VTK to H5grid converter added

.gitattributes

@@ -566,6 +566,8 @@ tools/h5hutcc.in -text
 tools/h5pAttrib.cc -text
 tools/h5pToGNUplot.cc -text
 tools/homdynToH5p.cc -text
+tools/vtk2h5grid/Makefile.am -text
+tools/vtk2h5grid/vtk2h5grid.cc -text
 visit_plugins/databases/H5Part/.depend -text
 visit_plugins/databases/H5Part/Makefile -text
 visit_plugins/databases/H5Part/README.txt -text

configure.ac

@@ -49,6 +49,13 @@ AC_ARG_ENABLE(
 	[Compile the MPI/IO interface [default=no]])],
 	[USE_PARALLEL=$enableval])
 
+AC_ARG_ENABLE(
+	[vtkconverter],
+	[AS_HELP_STRING([--enable-vtkconverter],
+	[Compile the vtk to H5hut converter for grids [default=no]])],
+	[ENABLE_VTKCONVERTER=$enableval])
+AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
+
 AC_ARG_WITH(
 	[hdf5],
 	[AC_HELP_STRING([--with-hdf5],
@@ -67,6 +74,12 @@ AC_ARG_WITH(
 	[path to lustre user API [default=""]])],
 	[LUSTREPATH=$withval], [LUSTREPATH=""])
 
+AC_ARG_WITH(
+	[vtk],
+	[AS_HELP_STRING([--with-vtk],
+	[path to VTK installation [default=""]])],
+	[VTK_PREFIX=$withval], [VTK_PREFIX=""])
+
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -364,6 +377,16 @@ fi
 
 LIBS="$LIBS -lz -lm"
 
+###############################################################################
+# TOOLS
+AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
+if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
+	AC_MSG_RESULT([yes])
+        # :TODO: add test whether we can compile/link a prog with vtk
+else
+	AC_MSG_RESULT([no])
+fi
+
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
@@ -400,6 +423,7 @@ AC_CONFIG_FILES([
         test/H5Fed/Makefile
 	tools/Makefile
 	tools/h5hutcc
+        tools/vtk2h5grid/Makefile
 ])
 
 AC_OUTPUT

tools/Makefile.am

@@ -1,6 +1,10 @@
 # tools level Makefile.am
 
-OBJEXT=o
+SUBDIRS =
+
+if ENABLE_VTKCONVERTER
+SUBDIRS +=	vtk2h5grid
+endif
 
 AM_LDFLAGS = -L../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@

tools/vtk2h5grid/Makefile.am

@@ -0,0 +1,16 @@
+AM_CPPFLAGS = -I${abs_top_builddir}/src/include -Wno-deprecated
+FFLAGS += -cpp $(AM_CPPFLAGS)
+LDFLAGS += -L${abs_top_builddir}/src/lib
+
+LDADD = 
+
+LDADD += -lH5hut -lH5hutC -lvtkCommon -lvtkIO
+
+
+bin_PROGRAMS = 
+
+bin_PROGRAMS += vtk2h5grid
+vtk2h5grid_SOURCES = vtk2h5grid.cc
+
+distclean-local:
+	$(RM) *~

