Merge branch 'develop' of ariadne.geophysik.rub.de:/data/git/pylot into develop

Conflicts:
	pylot/core/pick/earllatepicker.py
	pylot/core/pick/fmpicker.py
	pylot/core/pick/getSNR.py

QtPyLoT.py

@@ -29,7 +29,7 @@ from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
     QFileInfo, Qt
 from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
     QWidget, QHBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
-    QDialog, QErrorMessage, QApplication
+    QDialog, QErrorMessage, QApplication, QPixmap
 from obspy.core import UTCDateTime
 
 from pylot.core.read import Data, FilterOptions
@@ -38,12 +38,11 @@ from pylot.core.util import _getVersionString, FILTERDEFAULTS, fnConstructor, \
     NewEventDlg, createEvent, MPLWidget, PropertiesDlg, HelpForm, \
     DatastructureError, createAction, getLogin, createCreationInfo, PickDlg
 from pylot.core.util.structure import DATASTRUCTURE
-import qrc_resources
+import icons_rc
 
 # Version information
 __version__ = _getVersionString()
 
-
 class MainWindow(QMainWindow):
     closing = Signal()
 
@@ -101,8 +100,11 @@ class MainWindow(QMainWindow):
         except:
             self.startTime = UTCDateTime()
 
+        pylot_icon = QIcon()
+        pylot_icon.addPixmap(QPixmap(':/icons/pylot.ico'))
+
         self.setWindowTitle("PyLoT - do seismic processing the python way")
-        self.setWindowIcon(QIcon(":/icon.ico"))
+        self.setWindowIcon(pylot_icon)
 
         xlab = self.startTime.strftime('seconds since %Y/%m/%d %H:%M:%S (%Z)')
 
@@ -123,7 +125,15 @@ class MainWindow(QMainWindow):
         saveIcon = self.style().standardIcon(QStyle.SP_DriveHDIcon)
         helpIcon = self.style().standardIcon(QStyle.SP_DialogHelpButton)
         newIcon = self.style().standardIcon(QStyle.SP_FileIcon)
-        pickIcon = QIcon(':/pick.png')
+
+        # create resource icons
+        p_icon = QIcon()
+        p_icon.addPixmap(QPixmap(':/icons/picon.png'))
+        s_icon = QIcon()
+        s_icon.addPixmap(QPixmap(':/icons/sicon.png'))
+        print_icon = QIcon()
+        print_icon.addPixmap(QPixmap(':/icons/printer.png'))
+
         newEventAction = self.createAction(self, "&New event ...",
                                            self.createNewEvent,
                                            QKeySequence.New, newIcon,
@@ -140,10 +150,6 @@ class MainWindow(QMainWindow):
                                              "Ctrl+W", QIcon(":/wfIcon.png"),
                                              """Open waveform data (event will
                                              be closed).""")
-        selectStation = self.createAction(self, "Select station",
-                                          self.pickOnStation, "Alt+P", pickIcon,
-                                          "Select a station from overview "
-                                          "plot for picking")
         prefsEventAction = self.createAction(self, "Preferences",
                                              self.PyLoTprefs,
                                              QKeySequence.Preferences,
@@ -163,14 +169,14 @@ class MainWindow(QMainWindow):
                                              "Alt+F", QIcon(None),
                                              """Adjust filter parameters.""")
         self.selectPAction = self.createAction(self, "&P", self.alterPhase, "Alt+P",
-                                          QIcon(":/picon.png"),
+                                          p_icon,
                                           "Toggle P phase.", True)
         self.selectSAction = self.createAction(self, "&S", self.alterPhase, "Alt+S",
-                                          QIcon(":/sicon.png"),
+                                          s_icon,
                                           "Toggle S phase", True)
         printAction = self.createAction(self, "&Print event ...",
                                         self.printEvent, QKeySequence.Print,
-                                        QIcon(":/printer.png"),
+                                        print_icon,
                                         "Print waveform overview.")
         helpAction = self.createAction(self, "&Help ...", self.helpHelp,
                                        QKeySequence.HelpContents, helpIcon,
@@ -204,10 +210,10 @@ class MainWindow(QMainWindow):
         phaseToolBar.setObjectName("PhaseTools")
         self.addActions(phaseToolBar, phaseToolActions)
 
-        pickToolBar = self.addToolBar("PickTools")
+        # pickToolBar = self.addToolBar("PickTools")
-        pickToolActions = (selectStation, )
+        # pickToolActions = (selectStation, )
-        pickToolBar.setObjectName("PickTools")
+        # pickToolBar.setObjectName("PickTools")
-        self.addActions(pickToolBar, pickToolActions)
+        # self.addActions(pickToolBar, pickToolActions)
 
         self.eventLabel = QLabel()
         self.eventLabel.setFrameStyle(QFrame.StyledPanel | QFrame.Sunken)
@@ -336,9 +342,9 @@ class MainWindow(QMainWindow):
     def getPlotWidget(self):
         return self.DataPlot
 
-    def getWFID(self, event):
+    def getWFID(self, gui_event):
 
-        ycoord = event.ydata
+        ycoord = gui_event.ydata
 
         statID = int(round(ycoord))
 
