How can I selectively extract multidimensional data from an HDF5 file?

I'm new to manipulating HDF5 files on a low level, and I recently tried making a script to get some 3D data out of an HDF5 file. My HDF5 file dataset (x,y,z) is 14 x 29783 x 494 uint16. I'm trying to extract a 14 x 7001 x 494 portion of this, starting at y=89 (one-based index)and stopping at y=7089. Going off of examples in the low-level function documentation, here is my code:

plist='H5P_DEFAULT';
fid=H5F.open(imname);
dset_id=H5D.open(fid,'/Image');
dims=fliplr([14 7001 494]);  % get from data separation
mem_space_id=H5S.create_simple(3,dims,[]); % create cropped dataspace
file_space_id=H5D.get_space(dset_id);
offset = fliplr([0 88 0]); % Start at 89th column?
block = fliplr([14 7001 494]);
H5S.select_hyperslab(file_space_id,'H5S_SELECT_SET',offset,[],[],block);
data = H5D.read(dset_id,'H5ML_DEFAULT',mem_space_id,file_space_id,plist);
H5D.close(dset_id);
H5F.close(fid);

I get the following error at the H5D.read() statement: Error using hdf5lib2: The HDF5 library encountered an error during execution of the "H5Dread" function, "selection+offset not within extent". What am I doing wrong?

Answer 1

[per isakson]

Are you aware of HDF5 1.8 Matlab Examples?

I found them useful when I tried to use the low level support of HDF5 in Matlab. However, in my case the extra functionality of the low level api was not worth the trouble.