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[refactor] rewrote/simplified getQualitiesfromxml code, used function already implemented in phases.py

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Marcel Paffrath 2022-03-16 16:00:14 +01:00
parent 3cd17ff364
commit dd685d5d5e
5 changed files with 94 additions and 269 deletions
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6
PyLoT.py
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@ -89,7 +89,7 @@ from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.thread import Thread, Worker from pylot.core.util.thread import Thread, Worker
from pylot.core.util.version import get_git_version as _getVersionString from pylot.core.util.version import get_git_version as _getVersionString
from pylot.core.io.getEventListFromXML import geteventlistfromxml from pylot.core.io.getEventListFromXML import geteventlistfromxml
from pylot.core.io.getQualitiesfromxml import getQualitiesfromxml from pylot.core.io.phases import getQualitiesfromxml
from pylot.styles import style_settings from pylot.styles import style_settings
@ -1669,8 +1669,8 @@ class MainWindow(QMainWindow):
self.cmpw.show() self.cmpw.show()
def pickQualities(self): def pickQualities(self):
path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database'] path = self.get_current_event_path()
getQualitiesfromxml(path) getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'), plotflag=1)
return return
def eventlistXml(self): def eventlistXml(self):

138
pylot/core/io/getQualitiesfromxml.py
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@ -1,138 +0,0 @@
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
Uncertainties are tranformed into quality classes and visualized via histogram if desired.
Ludger Küperkoch, BESTEC GmbH, 07/2017
rev.: Ludger Küperkoch, igem, 10/2020
Edited for usage in PyLoT: Jeldrik Gaal, igem, 01/2022
"""
import glob
import matplotlib.pyplot as plt
import numpy as np
from obspy.core.event import read_events
def getQualitiesfromxml(path):
# uncertainties
ErrorsP = [0.02, 0.04, 0.08, 0.16]
ErrorsS = [0.04, 0.08, 0.16, 0.32]
Pw0 = []
Pw1 = []
Pw2 = []
Pw3 = []
Pw4 = []
Sw0 = []
Sw1 = []
Sw2 = []
Sw3 = []
Sw4 = []
# data path
dp = path + '/e*/*.xml'
# list of all available xml-files
xmlnames = glob.glob(dp)
# read all onset weights
for names in xmlnames:
print("Getting onset weights from {}".format(names))
cat = read_events(names)
arrivals = cat.events[0].picks
for Pick in arrivals:
if Pick.phase_hint[0] == 'P':
if Pick.time_errors.uncertainty <= ErrorsP[0]:
Pw0.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsP[0] and \
Pick.time_errors.uncertainty <= ErrorsP[1]:
Pw1.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsP[1] and \
Pick.time_errors.uncertainty <= ErrorsP[2]:
Pw2.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsP[2] and \
Pick.time_errors.uncertainty <= ErrorsP[3]:
Pw3.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsP[3]:
Pw4.append(Pick.time_errors.uncertainty)
else:
pass
elif Pick.phase_hint[0] == 'S':
if Pick.time_errors.uncertainty <= ErrorsS[0]:
Sw0.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsS[0] and \
Pick.time_errors.uncertainty <= ErrorsS[1]:
Sw1.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsS[1] and \
Pick.time_errors.uncertainty <= ErrorsS[2]:
Sw2.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsS[2] and \
Pick.time_errors.uncertainty <= ErrorsS[3]:
Sw3.append(Pick.time_errors.uncertainty)
elif Pick.time_errors.uncertainty > ErrorsS[3]:
Sw4.append(Pick.time_errors.uncertainty)
else:
pass
else:
print("Phase hint not defined for picking!")
pass
# get percentage of weights
numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
try:
P0perc = 100.0 / numPweights * len(Pw0)
except:
P0perc = 0
try:
P1perc = 100.0 / numPweights * len(Pw1)
except:
P1perc = 0
try:
P2perc = 100.0 / numPweights * len(Pw2)
except:
P2perc = 0
try:
P3perc = 100.0 / numPweights * len(Pw3)
except:
P3perc = 0
try:
P4perc = 100.0 / numPweights * len(Pw4)
except:
P4perc = 0
try:
S0perc = 100.0 / numSweights * len(Sw0)
except:
Soperc = 0
try:
S1perc = 100.0 / numSweights * len(Sw1)
except:
S1perc = 0
try:
S2perc = 100.0 / numSweights * len(Sw2)
except:
S2perc = 0
try:
S3perc = 100.0 / numSweights * len(Sw3)
except:
S3perc = 0
try:
S4perc = 100.0 / numSweights * len(Sw4)
except:
S4perc = 0
weights = ('0', '1', '2', '3', '4')
y_pos = np.arange(len(weights))
width = 0.34
p1, = plt.bar(0 - width, P0perc, width, color='black')
p2, = plt.bar(0, S0perc, width, color='red')
plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
plt.ylabel('%')
plt.xticks(y_pos, weights)
plt.xlim([-0.5, 4.5])
plt.xlabel('Qualities')
plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
plt.legend([p1, p2], ['P-Weights', 'S-Weights'])
plt.show()

