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Extending compound HDF5 dataset

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MrDan
MrDan 2016-5-3
编辑： bowen li 2018-5-22
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);
H5S.select_all(space);
% 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);
end
H5D.close(dset);
H5T.close (filetype);
H5T.close (memtype);
H5F.close(file);
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?
Thanks,
Daniel

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回答（1 个）

MrDan
MrDan 2016-5-3
编辑：per isakson 2016-5-3
I found the mistake myself by studying this: https://de.mathworks.com/matlabcentral/newsreader/view_thread/284377
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.
  2 个评论
Markus Krug
Markus Krug 2016-8-8
I have exactly the same problem but the above mentioned change did not solve the 'random' numbers for the extend dataset starting from row 4. Could you please post you solution.
Additonally I'm interested in extending compound datasets that are compressed. Did you do something similar? If yes any hint will be appreciated
bowen li
bowen li 2018-5-22
编辑：bowen li 2018-5-22
To fix the random number bug, replace
H5D.write(dset, memtype, 'H5S_ALL', space, 'H5P_DEFAULT',wdata);
throuth
memspace_id = H5S.create_simple(1,1,[]);
H5D.write(dset, memtype, memspace_id, space, 'H5P_DEFAULT',wdata);

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