MHO_ContainerHDF5Converter.hh

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#ifndef MHO_ContainerHDF5Converter_HH__
#define MHO_ContainerHDF5Converter_HH__
 
#include "MHO_ClassIdentity.hh"
#include "MHO_ExtensibleElement.hh"
#include "MHO_JSONHeaderWrapper.hh"
 
#include "MHO_Axis.hh"
#include "MHO_AxisPack.hh"
#include "MHO_ObjectTags.hh"
#include "MHO_ScalarContainer.hh"
#include "MHO_TableContainer.hh"
#include "MHO_Taggable.hh"
#include "MHO_VectorContainer.hh"
 
#include <sstream>
 
#include "hdf5.h"
#include "hdf5_hl.h" 
 
#include "MHO_NumpyTypeCode.hh"
#include "MHO_HDF5TypeCode.hh"
// #include "MHO_HDF5Attributes.hh"
// #include "MHO_HDF5Datasets.hh"
#include "MHO_HDF5ConversionHelpers.hh"
 
namespace hops
{
 
class MHO_HDF5Converter
{
    public:
        MHO_HDF5Converter(){};
        virtual ~MHO_HDF5Converter(){};
 
        virtual void SetObjectToConvert(MHO_Serializable* ) = 0;
        virtual void SetObjectMetaData(const mho_json& mdata){fMetaData = mdata;}
        virtual void WriteToHDF5File(hid_t /*file_id*/, std::string /*group_prefix*/) = 0;
 
    protected:
 
        mho_json fMetaData;
 
};
 
template< typename XContainerType > class MHO_ContainerHDF5Converter: public MHO_HDF5Converter
{
    public:
        MHO_ContainerHDF5Converter(): MHO_HDF5Converter() { fContainer = nullptr; }
 
        MHO_ContainerHDF5Converter(MHO_ExtensibleElement* element): MHO_HDF5Converter()
        {
            fContainer = dynamic_cast< XContainerType* >(element);
        }
 
        virtual ~MHO_ContainerHDF5Converter() {}
 
        virtual void SetObjectToConvert(MHO_Serializable* obj) { fContainer = dynamic_cast< XContainerType* >(obj); };
 
        virtual void WriteToHDF5File(hid_t file_id, std::string group_prefix)
        {
            if(fContainer != nullptr)
            {
                ConstructHDF5(file_id, group_prefix, fContainer);
            }
        }
 
    private:
        XContainerType* fContainer;
 
    protected:
 
        //unspecialized template doesn't do much
        template< typename XCheckType > void ConstructHDF5(hid_t /*file_id*/, std::string /*group_prefix*/, const XCheckType* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< XCheckType >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XCheckType >().as_string();
        };
 
        //use SFINAE to generate specialization for the rest of the container types
        //that we actually care about
 
        //scalar specialization
        template< typename XCheckType = XContainerType >
        typename std::enable_if< std::is_base_of< MHO_ScalarContainerBase, XCheckType >::value, void >::type
        ConstructHDF5(hid_t file_id, std::string group_prefix, const XContainerType* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< XContainerType >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XContainerType >().as_string();
            std::string object_uuid = obj->GetObjectUUID().as_string();
            msg_debug("hdf5interface", "creating scalar type for object with uuid: "<< object_uuid << eom);
            std::string item_group = group_prefix + "/" + object_uuid;
 
            if (H5Lexists(file_id, item_group.c_str(), H5P_DEFAULT) == 0) 
            {
                hid_t group_id = H5Gcreate(file_id, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                if(group_id < 0) 
                {
                    msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                }
                else
                {
                    std::string name = item_group + "/data";
                    //write the data
                    hid_t dataset_id = -1;
                    herr_t status = 
                    make_scalar_dataset< typename XContainerType::value_type >(file_id, dataset_id, name, fContainer->GetValue() );//fMetaData); 
                    H5Gclose(group_id);
                }
            }
        };
 
        //vector specialization (but not an axis!)
        template< typename XCheckType = XContainerType >
        typename std::enable_if< (std::is_base_of< MHO_VectorContainerBase, XCheckType >::value &&
                                  !std::is_base_of< MHO_AxisBase, XCheckType >::value),
                                 void >::type
        ConstructHDF5(hid_t file_id, std::string group_prefix, const XContainerType* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< XContainerType >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XContainerType >().as_string();
            std::string object_uuid = obj->GetObjectUUID().as_string();
            msg_debug("hdf5interface", "creating vector type for object with uuid: "<< object_uuid << eom);
 
            //grab the rank and dimensions
            hsize_t rank = 1;
            hsize_t dims[1];
            auto dim_array = fContainer->GetDimensionArray();
            for(std::size_t i=0; i<rank; i++){dims[i] = dim_array[i];}
            std::string item_group = group_prefix + "/" + object_uuid;
 
            if (H5Lexists(file_id, item_group.c_str(), H5P_DEFAULT) == 0) 
            {
                hid_t group_id = H5Gcreate(file_id, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                if(group_id < 0) 
                {
                    msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                }
                else
                {
                    std::string name = item_group + "/data";
                    //write the data
                    hid_t dataset_id = -1;
                    herr_t status = 
                    make_dataset< typename XContainerType::value_type >(file_id, dataset_id, name, rank, dims, fContainer->GetData(), fMetaData); 
 
                    H5Gclose(group_id);
                }
            }
        };
 
        //axis specialization
        template< typename XCheckType = XContainerType >
        typename std::enable_if< std::is_base_of< MHO_AxisBase, XCheckType >::value, void >::type
        ConstructHDF5(hid_t file_id, std::string group_prefix, const XContainerType* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< XContainerType >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XContainerType >().as_string();
            std::string object_uuid = obj->GetObjectUUID().as_string();
            msg_debug("hdf5interface", "creating axis type for object with uuid: "<< object_uuid << eom);
 
            //grab the rank and dimensions
            hsize_t rank = 1;
            hsize_t dims[1];
            auto dim_array = fContainer->GetDimensionArray();
            for(std::size_t i=0; i<rank; i++){dims[i] = dim_array[i];}
            std::string item_group = group_prefix + "/" + object_uuid;
 
            if (H5Lexists(file_id, item_group.c_str(), H5P_DEFAULT) == 0) 
            {
                hid_t group_id = H5Gcreate(file_id, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                if(group_id < 0) 
                {
                    msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                }
                else 
                {
                    std::string name = item_group + "/data";
                    //write the data
                    hid_t dataset_id = -1;
                    herr_t status = 
                    make_dataset< typename XContainerType::value_type >(file_id, dataset_id, name, rank, dims, fContainer->GetData(), fMetaData); 
 
                    H5Gclose(group_id);
                }
            }
        };
 
        //table specialization
        template< typename XCheckType = XContainerType >
        typename std::enable_if< std::is_base_of< MHO_TableContainerBase, XCheckType >::value, void >::type
        ConstructHDF5(hid_t file_id, std::string group_prefix, const XContainerType* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< XContainerType >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XContainerType >().as_string();
            std::string object_uuid = obj->GetObjectUUID().as_string();
            msg_debug("hdf5interface", "creating table type for object with uuid: "<< object_uuid << eom);
 
            //grab the rank and dimensions
            hsize_t rank = XContainerType::rank::value;
            hsize_t dims[XContainerType::rank::value];
            auto dim_array = obj->GetDimensionArray();
            for(std::size_t i=0; i<rank; i++){dims[i] = dim_array[i];}
 
            std::string item_group = group_prefix + "/" + object_uuid;
 
            if (H5Lexists(file_id, item_group.c_str(), H5P_DEFAULT) == 0) 
            {
                hid_t group_id = H5Gcreate(file_id, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                if(group_id < 0) 
                {
                    msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                }
                else 
                {
                    std::string name = item_group + "/data";
                    //write the data
                    hid_t dataset_id = -1;
                    herr_t status = 
                    make_dataset< typename XContainerType::value_type >(file_id, dataset_id, name, rank, dims, fContainer->GetData(), fMetaData); 
                    // make_dataset< typename XContainerType::value_type >(file_id, dataset_id, name, rank, dims, fContainer->GetData(), fMetaData["tags"]); 
 
                    //now attach the table axes
                    name = item_group;
                    AxisDumper axis_dumper(file_id, dataset_id, name, fMetaData);
                    for(std::size_t idx = 0; idx < obj->GetRank(); idx++)
                    {
                        axis_dumper.SetIndex(idx);
                        apply_at< typename XContainerType::axis_pack_tuple_type, AxisDumper >(*obj, idx, axis_dumper);
                    }
 
                    H5Gclose(group_id);
                }
            }
 
        };
 
        class AxisDumper
        {
            public:
                AxisDumper(hid_t file_id, hid_t ds_id, const std::string& parent, const mho_json& pmetadata):
                    fFileID(file_id), 
                    fDataSetID(ds_id), 
                    fParentName(parent),
                    fParentMetadata(pmetadata)
                {};
 
                AxisDumper(): fFileID(-1), fDataSetID(-1), fParentName(""){};
                ~AxisDumper(){};
        
                void SetIndex(std::size_t idx) { fIndex = idx; }
                void SetFileID(hid_t file_id){ fFileID = file_id; }
                void SetDataSetID(hid_t ds_id){ fDataSetID = ds_id; }
        
                template< typename XAxisType > void operator()(const XAxisType& axis)
                {
                    mho_json j;
                    std::string class_name = MHO_ClassIdentity::ClassName< XAxisType >();
                    std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< XAxisType >().as_string();
 
                    std::stringstream ssn;
                    ssn << "axis_" << fIndex;
                    std::string ax_name = ssn.str();
 
                    std::stringstream ss;
                    ss << fParentName << "/axis_";
                    ss << fIndex;
                    std::string item_group = ss.str();
 
                    if (H5Lexists(fFileID, item_group.c_str(), H5P_DEFAULT) == 0) 
                    {
                        hid_t group_id = H5Gcreate(fFileID, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                        if(group_id < 0) 
                        {
                            msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                        }
                        else 
                        {
                            std::string name = item_group + "/data";
 
