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pytheas.py
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pytheas.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
================================================================================
Pytheas: an open-source software solution for local shear-wave splitting studies
================================================================================
Pytheas is a tool that aims to introduce a new mentality in shear-wave splitting analysis
from local recordings, incorporating manual, semi- and fully- automatic methods under one
Graphical User Interface. Integrating databases and offering compatibility with popular data
and metadata file formats, Pytheas is designed with the simplification of analysis in mind,
while, at the same time, enhanching the effectiveness of processing and quality control of results.
Pytheas is released under the GNU GPLv3 license.
Authors: Spingos I. & Kaviris G. (c) 2019
Special thanks to Millas C. for testing the software and providing valuable feedback from the
very early stages of this endeavor!
For any issues, comments or suggestions please contact us at ispingos@geol.uoa.gr or through GitHub
at https://www.github.com/ispingos/pytheas-splitting
"""
LIC_STR=("""
Pytheas // PYThon sHear - wavE Analysis Suite
Copyright (C) 2019 Spingos I. & Kaviris G.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
For additional information, questions or suggestions
please contact: ispingos@geol.uoa.gr
""")
global VERSION
global VERDATE
VERSION="0.1.2"
VERDATE="19/12/2019"
## first get script's path
import os
global WORKDIR
WORKDIR=os.path.dirname(os.path.realpath(__file__))
## splash screen ##
print("..: Starting module imports...")
# using tk cause it's easier/faster for this (and is in the PSL)
import tkinter as tk
splroot=tk.Tk()
splroot.overrideredirect(True)
# get screen width/height and set as global
global SCWIDTH
global SCHEIGHT
SCWIDTH=splroot.winfo_screenwidth()
SCHEIGHT=splroot.winfo_screenheight()
# grab image file and get its dimensions
splfile=WORKDIR+os.sep+"etc/images/splash_color.png"
splimage=tk.PhotoImage(file=splfile)
iwidth=splimage.width(); iheight=splimage.height()
# scale it to 40% of screen for better display
scale=SCWIDTH*0.4/iwidth
splimage=splimage.subsample(int(round(1/scale)))
iwidth=splimage.width(); iheight=splimage.height()
# center image
x=(SCWIDTH-iwidth)/2
y=(SCHEIGHT-iheight)/2
splroot.geometry('%dx%d+%d+%d' % (iwidth, iheight, x, y))
# init canvas
canvas=tk.Canvas(splroot,height=iheight,width=iwidth)
canvas.create_image(iwidth/2,iheight/2,image=splimage)
canvas.pack()
# show splash
splroot.update()
## imports ##
print("..: Loading modules...")
import sys, shutil
import logging, traceback
import time, datetime
from glob import glob
import numpy as np
import scipy
from PyQt5 import QtWidgets, QtCore, QtGui
# ensure we're using Qt5 as the MPL backend
import matplotlib
matplotlib.use("Qt5Agg")
# continue with imports
from matplotlib import pyplot as plt
from matplotlib.figure import Figure
from matplotlib.ticker import LinearLocator, NullLocator
from matplotlib.collections import LineCollection
from matplotlib.backends.backend_qt5agg \
import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backend_bases import MouseEvent
import configparser
from obspy import read, Stream, UTCDateTime, read_events, read_inventory
from obspy.geodetics.base import degrees2kilometers, gps2dist_azimuth
from obspy.taup import TauPyModel
from obspy.taup.taup_create import get_builtin_model_files as taup_get_builtin_model_files
from obspy.taup.velocity_model import VelocityModel
# pytheas imports
from lib import eigenvalue as SC
from lib import clustering as TB
from lib import rotationcorrelation as RC
from lib import db_handler as DB
from lib import tools
from lib import parsers
# make 'logs' directory
try:
os.makedirs(WORKDIR+os.sep+"logs")
except: # if folder already exists
pass
# init the log file
logfile=WORKDIR+os.sep+"logs%s%s_Pytheas.log" % (os.sep,UTCDateTime().strftime("%Y%m%d%H%M%S"))
logging.basicConfig(
filename=logfile,
level=logging.DEBUG,
format='%(asctime)s %(levelname)s %(message)s'
)
# setup logging to terminal
terminal=logging.StreamHandler()
terminal.setLevel(logging.DEBUG)
terminal.setFormatter(logging.Formatter('%(asctime)s %(levelname)s %(message)s'))
logging.getLogger().addHandler(terminal)
# kill splash
splroot.destroy()
## Main Class ##
class Pytheas(QtWidgets.QMainWindow):
"""
Main class of the Pytheas software. Is responsible for building the
GUI and handling all functionality connected to it.
Uses a :class:`~PyQt5.QtWidgets.QMainWindow`
"""
def __init__(self):
"""Initiliaze main app window and setups labels, flags etc."""
logging.info("Start Application...")
# init the main window
QtWidgets.QMainWindow.__init__(self)
# check for default dirs. create them if needed
self.checkDefaultDirs()
# set icon and initial GUI params
self.appIcon=WORKDIR+os.sep+"etc/images/Pytheas_ICO.ico"
self.globalName="Pytheas"
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setFocusPolicy(QtCore.Qt.StrongFocus)
self.setWindowTitle(self.globalName+" v"+str(VERSION))
self.setWindowIcon(QtGui.QIcon(self.appIcon))
# set validators
self.validateInt=QtGui.QIntValidator()
self.validateFloat=QtGui.QDoubleValidator()
## set toolbar menus and actions
self.activateMenus=[]
# set file menu
logging.debug("Set File Menu...")
self.fileMenu=QtWidgets.QMenu("&File",self)
self.fileMenu.addAction("&Open Catalogue",self.openCatWindow,QtCore.Qt.SHIFT+QtCore.Qt.Key_O)
self.fileMenu.addAction("&Preferences",self.prefWindow,QtCore.Qt.SHIFT+QtCore.Qt.Key_P)
self.fileMenu.addSeparator()
self.fileMenu.addAction("&Quit",self.onlyQuit)
self.menuBar().addMenu(self.fileMenu) # Add Open menu to bar
# set database menu
logging.debug("Set Database Menu...")
self.dbMenu=QtWidgets.QMenu("&Database",self)
self.dbMenu.addAction("Save As...",self.saveAsDB)
self.dbMenu.addAction("Load New",self.loadNewDB)
self.dbMenu.addAction("Save Solution to Database",self.saveSolution,QtCore.Qt.CTRL+QtCore.Qt.Key_S)
self.dbMenu.addAction("Load Solution from Database",self.getSolution)
self.dbMenu.addAction("Export...",self.dbWindowQuery)
self.dbMenu.addAction("Export Active",self.exportActive)
self.dbMenu.addAction("Export Figure",self.exportFigure)
self.menuBar().addMenu(self.dbMenu) # add db menu bar
self.dbMenu.setEnabled(False)
self.activateMenus.append(self.dbMenu)
# set view menu
logging.debug("Set View Menu...")
self.viewMenu=QtWidgets.QMenu("&View",self)
self.viewMenu.addAction("&Grid",self.changeGrid)
self.actionGrid=self.viewMenu.actions()[0] # Since only one item so far. Maybe add an if check?
self.actionGrid.setCheckable(True)
self.actionGrid.setChecked(False)
self.viewMenu.addAction("&Center S",self.centerS)
self.viewMenu.addAction("&Set X Axis Limits",self.applyXAxisLimits)
self.menuBar().addMenu(self.viewMenu) # add view menu bar
self.viewMenu.setEnabled(False)
self.activateMenus.append(self.viewMenu)
# set visual inspection menu
logging.debug("Set Visual Inspection Menu...")
self.visualMenu=QtWidgets.QMenu("&Manual",self)
self.visualMenu.addAction("&Initial Stage",self.goToInitial,QtCore.Qt.CTRL+QtCore.Qt.Key_1)
self.visualMenu.addAction("&Rotated Stage",self.goToRotated,QtCore.Qt.CTRL+QtCore.Qt.Key_2)
self.visualMenu.addAction("&Corrected Stage",self.goToCorrected,QtCore.Qt.CTRL+QtCore.Qt.Key_3)
self.visualMenu.addSeparator()
self.visualMenu.addAction("&Set phi",self.getPhi)
self.visualMenu.addAction("&Set time-delay",self.applyTimedelay,QtCore.Qt.CTRL+QtCore.Qt.Key_D)
self.visualMenu.addAction("&Set grade",self.getGrade,QtCore.Qt.CTRL+QtCore.Qt.Key_X)
self.visualMenu.addAction("&Set comment",self.getComment,QtCore.Qt.CTRL+QtCore.Qt.Key_G)
self.menuBar().addMenu(self.visualMenu) # Add Visual menu to bar
self.visualMenu.setEnabled(False)
self.activateMenus.append(self.visualMenu)
# set other methods menu
self.splitMenu=QtWidgets.QMenu("&Splitting",self)
self.splitMenu.addAction("&Set Shear-wave Window",self.getMaxAin)
self.splitMenu.addSeparator()
self.actRT=QtWidgets.QAction("&ZRT", checkable=True, checked=True)
self.actQT=QtWidgets.QAction("&LQT", checkable=True, checked=False)
self.rotGrp=QtWidgets.QActionGroup(self, exclusive=True)
self.rotGrp.addAction(self.actRT)
self.rotGrp.addAction(self.actQT)
self.splitMenu.addAction(self.actRT)
self.splitMenu.addAction(self.actQT)
self.splitMenu.addSeparator()
self.splitMenu.addAction("&Rotation-Correlation",self.applyRC,QtCore.Qt.CTRL+QtCore.Qt.Key_K)
self.splitMenu.addAction("&Eigenvalue",lambda: self.applyEV('EV'),QtCore.Qt.CTRL+QtCore.Qt.Key_L)
self.splitMenu.addAction("&Minimum Energy",lambda: self.applyEV('ME'),QtCore.Qt.CTRL+QtCore.Qt.Key_E)
self.splitMenu.addSeparator()
self.splitMenu.addAction("&Cluster Analysis (EV)",lambda: self.applyCA('EV',self.stream,self.filtered,self.freqmin,self.freqmax,
self.sPick,self.baz,self.ain,True,False
),QtCore.Qt.CTRL+QtCore.Qt.Key_T)
self.splitMenu.addAction("&Cluster Analysis (ME)",lambda: self.applyCA('ME',self.stream,self.filtered,self.freqmin,self.freqmax,
self.sPick,self.baz,self.ain,True,False
),QtCore.Qt.CTRL+QtCore.Qt.Key_U)
self.splitMenu.addAction("&Cluster Analysis (RC)",lambda: self.applyCA('RC',self.stream,self.filtered,self.freqmin,self.freqmax,
self.sPick,self.baz,self.ain,True,False
),QtCore.Qt.CTRL+QtCore.Qt.Key_Y)
self.splitMenu.addSeparator()
self.splitMenu.addAction("&Catalogue Cluster Analysis",self.caMultWindow,QtCore.Qt.SHIFT+QtCore.Qt.Key_A)
self.menuBar().addMenu(self.splitMenu) # Add Splitting menu to bar
self.splitMenu.setEnabled(False)
self.activateMenus.append(self.splitMenu)
# set navigation menu
logging.debug("Set Navigation Menu...")
