Cannot get sweep number from nwb file

Technical
1

Hi, I want to load the nwb files from this dataset (DANDI Archive) but see the error when getting the sweep.

Here is the code:

from allensdk.core.nwb_data_set import NwbDataSet
file_name = 'C:/Users/swamylab/Downloads/sub-612905668_ses-614728579_icephys.nwb'
data_set = NwbDataSet(file_name)
data_set.get_experiment_sweep_numbers()

Here is the error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[36], line 4
      2 file_name = 'C:/Users/swamylab/Downloads/sub-612905668_ses-614728579_icephys.nwb'
      3 data_set = NwbDataSet(file_name)
----> 4 data_set.get_experiment_sweep_numbers()

File ~\anaconda3\envs\allensdk\Lib\site-packages\allensdk\core\nwb_data_set.py:320, in NwbDataSet.get_experiment_sweep_numbers(self)
    315 """ Get all of the sweep numbers for experiment epochs in the file,
    316 not including test sweeps. """
    318 with h5py.File(self.file_name, 'r') as f:
    319     sweeps = [int(e.split('_')[1])
--> 320               for e in f['epochs'].keys() if
    321               e.startswith('Experiment_')]
    322     return sweeps

File h5py\_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py\_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File ~\anaconda3\envs\allensdk\Lib\site-packages\h5py\_hl\group.py:357, in Group.__getitem__(self, name)
    355         raise ValueError("Invalid HDF5 object reference")
    356 elif isinstance(name, (bytes, str)):
--> 357     oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
    358 else:
    359     raise TypeError("Accessing a group is done with bytes or str, "
    360                     "not {}".format(type(name)))

File h5py\_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py\_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py\h5o.pyx:189, in h5py.h5o.open()

KeyError: "Unable to synchronously open object (object 'epochs' doesn't exist)"
2

I would recommend using the IPFX software package to work with the Patch-seq NWB files.

You would use code like this to do the equivalent of what you posted:

from ipfx.dataset.create import create_ephys_data_set

file_name = '/path/to/the/file/sub-612905668_ses-614728579_icephys.nwb'
data_set = create_ephys_data_set(nwb_file=file_name)
data_set.get_sweep_numbers()
3

Hi Gouwens, thank you for the instant reply and yes it works!

1 Like