Merge 0e316ab into 23e0208

CHANGELOG.txt

@@ -1,6 +1,7 @@
 1.0.3:
  - obspy.io.mseed:
    * ObsPy can now also read (Mini)SEED files with noise records. (see #1495)
+   * ObsPy can now read records with a data-offset of zero. (see #1509)
  - obspy.io.sac:
    * `SACTrace.lpspol` and `lcalda` are `True` and `False` by default, when
       created via `SACTrace.from_obspy_trace` with a `Trace` that has no SAC

obspy/io/mseed/scripts/recordanalyzer.py

@@ -217,7 +217,8 @@ def _get_blockettes(self):
         cur_blkt_offset = self.fixed_header['First blockette']
         # Loop until the beginning of the data is reached.
         while True:
-            if cur_blkt_offset >= self.fixed_header['Beginning of data']:
+            if len(self.blockettes) == \
+                    self.fixed_header["Number of blockettes that follow"]:
                 break
             # Seek to the offset.
             self.file.seek(self.record_offset + cur_blkt_offset, 0)

obspy/io/mseed/src/obspy-readbuffer.c

@@ -416,8 +416,11 @@ readMSEEDBuffer (char *mseed, int buflen, Selections *selections, flag
             }
         }
 
-        // Actually unpack the data if the flag is not set.
-        if (unpack_data != 0) {
+        // Actually unpack the data if the flag is not set and if the data
+        // offset is valid.
+        if ((unpack_data != 0) && (msr->fsdh->data_offset > 48) &&
+            (msr->fsdh->data_offset < msr->reclen) &&
+            (msr->samplecnt > 0)) {
             retval = msr_unpack_data (msr, swapflag, verbose);
         }
 

obspy/io/mseed/tests/test_mseed_special_issues.py

@@ -815,6 +815,59 @@ def test_read_file_with_various_noise_records(self):
         np.testing.assert_allclose(st[0].data, st[2].data)
         np.testing.assert_allclose(st[0].data, st[3].data)
 
+    def test_mseed_zero_data_offset(self):
+        """
+        Tests that a data offset of zero in the fixed header does not
+        confuse ObsPy.
+
+        The file contains three records: a normal one, followed by one with
+        a data-offset of zero, followed by another normal one.
+
+        This currently results in three returned traces:
+
+        * CH.PANIX..LHZ |
+          2016-08-21T01:41:19.000000Z - 2016-08-21T01:45:30.000000Z |
+          1.0 Hz, 252 samples
+        * CH.PANIX..LHZ |
+          2016-08-21T01:43:37.000000Z - 2016-08-21T01:43:37.000000Z |
+          1.0 Hz, 0 samples
+        * CH.PANIX..LHZ |
+          2016-08-21T01:45:31.000000Z - 2016-08-21T01:49:52.000000Z |
+          1.0 Hz, 262 samples
+        """
+        file = os.path.join(self.path, "data", "bizarre",
+                            "mseed_data_offset_0.mseed")
+        st = read(file)
+
+        self.assertEqual(len(st), 3)
+
+        tr = st[0]
+        self.assertEqual(tr.id, "CH.PANIX..LHZ")
+        self.assertEqual(tr.stats.starttime,
+                         UTCDateTime("2016-08-21T01:41:19.000000Z"))
+        self.assertEqual(tr.stats.endtime,
+                         UTCDateTime("2016-08-21T01:45:30.000000Z"))
+        self.assertEqual(tr.stats.npts, len(tr.data))
+        self.assertEqual(tr.stats.npts, 252)
+
+        tr = st[1]
+        self.assertEqual(tr.id, "CH.PANIX..LHZ")
+        self.assertEqual(tr.stats.starttime,
+                         UTCDateTime("2016-08-21T01:43:37.000000Z"))
+        self.assertEqual(tr.stats.endtime,
+                         UTCDateTime("2016-08-21T01:43:37.000000Z"))
+        self.assertEqual(tr.stats.npts, len(tr.data))
+        self.assertEqual(tr.stats.npts, 0)
+
+        tr = st[2]
+        self.assertEqual(tr.id, "CH.PANIX..LHZ")
+        self.assertEqual(tr.stats.starttime,
+                         UTCDateTime("2016-08-21T01:45:31.000000Z"))
+        self.assertEqual(tr.stats.endtime,
+                         UTCDateTime("2016-08-21T01:49:52.000000Z"))
+        self.assertEqual(tr.stats.npts, len(tr.data))
+        self.assertEqual(tr.stats.npts, 262)
+
 
