[update] increased robustness of correlation picker. If autoPyLoT fails on the stacked trace it tries to pick other stacked traces. Ignoring failed autoPyLoT picks can manually be set if they are not important (e.g. when only pick differences are important)

[minor] Commented out search for network name in metadata filename considered being unsafe

PyLoT.py

@@ -716,14 +716,14 @@ class MainWindow(QMainWindow):
         self.tabs.addTab(wf_tab, 'Waveform Plot')
         self.tabs.addTab(array_tab, 'Array Map')
         self.tabs.addTab(events_tab, 'Eventlist')
-        self.tabs.addTab(spectro_tab, 'Spectro')
+        #self.tabs.addTab(spectro_tab, 'Spectro')
 
         self.wf_layout.addWidget(self.no_data_label)
         self.wf_layout.addWidget(self.wf_scroll_area)
         self.wf_scroll_area.setWidgetResizable(True)
         self.init_array_tab()
         self.init_event_table()
-        self.init_spectro_tab()
+        #self.init_spectro_tab()
         self.tabs.setCurrentIndex(0)
 
         self.eventLabel = QLabel()
@@ -1011,7 +1011,7 @@ class MainWindow(QMainWindow):
         for event in events:
             for filename in filenames:
                 if os.path.isfile(filename) and event.pylot_id in filename:
-                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
+                    self.load_data(filename, draw=False, event=event, ask_user=False, merge_strategy=sld.merge_strategy)
                     refresh = True
         if not refresh:
             return
@@ -1020,8 +1020,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
-        if not ask_user:
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=True, merge_strategy='Overwrite',):
+        if ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1034,7 +1034,7 @@ class MainWindow(QMainWindow):
         if not event:
             event = self.get_current_event()
 
-        if event.picks:
+        if event.picks and ask_user:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Do you want to overwrite the data?',)
             overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
@@ -2196,7 +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)
 
@@ -2631,7 +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():
@@ -3590,7 +3590,7 @@ class MainWindow(QMainWindow):
     def calc_magnitude(self):
         self.init_metadata()
         if not self.metadata:
-            return None
+            return []
 
         wf_copy = self.get_data().getWFData().copy()
 
@@ -3599,6 +3599,10 @@ class MainWindow(QMainWindow):
         for station in np.unique(list(self.getPicks('manual').keys()) + list(self.getPicks('auto').keys())):
             wf_select += wf_copy.select(station=station)
 
+        if not wf_select:
+            logging.warning('Empty Stream in calc_magnitude. Return.')
+            return []
+
         corr_wf = restitute_data(wf_select, self.metadata)
         # calculate moment magnitude
         moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'),

README.md

@@ -54,33 +54,17 @@ In order to run PyLoT you need to install:
 
 #### Some handwork:
 
-PyLoT needs a properties folder on your system to work. It should be situated in your home directory
-(on Windows usually C:/Users/*username*):
-
-    mkdir ~/.pylot
-
-In the next step you have to copy some files to this directory:
-
-*for local distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_local.in ~/.pylot/pylot.in
-
-*for regional distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_regional.in ~/.pylot/pylot.in
-
-*for global distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_global.in ~/.pylot/pylot.in
-
-and some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling
+Some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling
 relation
 
     cp path-to-pylot/inputs/PILOT_TimeErrors.in path-to-pylot/inputs/richter_scaling.data ~/.pylot/
 
 You may need to do some modifications to these files. Especially folder names should be reviewed.
 
-PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
+PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10/11.
+
+## Example Dataset
+An example dataset with waveform data, metadata and automatic picks in the obspy-dmt dataset format for testing the teleseismic picking can be found at https://zenodo.org/doi/10.5281/zenodo.13759803
 
 ## Release notes
 
@@ -89,6 +73,7 @@ PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
 - event organisation in project files and waveform visualisation
 - consistent manual phase picking through predefined SNR dependant zoom level
 - consistent automatic phase picking routines using Higher Order Statistics, AIC and Autoregression
+- pick correlation correction for teleseismic waveforms
 - interactive tuning of auto-pick parameters
 - uniform uncertainty estimation from waveform's properties for automatic and manual picks
 - pdf representation and comparison of picks taking the uncertainty intrinsically into account
@@ -97,17 +82,17 @@ PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
 
 #### Known issues:
 
-We hope to solve these with the next release.
+Current release is still in development progress and has several issues. We are currently lacking manpower, but hope to assess many of the issues in the near future.
 
