Merge branch 'refs/heads/develop' into correlation_picker

# Conflicts:
#	pylot/core/pick/charfuns.py
#	tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in
#	tests/test_autopicker/test_autopylot.py

.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()
+            datapath = os.path.split(path)[0]
-            if system_name in ["Linux", "Darwin"]:
+            dirs = {
-                dirs = {
+                'datapath': datapath,
-                    '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)
-                }
         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]
+                box = self.parameterWidget.boxes[directory]
-                self.paraBox.setValue(box, dirs[directory])
+                self.parameterWidget.setValue(box, dirs[directory])
                 # show needed parameter in box
-                self.paraBox.show_parameter(directory)
+                self.parameterWidget.show_parameter(directory)
-            dirs_box = self.paraBox.get_groupbox_dialog('Directories')
+            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.datapath = new_rootpath
-        self.project.rootpath = new_rootpath
         for event in self.project.eventlist:
-            event.rootpath = new_rootpath
+            event.datapath = new_rootpath
-            event.path = os.path.join(event.rootpath, event.datapath, event.database, event.pylot_id)
+            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
@@ -2197,7 +2196,8 @@ class MainWindow(QMainWindow):
         if event.pylot_autopicks:
             self.drawPicks(picktype='auto')
         if event.pylot_picks or event.pylot_autopicks:
-            self.locateEventAction.setEnabled(True)
+            if not self._inputs.get('extent') == 'global':
+                self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
 
@@ -2427,7 +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
@@ -2632,7 +2632,6 @@ class MainWindow(QMainWindow):
                           picks=self.getPicksOnStation(station, 'manual'),
                           autopicks=self.getPicksOnStation(station, 'auto'),
                           metadata=self.metadata, event=event,
-                          model=self.inputs.get('taup_model'),
                           filteroptions=self.filteroptions, wftype=wftype,
                           show_comp_data=self.dataPlot.comp_checkbox.isChecked())
         if self.filterActionP.isChecked():
@@ -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)
+        obsdir = os.path.join(self._inputs['datapath'], eventname)
-        self.saveData(event=self.get_current_event(), directory=obsdir, outformats='.obs')
+        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:
+        if not self.parameterWidget:
-            self.paraBox = PylotParaBox(self._inputs, parent=self, windowflag=Qt.Window)
+            self.parameterWidget = PylotParameterWidget(self._inputs, parent=self, windowflag=Qt.Window)
-            self.paraBox.accepted.connect(self._setDirty)
+            self.parameterWidget.accepted.connect(self._setDirty)
-            self.paraBox.accepted.connect(self.filterOptionsFromParameter)
+            self.parameterWidget.accepted.connect(self.filterOptionsFromParameter)
         if show:
-            self.paraBox.params_to_gui()
+            self.parameterWidget.params_to_gui()
-            self.paraBox.show()
+            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)

README.md

@@ -11,7 +11,7 @@ PILOT has originally been developed in Mathworks' MatLab. In order to distribute
 problems, it has been decided to redevelop the software package in Python. The great work of the ObsPy group allows easy
 handling of a bunch of seismic data and PyLoT will benefit a lot compared to the former MatLab version.
 
-The development of PyLoT is part of the joint research project MAGS2 and AlpArray.
+The development of PyLoT is part of the joint research project MAGS2, AlpArray and AdriaArray.
 
 ## Installation
 
@@ -27,28 +27,30 @@ Afterwards run (from the PyLoT main directory where the files *requirements.txt*
     conda env create -f pylot.yml
 or
     
-    conda create --name pylot_38 --file requirements.txt
+    conda create -c conda-forge --name pylot_311 python=3.11 --file requirements.txt
 
-to create a new Anaconda environment called "pylot_38".
+to create a new Anaconda environment called *pylot_311*.
 
