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cgal/Mesh_3/include/CGAL/IO/vtk_io.h

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// Copyright (c) 2018 GeometryFactory (France).
// Copyright (c) 2004-2006 INRIA Sophia-Antipolis (France).
// Copyright (c) 2009 INRIA Sophia-Antipolis (France).
// All rights reserved.
//
// This file is part of CGAL (www.cgal.org).
// You can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation,
// either version 3 of the License, or (at your option) any later version.
//
// Licensees holding a valid commercial license may use this file in
// accordance with the commercial license agreement provided with the software.
//
// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
//
// $URL$
// $Id$
// SPDX-License-Identifier: GPL-3.0+
//
// Author(s) : Laurent RINEAU, Stephane Tayeb, Maxime Gimeno
#ifndef CGAL_VTK_IO_H
#define CGAL_VTK_IO_H
#include <CGAL/license/Mesh_3.h>
#include <fstream>
#include <vector>
#include <CGAL/Polygon_mesh_processing/internal/named_function_params.h>
#include <CGAL/Polygon_mesh_processing/internal/named_params_helper.h>
//todo try to factorize with functors
namespace CGAL{
// writes the appended data into the .vtu file
template <class FT>
void
write_vector(std::ostream& os,
const std::vector<FT>& vect)
{
const char* buffer = reinterpret_cast<const char*>(&(vect[0]));
std::size_t size = vect.size()*sizeof(FT);
os.write(reinterpret_cast<const char *>(&size), sizeof(std::size_t)); // number of bytes encoded
os.write(buffer, vect.size()*sizeof(FT)); // encoded data
}
template <class C3T3>
void
write_cells_tag(std::ostream& os,
const C3T3 & c3t3,
std::map<typename C3T3::Triangulation::Vertex_handle, std::size_t> & V,
bool binary,
std::size_t& offset)
{
typedef typename C3T3::Cells_in_complex_iterator Cell_iterator;
std::string formatattribute =
binary ? " format=\"appended\"" : " format=\"ascii\"";
std::string typeattribute;
switch(sizeof(std::size_t)) {
case 8: typeattribute = " type=\"UInt64\""; break;
case 4: typeattribute = " type=\"UInt32\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
// Write connectivity table
os << " <Cells>\n"
<< " <DataArray Name=\"connectivity\""
<< formatattribute << typeattribute;
if (binary) { // if binary output, just write the xml tag
os << " offset=\"" << offset << "\"/>\n";
offset += (4 * c3t3.number_of_cells() + 1) * sizeof(std::size_t);
// 4 indices (size_t) per cell + length of the encoded data (size_t)
}
else {
os << "\">\n";
for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
cit != c3t3.cells_in_complex_end() ;
++cit )
{
for (int i=0; i<4; i++)
os << V[cit->vertex(i)] << " ";
}
os << " </DataArray>\n";
}
// Write offsets
os << " <DataArray Name=\"offsets\""
<< formatattribute << typeattribute;
if (binary) { // if binary output, just write the xml tag
os << " offset=\"" << offset << "\"/>\n";
offset += (c3t3.number_of_cells() + 1) * sizeof(std::size_t);
// 1 offset (size_t) per cell + length of the encoded data (size_t)
}
else {
os << "\">\n";
std::size_t cells_offset = 0;
for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
cit != c3t3.cells_in_complex_end() ;
++cit )
{
cells_offset += 4;
os << cells_offset << " ";
}
os << " </DataArray>\n";
}
// Write cell type (tetrahedra == 10)
os << " <DataArray Name=\"types\""
<< formatattribute << " type=\"UInt8\"";
if (binary) {
os << " offset=\"" << offset << "\"/>\n";
offset += c3t3.number_of_cells() + sizeof(std::size_t);
// 1 unsigned char per cell + length of the encoded data (size_t)
}
else {
os << "\">\n";
for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
cit != c3t3.cells_in_complex_end() ;
