pop index out of range error in pixelclassification workflow

[soledis92]

There is an issue with dropping the channel axis during prediction export in the pixelclassification applet.

How to replicate:
During prediction export if the axis order in the image export options is set from e.g. yxc to yx (dropping the channel) after closing the options menu saving the project leads to an "pop index out of range IndexError". If the project is closed in that condition it can't be opened again.

The only work around to save the labels was to manually add an empty channel axis to the hdf5 project file. After that the project can be opened again.

Image of the error:

Cheers, Adrian

[snajder-r]

I can confirm the issue still persists in 1.3.2 rc1. Encountered this exact issue in the autocontext workflow when trying to save predictions as zyx instead of zyxc.

[k-dominik]

thx a lot for checking @snajder-r

[k-dominik]

can confirm this still is an issue

related (in a way): ilastik/volumina#263

[i3v]

I just ran into this and this when trying to export a prediction (Simple segmentation). The original image is yxzc (3D + 3 colors). I assumed that the prediction is 3D, so I set Transpose to Axis Order to zxy, which caused the error. (If I set zxyc instead, everything works as expected).

Once I get the "pop index out of range IndexError" error, there seem to be no way back - weird errors start to happen. Even and attempt to delete all exports (the "Delete All" button) causes an error:

---------------------------
SlotNotReadyError
---------------------------
Can't get data from slot <class 'lazyflow.operators.ioOperators.opExportSlot.OpExportSlot'>.ExportPath yet. It isn't ready. First upstream problem slot is: OpExportSlot/OpExportSlot.Input []: 	{_ready : False, has_mask : None, _dirty : False}

 (Advanced information about this error may be found in the log file: <...>\AppData\Local\ilastik\Logs\log.txt)

---------------------------
OK   
---------------------------

Moreover, (it looks like) I was stupid enough to save the project after the error.
As a result, my project file got damaged and the "pop index out of range" error was now preventing me from loading the project.

Thankfully, the fix was pretty easy. Just in case anyone would need this:

import h5py
input = r'C:\project\project.ilp'
with h5py.File(input,  "a") as f:
    del f['Prediction Export']

The versions of the python packages I used:

python = "==3.7.9"
h5py = "==3.7.0"

Based on "C:\Program Files\ilastik-1.4.0.post1-gpu\conda-meta").

Ilastik 1.4.0.post1.