Merge branch 'develop' into improve-util-utils

PyLoT.py

@@ -84,7 +84,7 @@ 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, PickQualitiesFromXml, \
-    SourceSpecWindow, ChooseWaveFormWindow
+    SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@@ -496,7 +496,6 @@ class MainWindow(QMainWindow):
                                                       icon=eventlist_xml_icon,
                                                       tip='Create an Eventlist from a XML File')
         self.eventlist_xml_action.setEnabled(False)
-
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -698,14 +697,17 @@ class MainWindow(QMainWindow):
         wf_tab = QtWidgets.QWidget(self)
         array_tab = QtWidgets.QWidget(self)
         events_tab = QtWidgets.QWidget(self)
+        spectro_tab = QtWidgets.QWidget(self)
 
         # init main widgets layouts
         self.wf_layout = QtWidgets.QVBoxLayout()
         self.array_layout = QtWidgets.QVBoxLayout()
         self.events_layout = QtWidgets.QVBoxLayout()
+        self.spectro_layout = QtWidgets.QVBoxLayout()
         wf_tab.setLayout(self.wf_layout)
         array_tab.setLayout(self.array_layout)
         events_tab.setLayout(self.events_layout)
+        spectro_tab.setLayout(self.spectro_layout)
 
         # tighten up layouts inside tabs
         for layout in [self.wf_layout, self.array_layout, self.events_layout]:
@@ -716,12 +718,14 @@ class MainWindow(QMainWindow):
         self.tabs.addTab(wf_tab, 'Waveform Plot')
         self.tabs.addTab(array_tab, 'Array Map')
         self.tabs.addTab(events_tab, 'Eventlist')
+        self.tabs.addTab(spectro_tab, 'Spectro')
 
         self.wf_layout.addWidget(self.no_data_label)
         self.wf_layout.addWidget(self.wf_scroll_area)
         self.wf_scroll_area.setWidgetResizable(True)
         self.init_array_tab()
         self.init_event_table()
+        self.init_spectro_tab()
         self.tabs.setCurrentIndex(0)
 
         self.eventLabel = QLabel()
@@ -734,16 +738,13 @@ class MainWindow(QMainWindow):
         _widget.setLayout(self._main_layout)
         _widget.showFullScreen()
 
-        self.logwidget = LogWidget(parent=None)
+
         if use_logwidget:
+            self.logwidget = LogWidget(parent=None)
             self.logwidget.show()
             self.stdout = self.logwidget.stdout
             self.stderr = self.logwidget.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
@@ -1678,20 +1679,20 @@ class MainWindow(QMainWindow):
 
     def pickQualities(self):
         path = self.get_current_event_path()
-        (_, _, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
+        (_, 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 
 
     # WIP JG
-    def eventlistXml2(self):
+    def eventlistXml(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):
+        # WIP JG
+    def spectogramView(self):
         global test
         stations = []
         names = []
@@ -1706,12 +1707,25 @@ class MainWindow(QMainWindow):
             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()
+
+        print (self.get_data().wfdata.traces[0])
+
+        test = SpectrogramTab(traces, self.get_data().wfdata)
+        height = self.tabs.widget(0).height()
+        width = self.tabs.widget(0).width()
+        self.tabs.setCurrentIndex(3)
+        figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
+        return figCanvas
+        #self.spectro_layout.addWidget()
+        # self.get_data().wfdata.spectrogram()
+        # self.tabs.addTab(figCanvas, 'Spectrogram')
+        # self.tabs[3] = figCanvas
+        # self.refreshTabs()
+        # test.show()
+
+
 
     def compareMulti(self):
         if not self.compareoptions:
@@ -1898,6 +1912,13 @@ class MainWindow(QMainWindow):
                     self.newWF(plot=False)
                 self.update_obspy_dmt()
                 self.refresh_array_map()
+        if self.tabs.currentIndex() == 3:
+            if self.spectroWidget != None:
+                self.spectro_layout.removeWidget(self.spectroWidget)
+            newSpectroWidget = self.spectogramView()
+            self.spectro_layout.addWidget(newSpectroWidget)
+            self.spectroWidget = newSpectroWidget
+
 