@@ -370,6 +376,10 @@ class MainWindow(QMainWindow):
         title = 'overview: {0} components'.format(zne_text[comp])
         wfst = self.getData().getWFData().select(component=comp)
         self.getPlotWidget().plotWFData(wfdata=wfst, title=title)
+        self.getPlotWidget().draw()
+        pos = self.getPlotWidget().getPlotDict().keys()
+        labels = [int(act) for act in pos]
+        self.getPlotWidget().setYTickLabels(pos, labels)
 
     def filterWaveformData(self):
         if self.getData():
@@ -444,7 +454,7 @@ class MainWindow(QMainWindow):
         return self.seismicPhase
 
     def getStationName(self, wfID):
-        return self.getPlotWidget().getPlotDict()[wfID]
+        return self.getPlotWidget().getPlotDict()[wfID][0]
 
     def alterPhase(self):
         pass
@@ -454,9 +464,9 @@ class MainWindow(QMainWindow):
         self.updateStatus('Seismic phase changed to '
                           '{0}'.format(self.getSeismicPhase()))
 
-    def pickOnStation(self, event):
+    def pickOnStation(self, gui_event):
 
-        wfID = self.getWFID(event)
+        wfID = self.getWFID(gui_event)
 
         station = self.getStationName(wfID)
         print 'picking on station {0}'.format(station)
@@ -517,13 +527,16 @@ class MainWindow(QMainWindow):
 
 def main():
     # create the Qt application
-    pylot_app = QApplication(sys.argv[0])
+    pylot_app = QApplication(sys.argv)
+
+    app_icon = QIcon()
+    app_icon.addPixmap(QPixmap(':/icons/pick.png'))
 
     # set Application Information
     pylot_app.setOrganizationName("Ruhr-University Bochum / MAGS2")
     pylot_app.setOrganizationDomain("rub.de")
     pylot_app.setApplicationName("PyLoT")
-    pylot_app.setWindowIcon(QIcon(":/icon.ico"))
+    pylot_app.setWindowIcon(app_icon)
 
     # create the main window
     pylot_form = MainWindow()

icons.qrc

@@ -5,6 +5,8 @@
 		<file>icons/picon.png</file>
 		<file>icons/sicon.png</file>
 		<file>icons/pick.png</file>
+        <file>icons/filter.png</file>
+        <file>icons/zoom.png</file>
     </qresource>
     <qresource prefix="/help">
         <file>help/index.html</file>

pylot/core/pick/earllatepicker.py

@@ -0,0 +1,27 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+"""
+   Created Mar 2015
+   Transcription of the rezipe of Diehl et al. (2009) for consistent phase
+   picking. For a given inital (the most likely) pick, the corresponding earliest
+   and latest possible pick is calculated based on noise measurements in front of
+   the most likely pick and signal wavelength derived from zero crossings.
+
+   :author: Ludger Kueperkoch / MAGS2 EP3 working group
+"""
+
+import argparse
+import obspy
+from pylot.core.pick.utils import earllatepicker
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--X', type=~obspy.core.stream.Stream, help='time series (seismogram) read with obspy module read')
+    parser.add_argument('--nfac', type=int, help='(noise factor), nfac times noise level to calculate latest possible pick')
+    parser.add_argument('--TSNR', type=tuple, help='length of time windows around pick used to determine SNR \
+                        [s] (Tnoise, Tgap, Tsignal)')
+    parser.add_argument('--Pick1', type=float, help='Onset time of most likely pick')
+    parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
+    args = parser.parse_args()
+    earllatepicker(args.X, args.nfac, args.TSNR, args.Pick1, args.iplot)

pylot/core/pick/fmpicker.py

@@ -0,0 +1,23 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+"""
+   Created Mar 2015
+   Function to derive first motion (polarity) for given phase onset based on zero crossings.
+
+   :author: MAGS2 EP3 working group / Ludger Kueperkoch
+"""
+
+import argparse
+import obspy
+from pylot.core.pick.utils import fmpicker
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--Xraw', type=~obspy.core.stream.Stream, help='unfiltered time series (seismogram) read with obspy module read')
+    parser.add_argument('--Xfilt', type=~obspy.core.stream.Stream, help='filtered time series (seismogram) read with obspy module read')
+    parser.add_argument('--pickwin', type=float, help='length of pick window [s] for first motion determination')
+    parser.add_argument('--Pick', type=float, help='Onset time of most likely pick')
+    parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
+    args = parser.parse_args()
+    fmpicker(args.Xraw, args.Xfilt, args.pickwin, args.Pick, args.iplot)
+

pylot/core/pick/getSNR.py

@@ -0,0 +1,30 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+"""
+   Created Mar/Apr 2015
+   Function to calculate SNR of certain part of seismogram relative
+   to given time. Returns SNR and SNR [dB].
+
+   :author: Ludger Kueperkoch /MAGS EP3 working group
+"""
+
+import argparse
+import obspy
+from pylot.core.pick.utils import getSNR
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--data', '-d', type=~obspy.core.stream.Stream,
+                        help='time series (seismogram) read with obspy module '
+                             'read',
+                        dest='data')
+    parser.add_argument('--tsnr', '-s', type=tuple,
+                        help='length of time windows around pick used to '
+                             'determine SNR [s] (Tnoise, Tgap, Tsignal)',
+                        dest='tsnr')
+    parser.add_argument('--time', '-t', type=float,
+                        help='initial time from which noise and signal windows '
+                             'are calculated',
+                        dest='time')
+    args = parser.parse_args()
+    print getSNR(args.data, args.tsnr, args.time)

