Extending compound HDF5 dataset

9 views (last 30 days)
MrDan on 3 May 2016
Edited: bowen li on 22 May 2018
Dear Forum,
I am trying to extend a dataset in Matlab with the low-level API. The underlying datatype is compound.
% create file
FILE ='myFile.h5';
file = H5F.create(FILE, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');
% create compound datatype
memtype = H5T.create ('H5T_COMPOUND', 32);
H5T.insert (memtype, 'serial_no', 0 ,'H5T_NATIVE_DOUBLE');
H5T.insert (memtype, 'location', 8, 'H5T_NATIVE_DOUBLE');
H5T.insert (memtype, 'wurz', 16, 'H5T_NATIVE_DOUBLE');
% create compound datatype
filetype = H5T.create ('H5T_COMPOUND', 32);
H5T.insert (filetype, 'serial_no', 0 ,'H5T_NATIVE_DOUBLE');
H5T.insert (filetype, 'location', 8, 'H5T_NATIVE_DOUBLE');
H5T.insert (filetype, 'wurz', 16, 'H5T_NATIVE_DOUBLE');
% create unlimited filespace
H5S_UNLIMITED = H5ML.get_constant_value('H5S_UNLIMITED');
maxdims = [H5S_UNLIMITED];
memspace = H5S.create_simple(1, fliplr(0), fliplr(maxdims));
% create data set
dcpl = H5P.create('H5P_DATASET_CREATE');
H5P.set_chunk (dcpl, fliplr(1));
dset = H5D.create(file, 'DS',filetype ,memspace, dcpl);
bSpace = H5D.get_space(dset);
%dset = H5D.create (file, 'DS', filetype, memspace, 'H5P_DEFAULT');
% fill element-wise
for i=1:10
% create test data
wdata.location = i;
wdata.serial_no = i*10;
wdata.wurz = -i*10;
% extend data set
H5D.extend(dset, i);
space = H5D.get_space(dset);
% select hyperslab
H5S.select_hyperslab(space,'H5S_SELECT_SET', i-1, 1, 1 ,1);
% write data
H5D.write(dset, memtype, 'H5S_ALL', space, 'H5P_DEFAULT',wdata);
% close file space
H5S.close (space);
H5T.close (filetype);
H5T.close (memtype);
Unfortunately my program does not do what I intend: Instead of filling element-wise, it will only copy the first compound data to the hdf5-file:
Output of dataset DS from HDF5 viewer:
serial_no location wurz
1.0 10.0 -10.0
0.0 0.0 0.0
0.0 0.0 0.0
-1.288480843725888E-231 -3.786504882356714E-270 -3.786504882356956E-270
4.9E-324 9.8117197E-315 9.81183448E-315
4.5792095E-316 9.8117197E-315 9.81183448E-315
9.792595565E-315 9.8117197E-315 9.81183448E-315
8.4E-323 4.9E-324 1.353122016E-315
9.79259493E-315 8.49433059E-315 2.121477727E-314
8.4E-323 9.790301677E-315 5.295032923E-315
Can anybody help?

Answers (1)

MrDan on 3 May 2016
Edited: per isakson on 3 May 2016
Finally, replacing this
memspace = H5S.create_simple(1, fliplr(0), fliplr(maxdims));
through this
memspace = H5S.create_simple(1, fliplr(1), fliplr(maxdims))
does the trick.
bowen li
bowen li on 22 May 2018
Edited: bowen li on 22 May 2018
To fix the random number bug, replace
H5D.write(dset, memtype, 'H5S_ALL', space, 'H5P_DEFAULT',wdata);
memspace_id = H5S.create_simple(1,1,[]);
H5D.write(dset, memtype, memspace_id, space, 'H5P_DEFAULT',wdata);

Sign in to comment.

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by