17 #define NOT_OPEN ((hid_t) -1)
19 #define STR_KEY_FILETYPE "filetype"
20 #define STR_FILETYPE_00 \
21 "_SHOGUN_SERIALIZABLE_HDF5_FILE_V_00_"
23 using namespace shogun;
25 CSerializableHdf5File::type_item_t::type_item_t(
const char* name_)
28 dims[0] = dims[1] = 0;
29 dspace = dtype = dset = NOT_OPEN;
36 CSerializableHdf5File::type_item_t::~type_item_t()
38 if (dset >= 0) H5Dclose(dset);
39 if (dtype >= 0) H5Tclose(dtype);
40 if (dspace >= 0) H5Sclose(dspace);
41 if (vltype != NULL)
SG_FREE(vltype);
46 CSerializableHdf5File::sizeof_sparsetype() {
47 return H5Tget_size(TYPE_INDEX) + H5Tget_size(H5T_STD_REF_OBJ);
50 CSerializableHdf5File::new_sparsetype()
52 hid_t result = H5Tcreate(H5T_COMPOUND, sizeof_sparsetype());
54 if (H5Tinsert(result, STR_SPARSE_FPTR, H5Tget_size(TYPE_INDEX),
61 CSerializableHdf5File::get_ref_sparstype(
void* sparse_buf) {
63 ((
char*) sparse_buf + H5Tget_size(TYPE_INDEX));
67 CSerializableHdf5File::new_sparseentrytype(EPrimitiveType ptype)
69 hid_t result = H5Tcreate(H5T_COMPOUND,
71 if (result < 0)
return NOT_OPEN;
73 if (H5Tinsert(result, STR_SPARSEENTRY_FINDEX,
76 if (H5Tinsert(result, STR_SPARSEENTRY_ENTRY,
TSGDataType
77 ::offset_sparseentry(ptype),
78 ptype2hdf5(ptype)) < 0)
return NOT_OPEN;
84 CSerializableHdf5File::ptype2hdf5(EPrimitiveType ptype)
88 switch (
sizeof (
bool)) {
89 case 1:
return H5T_NATIVE_UINT8;
90 case 2:
return H5T_NATIVE_UINT16;
91 case 4:
return H5T_NATIVE_UINT32;
92 case 8:
return H5T_NATIVE_UINT64;
96 case PT_CHAR:
return H5T_NATIVE_CHAR;
break;
97 case PT_INT8:
return H5T_NATIVE_INT8;
break;
98 case PT_UINT8:
return H5T_NATIVE_UINT8;
break;
99 case PT_INT16:
return H5T_NATIVE_INT16;
break;
100 case PT_UINT16:
return H5T_NATIVE_UINT16;
break;
101 case PT_INT32:
return H5T_NATIVE_INT32;
break;
102 case PT_UINT32:
return H5T_NATIVE_UINT32;
break;
103 case PT_INT64:
return H5T_NATIVE_INT64;
break;
104 case PT_UINT64:
return H5T_NATIVE_UINT64;
break;
105 case PT_FLOAT32:
return H5T_NATIVE_FLOAT;
break;
106 case PT_FLOAT64:
return H5T_NATIVE_DOUBLE;
break;
107 case PT_FLOATMAX:
return H5T_NATIVE_LDOUBLE;
break;
108 case PT_SGOBJECT:
return NOT_OPEN;
break;
115 CSerializableHdf5File::new_stype2hdf5(EStructType stype,
116 EPrimitiveType ptype)
118 hid_t result = ptype2hdf5(ptype);
121 case ST_NONE: result = H5Tcopy(result);
break;
122 case ST_STRING: result = H5Tvlen_create(result);
break;
123 case ST_SPARSE: result = new_sparsetype();
break;
131 CSerializableHdf5File::index2string(
136 case CT_SCALAR:
return false;
137 case CT_VECTOR:
case CT_SGVECTOR: snprintf(dest, n,
"y%u", y);
break;
138 case CT_MATRIX:
case CT_SGMATRIX: snprintf(dest, n,
"y%u_x%u", y, x);
break;
139 default:
return false;
146 CSerializableHdf5File::isequal_stype2hdf5(EStructType stype,
147 EPrimitiveType ptype,
150 hid_t pbuf = ptype2hdf5(ptype), pbuf2 = NOT_OPEN;
152 bool to_close =
false;
156 to_close =
true; pbuf = H5Tvlen_create(pbuf);
break;
158 to_close =
true; pbuf = new_sparsetype();
159 pbuf2 = new_sparseentrytype(ptype);
break;
162 bool result = (H5Tequal(htype, pbuf) > 0)
163 || (pbuf2 >= 0 && H5Tequal(htype, pbuf2) > 0);
165 if (pbuf2 >= 0 && H5Tclose(pbuf2) < 0)
return false;
166 if (to_close && H5Tclose(pbuf) < 0)
return false;
171 CSerializableHdf5File::dspace_select(EContainerType ctype,
index_t y,
174 type_item_t* m = m_stack_type.back();
176 if (H5Sselect_none(m->dspace) < 0)
return false;
181 case CT_SCALAR:
return false;
182 case CT_MATRIX:
case CT_SGMATRIX: coord[1] = x;
183 case CT_VECTOR:
case CT_SGVECTOR: coord[0] = y;
break;
184 default:
return false;
