writing nwb file with position data fails

[ajtritt]

Originally reported by: Loren Frank (Bitbucket: lmfrnk, GitHub: Unknown)

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Traceback (most recent call last):
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 280, in scalar_fill
dset = parent.require_dataset(name, data=data, shape=None, dtype=dtype)
File "/Users/loren/anaconda3/lib/python3.6/site-packages/h5py/_hl/group.py", line 136, in require_dataset
raise TypeError("Shapes do not match (existing %s vs new %s)" % (dset.shape, shape))
TypeError: Shapes do not match (existing () vs new None)

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

Traceback (most recent call last):
File "/Users/loren/Src/NWB/franklabnwb/convert_nspike.py", line 486, in
io.write(nwbf)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/io.py", line 25, in write
self.write_builder(f_builder)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 116, in write_builder
write_group(self.__file, name, gbldr.groups, gbldr.datasets, gbldr.attributes, gbldr.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 157, in write_group
builder.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 157, in write_group
builder.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 157, in write_group
builder.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 164, in write_group
builder.get('attributes'))
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 251, in write_dataset
dset = scalar_fill(parent, name, data)
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 282, in scalar_fill
raise Exception("Could not create scalar dataset %s in %s" % (name, parent.name)) from exc
Exception: Could not create scalar dataset reference_frame in /processing/Behavior Module/Position/Position Data

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• Bitbucket: https://bitbucket.org/lblneuro/pynwb/issue/34

[ajtritt]

Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):

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Hi Loren,

This looks like a problem when trying to create a file that already exists. I added some logic to deal with this. Please update and let me know if you still get this error.

Andrew

[ajtritt]

Original comment by Loren Frank (Bitbucket: lmfrnk, GitHub: Unknown):

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Great; I’ll test it out as soon as I can and get back to you…

Loren

Loren M. Frank

Professor
Howard Hughes Medical Institute
Kavli Institute for Fundamental Neuroscience
Department of Physiology
University of California, San Francisco
Office Phone: 415-502-7357

[ajtritt]

Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):

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From Loren:

Traceback (most recent call last):
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 327, in list_fill
data_dtype = __get_type(data)
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 221, in __get_type
raise ValueError('cannot determine type for empty data')
ValueError: cannot determine type for empty data

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

Traceback (most recent call last):
File "/Users/loren/Src/NWB/franklabnwb/convert_nspike.py", line 492, in
io.write(nwbf)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/io.py", line 25, in write
self.write_builder(f_builder)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 120, in write_builder
write_group(self.__file, name, gbldr.groups, gbldr.datasets, gbldr.attributes, gbldr.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 161, in write_group
builder.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 168, in write_group
builder.get('attributes'))
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 261, in write_dataset
dset = list_fill(parent, name, data)
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 329, in list_fill
raise Exception('cannot add %s to %s - could not determine type' % (name, parent.name)) from exc
Exception: cannot add tags to /epochs/day 3 - could not determine type

Process finished with exit code 1

[ajtritt]

Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):

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Merged in issue_34 (pull request #67)

fixing issue #34 and issue #35