"AddFileButton has been deleted" error during batch processing

Usage & Issues
#1

Hello everyone,

I have tried for the first time to run the batch-processing applet of the boundary-based segmentation workflow but I got this error while processing all the photos : “AddFileButton has been deleted”.

I saw on the internet that some people had the same problem but I couldn’t get anything to work. Has a solution to this problem been found ? Maybe in the latest version ? I am using ilastik-1.3.3post3 but maybe the version 1.4.0b9 has it fixed ?

Kind regards,

Antoine

#2

Maybe the headless mode will be the solution for me but my knowledge in coding isn’t strong enough so I don’t manage to get it working on my computer, could someone help me with it ? :slight_smile:

#3

Hi @Antoine_Cure,

this error is a bug that has not been fixed yet, unfortunately… Would sure be willing to help you set up the headless mode. There is not too much damage you can do there :slight_smile:

#4

By looking through the internet I think I found a solution that allows me to process images one by one. Is there any way to go faster ?

This is what I write in the command prompt :

call “c:\Program Files\ilastik-1.3.3post3\run-ilastik.bat” --headless --project=“path to project” --raw_data=“path to raw data” --probabilities=“path to probabilities” --export_source=“Multicut Segmentation” --output_filename_format=“path to output file”

#5

Hey @Antoine_Cure,

great that you found a solution already! Minor remark, you should use ilastik.exe that is in that folder, not the run_ilastik.bat.

What do you mean by faster?

  • ilastik should produce each single result faster?
    • probably not possible
  • you want to batch process many images and don’t want to do it 1 by 1 with waiting?
    • the script could be expanded to do that
  • You want to run multiple jobs in parallel?
    • while we don’t do it in batch processing, this could make sense on some more powerful machines.
#6

Great thanks for the correction !

Sorry by faster I meant, is there a way to batch process everything by expanding the code ?

#7

Hey @Antoine_Cure,

how to proceed there, totally depends on your background (and also maybe what you want to learn anyway).

A couple of ways this could be achieved:

  • using a batch script
  • using python, calling ilastik in a subprocess
  • going via Fiji, using the ilastik plugin in a macro there :slight_smile: