util.c File Reference

#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <ctype.h>
#include <hdf5.h>
#include "util.h"
#include "status.h"
#include "names-and-paths.h"

Include dependency graph for util.c:

Go to the source code of this file.

Macros
#define	VALGRIND_CHECK_MEM_IS_DEFINED(A, B)
#define	VALGRIND_MAKE_MEM_UNDEFINED(A, B)

Functions
void *	mhdf_malloc (size_t size, mhdf_Status *status)
void *	mhdf_realloc (void *ptr, size_t size, mhdf_Status *status)
size_t	mhdf_name_to_path (const char *name, char *path, size_t path_len)
static int	mhdf_hex_char (int c)
int	mhdf_path_to_name (const char *path, char *name)
char *	mhdf_name_to_path_copy (const char *name, mhdf_Status *status)
char *	mhdf_name_to_path_cat (const char *prefix, const char *name, mhdf_Status *status)
hid_t	mhdf_elem_group_from_handle (FileHandle *file_ptr, const char *elem_handle, mhdf_Status *status)
int	mhdf_create_scalar_attrib (hid_t object, const char *name, hid_t type, const void *value, mhdf_Status *status)
int	mhdf_read_scalar_attrib (hid_t object, const char *name, hid_t type, void *value, mhdf_Status *status)
static herr_t	find_attr_by_name (hid_t handle, const char *name, void *mydata)
int	mhdf_find_attribute (hid_t object, const char *attrib_name, unsigned int *index_out, mhdf_Status *status)
static herr_t	find_link_by_name (hid_t handle, const char *name, void *mydata)
int	mhdf_is_in_group (hid_t group, const char *name, mhdf_Status *status)
static int	mhdf_readwrite (hid_t data_id, int read, long offset, long count, hid_t type, void *array, hid_t io_prop, mhdf_Status *status)
static int	mhdf_readwrite_column (hid_t data_id, int read, int column, long offset, long count, hid_t type, void *array, hid_t io_prop, mhdf_Status *status)
int	mhdf_write_data (hid_t data_id, long offset, long count, hid_t type_id, const void *array, hid_t prop, mhdf_Status *status)
int	mhdf_read_data (hid_t data_id, long offset, long count, hid_t type_id, void *array, hid_t prop, mhdf_Status *status)
int	mhdf_read_column (hid_t data_id, int column, long offset, long count, hid_t type, void *array, hid_t prop, mhdf_Status *status)
int	mhdf_write_column (hid_t data_id, int column, long offset, long count, hid_t type, const void *array, hid_t prop, mhdf_Status *status)
hid_t	mhdf_create_table (hid_t group_id, const char *path, hid_t type, int rank, hsize_t *dims, mhdf_Status *status)
hid_t	mhdf_create_table_with_prop (hid_t group_id, const char *path, hid_t type, int rank, hsize_t *dims, hid_t create_prop, mhdf_Status *status)
hid_t	mhdf_open_table (hid_t group_id, const char *path, int columns, hsize_t *rows_out, mhdf_Status *status)
hid_t	mhdf_open_table2 (hid_t group_id, const char *path, int rank, hsize_t *dims_out, long *start_id_out, mhdf_Status *status)
hid_t	mhdf_open_table_simple (hid_t group_id, const char *path, mhdf_Status *status)
static int	qs_comp_int (const void *ptr1, const void *ptr2)
int	mhdf_compact_to_ranges (int *length, int *ids, int ordered)
hid_t	get_elem_type_enum (FileHandle *file_ptr, mhdf_Status *status)
int	mhdf_write_max_id (FileHandle *file_ptr, mhdf_Status *status)
static int	num_open (void)
void	mhdf_api_begin_internal (void)
void	mhdf_api_end_internal (int expected_diff, const char *filename, int linenumber)

Variables
static int	mhdf_api_handle_count = 0

Macro Definition Documentation

VALGRIND_CHECK_MEM_IS_DEFINED

#define VALGRIND_CHECK_MEM_IS_DEFINED	(		A,
			B
	)

MOAB, a Mesh-Oriented datABase, is a software component for creating, storing and accessing finite element mesh data.

Copyright 2004 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software.

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

Definition at line 28 of file util.c.

VALGRIND_MAKE_MEM_UNDEFINED

#define VALGRIND_MAKE_MEM_UNDEFINED	(		A,
			B
	)

Definition at line 29 of file util.c.

Function Documentation

find_attr_by_name()

static herr_t find_attr_by_name ( hid_t  handle, const char *  name, void *  mydata  )

static

Definition at line 246 of file util.c.

{
#endif
 /* empty statement to remove compiler warning */
 if( handle )
 {
 }
 return !strcmp( name, (const char*)mydata );
}

Referenced by mhdf_find_attribute().

find_link_by_name()

static herr_t find_link_by_name ( hid_t  handle, const char *  name, void *  mydata  )

static

Definition at line 271 of file util.c.

{
 /* empty statement to remove compiler warning */
 if( handle )
 {
 }
 return !strcmp( name, (const char*)mydata );
}

Referenced by mhdf_is_in_group().

get_elem_type_enum()

hid_t get_elem_type_enum	(	FileHandle *	file_ptr,
		mhdf_Status *	status
	)

Definition at line 786 of file util.c.

{
 hid_t result;
#if defined( H5Topen_vers ) && H5Topen_vers > 1
 result = H5Topen2( file_ptr->hdf_handle, TYPE_ENUM_PATH, H5P_DEFAULT );
#else
 result = H5Topen( file_ptr->hdf_handle, TYPE_ENUM_PATH );
#endif
 if( result < 0 ) mhdf_setFail( status, "Element type enum does not exist in file. Invalid file." );
 return result;
}

References struct_FileHandle::hdf_handle, mhdf_setFail(), and TYPE_ENUM_PATH.

Referenced by mhdf_addElement(), and mhdf_getElemName().

mhdf_api_begin_internal()

void mhdf_api_begin_internal

(

void

)

Definition at line 862 of file util.c.

{
 /* HDF5 docs are incorrect. Passing H5F_OBJ_ALL as the first
 arg to H5Fget_obj_count returns the total number of open
 handles, not just those in files (i.e. temporary types and such.)
 mhdf_api_handle_count = H5Fget_obj_count( H5F_OBJ_ALL, H5F_OBJ_ALL );
 Need to loop to get actual file handles:
 */
 mhdf_api_handle_count = num_open();
}

References mhdf_api_handle_count, and num_open().

mhdf_api_end_internal()

void mhdf_api_end_internal	(	int	expected_diff,
		const char *	filename,
		int	linenumber
	)

Definition at line 873 of file util.c.

{
 if( mhdf_api_handle_count + expected_diff != num_open() )
 {
 fprintf( stderr, "Unclosed handles at end of mhdf API call.\n" );
 fprintf( stderr, "Entered with %d, expected %d change, got %d.\n", mhdf_api_handle_count, expected_diff,
 num_open() );
 fprintf( stderr, "%s:%d\n", filename, linenumber );
 abort();
 }
 
 mhdf_api_handle_count = 0;
}

References mhdf_api_handle_count, and num_open().

mhdf_compact_to_ranges()

int mhdf_compact_to_ranges	(	int *	length,
		int *	ids,
		int	ordered
	)

Definition at line 733 of file util.c.

{
 int new_length = 0;
 int *iter, *end;
 int prev, count;
 int need_copy = 0;
 int *copy_ptr = 0, *w_iter;
 size_t blen;
 
 if( !ordered ) qsort( ids, *length, sizeof( int ), &qs_comp_int );
 
 iter = ids;
 end = ids + *length;
 while( iter != end )
 {
 prev = *( iter++ );
 while( iter < end && *( iter++ ) == ++prev )
 ;
 new_length += 2;
 if( new_length > ( iter - ids ) ) need_copy = 1;
 }
 
 if( new_length > *length ) return 0;
 
 if( need_copy )
 {
 blen = sizeof( int ) * *length;
 copy_ptr = (int*)malloc( blen );
 memcpy( copy_ptr, ids, blen );
 iter = copy_ptr;
 }
 else
 {
 iter = ids;
 }
 
 end = iter + *length;
 w_iter = ids;
 while( iter != end )
 {
 prev = *( iter++ );
 count = 1;
 while( iter < end && *( iter++ ) == ++prev )
 ;
 *( w_iter++ ) = prev - count;
 *( w_iter++ ) = count;
 }
 
 *length = new_length;
 if( need_copy ) free( copy_ptr );
 return 1;
}

References length(), and qs_comp_int().

mhdf_create_scalar_attrib()

int mhdf_create_scalar_attrib	(	hid_t	object,
		const char *	name,
		hid_t	type,
		const void *	value,
		mhdf_Status *	status
	)

Definition at line 164 of file util.c.

{
 hid_t dspace_id, attr_id;
 herr_t rval;
 
 dspace_id = H5Screate( H5S_SCALAR );
 if( dspace_id < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Screate_simple." );
 return 0;
 }
 
#if defined( H5Acreate_vers ) && H5Acreate_vers > 1
 attr_id = H5Acreate2( object, name, type, dspace_id, H5P_DEFAULT, H5P_DEFAULT );
#else
 attr_id = H5Acreate( object, name, type, dspace_id, H5P_DEFAULT );
#endif
 H5Sclose( dspace_id );
 if( attr_id < 0 )
 {
 mhdf_setFail( status, "Failed to create \"%s\" attrib.", name );
 return 0;
 }
 
 VALGRIND_CHECK_MEM_IS_DEFINED( value, H5Tget_size( type ) );
 rval = H5Awrite( attr_id, type, value );
 H5Aclose( attr_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Failed to write \"%s\" attrib.", name );
 return 0;
 }
 
 return 1;
}

References mhdf_setFail(), and VALGRIND_CHECK_MEM_IS_DEFINED.

Referenced by create_tag_common(), mhdf_addElement(), mhdf_createConnectivity(), mhdf_createFile(), mhdf_createNodeCoords(), mhdf_createPolyConnectivity(), mhdf_createSetMeta(), mhdf_createVarLenTag(), and store_tag_val_in_attrib().

mhdf_create_table()

hid_t mhdf_create_table	(	hid_t	group_id,
		const char *	path,
		hid_t	type,
		int	rank,
		hsize_t *	dims,
		mhdf_Status *	status
	)

Definition at line 563 of file util.c.

{
 return mhdf_create_table_with_prop( group_id, path, type, rank, dims, H5P_DEFAULT, status );
}

References mhdf_create_table_with_prop().

Referenced by mhdf_createAdjacency(), mhdf_createConnectivity(), mhdf_createDenseTagData(), mhdf_createNodeCoords(), mhdf_createPolyConnectivity(), mhdf_createSetChildren(), mhdf_createSetData(), mhdf_createSetMeta(), mhdf_createSetParents(), mhdf_createSparseTagData(), and mhdf_createVarLenTagData().

mhdf_create_table_with_prop()

hid_t mhdf_create_table_with_prop	(	hid_t	group_id,
		const char *	path,
		hid_t	type,
		int	rank,
		hsize_t *	dims,
		hid_t	create_prop,
		mhdf_Status *	status
	)

Definition at line 568 of file util.c.

{
 hid_t space_id, table_id;
 
 space_id = H5Screate_simple( rank, dims, NULL );
 if( space_id < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Screate_simple." );
 return -1;
 }
 
#if defined( H5Dcreate_vers ) && H5Dcreate_vers > 1
 table_id = H5Dcreate2( group_id, path, type, space_id, H5P_DEFAULT, create_prop, H5P_DEFAULT );
#else
 table_id = H5Dcreate( group_id, path, type, space_id, create_prop );
#endif
 H5Sclose( space_id );
 if( table_id < 0 )
 {
 mhdf_setFail( status, "HDF5 DataSet creation failed." );
 return -1;
 }
 
 mhdf_setOkay( status );
 return table_id;
}

References mhdf_setFail(), and mhdf_setOkay().

Referenced by mhdf_create_table().

mhdf_elem_group_from_handle()

hid_t mhdf_elem_group_from_handle	(	FileHandle *	file_ptr,
		const char *	elem_handle,
		mhdf_Status *	status
	)

Definition at line 146 of file util.c.

{
 char* path;
 hid_t result;
 
 path = mhdf_name_to_path_cat( ELEMENT_GROUP, elem_handle, status );
 if( NULL == path ) return -1;
 
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 result = H5Gopen2( file_ptr->hdf_handle, path, H5P_DEFAULT );
#else
 result = H5Gopen( file_ptr->hdf_handle, path );
#endif
 free( path );
 if( result < 0 ) mhdf_setFail( status, "Failed to open element group: \"%s\"", elem_handle );
 return result;
}

References ELEMENT_GROUP, struct_FileHandle::hdf_handle, mhdf_name_to_path_cat(), and mhdf_setFail().

Referenced by mhdf_createAdjacency(), mhdf_createConnectivity(), mhdf_createDenseTagData(), mhdf_createPolyConnectivity(), mhdf_getElemTypeName(), mhdf_haveAdjacency(), mhdf_haveDenseTag(), mhdf_isPolyElement(), mhdf_openAdjacency(), mhdf_openConnectivity(), mhdf_openConnectivitySimple(), mhdf_openDenseTagData(), and mhdf_openPolyConnectivity().

mhdf_find_attribute()

int mhdf_find_attribute	(	hid_t	object,
		const char *	attrib_name,
		unsigned int *	index_out,
		mhdf_Status *	status
	)

Definition at line 256 of file util.c.

{
 herr_t rval;
#if defined( H5Aiterate_vers ) && H5Aiterate_vers > 1
 hsize_t idx = 0;
 rval = H5Aiterate2( object, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &find_attr_by_name, (void*)attrib_name );
 *index_out = (unsigned int)idx;
#else
 *index_out = 0;
 rval = H5Aiterate( object, index_out, &find_attr_by_name, (void*)attrib_name );
#endif
 if( rval < 0 ) mhdf_setFail( status, "Internal error calling H5Aiterate." );
 return (int)rval;
}

References find_attr_by_name(), and mhdf_setFail().

Referenced by mhdf_getTagInfo(), mhdf_getTagValues(), mhdf_openSparseTagData(), and read_tag_attrib_data().

mhdf_hex_char()

static int mhdf_hex_char ( int  c )

static

Definition at line 85 of file util.c.