pylot/core/pick/getnoisewin.py

@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import numpy
+from pylot.core.pick.utils import getnoisewin
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--t', type=~numpy.array, help='numpy array of time stamps')
+    parser.add_argument('--t1', type=float, help='time from which relativ to it noise window is extracted')
+    parser.add_argument('--tnoise', type=float, help='length of time window [s] for noise part extraction')
+    parser.add_argument('--tgap', type=float, help='safety gap between signal (t1=onset) and noise')
+    args = parser.parse_args()
+    getnoisewin(args.t, args.t1, args.tnoise, args.tgap)

pylot/core/pick/getsignalwin.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import numpy
+from pylot.core.pick.utils import getsignalwin
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--t', type=~numpy.array, help='numpy array of time stamps')
+    parser.add_argument('--t1', type=float, help='time from which relativ to it signal window is extracted')
+    parser.add_argument('--tsignal', type=float, help='length of time window [s] for signal part extraction')
+    args = parser.parse_args()
+    getsignalwin(args.t, args.t1, args.tsignal)

pylot/core/pick/utils.py

@@ -11,7 +11,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from obspy.core import Stream
-import argparse
+
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     '''
@@ -45,8 +45,9 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     print 'earllatepicker: Get earliest and latest possible pick relative to most likely pick ...'
 
     x = X[0].data
-    t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate, X[0].stats.delta)
+    t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate,
-    #get latest possible pick
+                  X[0].stats.delta)
+    # get latest possible pick
     #get noise window
     inoise = getnoisewin(t, Pick1, TSNR[0], TSNR[1])
     #get signal window
@@ -68,18 +69,18 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
     zc = []
     zc.append(Pick1)
     i = 0
-    for j in range(isignal[0][1],isignal[0][len(t[isignal]) - 1]):
+    for j in range(isignal[0][1], isignal[0][len(t[isignal]) - 1]):
-        i = i+ 1
+        i = i + 1
-        if x[j-1] <= 0 and x[j] >= 0:
+        if x[j - 1] <= 0 and x[j] >= 0:
             zc.append(t[isignal][i])
-        elif x[j-1] > 0 and x[j] <= 0:
+        elif x[j - 1] > 0 and x[j] <= 0:
             zc.append(t[isignal][i])
         if len(zc) == 3:
             break
     #calculate maximum period T0 of signal out of zero crossings
     T0 = max(np.diff(zc))  #this is half wave length!
     #T0/4 is assumed as time difference between most likely and earliest possible pick!
-    EPick = Pick1 - T0/2
+    EPick = Pick1 - T0 / 2
 
     #get symmetric pick error as mean from earliest and latest possible pick
     #by weighting latest possible pick two times earliest possible pick
@@ -94,36 +95,31 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
         p3, = plt.plot(t[isignal], x[isignal], 'r')
         p4, = plt.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k')
         p5, = plt.plot(zc, [0, 0, 0], '*g', markersize=14)
-       plt.legend([p1, p2, p3, p4, p5], ['Data', 'Noise Window', 'Signal Window', 'Noise Level', 'Zero Crossings'], \
+        plt.legend([p1, p2, p3, p4, p5],
+                   ['Data', 'Noise Window', 'Signal Window', 'Noise Level',
+                    'Zero Crossings'], \
                    loc='best')
         plt.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], '--k')
         plt.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2)
-       plt.plot([LPick, LPick], [max(x)/2, -max(x)/2], '--k')
+        plt.plot([LPick, LPick], [max(x) / 2, -max(x) / 2], '--k')
-       plt.plot([EPick, EPick], [max(x)/2, -max(x)/2], '--k')
+        plt.plot([EPick, EPick], [max(x) / 2, -max(x) / 2], '--k')
-       plt.plot([Pick1 + PickError, Pick1 + PickError], [max(x)/2, -max(x)/2], 'r--')
+        plt.plot([Pick1 + PickError, Pick1 + PickError],
-       plt.plot([Pick1 - PickError, Pick1 - PickError], [max(x)/2, -max(x)/2], 'r--')
+                 [max(x) / 2, -max(x) / 2], 'r--')
+        plt.plot([Pick1 - PickError, Pick1 - PickError],
+                 [max(x) / 2, -max(x) / 2], 'r--')
         plt.xlabel('Time [s] since %s' % X[0].stats.starttime)
         plt.yticks([])
         ax = plt.gca()
         ax.set_xlim([t[inoise[0][0]] - 2, t[isignal[0][len(isignal) - 1]] + 3])
-       plt.title('Earliest-/Latest Possible/Most Likely Pick & Symmetric Pick Error, %s' % X[0].stats.station)
+        plt.title(
+            'Earliest-/Latest Possible/Most Likely Pick & Symmetric Pick Error, %s' %
+            X[0].stats.station)
         plt.show()
         raw_input()
         plt.close(iplot)
 
