Merge pull request #1005 from JuliaSprenger/add/neuraview

[neuralynx] add support for neuraview file header

Author: samuelgarcia

neo/rawio/neuralynxrawio/nlxheader.py

@@ -105,6 +105,13 @@ def _to_bool(txt):
                             r'  \(h:m:s\.ms\) (?P<time>\S+)',
             filename_regex=r'## File Name (?P<filename>\S+)',
             datetimeformat='%m/%d/%Y %H:%M:%S.%f'),
+        'neuraview2': dict(
+            datetime1_regex=r'## Date Opened: \(mm/dd/yyy\): (?P<date>\S+)'
+                            r' At Time: (?P<time>\S+)',
+            datetime2_regex=r'## Date Closed: \(mm/dd/yyy\): (?P<date>\S+)'
+                            r' At Time: (?P<time>\S+)',
+            filename_regex=r'## File Name: (?P<filename>\S+)',
+            datetimeformat='%m/%d/%Y %H:%M:%S'),
         # Cheetah after v 5.6.4 and default for others such as Pegasus
         'def': dict(
             datetime1_regex=r'-TimeCreated (?P<date>\S+) (?P<time>\S+)',
@@ -148,7 +155,7 @@ def __init__(self, filename):
             chid_entries = re.findall(r'\w+', self['channel_ids'])
             self['channel_ids'] = [int(c) for c in chid_entries]
         else:
-            self['channel_ids'] = [name]
+            self['channel_ids'] = ['unknown']
 
         # convert channel names
         if 'channel_names' in self:
@@ -158,7 +165,7 @@ def __init__(self, filename):
             assert len(self['channel_names']) == len(self['channel_ids']), \
                 'Number of channel ids does not match channel names.'
         else:
-            self['channel_names'] = [name] * len(self['channel_ids'])
+            self['channel_names'] = ['unknown'] * len(self['channel_ids'])
 
         # version and application name
         # older Cheetah versions with CheetahRev property
@@ -172,10 +179,15 @@ def __init__(self, filename):
             match = re.findall(pattern, self['ApplicationName'])
             assert len(match) == 1, 'impossible to find application name and version'
             self['ApplicationName'], app_version = match[0]
-        # BML Ncs file writing contained neither property, assume BML version 2
-        else:
+        # BML Ncs file contain neither property, but 'NLX_Base_Class_Type'
+        elif 'NLX_Base_Class_Type' in txt_header:
             self['ApplicationName'] = 'BML'
             app_version = "2.0"
+        # Neuraview Ncs file contained neither property nor
+        # NLX_Base_Class_Type information
+        else:
+            self['ApplicationName'] = 'Neuraview'
+            app_version = '2'
 
         self['ApplicationVersion'] = distutils.version.LooseVersion(app_version)
 
@@ -216,6 +228,9 @@ def __init__(self, filename):
         elif an == 'BML':
             hpd = NlxHeader.header_pattern_dicts['bml']
             av = "2"
+        elif an == 'Neuraview':
+            hpd = NlxHeader.header_pattern_dicts['neuraview2']
+            av = "2"
         else:
             an = "Unknown"
             av = "NA"

neo/test/iotest/test_neuralynxio.py

@@ -23,6 +23,19 @@ class CommonNeuralynxIOTest(BaseTestIO, unittest.TestCase, ):
     entities_to_download = TestNeuralynxRawIO.entities_to_download
     entities_to_test = TestNeuralynxRawIO.entities_to_test
 
+
+class TestCheetah_Neuraview(CommonNeuralynxIOTest, unittest.TestCase):
+    files_to_test = []
+
+    def test_read_block(self):
+        dirname = self.get_local_path('neuralynx/Neuraview_v2/original_data')
+        nio = NeuralynxIO(dirname=dirname, use_cache=False)
+        bl = nio.read_block()
+
+        # This dataset contains two event sets
+        self.assertEqual(len(bl.segments[0].events), 2)
+
+
 class TestCheetah_v551(CommonNeuralynxIOTest, unittest.TestCase):
     cheetah_version = '5.5.1'
     files_to_test = []