ValueError: TimeSeries.__init__: incorrect shape for 'timestamps' (got '(2, 356918)', expected '(None,)')

[sayali7]

What happened?

Hi,
I was trying to load .nwb file and I'm unable to open it because of the following error:

ValueError: TimeSeries.__init__: incorrect shape for 'timestamps' (got '(2, 356918)', expected '(None,)')

I saw an earlier post about this here ([https://github.com//issues/1180]), but I didn't find the solution.

Steps to Reproduce

from pynwb import NWBHDF5IO, NWBFile

io = NWBHDF5IO("./mouse485342.spikes.nwb", mode="r", load_namespaces=True)
nwbfile = io.read()

Traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in construct(self, **kwargs)
   1255         try:
-> 1256             obj = self.__new_container__(cls, builder.source, parent, builder.attributes.get(self.__spec.id_key()),
   1257                                          **kwargs)

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __new_container__(self, cls, container_source, parent, object_id, **kwargs)
   1268         # the automatic construct process during read, rather than by the user
-> 1269         obj.__init__(**kwargs)
   1270         obj._in_construct_mode = False  # reset to False to indicate that the construction of the object is complete

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
--> 643                 pargs = _check_args(args, kwargs)
    644                 return func(args[0], **pargs)

~/.local/lib/python3.10/site-packages/hdmf/utils.py in _check_args(args, kwargs)
    635                     msg = '%s: %s' % (func.__qualname__, ', '.join(parse_err))
--> 636                     raise ExceptionType(msg)
    637 

ValueError: TimeSeries.__init__: incorrect shape for 'timestamps' (got '(2, 356918)', expected '(None,)')

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

ConstructError                            Traceback (most recent call last)
/tmp/ipykernel_13858/3106899465.py in <module>
      1 io = NWBHDF5IO("./mouse485342.spikes.nwb", mode="r", load_namespaces=True)
----> 2 nwbfile = io.read()

~/.local/lib/python3.10/site-packages/hdmf/backends/hdf5/h5tools.py in read(self, **kwargs)
    477                                        % (self.source, self.__mode))
    478         try:
--> 479             return super().read(**kwargs)
    480         except UnsupportedOperation as e:
    481             if str(e) == 'Cannot build data. There are no values.':  # pragma: no cover

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/backends/io.py in read(self, **kwargs)
     58             # TODO also check that the keys are appropriate. print a better error message
     59             raise UnsupportedOperation('Cannot build data. There are no values.')
---> 60         container = self.__manager.construct(f_builder)
     61         container.read_io = self
     62         if self.herd_path is not None:

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    282                 # we are at the top of the hierarchy,
    283                 # so it must be time to resolve parents
--> 284                 result = self.__type_map.construct(builder, self, None)
    285                 self.__resolve_parents(result)
    286             self.prebuilt(result, builder)

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    793             raise ValueError('No ObjectMapper found for builder of type %s' % dt)
    794         else:
--> 795             return obj_mapper.construct(builder, build_manager, parent)
    796 
    797     @docval({"name": "container", "type": AbstractContainer, "doc": "the container to convert to a Builder"},

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in construct(self, **kwargs)
   1224         cls = manager.get_cls(builder)
   1225         # gather all subspecs
-> 1226         subspecs = self.__get_subspec_values(builder, self.spec, manager)
   1227         # get the constructor argument that each specification corresponds to
   1228         const_args = dict()

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_subspec_values(self, builder, spec, manager)
   1153                         ret[subspec] = self.__flatten(sub_builder, subspec, manager)
   1154             # now process groups and datasets
-> 1155             self.__get_sub_builders(groups, spec.groups, manager, ret)
   1156             self.__get_sub_builders(datasets, spec.datasets, manager, ret)
   1157         elif isinstance(spec, DatasetSpec):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_sub_builders(self, sub_builders, subspecs, manager, ret)
   1204                 if dt is None:
   1205                     # recurse
-> 1206                     ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
   1207                 else:
   1208                     ret[subspec] = manager.construct(sub_builder)

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_subspec_values(self, builder, spec, manager)
   1153                         ret[subspec] = self.__flatten(sub_builder, subspec, manager)
   1154             # now process groups and datasets
-> 1155             self.__get_sub_builders(groups, spec.groups, manager, ret)
   1156             self.__get_sub_builders(datasets, spec.datasets, manager, ret)
   1157         elif isinstance(spec, DatasetSpec):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_sub_builders(self, sub_builders, subspecs, manager, ret)
   1196                 sub_builder = builder_dt.get(dt)
   1197                 if sub_builder is not None:
-> 1198                     sub_builder = self.__flatten(sub_builder, subspec, manager)
   1199                     ret[subspec] = sub_builder
   1200             else:

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __flatten(self, sub_builder, subspec, manager)
   1209 
   1210     def __flatten(self, sub_builder, subspec, manager):
-> 1211         tmp = [manager.construct(b) for b in sub_builder]
   1212         if len(tmp) == 1 and not subspec.is_many():
   1213             tmp = tmp[0]

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in <listcomp>(.0)
   1209 
   1210     def __flatten(self, sub_builder, subspec, manager):
-> 1211         tmp = [manager.construct(b) for b in sub_builder]
   1212         if len(tmp) == 1 and not subspec.is_many():
   1213             tmp = tmp[0]

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    278             if parent_builder is not None:
    279                 parent = self._get_proxy_builder(parent_builder)
--> 280                 result = self.__type_map.construct(builder, self, parent)
    281             else:
    282                 # we are at the top of the hierarchy,

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    793             raise ValueError('No ObjectMapper found for builder of type %s' % dt)
    794         else:
--> 795             return obj_mapper.construct(builder, build_manager, parent)
    796 
    797     @docval({"name": "container", "type": AbstractContainer, "doc": "the container to convert to a Builder"},

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in construct(self, **kwargs)
   1224         cls = manager.get_cls(builder)
   1225         # gather all subspecs
-> 1226         subspecs = self.__get_subspec_values(builder, self.spec, manager)
   1227         # get the constructor argument that each specification corresponds to
   1228         const_args = dict()

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_subspec_values(self, builder, spec, manager)
   1153                         ret[subspec] = self.__flatten(sub_builder, subspec, manager)
   1154             # now process groups and datasets
-> 1155             self.__get_sub_builders(groups, spec.groups, manager, ret)
   1156             self.__get_sub_builders(datasets, spec.datasets, manager, ret)
   1157         elif isinstance(spec, DatasetSpec):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __get_sub_builders(self, sub_builders, subspecs, manager, ret)
   1196                 sub_builder = builder_dt.get(dt)
   1197                 if sub_builder is not None:
-> 1198                     sub_builder = self.__flatten(sub_builder, subspec, manager)
   1199                     ret[subspec] = sub_builder
   1200             else:

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in __flatten(self, sub_builder, subspec, manager)
   1209 
   1210     def __flatten(self, sub_builder, subspec, manager):
-> 1211         tmp = [manager.construct(b) for b in sub_builder]
   1212         if len(tmp) == 1 and not subspec.is_many():
   1213             tmp = tmp[0]

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in <listcomp>(.0)
   1209 
   1210     def __flatten(self, sub_builder, subspec, manager):
-> 1211         tmp = [manager.construct(b) for b in sub_builder]
   1212         if len(tmp) == 1 and not subspec.is_many():
   1213             tmp = tmp[0]

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    278             if parent_builder is not None:
    279                 parent = self._get_proxy_builder(parent_builder)
--> 280                 result = self.__type_map.construct(builder, self, parent)
    281             else:
    282                 # we are at the top of the hierarchy,

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/manager.py in construct(self, **kwargs)
    793             raise ValueError('No ObjectMapper found for builder of type %s' % dt)
    794         else:
--> 795             return obj_mapper.construct(builder, build_manager, parent)
    796 
    797     @docval({"name": "container", "type": AbstractContainer, "doc": "the container to convert to a Builder"},

~/.local/lib/python3.10/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    642             def func_call(*args, **kwargs):
    643                 pargs = _check_args(args, kwargs)
--> 644                 return func(args[0], **pargs)
    645         else:
    646             def func_call(*args, **kwargs):

~/.local/lib/python3.10/site-packages/hdmf/build/objectmapper.py in construct(self, **kwargs)
   1258         except Exception as ex:
   1259             msg = 'Could not construct %s object due to: %s' % (cls.__name__, ex)
-> 1260             raise ConstructError(builder, msg) from ex
   1261         return obj
   1262 

ConstructError: (root/processing/running/running_speed GroupBuilder {'attributes': {'comments': 'no comments', 'description': 'no description', 'help': 'General time series object', 'namespace': 'core', 'neurodata_type': 'TimeSeries'}, 'groups': {}, 'datasets': {'data': root/processing/running/running_speed/data DatasetBuilder {'attributes': {'conversion': 1.0, 'resolution': 0.0, 'unit': 'cm/s'}, 'data': <HDF5 dataset "data": shape (356918,), type "<f8">}, 'timestamps': root/processing/running/running_speed/timestamps DatasetBuilder {'attributes': {'interval': 1, 'unit': 'Seconds'}, 'data': <HDF5 dataset "timestamps": shape (2, 356918), type "<f8">}}, 'links': {}}, "Could not construct TimeSeries object due to: TimeSeries.__init__: incorrect shape for 'timestamps' (got '(2, 356918)', expected '(None,)')")

Operating System

Linux

Python Executable

Python

Python Version

3.10

Package Versions

pynwb: 2.5.0
hdmf: 3.9.0

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[rly]

@sayali7 Where did this NWB file come from? The timestamps field should be one dimensional, not two dimensional, so the file is not a valid NWB file.

[sayali7]

@rly The data was published with this 2021 paper, and can be downloaded from here. I tried reading the file called "mouse485342.spikes.nwb". I am not sure how else to read this data, if you have any alternative suggestions I would greatly appreciate it.

Thanks!