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byte-physics / x-to-nwb

Convert various patch-clamp data formats to NWBv2
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x-to-nwb (AttributeError: _stringsIndexed) #9

Open TeamPrigge opened 2 years ago

TeamPrigge commented 2 years ago

Dear Developers,

I recently tried to convert my abfV2 file into NWB but I am getting error right off the bat:

AttributeError: 'ABF' object has no attribute '_stringsIndexed'

I was wondering if anyone could helf solve the problem.

Best, Hassan

TeamPrigge commented 2 years ago

https://github.com/TeamPrigge/Problems/blob/main/XA9_0041_10062021_0010.abf

t-b commented 2 years ago

@TeamPrigge I presume you are the same Hassan which also emailed me.

When I'm converting the file with

$x-to-nwb XA9_0041_10062021_0010.abf

I'm getting

Converting XA9_0041_10062021_0010.abf
/home/firma/.pyenv/versions/3.8.6/lib/python3.8/site-packages/x_to_nwb/ABF2Converter.py:168: UserWarning: Could not find the JSON file XA9_0041_10062021_0010.json with settings.
  warnings.warn(f"Could not find the JSON file {settings} with settings.")
WARNING:pyabf.abf:fileGUID isn't truly unique (fileUUID is)
/home/firma/.pyenv/versions/3.8.6/lib/python3.8/site-packages/x_to_nwb/ABF2Converter.py:492: UserWarning: Could not find the scale factor for the stimset CC_longSquare_IV_ABA, using 1.0 as fallback.
  warnings.warn(
/home/firma/.pyenv/versions/3.8.6/lib/python3.8/site-packages/x_to_nwb/ABF2Converter.py:523: UserWarning: Could not find settings for amplifier unknown of channel PrimOut2.
  warnings.warn(f"Could not find settings for amplifier {amplifier} of channel {adcName}.")
/home/firma/.pyenv/versions/3.8.6/lib/python3.8/site-packages/x_to_nwb/ABF2Converter.py:523: UserWarning: Could not find settings for amplifier unknown of channel SecOut2.
  warnings.warn(f"Could not find settings for amplifier {amplifier} of channel {adcName}.")

Can you post what you got? Please also attach the output of pip show x-to-nwb pyabf.

MathkarP commented 1 year ago

Hello,

Has this issue been resolved? I am also getting the same error when I try to convert ABFv2 files to nwb.