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Merge branch 'refs/heads/develop' into correlation_picker

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# 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
This commit is contained in:
Marcel Paffrath 2024-08-29 16:37:15 +02:00
commit 424d42aa1c
13 changed files with 65847 additions and 43 deletions
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29
PyLoT.py
View File

@ -1031,22 +1031,23 @@ class MainWindow(QMainWindow):
if not fname:
return
qmb = QMessageBox(self, icon=QMessageBox.Question,
text='Do you want to overwrite this data?',)
overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
merge_button = qmb.addButton('Merge', QMessageBox.NoRole)
qmb.exec_()
if qmb.clickedButton() == overwrite_button:
merge_strategy = 'Overwrite'
elif qmb.clickedButton() == merge_button:
merge_strategy = 'Merge'
else:
return
if not event:
event = self.get_current_event()
if event.picks:
qmb = QMessageBox(self, icon=QMessageBox.Question,
text='Do you want to overwrite the data?',)
overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
merge_button = qmb.addButton('Merge', QMessageBox.NoRole)
qmb.exec_()
if qmb.clickedButton() == overwrite_button:
merge_strategy = 'Overwrite'
elif qmb.clickedButton() == merge_button:
merge_strategy = 'Merge'
else:
return
data = Data(self, event)
try:
data_new = Data(self, evtdata=str(fname))

15
autoPyLoT.py
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@ -184,15 +184,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
if not input_dict:
# started in production mode
datapath = datastructure.expandDataPath()
if fnames == 'None' and parameter['eventID'] == '*':
if fnames in [None, 'None'] and parameter['eventID'] == '*':
# multiple event processing
# read each event in database
events = [event for event in glob.glob(os.path.join(datapath, '*')) if
(os.path.isdir(event) and not event.endswith('EVENTS-INFO'))]
elif fnames == 'None' and parameter['eventID'] != '*' and not type(parameter['eventID']) == list:
elif fnames in [None, 'None'] and parameter['eventID'] != '*' and not type(parameter['eventID']) == list:
# single event processing
events = glob.glob(os.path.join(datapath, parameter['eventID']))
elif fnames == 'None' and type(parameter['eventID']) == list:
elif fnames in [None, 'None'] and type(parameter['eventID']) == list:
# multiple event processing
events = []
for eventID in parameter['eventID']:
@ -234,12 +234,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
data.get_evt_data().path = eventpath
print('Reading event data from filename {}...'.format(filename))
except Exception as e:
print('Could not read event from file {}: {}'.format(filename, e))
if type(e) == FileNotFoundError:
print('Creating new event file.')
else:
print('Could not read event from file {}: {}'.format(filename, e))
data = Data()
pylot_event = Event(eventpath) # event should be path to event directory
data.setEvtData(pylot_event)
if fnames == 'None':
data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
if fnames in [None, 'None']:
data.setWFData(glob.glob(os.path.join(event_datapath, '*')))
# the following is necessary because within
# multiple event processing no event ID is provided
# in autopylot.in

2
pylot/core/pick/charfuns.py
View File

@ -231,7 +231,7 @@ class AICcf(CharacteristicFunction):
ind = np.where(~np.isnan(xnp))[0]
if ind.size:
xnp[:ind[0]] = xnp[ind[0]]
xnp = signal.tukey(len(xnp), alpha=0.05) * xnp
xnp = tukey(len(xnp), alpha=0.05) * xnp
xnp = xnp - np.mean(xnp)
datlen = len(xnp)
k = np.arange(1, datlen)

