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AllenInstitute / npc_sessions

Tools for accessing and packaging data from behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.
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`690706_2023-11-28` units issue #97

Open bjhardcastle opened 4 months ago

bjhardcastle commented 4 months ago 
22:23:49 | root | INFO | Processing 690706_2023-11-28
22:23:56 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:12 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:12 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:17 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:33 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:41 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000
22:24:44 | aind-codeocean-api | INFO | https://codeocean.allenneuraldynamics.org/api/v1/data_assets?query=subject+id%3A+690706&start=0&limit=1000

fetching units:   0%|                                 | 0/6 [00:00<?, ?device/s]22:24:54 | aiobotocore.credentials | INFO | Found credentials in environment variables.
22:24:54 | aiobotocore.credentials | INFO | Found credentials in environment variables.
22:24:56 | aiobotocore.credentials | INFO | Found credentials in environment variables.
22:24:56 | aiobotocore.credentials | INFO | Found credentials in environment variables.

fetching units:  17%|████▏                    | 1/6 [00:02<00:13,  2.77s/device]

fetching units:  33%|████████▎                | 2/6 [00:08<00:18,  4.63s/device]

fetching units:  50%|████████████▌            | 3/6 [00:10<00:09,  3.17s/device]

fetching units:  67%|████████████████▋        | 4/6 [00:10<00:04,  2.06s/device]

fetching units:  83%|████████████████████▊    | 5/6 [00:10<00:01,  1.47s/device]

fetching units: 100%|█████████████████████████| 6/6 [00:11<00:00,  1.02s/device]
fetching units: 100%|█████████████████████████| 6/6 [00:11<00:00,  1.85s/device]

Processing jobs:  27%|██▋       | 28/103 [2:42:50<7:16:11, 348.95s/it]
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/scripts/write_sessions_to_nwb.py", line 90, in <module>
    main()
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/scripts/write_sessions_to_nwb.py", line 86, in main
    write_sessions_to_cache(**kwargs)  # type: ignore[misc, arg-type]
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/scripts/write_sessions_to_nwb.py", line 75, in write_sessions_to_cache
    helper(
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/scripts/write_sessions_to_nwb.py", line 27, in helper
    npc_sessions.write_and_upload_session_nwb(
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/utils/cache.py", line 192, in write_and_upload_session_nwb
    path = session.write_nwb_zarr(path=path, metadata_only=metadata_only)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 369, in write_nwb_zarr
    nwb = self.nwb if not metadata_only else self.metadata
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 332, in nwb
    analysis=self._analysis,
  File "/opt/conda/lib/python3.9/site-packages/npc_io/cached_property.py", line 78, in __get__
    val = self.func(instance)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 750, in _analysis
    modules.append(self.all_spike_histograms)
  File "/opt/conda/lib/python3.9/site-packages/npc_io/cached_property.py", line 78, in __get__
    val = self.func(instance)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 2632, in all_spike_histograms
    for probe in sorted(set(self.units.electrode_group_name[:])):
  File "/opt/conda/lib/python3.9/site-packages/npc_io/cached_property.py", line 78, in __get__
    val = self.func(instance)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 1429, in units
    for column in self._units.columns:
  File "/opt/conda/lib/python3.9/site-packages/npc_io/cached_property.py", line 78, in __get__
    val = self.func(instance)
  File "/opt/conda/lib/python3.9/site-packages/npc_sessions/sessions.py", line 1368, in _units
    units=npc_ephys.make_units_table_from_spike_interface_ks25(
  File "/opt/conda/lib/python3.9/site-packages/npc_ephys/units.py", line 284, in make_units_table_from_spike_interface_ks25
    return pd.concat(
  File "/opt/conda/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 382, in concat
    op = _Concatenator(
  File "/opt/conda/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 445, in __init__
    objs, keys = self._clean_keys_and_objs(objs, keys)
  File "/opt/conda/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 507, in _clean_keys_and_objs
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate