[Bug]: Error when opening SpikeGLX output, "key already in signals_info_dict"

[kailasas-um]

What happened?

Hi, I'm attempting to convert SpikeGLX ap.bin and lf.bin outputs into NWB format. When attempting to create a DataInterface object, I receive the error below. Any help in figuring out what's gone wrong would be greatly appreciated!

Steps to Reproduce

from neuroconv.datainterfaces import SpikeGLXRecordingInterface
path=f"[my-path]" 
interface = SpikeGLXRecordingInterface(file_path=path)

Traceback

>>> interface = SpikeGLXRecordingInterface(file_path=path)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/pydantic/validate_call_decorator.py", line 60, in wrapper_function
    return validate_call_wrapper(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/pydantic/_internal/_validate_call.py", line 96, in __call__
    res = self.__pydantic_validator__.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py", line 82, in __init__
    super().__init__(
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py", line 36, in __init__
    super().__init__(**source_data)
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/neuroconv/baseextractorinterface.py", line 37, in __init__
    self._extractor_instance = self.extractor(**self.extractor_kwargs)
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/spikeglx.py", line 65, in __init__
    NeoBaseRecordingExtractor.__init__(
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 188, in __init__
    _NeoBaseExtractor.__init__(self, block_index, **neo_kwargs)
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 27, in __init__
    self.neo_reader = self.get_neo_io_reader(self.NeoRawIOClass, **neo_kwargs)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 66, in get_neo_io_reader
    neo_reader.parse_header()
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/neo/rawio/baserawio.py", line 199, in parse_header
    self._parse_header()
  File "/nfs/turbo/*/processNeuropixels/lib/python3.12/site-packages/neo/rawio/spikeglxrawio.py", line 133, in _parse_header
    raise KeyError(f"key {key} is already in the signals_info_dict")
KeyError: "key (0, 'imec0.lf') is already in the signals_info_dict"

Operating System

Linux

Python Executable

Python

Python Version

3.12

Package Versions

annotated-types==0.7.0
asciitree==0.3.3
attrs==24.2.0
click==8.1.7
docstring_parser==0.16
faiss-cpu==1.9.0
fasteners==0.19
filelock==3.16.1
fsspec==2024.10.0
h5py==3.12.1
hdmf==3.14.5
hdmf_zarr==0.9.0
Jinja2==3.1.4
joblib==1.4.2
jsonschema==4.23.0
jsonschema-specifications==2024.10.1
kilosort==4.0.20
llvmlite==0.43.0
MarkupSafe==3.0.2
mpmath==1.3.0
neo==0.13.4
networkx==3.4.2
neuroconv==0.6.5
numba==0.60.0
numcodecs==0.14.0
numpy==1.26.4
nvidia-cublas-cu12==12.4.5.8
nvidia-cuda-cupti-cu12==12.4.127
nvidia-cuda-nvrtc-cu12==12.4.127
nvidia-cuda-runtime-cu12==12.4.127
nvidia-cudnn-cu12==9.1.0.70
nvidia-cufft-cu12==11.2.1.3
nvidia-curand-cu12==10.3.5.147
nvidia-cusolver-cu12==11.6.1.9
nvidia-cusparse-cu12==12.3.1.170
nvidia-nccl-cu12==2.21.5
nvidia-nvjitlink-cu12==12.4.127
nvidia-nvtx-cu12==12.4.127
packaging==24.2
pandas==2.2.3
parse==1.20.2
probeinterface==0.2.24
psutil==6.1.0
pydantic==2.9.2
pydantic_core==2.23.4
pynwb==2.8.2
python-dateutil==2.9.0.post0
pytz==2024.2
PyYAML==6.0.2
quantities==0.16.1
referencing==0.35.1
rpds-py==0.21.0
ruamel.yaml==0.18.6
ruamel.yaml.clib==0.2.12
scikit-learn==1.5.2
scipy==1.14.1
setuptools==75.5.0
six==1.16.0
spikeinterface==0.101.2
sympy==1.13.1
threadpoolctl==3.5.0
torch==2.5.1
tqdm==4.67.0
triton==3.1.0
typing_extensions==4.12.2
tzdata==2024.2
zarr==2.17.2

Code of Conduct

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[h-mayorquin]

Hi, thanks for raising an issue.

This seems like a neo issue. I would suggest trying the neo reader for spikeglx and if that fails it would produce a cleaner error trace which we can fix on the side.

Two questions:

1. Can you open an issue on neo if you get the error at the neo level.
2. Can you share the data with us so we can debug quicker?

[h-mayorquin]

Hi, I think I have an idea on what's causing this? Can you show me thee tree output of the folder that you are trying to convert?

[h-mayorquin]

I think this neo PR should solve this problem:
NeuralEnsemble/python-neo#1608

[h-mayorquin]

Ok, this should be solved wit the most recent changes on neo. I will be closing this. Feel free to open another issue if the problem persists.