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cgal/Polyhedron/demo/Polyhedron/Plugins/IO/VTK_io_plugin.cpp

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// Copyright (c) 2015 GeometryFactory (France). All rights reserved.
//
// This file is part of CGAL (www.cgal.org).
//
// $URL$
// $Id$
// SPDX-License-Identifier: GPL-3.0-or-later OR LicenseRef-Commercial
//
// Author(s) : Sebastien Loriot <sebastien.loriot@cgal.org>,
// Jane Tournois
//
#include <CGAL/SMDS_3/io_signature.h>
#include <QtCore/qglobal.h>
#include "Scene_surface_mesh_item.h"
#include "Scene_c3t3_item.h"
#include "Scene_polylines_item.h"
#include "Scene_points_with_normal_item.h"
#include <CGAL/Three/Polyhedron_demo_plugin_helper.h>
#include <CGAL/Three/Polyhedron_demo_io_plugin_interface.h>
#include <CGAL/Three/Three.h>
#include <QApplication>
#include <QMessageBox>
#include <QMainWindow>
#include <QFileDialog>
#include <QString>
#include <fstream>
#include <boost/graph/graph_traits.hpp>
#include <unordered_map>
#include <CGAL/boost/graph/properties.h>
#include <CGAL/boost/graph/Euler_operations.h>
#include <CGAL/property_map.h>
#include <CGAL/IO/Complex_3_in_triangulation_3_to_vtk.h>
#include <CGAL/SMDS_3/tet_soup_to_c3t3.h>
#include <CGAL/IO/output_to_vtu.h>
#include <CGAL/boost/graph/IO/VTK.h>
#include <CGAL/IO/VTK.h>
#include <vtkSmartPointer.h>
#include <vtkDataSetReader.h>
#include <vtkXMLPolyDataReader.h>
#include <vtkPolyDataWriter.h>
#include <vtkUnstructuredGrid.h>
#include <vtkXMLUnstructuredGridReader.h>
#include <vtkXMLUnstructuredGridWriter.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkPolyData.h>
#include <vtkIdTypeArray.h>
#include <vtkFieldData.h>
#include <vtkFloatArray.h>
#include <vtkDoubleArray.h>
#include <vtkCell.h>
#include <vtkCellData.h>
#include <vtkIdList.h>
#include <vtkAppendFilter.h>
#include <vtkSphereSource.h>
#include <vtkVersion.h>
#include <vtkPoints.h>
#include <vtkCellArray.h>
#include <vtkType.h>
#include <vtkCommand.h>
#include <CGAL/Named_function_parameters.h>
#include <CGAL/boost/graph/named_params_helper.h>
typedef Scene_surface_mesh_item Scene_facegraph_item;
typedef Scene_facegraph_item::Face_graph FaceGraph;
typedef boost::property_traits<boost::property_map<FaceGraph,
CGAL::vertex_point_t>::type>::value_type Point;
namespace CGAL{
template <class Point_3>
void extract_segments_from_vtkPointSet(vtkPointSet* poly_data,
std::vector< std::vector<Point_3> >& segments)
{
// get nb of points and cells
vtkIdType nb_points = poly_data->GetNumberOfPoints();
vtkIdType nb_cells = poly_data->GetNumberOfCells();
//extract points
std::vector<Point_3> point_map(nb_points);
for (vtkIdType i = 0; i<nb_points; ++i)
{
double coords[3];
poly_data->GetPoint(i, coords);
point_map[i]=Point_3(coords[0], coords[1], coords[2]);
}
//extract segments
for (vtkIdType i = 0; i<nb_cells; ++i)
{
if(poly_data->GetCellType(i) != 3
&& poly_data->GetCellType(i) != 4)
continue;
vtkCell* cell_ptr = poly_data->GetCell(i);
vtkIdType nb_vertices = cell_ptr->GetNumberOfPoints();
segments.push_back( std::vector<Point_3>() );
for(int j = 0; j < nb_vertices; ++j)
{
segments.back().push_back(point_map[cell_ptr->GetPointId(j)]);
}
}
}
template<typename VtkWriter, typename PM>
void polygon_mesh_to_vtkUnstructured(const PM& pmesh,//PolygonMesh
const char* filename)
{
typedef typename boost::graph_traits<PM>::vertex_descriptor vertex_descriptor;
typedef typename boost::graph_traits<PM>::face_descriptor face_descriptor;
typedef typename boost::graph_traits<PM>::halfedge_descriptor halfedge_descriptor;
typedef typename boost::property_map<PM, CGAL::vertex_point_t>::const_type VPMap;
typedef typename boost::property_map_value<PM, CGAL::vertex_point_t>::type Point_3;
VPMap vpmap = get(CGAL::vertex_point, pmesh);
vtkPoints* const vtk_points = vtkPoints::New();
vtkCellArray* const vtk_cells = vtkCellArray::New();
vtk_points->Allocate(num_vertices(pmesh));
vtk_cells->Allocate(num_faces(pmesh));
std::map<vertex_descriptor, vtkIdType> Vids;
vtkIdType inum = 0;
for(vertex_descriptor v : vertices(pmesh))
{
const Point_3& p = get(vpmap, v);
vtk_points->InsertNextPoint(CGAL::to_double(p.x()),
CGAL::to_double(p.y()),
CGAL::to_double(p.z()));
Vids[v] = inum++;
}
for(face_descriptor f : faces(pmesh))
{
vtkIdList* cell = vtkIdList::New();
for(halfedge_descriptor h :
halfedges_around_face(halfedge(f, pmesh), pmesh))
{
cell->InsertNextId(Vids[target(h, pmesh)]);
}
vtk_cells->InsertNextCell(cell);
cell->Delete();
}
vtkSmartPointer<vtkUnstructuredGrid> usg =
vtkSmartPointer<vtkUnstructuredGrid>::New();
usg->SetPoints(vtk_points);
vtk_points->Delete();
usg->SetCells(5,vtk_cells);
vtk_cells->Delete();
// Combine the two data sets
//vtkSmartPointer<vtkAppendFilter> appendFilter =
// vtkSmartPointer<vtkAppendFilter>::New();
//appendFilter->AddInputData(polydata);
//appendFilter->Update();
//vtkSmartPointer<vtkPolyData> unstructuredGrid =
// vtkSmartPointer<vtkPolyData>::New();
//unstructuredGrid->ShallowCopy(appendFilter->GetOutput());
// Write the unstructured grid
vtkSmartPointer<VtkWriter> writer =
vtkSmartPointer<VtkWriter>::New();
writer->SetFileName(filename);
writer->SetInputData(usg);
writer->Write();
}
}//end namespace CGAL
class Polyhedron_demo_vtk_plugin :
public QObject,
public CGAL::Three::Polyhedron_demo_io_plugin_interface
{
Q_OBJECT
Q_INTERFACES(CGAL::Three::Polyhedron_demo_io_plugin_interface)
Q_PLUGIN_METADATA(IID "com.geometryfactory.PolyhedronDemo.IOPluginInterface/1.90" FILE "vtk_io_plugin.json")
public:
typedef boost::graph_traits<FaceGraph>::vertex_descriptor vertex_descriptor;
typedef boost::graph_traits<FaceGraph>::face_descriptor face_descriptor;
QString nameFilters() const {
return "VTK XML UnstructuredGrid (*.vtu);;VTK PolyData files (*.vtk);; VTK XML PolyData (*.vtp)"; }
QString name() const { return "vtk_plugin"; }
bool canSave(const CGAL::Three::Scene_item* item)
{
return (qobject_cast<const Scene_facegraph_item*>(item)
|| qobject_cast<const Scene_c3t3_item*>(item));
}
bool save(QFileInfo fileinfo,QList<CGAL::Three::Scene_item*>& items)
{
Scene_item* item = items.front();
std::string extension = fileinfo.suffix().toLower().toStdString();
if ( extension != "vtk" && extension != "vtp" && extension != "vtu")
return false;
std::string output_filename = fileinfo.absoluteFilePath().toStdString();
const Scene_facegraph_item* poly_item =
qobject_cast<const Scene_facegraph_item*>(item);
if (poly_item)
{
if (extension != "vtp")
{
if(!CGAL::is_triangle_mesh(*poly_item->polyhedron()))
{
QMessageBox::warning(0, "Error",
"Cannot save a mesh in vtu format if "
"it is not pure triangle.");
return false;
}
CGAL::polygon_mesh_to_vtkUnstructured<vtkXMLUnstructuredGridWriter>(
*poly_item->polyhedron(),
output_filename.data());
}
else
{
const FaceGraph* mesh = poly_item->face_graph();
std::ofstream os(output_filename.data());
os << std::setprecision(16);
//write header
CGAL::IO::write_VTP(os, *mesh);
}
}
else
{
const Scene_c3t3_item* c3t3_item =
qobject_cast<const Scene_c3t3_item*>(item);
if(!c3t3_item || extension != "vtu")
return false;
std::ofstream os(output_filename.data());
os << std::setprecision(16);
const C3t3& c3t3 = c3t3_item->c3t3();
CGAL::IO::output_to_vtu(os, c3t3);
}
items.pop_front();
return true;
}
bool canLoad(QFileInfo) const { return true; }
QList<Scene_item*> load(QFileInfo fileinfo, bool& ok, bool add_to_scene)
{
std::string extension=fileinfo.suffix().toLower().toStdString();
if (extension != "vtk" && extension != "vtp" && extension != "vtu")
{
ok = false;
return QList<Scene_item*>();
}
std::string fname = fileinfo.absoluteFilePath().toStdString();
// Try to read .vtk in a facegraph
if(fileinfo.size() == 0)
{
CGAL::Three::Three::warning( tr("The file you are trying to load is empty."));
Scene_facegraph_item* item =
new Scene_facegraph_item();
item->setName(fileinfo.completeBaseName());
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(item);
return QList<Scene_item*>()<<item;
