Bugfix vtk reader data

example/IO/cmesh/vtk/t8_cmesh_read_from_vtk.cxx

@@ -34,15 +34,19 @@ along with t8code; if not, write to the Free Software Foundation, Inc.,
  * \param[in] prefix  The prefix of the file to read the mesh from
  * \param[in] comm    The communicator used in this example
  * \param[in] values_per_cell   The number of values per cell in the mesh.
+ * \param[in] partition         If set, partition the cmesh uniformly.
+ * \param[in] vtk_file_type     The type of the file to read.
+ * \param[in] user_package_id   The package id of the user application
+ * \param[in] out_prefix        The prefix of the output file.
  */
 void
 t8_forest_construct_from_vtk (const char *prefix, sc_MPI_Comm comm, const int values_per_cell, const int partition,
-                              vtk_file_type_t vtk_file_type, const char *out_prefix)
+                              vtk_file_type_t vtk_file_type, const int user_package_id, const char *out_prefix)
 {
   /* Read a poly-data file (.ply, .vtp, .obj, .stl, .vtk, .g) and construct a cmesh 
    * representing the mesh. If  there is any cell-data, it will be read too. 
    * Triangle-strips and polygons will be broken down to multiple triangles. */
-  t8_cmesh_t cmesh_in = t8_cmesh_vtk_reader (prefix, partition, 0, comm, vtk_file_type);
+  t8_cmesh_t cmesh_in = t8_cmesh_vtk_reader (prefix, partition, 0, comm, vtk_file_type, user_package_id, 0);
   if (cmesh_in == NULL) {
     t8_errorf ("Error reading file.\n");
     return;
@@ -123,7 +127,7 @@ main (int argc, char **argv)
   const char *out_file;
   sc_options_t *opt;
   char usage[BUFSIZ], help[BUFSIZ];
-  int sreturn;
+  int sreturn, user_application_package_id;
   int partition;
   int vtk_file_type_int;
   vtk_file_type_t vtk_file_type;
@@ -185,8 +189,10 @@ main (int argc, char **argv)
       vtk_file_type = VTK_FILE_ERROR;
       break;
     }
+    user_application_package_id = sc_package_register (NULL, SC_LP_DEFAULT, "user_application",
+                                                       "Dummy user application which accesses cmesh vtk data.");
     t8_forest_construct_from_vtk (vtk_file, sc_MPI_COMM_WORLD, num_keys, partition, (vtk_file_type_t) vtk_file_type,
-                                  out_file);
+                                  user_application_package_id, out_file);
   }
   sc_options_destroy (opt);
   sc_finalize ();

src/t8_cmesh/t8_cmesh.cxx

@@ -397,6 +397,13 @@ t8_cmesh_set_attribute (t8_cmesh_t cmesh, const t8_gloidx_t gtree_id, const int
                         void *const data, const size_t data_size, const int data_persists)
 {
   T8_ASSERT (t8_cmesh_is_initialized (cmesh));
+  T8_ASSERT (sc_package_is_registered (package_id));
+#if T8_ENABLE_DEBUG
+  // The key for t8code attributes must be in the range of possible keys.
+  if (package_id == t8_get_package_id ()) {
+    T8_ASSERT (key < T8_CMESH_NEXT_POSSIBLE_KEY && key >= 0);
+  }
+#endif
   SC_CHECK_ABORT (cmesh->set_from == NULL, "ERROR: Cannot add attributes to cmesh when deriving from another cmesh.\n");
 
   t8_stash_add_attribute (cmesh->stash, gtree_id, package_id, key, data_size, data, !data_persists);

src/t8_cmesh/t8_cmesh_examples.cxx

@@ -2760,7 +2760,8 @@ t8_cmesh_new_long_brick_pyramid (sc_MPI_Comm comm, int num_cubes)
 }
 
 t8_cmesh_t
-t8_cmesh_new_row_of_cubes (t8_locidx_t num_trees, const int set_attributes, const int do_partition, sc_MPI_Comm comm)
+t8_cmesh_new_row_of_cubes (t8_locidx_t num_trees, const int set_attributes, const int do_partition, sc_MPI_Comm comm,
+                           const int package_id)
 {
   T8_ASSERT (num_trees > 0);
 