self.navMenu=QtWidgets.QMenu("&Navigate",self)
self.navMenu.addAction("&Station List",self.stationsListWindow,QtCore.Qt.SHIFT+QtCore.Qt.Key_S)
self.navMenu.addAction("&Next Station",self.nextStation,QtCore.Qt.CTRL+QtCore.Qt.Key_W)
self.navMenu.addAction("&Previous Station",self.prevStation,QtCore.Qt.CTRL+QtCore.Qt.Key_Q)
self.navMenu.addSeparator()
self.navMenu.addAction("&Event List",self.eventsListWindow,QtCore.Qt.SHIFT+QtCore.Qt.Key_E)
self.navMenu.addAction("&Next Event",self.nextEvent,QtCore.Qt.SHIFT+QtCore.Qt.Key_N)
self.navMenu.addAction("&Previous Event",self.prevEvent,QtCore.Qt.SHIFT+QtCore.Qt.Key_B)
self.menuBar().addMenu(self.navMenu)
self.navMenu.setEnabled(False)
self.activateMenus.append(self.navMenu)
# set tools menu
logging.debug("Set Tools Menu...")
self.toolsMenu=QtWidgets.QMenu("&Tools",self)
self.toggleAR=QtWidgets.QAction("&AR-AIC", checkable=True, checked=False)
self.toggleAR.triggered.connect(self.changeAR)
self.toolsMenu.addAction(self.toggleAR)
self.toolsMenu.addSeparator()
self.toolsMenu.addAction("&Bandpass Filter",self.applyBandFilter,QtCore.Qt.CTRL+QtCore.Qt.Key_B)
self.toolsMenu.addAction("&Bandpass 1-20 Hz",self.applyFixed120Filter,QtCore.Qt.CTRL+QtCore.Qt.Key_F)
self.toolsMenu.addAction("&Bandpass 1-10 Hz",self.applyFixed110Filter,QtCore.Qt.CTRL+QtCore.Qt.Key_H)
self.toolsMenu.addAction("&Recommend Filter",self.applyRecFilter,QtCore.Qt.CTRL+QtCore.Qt.Key_A)
self.toolsMenu.addAction("&Remove filter",self.removeFilter,QtCore.Qt.CTRL+QtCore.Qt.Key_R)
self.toolsMenu.addAction("&Show Horizontal Spectra",self.plotSpectrum)
self.menuBar().addMenu(self.toolsMenu)
self.toolsMenu.setEnabled(False)
self.activateMenus.append(self.toolsMenu)
# disable actions to avoid errors before loading any data
for menu in self.activateMenus:
for action in menu.actions():
action.setEnabled(False)
# set the main widget and layout
logging.debug("Set Main Widget and Layout...")
self.mainWidg=QtWidgets.QWidget(self)
self.vLayout=QtWidgets.QVBoxLayout(self.mainWidg)
self.vLayout.setAlignment(QtCore.Qt.AlignCenter)
self.mainWidg.setStyleSheet("background-color:white;")
# Qt magic
self.dumWidg=QtWidgets.QWidget()
# set grid layout for the information widget
self.gLayout=QtWidgets.QGridLayout()
self.gLayout.setAlignment(QtCore.Qt.AlignCenter)
# set fonts for the information widget
self.lblFont=QtGui.QFont("Calibri",11,QtGui.QFont.Bold)
self.inpFont=QtGui.QFont("Calibri",11,QtGui.QFont.Normal)
# add the labels where information will be shown
self.lblOrigin=QtWidgets.QLabel("Pytheas v.%s" % VERSION,font=QtGui.QFont("Calibri",14,QtGui.QFont.Bold))
self.lblOrigin.setAlignment(QtCore.Qt.AlignCenter)
self.lblStation=QtWidgets.QLabel("V. Date: %s" % VERDATE,font=QtGui.QFont("Calibri",14,QtGui.QFont.Bold))
self.lblStation.setAlignment(QtCore.Qt.AlignCenter)
self.lblAIN=QtWidgets.QLabel("incidence ("+u"\u00b0"+"):",font=self.lblFont)
self.inpAIN=QtWidgets.QLabel("45",font=self.inpFont)
self.lblBAZ=QtWidgets.QLabel("backazimuth (N"+u"\u00b0"+"E):",font=self.lblFont)
self.inpBAZ=QtWidgets.QLabel("270",font=self.inpFont)
self.lblEPI=QtWidgets.QLabel("epicentral (km):",font=self.lblFont)
self.inpEPI=QtWidgets.QLabel("30",font=self.inpFont)
self.lblMAG=QtWidgets.QLabel("magnitude:",font=self.lblFont)
self.lblMAG.setFixedSize(64,20)
self.inpMAG=QtWidgets.QLabel("1.0",font=self.inpFont)
self.inpMAG.setFixedSize(32,20)
self.lblSNR=QtWidgets.QLabel("SNR:",font=self.lblFont)
self.inpSNR=QtWidgets.QLabel("5.9",font=self.inpFont)
self.lblSYS=QtWidgets.QLabel("System",font=self.lblFont)
self.inpSYS=QtWidgets.QLabel("ZNE",font=self.inpFont)
self.lblV2H=QtWidgets.QLabel("V<H",font=self.lblFont)
self.inpV2H=QtWidgets.QCheckBox()
