Comments (9)
alejoe91
commented on June 14, 2024
Hi @NilsNyberg
What version of h5py are you using? If it's >= 3, can you try again after downgrading to 2.10.0? The new version of h5py introduced some API changes at different levels and many packages still need to be updated.
Let me know if that works
Alessio
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NilsNyberg
commented on June 14, 2024
I was using the newest version, but tried downgrading to 2.10.0 now. I have confirmed it successfully downgraded to 2.10.0 via pip show h5py. I also again open the Anaconda console with administrative privileges. However, when I run the code I get the same error message.
I can also mention that I have tried different NWB files of different sizes (ranging from 0.66mb to 20+ gb) and I get the same error message on all of them. I haven't had a chance to try another computer yet, but gonna try to do it this afternoon.
I have attached the message again, in case you want to have a look:
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-5-5b1002091086> in <module>
3
4 recording_folder = 'nwb-dataset/'
----> 5 recording = se.NwbRecordingExtractor(recording_folder)
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\spikeextractors\extractors\nwbextractors\nwbextractors.py in __init__(self, file_path, electrical_series_name)
156 se.RecordingExtractor.__init__(self)
157 self._path = str(file_path)
--> 158 with NWBHDF5IO(self._path, 'r') as io:
159 nwbfile = io.read()
160 if electrical_series_name is not None:
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\pynwb\__init__.py in __init__(self, **kwargs)
244 elif manager is None:
245 manager = get_manager()
--> 246 super(NWBHDF5IO, self).__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm)
247
248 @docval({'name': 'src_io', 'type': HDMFIO, 'doc': 'the HDMFIO object for reading the data to export'},
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\backends\hdf5\h5tools.py in __init__(self, **kwargs)
66 self.__mode = mode
67 self.__file = file_obj
---> 68 super().__init__(manager, source=path)
69 self.__built = dict() # keep track of each builder for each dataset/group/link for each file
70 self.__read = dict() # keep track of which files have been read. Key is the filename value is the builder
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\backends\io.py in __init__(self, **kwargs)
15 self.__built = dict()
16 self.__source = getargs('source', kwargs)
---> 17 self.open()
18
19 @property
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\backends\hdf5\h5tools.py in open(self)
682 else:
683 kwargs = {}
--> 684 self.__file = File(self.source, open_flag, **kwargs)
685
686 def close(self):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\h5py\_hl\files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, **kwds)
406 fid = make_fid(name, mode, userblock_size,
407 fapl, fcpl=make_fcpl(track_order=track_order),
--> 408 swmr=swmr)
409
410 if isinstance(libver, tuple):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\h5py\_hl\files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
171 if swmr and swmr_support:
172 flags |= h5f.ACC_SWMR_READ
--> 173 fid = h5f.open(name, flags, fapl=fapl)
174 elif mode == 'r+':
175 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
h5py\_objects.pyx in h5py._objects.with_phil.wrapper()
h5py\_objects.pyx in h5py._objects.with_phil.wrapper()
h5py\h5f.pyx in h5py.h5f.open()
OSError: Unable to open file (unable to open file: name = 'nwb-dataset/', errno = 13, error message = 'Permission denied', flags = 0, o_flags = 0)
Any other suggestions for what might be causing the permission error?
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alejoe91
commented on June 14, 2024
Can you try to open it directly in NWB?
import pynwb
with pynwb.NWBHDF5IO('file-path.nwb', 'r') as io:
nwbfile = io.read()
If this fail as well, then the problem is somewher in the nwb file. Maybe you don't have the right file permissions?
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NilsNyberg
commented on June 14, 2024
I get the "No data_type found for builder root" error (I have attached it below). Doing a quick google search and found this: NeurodataWithoutBorders/pynwb#1077 suggesting this is likely due to the file being in NWB 1.0 and not 2.0. Does spikeinterface only work with NWB 2.0? If so, is there any way to get spikeinterface to work with NWB 1.0 as well?Afaik that is the only version of NWB that can be outputted by Open Ephys recordings (you can always record in another format and convert to NWB later I suppose, but would be great if spikeinterface would work with all the formats directly outputted by open ephys).