58
pylot/core/util/array_map.py
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@ -14,6 +14,8 @@ import obspy
from PySide2 import QtWidgets, QtGui
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from obspy import UTCDateTime
from pylot.core.util.utils import identifyPhaseID
from scipy.interpolate import griddata
@ -60,6 +62,7 @@ class Array_map(QtWidgets.QWidget):
self.parameter = parameter if parameter else parent._inputs
self.picks_rel = {}
self.picks_rel_mean_corrected = {}
self.marked_stations = []
self.highlighted_stations = []
@ -106,6 +109,7 @@ class Array_map(QtWidgets.QWidget):
self.map_reset_button = QtWidgets.QPushButton('Reset Map View')
self.save_map_button = QtWidgets.QPushButton('Save Map')
self.go2eq_button = QtWidgets.QPushButton('Go to Event Location')
self.subtract_mean_cb = QtWidgets.QCheckBox('Subtract mean')
self.main_box = QtWidgets.QVBoxLayout()
self.setLayout(self.main_box)
@ -152,6 +156,7 @@ class Array_map(QtWidgets.QWidget):
self.bot_row.addWidget(self.map_reset_button, 2)
self.bot_row.addWidget(self.go2eq_button, 2)
self.bot_row.addWidget(self.save_map_button, 2)
self.bot_row.addWidget(self.subtract_mean_cb, 0)
self.bot_row.addWidget(self.status_label, 5)
def init_colormap(self):
@ -212,6 +217,7 @@ class Array_map(QtWidgets.QWidget):
self.map_reset_button.clicked.connect(self.org_map_view)
self.go2eq_button.clicked.connect(self.go2eq)
self.save_map_button.clicked.connect(self.saveFigure)
self.subtract_mean_cb.stateChanged.connect(self.toggle_subtract_mean)
self.plotWidget.mpl_connect('motion_notify_event', self.mouse_moved)
self.plotWidget.mpl_connect('scroll_event', self.mouse_scroll)
@ -368,12 +374,6 @@ class Array_map(QtWidgets.QWidget):
def get_max_from_stations(self, key):
return self._from_dict(max, key)
def get_min_from_picks(self):
return min(self.picks_rel.values())
def get_max_from_picks(self):
return max(self.picks_rel.values())
def current_picks_dict(self):
picktype = self.comboBox_am.currentText().split(' ')[0]
auto_manu = {'auto': self.autopicks_dict,
@ -418,17 +418,17 @@ class Array_map(QtWidgets.QWidget):
print('Cannot display pick for station {}. Reason: {}'.format(station_name, e))
return picks, uncertainties
def get_picks_rel(picks):
def get_picks_rel(picks, func=min):
picks_rel = {}
picks_utc = []
for pick in picks.values():
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
picks_utc.append(pick)
if type(pick) is UTCDateTime:
picks_utc.append(pick.timestamp)
if picks_utc:
self._earliest_picktime = min(picks_utc)
self._reference_picktime = UTCDateTime(func(picks_utc))
for st_id, pick in picks.items():
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
pick -= self._earliest_picktime
if type(pick) is UTCDateTime:
pick -= self._reference_picktime
picks_rel[st_id] = pick
return picks_rel
@ -437,6 +437,15 @@ class Array_map(QtWidgets.QWidget):
self.picks, self.uncertainties = get_picks(self.stations_dict)
self.picks_rel = get_picks_rel(self.picks)
self.picks_rel_mean_corrected = get_picks_rel_mean_corr(self.picks)
def toggle_subtract_mean(self):
if self.subtract_mean_cb.isChecked():
cmap = 'seismic'
else:
cmap = 'viridis'
self.cmaps_box.setCurrentIndex(self.cmaps_box.findText(cmap))
self._refresh_drawings()
def init_lat_lon_dimensions(self):
# init minimum and maximum lon and lat dimensions
@ -467,11 +476,12 @@ class Array_map(QtWidgets.QWidget):
return stations, latitudes, longitudes
def get_picks_lat_lon(self):
picks_rel = self.picks_rel_mean_corrected if self.subtract_mean_cb.isChecked() else self.picks_rel
picks = []
uncertainties = []
latitudes = []
longitudes = []
for st_id, pick in self.picks_rel.items():
for st_id, pick in picks_rel.items():
picks.append(pick)
uncertainties.append(self.uncertainties.get(st_id))
latitudes.append(self.stations_dict[st_id]['latitude'])
@ -538,13 +548,20 @@ class Array_map(QtWidgets.QWidget):
print(message, e)
print(traceback.format_exc())
def draw_contour_filled(self, nlevel=50):
levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
def draw_contour_filled(self, nlevel=51):
if self.subtract_mean_cb.isChecked():
abs_max = self.get_residuals_absmax()
levels = np.linspace(-abs_max, abs_max, nlevel)
else:
levels = np.linspace(min(self.picks_rel.values()), max(self.picks_rel.values()), nlevel)
self.contourf = self.ax.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
alpha=0.4, zorder=8, cmap=self.get_colormap())
def get_residuals_absmax(self):
return np.max(np.absolute(list(self.picks_rel_mean_corrected.values())))
def get_colormap(self):
return plt.get_cmap(self.cmaps_box.currentText())
@ -575,7 +592,12 @@ class Array_map(QtWidgets.QWidget):
for uncertainty in uncertainties])
cmap = self.get_colormap()
self.sc_picked = self.ax.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
vmin = vmax = None
if self.subtract_mean_cb.isChecked():
vmin, vmax = -self.get_residuals_absmax(), self.get_residuals_absmax()
self.sc_picked = self.ax.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap, vmin=vmin, vmax=vmax,
c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
def annotate_ax(self):
@ -652,7 +674,9 @@ class Array_map(QtWidgets.QWidget):
if picks_available:
self.scatter_picked_stations()
if hasattr(self, 'sc_picked'):
self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime))
self.cbar = self.add_cbar(
label='Time relative to reference onset ({}) [s]'.format(self._reference_picktime)
)
self.comboBox_phase.setEnabled(True)
else:
self.comboBox_phase.setEnabled(False)

4
pylot/core/util/dataprocessing.py
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@ -27,6 +27,10 @@ class Metadata(object):
# saves which metadata files are from obspy dmt
self.obspy_dmt_invs = []
if inventory:
# make sure that no accidental backslashes mess up the path
if isinstance(inventory, str):
inventory = inventory.replace('\\', '/')
inventory = os.path.abspath(inventory)
if os.path.isdir(inventory):
self.add_inventory(inventory)
if os.path.isfile(inventory):

18672
tests/test_autopicker/PyLoT_20171010_063224.a_autopylot.xml Normal file
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6688
tests/test_autopicker/PyLoT_20171010_063224.a_corrected_taup_times_0.01-0.2_SKS.xml Normal file
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tests/test_autopicker/PyLoT_20171010_063224.a_corrected_taup_times_0.03-0.5_P.xml Normal file
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tests/test_autopicker/PyLoT_20171010_063224.a_correlated_0.01-0.2_SKS.xml Normal file
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tests/test_autopicker/PyLoT_20171010_063224.a_correlated_0.03-0.5_P.xml Normal file
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tests/test_autopicker/PyLoT_20171010_063224.a_saved_from_GUI.xml Normal file
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6
tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in
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@ -4,10 +4,8 @@
%Parameters are optimized for %extent data sets!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#main settings#
#rootpath# %project path
#datapath# %data path
#database# %name of data base
20171010_063224.a #eventID# %event ID for single event processing (* for all events found in database)
dmt_database_test #datapath# %data path
20171010_063224.a #eventID# %event ID for single event processing (* for all events found in database)
#invdir# %full path to inventory or dataless-seed file
PILOT #datastructure# %choose data structure
True #apverbose# %choose 'True' or 'False' for terminal output

42
tests/test_autopicker/test_autopylot.py
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@ -1,6 +1,8 @@
import os
import pytest
from obspy import read_events
from autoPyLoT import autoPyLoT
@ -8,7 +10,11 @@ class TestAutopickerGlobal():
def init(self):
self.params_infile = 'pylot_alparray_mantle_corr_stack_0.03-0.5.in'
self.test_event_dir = 'dmt_database_test'
self.fname_outfile_xml = os.path.join(
self.test_event_dir, '20171010_063224.a', 'PyLoT_20171010_063224.a_autopylot.xml'
)
# check if the input files exist
if not os.path.isfile(self.params_infile):
print(f'Test input file {os.path.abspath(self.params_infile)} not found.')
return False
@ -24,4 +30,38 @@ class TestAutopickerGlobal():
def test_autopicker(self):
assert self.init(), 'Initialization failed due to missing input files.'
#autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a')
# check for output file in test directory and remove it if necessary
if os.path.isfile(self.fname_outfile_xml):
os.remove(self.fname_outfile_xml)
autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a', obspyDMT_wfpath='processed')
# test for different known output files if they are identical or not
compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_autopylot.xml', True)
compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_saved_from_GUI.xml', True)
compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_corrected_taup_times_0.03-0.5_P.xml', False)
def compare_pickfiles(pickfile1: str, pickfile2: str, samefile: bool = True) -> None:
"""
Compare the pick times and errors from two pick files.
Parameters:
pickfile1 (str): The path to the first pick file.
pickfile2 (str): The path to the second pick file.
samefile (bool): A flag indicating whether the two files are expected to be the same. Defaults to True.
Returns:
None
"""
cat1 = read_events(pickfile1)
cat2 = read_events(pickfile2)
picks1 = sorted(cat1[0].picks, key=lambda pick: str(pick.waveform_id))
picks2 = sorted(cat2[0].picks, key=lambda pick: str(pick.waveform_id))
pick_times1 = [pick.time for pick in picks1]
pick_times2 = [pick.time for pick in picks2]
pick_terrs1 = [pick.time_errors for pick in picks1]
pick_terrs2 = [pick.time_errors for pick in picks2]
# check if times and errors are identical or not depending on the samefile flag
assert (pick_times1 == pick_times2) is samefile, 'Pick times error'
assert (pick_terrs1 == pick_terrs2) is samefile, 'Pick time errors errors'