Add a filter to HighFive

[LauZanMo]

I would like to ask whether there is a way to change the default filter of highfive to blosc, because the default filter,which is set to szip, is slow and my system has real-time requirements. I notice that the highfive code does not seem to support the setting of filter. Can it be implemented using the native HDF5 function ?

[LauZanMo]

I spent some time clarifying the structure of PropertyList in HighFive and found it very easy to add filter on this basis. First, I need to declare and implement the Blosc class in H5PropertyList.hpp and H5PropertyList_misc.hpp, respectively. Just like this:

# H5PropertyList.hpp

/// \implements PropertyInterface
class Blosc {
    public:
        explicit Blosc(unsigned level, unsigned shuffle, unsigned compressor);

    private:
        friend DataSetCreateProps;
        void apply(hid_t hid) const;
        unsigned _cd_values[7];
};



# H5PropertyList_misc.hpp

inline Blosc::Blosc(unsigned int level, unsigned int shuffle, unsigned int compressor) {
    _cd_values[4] = level;
    _cd_values[5] = shuffle;
    _cd_values[6] = compressor;
}

inline void Blosc::apply(const hid_t hid) const {
    detail::h5p_set_blosc(hid, _cd_values);
}

Then, as for the specific implementation function ‘detail::h5p_set_blosc’, I refer to the implementation of hdf5_blosc: #https://github.com/Blosc/hdf5-blosc/blob/master/src/example.c#L57 just like this:

# h5p_wrapper.hpp

#include "blosc_filter.h"
inline herr_t h5p_set_blosc(hid_t plist_id, const unsigned int *cd_values) {
    char *version, *date;
    if (register_blosc(&version, &date) < 0) {
        HDF5ErrMapper::ToException<PropertyException>("Blosc filter unavailable.");
    }
    
    herr_t err = H5Pset_filter(plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 7, cd_values);
    if (err < 0) {
        HDF5ErrMapper::ToException<PropertyException>("Error setting blosc property");
    }
    return err;
}

Of course I need to link hdf5-blosc dynamic library files:

# root CMakeLists.txt
# I install hdf5-blosc to the default path
set(blosc_filter_DIR /usr/local/lib/) 
target_link_libraries(HighFive INTERFACE blosc_filter)
target_link_directories(HighFive INTERFACE /usr/local/include/)

Finally I can write with blosc-filter!

HighFive::DataSetCreateProps props;
props.add(HighFive::Chunking({4,4}));
props.add(HighFive::Blosc(4, 1, BLOSC_BLOSCLZ));
// create dataset and write with this properties!

[alkino]

Do you think you can propose a PR with that? It looks exactly what you should do to add your own filter.

[LauZanMo]

OK, I'll submit a PR soon.