marcel/pylot
3
0
Fork 0
Code Issues 7 Pull Requests 1 Releases Wiki Activity

coppied files from Ludgers Laptop

Browse Source
This commit is contained in:
Marcel Paffrath
2017-04-06 13:16:28 +02:00
parent f5c06cd6b7
commit c90b061de9
56 changed files with 64030 additions and 244 deletions
Download Patch File Download Diff File Expand all files Collapse all files

0
pylot/core/util/__init__.py Executable file → Normal file
View File

18
pylot/core/util/dataprocessing.py
View File

@@ -180,8 +180,10 @@ def read_metadata(path_to_inventory):
invtype = key_for_set_value(inv)
if invtype is None:
raise IOError("Neither dataless-SEED file, inventory-xml file nor "
"RESP-file found!")
print("Neither dataless-SEED file, inventory-xml file nor "
"RESP-file found!")
print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
robj = None,
elif invtype == 'dless': # prevent multiple read of large dlsv
print("Reading metadata information from dataless-SEED file ...")
if len(inv[invtype]) == 1:
@@ -250,13 +252,23 @@ def restitute_data(data, invtype, inobj, unit='VEL', force=False):
else:
finv = invlist[0]
inventory = read_inventory(finv, format='STATIONXML')
elif invtype == None:
print("No restitution possible, as there are no station-meta data available!")
break
else:
data.remove(tr)
continue
# apply restitution to data
print("Correcting instrument at station %s, channel %s" \
% (tr.stats.station, tr.stats.channel))
try:
if invtype in ['resp', 'dless']:
tr.simulate(**kwargs)
try:
tr.simulate(**kwargs)
except ValueError as e:
vmsg = '{0}'.format(e)
print(vmsg)
else:
tr.attach_response(inventory)
tr.remove_response(output=unit,

10
pylot/core/util/defaults.py
View File

@@ -8,7 +8,9 @@ Created on Wed Feb 26 12:31:25 2014
import os
from pylot.core.loc import nll
from pylot.core.loc import hsat
from pylot.core.loc import hyposat
from pylot.core.loc import hypo71
from pylot.core.loc import hypodd
from pylot.core.loc import velest
@@ -43,10 +45,6 @@ FILTERDEFAULTS = readFilterInformation(os.path.join(os.path.expanduser('~'),
'.pylot',
'filter.in'))
AUTOMATIC_DEFAULTS = os.path.join(os.path.expanduser('~'),
'.pylot',
'autoPyLoT.in')
TIMEERROR_DEFAULTS = os.path.join(os.path.expanduser('~'),
'.pylot',
'PILOT_TimeErrors.in')
@@ -55,7 +53,7 @@ OUTPUTFORMATS = {'.xml': 'QUAKEML',
'.cnv': 'CNV',
'.obs': 'NLLOC_OBS'}
LOCTOOLS = dict(nll=nll, hsat=hsat, velest=velest)
LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=hypodd)
COMPPOSITION_MAP = dict(Z=2, N=1, E=0)
COMPPOSITION_MAP['1'] = 1

19
pylot/core/util/pdf.py
View File

@@ -51,8 +51,11 @@ def exp_parameter(te, tm, tl, eta):
sig1 = np.log(eta) / (te - tm)
sig2 = np.log(eta) / (tm - tl)
if np.isinf(sig1) == True:
sig1 = np.log(eta) / (tm - tl)
if np.isinf(sig2) == True:
sig2 = np.log(eta) / (te - tm)
a = 1 / (1 / sig1 + 1 / sig2)
return tm, sig1, sig2, a
@@ -237,7 +240,7 @@ class ProbabilityDensityFunction(object):
@classmethod
def from_pick(self, lbound, barycentre, rbound, incr=0.001, decfact=0.01,
type='gauss'):
type='exp'):
'''
Initialize a new ProbabilityDensityFunction object.
Takes incr, lbound, barycentre and rbound to derive x0 and the number
@@ -304,10 +307,14 @@ class ProbabilityDensityFunction(object):
:return float: rval
'''
rval = 0
for x in self.axis:
rval += x * self.data(x)
return rval * self.incr
#rval = 0
#for x in self.axis:
# rval += x * self.data(x)
rval = self.mu
# Not sure about this! That might not be the barycentre.
# However, for std calculation (next function)
# self.mu is also used!! (LK, 02/2017)
return rval
def standard_deviation(self):
mu = self.mu

