Types from header

doc/source/authors.rst

@@ -52,6 +52,7 @@ and may not be the current affiliation of a contributor.
 * rishidhingra@github
 * Hugo van Kemenade
 * Aitor Morales-Gregorio [13]
+* Peter N Steinmetz [22]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -74,6 +75,7 @@ and may not be the current affiliation of a contributor.
 19. IAL Developmental Neurobiology, Kazan Federal University, Kazan, Russia
 20. Harden Technologies, LLC
 21. Institut des Neurosciences Paris-Saclay, CNRS UMR 9197 - Université Paris-Sud, Gif-sur-Yvette, France
+22. Neurtex Brain Research Institute, Dallas, TX, USAs
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

neo/rawio/neuralynxrawio.py

@@ -108,7 +108,7 @@ def _parse_header(self):
                 continue
 
             # All file have more or less the same header structure
-            info = NlxHeader.buildForFile(filename)
+            info = NlxHeader.build_for_file(filename)
             chan_names = info['channel_names']
             chan_ids = info['channel_ids']
 
@@ -227,7 +227,7 @@ def _parse_header(self):
         self._timestamp_limits = None
         self._nb_segment = 1
 
-        # Read ncs files for gaps detection and nb_segment computation.
+        # Read ncs files for gap detection and nb_segment computation.
         # :TODO: current algorithm depends on side-effect of read_ncs_files on
         #   self._sigs_memmap, self._sigs_t_start, self._sigs_t_stop,
         #   self._sigs_length, self._nb_segment, self._timestamp_limits
@@ -661,6 +661,7 @@ def _to_bool(txt):
         ('ApplicationName', '', None),  # also include version number when present
         ('AcquisitionSystem', '', None),
         ('ReferenceChannel', '', None),
+        ('NLX_Base_Class_Type', '', None)  # in version 4 and earlier versions of Cheetah
     ]
 
     # Filename and datetime may appear in header lines starting with # at
@@ -694,7 +695,7 @@ def _to_bool(txt):
             datetimeformat='%Y/%m/%d %H:%M:%S')
     }
 
-    def buildForFile(filename):
+    def build_for_file(filename):
         """
         Factory function to build NlxHeader for a given file.
         """
@@ -809,6 +810,48 @@ def buildForFile(filename):
 
         return info
 
+    def type_of_recording(self):
+        """
+        Determines type of recording in Ncs file with this header.
+
+        RETURN:
+            one of 'PRE4','BML','DIGITALLYNX','DIGITALLYNXSX','UNKNOWN'
+        """
+
+        if 'NLX_Base_Class_Type' in self:
+
+            # older style standard neuralynx acquisition with rounded sampling frequency
+            if self['NLX_Base_Class_Type'] == 'CscAcqEnt':
+                return 'PRE4'
+
+            # BML style with fractional frequency and microsPerSamp
+            elif self['NLX_Base_Class_Type'] == 'BmlAcq':
+                return 'BML'
+
+            else:
+                return 'UNKNOWN'
+
+        elif 'HardwareSubSystemType' in self:
+
+            # DigitalLynx
+            if self['HardwareSubSystemType'] == 'DigitalLynx':
+                return 'DIGITALLYNX'
+
+            # DigitalLynxSX
+            elif self['HardwareSubSystemType'] == 'DigitalLynxSX':
+                return 'DIGITALLYNXSX'
+
+        elif 'FileType' in self:
+
+            if self['FileVersion'] in ['3.3', '3.4']:
+                return self['AcquisitionSystem'].split()[1].upper()
+
+            else:
+                return 'UNKNOWN'
+
+        else:
+            return 'UNKNOWN'
+
 
 class NcsHeader():
     """

neo/test/iotest/test_neuralynxio.py

@@ -22,12 +22,14 @@
 class CommonNeuralynxIOTest(BaseTestIO, unittest.TestCase, ):
     ioclass = NeuralynxIO
     files_to_test = [
+        # 'Cheetah_v4.0.2/original_data',
         'Cheetah_v5.5.1/original_data',
         'Cheetah_v5.6.3/original_data',
         'Cheetah_v5.7.4/original_data',
         'Pegasus_v2.1.1',
         'Cheetah_v6.3.2/incomplete_blocks']
     files_to_download = [
+        'Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs',
         'Cheetah_v5.5.1/original_data/CheetahLogFile.txt',
         'Cheetah_v5.5.1/original_data/CheetahLostADRecords.txt',
         'Cheetah_v5.5.1/original_data/Events.nev',

neo/test/rawiotest/test_neuralynxrawio.py

@@ -2,6 +2,7 @@
 
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
+from neo.rawio.neuralynxrawio import NlxHeader
 
 import logging
 
@@ -11,12 +12,13 @@
 class TestNeuralynxRawIO(BaseTestRawIO, unittest.TestCase, ):
     rawioclass = NeuralynxRawIO
     entities_to_test = [
+        # 'Cheetah_v4.0.2/original_data',
         'Cheetah_v5.5.1/original_data',
         'Cheetah_v5.6.3/original_data',
         'Cheetah_v5.7.4/original_data',
-        'Cheetah_v6.3.2/incomplete_blocks'
-    ]
+        'Cheetah_v6.3.2/incomplete_blocks']
     files_to_download = [
+        'Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs',
         'Cheetah_v5.5.1/original_data/CheetahLogFile.txt',
         'Cheetah_v5.5.1/original_data/CheetahLostADRecords.txt',
         'Cheetah_v5.5.1/original_data/Events.nev',
@@ -61,5 +63,28 @@ class TestNeuralynxRawIO(BaseTestRawIO, unittest.TestCase, ):
         'Cheetah_v6.3.2/incomplete_blocks/README.txt']
 
 
+class TestNcsRecordingType(TestNeuralynxRawIO, unittest.TestCase):
+    """
+    Test of decoding of NlxHeader for type of recording.
+    """
+
+    ncsTypeTestFiles = [
+        ('Cheetah_v4.0.2/original_data/CSC14_trunc.Ncs', 'PRE4'),
+        ('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'),
+        ('Cheetah_v5.6.3/original_data/TT1.ntt', 'DIGITALLYNXSX'),
+        ('Cheetah_v5.7.4/original_data/CSC1.ncs', 'DIGITALLYNXSX'),
+        ('Cheetah_v6.3.2/incomplete_blocks/CSC1_reduced.ncs', 'DIGITALLYNXSX')]
+
+    def test_recording_types(self):
+
+        for typeTest in self.ncsTypeTestFiles:
+
+            filename = self.get_filename_path(typeTest[0])
+            hdr = NlxHeader.build_for_file(filename)
+            self.assertEqual(hdr.type_of_recording(), typeTest[1])
+
+
 if __name__ == "__main__":
     unittest.main()