 def suite():
     return unittest.makeSuite(MSEEDSpecialIssueTestCase, 'test')

obspy/io/mseed/tests/test_recordanalyzer.py

@@ -103,6 +103,96 @@ def test_second_record(self):
         self.assertEqual(expected.encode('utf-8'),
                          out.stdout)
 
+    def test_record_with_data_offset_zero(self):
+        """
+        The test file has a middle record which has data offset zero. Make
+        sure it can be read, as well as the following record.
+        """
+        filename = os.path.join(os.path.dirname(__file__), 'data', 'bizarre',
+                                'mseed_data_offset_0.mseed')
+
+        with CatchOutput() as out:
+            obspy_recordanalyzer(['-n', '1', filename])
+
+        expected = '''FILE: %s
+Record Number: 1
+Record Offset: 512 byte
+Header Endianness: Big Endian
+
+FIXED SECTION OF DATA HEADER
+	Sequence number: 1
+	Data header/quality indicator: D
+	Station identifier code: PANIX
+	Location identifier: 
+	Channel identifier: LHZ
+	Network code: CH
+	Record start time: 2016-08-21T01:43:37.000000Z
+	Number of samples: 0
+	Sample rate factor: 1
+	Sample rate multiplier: 1
+	Activity flags: 4
+	I/O and clock flags: 0
+	Data quality flags: 0
+	Number of blockettes that follow: 2
+	Time correction: 0
+	Beginning of data: 0
+	First blockette: 48
+
+BLOCKETTES
+	1000:	Encoding Format: 11
+		Word Order: 1
+		Data Record Length: 9
+	201:	NOT YET IMPLEMENTED
+
+CALCULATED VALUES
+	Corrected Starttime: 2016-08-21T01:43:37.000000Z
+
+''' % (filename,)  # noqa
+        self.assertEqual(expected.encode('utf-8'),
+                         out.stdout)
+
+        with CatchOutput() as out:
+            obspy_recordanalyzer(['-n', '2', filename])
+
+        expected = '''FILE: %s
+Record Number: 2
+Record Offset: 1024 byte
+Header Endianness: Big Endian
+
+FIXED SECTION OF DATA HEADER
+	Sequence number: 189
+	Data header/quality indicator: D
+	Station identifier code: PANIX
+	Location identifier: 
+	Channel identifier: LHZ
+	Network code: CH
+	Record start time: 2016-08-21T01:45:31.000000Z
+	Number of samples: 262
+	Sample rate factor: 1
+	Sample rate multiplier: 1
+	Activity flags: 68
+	I/O and clock flags: 32
+	Data quality flags: 0
+	Number of blockettes that follow: 2
+	Time correction: 0
+	Beginning of data: 64
+	First blockette: 48
+
+BLOCKETTES
+	1000:	Encoding Format: 11
+		Word Order: 1
+		Data Record Length: 9
+	1001:	Timing quality: 100
+		mu_sec: 0
+		Frame count: 7
+
+CALCULATED VALUES
+	Corrected Starttime: 2016-08-21T01:45:31.000000Z
+
+''' % (filename,)  # noqa
+        self.assertEqual(expected.encode('utf-8'),
+                         out.stdout)
+
 
 def suite():
     return unittest.makeSuite(RecordAnalyserTestCase, 'test')