From: bangerth Date: Mon, 7 Oct 2013 13:43:08 +0000 (+0000) Subject: Patch by Mayank Subharwal and Andreas Putz: Make GridIn read VTK files as well. X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=994790bebcdafbd6227a726091f70dee907cc927;p=dealii-svn.git Patch by Mayank Subharwal and Andreas Putz: Make GridIn read VTK files as well. git-svn-id: https://svn.dealii.org/trunk@31163 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h index cb3806c104..7cdcdd827e 100644 --- a/deal.II/doc/news/changes.h +++ b/deal.II/doc/news/changes.h @@ -145,6 +145,12 @@ inconvenience this causes.

Specific improvements

    +
  1. + New: GridIn::read_vtk() reads 2d and 3d meshes in VTK format. +
    + (Mayank Sabharwal, Andreas Putz, 2013/10/07) +
    2. +
  2. Fixed: ConstraintMatrix would not compress() the IndexSet in the constructor leading to crashes that only happen in release mode. This is now fixed. diff --git a/deal.II/include/deal.II/grid/grid_in.h b/deal.II/include/deal.II/grid/grid_in.h index 5d4997ec38..2562f2870e 100644 --- a/deal.II/include/deal.II/grid/grid_in.h +++ b/deal.II/include/deal.II/grid/grid_in.h @@ -36,7 +36,7 @@ struct SubCellData; /** * This class implements an input mechanism for grid data. It allows to read a * grid structure into a triangulation object. At present, UCD (unstructured - * cell data), DB Mesh, XDA, Gmsh, Tecplot, NetCDF, UNV, and Cubit are supported as + * cell data), DB Mesh, XDA, Gmsh, Tecplot, NetCDF, UNV, VTK, and Cubit are supported as * input format for grid data. Any numerical data other than geometric * (vertex locations) and topological (how vertices form cells) information is * ignored. @@ -177,6 +177,37 @@ struct SubCellData; * mesh is built up, and 4) all numbers that might be associated with some of * the internal faces of this compound mesh are removed. * + *
  3. VTK format: VTK Unstructured Grid Legacy file reader + * generator. The reader can handle only Unstructured Grid format of data + * at present for 2D & 3D geometries. + * The documentation for the general legacy vtk file, including Unstructured Grid format + * can be found here: + * http://www.cacr.caltech.edu/~slombey/asci/vtk/vtk_formats.simple.html + * + * The VTK format requires the vertices to be + * in following ordering: in 2d + * @verbatim + * 3-----2 + * | | + * | | + * | | + * 0-----1 + * @endverbatim + * and in 3d + * @verbatim + * 7-------6 7-------6 + * /| | / /| + * / | | / / | + * / | | / / | + * 4 | | 4-------5 | + * | 3-------2 | | 2 + * | / / | | / + * | / / | | / + * |/ / | |/ + * 0-------1 0-------1 + * @endverbatim + * + * *
  4. Cubit format: deal.II doesn't directly support importing from * Cubit at this time. However, Cubit can export in UCD format using a simple * plug-in, and the resulting UCD file can then be read by this class. The @@ -310,7 +341,9 @@ public: /// Use read_netcdf() netcdf, /// Use read_tecplot() - tecplot + tecplot, + /// Use read_vtk() + vtk }; /** @@ -342,16 +375,24 @@ public: */ void read (const std::string &in, Format format=Default); + /** + * Read grid data from an vtk file. + * Numerical data is ignored. + * + * @author Mayank Sabharwal, Andreas Putz, 2013 + */ + void read_vtk(std::istream &in); + /** * Read grid data from an unv * file as generated by the * Salome mesh generator. * Numerical data is ignored. - * - * Note the comments on - * generating this file format in - * the general documentation of - * this class. + * + * Note the comments on + * generating this file format in + * the general documentation of + * this class. */ void read_unv(std::istream &in); diff --git a/deal.II/source/grid/grid_in.cc b/deal.II/source/grid/grid_in.cc index 158de1331a..e61de813d6 100644 --- a/deal.II/source/grid/grid_in.cc +++ b/deal.II/source/grid/grid_in.cc @@ -17,6 +17,7 @@ #include #include +#include #include #include @@ -51,9 +52,294 @@ void GridIn::attach_triangulation (Triangulation & -// --- --- -// --- read_unv --- -// --- --- +template +void GridIn::read_vtk(std::istream &in) +{ + Assert((dim == 2)||(dim == 3), ExcNotImplemented()); + std::string line; + std::string text[4]; + text[0] = "# vtk DataFile Version 3.0"; + text[1] = "vtk output"; + text[2] = "ASCII"; + text[3] = "DATASET UNSTRUCTURED_GRID"; + + for(unsigned int i = 0;i < 4;i++)//Checking for the match between initial strings/text in the file. + { + getline(in,line); + + AssertThrow (line.compare(text[i]) == 0, + ExcMessage(std::string("While reading VTK file, failed to find <") + + text[i] + ">")); + } + + ///////////////////Declaring storage and mappings////////////////// + + std::vector< Point > vertices;//vector of vertices + std::vector< CellData > cells;//vector of cells + SubCellData subcelldata;//subcell data that includes bounds and material IDs. + std::map vertex_indices; // # vert in unv (key) ---> # vert in deal.II (value) + std::map cell_indices; // # cell in unv (key) ---> # cell in deal.II (value) + std::map quad_indices; // # quad in unv (key) ---> # quad in deal.II (value) + std::map line_indices; // # line in unv(key) ---> # line in deal.II (value) + + unsigned int no_vertices, no_quads=0,no_lines=0; + + char keyword_1[7],keyword_2[6],keyword_3[10] ;//keywords for the three types of data + + in.get(keyword_1, 7); + + //////////////////Processing the POINTS section/////////////// + + if (std::strcmp(keyword_1,"POINTS") == 0)//comparing the keyword points + { + in>>no_vertices;// taking the no. of vertices + in.ignore(256, '\n');//ignoring the number beside the total no. of points. + + for(unsigned int count = 0; count < no_vertices; count++)//loop to read three values till the no . vertices is satisfied + { + // VTK format always specifies vertex coordinates with 3 components + Point<3> x; + in >> x(0) >> x(1) >> x(2); + + vertices.push_back(Point()); + for (unsigned int d=0; d>total_cells; + in.ignore(256,'\n'); + + if (dim == 3) + { + for(unsigned int count = 0; count < total_cells; count++) + { + in>>type; + + if(type == 8) + { + + cells.push_back(CellData()); + + for(j = 0; j < type; j++)//loop to feed data + in >> cells.back().vertices[j]; + + cells.back().material_id = 0; + + for(j = 0; j < type; j++)//loop to feed the data of the vertices to the cell + { + cells.back().vertices[j] = vertex_indices[cells.back().vertices[j]]; + } + cell_indices[count] = count; + no_cells++; + } + + else if ( type == 4) + { + + subcelldata.boundary_quads.push_back(CellData<2>()); + int no_quads = 0; + + for(j = 0; j < type; j++)//loop to feed the data to the boundary + { + in >> subcelldata.boundary_quads.back().vertices[j]; + } + subcelldata.boundary_quads.back().material_id = 0; + for(unsigned int j = 0; j < type; j++) + { + subcelldata.boundary_quads.back().vertices[j] = vertex_indices[subcelldata.boundary_quads.back().vertices[j]]; + } + quad_indices[count] = count + 1; + no_quads++; + } + + else + AssertThrow (false, + ExcMessage ("While reading VTK file, unknown file type encountered")); + } + } + + else if (dim == 2) + { + for(unsigned int count = 0; count < total_cells; count++) + { + in>>type; + + if(type == 4) + { + cells.push_back(CellData()); + + for(j = 0; j < type; j++)//loop to feed data + in >> cells.back().vertices[j]; + + cells.back().material_id = 0; + + for(j = 0; j < type; j++)//loop to feed the data of the vertices to the cell + { + cells.back().vertices[j] = vertex_indices[cells.back().vertices[j]]; + } + cell_indices[count] = count; + no_cells++; + } + + else if(type == 2) + { + //If this is encountered, the pointer comes out of the loop + //and starts processing boundaries. + subcelldata.boundary_lines.push_back(CellData<1>()); + int no_lines = 0; + + for(j = 0; j < type; j++)//loop to feed the data to the boundary + { + in >> subcelldata.boundary_lines.back().vertices[j]; + } + subcelldata.boundary_lines.back().material_id = 0; + for(unsigned int j = 0; j < type; j++) + { + subcelldata.boundary_lines.back().vertices[j] = vertex_indices[subcelldata.boundary_lines.back().vertices[j]]; + } + line_indices[count] = count + 1; + no_lines++; + } + + else + AssertThrow (false, + ExcMessage ("While reading VTK file, unknown file type encountered")); + } + } + else + AssertThrow (false, + ExcMessage ("While reading VTK file, failed to find CELLS section")); + + /////////////////////Processing the CELL_TYPES section//////////////////////// + + in>>keyword_3; + + if (std::strcmp(keyword_3,"CELL_TYPES") == 0)//Entering the cell_types section and ignoring data. + { + in.ignore(256, '\n'); + + while(!in.eof()) + { + in>>keyword_3; + if(std::strcmp(keyword_3,"12") && std::strcmp(keyword_3,"9")) + { + break; + } + } + } + + ////////////////////////Processing the CELL_DATA section///////////////////////////// + + if (std::strcmp(keyword_3,"CELL_DATA") == 0) + { + int no_ids; + in>>no_ids; + + std::string linenew; + std::string textnew[2]; + textnew[0] = "SCALARS MaterialID double"; + textnew[1] = "LOOKUP_TABLE default"; + + in.ignore(256, '\n'); + + for(unsigned int i = 0;i < 2;i++) + { + getline(in,linenew); + + if(linenew.compare(textnew[i]) == 0) + {} + else + AssertThrow (false, + ExcMessage (std::string("While reading VTK file, failed to find <") + + textnew[i] + "> section")); + } + + for(unsigned int i = 0; i < no_cells; i++)//assigning IDs to cells. + { + int id; + in>>id; + cells[cell_indices[i]].material_id = id; + } + + if (dim == 3) + { + for(unsigned int i = 0; i < no_quads; i++)//assigning IDs to bounds. + { + int id; + in>>id; + subcelldata.boundary_quads[quad_indices[i]].material_id = id; + } + } + else if (dim == 2) + { + for(unsigned int i = 0; i < no_lines; i++)//assigning IDs to bounds. + { + int id; + in>>id; + subcelldata.boundary_lines[line_indices[i]].material_id = id; + } + } + } + else + AssertThrow (false, + ExcMessage ("While reading VTK file, failed to find CELL_DATA section")); + + + Assert(subcelldata.check_consistency(dim), ExcInternalError()); + + GridTools::delete_unused_vertices(vertices, + cells, + subcelldata); + + if(dim == spacedim) + GridReordering::invert_all_cells_of_negative_grid(vertices, + cells); + + GridReordering::reorder_cells(cells); + tria->create_triangulation_compatibility(vertices, + cells, + subcelldata); + + return; + } + else + AssertThrow (false, + ExcMessage ("While reading VTK file, failed to find CELLS section")); +} + + template void GridIn::read_unv(std::istream &in) @@ -230,18 +516,18 @@ void GridIn::read_unv(std::istream &in) AssertThrow(in, ExcIO()); in >> id; - int n_lines = (n_entities%2 == 0)?(n_entities/2):((n_entities+1)/2); + const unsigned int n_lines = (n_entities%2 == 0)?(n_entities/2):((n_entities+1)/2); - for (int no_line = 0; no_line < n_lines; no_line++) + for (unsigned int no_line = 0; no_line < n_lines; no_line++) { - int n_fragments; + unsigned int n_fragments; if (no_line == n_lines-1) n_fragments = (n_entities%2 == 0)?(2):(1); else n_fragments = 2; - for (int no_fragment = 0; no_fragment < n_fragments; no_fragment++) + for (unsigned int no_fragment = 0; no_fragment < n_fragments; no_fragment++) { AssertThrow(in, ExcIO()); in >> dummy >> no >> dummy >> dummy; @@ -2355,6 +2641,10 @@ void GridIn::read (std::istream &in, read_msh (in); return; + case vtk: + read_vtk (in); + return; + case unv: read_unv (in); return; @@ -2395,6 +2685,8 @@ GridIn::default_suffix (const Format format) return ".dbmesh"; case msh: return ".msh"; + case vtk: + return ".vtk"; case unv: return ".unv"; case ucd: @@ -2426,6 +2718,9 @@ GridIn::parse_format (const std::string &format_name) if (format_name == "unv") return unv; + if (format_name == "vtk") + return vtk; + if (format_name == "inp") return ucd; @@ -2469,7 +2764,7 @@ GridIn::parse_format (const std::string &format_name) template std::string GridIn::get_format_names () { - return "dbmesh|msh|unv|ucd|xda|netcdf|tecplot"; + return "dbmesh|msh|unv|vtk|ucd|xda|netcdf|tecplot"; } diff --git a/tests/deal.II/grid_in_vtk_2d.cc b/tests/deal.II/grid_in_vtk_2d.cc new file mode 100644 index 0000000000..f78e9e7b5a --- /dev/null +++ b/tests/deal.II/grid_in_vtk_2d.cc @@ -0,0 +1,72 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 2002 - 2013 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, 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. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// read a 2d file in the VTK format + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +std::ofstream logfile("grid_in_vtk_2d/output"); + + +template +void check_file (const std::string name, + typename GridIn::Format format) +{ + Triangulation tria; + GridIn gi; + gi.attach_triangulation (tria); + gi.read(name, format); + deallog << name + << '\t' << tria.n_vertices() + << '\t' << tria.n_cells() + << std::endl; + + GridOut grid_out; + grid_out.write_gnuplot (tria, deallog.get_file_stream()); +} + +void filename_resolution() +{ + check_file<2> (std::string("grid_in_vtk_2d/mesh"), GridIn<2>::vtk); +} + + +int main () +{ + deallog << std::setprecision (2); + logfile << std::setprecision (2); + deallog.attach(logfile); + deallog.depth_console(0); + deallog.threshold_double(1.e-10); + + filename_resolution(); +} + diff --git a/tests/deal.II/grid_in_vtk_2d/cmp/generic b/tests/deal.II/grid_in_vtk_2d/cmp/generic new file mode 100644 index 0000000000..34d6bb61c2 --- /dev/null +++ b/tests/deal.II/grid_in_vtk_2d/cmp/generic @@ -0,0 +1,9 @@ + +DEAL::grid_in_vtk_2d/mesh 4 1 +-0.50 -0.50 0 1 +0.50 -0.50 0 1 +0.50 0.50 0 1 +-0.50 0.50 0 1 +-0.50 -0.50 0 1 + + diff --git a/tests/deal.II/grid_in_vtk_2d/mesh b/tests/deal.II/grid_in_vtk_2d/mesh new file mode 100644 index 0000000000..6e1d90b7ed --- /dev/null +++ b/tests/deal.II/grid_in_vtk_2d/mesh @@ -0,0 +1,13 @@ +# vtk DataFile Version 3.0 +vtk output +ASCII +DATASET UNSTRUCTURED_GRID +POINTS 4 float +-0.5 -0.5 0 0.5 -0.5 0 -0.5 0.5 0 +0.5 0.5 0 +CELLS 1 5 +4 0 1 3 2 +CELL_DATA 1 +SCALARS MaterialID double +LOOKUP_TABLE default +1 \ No newline at end of file diff --git a/tests/deal.II/grid_in_vtk_2d/mesh.msh b/tests/deal.II/grid_in_vtk_2d/mesh.msh new file mode 100644 index 0000000000..1b265ca0fb --- /dev/null +++ b/tests/deal.II/grid_in_vtk_2d/mesh.msh @@ -0,0 +1,474 @@ +$NOD +216 +3 0 0 0 +4 0 1 0 +5 1 1 0 +6 1 0 0 +8 0.7 0.5 0 +9 0.3 0.5 0 +1647 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option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// read a 3d file in the VTK format + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +std::ofstream logfile("grid_in_vtk_3d/output"); + + +template +void check_file (const std::string name, + typename GridIn::Format format) +{ + Triangulation tria; + GridIn gi; + gi.attach_triangulation (tria); + gi.read(name, format); + deallog << name + << '\t' << tria.n_vertices() + << '\t' << tria.n_cells() + << std::endl; + + GridOut grid_out; + grid_out.write_gnuplot (tria, deallog.get_file_stream()); +} + +void filename_resolution() +{ + check_file<3> (std::string("grid_in_vtk_3d/mesh"), GridIn<3>::vtk); +} + + +int main () +{ + deallog << std::setprecision (2); + logfile << std::setprecision (2); + deallog.attach(logfile); + deallog.depth_console(0); + deallog.threshold_double(1.e-10); + + filename_resolution(); +} + diff --git a/tests/deal.II/grid_in_vtk_3d/cmp/generic b/tests/deal.II/grid_in_vtk_3d/cmp/generic new file mode 100644 index 0000000000..a023078bb6 --- /dev/null +++ b/tests/deal.II/grid_in_vtk_3d/cmp/generic @@ -0,0 +1,3002 @@ + +DEAL::grid_in_vtk_3d/mesh 216 125 +0.0 0.0 1.0 0 0 +1.0 0.0 1.0 0 0 +1.0 1.0 1.0 0 0 +0.0 1.0 1.0 0 0 +0.0 0.0 1.0 0 0 + +0.0 0.0 0.0 0 0 +1.0 0.0 0.0 0 0 +1.0 1.0 0.0 0 0 +0.0 1.0 0.0 0 0 +0.0 0.0 0.0 0 0 + +0.0 0.0 1.0 0 0 +0.0 0.0 0.0 0 0 + +1.0 0.0 1.0 0 0 +1.0 0.0 0.0 0 0 + +1.0 1.0 1.0 0 0 +1.0 1.0 0.0 0 0 + +0.0 1.0 1.0 0 0 +0.0 1.0 0.0 0 0 + +0.0 0.0 2.0 0 0 +1.0 0.0 2.0 0 0 +1.0 1.0 2.0 0 0 +0.0 1.0 2.0 0 0 +0.0 0.0 2.0 0 0 + +0.0 0.0 1.0 0 0 +1.0 0.0 1.0 0 0 +1.0 1.0 1.0 0 0 +0.0 1.0 1.0 0 0 +0.0 0.0 1.0 0 0 + +0.0 0.0 2.0 0 0 +0.0 0.0 1.0 0 0 + +1.0 0.0 2.0 0 0 +1.0 0.0 1.0 0 0 + +1.0 1.0 2.0 0 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