}
vtkSmartPointer<vtkPointSet> data;
vtkSmartPointer<CGAL::IO::internal::ErrorObserverVtk> obs =
vtkSmartPointer<CGAL::IO::internal::ErrorObserverVtk>::New();
if (extension=="vtp")
data = CGAL::IO::internal::read_vtk_file<vtkXMLPolyDataReader>(fname,obs)
->GetOutput();
else
if (extension=="vtu")
data = CGAL::IO::internal::read_vtk_file<vtkXMLUnstructuredGridReader>(fname,obs)
->GetOutput();
else{
//read non-XML data
vtkSmartPointer<vtkDataSetReader> reader =
CGAL::IO::internal::read_vtk_file<vtkDataSetReader>(fname,obs);
data = vtkPolyData::SafeDownCast(reader->GetOutput());
if (!data)
data = vtkUnstructuredGrid::SafeDownCast(reader->GetOutput());
}
if (obs->GetError())
{
QMessageBox msgBox;
msgBox.setText("This type of data can't be opened");
msgBox.setInformativeText(QString("VTK error message :\n")
.append(QString(obs->GetErrorMessage().data())));
msgBox.setStandardButtons(QMessageBox::Ok);
msgBox.setIcon(QMessageBox::Critical);
msgBox.exec();
ok = false;
return QList<Scene_item*>();
}
if (obs->GetWarning())
{
QMessageBox msgBox;
msgBox.setText("This file generates a warning");
msgBox.setInformativeText(QString("VTK warning message :\n")
.append(QString(obs->GetWarningMessage().data())));
msgBox.setStandardButtons(QMessageBox::Ok);
msgBox.setIcon(QMessageBox::Warning);
msgBox.exec();
}
//check celltypes
bool is_polygon_mesh(false),
is_c3t3(false),
is_polyline(false);
for(int i = 0; i< data->GetNumberOfCells(); ++i)
{
int t = data->GetCellType(i);
if( t == 5 || t == 7 || t == 9) //tri, quad or polygon
is_polygon_mesh = true;
else if(t == 10) //tetrahedron
is_c3t3 = true;
else if( t == 3 || t == 4) //line or polyline
is_polyline = true;
}
Scene_group_item* group = nullptr;
if((is_polygon_mesh && is_c3t3)
|| (is_polygon_mesh && is_polyline)
|| (is_c3t3 && is_polyline) )
{
group = new Scene_group_item(fileinfo.baseName());
}
if(is_polygon_mesh)
{
auto poly = std::make_unique<FaceGraph>();
Scene_item* poly_item = nullptr;
if (CGAL::IO::internal::vtkPointSet_to_polygon_mesh(data, *poly, CGAL::parameters::default_values()))
{
poly_item = new Scene_facegraph_item(poly.release());
} else {
poly.reset(nullptr);
std::vector<Point_3> points;
std::vector<std::vector<std::size_t> > polygons;
if (CGAL::IO::internal::vtkPointSet_to_polygon_soup(data, points, polygons, CGAL::parameters::default_values()))
{
auto soup_item = new Scene_polygon_soup_item();
soup_item->load(points, polygons);
poly_item = soup_item;
}
}
if(poly_item) {
if(group)
{
poly_item->setName(QString("%1_faces").arg(fileinfo.baseName()));
CGAL::Three::Three::scene()->addItem(poly_item);
CGAL::Three::Three::scene()->changeGroup(poly_item, group);
}
else{
poly_item->setName(fileinfo.baseName());
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(poly_item);
return QList<Scene_item*>()<<poly_item;
}
}
}
if (is_c3t3)
{
typedef std::array<int, 3> Facet; // 3 = id
typedef std::array<int, 4> Tet; // first 4 = id, fifth = reference
Scene_c3t3_item* c3t3_item = new Scene_c3t3_item();
c3t3_item->set_valid(false);
//build a triangulation from data:
std::vector<Tr::Point> points;
vtkPoints* dataP = data->GetPoints();;
for(int i = 0; i< data->GetNumberOfPoints(); ++i)
{
double *p = dataP->GetPoint(i);
points.push_back(Tr::Point(p[0],p[1],p[2]));
}
std::vector<Tet> finite_cells;
std::vector<C3t3::Subdomain_index> subdomains;
bool has_mesh_domain = data->GetCellData()->HasArray("MeshDomain");
vtkDataArray* domains = data->GetCellData()->GetArray("MeshDomain");
for(int i = 0; i< data->GetNumberOfCells(); ++i)
{
if(data->GetCellType(i) != 10 )
continue;
vtkIdList* pids = data->GetCell(i)->GetPointIds();
Tet cell;
for(int j = 0; j<4; ++j)
cell[j] = pids->GetId(j);
finite_cells.push_back(cell);
const auto si = has_mesh_domain
? static_cast<int>(domains->GetComponent(i, 0))
: 1;
subdomains.push_back(si);
}
std::map<Facet, int> border_facets;
//Preprocessing for build_triangulation
//check for orientation and swap in cells if not good.
