Fixes for cheetah v5.4.0

neo/rawio/neuralynxrawio/nlxheader.py

@@ -89,6 +89,14 @@ def _to_bool(txt):
                             r'  At Time: (?P<time>\S+)',
             filename_regex=r'## File Name: (?P<filename>\S+)',
             datetimeformat='%m/%d/%Y %H:%M:%S.%f'),
+        # Cheetah version 5.4.0
+        'v5.4.0': dict(
+            datetime1_regex=r'## Time Opened \(m/d/y\): (?P<date>\S+)'
+                            r'  At Time: (?P<time>\S+)',
+            datetime2_regex=r'## Time Closed \(m/d/y\): (?P<date>\S+)'
+                            r'  At Time: (?P<time>\S+)',
+            filename_regex=r'## File Name: (?P<filename>\S+)',
+            datetimeformat='%m/%d/%Y %H:%M:%S.%f'),
         # Cheetah version 5 before and including v 5.6.4 as well as version 1
         'bv5.6.4': dict(
             datetime1_regex=r'## Time Opened \(m/d/y\): (?P<date>\S+)'
@@ -199,25 +207,40 @@ def __init__(self, filename):
                 hpd = NlxHeader.header_pattern_dicts['bv5.6.4']
             elif av < '5':
                 hpd = NlxHeader.header_pattern_dicts['bv5']
+            elif av <= '5.4.0':
+                hpd = NlxHeader.header_pattern_dicts['v5.4.0']
             elif av <= '5.6.4':
                 hpd = NlxHeader.header_pattern_dicts['bv5.6.4']
             else:
                 hpd = NlxHeader.header_pattern_dicts['def']
         elif an == 'BML':
             hpd = NlxHeader.header_pattern_dicts['bml']
+            av = "2"
         else:
+            an = "Unknown"
+            av = "NA"
             hpd = NlxHeader.header_pattern_dicts['def']
 
         # opening time
-        dt1 = re.search(hpd['datetime1_regex'], txt_header).groupdict()
-        self['recording_opened'] = datetime.datetime.strptime(
-            dt1['date'] + ' ' + dt1['time'], hpd['datetimeformat'])
+        sr = re.search(hpd['datetime1_regex'], txt_header)
+        if not sr:
+            raise IOError("No matching header open date/time for application {} " +
+                          "version {}. Please contact developers.".format(an, av))
+        else:
+            dt1 = sr.groupdict()
+            self['recording_opened'] = datetime.datetime.strptime(
+                dt1['date'] + ' ' + dt1['time'], hpd['datetimeformat'])
 
         # close time, if available
         if 'datetime2_regex' in hpd:
-            dt2 = re.search(hpd['datetime2_regex'], txt_header).groupdict()
-            self['recording_closed'] = datetime.datetime.strptime(
-                dt2['date'] + ' ' + dt2['time'], hpd['datetimeformat'])
+            sr = re.search(hpd['datetime2_regex'], txt_header)
+            if not sr:
+                raise IOError("No matching header close date/time for application {} " +
+                              "version {}. Please contact developers.".format(an, av))
+            else:
+                dt2 = sr.groupdict()
+                self['recording_closed'] = datetime.datetime.strptime(
+                    dt2['date'] + ' ' + dt2['time'], hpd['datetimeformat'])
 
     def type_of_recording(self):
         """

