Data Export Error in Ilastik Object Classification Pipeline

Hi Guys,

I’m encountering an error that appears similar to this:

When attempting to export either object predictions or probabilities as multipage tiffs (or multipage tiff sequences) from an object classification pipeline, I get the following error:

Capture

This seems to be specific to a particular pipeline I’ve created. Pretty sure I’ve managed to export data in this format before without any problems.

I’m using Ilastik version 1.3.3post1.

Thanks,

D.

Hi @djpbarry,

that doesn’t sounds/look nice.

The error is happening in the library (vigra) we use to write tiffs. I haven’t been able to track down the exact cause just yet. I think the only workaround now would be to export to hdf5 and then maybe write a fiji macro that does the conversion?

Hi @k-dominik,

So that’s what I thought at first, that there’s something going on with the TIFF writing.

But, on further investigation, it seems the error is appearing regardless of the file format I choose. For example, if I try to export to h5:

Capture

Hey @djpbarry,

that’s unfortunate. So reading the image might be the problem. Are you reading tiff files? If so can you open this particular image in ilastik without problems?
Really puzzling, but getting to the root of this would be really good.

Hi @k-dominik,

Yep, no problem reading the files, which are indeed TIFFs. The inputs are raw images plus pixel probabilities from a pixel classification pipeline.

Absolutely no problem at any stage loading the images or training the object classifier - only problem is with the data export (which only seems to have surfaced today).

:confused:

Is this behavior reproducible with a single of your datasets? If so it would be great if you can share it with us (you can do so privately via team@ilastik.org) so we can have a closer look!

Sure @k-dominik, I’ll put something together and send it over.

D.

Hi djpbarry, thanks for providing the data, I can definitely reproduce it. So far I can tell you, that ilastik seems to have a problem with your probabilities file --> it will hang when you try to go to the last time slice :open_mouth: - So I’m looking into this now - fiji seems to be able to open the prob file just fine, so the problem is likely on our side (or with one of our tiff reading libs).

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btw, some side question, have you produced the probability file with ilastik?

Yes, that’s correct.

Hey @k-dominik,

Just wondering if there’s any further info on this?

D.

Honestly I didn’t have time to look further into it.

I would, for now advice to export the offending file again (from pixel classification), maybe to h5, and then try it again. Would this be a viable solution for you?

On the long run the problem of handling corrupt .tiff files (or any corrupt files for that matter) more gracefully that needs to be fixed on our side, of course.

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Sure, I’ll give it a try.