#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <H5Fpublic.h>
#include <H5Ppublic.h>
#include <H5Gpublic.h>
#include <H5Spublic.h>
#include <H5Tpublic.h>
#include <H5Apublic.h>
#include "mhdf.h"
#include "status.h"
#include "names-and-paths.h"
#include "util.h"
#include "file-handle.h"

Include dependency graph for file.c:

Functions
static int	make_hdf_group (const char path, hid_t file, size_t size, mhdf_Status status)
mhdf_FileHandle	mhdf_createFile (const char filename, int overwrite, const char elem_type_list, size_t elem_list_len, hid_t id_type, mhdf_Status status)
	Create a new file.
mhdf_FileHandle	mhdf_openFile (const char filename, int writeable, unsigned long max_id_out, hid_t id_type, mhdf_Status *status)
	Open an existing file.
int	mhdf_countOpenHandles (mhdf_FileHandle file_handle)
	Get number of open HDF5 objects from file.
static herr_t	get_max_id (hid_t group_id, const char subgroup, const char datatable, unsigned long *data)
static herr_t	max_id_iter (hid_t group_id, const char name, void data)
static int	scan_for_max_id (FileHandle file_ptr, mhdf_Status status)
mhdf_FileHandle	mhdf_openFileWithOpt (const char filename, int writable, unsigned long max_id_out, hid_t id_type, hid_t access_prop, mhdf_Status *status)
	Open an existing file with options.
void	mhdf_getElemName (mhdf_FileHandle file_handle, unsigned int type_index, char buffer, size_t buf_size, mhdf_Status status)
	Given an element type Id, get the name. Fails if buffer is not of sufficient size.
int	mhdf_checkOpenHandles (mhdf_FileHandle handle, mhdf_Status *status)
void	mhdf_closeFile (mhdf_FileHandle handle, mhdf_Status *status)
	Close the file.
void	mhdf_closeData (mhdf_FileHandle file, hid_t handle, mhdf_Status *status)
	Common close function for all data handle types.
void	mhdf_addElement (mhdf_FileHandle file_handle, const char name, unsigned int elem_type, mhdf_Status status)
	Add a new table of element data to the file.
char **	mhdf_getElemHandles (mhdf_FileHandle file_handle, unsigned int count_out, mhdf_Status status)
	Get the list of element groups in the file.
void	mhdf_getElemTypeName (mhdf_FileHandle file_handle, const char elem_handle, char buffer, size_t buf_len, mhdf_Status *status)
	Get the element type name for a given element group handle.
const char *	mhdf_node_type_handle (void)
	Get an mhdf_ElemHandle object for the node data.
const char *	mhdf_set_type_handle (void)
	Return a special element group handle used to specify the set group.
int	mhdf_isPolyElement (mhdf_FileHandle file_handle, const char elem_handle, mhdf_Status status)
	Check if an element group contains polygon or polyhedron.
void	mhdf_writeHistory (mhdf_FileHandle file_handle, const char *strings, int num_strings, mhdf_Status status)
	Write the file history as a list of strings.
char **	mhdf_readHistory (mhdf_FileHandle file_handle, int num_strings, mhdf_Status status)
	Read the file history as a list of strings.
void	mhdf_getNextStartId (mhdf_FileHandle file, mhdf_index_t start_id_out, mhdf_Status status)
	Get start ID that will be assigned to next created dataset.

Function Documentation

static herr_t get_max_id	(	hid_t	group_id,
		const char *	subgroup,
		const char *	datatable,
		unsigned long *	data
	)		`[static]`

Definition at line 155 of file file.c.

References rank, and START_ID_ATTRIB.

Referenced by max_id_iter(), and scan_for_max_id().