self.inpV2H.setChecked(False)
self.inpV2H.toggled.connect(self.disableV2HToggle)
self.lblPHI=QtWidgets.QLabel("φ (N"+u"\u00b0"+"E):",font=self.lblFont)
self.inpPHI=QtWidgets.QLabel("130",font=self.inpFont)
self.lblTD=QtWidgets.QLabel("t<sub>d</sub> (ms): ",font=self.lblFont)
self.inpTD=QtWidgets.QLabel("50",font=self.inpFont)
self.lblPOL=QtWidgets.QLabel("pol (N"+u"\u00b0"+"E):",font=self.lblFont)
self.inpPOL=QtWidgets.QLabel("30",font=self.inpFont)
self.lblGRD=QtWidgets.QLabel("grade: ",font=self.lblFont)
self.lblGRD.setFixedSize(64,20)
self.inpGRD=QtWidgets.QLabel("X",font=self.inpFont)
self.inpGRD.setFixedSize(32,20)
self.lblFLT=QtWidgets.QLabel("Filter (Hz):",font=self.lblFont)
self.inpFLT=QtWidgets.QLabel("1.0|20.0",font=self.inpFont)
self.lblORN=QtWidgets.QLabel("Orient",font=self.lblFont)
self.inpORN=QtWidgets.QLabel("0.0",font=self.inpFont)
self.lblMET=QtWidgets.QLabel("Method:",font=self.lblFont)
self.inpMET=QtWidgets.QLabel("MAN",font=self.inpFont)
# add labels to grid
# first int is row, second int is column
self.gLayout.addWidget(self.lblOrigin,1,5)
self.gLayout.addWidget(self.lblStation,1,7)
self.gLayout.addWidget(self.lblAIN,2,1)
self.gLayout.addWidget(self.inpAIN,2,2)
self.gLayout.addWidget(self.lblBAZ,2,3)
self.gLayout.addWidget(self.inpBAZ,2,4)
self.gLayout.addWidget(self.lblEPI,2,5)
self.gLayout.addWidget(self.inpEPI,2,6)
self.gLayout.addWidget(self.lblMAG,2,7)
self.gLayout.addWidget(self.inpMAG,2,8)
self.gLayout.addWidget(self.lblSNR,2,9)
self.gLayout.addWidget(self.inpSNR,2,10)
self.gLayout.addWidget(self.lblSYS,2,11)
self.gLayout.addWidget(self.inpSYS,2,12)
self.gLayout.addWidget(self.lblV2H,2,13)
self.gLayout.addWidget(self.inpV2H,2,14)
self.gLayout.addWidget(self.lblPHI,3,1)
self.gLayout.addWidget(self.inpPHI,3,2)
self.gLayout.addWidget(self.lblTD,3,3)
self.gLayout.addWidget(self.inpTD,3,4)
self.gLayout.addWidget(self.lblPOL,3,5)
self.gLayout.addWidget(self.inpPOL,3,6)
self.gLayout.addWidget(self.lblGRD,3,7)
self.gLayout.addWidget(self.inpGRD,3,8)
self.gLayout.addWidget(self.lblORN,3,9)
self.gLayout.addWidget(self.inpORN,3,10)
self.gLayout.addWidget(self.lblFLT,3,11)
self.gLayout.addWidget(self.inpFLT,3,12)
self.gLayout.addWidget(self.lblMET,3,13)
self.gLayout.addWidget(self.inpMET,3,14)
# add the grid layout to the dummy widget and add it to
# the main layout
self.dumWidg.setLayout(self.gLayout)
self.vLayout.addWidget(self.dumWidg)
# make the placeholder MPL plot and add it to the main widget
logging.debug("Add Matplotlib plot...")
self.figDict=self.makeFig()
self.activeFig=self.figDict["FIGURE"]
self.axZ=self.figDict["TRACE"]["Z"]
self.axN=self.figDict["TRACE"]["N"]
self.axE=self.figDict["TRACE"]["E"]
self.axPolar=self.figDict["POLAR"]
self.axPart1=self.figDict["HOD1"]
self.axPart2=self.figDict["HOD2"]
self.axPart3=self.figDict["HOD3"]
self.colPal=self.figDict["PALETTE"]
self.addFig(self.activeFig)
# read configuration files
self.generalCNF=parsers.parseGeneralCnf(WORKDIR+os.sep+"etc%soptions%sgeneral.cnf"%(os.sep,os.sep))
self.pkCNF=parsers.parsePickerCnf(WORKDIR+os.sep+"etc%soptions%spicker.cnf"%(os.sep,os.sep))
self.caCNF=parsers.parseClusteringCnf(WORKDIR+os.sep+"etc%soptions%sclustering.cnf"%(os.sep,os.sep))
self.tpCNF=parsers.parseTaupCnf(WORKDIR+os.sep+"etc%soptions%staup.cnf"%(os.sep,os.sep))
self.gradeCNF=parsers.parseGradeCnf(WORKDIR+os.sep+"etc%soptions%sgrading.cnf"%(os.sep,os.sep))
# small hack
self.caCNF.maxTd=self.generalCNF.maxTd
# clean logs
self.cleanLogs()
# read inventory
try:
self.inventory, self.xmlInventory = self.readStations(self.tpCNF.stations)
logging.info(str(self.inventory))
except: # no station file! show a warning to the user...
