What is the structure of HDF5 / h5 file

m.ded · September 13, 2023, 11:26am

I use ANTs GitHub - ANTsX/ANTs: Advanced Normalization Tools (ANTs) to to create deformation fields in HDF5 format.
ANTs h5 transform files come from the ITK underlying IO system.

I would like to understand the structure of these h5 files to enable conversion from Elastix .nii file to .h5 file.
However, I do not understand all the values that are in the file. It contains a group “TransformGroup” which in turn contains groups “0”, “1” and “2”.

For example, “1” and “2” contains a dataset “TransformFixedParameters”. But I don’t understand what the values represent.

dzenanz · September 13, 2023, 12:38pm

Does taking a look at this section and the rest of this file help?

github.com

InsightSoftwareConsortium/ITK/blob/v5.3.0/Modules/IO/TransformHDF5/src/itkHDF5TransformIO.cxx#L470-L501


      
          // HDF uses hierarchical paths to find particular data
          // in a file. These strings are used by both reading and
          // writing.
          const std::string HDF5CommonPathNames::transformGroupName(std::string("/TransformGroup"));
          const std::string HDF5CommonPathNames::transformTypeName("/TransformType");
          
          const std::string HDF5CommonPathNames::transformFixedNameMisspelled("/TranformFixedParameters");
          const std::string HDF5CommonPathNames::transformParamsNameMisspelled("/TranformParameters");
          const std::string HDF5CommonPathNames::transformFixedName("/TransformFixedParameters");
          const std::string HDF5CommonPathNames::transformParamsName("/TransformParameters");
          
          const std::string HDF5CommonPathNames::ItkVersion("/ITKVersion");
          const std::string HDF5CommonPathNames::HDFVersion("/HDFVersion");
          const std::string HDF5CommonPathNames::OSName("/OSName");
          const std::string HDF5CommonPathNames::OSVersion("/OSVersion");
          
          
          // I couldn't figure out a way to represent transforms
          // excepts as groups -- the HDF5 composite only allows
          // fixed-size structures.

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m.ded · September 13, 2023, 3:31pm

Thank you, but not really. I am not that familial with C++. I read the code and the method WriteFixedParameters but I can’t figure out what information transformFixedNameMisspelled, transformParamsNameMisspelled and transformFixedName store. in the ANTs-HDF5-file.

dzenanz · September 13, 2023, 4:05pm

This comment explains the 0,1,2 group names?

github.com

InsightSoftwareConsortium/ITK/blob/v5.3.0/Modules/IO/TransformHDF5/src/itkHDF5TransformIO.cxx#L490-L492


      
          // Since (for now) transforms are ordered in a file, but
          // not named, I name them by their order in the file,
          // beginning with zero.

For conversion, maybe read in the .nii image, set it to a DisplacementFieldTransform, and then write it using TransformFileWriter?

matt.mccormick · September 22, 2023, 8:43pm

Hi,

The TransformFixedParameters are the transformation parameters that are not optimized during registration. Other parameters are optimized during registration. Transform parameters are described in the ITK Software Guide.