PyLoT.py

@@ -2196,7 +2196,6 @@ class MainWindow(QMainWindow):
         if event.pylot_autopicks:
             self.drawPicks(picktype='auto')
         if event.pylot_picks or event.pylot_autopicks:
-            if not self._inputs.get('extent') == 'global':
             self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
@@ -2632,6 +2631,7 @@ 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 Qt libraries to be installed first.
+and the Qt4 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': 'iasp91',
+                           'value': None,
                            'namestring': 'TauPy model'},
 
             'taup_phases': {'type': str,

pylot/core/pick/charfuns.py

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

@@ -521,6 +521,7 @@ 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

@@ -1871,14 +1871,13 @@ 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, wftype=None):
+                 event=None, filteroptions=None, model=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
@@ -2271,8 +2270,8 @@ class PickDlg(QDialog):
         arrivals = func[plot](source_origin.depth,
                               source_origin.latitude,
                               source_origin.longitude,
-                              station_coords.get('latitude'),
-                              station_coords.get('longitude'),
+                              station_coords['latitude'],
+                              station_coords['longitude'],
                               phases)
         self.arrivals = arrivals
 

pylot/correlation/__init__.py

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

pylot/correlation/parameters_adriaarray.yaml

@@ -1,90 +0,0 @@
-#############################  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

@@ -1,40 +0,0 @@
-#!/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

@@ -1,23 +0,0 @@
-#!/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

@@ -1,61 +0,0 @@
-#!/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

@@ -1,76 +0,0 @@
-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)