Merge pull request #1257 from PeterNSteinmetz/CheetahV5.6.0FixesOnly

After discussion among the maintainers we decided to merge this, but we should look at this again to check if the values are available in the info dictionary.

neo/rawio/neuralynxrawio/ncssections.py

@@ -438,7 +438,7 @@ def build_for_ncs_file(ncsMemMap, nlxHdr):
 
         # digital lynx style with fractional frequency and micros per samp determined from
         # block times
-        elif acqType == "DIGITALLYNX" or acqType == "DIGITALLYNXSX" or acqType == 'CHEETAH64' or acqType == 'RAWDATAFILE':
+        elif acqType in ["DIGITALLYNX", "DIGITALLYNXSX", 'CHEETAH64', 'CHEETAH560', 'RAWDATAFILE']:
             nomFreq = nlxHdr['sampling_rate']
             nb = NcsSectionsFactory._buildForMaxGap(ncsMemMap, nomFreq)
 

neo/rawio/neuralynxrawio/neuralynxrawio.py

@@ -850,20 +850,21 @@ def get_nse_or_ntt_dtype(info, ext):
     """
     dtype = [('timestamp', 'uint64'), ('channel_id', 'uint32'), ('unit_id', 'uint32')]
 
-    # count feature
-    nb_feature = 0
-    for k in info.keys():
-        if k.startswith('Feature '):
-            nb_feature += 1
+    # for purpose of dtypes, features in the file are always fixed 8 presently,
+    # whether mentioned in the header or not. Features may not be listed in the header
+    # if no feature names are assigned in Neuralynx software.
+    nb_feature = 8
     dtype += [('features', 'int32', (nb_feature,))]
 
-    # count sample
+    # Number of samples are fixed in the file at 32 for .nse 32 * 4 for .ntt.
+    # WaveformLength may or may not be listed in the file depending on settings
+    # in the Neuralynx software, so don't try retrieving it.
     if ext == 'nse':
-        nb_sample = info['WaveformLength']
+        nb_sample = 32
         dtype += [('samples', 'int16', (nb_sample,))]
     elif ext == 'ntt':
-        nb_sample = info['WaveformLength']
-        nb_chan = 4  # check this if not tetrode
+        nb_sample = 32
+        nb_chan = 4
         dtype += [('samples', 'int16', (nb_sample, nb_chan))]
 
     return dtype

neo/rawio/neuralynxrawio/nlxheader.py

@@ -97,6 +97,12 @@ 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 5.6.0, some range of versions in between
+        'v5.6.0': dict(
+            datetime1_regex=r'## Time Opened: \(m/d/y\): (?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+)'
@@ -223,6 +229,8 @@ def __init__(self, filename):
                 hpd = NlxHeader.header_pattern_dicts['bv5']
             elif av <= Version('5.4.0'):
                 hpd = NlxHeader.header_pattern_dicts['v5.4.0']
+            elif av == Version('5.6.0'):
+                hpd = NlxHeader.header_pattern_dicts['v5.6.0']
             elif av <= Version('5.6.4'):
                 hpd = NlxHeader.header_pattern_dicts['bv5.6.4']
             else:
@@ -303,11 +311,11 @@ def type_of_recording(self):
 
         elif 'FileType' in self:
 
-            if self['FileVersion'] in ['3.3', '3.4']:
+            if 'FileVersion' in self and self['FileVersion'] in ['3.3', '3.4']:
                 return self['AcquisitionSystem'].split()[1].upper()
 
             else:
-                return 'UNKNOWN'
+                return 'CHEETAH560' # only known case of FileType without FileVersion
 
         else:
             return 'UNKNOWN'