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Fix neuralynx channel ids and names and add ATLAS acq type #1107

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Merged
samuelgarcia merged 3 commits into from
Mar 31, 2022
Merged

Fix neuralynx channel ids and names and add ATLAS acq type #1107

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80f4bc1
[neuralynx] fix channel id and name detection from header
Mar 24, 2022
fd7bf28
[neuralynx] add ATLAS acquisition type
Mar 24, 2022
1093e08
[neuralynx] add support for 'Cheetah64' subsystem
Mar 28, 2022
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6 changes: 3 additions & 3 deletions neo/rawio/neuralynxrawio/ncssections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
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11 changes: 9 additions & 2 deletions neo/rawio/neuralynxrawio/nlxheader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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']), \
Expand Down Expand Up @@ -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']:
Expand Down