 Afterwards activate the environment by typing
 
-    conda activate pylot_38
+    conda activate pylot_311
 
 #### Prerequisites:
 
 In order to run PyLoT you need to install:
 
 - Python 3
-- obspy
-- pyside2
-- pyqtgraph
 - cartopy
+- joblib
+- obspy
+- pyaml
+- pyqtgraph
+- pyside2
 
 (the following are already dependencies of the above packages):
 - scipy
 - numpy
-- matplotlib <= 3.3.x
+- matplotlib
 
 #### Some handwork:
 
@@ -108,4 +110,4 @@ Others: A. Bruestle, T. Meier, W. Friederich
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-April 2022
+August 2024

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'),
+        dsfields = {'dpath': parameter.get('datapath'),}
-                    'dpath': parameter.get('datapath'),
-                    'dbase': parameter.get('database')}
 
-        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'],
+            datapath = parameter['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':
+            if fnames in [None, 'None']:
-                data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
+                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 datapath)
-                                                   #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                                                        

inputs/pylot_local.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/DATA/Insheim                                      #rootpath#       %project path                                                                                        
+/DATA/Insheim/EVENT_DATA/LOCAL/2018.02_Insheim     #datapath#       %data path
-EVENT_DATA/LOCAL                                   #datapath#       %data path                                                                                           
+e0006.038.18                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
-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/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                                                        

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 datapath)
-                                                   #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                                                        

pylot.yml

@@ -1,14 +1,12 @@
-name: pylot_38
+name: pylot_311
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - cartopy=0.20.2
+  - cartopy=0.23.0=py311hcf9f919_1
-  - matplotlib-base=3.3.4
+  - joblib=1.4.2=pyhd8ed1ab_0
-  - numpy=1.22.3
+  - obspy=1.4.1=py311he736701_3
-  - obspy=1.3.0
+  - pyaml=24.7.0=pyhd8ed1ab_0
-  - pyqtgraph=0.12.4
+  - pyqtgraph=0.13.7=pyhd8ed1ab_0
-  - pyside2>=5.13.2
+  - pyside2=5.15.8=py311h3d699ce_4
-  - python=3.8.12
+  - pytest=8.3.2=pyhd8ed1ab_0
-  - qt>=5.12.9
-  - scipy=1.8.0

pylot/__init__.py

@@ -9,7 +9,7 @@ PyLoT - the Python picking and Localization Tool
 
 This python library contains a graphical user interfaces for picking
 seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
-and the Qt4 libraries to be installed first.
+and the Qt libraries to be installed first.
 
 PILOT has been developed in Mathworks' MatLab. In order to distribute
 PILOT without facing portability problems, it has been decided to re-

pylot/core/io/default_parameters.py

@@ -6,24 +6,14 @@ import numpy as np
 Default parameters used for picking
 """
 
-defaults = {'rootpath': {'type': str,
+defaults = {'datapath': {'type': str,
-                         'tooltip': 'project path',
+                         'tooltip': 'path to eventfolders',
-                         'value': '',
-                         'namestring': 'Root path'},
-
-            'datapath': {'type': str,
-                         'tooltip': 'data path',
                          'value': '',
                          'namestring': 'Data path'},
 
-            'database': {'type': str,
-                         'tooltip': 'name of data base',
-                         'value': '',
-                         'namestring': 'Database path'},
-
             'eventID': {'type': str,
-                        'tooltip': 'event ID for single event processing (* for all events found in database)',
+                        'tooltip': 'event ID for single event processing (* for all events found in datapath)',
-                        'value': '',
+                        'value': '*',
                         'namestring': 'Event ID'},
 
             'extent': {'type': str,
@@ -511,7 +501,7 @@ defaults = {'rootpath': {'type': str,
 
             'taup_model': {'type': str,
                            'tooltip': 'Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
-                           'value': None,
+                           'value': 'iasp91',
                            'namestring': 'TauPy model'},
 
             'taup_phases': {'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:
+        else:
-            return None
+            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/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
@@ -227,7 +231,7 @@ 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)

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_xlim = self.ax.get_xlim()
-        self.org_ylim = self.canvas.axes.get_ylim()
+        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.ax.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_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.canvas = MplCanvas(projection=self.projection)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
         else:
-            self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
+            self.canvas = MplCanvas(extern_axes=self.extern_plot_axes)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+
+        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.ax.add_feature(cf.LAND)
-        self.canvas.axes = plt.axes(projection=ccrs.PlateCarree())
+        self.ax.add_feature(cf.OCEAN)
-        self.canvas.axes.add_feature(cf.LAND)
+        self.ax.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
-        self.canvas.axes.add_feature(cf.OCEAN)
+        self.ax.add_feature(cf.BORDERS, alpha=0.7)
-        self.canvas.axes.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
+        self.ax.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.add_feature(cf.BORDERS, alpha=0.7)
+        self.ax.add_feature(cf.RIVERS, linewidth=1)
-        self.canvas.axes.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.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',
+        self.gridlines = self.ax.gridlines(draw_labels=False, alpha=0.6, color='gray',
-                                                    linewidth=self.linewidth / 2, zorder=7)
+                                           linewidth=self.linewidth / 2, zorder=7, crs=ccrs.PlateCarree())
-        # 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
 