logging.exception("Could not find station file %s" % self.tpCNF.stations)
winTitle="StationXML Warning"
genText="Could not read the StationXML!"
infText="Could not read %s " % self.tpCNF.stations
self.warnMsgBox(genText,infText,winTitle)
self.inventory=None
# set flags and various initial parameters
self.flagReset()
self.maxAin=np.inf
# all done!
logging.debug("Set focus, central widget and navigation toolbar...")
self.setCentralWidget(self.mainWidg)
## SCIENCE FUNCTIONS ##
def calcV2H(self,pick,start=-0.5,end=0.5):
"""
Calculate the vertical to horizontal ratio of amplitudes for both
channels.
:type pick: float
:param pick: the arrival of the S-wave relative to the trace's start time (in s)
:type start: float, optional
:param start: start of the window for which the V/H ratio will be calculated,
relative to the S-arrival (in s). Defaults to -0.5.
:type end: float, optional
:param end: end of the window for which the V/H ratio will be calculated,
relative to the S-arrival (in s). Defaults to 0.5.
:returns: True if V<H and False if V>H
"""
## adjust windows to S pick
sps=self.stream[0].stats.sampling_rate
winstart=pick+start
idxstart=int(np.floor(sps*winstart))
winend=pick+end
idxend=int(np.ceil(sps*winend))
if (idxstart < 0) or (idxend > self.stream[0].stats.npts):
logging.warning("Not enough samples for V2H based on pick")
return False
## get arrays
H1="N"; H2="E"
if self.stageRotated: H1="R"; H2="T"
Z=self.stream.select(component="Z")[0].data[idxstart:idxend]
N=self.stream.select(component=H1)[0].data[idxstart:idxend]
E=self.stream.select(component=H2)[0].data[idxstart:idxend]
## return the ratios
return any((np.abs(Z).max()<np.abs(N).max(),np.abs(Z).max()<np.abs(E).max()))
def calcSNR(self,pick,winNoise=None,winSignal=None):
"""
Calculates the Signal-to-Noise Ratio (SNR) around the S-arrival (if picked)
or the middle of the selected signal window. The equation used is:
SNR = ( RMSsignal / RMSnoise)**2, where RMS = sqrt(sum(A**2))
The SNR is acquired for each horizontal component and their mean is defined
as the final value.
:type pick: float
:param pick: the arrival of the S-wave relative to the trace's start time (in s)
:type winNoise: float or None, optional
:param winNoise: start of the noise window (its end is the S-arrival/middle of window).
If None, its value is acquired from the Preferences. Defaults to None.
:type winSignal: float or None, optional
:param winSignal: end of the signal window (its start is the S-arrival/middle of window).
If None, its value is acquired from the Preferences. Defaults to None.
:returns: the average SNR of the horizontal waveforms
"""
# get windows bounds from Preferences?
if winNoise is None: winNoise=self.generalCNF.snrStart
if winSignal is None: winSignal=self.generalCNF.snrEnd
# grab the two horizontal waveforms
if self.stageRotated:
M1=self.stream.select(component="R")[0].data
M2=self.stream.select(component="T")[0].data
else:
M1=self.stream.select(component="N")[0].data
M2=self.stream.select(component="E")[0].data
# get indices of the signal and noise windows
idxNoise=int(np.floor((pick+winNoise)*self.stream[0].stats.sampling_rate))
idxSignl=int(np.ceil((pick+winSignal)*self.stream[0].stats.sampling_rate))
# however, if the bounds are beyond the length of the waveform...
if (idxNoise < 0) or (idxSignl > self.stream[0].stats.npts):
logging.warning("Not enough samples for SNR based on pick")
return 0
idxPick=int(pick*self.stream[0].stats.sampling_rate)
# calculate SNR for N/F channels
noise=M1[idxNoise:idxSignl]
signl=M1[idxPick:idxSignl]
RMSnoise=np.sqrt(np.mean(noise**2))
RMSsignl=np.sqrt(np.mean(signl**2))
SNR1=(RMSsignl/RMSnoise)**2
# calculate SNR for E/S channels
noise=M2[idxNoise:idxSignl]
signl=M2[idxPick:idxSignl]
RMSnoise=np.sqrt(np.mean(noise**2))
RMSsignl=np.sqrt(np.mean(signl**2))
SNR2=(RMSsignl/RMSnoise)**2
# get average SNR
SNR=(SNR1+SNR2)/2.0
if tools.isnone(SNR): # final check, just to be sure
SNR=0.0
return SNR
def tdCheck(self,td):
"""
Checks that the input time delay value is proper according to the
sampling rate and corrects it if it isn't.
:type td: float
:param td: the input time-delay (in s)
:returns: the corrected time-delay
"""
logging.debug("input td: "+str(td))
# get values straight from the trace object
df=self.stream[0].stats.delta
sps=self.stream[0].stats.sampling_rate
# convert dt to samples
td*=sps
# if no modulo then is fine
if td % sps:
td=np.ceil(td)
td*=df # convert back to s
logging.debug("input td was corrected to "+str(td))
else:
td*=df # convert back to s
logging.debug("input td is correct!")
return td
def rotation(self,phi,stream,method):
"""
Rotate the traces according to the measured Sfast polarization.
