)
         rms = abs(x1)
 
@@ -874,6 +882,10 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
         fig._tight = True
         ax = fig.add_subplot(111)
         ax.plot(t, rms, color=linecolor, linewidth=0.7, label='RMS Data')
+        ax.plot(t, x1, 'k', alpha=0.3, lw=0.3, zorder=0)
+        if x2 is not None and x3 is not None:
+            ax.plot(t, x2, 'r', alpha=0.3, lw=0.3, zorder=0)
+            ax.plot(t, x3, 'g', alpha=0.3, lw=0.3, zorder=0)
         ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
         ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
         ax.plot([t[isignal[0]], t[isignal[len(isignal) - 1]]],
@@ -883,6 +895,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
         ax.set_xlabel('Time [s] since %s' % X[0].stats.starttime)
         ax.set_ylabel('Counts')
         ax.set_title('Check for Signal Length, Station %s' % X[0].stats.station)
+        ax.set_xlim(pickparams["pstart"], pickparams["pstop"])
         ax.set_yticks([])
         if plt_flag == 1:
             fig.show()

pylot/core/util/array_map.py

@@ -5,14 +5,17 @@ import traceback
 
 import cartopy.crs as ccrs
 import cartopy.feature as cf
+from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
 import matplotlib
 import matplotlib.patheffects as PathEffects
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy
-from PySide2 import QtWidgets
+from PySide2 import QtWidgets, QtGui
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from obspy import UTCDateTime
+
 from pylot.core.util.utils import identifyPhaseID
 from scipy.interpolate import griddata
 
@@ -24,10 +27,10 @@ matplotlib.use('Qt5Agg')
 
 class MplCanvas(FigureCanvas):
 
-    def __init__(self, parent=None, extern_axes=None, width=5, height=4, dpi=100):
+    def __init__(self, extern_axes=None, projection=None, width=15, height=5, dpi=100):
         if extern_axes is None:
             self.fig = plt.figure(figsize=(width, height), dpi=dpi)
-            self.axes = self.fig.add_subplot(111)
+            self.axes = self.fig.add_subplot(111, projection=projection)
         else:
             self.fig = extern_axes.figure
             self.axes = extern_axes
@@ -59,24 +62,30 @@ class Array_map(QtWidgets.QWidget):
         self.parameter = parameter if parameter else parent._inputs
 
         self.picks_rel = {}
+        self.picks_rel_mean_corrected = {}
         self.marked_stations = []
         self.highlighted_stations = []
 
         # call functions to draw everything
+        self.projection = ccrs.PlateCarree()
         self.init_graphics()
+        self.ax = self.canvas.axes
+        self.ax.set_adjustable('datalim')
+
         self.init_stations()
         self.init_crtpyMap()
         self.init_map()
+
         # set original map limits to fall back on when home button is pressed
-        self.org_xlim = self.canvas.axes.get_xlim()
-        self.org_ylim = self.canvas.axes.get_ylim()
+        self.org_xlim = self.ax.get_xlim()
+        self.org_ylim = self.ax.get_ylim()
+
         # initial map without event
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
 
         self._style = None if not hasattr(parent, '_style') else parent._style
 
-
     def init_map(self):
         self.init_colormap()
         self.connectSignals()
@@ -89,23 +98,24 @@ class Array_map(QtWidgets.QWidget):
         # initialize figure elements
 
         if self.extern_plot_axes is None:
-            self.canvas = MplCanvas(self)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+            self.canvas = MplCanvas(projection=self.projection)
         else:
-            self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+            self.canvas = MplCanvas(extern_axes=self.extern_plot_axes)
+
+        self.plotWidget = self.canvas
 