++cit )
os << "10 ";
os << " </DataArray>\n";
}
os << " </Cells>\n";
}
template <class C3T3>
void
write_cells(std::ostream& os,
const C3T3 & c3t3,
std::map<typename C3T3::Triangulation::Vertex_handle, std::size_t> & V,
std::vector<float>& mids)
{
typedef typename C3T3::Cells_in_complex_iterator Cell_iterator;
std::vector<std::size_t> connectivity_table;
std::vector<std::size_t> offsets;
std::vector<unsigned char> cell_type(c3t3.number_of_cells(),10); // tetrahedra == 10
std::size_t off = 0;
for( Cell_iterator cit = c3t3.cells_in_complex_begin() ;
cit != c3t3.cells_in_complex_end() ;
++cit )
{
off += 4;
offsets.push_back(off);
for (int i=0; i<4; i++)
connectivity_table.push_back(V[cit->vertex(i)]);
mids.push_back(cit->subdomain_index());
}
write_vector<std::size_t>(os,connectivity_table);
write_vector<std::size_t>(os,offsets);
write_vector<unsigned char>(os,cell_type);
}
// writes the polys appended data at the end of the .vtp file
template <class Mesh,
typename NamedParameters>
void
write_polys(std::ostream& os,
const Mesh & mesh,
const NamedParameters& np)
{
typedef typename boost::graph_traits<Mesh>::vertex_descriptor vertex_descriptor;
typedef typename boost::graph_traits<Mesh>::face_iterator face_iterator;
typedef typename CGAL::Polygon_mesh_processing::GetVertexPointMap<Mesh, NamedParameters>::const_type Vpmap;
typedef typename CGAL::Polygon_mesh_processing::GetVertexIndexMap<Mesh, NamedParameters>::type Vimap;
Vimap V = choose_param(get_param(np, CGAL::internal_np::vertex_index),
get_const_property_map(CGAL::internal_np::vertex_index, mesh));
typedef typename boost::property_traits<Vpmap>::value_type Point_t;
typedef typename CGAL::Kernel_traits<Point_t>::Kernel Gt;
std::vector<std::size_t> connectivity_table;
std::vector<std::size_t> offsets;
std::vector<unsigned char> cell_type(num_faces(mesh),5); // triangle == 5
std::size_t off = 0;
for( face_iterator fit = faces(mesh).begin() ;
fit != faces(mesh).end() ;
++fit )
{
off += 3;
offsets.push_back(off);
BOOST_FOREACH(vertex_descriptor v,
vertices_around_face(halfedge(*fit, mesh), mesh))
connectivity_table.push_back(V[v]);
}
write_vector<std::size_t>(os,connectivity_table);
write_vector<std::size_t>(os,offsets);
write_vector<unsigned char>(os,cell_type);
}
//todo use named params for maps
template <class Mesh,
typename NamedParameters>
void
write_polys_tag(std::ostream& os,
const Mesh & mesh,
bool binary,
std::size_t& offset,
const NamedParameters& np)
{
typedef typename boost::graph_traits<Mesh>::vertex_descriptor vertex_descriptor;
typedef typename boost::graph_traits<Mesh>::face_iterator face_iterator;
typedef typename CGAL::Polygon_mesh_processing::GetVertexPointMap<Mesh, NamedParameters>::const_type Vpmap;
typedef typename CGAL::Polygon_mesh_processing::GetVertexIndexMap<Mesh, NamedParameters>::type Vimap;
Vimap V = choose_param(get_param(np, CGAL::internal_np::vertex_index),
get_const_property_map(CGAL::internal_np::vertex_index, mesh));
typedef typename boost::property_traits<Vpmap>::value_type Point_t;
typedef typename CGAL::Kernel_traits<Point_t>::Kernel Gt;
std::string formatattribute =
binary ? " format=\"appended\"" : " format=\"ascii\"";
std::string typeattribute;
switch(sizeof(std::size_t)) {
case 8: typeattribute = " type=\"UInt64\""; break;
case 4: typeattribute = " type=\"UInt32\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
// Write connectivity table
os << " <Polys>\n"
<< " <DataArray Name=\"connectivity\""
<< formatattribute << typeattribute;
if (binary) { // if binary output, just write the xml tag
os << " offset=\"" << offset << "\"/>\n";
offset += (3 * num_faces(mesh)+ 1) * sizeof(std::size_t);