 ## Staff
 
-Original author(s): M. Rische, S. Wehling-Benatelli, L. Kueperkoch, M. Bischoff (PILOT)
+Developer(s): M. Paffrath, S. Wehling-Benatelli, L. Kueperkoch, D. Arnold, K. Cökerim, K. Olbert, M. Bischoff, C. Wollin, M. Rische, S. Zimmermann
 
-Developer(s): S. Wehling-Benatelli, M. Paffrath, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, D. Arnold, K. Cökerim, S. Zimmermann
+Original author(s): M. Rische, S. Wehling-Benatelli, L. Kueperkoch, M. Bischoff (PILOT)
 
 Others: A. Bruestle, T. Meier, W. Friederich
 
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-August 2024
+March 2025

docs/correlation.md

@@ -0,0 +1,77 @@
+# Pick-Correlation Correction
+
+## Introduction
+Currently, the pick-correlation correction algorithm is not accessible from they PyLoT GUI. The main file *pick_correlation_correction.py* is located in the directory *pylot\correlation*.
+The program only works for an obspy dmt database structure.
+
+The basic workflow of the algorithm is shown in the following diagram. The first step **(1)** is the normal (automatic) picking procedure in PyLoT. Everything from step **(2)** to **(5)** is part of the correlation correction algorithm.
+
+*Note: The first step is not required in case theoretical onsets are used instead of external picks when the parameter use_taupy_onsets is set to True. However, an existing event quakeML (.xml) file generated by PyLoT might be required for each event in case not external picks are used.*
+
+![images/workflow_stacking.png](images/workflow_stacking.png)
+
+A detailed description of the algorithm can be found in the corresponding publication:
+
+*Paffrath, M., Friederich, W., and the AlpArray and AlpArray-SWATH D Working Groups: Teleseismic P waves at the AlpArray seismic network: wave fronts, absolute travel times and travel-time residuals, Solid Earth, 12, 1635–1660, https://doi.org/10.5194/se-12-1635-2021, 2021.*
+
+## How to use
+To use the program you have to call the main program providing two mandatory arguments: a path to the obspy dmt database folder *dmt_database_path* and the path to the PyLoT infile *pylot.in* for picking of the beam trace:
+
+```python pick_correlation_correction.py dmt_database_path pylot.in```
+
+By default, the parameter file *parameters.yaml* is used. You can use the command line option *--params* to specify a different parameter file and other optional arguments such as *-pd* for plotting detailed information or *-n 4* to use 4 cores for parallel processing:
+
+```python pick_correlation_correction.py dmt_database_path pylot.in --params parameters_adriaarray.yaml -pd -n 4```
+
+## Cross-Correlation Parameters
+
+The program uses the parameters in the file *parameters.yaml* by default. You can use the command line option *--params* to specify a different parameter file. An example of the parameter file is provided in the *correlation\parameters.yaml* file.
+
+In the top level of the parameter file the logging level *logging* can be set, as well as a list of pick phases *pick_phases* (e.g. ['P', 'S']).
+
+For each pick phase the different parameters can be set in the first sub-level of the parameter file, e.g.:
+
+```yaml
+logging: info
+pick_phases: ['P', 'S']
+
+P:
+ min_corr_stacking: 0.8
+ min_corr_export: 0.6
+ [...]
+
+S:
+ min_corr_stacking: 0.7
+ [...]
+```
+
+The following parameters are available:
+
+
+| Parameter Name                 | Description                                                                                        | Parameter Type |
+|--------------------------------|----------------------------------------------------------------------------------------------------|----------------|
+| min_corr_stacking              | Minimum correlation coefficient for building beam trace                                            | float          |
+| min_corr_export                | Minimum correlation coefficient for pick export                                                    | float          |
+| min_stack                      | Minimum number of stations for building beam trace                                                 | int            |
+| t_before                       | Correlation window before reference pick                                                           | float          |
+| t_after                        | Correlation window after reference pick                                                            | float          |
+| cc_maxlag                      | Maximum shift for initial correlation                                                              | float          |
+| cc_maxlag2                     | Maximum shift for second (final) correlation (also for calculating pick uncertainty)               | float          |
+| initial_pick_outlier_threshold | Threshold for excluding large outliers of initial (AIC) picks                                      | float          |
+| export_threshold               | Automatically exclude all onsets which deviate more than this threshold from corrected taup onsets | float          |
+| min_picks_export               | Minimum number of correlated picks for export                                                      | int            |
+| min_picks_autopylot            | Minimum number of reference auto picks to continue with event                                      | int            |
+| check_RMS                      | Do RMS check to search for restitution errors (very experimental)                                  | bool           |
+| use_taupy_onsets               | Use taupy onsets as reference picks instead of external picks                                      | bool           |
+| station_list                   | Use the following stations as reference for stacking                                               | list[str]      |
+| use_stacked_trace              | Use existing stacked trace if found (spare re-computation)                                         | bool           |
+| data_dir                       | obspyDMT data subdirectory (e.g. 'raw', 'processed')                                               | str            |
+| pickfile_extension             | Use quakeML files (PyLoT output) with the following extension                                      | str            |
+| dt_stacking                    | Time difference for stacking window (in seconds)                                                   | list[float]    |
+| filter_options                 | Filter for first correlation (rough)                                                               | dict           |
+| filter_options_final           | Filter for second correlation (fine)                                                               | dict           |
+| filter_type                    | Filter type (e.g. bandpass)                                                                        | str            |
+| sampfreq                       | Sampling frequency (in Hz)                                                                         | float          |
+
+## Example Dataset
+An example dataset with waveform data, metadata and automatic picks in the obspy-dmt dataset format for testing can be found at https://zenodo.org/doi/10.5281/zenodo.13759803