{
    unsigned long id;
    hid_t elem_id, conn_id, attr_id, space_id;
    herr_t rval;
    int rank;
    hsize_t dims[2];

#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
    elem_id = H5Gopen2( group_id, subgroup, H5P_DEFAULT );
#else
    elem_id      = H5Gopen( group_id, subgroup );
#endif
    if( elem_id < 0 ) return (herr_t)-1;

#if defined( H5Dopen_vers ) && H5Dopen_vers > 1
    conn_id = H5Dopen2( elem_id, datatable, H5P_DEFAULT );
#else
    conn_id      = H5Dopen( elem_id, datatable );
#endif
    H5Gclose( elem_id );
    if( conn_id < 0 ) return (herr_t)-1;

    space_id = H5Dget_space( conn_id );
    if( space_id < 0 )
    {
        H5Dclose( conn_id );
        return -1;
    }

    rank = H5Sget_simple_extent_ndims( space_id );
    if( rank <= 0 || rank > 2 )
    {
        H5Dclose( conn_id );
        H5Sclose( space_id );
        return -1;
    }

    rval = H5Sget_simple_extent_dims( space_id, dims, NULL );
    H5Sclose( space_id );
    if( rval < 0 )
    {
        H5Dclose( conn_id );
        return -1;
    }

    attr_id = H5Aopen_name( conn_id, START_ID_ATTRIB );
    H5Dclose( conn_id );
    if( attr_id < 0 ) return (herr_t)-1;

    rval = H5Aread( attr_id, H5T_NATIVE_ULONG, &id );
    H5Aclose( attr_id );
    if( rval < 0 ) return rval;

    id += dims[0];
    if( id > *data ) *data = id;
    return 0;
}

static int make_hdf_group	(	const char *	path,
		hid_t	file,
		size_t	size,
		mhdf_Status *	status
	)		`[static]`

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

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 713 of file file.c.

References mhdf_setFail().

Referenced by mhdf_createFile().

{
#if defined( H5Gcreate_vers ) && H5Gcreate_vers > 1
    hid_t handle = H5Gcreate2( file, path, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
    /* empty statement to avoid compiler warning */
    if( sz )
    {
    }
#else
    hid_t handle = H5Gcreate( file, path, sz );
#endif
    if( handle < 0 )
    {
        mhdf_setFail( status, "Failed to create \"%s\" group.", path );
        return 0;
    }
    else
    {
        H5Gclose( handle );
        return 1;
    }
}

static herr_t max_id_iter	(	hid_t	group_id,
		const char *	name,
		void *	data
	)		`[static]`

Definition at line 214 of file file.c.

References CONNECTIVITY_NAME, and get_max_id().

Referenced by scan_for_max_id().

{
    return get_max_id( group_id, name, CONNECTIVITY_NAME, (unsigned long*)data );
}

static int scan_for_max_id	(	FileHandle *	file_ptr,
		mhdf_Status *	status
	)		`[static]`

Definition at line 219 of file file.c.

References ELEMENT_GROUP_NAME, get_max_id(), struct_FileHandle::hdf_handle, struct_FileHandle::max_id, MAX_ID_ATTRIB, max_id_iter(), mhdf_is_in_group(), mhdf_read_scalar_attrib(), mhdf_setFail(), NODE_GROUP_NAME, ROOT_GROUP, SET_GROUP_NAME, and SET_META_NAME.

Referenced by mhdf_openFileWithOpt().

{
    hid_t group_id;
    herr_t rval;

    /* Check for new format, with max_id as attrib of root group */
#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 - invalid file." );
        return 0;
    }
    if( mhdf_read_scalar_attrib( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, &file_ptr->max_id, status ) )
    {
        H5Gclose( group_id );
        return 1;
    }

    /* Didn't find it, scan the elements group */
    rval = H5Giterate( group_id, ELEMENT_GROUP_NAME, 0, &max_id_iter, &file_ptr->max_id );
    if( rval )
    {
        H5Gclose( group_id );
        mhdf_setFail( status, "Internal error -- invalid file." );
        return 0;
    }

    /* Check node table too */
    rval = get_max_id( group_id, NODE_GROUP_NAME, "coordinates", (unsigned long*)( &file_ptr->max_id ) );
    if( rval )
    {
        H5Gclose( group_id );
        mhdf_setFail( status, "Internal error -- invalid file." );
        return 0;
    }

    /* Check set table, if it exists */
    rval = mhdf_is_in_group( group_id, SET_GROUP_NAME, status );
    if( rval < 1 )
    {
        H5Gclose( group_id );
        return !rval;
    }
    rval = get_max_id( group_id, SET_GROUP_NAME, SET_META_NAME, (unsigned long*)( &file_ptr->max_id ) );
    H5Gclose( group_id );
    if( rval )
    {
        mhdf_setFail( status, "Internal error -- invalid file." );
        return 0;
    }

    return 1;
}

Functions

Function Documentation