186 if (H5Sselect_elements(m->dspace, H5S_SELECT_SET, 1, coord) < 0)
193 CSerializableHdf5File::attr_write_scalar(
194 hid_t datatype,
const char* name,
const void* val)
197 if ((dspace = H5Screate_simple(0, NULL, NULL)) < 0)
return false;
199 if ((dtype = H5Tcopy(datatype)) < 0)
return false;
201 if ((attr = H5Acreate2(
202 m_stack_h5stream.back(), name, dtype, dspace,
203 H5P_DEFAULT, H5P_DEFAULT)) < 0)
return false;
205 if (H5Awrite(attr, datatype, val) < 0)
return false;
207 if (H5Aclose(attr) < 0)
return false;
208 if (H5Tclose(dtype) < 0)
return false;
209 if (H5Sclose(dspace) < 0)
return false;
215 CSerializableHdf5File::attr_write_string(
216 const char* name,
const char* val)
219 if ((dtype = H5Tcopy(H5T_C_S1)) < 0)
return false;
220 if (H5Tset_size(dtype, strlen(val)+1) < 0)
return false;
222 if (!attr_write_scalar(dtype, name, val))
return false;
224 if (H5Tclose(dtype) < 0)
return false;
230 CSerializableHdf5File::attr_exists(
const char* name)
232 return H5Aexists(m_stack_h5stream.back(), name) > 0;
236 CSerializableHdf5File::attr_get_size(
const char* name)
238 if (!attr_exists(name))
return 0;
241 if ((attr = H5Aopen(m_stack_h5stream.back(), name, H5P_DEFAULT))
245 if ((dtype = H5Aget_type(attr)) < 0)
return 0;
247 size_t result = H5Tget_size(dtype);
249 if (H5Tclose(dtype) < 0)
return 0;
250 if (H5Aclose(attr) < 0)
return 0;
256 CSerializableHdf5File::attr_read_scalar(
257 hid_t datatype,
const char* name,
void* val)
259 if (!attr_exists(name))
return false;
262 if ((attr = H5Aopen(m_stack_h5stream.back(), name, H5P_DEFAULT))
266 if ((dspace = H5Aget_space(attr)) < 0)
return false;
267 if (H5Sget_simple_extent_type(dspace) != H5S_SCALAR)
return false;
270 if ((dtype = H5Aget_type(attr)) < 0)
return false;
271 if (H5Tequal(datatype, dtype) <= 0)
return false;
273 if (H5Aread(attr, datatype, val) < 0)
return false;
275 if (H5Tclose(dtype) < 0)
return false;
276 if (H5Sclose(dspace) < 0)
return false;
277 if (H5Aclose(attr) < 0)
return false;
283 CSerializableHdf5File::attr_read_string(
284 const char* name,
char* val,
size_t n)
286 size_t size = attr_get_size(name);
287 if (size == 0 || size > n)
return false;
290 if ((dtype = H5Tcopy(H5T_C_S1)) < 0)
return false;
291 if (H5Tset_size(dtype, size) < 0)
return false;
293 if (!attr_read_scalar(dtype, name, val))
return false;
295 if (H5Tclose(dtype) < 0)
return false;
301 CSerializableHdf5File::group_create(
const char* name,
307 snprintf(gname,
STRING_LEN,
"%s%s", prefix, name);
309 m_stack_h5stream.push_back(
310 ngroup = H5Gcreate2(m_stack_h5stream.back(), gname, H5P_DEFAULT,
311 H5P_DEFAULT, H5P_DEFAULT));
312 if (ngroup < 0)
return false;
318 CSerializableHdf5File::group_open(
const char* name,
324 snprintf(gname,
STRING_LEN,
"%s%s", prefix, name);
326 m_stack_h5stream.push_back(
327 group = H5Gopen2(m_stack_h5stream.back(), gname, H5P_DEFAULT));
328 if (group < 0)
return false;
334 CSerializableHdf5File::group_close()
336 if (H5Gclose(m_stack_h5stream.back()) < 0)
return false;
337 m_stack_h5stream.pop_back();
342 CSerializableHdf5File::CSerializableHdf5File()
345 CSerializableHdf5File::CSerializableHdf5File(
const char* fname,
char rw)
348 CSerializableFile::init(NULL, rw, fname);
352 CSerializableHdf5File::~CSerializableHdf5File()
354 while (m_stack_type.get_num_elements() > 0) {
355 delete m_stack_type.back(); m_stack_type.pop_back();
362 CSerializableHdf5File::new_reader(
char* dest_version,
size_t n)
364 if (!attr_read_string(STR_KEY_FILETYPE, dest_version, n))
367 if (strcmp(STR_FILETYPE_00, dest_version) == 0)
368 return new SerializableHdf5Reader00(
this);
374 CSerializableHdf5File::init(
const char* fname)
376 if (m_filename == NULL || *m_filename ==
'\0') {
377 SG_WARNING(
"Filename not given for opening file!\n");
381 hid_t h5stream = NOT_OPEN;
384 h5stream = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT,
388 h5stream = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
391 SG_WARNING(
"Could not open file `%s', unknown mode!\n",
397 SG_WARNING(
"Could not open file `%s'!\n", m_filename);
401 m_stack_h5stream.push_back(h5stream);
404 if (!attr_write_string(STR_KEY_FILETYPE, STR_FILETYPE_00)) {
405 SG_WARNING(
"%s: Could not open file for writing during "
406 "writing filetype!\n", fname);
416 CSerializableHdf5File::close()
418 while (m_stack_h5stream.get_num_elements() > 1) {
419 if (m_stack_h5stream.back() >= 0)
420 H5Gclose(m_stack_h5stream.back());
421 m_stack_h5stream.pop_back();
424 if (m_stack_h5stream.get_num_elements() == 1) {
425 if (m_stack_h5stream.back() >= 0)
426 H5Fclose(m_stack_h5stream.back());
427 m_stack_h5stream.pop_back();
432 CSerializableHdf5File::is_opened()
434 return m_stack_h5stream.get_num_elements() > 0;
438 CSerializableHdf5File::write_scalar_wrapped(
441 type_item_t* m = m_stack_type.back();
445 if (m->y != 0 || m->x != 0)
return true;
449 m->vltype[m->x*m->dims[1] + m->y].p = (
void*) param;
452 < (
index_t) m->vltype[m->x*m->dims[1] + m->y].len-1)
453 || ((type->
m_ctype == CT_VECTOR || type->
m_ctype == CT_SGVECTOR) && m->y
456 && (m->x < (
index_t) m->dims[0]-1
457 || m->y < (
index_t) m->dims[1]-1)))
461 if (m->sub_y != 0)
return true;
463 default:
return false;
472 if (H5Dwrite(m->dset, mem_type_id, H5S_ALL, H5S_ALL,
473 H5P_DEFAULT, param) < 0)
return false;
476 if (H5Dwrite(m->dset, mem_type_id, H5S_ALL, H5S_ALL,
477 H5P_DEFAULT, m->vltype) < 0)
return false;
480 if (H5Dwrite(m->dset, m->dtype, H5S_ALL, H5S_ALL,
481 H5P_DEFAULT, m->sparse_ptr) < 0)
return false;
483 default:
return false;
486 if (H5Tclose(mem_type_id) < 0)
return false;
492 CSerializableHdf5File::write_cont_begin_wrapped(
495 hbool_t bool_buf =
true;
497 if (type->
m_ptype != PT_SGOBJECT)
return true;
499 if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_CONT, &bool_buf))
504 if (!attr_write_string(STR_CTYPE_NAME, ctype_buf))
return false;
510 SG_ERROR(
"write_cont_begin_wrapped(): Implementation error "
511 "during writing Hdf5File!");
513 case CT_MATRIX:
case CT_SGMATRIX:
514 if (!attr_write_scalar(TYPE_INDEX, STR_LENGTH_X, &len_real_x))
517 case CT_VECTOR:
case CT_SGVECTOR:
518 if (!attr_write_scalar(TYPE_INDEX, STR_LENGTH_Y, &len_real_y))
521 default:
return false;
528 CSerializableHdf5File::write_cont_end_wrapped(
535 CSerializableHdf5File::write_string_begin_wrapped(
538 type_item_t* m = m_stack_type.back();
540 m->vltype[m->x*m->dims[1] + m->y].len = length;
546 CSerializableHdf5File::write_string_end_wrapped(
553 CSerializableHdf5File::write_stringentry_begin_wrapped(
556 type_item_t* m = m_stack_type.back();
564 CSerializableHdf5File::write_stringentry_end_wrapped(
571 CSerializableHdf5File::write_sparse_begin_wrapped(
574 type_item_t* m_prev = m_stack_type.back();
576 if(!dspace_select(type->
m_ctype, m_prev->y, m_prev->x))
579 type_item_t* m =
new type_item_t(m_stack_type.back()->name);
580 m_stack_type.push_back(m);
584 if (m_prev->y == 0 && m_prev->x == 0) {
585 hbool_t bool_buf =
true;
586 if (!group_create(m->name, STR_GROUP_PREFIX))
return false;
588 if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_SPARSE,
589 &bool_buf))
return false;
591 if (!group_open(m->name, STR_GROUP_PREFIX))
