added

.gitattributes

@@ -429,6 +429,9 @@ src/h5_core/h5t_openclose.h -text
 src/h5_core/h5t_readwrite.c -text
 src/h5_core/h5t_readwrite.h -text
 src/h5_core/h5t_readwrite_private.h -text
+src/h5_core/h5t_retrieve.c -text
+src/h5_core/h5t_retrieve.h -text
+src/h5_core/h5t_retrieve_private.h -text
 src/h5_core/h5t_storemesh.c -text
 src/h5_core/h5t_storemesh.h -text
 src/h5_core/h5t_storemesh_private.h -text

src/h5_core/h5t_retrieve.c

@@ -0,0 +1,304 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>	/* va_arg - System dependent ?! */
+#include <string.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <hdf5.h>
+
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_core_private.h"
+
+h5_err_t
+h5t_begin_traverse_vertices (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_vertex_iterator_t *iter = &t->iters.vertex; 
+
+	iter->cur_vid = -1;
+	return H5_SUCCESS;
+}
+
+h5_id_t
+h5t_traverse_vertices (
+	h5_file_t * f,			/*!< file handle		*/
+	h5_id_t * const id,		/*!< OUT: global vertex id	*/
+	h5_float64_t P[3]		/*!< OUT: coordinates		*/
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_vertex_iterator_t *iter = &t->iters.vertex; 
+
+	if ( iter->cur_vid+1 >= t->num_vertices[t->cur_level] ) {
+		h5_debug ( f, "Traversing done!" );
+		return H5_NOK;
+	}
+	h5_vertex_t *vertex = &t->vertices[++iter->cur_vid];
+	*id = vertex->global_vid;
+	memcpy ( P, &vertex->P, sizeof ( vertex->P ) );
+
+	return iter->cur_vid;
+}
+
+h5_err_t
+h5t_end_traverse_vertices (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_vertex_iterator_t *iter = &t->iters.vertex; 
+
+	iter->cur_vid = -1;
+	return H5_SUCCESS;
+}
+
+/*
+  Test whether given element is on current level. This is the case, if
+  - the level_id of the element is <= the current level
+  - and, if any, the direct children is on a level > the current level
+*/
+h5_err_t
+_h5t_elem_is_on_cur_level (
+	h5_file_t * const f,
+	h5_elem_ldta_t *el_dta 
+	) {
+	h5t_fdata_t *t = f->t;
+	if ( ( el_dta->level_id > t->cur_level ) ||
+	     ( (el_dta->local_child_eid >= 0) &&
+	       (el_dta->local_child_eid < t->num_elems[t->cur_level]) ) ) {
+		return H5_NOK;
+	}
+	return H5_SUCCESS;
+}
+
+/*
+  Skip elements which have been refined on a level <= the current one.
+*/
+h5_id_t
+_skip_to_next_elem_on_level (
+	h5_file_t * f,
+	h5_id_t *eid
+	) {
+	h5t_fdata_t *t = f->t;
+	h5_elem_ldta_t *el_dta;
+
+	do {
+		(*eid)++;
+		if ( *eid >= t->num_elems[t->cur_level] ) {
+			return h5_error_internal (
+				f, __FILE__, __func__, __LINE__ );
+		}
+		el_dta = &t->elems_ldta[*eid];
+	}
+	while ( _h5t_elem_is_on_cur_level ( f, el_dta ) == H5_NOK );
+	return *eid;
+}
+
+h5_err_t
+h5t_begin_traverse_edges (
+	h5_file_t * const f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.edge; 
+
+	iter->cur_eid = 0;
+	TRY ( _skip_to_next_elem_on_level ( f, &iter->cur_eid ) );
+	iter->cur_fid = -1;
+	return H5_SUCCESS;
+}
+
+h5_id_t
+h5t_traverse_edges (
+	h5_file_t * const f,
+	h5_id_t *local_vids
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.edge; 
+	h5_te_node_t *te;
+	h5_size_t i;
+	do {
+		if ( iter->cur_fid >= 5 ) {
+			if ( iter->cur_eid+1 >= t->num_elems[t->cur_level] ) {
+				h5_debug ( f, "Traversing done!" );
+				return H5_NOK;
+			}
+			TRY ( _skip_to_next_elem_on_level (
+				      f, &iter->cur_eid ) );
+			iter->cur_fid = 0;
+		} else {
+			iter->cur_fid++;
+		}
+		TRY ( _h5t_find_te2 (
+			      f, &te, iter->cur_fid, iter->cur_eid ) );
+		/* skip to first element which is on current level */
+		i = -1;
+		h5_elem_ldta_t *el_dta;
+		do {
+			i++;
+			h5_id_t eid = _h5t_get_elem_id ( te->value.items[i] );
+			el_dta = &t->elems_ldta[eid];
+		} while ( _h5t_elem_is_on_cur_level ( f, el_dta ) == H5_NOK );
+	} while ( iter->cur_eid != _h5t_get_elem_id(te->value.items[i]) );
