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@@ -144,26 +144,6 @@ for iSess = 1:numel(sessionID)
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end
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[inds, waveformIndexIndex] = util.create_indexed_column(waveformIndexIndex');
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- % Convert rel_horz_pos, rel_vert_pos, and waveform_mean to cell arrays of
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- % strings. For some reason I cannot store them in the NWB file in any
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- % other form than strings on one machine but not the other. So if you
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- % encounter an hdf5lib2 error. You may need to uncomment the code lines
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- % below and use variables converted to cell arrays of strings. Also don't
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- % forget to correct lines number 198, 201, and 226.
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- % For more details see https://github.com/NeurodataWithoutBorders/matnwb/issues/462
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-% if ~isempty(spikes)
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-% rel_horz_pos = num2cell(cell2mat(table2array(metadata(:,7)))./1000);
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-% rel_vert_pos = num2cell(cell2mat(table2array(metadata(:,8)))./1000);
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-% for iUnit = 1:numel(rel_horz_pos)
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-% rel_horz_pos{iUnit} = num2str(rel_horz_pos{iUnit});
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-% rel_vert_pos{iUnit} = num2str(rel_vert_pos{iUnit});
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-% waveformMeans{iUnit} = num2str(waveformMeans{iUnit});
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-% end
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-% else
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-% rel_horz_pos = [];
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-% rel_vert_pos = [];
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-% end
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-
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% Store spiking and waveform data inside the nwb object
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% see https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/Units.html
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if ~isempty(spikes)
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@@ -195,10 +175,10 @@ for iSess = 1:numel(sessionID)
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'data', cell2mat(metadata{:,6}), ...
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'description', 'Local probe channel with the largest cluster waveform amplitude'), ...
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'rel_horz_pos', types.hdmf_common.VectorData( ...
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- 'data', cell2mat(metadata{:,7})./1000, ... % use rel_horz_pos in Matlab R2021a
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+ 'data', cell2mat(metadata{:,7})./1000, ...
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'description', 'Probe-relative horizontal position in mm'), ...
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'rel_vert_pos', types.hdmf_common.VectorData( ...
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- 'data', cell2mat(metadata{:,8})./1000, ... % use rel_vert_pos in Matlab R2021a
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+ 'data', cell2mat(metadata{:,8})./1000, ...
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'description', 'Probe tip-relative vertical position in mm'), ...
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'isi_violations', types.hdmf_common.VectorData( ...
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'data', cell2mat(metadata{:,9}), ...
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@@ -223,7 +203,7 @@ for iSess = 1:numel(sessionID)
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'description', 'Probe recording channels', ...
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'data', cell2mat(table2array(metadata(:,1)))), ...
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'waveform_mean', types.hdmf_common.VectorData( ...
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- 'data', cell2mat(waveformMeans), ... % use waveformMeans Matlab R2021a
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+ 'data', cell2mat(waveformMeans), ...
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'description', ['Mean waveforms on the probe channel with the largest waveform amplitude.' ...
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'MUA waveforms are excluded. The order that waveforms are stored match the order of units in the unit table.']) ...
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);
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@@ -288,6 +268,10 @@ for iSess = 1:numel(sessionID)
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end
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% Save the NWB file for the session
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+ % If you encounter an hdf5lib2 error, you may need make sure that you are
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+ % not storing cell arrays of numbers in VectorData and that you delete
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+ % old NWB files rather than try overwriting them. For more details see
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+ % https://github.com/NeurodataWithoutBorders/matnwb/issues/462
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if iSess < 10
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nwbExport(nwb, [animalDerivedDataFolderNWB filesep 'ecephys_session_0' num2str(iSess) '.nwb']);
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else
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dervinism