211
pylot/core/io/phases.py
View File

@ -17,7 +17,7 @@ from pylot.core.io.location import create_event, \
create_magnitude create_magnitude
from pylot.core.pick.utils import select_for_phase, get_quality_class from pylot.core.pick.utils import select_for_phase, get_quality_class
from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \ from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
backtransformFilterString backtransformFilterString, loopIdentifyPhase, identifyPhase
def add_amplitudes(event, amplitudes): def add_amplitudes(event, amplitudes):
@ -375,7 +375,6 @@ def picks_from_picksdict(picks, creation_info=None):
def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0): def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
import glob
# TODO: change root to datapath # TODO: change root to datapath
db_root = os.path.join(root_dir, db_dir) db_root = os.path.join(root_dir, db_dir)
evt_list = glob.glob1(db_root, 'e????.???.??') evt_list = glob.glob1(db_root, 'e????.???.??')
@ -1056,37 +1055,60 @@ def merge_picks(event, picks):
return event return event
def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1): def getQualitiesfromxml(path, errorsP, errorsS, plotflag=1, figure=None, verbosity=0):
""" """
Script to get onset uncertainties from Quakeml.xml files created by PyLoT. Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
Uncertainties are tranformed into quality classes and visualized via histogram if desired. Uncertainties are tranformed into quality classes and visualized via histogram if desired.
Ludger Küperkoch, BESTEC GmbH, 07/2017 Ludger Küperkoch, BESTEC GmbH, 07/2017
:param xmlnames: list of xml obspy event files containing picks :param path: path containing xml files
:type xmlnames: list :type path: str
:param ErrorsP: time errors of P waves for the four discrete quality classes :param errorsP: time errors of P waves for the four discrete quality classes
:type ErrorsP: :type errorsP:
:param ErrorsS: time errors of S waves for the four discrete quality classes :param errorsS: time errors of S waves for the four discrete quality classes
:type ErrorsS: :type errorsS:
:param plotflag: :param plotflag:
:type plotflag: :type plotflag:
:return: :return:
:rtype: :rtype:
""" """
from pylot.core.pick.utils import get_quality_class def calc_perc(uncertainties, ntotal):
from pylot.core.util.utils import loopIdentifyPhase, identifyPhase if len(uncertainties) == 0:
return 0
else:
return 100 / ntotal * len(uncertainties)
def calc_weight_perc(psweights, weight_ids):
# count total number of list items for this phase
numWeights = np.sum([len(weight) for weight in psweights.values()])
# iterate over all available weights to return a list with percentages for plotting
plot_list = []
for weight_id in weight_ids:
plot_list.append(calc_perc(psweights[weight_id], numWeights))
return plot_list, numWeights
xmlnames = glob.glob(os.path.join(path, '*.xml'))
if len(xmlnames) == 0:
print(f'No files found in path {path}.')
return False
# first define possible phases here
phases = ['P', 'S']
# define possible weights (0-4)
weight_ids = list(range(5))
# put both error lists in a dictionary with P/S key so that amount of code can be halfed by simply using P/S as key
errors = dict(P=errorsP, S=errorsS)
# create dictionaries for each phase (P/S) with a dictionary of empty list for each weight defined in weights
# tuple above
weights = {}
for phase in phases:
weights[phase] = {weight_id: [] for weight_id in weight_ids}
# read all onset weights
Pw0 = []
Pw1 = []
Pw2 = []
Pw3 = []
Pw4 = []
Sw0 = []
Sw1 = []
Sw2 = []
Sw3 = []
Sw4 = []
for names in xmlnames: for names in xmlnames:
print("Getting onset weights from {}".format(names)) print("Getting onset weights from {}".format(names))
cat = read_events(names) cat = read_events(names)
@ -1094,119 +1116,60 @@ def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
arrivals = cat.events[0].picks arrivals = cat.events[0].picks
arrivals_copy = cat_copy.events[0].picks arrivals_copy = cat_copy.events[0].picks
# Prefere manual picks if qualities are sufficient! # Prefere manual picks if qualities are sufficient!
for Pick in arrivals: for pick in arrivals:
if Pick.method_id.id.split('/')[1] == 'manual': if pick.method_id.id.split('/')[1] == 'manual':
mstation = Pick.waveform_id.station_code mstation = pick.waveform_id.station_code
mstation_ext = mstation + '_' mstation_ext = mstation + '_'
for mpick in arrivals_copy: for mpick in arrivals_copy:
phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint)) phase = identifyPhase(loopIdentifyPhase(pick.phase_hint)) # MP MP catch if this fails?
if phase == 'P': if ((mpick.waveform_id.station_code == mstation) or
if ((mpick.waveform_id.station_code == mstation) or (mpick.waveform_id.station_code == mstation_ext)) and \
(mpick.waveform_id.station_code == mstation_ext)) and \ (mpick.method_id.id.split('/')[1] == 'auto') and \
(mpick.method_id.id.split('/')[1] == 'auto') and \ (mpick.time_errors['uncertainty'] <= errors[phase][3]):
(mpick.time_errors['uncertainty'] <= ErrorsP[3]): del mpick
del mpick break
break
elif phase == 'S':
if ((mpick.waveform_id.station_code == mstation) or
(mpick.waveform_id.station_code == mstation_ext)) and \
(mpick.method_id.id.split('/')[1] == 'auto') and \
(mpick.time_errors['uncertainty'] <= ErrorsS[3]):
del mpick
break
lendiff = len(arrivals) - len(arrivals_copy) lendiff = len(arrivals) - len(arrivals_copy)
if lendiff != 0: if lendiff != 0:
print("Found manual as well as automatic picks, prefered the {} manual ones!".format(lendiff)) print("Found manual as well as automatic picks, prefered the {} manual ones!".format(lendiff))
for Pick in arrivals_copy: for pick in arrivals_copy:
phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint)) phase = identifyPhase(loopIdentifyPhase(pick.phase_hint))
if phase == 'P': uncertainty = pick.time_errors.uncertainty
Pqual = get_quality_class(Pick.time_errors.uncertainty, ErrorsP) if not uncertainty:
if Pqual == 0: if verbosity > 0:
Pw0.append(Pick.time_errors.uncertainty) print('No uncertainty, pick {} invalid!'.format(pick.method_id.id))
elif Pqual == 1: continue
Pw1.append(Pick.time_errors.uncertainty) # check P/S phase
elif Pqual == 2: if phase not in phases:
Pw2.append(Pick.time_errors.uncertainty)
elif Pqual == 3:
Pw3.append(Pick.time_errors.uncertainty)
elif Pqual == 4:
Pw4.append(Pick.time_errors.uncertainty)
elif phase == 'S':
Squal = get_quality_class(Pick.time_errors.uncertainty, ErrorsS)
if Squal == 0:
Sw0.append(Pick.time_errors.uncertainty)
elif Squal == 1:
Sw1.append(Pick.time_errors.uncertainty)
elif Squal == 2:
Sw2.append(Pick.time_errors.uncertainty)
elif Squal == 3:
Sw3.append(Pick.time_errors.uncertainty)
elif Squal == 4:
Sw4.append(Pick.time_errors.uncertainty)
else:
print("Phase hint not defined for picking!") print("Phase hint not defined for picking!")
pass continue
qual = get_quality_class(uncertainty, errors[phase])
weights[phase][qual].append(uncertainty)
if plotflag == 0: if plotflag == 0:
Punc = [Pw0, Pw1, Pw2, Pw3, Pw4] p_unc = [weights['P'][weight_id] for weight_id in weight_ids]
Sunc = [Sw0, Sw1, Sw2, Sw3, Sw4] s_unc = [weights['S'][weight_id] for weight_id in weight_ids]
return Punc, Sunc return p_unc, s_unc
else: else:
if not figure:
fig = plt.figure()
ax = fig.add_subplot(111)
# get percentage of weights # get percentage of weights
numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)]) listP, numPweights = calc_weight_perc(weights['P'], weight_ids)
numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)]) listS, numSweights = calc_weight_perc(weights['S'], weight_ids)
if len(Pw0) > 0:
P0perc = 100 / numPweights * len(Pw0)
else:
P0perc = 0
if len(Pw1) > 0:
P1perc = 100 / numPweights * len(Pw1)
else:
P1perc = 0
if len(Pw2) > 0:
P2perc = 100 / numPweights * len(Pw2)
else:
P2perc = 0
if len(Pw3) > 0:
P3perc = 100 / numPweights * len(Pw3)
else:
P3perc = 0
if len(Pw4) > 0:
P4perc = 100 / numPweights * len(Pw4)
else:
P4perc = 0
if len(Sw0) > 0:
S0perc = 100 / numSweights * len(Sw0)
else:
S0perc = 0
if len(Sw1) > 0:
S1perc = 100 / numSweights * len(Sw1)
else:
S1perc = 0
if len(Sw2) > 0:
S2perc = 100 / numSweights * len(Sw2)
else:
S2perc = 0
if len(Sw3) > 0:
S3perc = 100 / numSweights * len(Sw3)
else:
S3perc = 0
if len(Sw4) > 0:
S4perc = 100 / numSweights * len(Sw4)
else:
S4perc = 0
weights = ('0', '1', '2', '3', '4') y_pos = np.arange(len(weight_ids))
y_pos = np.arange(len(weights))
width = 0.34 width = 0.34
plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black') ax.bar(y_pos - width, listP, width, color='black')
plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red') ax.bar(y_pos, listS, width, color='red')
plt.ylabel('%') ax.set_ylabel('%')
plt.xticks(y_pos, weights) ax.set_xticks(y_pos, weight_ids)
plt.xlim([-0.5, 4.5]) ax.set_xlim([-0.5, 4.5])
plt.xlabel('Qualities') ax.set_xlabel('Qualities')
plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights)) ax.set_title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
plt.show()
return [P0perc, P1perc, P2perc, P3perc, P4perc], [S0perc, S1perc, S2perc, S3perc, S4perc] if not figure:
fig.show()
return listP, listS

