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ome / omero-guide-ilastik

BSD 2-Clause "Simplified" License
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install from conda-forge channel #33

Closed jburel closed 2 years ago

jburel commented 2 years ago

Use conda-forge channel instead of ome one see See https://github.com/ome/conda-omero-py/issues/26

github-actions[bot] commented 2 years ago

Binder :point_left: Launch a binder notebook on branch installation

pwalczysko commented 2 years ago

builds okay on MyBinder.

The pixel_classification notebook works fine. But the pixel_classification_zarr ends repeatedly with "dead kernel" and the only option is to restart, then, new run of notebook, and the same repeats again. It happens when ilastik is working, and the last output before the freeze is

NFO lazyflow.utility.bigRequestStreamer: Chose blockshape: (1, 92, 92, 92, 2)

INFO:lazyflow.utility.bigRequestStreamer:Chose blockshape: (1, 92, 92, 92, 2)

INFO lazyflow.utility.bigRequestStreamer: Estimated RAM usage per block is 748.6MiB

INFO:lazyflow.utility.bigRequestStreamer:Estimated RAM usage per block is 748.6MiB
WARNING arraytypes.py(1263): FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
WARNING arraytypes.py(1269): FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
pwalczysko commented 2 years ago

the idr0062_pixel_classification_zarr notebook is working fine too. So out of 3 notebooks, 1 is not working (pixel_class.._zarr)

jburel commented 2 years ago

Thanks I need to review the zarr section. This outside the scope of this PR.