docs/tuning.md

@@ -6,122 +6,123 @@ A description of the parameters used for determining automatic picks.
 
 Parameters applied to the traces before picking algorithm starts.
 
-| Name                | Description                                                                                                                                                                                                             |
-|---------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *P Start*, *P
-Stop* | Define time interval relative to trace start time for CF calculation on vertical trace. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue.    |
-| *S Start*, *S
-Stop* | Define time interval relative to trace start time for CF calculation on horizontal traces. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue. |
-| *Bandpass
-Z1*       | Filter settings for Butterworth bandpass applied to vertical trace for calculation of initial P pick.                                                                                                                   |
-| *Bandpass
-Z2*       | Filter settings for Butterworth bandpass applied to vertical trace for calculation of precise P pick.                                                                                                                   |
-| *Bandpass
-H1*       | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of initial S pick.                                                                                                                |
-| *Bandpass
-H2*       | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of precise S pick.                                                                                                                |
+| Name          | Description                                                                                                                                                                                                             |
+|---------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *P Start*, *P |                                                                                                                                                                                                                         |
+| Stop*         | Define time interval relative to trace start time for CF calculation on vertical trace. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue.    |
+| *S Start*, *S |                                                                                                                                                                                                                         |
+| Stop*         | Define time interval relative to trace start time for CF calculation on horizontal traces. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue. |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| Z1*           | Filter settings for Butterworth bandpass applied to vertical trace for calculation of initial P pick.                                                                                                                   |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| Z2*           | Filter settings for Butterworth bandpass applied to vertical trace for calculation of precise P pick.                                                                                                                   |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| H1*           | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of initial S pick.                                                                                                                |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| H2*           | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of precise S pick.                                                                                                                |
 
 ## Inital P pick
 
 Parameters used for determination of initial P pick.
 
-| Name         | Description                                                                                                                  |
-|--------------|------------------------------------------------------------------------------------------------------------------------------|
-| *
-tLTA*       | Size of gliding LTA window in seconds used for calculation of HOS-CF.                                                        |
-| *pickwin
-P*  | Size of time window in seconds in which the minimum of the AIC-CF in front of the maximum of the HOS-CF is determined.       |
-| *
-AICtsmooth* | Average of samples in this time window will be used for smoothing of the AIC-CF.                                             |
-| *
-checkwinP*  | Time in front of the global maximum of the HOS-CF in which to search for a second local extrema.                             |
-| *minfactorP* | Used with *
-checkwinP*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorP*. |
-| *
-tsignal*    | Time window in seconds after the initial P pick used for determining signal amplitude.                                       |
-| *
-tnoise*     | Time window in seconds in front of initial P pick used for determining noise amplitude.                                      |
-| *tsafetey*   | Time in seconds between *tsignal* and *
-tnoise*.                                                                              |
-| *
-tslope*     | Time window in seconds after initial P pick in which the slope of the onset is calculated.                                   |
+| Name                                                                                                              | Description                                                                                                            |
+|-------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|
+| *                                                                                                                 |                                                                                                                        |
+| tLTA*                                                                                                             | Size of gliding LTA window in seconds used for calculation of HOS-CF.                                                  |
+| *pickwin                                                                                                          |                                                                                                                        |
+| P*                                                                                                                | Size of time window in seconds in which the minimum of the AIC-CF in front of the maximum of the HOS-CF is determined. |
+| *                                                                                                                 |                                                                                                                        |
+| AICtsmooth*                                                                                                       | Average of samples in this time window will be used for smoothing of the AIC-CF.                                       |
+| *                                                                                                                 |                                                                                                                        |
+| checkwinP*                                                                                                        | Time in front of the global maximum of the HOS-CF in which to search for a second local extrema.                       |
+| *minfactorP*                                                                                                      | Used with *                                                                                                            |
+| checkwinP*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorP*. |                                                                                                                        |
+| *                                                                                                                 |                                                                                                                        |
+| tsignal*                                                                                                          | Time window in seconds after the initial P pick used for determining signal amplitude.                                 |
+| *                                                                                                                 |                                                                                                                        |
+| tnoise*                                                                                                           | Time window in seconds in front of initial P pick used for determining noise amplitude.                                |
+| *tsafetey*                                                                                                        | Time in seconds between *tsignal* and *                                                                                |
+| tnoise*.                                                                                                          |                                                                                                                        |
+| *                                                                                                                 |                                                                                                                        |
+| tslope*                                                                                                           | Time window in seconds after initial P pick in which the slope of the onset is calculated.                             |
 
 ## Inital S pick
 
 Parameters used for determination of initial S pick
 
-| Name          | Description                                                                                                                  |
-|---------------|------------------------------------------------------------------------------------------------------------------------------|
-| *
-tdet1h*      | Length of time window in seconds in which AR params of the waveform are determined.                                          |
-| *
-tpred1h*     | Length of time window in seconds in which the waveform is predicted using the AR model.                                      |
-| *
-AICtsmoothS* | Average of samples in this time window is used for smoothing the AIC-CF.                                                     |
-| *
-pickwinS*    | Time window in which the minimum in the AIC-CF in front of the maximum in the ARH-CF is determined.                          |
-| *
-checkwinS*   | Time in front of the global maximum of the ARH-CF in which to search for a second local extrema.                             |
-| *minfactorP*  | Used with *
-checkwinS*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorS*. |
-| *
-tsignal*     | Time window in seconds after the initial P pick used for determining signal amplitude.                                       |
-| *
-tnoise*      | Time window in seconds in front of initial P pick used for determining noise amplitude.                                      |
-| *tsafetey*    | Time in seconds between *tsignal* and *
-tnoise*.                                                                              |
-| *
-tslope*      | Time window in seconds after initial P pick in which the slope of the onset is calculated.                                   |
+| Name                                                                                                              | Description                                                                                         |
+|-------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------|
+| *                                                                                                                 |                                                                                                     |
+| tdet1h*                                                                                                           | Length of time window in seconds in which AR params of the waveform are determined.                 |
+| *                                                                                                                 |                                                                                                     |
+| tpred1h*                                                                                                          | Length of time window in seconds in which the waveform is predicted using the AR model.             |
+| *                                                                                                                 |                                                                                                     |
+| AICtsmoothS*                                                                                                      | Average of samples in this time window is used for smoothing the AIC-CF.                            |
+| *                                                                                                                 |                                                                                                     |
+| pickwinS*                                                                                                         | Time window in which the minimum in the AIC-CF in front of the maximum in the ARH-CF is determined. |
+| *                                                                                                                 |                                                                                                     |
+| checkwinS*                                                                                                        | Time in front of the global maximum of the ARH-CF in which to search for a second local extrema.    |
+| *minfactorP*                                                                                                      | Used with *                                                                                         |
+| checkwinS*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorS*. |                                                                                                     |
+| *                                                                                                                 |                                                                                                     |
+| tsignal*                                                                                                          | Time window in seconds after the initial P pick used for determining signal amplitude.              |
+| *                                                                                                                 |                                                                                                     |
+| tnoise*                                                                                                           | Time window in seconds in front of initial P pick used for determining noise amplitude.             |
+| *tsafetey*                                                                                                        | Time in seconds between *tsignal* and *                                                             |
+| tnoise*.                                                                                                          |                                                                                                     |
+| *                                                                                                                 |                                                                                                     |
+| tslope*                                                                                                           | Time window in seconds after initial P pick in which the slope of the onset is calculated.          |
 