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

@ -1320,7 +1320,7 @@ def get_quality_class(uncertainty, weight_classes):
:return: quality of pick (0-4) :return: quality of pick (0-4)
:rtype: int :rtype: int
""" """
if not uncertainty: return max(weight_classes) if not uncertainty: return len(weight_classes)
try: try:
# create generator expression containing all indices of values in weight classes that are >= than uncertainty. # create generator expression containing all indices of values in weight classes that are >= than uncertainty.
# call next on it once to receive first value # call next on it once to receive first value

6
tests/test_get_qualities_from_xml.py
View File

@ -5,7 +5,7 @@ from pylot.core.io.phases import getQualitiesfromxml
class TestQualityFromXML(unittest.TestCase): class TestQualityFromXML(unittest.TestCase):
def setUp(self): def setUp(self):
self.xmlpaths = ['PyLoT_e0019.048.13.xml'] self.path = '.'
self.ErrorsP = [0.02, 0.04, 0.08, 0.16] self.ErrorsP = [0.02, 0.04, 0.08, 0.16]
self.ErrorsS = [0.04, 0.08, 0.16, 0.32] self.ErrorsS = [0.04, 0.08, 0.16, 0.32]
self.test0_result = [[0.0136956521739, 0.0126, 0.0101612903226, 0.00734848484849, 0.0135069444444, self.test0_result = [[0.0136956521739, 0.0126, 0.0101612903226, 0.00734848484849, 0.0135069444444,
@ -23,10 +23,10 @@ class TestQualityFromXML(unittest.TestCase):
[92.0, 4.0, 4.0, 0, 0] [92.0, 4.0, 4.0, 0, 0]
def test_result_plotflag0(self): def test_result_plotflag0(self):
self.assertEqual(getQualitiesfromxml(self.xmlpaths, self.ErrorsP, self.ErrorsS, 0), self.test0_result) self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 0), self.test0_result)
def test_result_plotflag1(self): def test_result_plotflag1(self):
self.assertEqual(getQualitiesfromxml(self.xmlpaths, self.ErrorsP, self.ErrorsS, 1), self.test1_result) self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 1), self.test1_result)
if __name__ == '__main__': if __name__ == '__main__':