return false;
592 if (!attr_exists(STR_IS_SPARSE))
return false;
595 m->rank = 1; m->dims[0] = length;
596 if (m->dims[0] == 0) m->dspace = H5Screate(H5S_NULL);
598 if (m->dspace < 0 && (m->dspace = H5Screate_simple(
599 m->rank, m->dims, NULL)) < 0)
601 if ((m->dtype = new_sparseentrytype(type->
m_ptype)) < 0)
607 if ((m->dset = H5Dcreate2(
608 m_stack_h5stream.back(), name, m->dtype, m->dspace,
609 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
614 char* buf =
SG_MALLOC(
char, sizeof_sparsetype());
617 if ((mem_type_id = new_sparsetype()) < 0)
return false;
620 if ((mem_space_id = H5Screate_simple(0, NULL, NULL)) < 0)
623 hobj_ref_t* sparse_ref = get_ref_sparstype(buf);
624 if (H5Rcreate(sparse_ref, m_stack_h5stream.back(), name,
625 H5R_OBJECT, -1) < 0)
return false;
627 if (H5Dwrite(m_prev->dset, mem_type_id, mem_space_id,
628 m_prev->dspace, H5P_DEFAULT, buf) < 0)
return false;
630 if (H5Sclose(mem_space_id) < 0)
return false;
631 if (H5Tclose(mem_type_id) < 0)
return false;
639 CSerializableHdf5File::write_sparse_end_wrapped(
642 if (!group_close())
return false;
643 delete m_stack_type.back(); m_stack_type.pop_back();
649 CSerializableHdf5File::write_sparseentry_begin_wrapped(
653 type_item_t* m = m_stack_type.back();
662 CSerializableHdf5File::write_sparseentry_end_wrapped(
670 CSerializableHdf5File::write_item_begin_wrapped(
673 type_item_t* m = m_stack_type.back();
676 if (type->
m_ptype != PT_SGOBJECT)
return true;
681 if (!group_create(name,
""))
return false;
687 CSerializableHdf5File::write_item_end_wrapped(
690 if (type->
m_ptype == PT_SGOBJECT)
691 if (!group_close())
return false;
697 CSerializableHdf5File::write_sgserializable_begin_wrapped(
698 const TSGDataType* type,
const char* sgserializable_name,
699 EPrimitiveType
generic)
701 hbool_t bool_buf =
true;
703 if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_SGSERIALIZABLE,
704 &bool_buf))
return false;
706 if (*sgserializable_name ==
'\0') {
707 if (!attr_write_scalar(H5T_NATIVE_HBOOL, STR_IS_NULL,
713 if (!attr_write_string(STR_INSTANCE_NAME, sgserializable_name))
719 if (!attr_write_string(STR_GENERIC_NAME, buf))
return false;
726 CSerializableHdf5File::write_sgserializable_end_wrapped(
727 const TSGDataType* type,
const char* sgserializable_name,
728 EPrimitiveType
generic)
734 CSerializableHdf5File::write_type_begin_wrapped(
735 const TSGDataType* type,
const char* name,
const char* prefix)
737 type_item_t* m =
new type_item_t(name); m_stack_type.push_back(m);
739 if (type->
m_ptype == PT_SGOBJECT) {
740 if (!group_create(name,
""))
return false;
751 case CT_VECTOR:
case CT_SGVECTOR:
753 if (m->dims[0] == 0) m->dspace = H5Screate(H5S_NULL);
754 if (type->
m_stype == ST_STRING)
755 m->vltype =
SG_MALLOC(hvl_t, m->dims[0]);
757 case CT_MATRIX:
case CT_SGMATRIX:
760 if (m->dims[0] *m->dims[1] == 0)
761 m->dspace = H5Screate(H5S_NULL);
762 if (type->
m_stype == ST_STRING)
763 m->vltype =
SG_MALLOC(hvl_t, m->dims[0] *m->dims[1]);
765 default:
return false;
768 if (m->dspace < 0 && (m->dspace = H5Screate_simple(
769 m->rank, m->dims, NULL)) < 0)
771 if ((m->dtype = new_stype2hdf5(type->
m_stype, type->
m_ptype)) < 0)
774 if ((m->dset = H5Dcreate2(
775 m_stack_h5stream.back(), name, m->dtype, m->dspace,
776 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
783 CSerializableHdf5File::write_type_end_wrapped(
784 const TSGDataType* type,
const char* name,
const char* prefix)
786 if (type->
m_ptype == PT_SGOBJECT)
787 if (!group_close())
return false;
789 delete m_stack_type.back(); m_stack_type.pop_back();