non-working commit of autoPyLoT functionality in overview window

QtPyLoT.py

@@ -34,15 +34,16 @@ from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
 from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
     QWidget, QHBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
     QDialog, QErrorMessage, QApplication, QPixmap, QMessageBox, QSplashScreen, \
-    QActionGroup
+    QActionGroup, QListWidget
 import numpy as np
 from obspy.core import UTCDateTime
 
-from pylot.core.read import Data, FilterOptions
+from pylot.core.read import Data, FilterOptions, AutoPickParameter
 from pylot.core.util import _getVersionString, FILTERDEFAULTS, fnConstructor, \
     checkurl, FormatError, FilterOptionsDialog, \
     NewEventDlg, createEvent, MPLWidget, PropertiesDlg, HelpForm, \
     DatastructureError, createAction, getLogin, createCreationInfo, PickDlg
+from pylot.core.util.thread import WorkerThread
 from pylot.core.util.structure import DATASTRUCTURE
 import icons_rc
 
@@ -147,11 +148,13 @@ class MainWindow(QMainWindow):
         filter_icon = QIcon()
         filter_icon.addPixmap(QPixmap(':/icons/filter.png'))
         z_icon = QIcon()
-        z_icon.addPixmap((QPixmap(':/icons/key_Z.png')))
+        z_icon.addPixmap(QPixmap(':/icons/key_Z.png'))
         n_icon = QIcon()
-        n_icon.addPixmap((QPixmap(':/icons/key_N.png')))
+        n_icon.addPixmap(QPixmap(':/icons/key_N.png'))
         e_icon = QIcon()
-        e_icon.addPixmap((QPixmap(':/icons/key_E.png')))
+        e_icon.addPixmap(QPixmap(':/icons/key_E.png'))
+        auto_icon = QIcon()
+        auto_icon.addPixmap(QPixmap(':/icons/sync.png'))
 
         newEventAction = self.createAction(self, "&New event ...",
                                            self.createNewEvent,
@@ -261,6 +264,17 @@ class MainWindow(QMainWindow):
         componentToolBar.setObjectName("PhaseTools")
         self.addActions(componentToolBar, componentActions)
 
+        auto_pick = self.createAction(parent=self, text='autoPick',
+                                      slot=self.autoPick, shortcut='Alt+Ctrl+A',
+                                      icon=auto_icon, tip='Automatically pick'
+                                                          ' the entire dataset'
+                                                          ' displayed!',
+                                      checkable=False)
+
+        autoPickToolBar = self.addToolBar("autoPyLoT")
+        autoPickActions = (auto_pick,)
+        self.addActions(autoPickToolBar, autoPickActions)
+
         # pickToolBar = self.addToolBar("PickTools")
         # pickToolActions = (selectStation, )
         # pickToolBar.setObjectName("PickTools")
@@ -570,6 +584,20 @@ class MainWindow(QMainWindow):
         else:
             self.updateStatus('picks discarded ({0})'.format(station))
 
+    def autoPick(self):
+        list = QListWidget()
+        autopick_parameter = AutoPickParameter('autoPyLoT_local.in')
+        list.addItem(str(autopick_parameter))
+
+        # Create the worker thread and run it
+        self.thread = WorkerThread(parent=self,
+                                   func=autopickevent,
+                                   data=self.getData().getWFData(),
+                                   param=autopick_parameter)
+        self.thread.message.connect(list.addItem)
+        self.thread.start()
+
+
     def addPicks(self, station, picks):
         stat_picks = self.getPicksOnStation(station)
         if not stat_picks:

icons.qrc

@@ -15,6 +15,7 @@
         <file>icons/key_W.png</file>
 		<file>icons/key_Z.png</file>
         <file>icons/filter.png</file>
+        <file>icons/sync.png</file>
         <file>icons/zoom_in.png</file>
         <file>icons/zoom_out.png</file>
         <file>splash/splash.png</file>

pylot/core/pick/utils.py

@@ -12,8 +12,25 @@ import numpy as np
 import scipy as sc
 import matplotlib.pyplot as plt
 from obspy.core import Stream, UTCDateTime
+from pylot.core.pick.run_autopicking import run_autopicking
 import warnings
 import pdb
+
+def autopickevent(data, param):
+    stations = []
+
+    for n in len(data):
+        station = data[n].stats.station
+        if station not in stations:
+            stations.append(station)
+        else:
+            continue
+
+    for station in stations:
+        topick = data.select(station=station)
+
+        stat_picks = run_autopicking(topick, param)
+
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     '''
     Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
@@ -254,7 +271,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
                 FM = '+'
             elif P1[0] > 0 and P2[0] <= 0:
                 FM = '+'
-           
+
         print 'fmpicker: Found polarity %s' % FM
 
