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notmatthancock / pylidc

An object relational mapping for the LIDC dataset using sqlalchemy.
https://pylidc.github.io
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handling IOError exception when trying to load missing dicom files #5

Closed violeta7 closed 7 years ago

violeta7 commented 7 years ago

Recently, I have used PyLIDC a lot. This is a great project. I found a small bug when I am using it. LIDC-IDRI dataset often does not have files which is in the filename DB of PyLIDC. It raise an IOError exception, and kills a program.

notmatthancock commented 7 years ago

It'd be preferable if you created an issue before the pull request, so that we can pin down more precisely the source of the error and how your patch fixes it. Also, I think you have a typo in your patch. Lastly, I suspect that your issue may the same as this one, which was patched and added to the latest pip version. Try upgrading pylidc to the most recent version, i.e. pip install --upgrade pylidc.

violeta7 commented 7 years ago

Yes, It looks like similar with the issue, but please be sure that this can happen not only 000000.dcm but also there is missing files in the middle. And I will make an issue before pull the request next time.

notmatthancock commented 7 years ago

I see what you are saying, and catching an error might be a good last resort. However, my concerns are (1) we don't understand if and where this problem actually occurs, and (2) I'm not sure if loading the images with a slice missing from the middle might break another function down-the-line.

Do you still experience your issue if you use the latest version of pylidc with your patch excluded? If so, please open an issue so we can pin-point where the problem is occurring, and so that we can potentially write a more robust fix.

notmatthancock commented 7 years ago

see #7