// 3 indices (size_t) per triangle + length of the encoded data (size_t)
}
else {
os << "\">\n";
for( face_iterator fit = faces(mesh).begin() ;
fit != faces(mesh).end() ;
++fit )
{
BOOST_FOREACH(vertex_descriptor v,
vertices_around_face(halfedge(*fit, mesh), mesh))
os << V[v] << " ";
}
os << " </DataArray>\n";
}
// Write offsets
os << " <DataArray Name=\"offsets\""
<< formatattribute << typeattribute;
if (binary) { // if binary output, just write the xml tag
os << " offset=\"" << offset << "\"/>\n";
offset += (num_faces(mesh) + 1) * sizeof(std::size_t);
// 1 offset (size_t) per triangle + length of the encoded data (size_t)
}
else {
os << "\">\n";
std::size_t polys_offset = 0;
for( face_iterator fit = faces(mesh).begin() ;
fit != faces(mesh).end() ;
++fit )
{
polys_offset += 3;
os << polys_offset << " ";
}
os << " </DataArray>\n";
}
// Write cell type (triangle == 5)
os << " <DataArray Name=\"types\""
<< formatattribute << " type=\"UInt8\"";
if (binary) {
os << " offset=\"" << offset << "\"/>\n";
offset += num_faces(mesh) + sizeof(std::size_t);
// 1 unsigned char per cell + length of the encoded data (size_t)
}
else {
os << "\">\n";
for(std::size_t i = 0; i< num_faces(mesh); ++i)
os << "5 ";
os << " </DataArray>\n";
}
os << " </Polys>\n";
}
// writes the points tags before binary data is appended
template <class Tr>
void
write_points_tag(std::ostream& os,
const Tr & tr,
std::map<typename Tr::Vertex_handle, std::size_t> & V,
bool binary,
std::size_t& offset)
{
std::size_t dim = 3;
typedef typename Tr::Finite_vertices_iterator Finite_vertices_iterator;
typedef typename Tr::Geom_traits Gt;
typedef typename Gt::FT FT;
std::size_t inum = 0;
std::string format = binary ? "appended" : "ascii";
std::string type = (sizeof(FT) == 8) ? "Float64" : "Float32";
os << " <Points>\n"
<< " <DataArray type =\"" << type << "\" NumberOfComponents=\"3\" format=\""
<< format;
if (binary) {
os << "\" offset=\"" << offset << "\"/>\n";
offset += 3 * tr.number_of_vertices() * sizeof(FT) + sizeof(std::size_t);
// dim coords per points + length of the encoded data (size_t)
}
else {
os << "\">\n";
for( Finite_vertices_iterator vit = tr.finite_vertices_begin();
vit != tr.finite_vertices_end();
++vit)
{
V[vit] = inum++;
os << vit->point()[0] << " ";
os << vit->point()[1] << " ";
if(dim == 3)
os << vit->point()[2] << " ";
else
os << 0.0 << " ";
}
os << " </DataArray>\n";
}
os << " </Points>\n";
}
//todo : use namedparams for points and ids
//overload for facegraph
template <class Mesh,
typename NamedParameters>
void
write_points_tag(std::ostream& os,
const Mesh & mesh,
bool binary,
std::size_t& offset,
const NamedParameters& np)
{
typedef typename boost::graph_traits<Mesh>::vertex_iterator vertex_iterator;
typedef typename CGAL::Polygon_mesh_processing::GetVertexPointMap<Mesh, NamedParameters>::const_type Vpmap;
Vpmap vpm = choose_param(get_param(np, CGAL::vertex_point),
get_const_property_map(CGAL::vertex_point, mesh));
typedef typename boost::property_traits<Vpmap>::value_type Point_t;
typedef typename CGAL::Kernel_traits<Point_t>::Kernel Gt;
typedef typename Gt::FT FT;
std::string format = binary ? "appended" : "ascii";
std::string type = (sizeof(FT) == 8) ? "Float64" : "Float32";
os << " <Points>\n"
<< " <DataArray type =\"" << type << "\" NumberOfComponents=\"3\" format=\""
<< format;
if (binary) {
os << "\" offset=\"" << offset << "\"/>\n";
offset += 3 * num_vertices(mesh) * sizeof(FT) + sizeof(std::size_t);
// 3 coords per points + length of the encoded data (size_t)
}
else {
os << "\">\n";
for( vertex_iterator vit = vertices(mesh).begin();
vit != vertices(mesh).end();
