NotImplementedError: This meta file version of spikeglxis not implemented spikinterface 0.98.1

[gmaggi]

Hi,

One of the users of spikeinterface has a single recording which is in a directory together to its metafile.. Te full content of the dir is: sh0br80bvd_g0_tcat.imec0.ap.bin sh0br80bvd_g0_tcat.imec0.ap.meta sh0br80bvd_g0_tcat.imec0.lf.bin sh0br80bvd_g0_tcat.imec0.lf.meta

we are running se.read_spikeglx( DIRPATH , stream_id = 'imec0.ap')
and we get (last part of the error)

File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/spikeglxrawio.py", line 406, in extract_stream_info raise NotImplementedError('This meta file version of spikeglx' NotImplementedError: This meta file version of spikeglxis not implemented

any idea what is the issue could be?

thanks!

[alejoe91]

Can you share the .meta file?

[gmaggi]

I just sent it to your gmail. Sorry if this is not the right way of sharing it

[alejoe91]

Thanks! It works on my side! What version of neo are you using? Can you pip install -U neo to be sure?

[gmaggi]

python -c "import neo; print(neo.__version__)" 0.12.0 that is the current one, do I still need to update?

…

On Aug 31, 2023, at 1:25 PM, Alessio Buccino ***@***.***> wrote: Thanks! It works on my side! What version of neo are you using? Can you pip install -U neo to be sure? — Reply to this email directly, view it on GitHub <#1949 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVZDCPSAFRFNW7EMI53QFTXYBYEDANCNFSM6AAAAAA4FZTASY>. You are receiving this because you authored the thread.

[gmaggi]

neo 0.12.0 seems to be the latest one. The update did not fix the issue.
The spikeinterface we have is 0.98.1

[alejoe91]

Can you paste the full error?

[gmaggi]

Traceback (most recent call last):
  File "/opt/git_nerf_common/nerf_spikeinterface/nerf_spikeinterface_pipeline.py", line 350, in <module>
    recording = run_extractor()
  File "/opt/git_nerf_common/nerf_spikeinterface/nerf_spikeinterface_pipeline.py", line 218, in run_extractor
    subrecording = se.read_spikeglx( Path(args.INPUTFILE) , stream_id = 'imec0.ap')
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/spikeinterface/extractors/neoextractors/spikeglx.py", line 51, in __init__
    NeoBaseRecordingExtractor.__init__(
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 185, in __init__
    _NeoBaseExtractor.__init__(self, block_index, **neo_kwargs)
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 25, in __init__
    self.neo_reader = self.get_neo_io_reader(self.NeoRawIOClass, **neo_kwargs)
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 64, in get_neo_io_reader
    neo_reader.parse_header()
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/baserawio.py", line 179, in parse_header
    self._parse_header()
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/spikeglxrawio.py", line 81, in _parse_header
    self.signals_info_list = scan_files(self.dirname)
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/spikeglxrawio.py", line 254, in scan_files
    info = extract_stream_info(meta_filename, meta)
  File "/opt/anaconda/anaconda3/envs/spikeinterfacefull_0.98.1/lib/python3.10/site-packages/neo/rawio/spikeglxrawio.py", line 406, in extract_stream_info
    raise NotImplementedError('This meta file version of spikeglx'
NotImplementedError: This meta file version of spikeglxis not implemented

[alejoe91]

Ah! I think that the problem is that it's a NP2 probe (imDatPrb_type=24), but you have LF streams too! NP2 probes should only generate AP streams, since they are broad-band...

Can you confirm you are using a NP2-4 shank probe?

[Shrh627]

Hi,
Yes, we are using a 4-shank NP2.0 probe. I also need to mention that I found a difference between the raw data meta file and the output of the CatGT.

catGTCmdline0=<CatGT -dir=E:/Data/ephys/raw/Chronic/SH049/230823/sh0br80bvd_g0/sh0br80bvd_g0_imec0 -run=sh0br80bvd -g=0 -t=0 -no_run_fld -t_miss_ok -prb=0 -ap -lf -aphipass=300 -aplopass=5000 -lfhipass=1 -lflopass=300 -gbldmx -gfix=0.4,0.1,0.02 -dest=//nerffs17/boninlabwip2023/data/ephys/shahriar/Raw/NP2.0/Chronic/SH049/230823>
catGVals=0,0
catNFiles=1
catTVals=0,0

These lines are in the output of the CatGT .meta file which is not in the GLX output file.

[alejoe91]

Do you have lf.bin in the original folder (before CatGT)?

[Shrh627]

No, I don't.

[alejoe91]

Then try to move them somewhere else! It should work! We made that assumption that NP2 only has ap, but if CatGT produces an lf too we'll probably need to relax thta assumption

[gmaggi]

Putting only the ap* files in a dir works fine.
Thanks!!

[gmaggi]

Then try to move them somewhere else! It should work! We made that assumption that NP2 only has ap, but if CatGT produces an lf too we'll probably need to relax thta assumption

Hi @alejoe91 , would this assumption be relaxed in the next version?

[alejoe91]

Yes: see NeuralEnsemble/python-neo#1327

[alejoe91]

Closing because related to NEO (and already fixed in SI)