reading of vertices and tets added

src/h5/t_readwrite.c

@@ -152,7 +152,7 @@ _write_vertices (
 	struct h5t_fdata *t = &f->t;
 	h5_err_t h5err;
 
-	if ( t->num_vertices <= 0 ) return H5_SUCCESS;
+	if ( t->num_vertices <= 0 ) return H5_SUCCESS;  /* ???? */
 
  	if ( t->coord_gid < 0 ) {
 		h5err = _open_coord_group ( f );
@@ -245,6 +245,7 @@ _write_data (
 	h5_err_t h5err;
 
 	if ( t->num_levels <= 0 ) return 0;
+	if ( t->new_mesh < 0 ) return 0;
 
 	if ( t->topo_gid < 0 ) {
 		h5err = _open_topo_group ( f );
@@ -320,22 +321,6 @@ _h5t_close_step (
 	return H5_SUCCESS;
 }
 
-h5_err_t
-_h5t_create_mesh (
-	h5_file *f		/*!< file handle */
-	) {
-
-	struct h5t_fdata *t = &f->t;
-	h5_err_t h5err = H5_SUCCESS;
-
-	h5err = _open_mesh_group ( f );
-	if ( h5err < 0 ) return h5err;
-
-	t->num_levels = 0;
-
-	return h5err;
-}
-
 h5_err_t
 _h5t_close_mesh (
 	h5_file *f		/*!< file handle */
@@ -361,65 +346,106 @@ h5_size_t
 H5t_get_num_meshes (
 	h5_file * f
 	) {
-	return -1;
-}
-
-h5_err_t
-H5t_set_mesh (
-	h5_file * f,
-	const h5_id_t id
-	) {
-	return -1;
-}
-
-h5_id_t
-H5t_add_mesh (
-	h5_file * f
-	) {
-	struct h5t_fdata *t = &f->t;
-	h5_err_t h5err = H5_SUCCESS;
-
-	/*
-	  - close current mesh
-	  - count number of objects in /TOPO - this is the number of stored
-	  meshes.
-	  - create new group
-	*/
-	h5err = _h5t_close_mesh ( f );
-	if ( h5err < 0 ) return h5err;
-
-	h5err = _open_topo_group ( f );
-	if ( h5err < 0 ) return h5err;
-
-	t->cur_mesh = (h5_id_t)H5_get_num_objects (
+	return (h5_size_t)H5_get_num_objects (
 		f->root_gid,
 		H5T_CONTAINER_GRPNAME,
 		H5G_GROUP );
-	if ( t->cur_mesh < 0 ) return t->cur_mesh;
-	if ( t->new_mesh < 0 )
-		t->new_mesh = t->cur_mesh;
-
-	snprintf ( t->mesh_name, sizeof ( t->mesh_name ), "Mesh#%d", t->cur_mesh );
-
-	h5err = _h5t_create_mesh ( f );
-	if ( h5err < 0 ) return h5err;
-
-	return t->cur_mesh;
 }
 
+/*
+  If the value of parameter \c id is \c -1, a new mesh will be appended.
+  After calling this function, the number of levels is stored in the
+  file structure.
+*/
+h5_err_t
+H5t_open_mesh (
+	h5_file * f,
+	h5_id_t id
+	) {
+	struct h5t_fdata *t = &f->t;
+
+	h5_err_t h5err = _h5t_close_mesh ( f );
+	if ( h5err < 0 ) return h5err;
+
+	if ( t->num_meshes < 0 ) {
+		h5_size_t result = H5t_get_num_meshes ( f );
+		t->num_meshes = ( result > 0 ? result : 0 );
+	}
+	if ( (id < -1) || (id >= t->num_meshes) ) {
+		return HANDLE_H5_OUT_OF_RANGE_ERR( "mesh", id );
+	}
+	if ( id == -1 ) {  /* append new mesh */
+		id = t->num_meshes;
+	}
+	snprintf ( t->mesh_name, sizeof (t->mesh_name), "Mesh#%d", id );
+
+	h5err = _open_mesh_group ( f );
+	if ( h5err < 0 ) return h5err;
+
+	t->cur_mesh = id;
+
+	if ( id != t->num_meshes ) {	/* open existing */
+		t->num_levels = H5t_get_num_levels ( f );
+		if ( t->num_levels < 0 ) return t->num_levels;
+	} else {			/* append new */
+		t->num_meshes++;
+		if ( t->new_mesh < 0 )
+			t->new_mesh = id;
+		t->num_levels = 0;
+	} 
+
+	return H5_SUCCESS;
+}
+
+/*
+  Number of levels: Number of elements in dataset H5T_COORD3D_NUM_ELEMS_DSNAME
+ */
 h5_size_t
 H5t_get_num_levels (
 	h5_file * f
 	) {
-	return -1;
+	struct h5t_fdata *t = &f->t;
+	h5_err_t h5err;
+
+	if ( t->num_levels >= 0 ) return t->num_levels;
+	if ( t->cur_mesh < 0 ) {
+		return HANDLE_H5_UNDEF_MESH_ERR;
+	}
+	if ( t->coord_gid < 0 ) {
+		h5err = _open_coord_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	hid_t dset_id = H5Dopen ( t->coord_gid, H5T_COORD3D_NUM_ELEMS_DSNAME );
+	if ( dset_id < 0 )
+		return HANDLE_H5D_OPEN_ERR ( H5T_COORD3D_NUM_ELEMS_DSNAME );
+	hid_t space_id = H5Dget_space( dset_id );
+	if ( space_id < 0 )
+		return HANDLE_H5D_GET_SPACE_ERR;
+	hssize_t size = H5Sget_simple_extent_npoints ( space_id );
+	if ( size < 0 )
+		return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR;
+
+	herr_t herr = H5Sclose ( space_id );
+	if ( herr < 0 )
+		return HANDLE_H5S_CLOSE_ERR;
+	t->num_levels = size;
+	return size;
 }
 
 h5_err_t
-H5t_set_level (
+H5t_open_level (
 	h5_file * f,
 	const h5_id_t id
 	) {
-	return -1;
+	struct h5t_fdata *t = &f->t;
+
+	if ( (id < 0) || (id >= t->num_levels) )
+		return HANDLE_H5_OUT_OF_RANGE_ERR ( "Level", id );
+	t->cur_level = id;
+	t->last_retrieved_vertex_id = -1;
+	t->last_retrieved_tet_id = -1;
+
+	return H5_SUCCESS;
 }
 
 h5_id_t
@@ -469,11 +495,10 @@ H5t_add_num_vertices (
 	}
 	ssize_t num_elems = (t->cur_level > 0 ?
 			     t->num_vertices[t->cur_level-1] + num : num);
-
 	t->num_vertices[t->cur_level] = num_elems;
-	t->vertices = realloc (
-		t->vertices, num_elems*sizeof ( t->vertices[0] ) );
-
+	ssize_t num_bytes = num_elems*sizeof ( t->vertices[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->vertices = realloc (	t->vertices, num_bytes );
 	if ( t->vertices == NULL ) {
 		return HANDLE_H5_NOMEM_ERR;
 	}
@@ -481,6 +506,108 @@ H5t_add_num_vertices (
 	return num;
 }
 
