bugfix: correct erroneous and add new doctests

PyLoT.py

@@ -496,6 +496,7 @@ 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,
@@ -1403,8 +1404,6 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
-            #phaseErrors = {'P': self._inputs['timeerrorsP'],
-            #               'S': self._inputs['timeerrorsS']}
 
             man_au_picks = {'manual': event.pylot_picks,
                             'auto': event.pylot_autopicks}
@@ -1473,7 +1472,6 @@ class MainWindow(QMainWindow):
 
             for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
                 npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
-                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
                 item_np.setText(npicks_str)
 
             item_ref = QStandardItem()  # str(event_ref))
@@ -1718,8 +1716,6 @@ 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()
 
         print (self.get_data().wfdata.traces[0])
 
@@ -1729,14 +1725,6 @@ class MainWindow(QMainWindow):
         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:
@@ -1896,7 +1884,6 @@ class MainWindow(QMainWindow):
         # which will read in data input twice. Therefore current tab is changed to 0
         # in loadProject before calling this function.
         self.fill_eventbox()
-        #print(f'{self.get_current_event()=}')
         plotted = False
         if self.tabs.currentIndex() == 2:
             self.init_event_table()

pylot/core/pick/utils.py

@@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P1 = np.polyfit(xslope1, xraw[islope1], 1)
                 datafit1 = np.polyval(P1, xslope1)
-            except Exception as e:
+            except ValueError as e:
                 print("fmpicker: Problems with data fit! {}".format(e))
                 print("Skip first motion determination!")
                 return FM
@@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P2 = np.polyfit(xslope2, xfilt[islope2], 1)
                 datafit2 = np.polyval(P2, xslope2)
-            except Exception as e:
+            except ValueError as e:
                 emsg = 'fmpicker: polyfit failed: {}'.format(e)
                 print(emsg)
                 return FM

pylot/core/util/utils.py

@@ -333,18 +333,37 @@ def get_bool(value):
     """
     Convert string representations of bools to their true boolean value
     :param value:
-    :type value: str, bool
+    :type value: str, bool, int, float
     :return: true boolean value
     :rtype: bool
+
+    >>> get_bool(True)
+    True
+    >>> get_bool(False)
+    False
+    >>> get_bool(0)
+    False
+    >>> get_bool(0.)
+    False
+    >>> get_bool(0.1)
+    True
+    >>> get_bool(2)
+    True
+    >>> get_bool(-1)
+    False
+    >>> get_bool(-0.3)
+    False
     """
-    if type(value) is bool:
+    if type(value) == bool:
         return value
     elif value in ['True', 'true']:
         return True
     elif value in ['False', 'false']:
         return False
+    elif value > 0. or value > 0:
+        return True
     else:
-        return bool(value)
+        return False
 
 def four_digits(year):
     """
@@ -355,8 +374,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
+    >>> four_digits(75)
-    1920
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -513,6 +532,11 @@ def is_executable(fn):
     :param fn: path to the file to be tested
     :return: True or False
     :rtype: bool
+
+    >>> is_executable('/bin/ls')
+    True
+    >>> is_executable('/var/log/system.log')
+    False
     """
     return os.path.isfile(fn) and os.access(fn, os.X_OK)
 
@@ -619,13 +643,13 @@ def find_horizontals(data):
     :param data: waveform data
     :type data: `obspy.core.stream.Stream`
     :return: components list
-    :rtype: list
+    :rtype: List(str)
 
     ..example::
 
     >>> st = read()
     >>> find_horizontals(st)
-    [u'N', u'E']
+    ['N', 'E']
     """
     rval = []
     for tr in data:
@@ -819,6 +843,19 @@ def trim_station_components(data, trim_start=True, trim_end=True):
     return data
 
 
+def merge_stream(stream):
+    gaps = stream.get_gaps()
+    if gaps:
+        # list of merged stations (seed_ids)
+        merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
+        stream.merge(method=1)
+        print('Merged the following stations because of gaps:')
+        for merged_station in merged:
+            print(merged_station)
+
+    return stream, gaps
+
+
 def check4gapsAndRemove(data):
     """
     check for gaps in Stream and remove them
@@ -839,12 +876,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check_for_gaps_and_merge(data):
+def check4gapsAndMerge(data):
     """
     check for gaps in Stream and merge if gaps are found
     :param data: stream of seismic data
     :type data: `~obspy.core.stream.Stream`
-    :return: data stream, gaps returned from obspy get_gaps
+    :return: data stream
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -855,7 +892,7 @@ def check_for_gaps_and_merge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data, gaps
+    return data
 
 
 def check4doubled(data):
@@ -927,11 +964,11 @@ def get_possible_pylot_eventfile_extensions(event, fext):
 
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -987,7 +1024,7 @@ def check4rotated(data, metadata=None, verbosity=1):
         if len(wfs_in) < 3:
             print(f"Stream {wfs_in=}, has not enough components to rotate.")
             return wfs_in
-        
+
         # check if any traces in this station need to be rotated
         trace_ids = [trace.id for trace in wfs_in]
         if not rotation_required(trace_ids):
@@ -1155,7 +1192,6 @@ def identifyPhase(phase):
         return False
 
 
-@lru_cache
 def identifyPhaseID(phase):
     """
     Returns phase id (capital P or S)

pylot/core/util/widgets.py

@@ -897,8 +897,6 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
-        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
-
         # list containing tuples of network, station, channel (for sorting)
         nslc = []
         for trace in st_select:
@@ -5788,10 +5786,7 @@ class ChooseWaveFormWindow(QWidget):
     def submit(self):
         matplotlib.pyplot.close(self.currentSpectro)
         t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        #self.currentSpectro = self.traces[
+        self.applyFFT()
-        #    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']
@@ -5886,21 +5881,6 @@ class SpectrogramTab(QWidget):
                           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
 
@@ -5909,24 +5889,8 @@ class SpectrogramTab(QWidget):
         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()