Load file from open repository with unknown nwb version

[lepmik]

Hi I'm trying to load files from this open repository shared by the barry lab

https://www.dropbox.com/sh/zdanporcx0v3s10/AADa3Cy2siUd0Co3B7yyGNBga?dl=0

When trying to load the file with pynwb I get the following error

from pynwb import NWBHDF5IO, NWBFile, TimeSeries
raw_io = NWBHDF5IO("Markus Frey - R2470_experiment_1.nwb", "r")
nwb_in = raw_io.read()

TypeError: Missing NWB version in file. The file is not a valid NWB file.

Is there any way I can open the file?

[oruebel]

I have not had a chance to look at the file, but the fact that the NWB version is missing seems to indicate that the file is likely a NWB version 1.x file. PyNWB and MatNWB support NWB 2.0 and up (see https://nwb-overview.readthedocs.io/en/latest/faq.html#nwb-1-vs-2). I can take a look later to further confirm. If the file is indeed 1.x then you should still be able to open the file directly via HDF5.

Here a list of HDF5 tools that are useful inspect the raw HDF5 file https://nwb-overview.readthedocs.io/en/latest/tools/hdftools/hdftools.html#analysistools-hdftools In Python you can also use h5py directly to open the file.

import h5py
nwb_file = h5py.File("Markus Frey - R2470_experiment_1.nwb", "r")

The HDF5 tools are not aware of the NWB schema, so they are missing PyNWB convenience functionality, but they should get you access to the data.

[lepmik]

Hi, thanks for the reply, I managed to get the data with h5py 😀 tor. 21. des. 2023, 21:19 skrev Oliver Ruebel ***@***.***>:

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I have not had a chance to look at the file, but the fact that the NWB version is missing seems to indicate that the file is likely a NWB version 1.x file. PyNWB and MatNWB support NWB 2.0 and up (see https://nwb-overview.readthedocs.io/en/latest/faq.html#nwb-1-vs-2). I can take a look later to further confirm. If the file is indeed 1.x then you should still be able to open the file directly via HDF5. Here a list of HDF5 tools that are useful inspect the raw HDF5 file https://nwb-overview.readthedocs.io/en/latest/tools/hdftools/hdftools.html#analysistools-hdftools In Python you can also use h5py directly to open the file. import h5py nwb_file = h5py.File("Markus Frey - R2470_experiment_1.nwb", "r") The HDF5 tools are not aware of the NWB schema, so they are missing PyNWB convenience functionality, but they should get you access to the data. — Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2CP4BN4ASGS6UQQIYHORDYKSKUXAVCNFSM6AAAAABA6RIUMOVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSMRRHAYTA> . You are receiving this because you authored the thread.Message ID: <NeurodataWithoutBorders/helpdesk/repo-discussions/65/comments/7921810@ github.com>