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juglab / cryoCARE_pip

PIP package of cryoCARE
BSD 3-Clause "New" or "Revised" License
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n_tiles [1,1,1] produces black volume #16

Closed thorstenwagner closed 2 years ago

thorstenwagner commented 2 years ago

Hi,

when I run cryoCARE on my local setup, it typically crashes with a OOM error and then tries n_tiles (1,1, 2) and runs through. The results look fine :-)

If I run the same cryoCARE setup on our cluster with RTX6000 GPUs it only produces a black volume. However, if you set n_tiles to (1,1,2) in the prediction config, it works well.

So, there seems to be bug when running it only on a single tile. Any ideas @tibuch ?

Best, Thorsten

tibuch commented 2 years ago

Hi,

Thank you for reporting!

I think the issue originates from here. Instead of writing the prediction into the provided output it is returned :frowning:

Best, Tim-Oliver

thorstenwagner commented 2 years ago

Ah, interesting! Thanks for the hint! I think it should be straight forward to fix it? I just need to have a look on format of the output volume. Or do you know off the top of your head how to fix it?

tibuch commented 2 years ago

Unfortunately not. Maybe this works? But I would have to dig a bit to understand again what I did there :sweat_smile:

thorstenwagner commented 2 years ago

Alright, analyzed the problem a bit using a tiny test sample:

Provided output shape is: (104, 232, 232, 1) pred shape is: (104, 232, 232, 1)

I will try a fix ^^

thorstenwagner commented 2 years ago

The fix works for me. If you are fine with it, I would merge it.

tibuch commented 2 years ago

Looks good to me, please go ahead.

thorstenwagner commented 2 years ago

Thanks for checking! I merged it. I close this issue.