random_forest_hdf5_impex.hxx

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#ifndef VIGRA_RANDOM_FOREST_IMPEX_HDF5_HXX
#define VIGRA_RANDOM_FOREST_IMPEX_HDF5_HXX
 
#include "config.hxx"
#include "random_forest.hxx"
#include "hdf5impex.hxx"
#include <algorithm>
#include <string>
 
namespace vigra
{
 
static const char *const rf_hdf5_options       = "_options";
static const char *const rf_hdf5_ext_param     = "_ext_param";
static const char *const rf_hdf5_labels        = "labels";
static const char *const rf_hdf5_topology      = "topology";
static const char *const rf_hdf5_parameters    = "parameters";
static const char *const rf_hdf5_tree          = "Tree_";
static const char *const rf_hdf5_version_group = ".";
static const char *const rf_hdf5_version_tag   = "vigra_random_forest_version";
static const double      rf_hdf5_version       =  0.1;
 
namespace detail
{
 
VIGRA_EXPORT void options_import_HDF5(HDF5File &, RandomForestOptions &,
                                      const std::string &);
 
VIGRA_EXPORT void options_export_HDF5(HDF5File &, const RandomForestOptions &,
                                      const std::string &);
 
VIGRA_EXPORT void dt_import_HDF5(HDF5File &, detail::DecisionTree &,
                                 const std::string &);
 
VIGRA_EXPORT void dt_export_HDF5(HDF5File &, const detail::DecisionTree &,
                                 const std::string &);
 
template<class X>
void rf_import_HDF5_to_map(HDF5File & h5context, X & param,
                           const char *const ignored_label = 0)
{
    // read a map containing all the double fields
    typedef typename X::map_type map_type;
    typedef std::pair<typename map_type::iterator, bool> inserter_type;
    typedef typename map_type::value_type value_type;
    typedef typename map_type::mapped_type mapped_type;
 
    map_type serialized_param;
    bool ignored_seen = ignored_label == 0;
 
    std::vector<std::string> names = h5context.ls();
    std::vector<std::string>::const_iterator j;
    for (j = names.begin(); j != names.end(); ++j)
    {
        if (ignored_label && *j == ignored_label)
        {
            ignored_seen = true;
            continue;
        }
        // get sort of an iterator to a new empty array vector in the map ...
        inserter_type new_array
            = serialized_param.insert(value_type(*j, mapped_type()));
        // ... and read the data into that place.
        h5context.readAndResize(*j, (*(new_array.first)).second);
    }
    vigra_precondition(ignored_seen, "rf_import_HDF5_to_map(): "
                                                         "labels are missing.");
    param.make_from_map(serialized_param);
}
 
template<class T>
void problemspec_import_HDF5(HDF5File & h5context, ProblemSpec<T> & param,
                             const std::string & name)
{
    h5context.cd(name);
    rf_import_HDF5_to_map(h5context, param, rf_hdf5_labels);
    // load_class_labels
    ArrayVector<T> labels;
    h5context.readAndResize(rf_hdf5_labels, labels);
    param.classes_(labels.begin(), labels.end());
    h5context.cd_up();
}
 
template<class X>
void rf_export_map_to_HDF5(HDF5File & h5context, const X & param)
{
    typedef typename X::map_type map_type;
    map_type serialized_param;
    // get a map containing all the double fields
    param.make_map(serialized_param);
    typename map_type::const_iterator j;
    for (j = serialized_param.begin(); j != serialized_param.end(); ++j)
        h5context.write(j->first, j->second);
}
 
template<class T>
void problemspec_export_HDF5(HDF5File & h5context, ProblemSpec<T> const & param,
                             const std::string & name)
{
    h5context.cd_mk(name);
    rf_export_map_to_HDF5(h5context, param);
    h5context.write(rf_hdf5_labels, param.classes);
    h5context.cd_up();
}
 
struct padded_number_string_data;
class VIGRA_EXPORT padded_number_string
{
private:
    padded_number_string_data* padded_number;
protected:
    padded_number_string(const padded_number_string &);
    void operator=(const padded_number_string &);
public:
    padded_number_string(int n);
    std::string operator()(int k) const;
    ~padded_number_string();
};
 
inline std::string get_cwd(HDF5File & h5context)
{
    return h5context.get_absolute_path(h5context.pwd());
}
 
} // namespace detail
 
/** \brief Save a random forest to an HDF5File object into a specified HDF5
           group.
 
