From 888647c47a231ebaf6c0739c8cc09a5b09d0bd79 Mon Sep 17 00:00:00 2001 From: Vaishnavi Kale Date: Thu, 14 Nov 2024 16:12:28 -0700 Subject: [PATCH] Read meshes with field data in read_vtk() --- include/deal.II/grid/grid_in.h | 21 + source/grid/grid_in.cc | 150 +- tests/grid/grid_in_vtk_2d_field_data.cc | 93 ++ tests/grid/grid_in_vtk_2d_field_data.output | 1602 +++++++++++++++++++ tests/grid/grid_in_vtk_2d_field_data/mesh | 743 +++++++++ 5 files changed, 2574 insertions(+), 35 deletions(-) create mode 100644 tests/grid/grid_in_vtk_2d_field_data.cc create mode 100644 tests/grid/grid_in_vtk_2d_field_data.output create mode 100644 tests/grid/grid_in_vtk_2d_field_data/mesh diff --git a/include/deal.II/grid/grid_in.h b/include/deal.II/grid/grid_in.h index b5fb6e8fa4..cc25583cb8 100644 --- a/include/deal.II/grid/grid_in.h +++ b/include/deal.II/grid/grid_in.h @@ -23,6 +23,7 @@ #include #include +#include #include #include @@ -878,6 +879,17 @@ public: std::to_string(arg1) + " lines and " + std::to_string(arg2) + " facets (surface triangles or quadrilaterals)."); + /** + * Return a map containing field data. The format of the returned map is as + * follows: + * - std::string stores the name of the field data (identifier) as specified + * in the external mesh + * - std::vector stores value for the given identifier in each cell. + * To access the value use field_data[name_field][cell_id]. + */ + const std::map> & + get_field_data() const; + protected: /** * Store address of the triangulation to be fed with the data read in. @@ -948,6 +960,15 @@ private: * Input format used by read() if no format is given. */ Format default_format; + + /** + * Data member that stores cell data. The format is as follows: + * - std::string stores the name of the field data (identifier) as specified + * in the external mesh + * - std::vector stores value for the given identifier in each + * cell_id. To access the value use field_data[name_field][cell_id]. + */ + std::map> field_data; }; /* -------------- declaration of explicit specializations ------------- */ diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index 3483130d77..3609794bc0 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -163,10 +163,11 @@ GridIn::read_vtk(std::istream &in) { std::string line; - // verify that the first, third and fourth lines match - // expectations. the second line of the file may essentially be - // anything the author of the file chose to identify what's in - // there, so we just ensure that we can read it + // verify that the third and fourth lines match + // expectations. the first line is not checked to allow use of + // different vtk versions and the second line of the file may + // essentially be anything the author of the file chose to + // identify what's in there, so we just ensure that we can read it. { std::string text[4]; text[0] = "# vtk DataFile Version 3.0"; @@ -177,7 +178,7 @@ GridIn::read_vtk(std::istream &in) for (unsigned int i = 0; i < 4; ++i) { getline(in, line); - if (i != 1) + if (i == 2 || i == 3) AssertThrow( line.compare(text[i]) == 0, ExcMessage( @@ -433,35 +434,41 @@ GridIn::read_vtk(std::istream &in) for (unsigned int i = 0; i < n_ints; ++i) in >> tmp_int; + + // Processing the CELL_DATA and FIELD_DATA sections + // Ignore everything up to CELL_DATA while (in >> keyword) - if (keyword == "CELL_DATA") - { - unsigned int n_ids; - in >> n_ids; - - AssertThrow(n_ids == n_geometric_objects, - ExcMessage("The VTK reader found a CELL_DATA statement " - "that lists a total of " + - Utilities::int_to_string(n_ids) + - " cell data objects, but this needs to " - "equal the number of cells (which is " + - Utilities::int_to_string(cells.size()) + - ") plus the number of quads (" + - Utilities::int_to_string( - subcelldata.boundary_quads.size()) + - " in 3d or the number of lines (" + - Utilities::int_to_string( - subcelldata.boundary_lines.size()) + - ") in 2d.")); - - const std::vector data_sets{"MaterialID", - "ManifoldID"}; - - for (unsigned int i = 0; i < data_sets.size(); ++i) - { - // Ignore everything until we get to a SCALARS data set - while (in >> keyword) + { + if (keyword == "CELL_DATA") + { + unsigned int n_ids; + in >> n_ids; + + AssertThrow( + n_ids == n_geometric_objects, + ExcMessage( + "The VTK reader found a CELL_DATA statement " + "that lists a total of " + + Utilities::int_to_string(n_ids) + + " cell data objects, but this needs to " + "equal the number of cells (which is " + + Utilities::int_to_string(cells.size()) + + ") plus the number of quads (" + + Utilities::int_to_string(subcelldata.boundary_quads.size()) + + " in 3d or the number of lines (" + + Utilities::int_to_string(subcelldata.boundary_lines.size()) + + ") in 2d.")); + + const std::vector data_sets{"MaterialID", + "ManifoldID"}; + + in >> keyword; + for (unsigned