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Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
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Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
#include "mhdf.h"#include "util.h"#include "status.h"#include <assert.h>#include <stdlib.h>#include <string.h>#include <H5Tpublic.h>#include <H5Dpublic.h>#include <H5Ppublic.h>
Include dependency graph for file-desc.c:Go to the source code of this file.
Defines | |
| #define | FIX_OFFSET(TYPE, FIELD) |
Functions | |
| static struct mhdf_FileDesc * | alloc_file_desc (mhdf_Status *status) |
| static void * | realloc_data (struct mhdf_FileDesc **data, size_t append_bytes, mhdf_Status *status, int alignment) |
| void | mhdf_fixFileDesc (struct mhdf_FileDesc *copy_ptr, const struct mhdf_FileDesc *orig_addr) |
| Fix nested pointers for copied/moved FileDesc struct. | |
| static struct mhdf_FileDesc * | get_elem_desc (mhdf_FileHandle file_handle, struct mhdf_FileDesc *result, const char *elem_handle, int idx, mhdf_Status *status) |
| static unsigned | get_file_id_size (hid_t file_id_type, mhdf_Status *status) |
| static struct mhdf_FileDesc * | get_tag_desc (mhdf_FileHandle file_handle, struct mhdf_FileDesc *result, const char *name, int idx, hid_t type, mhdf_Status *status) |
| static void | free_string_list (char **list, int count) |
| struct mhdf_FileDesc * | mhdf_getFileSummary (mhdf_FileHandle file_handle, hid_t file_id_type, mhdf_Status *status, int extraSetInfo) |
| Get summary of data tables contained within file. | |
Variables | |
| static char | buffer [512] |
| #define FIX_OFFSET | ( | TYPE, | |
| FIELD | |||
| ) |
if( copy_ptr->FIELD != NULL ) \ copy_ptr->FIELD = (TYPE)( ( (char*)( copy_ptr->FIELD ) - (char*)orig_addr ) + (char*)copy_ptr )
Definition at line 73 of file file-desc.c.
Referenced by mhdf_fixFileDesc().
| static struct mhdf_FileDesc * alloc_file_desc | ( | mhdf_Status * | status | ) | [static, read] |
Definition at line 15 of file file-desc.c.
References mhdf_isError(), mhdf_malloc(), mhdf_FileDesc::offset, and mhdf_FileDesc::total_size.
Referenced by mhdf_getFileSummary().
{
struct mhdf_FileDesc* result;
/* allocate a little short of a page */
result = (struct mhdf_FileDesc*)mhdf_malloc( 4000, status );
if( mhdf_isError( status ) ) return 0;
memset( result, 0, sizeof( struct mhdf_FileDesc ) );
result->total_size = 4000;
result->offset = ( (unsigned char*)result ) + sizeof( struct mhdf_FileDesc );
return result;
}
| static void free_string_list | ( | char ** | list, |
| int | count | ||
| ) | [static] |
Definition at line 377 of file file-desc.c.
Referenced by mhdf_getFileSummary().
{
int i;
for( i = 0; i < count; ++i )
free( list[i] );
free( list );
}
| static struct mhdf_FileDesc* get_elem_desc | ( | mhdf_FileHandle | file_handle, |
| struct mhdf_FileDesc * | result, | ||
| const char * | elem_handle, | ||
| int | idx, | ||
| mhdf_Status * | status | ||
| ) | [static, read] |
Definition at line 120 of file file-desc.c.
References buffer, mhdf_EntDesc::count, mhdf_EntDesc::dense_tag_indices, mhdf_ElemDesc::desc, mhdf_FileDesc::elems, mhdf_ElemDesc::handle, mhdf_ElemDesc::have_adj, mhdf_closeData(), mhdf_getElemTypeName(), mhdf_haveAdjacency(), mhdf_isError(), mhdf_isPolyElement(), mhdf_openConnectivity(), mhdf_openPolyConnectivity(), mhdf_EntDesc::num_dense_tags, realloc_data(), mhdf_EntDesc::start_id, mhdf_ElemDesc::type, and mhdf_EntDesc::vals_per_ent.
Referenced by mhdf_getFileSummary().
{
hid_t id_pair[2];
int poly;
void* ptr;
long junk;
ptr = realloc_data( &result, strlen( elem_handle ) + 1, status, sizeof(char) );
if( !ptr ) return NULL;
strcpy( ptr, elem_handle );
result->elems[idx].handle = ptr;
mhdf_getElemTypeName( file_handle, elem_handle, buffer, sizeof( buffer ), status );
if( mhdf_isError( status ) )
{
free( result );
return NULL;
}
ptr = realloc_data( &result, strlen( buffer ) + 1, status, sizeof(char) );
if( !ptr ) return NULL;
strcpy( ptr, buffer );
result->elems[idx].type = ptr;
poly = mhdf_isPolyElement( file_handle, elem_handle, status );
if( mhdf_isError( status ) )
{
free( result );
return NULL;
}
if( !poly )
{
id_pair[0] = mhdf_openConnectivity( file_handle, elem_handle, &result->elems[idx].desc.vals_per_ent,
&result->elems[idx].desc.count, &result->elems[idx].desc.start_id, status );
if( id_pair[0] < 0 )
{
free( result );
return NULL;
}
mhdf_closeData( file_handle, id_pair[0], status );
}
else
{
result->elems[idx].desc.vals_per_ent = -1;
mhdf_openPolyConnectivity( file_handle, elem_handle, &result->elems[idx].desc.count, &junk,
&result->elems[idx].desc.start_id, id_pair, status );
if( id_pair[0] < 0 )
{
free( result );
return NULL;
}
mhdf_closeData( file_handle, id_pair[0], status );
mhdf_closeData( file_handle, id_pair[1], status );
}
result->elems[idx].desc.dense_tag_indices = NULL;
result->elems[idx].desc.num_dense_tags = 0;
result->elems[idx].have_adj = mhdf_haveAdjacency( file_handle, result->elems[idx].handle, status );
if( mhdf_isError( status ) )
{
free( result );
return 0;
}
return result;
}
| static unsigned get_file_id_size | ( | hid_t | file_id_type, |
| mhdf_Status * | status | ||
| ) | [static] |
Definition at line 192 of file file-desc.c.
References mhdf_setFail().
Referenced by get_tag_desc().
{
if( H5Tget_class( file_id_type ) != H5T_INTEGER )
{
mhdf_setFail( status, "Invalid handle or type class for file ID type." );
return 0;
}
return H5Tget_size( file_id_type );
}
| static struct mhdf_FileDesc* get_tag_desc | ( | mhdf_FileHandle | file_handle, |
| struct mhdf_FileDesc * | result, | ||
| const char * | name, | ||
| int | idx, | ||
| hid_t | type, | ||
| mhdf_Status * | status | ||
| ) | [static, read] |
Definition at line 203 of file file-desc.c.
References mhdf_TagDesc::bytes, mhdf_TagDesc::default_value, mhdf_TagDesc::default_value_size, get_file_id_size(), mhdf_TagDesc::global_value, mhdf_TagDesc::global_value_size, mhdf_TagDesc::have_sparse, mhdf_BITFIELD, mhdf_BOOLEAN, mhdf_ENTITY_ID, mhdf_FLOAT, mhdf_getTagInfo(), mhdf_getTagValues(), mhdf_INTEGER, mhdf_isError(), mhdf_OPAQUE, mhdf_setFail(), mhdf_TagDesc::name, realloc_data(), size, mhdf_TagDesc::size, mhdf_TagDesc::storage, mhdf_FileDesc::tags, and mhdf_TagDesc::type.
Referenced by mhdf_getFileSummary().
