Ilastik index export error

Usage & Issues
#1

@k-dominik maybe you can help me out here. I just made a simple object classification pipeline for a 3D image and tried to export the results but I am getting an unhelpful index out of bounds error. The image itself is exported fine, the issue seems to be writing the results table (csv and h5 options both produce this).

Screen Shot 2020-04-12 at 12.32.39 PM
Screen Shot 2020-04-12 at 12.32.39 PM2506×1608 713 KB

Looking at the ilastik log it looks like the index error is being thrown by do_export https://github.com/ilastik/ilastik/blob/31a2233731cde7934f95721ba70a33a2b1a74be3/ilastik/applets/objectClassification/opObjectClassification.py#L835

Happy to send you the ilp, log files, and example image to reproduce if that helps. I am using Ilastik 1.3.3post2-OSX

#2

Hi @Nick_George,

is it possible that you don’t have any objects in this image at all? Otherwise, yes, I’d need the project file (and input image) to be able to reproduce. Would you mind uploading them here?

#3

@k-dominik it seems to be highlighting several objects, so I don’t think that is the issue. I just uploaded both to the link you provided. Thanks for looking into this for me the segmentation looks really nice.

#4

Hi @Nick_George,

thank you for providing the files! I could reproduce the error.

So it seems you have not trained the object classifier. Do I assume correctly, that you are only interested in the object features? In any case the problem you ran into should be handled more gracefully than just throwing an error that is not very informative. So in order to resolve this, you have to annotate at least one object (so in the “Object Classification” applet, click on one object so it is labeled). Then the error should go away.

On a side note: We do not recommend to use the combined pixel + object classification workflow. It’s there for demo purposes really. Ideally you’d be splitting your workflow and do pixel classification first, export the output and use it in a new, object classification project.

Cheers
Dominik

#5

Thanks for looking into that @k-dominik, selecting a few objects looks like it solved my problem! I did not realize the combined workflow was not recommended. I’ll try the alternate workflow and see how that goes this week!