 ## Precise P pick
 
 Parameters used for determination of precise P pick.
 
-| Name         | Description                                                                                                                                                                                                             |
-|--------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *Precalcwin* | Time window in seconds for recalculation of the HOS-CF. The new CF will be two times the size of *
-Precalcwin*, since it will be calculated from the initial pick to +/- *Precalcwin*.                                   |
-| *
-tsmoothP*   | Average of samples in this time window will be used for smoothing the second HOS-CF.                                                                                                                                    |
-| *
-ausP*       | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed HOS-CF is found when the previous sample is larger or equal to the current sample times (1+*
-ausP*). |
+| Name                                                                                | Description                                                                                                                                                                                                      |
+|-------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *Precalcwin*                                                                        | Time window in seconds for recalculation of the HOS-CF. The new CF will be two times the size of *                                                                                                               |
+| Precalcwin*, since it will be calculated from the initial pick to +/- *Precalcwin*. |                                                                                                                                                                                                                  |
+| *                                                                                   |                                                                                                                                                                                                                  |
+| tsmoothP*                                                                           | Average of samples in this time window will be used for smoothing the second HOS-CF.                                                                                                                             |
+| *                                                                                   |                                                                                                                                                                                                                  |
+| ausP*                                                                               | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed HOS-CF is found when the previous sample is larger or equal to the current sample times (1+* |
+| ausP*).                                                                             |                                                                                                                                                                                                                  |
 
 ## Precise S pick
 
 Parameters used for determination of precise S pick.
 
-| Name         | Description                                                                                                                                                                                                             |
-|--------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-tdet2h*     | Time window for determination of AR coefficients.                                                                                                                                                                       |
-| *
-tpred2h*    | Time window in which the waveform is predicted using the determined AR parameters.                                                                                                                                      |
-| *Srecalcwin* | Time window for recalculation of ARH-CF. New CF will be calculated from initial pick +/- *
-Srecalcwin*.                                                                                                                  |
-| *
-tsmoothS*   | Average of samples in this time window will be used for smoothing the second ARH-CF.                                                                                                                                    |
-| *
-ausS*       | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed ARH-CF is found when the previous sample is larger or equal to the current sample times (1+*
-ausS*). |
-| *
-pickwinS*   | Time window around initial pick in which to look for a precise pick.                                                                                                                                                    |
+| Name         | Description                                                                                                                                                                                                      |
+|--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *            |                                                                                                                                                                                                                  |
+| tdet2h*      | Time window for determination of AR coefficients.                                                                                                                                                                |
+| *            |                                                                                                                                                                                                                  |
+| tpred2h*     | Time window in which the waveform is predicted using the determined AR parameters.                                                                                                                               |
+| *Srecalcwin* | Time window for recalculation of ARH-CF. New CF will be calculated from initial pick +/- *                                                                                                                       |
+| Srecalcwin*. |                                                                                                                                                                                                                  |
+| *            |                                                                                                                                                                                                                  |
+| tsmoothS*    | Average of samples in this time window will be used for smoothing the second ARH-CF.                                                                                                                             |
+| *            |                                                                                                                                                                                                                  |
+| ausS*        | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed ARH-CF is found when the previous sample is larger or equal to the current sample times (1+* |
+| ausS*).      |                                                                                                                                                                                                                  |
+| *            |                                                                                                                                                                                                                  |
+| pickwinS*    | Time window around initial pick in which to look for a precise pick.                                                                                                                                             |
 
 ## Pick quality control
 
 Parameters used for checking quality and integrity of automatic picks.
 
