Open bendichter opened 4 years ago
actually the dev branches should work, but I'm not sure about the current releases. I'll let you know when there's a new release.
I updated to pynwb == pynwb-1.1.0.post0.dev5
& hdmf == 1.3.2.post0.dev6
I had no problems during the read out of the NWB files; however, during the export (write out), I encountered this error:
Traceback (most recent call last): File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/backends/hdf5/h5tools.py", line 966, in __list_fill__ dset = parent.create_dataset(name, shape=data_shape, dtype=dtype, io_settings) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/h5py/_hl/group.py", line 105, in create_dataset dsid = dataset.make_new_dset(self, shape, dtype, data, kwds) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/h5py/_hl/dataset.py", line 93, in make_new_dset tid = h5t.py_create(dtype, logical=1) File "h5py/h5t.pyx", line 1450, in h5py.h5t.py_create (-------src-dir--------/h5py/h5t.c:16211) File "h5py/h5t.pyx", line 1470, in h5py.h5t.py_create (-------src-dir--------/h5py/h5t.c:16042) File "h5py/h5t.pyx", line 1531, in h5py.h5t.py_create (-------src-dir--------/h5py/h5t.c:16002) TypeError: No conversion path for dtype: dtype('<U')
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "
When using the updated packages (those published on PyPi), hdmf == 1.3.2
& pynwb == 1.1.0
, I encounter the following error during the export (write out) of the NWB files:
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/RutishauserLabtoNWB/events/newolddelay/python/export/no2nwb_main.py", line 64, in NO2NWB_export nwbfile = no2nwb.no2nwb(NOdata, session_nr, subjects_ini, path_to_data) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/RutishauserLabtoNWB/events/newolddelay/python/export/no2nwb.py", line 241, in no2nwb nwbfile.add_trial_column('stim_on_time', 'the time when the stimulus is shown') File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/file.py", line 527, in add_trial_column self.__check_trials() File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/file.py", line 519, in __check_trials self.trials = TimeIntervals('trials', 'experimental trials') File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/epoch.py", line 31, in __init__ call_docval_func(super(TimeIntervals, self).__init__, kwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func return func(*fargs, **fkwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 942, in __init__ id = ElementIdentifiers('id') File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 401, in __init__ call_docval_func(super(ElementIdentifiers, self).__init__, kwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func return func(*fargs, **fkwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 281, in __init__ call_docval_func(super(NWBData, self).__init__, kwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func return func(*fargs, **fkwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call return func(self, **parsed['args']) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 34, in __init__ call_docval_func(super(NWBBaseType, self).__init__, kwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func return func(*fargs, **fkwargs) File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 436, in func_call raise_from(ExceptionType(msg), None) File "<string>", line 2, in raise_from TypeError: None is not allowed for 'data' (expected 'ndarray, list, tuple, Dataset, HDMFDataset or data', not None)
And I get this error (during the read out) of the NWB files:
`Traceback (most recent call last):
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/build/map.py", line 1207, in construct
obj.init(kwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call
return func(self, parsed['args'])
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 401, in init
call_docval_func(super(ElementIdentifiers, self).init, kwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func
return func(fargs, fkwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call
return func(self, parsed['args'])
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 281, in init
call_docval_func(super(NWBData, self).init, kwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func
return func(fargs, fkwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 438, in func_call
return func(self, parsed['args'])
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/pynwb/core.py", line 34, in init
call_docval_func(super(NWBBaseType, self).init, kwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 327, in call_docval_func
return func(*fargs, **fkwargs)
File "/Users/nandchandravadia/anaconda/lib/python3.5/site-packages/hdmf/utils.py", line 436, in func_call
raise_from(ExceptionType(msg), None)
File "
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "
@nandchandravadia thanks I am seeing this too. I'll raise the issue.
Could you test the code with the latest releases for pynwb and hdmf? I think it should work now