+	memcpy ( local_vids, te->key.vids, 2*sizeof(h5_id_t) );
+
+	return te->value.items[0];
+}
+
+h5_err_t
+h5t_end_traverse_edges (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.edge; 
+
+	iter->cur_eid = 0;
+	iter->cur_fid = -1;
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5t_begin_traverse_triangles (
+	h5_file_t * const f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.triangle; 
+
+	iter->cur_eid = 0;
+	TRY ( _skip_to_next_elem_on_level ( f, &iter->cur_eid ) );
+	iter->cur_fid = -1;
+	return H5_SUCCESS;
+}
+
+h5_id_t
+h5t_traverse_triangles (
+	h5_file_t * const f,
+	h5_id_t *local_vids
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.triangle; 
+	h5_td_node_t *td;
+	h5_size_t i;
+	do {
+		if ( iter->cur_fid >= 3 ) {
+			if ( iter->cur_eid+1 >= t->num_elems[t->cur_level] ) {
+				h5_debug ( f, "Traversing done!" );
+				return H5_NOK;
+			}
+			TRY ( _skip_to_next_elem_on_level (
+				      f, &iter->cur_eid ) );
+			iter->cur_fid = 0;
+		} else {
+			iter->cur_fid++;
+		}
+		TRY ( _h5t_find_td2 (
+			      f, &td, iter->cur_fid, iter->cur_eid ) );
+		/* skip to first element which is on current level */
+		i = -1;
+		h5_elem_ldta_t *el_dta;
+		do {
+			i++;
+			h5_id_t eid = _h5t_get_elem_id ( td->value.items[i] );
+			el_dta = &t->elems_ldta[eid];
+		} while ( _h5t_elem_is_on_cur_level ( f, el_dta ) == H5_NOK );
+	} while ( iter->cur_eid != _h5t_get_elem_id(td->value.items[i]) );
+	memcpy ( local_vids, td->key.vids, 3*sizeof(h5_id_t) );
+
+	return td->value.items[0];
+}
+
+h5_err_t
+h5t_end_traverse_triangles (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_entity_iterator_t *iter = &t->iters.triangle; 
+
+	iter->cur_eid = 0;
+	iter->cur_fid = -1;
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5t_begin_traverse_elems (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_elem_iterator_t *iter = &t->iters.elem; 
+
+	iter->cur_eid = -1;
+	return H5_SUCCESS;
+}
+
+/*!
+  \param[in]	f		file handle
+  \param[out]	global_eid	Global element id
+  \param[out]	local_parent_id	Local parent id
+  \param[out]	vids		Local vertex id
+*/
+h5_id_t
+h5t_traverse_elems (
+	h5_file_t * const f,
+	h5_id_t * const global_eid,
+	h5_id_t * const local_parent_id,
+	h5_id_t *local_vids
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_elem_iterator_t *iter = &t->iters.elem; 
+	h5_elem_t *elem;
+	h5_elem_ldta_t *elem_data;
+	h5_id_t local_child_eid;
+	h5_id_t refined_on_level = -1;
+
+	if ( iter->cur_eid+1 >= t->num_elems[t->cur_level] ) {
+		h5_debug ( f, "Traversing done!" );
+		return H5_NOK;
+	}
+
+	/*
+	  Skip elements which have been refined on a level <= the current one.
+	*/
+	do {
+		++iter->cur_eid;
+		elem_data = &t->elems_ldta[iter->cur_eid];
+		local_child_eid = elem_data->local_child_eid;
+		refined_on_level = ( local_child_eid >= 0 ) ?
+			t->elems_ldta[local_child_eid].level_id :
+			t->cur_level+1;   /* this means "not refined" */
+	}
+	while ( refined_on_level <= t->cur_level );
+
+	switch ( t->mesh_type ) {
+	case H5_OID_TETRAHEDRON:
+		elem = (h5_elem_t*)&t->elems.tets[iter->cur_eid];
+		break;
+	case H5_OID_TRIANGLE:
+		elem = (h5_elem_t*)&t->elems.tris[iter->cur_eid];
+		break;
+	default:
+		return h5_error_internal (
+			f, __FILE__, __func__, __LINE__ );
+	}
+
+	if ( iter->cur_eid >= t->num_elems[t->cur_level] ) {
+		return h5_error_internal (
+			f, __FILE__, __func__, __LINE__ );
+	}
+	*global_eid = elem->global_eid;
+	*local_parent_id = elem_data->local_parent_eid;
+	memcpy (
+		local_vids,
+		elem_data->local_vids,
+		sizeof ( elem_data->local_vids[0] ) * t->mesh_type );
+
+	return iter->cur_eid;
+}
+
+h5_err_t
+h5t_end_traverse_elems (
+	h5_file_t * f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5t_elem_iterator_t *iter = &t->iters.elem; 
+	iter->cur_eid = -1;
+	return H5_SUCCESS;
+}
+