++vit)
{
os << get(vpm, *vit).x() << " " << get(vpm, *vit).y() << " "
<< get(vpm, *vit).z() << " ";
}
os << " </DataArray>\n";
}
os << " </Points>\n";
}
// writes the points appended data at the end of the .vtu file
template <class Tr>
void
write_points(std::ostream& os,
const Tr & tr,
std::map<typename Tr::Vertex_handle,
std::size_t> & V)
{
std::size_t dim = 3;
typedef typename Tr::Finite_vertices_iterator Finite_vertices_iterator;
typedef typename Tr::Geom_traits Gt;
typedef typename Gt::FT FT;
std::size_t inum = 0;
std::vector<FT> coordinates;
for( Finite_vertices_iterator vit = tr.finite_vertices_begin();
vit != tr.finite_vertices_end();
++vit)
{
V[vit] = inum++; // binary output => the map has not been filled yet
coordinates.push_back(vit->point()[0]);
coordinates.push_back(vit->point()[1]);
coordinates.push_back(dim == 3 ? vit->point()[2] : 0.0);
}
write_vector<FT>(os,coordinates);
}
// writes the points appended data at the end of the .vtp file
template <class Mesh,
class NamedParameters>
void
write_polys_points(std::ostream& os,
const Mesh & mesh,
const NamedParameters& np)
{
typedef typename boost::graph_traits<Mesh>::vertex_iterator vertex_iterator;
typedef typename CGAL::Polygon_mesh_processing::GetVertexPointMap<Mesh, NamedParameters>::const_type Vpmap;
Vpmap vpm = choose_param(get_param(np, CGAL::vertex_point),
get_const_property_map(CGAL::vertex_point, mesh));
typedef typename boost::property_traits<Vpmap>::value_type Point_t;
typedef typename CGAL::Kernel_traits<Point_t>::Kernel Gt;
typedef typename Gt::FT FT;
std::vector<FT> coordinates;
for( vertex_iterator vit = vertices(mesh).begin();
vit != vertices(mesh).end();
++vit)
{
coordinates.push_back(get(vpm, *vit).x());
coordinates.push_back(get(vpm, *vit).y());
coordinates.push_back(get(vpm, *vit).z());
}
write_vector<FT>(os,coordinates);
}
// writes the attribute tags before binary data is appended
template <class T>
void
write_attribute_tag(std::ostream& os,
const std::string& attr_name,
const std::vector<T>& attribute,
bool binary,
std::size_t& offset)
{
std::string format = binary ? "appended" : "ascii";
std::string type = (sizeof(T) == 8) ? "Float64" : "Float32";
os << " <DataArray type=\"" << type << "\" Name=\"" << attr_name << "\" format=\"" << format;
if (binary) {
os << "\" offset=\"" << offset << "\"/>\n";
offset += attribute.size() * sizeof(T) + sizeof(std::size_t);
}
else {
typedef typename std::vector<T>::const_iterator Iterator;
os << "\">\n";
for (Iterator it = attribute.begin();
it != attribute.end();
++it )
os << *it << " ";
os << " </DataArray>\n";
}
}
// writes the attributes appended data at the end of the .vtu file
template <typename FT>
void
write_attributes(std::ostream& os,
const std::vector<FT>& att)
{
write_vector(os,att);
}
//public API
//!
//! \brief write_polydata_3 writes the content of a triangulated surface mesh in the .vtp
//! XML format.
//!
//! \tparam TriangleMesh a model of `FaceListGraph` with triangle faces.
//! \tparam NamedParameters a sequence of \ref pmp_namedparameters "Named Parameters"
//!
//! \param os a `std::ostream`.
//! \param mesh an instance of `TriangleMesh` to be written.
//! \param binary decides if the data should be written in binary(`true`)
//! or in ASCII(`false`).
//! \param np optional sequence of \ref pmp_namedparameters "Named Parameters" among the
//! ones listed below
//!
//! \cgalNamedParamsBegin
//! \cgalParamBegin{vertex_point_map} the property map with the points associated to
//! the vertices of `mesh`. If this parameter is omitted, an internal property map for
//! `CGAL::vertex_point_t` must be available in `TriangleMesh`.
//! \cgalParamEnd
//! \cgalParamBegin{vertex_index_map} the property map with the indices associated to
//! the vertices of `mesh`. If this parameter is omitted, an internal property map for
//! `CGAL::vertex_index_t` must be available in `TriangleMesh`.
//! \cgalParamEnd
//! \cgalNamedParamsEnd
template<class TriangleMesh,
class NamedParameters>
void write_polydata(std::ostream& os,
const TriangleMesh& mesh,
bool binary,
const NamedParameters& np)
{
os << "<?xml version=\"1.0\"?>\n"
<< "<VTKFile type=\"PolyData\" version=\"0.1\"";
#ifdef CGAL_LITTLE_ENDIAN
os << " byte_order=\"LittleEndian\"";
#else // CGAL_BIG_ENDIAN
os << " byte_order=\"BigEndian\"";
#endif
switch(sizeof(std::size_t)) {
case 4: os << " header_type=\"UInt32\""; break;
case 8: os << " header_type=\"UInt64\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
os << ">\n"
<< " <PolyData>" << "\n";
os << " <Piece NumberOfPoints=\"" << num_vertices(mesh)
<< "\" NumberOfPolys=\"" << num_faces(mesh) << "\">\n";
std::size_t offset = 0;
write_points_tag(os,mesh,binary,offset, np);
write_polys_tag(os,mesh,binary,offset, np);
os << " </Piece>\n"
<< " </PolyData>\n";
if (binary) {
os << "<AppendedData encoding=\"raw\">\n_";
write_polys_points(os,mesh, np);
write_polys(os,mesh, np);
}
os << "</VTKFile>\n";
}
template<class TriangleMesh>
void write_polydata(std::ostream& os,
const TriangleMesh& mesh,
bool binary = true)
{
write_polydata(os, mesh, binary, CGAL::parameters::all_default());
}
//!
//! \brief write_unstructured_grid_3 writes the content of a `C3t3` in the .vtu
//! XML format.
//!
//! \tparam C3T3 a model of `MeshComplexWithFeatures_3InTriangulation_3`.
//!
//! \param os a `std::ostream`.
//! \param c3t3 an instance of `C3T3` to be written.
//! \param binary decides if the data should be written in binary(`true`)
//! or in ASCII(`false`).
//!
template <class C3T3>
void write_unstructured_grid_3(std::ostream& os,
const C3T3& c3t3)
{
typedef typename C3T3::Triangulation Tr;
typedef typename Tr::Vertex_handle Vertex_handle;
const Tr& tr = c3t3.triangulation();
std::map<Vertex_handle, std::size_t> V;
//write header
os << "<?xml version=\"1.0\"?>\n"
<< "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\"";
#ifdef CGAL_LITTLE_ENDIAN
os << " byte_order=\"LittleEndian\"";
#else // CGAL_BIG_ENDIAN
os << " byte_order=\"BigEndian\"";
#endif
switch(sizeof(std::size_t)) {
case 4: os << " header_type=\"UInt32\""; break;
case 8: os << " header_type=\"UInt64\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
os << ">\n"
<< " <UnstructuredGrid>" << "\n";
os << " <Piece NumberOfPoints=\"" << tr.number_of_vertices()
<< "\" NumberOfCells=\"" << c3t3.number_of_cells() << "\">\n";
bool binary = true;
std::size_t offset = 0;
write_points_tag(os,tr,V,binary,offset);
write_cells_tag(os,c3t3,V,binary,offset);
std::vector<float> mids;
os << " <CellData Domain=\"MeshDomain";
os << "\">\n";
write_attribute_tag(os,"MeshDomain",mids,binary,offset);
os << " </CellData>\n";
os << " </Piece>\n"
<< " </UnstructuredGrid>\n";
if (binary) {
os << "<AppendedData encoding=\"raw\">\n_";
write_points(os,tr,V); // write points before cells to fill the std::map V
write_cells(os,c3t3,V, mids);//todo mids should be filled by write_attribute_tag
write_attributes(os,mids);
}
os << "</VTKFile>\n";
}
} //end CGAL
#endif // CGAL_VTK_IO_H
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