for(std::size_t i=0; i<finite_cells.size(); ++i)
{
Point_3 test_points[4];
for (int j = 0; j < 4; ++j)
{
Tr::Point tp = points[finite_cells[i][j]];
test_points[j] = Point_3(tp.x(), tp.y(), tp.z());
}
if(CGAL::orientation(test_points[0], test_points[1], test_points[2], test_points[3])
!= CGAL::POSITIVE)
{
std::swap(finite_cells[i][1], finite_cells[i][3]);
}
}
CGAL::SMDS_3::build_triangulation_with_subdomains_range(
c3t3_item->c3t3().triangulation(),
points, finite_cells, subdomains, border_facets,
false, false, true);
for( C3t3::Triangulation::Finite_cells_iterator
cit = c3t3_item->c3t3().triangulation().finite_cells_begin();
cit != c3t3_item->c3t3().triangulation().finite_cells_end();
++cit)
{
CGAL_assertion(cit->info() >= 0);
c3t3_item->c3t3().add_to_complex(cit, cit->info());
for(int i=0; i < 4; ++i)
{
if(cit->surface_patch_index(i)>0)
{
c3t3_item->c3t3().add_to_complex(cit, i, cit->surface_patch_index(i));
}
}
}
//if there is no facet in the complex, we add the border facets.
if(c3t3_item->c3t3().number_of_facets_in_complex() == 0)
{
for( C3t3::Triangulation::Finite_facets_iterator
fit = c3t3_item->c3t3().triangulation().finite_facets_begin();
fit != c3t3_item->c3t3().triangulation().finite_facets_end();
++fit)
{
typedef C3t3::Triangulation::Cell_handle Cell_handle;
Cell_handle c = fit->first;
Cell_handle nc = c->neighbor(fit->second);
// By definition, Subdomain_index() is supposed to be the id of the exterior
if(c->subdomain_index() != C3t3::Triangulation::Cell::Subdomain_index() &&
nc->subdomain_index() == C3t3::Triangulation::Cell::Subdomain_index())
{
// Color the border facet with the index of its cell
c3t3_item->c3t3().add_to_complex(c, fit->second, c->subdomain_index());
}
}
}
c3t3_item->c3t3_changed();
c3t3_item->resetCutPlane();
if(group)
{
c3t3_item->setName(QString("%1_tetrahedra").arg(fileinfo.baseName()));
CGAL::Three::Three::scene()->addItem(c3t3_item);
CGAL::Three::Three::scene()->changeGroup(c3t3_item, group);
}
else{
c3t3_item->setName(fileinfo.baseName());
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(c3t3_item);
return QList<Scene_item*>()<<c3t3_item;
}
}
if(is_polyline)
{
std::vector< std::vector<Point> > segments;
extract_segments_from_vtkPointSet(data,segments);
Scene_polylines_item* polyline_item = new Scene_polylines_item();
for(const std::vector<Point>& segment : segments)
polyline_item->polylines.push_back(segment);
if(group)
{
polyline_item->setName(QString("%1_lines").arg(fileinfo.baseName()));
CGAL::Three::Three::scene()->addItem(polyline_item);
CGAL::Three::Three::scene()->changeGroup(polyline_item, group);
}
else{
polyline_item->setName(fileinfo.baseName());
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(polyline_item);
return QList<Scene_item*>()<<polyline_item;
}
}
if(group){
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(group);
return QList<Scene_item*>()<<group;
}
QApplication::restoreOverrideCursor();
QMessageBox::warning(CGAL::Three::Three::mainWindow(),
"Problematic file",
"Cell type not recognized. Only points will be displayed.");
QApplication::setOverrideCursor(Qt::WaitCursor);
Scene_points_with_normal_item* point_item = new Scene_points_with_normal_item();
for(int i=0; i< data->GetNumberOfPoints(); ++i)
{
double* p = data->GetPoint(i);
point_item->point_set()->insert(Point_3(p[0], p[1], p[2]));
}
point_item->setName(fileinfo.baseName());
ok = true;
if(add_to_scene)
CGAL::Three::Three::scene()->addItem(point_item);
return QList<Scene_item*>()<<point_item;
}
}; // end Polyhedron_demo_vtk_plugin
#include "VTK_io_plugin.moc"
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