     return EPick, LPick, PickError
 
-if __name__ == "__main__":
-   parser = argparse.ArgumentParser()
-   parser.add_argument('--X', type=~obspy.core.stream.Stream, help='time series (seismogram) read with obspy module read')
-   parser.add_argument('--nfac', type=int, help='(noise factor), nfac times noise level to calculate latest possible pick')
-   parser.add_argument('--TSNR', type=tuple, help='length of time windows around pick used to determine SNR \
-                       [s] (Tnoise, Tgap, Tsignal)')
-   parser.add_argument('--Pick1', type=float, help='Onset time of most likely pick')
-   parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
-   args = parser.parse_args()
-   earllatepicker(args.X, args.nfac, args.TSNR, args.Pick1, args.iplot)
-
 
 def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
     '''
@@ -156,9 +152,11 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
 
         xraw = Xraw[0].data
         xfilt = Xfilt[0].data
-       t = np.arange(0, Xraw[0].stats.npts / Xraw[0].stats.sampling_rate, Xraw[0].stats.delta)
+        t = np.arange(0, Xraw[0].stats.npts / Xraw[0].stats.sampling_rate,
-       #get pick window
+                      Xraw[0].stats.delta)
-       ipick = np.where((t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
+        # get pick window
+        ipick = np.where(
+            (t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
         #remove mean
         xraw[ipick] = xraw[ipick] - np.mean(xraw[ipick])
         xfilt[ipick] = xfilt[ipick] - np.mean(xfilt[ipick])
@@ -170,12 +168,12 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
         zc1.append(Pick)
         index1 = []
         i = 0
-       for j in range(ipick[0][1],ipick[0][len(t[ipick]) - 1]):
+        for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
-           i = i+ 1
+            i = i + 1
-           if xraw[j-1] <= 0 and xraw[j] >= 0:
+            if xraw[j - 1] <= 0 and xraw[j] >= 0:
                 zc1.append(t[ipick][i])
                 index1.append(i)
-           elif xraw[j-1] > 0 and xraw[j] <= 0:
+            elif xraw[j - 1] > 0 and xraw[j] <= 0:
                 zc1.append(t[ipick][i])
                 index1.append(i)
             if len(zc1) == 3:
@@ -205,12 +203,12 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
         zc2.append(Pick)
         index2 = []
         i = 0
-       for j in range(ipick[0][1],ipick[0][len(t[ipick]) - 1]):
+        for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
-           i = i+ 1
+            i = i + 1
-           if xfilt[j-1] <= 0 and xfilt[j] >= 0:
+            if xfilt[j - 1] <= 0 and xfilt[j] >= 0:
                 zc2.append(t[ipick][i])
                 index2.append(i)
-           elif xfilt[j-1] > 0 and xfilt[j] <= 0:
+            elif xfilt[j - 1] > 0 and xfilt[j] <= 0:
                 zc2.append(t[ipick][i])
                 index2.append(i)
             if len(zc2) == 3:
@@ -240,7 +238,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
                 FM = 'D'
             elif P1[0] >= 0 and P2[0] < 0:
                 FM = '-'
-          elif P1[0] < 0 and P2[0]>= 0:
+            elif P1[0] < 0 and P2[0] >= 0:
                 FM = '-'
             elif P1[0] > 0 and P2[0] > 0:
                 FM = 'U'
@@ -251,32 +249,37 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
 
     if iplot is not None:
         plt.figure(iplot)
-       plt.subplot(2,1,1)
+        plt.subplot(2, 1, 1)
         plt.plot(t, xraw, 'k')
         p1, = plt.plot([Pick, Pick], [max(xraw), -max(xraw)], 'b', linewidth=2)
         if P1 is not None:
             p2, = plt.plot(t[islope1], xraw[islope1])
             p3, = plt.plot(zc1, np.zeros(len(zc1)), '*g', markersize=14)
             p4, = plt.plot(t[islope1], datafit1, '--g', linewidth=2)
-          plt.legend([p1, p2, p3, p4], ['Pick', 'Slope Window', 'Zero Crossings', 'Slope'], \
+            plt.legend([p1, p2, p3, p4],
+                       ['Pick', 'Slope Window', 'Zero Crossings', 'Slope'], \
                        loc='best')
             plt.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
             ax = plt.gca()
-          ax.set_xlim([t[islope1[0][0]] - 0.1, t[islope1[0][len(islope1) - 1]] + 0.3])
+            ax.set_xlim(
+                [t[islope1[0][0]] - 0.1, t[islope1[0][len(islope1) - 1]] + 0.3])
         plt.yticks([])
-       plt.title('First-Motion Determination, %s, Unfiltered Data' % Xraw[0].stats.station)
+        plt.title('First-Motion Determination, %s, Unfiltered Data' % Xraw[
+            0].stats.station)
 