{
 if( isdigit( c ) )
 return c - '0';
 else
 return toupper( c ) - ( 'A' - 10 );
}

Referenced by mhdf_path_to_name().

mhdf_is_in_group()

int mhdf_is_in_group	(	hid_t	group,
		const char *	name,
		mhdf_Status *	status
	)

Definition at line 280 of file util.c.

{
 int rval;
 rval = H5Giterate( group, ".", NULL, &find_link_by_name, (void*)name );
 if( rval < 0 ) mhdf_setFail( status, "Internal error in H5Giterate." );
 return rval;
}

References find_link_by_name(), and mhdf_setFail().

Referenced by mhdf_getTagInfo(), mhdf_haveAdjacency(), mhdf_haveDenseTag(), mhdf_haveNodes(), mhdf_haveSets(), mhdf_isPolyElement(), mhdf_readHistory(), and scan_for_max_id().

mhdf_malloc()

void* mhdf_malloc	(	size_t	size,
		mhdf_Status *	status
	)

MOAB, a Mesh-Oriented datABase, is a software component for creating, storing and accessing finite element mesh data.

Copyright 2004 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software.

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

Definition at line 32 of file util.c.

{
 void* result;
 result = malloc( size );
 if( !result ) mhdf_setFail( status, "Allocation of %d bytes failed.\n", (int)size );
 return result;
}

References mhdf_setFail(), and size.

Referenced by alloc_file_desc(), mhdf_addElement(), mhdf_alloc_FileHandle(), mhdf_createDenseTagData(), mhdf_getElemHandles(), mhdf_getFileSummary(), mhdf_getTagNames(), mhdf_name_to_path_cat(), mhdf_name_to_path_copy(), mhdf_openDenseTagData(), and mhdf_readHistory().

mhdf_name_to_path()

size_t mhdf_name_to_path	(	const char *	name,
		char *	path,
		size_t	path_len
	)

Definition at line 48 of file util.c.

{
 size_t length = 1;
 unsigned char* iter;
 
 if( 0 == strcmp( name, "." ) )
 {
 if( path_len >= 4 ) sprintf( path, "\\%02X", (int)*name );
 return 4;
 }
 
 for( iter = (unsigned char*)name; *iter; ++iter )
 {
 if( iscntrl( *iter ) || *iter == '/' || *iter == '\\' || *iter > 127 )
 length += 3;
 else
 length += 1;
 }
 if( path_len < length ) return length;
 
 for( iter = (unsigned char*)name; *iter; ++iter )
 {
 if( iscntrl( *iter ) || *iter == '/' || *iter == '\\' || *iter > 127 )
 {
 sprintf( path, "\\%02X", (int)( *iter ) );
 path += 3;
 }
 else
 {
 *( path++ ) = *iter;
 }
 }
 
 *path = '\0';
 return length;
}

References length().

Referenced by mhdf_addElement(), mhdf_createDenseTagData(), mhdf_name_to_path_cat(), mhdf_name_to_path_copy(), and mhdf_openDenseTagData().

mhdf_name_to_path_cat()

char* mhdf_name_to_path_cat	(	const char *	prefix,
		const char *	name,
		mhdf_Status *	status
	)

Definition at line 131 of file util.c.

{
 size_t size, plen;
 char* buffer;
 
 plen = strlen( prefix );
 size = mhdf_name_to_path( name, NULL, 0 ) + 1;
 buffer = (char*)mhdf_malloc( size + plen, status );
 if( !buffer ) return NULL;
 
 memcpy( buffer, prefix, plen );
 mhdf_name_to_path( name, buffer + plen, size );
 return buffer;
}

References buffer, mhdf_malloc(), mhdf_name_to_path(), and size.

Referenced by mhdf_elem_group_from_handle().

mhdf_name_to_path_copy()

char* mhdf_name_to_path_copy	(	const char *	name,
		mhdf_Status *	status
	)

Definition at line 118 of file util.c.

{
 size_t size;
 char* buffer;
 
 size = mhdf_name_to_path( name, NULL, 0 );
 buffer = (char*)mhdf_malloc( size, status );
 if( !buffer ) return NULL;
 
 mhdf_name_to_path( name, buffer, size );
 return buffer;
}

References buffer, mhdf_malloc(), mhdf_name_to_path(), and size.

Referenced by create_tag_common(), get_tag(), mhdf_getTagDataType(), and mhdf_haveDenseTag().

mhdf_open_table()

hid_t mhdf_open_table	(	hid_t	group_id,
		const char *	path,
		int	columns,
		hsize_t *	rows_out,
		mhdf_Status *	status
	)

Definition at line 601 of file util.c.