     def newWF(self, event=None, plot=True):
         '''
@@ -2155,6 +2176,7 @@ class MainWindow(QMainWindow):
             self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
+
         if True in self.comparable.values():
             self.compare_action.setEnabled(True)
         self.draw()
@@ -3128,7 +3150,7 @@ class MainWindow(QMainWindow):
         phasefile = os.path.join(obsdir, filename + '.obs')
         lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
         try:
-            lt.locate(ctrfile, self.obspy_dmt)
+            lt.locate(ctrfile, self._inputs)
         except RuntimeError as e:
             print(e.message)
         # finally:
@@ -3182,7 +3204,7 @@ class MainWindow(QMainWindow):
         '''
         if checked: pass  # dummy argument for QAction trigger signal
         self.tabs.setCurrentIndex(1)
-        # if there is no metadata (invetories is an empty list), just initialize the default empty tab
+        # if there is no metadata (inventories is an empty list), just initialize the default empty tab
         if not self.metadata.inventories:
             self.init_array_tab()
             return
@@ -3204,6 +3226,15 @@ class MainWindow(QMainWindow):
         self.tabs.setCurrentIndex(index)
         self.refresh_array_map()
 
+    def init_spectro_tab(self):
+        '''
+        Init spectrogram tab with currently selected event.
+        '''
+        self.spectroWidget = None
+        #self.spectro_layout.addWidget( self.spectogramView() )
+        pass
+
+
     def array_map_thread(self):
         '''
         Start modal thread to init the array_map object.

pylot/core/io/data.py

@@ -260,7 +260,6 @@ class Data(object):
         can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
         """
         from pylot.core.util.defaults import OUTPUTFORMATS
-
         if not type(fcheck) == list:
             fcheck = [fcheck]
 
@@ -321,35 +320,61 @@ class Data(object):
             if lendiff != 0:
                 print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
 
+
+            no_uncertainties_p = []
+            no_uncertainties_s = []
             if upperErrors:
                 # check for pick uncertainties exceeding adjusted upper errors
                 # Picks with larger uncertainties will not be saved in output file!
                 for j in range(len(picks)):
                     for i in range(len(picks_copy)):
                         if picks_copy[i].phase_hint[0] == 'P':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                 #   picks_copy[i].waveform_id.station_code,
+                                  #  picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
+                                    no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+                            #print ("checking for upper_uncertainty")
+                            if  (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                    (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[0]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} P-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
                         if picks_copy[i].phase_hint[0] == 'S':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                    #picks_copy[i].waveform_id.station_code,
+                                    #picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
+                                    no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+
+                            if (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[1]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} S-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
+            for s in no_uncertainties_p:
+                print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
+            for s in no_uncertainties_s:
+                print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
 
             if fnext == '.obs':
                 try:

pylot/core/io/phases.py

@@ -517,7 +517,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 try:
                     fm = arrivals[key]['P']['fm']
                 except KeyError as e:
@@ -551,7 +551,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                                                                            ss_ms,
                                                                                            pweight))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 fm = '?'
                 onset = arrivals[key]['S']['mpp']
                 year = onset.year
@@ -670,7 +670,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P') and arrivals[key]['P']['mpp'] is not None:
+            if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
                 if arrivals[key]['P']['weight'] < 4:
                     Ponset = arrivals[key]['P']['mpp']
                     pyear = Ponset.year
@@ -699,7 +699,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
                               % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 if arrivals[key]['S']['weight'] < 4:
                     Sonset = arrivals[key]['S']['mpp']
                     syear = Sonset.year
@@ -768,7 +768,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
             # P onsets
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
@@ -782,7 +782,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     else:
                         fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
                         # S onsets
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 if usedarrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
@@ -828,13 +828,13 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 # P onsets
                 if usedarrivals[key]['P']['weight'] < 4:
                     Ponset = usedarrivals[key]['P']['mpp']
                     Prt = Ponset - stime  # onset time relative to source time
                     fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 # S onsets
                 if usedarrivals[key]['S']['weight'] < 4:
                     Sonset = usedarrivals[key]['S']['mpp']
@@ -879,7 +879,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
                     stat = key
                     for i in range(len(picks)):
@@ -961,7 +961,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         # write phase lines
         for key in arrivals:
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
                     stat = key
                     ccode = arrivals[key]['P']['channel']
@@ -1014,7 +1014,6 @@ def chooseArrivals(arrivals):
     :return: arrivals but with the manual picks prefered if possible
     """
     # If len of arrivals is greater than 2 it comes from autopicking so only autopicks are available
-    print("=== CHOOSE ===")
     if len(arrivals) > 2:
         return arrivals
     if arrivals['auto'] and arrivals['manual']:

pylot/core/util/thread.py

@@ -41,7 +41,8 @@ class Thread(QThread):
             exctype, value = sys.exc_info()[:2]
             self._executedErrorInfo = '{} {} {}'. \
                 format(exctype, value, traceback.format_exc())
-        sys.stdout = self.old_stdout
+        if self.redirect_stdout:
+            sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:

pylot/core/util/widgets.py

@@ -5663,9 +5663,23 @@ class ChooseWaveFormWindow(QWidget):
     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()
+        #self.currentSpectro = self.traces[
+        #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
+        #self.currentSpectro.show()
+        applyFFT()
+
+    def applyFFT(self, trace):
+        tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
+
+    def applyFFTs(self, tra):
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
 
     def submitN(self):
         matplotlib.pyplot.close(self.currentSpectro)
@@ -5681,13 +5695,6 @@ class ChooseWaveFormWindow(QWidget):
             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:
@@ -5714,7 +5721,87 @@ class ChooseWaveFormWindow(QWidget):
         pass
 
 
+class SpectrogramTab(QWidget):
+    def __init__(self, traces, wfdata, parent=None):
+        super(SpectrogramTab, self).__init__(parent)
+        self.setupUi()
+        self.traces = traces
+        self.wfdata = wfdata
+
+    def setupUi(self):
+        pass
+    def makeSpecFig(self, direction = 'Z', height = 0, width = 0, parent = None):
+
+        i = 0
+        grams = []
+        figure, axis = matplotlib.pyplot.subplots(len(self.traces), sharex=True)
+
+        start, end = full_range(self.wfdata)
+
+        if height != 0 and width != 0:
+            figure.figsize = (width, height)
+            figure.set_figwidth = width
+            figure.set_figheight = height
+
+        #figure.tight_layout()
+
+        for t in self.traces:
+            tra = self.traces[t][direction]
+            #print(start, end)
+
+            # Set Title
+            if i == 0:
+                if direction == 'Z':
+                    figure.suptitle("section: vertical components")
+                elif direction == 'E':
+                    figure.suptitle("section: east-west components")
+                elif direction == 'N':
+                    figure.suptitle("section: north-south components")
+                axis[i].vlines(0, axis[i].get_ylim()[0], axis[i].get_ylim()[1],
+                          colors='m', linestyles='dashed',
+                          linewidth=2)
+
+            # Different axis settings for visual improvements
+            # axis[i].set_xlim(left=0, right=end - start)
+            # axis[i].spines['top'].set_visible(False)
+            # axis[i].spines['right'].set_visible(False)
+            # # axis[i].spines['left'].set_visible(False)
+
+            # axis[i].tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
+            # if not (len(self.traces) == i - 1):
+                # axis[i].spines['bottom'].set_visible(False)
+            # axis[i].set_yticks([])
+            # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+
+            #ax.axhline(n, color="0.5", lw=0.5)
+
+
+            grams.append(tra.spectrogram(show=False, axes=axis[i]))
+            i+=1
+
+        #figure.setXLims([0, end - start])
+        figure.set_tight_layout(True)
+        fC = FigureCanvas(figure)
+        return fC
+
+    #for t in self.traces:
+       # tra = self.traces[t]['Z']
+       # transformed = abs(np.fft.rfft(tra.data))
+       # axis[i].plot(transformed, label=t)
+       # # axis[i].tick_params(labelbottom=False)
+       # axis[i].spines['top'].set_visible(False)
+       # axis[i].spines['right'].set_visible(False)
+       # axis[i].spines['left'].set_visible(False)
+       # if not (len(self.traces) == i - 1):
+       #     axis[i].spines['bottom'].set_visible(False)
+       # axis[i].set_yticks([])
+       # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+       # # axis[i].axis('off')
+       # i += 1
+       # # self.applyFFTs(t)
+
+
 if __name__ == '__main__':
     import doctest
 
-    doctest.testmod()
+    doctest.testmod()