    The random forest is saved as a set of HDF5 datasets, groups, and
    attributes below a certain HDF5 group (default: current group of the
    HDF5File object). No additional data should be stored in that group.
 
    \param rf        Random forest object to be exported
    \param h5context HDF5File object to use
    \param pathname  If empty or not supplied, save the random forest to the
                     current group of the HDF5File object. Otherwise, save to a
                     new-created group specified by the path name, which may
                     be either relative or absolute.
*/
template<class T, class Tag>
void rf_export_HDF5(const RandomForest<T, Tag> & rf,
                    HDF5File & h5context,
                    const std::string & pathname = "")
{
    std::string cwd;
    if (pathname.size()) {
        cwd = detail::get_cwd(h5context);
        h5context.cd_mk(pathname);
    }
    // version attribute
    h5context.writeAttribute(rf_hdf5_version_group, rf_hdf5_version_tag,
                             rf_hdf5_version);
    // save serialized options
    detail::options_export_HDF5(h5context, rf.options(), rf_hdf5_options);
    // save external parameters
    detail::problemspec_export_HDF5(h5context, rf.ext_param(),
                                    rf_hdf5_ext_param);
    // save trees
    int tree_count = rf.options_.tree_count_;
    detail::padded_number_string tree_number(tree_count);
    for (int i = 0; i < tree_count; ++i)
        detail::dt_export_HDF5(h5context, rf.tree(i),
                                                 rf_hdf5_tree + tree_number(i));
 
    if (pathname.size())
        h5context.cd(cwd);
}
 
/** \brief Save a random forest to a named HDF5 file into a specified HDF5
           group.
 
    The random forest is saved as a set of HDF5 datasets, groups, and
    attributes below a certain HDF5 group (default: root). No additional data
    should be stored in that group.
 
    \param rf       Random forest object to be exported
    \param filename Name of an HDF5 file to open
    \param pathname If empty or not supplied, save the random forest to the
                    root group of the HDF5 file. Otherwise, save to a
                    new-created group specified by the path name (relative
                    to the root group).
*/
template<class T, class Tag>
void rf_export_HDF5(const RandomForest<T, Tag> & rf,
                    const std::string & filename,
                    const std::string & pathname = "")
{
    HDF5File h5context(filename , HDF5File::Open);
    rf_export_HDF5(rf, h5context, pathname);
}
 
/** \brief Save a random forest to an HDF5 file specified by its id
 
    The random forest is saved as a set of HDF5 datasets, groups, and
    attributes below a certain HDF5 group (default: root). No additional data
    should be stored in that group.
 
    \warning In case the underlying HDF5 library used by Vigra is not
    exactly the same library used to open the file with the given id, this
    method will lead to crashes.
 
    \param rf       Random forest object to be exported
    \param outf_id  HDF5 file id
    \param pathname If empty or not supplied, save the random forest to the
                    root group of the HDF5 file. Otherwise, save to a
                    new-created group specified by the path name (relative
                    to the root group).
*/
template<class T, class Tag>
void rf_export_HDF5(const RandomForest<T, Tag> & rf,
                    hid_t outf_id,
                    const std::string & pathname = "")
{
    HDF5HandleShared fileHandle(outf_id, NULL, "");
    HDF5File h5context(fileHandle, pathname);
    rf_export_HDF5(rf, h5context);
}
 
/** \brief Read a random forest from an HDF5File object's specified group.
 
    The random forest is read from a certain HDF5 group (default: current group
    of the HDF5File object) as a set of HDF5 datasets, groups, and
    attributes. No additional data should be present in that group.
 