src/h5_core/h5t_retrieve.h

@@ -0,0 +1,72 @@
+#ifndef __H5T_RETRIEVE_H
+#define __H5T_RETRIEVE_H
+
+h5_err_t
+h5t_begin_traverse_vertices (
+	h5_file_t * f
+	);
+
+h5_id_t
+h5t_traverse_vertices (
+	h5_file_t * f,
+	h5_id_t * const  id,
+	h5_float64_t P[3]
+	);
+
+h5_err_t
+h5t_end_traverse_vertices (
+	h5_file_t * f
+	);
+
+h5_err_t
+h5t_begin_traverse_edges (
+	h5_file_t * const f
+	);
+
+h5_id_t
+h5t_traverse_edges (
+	h5_file_t * const f,
+	h5_id_t *local_vids
+	);
+
+h5_err_t
+h5t_end_traverse_edges (
+	h5_file_t * f
+	);
+
+h5_err_t
+h5t_begin_traverse_triangles (
+	h5_file_t * const f
+	);
+
+h5_id_t
+h5t_traverse_triangles (
+	h5_file_t * const f,
+	h5_id_t *local_vids
+	);
+
+h5_err_t
+h5t_end_traverse_triangles (
+	h5_file_t * f
+	);
+
+h5_err_t
+h5t_begin_traverse_elems (
+	h5_file_t * f
+	);
+
+h5_id_t
+h5t_traverse_elems (
+	h5_file_t * f,
+	h5_id_t * const id,
+	h5_id_t * const parent_id,
+	h5_id_t * vids
+	);
+
+h5_err_t
+h5t_end_traverse_elems (
+	h5_file_t * const f
+	);
+
+
+#endif

src/h5_core/h5t_retrieve_private.h

@@ -0,0 +1,10 @@
+#ifndef __H5T_RETRIEVE_PRIVATE_H
+#define __H5T_RETRIEVE_PRIVATE_H
+
+h5_err_t
+_h5t_elem_is_on_cur_level (
+	h5_file_t * const f,
+	h5_elem_ldta_t *el_dta 
+	);
+
+#endif