[Bug]: IndexError: list index out of range, .abf conversion

[eastmanlewis]

What happened?

Trying to convert .abf to nwb, I run into an IndexError: list index out of range at (I believe) the conversion step. In my environment I installed the tdt conversion package first and then the abf conversion package to work around an issue I ran into when I tried running the code having installed the abf package only. I will submit a second bug report for that if it will be helpful.

Steps to Reproduce

from datetime import datetime
from zoneinfo import ZoneInfo
from pathlib import Path
from neuroconv.datainterfaces import AbfInterface

# Metadata info
icephys_metadata = {
    "cell_id": "20220818001",
    "slice_id": "20220818001",
    "targeted_layer": "L2-3(medial)",
    "inferred_layer": "",
    "recording_sessions": [
        {
            "abf_file_name": "File_axon_5.abf",
            "stimulus_type": "long_square",
            "icephys_experiment_type": "voltage_clamp"
        }
    ]
}

# Instantiate data interface
interface = AbfInterface(
    file_paths=[fr"C:\Users\eastm\OneDrive\Desktop\2024_06_07_0000.abf"],
    icephys_metadata=icephys_metadata
)

# Get metadata from source data and modify any values you want
metadata = interface.get_metadata()
metadata['NWBFile'].update(
    identifier="ID1234",
    session_description="Intracellular electrophysiology experiment.",
    lab="my lab name",                       # <-- optional
    institution="My University",             # <-- optional
    experimenter=["John Doe", "Jane Doe"],   # <-- optional
)
metadata["Subject"] = dict(
    subject_id="subject_ID123",
    species="Mus musculus",
    sex="M",
    date_of_birth="2022-03-15T00:00:00"
)

# Run conversion
nwbfile_path = r'C:/Users/eastm/OneDrive/Desktop/test_nwb_2024_06_07_0000.nwb'
interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

Traceback

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[25], line 45
     43 # Run conversion
     44 nwbfile_path = r'C:/Users/eastm/OneDrive/Desktop/test_nwb_2024_06_07_0000.nwb'
---> 45 interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

File ~\.conda\envs\neuroconv_tdt\Lib\site-packages\neuroconv\basedatainterface.py:196, in BaseDataInterface.run_conversion(self, nwbfile_path, nwbfile, metadata, overwrite, backend, backend_configuration, **conversion_options)
    192 append_mode = file_initially_exists and not overwrite
    194 self.validate_metadata(metadata=metadata, append_mode=append_mode)
--> 196 with make_or_load_nwbfile(
    197     nwbfile_path=nwbfile_path,
    198     nwbfile=nwbfile,
    199     metadata=metadata,
    200     overwrite=overwrite,
    201     backend=backend,
    202     verbose=getattr(self, "verbose", False),
    203 ) as nwbfile_out:
    204     if no_nwbfile_provided:
    205         self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)

File ~\.conda\envs\neuroconv_tdt\Lib\contextlib.py:137, in _GeneratorContextManager.__enter__(self)
    135 del self.args, self.kwds, self.func
    136 try:
--> 137     return next(self.gen)
    138 except StopIteration:
    139     raise RuntimeError("generator didn't yield") from None

File ~\.conda\envs\neuroconv_tdt\Lib\site-packages\neuroconv\tools\nwb_helpers\_metadata_and_file_helpers.py:235, in make_or_load_nwbfile(nwbfile_path, nwbfile, metadata, overwrite, backend, verbose)
    229     assert (
    230         len(backends_that_can_read) <= 1
    231     ), "More than one backend is capable of reading the file! Please raise an issue describing your file."
    232     if backend not in backends_that_can_read:
    233         raise IOError(
    234             f"The chosen backend ('{backend}') is unable to read the file! "
--> 235             f"Please select '{backends_that_can_read[0]}' instead."
    236         )
    237 else:
    238     load_kwargs.update(mode="w")