         # initialize GUI elements
         self.status_label = QtWidgets.QLabel()
         self.map_reset_button = QtWidgets.QPushButton('Reset Map View')
         self.save_map_button = QtWidgets.QPushButton('Save Map')
         self.go2eq_button = QtWidgets.QPushButton('Go to Event Location')
+        self.subtract_mean_cb = QtWidgets.QCheckBox('Subtract mean')
 
         self.main_box = QtWidgets.QVBoxLayout()
         self.setLayout(self.main_box)
 
         self.top_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.top_row, 1)
+        self.main_box.addLayout(self.top_row, 0)
 
         self.comboBox_phase = QtWidgets.QComboBox()
         self.comboBox_phase.insertItem(0, 'P')
@@ -138,14 +148,15 @@ class Array_map(QtWidgets.QWidget):
         self.top_row.addWidget(self.auto_refresh_box)
         self.top_row.addWidget(self.refresh_button)
 
-        self.main_box.addWidget(self.plotWidget, 1)
+        self.main_box.addWidget(self.plotWidget, 10)
 
         self.bot_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.bot_row, 0.3)
+        self.main_box.addLayout(self.bot_row, 0)
         self.bot_row.addWidget(QtWidgets.QLabel(''), 5)
         self.bot_row.addWidget(self.map_reset_button, 2)
         self.bot_row.addWidget(self.go2eq_button, 2)
         self.bot_row.addWidget(self.save_map_button, 2)
+        self.bot_row.addWidget(self.subtract_mean_cb, 0)
         self.bot_row.addWidget(self.status_label, 5)
 
     def init_colormap(self):
@@ -153,14 +164,12 @@ class Array_map(QtWidgets.QWidget):
         self.init_lat_lon_grid()
 
     def init_crtpyMap(self):
-        self.canvas.axes.cla()
-        self.canvas.axes = plt.axes(projection=ccrs.PlateCarree())
-        self.canvas.axes.add_feature(cf.LAND)
-        self.canvas.axes.add_feature(cf.OCEAN)
-        self.canvas.axes.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
-        self.canvas.axes.add_feature(cf.BORDERS, alpha=0.7)
-        self.canvas.axes.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.add_feature(cf.RIVERS, linewidth=1)
+        self.ax.add_feature(cf.LAND)
+        self.ax.add_feature(cf.OCEAN)
+        self.ax.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
+        self.ax.add_feature(cf.BORDERS, alpha=0.7)
+        self.ax.add_feature(cf.LAKES, alpha=0.7)
+        self.ax.add_feature(cf.RIVERS, linewidth=1)
 
         # parallels and meridians
         self.add_merid_paral()
@@ -168,12 +177,8 @@ class Array_map(QtWidgets.QWidget):
         self.canvas.fig.tight_layout()
 
     def add_merid_paral(self):
-        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.6, color='gray',
-                                                    linewidth=self.linewidth / 2, zorder=7)
-        # TODO: current cartopy version does not support label removal. Devs are working on it.
-        #  Should be fixed in coming cartopy versions
-        # self.gridlines.xformatter = LONGITUDE_FORMATTER
-        # self.gridlines.yformatter = LATITUDE_FORMATTER
+        self.gridlines = self.ax.gridlines(draw_labels=False, alpha=0.6, color='gray',
+                                           linewidth=self.linewidth / 2, zorder=7, crs=ccrs.PlateCarree())
 
     def remove_merid_paral(self):
         if len(self.gridlines.xline_artists):
@@ -181,24 +186,24 @@ class Array_map(QtWidgets.QWidget):
             self.gridlines.yline_artists[0].remove()
 
     def org_map_view(self):
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
         # parallels and meridians
-        self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.remove_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.canvas.draw_idle()
 
     def go2eq(self):
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.canvas.axes.set_xlim(lons - 10, lons + 10)
-            self.canvas.axes.set_ylim(lats - 5, lats + 5)
+            self.ax.set_xlim(lons - 10, lons + 10)
+            self.ax.set_ylim(lats - 5, lats + 5)
             # parallels and meridians
-            self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.remove_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.canvas.draw_idle()
 
         else:
             self.status_label.setText('No event information available')
@@ -212,6 +217,7 @@ class Array_map(QtWidgets.QWidget):
         self.map_reset_button.clicked.connect(self.org_map_view)
         self.go2eq_button.clicked.connect(self.go2eq)
         self.save_map_button.clicked.connect(self.saveFigure)
+        self.subtract_mean_cb.stateChanged.connect(self.toggle_subtract_mean)
 
         self.plotWidget.mpl_connect('motion_notify_event', self.mouse_moved)
         self.plotWidget.mpl_connect('scroll_event', self.mouse_scroll)
@@ -220,21 +226,32 @@ class Array_map(QtWidgets.QWidget):
 