     if iplot > 1:
@@ -530,7 +547,7 @@ def wadaticheck(pickdic, dttolerance, iplot):
     	print 'wadaticheck: Not enough S-P times available for reliable regression!'
         print 'Skip wadati check!'
         wfitflag = 1
-    
+
     # plot results
     if iplot > 1:
     	plt.figure(iplot)
@@ -615,12 +632,12 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
         print 'checksignallength: Signal shorter than required minimum signal length!'
         print 'Presumably picked noise peak, pick is rejected!'
         returnflag = 0
-    
+
     if iplot == 2:
         plt.figure(iplot)
     	p1, = plt.plot(t,x, 'k')
         p2, = plt.plot(t[inoise], e[inoise], 'c')
-        p3, = plt.plot(t[isignal],e[isignal], 'r') 
+        p3, = plt.plot(t[isignal],e[isignal], 'r')
         p2, = plt.plot(t[inoise], e[inoise])
         p3, = plt.plot(t[isignal],e[isignal], 'r')
         p4, = plt.plot([t[isignal[0]], t[isignal[len(isignal)-1]]], \
@@ -642,7 +659,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
 
 def checkPonsets(pickdic, dttolerance, iplot):
     '''
-    Function to check statistics of P-onset times: Control deviation from 
+    Function to check statistics of P-onset times: Control deviation from
     median (maximum adjusted deviation = dttolerance) and apply pseudo-
     bootstrapping jackknife.
 
@@ -722,7 +739,7 @@ def checkPonsets(pickdic, dttolerance, iplot):
         for i in range(0, len(Ppicks)):
         	plt.text(i, Ppicks[i] + 0.2, stations[i])
 
-        plt.xlabel('Number of P Picks') 
+        plt.xlabel('Number of P Picks')
         plt.ylabel('Onset Time [s] from 1.1.1970')
         plt.legend([p1, p2, p3], ['Skipped P Picks', 'Good P Picks', 'Median'], \
                     loc='best')
@@ -751,7 +768,7 @@ def jackknife(X, phi, h):
     : param: h, size of subgroups, optinal, default = 1
     : type:  integer
     '''
-    
+
     PHI_jack = None
     PHI_pseudo = None
     PHI_sub = None
@@ -786,7 +803,7 @@ def jackknife(X, phi, h):
                 	phi_sub = np.var(xx)
                 elif phi == 'MED':
                 	phi_sub = np.median(xx)
-               
+
                 PHI_sub.append(phi_sub)
                 # pseudo values
                 phi_pseudo = g * phi_sc - ((g - 1) * phi_sub)
@@ -799,21 +816,21 @@ def jackknife(X, phi, h):
 
 def checkZ4S(X, pick, zfac, checkwin, iplot):
     '''
-    Function to compare energy content of vertical trace with 
+    Function to compare energy content of vertical trace with
-    energy content of horizontal traces to detect spuriously 
+    energy content of horizontal traces to detect spuriously
     picked S onsets instead of P onsets. Usually, P coda shows
     larger longitudal energy on vertical trace than on horizontal
     traces, where the transversal energy is larger within S coda.
-    Be careful: there are special circumstances, where this is not 
+    Be careful: there are special circumstances, where this is not
     the case!
 
     : param: X, fitered(!) time series, three traces
-    : type:  `~obspy.core.stream.Stream` 
+    : type:  `~obspy.core.stream.Stream`
 
     : param: pick, initial (AIC) P onset time
     : type:  float
-    
+
-    : param: zfac, factor for threshold determination, 
+    : param: zfac, factor for threshold determination,
              vertical energy must exceed coda level times zfac
              to declare a pick as P onset
     : type:  float
@@ -841,7 +858,7 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
     ndat = X.select(component="N")
     if len(ndat) == 0:  # check for other components
         ndat = X.select(component="1")
-    
+
 
     z = zdat[0].data
     tz = np.arange(0, zdat[0].stats.npts / zdat[0].stats.sampling_rate,
@@ -863,7 +880,7 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
     # calculate energy levels
     zcodalevel = max(absz[isignal])
     encodalevel = max(absen[isignal])
-    
+
     # calculate threshold
     minsiglevel = encodalevel * zfac
 
@@ -873,7 +890,7 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
     	print 'checkZ4S: Maybe S onset? Skip this P pick!'
     else:
         print 'checkZ4S: P onset passes checkZ4S test!'
-        returnflag = 1      
+        returnflag = 1
 
     if iplot > 1:
     	te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,

pylot/core/util/thread.py

@@ -4,8 +4,9 @@ from PySide.QtCore import QThread, Signal
 class WorkerThread(QThread):
     message = Signal(str)
 
-    def __init__(self, func, data, param):
+    def __init__(self, parent, func, data, param):
         super(WorkerThread, self).__init__()
+        self.setParent(parent)
         self.func = func
         self.data = data
         self.param = param
@@ -13,7 +14,12 @@ class WorkerThread(QThread):
     def run(self):
         sys.stdout = self
 
-        self.func(self.data, self.param)
+        picks = self.func(self.data, self.param)
+
+        try:
+            self.parent().addPicks(picks)
+        except AttributeError:
+            print picks
 
     def write(self, text):
         self.message.emit(text)