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NeuralEnsemble / python-neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats
http://neo.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Spikeglx: parse tcat input #1511

Open tabedzki opened 3 months ago

tabedzki commented 3 months ago

Describe the bug I am unable to read in my lf files when using SpikeGLXRawIO. The file structure is currently as below. When I had all the lf files be t0 instead of tcat it worked flawlessly. 

ya008_20240525_g0
├── ya008_20240525_g0_ct_offsets.txt
├── ya008_20240525_g0_fyi.txt
├── ya008_20240525_g0_imec0
│  ├── ya008_20240525_g0_t0.imec0.ap.bin
│  ├── ya008_20240525_g0_t0.imec0.ap.meta
│  ├── ya008_20240525_g0_tcat.imec0.lf.bin
│  └── ya008_20240525_g0_tcat.imec0.lf.meta
├── ya008_20240525_g0_imec1
│  ├── ya008_20240525_g0_t0.imec1.ap.bin
│  ├── ya008_20240525_g0_t0.imec1.ap.meta
│  ├── ya008_20240525_g0_tcat.imec1.lf.bin
│  └── ya008_20240525_g0_tcat.imec1.lf.meta
├── ya008_20240525_g0_t0.nidq.bin
└── ya008_20240525_g0_t0.nidq.meta

To Reproduce

(neuroconv_312) ➜  test2 ipython
Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.26.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import neo.rawio

In [2]: reader = neo.rawio.SpikeGLXRawIO(dirname='./ya008_20240525_g0')

In [3]: reader.parse_header()
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[3], line 1
----> 1 reader.parse_header()

File /scratch/ct5868/.conda/envs/neuroconv_312/lib/python3.12/site-packages/neo/rawio/baserawio.py:189, in BaseRawIO.parse_header(self)
    176 """
    177 Parses the header of the file(s) to allow for faster computations
    178 for all other functions
    179
    180 """
    181 # this must create
    182 # self.header['nb_block']
    183 # self.header['nb_segment']
   (...)
    186 # self.header['spike_channels']
    187 # self.header['event_channels']
--> 189 self._parse_header()
    190 self._check_stream_signal_channel_characteristics()
    191 self.is_header_parsed = True

File /scratch/ct5868/.conda/envs/neuroconv_312/lib/python3.12/site-packages/neo/rawio/spikeglxrawio.py:147, in SpikeGLXRawIO._parse_header(self)
    144 signal_channels = []
    145 for stream_name in stream_names:
    146     # take first segment
--> 147     info = self.signals_info_dict[0, stream_name]
    149     stream_id = stream_name
    150     stream_index = stream_names.index(info["stream_name"])

KeyError: (0, 'imec1.ap')

Environment:

Related to #1501 #1390

I am happy to provide access to the meta files. The SpikeGLX data is rather large so if having access to that would be necessary, I'd have to ask IT how to best distribute that data.

samuelgarcia commented 3 months ago

@alejoe91 can you handle this ?