     # set mouse events -----------------------------------------------------
     def mouse_moved(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
+        else:
+            cont, inds = self.sc.contains(event)
         lat = event.ydata
         lon = event.xdata
-        self.status_label.setText('Latitude: {:3.5f}, Longitude: {:3.5f}'.format(lat, lon))
+        text = f'Longitude: {lon:3.3f}, Latitude: {lat:3.3f}'
+
+        if cont:
+            indices = inds['ind']
+            text += ' | Station: ' if len(indices) == 1 else ' | Stations: '
+            text += ' - '.join([self._station_onpick_ids[index] for index in indices[:5]])
+            if len(indices) > 5:
+                text += '...'
+
+        self.status_label.setText(text)
 
     def mouse_scroll(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
 
         zoom = {'up': 1. / 2., 'down': 2.}
 
         if event.button in zoom:
-            xlim = self.canvas.axes.get_xlim()
-            ylim = self.canvas.axes.get_ylim()
+            xlim = self.ax.get_xlim()
+            ylim = self.ax.get_ylim()
 
             x, y = event.xdata, event.ydata
 
@@ -246,24 +263,24 @@ class Array_map(QtWidgets.QWidget):
             yb = y - 0.5 * ydiff
             yt = y + 0.5 * ydiff
 
-            self.canvas.axes.set_xlim(xl, xr)
-            self.canvas.axes.set_ylim(yb, yt)
+            self.ax.set_xlim(xl, xr)
+            self.ax.set_ylim(yb, yt)
             # parallels and meridians
-            self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.remove_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.ax.figure.canvas.draw_idle()
 
     def mouseLeftPress(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         self.map_x = event.xdata
         self.map_y = event.ydata
-        self.map_xlim = self.canvas.axes.get_xlim()
-        self.map_ylim = self.canvas.axes.get_ylim()
+        self.map_xlim = self.ax.get_xlim()
+        self.map_ylim = self.ax.get_ylim()
 
     def mouseLeftRelease(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         new_x = event.xdata
         new_y = event.ydata
@@ -271,13 +288,13 @@ class Array_map(QtWidgets.QWidget):
         dx = new_x - self.map_x
         dy = new_y - self.map_y
 
-        self.canvas.axes.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
-        self.canvas.axes.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
+        self.ax.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
+        self.ax.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
         # parallels and meridians
-        self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.remove_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.ax.figure.canvas.draw_idle()
 
     def onpick(self, event):
         btn_msg = {1: ' in selection. Aborted', 2: ' to delete a pick on. Aborted', 3: ' to display info.'}
@@ -357,12 +374,6 @@ class Array_map(QtWidgets.QWidget):
     def get_max_from_stations(self, key):
         return self._from_dict(max, key)
 
-    def get_min_from_picks(self):
-        return min(self.picks_rel.values())
-
-    def get_max_from_picks(self):
-        return max(self.picks_rel.values())
-
     def current_picks_dict(self):
         picktype = self.comboBox_am.currentText().split(' ')[0]
         auto_manu = {'auto': self.autopicks_dict,
@@ -407,22 +418,34 @@ class Array_map(QtWidgets.QWidget):
                     print('Cannot display pick for station {}. Reason: {}'.format(station_name, e))
             return picks, uncertainties
 