{
void* ptr;
int have_default, have_global;
int valsize, size, close_type = 0;
hsize_t array_len;
ptr = realloc_data( &result, strlen( name ) + 1, status, sizeof(char) );
if( NULL == ptr ) return NULL;
strcpy( ptr, name );
result->tags[idx].name = ptr;
mhdf_getTagInfo( file_handle, name, &result->tags[idx].type, &result->tags[idx].size, &result->tags[idx].storage,
&have_default, &have_global, &result->tags[idx].have_sparse, status );
if( mhdf_isError( status ) )
{
free( result );
return NULL;
}
/* For variable length tags, have_default and have_global will
contain the size of the respective values. For fixed-length
tags, they are either zero or one. Simplify later code by
making them contain the size for both cases. */
valsize = result->tags[idx].size;
if( result->tags[idx].size >= 0 )
{
if( have_default ) have_default = valsize;
if( have_global ) have_global = valsize;
}
result->tags[idx].default_value = NULL;
result->tags[idx].default_value_size = have_default;
result->tags[idx].global_value = NULL;
result->tags[idx].global_value_size = have_global;
switch( result->tags[idx].type )
{
case mhdf_OPAQUE:
type = 0;
break;
case mhdf_BOOLEAN:
type = H5T_NATIVE_UCHAR;
break;
case mhdf_INTEGER:
type = H5T_NATIVE_INT;
have_default *= sizeof( int );
have_global *= sizeof( int );
valsize *= sizeof( int );
break;
case mhdf_FLOAT:
type = H5T_NATIVE_DOUBLE;
have_default *= sizeof( double );
have_global *= sizeof( double );
valsize *= sizeof( double );
break;
case mhdf_BITFIELD:
have_default = ( have_default + 7 ) / 8;
have_global = ( have_global + 7 ) / 8;
valsize = ( valsize + 7 ) / 8;
switch( valsize )
{
case 1:
type = H5Tcopy( H5T_NATIVE_B8 );
break;
case 2:
type = H5Tcopy( H5T_NATIVE_B16 );
break;
case 3:
case 4:
valsize += 4 - valsize; // to avoid fallthrough warning
type = H5Tcopy( H5T_NATIVE_B32 );
break;
case 5:
case 6:
case 7:
case 8:
valsize += 8 - valsize; // to avoid fallthrough warning
type = H5Tcopy( H5T_NATIVE_B64 );
break;
default:
free( result );
mhdf_setFail( status, "Cannot create a bit tag larger than 64-bits. %d bits requested.\n",
(int)valsize );
return NULL;
}
close_type = 1;
break;
case mhdf_ENTITY_ID:
if( 0 == type ) type = H5T_NATIVE_ULONG;
size = get_file_id_size( type, status );
if( !size )
{
free( result );
return NULL;
}
have_default *= size;
have_global *= size;
valsize *= size;
break;
default:
mhdf_setFail( status, "Unknown mhdf_TagDataType value (%d) for tag (\"%s\")", (int)result->tags[idx].type,
name );
free( result );
return NULL;
}
result->tags[idx].bytes = valsize;
if( result->tags[idx].type != mhdf_OPAQUE && result->tags[idx].type != mhdf_BITFIELD && result->tags[idx].size > 1 )
{
close_type = 1;
array_len = result->tags[idx].size;
#if defined( H5Tarray_create_vers ) && H5Tarray_create_vers > 1
type = H5Tarray_create2( type, 1, &array_len );
#else
type = H5Tarray_create( type, 1, &array_len, 0 );
#endif
if( type < 0 )
{
mhdf_setFail( status, "H5Tarray_create failed for tag (\"%s\")", name );
free( result );
return NULL;
}
}
if( have_default || have_global )
{
if( have_default )
{
ptr = realloc_data( &result, have_default, status, sizeof(int) );
if( NULL == ptr )
{
if( close_type )
{
H5Tclose( type );
}
return NULL;
}
result->tags[idx].default_value = ptr;
}
if( have_global )
{
ptr = realloc_data( &result, have_global, status, sizeof(int) );
if( NULL == ptr )
{
if( close_type )
{
H5Tclose( type );
}
return NULL;
}
result->tags[idx].global_value = ptr;
}
mhdf_getTagValues( file_handle, name, type, result->tags[idx].default_value, result->tags[idx].global_value,
status );
if( close_type )
{
H5Tclose( type );
}
if( mhdf_isError( status ) )
{
free( result );
return NULL;
}
}
return result;
}
| static void * realloc_data | ( | struct mhdf_FileDesc ** | data, |
| size_t | append_bytes, | ||
| mhdf_Status * | status, | ||
| int | alignment | ||
| ) | [static] |
Definition at line 28 of file file-desc.c.