:type phi: float
:param phi: the Sfast polarization direction
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: the stream containing the waveforms to be rotated
:type method: str
:param method: determines which rotation to perform. Must be either
"NE->RT" or "RT->NE".
:returns: the Stream object with the rotated waveforms.
"""
# first check start times. Differences of 1 sample or less
# are allowed.
delta=stream[0].stats.delta
try:
startNorth=stream.select(component="N")[0].stats.starttime
startEast=stream.select(component="E")[0].stats.starttime
except IndexError:
startNorth=stream.select(component="R")[0].stats.starttime
startEast=stream.select(component="T")[0].stats.starttime
if abs(startNorth - startEast) > delta:
raise ValueError("Components are not synced!")
# make the rotation matrix
M=tools.Rmatrix2D(phi)
# according to requested rotation
if method.upper() == "NE->RT":
ne=np.asarray((
stream.select(component="N")[0].data,
stream.select(component="E")[0].data
))
rt=np.dot(M,ne)
# assign new values to stream
stream.select(component="N")[0].data=rt[0]
stream.select(component="N")[0].stats.channel=\
stream.select(component="N")[0].stats.channel[:2]+"R"
stream.select(component="E")[0].data=rt[1]
stream.select(component="E")[0].stats.channel=\
stream.select(component="E")[0].stats.channel[:2]+"T"
elif method.upper() == "RT->NE":
rt=np.asarray((
stream.select(component="R")[0].data,
stream.select(component="T")[0].data
))
ne=np.dot(M.T,rt)
# assign new values to stream
stream.select(component="R")[0].data=ne[0]
stream.select(component="R")[0].stats.channel=\
stream.select(component="R")[0].stats.channel[:2]+"N"
stream.select(component="T")[0].data=ne[1]
stream.select(component="T")[0].stats.channel=\
stream.select(component="T")[0].stats.channel[:2]+"E"
return stream
def timedelay(self,td,stream,warning=True):
"""
Wrapper for adding the time-delay to the slow (transverse) component. Changes
occur in-place, so a new stream is not returned.
:type td: float
:param td: the time-delay
:type stream: :class:`~obspy.core.stream.Stream`
:param stream: stream where the time-delay will be added to
:type warning: bool, optional
:param warning: selects whether to log a warning if the time-delay
is attempted to be added in the initial stage. Defaults to True.
"""
if warning:
if not self.stageRotated and not self.stageCorrected:
logging.warning("Traces aren't rotated!")
return
try:
return tools.timedelay(td,stream)
except IndexError:
logging.warning("Traces have not been rotated!")
## ARCHIVING FUNCTIONS ##
def checkDefaultDirs(self):
"""Make the default directories."""
if not os.path.isdir(WORKDIR+os.sep+"etc%sindex"%os.sep):
os.makedirs(WORKDIR+os.sep+"etc%sindex"%os.sep)
logging.debug("Created etc%sindex."%os.sep)
if not os.path.isdir(WORKDIR+os.sep+"etc%soptions"%os.sep):
os.makedirs(WORKDIR+os.sep+"etc%soptions"%os.sep)
logging.debug("Created etc%soptions."%os.sep)
if not os.path.isdir(WORKDIR+os.sep+"etc%sevcor"%os.sep):
os.makedirs(WORKDIR+os.sep+"etc%sevcor"%os.sep)
logging.debug("Created etc%sevcor"%os.sep)
def getTree(self,path):
"""
Get tree of directories that contain waveforms. It is mandatory for the
final branch to be named after the event code, e.g. %Y-%m-%d-%H-%M-%S
:type path: str
:param path: master directory that contains separate event folders.
:returns: a list of the event directories found
"""
fullEvents={}; n=0
for root,dirs,files in os.walk(path):
if files and not dirs:
n+=1
logging.debug("Adding path to event %i"%n)
fullEvents[os.path.split(root)[-1]]=root
return fullEvents
def getActiveStations(self):
"""
Gets station names that exist both in the waveform directory of the
active event and have arrivals in the catalogue.