     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.ax.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_ylim(self.org_ylim[0], self.org_ylim[1])
         # parallels and meridians
-        self.remove_merid_paral()
+        #self.remove_merid_paral()
-        self.add_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.ax.set_xlim(lons - 10, lons + 10)
-            self.canvas.axes.set_ylim(lats - 5, lats + 5)
+            self.ax.set_ylim(lats - 5, lats + 5)
             # parallels and meridians
-            self.remove_merid_paral()
+            #self.remove_merid_paral()
-            self.add_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()
+            xlim = self.ax.get_xlim()
-            ylim = self.canvas.axes.get_ylim()
+            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.ax.set_xlim(xl, xr)
-            self.canvas.axes.set_ylim(yb, yt)
+            self.ax.set_ylim(yb, yt)
             # parallels and meridians
-            self.remove_merid_paral()
+            #self.remove_merid_paral()
-            self.add_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_xlim = self.ax.get_xlim()
-        self.map_ylim = self.canvas.axes.get_ylim()
+        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.ax.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_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
         # parallels and meridians
-        self.remove_merid_paral()
+        #self.remove_merid_paral()
-        self.add_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:
+                if type(pick) is UTCDateTime:
-                    picks_utc.append(pick)
+                    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:
+                    if type(pick) is UTCDateTime:
-                        pick -= self._earliest_picktime
+                        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'])
@@ -469,13 +493,20 @@ 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,
+        self.highlighted_stations.append(self.ax.scatter(lon, lat, s=self.pointsize, edgecolors=color,
-                                                                  facecolors='none', zorder=12,
+                                                         facecolors='none', zorder=12,
-                                                                  transform=ccrs.PlateCarree(), label='deleted'))
+                                                         transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        wfdata = self._parent.get_data().getWFData()
+        try:
-        wfdata_comp = self._parent.get_data().getWFDataComp()
+            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]
             pyl_mw = self._parent
@@ -490,7 +521,6 @@ class Array_map(QtWidgets.QWidget):
                                   picks=self._parent.get_current_event().getPick(station),
                                   autopicks=self._parent.get_current_event().getAutopick(station),
                                   filteroptions=self._parent.filteroptions, metadata=self.metadata,
-                                  model=self.parameter.get('taup_model'),
                                   event=pyl_mw.get_current_event())
             except Exception as e:
                 message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
@@ -518,12 +548,19 @@ class Array_map(QtWidgets.QWidget):
                 print(message, e)
                 print(traceback.format_exc())
 
-    def draw_contour_filled(self, nlevel=50):
+    def draw_contour_filled(self, nlevel=51):
-        levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
+        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,
+        self.contourf = self.ax.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                                  linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
+                                         linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
-                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())
+                                         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())
@@ -531,18 +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='.',
+        self.sc = self.ax.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
-                                           zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
+                                  zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
-                                           transform=ccrs.PlateCarree())
+                                  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,
+            self.sc_event = self.ax.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
-                                                     label='Event (might be outside map region)', marker='*',
+                                            label='Event (might be outside map region)', marker='*',
-                                                     edgecolors='black',
+                                            edgecolors='black',
-                                                     transform=ccrs.PlateCarree())
+                                            transform=ccrs.PlateCarree())
 
     def scatter_picked_stations(self):
         picks, uncertainties, lats, lons = self.get_picks_lat_lon()
@@ -555,8 +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 = []
@@ -574,20 +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.,
+                self.ax.annotate(f'{st}', xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
-                                          fontweight='semibold', color=color, alpha=0.8,
+                                 fontweight='semibold', color=color, alpha=0.8,
-                                          transform=ccrs.PlateCarree(), zorder=14,
+                                 transform=ccrs.PlateCarree(), zorder=14,
-                                          path_effects=[PathEffects.withStroke(
+                                 path_effects=[PathEffects.withStroke(
-                                              linewidth=self.pointsize / 15., foreground='k')]))
+                                     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)
+        self.cbax_bg = inset_axes(self.ax, width="6%", height="75%", loc=5)
-        cbax = inset_axes(self.canvas.axes, width='2%', height='70%', loc=5)
+        cbax = inset_axes(self.ax, width='2%', height='70%', loc=5)
-        cbar = self.canvas.axes.figure.colorbar(self.sc_picked, cax=cbax)
+        cbar = self.ax.figure.colorbar(self.sc_picked, cax=cbax)
         cbar.set_label(label)
         cbax.yaxis.tick_left()
         cbax.yaxis.set_label_position('left')
@@ -632,7 +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