-        def get_picks_rel(picks):
+        def get_picks_rel(picks, func=min):
             picks_rel = {}
             picks_utc = []
             for pick in picks.values():
-                if type(pick) is obspy.core.utcdatetime.UTCDateTime:
-                    picks_utc.append(pick)
+                if type(pick) is UTCDateTime:
+                    picks_utc.append(pick.timestamp)
             if picks_utc:
-                self._earliest_picktime = min(picks_utc)
+                self._reference_picktime = UTCDateTime(func(picks_utc))
                 for st_id, pick in picks.items():
-                    if type(pick) is obspy.core.utcdatetime.UTCDateTime:
-                        pick -= self._earliest_picktime
+                    if type(pick) is UTCDateTime:
+                        pick -= self._reference_picktime
                     picks_rel[st_id] = pick
             return picks_rel
 
+        def get_picks_rel_mean_corr(picks):
+            return get_picks_rel(picks, func=np.nanmean)
+
         self.picks, self.uncertainties = get_picks(self.stations_dict)
         self.picks_rel = get_picks_rel(self.picks)
+        self.picks_rel_mean_corrected = get_picks_rel_mean_corr(self.picks)
+
+    def toggle_subtract_mean(self):
+        if self.subtract_mean_cb.isChecked():
+            cmap = 'seismic'
+        else:
+            cmap = 'viridis'
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText(cmap))
+        self._refresh_drawings()
 
     def init_lat_lon_dimensions(self):
         # init minimum and maximum lon and lat dimensions
@@ -453,11 +476,12 @@ class Array_map(QtWidgets.QWidget):
         return stations, latitudes, longitudes
 
     def get_picks_lat_lon(self):
+        picks_rel = self.picks_rel_mean_corrected if self.subtract_mean_cb.isChecked() else self.picks_rel
         picks = []
         uncertainties = []
         latitudes = []
         longitudes = []
-        for st_id, pick in self.picks_rel.items():
+        for st_id, pick in picks_rel.items():
             picks.append(pick)
             uncertainties.append(self.uncertainties.get(st_id))
             latitudes.append(self.stations_dict[st_id]['latitude'])
@@ -469,12 +493,19 @@ class Array_map(QtWidgets.QWidget):
         stat_dict = self.stations_dict['{}.{}'.format(network, station)]
         lat = stat_dict['latitude']
         lon = stat_dict['longitude']
-        self.highlighted_stations.append(self.canvas.axes.scatter(lon, lat, s=self.pointsize, edgecolors=color,
-                                                                  facecolors='none', zorder=12,
-                                                                  transform=ccrs.PlateCarree(), label='deleted'))
+        self.highlighted_stations.append(self.ax.scatter(lon, lat, s=self.pointsize, edgecolors=color,
+                                                         facecolors='none', zorder=12,
+                                                         transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        wfdata = self._parent.get_data().getWFData()
+        try:
+            wfdata = self._parent.get_data().getWFData()
+        except AttributeError:
+            QtWidgets.QMessageBox.warning(
+                self, "PyLoT Warning",
+                "No waveform data found. Check if they were already loaded in Waveform plot tab."
+            )
+            return
         wfdata_comp = self._parent.get_data().getAltWFdata()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
@@ -517,12 +548,19 @@ class Array_map(QtWidgets.QWidget):
                 print(message, e)
                 print(traceback.format_exc())
 
-    def draw_contour_filled(self, nlevel=50):
-        levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
+    def draw_contour_filled(self, nlevel=51):
+        if self.subtract_mean_cb.isChecked():
+            abs_max = self.get_residuals_absmax()
+            levels = np.linspace(-abs_max, abs_max, nlevel)
+        else:
+            levels = np.linspace(min(self.picks_rel.values()), max(self.picks_rel.values()), nlevel)
 
-        self.contourf = self.canvas.axes.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                                  linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
-                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())
+        self.contourf = self.ax.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
+                                         linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
+                                         alpha=0.4, zorder=8, cmap=self.get_colormap())
+
+    def get_residuals_absmax(self):
+        return np.max(np.absolute(list(self.picks_rel_mean_corrected.values())))
 
     def get_colormap(self):
         return plt.get_cmap(self.cmaps_box.currentText())
@@ -530,18 +568,18 @@ class Array_map(QtWidgets.QWidget):
     def scatter_all_stations(self):
         stations, lats, lons = self.get_st_lat_lon_for_plot()
 