:returns: a list of the station names
"""
evFolder=self.fullEvents[self.activeEvent]
staList=sorted(
self.statsDict[self.activeEvent],
key=lambda x:self.statsDict[self.activeEvent][x]["AN"]
)
activeStations=[]
for station in staList:
path=evFolder+os.sep+"*."+station+".*"
try:
if glob(path)[0]:
activeStations.append(station)
except:
pass
return activeStations
def getActiveEvents(self):
"""
Gets events that exist both in the data directory and the
catalogue
:returns: a list of the active events
"""
activeEvents=[]
for event in sorted(self.evsDict):
try:
path=self.fullEvents[event]
if glob(path)[0]:
activeEvents.append(event)
except:
continue
return activeEvents
def readStations(self,staFile):
"""
Read the stations information file. Must be either a
StationXML or an ASCII file in the format:
station network latitude longitude elevation
:type staFile: str
:param staFile: path to the station information file
:returns: if the file is StationXML returns a tuple with
(a dict containing the station information,
the :class:`~obspy.core.stream.Inventory` object),
otherwise returns (a dict containing the station information, None)
"""
try:
# simple check to validate file is of xml type, as obspy's
# read_inventory sometimes parses non-xml files as xml
with open(staFile, 'r') as fid:
check_line = fid.readline()
if not '?xml version' in check_line:
raise TypeError('Input file is not StationXML')
# read the xml
xml=read_inventory(staFile)
inventory={}
for net in xml:
for sta in net:
inventory.update({sta.code:{"network":net.code,"latitude":sta.latitude,
"longitude":sta.longitude,"elevation":sta.elevation}})
return inventory, xml
except TypeError:
xml=None
with open(staFile,"r") as fid:
staLines=fid.readlines()
return {x.split()[0]:
{
"network":x.split()[1],"latitude":float(x.split()[2]),
"longitude":float(x.split()[3]),"elevation":float(x.split()[4])
} for x in staLines
}, xml
except:
raise IOError("Could not read station file %s" % staFile)
def readEventCat(self,catFile):
"""
Read a simple catalogue file in the format of:
(origin time must be in the first 23 columns)
year mo da hr mn second latit longi depth magnitude
^
23
:type catFile: str
:param catFile: path to the catalogue file
:returns: (dict with event information, dict with arrival information)
"""
# initialize dictionaries
evsDict={}; statsDict={}
frmt="%Y-%m-%d-%H-%M-%S"
# read the file
with open(catFile,"r") as fid: catLines=fid.readlines()
for evid,line in enumerate(catLines):
try:
evDict=tools.initPytheasDict("event")
origin=UTCDateTime(line[:23])
dateKey=origin.strftime(frmt)
evlat=float(line[23:].strip().split()[0])
evlon=float(line[23:].strip().split()[1])
evdep=float(line[23:].strip().split()[2])
if not evdep:
evdep = 0.1 # temporary fix
mag=float(line[23:].strip().split()[3])
evDict["YEAR"]=origin.year
evDict["Mo"]=origin.month
evDict["Da"]=origin.day
evDict["HR"]=origin.hour
evDict["MN"]=origin.minute
evDict["SEC"]=origin.second+origin.microsecond/10**6
evDict["ORIGIN"]=origin
evDict["LAT"]=evlat; evDict["LON"]=evlon; evDict["DEPTH"]=evdep
evDict["MAG"]=mag; evDict["evID"]=str(evid)
# start adding stations
statsDict.update({dateKey:{}})
for station in sorted(self.inventory):
try:
staDict=tools.initPytheasDict("station")
# get distance and azimuth
dist,az,baz=gps2dist_azimuth(evlat,evlon,
self.inventory[station]["latitude"],
self.inventory[station]["longitude"])
# calculate ain for direct linear raypath #
ain=np.rad2deg(np.arctan((dist/1000.)/evdep))
# store values to dictionary
staDict['STA']=station
staDict['NET']=self.inventory[station]['network']
staDict['DIST']=dist/1000.
staDict['BAZ']=baz; staDict['AN']=ain
statsDict[dateKey].update({station:staDict})
except:
logging.exception("Could not process %s for %s" % (station,dateKey))
continue
# store values
evsDict.update({dateKey:evDict})
except:
logging.exception("Could not process %s" % dateKey)
continue
return evsDict,statsDict
def readQML(self,qmlFile):
"""
Read a QuakeML file.
:type catFile: str
:param catFile: path to the QuakeML file
:returns: (dict with event information, dict with arrival information)
"""
# Set event ID before running any loops
evID=0
# Read the actual QuakeML file.
logging.info("Attempting to read %s"%qmlFile)
try:
events=read_events(qmlFile)
except:
logging.exception("Could not read %s"%qmlFile)
return
# Create a dictionary for the event and arrival information.
evsDict={}; statsDict={}
for evid,event in enumerate(events):
try:
# first, update the evDict object
prefOrig=event.preferred_origin()
rid=prefOrig.resource_id
origin=prefOrig.time
originZero=UTCDateTime(year=origin.year,month=origin.month,day=origin.day,
hour=origin.hour,minute=origin.minute,second=0)
lat=prefOrig.latitude
lon=prefOrig.longitude
if tools.isnone(lat) or tools.isnone(lon):
logging.warning('Event %s does not have location information. Skipping...' % origin)
continue
try:
dep = prefOrig.depth / 1000. # depth should be in km
if not dep:
dep = 0.1 # temporary fix
except TypeError: # is depth None?
dep = 0.1
# set pref mag before searching for corresponding r-id
mag=event.preferred_magnitude()
if mag is None:
magVal=np.nan
else:
for magRef in event.magnitudes:
if magRef.origin_id == rid:
mag=magRef
magVal=mag.mag
# parse to evDict object
evDict={'YEAR':origin.year,'Mo':origin.month,'Da':origin.day,'HR':origin.hour,
'MN':origin.minute,'SEC':origin.second+origin.microsecond/10**6, 'ORIGIN':origin,
'LAT':lat,'LON':lon,'DEPTH':dep,
'MAG':magVal,'evID':str(evid)}
frmt="%Y-%m-%d-%H-%M-%S"
dateKey=origin.strftime(frmt)
# now, need to make the staDict object
picksRef=event.picks; staDict={}; picks={}
for arr in prefOrig.arrivals:
pid=arr.pick_id
phase=arr.phase
# get the epicentral distance
try: # distance should be written in the file
dist=degrees2kilometers(arr.distance)
except:
dist=None
# get the backazimuth
try:
baz=arr.backazimuth
except AttributeError: # if baz is not there, maybe az?
try:
baz=(arr.azimuth+180) % 360
except: # no az either?
baz=None
# get the angle of incidence
try: # if ain is not written
ain=arr.incidence_angle
except AttributeError: # maybe the takeoff is
try:
# calcualte the incidence angle from the takeoff
# as seen in Kapetanidis (2017).
ih=arr.takeoff_angle # takeoff angle
vTop=np.float(self.vmodel.evaluate_below(0,'s')) # velocity at station
vSrc=np.float(self.vmodel.evaluate_below(dep,'s')) # velocity at source
ain=np.rad2deg(np.arcsin((vTop/vSrc)*np.sin(np.deg2rad(ih))))
except:
ain=np.nan
## TODO: this should be added as a user-switch
##if dist > degrees2kilometers(1): # accept ONLY local phases. should this be a user option?
