Merge pull request #2021 from obspy/patch-nordic-amps

nordic: Bug-fix amplitude and wavefile write

CHANGELOG.txt

@@ -17,6 +17,9 @@
      (see #1981, #2057).
    * Fix util.get_start_and_end_time returning sample rate = 0 when
      sample rate = 1 (see #2069)
+ - obspy.io.nordic
+   * Bug-fix for amplitudes without magnitude_hint (see #2021)
+   * Bug-fix for wavefiles with full path stripping (see #2021)
  - obspy.io.reftek:
    * Fix problems reading some Reftek 130 files, presumably due to floating
      point accuracy issues in comparing timestamps. Internal representation of
@@ -35,7 +38,6 @@
      npz file that was written with a newer version of the npz representation
      than is used by current ObsPy version (see #2051)
 
-
 1.1.0: (doi: 10.5281/zenodo.165135)
  - General:
    * Read support for Guralp Compressed Format (GCF) waveform data,

obspy/io/nordic/core.py

@@ -957,7 +957,7 @@ def _write_nordic(event, filename, userid='OBSP', evtype='L', outdir='.',
     # Write line 3 of s-file
     for wavefile in wavefiles:
         sfile.write(' ' + os.path.basename(wavefile) +
-                    '6'.rjust(79 - len(wavefile)) + '\n')
+                    '6'.rjust(79 - len(os.path.basename(wavefile))) + '\n')
     # Write final line of s-file
     sfile.write(' STAT SP IPHASW D HRMM SECON CODA AMPLIT PERI AZIMU' +
                 ' VELO AIN AR TRES W  DIS CAZ7\n')
@@ -1109,7 +1109,8 @@ def nordpick(event):
                 else:
                     amp = None
                 coda = ' '
-                if amplitude.magnitude_hint.upper() == 'ML':
+                mag_hint = (amplitude.magnitude_hint or amplitude.type)
+                if mag_hint is not None and mag_hint.upper() in ['AML', 'ML']:
                     phase_hint = 'IAML'
                     impulsivity = ' '
             else:

obspy/io/nordic/tests/test_nordic.py

@@ -105,6 +105,10 @@ def test_read_write(self):
                          test_ev.amplitudes[0].period)
         self.assertEqual(read_ev.amplitudes[0].snr,
                          test_ev.amplitudes[0].snr)
+        self.assertEqual(read_ev.amplitudes[2].period,
+                         test_ev.amplitudes[2].period)
+        self.assertEqual(read_ev.amplitudes[2].snr,
+                         test_ev.amplitudes[2].snr)
         # Check coda magnitude pick
         # Resource ids get overwritten because you can't have two the same in
         # memory
@@ -385,6 +389,25 @@ def test_read_wavename(self):
         testing_path = os.path.join(self.testing_path, '01-0411-15L.S201309')
         wavefiles = readwavename(testing_path)
         self.assertEqual(len(wavefiles), 1)
+        # Test that full paths are handled
+        test_event = full_test_event()
+        # Add the event to a catalogue which can be used for QuakeML testing
+        test_cat = Catalog()
+        test_cat += test_event
+        # Check the read-write s-file functionality
+        with TemporaryWorkingDirectory():
+            sfile = _write_nordic(
+                test_cat[0], filename=None, userid='TEST', evtype='L',
+                outdir='.', wavefiles=['walrus/test'], explosion=True,
+                overwrite=True)
+            self.assertEqual(readwavename(sfile), ['test'])
+        # Check that multiple wavefiles are read properly
+        with TemporaryWorkingDirectory():
+            sfile = _write_nordic(
+                test_cat[0], filename=None, userid='TEST', evtype='L',
+                outdir='.', wavefiles=['walrus/test', 'albert'],
+                explosion=True, overwrite=True)
+            self.assertEqual(readwavename(sfile), ['test', 'albert'])
 
     def test_read_event(self):
         """
@@ -641,11 +664,14 @@ def _test_similarity(event_1, event_2, verbose=False):
     for amp_1, amp_2 in zip(event_1.amplitudes, event_2.amplitudes):
         # Assuming same ordering of amplitudes
         for key in amp_1.keys():
-            if key not in ["resource_id", "pick_id", "waveform_id", "snr"]:
+            if key not in ["resource_id", "pick_id", "waveform_id", "snr",
+                           "magnitude_hint", 'type']:
                 if not amp_1[key] == amp_2[key]:
                     if verbose:
                         print('%s is not the same as %s for key %s' %
                               (amp_1[key], amp_2[key], key))
+                        print(amp_1)
+                        print(amp_2)
                     return False
             elif key == "waveform_id":
                 if pick_1[key].station_code != pick_2[key].station_code:
@@ -661,6 +687,15 @@ def _test_similarity(event_1, event_2, verbose=False):
                     if verbose:
                         print('Channel codes do not match')
                     return False
+            elif key in ["magnitude_hint", "type"]:
+                # Reading back in will define both, but input event might have
+                # None
+                if amp_1[key] is not None:
+                    if not amp_1[key] == amp_2[key]:
+                        if verbose:
+                            print('%s is not the same as %s for key %s' %
+                                  (amp_1[key], amp_2[key], key))
+                        return False
     return True
 
 
@@ -699,52 +734,49 @@ def full_test_event():
                                       network_code='NZ')
     _waveform_id_2 = WaveformStreamID(station_code='WTSZ', channel_code='BH1',
                                       network_code=' ')
-    # Pick to associate with amplitude
-    test_event.picks.append(
+    # Pick to associate with amplitude - 0
+    test_event.picks = [
         Pick(waveform_id=_waveform_id_1, phase_hint='IAML',
              polarity='undecidable', time=UTCDateTime("2012-03-26") + 1.68,
-             evaluation_mode="manual"))
-    # Need a second pick for coda
-    test_event.picks.append(
+             evaluation_mode="manual"),
         Pick(waveform_id=_waveform_id_1, onset='impulsive', phase_hint='PN',
              polarity='positive', time=UTCDateTime("2012-03-26") + 1.68,
-             evaluation_mode="manual"))
-    # Unassociated pick
-    test_event.picks.append(
+             evaluation_mode="manual"),
+        Pick(waveform_id=_waveform_id_1, phase_hint='IAML',
+             polarity='undecidable', time=UTCDateTime("2012-03-26") + 1.68,
+             evaluation_mode="manual"),
         Pick(waveform_id=_waveform_id_2, onset='impulsive', phase_hint='SG',
              polarity='undecidable', time=UTCDateTime("2012-03-26") + 1.72,
-             evaluation_mode="manual"))
-    # Unassociated pick
-    test_event.picks.append(
+             evaluation_mode="manual"),
         Pick(waveform_id=_waveform_id_2, onset='impulsive', phase_hint='PN',
              polarity='undecidable', time=UTCDateTime("2012-03-26") + 1.62,
-             evaluation_mode="automatic"))
+             evaluation_mode="automatic")]
     # Test a generic local magnitude amplitude pick
-    test_event.amplitudes.append(
+    test_event.amplitudes = [
         Amplitude(generic_amplitude=2.0, period=0.4,
                   pick_id=test_event.picks[0].resource_id,
                   waveform_id=test_event.picks[0].waveform_id, unit='m',
-                  magnitude_hint='ML', category='point', type='AML'))
-    # Test a coda magnitude pick
-    test_event.amplitudes.append(
+                  magnitude_hint='ML', category='point', type='AML'),
         Amplitude(generic_amplitude=10,
                   pick_id=test_event.picks[1].resource_id,
                   waveform_id=test_event.picks[1].waveform_id, type='END',
                   category='duration', unit='s', magnitude_hint='Mc',
-                  snr=2.3))
-    test_event.origins[0].arrivals.append(
+                  snr=2.3),
+        Amplitude(generic_amplitude=5.0, period=0.6,
+                  pick_id=test_event.picks[2].resource_id,
+                  waveform_id=test_event.picks[0].waveform_id, unit='m',
+                  category='point', type='AML')]
+    test_event.origins[0].arrivals = [
         Arrival(time_weight=0, phase=test_event.picks[1].phase_hint,
-                pick_id=test_event.picks[1].resource_id))
-    test_event.origins[0].arrivals.append(
-        Arrival(time_weight=2, phase=test_event.picks[2].phase_hint,
-                pick_id=test_event.picks[2].resource_id,
-                backazimuth_residual=5, time_residual=0.2, distance=15,
-                azimuth=25))
-    test_event.origins[0].arrivals.append(
+                pick_id=test_event.picks[1].resource_id),
         Arrival(time_weight=2, phase=test_event.picks[3].phase_hint,
                 pick_id=test_event.picks[3].resource_id,
                 backazimuth_residual=5, time_residual=0.2, distance=15,
-                azimuth=25))
+                azimuth=25),
+        Arrival(time_weight=2, phase=test_event.picks[4].phase_hint,
+                pick_id=test_event.picks[4].resource_id,
+                backazimuth_residual=5, time_residual=0.2, distance=15,
+                azimuth=25)]
     return test_event