Dandiset 000021 error with nwbRead

[BrockMCarlson]

What happened?

Dandiset 000021 NWB files do not load into the matlab workspace using nwbRead. Other nwb files from other dandisets do seem to load. I suspect there may be something specific to the nwb file format in the 000021 dandiset that prevents nwbRead completion.

Steps to Reproduce

%% Load NWB _00021 - does not work
clear
cd matnwb
addpath(genpath(pwd));
generateCore(); % generate the most recent nwb-schema release.

% File string generation to 000021 dandiset file location on the local machine.
% For the purposes of this test, we have used individual files from the sub-699733573 and sub-703279277 folders under dandiset 000021

fileStorageFile = 'C:\NeuroDataReHack';
cd(fileStorageFile)
nwbFileName_21 = 'sub-699733573_ses-715093703.nwb';
nwbFile_21 = strcat(fileStorageFile,filesep,nwbFileName_21);

% load
nwb_21 = nwbRead(nwbFile_21);

Error Message

Error using logical
Conversion to logical from cell is not possible.

Error in types.util.correctType (line 58)
        val = logical(val);

Error in types.util.checkDtype (line 96)
correctedValue = types.util.correctType(val, type);

Error in types.ndx_aibs_ecephys.EcephysElectrodeGroup/validate_has_lfp_data (line 64)
        val = types.util.checkDtype('has_lfp_data', 'logical', val);

Error in types.ndx_aibs_ecephys.EcephysElectrodeGroup/set.has_lfp_data (line 35)
        obj.has_lfp_data = obj.validate_has_lfp_data(val);

Error in types.ndx_aibs_ecephys.EcephysElectrodeGroup (line 26)
        obj.has_lfp_data = p.Results.has_lfp_data;

Error in io.parseGroup (line 85)
    parsed = eval([Type.typename '(kwargs{:})']);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in nwbRead (line 59)
nwb = io.parseGroup(filename, h5info(filename), Blacklist);

Error in loadNWBfiles (line 40)
nwb_21 = nwbRead(nwbFile_21);

Operating System

Windows

Matlab Version

'9.12.0.1975300 (R2022a) Update 3'

Code of Conduct

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[lawrence-mbf]

Hi @BrockMCarlson,

Are you using a release version of MatNWB or the tip of the master branch?

[BrockMCarlson]

Hi @lawrence-mbf . Thanks! I have tried cloning the repo from the github master branch. I have also deleted that download and re-tried the process with the Mathworks FileExchange release. I believe both of these are the tip of the master branch, correct?

[lawrence-mbf]

@BrockMCarlson I believe so. I will look into this.

[lawrence-mbf]

This is due to how booleans are encoded in h5py as HDF5 does not provide boolean data on its own. Related to #458

[lawrence-mbf]

Hi @BrockMCarlson Since bool support has been merged, the only issue is just due to this long outstanding issue with waveform_mean #43

[lawrence-mbf]

The waveform_mean issue is tracked in #238