-       plt.subplot(2,1,2)
+        plt.subplot(2, 1, 2)
         plt.title('First-Motion Determination, Filtered Data')
         plt.plot(t, xfilt, 'k')
-       p1, = plt.plot([Pick, Pick], [max(xfilt), -max(xfilt)], 'b', linewidth=2)
+        p1, = plt.plot([Pick, Pick], [max(xfilt), -max(xfilt)], 'b',
+                       linewidth=2)
         if P2 is not None:
             p2, = plt.plot(t[islope2], xfilt[islope2])
             p3, = plt.plot(zc2, np.zeros(len(zc2)), '*g', markersize=14)
             p4, = plt.plot(t[islope2], datafit2, '--g', linewidth=2)
             plt.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
             ax = plt.gca()
-          ax.set_xlim([t[islope2[0][0]] - 0.1, t[islope2[0][len(islope2) - 1]] + 0.3])
+            ax.set_xlim(
+                [t[islope2[0][0]] - 0.1, t[islope2[0][len(islope2) - 1]] + 0.3])
         plt.xlabel('Time [s] since %s' % Xraw[0].stats.starttime)
         plt.yticks([])
         plt.show()
@@ -285,16 +288,6 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
 
     return FM
 
-if __name__ == "__main__":
-   parser = argparse.ArgumentParser()
-   parser.add_argument('--Xraw', type=~obspy.core.stream.Stream, help='unfiltered time series (seismogram) read with obspy module read')
-   parser.add_argument('--Xfilt', type=~obspy.core.stream.Stream, help='filtered time series (seismogram) read with obspy module read')
-   parser.add_argument('--pickwin', type=float, help='length of pick window [s] for first motion determination')
-   parser.add_argument('--Pick', type=float, help='Onset time of most likely pick')
-   parser.add_argument('--iplot', type=int, help='if set, figure no. iplot occurs')
-   args = parser.parse_args()
-   earllatepicker(args.Xraw, args.Xfilt, args.pickwin, args.Pick, args.iplot)
-
 
 def getSNR(X, TSNR, t1):
     '''
@@ -314,12 +307,13 @@ def getSNR(X, TSNR, t1):
 
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
-    SNR = None
-    SNRdB = None
     x = X[0].data
-    t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate, X[0].stats.delta)
+    t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate,
-    #get noise window
+                  X[0].stats.delta)
+
+    # get noise window
     inoise = getnoisewin(t, t1, TSNR[0], TSNR[1])
+
     #get signal window
     isignal = getsignalwin(t, t1, TSNR[2])
     if np.size(inoise) < 1:
@@ -330,19 +324,11 @@ def getSNR(X, TSNR, t1):
         return
 
     #calculate ratios
-    SNR = max(abs(x[isignal])) / np.mean(abs(x[inoise]))
+    noiselevel = np.mean(abs(x[inoise]))
+    SNR = max(abs(x[isignal])) / noiselevel
     SNRdB = 20 * np.log10(SNR)
 
-    return SNR, SNRdB
+    return SNR, SNRdB, noiselevel
-
-if __name__ == "__main__":
-   parser = argparse.ArgumentParser()
-   parser.add_argument('--X', type=~obspy.core.stream.Stream, help='time series (seismogram) read with obspy module read')
-   parser.add_argument('--TSNR', type=tuple, help='length of time windows around pick used to determine SNR \
-                       [s] (Tnoise, Tgap, Tsignal)')
-   parser.add_argument('--t1', type=float, help='initial time from which noise and signal windows are calculated')
-   args = parser.parse_args()
-   getSNR(args.X, args.TSNR, args.t1)
 
 
 def getnoisewin(t, t1, tnoise, tgap):
@@ -365,7 +351,7 @@ def getnoisewin(t, t1, tnoise, tgap):
     '''
 
     inoise = None
-    #get noise window
+    # get noise window
     inoise = np.where((t <= max([t1 - tgap, 0])) \
                       & (t >= max([t1 - tnoise - tgap, 0])))
     if np.size(inoise) < 1:
@@ -373,14 +359,6 @@ def getnoisewin(t, t1, tnoise, tgap):
 
     return inoise
 
-if __name__ == "__main__":
-   parser = argparse.ArgumentParser()
-   parser.add_argument('--t', type=array, help='numpy array of time stamps')
-   parser.add_argument('--t1', type=float, help='time from which relativ to it noise window is extracted')
-   parser.add_argument('--tnoise', type=float, help='length of time window [s] for noise part extraction')
-   parser.add_argument('--tgap', type=float, help='safety gap between signal (t1=onset) and noise') 
-   args = parser.parse_args()
-   getnoisewin(args.t, args.t1, args.tnoise, args.tgap)
 
 def getsignalwin(t, t1, tsignal):
     '''
@@ -398,7 +376,7 @@ def getsignalwin(t, t1, tsignal):
     '''
 
     inoise = None
-    #get signal window
+    # get signal window
     isignal = np.where((t <= min([t1 + tsignal, len(t)])) \
                        & (t >= t1))
     if np.size(isignal) < 1:
@@ -406,10 +384,4 @@ def getsignalwin(t, t1, tsignal):
 
     return isignal
 
-if __name__ == "__main__":
+
-   parser = argparse.ArgumentParser()
-   parser.add_argument('--t', type=array, help='numpy array of time stamps')
-   parser.add_argument('--t1', type=float, help='time from which relativ to it signal window is extracted')
-   parser.add_argument('--tsignal', type=float, help='length of time window [s] for signal part extraction')
-   args = parser.parse_args()
-   getsignalwin(args.t, args.t1, args.tsignal)

pylot/core/util/widgets.py

@@ -14,34 +14,18 @@ matplotlib.rcParams['backend.qt4'] = 'PySide'
 