References mhdf_fixFileDesc(), mhdf_isError(), mhdf_realloc(), mhdf_FileDesc::offset, and mhdf_FileDesc::total_size.
Referenced by get_elem_desc(), get_tag_desc(), and mhdf_getFileSummary().
{
void* result_ptr;
struct mhdf_FileDesc* const input_ptr = *data;
unsigned char* mem_ptr = (unsigned char*)input_ptr;
size_t new_size, occupied_size = input_ptr->offset - mem_ptr;
int append_bytes_padded = append_bytes + alignment - 1;
/* if the end of the allocated space is before the end of the required space */
if( mem_ptr + input_ptr->total_size < input_ptr->offset + append_bytes_padded )
{
if( append_bytes_padded < input_ptr->total_size )
new_size = 2 * input_ptr->total_size;
else
new_size = input_ptr->total_size + append_bytes_padded;
*data = (struct mhdf_FileDesc*)mhdf_realloc( *data, new_size, status );
if( mhdf_isError( status ) ) return 0;
/* if realloc moved us to a different location in memory,
* we need to update all of the internal pointers to
* new locations relative to the start of the struct */
if( *data != input_ptr )
{
mhdf_fixFileDesc( *data, input_ptr );
mem_ptr = (unsigned char*)( *data );
( *data )->offset = mem_ptr + occupied_size;
}
( *data )->total_size = new_size;
}
result_ptr = ( *data )->offset;
/* need to make this return pointer aligned */
uintptr_t addr = (uintptr_t)(( *data )->offset);
int pad = addr%alignment;
if (pad > 0)
{
( *data )->offset += (alignment-pad);
result_ptr = ( *data )->offset;
}
/*printf("new address %p \n", result_ptr);*/
( *data )->offset += append_bytes;
return result_ptr;
}
char buffer[512] [static] |
Definition at line 13 of file file-desc.c.
Referenced by check_valid_adjacencies(), check_valid_elem_conn(), check_valid_poly_conn(), file_exists(), get_elem_desc(), moab::ReadHDF5::get_tagged_entities(), moab::INT_IO_ERROR(), is_acis_bin_file(), is_acis_txt_file(), moab::ReadCGM::is_cubit_file(), is_cubit_file(), moab::ReadCGM::is_facet_file(), moab::ReadCGM::is_iges_file(), is_iges_file(), moab::ReadCGM::is_occ_brep_file(), is_occ_brep_file(), moab::ReadCGM::is_step_file(), is_step_file(), moab::mem_to_string(), mhdf_getElemHandles(), mhdf_name_to_path_cat(), mhdf_name_to_path_copy(), moab::mpi_err_str(), moab::WriteHDF5::ExportSet::name(), print_error(), print_iGeom_error(), print_iMesh_error(), moab::ErrorOutput::print_real(), moab::DebugOutput::print_real(), moab::ReadHDF5::read_adjacencies(), moab::ReadHDF5::read_elems(), moab::ReadHDF5::read_node_adj_elems(), moab::ReadHDF5::read_nodes(), moab::ReadHDF5VarLen::read_offsets(), moab::ReadHDF5::read_poly(), moab::ReadHDF5::read_set_data(), moab::ReadHDF5::read_tag_values_partial(), moab::ReadHDF5::read_var_len_tag(), moab::ParCommGraph::receive_mesh(), moab::ParCommGraph::receive_tag_values(), moab::ReorderTool::reorder_tag_data(), moab::ReadHDF5::search_tag_values(), moab::ParCommGraph::send_graph_partition(), moab::ParCommGraph::send_mesh_parts(), moab::ParCommGraph::send_tag_values(), moab::ReadHDF5::store_file_ids(), moab::ReadHDF5::store_sets_file_ids(), string_tag_value(), moab::WriteHDF5::write_adjacencies(), moab::WriteHDF5::write_elems(), moab::WriteHDF5::write_nodes(), moab::WriteHDF5::write_set_data(), moab::WriteHDF5::write_sets(), and moab::WriteHDF5::write_var_len_data().
1.7.6.1.
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