                            mho_json mdata;
                            if(fParentMetadata.contains(ax_name))
                            {
                                mdata = fParentMetadata[ax_name];
                            }
                            msg_debug("hdf5interface", "creating an axis object with name: " << name<< eom);
 
                            //copy the data into a temporary vector (needed to deal with string axes)
                            std::size_t n = axis.GetSize();
                            std::vector< typename XAxisType::value_type > axis_data;
                            for(std::size_t i=0; i<n; i++){axis_data.push_back( axis.at(i) ); }
                
                            hsize_t dims[1];
                            dims[0] = n;
                            hid_t dataset_id = -1;
                            herr_t status = 
                            make_scale< typename XAxisType::value_type >(fFileID, fDataSetID, fIndex, item_group, name, &axis_data, mdata);
 
                            H5Gclose(group_id);
                        }
                    }
                };
 
            private:
 
                hid_t fFileID;
                hid_t fDataSetID;
                std::string fParentName;
                std::size_t fIndex;
                const mho_json& fParentMetadata;
 
        };
};
 
 
 
 
 
 
 
 
template<> class MHO_ContainerHDF5Converter< MHO_ObjectTags >: public MHO_HDF5Converter
{
    public:
        MHO_ContainerHDF5Converter(): MHO_HDF5Converter() { fContainer = nullptr; }
 
        MHO_ContainerHDF5Converter(MHO_ExtensibleElement* element): MHO_HDF5Converter()
        {
            fContainer = dynamic_cast< MHO_ObjectTags* >(element);
        }
 
        virtual ~MHO_ContainerHDF5Converter() {}
 
        virtual void SetObjectToConvert(MHO_Serializable* obj) { fContainer = dynamic_cast< MHO_ObjectTags* >(obj); };
 
        virtual void WriteToHDF5File(hid_t file_id, std::string group_prefix)
        {
            if(fContainer != nullptr)
            {
                ConstructHDF5(file_id, group_prefix, fContainer);
            }
        }
 
    private:
 
        void ConstructHDF5(hid_t file_id, std::string group_prefix, const MHO_ObjectTags* obj)
        {
            std::string class_name = MHO_ClassIdentity::ClassName< MHO_ObjectTags >();
            std::string class_uuid = MHO_ClassIdentity::GetUUIDFromClass< MHO_ObjectTags >().as_string();
            std::string object_uuid = obj->GetObjectUUID().as_string();
            msg_debug("hdf5interface", "creating tag type for object with uuid: "<< object_uuid << eom);
 
            std::string item_group = group_prefix + "/" + object_uuid;
 
            if (H5Lexists(file_id, item_group.c_str(), H5P_DEFAULT) == 0) 
            {
                hid_t group_id = H5Gcreate(file_id, item_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                if(group_id < 0) 
                {
                    msg_error("hdf5interface", "failed to create HDF5 group: "<< item_group << eom);
                }
                else 
                {
                    std::string name = item_group + "/uuid_set";
                    //the data we want to store is a vector of the object UUIDs that we are tagging 
                    std::vector< MHO_UUID > uvec = obj->GetAllObjectUUIDs();
                    //now convert these to a vector of strings
                    std::vector< std::string > uuid_vec;
                    for(std::size_t i=0; i<uvec.size(); i++){uuid_vec.push_back( uvec[i].as_string() );}
                    mho_json mdata = obj->GetMetaDataAsJSON();
 
                    mdata["class_name"] = class_name;
                    mdata["class_uuid"] = class_uuid;
                    hid_t dataset_id = -1;
                    herr_t status =
                    make_string_vector_dataset(file_id, dataset_id, name, &uuid_vec, mdata);
 
                    //store plot data as a separate object
                    if(mdata.contains("plot_data"))
                    {
                        std::string plot_group = item_group + "/" + "plot_data";
                        hid_t plot_group_id = H5Gcreate(file_id, plot_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                        json_to_hdf5_attributes(mdata["plot_data"], plot_group_id);
                        H5Gclose(plot_group_id);
                        // hid_t pd_dset_id = -1;
                        // std::string plot_data_name = item_group + "/plot_data";
                        // std::string plot_data = mdata["plot_data"].dump();
                        // make_scalar_dataset(file_id, pd_dset_id, plot_data_name, plot_data);
                    }
 
                    //store paramters as a separate object
                    if(mdata.contains("parameters"))
                    {
                        std::string param_group = item_group + "/" + "parameters";
                        hid_t param_group_id = H5Gcreate(file_id, param_group.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                        json_to_hdf5_attributes(mdata["parameters"], param_group_id);
                        H5Gclose(param_group_id);
 
                        // hid_t pm_dset_id = -1;
                        // std::string param_data_name = item_group + "/parameters";
                        // std::string param_data = mdata["parameters"].dump();
                        // make_scalar_dataset(file_id, pm_dset_id, param_data_name, param_data);
                    }
 
                    H5Gclose(group_id);
                }
            }
        };
 
        MHO_ObjectTags* fContainer;
};
 
} // namespace hops
 
#endif