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_qt4agg import FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg
 from matplotlib.widgets import MultiCursor
-from PySide.QtGui import (QAction,
+from PySide.QtGui import QAction, QApplication,QComboBox, QDateTimeEdit,\
-                          QApplication,
+    QDialog, QDialogButtonBox, QDoubleSpinBox, QGroupBox, QGridLayout,\
-                          QComboBox,
+    QIcon, QKeySequence, QLabel, QLineEdit, QMessageBox, QPixmap, QSpinBox,\
-                          QDateTimeEdit,
+    QTabWidget, QToolBar, QVBoxLayout, QWidget
-                          QDialog,
+from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
-                          QDialogButtonBox,
-                          QDoubleSpinBox,
-                          QGroupBox,
-                          QGridLayout,
-                          QHBoxLayout,
-                          QIcon,
-                          QKeySequence,
-                          QLabel,
-                          QLineEdit,
-                          QMessageBox,
-                          QSpinBox,
-                          QTabWidget,
-                          QToolBar,
-                          QVBoxLayout,
-                          QWidget)
-from PySide.QtCore import (QSettings,
-                           Qt,
-                           QUrl,
-                           Signal,
-                           Slot)
 from PySide.QtWebKit import QWebView
+from obspy import Stream, UTCDateTime
+from obspy.core.event import Pick, WaveformStreamID
 from pylot.core.read import FilterOptions
+from pylot.core.pick.utils import getSNR
 from pylot.core.util.defaults import OUTPUTFORMATS
 from pylot.core.util import prepTimeAxis, getGlobalTimes
 
@@ -71,6 +55,7 @@ class MPLWidget(FigureCanvas):
         self._parent = None
         self.setParent(parent)
         self.figure = Figure()
+        self.figure.set_facecolor((.92, .92, .92))
         # attribute plotdict is an dictionary connecting position and a name
         self.plotdict = dict()
         # create axes
@@ -91,39 +76,58 @@ class MPLWidget(FigureCanvas):
     def setPlotDict(self, key, value):
         self.plotdict[key] = value
 
+    def clearPlotDict(self):
+        self.plotdict = dict()
+
     def getParent(self):
         return self._parent
 
     def setParent(self, parent):
         self._parent = parent
 
-    def plotWFData(self, wfdata, title = None):
+    def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None):
-        self.axes.lines = []
+        self.axes.cla()
+        self.clearPlotDict()
         wfstart = getGlobalTimes(wfdata)[0]
         for n, trace in enumerate(wfdata):
+            channel = trace.stats.channel
             station = trace.stats.station
-            print('plotting station: %s' % station)
+            msg = 'plotting %s channel of station %s' % (channel, station)
+            print(msg)
             stime = trace.stats.starttime - wfstart
             time_ax = prepTimeAxis(stime, trace)
             trace.detrend()
             trace.detrend('demean')
             trace.normalize(trace.data.max() * 2)
             self.axes.plot(time_ax, trace.data + n, 'k')
-            self.axes.hold(True)
             xlabel = 'seconds since {0}'.format(wfstart)
             ylabel = ''
             self.updateWidget(xlabel, ylabel, title)
-            self.setPlotDict(n, station)
+            self.setPlotDict(n, (station, channel))
         self.axes.autoscale(tight=True)
+        if zoomx:
+            self.axes.set_xlim(zoomx)
+        if zoomy:
+            self.axes.set_ylim(zoomy)
+        self.draw()
+
+    def setYTickLabels(self, pos, labels):
+        self.axes.set_yticks(pos)
+        self.axes.set_yticklabels(labels)
+        self.draw()
 
     def updateXLabel(self, text):
         self.axes.set_xlabel(text)
+        self.draw()
+
 
     def updateYLabel(self, text):
         self.axes.set_ylabel(text)
+        self.draw()
 
     def updateTitle(self, text):
         self.axes.set_title(text)
+        self.draw()
 
     def updateWidget(self, xlabel, ylabel, title):
         self.updateXLabel(xlabel)
@@ -237,6 +241,12 @@ class PickDlg(QDialog):
         self.station = station
         self.rotate = rotate
         self.components = 'ZNE'
+        self.picks = {}
+
+        # initialize panning attributes
+        self.press = None
+        self.xpress = None
+        self.ypress = None
 
         # set attribute holding data
         if data is None:
@@ -259,17 +269,50 @@ class PickDlg(QDialog):
         # plot data
         self.getPlotWidget().plotWFData(wfdata=self.getWFData(),
                                         title=self.getStation())
+        self.limits = {'xlims' : self.getPlotWidget().axes.get_xlim(),
+                       'ylims' : self.getPlotWidget().axes.get_ylim()}
+        self.apd = self.getWFData()
+
+        # set plot labels
+
+        self.setPlotLabels()
+
+        # connect button press event to an action
+        self.cidpress = self.connectPressEvent(self.panPress)
+        self.cidmotion = self.connectMotionEvent()
+        self.cidrelease = self.connectReleaseEvent()
+        self.cidscroll = self.connectScrollEvent()
 
     def setupUi(self):
 