{
 hid_t table_id, space_id;
 hsize_t dims[2];
 int rank;
 
#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
 table_id = H5Dopen2( group_id, path, H5P_DEFAULT );
#else
 table_id = H5Dopen( group_id, path );
#endif
 if( table_id < 0 )
 {
 mhdf_setFail( status, "HDF5 DataSet creation failed." );
 return -1;
 }
 
 space_id = H5Dget_space( table_id );
 if( space_id < 0 )
 {
 mhdf_setFail( status, "Internal error in H5Dget_space." );
 H5Dclose( table_id );
 return -1;
 }
 
 rank = H5Sget_simple_extent_ndims( space_id );
 if( rank != ( columns ? 1 : 2 ) )
 {
 mhdf_setFail( status, "Incorrect DataSpace for DataSet." );
 H5Sclose( space_id );
 H5Dclose( table_id );
 return -1;
 }
 
 rank = H5Sget_simple_extent_dims( space_id, dims, NULL );
 H5Sclose( space_id );
 if( rank < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Sget_simple_extent_dims." );
 H5Dclose( table_id );
 return -1;
 }
 
 *rows_out = dims[0];
 mhdf_setOkay( status );
 return table_id;
}

References mhdf_setFail(), and mhdf_setOkay().

Referenced by mhdf_openAdjacency(), mhdf_openDenseTagData(), mhdf_openPolyConnectivity(), mhdf_openSetChildren(), mhdf_openSetData(), mhdf_openSetParents(), and mhdf_openSparseTagData().

mhdf_open_table2()

hid_t mhdf_open_table2	(	hid_t	group_id,
		const char *	path,
		int	rank,
		hsize_t *	dims_out,
		long *	start_id_out,
		mhdf_Status *	status
	)

Definition at line 649 of file util.c.

{
 hid_t table_id, space_id;
 
#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
 table_id = H5Dopen2( group_id, path, H5P_DEFAULT );
#else
 table_id = H5Dopen( group_id, path );
#endif
 if( table_id < 0 )
 {
 mhdf_setFail( status, "HDF5 DataSet creation failed." );
 return -1;
 }
 
 space_id = H5Dget_space( table_id );
 if( space_id < 0 )
 {
 mhdf_setFail( status, "Internal error in H5Dget_space." );
 H5Dclose( table_id );
 return -1;
 }
 
 if( H5Sget_simple_extent_ndims( space_id ) != rank )
 {
 mhdf_setFail( status, "Incorrect DataSpace for DataSet." );
 H5Sclose( space_id );
 H5Dclose( table_id );
 return -1;
 }
 
 rank = H5Sget_simple_extent_dims( space_id, dims_out, NULL );
 H5Sclose( space_id );
 if( rank < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Sget_simple_extent_dims." );
 H5Dclose( table_id );
 return -1;
 }
 
 if( !mhdf_read_scalar_attrib( table_id, START_ID_ATTRIB, H5T_NATIVE_LONG, start_id_out, status ) )
 {
 mhdf_setFail( status, "File format error. Failed to retreive ID offset." );
 H5Dclose( table_id );
 return -1;
 }
 
 mhdf_setOkay( status );
 return table_id;
}

References mhdf_read_scalar_attrib(), mhdf_setFail(), mhdf_setOkay(), and START_ID_ATTRIB.

Referenced by mhdf_openConnectivity(), mhdf_openNodeCoords(), and mhdf_openSetMeta().

mhdf_open_table_simple()

hid_t mhdf_open_table_simple	(	hid_t	group_id,
		const char *	path,
		mhdf_Status *	status
	)

Definition at line 705 of file util.c.

{
 hid_t table_id;
 
#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
 table_id = H5Dopen2( group_id, path, H5P_DEFAULT );
#else
 table_id = H5Dopen( group_id, path );
#endif
 if( table_id < 0 )
 {
 mhdf_setFail( status, "HDF5 DataSet creation failed." );
 }
 else
 {
 mhdf_setOkay( status );
 }
 
 return table_id;
}

References mhdf_setFail(), and mhdf_setOkay().

Referenced by mhdf_openConnectivitySimple(), mhdf_openNodeCoordsSimple(), and mhdf_openSetMetaSimple().

mhdf_path_to_name()

int mhdf_path_to_name	(	const char *	path,
		char *	name
	)

Definition at line 93 of file util.c.

{
 const char* iter;
 char c1, c2;
 
 for( iter = path; *iter; ++iter, ++name )
 {
 if( *iter == '\\' )
 {
 c1 = *++iter;
 c2 = *++iter;
 if( !isxdigit( c1 ) || !isxdigit( c2 ) ) return 0;
 
 *name = (char)( 16 * mhdf_hex_char( c1 ) + mhdf_hex_char( c2 ) );
 }
 else
 {
 *name = *iter;
 }
 }
 
 *name = '\0';
 return 1;
}

References mhdf_hex_char().

Referenced by mhdf_addElement(), mhdf_getElemHandles(), and mhdf_getTagNames().

mhdf_read_column()

int mhdf_read_column	(	hid_t	data_id,
		int	column,
		long	offset,
		long	count,
		hid_t	type,
		void *	array,
		hid_t	prop,
		mhdf_Status *	status
	)

Definition at line 539 of file util.c.

{
 return mhdf_readwrite_column( data_id, 1, column, offset, count, type, array, prop, status );
}

References mhdf_readwrite_column().

Referenced by mhdf_readNodeCoord(), and mhdf_readNodeCoordWithOpt().

mhdf_read_data()

int mhdf_read_data	(	hid_t	data_id,
		long	offset,
		long	count,
		hid_t	type_id,
		void *	array,
		hid_t	prop,
		mhdf_Status *	status
	)

Definition at line 528 of file util.c.

{
 return mhdf_readwrite( data_id, 1, offset, count, type_id, array, prop, status );
}

References mhdf_readwrite().

Referenced by mhdf_getFileSummary(), mhdf_readAdjacency(), mhdf_readAdjacencyWithOpt(), mhdf_readConnectivity(), mhdf_readConnectivityWithOpt(), mhdf_readNodeCoords(), mhdf_readNodeCoordsWithOpt(), mhdf_readPolyConnIDs(), mhdf_readPolyConnIDsWithOpt(), mhdf_readPolyConnIndices(), mhdf_readPolyConnIndicesWithOpt(), mhdf_readSetData(), mhdf_readSetDataWithOpt(), mhdf_readSetParentsChildren(), mhdf_readSetParentsChildrenWithOpt(), mhdf_readSparseTagEntities(), mhdf_readSparseTagEntitiesWithOpt(), mhdf_readSparseTagIndices(), mhdf_readSparseTagIndicesWithOpt(), and mhdf_readTagValuesWithOpt().

mhdf_read_scalar_attrib()

int mhdf_read_scalar_attrib	(	hid_t	object,
		const char *	name,
		hid_t	type,
		void *	value,
		mhdf_Status *	status
	)

Definition at line 200 of file util.c.

{
 hid_t attr_id, type_id;
 herr_t rval;
 
 attr_id = H5Aopen_name( object, name );
 if( attr_id < 0 )
 {
 mhdf_setFail( status, "Failed to create \"%s\" attrib.", name );
 return 0;
 }
 
 if( type > 0 )
 {
 type_id = type;
 }
 else
 {
 type_id = H5Aget_type( attr_id );
 if( type_id < 0 )
 {
 H5Aclose( attr_id );
 return 0;
 }
 }
 
 rval = H5Aread( attr_id, type_id, value );
 H5Aclose( attr_id );
 if( type < 1 ) H5Tclose( type_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Failed to read \"%s\" attrib.", name );
 return 0;
 }
 
 return 1;
}

References mhdf_setFail().

Referenced by mhdf_getTagInfo(), mhdf_open_table2(), mhdf_openPolyConnectivity(), read_tag_attrib_data(), and scan_for_max_id().

mhdf_readwrite()

static int mhdf_readwrite ( hid_t  data_id, int  read, long  offset, long  count, hid_t  type, void *  array, hid_t  io_prop, mhdf_Status *  status  )

static

Definition at line 288 of file util.c.

{
 hid_t slab_id, mem_id;
 hsize_t offsets[2], counts[2] = { 1, 1 };
 herr_t rval;
 int dims;
 /*#if (1000 * H5_VERS_MAJOR + H5_VERS_MINOR) < 1008*/
 const hsize_t one = 1;
 /*#endif*/
 
 if( offset < 0 || count < 0 )
 {
 mhdf_setFail( status,
 "Invalid input for %s: "
 "offset = %ld, count = %ld\n",
 read ? "read" : "write", offset, count );
 return 0;
 }
 
 slab_id = H5Dget_space( data_id );
 if( slab_id < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Dget_space." );
 return 0;
 }
 
 dims = H5Sget_simple_extent_ndims( slab_id );
 if( dims < 1 || dims > 2 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error: unexpected dataset rank: %d.", dims );
 return 0;
 }
 
 dims = H5Sget_simple_extent_dims( slab_id, counts, NULL );
 if( dims < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Sget_simple_extend_dims." );
 return 0;
 }
 
 if( (unsigned long)( offset + count ) > counts[0] )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Requested %s of rows %ld to %ld of a %ld row table.\n", read ? "read" : "write", offset,
 offset + count - 1, (long)counts[dims - 1] );
 return 0;
 }
 
 counts[0] = (hsize_t)count;
 offsets[0] = (hsize_t)offset;
 offsets[1] = 0;
 if( count )
 rval = H5Sselect_hyperslab( slab_id, H5S_SELECT_SET, offsets, NULL, counts, NULL );
 else
 rval = H5Sselect_none( slab_id );
 if( rval < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Sselect_hyperslab." );
 return 0;
 }
 
 if( count )
 mem_id = H5Screate_simple( dims, counts, NULL );
 else
 {
 /*#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR >= 8
 mem_id = H5Screate(H5S_NULL);
 #else*/
 mem_id = H5Screate_simple( 1, &one, NULL );
 if( mem_id && 0 > H5Sselect_none( mem_id ) )
 {
 H5Sclose( mem_id );
 mem_id = -1;
 }
 /*#endif*/
 }
 
 if( mem_id < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Screate_simple." );
 return 0;
 }
 
 if( read )
 rval = H5Dread( data_id, type, mem_id, slab_id, io_prop, array );
 else
 {
 VALGRIND_CHECK_MEM_IS_DEFINED( array, counts[0] * counts[1] * H5Tget_size( type ) );
 rval = H5Dwrite( data_id, type, mem_id, slab_id, io_prop, array );
 }
 H5Sclose( slab_id );
 H5Sclose( mem_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5D%s.", read ? "read" : "write" );
 return 0;
 }
 
 mhdf_setOkay( status );
 return 1;
}

References mhdf_setFail(), mhdf_setOkay(), and VALGRIND_CHECK_MEM_IS_DEFINED.

Referenced by mhdf_read_data(), and mhdf_write_data().

mhdf_readwrite_column()

static int mhdf_readwrite_column ( hid_t  data_id, int  read, int  column, long  offset, long  count, hid_t  type, void *  array, hid_t  io_prop, mhdf_Status *  status  )

static

Definition at line 401 of file util.c.

{
 hid_t slab_id, mem_id;
 hsize_t offsets[2], counts[2];
 herr_t rval;
 int dims;
 /*#if (1000 * H5_VERS_MAJOR + H5_VERS_MINOR) < 1008*/
 const hsize_t one = 1;
 /*#endif*/
 
 if( column < 0 || offset < 0 || count < 0 )
 {
 mhdf_setFail( status,
 "Invalid input for %s: "
 "column = %d, offset = %ld, count = %ld\n",
 read ? "read" : "write", column, offset, count );
 return 0;
 }
 
 slab_id = H5Dget_space( data_id );
 if( slab_id < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5Dget_space." );
 return 0;
 }
 
 dims = H5Sget_simple_extent_ndims( slab_id );
 if( dims < 1 || dims > 2 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error: unexpected dataset rank: %d.", dims );
 return 0;
 }
 
 dims = H5Sget_simple_extent_dims( slab_id, counts, NULL );
 if( dims < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Sget_simple_extend_dims." );
 return 0;
 }
 
 if( (unsigned long)( offset + count ) > counts[0] || (unsigned long)column > counts[1] )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Requested %s of (%ld,%d)->(%ld,%ld) of (%ld, %ld) table.\n", read ? "read" : "write",
 offset, column, offset + count - 1, column, (long)counts[0], (long)counts[1] );
 return 0;
 }
 
 counts[0] = (hsize_t)count;
 offsets[0] = (hsize_t)offset;
 counts[1] = 1;
 offsets[1] = column;
 if( count )
 rval = H5Sselect_hyperslab( slab_id, H5S_SELECT_SET, offsets, NULL, counts, NULL );
 else
 rval = H5Sselect_none( slab_id );
 if( rval < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Sselect_hyperslab." );
 return 0;
 }
 
 if( count )
 mem_id = H5Screate_simple( dims, counts, NULL );
 else
 {
 /*#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR >= 8
 mem_id = H5Screate(H5S_NULL);
 #else*/
 mem_id = H5Screate_simple( 1, &one, NULL );
 if( mem_id && 0 > H5Sselect_none( mem_id ) )
 {
 H5Sclose( mem_id );
 mem_id = -1;
 }
 /*#endif*/
 }
 
 if( mem_id < 0 )
 {
 H5Sclose( slab_id );
 mhdf_setFail( status, "Internal error calling H5Screate_simple." );
 return 0;
 }
 
 if( read )
 rval = H5Dread( data_id, type, mem_id, slab_id, io_prop, array );
 else
 {
 VALGRIND_CHECK_MEM_IS_DEFINED( array, count * H5Tget_size( type ) );
 rval = H5Dwrite( data_id, type, mem_id, slab_id, io_prop, array );
 VALGRIND_MAKE_MEM_UNDEFINED( array, count * H5Tget_size( type ) );
 }
 H5Sclose( slab_id );
 H5Sclose( mem_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Internal error calling H5D%s.", read ? "read" : "write" );
 return 0;
 }
 
 mhdf_setOkay( status );
 return 1;
}

References mhdf_setFail(), mhdf_setOkay(), VALGRIND_CHECK_MEM_IS_DEFINED, and VALGRIND_MAKE_MEM_UNDEFINED.

Referenced by mhdf_read_column(), and mhdf_write_column().

mhdf_realloc()

void* mhdf_realloc	(	void *	ptr,
		size_t	size,
		mhdf_Status *	status
	)

Definition at line 40 of file util.c.

{
 void* result;
 result = realloc( ptr, size );
 if( !result ) mhdf_setFail( status, "Allocation of %d bytes failed.\n", (int)size );
 return result;
}

References mhdf_setFail(), and size.

