Merge remote-tracking branch 'origin/develop' into develop

PyLoT.py

@@ -60,7 +60,7 @@ except ImportError:
     from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 
-from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
+from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude, calcsourcespec
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import FilterOptions, PylotParameter
 from autoPyLoT import autoPyLoT
@@ -83,7 +83,8 @@ from pylot.core.io.location import create_creation_info, create_event
 from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
-    CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget
+    CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
+    SourceSpecWindow, ChooseWaveFormWindow
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@@ -734,12 +735,22 @@ class MainWindow(QMainWindow):
         if use_logwidget:
             self.logwidget = LogWidget(parent=None)
             self.logwidget.show()
+            self.stdout = self.logwidget.stdout
+            self.stderr = self.logwidget.stderr
 
-            sys.stdout = self.logwidget.stdout
-            sys.stderr = self.logwidget.stderr
+            sys.stdout = self.stdout
+            sys.stderr = self.stderr
+
+            # Not sure why but the lines above kept messing with the Ouput even with use_logwidget disabled
+            sys.stdout = self.stdout
+            sys.stderr = self.stderr
 
         self.setCentralWidget(_widget)
 
+        # Need to store PickQualities Window somewhere so it doesnt disappear
+        self.pickQualitiesWindow = None
+
+
     def init_wfWidget(self):
         xlab = self.startTime.strftime('seconds since %Y/%m/%d %H:%M:%S (%Z)')
         plottitle = None  # "Overview: {0} components ".format(self.getComponent())
@@ -1668,15 +1679,41 @@ class MainWindow(QMainWindow):
 
     def pickQualities(self):
         path = self.get_current_event_path()
-        getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'), plotflag=1)
-        return
+        (_, _, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
+        self.pickQualitiesWindow = PickQualitiesFromXml(figure=plot, path=self.get_current_event_path(),inputVar=self._inputs)
+        self.pickQualitiesWindow.showUI()
+        return 
 
-    def eventlistXml(self):
+    # WIP JG
+    def eventlistXml2(self):
         path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
         outpath = self.project.location[:self.project.location.rfind('/')]
         geteventlistfromxml(path, outpath)
         return
 
+    # WIP JG
+    def eventlistXml(self):
+        global test
+        stations = []
+        names = []
+        traces = {}
+        for tr in self.get_data().wfdata.traces:
+            if not tr.stats.station in stations:
+                stations.append(tr.stats.station)
+                names.append(tr.stats.network + '.' + tr.stats.station)
+        for station in stations:
+            traces[station] = {}
+        for ch in ['Z', 'N', 'E']:
+            for tr in self.get_data().wfdata.select(component=ch).traces:
+                traces[tr.stats.station][ch] = tr
+
+
+        names.sort()
+        a = self.get_current_event()
+        test = ChooseWaveFormWindow(WaveForms=names, traces=traces, stream=self.get_data())
+        #self.get_data().wfdata.spectrogram()
+        test.show()
+
     def compareMulti(self):
         if not self.compareoptions:
             return
@@ -3075,11 +3112,13 @@ class MainWindow(QMainWindow):
         lt = locateTool[loctool]
         # get working directory
         locroot = parameter['nllocroot']
+        #locroot = 'E:/NLL/src/Insheim'
         if locroot is None:
             self.PyLoTprefs()
             self.locate_event()
 
         ctrfile = os.path.join(locroot, 'run', parameter['ctrfile'])
+        #ctrfile = 'E:/NLL/src/Insheim/run/Insheim_min1d032016.in'
         ttt = parameter['ttpatter']
         outfile = parameter['outpatter']
         eventname = self.get_current_event_name()
@@ -3090,7 +3129,7 @@ class MainWindow(QMainWindow):
         phasefile = os.path.join(obsdir, filename + '.obs')
         lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
         try:
-            lt.locate(ctrfile)
+            lt.locate(ctrfile, self.obspy_dmt)
         except RuntimeError as e:
             print(e.message)
         # finally:
@@ -3495,7 +3534,7 @@ class MainWindow(QMainWindow):
 
         wf_select = Stream()
         # restitute only picked traces
-        for station in np.unique(self.getPicks('manual').keys() + self.getPicks('auto').keys()):
+        for station in np.unique(list(self.getPicks('manual').keys()) + list(self.getPicks('auto').keys())):
             wf_select += wf_copy.select(station=station)
 
         corr_wf = restitute_data(wf_select, self.metadata)

pylot/core/analysis/magnitude.py

@@ -144,6 +144,10 @@ class Magnitude(object):
                     azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
             else:
                 # no scaling necessary
+                # Temporary fix needs rework
+                if (len(self.magnitudes.keys()) == 0):
+                    print("Error in local magnitude calculation ")
+                    return None
                 mag = ope.Magnitude(
                     mag=np.median([M.mag for M in self.magnitudes.values()]),
                     magnitude_type=self.type,
@@ -432,6 +436,40 @@ class MomentMagnitude(Magnitude):
             self.event.station_magnitudes.append(magnitude)
             self.magnitudes = (station, magnitude)
 
