minor improvement to ingest pykilosort - update NWB export (include raw data)

Hi Thinh @ttngu207

I did some tests with the latest code, but still got the same error even with Susu and Dave’s data.

Everything looked fine (writing and reading nwb) until I tried to actually retrieve the data inside it. For exampe, when I ran nwb_reload.units.to_dataframe() or nwb_reload.trials.to_dataframe(), I got

...

/opt/conda/lib/python3.7/site-packages/cached_property.py in __get__(self, obj, cls)
     34             return self._wrap_in_coroutine(obj)
     35 
---> 36         value = obj.__dict__[self.func.__name__] = self.func(obj)
     37         return value
     38 

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

/opt/conda/lib/python3.7/site-packages/h5py/_hl/dataset.py in _extent_type(self)
    543     def _extent_type(self):
    544         """Get extent type for this dataset - SIMPLE, SCALAR or NULL"""
--> 545         return self.id.get_space().get_simple_extent_type()
    546 
    547     @cached_property

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5d.pyx in h5py.h5d.DatasetID.get_space()

ValueError: Invalid dataset identifier (invalid dataset identifier)

Please see the last part of this notebook and the same error in this notebook (with my data).

Have you tried the same on your side?

Currently I'm using a workaround to retrieve data by native h5py (see this notebook)

Thanks, Han

mesoscale-activity-map / map-ephys

minor improvement to ingest pykilosort - update NWB export (include raw data) #262