IndexError: list index out of range

Operating System

Windows

Python Executable

Conda

Python Version

3.11

Package Versions

annotated-types==0.7.0
anyio @ file:///C:/b/abs_31grv7a7bl/croot/anyio_1729121290992/work
argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work
argon2-cffi-bindings @ file:///C:/b/abs_f11axiliot/croot/argon2-cffi-bindings_1736182463870/work
asciitree==0.3.3
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async-lru @ file:///C:/b/abs_e0hjkvwwb5/croot/async-lru_1699554572212/work
attrs @ file:///C:/b/abs_89hmquz5ga/croot/attrs_1734533130810/work
babel @ file:///C:/b/abs_ffzt1bmjth/croot/babel_1737454394148/work
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decorator @ file:///opt/conda/conda-bld/decorator_1643638310831/work
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Deprecated==1.2.15
docstring_parser==0.16
executing @ file:///opt/conda/conda-bld/executing_1646925071911/work
fasteners==0.19
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h11 @ file:///C:/b/abs_1czwoyexjf/croot/h11_1706652332846/work
h5py==3.12.1
hdmf==3.14.5
hdmf_zarr==0.9.0
httpcore @ file:///C:/b/abs_55n7g233bw/croot/httpcore_1706728507241/work
httpx @ file:///C:/b/abs_43e135shby/croot/httpx_1723474830126/work
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ipykernel @ file:///C:/b/abs_5etv6sld_j/croot/ipykernel_1728665608850/work
ipython @ file:///C:/b/abs_8eyhzleyrk/croot/ipython_1734548134403/work
ipywidgets==8.1.5
jedi @ file:///C:/b/abs_3a2kbnlclc/croot/jedi_1733987412687/work
Jinja2 @ file:///C:/b/abs_ddyeze2h6_/croot/jinja2_1730903330414/work
json5 @ file:///C:/b/abs_743lprxrv5/croot/json5_1730786818336/work
jsonschema @ file:///C:/b/abs_394_t6__xq/croot/jsonschema_1728486718320/work
jsonschema-specifications @ file:///C:/b/abs_0brvm6vryw/croot/jsonschema-specifications_1699032417323/work
jupyter-events @ file:///C:/b/abs_c2m9s5b5m5/croot/jupyter_events_1718738115254/work
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jupyter_client @ file:///C:/b/abs_a6h3c8hfdq/croot/jupyter_client_1699455939372/work
jupyter_core @ file:///C:/b/abs_beftpbuevw/croot/jupyter_core_1718818307097/work
jupyter_server @ file:///C:/b/abs_9a333nh6yu/croot/jupyter_server_1718827092223/work
jupyter_server_terminals @ file:///C:/b/abs_ec0dq4b50j/croot/jupyter_server_terminals_1686870763512/work
jupyterlab @ file:///C:/b/abs_88qjk9lo2r/croot/jupyterlab_1725895228333/work
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jupyterlab_server @ file:///C:/b/abs_fdi5r_tpjc/croot/jupyterlab_server_1725865372811/work
jupyterlab_widgets==3.0.13
MarkupSafe @ file:///C:/b/abs_a9k8j__c_q/croot/markupsafe_1736370039866/work
matplotlib-inline @ file:///C:/ci_311/matplotlib-inline_1676425798036/work
mistune @ file:///C:/ci_311/mistune_1676425111783/work
nbclient @ file:///C:/b/abs_cal0q5fyju/croot/nbclient_1698934263135/work
nbconvert @ file:///C:/b/abs_ac6qnzi3no/croot/nbconvert_1728050663985/work
nbformat @ file:///C:/b/abs_c2jkw46etm/croot/nbformat_1728050303821/work
ndx-dandi-icephys==0.4.0
neo==0.14.0
nest-asyncio @ file:///C:/b/abs_65d6lblmoi/croot/nest-asyncio_1708532721305/work
neuroconv==0.6.7
notebook @ file:///C:/b/abs_feeub5ouq6/croot/notebook_1727197380211/work
notebook_shim @ file:///C:/b/abs_a5xysln3lb/croot/notebook-shim_1699455926920/work
numcodecs==0.15.0
numpy==1.26.4
overrides @ file:///C:/b/abs_cfh89c8yf4/croot/overrides_1699371165349/work
packaging @ file:///C:/b/abs_3by6s2fa66/croot/packaging_1734472138782/work
pandas==2.2.3
