napari failing on labels v0.2 version of idr:6001247

[joshmoore]

(z) /tmp $NAPARI_CATCH_ERRORS=0 napari 6001247.zarr/
/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/__main__.py:419: UserWarning: pythonw executable not found.
To unfreeze the menubar on macOS, click away from napari to another app, then reactivate napari. To avoid this problem, please install python.app in conda using:
conda install -c conda-forge python.app
  warnings.warn(msg)
WARNING: Layer-backing can not be explicitly controlled on 10.14 when built against the 10.14 SDK
15:00:36 WARNING Layer-backing can not be explicitly controlled on 10.14 when built against the 10.14 SDK
Traceback (most recent call last):
  File "/usr/local/anaconda3/envs/z/bin/napari", line 8, in <module>
    sys.exit(main())
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/__main__.py", line 420, in main
    _run()
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/__main__.py", line 304, in _run
    viewer = view_path(  # noqa: F841
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/view_layers.py", line 169, in view_path
    return _make_viewer_then('open', args, kwargs)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/view_layers.py", line 119, in _make_viewer_then
    method(*args, **kwargs)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/components/viewer_model.py", line 856, in open
    self._add_layers_with_plugins(
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/components/viewer_model.py", line 929, in _add_layers_with_plugins
    added.extend(self._add_layer_from_data(*_data))
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/components/viewer_model.py", line 1006, in _add_layer_from_data
    raise exc
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/components/viewer_model.py", line 1003, in _add_layer_from_data
    layer = add_method(data, **(meta or {}))
  File "<string>", line 4, in add_labels
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 202, in __init__
    self._properties, self._label_index = self._prepare_properties(
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 429, in _prepare_properties
    label_index = cls._map_index(properties)
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 511, in _map_index
    max_len = max(len(x) for x in properties.values())
  File "/usr/local/anaconda3/envs/z/lib/python3.9/site-packages/napari/layers/labels/labels.py", line 511, in <genexpr>
    max_len = max(len(x) for x in properties.values())
TypeError: len() of unsized object

[jni]

eek! @joshmoore what are you passing in as properties=? Looking at the _prepare_properties code, we check for None or empty dicts or dataframes... Anyway here's the offending function:

https://github.com/napari/napari/blob/d310847f0c79f062daadecb8a159e8972c074470/napari/layers/labels/labels.py#L507-L512

and as far as I can tell that input should indeed be a Dict[str: np.ndarray] unless you are passing in something unexpected here... But I might be missing something.

Can this be replicated with an IDR URL?

[joshmoore]

Not offhand, but then I've upgraded in an attempt to get things working. I imagine I need to get the above into an integration test of some form.

[will-moore]

I'd missed this issue but found the same bug yesterday. See https://forum.image.sc/t/napari-labels-layer-properties/57649

At some point in the past, I believe the labels properties was a dict of label_value (int): {"key": "value"} but it is now "key": [list, of, values, for, each, label].

Not sure when that change happened. Don't know how to find older napari docs and couldn't find a relevant PR.