9
pylot/core/util/thread.py
View File

@@ -7,17 +7,18 @@ class AutoPickThread(QThread):
message = Signal(str)
finished = Signal()
def __init__(self, parent, func, data, param):
def __init__(self, parent, func, infile, fnames, savepath):
super(AutoPickThread, self).__init__()
self.setParent(parent)
self.func = func
self.data = data
self.param = param
self.infile = infile
self.fnames = fnames
self.savepath = savepath
def run(self):
sys.stdout = self
picks = self.func(self.data, self.param)
picks = self.func(self.infile, self.fnames, self.savepath)
print("Autopicking finished!\n")

9
pylot/core/util/utils.py
View File

@@ -477,7 +477,7 @@ def runProgram(cmd, parameter=None):
subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
def which(program):
def which(program, infile=None):
"""
takes a program name and returns the full path to the executable or None
modified after: http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
@@ -490,7 +490,12 @@ def which(program):
for key in settings.allKeys():
if 'binPath' in key:
os.environ['PATH'] += ':{0}'.format(settings.value(key))
bpath = os.path.join(os.path.expanduser('~'), '.pylot', 'autoPyLoT.in')
if infile is None:
# use default parameter-file name
bpath = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
else:
bpath = os.path.join(os.path.expanduser('~'), '.pylot', infile)
if os.path.exists(bpath):
nllocpath = ":" + AutoPickParameter(bpath).get('nllocbin')
os.environ['PATH'] += nllocpath

0
pylot/core/util/version.py Executable file → Normal file
View File

150
pylot/core/util/widgets.py
View File

@@ -5,12 +5,15 @@ Created on Wed Mar 19 11:27:35 2014
@author: sebastianw
"""
import os
import getpass
import warnings
import copy
import datetime
import numpy as np
from matplotlib.figure import Figure
from pylot.core.util.utils import find_horizontals
try:
from matplotlib.backends.backend_qt4agg import FigureCanvas
@@ -26,7 +29,7 @@ from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \
from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
from PySide.QtWebKit import QWebView
from obspy import Stream, UTCDateTime
from pylot.core.io.inputs import FilterOptions
from pylot.core.io.inputs import FilterOptions, AutoPickParameter
from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
getResolutionWindow
from pylot.core.pick.compare import Comparison
@@ -49,7 +52,12 @@ def getDataType(parent):
def plot_pdf(_axes, x, y, annotation, bbox_props, xlabel=None, ylabel=None,
title=None):
_axes.plot(x, y)
# try method or data
try:
_axes.plot(x, y()) # y provided as method
except:
_axes.plot(x, y) # y provided as data
if title:
_axes.set_title(title)
if xlabel:
@@ -235,23 +243,23 @@ class ComparisonDialog(QDialog):
x, y, std, exp = pdf.axis, pdf.data, pdf.standard_deviation(), \
pdf.expectation()
annotation = "{phase} difference on {station}\n" \
"expectation: {exp}\n" \
"std: {std}".format(station=station, phase=phase,
std=std, exp=exp)
annotation = "%s difference on %s\n" \
"expectation: %7.4f s\n" \
"std: %7.4f s" % (phase, station,
exp, std)
bbox_props = dict(boxstyle='round', facecolor='lightgrey', alpha=.7)
plot_pdf(_axes, x, y, annotation, bbox_props, 'time difference [s]',
'propability density [-]', phase)
'propability density [-]', phase)
pdf_a = copy.deepcopy(self.data.get('auto')[station][phase])
pdf_m = copy.deepcopy(self.data.get('manu')[station][phase])
xauto, yauto, stdauto, expauto, alim = pdf_a.axis, pdf_a.data, \
xauto, yauto, stdauto, expauto, alim = pdf_a.axis, pdf_a.data(), \
pdf_a.standard_deviation(), \
pdf_a.expectation(), \
pdf_a.limits()
xmanu, ymanu, stdmanu, expmanu, mlim = pdf_m.axis, pdf_m.data, \
xmanu, ymanu, stdmanu, expmanu, mlim = pdf_m.axis, pdf_m.data(), \
pdf_m.standard_deviation(), \
pdf_m.expectation(), \
pdf_m.limits()
@@ -259,21 +267,19 @@ class ComparisonDialog(QDialog):
lims = clims(alim, mlim)
# relative x axis
x0 = lims[0]
xmanu -= x0
xmanu -= x0
xauto -= x0
lims = [lim - x0 for lim in lims]
x0 = UTCDateTime(x0)
# set annotation text
mannotation = "probability density for manual pick\n" \
"expectation: {exp}\n" \
"std: {std}".format(std=stdmanu,
exp=expmanu-x0.timestamp)
mannotation = "probability density of manual pick\n" \
"expectation: %7.4f s\n" \
"std: %7.4f s" % (expmanu-x0.timestamp, stdmanu)
aannotation = "probability density for automatic pick\n" \
"expectation: {exp}\n" \
"std: {std}".format(std=stdauto,
exp=expauto-x0.timestamp)
aannotation = "probability density of automatic pick\n" \
"expectation: %7.4f s\n" \
"std: %7.4f s" % (expauto-x0.timestamp, stdauto)
_ax1 = plot_pdf(_ax1, xmanu, ymanu, mannotation,
bbox_props=bbox_props, xlabel='seconds since '
@@ -504,15 +510,17 @@ class WaveformWidget(FigureCanvas):
class PickDlg(QDialog):
def __init__(self, parent=None, data=None, station=None, picks=None,
rotate=False):
rotate=False, infile=None):
super(PickDlg, self).__init__(parent)
# initialize attributes
self.infile = infile
self.station = station
self.rotate = rotate
self.components = 'ZNE'
settings = QSettings()
self._user = settings.value('user/Login', 'anonymous')
pylot_user = getpass.getuser()
self._user = settings.value('user/Login', pylot_user)
if picks:
self.picks = picks
else:
@@ -704,6 +712,9 @@ class PickDlg(QDialog):
self.cidrelease = self.connectReleaseEvent(self.panRelease)
self.cidscroll = self.connectScrollEvent(self.scrollZoom)
def getinfile(self):
return self.infile
def getStartTime(self):
return self.stime
@@ -806,6 +817,7 @@ class PickDlg(QDialog):
self.disconnectMotionEvent()
self.cidpress = self.connectPressEvent(self.setPick)
print(self.selectPhase.currentText())
if self.selectPhase.currentText().upper().startswith('P'):
self.setIniPickP(gui_event, wfdata, trace_number)
elif self.selectPhase.currentText().upper().startswith('S'):
@@ -819,14 +831,14 @@ class PickDlg(QDialog):
def setIniPickP(self, gui_event, wfdata, trace_number):
parameter = AutoPickParameter(self.getinfile())
ini_pick = gui_event.xdata
settings = QSettings()
nfac = settings.value('picking/nfac_P', 1.3)
noise_win = settings.value('picking/noise_win_P', 5.)
gap_win = settings.value('picking/gap_win_P', .2)
signal_win = settings.value('picking/signal_win_P', 3.)
nfac = parameter.get('nfacP')
twins = parameter.get('tsnrz')
noise_win = twins[0]
gap_win = twins[1]
signal_win = twins[2]
itrace = int(trace_number)
while itrace > len(wfdata) - 1:
@@ -868,14 +880,14 @@ class PickDlg(QDialog):
def setIniPickS(self, gui_event, wfdata):
parameter = AutoPickParameter(self.getinfile())
ini_pick = gui_event.xdata
settings = QSettings()
nfac = settings.value('picking/nfac_S', 1.5)
noise_win = settings.value('picking/noise_win_S', 5.)
gap_win = settings.value('picking/gap_win_S', .2)
signal_win = settings.value('picking/signal_win_S', 3.)
nfac = parameter.get('nfacS')
twins = parameter.get('tsnrh')
noise_win = twins[0]
gap_win = twins[1]
signal_win = twins[2]
# copy data for plotting
data = self.getWFData().copy()
@@ -922,6 +934,8 @@ class PickDlg(QDialog):
def setPick(self, gui_event):
parameter = AutoPickParameter(self.getinfile())
# get axes limits
self.updateCurrentLimits()
@@ -941,7 +955,14 @@ class PickDlg(QDialog):
wfdata.filter(**filteroptions)
# get earliest and latest possible pick and symmetric pick error
[epp, lpp, spe] = earllatepicker(wfdata, 1.5, (5., .5, 2.), pick)
if wfdata[0].stats.channel[2] == 'Z' or wfdata[0].stats.channel[2] == '3':
nfac = parameter.get('nfacP')
TSNR = parameter.get('tsnrz')
else:
nfac = parameter.get('nfacS')
TSNR = parameter.get('tsnrh')
[epp, lpp, spe] = earllatepicker(wfdata, nfac, (TSNR[0], TSNR[1], TSNR[2]), pick)
# return absolute time values for phases
stime = self.getStartTime()
@@ -951,7 +972,8 @@ class PickDlg(QDialog):
# save pick times for actual phase
phasepicks = dict(epp=epp, lpp=lpp, mpp=mpp, spe=spe,
picker=self.getUser())
picker='manual', channel=channel,
network=wfdata[0].stats.network)
try:
oldphasepick = self.picks[phase]
@@ -1171,13 +1193,15 @@ class PickDlg(QDialog):
class PropertiesDlg(QDialog):
def __init__(self, parent=None):
def __init__(self, parent=None, infile=None):
super(PropertiesDlg, self).__init__(parent)
self.infile = infile
appName = QApplication.applicationName()
self.setWindowTitle("{0} Properties".format(appName))
self.tabWidget = QTabWidget()
self.tabWidget.addTab(InputsTab(self), "Inputs")
self.tabWidget.addTab(OutputsTab(self), "Outputs")
@@ -1186,7 +1210,8 @@ class PropertiesDlg(QDialog):
self.tabWidget.addTab(LocalisationTab(self), "Loc Tools")
self.buttonBox = QDialogButtonBox(QDialogButtonBox.Ok |
QDialogButtonBox.Apply |
QDialogButtonBox.Close)
QDialogButtonBox.Close |
QDialogButtonBox.RestoreDefaults)
layout = QVBoxLayout()
layout.addWidget(self.tabWidget)
@@ -1195,8 +1220,11 @@ class PropertiesDlg(QDialog):
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.buttonBox.button(QDialogButtonBox.Apply).clicked.connect(
self.apply)
self.buttonBox.button(QDialogButtonBox.Apply).clicked.connect(self.apply)
self.buttonBox.button(QDialogButtonBox.RestoreDefaults).clicked.connect(self.restore)
def getinfile(self):
return self.infile
def accept(self, *args, **kwargs):
self.apply()
@@ -1209,6 +1237,14 @@ class PropertiesDlg(QDialog):
if values is not None:
self.setValues(values)
def restore(self):
for widint in range(self.tabWidget.count()):
curwid = self.tabWidget.widget(widint)
values = curwid.resetValues(self.getinfile())
if values is not None:
self.setValues(values)
@staticmethod
def setValues(tabValues):
settings = QSettings()
@@ -1224,16 +1260,19 @@ class PropTab(QWidget):
def getValues(self):
return None
def resetValues(self, infile=None):
return None
class InputsTab(PropTab):
def __init__(self, parent):
def __init__(self, parent, infile=None):
super(InputsTab, self).__init__(parent)
settings = QSettings()
pylot_user = getpass.getuser()
fulluser = settings.value("user/FullName")
login = settings.value("user/Login")
fullNameLabel = QLabel("Full name for user '{0}': ".format(login))
fullNameLabel = QLabel("Full name for user '{0}': ".format(pylot_user))
# get the full name of the actual user
self.fullNameEdit = QLineEdit()
@@ -1276,9 +1315,24 @@ class InputsTab(PropTab):
"data/Structure": self.structureSelect.currentText()}
return values
def resetValues(self, infile):
para = AutoPickParameter(infile)
datstruct = para.get('datastructure')
if datstruct == 'SeisComp':
index = 0
else:
index = 2
datapath = para.get('datapath')
rootpath = para.get('rootpath')
database = para.get('database')
path = os.path.join(os.path.expanduser('~'), rootpath, datapath, database)
values = {"data/dataRoot": self.dataDirEdit.setText("%s" % path),
"user/FullName": self.fullNameEdit.text(),
"data/Structure": self.structureSelect.setCurrentIndex(index)}
return values
class OutputsTab(PropTab):
def __init__(self, parent=None):
def __init__(self, parent=None, infile=None):
super(OutputsTab, self).__init__(parent)
settings = QSettings()
@@ -1302,6 +1356,9 @@ class OutputsTab(PropTab):
values = {"output/Format": self.eventOutputComboBox.currentText()}
return values
def resetValues(self, infile):
values = {"output/Format": self.eventOutputComboBox.setCurrentIndex(1)}
return values
class PhasesTab(PropTab):
def __init__(self, parent=None):
@@ -1318,7 +1375,7 @@ class GraphicsTab(PropTab):
class LocalisationTab(PropTab):
def __init__(self, parent=None):
def __init__(self, parent=None, infile=None):
super(LocalisationTab, self).__init__(parent)
settings = QSettings()
@@ -1388,6 +1445,13 @@ class LocalisationTab(PropTab):
"loc/tool": loctool}
return values
def resetValues(self, infile):
para = AutoPickParameter(infile)
nllocroot = para.get('nllocroot')
nllocbin = para.get('nllocbin')
loctool = self.locToolComboBox.setCurrentIndex(3)
values = {"nll/rootPath": self.rootedit.setText("%s" % nllocroot),
"nll/binPath": self.binedit.setText("%s" % nllocbin)}
class NewEventDlg(QDialog):
def __init__(self, parent=None, titleString="Create a new event"):