@@ -2793,10 +2794,8 @@ t8_cmesh_new_row_of_cubes (t8_locidx_t num_trees, const int set_attributes, cons
     }
     /* Set two more dummy attributes - tree_id & num_trees. */
     if (set_attributes) {
-      t8_cmesh_set_attribute (cmesh, tree_id, t8_get_package_id (), T8_CMESH_NEXT_POSSIBLE_KEY, &tree_id,
-                              sizeof (t8_locidx_t), 0);
-      t8_cmesh_set_attribute (cmesh, tree_id, t8_get_package_id (), T8_CMESH_NEXT_POSSIBLE_KEY + 1, &num_trees,
-                              sizeof (t8_locidx_t), 0);
+      t8_cmesh_set_attribute (cmesh, tree_id, package_id, 0, &tree_id, sizeof (t8_locidx_t), 0);
+      t8_cmesh_set_attribute (cmesh, tree_id, package_id, 1, &num_trees, sizeof (t8_locidx_t), 0);
     }
   }
 

src/t8_cmesh/t8_cmesh_examples.h

@@ -374,13 +374,16 @@ t8_cmesh_new_long_brick_pyramid (sc_MPI_Comm comm, int num_cubes);
 
 /** Construct \a num_trees many cubes each of length 1 connected along the x-axis 
  * without any additional attributes than the tree-vertices, or with additional attributes.
- * \param [in] num_trees     The number of trees along the x-axis
- * \param [in] set_attributes    If 1, set tree_id and num_trees as additional attribute for each tree.
- * \param [in] comm          The MPI communicator used to commit the cmesh
- * \return                   A cmesh with \a num_trees many hexahedrons.
+ * \param [in] num_trees       The number of trees along the x-axis
+ * \param [in] set_attributes  If 1, set tree_id and num_trees as additional attribute for each tree.
+ * \param [in] do_partition    Partition the cmesh.
+ * \param [in] comm            The MPI communicator used to commit the cmesh.
+ * \param [in] package_id      The package id to use for the cmesh. Cannot be the t8 or sc package id.
+ * \return                     A cmesh with \a num_trees many hexahedrons.
  */
 t8_cmesh_t
-t8_cmesh_new_row_of_cubes (t8_locidx_t num_trees, const int set_attributes, const int do_partition, sc_MPI_Comm comm);
+t8_cmesh_new_row_of_cubes (t8_locidx_t num_trees, const int set_attributes, const int do_partition, sc_MPI_Comm comm,
+                           const int package_id);
 
 /** Construct a quadrangulated disk of given radius.
  * \param [in] radius        Radius of the sphere.

src/t8_cmesh/t8_cmesh_vtk_reader.cxx

@@ -31,9 +31,9 @@ T8_EXTERN_C_BEGIN ();
 
 t8_cmesh_t
 t8_cmesh_vtk_reader (const char *filename, const int partition, const int main_proc, sc_MPI_Comm comm,
-                     const vtk_file_type_t vtk_file_type)
+                     const vtk_file_type_t vtk_file_type, const int package_id, const int starting_key)
 {
-  return t8_vtk_reader_cmesh (filename, partition, main_proc, comm, vtk_file_type);
+  return t8_vtk_reader_cmesh (filename, partition, main_proc, comm, vtk_file_type, package_id, starting_key);
 }
 
 T8_EXTERN_C_END ();

src/t8_cmesh_vtk_reader.hxx

@@ -46,11 +46,13 @@ T8_EXTERN_C_BEGIN ();
  * \param[in] main_proc     The main reading processor
  * \param[in] comm          An mpi-communicator
  * \param[in] vtk_file_type A vtk-filetype that is readable by t8code. 
+ * \param[in] package_id    The package id of the application. It is generated with the usage of \ref sc_package_register.  
+ * \param[in] starting_key  If the application already registered attributes, the starting key is used so that the existing attributes are not overwritten.
  * \return                  A committed cmesh.
  */
 t8_cmesh_t
 t8_cmesh_vtk_reader (const char *filename, const int partition, const int main_proc, sc_MPI_Comm comm,
-                     const vtk_file_type_t vtk_file_type);
+                     const vtk_file_type_t vtk_file_type, const int package_id, const int starting_key);
 
 T8_EXTERN_C_END ();
 

src/t8_vtk/t8_vtk_reader.cxx

@@ -224,7 +224,7 @@ t8_get_dimension (vtkSmartPointer<vtkDataSet> vtkGrid)
 
 static void
 t8_vtk_iterate_cells (vtkSmartPointer<vtkDataSet> vtkGrid, t8_cmesh_t cmesh, const t8_gloidx_t first_tree,
-                      [[maybe_unused]] sc_MPI_Comm comm)
+                      [[maybe_unused]] sc_MPI_Comm comm, const int package_id, const int starting_key)
 {
   double **tuples = NULL;
   size_t *data_size = NULL;
@@ -284,7 +284,7 @@ t8_vtk_iterate_cells (vtkSmartPointer<vtkDataSet> vtkGrid, t8_cmesh_t cmesh, con
       const t8_gloidx_t cell_id = cell_it->GetCellId ();
       vtkDataArray *data = cell_data->GetArray (dtype);
       data->GetTuple (cell_id, tuples[dtype]);
-      t8_cmesh_set_attribute (cmesh, tree_id, t8_get_package_id (), dtype + 1, tuples[dtype], data_size[dtype], 0);
+      t8_cmesh_set_attribute (cmesh, tree_id, package_id, dtype + starting_key, tuples[dtype], data_size[dtype], 0);
     }
     tree_id++;
   }
@@ -341,8 +341,11 @@ t8_vtk_partition (t8_cmesh_t cmesh, const int mpirank, const int mpisize, t8_glo
 
 t8_cmesh_t
 t8_vtkGrid_to_cmesh (vtkSmartPointer<vtkDataSet> vtkGrid, const int partition, const int main_proc,
-                     const int distributed_grid, sc_MPI_Comm comm)
+                     const int distributed_grid, sc_MPI_Comm comm, const int package_id, const int starting_key)
 {
+  T8_ASSERT (package_id != t8_get_package_id ());
+  T8_ASSERT (package_id != sc_get_package_id ());
+  T8_ASSERT (sc_package_is_registered (package_id));
   t8_cmesh_t cmesh;
   int mpisize;
   int mpirank;
@@ -388,7 +391,7 @@ t8_vtkGrid_to_cmesh (vtkSmartPointer<vtkDataSet> vtkGrid, const int partition, c
    * - We use a parallel file-type and use a partitioned read, every proc translates its chunk of the grid. 
    */
   if (!partition || mpirank == main_proc || distributed_grid) {
-    t8_vtk_iterate_cells (vtkGrid, cmesh, first_tree, comm);
+    t8_vtk_iterate_cells (vtkGrid, cmesh, first_tree, comm, package_id, starting_key);
   }
 
   if (cmesh != NULL) {
@@ -499,13 +502,15 @@ t8_vtk_reader_pointSet (const char *filename, const int partition, const int mai
 t8_cmesh_t
 t8_vtk_reader_cmesh ([[maybe_unused]] const char *filename, [[maybe_unused]] const int partition,
                      [[maybe_unused]] const int main_proc, [[maybe_unused]] sc_MPI_Comm comm,
-                     [[maybe_unused]] const vtk_file_type_t vtk_file_type)
+                     [[maybe_unused]] const vtk_file_type_t vtk_file_type, [[maybe_unused]] const int package_id,
+                     [[maybe_unused]] const int starting_key)
 {
 #if T8_ENABLE_VTK
   vtkSmartPointer<vtkDataSet> vtkGrid = t8_vtk_reader (filename, partition, main_proc, comm, vtk_file_type);
   if (vtkGrid != NULL) {
     const int distributed_grid = (vtk_file_type & VTK_PARALLEL_FILE) && partition;
-    t8_cmesh_t cmesh = t8_vtkGrid_to_cmesh (vtkGrid, partition, main_proc, distributed_grid, comm);
+    t8_cmesh_t cmesh
+      = t8_vtkGrid_to_cmesh (vtkGrid, partition, main_proc, distributed_grid, comm, package_id, starting_key);
     T8_ASSERT (cmesh != NULL);
     return cmesh;
   }

src/t8_vtk/t8_vtk_reader.hxx

@@ -39,18 +39,20 @@ T8_EXTERN_C_BEGIN ();
 
 /**
  * Given a pointer to a vtkDataSet a cmesh representing the vtkDataSet is
- * constructed and can be shared over the processes. 
+ * constructed and can be shared over the processes. The vtk data arrays will be associated with the trees.
  * 
  * \param[in] vtkGrid A pointer to a vtkDataSet
  * \param[in] partition Flag if the cmesh should be partitioned
  * \param[in] main_proc The main reading process
  * \param[in] distributed_grid Flag if the vtkGrid is distributed over several procs. 
  * \param[in] comm The communicator. 
- * \return t8_cmesh_t 
+ * \param[in] package_id The package id of the application. It is generated with the usage of \ref sc_package_register.
+ * \param[in] starting_key If the application already registered attributes, the starting key is used so that the existing attributes are not overwritten.
+ * \return The committed cmesh 
  */
 t8_cmesh_t
 t8_vtkGrid_to_cmesh (vtkSmartPointer<vtkDataSet> vtkGrid, const int partition, const int main_proc,
-                     const int distributed_grid, sc_MPI_Comm comm);
+                     const int distributed_grid, sc_MPI_Comm comm, const int package_id, const int starting_key);
 
 /**
  * Given a pointer to a vtkDataSet a vtkPointSet storing a set of points of
@@ -106,7 +108,9 @@ t8_vtk_reader_pointSet (const char *filename, const int partition, const int mai
  * Given a filename to a vtkUnstructuredGrid or vtkPolyData read the file and
  * construct a cmesh. This is a two stage process. First the file is read and
  * stored in a vtkDataSet using \a t8_vtk_reader and \a t8_file_to_vtkGrid. 
- * In the second stage a cmesh is constructed from the vtkDataSet using \a t8_vtkGrid_to_cmesh. 
+ * In the second stage a cmesh is constructed from the vtkDataSet using \a t8_vtkGrid_to_cmesh.
+ * The vtk data arrays will be associated with the cmesh trees and saved as tree attributes using the 
+ * provided user application \a package_id. The keys for the tree attributes start at \a starting_key.
  * 
  * Both stages use the vtk-library, therefore the function is only available if 
  * t8code is linked against VTK. 
@@ -116,12 +120,14 @@ t8_vtk_reader_pointSet (const char *filename, const int partition, const int mai
  * \param[in] partition     Flag if the constructed mesh should be partitioned
  * \param[in] main_proc     The main reading processor
  * \param[in] comm          An mpi-communicator
- * \param[in] vtk_file_type A vtk-filetype that is readable by t8code. 
+ * \param[in] vtk_file_type A vtk-filetype that is readable by t8code.
+ * \param[in] package_id    The package id of the application. It is generated with the usage of \ref sc_package_register.  
+ * \param[in] starting_key  If the application already registered attributes, the starting key is used so that the existing attributes are not overwritten.
  * \return                  A committed cmesh.
  */
 t8_cmesh_t
 t8_vtk_reader_cmesh (const char *filename, const int partition, const int main_proc, sc_MPI_Comm comm,
-                     const vtk_file_type_t vtk_file_type);
+                     const vtk_file_type_t vtk_file_type, const int package_id, const int starting_key);
 
 T8_EXTERN_C_END ();