lorenfranklab / franklab-nwb-hack Goto Github PK
View Code? Open in Web Editor NEWFrank Lab code demoing NWB development (e.g. at Hackathons)
Frank Lab code demoing NWB development (e.g. at Hackathons)
Hello, thanks for the notebook, I'm really appreciating the clear description with the mapping of the experiment concepts with pynwb objects.
I'm having a problem loading the file at https://www.dropbox.com/s/92jkkse2c7lm7qe/bon04.nwb?dl=0:
Exception: ('File error', ValueError('Error reading the NWB file.', ("'franklab' not a namespace",)))
I'm using the last dev version. Maybe a patched version of pynwb was used to generate the file?
Thanks in advance.
when trying to run the notebook to convert data to NWB:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-10-04a926256d6c> in <module>
43 pos_series = position['spatial_series']
44 sleep_fig = flh.plot_position_by_epochs(animal, pos_series, np.array(epoch_time_ivls),
---> 45 sleep_epochs, 'Sleep box epochs: animal %s, day %s' % (animal, day))
46 wtrackA_fig = flh.plot_position_by_epochs(animal, pos_series, np.array(epoch_time_ivls),
47 wtrackA_epochs, 'W-track A epochs: animal %s, day %s' % (animal, day))
~/dev/franklab-nwb-hack/hackathon-6/fl_extension_helpers.py in plot_position_by_epochs(animal, pos_series, epoch_ivls, epochs, title)
227 samples = pd.DataFrame(data=pos_series.data[()], columns=['x', 'y'])
228 sample_times = pos_series.timestamps[()]
--> 229 valid_intervals = query.TimeIntervals(epoch_ivls)
230 position = query.ContinuousData(samples=samples,
231 sample_times=sample_times,
~/dev/franklab-nwb-hack/hackathon-6/nwb_query.py in __init__(self, bounds)
55
56 def __init__(self, bounds=None):
---> 57 self.intervals = self.__make_intervals(bounds)
58
59 def __make_intervals(self, bounds):
~/dev/franklab-nwb-hack/hackathon-6/nwb_query.py in __make_intervals(self, bounds)
63 elif (isinstance(bounds, np.ndarray) and bounds.ndim == 2 and bounds.shape[1] == 2):
64 # input is a 2D (m x 2) numpy array
---> 65 intervals = iv.empty()
66 for ivl in bounds:
67 intervals = intervals | iv.closed(*ivl)
AttributeError: module 'intervals' has no attribute 'empty'
@tjd2002 What "intervals" package are you using? Running pip install intervals
does not seem to work.
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