    \param rf        Random forest object to be imported
    \param h5context HDF5File object to use
    \param pathname  If empty or not supplied, read from the random forest
                     from the current group of the HDF5File object. Otherwise,
                     use the group specified by the path name, which may
                     be either relative or absolute.
*/
template<class T, class Tag>
bool rf_import_HDF5(RandomForest<T, Tag> & rf,
                    HDF5File & h5context,
                    const std::string & pathname = "")
{
    std::string cwd;
    if (pathname.size()) {
        cwd = detail::get_cwd(h5context);
        h5context.cd(pathname);
    }
    // version attribute
    if (h5context.existsAttribute(rf_hdf5_version_group, rf_hdf5_version_tag))
    {
        double read_version;
        h5context.readAttribute(rf_hdf5_version_group, rf_hdf5_version_tag,
                                read_version);
        vigra_precondition(read_version <= rf_hdf5_version,
                          "rf_import_HDF5(): unexpected file format version.");
    }
    // get serialized options
    detail::options_import_HDF5(h5context, rf.options_, rf_hdf5_options);
    // get external parameters
    detail::problemspec_import_HDF5(h5context, rf.ext_param_,
                                    rf_hdf5_ext_param);
    rf.trees_.clear();
    // get all groups in base path
    // no check for the rf_hdf5_tree prefix...
    std::vector<std::string> names = h5context.ls();
    // HDF5File::ls() uses H5_ITER_NATIVE, which does not guarantee alphabetical
    // order. Sort so that trees are imported in the same order they were exported.
    std::sort(names.begin(), names.end());
    std::vector<std::string>::const_iterator j;
    for (j = names.begin(); j != names.end(); ++j)
    {
        if ((*j->rbegin() == '/') && (*j->begin() != '_')) // skip the above
        {
            rf.trees_.push_back(detail::DecisionTree(rf.ext_param_));
            detail::dt_import_HDF5(h5context, rf.trees_.back(), *j);
        }
    }
    if (pathname.size())
        h5context.cd(cwd);
    return true;
}
 
/** \brief Read a random forest from a named HDF5 file's specified group.
 
    The random forest is read from a certain HDF5 group (default: root group
    of the HDF5 file) as a set of HDF5 datasets, groups, and attributes.
    No additional data should be present in that group.
 
    \param rf        Random forest object to be imported
    \param filename Name of an HDF5 file to open
    \param pathname  If empty or not supplied, read from the random forest
                     from the current group of the HDF5 file. Otherwise,
                     use the group specified by the path name, which may
                     be either relative or absolute.
*/
template<class T, class Tag>
bool rf_import_HDF5(RandomForest<T, Tag> & rf,
                    const std::string & filename,
                    const std::string & pathname = "")
{
    HDF5File h5context(filename, HDF5File::OpenReadOnly);
    return rf_import_HDF5(rf, h5context, pathname);
}
 
/** \brief Read a random forest from an HDF5 file specified by its id.
 
    The random forest is read from a certain HDF5 group (default: root group
    of the HDF5 file) as a set of HDF5 datasets, groups, and attributes.
    No additional data should be present in that group.
 
    \warning In case the underlying HDF5 library used by Vigra is not
    exactly the same library used to open the file with the given id, this
    method will lead to crashes.
 
    \param rf        Random forest object to be imported
    \param inf_id   HDF5 file id
    \param pathname  If empty or not supplied, read from the random forest
                     from the current group of the HDF5 file. Otherwise,
                     use the group specified by the path name, which may
                     be either relative or absolute.
*/
template<class T, class Tag>
bool rf_import_HDF5(RandomForest<T, Tag> & rf,
                    hid_t inf_id,
                    const std::string & pathname = "")
{
    HDF5HandleShared fileHandle(inf_id, NULL, "");
    HDF5File h5context(fileHandle, pathname, true);
    return rf_import_HDF5(rf, h5context);
}
 
} // namespace vigra
 
#endif // VIGRA_RANDOM_FOREST_HDF5_IMPEX_HXX