Merge branch 'refs/heads/correlation_picker' into develop
This commit is contained in:
commit
41c9183be3
4
PyLoT.py
4
PyLoT.py
@ -2196,7 +2196,8 @@ class MainWindow(QMainWindow):
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if event.pylot_autopicks:
|
if event.pylot_autopicks:
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self.drawPicks(picktype='auto')
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self.drawPicks(picktype='auto')
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if event.pylot_picks or event.pylot_autopicks:
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if event.pylot_picks or event.pylot_autopicks:
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self.locateEventAction.setEnabled(True)
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if not self._inputs.get('extent') == 'global':
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self.locateEventAction.setEnabled(True)
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self.qualities_action.setEnabled(True)
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self.qualities_action.setEnabled(True)
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self.eventlist_xml_action.setEnabled(True)
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self.eventlist_xml_action.setEnabled(True)
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@ -2631,7 +2632,6 @@ class MainWindow(QMainWindow):
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picks=self.getPicksOnStation(station, 'manual'),
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picks=self.getPicksOnStation(station, 'manual'),
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autopicks=self.getPicksOnStation(station, 'auto'),
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autopicks=self.getPicksOnStation(station, 'auto'),
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metadata=self.metadata, event=event,
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metadata=self.metadata, event=event,
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model=self.inputs.get('taup_model'),
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filteroptions=self.filteroptions, wftype=wftype,
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filteroptions=self.filteroptions, wftype=wftype,
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show_comp_data=self.dataPlot.comp_checkbox.isChecked())
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show_comp_data=self.dataPlot.comp_checkbox.isChecked())
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if self.filterActionP.isChecked():
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if self.filterActionP.isChecked():
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@ -9,7 +9,7 @@ PyLoT - the Python picking and Localization Tool
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This python library contains a graphical user interfaces for picking
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This python library contains a graphical user interfaces for picking
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seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
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seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
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and the Qt4 libraries to be installed first.
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and the Qt libraries to be installed first.
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|
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PILOT has been developed in Mathworks' MatLab. In order to distribute
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PILOT has been developed in Mathworks' MatLab. In order to distribute
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PILOT without facing portability problems, it has been decided to re-
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PILOT without facing portability problems, it has been decided to re-
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@ -501,7 +501,7 @@ defaults = {'datapath': {'type': str,
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'taup_model': {'type': str,
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'taup_model': {'type': str,
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'tooltip': 'Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
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'tooltip': 'Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
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'value': None,
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'value': 'iasp91',
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'namestring': 'TauPy model'},
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'namestring': 'TauPy model'},
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'taup_phases': {'type': str,
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'taup_phases': {'type': str,
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@ -21,6 +21,7 @@ try:
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from scipy.signal import tukey
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from scipy.signal import tukey
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except ImportError:
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except ImportError:
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from scipy.signal.windows import tukey
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from scipy.signal.windows import tukey
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from obspy.core import Stream
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from obspy.core import Stream
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from pylot.core.pick.utils import PickingFailedException
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from pylot.core.pick.utils import PickingFailedException
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@ -521,7 +521,6 @@ class Array_map(QtWidgets.QWidget):
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picks=self._parent.get_current_event().getPick(station),
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picks=self._parent.get_current_event().getPick(station),
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autopicks=self._parent.get_current_event().getAutopick(station),
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autopicks=self._parent.get_current_event().getAutopick(station),
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filteroptions=self._parent.filteroptions, metadata=self.metadata,
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filteroptions=self._parent.filteroptions, metadata=self.metadata,
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model=self.parameter.get('taup_model'),
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event=pyl_mw.get_current_event())
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event=pyl_mw.get_current_event())
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except Exception as e:
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except Exception as e:
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message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
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message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
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@ -1871,13 +1871,14 @@ class PickDlg(QDialog):
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def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
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def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
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autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
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autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
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event=None, filteroptions=None, model=None, wftype=None):
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event=None, filteroptions=None, wftype=None):
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super(PickDlg, self).__init__(parent, Qt.Window)
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super(PickDlg, self).__init__(parent, Qt.Window)
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self.orig_parent = parent
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self.orig_parent = parent
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self.setAttribute(Qt.WA_DeleteOnClose)
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self.setAttribute(Qt.WA_DeleteOnClose)
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# initialize attributes
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# initialize attributes
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self.parameter = parameter
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self.parameter = parameter
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model = self.parameter.get('taup_model')
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self._embedded = embedded
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self._embedded = embedded
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self.showCompData = show_comp_data
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self.showCompData = show_comp_data
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self.station = station
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self.station = station
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@ -2270,8 +2271,8 @@ class PickDlg(QDialog):
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arrivals = func[plot](source_origin.depth,
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arrivals = func[plot](source_origin.depth,
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source_origin.latitude,
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source_origin.latitude,
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source_origin.longitude,
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source_origin.longitude,
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station_coords['latitude'],
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station_coords.get('latitude'),
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station_coords['longitude'],
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station_coords.get('longitude'),
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phases)
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phases)
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self.arrivals = arrivals
