The MiCrONS Datasets tutorial

[aquineuro]

I followed the instructions from https://navis.readthedocs.io/en/latest/source/tutorials/microns_tut.html and I got the following error when I try to promp the content of the variable "inh". Please could you help me or tell me where I should look like for an answer. Thanks a lot. Sébastien

Traceback (most recent call last):
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\IPython\core\interactiveshell.py", line 3437, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-20-2830aab9af73>", line 2, in <module>
    inh = mi.fetch_neurons(inh_ids, lod=2, with_synapses=False)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\navis\interfaces\microns.py", line 180, in fetch_neurons
    vol = get_cloudvol(url)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\navis\interfaces\microns.py", line 82, in get_cloudvol
    return cv.CloudVolume(url, cache=cache, use_https=True, progress=False)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\cloudvolume.py", line 228, in __new__
    return REGISTERED_PLUGINS[path.format](**kwargs)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\datasource\precomputed\__init__.py", line 99, in create_precomputed
    mesh = PrecomputedMeshSource(meta, cache_service, config, readonly)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\datasource\precomputed\mesh\__init__.py", line 17, in __new__
    mesh_meta = PrecomputedMeshMetadata(meta, cache)
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\datasource\precomputed\mesh\metadata.py", line 17, in __init__
    self.info = self.fetch_info()
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\datasource\precomputed\mesh\metadata.py", line 71, in fetch_info
    info = self.cache.download_json(self.meta.join(self.mesh_path, 'info'))
  File "C:\Users\sebas\anaconda3\envs\test\lib\site-packages\cloudvolume\cacheservice.py", line 343, in download_json
    res = res[path]
KeyError: 'mesh/info'

[schlegelp]

This error originates from the cloud-volume package which navis uses to fetch meshes, etc. from MICRoNS datasets. It looks like it's failing to read the meta data when first initialising the connection.

I just tried running it on my machine and it works just fine. Two things for you to try/report back on:

1. Restart your Python session and try again - maybe the backend for the MICrONS data had a temporary hiccup.
2. Make sure you have the most up-to-date version of cloud-volume (I tried with both the most recent 7.0.0 and an earlier 6.1.0.

Let me know if one of the two works. Otherwise we'll have to dig deeper.

[aquineuro]

Thanks for answering quickly, I appreciate!

1. I restarted my ipython
2. I have the version 7.0.0 of cloud-volume

But still I can't fetch the data, is there any authentification I could have missed or did badly ?

Thanks again. Sébastien

[schlegelp]

Mhm.... that's strange. Could you perhaps try running this:

>>> from cloudvolume import CloudVolume
>>> vol = CloudVolume('precomputed://gs://iarpa_microns/minnie/minnie65/seg', cache=True, use_https=True)

See if that throws the same error?

[aquineuro]

Yes I got the same error.

[aquineuro]

I am working on windows 10.

[aquineuro]

If I do this ; vol = CloudVolume('precomputed://gs://iarpa_microns/minnie/minnie65/seg') I don't get an error

[aquineuro]

It's the "cache=True" argument which is causing the error

[schlegelp]

Ah OK. I can push a workaround for that issue to navis but will also open an issue in the cloud-volume repo. Will keep you posted here.

[aquineuro]

Thank you very much .

[schlegelp]

FYI: this should be fixed if you update to the newest version of cloud-volume.

[schlegelp]

Closing assuming this is fixed.