Referenced by realloc_data().

mhdf_write_column()

int mhdf_write_column	(	hid_t	data_id,
		int	column,
		long	offset,
		long	count,
		hid_t	type,
		const void *	array,
		hid_t	prop,
		mhdf_Status *	status
	)

Definition at line 551 of file util.c.

{
 return mhdf_readwrite_column( data_id, 0, column, offset, count, type, (void*)array, prop, status );
}

References mhdf_readwrite_column().

Referenced by mhdf_writeNodeCoord(), and mhdf_writeNodeCoordWithOpt().

mhdf_write_data()

int mhdf_write_data	(	hid_t	data_id,
		long	offset,
		long	count,
		hid_t	type_id,
		const void *	array,
		hid_t	prop,
		mhdf_Status *	status
	)

Definition at line 517 of file util.c.

{
 return mhdf_readwrite( data_id, 0, offset, count, type_id, (void*)array, prop, status );
}

References mhdf_readwrite().

Referenced by mhdf_writeAdjacency(), mhdf_writeAdjacencyWithOpt(), mhdf_writeConnectivity(), mhdf_writeConnectivityWithOpt(), mhdf_writeNodeCoords(), mhdf_writeNodeCoordsWithOpt(), mhdf_writePolyConnIDs(), mhdf_writePolyConnIDsWithOpt(), mhdf_writePolyConnIndices(), mhdf_writePolyConnIndicesWithOpt(), mhdf_writeSetData(), mhdf_writeSetDataWithOpt(), mhdf_writeSetParentsChildren(), mhdf_writeSetParentsChildrenWithOpt(), mhdf_writeSparseTagEntities(), mhdf_writeSparseTagEntitiesWithOpt(), mhdf_writeSparseTagIndices(), mhdf_writeSparseTagIndicesWithOpt(), and mhdf_writeTagValuesWithOpt().

mhdf_write_max_id()

int mhdf_write_max_id	(	FileHandle *	file_ptr,
		mhdf_Status *	status
	)

Definition at line 798 of file util.c.

{
 hid_t group_id, attr_id, space_id;
 herr_t rval;
 
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Internal error -- file invalid." );
 return 0;
 }
 
 attr_id = H5Aopen_name( group_id, MAX_ID_ATTRIB );
 if( attr_id < 0 )
 {
 space_id = H5Screate( H5S_SCALAR );
#if defined( H5Acreate_vers ) && H5Acreate_vers > 1
 attr_id = H5Acreate2( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, space_id, H5P_DEFAULT, H5P_DEFAULT );
#else
 attr_id = H5Acreate( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, space_id, H5P_DEFAULT );
#endif
 H5Sclose( space_id );
 }
 H5Gclose( group_id );
 if( attr_id < 0 )
 {
 mhdf_setFail( status, "Failed to create attribute \"%s\" on \"%s\"", MAX_ID_ATTRIB, ROOT_GROUP );
 return 0;
 }
 
 rval = H5Awrite( attr_id, H5T_NATIVE_ULONG, &file_ptr->max_id );
 H5Aclose( attr_id );
 if( rval < 0 )
 {
 mhdf_setFail( status, "Failed to write \"%s\" attrib.", MAX_ID_ATTRIB );
 return 0;
 }
 
 return 1;
}

References struct_FileHandle::hdf_handle, struct_FileHandle::max_id, MAX_ID_ATTRIB, mhdf_setFail(), and ROOT_GROUP.

Referenced by mhdf_createConnectivity(), mhdf_createNodeCoords(), mhdf_createPolyConnectivity(), and mhdf_createSetMeta().

num_open()

static int num_open ( void  )

static

Definition at line 845 of file util.c.

{
 hid_t list[64];
 int nf, rval, i, count = 0;
 
 nf = H5Fget_obj_ids( H5F_OBJ_ALL, H5F_OBJ_FILE, sizeof( list ) / sizeof( hid_t ), list );
 if( nf <= 0 || nf > 64 ) return 0;
 
 for( i = 0; i < nf; i++ )
 {
 rval = H5Fget_obj_count( list[i], H5F_OBJ_ALL );
 if( rval > 0 ) count += rval;
 }
 
 return count;
}

Referenced by mhdf_api_begin_internal(), and mhdf_api_end_internal().

qs_comp_int()

static int qs_comp_int ( const void *  ptr1, const void *  ptr2  )

static

Definition at line 726 of file util.c.

{
 const int* left = (const int*)ptr1;
 const int* right = (const int*)ptr2;
 return *left < *right ? -1 : *left > *right ? 1 : 0;
}

Referenced by mhdf_compact_to_ranges().

Variable Documentation

mhdf_api_handle_count

int mhdf_api_handle_count = 0

static

Definition at line 843 of file util.c.

Referenced by mhdf_api_begin_internal(), and mhdf_api_end_internal().