tools/vtk2h5grid/vtk2h5grid.cc

@@ -0,0 +1,203 @@
+#include <sys/stat.h>
+#include <stdio.h>
+#include <stdarg.h>
+#include <getopt.h>
+#include <errno.h>
+
+#include <map>
+
+
+#include <vtkSmartPointer.h>
+#include <vtkExtractEdges.h>
+#include "vtkUnstructuredGrid.h"
+#include "vtkUnstructuredGridReader.h"
+
+#include "H5hut.h"
+
+const char* version = "0.1.0";
+int convert_boundary = 1;
+int convert_volume = 0;
+const struct option longopts[] = {
+        {"version",     no_argument, 0,                 'v'},
+        {"help",        no_argument, 0,                 'h'},
+        {"boundary",    no_argument, &convert_boundary, 1},
+        {"volume",      no_argument, &convert_volume,   1},
+        {"no-boundary", no_argument, &convert_boundary, 0},
+        {"no-volume",   no_argument, &convert_volume,   0},
+        {0,0,0,0},
+};
+
+typedef std::map<int, size_t> IdMap;
+
+static void
+usage (
+        char* cmd
+        ) {
+        std::cout << std::endl << "Usage: " << std::endl;
+        std::cout << "  " << cmd << " [OPTIONS] FILE..." << std::endl << std::endl;
+        std::cout << "Options:" << std::endl;
+        std::cout << "  --(no-)boundary   do (not) convert boundary triangles." << std::endl;
+        std::cout << "                    default is yes" << std::endl;
+        std::cout << "  --(no-)volume     do (not) convert volume mesh." << std::endl;
+        std::cout << "                    default is no" << std::endl;
+        std::cout << std::endl;
+        exit (1);
+}
+
+static void
+print_version (
+        char* cmd
+        ) {
+        std::cout << "Version: " << cmd << " " << version << std::endl;
+        exit (1);
+}
+
+static int
+init (
+        int argc,
+        char* argv[]
+        ) {
+        int index;
+        int iarg = 0;
+
+        //turn off getopt error message
+        opterr = 1; 
+
+        while(iarg != -1) {
+                iarg = getopt_long(argc, argv, "vh?", longopts, &index);
+
+                switch (iarg) {
+                case 'h':
+                case '?':
+                        usage (argv[0]);
+                        break;
+
+                case 'v':
+                        print_version (argv[0]);
+                        break;
+                }
+        }
+        return argc - optind;
+}
+
+void
+convert_vtk2h5grid (
+        vtkUnstructuredGrid* vtk_grid,
+        h5t_mesh_t* h5_grid,
+        int cell_type
+        ) {
+        IdMap idmap;
+        vtkIdType num_vtk_cells = vtk_grid->GetNumberOfCells ();
+        h5_loc_idx_t (*cells)[4] = new h5_loc_idx_t[num_vtk_cells][4];
+        int h5_cell_idx = 0;
+        int h5_vertex_idx = 0;
+        H5FedBeginStoreVertices (h5_grid, num_vtk_cells);
+        for (vtkIdType vtk_cell_id = 0; vtk_cell_id < num_vtk_cells; vtk_cell_id++) {
+                if (vtk_grid->GetCellType (vtk_cell_id) != cell_type) 
+                        continue;
+                
+                vtkIdType num_pts;
+                vtkIdType* pts;
+                vtk_grid->GetCellPoints (vtk_cell_id, num_pts, pts);
+                for (vtkIdType i = 0; i < num_pts; i++) {
+                        IdMap::iterator it = idmap.find (pts[i]);
+                        if (it == idmap.end ()) {
+                                // add point to H5hut mesh
+                                double pt[3];
+                                vtk_grid->GetPoint (pts[i], pt);
+                                H5FedStoreVertex (h5_grid, -1, pt);
+                                // map pt index in vtk file to pt index in H5hut file
+                                idmap.insert (IdMap::value_type (pts[i], h5_vertex_idx));
+                                cells[h5_cell_idx][i] = h5_vertex_idx++;
+                        } else {
+                                cells[h5_cell_idx][i] = it->second;
+                        }
+                }
+                h5_cell_idx++;
+        }
+        H5FedEndStoreVertices (h5_grid);
+        int num_h5_vertices = h5_vertex_idx;
+        int num_h5_cells = h5_cell_idx;
+        cout << "  number of points in mesh: " << num_h5_vertices << endl;
+        cout << "  number of cells in mesh:  " << num_h5_cells << endl;
+        // add tetrahedra to H5hut file
+        H5FedBeginStoreElements (h5_grid, num_vtk_cells);
+        for (int i = 0; i < num_h5_cells; i++) {
+                H5FedStoreElement (h5_grid, cells[i]);
+        }
+        H5FedEndStoreElements (h5_grid);
+        delete cells;
+}
+
+h5_err_t
+H5Errorhandler (
+	const char* fmt,
+	va_list ap
+	) {
+	vfprintf (stderr, fmt, ap);
+        exit (42);
+	return -2;
+}
+
+int
+main (
+        int argc,
+        char* argv[]
+        ) {
+
+        argc = init (argc, argv);
+        if (argc == 0) {
+                std::cout << "No file(s) to convert?!" << std::endl;
+                usage (argv[0]);
+        }
+        argv += optind;
+        H5SetErrorHandler (H5Errorhandler);
+        for (int i = 0; i < argc; i++) {
+                std::string vtk_filename = argv[i];
+                std::string h5grid_filename = vtk_filename.substr (0, vtk_filename.find_last_of ('.')) + ".h5";
+                struct stat st;
+                if (stat (vtk_filename.c_str(), &st) < 0) {
+                        perror (vtk_filename.c_str());
+                        exit (1);
+                }
+                if (!(st.st_mode & S_IRUSR)) {
+                        std::cerr << vtk_filename << ": not readable" << std::endl;
+                        exit (1);
+                }
+                if (stat (h5grid_filename.c_str(), &st) == 0) {
+                        std::cerr << h5grid_filename << ": already exits" << std::endl;
+                        exit (1);
+                }
+                if (errno != ENOENT) {
+                        perror (h5grid_filename.c_str());
+                        exit (1);
+                }
+                std::cout << vtk_filename << ": converting ...." << std::endl;
+
+                // read vtk file
+                vtkSmartPointer<vtkUnstructuredGridReader> reader =
+                        vtkSmartPointer<vtkUnstructuredGridReader>::New ();
+                reader->SetFileName (vtk_filename.c_str ());
+                reader->Update ();
+                vtkUnstructuredGrid* vtk_grid = reader->GetOutput ();
+
+                // open new H5hut file
+                h5_file_t* f = H5OpenFile (h5grid_filename.c_str(), H5_O_WRONLY, 0);
+
+                h5t_mesh_t* h5_grid;
+                if (convert_boundary) {
+                        // add boundary mesh
+                        H5FedAddTriangleMesh (f, "0", &h5_grid);
+                        convert_vtk2h5grid (vtk_grid, h5_grid, VTK_TRIANGLE);
+                        H5FedCloseMesh (h5_grid);
+                }
+                if (convert_volume) {
+                        // add volume mesh
+                        H5FedAddTetrahedralMesh (f, "0", &h5_grid);
+                        convert_vtk2h5grid (vtk_grid, h5_grid, VTK_TETRA);
+                        H5FedCloseMesh (h5_grid);
+                }
+                H5CloseFile (f);
+        }
+        return 0;
+}