for General Purpose handling of hdf5 files

Collaboration diagram for for General Purpose handling of hdf5 files:

Classes
class	XmippH5File

Typedefs
typedef std::pair< H5FileProvider, String >	H5infoProvider

Enumerations
enum	H5FileProvider { NONE, MISTRAL, EMAN }

Functions
std::map< String, H5infoProvider >	createProviderMap ()
H5infoProvider	getProvider (hid_t fhdf5)
herr_t	showObjectInfo (hid_t group, const char *name, void *op_data)

Variables
const std::map< String, H5infoProvider >	H5ProviderMap = createProviderMap()

Detailed Description

Typedef Documentation

H5infoProvider

typedef std::pair<H5FileProvider, String> H5infoProvider

Definition at line 51 of file xmipp_hdf5.h.

Enumeration Type Documentation

H5FileProvider

enum H5FileProvider

Enumerator
NONE
MISTRAL
EMAN

Definition at line 43 of file xmipp_hdf5.h.

{
    NONE,
    MISTRAL,
    EMAN
} ;

Function Documentation

createProviderMap()

std::map<String, H5infoProvider > createProviderMap

(

)

Definition at line 102 of file xmipp_hdf5.cpp.

{
    std::map<String, H5infoProvider > m;
    m["NXtomo"] = std::make_pair(MISTRAL, "/NXtomo/instrument/sample/data");
    m["TomoNormalized"] = std::make_pair(MISTRAL, "/TomoNormalized/TomoNormalized");
    m["MDF"]  = std::make_pair(EMAN,    "/MDF/images/%i/image");
    return m;
}

getProvider()

H5infoProvider getProvider

(

hid_t

fhdf5

)

Return the default dataset name according to the typical group name of the root

Parameters

fhdf5

hdf5 file hander

Returns

Default dataset name for a file provider

Definition at line 202 of file xmipp_hdf5.cpp.

{
    H5infoProvider provider;

    size_t maxSize = 1024;
    char groupName[1024];
    char memName[1024];

    hid_t gid;
    ssize_t len;

    gid = H5Gopen(fhdf5,"/", H5P_DEFAULT);

    len = H5Iget_name(gid, groupName, maxSize);

    if (len == 0)
        REPORT_ERROR(ERR_VALUE_EMPTY, "rwHDF5: Empty structure in file.");

    len = H5Gget_objname_by_idx(gid, 0, memName, maxSize);

    H5Gclose(gid);

    typedef std::map<String, H5infoProvider >::const_iterator it_type;

    for ( it_type it = H5ProviderMap.begin(); it != H5ProviderMap.end(); it++)
    {
        if ( strcmp(memName,it->first.c_str() ) == 0 )
            return it->second;
    }

    return std::make_pair(NONE , "");

//    REPORT_ERROR(ERR_IO, "rwHDF5: Unknown file provider. Default dataset unknown.");

}

showObjectInfo()

herr_t showObjectInfo	(	hid_t	group,
		const char *	name,
		void *	op_data
	)

Definition at line 36 of file xmipp_hdf5.cpp.

{
    H5TreeInfo &h5Info = *((H5TreeInfo*)op_data);
    std::ostream &out = *(h5Info.out);

    hsize_t nobj;
    herr_t err=0;
    hid_t grpid, dsid;

    H5G_stat_t statbuf;

    // Print the object name
    out <<  formatString("%s%s - ", h5Info.rootname.c_str(), name);

    H5Gget_objinfo(objId, name, 0, &statbuf);
    /*
     * process each object according to its type
     */
    switch(statbuf.type)
    {
    case H5G_LINK:
        out <<  " SYM_LINK:\n";
        //        do_link(gid,memb_name);
        break;
    case H5G_GROUP:
        {
            String rootname = h5Info.rootname;
            h5Info.rootname += (String)name + "/";

            grpid = H5Gopen(objId,name, H5P_DEFAULT);
            err = H5Gget_num_objs(grpid, &nobj);
            out <<  formatString("Group {%d elements}\n", nobj);

            H5Giterate(objId, name, NULL, showObjectInfo, &h5Info);
            h5Info.rootname = rootname;
            break;
        }
    case H5G_DATASET:
        out <<  "Dataset {";
        dsid = H5Dopen(objId, name, H5P_DEFAULT);
        hsize_t dims[4];
        hid_t filespace;
        int rank;
        filespace = H5Dget_space(dsid);    /* Get filespace handle first. */
        rank  = H5Sget_simple_extent_dims(filespace, dims, NULL);

        for (int k = 0; k < rank-1; ++k)
            out << dims[k] << ", ";

        out << dims[rank-1] << "}\n";
        H5Dclose(dsid);
        break;
    case H5G_TYPE:
            out <<  " Data type:\n";
        //        idType = H5Topen(objId,memb_name, H5P_DEFAULT);
        //        H5Tclose(idType);
        break;
    default:
            out << " unknown?\n";
        break;
    }
    return err;
}

Variable Documentation

H5ProviderMap

const std::map<String, H5infoProvider > H5ProviderMap = createProviderMap()

Global declaration of a map to distinguish the h5file provider

Definition at line 56 of file xmipp_hdf5.h.