+    # WIP JG
+    def getSourceSpec(self):
+        for a in self.arrivals:
+            if a.phase not in 'pP':
+                continue
+            # make sure calculating Mo only from reliable onsets
+            # NLLoc: time_weight = 0 => do not use onset!
+            if a.time_weight == 0:
+                continue
+            pick = a.pick_id.get_referred_object()
+            station = pick.waveform_id.station_code
+            if len(self.stream) <= 2:
+                print("Station:" '{0}'.format(station))
+                print("WARNING: No instrument corrected data available,"
+                      " no magnitude calculation possible! Go on.")
+                continue
+            wf = self.stream.select(station=station)
+            if not wf:
+                continue
+            try:
+                scopy = wf.copy()
+            except AssertionError:
+                print("WARNING: Something's wrong with the data,"
+                      "station {},"
+                      "no calculation of moment magnitude possible! Go on.".format(station))
+                continue
+            onset = pick.time
+            distance = degrees2kilometers(a.distance)
+            azimuth = a.azimuth
+            incidence = a.takeoff_angle
+            w0, fc, plt = calcsourcespec(scopy, onset, self.p_velocity, distance,
+                                    azimuth, incidence, self.p_attenuation,
+                                    3, self.verbose)
+            return w0, fc, plt
 
 def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):
     '''
@@ -602,7 +640,7 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
         N = min(int(np.power(m, 2)), 16384)
         # N = int(np.power(m, 2))
         y = dt * np.fft.fft(xdat, N)
-        Y = abs(y[: N / 2])
+        Y = abs(y[: int(N / 2)])
         L = (N - 1) / freq
         f = np.arange(0, fny, 1 / L)
 
@@ -679,6 +717,8 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
             plt.xlabel('Frequency [Hz]')
             plt.ylabel('Amplitude [m/Hz]')
             plt.grid()
+            if iplot == 3:
+                return w0, Fc, plt
             plt.show()
             try:
                 input()

pylot/core/loc/nll.py

@@ -82,7 +82,7 @@ def locate(fnin, parameter=None):
     :param fnin: external program name
     :return: None
     """
-    exe_path = which('NLLoc', parameter)
+    exe_path = parameter['nllocbin'] + '/bin/NLLoc'    
     if exe_path is None:
         raise NLLocError('NonLinLoc executable not found; check your '
                          'environment variables')

pylot/core/pick/charfuns.py

@@ -16,10 +16,9 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 
 :author: MAGS2 EP3 working group
 """
-
 import numpy as np
-from obspy.core import Stream
 from scipy import signal
+from obspy.core import Stream
 
 
 class CharacteristicFunction(object):
@@ -259,7 +258,7 @@ class HOScf(CharacteristicFunction):
         """
         Function to calculate skewness (statistics of order 3) or kurtosis
         (statistics of order 4), using one long moving window, as published
-        in Kueperkoch et al. (2010).
+        in Kueperkoch et al. (2010), or order 2, i.e. STA/LTA.
         :param data: data, time series (whether seismogram or CF)
         :type data: tuple
         :return: HOS cf
@@ -276,28 +275,47 @@ class HOScf(CharacteristicFunction):
         elif self.getOrder() == 4:  # this is kurtosis
             y = np.power(xnp, 4)
             y1 = np.power(xnp, 2)
+        elif self.getOrder() == 2:  # this is variance, used for STA/LTA processing
+            y = np.power(xnp, 2)
+            y1 = np.power(xnp, 2)
 
