Merge pull request #1107 from JuliaSprenger/fix/neuralynx_header

Fix neuralynx channel ids and names and add ATLAS acq type

Author: samuelgarcia

neo/rawio/neuralynxrawio/ncssections.py

@@ -411,12 +411,12 @@ 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":
+        elif acqType == "DIGITALLYNX" or acqType == "DIGITALLYNXSX" or acqType == 'CHEETAH64':
             nomFreq = nlxHdr['sampling_rate']
             nb = NcsSectionsFactory._buildForMaxGap(ncsMemMap, nomFreq)
 
-        # BML style with fractional frequency and micros per samp
-        elif acqType == "BML":
+        # BML & ATLAS style with fractional frequency and micros per samp
+        elif acqType == "BML" or acqType == "ATLAS":
             sampFreqUsed = nlxHdr['sampling_rate']
             nb = NcsSectionsFactory._buildGivenActualFrequency(ncsMemMap, sampFreqUsed,
                                                                math.floor(sampFreqUsed))

neo/rawio/neuralynxrawio/nlxheader.py

@@ -152,14 +152,14 @@ def __init__(self, filename):
 
         # convert channel ids
         if 'channel_ids' in self:
-            chid_entries = re.findall(r'\w+', self['channel_ids'])
+            chid_entries = re.findall(r'\S+', self['channel_ids'])
             self['channel_ids'] = [int(c) for c in chid_entries]
         else:
             self['channel_ids'] = ['unknown']
 
         # convert channel names
         if 'channel_names' in self:
-            name_entries = re.findall(r'\w+', self['channel_names'])
+            name_entries = re.findall(r'\S+', self['channel_names'])
             if len(name_entries) == 1:
                 self['channel_names'] = name_entries * len(self['channel_ids'])
             assert len(self['channel_names']) == len(self['channel_ids']), \
@@ -288,6 +288,13 @@ def type_of_recording(self):
             elif self['HardwareSubSystemType'] == 'DigitalLynxSX':
                 return 'DIGITALLYNXSX'
 
+            # Cheetah64
+            elif self['HardwareSubSystemType'] == 'Cheetah64':
+                return 'CHEETAH64'
+
+            else:
+                return 'UNKNOWN'
+
         elif 'FileType' in self:
 
             if self['FileVersion'] in ['3.3', '3.4']: