`PRB2_4_2_0640_0` not supported?
Closed this issue · 2 comments
TheChymera commented
Hello, I'm having issues converting some neuropixels (spikeglx) data to NWB, and it seems the package giving the error is probeinterface
.
Is this something that's really missing and should be added by you, or are some of the higher-level packages at fault?
(reposit) [typhon]/mnt/DATA/data/studies/manish/mvmnda/rawdata/code ❱ cat reposit.py
from datetime import datetime
from dateutil import tz
from pathlib import Path
from neuroconv.converters import SpikeGLXConverterPipe
import json
dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/Ach_DualPixel_7_14_23/Ach_DualPixel_7_14_23_g0"
#dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/sub-pixelfiber/M387-2023-10-20_g0"
#dir_path = "../../sourcedata/M387-2023-10-20_g0"
converter = SpikeGLXConverterPipe(folder_path=dir_path)
# Extract what metadata we can from the source files
metadata = converter.get_metadata()
# The following doesn't work as per the guide ( https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/recording/spikeglx.html#single-stream ), apparently no session_start_time is read in:
#session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=tz.gettz("US/Pacific"))
# So we do:
session_start_time = datetime.now(tz.tzlocal())
metadata["NWBFile"].update(session_start_time=session_start_time)
# Choose a path for saving the nwb file and run the conversion
nwbfile_path = "/mnt/DATA/data/studies/manish/mvmnda/rawdata/my_spikeglx_session.nwb"
converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
(reposit) [typhon]/mnt/DATA/data/studies/manish/mvmnda/rawdata/code ❱ python reposit.py
Traceback (most recent call last):
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/reposit.py", line 10, in <module>
converter = SpikeGLXConverterPipe(folder_path=dir_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxconverter.py", line 64, in __init__
interface = SpikeGLXRecordingInterface(file_path=file_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py", line 76, in __init__
super().__init__(
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py", line 32, in __init__
self.recording_extractor = self.get_extractor()(**source_data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/spikeinterface/extractors/neoextractors/spikeglx.py", line 63, in __init__
probe = pi.read_spikeglx(meta_filename)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/probeinterface/io.py", line 1262, in read_spikeglx
probe = _read_imro_string(imro_str=imro_table, imDatPrb_pn=imDatPrb_pn)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/DATA/data/studies/manish/mvmnda/rawdata/code/venvs/reposit/lib/python3.11/site-packages/probeinterface/io.py", line 1094, in _read_imro_string
raise NotImplementedError(f"Probe part number {imDatPrb_pn} is not supported yet")
NotImplementedError: Probe part number PRB2_4_2_0640_0 is not supported yet
yarikoptic commented
may be would be easier to figure out if a sample file is shared somewhere?
alejoe91 commented
Hi guys, I'll make a PR to add that probe part number to the internal list.
@TheChymera do you know what NP probe model PRB2_4_2_0640_0
corresponds to?