         # Initialisation
         # t2: long term moving window
         ilta = int(round(self.getTime2() / self.getIncrement()))
+        ista = int(round((self.getTime2() / 10) / self.getIncrement()))  # TODO: still hard coded!!
         lta = y[0]
         lta1 = y1[0]
+        sta = y[0]
         # moving windows
         LTA = np.zeros(len(xnp))
+        STA = np.zeros(len(xnp))
         for j in range(0, len(xnp)):
             if j < 4:
                 LTA[j] = 0
+                STA[j] = 0
+            elif j <= ista:
+                lta = (y[j] + lta * (j - 1)) / j
+                if self.getOrder() == 2:
+                    sta = (y[j] + sta * (j - 1)) / j
+            # elif j < 4:
             elif j <= ilta:
                 lta = (y[j] + lta * (j - 1)) / j
                 lta1 = (y1[j] + lta1 * (j - 1)) / j
+                if self.getOrder() == 2:
+                    sta = (y[j] - y[j - ista]) / ista + sta
             else:
                 lta = (y[j] - y[j - ilta]) / ilta + lta
                 lta1 = (y1[j] - y1[j - ilta]) / ilta + lta1
+                if self.getOrder() == 2:
+                    sta = (y[j] - y[j - ista]) / ista + sta
             # define LTA
             if self.getOrder() == 3:
                 LTA[j] = lta / np.power(lta1, 1.5)
             elif self.getOrder() == 4:
                 LTA[j] = lta / np.power(lta1, 2)
+            else:
+                LTA[j] = lta
+                STA[j] = sta
 
         # remove NaN's with first not-NaN-value,
         # so autopicker doesnt pick discontinuity at start of the trace
@@ -306,7 +324,10 @@ class HOScf(CharacteristicFunction):
             first = ind[0]
             LTA[:first] = LTA[first]
 
-        self.cf = LTA
+        if self.getOrder() > 2:
+            self.cf = LTA
+        else:  # order 2 means STA/LTA!
+            self.cf = STA / LTA
         self.xcf = x
 
 

pylot/core/util/gui.py

@@ -56,7 +56,7 @@ def which(program, parameter):
         nllocpath = ":" + parameter.get('nllocbin')
         os.environ['PATH'] += nllocpath
     except Exception as e:
-        print(e.message)
+        print(e)
 
     def is_exe(fpath):
         return os.path.exists(fpath) and os.access(fpath, os.X_OK)

pylot/core/util/widgets.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """
 Created on Wed Mar 19 11:27:35 2014
-
 @author: sebastianw
 """
 
@@ -3161,7 +3160,6 @@ class CanvasWidget(QWidget):
 class MultiEventWidget(QWidget):
     start = Signal()
     '''
-
     '''
 
     def __init__(self, options=None, parent=None, windowflag=Qt.Window):
@@ -3438,7 +3436,6 @@ class TuneAutopicker(QWidget):
     update = QtCore.Signal(str)
     '''
     QWidget used to modifiy and test picking parameters for autopicking algorithm.
-
     :param: parent
     :type: PyLoT Mainwindow
     '''
@@ -3959,10 +3956,8 @@ class PylotParaBox(QtWidgets.QWidget):
     def __init__(self, parameter, parent=None, windowflag=Qt.Window):
         '''
         Generate Widget containing parameters for PyLoT.
-
         :param: parameter
         :type: PylotParameter (object)
-
         '''
         QtWidgets.QWidget.__init__(self, parent, windowflag)
         self.parameter = parameter
@@ -5561,7 +5556,165 @@ class HelpForm(QDialog):
         self.pageLabel.setText(self.webBrowser.title())
 
