MatNWB <-> HDF5 Dimension Mapping
Create Table
First, create an expandable TimeIntervals table of height 10.
% Define VectorData objects for each column
% 1D column
start_col = types.hdmf_common.VectorData( ...
'description', 'start times column', ...
'data', types.untyped.DataPipe( ...
'data', 1:10, ... # maps onto HDF5 dataset of size (10, )
'maxSize', Inf ...
) ...
);
% 1D column
stop_col = types.hdmf_common.VectorData( ...
'description', 'stop times column', ...
'data', types.untyped.DataPipe( ...
'data', 1:10, ... # maps onto HDF5 dataset of size (10, 1)
'maxSize', [1 Inf], ...
'axis', 2 ...
) ...
);
% 1D column
cond_col = types.hdmf_common.VectorData( ...
'description', 'condition column', ...
'data', types.untyped.DataPipe( ...
'data', randi(2,10,1), ... # maps onto HDF5 dataset of size (1, 10)
'maxSize', [Inf, 1], ...
'axis', 1 ...
) ...
);
% 4D column
randomval_col = types.hdmf_common.VectorData( ...
'description', 'randomvalues column', ...
'data', types.untyped.DataPipe( ...
'data', rand(5,2,3,10), ... # maps onto HDF5 dataset of size (10, 3, 2, 5)
'maxSize', [5, 2, 3, Inf], ...
'axis', 4 ...
) ...
);
% 1D column
ids_col = types.hdmf_common.ElementIdentifiers( ...
'data', types.untyped.DataPipe( ...
'data', (0:9), ... # maps onto HDF5 dataset of size (10, )
'maxSize', Inf ...
) ...
);
% Create table
trials_table = types.core.TimeIntervals(...
'description', 'test dynamic table column',...
'colnames', {'start_time', 'stop_time', 'randomvalues', 'conditions'}, ...
'start_time', start_col, ...
'stop_time', stop_col, ...
'conditions', cond_col, ...
'randomvalues', randomval_col, ...
'id', ids_col ...
);
Export Table
Create NWB file with expandable TimeIntervals table and export.
% Create NwbFile object with required arguments
file = NwbFile( ...
'session_start_time', '2022-01-01 00:00:00', ...
'identifier', 'ident1', ...
'session_description', 'test file' ...
);
% Assign to intervals_trials
file.intervals_trials = trials_table;
% Export
nwbExport(file, 'testFileWithDataPipes.nwb');
You can examine the dimensions of the datasets on file using HDFView. Screenshots for this file are below.