neo/test/iotest/test_neuralynxio.py

@@ -26,6 +26,7 @@ class CommonNeuralynxIOTest(BaseTestIO, unittest.TestCase, ):
         'BML_unfilledsplit/original_data',
         'Cheetah_v1.1.0/original_data',
         'Cheetah_v4.0.2/original_data',
+        'Cheetah_v5.4.0/original_data',
         'Cheetah_v5.5.1/original_data',
         'Cheetah_v5.6.3/original_data',
         'Cheetah_v5.7.4/original_data',
@@ -44,6 +45,8 @@ class CommonNeuralynxIOTest(BaseTestIO, unittest.TestCase, ):
         'Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs',
         'Cheetah_v4.0.2/plain_data/CSC14_trunc.txt',
         'Cheetah_v4.0.2/README.txt',
+        'Cheetah_v5.4.0/original_data/CSC5_trunc.Ncs',
+        'Cheetah_v5.4.0/plain_data/CSC5_trunc.txt',
         'Cheetah_v5.5.1/original_data/CheetahLogFile.txt',
         'Cheetah_v5.5.1/original_data/CheetahLostADRecords.txt',
         'Cheetah_v5.5.1/original_data/Events.nev',
@@ -311,7 +314,7 @@ def _load_plaindata(self, filename, numSamps):
             #     np.testing.assert_allclose(plain_data[:numToTest],
             #                                anasig.magnitude[:numToTest, 0] * gain_factor_0,
             #                                rtol=0.01, err_msg=" for file " + filename)
-    @unittest.skip
+    @unittest.skip("nse failing for now as per issue #907")
     def test_keep_original_spike_times(self):
         for session in self.files_to_test:
             dirname = self.get_filename_path(session)
@@ -322,7 +325,7 @@ def test_keep_original_spike_times(self):
                 filename = st.file_origin.replace('original_data', 'plain_data')
                 if '.nse' in st.file_origin:
                     filename = filename.replace('.nse', '.txt')
-                    times_column = 0
+                    times_column = 1
                     plain_data = np.loadtxt(filename)[:, times_column]
                 elif '.ntt' in st.file_origin:
                     filename = filename.replace('.ntt', '.txt')

neo/test/rawiotest/test_neuralynxrawio.py

@@ -19,6 +19,7 @@ class TestNeuralynxRawIO(BaseTestRawIO, unittest.TestCase, ):
         'BML_unfilledsplit/original_data',
         'Cheetah_v1.1.0/original_data',
         'Cheetah_v4.0.2/original_data',
+        'Cheetah_v5.4.0/original_data',
         'Cheetah_v5.5.1/original_data',
         'Cheetah_v5.6.3/original_data',
         'Cheetah_v5.7.4/original_data',
@@ -36,6 +37,8 @@ class TestNeuralynxRawIO(BaseTestRawIO, unittest.TestCase, ):
         'Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs',
         'Cheetah_v4.0.2/plain_data/CSC14_trunc.txt',
         'Cheetah_v4.0.2/README.txt',
+        'Cheetah_v5.4.0/original_data/CSC5_trunc.Ncs',
+        'Cheetah_v5.4.0/plain_data/CSC5_trunc.txt',
         'Cheetah_v5.5.1/original_data/CheetahLogFile.txt',
         'Cheetah_v5.5.1/original_data/CheetahLostADRecords.txt',
         'Cheetah_v5.5.1/original_data/Events.nev',
@@ -79,7 +82,7 @@ class TestNeuralynxRawIO(BaseTestRawIO, unittest.TestCase, ):
         'Cheetah_v6.3.2/incomplete_blocks/Events.nev',
         'Cheetah_v6.3.2/incomplete_blocks/README.txt']
 
-    def test_read_ncs_files_sideeffects(self):
+    def test_scan_ncs_files(self):
 
         # Test BML style of Ncs files, similar to PRE4 but with fractional frequency
         # in the header and fractional microsPerSamp, which is then rounded as appropriate
@@ -124,7 +127,8 @@ def test_read_ncs_files_sideeffects(self):
         # three blocks of records. Gaps are on the order of 60 microseconds or so.
         rawio = NeuralynxRawIO(self.get_filename_path('Cheetah_v6.3.2/incomplete_blocks'))
         rawio.parse_header()
-        # test values here from direct inspection of .ncs file
+        # test values here from direct inspection of .ncs file, except for 3rd block
+        # t_stop, which is extended due to events past the last block of ncs records.
         self.assertEqual(rawio._nb_segment, 3)
         self.assertListEqual(rawio._timestamp_limits, [(8408806811, 8427831990),
                                                        (8427832053, 8487768498),
@@ -143,6 +147,7 @@ class TestNcsRecordingType(TestNeuralynxRawIO, unittest.TestCase):
 
     ncsTypeTestFiles = [
         ('Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs', 'PRE4'),
+        ('Cheetah_v5.4.0/original_data/CSC5_trunc.Ncs', 'DIGITALLYNX'),
         ('Cheetah_v5.5.1/original_data/STet3a.nse', 'DIGITALLYNXSX'),
         ('Cheetah_v5.5.1/original_data/Tet3a.ncs', 'DIGITALLYNXSX'),
         ('Cheetah_v5.6.3/original_data/CSC1.ncs', 'DIGITALLYNXSX'),