error opening icephys file #115
Description
dandiset: 001183
path: sub-2020-02-15-0006/sub-2020-02-15-0006_icephys.nwb
This is an icephys file. I can download it and open it in PyNWB, but when I try to open it in using lindi it throws an error.
# this works
import pynwb
fpath = "/Users/bdichter/Downloads/sub-2020-02-15-0006_icephys.nwb"
pynwb.NWBHDF5IO(fpath,"r").read()
# this does not work
import lindi
download_url = 'https://api.dandiarchive.org/api/dandisets/001183/versions/draft/assets/89d74f56-fa79-4162-b6e6-cd5c2659f7ad/download/'
f = lindi.LindiH5pyFile.from_hdf5_file(download_url)
nwb = pynwb.NWBHDF5IO(file=f, mode='r').read()---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[135], line 4
2 download_url = 'https://api.dandiarchive.org/api/dandisets/001183/versions/draft/assets/89d74f56-fa79-4162-b6e6-cd5c2659f7ad/download/'
3 f = lindi.LindiH5pyFile.from_hdf5_file(download_url)
----> 4 nwb = pynwb.NWBHDF5IO(file=f, mode='r').read()
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/pynwb/__init__.py:489, in NWBHDF5IO.read(self, **kwargs)
486 raise TypeError("NWB version %s not supported. PyNWB supports NWB files version 2 and above." %
487 str(file_version_str))
488 # read the file
--> 489 file = super().read(**kwargs)
490 return file
File ~/miniconda3/lib/python3.12/site-packages/hdmf/backends/hdf5/h5tools.py:458, in HDF5IO.read(self, **kwargs)
455 raise UnsupportedOperation("Cannot read from file %s in mode '%s'. Please use mode 'r', 'r+', or 'a'."
456 % (self.source, self.__mode))
457 try:
--> 458 return super().read(**kwargs)
459 except UnsupportedOperation as e:
460 if str(e) == 'Cannot build data. There are no values.': # pragma: no cover
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/backends/io.py:60, in HDMFIO.read(self, **kwargs)
57 if all(len(v) == 0 for v in f_builder.values()):
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:
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:286, in BuildManager.construct(self, **kwargs)
282 result = self.__type_map.construct(builder, self, parent)
283 else:
284 # we are at the top of the hierarchy,
285 # so it must be time to resolve parents
--> 286 result = self.__type_map.construct(builder, self, None)
287 self.__resolve_parents(result)
288 self.prebuilt(result, builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:813, in TypeMap.construct(self, **kwargs)
811 raise ValueError('No ObjectMapper found for builder of type %s' % dt)
812 else:
--> 813 return obj_mapper.construct(builder, build_manager, parent)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/pynwb/io/file.py:161, in NWBFileMap.construct(self, **kwargs)
157 builder.groups['bands'].attributes['namespace'] = 'core'
159 apply_to_child_builders(nwbfile_builder, [update_builder_frequency_bands_table])
--> 161 return super().construct(**kwargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1338, in ObjectMapper.construct(self, **kwargs)
1336 cls = manager.get_cls(builder)
1337 # gather all subspecs
-> 1338 subspecs = self.__get_subspec_values(builder, self.spec, manager)
1339 # get the constructor argument that each specification corresponds to
1340 const_args = dict()
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1267, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1265 ret[subspec] = self.__flatten(sub_builder, subspec, manager)
1266 # now process groups and datasets
-> 1267 self.__get_sub_builders(groups, spec.groups, manager, ret)
1268 self.__get_sub_builders(datasets, spec.datasets, manager, ret)
1269 elif isinstance(spec, DatasetSpec):
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1318, in ObjectMapper.__get_sub_builders(self, sub_builders, subspecs, manager, ret)
1315 continue
1316 if dt is None:
1317 # recurse
-> 1318 ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
1319 else:
1320 ret[subspec] = manager.construct(sub_builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1267, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1265 ret[subspec] = self.__flatten(sub_builder, subspec, manager)
1266 # now process groups and datasets
-> 1267 self.__get_sub_builders(groups, spec.groups, manager, ret)
1268 self.__get_sub_builders(datasets, spec.datasets, manager, ret)
1269 elif isinstance(spec, DatasetSpec):
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1318, in ObjectMapper.__get_sub_builders(self, sub_builders, subspecs, manager, ret)
1315 continue
1316 if dt is None:
1317 # recurse
-> 1318 ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
1319 else:
1320 ret[subspec] = manager.construct(sub_builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1267, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1265 ret[subspec] = self.__flatten(sub_builder, subspec, manager)
1266 # now process groups and datasets
-> 1267 self.__get_sub_builders(groups, spec.groups, manager, ret)
1268 self.__get_sub_builders(datasets, spec.datasets, manager, ret)
1269 elif isinstance(spec, DatasetSpec):
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1320, in ObjectMapper.__get_sub_builders(self, sub_builders, subspecs, manager, ret)
1318 ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
1319 else:
-> 1320 ret[subspec] = manager.construct(sub_builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:282, in BuildManager.construct(self, **kwargs)
280 if parent_builder is not None:
281 parent = self._get_proxy_builder(parent_builder)
--> 282 result = self.__type_map.construct(builder, self, parent)
283 else:
284 # we are at the top of the hierarchy,
285 # so it must be time to resolve parents
286 result = self.__type_map.construct(builder, self, None)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:813, in TypeMap.construct(self, **kwargs)
811 raise ValueError('No ObjectMapper found for builder of type %s' % dt)
812 else:
--> 813 return obj_mapper.construct(builder, build_manager, parent)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1338, in ObjectMapper.construct(self, **kwargs)
