How to get attribute value from a group?

[haziq-zur]

Hi all,

I have a .h5 file generated from an instrument and doing a hdf5 file parser to extract the content and expose it into a map. The file structure that I have is as below.

I manage to get the array of data from the dataset, but I try to get the attribute of the parent I'm having an exception ->
System.ArgumentException: 'Must provide at least one rank.'

I use the method hdf5.ReadAttribute<int>(wvf_group_id, "NumWaveforms")

[flappah]

No answer but just to add at this, it also happens to me. I try to read an attribute of an enumerated type but am only interested in the byte value of the attribute and not the enumeration. So I use the same method as OP. And then the same error occurs. "Must provide at least one rank".

[LiorBanai]

Hi @haziq-zur and @flappah can you attach an example file for me to test? I'll try to get to it in few days

[flappah]

Hi Lior,

sure! This is the code I use. It is more or less equivalent to the other code I posted only then without going to the underlying HDF group p/invoke wrapper:

            var fileId = Hdf5.OpenFile(fileName);
            var groupId = Hdf5.CreateOrOpenGroup(fileId, "/SurfaceCurrent");
            byte dataCodingFormat = 0;
            try
            {
                dataCodingFormat = Hdf5.ReadAttribute<byte>(groupId, "dataCodingFormat");
            }
            finally
            {
                Hdf5.CloseGroup(groupId);
                Hdf5.CloseFile(fileId);
            }

[flappah]

BTW, it's part of a project I'm currently doing that can read IHO's S1xx standards. Right now I'm implementing S-111 that needs to read data from HDF5. To get a feel for the broader context it's on https://github.com/flappah/S1XViewer in the file https://github.com/flappah/S1XViewer/blob/master/S1XViewer.HDF/S111ProductSupport.cs

[haziq-zur]

Hi @LiorBanai,

I have attached the file that I used to extract data below.
cwaveformfloat.zip

Using the HDFView Tools, I can clearly see that there are some attribute in the /Waveforms group as posted previously. I did try using Hdf5.ReadTreeFileStructure() and Hdf5.ReadFlatFileStructure() to get the whole structure of the hdf5 file but the attribute content is showing zero which is weird since the HDFView can clearly show the attribute and its value.

[flappah]

BTW, I managed to bypass the issue by just going to the underlying HDF-Group C wrapper. In my specific example I needed to retrieve the byte value (unsigned int 8 bit) which is the actual storage of the enumerated attribute type. The following code does this without a problem:

        public override int GetDataCodingFormat(string fileName)
        {
            var fileId = H5F.open(fileName, H5F.ACC_RDONLY, H5P.DEFAULT);
            var groupId = H5G.open(fileId, Encoding.ASCII.GetBytes("/SurfaceCurrent"), H5P.DEFAULT);
            var attribId = H5A.open(groupId, Encoding.ASCII.GetBytes("dataCodingFormat"), H5P.DEFAULT);
 
            var value = new byte[2];
            var handle = GCHandle.Alloc(value, GCHandleType.Pinned);
            try
            {
                if (H5A.read(attribId, H5T.NATIVE_UINT8, handle.AddrOfPinnedObject()) == 0)
                {
                    var returnValue = BitConverter.ToInt16(value, 0);
                    return returnValue;
                }
            }
            finally
            {
                handle.Free();
                H5A.close(attribId);
                H5G.close(groupId);
                H5F.close(fileId);
            }
 
            return -1;
        }

Maybe this can also help you out!

[edited: made code sample complete]

[haziq-zur]

Hi @flappah,

I have tried your suggestion on using the underlying C wrapper to get the attribute and manage to get the attribute value that I want. For now, it is a matter of creating a looping function to iterate over all the attributes present in the groups/datasets. Thanks a lot for your help. For now, I will mark this as answer as I can use it to achieve my goals. But would like to know more on what happen with HDF5-CSharp not able to directly get the attribute. Thanks again.