-        self.sc = self.canvas.axes.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
-                                           zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
-                                           transform=ccrs.PlateCarree())
+        self.sc = self.ax.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
+                                  zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
+                                  transform=ccrs.PlateCarree())
 
         self.cid = self.plotWidget.mpl_connect('pick_event', self.onpick)
         self._station_onpick_ids = stations
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.sc_event = self.canvas.axes.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
-                                                     label='Event (might be outside map region)', marker='*',
-                                                     edgecolors='black',
-                                                     transform=ccrs.PlateCarree())
+            self.sc_event = self.ax.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
+                                            label='Event (might be outside map region)', marker='*',
+                                            edgecolors='black',
+                                            transform=ccrs.PlateCarree())
 
     def scatter_picked_stations(self):
         picks, uncertainties, lats, lons = self.get_picks_lat_lon()
@@ -554,8 +592,13 @@ class Array_map(QtWidgets.QWidget):
                           for uncertainty in uncertainties])
 
         cmap = self.get_colormap()
-        self.sc_picked = self.canvas.axes.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
-                                                  c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
+
+        vmin = vmax = None
+        if self.subtract_mean_cb.isChecked():
+            vmin, vmax = -self.get_residuals_absmax(), self.get_residuals_absmax()
+
+        self.sc_picked = self.ax.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap, vmin=vmin, vmax=vmax,
+                                         c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
 
     def annotate_ax(self):
         self.annotations = []
@@ -573,20 +616,20 @@ class Array_map(QtWidgets.QWidget):
             if st in self.marked_stations:
                 color = 'red'
             self.annotations.append(
-                self.canvas.axes.annotate(' %s' % st, xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
-                                          fontweight='semibold', color=color, alpha=0.8,
-                                          transform=ccrs.PlateCarree(), zorder=14,
-                                          path_effects=[PathEffects.withStroke(
-                                              linewidth=self.pointsize / 15., foreground='k')]))
+                self.ax.annotate(f'{st}', xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
+                                 fontweight='semibold', color=color, alpha=0.8,
+                                 transform=ccrs.PlateCarree(), zorder=14,
+                                 path_effects=[PathEffects.withStroke(
+                                     linewidth=self.pointsize / 15., foreground='k')]))
 
-        self.legend = self.canvas.axes.legend(loc=1, framealpha=1)
+        self.legend = self.ax.legend(loc=1, framealpha=1)
         self.legend.set_zorder(100)
         self.legend.get_frame().set_facecolor((1, 1, 1, 0.95))
 
     def add_cbar(self, label):
-        self.cbax_bg = inset_axes(self.canvas.axes, width="6%", height="75%", loc=5)
-        cbax = inset_axes(self.canvas.axes, width='2%', height='70%', loc=5)
-        cbar = self.canvas.axes.figure.colorbar(self.sc_picked, cax=cbax)
+        self.cbax_bg = inset_axes(self.ax, width="6%", height="75%", loc=5)
+        cbax = inset_axes(self.ax, width='2%', height='70%', loc=5)
+        cbar = self.ax.figure.colorbar(self.sc_picked, cax=cbax)
         cbar.set_label(label)
         cbax.yaxis.tick_left()
         cbax.yaxis.set_label_position('left')
@@ -631,7 +674,9 @@ class Array_map(QtWidgets.QWidget):
         if picks_available:
             self.scatter_picked_stations()
             if hasattr(self, 'sc_picked'):
-                self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime))
+                self.cbar = self.add_cbar(
+                    label='Time relative to reference onset ({}) [s]'.format(self._reference_picktime)
+                )
             self.comboBox_phase.setEnabled(True)
         else:
             self.comboBox_phase.setEnabled(False)

