CODEWITHSUNDEEP
matlabdatasethdf5
medicine_man
medicine_man

Reputation: 321

Write Matrix Data to Each Member of Datatype in HDF5 file via MATLAB

This is my first go at trying to create an HDF5 file from scratch using the Low-Level commands via MATLAB.

My issue is that I am having a hard time trying to write data to each specific member in the datatype on my dataset.

First, I create a new HDF5 file, and set the right layer of groups:

new_h5 = H5F.create('new_hdf5_file.h5','H5F_ACC_TRUNC','H5P_DEFAULT','H5P_DEFAULT');
new_h5 = H5G.create(new_h5,'first','H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');
new_h5 = H5G.create(new_h5,'second','H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');

Then, I create my datatype:

datatype = H5T.create('H5T_compound',20);
H5T.insert(datatype,'first_element',0,'H5T_NATIVE_INT');
H5T.insert(datatype,'second_element',4,'H5T_NATIVE_DOUBLE');
H5T.insert(datatype,'third_element',12,'H5T_NATIVE_DOUBLE');

Then, I format that into my dataset:

new_h5 = H5D.create(new_h5,'location',datatype,H5S.create('H5S_SCALAR'),'H5P_DEFAULT');
subset = H5D.get_type(H5D.open(new_h5,'/first/second/location'));
mem_type = H5T.get_member_type(subset,0);

I receive an error with the following command:

H5D.write(mem_type,'H5ML_DEFAULT','H5S_ALL','H5S_ALL','H5P_DEFAULT',data);

Error using hdf5lib2

Unhandled HDF5 class (H5T_NO_CLASS) encountered. It is not possible to write to this attribute or dataset.

So, I try this method instead:

new_h5 = H5D.create(new_h5,'location',datatype,H5S.create_simple(2,dims,dims),'H5P_DEFAULT'); %where dims are the dimensions of all matrices of data structure
H5D.write(mem_type,'H5ML_DEFAULT','H5S_ALL','H5S_ALL','H5P_DEFAULT',data); %where data is a structure

I receive an error with this following command:

H5D.write(mem_type,'H5ML_DEFAULT','H5S_ALL','H5S_ALL','H5P_DEFAULT',data);

Error using hdf5lib2

Attempted to transfer too many values to or from the library buffer.

When looking here for the XML tags for the error messages, it describes the above error as "illegalArrayAccess." Apparently, according to this question, you can only write to 4 members without the buffer throwing an error?

Is this correct? How can I correctly write to each member. I am about to reach my mental limit trying to figure this one out.

EDIT:

References kept here for general information:

HDF5 Compound Datatypes Example

HDF5 Compount Datatypes

H5D.write MATLAB Command

Upvotes: 3

Views: 683

Answers (1)

medicine_man
medicine_man

Reputation: 321

I found out why I cannot write data. I have solved the problem. I had my dimensions set incorrectly (which is code I forgot to include originally). My apologies. I had my dimensions like this:

dims = fliplr(size(data_matrix));

Where dims was a 15x250 matrix. The error was in that the buffer was unable to write a 250x15 matrix for each member, because it only had data for a 250x1 for each member.

The following code will (generically) work for writing data to each member:

new_h5 = H5F.create('new_hdf5_file.h5','H5F_ACC_TRUNC','H5P_DEFAULT','H5P_DEFAULT');
new_h5 = H5G.create(new_h5,'first','H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');
new_h5 = H5G.create(new_h5,'second','H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');
datatype = H5T.create('H5T_compound',20);
H5T.insert(datatype,'first_element',0,'H5T_NATIVE_INT');
H5T.insert(datatype,'second_element',4,'H5T_NATIVE_DOUBLE');
H5T.insert(datatype,'third_element',12,'H5T_NATIVE_DOUBLE');
dims = fliplr(size(data_matrix)); dims = [1 dims(1,2)];
new_h5 = H5D.create(new_h5,'location',datatype,H5S.create_simple(2,dims,dims),'H5P_DEFAULT'); 
H5D.write(new_h5,'H5ML_DEFAULT','H5S_ALL','H5S_ALL','H5P_DEFAULT',data_structure);

where data_matrix is a 15x250 matrix containing all data, and where data_structure is a sctucture containing 15 fields, each 250x1 in size.

Upvotes: 2

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