 
+class PickQualitiesFromXml(QWidget):
+    """
+            PyLoT widget PickQualitiesFromXml is a QWidget object. It is an UI that enables the user
+            to create a plot showing the pick qualities in the event selected inside the QComboBox created
+            by this Widget. The user can also choose to select all Events.
+            The plot is being shown by a FigureCanvas from matlplotlib.
+    """
+
+    def __init__(self, parent=None, figure=Figure(), path="", inputVar=None):
+        super(PickQualitiesFromXml, self).__init__(parent)
+
+        self.fig = figure
+        self.chooseBox = QComboBox()
+        self.path = path
+        self.inputs = inputVar
+        self.setupUi()
+
+    def setupUi(self):
+        self.setWindowTitle("Get pick qualities from xml files")
+        self.main_layout = QtWidgets.QVBoxLayout()
+        self.figureC = FigureCanvas(self.fig)
+        self.chooseBox = self.createComboBox()
+        if self.chooseBox:
+            self.main_layout.addWidget(self.chooseBox)
+        self.main_layout.addWidget(self.figureC)
+        self.setLayout(self.main_layout)
+
+    def showUI(self):
+        self.show()
+
+    # Creates a QComboBox and adds all events in the current folder as options. Also gives the option to choose all events
+    def createComboBox(self):
+        self.chooseBox.addItems(glob.glob(os.path.join(os.path.dirname(self.path) + "/*/", '*.xml')))
+        self.chooseBox.addItem("All")
+        self.chooseBox.currentIndexChanged.connect(self.selectionChanged)
+        self.chooseBox.setCurrentIndex(self.chooseBox.count() - 1)
+        return self.chooseBox
+
+    # Function that gets called when the user changes the current selection in the QComboBox. Redraws the plot with the new data
+    def selectionChanged(self):
+        self.figureC.setParent(None)
+        if self.chooseBox.currentIndex() == self.chooseBox.count() - 1:
+            (_, _, plot) = getQualitiesfromxml(self.path, self.inputs.get('timeerrorsP'),
+                                               self.inputs.get('timeerrorsS'), plotflag=1)
+            self.figureC = FigureCanvas(plot)
+        else:
+            (_, _, plot) = getQualitiesfromxml(self.path, self.inputs.get('timeerrorsP'),
+                                               self.inputs.get('timeerrorsS'), plotflag=1,
+                                               xmlnames=[self.chooseBox.currentText()])
+            self.figureC = FigureCanvas(plot)
+        self.figureC.draw()
+        self.main_layout.addWidget(self.figureC)
+        self.setLayout(self.main_layout)
+
+
+class SourceSpecWindow(QWidget):
+    def __init__(self, parent=None, figure=Figure()):
+        super(SourceSpecWindow, self).__init__(parent)
+        self.main_layout = QVBoxLayout()
+        self.setWindowTitle("Display source spectrum from selected trace")
+        self.fig = figure
+
+    def setupUi(self):
+        self.figureC = FigureCanvas(self.fig)
+        self.main_layout.addWidget(self.figureC)
+        self.setLayout(self.main_layout)
+
+
+class ChooseWaveFormWindow(QWidget):
+    def __init__(self, parent=None, WaveForms=[], traces=[], stream=None, chooseB=False):
+        super(ChooseWaveFormWindow, self).__init__(parent)
+        self.main_layout = QVBoxLayout()
+        self.setWindowTitle("Choose trace to display source spectrum")
+        self.wFs = WaveForms
+        self.chooseBoxTraces = QComboBox()
+        self.chooseBoxComponent = QComboBox()
+        self.submitButton = QPushButton(text='test')
+
+        self.chooseB = chooseB
+
+        self.verticalButton = QPushButton(text='Z')
+        self.northButton = QPushButton(text='N')
+        self.eastButton = QPushButton(text='E')
+        self.component = ''
+
+        self.traces = traces
+        self.stream = stream
+        self.setupUI()
+        self.currentSpectro = Figure()
+
+    def setupUI(self):
+        self.submitButton.clicked.connect(self.submit)
+        self.createComboBoxTraces()
+        self.main_layout.addWidget(self.chooseBoxTraces)
+
+        if self.chooseB:
+            self.createComboBoxComponent()
+            self.main_layout.addWidget(self.submitButton)
+            self.main_layout.addWidget(self.chooseBoxComponent)
+        else:
+            self.createButtonsComponent()
+
+        self.setLayout(self.main_layout)
+
+    def submit(self):
+        matplotlib.pyplot.close(self.currentSpectro)
+        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
+
+    def submitN(self):
+        matplotlib.pyplot.close(self.currentSpectro)
+        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]]['N'].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
+
+    def submitE(self):
+        matplotlib.pyplot.close(self.currentSpectro)
+        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]]['E'].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
+
+    def submitZ(self):
+        matplotlib.pyplot.close(self.currentSpectro)
+        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]]['Z'].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
+
+    # Creates a QComboBox and adds all traces provided
+    def createComboBoxTraces(self):
+        if len(self.wFs) <= 0:
+            raise 'No traces provided'
+        self.chooseBoxTraces.addItems(self.wFs)
+        self.chooseBoxTraces.currentIndexChanged.connect(self.selectionChanged)
+        self.chooseBoxTraces.setCurrentIndex(0)
+        return self.chooseBoxTraces
+
+    def createButtonsComponent(self):
+        self.northButton.clicked.connect(self.submitN)
+        self.eastButton.clicked.connect(self.submitE)
+        self.verticalButton.clicked.connect(self.submitZ)
+
+        self.main_layout.addWidget(self.verticalButton)
+        self.main_layout.addWidget(self.northButton)
+        self.main_layout.addWidget(self.eastButton)
+
+    def createComboBoxComponent(self):
+        self.chooseBoxComponent.addItems(['Z', 'N', 'E'])
+
+    # Function that gets called when the user changes the current selection in the QComboBox.
+    def selectionChanged(self):
+        pass
+
+
 if __name__ == '__main__':
     import doctest
 
-    doctest.testmod()
+    doctest.testmod()