pylot/core/util/dataprocessing.py

@@ -27,6 +27,10 @@ class Metadata(object):
         # saves which metadata files are from obspy dmt
         self.obspy_dmt_invs = []
         if inventory:
+            # make sure that no accidental backslashes mess up the path
+            if isinstance(inventory, str):
+                inventory = inventory.replace('\\', '/')
+                inventory = os.path.abspath(inventory)
             if os.path.isdir(inventory):
                 self.add_inventory(inventory)
             if os.path.isfile(inventory):

pylot/core/util/event.py

@@ -22,14 +22,11 @@ class Event(ObsPyEvent):
         :param path: path to event directory
         :type path: str
         """
-        # TODO: remove rootpath and database
         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 = os.path.split(path)[0]  # path.split('/')[-3]
-        self.rootpath = '/' + os.path.join(*path.split('/')[:-3])
         self.pylot_autopicks = {}
         self.pylot_picks = {}
         self.notes = ''

pylot/core/util/utils.py

@@ -1076,7 +1076,7 @@ def check4rotated(data, metadata=None, verbosity=1):
             return wfs_in
 
         # check metadata quality
-        t_start = full_range(wfs_in)
+        t_start = full_range(wfs_in)[0]
         try:
             azimuths = []
             dips = []
@@ -1084,8 +1084,9 @@ def check4rotated(data, metadata=None, verbosity=1):
                 azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
                 dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
         except (KeyError, TypeError) as err:
-            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
-                  f"available in metadata. Stream remains unchanged.")
+            logging.warning(f"Rotating not possible, not all azimuth and dip information "
+                            f"available in metadata. Stream remains unchanged.")
+            logging.debug(f"Rotating not possible, {err=}, {type(err)=}")
             return wfs_in
         except Exception as err:
             print(f"Unexpected {err=}, {type(err)=}")

pylot/core/util/widgets.py

@@ -8,6 +8,7 @@ import copy
 import datetime
 import getpass
 import glob
+import logging
 import multiprocessing
 import os
 import subprocess
@@ -3836,7 +3837,7 @@ class TuneAutopicker(QWidget):
         self.stb_names = ['aicARHfig', 'refSpick', 'el_S1pick', 'el_S2pick']
 
     def add_parameters(self):
-        self.paraBox = PylotParaBox(self.parameter, parent=self, windowflag=Qt.Widget)
+        self.paraBox = PylotParameterWidget(self.parameter, parent=self, windowflag=Qt.Widget)
         self.paraBox.set_tune_mode(True)
         self.update_eventID()
         self.parameter_layout.addWidget(self.paraBox)
@@ -4203,7 +4204,7 @@ class TuneAutopicker(QWidget):
         self.qmb.show()
 
 
-class PylotParaBox(QtWidgets.QWidget):
+class PylotParameterWidget(QtWidgets.QWidget):
     accepted = QtCore.Signal(str)
     rejected = QtCore.Signal(str)
 
@@ -4317,6 +4318,11 @@ class PylotParaBox(QtWidgets.QWidget):
         grid = QtWidgets.QGridLayout()
 
         for index1, name in enumerate(parameter_names):
+            if name in ['rootpath', 'database']:
+                logging.warning(
+                    f'Deprecated parameter loaded: {name}. Check if datapath is still correct in parameter widget.'
+                )
+                continue
             default_item = self.parameter.get_defaults()[name]
             tooltip = default_item['tooltip']
             tooltip += ' | type: {}'.format(default_item['type'])
@@ -4886,7 +4892,7 @@ class PropTab(QWidget):
     def getValues(self):
         return None
 
-    def resetValues(self, infile=None):
+    def resetValues(self, infile):
         return None
 