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
parse==1.20.2
parso @ file:///C:/b/abs_834b4mj92b/croot/parso_1733963322289/work
platformdirs @ file:///C:/b/abs_b6z_yqw_ii/croot/platformdirs_1692205479426/work
probeinterface==0.2.24
prometheus_client @ file:///C:/b/abs_e7l07zkc4b/croot/prometheus_client_1731961599071/work
prompt-toolkit @ file:///C:/b/abs_68uwr58ed1/croot/prompt-toolkit_1704404394082/work
psutil @ file:///C:/b/abs_b5gv3mn55h/croot/psutil_1736371546320/work
pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
pydantic==2.10.5
pydantic_core==2.27.2
Pygments @ file:///C:/b/abs_fay9dpq4n_/croot/pygments_1684279990574/work
pynwb==2.8.3
PySocks @ file:///C:/ci_311/pysocks_1676425991111/work
python-dateutil @ file:///C:/b/abs_3au_koqnbs/croot/python-dateutil_1716495777160/work
python-json-logger @ file:///C:/b/abs_0cm_mnox0z/croot/python-json-logger_1734370042436/work
pytz==2024.2
pywin32==308
pywinpty @ file:///C:/b/abs_6696uz5mru/croot/pywinpty_1733514639618/work
PyYAML @ file:///C:/b/abs_14xkfs39bx/croot/pyyaml_1728657968772/work
pyzmq @ file:///C:/b/abs_f3yte6j5yn/croot/pyzmq_1734711069724/work
quantities==0.16.1
referencing @ file:///C:/b/abs_09f4hj6adf/croot/referencing_1699012097448/work
requests @ file:///C:/b/abs_c3508vg8ez/croot/requests_1731000584867/work
rfc3339-validator @ file:///C:/b/abs_ddfmseb_vm/croot/rfc3339-validator_1683077054906/work
rfc3986-validator @ file:///C:/b/abs_6e9azihr8o/croot/rfc3986-validator_1683059049737/work
rpds-py @ file:///C:/b/abs_0c6z5kcdb6/croot/rpds-py_1736545465023/work
ruamel.yaml==0.18.10
ruamel.yaml.clib==0.2.12
scipy==1.15.1
Send2Trash @ file:///C:/b/abs_7e73ol18dl/croot/send2trash_1736542724140/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
sniffio @ file:///C:/b/abs_3akdewudo_/croot/sniffio_1705431337396/work
soupsieve @ file:///C:/b/abs_bbsvy9t4pl/croot/soupsieve_1696347611357/work
spikeinterface==0.101.2
stack-data @ file:///opt/conda/conda-bld/stack_data_1646927590127/work
terminado @ file:///C:/ci_311/terminado_1678228513830/work
threadpoolctl==3.5.0
tinycss2 @ file:///C:/ci_311/tinycss2_1676425376744/work
tornado @ file:///C:/b/abs_7cyu943ybx/croot/tornado_1733960510898/work
tqdm==4.67.1
traitlets @ file:///C:/b/abs_bfsnoxl4pq/croot/traitlets_1718227069245/work
typing_extensions @ file:///C:/b/abs_0ffjxtihug/croot/typing_extensions_1734714875646/work
tzdata==2025.1
urllib3 @ file:///C:/b/abs_7bst06lizn/croot/urllib3_1737133657081/work
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webencodings==0.5.1
websocket-client @ file:///C:/b/abs_5dmnxxoci9/croot/websocket-client_1715878351319/work
widgetsnbextension==4.0.13
win-inet-pton @ file:///C:/ci_311/win_inet_pton_1676425458225/work
wrapt==1.17.2
zarr==2.17.2

Code of Conduct

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[h-mayorquin]

Hi, thanks a lot for filling an issue. Can you try adding overwrite=True to the following lines:

# Run conversion
nwbfile_path = r'C:/Users/eastm/OneDrive/Desktop/test_nwb_2024_06_07_0000.nwb'
interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)

And let me know if that fixes the issue?

[laurelrr]

I was having a similar error and the 'overwrite=True' fixed it for me. Thanks!

[eastmanlewis]

overwrite=True seems to be working for me as well, thanks! I'm getting an .nwb file now and no errors from running the code. This is my first foray into nwb format and I'm still working on viewing the file that the code produced, so I can't speak to that. Thanks again for the quick help!!