Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Fallback plugin logic faulty

See original GitHub issue

🐛 Bug

Dragging and dropping an (apparently malformed 😅) multiscale .zarr folder to napari gave me the following error:

INFO:napari_plugin_engine.manager:loaded 3 plugins:
  <module 'napari.plugins._builtins' from '/Users/jni/conda/envs/all/lib/python3.8/site-packages/napari/plugins/_builtins.py'>
  <module 'napari_svg' from '/Users/jni/conda/envs/all/lib/python3.8/site-packages/napari_svg/__init__.py'>
  <module 'ome_zarr' from '/Users/jni/conda/envs/all/lib/python3.8/site-packages/ome_zarr.py'>
  <module 'napari_plugin_engine' from '/Users/jni/conda/envs/all/lib/python3.8/site-packages/napari_plugin_engine/__init__.py'>
ERROR:napari.plugins.io:PluginError: Error in plugin 'builtins', hook 'napari_get_reader': local variable 'image' referenced before assignment
  Cause was: local variable 'image' referenced before assignment
    version: 0.3.0
    package: napari

ERROR:napari.components.add_layers_mixin:No plugin found capable of reading /Volumes/datac/napari-data/covid-gut/.

Note “local variable image referenced before assignment”. This should never happen.

Issue Analytics

State:
Created 3 years ago
Reactions:1
Comments:9 (9 by maintainers)

Top GitHub Comments

1reaction

tlambert03commented, May 7, 2020

I can’t get the stack trace if I launched napari from the command line.

not even in the plugin error reporter? under builtins?

ohhh … do you mean you launch it with a filepath and it quits immediately?? hadn’t thought about that!

1reaction

jnicommented, May 7, 2020

Another logic issue: if data is a list BUT the arrays are not in decreasing order of size, we throw an AttributeError:

~/conda/envs/all/lib/python3.8/site-packages/napari/layers/image/image.py in __init__(self, data, rgb, colormap, contrast_limits, gamma, interpolation, rendering, iso_threshold, attenuation, name, metadata, scale, translate, opacity, blending, visible, multiscale)
    162             init_shape = data[0].shape
    163         else:
--> 164             init_shape = data.shape
    165
    166         # Determine if rgb

AttributeError: 'list' object has no attribute 'shape'

In this case this happened because the plugin (I’m still trying to figure out why) ended up providing the arrays in lexicographical (0, 1, 10, 2) order rather than numerical.

We should detect malformed data and quit gracefully (or re-sort, but I like that less), rather than crash with a mysterious error.