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AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data
https://allensdk.readthedocs.io/en/latest/
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KeyError: 'sweeps_by_type' #2711

Open win2dvp21 opened 11 months ago

win2dvp21 commented 11 months ago

Describe the bug I want to simulate the model you provide in cell_type, but I keep getting a key error: sweeps_by_type is not present, and indeed it is not present in the manifest.json I downloaded.

To Reproduce I followed your documetation. Here

Download biophysical model

from allensdk.api.queries.biophysical_api import BiophysicalApi

bp = BiophysicalApi()
bp.cache_stimulus = True
neuronal_model_id = 473863035
bp.cache_data(neuronal_model_id, working_directory='neuronal_model')

Run the simulation

cd neuronal_model
nrnivmodl ./modfiles # until this code, it was working fine.
python3 -m allensdk.model.biophysical.runner manifest.json # perisomatic models

Expected behavior I just want the model simulation you provided to work.

Actual Behavior python3 -m allensdk.model.biophysical.runner manifest.json

When I run the above code, I get the following error.

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/python3.8/site-packages/allensdk/model/biophysical/runner.py", li                                                                                                                        ne 119, in run_sync
    sweeps_by_type = run_params['sweeps_by_type']
KeyError: 'sweeps_by_type'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/python3.8/site-packages/allensdk/model/biophysical/runner.py", li                                                                                                                        ne 240, in <module>
    run(vars(schema))
  File "/python3.8/site-packages/allensdk/model/biophysical/runner.py", li                                                                                                                        ne 87, in run
    pool.map(partial(run_sync, description), [[sweep] for sweep in sweeps])
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
KeyError: 'sweeps_by_type'

Environment (please complete the following information):

Additional context After seeing the above error, I checked the manifest.json file and it didn't have sweeps_by_type, so I downloaded the model from LINK via Download model, checked the manifest.json of that file and it had sweeps_by_type. Then I overwrote it into the existing manifest.json, but I still got the error.

The error I was getting was the following, repeated over and over again.

/allensdk/ephys/ephys_features.py:1143: RuntimeWarning: Mean of empty slice.
  new_thresh_frac = min_thresh / all_upstrokes.mean()
/python3.8/site-packages/numpy/core/_methods.py:188: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)