1336 cls = manager.get_cls(builder)
1337 # gather all subspecs
-> 1338 subspecs = self.__get_subspec_values(builder, self.spec, manager)
1339 # get the constructor argument that each specification corresponds to
1340 const_args = dict()
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1267, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1265 ret[subspec] = self.__flatten(sub_builder, subspec, manager)
1266 # now process groups and datasets
-> 1267 self.__get_sub_builders(groups, spec.groups, manager, ret)
1268 self.__get_sub_builders(datasets, spec.datasets, manager, ret)
1269 elif isinstance(spec, DatasetSpec):
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1320, in ObjectMapper.__get_sub_builders(self, sub_builders, subspecs, manager, ret)
1318 ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
1319 else:
-> 1320 ret[subspec] = manager.construct(sub_builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:282, in BuildManager.construct(self, **kwargs)
280 if parent_builder is not None:
281 parent = self._get_proxy_builder(parent_builder)
--> 282 result = self.__type_map.construct(builder, self, parent)
283 else:
284 # we are at the top of the hierarchy,
285 # so it must be time to resolve parents
286 result = self.__type_map.construct(builder, self, None)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:813, in TypeMap.construct(self, **kwargs)
811 raise ValueError('No ObjectMapper found for builder of type %s' % dt)
812 else:
--> 813 return obj_mapper.construct(builder, build_manager, parent)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1338, in ObjectMapper.construct(self, **kwargs)
1336 cls = manager.get_cls(builder)
1337 # gather all subspecs
-> 1338 subspecs = self.__get_subspec_values(builder, self.spec, manager)
1339 # get the constructor argument that each specification corresponds to
1340 const_args = dict()
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1268, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1266 # now process groups and datasets
1267 self.__get_sub_builders(groups, spec.groups, manager, ret)
-> 1268 self.__get_sub_builders(datasets, spec.datasets, manager, ret)
1269 elif isinstance(spec, DatasetSpec):
1270 if not isinstance(builder, DatasetBuilder): # pragma: no cover
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1320, in ObjectMapper.__get_sub_builders(self, sub_builders, subspecs, manager, ret)
1318 ret.update(self.__get_subspec_values(sub_builder, subspec, manager))
1319 else:
-> 1320 ret[subspec] = manager.construct(sub_builder)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:282, in BuildManager.construct(self, **kwargs)
280 if parent_builder is not None:
281 parent = self._get_proxy_builder(parent_builder)
--> 282 result = self.__type_map.construct(builder, self, parent)
283 else:
284 # we are at the top of the hierarchy,
285 # so it must be time to resolve parents
286 result = self.__type_map.construct(builder, self, None)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/manager.py:813, in TypeMap.construct(self, **kwargs)
811 raise ValueError('No ObjectMapper found for builder of type %s' % dt)
812 else:
--> 813 return obj_mapper.construct(builder, build_manager, parent)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/utils.py:578, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
576 def func_call(*args, **kwargs):
577 pargs = _check_args(args, kwargs)
--> 578 return func(args[0], **pargs)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1338, in ObjectMapper.construct(self, **kwargs)
1336 cls = manager.get_cls(builder)
1337 # gather all subspecs
-> 1338 subspecs = self.__get_subspec_values(builder, self.spec, manager)
1339 # get the constructor argument that each specification corresponds to
1340 const_args = dict()
File ~/miniconda3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1273, in ObjectMapper.__get_subspec_values(self, builder, spec, manager)
1270 if not isinstance(builder, DatasetBuilder): # pragma: no cover
1271 raise ValueError("__get_subspec_values - must pass DatasetBuilder with DatasetSpec")
1272 if (spec.shape is None and getattr(builder.data, 'shape', None) == (1,) and
-> 1273 type(builder.data[0]) is not np.void):
1274 # if a scalar dataset is expected and a 1-element non-compound dataset is given, then read the dataset
1275 builder['data'] = builder.data[0] # use dictionary reference instead of .data to bypass error
1276 ret[spec] = self.__check_ref_resolver(builder.data)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/backends/hdf5/h5_utils.py:231, in AbstractH5TableDataset.__getitem__(self, arg)
230 def __getitem__(self, arg):
--> 231 rows = copy(super().__getitem__(arg))
232 if np.issubdtype(type(arg), np.integer):
233 self.__swap_refs(rows)
File ~/miniconda3/lib/python3.12/site-packages/hdmf/query.py:20, in HDMFDataset.__getitem__(self, key)
18 def __getitem__(self, key):
19 idx = self.__evaluate_key(key)
---> 20 return self.dataset[idx]
File ~/miniconda3/lib/python3.12/site-packages/lindi/LindiH5pyFile/LindiH5pyDataset.py:180, in LindiH5pyDataset.__getitem__(self, args, new_dtype)
178 if new_dtype is not None:
179 raise Exception("new_dtype is not supported for zarr.Array")
--> 180 return self._get_item_for_zarr(self._zarr_array, args)
File ~/miniconda3/lib/python3.12/site-packages/lindi/LindiH5pyFile/LindiH5pyDataset.py:217, in LindiH5pyDataset._get_item_for_zarr(self, zarr_array, selection)
215 return ret
216 else:
--> 217 raise TypeError(
218 f"Compound dataset {self.name} does not support selection with {selection}"
219 )
221 # We use zarr's slicing, except in the case of a scalar dataset
222 if self.ndim == 0:
223 # make sure selection is ()
TypeError: Compound dataset /general/intracellular_ephys/intracellular_recordings/stimuli/stimulus does not support selection with 0