374 lines
11 KiB
C++
374 lines
11 KiB
C++
// Copyright (c) 2018 GeometryFactory (France).
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// Copyright (c) 2004-2006 INRIA Sophia-Antipolis (France).
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// Copyright (c) 2009 INRIA Sophia-Antipolis (France).
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// All rights reserved.
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//
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// This file is part of CGAL (www.cgal.org).
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//
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// $URL: https://github.com/CGAL/cgal/blob/v5.1/Mesh_3/include/CGAL/IO/output_to_vtu.h $
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// $Id: output_to_vtu.h 0779373 2020-03-26T13:31:46+01:00 Sébastien Loriot
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// SPDX-License-Identifier: GPL-3.0-or-later OR LicenseRef-Commercial
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//
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// Author(s) : Laurent RINEAU, Stephane Tayeb, Maxime Gimeno
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#ifndef CGAL_OUTPUT_TO_VTU_H
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#define CGAL_OUTPUT_TO_VTU_H
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#include <CGAL/license/Mesh_3.h>
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#include <iostream>
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#include <vector>
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#include <map>
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#include <CGAL/assertions.h>
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#include <CGAL/IO/io.h>
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#include <CGAL/IO/write_vtk.h>
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#include <boost/variant.hpp>
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//todo try to factorize with functors
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namespace CGAL{
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template <class C3T3>
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void
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write_cells_tag(std::ostream& os,
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const C3T3 & c3t3,
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std::map<typename C3T3::Triangulation::Vertex_handle, std::size_t> & V,
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bool binary,
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std::size_t& offset)
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{
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typedef typename C3T3::Cells_in_complex_iterator Cell_iterator;
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std::string formatattribute =
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binary ? " format=\"appended\"" : " format=\"ascii\"";
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std::string typeattribute;
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switch(sizeof(std::size_t)) {
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case 8: typeattribute = " type=\"UInt64\""; break;
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case 4: typeattribute = " type=\"UInt32\""; break;
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default: CGAL_error_msg("Unknown size of std::size_t");
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}
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// Write connectivity table
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os << " <Cells>\n"
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<< " <DataArray Name=\"connectivity\""
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<< formatattribute << typeattribute;
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if (binary) { // if binary output, just write the xml tag
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os << " offset=\"" << offset << "\"/>\n";
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offset += (4 * c3t3.number_of_cells() + 1) * sizeof(std::size_t);
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// 4 indices (size_t) per cell + length of the encoded data (size_t)
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}
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else {
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os << ">\n";
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for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
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cit != c3t3.cells_in_complex_end() ;
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++cit )
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{
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for (int i=0; i<4; i++)
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os << V[cit->vertex(i)] << " ";
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}
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os << "\n </DataArray>\n";
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}
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// Write offsets
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os << " <DataArray Name=\"offsets\""
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<< formatattribute << typeattribute;
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if (binary) { // if binary output, just write the xml tag
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os << " offset=\"" << offset << "\"/>\n";
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offset += (c3t3.number_of_cells() + 1) * sizeof(std::size_t);
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// 1 offset (size_t) per cell + length of the encoded data (size_t)
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}
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else {
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os << ">\n";
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std::size_t cells_offset = 0;
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for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
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cit != c3t3.cells_in_complex_end() ;
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++cit )
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{
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cells_offset += 4;
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os << cells_offset << " ";
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}
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os << "\n </DataArray>\n";
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}
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// Write cell type (tetrahedra == 10)
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os << " <DataArray Name=\"types\""
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<< formatattribute << " type=\"UInt8\"";
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if (binary) {
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os << " offset=\"" << offset << "\"/>\n";
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offset += c3t3.number_of_cells() + sizeof(std::size_t);
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// 1 unsigned char per cell + length of the encoded data (size_t)
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}
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else {
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os << ">\n";
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for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
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cit != c3t3.cells_in_complex_end() ;
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++cit )
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os << "10 ";
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os << "\n </DataArray>\n";
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}
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os << " </Cells>\n";
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}
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template <class C3T3>
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void
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write_cells(std::ostream& os,
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const C3T3 & c3t3,
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std::map<typename C3T3::Triangulation::Vertex_handle, std::size_t> & V)
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{
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typedef typename C3T3::Cells_in_complex_iterator Cell_iterator;
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std::vector<std::size_t> connectivity_table;
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std::vector<std::size_t> offsets;
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std::vector<unsigned char> cell_type(c3t3.number_of_cells(),10); // tetrahedra == 10
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std::size_t off = 0;
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for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
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cit != c3t3.cells_in_complex_end() ;
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++cit )
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{
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off += 4;
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offsets.push_back(off);
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for (int i=0; i<4; i++)
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connectivity_table.push_back(V[cit->vertex(i)]);
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}
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write_vector<std::size_t>(os,connectivity_table);
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write_vector<std::size_t>(os,offsets);
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write_vector<unsigned char>(os,cell_type);
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}
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template <class Tr>
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void
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write_c3t3_points_tag(std::ostream& os,
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const Tr & tr,
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std::size_t size_of_vertices,
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std::map<typename Tr::Vertex_handle, std::size_t> & V,
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bool binary,
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std::size_t& offset)
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{
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std::size_t dim = 3;
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typedef typename Tr::Finite_vertices_iterator Finite_vertices_iterator;
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typedef typename Tr::Geom_traits Gt;
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typedef typename Gt::FT FT;
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std::size_t inum = 0;
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std::string format = binary ? "appended" : "ascii";
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std::string type = (sizeof(FT) == 8) ? "Float64" : "Float32";
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os << " <Points>\n"
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<< " <DataArray type =\"" << type << "\" NumberOfComponents=\"3\" format=\""
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<< format;
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if (binary) {
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os << "\" offset=\"" << offset << "\"/>\n";
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offset += 3 * size_of_vertices * sizeof(FT) + sizeof(std::size_t);
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// dim coords per points + length of the encoded data (size_t)
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}
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else {
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os << "\">\n";
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for( Finite_vertices_iterator vit = tr.finite_vertices_begin();
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vit != tr.finite_vertices_end();
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++vit)
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{
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if(vit->in_dimension() <= -1) continue;
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V[vit] = inum++;
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os << vit->point()[0] << " ";
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os << vit->point()[1] << " ";
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if(dim == 3)
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os << vit->point()[2] << " ";
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else
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os << 0.0 << " ";
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}
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os << "\n </DataArray>\n";
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}
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os << " </Points>\n";
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}
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// writes the points appended data at the end of the .vtu file
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template <class Tr>
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void
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write_c3t3_points(std::ostream& os,
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const Tr & tr,
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std::map<typename Tr::Vertex_handle,
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std::size_t> & V)
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{
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std::size_t dim = 3;
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typedef typename Tr::Finite_vertices_iterator Finite_vertices_iterator;
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typedef typename Tr::Geom_traits Gt;
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typedef typename Gt::FT FT;
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std::size_t inum = 0;
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std::vector<FT> coordinates;
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for( Finite_vertices_iterator vit = tr.finite_vertices_begin();
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vit != tr.finite_vertices_end();
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++vit)
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{
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if(vit->in_dimension() <= -1) continue;
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V[vit] = inum++; // binary output => the map has not been filled yet
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coordinates.push_back(vit->point()[0]);
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coordinates.push_back(vit->point()[1]);
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coordinates.push_back(dim == 3 ? vit->point()[2] : 0.0);
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}
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write_vector<FT>(os,coordinates);
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}
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// writes the attribute tags before binary data is appended
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template <class T>
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void
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write_attribute_tag(std::ostream& os,
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const std::string& attr_name,
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const std::vector<T>& attribute,
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bool binary,
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std::size_t& offset)
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{
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std::string format = binary ? "appended" : "ascii";
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std::string type = "";
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if(std::is_floating_point<T>::value)
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{
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type = (sizeof(T) == 8) ? "Float64" : "Float32";
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}
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else
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{
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if(sizeof(T) == 1)
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type = "UInt8";
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else if(sizeof(T) == 4)
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type = "UInt32";
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else
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type = "UInt64";
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}
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os << " <DataArray type=\"" << type << "\" Name=\"" << attr_name << "\" format=\"" << format;
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if (binary) {
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os << "\" offset=\"" << offset << "\"/>\n";
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offset += attribute.size() * sizeof(T) + sizeof(std::size_t);
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}
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else {
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typedef typename std::vector<T>::const_iterator Iterator;
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os << "\">\n";
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for (Iterator it = attribute.begin();
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it != attribute.end();
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++it )
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os << *it << " ";
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os << "\n </DataArray>\n";
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}
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}
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// writes the attributes appended data at the end of the .vtu file
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template <typename FT>
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void
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write_attributes(std::ostream& os,
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const std::vector<FT>& att)
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{
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write_vector(os,att);
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}
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enum VTU_ATTRIBUTE_TYPE{
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DOUBLE=0,
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UNIT_8,
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SIZE_TYPE
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};
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typedef boost::variant<const std::vector<double>*, const std::vector<uint8_t>*, const std::vector<std::size_t>* > Vtu_attributes;
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template <class C3T3>
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void output_to_vtu_with_attributes(std::ostream& os,
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const C3T3& c3t3,
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std::vector<std::pair<const char*, Vtu_attributes> >&attributes,
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IO::Mode mode = IO::BINARY)
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{
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//CGAL_assertion(attributes.size() == attribute_types.size());
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typedef typename C3T3::Triangulation Tr;
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typedef typename Tr::Vertex_handle Vertex_handle;
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const Tr& tr = c3t3.triangulation();
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std::map<Vertex_handle, std::size_t> V;
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//write header
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os << "<?xml version=\"1.0\"?>\n"
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<< "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\"";
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#ifdef CGAL_LITTLE_ENDIAN
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os << " byte_order=\"LittleEndian\"";
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#else // CGAL_BIG_ENDIAN
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os << " byte_order=\"BigEndian\"";
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#endif
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switch(sizeof(std::size_t)) {
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case 4: os << " header_type=\"UInt32\""; break;
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case 8: os << " header_type=\"UInt64\""; break;
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default: CGAL_error_msg("Unknown size of std::size_t");
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}
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os << ">\n"
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<< " <UnstructuredGrid>" << "\n";
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const std::size_t number_of_vertices =
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tr.number_of_vertices() - c3t3.number_of_far_points();
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os << " <Piece NumberOfPoints=\"" << number_of_vertices
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<< "\" NumberOfCells=\"" << c3t3.number_of_cells() << "\">\n";
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std::size_t offset = 0;
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const bool binary = (mode == IO::BINARY);
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write_c3t3_points_tag(os,tr,number_of_vertices,V,binary,offset);
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write_cells_tag(os,c3t3,V,binary,offset); // fills V if the mode is ASCII
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os << " <CellData Scalars=\""<<attributes.front().first<<"\">\n";
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for(std::size_t i = 0; i< attributes.size(); ++i)
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{
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switch(attributes[i].second.which()){
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case 0:
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write_attribute_tag(os,attributes[i].first, *boost::get<const std::vector<double>* >(attributes[i].second), binary,offset);
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break;
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case 1:
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write_attribute_tag(os,attributes[i].first, *boost::get<const std::vector<uint8_t>* >(attributes[i].second), binary,offset);
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break;
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default:
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write_attribute_tag(os,attributes[i].first, *boost::get<const std::vector<std::size_t>* >(attributes[i].second), binary,offset);
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break;
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}
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}
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os << " </CellData>\n";
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os << " </Piece>\n"
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<< " </UnstructuredGrid>\n";
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if (binary) {
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os << "<AppendedData encoding=\"raw\">\n_";
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write_c3t3_points(os,tr,V); // fills V if the mode is BINARY
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write_cells(os,c3t3,V);
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for(std::size_t i = 0; i< attributes.size(); ++i)
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switch(attributes[i].second.which()){
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case 0:
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write_attributes(os, *boost::get<const std::vector<double>* >(attributes[i].second));
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break;
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case 1:
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write_attributes(os, *boost::get<const std::vector<uint8_t>* >(attributes[i].second));
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break;
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default:
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write_attributes(os, *boost::get<const std::vector<std::size_t>* >(attributes[i].second));
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break;
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}
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}
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os << "</VTKFile>\n";
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}
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//public API
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template <class C3T3>
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void output_to_vtu(std::ostream& os,
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const C3T3& c3t3,
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IO::Mode mode = IO::BINARY)
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{
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typedef typename C3T3::Cells_in_complex_iterator Cell_iterator;
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std::vector<double> mids;
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for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
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cit != c3t3.cells_in_complex_end() ;
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++cit )
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{
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double v = cit->subdomain_index();
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mids.push_back(v);
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}
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std::vector<std::pair<const char*, Vtu_attributes > > atts;
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Vtu_attributes v = &mids;
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atts.push_back(std::make_pair("MeshDomain", v));
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output_to_vtu_with_attributes(os, c3t3, atts, mode);
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}
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} //end CGAL
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#endif // CGAL_VTK_IO_H
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