-| Name                                       | Description                                                                                                                                                                                                                                                                    |
-|--------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-minAICPslope*                             | Initial P picks with a slope lower than this value will be discared.                                                                                                                                                                                                           |
-| *
-minAICPSNR*                               | Initial P picks with a SNR below this value will be discarded.                                                                                                                                                                                                                 |
-| *
-minAICSslope*                             | Initial S picks with a slope lower than this value will be discarded.                                                                                                                                                                                                          |
-| *
-minAICSSNR*                               | Initial S picks with a SNR below this value will be discarded.                                                                                                                                                                                                                 |
-| *minsiglength*, *noisefacor*. *minpercent* | Parameters for checking signal length. In the time window of size *
+| Name                                       | Description                                                           |
+|--------------------------------------------|-----------------------------------------------------------------------|
+| *                                          |                                                                       |
+| minAICPslope*                              | Initial P picks with a slope lower than this value will be discared.  |
+| *                                          |                                                                       |
+| minAICPSNR*                                | Initial P picks with a SNR below this value will be discarded.        |
+| *                                          |                                                                       |
+| minAICSslope*                              | Initial S picks with a slope lower than this value will be discarded. |
+| *                                          |                                                                       |
+| minAICSSNR*                                | Initial S picks with a SNR below this value will be discarded.        |
+| *minsiglength*, *noisefacor*. *minpercent* | Parameters for checking signal length. In the time window of size *   |
+
 minsiglength* after the initial P pick *
 minpercent* of samples have to be larger than the RMS value.                                                                                                        |
 | *
@@ -139,12 +140,12 @@ wdttolerance*                             | Maximum allowed deviation of S onset
 
 Parameters for discrete quality classes.
 
-| Name             | Description                                                                                                                                                                                                           |
-|------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-timeerrorsP*    | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for P onsets.                                                                           |
-| *
-timeerrorsS*    | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for S onsets.                                                                           |
-| *nfacP*, *nfacS* | For determination of latest possible onset time. The time when the signal reaches an amplitude of *
-nfac* * mean value of the RMS amplitude in the time window *tnoise* corresponds to the latest possible onset time. |
+| Name                                                                                                               | Description                                                                                                                                 |
+|--------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
+| *                                                                                                                  |                                                                                                                                             |
+| timeerrorsP*                                                                                                       | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for P onsets. |
+| *                                                                                                                  |                                                                                                                                             |
+| timeerrorsS*                                                                                                       | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for S onsets. |
+| *nfacP*, *nfacS*                                                                                                   | For determination of latest possible onset time. The time when the signal reaches an amplitude of *                                         |
+| nfac* * mean value of the RMS amplitude in the time window *tnoise* corresponds to the latest possible onset time. |                                                                                                                                             |
 

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/data.py

@@ -36,8 +36,17 @@ class Data(object):
     loaded event. Container object holding, e.g. phase arrivals, etc.
     """
 
-    def __init__(self, parent=None, evtdata=None):
+    def __init__(self, parent=None, evtdata=None, picking_parameter=None):
         self._parent = parent
+
+        if not picking_parameter:
+            if hasattr(parent, '_inputs'):
+                picking_parameter = parent._inputs
+            else:
+                logging.warning('No picking parameters found! Using default input parameters!!!')
+                picking_parameter = PylotParameter()
+        self.picking_parameter = picking_parameter
+
         if self.getParent():
             self.comp = parent.getComponent()
         else:
@@ -403,23 +412,19 @@ class Data(object):
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.cnv':
                 try:
-                    velest.export(picks_copy, fnout + fnext, eventinfo=self.get_evt_data())
+                    velest.export(picks_copy, fnout + fnext, self.picking_parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '_focmec.in':
                 try:
-                    parameter = PylotParameter()
-                    logging.warning('Using default input parameter')
-                    focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
+                    focmec.export(picks_copy, fnout + fnext, self.picking_parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.pha':
                 try:
-                    parameter = PylotParameter()
-                    logging.warning('Using default input parameter')
-                    hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
+                    hypodd.export(picks_copy, fnout + fnext, self.picking_parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))

pylot/core/io/default_parameters.py

@@ -501,7 +501,7 @@ defaults = {'datapath': {'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,