int i = 0; i < data_sets.size(); ++i) + { + // Ignore everything until we get to a SCALARS data set + + std::cout << "keyword: " << keyword << std::endl; if (keyword == "SCALARS") { // Now see if we know about this type of data set, @@ -568,8 +575,76 @@ GridIn::read_vtk(std::istream &in) } } } - } - } + // check if a second SCALAR exists. If so, read the new + // keyword SCALARS, otherwise, return to the bookmarked + // position. + std::streampos oldpos = in.tellg(); + in >> keyword; + if (keyword == "SCALARS") + continue; + else + in.seekg(oldpos); + } + } + + + // Addition of FIELD DATA: + + + else if (keyword == "FIELD") + { + unsigned int n_fields; + in >> keyword; + AssertThrow( + keyword == "FieldData", + ExcMessage( + "While reading VTK file, missing keyword FieldData")); + + in >> n_fields; + + for (unsigned int i = 0; i < n_fields; ++i) + { + std::string section_name; + std::string data_type; + unsigned int temp, n_ids; + double data; + in >> section_name; + in >> temp; + in >> n_ids; + AssertThrow( + n_ids == n_geometric_objects, + ExcMessage( + "The VTK reader found a FIELD statement " + "that lists a total of " + + Utilities::int_to_string(n_ids) + + " cell data objects, but this needs to equal the number of cells (which is " + + Utilities::int_to_string(cells.size()) + + ") plus the number of quads (" + + Utilities::int_to_string( + subcelldata.boundary_quads.size()) + + " in 3d or the number of lines (" + + Utilities::int_to_string( + subcelldata.boundary_lines.size()) + + ") in 2d.")); + in >> data_type; + std::vector temp_data; + temp_data.resize(n_ids); + for (unsigned int j = 0; j < n_ids; ++j) + { + in >> data; + if (j < cells.size()) + temp_data[j] = data; + } + this->field_data[section_name] = std::move(temp_data); + } + } + else + { + // just ignore a line that doesn't start with any of the + // recognized tags + } + } // end of while loop + Assert(subcelldata.check_consistency(dim), ExcInternalError()); apply_grid_fixup_functions(vertices, cells, subcelldata); tria->create_triangulation(vertices, cells, subcelldata); @@ -580,7 +655,12 @@ GridIn::read_vtk(std::istream &in) "While reading VTK file, failed to find CELLS section")); } - +template +const std::map> & +GridIn::get_field_data() const +{ + return this->field_data; +} template void diff --git a/tests/grid/grid_in_vtk_2d_field_data.cc b/tests/grid/grid_in_vtk_2d_field_data.cc new file mode 100644 index 0000000000..c604cc5a0c --- /dev/null +++ b/tests/grid/grid_in_vtk_2d_field_data.cc @@ -0,0 +1,93 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2002 - 2018 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.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// read a 2d file in the VTK format with field data + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include + +#include "../tests.h" + +template +void +check_file(const std::string name, typename GridIn::Format format) +{ + Triangulation triangulation; + GridIn gridin; + GridOut gridout; + + gridin.attach_triangulation(triangulation); + gridin.read(name, format); + deallog << '\t' << triangulation.n_vertices() << '\t' + << triangulation.n_cells() << std::endl; + std::map> field_data; + + field_data = gridin.get_field_data(); + if (field_data.size() > 0) + { + std::map>::const_iterator iter = + field_data.find("Density"); + if (iter != field_data.end()) + { + std::vector cell_density = iter->second; + for (typename Triangulation::active_cell_iterator cell = + triangulation.begin_active(); + cell != triangulation.end(); + ++cell) + { + // store cell ID as a string + std::string text = boost::lexical_cast(cell->id()); + // Convert the string containing cell ID to an integer + boost::char_separator sep{"_"}; + boost::tokenizer> tokens(text, sep); + unsigned int cell_id = + boost::lexical_cast(*(tokens.begin())); + deallog << '\t' << cell_density[cell_id] << std::endl; + } + } + } + + gridout.write_gnuplot(triangulation, deallog.get_file_stream()); +} + +void +filename_resolution() +{ + check_file<2>(std::string(SOURCE_DIR "/grid_in_vtk_2d_field_data/mesh"), + GridIn<2>::vtk); +} + + +int +main() +{ + initlog(); + deallog << std::setprecision(2); + + filename_resolution(); +} diff --git a/tests/grid/grid_in_vtk_2d_field_data.output b/tests/grid/grid_in_vtk_2d_field_data.output new file mode 100644 index 0000000000..afc111ec6a --- /dev/null +++ b/tests/grid/grid_in_vtk_2d_field_data.output @@ -0,0 +1,1602 @@ + +DEAL:: 246 200 +DEAL:: 0.88 +DEAL:: 0.57 +DEAL:: 0.65 +DEAL:: 0.26 +DEAL:: 0.32 +DEAL:: 0.50 +DEAL:: 0.32 +DEAL:: 0.52 +DEAL:: 0.22 +DEAL:: 0.64 +DEAL:: 0.0026 +DEAL:: 0.33 +DEAL:: 0.32 +DEAL:: 0.71 +DEAL:: 0.86 +DEAL:: 0.33 +DEAL:: 0.30 +DEAL:: 0.76 +DEAL:: 0.48 +DEAL:: 0.71 +DEAL:: 0.69 +DEAL:: 0.53 +DEAL:: 0.93 +DEAL:: 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