Using the following code
import pynwb
fpath = 'E:/spiketutorials/NWB_Developer_Breakout_Session_Sep2020/nwb-dataset/experiment_1.nwb'
with pynwb.NWBHDF5IO('experiment_1.nwb', 'r') as io:
nwbfile = io.read()
gives
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-9-d7594c4c141d> in <module>
2 fpath = 'E:/spiketutorials/NWB_Developer_Breakout_Session_Sep2020/nwb-dataset/experiment_1.nwb'
3 with pynwb.NWBHDF5IO('experiment_1.nwb', 'r') as io:
----> 4 nwbfile = io.read()
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\backends\hdf5\h5tools.py in read(self, **kwargs)
412 % (self.source, self.__mode))
413 try:
--> 414 return call_docval_func(super().read, kwargs)
415 except UnsupportedOperation as e:
416 if str(e) == 'Cannot build data. There are no values.': # pragma: no cover
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in call_docval_func(func, kwargs)
403 def call_docval_func(func, kwargs):
404 fargs, fkwargs = fmt_docval_args(func, kwargs)
--> 405 return func(*fargs, **fkwargs)
406
407
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\backends\io.py in read(self, **kwargs)
34 # TODO also check that the keys are appropriate. print a better error message
35 raise UnsupportedOperation('Cannot build data. There are no values.')
---> 36 container = self.__manager.construct(f_builder)
37 return container
38
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\build\manager.py in construct(self, **kwargs)
236 # we are at the top of the hierarchy,
237 # so it must be time to resolve parents
--> 238 result = self.__type_map.construct(builder, self, None)
239 self.__resolve_parents(result)
240 self.prebuilt(result, builder)
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\build\manager.py in construct(self, **kwargs)
850 if build_manager is None:
851 build_manager = BuildManager(self)
--> 852 obj_mapper = self.get_map(builder)
853 if obj_mapper is None:
854 dt = builder.attributes[self.namespace_catalog.group_spec_cls.type_key()]
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\build\manager.py in get_map(self, **kwargs)
770 data_type = self.get_builder_dt(obj)
771 namespace = self.get_builder_ns(obj)
--> 772 container_cls = self.get_cls(obj)
773 # now build the ObjectMapper class
774 mapper = self.__mappers.get(container_cls)
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\utils.py in func_call(*args, **kwargs)
559 def func_call(*args, **kwargs):
560 pargs = _check_args(args, kwargs)
--> 561 return func(args[0], **pargs)
562 else:
563 def func_call(*args, **kwargs):
c:\users\julie\miniconda3\envs\spiketutorial\lib\site-packages\hdmf\build\manager.py in get_cls(self, **kwargs)
699 data_type = self.get_builder_dt(builder)
700 if data_type is None:
--> 701 raise ValueError("No data_type found for builder %s" % builder.path)
702 namespace = self.get_builder_ns(builder)
703 if namespace is None:
ValueError: No data_type found for builder root
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alejoe91
commented on June 14, 2024
@bendichter maybe it'd make sense to keep back-compatibility with NWB 1.0? But I guess that would require to have an old version of pynwb installed? Is there a way to open 1.0 files with the current pynwb version?
@NilsNyberg at the moment only 2.0 is supported unfortunately. Sorry about that!
I recommend saving Open Ephys data to binary and using the OpenEphysRecordingExtractor for the moment
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NilsNyberg
commented on June 14, 2024
Thanks for the help (again!) - yeah I think for future-proofing I'd better move to binary instead... It's a shame Open Ephys does not yet give the availability to save directly to NWB 2.0, but I think its a work in progress at least.
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alejoe91
commented on June 14, 2024
No worries at all :)
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bendichter
commented on June 14, 2024
@alejoe91, unfortunately there is no way to open NWB 1.0 files with pynwb, and they are unlikely to support it going forward. It would be nice to support OpenEphys data in spikeextractors, particularly if in a version of NWB. It would be easiest to do this via h5py. @NilsNyberg, can you share an example file?
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samuelgarcia
commented on June 14, 2024
Can we close this ?
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