+/*
+  read everything with this function !?
+*/
+static h5_err_t
+_read_dataset (
+	h5_file * f,
+	hid_t group_id,
+	const char dataset_name[],
+	hid_t type_id,
+	hid_t (*open_mem_space)(h5_file*,hid_t),
+	hid_t (*open_file_space)(h5_file*,hid_t),
+	void * const data ) {
+
+	hid_t dataset_id = H5Dopen ( group_id, dataset_name );
+	if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( dataset_name );
+
+	hid_t mem_space_id = (*open_mem_space)( f, dataset_id );
+	if ( mem_space_id < 0 ) return mem_space_id;
+	hid_t file_space_id = (*open_file_space)( f, dataset_id );
+	if ( file_space_id < 0 ) return file_space_id;
+
+	herr_t herr = H5Dread (
+		dataset_id,
+		type_id,
+		mem_space_id,
+		file_space_id,
+		f->xfer_prop,
+		data );
+	if ( herr < 0 )
+		return HANDLE_H5D_READ_ERR ( H5_get_objname ( dataset_id ) );
+
+	if ( file_space_id != H5S_ALL ) {
+		herr = H5Sclose ( file_space_id );
+		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
+	}
+
+	if ( mem_space_id != H5S_ALL )
+		herr = H5Sclose ( mem_space_id );
+		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
+
+	herr = H5Dclose ( dataset_id );
+	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
+
+	return H5_SUCCESS;
+}
+
+static hid_t
+_open_mem_space_vertices (
+	h5_file * f,
+	hid_t dataset_id
+	) {
+	return H5S_ALL;
+}
+
+static hid_t
+_open_file_space_vertices (
+	h5_file * f,
+	hid_t dataset_id
+	) {
+	return H5S_ALL;
+}
+
+static hid_t
+_open_space_all (
+	h5_file * f,
+	hid_t dataset_id
+	) {
+	return H5S_ALL;
+}
+
+static h5_err_t
+_read_num_vertices (
+	h5_file * f
+	) {
+	h5_err_t h5err;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_level < 0 ) 
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
+ 	if ( t->coord_gid < 0 ) {
+		h5err = _open_coord_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	ssize_t num_bytes = t->num_levels*sizeof ( t->num_vertices[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->num_vertices = realloc ( t->num_vertices, num_bytes );
+	if ( t->num_vertices == NULL )
+		return HANDLE_H5_NOMEM_ERR;
+	h5err = _read_dataset (
+		f,
+		t->coord_gid,
+		H5T_COORD3D_NUM_ELEMS_DSNAME,
+		H5T_NATIVE_INT32,
+		_open_space_all,
+		_open_space_all,
+		t->num_vertices );
+	if ( h5err < 0 ) return h5err;
+
+	return H5_SUCCESS;
+}
+
 static h5_err_t
 _read_vertices (
 	h5_file * f
@@ -488,18 +615,35 @@ _read_vertices (
 	h5_err_t h5err;
 	struct h5t_fdata *t = &f->t;
 
-	if ( t->topo_gid < 0 ) {
-		h5err = _open_topo_group ( f );
-		if ( h5err < 0 ) return h5err;
-	}
+	if ( t->cur_level < 0 ) 
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
  	if ( t->coord_gid < 0 ) {
 		h5err = _open_coord_group ( f );
 		if ( h5err < 0 ) return h5err;
 	}
 
-	/*
-	  get number of levels
-	*/
+	if ( t->num_vertices == NULL ) {
+		h5err = _read_num_vertices ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+
+	ssize_t num_elems = t->num_vertices[t->num_levels-1];
+	ssize_t num_bytes = num_elems*sizeof ( t->vertices[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->vertices = realloc (	t->vertices, num_bytes );
+	if ( t->vertices == NULL )
+		return HANDLE_H5_NOMEM_ERR;
+	h5err = _read_dataset (
+		f,
+		t->coord_gid,
+		H5T_COORD3D_DSNAME,
+		t->vertex_tid,
+		_open_mem_space_vertices,
+		_open_file_space_vertices,
+		t->vertices );
+	if ( h5err < 0 ) return h5err;
+
 	return H5_SUCCESS;
 }
 
@@ -515,8 +659,8 @@ H5t_get_num_vertices (
 	if ( t->cur_level < 0 ) {
 		return HANDLE_H5_UNDEF_LEVEL_ERR;
 	}
-	if ( t->vertices == NULL ) {
-		h5_err_t h5err = _read_vertices ( f );
+	if ( t->num_vertices == NULL ) {
+		h5_err_t h5err = _read_num_vertices ( f );
 		if ( h5err < 0 ) return h5err;
 	}
 	return t->num_vertices[t->cur_level];
@@ -530,11 +674,31 @@ H5t_store_vertex (
 	) {
 	struct h5t_fdata *t = &f->t;
 
-	if ( t->cur_level < 0 )
-		return H5_ERR_INVAL;
+	/*
+	  more than allocated
+	*/
+	if ( t->last_stored_vertex_id+1 >= t->num_vertices[t->cur_level] ) 
+		return HANDLE_H5_OVERFLOW_ERR( "vertex",
+					       t->num_vertices[t->cur_level] );
 
-	if ( t->last_stored_vertex_id+1 >= t->num_vertices[t->cur_level] )
-		return H5_ERR_INVAL;
+	/*
+	  missing call to add the first level
+	 */
+	if ( t->cur_level < 0 )
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
+	/*
+	  check id
+	*/
+	if ( (t->cur_level == 0) && (
+		     (id < 0) || (id >= t->num_vertices[0]) ) ) {
+		return HANDLE_H5_OUT_OF_RANGE_ERR( "vertex", id );
+	}
+	if ( (t->cur_level > 0) && (
+		     (id <  t->num_vertices[t->cur_level-1]) ||
+		     (id >= t->num_vertices[t->cur_level]) ) ) {
+		return HANDLE_H5_OUT_OF_RANGE_ERR( "vertex", id );
+	}
 
 	h5_vertex *vertex = &t->vertices[++t->last_stored_vertex_id];
 	vertex->id = id;
@@ -555,10 +719,24 @@ H5t_get_vertex_ids (
 h5_id_t
 H5t_get_vertex (
 	h5_file * f,			/*!< file handle		*/
-	h5_id_t * const id,		/*!< global vertex id or -1	*/
-	h5_float64_t * const P[3]	/*!< coordinates		*/
+	h5_id_t * const id,		/*!< global vertex		*/
+	h5_float64_t P[3]		/*!< coordinates		*/
 	) {
-	return -1;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->vertices == NULL ) {
+		h5_err_t h5err = _read_vertices ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	if ( t->last_retrieved_vertex_id+1 >= t->num_vertices[t->cur_level] ) {
+		H5_warn ( "Trying to read more tets than available!" );
+		return -1;
+	}
+	h5_vertex *vertex = &t->vertices[++t->last_retrieved_vertex_id];
+	*id = vertex->id;
+	memcpy ( P, &vertex->P, sizeof ( vertex->P ) );
+
+	return t->last_retrieved_vertex_id;
 }
 
 h5_size_t
@@ -576,7 +754,7 @@ H5t_add_num_tets (
 			    num + t->num_tets_on_level[t->cur_level-1] : num;
 
 	ssize_t num_bytes = num_tets*sizeof ( t->tets[0] );
-	H5_debug ( "Allocating %d bytes.", num_bytes ); 
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
 	t->tets = realloc ( t->tets, num_bytes );
 	if ( t->tets == NULL ) {
 		return H5_ERR_NOMEM;
@@ -589,12 +767,6 @@ H5t_add_num_tets (
 	return num;
 }
 
-h5_size_t
-H5t_get_num_tets (
-	h5_file * f
-	) {
-	return -1;
-}
 
 h5_id_t
 H5t_store_tet (
@@ -663,13 +835,179 @@ H5t_store_tet (
 	return t->last_stored_vertex_id;
 }
 
+static h5_err_t
+_read_num_tets (
+	h5_file * f
+	) {
+
+
+	h5_err_t h5err;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_level < 0 ) 
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
+ 	if ( t->vmesh_gid < 0 ) {
+		h5err = _open_vmesh_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	ssize_t num_bytes = t->num_levels*sizeof ( t->num_tets[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->num_tets = realloc ( t->num_tets, num_bytes );
+	if ( t->num_tets == NULL )
+		return HANDLE_H5_NOMEM_ERR;
+	h5err = _read_dataset (
+		f,
+		t->vmesh_gid,
+		H5T_TETMESH_NUM_ELEMS_DSNAME,
+		H5T_NATIVE_INT32,
+		_open_space_all,
+		_open_space_all,
+		t->num_tets );
+	if ( h5err < 0 ) return h5err;
+
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+_read_num_tets_on_level (
+	h5_file * f
+	) {
+
+	h5_err_t h5err;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_level < 0 ) 
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
+ 	if ( t->vmesh_gid < 0 ) {
+		h5err = _open_vmesh_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	ssize_t num_bytes = t->num_levels*sizeof ( t->num_tets_on_level[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->num_tets_on_level = realloc ( t->num_tets_on_level, num_bytes );
+	if ( t->num_tets_on_level == NULL )
+		return HANDLE_H5_NOMEM_ERR;
+	h5err = _read_dataset (
+		f,
+		t->vmesh_gid,
+		H5T_TETMESH_NUM_ELEMS_ON_LEVEL_DSNAME,
+		H5T_NATIVE_INT32,
+		_open_space_all,
+		_open_space_all,
+		t->num_tets_on_level );
+	if ( h5err < 0 ) return h5err;
+
+	return H5_SUCCESS;
+}
+
+static hid_t
+_open_mem_space_tets (
+	h5_file * f,
+	hid_t dataset_id
+	) {
+	return H5S_ALL;
+}
+
+static hid_t
+_open_file_space_tets (
+	h5_file * f,
+	hid_t dataset_id
+	) {
+	return H5S_ALL;
+}
+
+static h5_err_t
+_read_tets (
+	h5_file * f
+	) {
+	h5_err_t h5err;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_level < 0 ) 
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+
+ 	if ( t->vmesh_gid < 0 ) {
+		h5err = _open_vmesh_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+
+	if ( t->num_tets == NULL ) {
+		h5err = _read_num_tets ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+
+	ssize_t num_elems = t->num_tets[t->num_levels-1];
+	ssize_t num_bytes = num_elems*sizeof ( t->tets[0] );
+	H5_debug ( "Allocating %ld bytes.", num_bytes ); 
+	t->tets = realloc (	t->tets, num_bytes );
+	if ( t->tets == NULL )
+		return HANDLE_H5_NOMEM_ERR;
+	h5err = _read_dataset (
+		f,
+		t->vmesh_gid,
+		H5T_TETMESH_DSNAME,
+		t->tet_tid,
+		_open_mem_space_tets,
+		_open_file_space_tets,
+		t->tets );
+	if ( h5err < 0 ) return h5err;
+
+	return H5_SUCCESS;
+}
+
+h5_size_t
+H5t_get_num_tets (
+	h5_file * f
+	) {
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_mesh < 0 ) {
+		return HANDLE_H5_UNDEF_MESH_ERR;
+	}
+	if ( t->cur_level < 0 ) {
+		return HANDLE_H5_UNDEF_LEVEL_ERR;
+	}
+	if ( t->num_tets_on_level == NULL ) {
+		h5_err_t h5err = _read_num_tets_on_level ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	return t->num_tets_on_level[t->cur_level];
+}
+
 h5_id_t
 H5t_get_tet (
 	h5_file * f,
-	h5_id_t * const tet_id,		/*!< global tetrahedron id	*/
+	h5_id_t * const id,		/*!< global tetrahedron id	*/
 	h5_id_t * const parent_id,	/*!< global parent id
 					     if level \c >0 else \c -1	*/
-	h5_id_t * const vertex_ids[4]	/*!< tuple with vertex id's	*/
+	h5_id_t ids[4]			/*!< tuple with vertex id's	*/
 	) {
-	return -1;
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->tets == NULL ) {
+		h5_err_t h5err = _read_tets ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	if ( t->last_retrieved_tet_id+1 >= t->num_tets[t->cur_level] ) {
+		H5_warn ( "Trying to read more tets than available!" );
+		return -1;
+	}
+	h5_tetrahedron *tet = &t->tets[++t->last_retrieved_tet_id];
+
+	while ( (tet->refined_on_level != -1) &&
+		(tet->refined_on_level <= t->cur_level) ){
+		tet++;
+		t->last_retrieved_tet_id++;
+		if ( t->last_retrieved_tet_id >= t->num_tets[t->cur_level] ) {
+			return HANDLE_H5_INTERNAL_ERR;
+		}
+	}
+
+	*id = tet->id;
+	*parent_id = tet->parent_id;
+	memcpy ( ids, &tet->vertex_ids, sizeof ( tet->vertex_ids ) );
+
+	return t->last_retrieved_tet_id;
 }