SerializableHdf5File.cpp

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2010 Soeren Sonnenburg
 * Copyright (C) 2010 Berlin Institute of Technology
 */

#include "lib/config.h"
#ifdef HAVE_HDF5

#include "lib/SerializableHdf5File.h"
#include "lib/SerializableHdf5Reader00.h"

#define NOT_OPEN                   ((hid_t) -1)

#define STR_KEY_FILETYPE           "filetype"
#define STR_FILETYPE_00 \
    "_SHOGUN_SERIALIZABLE_HDF5_FILE_V_00_"

using namespace shogun;

CSerializableHdf5File::type_item_t::type_item_t(const char* name_)
{
    rank = 0;
    dims[0] = dims[1] = 0;
    dspace = dtype = dset = NOT_OPEN;
    vltype = NULL;
    y = x = sub_y = 0;
    sparse_ptr = NULL;
    name = name_;
}

CSerializableHdf5File::type_item_t::~type_item_t(void)
{
    if (dset >= 0) H5Dclose(dset);
    if (dtype >= 0) H5Tclose(dtype);
    if (dspace >= 0) H5Sclose(dspace);
    if (vltype != NULL) delete[] vltype;
    /* Do not delete SPARSE_PTR  */
}

hid_t
CSerializableHdf5File::sizeof_sparsetype(void) {
    return H5Tget_size(TYPE_INDEX) + H5Tget_size(H5T_STD_REF_OBJ);
}
hid_t
CSerializableHdf5File::new_sparsetype(void)
{
    hid_t result = H5Tcreate(H5T_COMPOUND, sizeof_sparsetype());

    if (H5Tinsert(result, STR_SPARSE_VINDEX, 0, TYPE_INDEX) < 0)
        return NOT_OPEN;
    if (H5Tinsert(result, STR_SPARSE_FPTR, H5Tget_size(TYPE_INDEX),
                  H5T_STD_REF_OBJ) < 0)
        return NOT_OPEN;

    return result;
}
hobj_ref_t*
CSerializableHdf5File::get_ref_sparstype(void* sparse_buf) {
    return (hobj_ref_t*)
        ((char*) sparse_buf + H5Tget_size(TYPE_INDEX));
}

hid_t
CSerializableHdf5File::new_sparseentrytype(EPrimitiveType ptype)
{
    hid_t result = H5Tcreate(H5T_COMPOUND,
                             TSGDataType::sizeof_sparseentry(ptype));
    if (result < 0) return NOT_OPEN;

    if (H5Tinsert(result, STR_SPARSEENTRY_FINDEX,
                  HOFFSET(TSparseEntry<char>, feat_index), TYPE_INDEX)
        < 0) return NOT_OPEN;
    if (H5Tinsert(result, STR_SPARSEENTRY_ENTRY, TSGDataType
                  ::offset_sparseentry(ptype),
                  ptype2hdf5(ptype)) < 0) return NOT_OPEN;

    return result;
}

hid_t
CSerializableHdf5File::ptype2hdf5(EPrimitiveType ptype)
{
    switch (ptype) {
    case PT_BOOL:
        switch (sizeof (bool)) {
        case 1: return H5T_NATIVE_UINT8;
        case 2: return H5T_NATIVE_UINT16;
        case 4: return H5T_NATIVE_UINT32;
        case 8: return H5T_NATIVE_UINT64;
        default: break;
        }
        break;
    case PT_CHAR: return H5T_NATIVE_CHAR; break;
    case PT_INT8: return H5T_NATIVE_INT8; break;
    case PT_UINT8: return H5T_NATIVE_UINT8; break;
    case PT_INT16: return H5T_NATIVE_INT16; break;
    case PT_UINT16: return H5T_NATIVE_UINT16; break;
    case PT_INT32: return H5T_NATIVE_INT32; break;
    case PT_UINT32: return H5T_NATIVE_UINT32; break;
    case PT_INT64: return H5T_NATIVE_INT64; break;
    case PT_UINT64: return H5T_NATIVE_UINT64; break;
    case PT_FLOAT32: return H5T_NATIVE_FLOAT; break;
    case PT_FLOAT64: return H5T_NATIVE_DOUBLE; break;
    case PT_FLOATMAX: return H5T_NATIVE_LDOUBLE; break;
    case PT_SGOBJECT: return NOT_OPEN; break;
    }

    return NOT_OPEN;
}

hid_t
CSerializableHdf5File::new_stype2hdf5(EStructType stype,
                                      EPrimitiveType ptype)
{
    hid_t result = ptype2hdf5(ptype);

    switch (stype) {
    case ST_NONE: result = H5Tcopy(result); break;
    case ST_STRING: result = H5Tvlen_create(result); break;
    case ST_SPARSE: result = new_sparsetype(); break;
    }

    return result;
}

bool
CSerializableHdf5File::index2string(
    char* dest, size_t n, EContainerType ctype, index_t y, index_t x)
{
    switch (ctype) {
    case CT_SCALAR: return false;
    case CT_VECTOR: snprintf(dest, n, "y%u", y); break;
    case CT_MATRIX: snprintf(dest, n, "y%u_x%u", y, x); break;
    }

    return true;
}

bool
CSerializableHdf5File::isequal_stype2hdf5(EStructType stype,
                                          EPrimitiveType ptype,
                                          hid_t htype)
{
    hid_t pbuf = ptype2hdf5(ptype), pbuf2 = NOT_OPEN;

    bool to_close = false;
    switch (stype) {
    case ST_NONE: break;
    case ST_STRING:
        to_close = true; pbuf = H5Tvlen_create(pbuf); break;
    case ST_SPARSE:
        to_close = true; pbuf = new_sparsetype();
        pbuf2 = new_sparseentrytype(ptype); break;
    }

    bool result = (H5Tequal(htype, pbuf) > 0)
        || (pbuf2 >= 0 && H5Tequal(htype, pbuf2) > 0);

    if (pbuf2 >= 0 && H5Tclose(pbuf2) < 0) return false;
    if (to_close && H5Tclose(pbuf) < 0) return false;
    return result;
}

bool
CSerializableHdf5File::dspace_select(EContainerType ctype, index_t y,
                                     index_t x)
{
    type_item_t* m = m_stack_type.back();

    if (H5Sselect_none(m->dspace) < 0) return false;

    hsize_t coord[2];
    switch (ctype) {
    case CT_SCALAR: return false;
    case CT_MATRIX: coord[1] = x; /* break;  */
    case CT_VECTOR: coord[0] = y; break;
    }
    if (H5Sselect_elements(m->dspace, H5S_SELECT_SET, 1, coord) < 0)
        return false;

    return true;
}

bool
CSerializableHdf5File::attr_write_scalar(
    hid_t datatype, const char* name, const void* val)
{
    hid_t dspace;
    if ((dspace = H5Screate_simple(0, NULL, NULL)) < 0) return false;
    hid_t dtype;
    if ((dtype = H5Tcopy(datatype)) < 0) return false;
    hid_t attr;
    if ((attr = H5Acreate2(
             m_stack_h5stream.back(), name, dtype, dspace,
             H5P_DEFAULT, H5P_DEFAULT)) < 0) return false;

    if (H5Awrite(attr, datatype, val) < 0) return false;

    if (H5Aclose(attr) < 0) return false;
    if (H5Tclose(dtype) < 0) return false;
    if (H5Sclose(dspace) < 0) return false;

    return true;
}

bool
CSerializableHdf5File::attr_write_string(
    const char* name, const char* val)
{
    hid_t dtype;
    if ((dtype = H5Tcopy(H5T_C_S1)) < 0) return false;
    if (H5Tset_size(dtype, strlen(val)+1) < 0) return false;

    if (!attr_write_scalar(dtype, name, val)) return false;

    if (H5Tclose(dtype) < 0) return false;

    return true;
}

bool
CSerializableHdf5File::attr_exists(const char* name)
{
    return H5Aexists(m_stack_h5stream.back(), name) > 0;
}

size_t
CSerializableHdf5File::attr_get_size(const char* name)
{
    if (!attr_exists(name)) return 0;

    hid_t attr;
    if ((attr = H5Aopen(m_stack_h5stream.back(), name, H5P_DEFAULT))
        < 0) return 0;

    hid_t dtype;
    if ((dtype = H5Aget_type(attr)) < 0) return 0;

    size_t result = H5Tget_size(dtype);

    if (H5Tclose(dtype) < 0) return 0;
    if (H5Aclose(attr) < 0) return 0;

    return result;
}

bool
CSerializableHdf5File::attr_read_scalar(
    hid_t datatype, const char* name, void* val)
{
    if (!attr_exists(name)) return false;

    hid_t attr;
    if ((attr = H5Aopen(m_stack_h5stream.back(), name, H5P_DEFAULT))
        < 0) return false;

    hid_t dspace;
    if ((dspace = H5Aget_space(attr)) < 0) return false;
    if (H5Sget_simple_extent_type(dspace) != H5S_SCALAR) return false;

    hid_t dtype;
    if ((dtype = H5Aget_type(attr)) < 0) return false;
    if (H5Tequal(datatype, dtype) <= 0) return false;

    if (H5Aread(attr, datatype, val) < 0) return false;

    if (H5Tclose(dtype) < 0) return false;
    if (H5Sclose(dspace) < 0) return false;
    if (H5Aclose(attr) < 0) return false;

    return true;
}

bool
CSerializableHdf5File::attr_read_string(
    const char* name, char* val, size_t n)
{
    size_t size = attr_get_size(name);
    if (size == 0 || size > n) return false;

    hid_t dtype;
    if ((dtype = H5Tcopy(H5T_C_S1)) < 0) return false;
    if (H5Tset_size(dtype, size) < 0) return false;

    if (!attr_read_scalar(dtype, name, val)) return false;

    if (H5Tclose(dtype) < 0) return false;

    return true;
}

bool
CSerializableHdf5File::group_create(const char* name,
                                    const char* prefix)
{
    hid_t ngroup;
    string_t gname;

    snprintf(gname, STRING_LEN, "%s%s", prefix, name);

    m_stack_h5stream.push_back(
        ngroup = H5Gcreate2(m_stack_h5stream.back(), gname, H5P_DEFAULT,
                            H5P_DEFAULT, H5P_DEFAULT));
    if (ngroup < 0) return false;

    return true;
}

bool
CSerializableHdf5File::group_open(const char* name,
                                  const char* prefix)
{
    hid_t group;
    string_t gname;

    snprintf(gname, STRING_LEN, "%s%s", prefix, name);

    m_stack_h5stream.push_back(
        group = H5Gopen2(m_stack_h5stream.back(), gname, H5P_DEFAULT));
    if (group < 0) return false;

    return true;
}

bool
CSerializableHdf5File::group_close(void)
{
    if (H5Gclose(m_stack_h5stream.back()) < 0) return false;
    m_stack_h5stream.pop_back();

    return true;
}

CSerializableHdf5File::CSerializableHdf5File(void)
    :CSerializableFile() { init(""); }

CSerializableHdf5File::CSerializableHdf5File(const char* fname, char rw)
    :CSerializableFile()
{
    CSerializableFile::init(NULL, rw, fname);
    init(fname);
}

CSerializableHdf5File::~CSerializableHdf5File()
{
    while (m_stack_type.get_num_elements() > 0) {
        delete m_stack_type.back(); m_stack_type.pop_back();
    }

    close();
}

CSerializableFile::TSerializableReader*
CSerializableHdf5File::new_reader(char* dest_version, size_t n)
{
    if (!attr_read_string(STR_KEY_FILETYPE, dest_version, n))
        return NULL;

    if (strcmp(STR_FILETYPE_00, dest_version) == 0)
        return new SerializableHdf5Reader00(this);

    return NULL;
}

void
CSerializableHdf5File::init(const char* fname)
{
    if (m_filename == NULL || *m_filename == '\0') {
        SG_WARNING("Filename not given for opening file!\n");
        close(); return;
    }

    hid_t h5stream = NOT_OPEN;
    switch (m_task) {
    case 'w':
        h5stream = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT,
                             H5P_DEFAULT);
        break;
    case 'r':
        h5stream = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
        break;
    default:
        SG_WARNING("Could not open file `%s', unknown mode!\n",
                   m_filename);
        close(); return;
    }

    if (h5stream < 0) {
        SG_WARNING("Could not open file `%s'!\n", m_filename);
        close(); return;
    }

    m_stack_h5stream.push_back(h5stream);
    switch (m_task) {
    case 'w':
        if (!attr_write_string(STR_KEY_FILETYPE, STR_FILETYPE_00)) {
            SG_WARNING("%s: Could not open file for writing during "
                       "writing filetype!\n", fname);
            close(); return;
        }
        break;
    case 'r': break;
    default: break;
    }
}

void
CSerializableHdf5File::close(void)
{
    while (m_stack_h5stream.get_num_elements() > 1) {
        if (m_stack_h5stream.back() >= 0)
            H5Gclose(m_stack_h5stream.back());
        m_stack_h5stream.pop_back();
    }

    if (m_stack_h5stream.get_num_elements() == 1) {
        if (m_stack_h5stream.back() >= 0)
            H5Fclose(m_stack_h5stream.back());
        m_stack_h5stream.pop_back();
    }
}

bool
CSerializableHdf5File::is_opened(void)
{
    return m_stack_h5stream.get_num_elements() > 0;
}

bool
CSerializableHdf5File::write_scalar_wrapped(
    const TSGDataType* type, const void* param)
{
    type_item_t* m = m_stack_type.back();

    switch (type->m_stype) {
    case ST_NONE:
        if (m->y != 0 || m->x != 0) return true;
        break;
    case ST_STRING:
        if (m->sub_y == 0)
            m->vltype[m->x*m->dims[1] + m->y].p = (void*) param;

        if ((m->sub_y
             < (index_t) m->vltype[m->x*m->dims[1] + m->y].len-1)
            || (type->m_ctype == CT_VECTOR && m->y
                < (index_t) m->dims[0]-1)
            || (type->m_ctype == CT_MATRIX
                && (m->x < (index_t) m->dims[0]-1
                    || m->y < (index_t) m->dims[1]-1)))
            return true;
        break;
    case ST_SPARSE:
        if (m->sub_y != 0) return true;
        break;
    }

    hid_t mem_type_id;
    if ((mem_type_id = new_stype2hdf5(type->m_stype, type->m_ptype)
            ) < 0) return false;

    switch (type->m_stype) {
    case ST_NONE:
        if (H5Dwrite(m->dset, mem_type_id, H5S_ALL, H5S_ALL,
                     H5P_DEFAULT, param) < 0) return false;
        break;
    case ST_STRING:
        if (H5Dwrite(m->dset, mem_type_id, H5S_ALL, H5S_ALL,
                     H5P_DEFAULT, m->vltype) < 0) return false;
        break;
    case ST_SPARSE:
        if (H5Dwrite(m->dset, m->dtype, H5S_ALL, H5S_ALL,
                     H5P_DEFAULT, m->sparse_ptr) < 0) return false;
        break;
    }

    if (H5Tclose(mem_type_id) < 0) return false;

    return true;
}

bool
CSerializableHdf5File::write_cont_begin_wrapped(
    const TSGDataType* type, index_t len_real_y, index_t len_real_x)
{
    hbool_t bool_buf = true;

    if (type->m_ptype != PT_SGOBJECT) return true;

    if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_CONT, &bool_buf))
        return false;

    string_t ctype_buf;
    type->to_string(ctype_buf, STRING_LEN);
    if (!attr_write_string(STR_CTYPE_NAME, ctype_buf)) return false;

    switch (type->m_ctype) {
    case CT_SCALAR:
        SG_ERROR("write_cont_begin_wrapped(): Implementation error "
                 "during writing Hdf5File!");
        return false;
    case CT_MATRIX:
        if (!attr_write_scalar(TYPE_INDEX, STR_LENGTH_X, &len_real_x))
            return false;
        /* break;  */
    case CT_VECTOR:
        if (!attr_write_scalar(TYPE_INDEX, STR_LENGTH_Y, &len_real_y))
            return false;
        break;
    }

    return true;
}

bool
CSerializableHdf5File::write_cont_end_wrapped(
    const TSGDataType* type, index_t len_real_y, index_t len_real_x)
{
    return true;
}

bool
CSerializableHdf5File::write_string_begin_wrapped(
    const TSGDataType* type, index_t length)
{
    type_item_t* m = m_stack_type.back();

    m->vltype[m->x*m->dims[1] + m->y].len = length;

    return true;
}

bool
CSerializableHdf5File::write_string_end_wrapped(
    const TSGDataType* type, index_t length)
{
    return true;
}

bool
CSerializableHdf5File::write_stringentry_begin_wrapped(
    const TSGDataType* type, index_t y)
{
    type_item_t* m = m_stack_type.back();

    m->sub_y = y;

    return true;
}

bool
CSerializableHdf5File::write_stringentry_end_wrapped(
    const TSGDataType* type, index_t y)
{
    return true;
}

bool
CSerializableHdf5File::write_sparse_begin_wrapped(
    const TSGDataType* type, index_t vec_index,
    index_t length)
{
    type_item_t* m_prev = m_stack_type.back();

    if(!dspace_select(type->m_ctype, m_prev->y, m_prev->x))
        return false;

    type_item_t* m = new type_item_t(m_stack_type.back()->name);
    m_stack_type.push_back(m);

    /* ************************************************************ */

    if (m_prev->y == 0 && m_prev->x == 0) {
        hbool_t bool_buf = true;
        if (!group_create(m->name, STR_GROUP_PREFIX)) return false;

        if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_SPARSE,
                               &bool_buf)) return false;
    } else {
        if (!group_open(m->name, STR_GROUP_PREFIX)) return false;
        if (!attr_exists(STR_IS_SPARSE)) return false;
    }

    m->rank = 1; m->dims[0] = length;
    if (m->dims[0] == 0) m->dspace = H5Screate(H5S_NULL);

    if (m->dspace < 0 && (m->dspace = H5Screate_simple(
                              m->rank, m->dims, NULL)) < 0)
        return false;
    if ((m->dtype = new_sparseentrytype(type->m_ptype)) < 0)
        return false;

    string_t name;
    index2string(name, STRING_LEN, type->m_ctype, m_prev->y,
                 m_prev->x);
    if ((m->dset = H5Dcreate2(
             m_stack_h5stream.back(), name, m->dtype, m->dspace,
             H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
        return false;

    /* ************************************************************ */

    char* buf = new char[sizeof_sparsetype()];

    *(index_t*) buf = vec_index;

    hid_t mem_type_id;
    if ((mem_type_id = new_sparsetype()) < 0) return false;

    hid_t mem_space_id;
    if ((mem_space_id = H5Screate_simple(0, NULL, NULL)) < 0)
        return false;

    hobj_ref_t* sparse_ref = get_ref_sparstype(buf);
    if (H5Rcreate(sparse_ref, m_stack_h5stream.back(), name,
                  H5R_OBJECT, -1) < 0) return false;

    if (H5Dwrite(m_prev->dset, mem_type_id, mem_space_id,
                 m_prev->dspace, H5P_DEFAULT, buf) < 0) return false;

    if (H5Sclose(mem_space_id) < 0) return false;
    if (H5Tclose(mem_type_id) < 0) return false;

    delete buf;

    return true;
}

bool
CSerializableHdf5File::write_sparse_end_wrapped(
    const TSGDataType* type, index_t vec_index,
    index_t length)
{
    if (!group_close()) return false;
    delete m_stack_type.back(); m_stack_type.pop_back();

    return true;
}

bool
CSerializableHdf5File::write_sparseentry_begin_wrapped(
    const TSGDataType* type, const TSparseEntry<char>* first_entry,
    index_t feat_index, index_t y)
{
    type_item_t* m = m_stack_type.back();

    m->sparse_ptr = (TSparseEntry<char>*) first_entry;
    m->sub_y = y;

    return true;
}

bool
CSerializableHdf5File::write_sparseentry_end_wrapped(
    const TSGDataType* type, const TSparseEntry<char>* first_entry,
    index_t feat_index, index_t y)
{
    return true;
}

bool
CSerializableHdf5File::write_item_begin_wrapped(
    const TSGDataType* type, index_t y, index_t x)
{
    type_item_t* m = m_stack_type.back();
    m->y = y; m->x = x;

    if (type->m_ptype != PT_SGOBJECT) return true;

    string_t name;
    if (!index2string(name, STRING_LEN, type->m_ctype, y, x))
        return false;
    if (!group_create(name, "")) return false;

    return true;
}

bool
CSerializableHdf5File::write_item_end_wrapped(
    const TSGDataType* type, index_t y, index_t x)
{
    if (type->m_ptype == PT_SGOBJECT)
        if (!group_close()) return false;

    return true;
}

bool
CSerializableHdf5File::write_sgserializable_begin_wrapped(
    const TSGDataType* type, const char* sgserializable_name,
    EPrimitiveType generic)
{
    hbool_t bool_buf = true;

    if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_SGSERIALIZABLE,
                           &bool_buf)) return false;

    if (*sgserializable_name == '\0') {
        if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_NULL,
                               &bool_buf))
            return false;
        return true;
    }

    if (!attr_write_string(STR_INSTANCE_NAME, sgserializable_name))
        return false;

    if (generic != PT_NOT_GENERIC) {
        string_t buf;
        TSGDataType::ptype_to_string(buf, generic, STRING_LEN);
        if (!attr_write_string(STR_GENERIC_NAME, buf)) return false;
    }

    return true;
}

bool
CSerializableHdf5File::write_sgserializable_end_wrapped(
    const TSGDataType* type, const char* sgserializable_name,
    EPrimitiveType generic)
{
    return true;
}

bool
CSerializableHdf5File::write_type_begin_wrapped(
    const TSGDataType* type, const char* name, const char* prefix)
{
    type_item_t* m = new type_item_t(name); m_stack_type.push_back(m);

    if (type->m_ptype == PT_SGOBJECT) {
        if (!group_create(name, "")) return false;
        return true;
    }

    switch (type->m_ctype) {
    case CT_SCALAR:
        m->rank = 0;
        if (type->m_stype == ST_STRING) m->vltype = new hvl_t[1];
        break;
    case CT_VECTOR:
        m->rank = 1; m->dims[0] = *type->m_length_y;
        if (m->dims[0] == 0) m->dspace = H5Screate(H5S_NULL);
        if (type->m_stype == ST_STRING)
            m->vltype = new hvl_t[m->dims[0]];
        break;
    case CT_MATRIX:
        m->rank = 2;
        m->dims[0] = *type->m_length_x; m->dims[1] = *type->m_length_y;
        if (m->dims[0] *m->dims[1] == 0)
            m->dspace = H5Screate(H5S_NULL);
        if (type->m_stype == ST_STRING)
            m->vltype = new hvl_t[m->dims[0] *m->dims[1]];
        break;
    }

    if (m->dspace < 0 && (m->dspace = H5Screate_simple(
                              m->rank, m->dims, NULL)) < 0)
        return false;
    if ((m->dtype = new_stype2hdf5(type->m_stype, type->m_ptype)) < 0)
        return false;

    if ((m->dset = H5Dcreate2(
             m_stack_h5stream.back(), name, m->dtype, m->dspace,
             H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
        return false;

    return true;
}

bool
CSerializableHdf5File::write_type_end_wrapped(
    const TSGDataType* type, const char* name, const char* prefix)
{
    if (type->m_ptype == PT_SGOBJECT)
        if (!group_close()) return false;

    delete m_stack_type.back(); m_stack_type.pop_back();
    return true;
}

#endif /* HAVE_HDF5  */