 
@@ -4983,12 +4989,7 @@ class InputsTab(PropTab):
         else:
             index = 2
         datapath = para.get('datapath') if not para.get('datapath') is None else ''
-        rootpath = para.get('rootpath') if not para.get('rootpath') is None else ''
-        database = para.get('database') if not para.get('database') is None else ''
-        if isinstance(database, int):
-            database = str(database)
-        path = os.path.join(os.path.expanduser('~'), rootpath, datapath, database)
-        values = {"data/dataRoot": self.dataDirEdit.setText("%s" % path),
+        values = {"data/dataRoot": self.dataDirEdit.setText("%s" % datapath),
                   "user/FullName": self.fullNameEdit.text(),
                   "data/Structure": self.structureSelect.setCurrentIndex(index),
                   "tstart": self.tstartBox.setValue(0),

tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-                                                   #rootpath#       %project path                                                                                        
-                                                   #datapath#       %data path                                                                                           
-                                                   #database#       %name of data base                                                                                   
-20171010_063224.a                                  #eventID#        %event ID for single event processing (* for all events found in database)                           
+dmt_database_test                                  #datapath#       %data path
+20171010_063224.a                                  #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                                                        

tests/test_autopicker/test_autopylot.py

@@ -1,6 +1,8 @@
 import os
 import pytest
 
+from obspy import read_events
+
 from autoPyLoT import autoPyLoT
 
 
@@ -8,7 +10,11 @@ class TestAutopickerGlobal():
     def init(self):
         self.params_infile = 'pylot_alparray_mantle_corr_stack_0.03-0.5.in'
         self.test_event_dir = 'dmt_database_test'
+        self.fname_outfile_xml = os.path.join(
+            self.test_event_dir, '20171010_063224.a', 'PyLoT_20171010_063224.a_autopylot.xml'
+        )
 
+        # check if the input files exist
         if not os.path.isfile(self.params_infile):
             print(f'Test input file {os.path.abspath(self.params_infile)} not found.')
             return False
@@ -24,4 +30,38 @@ class TestAutopickerGlobal():
 
     def test_autopicker(self):
         assert self.init(), 'Initialization failed due to missing input files.'
-        #autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a')
+        # check for output file in test directory and remove it if necessary
+        if os.path.isfile(self.fname_outfile_xml):
+            os.remove(self.fname_outfile_xml)
+        autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a', obspyDMT_wfpath='processed')
+
+        # test for different known output files if they are identical or not
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_autopylot.xml', True)
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_saved_from_GUI.xml', True)
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_corrected_taup_times_0.03-0.5_P.xml', False)
+
+
+def compare_pickfiles(pickfile1: str, pickfile2: str, samefile: bool = True) -> None:
+    """
+    Compare the pick times and errors from two pick files.
+
+    Parameters:
+        pickfile1 (str): The path to the first pick file.
+        pickfile2 (str): The path to the second pick file.
+        samefile (bool): A flag indicating whether the two files are expected to be the same. Defaults to True.
+
+    Returns:
+        None
+    """
+    cat1 = read_events(pickfile1)
+    cat2 = read_events(pickfile2)
+    picks1 = sorted(cat1[0].picks, key=lambda pick: str(pick.waveform_id))
+    picks2 = sorted(cat2[0].picks, key=lambda pick: str(pick.waveform_id))
+    pick_times1 = [pick.time for pick in picks1]
+    pick_times2 = [pick.time for pick in picks2]
+    pick_terrs1 = [pick.time_errors for pick in picks1]
+    pick_terrs2 = [pick.time_errors for pick in picks2]
+
+    # check if times and errors are identical or not depending on the samefile flag
+    assert (pick_times1 == pick_times2) is samefile, 'Pick times error'
+    assert (pick_terrs1 == pick_terrs2) is samefile, 'Pick time errors errors'

tests/test_autopickstation/autoPyLoT_global_taupy_false.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/home/darius                                       #rootpath#       %project path                                                                                        
-alparray                                           #datapath#       %data path                                                                                           
-waveforms_used                                     #database#       %name of data base                                                                                   
-e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/home/darius/alparray/waveforms_used               #datapath#       %data path
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /home/darius/alparray/metadata                     #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 875.0                                              #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 False                                              #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
+P,Pdiff,S,Sdiff                                    #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 0.01 0.1                                           #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]                                    
 0.01 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