pylot/core/io/inputs.py

@@ -53,10 +53,16 @@ class PylotParameter(object):
         self.__parameter = {}
         self._verbosity = verbosity
         self._parFileCont = {}
+
         # io from parsed arguments alternatively
         for key, val in kwargs.items():
             self._parFileCont[key] = val
         self.from_file()
+
+        # if no filename or kwargs given, use default values
+        if not fnin and not kwargs:
+            self.reset_defaults()
+
         if fnout:
             self.export2File(fnout)
 

pylot/core/io/phases.py

@@ -278,7 +278,6 @@ def picksdict_from_picks(evt, parameter=None):
         weight = phase.get('weight')
         if not weight:
             if not parameter:
-                logging.warning('Using ')
                 logging.warning('Using default input parameter')
                 parameter = PylotParameter()
             pick.phase_hint = identifyPhase(pick.phase_hint)
@@ -513,7 +512,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # 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('datapath'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
+        arrivals = chooseArrivals(arrivals)
         for key in arrivals:
             # P onsets
             if 'P' in arrivals[key]:
@@ -666,7 +665,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('%s, event %s \n' % (parameter.get('datapath'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
+        arrivals = chooseArrivals(arrivals)
         for key in arrivals:
             # P onsets
             if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
@@ -757,11 +756,11 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             cns, eventsource['longitude'], cew, eventsource['depth'], eventinfo.magnitudes[0]['mag'], ifx))
         n = 0
         # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
+        if isinstance(arrivals, dict) is False:
             # convert pick object (PyLoT) into dictionary
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
+            arrivals = picksdict_from_picks(evt, parameter=parameter)
         # check for automatic and manual picks
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
@@ -822,7 +821,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             # convert pick object (PyLoT) into dictionary
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
+            arrivals = picksdict_from_picks(evt, parameter=parameter)
         # check for automatic and manual picks
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
@@ -873,7 +872,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
             # convert pick object (PyLoT) into dictionary
             evt = ope.Event(resource_id=eventinfo['resource_id'])
             evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
+            arrivals = picksdict_from_picks(evt, parameter=parameter)
         # check for automatic and manual picks
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)

pylot/core/pick/charfuns.py

@@ -21,6 +21,7 @@ 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

pylot/core/util/array_map.py

@@ -134,8 +134,8 @@ class Array_map(QtWidgets.QWidget):
         self.cmaps_box = QtWidgets.QComboBox()
         self.cmaps_box.setMaxVisibleItems(20)
         [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
-        # try to set to viridis as default
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('viridis'))
+        # try to set to plasma as default
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('plasma'))
 
         self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
@@ -521,7 +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)

pylot/core/util/dataprocessing.py

@@ -59,6 +59,8 @@ class Metadata(object):
         :type path_to_inventory: str
         :return: None
         """
+        path_to_inventory = path_to_inventory.replace('\\', '/')
+        path_to_inventory = os.path.abspath(path_to_inventory)
         assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory)
         if path_to_inventory not in self.inventories:
             self.inventories.append(path_to_inventory)
@@ -218,9 +220,9 @@ class Metadata(object):
                     network_name = network.code
                     if not station_name in self.stations_dict.keys():
                         st_id = '{}.{}'.format(network_name, station_name)
-                        self.stations_dict[st_id] = {'latitude': station[0].latitude,
-                                                     'longitude': station[0].longitude,
-                                                     'elevation': station[0].elevation}
+                        self.stations_dict[st_id] = {'latitude': station.latitude,
+                                                     'longitude': station.longitude,
+                                                     'elevation': station.elevation}
 
         read_stat = {'xml': stat_info_from_inventory,
                      'dless': stat_info_from_parser}
@@ -266,9 +268,6 @@ class Metadata(object):
         if not fnames:
             # search for station name in filename
             fnames = glob.glob(os.path.join(path_to_inventory, '*' + station + '*'))
-        if not fnames:
-            # search for network name in filename
-            fnames = glob.glob(os.path.join(path_to_inventory, '*' + network + '*'))
         if not fnames:
             if self.verbosity:
                 print('Could not find filenames matching station name, network name or seed id')
@@ -280,7 +279,7 @@ class Metadata(object):
                     continue
             invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
             try:
-                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
+                robj.get_coordinates(station_seed_id)
                 self.inventory_files[fname] = {'invtype': invtype,
                                                'data': robj}
                 if station_seed_id in self.seed_ids.keys():
@@ -288,6 +287,7 @@ class Metadata(object):
                 self.seed_ids[station_seed_id] = fname
                 return True
             except Exception as e:
+                logging.warning(e)
                 continue
         print('Could not find metadata for station_seed_id {} in path {}'.format(station_seed_id, path_to_inventory))
 
