Merge branch 'refs/heads/correlation_picker' into develop

# 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

PyLoT.py

@@ -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():

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

@@ -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/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

@@ -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/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.get('latitude'),
-                              station_coords['longitude'],
+                              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 +1,90 @@
+#############################  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

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)