tjr1
commented
6 months ago I also can't read any .nwb files with neo due to this error. @CodyCBakerPhD , might you have an idea on this one?
Open Idavr opened 7 months ago
tjr1
commented
6 months ago I also can't read any .nwb files with neo due to this error. @CodyCBakerPhD , might you have an idea on this one?
Moritz-Alexander-Kern
commented
3 months ago I encountered the same issue
The .nwb file is publicly available, here:
https://dandiarchive.org/dandiset/000473/0.230417.1502/files?location=sub-216301&page=1
Code to reproduce:
from neo.io import NWBIO
filepath = "sub-216301_ses-216301-20200521-probe0_ecephys+ogen.nwb"
io = NWBIO(f"{filepath}",'r')
block = io.read_block(block_index=1)Output:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[3], line 3
1 filepath = "sub-216301_ses-216301-20200521-probe0_ecephys+ogen.nwb"
2 io = NWBIO(f"{filepath}",'r')
----> 3 block = io.read_block(block_index=1)
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/io/nwbio.py:287, in NWBIO.read_block(self, lazy, block_index, **kargs)
283 def read_block(self, lazy=False, block_index=0, **kargs):
284 """
285 Load the first block in the file.
286 """
--> 287 return self.read_all_blocks(lazy=lazy)[block_index]
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/io/nwbio.py:277, in NWBIO.read_all_blocks(self, lazy, **kwargs)
275 self._blocks = {}
276 self._read_acquisition_group(lazy=lazy)
--> 277 self._read_stimulus_group(lazy)
278 self._read_units(lazy=lazy)
279 self._read_epochs_group(lazy)
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/io/nwbio.py:397, in NWBIO._read_stimulus_group(self, lazy)
396 def _read_stimulus_group(self, lazy):
--> 397 self._read_timeseries_group("stimulus", lazy)
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/io/nwbio.py:358, in NWBIO._read_timeseries_group(self, group_name, lazy)
356 block_name = hierarchy["block"]
357 segment_name = hierarchy["segment"]
--> 358 segment = self._get_segment(block_name, segment_name)
359 if isinstance(timeseries, pynwb.misc.AnnotationSeries):
360 event = EventProxy(timeseries, group_name)
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/io/nwbio.py:297, in NWBIO._get_segment(self, block_name, segment_name)
295 block = self._blocks[block_name]
296 else:
--> 297 block = Block(name=block_name, **self.global_block_metadata)
298 self._blocks[block_name] = block
299 segment = None
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/core/block.py:96, in Block.__init__(self, name, description, file_origin, file_datetime, rec_datetime, index, **annotations)
83 def __init__(
84 self,
85 name=None,
(...)
91 **annotations,
92 ):
93 """
94 Initialize a new :class:`Block` instance.
95 """
---> 96 super().__init__(name=name, description=description, file_origin=file_origin, **annotations)
98 self.file_datetime = file_datetime
99 self.rec_datetime = rec_datetime
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/core/container.py:204, in Container.__init__(self, name, description, file_origin, **annotations)
200 def __init__(self, name=None, description=None, file_origin=None, **annotations):
201 """
202 Initialize a new :class:`Container` instance.
203 """
--> 204 super().__init__(name=name, description=description, file_origin=file_origin, **annotations)
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/core/baseneo.py:301, in BaseNeo.__init__(self, name, description, file_origin, **annotations)
293 """
294 This is the base constructor for all Neo objects.
295
(...)
298 :class:`BaseNeo` or the child class.
299 """
300 # create `annotations` for additional arguments
--> 301 _check_annotations(annotations)
302 self.annotations = annotations
304 # these attributes are recommended for all objects.
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/core/baseneo.py:74, in _check_annotations(value)
72 if not isinstance(key, str):
73 raise TypeError(f"Annotations keys must be strings not of type {type(key)}")
---> 74 _check_annotations(element)
75 elif isinstance(value, (list, tuple)):
76 for element in value:
File ~/DANDI/.venv/lib/python3.10/site-packages/neo/core/baseneo.py:79, in _check_annotations(value)
77 _check_annotations(element)
78 elif not isinstance(value, ALLOWED_ANNOTATION_TYPES):
---> 79 raise ValueError(f"Invalid annotation. Annotations of type {type(value)} are not" f"allowed")
ValueError: Invalid annotation. Annotations of type <class 'hdmf.utils.StrDataset'> are notallowedWith:
OS: Ubuntu 22.04.4 LTS
Python 3.10.12
Package Version
------------------------- -----------
h5py 3.11.0
hdmf 3.14.0
neo 0.13.1
numpy 1.26.4
pynwb 2.8.0
quantities 0.15.0
This is related to: https://github.com/NeuralEnsemble/elephant/issues/627
apdavison
commented
3 months ago Hi everyone, sorry for the delay in starting to address this. Please try to read the file using the code in the linked pull request (#1502). That code allows me to read the test file from DANDI, but there are many warnings, so I suspect there are still problems to fix, and I will look into this further in a couple of weeks. All feedback is welcome!
Greetings everyone! I hope someone here can help with solving a very basic issue.
Currently I am trying to read a .nwb file using NWBIO like this:
from pynwb import NWBFile, NWBHDF5IO from neo.io import NWBIO
file = '/745606_20231213-probe0.nwb'
reader = NWBIO(file) data_neo = reader.read() print(data_neo)
Environment:
I saw some previous issues with reading .nwb files, but not with this exact ValueError. Any assistance in very much appreciated!
Best,
Idavr