AllenNeuralDynamics / AllenNeuralDynamics/aind-ecephys-nwb

mmap length greater than file size

Ouverte
#14 2 commentaires 0 réactions 0 personnes assignées Voir sur GitHub
Langage dominant
Python
Étoiles
0
Forks
1
Métriques de merge des PR
Aucune PR mergée en 30 j

Description

Working with a 2 segment openephys recording i end up with the following `ValueError`:
```
Command error:
File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 541, in write_group
self.write_dataset(
File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1132, in write_dataset
self.__dci_queue.exhaust_queue()
File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/utils.py", line 217, in exhaust_queue
if self.__write_chunk__(zarr_dataset, iterator):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/utils.py", line 77, in __write_chunk__
chunk_i = next(data)
^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/hdmf/data_utils.py", line 405, in __next__
return DataChunk(data=self._get_data(selection=buffer_selection), selection=buffer_selection)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/neuroconv/tools/spikeinterface/spikeinterfacerecordingdatachunkiterator.py", line 96, in _get_data
return self.recording.get_traces(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/core/baserecording.py", line 340, in get_traces
traces = rs.get_traces(start_frame=start_frame, end_frame=end_frame, channel_indices=channel_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/preprocessing/filter.py", line 162, in get_traces
traces_chunk, left_margin, right_margin = get_chunk_with_margin(
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/core/recording_tools.py", line 863, in get_chunk_with_margin
traces_chunk = rec_segment.get_traces(
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/preprocessing/decimate.py", line 130, in get_traces
return self._parent_segment.get_traces(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/core/channelslice.py", line 101, in get_traces
traces = self._parent_recording_segment.get_traces(start_frame, end_frame, parent_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 367, in get_traces
raw_traces = self.neo_reader.get_analogsignal_chunk(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/neo/rawio/baserawio.py", line 1006, in get_analogsignal_chunk
raw_chunk = self._get_analogsignal_chunk(block_index, seg_index, i_start, i_stop, stream_index, channel_indexes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/neo/rawio/baserawio.py", line 1621, in _get_analogsignal_chunk
raw_sigs = get_memmap_chunk_from_opened_file(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/neo/rawio/utils.py", line 46, in get_memmap_chunk_from_opened_file
memmap_obj = mmap.mmap(fid.fileno(), length=length, access=mmap.ACCESS_READ, offset=memmap_offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: mmap length is greater than file size
```

Guide de contribution

Aucun guide de contribution indexé pour ce dépôt

Évaluation

Cette issue n'a pas encore été évaluée.

Recevez les nouvelles issues par e-mail

Un résumé court des issues GitHub adaptées aux débutants.