@@ -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 "
+            logging.warning(f"Rotating not possible, not all azimuth and dip information "
-                  f"available in metadata. Stream remains unchanged.")
+                            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
@@ -1870,13 +1871,14 @@ class PickDlg(QDialog):
 
     def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
                  autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
-                 event=None, filteroptions=None, model=None, wftype=None):
+                 event=None, filteroptions=None, wftype=None):
         super(PickDlg, self).__init__(parent, Qt.Window)
         self.orig_parent = parent
         self.setAttribute(Qt.WA_DeleteOnClose)
 
         # initialize attributes
         self.parameter = parameter
+        model = self.parameter.get('taup_model')
         self._embedded = embedded
         self.showCompData = show_comp_data
         self.station = station
@@ -2269,8 +2271,8 @@ class PickDlg(QDialog):
         arrivals = func[plot](source_origin.depth,
                               source_origin.latitude,
                               source_origin.longitude,
-                              station_coords['latitude'],
+                              station_coords.get('latitude'),
-                              station_coords['longitude'],
+                              station_coords.get('longitude'),
                               phases)
         self.arrivals = arrivals
 
@@ -3835,7 +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)
@@ -4202,7 +4204,7 @@ class TuneAutopicker(QWidget):
         self.qmb.show()
 
 
-class PylotParaBox(QtWidgets.QWidget):
+class PylotParameterWidget(QtWidgets.QWidget):
     accepted = QtCore.Signal(str)
     rejected = QtCore.Signal(str)
 
@@ -4316,6 +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'])
@@ -4885,7 +4892,7 @@ class PropTab(QWidget):
     def getValues(self):
         return None
 
-    def resetValues(self, infile=None):
+    def resetValues(self, infile):
         return None
 
 
@@ -4982,12 +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 ''
+        values = {"data/dataRoot": self.dataDirEdit.setText("%s" % datapath),
-        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),
                   "user/FullName": self.fullNameEdit.text(),
                   "data/Structure": self.structureSelect.setCurrentIndex(index),
                   "tstart": self.tstartBox.setValue(0),

pylot/correlation/__init__.py

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

pylot/correlation/parameters_adriaarray.yaml

@@ -0,0 +1,90 @@
+#############################  correlation parameters  #####################################
+# min_corr_stacking: minimum correlation coefficient for building beam trace
+# min_corr_export: minimum correlation coefficient for pick export
+# min_stack: minimum number of stations for building beam trace
+# t_before: correlation window before pick
+# t_after: correlation window after pick#
+# cc_maxlag: maximum shift for initial correlation
+# cc_maxlag2: maximum shift for second (final) correlation (also for calculating pick uncertainty)
+# initial_pick_outlier_threshold: (hopefully) threshold for excluding large outliers of initial (AIC) picks
+# export_threshold: automatically exclude all onsets which deviate more than this threshold from corrected taup onsets
+# min_picks_export: minimum number of correlated picks for export
+# min_picks_autopylot: minimum number of reference autopicks picks to continue with event
+# check_RMS: do RMS check to search for restitution errors (very experimental)
+# use_taupy_onsets: use taupy onsets as reference picks instead of external picks
+# station_list: use the following stations as reference for stacking
+# use_stacked_trace: use existing stacked trace if found (spare re-computation)
+# data_dir: obspyDMT data subdirectory (e.g. 'raw', 'processed')
+# pickfile_extension: use quakeML files (PyLoT output) with the following extension, e.g. '_autopylot' for pickfiles
+#                     such as 'PyLoT_20170501_141822_autopylot.xml'
+
+logging: info
+pick_phases: ['P', 'S']
+
+# P-phase
+P:
+  min_corr_stacking: 0.8
+  min_corr_export: 0.6
+  min_stack: 20
+  t_before: 30.
+  t_after: 50.
+  cc_maxlag: 50.
+  cc_maxlag2: 5.
+  initial_pick_outlier_threshold: 30.
+  export_threshold: 2.5
+  min_picks_export: 100
+  min_picks_autopylot: 50
+  check_RMS: True
+  use_taupy_onsets: False
+  station_list: ['HU.MORH', 'HU.TIH',  'OX.FUSE', 'OX.BAD']
+  use_stacked_trace: False
+  data_dir: 'processed'
+  pickfile_extension: '_autopylot'
+  dt_stacking: [250, 250]
+
+  # filter for first correlation (rough)
+  filter_options:
+    freqmax: 0.5
+    freqmin: 0.03
+  # filter for second correlation (fine)
+  filter_options_final:
+    freqmax: 0.5
+    freqmin: 0.03
+
+  filter_type: bandpass
+  sampfreq: 20.0
+
+# S-phase
+S:
+  min_corr_stacking: 0.7
+  min_corr_export: 0.6
+  min_stack: 20
+  t_before: 60.
+  t_after: 60.
+  cc_maxlag: 100.
+  cc_maxlag2: 25.
+  initial_pick_outlier_threshold: 30.
+  export_threshold: 5.0
+  min_picks_export: 200
+  min_picks_autopylot: 50
+  check_RMS: True
+  use_taupy_onsets: False
+  station_list: ['HU.MORH','HU.TIH',  'OX.FUSE', 'OX.BAD']
+  use_stacked_trace: False
+  data_dir: 'processed'
+  pickfile_extension: '_autopylot'
+  dt_stacking: [250, 250]
+
+  # filter for first correlation (rough)
+  filter_options:
+    freqmax: 0.1
+    freqmin: 0.01
+
+  # filter for second correlation (fine)
+  filter_options_final:
+    freqmax: 0.2
+    freqmin: 0.01
+
+  filter_type: bandpass
+  sampfreq: 20.0
+

