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marksgraham / OCT-Converter

Tools for extracting the raw optical coherence tomography (OCT) and fundus data from proprietary file formats.
https://pypi.org/project/oct-converter/
MIT License
199 stars 72 forks source link

fda.read_oct_volume gives No decoders are available error #52

Closed YaseminTurkan closed 2 years ago

YaseminTurkan commented 2 years ago

Hi Mark,

Thanks a lot for the library. I will be using it a lot for my Ph D. Thesis

I am trying to read UKBiobank file in fda format. I got the following error: "No decoders are available error"

I nhave debuf-gged the code in function read_oct_volume (self) there is a function called slice = decode (raw_slice) which calls from pylibjpeg
in the decode function decoders = get_getcoders() returns empty set. I have installed all the files.

Am I missing something?
Thanks again for your great support for the library Best Yasemin

marksgraham commented 2 years ago

Hi,

Could you tell me what version of Python and pylibjpeg you're using?

YaseminTurkan commented 2 years ago

python 3.7.9 pylibjpeg 1.4.0

marksgraham commented 2 years ago

Any chance you can send me an example of the .fda file this fails on? Or check whether it works for you using the example .fda file you can download from here: https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=31

YaseminTurkan commented 2 years ago

it gives the same error when I test with the data in your link. My downloaded UK Biobank files are in the attachment UKBiobank.zip

marksgraham commented 2 years ago

Hm these all work fine for me. What OS are you using? Can you send me the full output of pip list?

YaseminTurkan commented 2 years ago

I found the issue, it has been with the environment variables. I needed to reboot my PC after the installation of the libraries. (By the way, I was running on Windows 10)

Thanks a lot for your all help. Very much appreciated. I will be using your library a lot during my Ph. D. Thesis :)

marksgraham commented 2 years ago

That's great, glad it is all working now 👍