Ilastik - back compatability or update old files?


I was hoping something had already encountered this issue and found a solution.

I have an old Ilastik workflow, pixel classification, made in 1.3.2.

I can’t open this in a new version of Ilastik 1.3.3.post3. It makes a window with fail to load It gives me a long list of errors in command window, it ends in a assertion error:
File “C:\Program Files\ilastik-1.3.3post3\lib\site-packages\ndstructs\”, line 84, in init
assert len(arr.shape) == len(axiskeys)

I am running this on a windows 10 machine. The old ilastik could have been created in an older version of ilastik (hard to tell, because I lost the software after an hdd malfunction), but I can open it in 1.3.2.

My question
Does anybody know why this is happening? Or is it just me?
Is this a known issue? I couldn’t find it on their git?
Is there a way update the .ilp file to make it accessible to 1.3.3?
Should I make a report in the git?

Hi @JesD12,

bummer that you ran into this. It is not exactly unknown (there is an issue on our github). I couldn’t reproduce this particular problem but we had quite some changes in that code since the original report. Could I maybe ask you to try the latest beta version of ilastik (1.4.0b7)?

Hi @k-dominik
Thank you for getting back so soon. I tried the newest version (1.4.0b7) but it gives the same error.
I then tried it on some of my other project also created with 1.3.2, and they did work, so I did a little more trouble-shooting. It turns out I only seem to have this issue when the input files are .h5 file format.

Here is what I did:
I created projects in the 1.3.2 added a few image files, minimal feature and training, and then save. Then I tried opening them with 1.3.3.
I tried several different differnet data format (multi channel/2D/3D), but the only difference that seems to matter was whether the input data was .h5 or tiff.
The project with tif files could be opened in 1.3.3 whereas
the project with .h5 file format would give me this error.

Let me know if you want the project files, or if you want me to do any more testing.
Also sorry I missed the issue in your git, I thought I looked through all of it. Let me know if you want me to also post this in the thread on git.

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Hi @JesD12,

thank you very much for trying the beta and also for going through the effort to make the issue reproducible.

I have tried your instructions on linux and windows but couldn’t get it to fail. So it would be really great if you could upload some example data, and possibly an example project, too. You could drop the files conveniently here (note, this link is only active for two days).


Hi again @k-dominik
I have uploaded the files (maybe twice, sorry). It includes 3 files:
the ilp file, the h5 image file and a txt file with the message from the cmd promt window.

I am using it on a windows 10 computer, and the h5 file was generated with the ilastik plugin to fiji.

Let me know if there is more I can do. And thanks a lot for this support.



Hi @JesD12,

thank yo very much for uploading. I didn’t have time to look into it yet any further than confirming that I can produce the error now. So that’s one step closer to resolving the issue for sure!

Cheers :slight_smile:

just a quick update, we’ll have an updated beta version by the end of this week where this bug disappears.

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Thanks a lot @k-dominik, that would be highly appreciated, and will for sure try it out.

okay, it is taking a tad longer than expected (unrelated to your issue). I’ll ping you here, once it’s ready

Hi @JesD12

our 1.4.0b8 version should resolve this issue:

Hi @k-dominik

I have tried it and can confirm it has solved the issue. Thank you very much.

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