sridharjagannathan / pyroglancer Goto Github PK

Traceback (most recent call last):
  File "/Users/sri/Documents/Python/neuroglancer/python/neuroglancer/sockjs_handler.py", line 52, in _on_changed
    provider = self.credentials_manager.get(parsed_key['key'], parsed_key.get('parameters'))
  File "/Users/sri/Documents/Python/neuroglancer/python/neuroglancer/credentials_provider.py", line 31, in get
    return self._providers[key](parameters)
KeyError: 'DVID'

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  Using cached pyOpenSSL-16.0.0-py2.py3-none-any.whl (45 kB)
  Using cached pyOpenSSL-0.15.1-py2.py3-none-any.whl (102 kB)
  Using cached pyOpenSSL-0.15-py2.py3-none-any.whl (102 kB)
  Using cached pyOpenSSL-0.14.tar.gz (128 kB)

{"@type": "neuroglancer_segment_properties", "inline": {"ids": ["100", "101", "102"], "properties": [{"id": "label", "type": "label", "values": ["AAA", "BBB", "CCC"]}]}}

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-12-63b0b2ba0a2e> in <module>
----> 1 tmpviewer = add_flywirelayer(flywireurl2dict(shorturl), layer_kws = {'type': 'volumes','name': 'vfb_' + vfbmeshes_dict[first_mesh].name,
      2                                                         'source': vfb2flywiremeshes[first_mesh],'color': 'magenta'})

/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pyroglancer/flywire.py in flywireurl2dict(flywireurl)
     56     if 'json_url' in querystring:
     57         # Get the layers from the json file as query
---> 58         token = cloudvolume.secrets.chunkedgraph_credentials['token']
     59         response = requests.get(querystring['json_url'][0], headers={'Authorization': f"Bearer {token}"})
     60         response.raise_for_status()

AttributeError: module 'cloudvolume.secrets' has no attribute 'chunkedgraph_credentials'

AttributeError                            Traceback (most recent call last)
Input In [31], in <module>
----> 1 uploadskeletons(swcs, skel_ids, skel_names, hostdirectory, 'longest_neurites')

File ~/miniforge3/envs/newpyg2/lib/python3.9/site-packages/pyroglancer/skeletons.py:143, in uploadskeletons(skelsource, skelseglist, skelnamelist, path, layer_name)
    121 def uploadskeletons(skelsource, skelseglist, skelnamelist, path, layer_name):
    122     """Upload skeleton (of cloudvolume class) to a local server.
    123 
    124     Parameters
   (...)
    140         object of cloudvolume class
    141     """
    142     info = {"@type": "neuroglancer_skeletons",
--> 143             "transform": skelsource[0].transform.flatten(),
    144             "vertex_attributes": [{"id": "radius", "data_type": "float32", "num_components": 1}],
    145             "scales": "um"}
    146     path = 'file://' + path + '/precomputed/' + layer_name
    147     cv = CloudVolume(path, info=info)

File ~/miniforge3/envs/newpyg2/lib/python3.9/site-packages/navis/core/skeleton.py:199, in TreeNeuron.__getattr__(self, key)
    193 """We will use this magic method to calculate some attributes on-demand."""
    194 # Note that we're mixing @property and __getattr__ which causes problems:
    195 # if a @property raises an Exception, Python falls back to __getattr__
    196 # and traceback is lost!
    197 
    198 # Last ditch effort - maybe the base class knows the key?
--> 199 return super().__getattr__(key)

File ~/miniforge3/envs/newpyg2/lib/python3.9/site-packages/navis/core/base.py:156, in BaseNeuron.__getattr__(self, key)
    153             return 'NA'
    154     return None
--> 156 raise AttributeError(f'Attribute "{key}" not found')

AttributeError: Attribute "transform" not found