How to save mat files as h5 files?

I have cell arrays saved as a .mat file and I want to transform this into a .h5 file.

How do I transform a .mat file into a .h5 file?

I have read that we should try to use hdf5write or h5write to do so, but I do not understand how to use these functions.

I am trying to use a code written by a colleague that processes data as .h5 files , but does not do so with .mat files, unfortunately my data is all in .mat files.

[Stephen23]

https://www.mathworks.com/help/matlab/ref/load.html

https://www.mathworks.com/help/matlab/hdf5-files.html

https://www.mathworks.com/help/matlab/import_export/process-a-sequence-of-files.html

In most cases LOADing into an output variable is more robust.

[Gordon]

Thankyou for your help. My problem is that I do not understand how to correctly use the h5read and h5create functions.

I have attempted loading my file, but because it is a 1x1 struct with 70 fields, I don't know what to do.

Answer 1

[Abhaya]

Hi Gordon,

I understand that you want to convert a 1x1 struct with 70 fields, to an H5 file using ‘h5write’ function. However, the ‘h5write’ function does not inherently support writing structs directly into H5 files.

To save the struct into an H5 file, you will need to manually iterate over each field in the struct and write each one as a separate dataset in the HDF5 file.

Please refer to the following sample code for better understanding.

%Simple struct with two fields 
dataStruct = struct(); 
dataStruct.field1 = rand(3);          
dataStruct.field2 = [1, 2, 3, 4, 5];  

h5filename = 'dataStruct.h5'; 

% Get the field names of the struct 
fields = fieldnames(dataStruct); 

% Loop over each field in the struct 
for i = 1:length(fields) 
    fieldName = fields{i};           
    fieldData = dataStruct.(fieldName); % Access the data in the field 
    
    % Determine the size of the field data 
    dataSize = size(fieldData); 
    
    % Create a dataset for each struct field and write into it 
    h5create(h5filename, ['/' fieldName], dataSize); 
    h5write(h5filename, ['/' fieldName], fieldData); 
end 

For more information, please refer to the MATLAB documentations linked below.

• https://www.mathworks.com/help/matlab/ref/h5create.html
• https://www.mathworks.com/help/matlab/ref/h5write.html

Hope it solves your query.