TDT read issue when 'StoreName' key is missing from header
Closed this issue · 2 comments
weiglszonja commented
Describe the bug
I'm having issues with reading TDT files (not sure where to check the TDT version, but these files are from 2014), where
'StoreName' key is missing from one of the entries in info:
python-neo/neo/rawio/tdtrawio.py
Line 553 in c96ec93
Here is a snippet how the infos look like for one the problematic files:
[
OrderedDict({'NumPoints': b'32', 'DataFormat': b'0', 'SampleFreq': b'24414.062500'}),
...
OrderedDict({'StoreName': b'Conx', 'HeadName': b'Conx', 'Enabled': b'1', 'CircType': b'5', 'NumChan': b'20', 'StrobeMode': b'0', 'TankEvType': b'33025', 'NumPoints': b'2048', 'DataFormat': b'2', 'SampleFreq': b'24414.062500'}),
...
OrderedDict({'StoreName': b'LFPx', 'HeadName': b'LFPx', 'Enabled': b'1', 'CircType': b'5', 'NumChan': b'4', 'StrobeMode': b'0', 'TankEvType': b'33025', 'NumPoints': b'64', 'DataFormat': b'0', 'SampleFreq': b'1017.252625'})]
]
I'm not sure what signal the first entry should correspond to, the neural signals have the 'Conx' stream name.
Is there a way to fix this?
To Reproduce
I can share one of these files privately.
Additional context
Traceback (most recent call last):
File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/pydevd.py", line 1534, in _exec
pydev_imports.execfile(file, globals, locals) # execute the script
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/Users/weian/catalystneuro/turner-lab-to-nwb/check_datalist.py", line 11, in <module>
stream_names, stream_ids = TdtRecordingExtractor.get_streams(folder_path=problematic_files[0])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/weian/anaconda3/envs/turner_lab_to_nwb_env/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 71, in get_streams
neo_reader = cls.get_neo_io_reader(cls.NeoRawIOClass, **neo_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/weian/anaconda3/envs/turner_lab_to_nwb_env/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 64, in get_neo_io_reader
neo_reader.parse_header()
File "/Users/weian/anaconda3/envs/turner_lab_to_nwb_env/lib/python3.12/site-packages/neo/rawio/baserawio.py", line 179, in parse_header
self._parse_header()
File "/Users/weian/anaconda3/envs/turner_lab_to_nwb_env/lib/python3.12/site-packages/neo/rawio/tdtrawio.py", line 101, in _parse_header
_info_channel_groups = read_tbk(tbk_filename)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/weian/anaconda3/envs/turner_lab_to_nwb_env/lib/python3.12/site-packages/neo/rawio/tdtrawio.py", line 542, in read_tbk
v = np.dtype(dt).type(info[k])
~~~~^^^
KeyError: 'StoreName'alejoe91 commented
Hi @weiglszonja
Would you have time to try to make a PR with a fix? Basically running that line only if StoreName in info
weiglszonja commented