How to convert a large .mat file of (default format ~ 7) to a 7.3 MAT-file / HDF5 based format when the file is too large to load.

I have a program which exports .mat files in the default .mat format - I believe it v7 MAT-file? Due to the size I am unable to load the .mat file. When attempting to load the .mat file I receive an "Error using load. Cannot read file X". I have no control over the output of the program used to generate the .mat file. Is there a way in which the .mat file may be accessed to retrieve the content? Ideally I would like to retrieve the data and save it in a v7.3 MAT-file format. Thanks!

Answer 1

[Walter Roberson]

-v7 format .mat files cannot have any component which is larger than 2 gigabytes. This suggests a strategy of using load() to request particular variables from the -v7 .mat file, and write the contents to the -v7.3 .mat file (possibly using matFile)

[Jamie]

Hi Walter, thanks for the extremely quick response!! I was incorrect. The matfiles are of the format 5.0. Can we request elements/vars from a 5.0 format .mat in the same manner?

[Jamie]

Found it - page 1-4. https://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf.

How to view the contents of a large .mat: http://au.mathworks.com/help/matlab/import_export/view-the-contents-of-a-mat-file.html

[Walter Roberson]

"5.0" format shows up for both -v5 and -v7 files, but not for -v7.3 files.

[Walter Roberson]

You can use whos to find the names of the variables, and then you can loop over the names with load()

in_matname = 'YourMatFileName.mat';
out_matname = 'NewMatFileName.mat';

S = whos('-file', in_matname);
for K = 1 : length(S)
  thisvarname = S.name;
  datastruct = load(in_matname, thisvarname);
  save(out_matname, '-v7.3', '-struct', 'datastruct', '-append');
end

[Jamie]

Excellent! Thanks for your help. Avid reader of your many posts!

[Gaël]

I'm really new to matlab but I had to update the code like this to get it run:

in_matname = 'YourMatFileName.mat';
out_matname = 'NewMatFileName.mat';

S = whos('-file', in_matname);

for K = 1 : length(S)
  thisvarname = S(K).name;
  % disp(K);
  % disp(thisvarname);
  datastruct = load(in_matname, thisvarname);
  if K == 1
    save(out_matname, '-v7.3', '-struct', 'datastruct');
  else
    save(out_matname, '-struct', 'datastruct', '-append');   
  end
end