+        # create matplotlib toolbar to inherit functionality
+        self.figToolBar = NavigationToolbar2QTAgg(self.getPlotWidget(), self)
+        self.figToolBar.hide()
+
+        # create icons
+        filter_icon = QIcon()
+        filter_icon.addPixmap(QPixmap(':/icons/filter.png'))
+
+        zoom_icon = QIcon()
+        zoom_icon.addPixmap(QPixmap(':/icons/zoom.png'))
+
+
         # create actions
         self.filterAction = createAction(parent=self, text='Filter',
                                          slot=self.filterWFData,
-                                         icon=QIcon(':/filter.png'),
+                                         icon=filter_icon,
-                                         tip='Filter waveforms',
+                                         tip='Toggle filtered/original'
+                                             ' waveforms',
                                          checkable=True)
         self.selectPhase = QComboBox()
-        self.selectPhase.addItems(['Pn', 'Pg', 'P1', 'P2'])
+        self.selectPhase.addItems([None, 'Pn', 'Pg', 'P1', 'P2'])
+
+
+
+        self.zoomAction = createAction(parent=self, text='Zoom',
+                                       slot=self.zoom, icon=zoom_icon,
+                                       tip='Zoom into waveform',
+                                       checkable=True)
 
         # layout the outermost appearance of the Pick Dialog
         _outerlayout = QVBoxLayout()
@@ -280,19 +323,64 @@ class PickDlg(QDialog):
         _dialtoolbar.addAction(self.filterAction)
         _dialtoolbar.addWidget(self.selectPhase)
 
-        _innerlayout = QHBoxLayout()
+        _innerlayout = QVBoxLayout()
 
-        _toolslayout = QVBoxLayout()
-        _toolslabel = QLabel('Place for Tools')
-        _toolslayout.addWidget(_toolslabel)
-
-        _innerlayout.addLayout(_toolslayout)
         _innerlayout.addWidget(self.multicompfig)
+        _buttonbox = QDialogButtonBox(QDialogButtonBox.Apply |
+                                      QDialogButtonBox.Ok |
+                                      QDialogButtonBox.Cancel)
+
+        _innerlayout.addWidget(_buttonbox)
 
         _outerlayout.addWidget(_dialtoolbar)
         _outerlayout.addLayout(_innerlayout)
+
+        self.selectPhase.currentIndexChanged.connect(self.verifyPhaseSelection)
+
         self.setLayout(_outerlayout)
 
+    def disconnectPressEvent(self):
+        self.getPlotWidget().mpl_disconnect(self.cidpress)
+
+    def connectPressEvent(self, slot):
+        widget = self.getPlotWidget()
+        return widget.mpl_connect('button_press_event', slot)
+
+    def reconnectPressEvent(self, slot):
+        self.disconnectPressEvent()
+        return self.connectPressEvent(slot)
+
+    def disconnectScrollEvent(self):
+        widget = self.getPlotWidget()
+        widget.mpl_disconnect(self.cidscroll)
+
+    def connectScrollEvent(self):
+        widget = self.getPlotWidget()
+        return widget.mpl_connect('scroll_event', self.scrollZoom)
+
+    def disconnectMotionEvent(self):
+        widget = self.getPlotWidget()
+        widget.mpl_disconnect(self.cidmotion)
+
+    def connectMotionEvent(self):
+        widget = self.getPlotWidget()
+        return widget.mpl_connect('motion_notify_event', self.panMotion)
+
+    def disconnectReleaseEvent(self):
+        widget = self.getPlotWidget()
+        widget.mpl_disconnect(self.cidrelease)
+
+    def connectReleaseEvent(self):
+        widget = self.getPlotWidget()
+        return widget.mpl_connect('button_release_event', self.panRelease)
+
+    def verifyPhaseSelection(self):
+        phase = self.selectPhase.currentText()
+        if phase:
+            self.disconnectReleaseEvent()
+            self.disconnectScrollEvent()
+            self.disconnectMotionEvent()
+            self.reconnectPressEvent(self.setIniPick)
 
     def getComponents(self):
         return self.components
@@ -303,14 +391,196 @@ class PickDlg(QDialog):
     def getPlotWidget(self):
         return self.multicompfig
 
+    def getChannelID(self, key):
+        return self.getPlotWidget().getPlotDict()[int(key)][1]
+
     def getWFData(self):
         return self.data
 
-    def filterWFData(self):
+    def selectWFData(self, channel):
-        data = self.getWFData().copy().filter(type='bandpass', freqmin=.5, freqmax=15.)
+        component = channel[-1].upper()
-        title = self.getStation() + ' (filtered)'
+        wfdata = Stream()
-        self.getPlotWidget().plotWFData(wfdata=data, title=title)
+        def selectTrace(trace, components):
+            if trace.stats.channel[-1].upper() in components:
+                return trace
 