pylot/correlation/submit_pick_corr_correction.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+#ulimit -s 8192
+#ulimit -v $(ulimit -v | awk '{printf("%d",$1*0.95)}')
+#ulimit -v
+
+#655360
+
+source /opt/anaconda3/etc/profile.d/conda.sh
+conda activate pylot_311
+NSLOTS=20
+
+#qsub -l low -cwd -l "os=*stretch" -pe smp 40 submit_pick_corr_correction.sh
+#$ -l low
+#$ -l h_vmem=6G
+#$ -cwd
+#$ -pe smp 20
+#$ -N corr_pick
+
+
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/pylot_tools/"
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/"
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/pylot/"
+
+#export MKL_NUM_THREADS=${NSLOTS:=1}
+#export NUMEXPR_NUM_THREADS=${NSLOTS:=1}
+#export OMP_NUM_THREADS=${NSLOTS:=1}
+
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 0 -istop 100
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 100 -istop 200
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M6.0-6.5' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 0 -istop 100
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 100 -istop 200
+#python pick_correlation_correction.py 'H:\sciebo\dmt_database' 'H:\Sciebo\dmt_database\pylot_alparray_mantle_corr_S_0.01-0.2.in' -pd -n 4 -t
+
+pylot_infile='/home/marcel/.pylot/pylot_alparray_syn_fwi_mk6_it3.in'
+#pylot_infile='/home/marcel/.pylot/pylot_adriaarray_corr_P_and_S.in'
+
+# THIS SCRIPT SHOLD BE CALLED BY "submit_to_grid_engine.py" using the following line:
+python pick_correlation_correction.py $1 $pylot_infile -pd -n ${NSLOTS:=1} -istart $2 --params 'parameters_fwi_mk6_it3.yaml'
+#--event_blacklist eventlist.txt

pylot/correlation/submit_to_grid_engine.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+
+import subprocess
+
+fnames = [
+    ('/data/AlpArray_Data/dmt_database_synth_model_mk6_it3_no_rotation', 0),
+          ]
+
+#fnames = [('/data/AlpArray_Data/dmt_database_mantle_0.01-0.2_SKS-phase', 0),
+#          ('/data/AlpArray_Data/dmt_database_mantle_0.01-0.2_S-phase', 0),]
+
+####
+script_location = '/home/marcel/VersionCtrl/git/code_base/correlation_picker/submit_pick_corr_correction.sh'
+####
+
+for fnin, istart in fnames:
+    input_cmds = f'qsub -q low.q@minos15,low.q@minos14,low.q@minos13,low.q@minos12,low.q@minos11 {script_location} {fnin} {istart}'
+
+    print(input_cmds)
+    print(subprocess.check_output(input_cmds.split()))
+
+
+