@@ -652,6 +652,8 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
     """
 
     # data = remove_underscores(data)
+    if not data:
+        return
 
     # loop over traces
     input_tuples = []
@@ -659,9 +661,14 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
         input_tuples.append((tr, metadata, unit, force))
         data.remove(tr)
 
-    pool = gen_Pool(ncores)
-    result = pool.imap_unordered(restitute_trace, input_tuples)
-    pool.close()
+    if ncores == 0:
+        result = []
+        for input_tuple in input_tuples:
+            result.append(restitute_trace(input_tuple))
+    else:
+        pool = gen_Pool(ncores)
+        result = pool.imap_unordered(restitute_trace, input_tuples)
+        pool.close()
 
     for tr, remove_trace in result:
         if not remove_trace:

pylot/core/util/utils.py

@@ -51,7 +51,6 @@ def readDefaultFilterInformation():
     :rtype: dict
     """
     pparam = PylotParameter()
-    pparam.reset_defaults()
     return readFilterInformation(pparam)
 
 

pylot/core/util/widgets.py

@@ -1871,13 +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
@@ -2270,8 +2271,8 @@ class PickDlg(QDialog):
         arrivals = func[plot](source_origin.depth,
                               source_origin.latitude,
                               source_origin.longitude,
-                              station_coords['latitude'],
-                              station_coords['longitude'],
+                              station_coords.get('latitude'),
+                              station_coords.get('longitude'),
                               phases)
         self.arrivals = arrivals
 

pylot/correlation/__init__.py

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

pylot/correlation/parameters_adriaarray.yaml

@@ -0,0 +1,101 @@
+#############################  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 auto 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'
+# dt_stacking: time shift for stacking (e.g. [0, 250] for 0 and 250 seconds shift)
+# filter_options: filter for first correlation (rough)
+# filter_options_final: filter for second correlation (fine)
+# filter_type: e.g. 'bandpass'
+# sampfreq: sampling frequency of the data
+
+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
+
+  # ignore if autopylot fails to pick master-trace (not recommended if absolute onset times matter)
+  ignore_autopylot_fail_on_master: True
+
+# 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
+
+  # ignore if autopylot fails to pick master-trace (not recommended if absolute onset times matter)
+  ignore_autopylot_fail_on_master: True
+

pylot/correlation/submit_pick_corr_correction.sh

@@ -0,0 +1,41 @@
+#!/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:
+# use -pd for detailed plots in eventdir/correlation_XX_XX/figures
+python pick_correlation_correction.py $1 $pylot_infile -n ${NSLOTS:=1} -istart $2 --params 'parameters_adriaarray.yaml' # -pd
+#--event_blacklist eventlist.txt

pylot/correlation/submit_to_grid_engine.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+import subprocess
+
+fnames = [
+    ('/data/AdriaArray_Data/dmt_database_mantle_M5.0-5.4', 0),
+    ('/data/AdriaArray_Data/dmt_database_mantle_M5.4-5.7', 0),
+    ('/data/AdriaArray_Data/dmt_database_mantle_M5.7-6.0', 0),
+    ('/data/AdriaArray_Data/dmt_database_mantle_M6.0-6.3', 0),
+    ('/data/AdriaArray_Data/dmt_database_mantle_M6.3-10.0', 0),
+    # ('/data/AdriaArray_Data/dmt_database_ISC_mantle_M5.0-5.4', 0),
+    # ('/data/AdriaArray_Data/dmt_database_ISC_mantle_M5.4-5.7', 0),
+    # ('/data/AdriaArray_Data/dmt_database_ISC_mantle_M5.7-6.0', 0),
+    # ('/data/AdriaArray_Data/dmt_database_ISC_mantle_M6.0-10.0', 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/pylot/pylot/correlation/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

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)