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[Bug]: DataStub errors out if trying to retrieve data with empty indices #595

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ehennestad opened this issue Sep 14, 2024 · 2 comments · May be fixed by #605
Open
2 tasks done

[Bug]: DataStub errors out if trying to retrieve data with empty indices #595

ehennestad opened this issue Sep 14, 2024 · 2 comments · May be fixed by #605
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status: need verification potentially solved, but needs verification topic: matnwb-api related to improving the matnwb api

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@ehennestad
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What happened?

I ran the convertTrials tutorial (branch: 515-fix-convert-trials-tutorial) and tried to run the following:

Steps to Reproduce

nwbIn = nwbRead(nwbFilePath);
nwbIn.intervals_trials.toTable()

Error Message

Error using hdf5lib2
The HDF5 library encountered an error and produced the following stack trace information:

    H5Sselect_elements    elements not specified

Error in H5S.select_elements (line 43)
H5ML.hdf5lib2('H5Sselect_elements', space_id, op, h5_coord);

Error in types.untyped.DataStub/load_mat_style (line 52)
        H5S.select_elements(readSpaceId, 'H5S_SELECT_SET', ...

Error in indexing (line 169)
                data = obj.load_mat_style(CurrentSubRef.subs{:});

Error in types.util.dynamictable.getRow>select (line 170)
        selected = Vector.data(selectInd{:});

Error in types.util.dynamictable.getRow>select (line 205)
        selected{iRange} = select(DynamicTable,...

Error in types.util.dynamictable.getRow (line 49)
    row{i} = select(DynamicTable, indexNames, ind);

Error in types.hdmf_common.DynamicTable/getRow (line 120)
        row = types.util.dynamictable.getRow(obj, id, varargin{:});

Error in types.util.dynamictable.nwbToTable (line 81)
matlabTable = [matlabTable DynamicTable.getRow( ...

Error in types.hdmf_common.DynamicTable/toTable (line 124)
        table = types.util.dynamictable.nwbToTable(obj, varargin{:});

Operating System

macOS

Matlab Version

R2023b

Code of Conduct
@ehennestad
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The error occurs because some of the rows in timeseries_index of the intervals_trials are empty, i.e does not point to any timeseries.

In MATLAB, it is possible to use empty indices, and this could be implemented for DataStub as well.

e.g.

a = struct

a = 

  struct with no fields.

K>> a([])

ans = 

  0×0 empty struct array with no fields.

ehennestad added a commit that referenced this issue Sep 14, 2024
@ehennestad
Coarse fix for #595
fc9ca2a
@ehennestad
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@bendichter @lawrence-mbf
I added a proposed fix and it works in the specific case where this error happens. It is not a very general fix, and there may be better ways to solve this?

@ehennestad ehennestad self-assigned this Sep 17, 2024
@ehennestad ehennestad reopened this Oct 31, 2024
@ehennestad ehennestad added the status: need verification potentially solved, but needs verification label Oct 31, 2024
@ehennestad ehennestad linked a pull request Oct 31, 2024 that will close this issue
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@ehennestad ehennestad added the topic: matnwb-api related to improving the matnwb api label Nov 1, 2024
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595 Allow using empty indices for datastub NeurodataWithoutBorders/matnwb
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