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self.arrivals = arrivals
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2
pylot/correlation/__init__.py
Normal file
2
pylot/correlation/__init__.py
Normal file
@ -0,0 +1,2 @@
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# -*- coding: utf-8 -*-
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#
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90
pylot/correlation/parameters_adriaarray.yaml
Normal file
90
pylot/correlation/parameters_adriaarray.yaml
Normal file
@ -0,0 +1,90 @@
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############################# correlation parameters #####################################
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# min_corr_stacking: minimum correlation coefficient for building beam trace
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# min_corr_export: minimum correlation coefficient for pick export
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# min_stack: minimum number of stations for building beam trace
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# t_before: correlation window before pick
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# t_after: correlation window after pick#
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# cc_maxlag: maximum shift for initial correlation
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# cc_maxlag2: maximum shift for second (final) correlation (also for calculating pick uncertainty)
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# initial_pick_outlier_threshold: (hopefully) threshold for excluding large outliers of initial (AIC) picks
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# export_threshold: automatically exclude all onsets which deviate more than this threshold from corrected taup onsets
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# min_picks_export: minimum number of correlated picks for export
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# min_picks_autopylot: minimum number of reference autopicks picks to continue with event
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# check_RMS: do RMS check to search for restitution errors (very experimental)
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# use_taupy_onsets: use taupy onsets as reference picks instead of external picks
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# station_list: use the following stations as reference for stacking
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# use_stacked_trace: use existing stacked trace if found (spare re-computation)
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# data_dir: obspyDMT data subdirectory (e.g. 'raw', 'processed')
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# pickfile_extension: use quakeML files (PyLoT output) with the following extension, e.g. '_autopylot' for pickfiles
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# such as 'PyLoT_20170501_141822_autopylot.xml'
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logging: info
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pick_phases: ['P', 'S']
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# P-phase
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P:
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min_corr_stacking: 0.8
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min_corr_export: 0.6
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min_stack: 20
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t_before: 30.
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t_after: 50.
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cc_maxlag: 50.
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cc_maxlag2: 5.
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initial_pick_outlier_threshold: 30.
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export_threshold: 2.5
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min_picks_export: 100
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min_picks_autopylot: 50
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check_RMS: True
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use_taupy_onsets: False
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station_list: ['HU.MORH', 'HU.TIH', 'OX.FUSE', 'OX.BAD']
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use_stacked_trace: False
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data_dir: 'processed'
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pickfile_extension: '_autopylot'
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dt_stacking: [250, 250]
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# filter for first correlation (rough)
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filter_options:
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freqmax: 0.5
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freqmin: 0.03
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# filter for second correlation (fine)
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filter_options_final:
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freqmax: 0.5
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freqmin: 0.03
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filter_type: bandpass
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sampfreq: 20.0
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# S-phase
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S:
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min_corr_stacking: 0.7
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min_corr_export: 0.6
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min_stack: 20
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t_before: 60.
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t_after: 60.
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cc_maxlag: 100.
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cc_maxlag2: 25.
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initial_pick_outlier_threshold: 30.
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export_threshold: 5.0
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min_picks_export: 200
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min_picks_autopylot: 50
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check_RMS: True
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use_taupy_onsets: False
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station_list: ['HU.MORH','HU.TIH', 'OX.FUSE', 'OX.BAD']
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use_stacked_trace: False
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data_dir: 'processed'
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pickfile_extension: '_autopylot'
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dt_stacking: [250, 250]
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|
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# filter for first correlation (rough)
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filter_options:
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freqmax: 0.1
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freqmin: 0.01
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|
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# filter for second correlation (fine)
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filter_options_final:
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freqmax: 0.2
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freqmin: 0.01
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|
filter_type: bandpass
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sampfreq: 20.0
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|
1987
pylot/correlation/pick_correlation_correction.py
Normal file
1987
pylot/correlation/pick_correlation_correction.py
Normal file
File diff suppressed because it is too large
Load Diff
40
pylot/correlation/submit_pick_corr_correction.sh
Executable file
40
pylot/correlation/submit_pick_corr_correction.sh
Executable file
@ -0,0 +1,40 @@
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|
#!/bin/bash
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|
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|
#ulimit -s 8192
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|
#ulimit -v $(ulimit -v | awk '{printf("%d",$1*0.95)}')
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|
#ulimit -v
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|
|
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|
#655360
|
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|
|
||||||
|
source /opt/anaconda3/etc/profile.d/conda.sh
|
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|
conda activate pylot_311
|
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|
NSLOTS=20
|
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|
|
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|
#qsub -l low -cwd -l "os=*stretch" -pe smp 40 submit_pick_corr_correction.sh
|
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|
#$ -l low
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|
#$ -l h_vmem=6G
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|
#$ -cwd
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|
#$ -pe smp 20
|
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|
#$ -N corr_pick
|
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|
|
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|
|
||||||
|
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=${NSLOTS:=1}
|
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|
#export OMP_NUM_THREADS=${NSLOTS:=1}
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||||||
|
|
||||||
|
#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
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||||||
|
#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'
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||||||
|
#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
|
23
pylot/correlation/submit_to_grid_engine.py
Executable file
23
pylot/correlation/submit_to_grid_engine.py
Executable file
@ -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()))
|
||||||
|
|
||||||
|
|
||||||
|
|
61
pylot/correlation/utils.py
Normal file
61
pylot/correlation/utils.py
Normal file
@ -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)
|
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|
return metadata
|
@ -0,0 +1,76 @@
|
|||||||
|
import pytest
|
||||||
|
from obspy import read, Trace, UTCDateTime
|
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|
|
||||||
|
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)
|
Loading…
Reference in New Issue
Block a user