pylot/correlation/utils.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import glob
+import json
+
+from obspy import read_events
+
+from pylot.core.util.dataprocessing import Metadata
+from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
+
+
+def get_event_obspy_dmt(eventdir):
+    event_pkl_file = os.path.join(eventdir, 'info', 'event.pkl')
+    if not os.path.exists(event_pkl_file):
+        raise IOError('Could not find event path for event: {}'.format(eventdir))
+    event = qml_from_obspyDMT(event_pkl_file)
+    return event
+
+
+def get_event_pylot(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = os.path.join(eventdir, 'PyLoT_{}{}.xml'.format(event_id, extension))
+    if not os.path.isfile(filename):
+        return
+    cat = read_events(filename)
+    return cat[0]
+
+
+def get_event_id(eventdir):
+    event_id = os.path.split(eventdir)[-1]
+    return event_id
+
+
+def get_picks(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = 'PyLoT_{}{}.xml'
+    filename = filename.format(event_id, extension)
+    fpath = os.path.join(eventdir, filename)
+    fpaths = glob.glob(fpath)
+    if len(fpaths) == 1:
+        cat = read_events(fpaths[0])
+        picks = cat[0].picks
+        return picks
+    elif len(fpaths) == 0:
+        print('get_picks: File not found: {}'.format(fpath))
+        return
+    print(f'WARNING: Ambiguous pick file specification. Found the following pick files {fpaths}\nFilemask: {fpath}')
+    return
+
+
+def write_json(object, fname):
+    with open(fname, 'w') as outfile:
+        json.dump(object, outfile, sort_keys=True, indent=4)
+
+
+def get_metadata(eventdir):
+    metadata_path = os.path.join(eventdir, 'resp')
+    metadata = Metadata(inventory=metadata_path, verbosity=0)
+    return metadata

requirements.txt

@@ -1,12 +1,7 @@
-# This file may be used to create an environment using:
+Cartopy==0.23.0
-# $ conda create --name <env> --file <this file>
+joblib==1.4.2
-# platform: win-64
+obspy==1.4.1
-cartopy=0.20.2
+pyaml==24.7.0
-matplotlib-base=3.3.4
+pyqtgraph==0.13.7
-numpy=1.22.3
+PySide2==5.15.8
-obspy=1.3.0
+pytest==8.3.2
-pyqtgraph=0.12.4
-pyside2=5.13.2
-python=3.8.12
-qt=5.12.9
-scipy=1.8.0

tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in

@@ -0,0 +1,99 @@
+%This is a parameter input file for PyLoT/autoPyLoT.
+%All main and special settings regarding data handling
+%and picking are to be set here!
+%Parameters are optimized for %extent data sets!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#main settings#
+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                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#NLLoc settings#
+None                                               #nllocbin#       %path to NLLoc executable                                                                            
+None                                               #nllocroot#      %root of NLLoc-processing directory                                                                  
+None                                               #phasefile#      %name of autoPyLoT-output phase file for NLLoc                                                       
+None                                               #ctrfile#        %name of autoPyLoT-output control file for NLLoc                                                     
+ttime                                              #ttpatter#       %pattern of NLLoc ttimes from grid                                                                   
+AUTOLOC_nlloc                                      #outpatter#      %pattern of NLLoc-output file                                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#parameters for seismic moment estimation#
+3530.0                                             #vp#             %average P-wave velocity                                                                             
+2500.0                                             #rho#            %average rock density [kg/m^3]                                                                       
+300.0 0.8                                          #Qp#             %quality factor for P waves (Qp*f^a); list(Qp, a)                                                    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#settings local magnitude#
+1.0 1.0 1.0                                        #WAscaling#      %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]                           If zeros are set, original Richter magnitude is calculated!
+1.0 1.0                                            #magscaling#     %Scaling relation for derived local magnitude [a*Ml+b].                            If zeros are set, no scaling of network magnitude is applied!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#filter settings#
+0.03 0.03                                          #minfreq#        %Lower filter frequency [P, S]                                                                       
+0.5 0.5                                            #maxfreq#        %Upper filter frequency [P, S]                                                                       
+4 4                                                #filter_order#   %filter order [P, S]                                                                                 
+bandpass bandpass                                  #filter_type#    %filter type (bandpass, bandstop, lowpass, highpass) [P, S]                                          
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#common settings picker#
+global                                             #extent#         %extent of array ("local", "regional" or "global")                                                   
+-100.0                                             #pstart#         %start time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)     
+50.0                                               #pstop#          %end time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)       
+-50.0                                              #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
+50.0                                               #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                                 
+ak135                                              #taup_model#     %Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+P,Pdiff,S,SKS                                      #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
+0.03 0.5                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
+0.01 0.5                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
+0.03 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     
+0.01 0.5                                           #bph2#           %lower/upper corner freq. of second band pass filter z-comp. [Hz]                                    
+#special settings for calculating CF#
+%!!Edit the following only if you know what you are doing!!%
+#Z-component#
+HOS                                                #algoP#          %choose algorithm for P-onset determination (HOS, ARZ, or AR3)                                       
+300.0                                              #tlta#           %for HOS-/AR-AIC-picker, length of LTA window [s]                                                    
+4                                                  #hosorder#       %for HOS-picker, order of Higher Order Statistics                                                    
+2                                                  #Parorder#       %for AR-picker, order of AR process of Z-component                                                   
+16.0                                               #tdet1z#         %for AR-picker, length of AR determination window [s] for Z-component, 1st pick                      
+10.0                                               #tpred1z#        %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick                         
+12.0                                               #tdet2z#         %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick                      
+6.0                                                #tpred2z#        %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick                         
+0.001                                              #addnoise#       %add noise to seismogram for stable AR prediction                                                    
+60.0 5.0 20.0 12.0                                 #tsnrz#          %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]     
+50.0                                               #pickwinP#       %for initial AIC pick, length of P-pick window [s]                                                   
+30.0                                               #Precalcwin#     %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)                        
+2.0                                                #aictsmooth#     %for HOS/AR, take average of samples for smoothing of AIC-function [s]                               
+2.0                                                #tsmoothP#       %for HOS/AR, take average of samples in this time window for smoothing CF [s]                        
+0.006                                              #ausP#           %for HOS/AR, artificial uplift of samples (aus) of CF (P)                                            
+2.0                                                #nfacP#          %for HOS/AR, noise factor for noise level determination (P)                                          
+#H-components#
+ARH                                                #algoS#          %choose algorithm for S-onset determination (ARH or AR3)                                             
+12.0                                               #tdet1h#         %for HOS/AR, length of AR-determination window [s], H-components, 1st pick                           
+6.0                                                #tpred1h#        %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick                              
+8.0                                                #tdet2h#         %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick                            
+4.0                                                #tpred2h#        %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick                              
+4                                                  #Sarorder#       %for AR-picker, order of AR process of H-components                                                  
+100.0                                              #Srecalcwin#     %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)                             
+195.0                                              #pickwinS#       %for initial AIC pick, length of S-pick window [s]                                                   
+60.0 10.0 30.0 12.0                                #tsnrh#          %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]    
+22.0                                               #aictsmoothS#    %for AIC-picker, take average of samples in this time window for smoothing of AIC-function [s]       
+20.0                                               #tsmoothS#       %for AR-picker, take average of samples for smoothing CF [s] (S)                                     
+0.001                                              #ausS#           %for HOS/AR, artificial uplift of samples (aus) of CF (S)                                            
+2.0                                                #nfacS#          %for AR-picker, noise factor for noise level determination (S)                                       
+#first-motion picker#
+1                                                  #minfmweight#    %minimum required P weight for first-motion determination                                            
+3.0                                                #minFMSNR#       %miniumum required SNR for first-motion determination                                                
+10.0                                               #fmpickwin#      %pick window [s] around P onset for calculating zero crossings                                       
+#quality assessment#
+0.1 0.2 0.4 0.8                                    #timeerrorsP#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P                           
+4.0 8.0 16.0 32.0                                  #timeerrorsS#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S                           
+0.005                                              #minAICPslope#   %below this slope [counts/s] the initial P pick is rejected                                          
+1.1                                                #minAICPSNR#     %below this SNR the initial P pick is rejected                                                       
+0.002                                              #minAICSslope#   %below this slope [counts/s] the initial S pick is rejected                                          
+1.3                                                #minAICSSNR#     %below this SNR the initial S pick is rejected                                                       
+20.0                                               #minsiglength#   %length of signal part for which amplitudes must exceed noiselevel [s]                               
+1.0                                                #noisefactor#    %noiselevel*noisefactor=threshold                                                                    
+10.0                                               #minpercent#     %required percentage of amplitudes exceeding threshold                                               
+0.1                                                #zfac#           %P-amplitude must exceed at least zfac times RMS-S amplitude                                         
+100.0                                              #mdttolerance#   %maximum allowed deviation of P picks from median [s]                                                
+50.0                                               #wdttolerance#   %maximum allowed deviation from Wadati-diagram                                                       
+25.0                                               #jackfactor#     %pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor

tests/test_autopicker/test_autopylot.py

@@ -0,0 +1,67 @@
+import os
+import pytest
+
+from obspy import read_events
+
+from autoPyLoT import autoPyLoT
+
+
+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
+
+        if not os.path.exists(self.test_event_dir):
+            print(
+                f'Test event directory not found at location "{os.path.abspath(self.test_event_dir)}". '
+                f'Make sure to load it from the website first.'
+            )
+            return False
+
+        return True
+
+    def test_autopicker(self):
+        assert self.init(), 'Initialization failed due to missing input files.'
+        # 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                                                                                        
+/home/darius/alparray/waveforms_used               #datapath#       %data path
-alparray                                           #datapath#       %data path                                                                                           
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
-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/metadata                     #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_autopickstation/autoPyLoT_global_taupy_true.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/home/darius                                       #rootpath#       %project path                                                                                        
+/home/darius/alparray/waveforms_used               #datapath#       %data path
-alparray                                           #datapath#       %data path                                                                                           
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
-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/metadata                     #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_pick_correlation_correction/test_pick_correlation_correction.py

@@ -0,0 +1,76 @@
+import pytest
+from obspy import read, Trace, UTCDateTime
+
+from pylot.correlation.pick_correlation_correction import XCorrPickCorrection
+
+
+class TestXCorrPickCorrection():
+    def setup(self):
+        self.make_test_traces()
+        self.make_test_picks()
+        self.t_before = 2.
+        self.t_after = 2.
+        self.cc_maxlag = 0.5
+
+    def make_test_traces(self):
+        # take first trace of test Stream from obspy
+        tr1 = read()[0]
+        # filter trace
+        tr1.filter('bandpass', freqmin=1, freqmax=20)
+        # make a copy and shift the copy by 0.1 s
+        tr2 = tr1.copy()
+        tr2.stats.starttime += 0.1
+
+        self.trace1 = tr1
+        self.trace2 = tr2
+
+    def make_test_picks(self):
+        # create an artificial reference pick on reference trace (trace1) and another one on the 0.1 s shifted trace
+        self.tpick1 = UTCDateTime('2009-08-24T00:20:07.7')
+        # shift the second pick by 0.2 s, the correction should be around 0.1 s now
+        self.tpick2 = self.tpick1 + 0.2
+
+    def test_slice_trace_okay(self):
+
+        self.setup()
+        xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                   t_before=self.t_before, t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+
+        test_trace = self.trace1
+        pick_time = self.tpick2
+
+        sliced_trace = xcpc.slice_trace(test_trace, pick_time)
+        assert ((sliced_trace.stats.starttime == pick_time - self.t_before - self.cc_maxlag / 2)
+                and (sliced_trace.stats.endtime == pick_time + self.t_after + self.cc_maxlag / 2))
+
+    def test_slice_trace_fails(self):
+        self.setup()
+
+        test_trace = self.trace1
+        pick_time = self.tpick1
+
+        with pytest.raises(ValueError):
+            xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                       t_before=self.t_before + 20, t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+            xcpc.slice_trace(test_trace, pick_time)
+
+        with pytest.raises(ValueError):
+            xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                       t_before=self.t_before, t_after=self.t_after + 50, cc_maxlag=self.cc_maxlag)
+            xcpc.slice_trace(test_trace, pick_time)
+
+    def test_cross_correlation(self):
+        self.setup()
+
+        # create XCorrPickCorrection object
+        xcpc = XCorrPickCorrection(self.tpick1, self.trace1, self.tpick2, self.trace2, t_before=self.t_before,
+                                   t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+
+        # execute correlation
+        correction, cc_max, uncert, fwfm = xcpc.cross_correlation(False, '', '')
+
+        # define awaited test result
+        test_result = (-0.09983091718314982, 0.9578431835689154, 0.0015285160561610929, 0.03625786256084631)
+
+        # check results
+        assert pytest.approx(test_result, rel=1e-6) == (correction, cc_max, uncert, fwfm)