+        if component == 'E' or component == 'N':
+            for trace in self.getWFData():
+                trace = selectTrace(trace, 'NE')
+                if trace:
+                    wfdata.append(trace)
+        elif component == 'Z':
+            wfdata = self.getWFData().select(component=component)
+        return wfdata
+
+    def getPicks(self):
+        return self.picks
+
+    def getAPD(self):
+        return self.apd
+
+    def updateAPD(self, wfdata):
+        self.apd = wfdata
+
+    def setIniPick(self, gui_event):
+        channel = self.getChannelID(round(gui_event.ydata))
+        wfdata = self.selectWFData(channel)
+
+        self.disconnectScrollEvent()
+
+        self.cidpress = self.reconnectPressEvent(self.setPick)
+
+        ini_pick = gui_event.xdata
+
+        # calculate the resolution window width from SNR
+        #       SNR >= 3    ->  2 sec    HRW
+        #   3 > SNR >= 2    ->  5 sec    MRW
+        #   2 > SNR >= 1.5  -> 10 sec    LRW
+        # 1.5 > SNR         -> 15 sec   VLRW
+        # see also Diehl et al. 2009
+
+        res_wins = {
+            'HRW' : 2.,
+            'MRW' : 5.,
+            'LRW' : 10.,
+            'VLRW' : 15.
+        }
+
+        result = getSNR(wfdata, (10., 2., 1.5), ini_pick)
+
+        snr = result[0]
+        noiselevel = result[2] * 1.5
+
+        if snr < 1.5:
+            x_res = res_wins['VLRW']
+        elif snr < 2.:
+            x_res = res_wins['LRW']
+        elif snr < 3.:
+            x_res = res_wins['MRW']
+        else:
+            x_res = res_wins['HRW']
+        x_res /= 2
+
+        zoomx = [ini_pick - x_res, ini_pick + x_res]
+        zoomy = [noiselevel * 1.5, -noiselevel * 1.5]
+        self.getPlotWidget().plotWFData(wfdata=wfdata,
+                                        title=self.getStation() +
+                                              ' picking mode',
+                                        zoomx=zoomx,
+                                        zoomy=zoomy)
+        self.updateAPD(wfdata)
+
+        # reset labels
+        self.setPlotLabels()
+
+    def setPick(self, gui_event):
+        pick = gui_event.xdata
+        ax = self.getPlotWidget().axes
+
+        ylims = ax.get_ylim()
+
+        ax.plot([pick, pick], ylims, 'r--')
+        self.getPlotWidget().draw()
+
+    def panPress(self, gui_event):
+        ax = self.getPlotWidget().axes
+        if gui_event.inaxes != ax: return
+        self.cur_xlim = ax.get_xlim()
+        self.cur_ylim = ax.get_ylim()
+        self.press = gui_event.xdata, gui_event.ydata
+        self.xpress, self.ypress = self.press
+
+    def panRelease(self, gui_event):
+        ax = self.getPlotWidget().axes
+        self.press = None
+        ax.figure.canvas.draw()
+
+    def panMotion(self, gui_event):
+        ax = self.getPlotWidget().axes
+        if self.press is None: return
+        if gui_event.inaxes != ax: return
+        dx = gui_event.xdata - self.xpress
+        dy = gui_event.ydata - self.ypress
+        self.cur_xlim -= dx
+        self.cur_ylim -= dy
+        ax.set_xlim(self.cur_xlim)
+        ax.set_ylim(self.cur_ylim)
+
+        ax.figure.canvas.draw()
+
+    def filterWFData(self):
+        ax = self.getPlotWidget().axes
+        ylims = ax.get_ylim()
+        xlims = ax.get_xlim()
+        if self.filterAction.isChecked():
+            data = self.getAPD().copy()
+            data.filter(type='bandpass', freqmin=.5, freqmax=15.)
+            title = self.getStation() + ' (filtered)'
+        else:
+            data = self.getAPD().copy()
+            title = self.getStation()
+        self.getPlotWidget().plotWFData(wfdata=data, title=title, zoomx=xlims,
+                                        zoomy=ylims)
+        self.setPlotLabels()
+
+    def setPlotLabels(self):
+
+        # get channel labels
+        pos = self.getPlotWidget().getPlotDict().keys()
+        labels = [self.getPlotWidget().getPlotDict()[key][1] for key in pos]
+
+        # set channel labels
+        self.getPlotWidget().setYTickLabels(pos, labels)
+
+    def zoom(self):
+        if self.zoomAction.isChecked():
+            self.disconnectPressEvent()
+            self.figToolBar.zoom()
+        else:
+            self.connectPressEvent(self.setIniPick)
+
+    def scrollZoom(self, gui_event, factor=2.):
+
+        widget = self.getPlotWidget()
+
+        curr_xlim = widget.axes.get_xlim()
+        curr_ylim = widget.axes.get_ylim()
+
+        if gui_event.button == 'up':
+            scale_factor = 1/factor
+        elif gui_event.button == 'down':
+            # deal with zoom out
+            scale_factor = factor
+        else:
+            # deal with something that should never happen
+            scale_factor = 1
+            print gui_event.button
+
+        new_xlim = gui_event.xdata - scale_factor * (gui_event.xdata - curr_xlim)
+        new_ylim = gui_event.ydata - scale_factor * (gui_event.ydata - curr_ylim)
+
+        new_xlim.sort()
+        new_xlim[0] = max(new_xlim[0], self.limits['xlims'][0])
+        new_xlim[1] = min(new_xlim[1], self.limits['xlims'][1])
+        new_ylim.sort()
+        new_ylim[0] = max(new_ylim[0], self.limits['ylims'][0])
+        new_ylim[1] = min(new_ylim[1], self.limits['ylims'][1])
+
+        widget.axes.set_xlim(new_xlim)
+        widget.axes.set_ylim(new_ylim)
+        widget.draw()
+
+    def apply(self):
+        picks = self.getPicks()
+        for pick in picks:
+            print pick
+
+    def reject(self):
+        QDialog.reject(self)
+
+    def accept(self):
+        self.apply()
+        QDialog.accept(self)
 
 class PropertiesDlg(QDialog):