## continue
# check for phase and select
if phase not in ["p","P","s","S"]: # "P"/"S" accepted only cause of erroneous registration
continue # of direct upward local phases in the QuakeML
for tmp in picksRef: # get the station info for the arrival
if tmp.resource_id == pid: # match arrival to pick
station=tmp.waveform_id.station_code
network=tmp.waveform_id.network_code
component=tmp.waveform_id.channel_code
ptime=tmp.time
if not network: # can this happen?
network="XX" # should skip in that case?
if not station:
station="XXX"
continue
if not component:
component="XXX"
if any((tools.isnone(ain), tools.isnone(baz), tools.isnone(dist))):
# get distance and azimuth
if station not in self.inventory:
continue
gps=gps2dist_azimuth(
lat,lon,
self.inventory[station]["latitude"],
self.inventory[station]["longitude"]
)
# replace values where needed
if tools.isnone(dist):
dist=gps[0]/1000.
if tools.isnone(baz):
baz=gps[2]
if tools.isnone(ain):
# calculate ain for direct linear raypath
ain=np.rad2deg(np.arctan((dist)/dep))
if tools.isnone(ain): ain = 90.0
# get phase information
if phase in ['p','P']:
temp={'STA':station,'NET':network,'COM':component,
'DIST':dist,'BAZ':baz,'AN':ain,
'SECP':ptime-originZero,'TOBSP':ptime-origin}
if station in staDict:
staDict[station].update(temp)
else:
staDict.update({station:temp})
elif phase in ['s','S']:
temp={'STA':station,'NET':network,'COM':component, # re-adding these in case no
'DIST':dist,'BAZ':baz,'AN':ain, # P-arrival was found in the
'SECS':ptime-originZero,'TOBSS':ptime-origin} # QuakeML
if station in staDict:
staDict[station].update(temp)
else:
staDict.update({station:temp})
if not staDict:
logging.warning("No picks found for %s" % dateKey)
for station in sorted(self.inventory):
try:
tempDict=tools.initPytheasDict("station")
# get distance and azimuth
dist,az,baz=gps2dist_azimuth(lat,lon,
self.inventory[station]["latitude"],
self.inventory[station]["longitude"])
# calculate ain for direct linear raypath #
if not dep:
dep = 0.1 # temporary fix
ain=np.rad2deg(np.arctan((dist/1000.)/dep))
if tools.isnone(ain):
ain = 0.0
# store values to dictionary
tempDict['STA']=station
tempDict['NET']=self.inventory[station]['network']
tempDict['DIST']=dist/1000.
tempDict['BAZ']=baz
tempDict['AN']=ain
staDict.update({station:tempDict})
except:
logging.exception("Could not process %s for %s" % (station,dateKey))
continue
evsDict.update({dateKey:evDict})
evsDict[dateKey]['NSTA']=len(staDict)
statsDict.update({dateKey:staDict})
except:
logging.exception("Could not parse %s from catalogue, skipping..." % evid)
return evsDict,statsDict
def eventCorrect(self,evPath,evsDict,statsDict):
"""
Corrects the keys of events and stations dictionaries to be
in accordance with event ids acquired from the folder search.
:type evPath: tuple-like
:param evPath: tuple-like of event codes found in the data directory
:type evsDict: dict
:param evsDict: dict containing all the event information acquired from the
catalogue
:type statsDict: dict
:param statsDict: dict containing all the arrival information acquired from the
catalogue
:returns: (event information dict, arrival information dict) both with corrected
event code keys (i.e. the origin times from the catalogue were replaced with
the matched ones from the data directory)
"""
tOff=self.generalCNF.matching
keyTrash=[]
logging.debug("Performing keys correction...")
# get previous corrections
try: # if it exists
with open(WORKDIR+os.sep+"etc%sevcor%sevcor.dat"%(os.sep,os.sep)) as fid:
corList=fid.readlines()
corDict={x.split()[0].strip():x.split()[1].strip() for x in corList}
except IOError: # if file doesn't exist
with open(WORKDIR+os.sep+"etc%sevcor%sevcor.dat"%(os.sep,os.sep),"w") as fid:
fid.write("# INITIAL CORRECTED \n")
corDict={}
# get keys. catalogue keys are rounded to 0 microseconds
catalogueKeys=np.asarray([round(UTCDateTime(x).timestamp) for x in sorted(evsDict)])
directoryKeys=np.asarray([UTCDateTime(y).timestamp for y in sorted(evPath)])
keyFrmt="%Y-%m-%d-%H-%M-%S"
# we want to match the CATALOGUE keys to the DIRECTORY keys
for eTms in catalogueKeys: