List all datasets and groups of an hdf5 file

Hello!

I am trying to compile all group names and dataset names into a couple cell arrays from an hdf5 file. In python i can accomplish something similar using the visit command. It looks like the low level Matlab comands do contain a visit function as well, but I may not be using it correctly.

Edit: I wanted to clarify there are nested groups/datasets in the file, so recursion is needed to traverse the hdf5 objects.

% Python example for getting all datasets:  
keys = []
with h5py.File(filepath, 'r+') as f: 
        f.visit(lambda key : keys.append(key) if isinstance(f[key], h5py.Dataset) else None)

I tried the following code but it's returning all keys as groups, even though some of them are datasets.

    s = struct
    s.datasets = {};
    s.groups = {}; 
    fid = H5F.open(fileName, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
    [status sOut] = H5O.visit(fid, 'H5_INDEX_NAME', 'H5_ITER_NATIVE', @getObjInfo, s);
    
    function [status, sOut] = getObjInfo(objId, name, sIn)
    
        obj_info=H5O.get_info(objId);
        disp(obj_info.nlinks)
        switch(obj_info.type)
            case H5ML.get_constant_value('H5G_LINK')
                fprintf('Object #%s is a link.\n', name);
            case H5ML.get_constant_value('H5G_GROUP')
                fprintf('Object #%s is a group.\n', name);
                  sIn.groups{end+1} = name;
            case H5ML.get_constant_value('H5G_DATASET')
                fprintf('Object #%s is a dataset.\n', name);
                  sIn.datasets{end+1} = name; 
            case H5ML.get_constant_value('H5G_TYPE')
               fprintf('Object #%s is a named datatype.\n', name);
        end
        status = 0; % keep iterating
        sOut = sIn; 
    end

[Walter Roberson]

Out of curiosity, what happens if you put the case for H5G_DATASET before the case for H5G_GROUP ?

Answer 1

[LostInMatlabtion]

Looks like it works if i change to the following:

  function [status, sOut] = getObjInfo(rootID, name, sIn)
    objID = H5O.open(rootID, name, 'H5P_DEFAULT');
    obj_info=H5O.get_info(objID);
    H5O.close(objID);