tests/test_autopickstation/autoPyLoT_global_taupy_true.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/home/darius                                       #rootpath#       %project path                                                                                        
-alparray                                           #datapath#       %data path                                                                                           
-waveforms_used                                     #database#       %name of data base                                                                                   
-e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/home/darius/alparray/waveforms_used               #datapath#       %data path
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /home/darius/alparray/metadata                     #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 875.0                                              #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
+P,Pdiff,S,Sdiff                                    #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 0.01 0.1                                           #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]                                    
 0.01 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

tests/test_autopickstation/test_autopickstation.py

@@ -1,6 +1,7 @@
 import os
 import sys
 import unittest
+import pytest
 
 import obspy
 from obspy import UTCDateTime
@@ -105,7 +106,6 @@ class TestAutopickStation(unittest.TestCase):
         # show complete diff when difference in results dictionaries are found
         self.maxDiff = None
 
-    # @skip("Works")
     def test_autopickstation_taupy_disabled_gra1(self):
         expected = {
             'P': {'picker': 'auto', 'snrdb': 15.405649120980094, 'weight': 0, 'Mo': None, 'marked': [], 'Mw': None,
@@ -121,8 +121,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra1, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_taupy_enabled_gra1(self):
@@ -140,8 +140,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra1, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_taupy_disabled_gra2(self):
@@ -157,8 +157,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra2, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA2', station)
 
     def test_autopickstation_taupy_enabled_gra2(self):
@@ -175,8 +175,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra2, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA2', station)
 
     def test_autopickstation_taupy_disabled_ech(self):
@@ -190,8 +190,8 @@ class TestAutopickStation(unittest.TestCase):
                           'fm': None, 'spe': None, 'channel': u'LHE'}}
         with HidePrints():
             result, station = autopickstation(wfstream=self.ech, pickparam=self.pickparam_taupy_disabled)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('ECH', station)
 
     def test_autopickstation_taupy_enabled_ech(self):
@@ -208,8 +208,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.ech, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('ECH', station)
 
     def test_autopickstation_taupy_disabled_fiesa(self):
@@ -224,8 +224,8 @@ class TestAutopickStation(unittest.TestCase):
                           'fm': None, 'spe': None, 'channel': u'LHE'}}
         with HidePrints():
             result, station = autopickstation(wfstream=self.fiesa, pickparam=self.pickparam_taupy_disabled)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('FIESA', station)
 
     def test_autopickstation_taupy_enabled_fiesa(self):
@@ -242,8 +242,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.fiesa, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('FIESA', station)
 
     def test_autopickstation_gra1_z_comp_missing(self):
@@ -272,7 +272,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=wfstream, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_a106_taupy_enabled(self):
@@ -290,7 +291,9 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.a106, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
+
 
     def test_autopickstation_station_missing_in_metadata(self):
         """This station is not in the metadata, but Taupy is enabled. Taupy should exit cleanly and modify the starttime
@@ -311,8 +314,37 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.a005a, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
 
 
+def run_dict_comparison(result, expected):
+    for key, expected_value in expected.items():
+        if isinstance(expected_value, dict):
+            run_dict_comparison(result[key], expected[key])
+        else:
+            res = result[key]
+            if isinstance(res, UTCDateTime) and isinstance(expected_value, UTCDateTime):
+                res = res.timestamp
+                expected_value = expected_value.timestamp
+            assert expected_value == pytest.approx(res), f'{key}: {expected_value} != {res}'
+
+
+def compare_dicts(result, expected, hint=''):
+    try:
+        run_dict_comparison(result, expected)
+    except AssertionError:
+        raise AssertionError(f'{hint}Dictionaries not equal.'
+                             f'\n\n<<Expected>>\n{pretty_print_dict(expected)}'
+                             f'\n\n<<Result>>\n{pretty_print_dict(result)}')
+
+
+def pretty_print_dict(dct):
+    retstr = ''
+    for key, value in sorted(dct.items(), key=lambda x: x[0]):
+        retstr += f"{key} : {value}\n"
+
+    return retstr
+
 if __name__ == '__main__':
     unittest.main()