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/* Copyright (c) 2007 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* |
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* AlphaShape.cpp |
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* |
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* Purpose: To calculate convexhull, hull volume and radius |
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* using the CGAL library. |
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* |
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* Created by Charles F. Vardeman II on 11 Dec 2006. |
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* @author Charles F. Vardeman II |
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* @version $Id: AlphaShape.cpp,v 1.2 2008-05-14 14:31:48 chuckv Exp $ |
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* |
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*/ |
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|
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#include "math/AlphaShape.hpp" |
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|
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#include <iostream> |
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#include <list> |
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#include <fstream> |
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#include <CGAL/IO/Geomview_stream.h> |
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#include <CGAL/IO/alpha_shape_geomview_ostream_3.h> |
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|
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#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> |
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#include <CGAL/Delaunay_triangulation_3.h> |
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#include <CGAL/Triangulation_hierarchy_3.h> |
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#include <CGAL/Alpha_shape_3.h> |
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#include <CGAL/Tetrahedron_3.h> |
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|
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|
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struct K : CGAL::Exact_predicates_inexact_constructions_kernel {}; |
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|
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typedef CGAL::Alpha_shape_vertex_base_3<K> Vb; |
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typedef CGAL::Triangulation_hierarchy_vertex_base_3<Vb> Vbh; |
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typedef CGAL::Alpha_shape_cell_base_3<K> Fb; |
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typedef CGAL::Triangulation_data_structure_3<Vbh,Fb> Tds; |
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typedef CGAL::Delaunay_triangulation_3<K,Tds> Delaunay; |
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typedef CGAL::Triangulation_hierarchy_3<Delaunay> Delaunay_hierarchy; |
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typedef CGAL::Alpha_shape_3<Delaunay_hierarchy> Alpha_shape_3; |
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|
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typedef K::Point_3 Point; |
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typedef Alpha_shape_3::Alpha_iterator Alpha_iterator; |
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typedef Alpha_shape_3::NT NT; |
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typedef Alpha_shape_3::Cell_handle Cell_handle; |
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typedef Alpha_shape_3::Vertex_handle Vertex_handle; |
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typedef Alpha_shape_3::Facet Facet; |
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typedef Alpha_shape_3::Edge Edge; |
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typedef CGAL::Tetrahedron_3<K> Tetrahedron; |
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|
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|
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|
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|
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using namespace oopse; |
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|
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AlphaShape::AlphaShape(){} |
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|
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|
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bool AlphaShape::genHull(std::vector<Vector3d> pos) |
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{ |
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Delaunay_hierarchy dt; |
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//points.reserve(pos.size()); |
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// Copy the positon vector into a points vector for cgal. |
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for (unsigned int i = 0; i < pos.size(); ++i) |
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{ |
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Point pt(pos[i][0],pos[i][1],pos[i][2]); |
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dt.insert(pt); |
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} |
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|
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/* Generate Alpha Shape */ |
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std::cout << "Generating alpha shape" << std::endl; |
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Alpha_shape_3 ashape(dt); |
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|
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/* |
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CGAL::Geomview_stream gv(CGAL::Bbox_3(0,0,0, 2, 2, 2)); |
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gv.set_line_width(4); |
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gv.set_trace(false); |
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gv.set_bg_color(CGAL::Color(0, 200, 200)); |
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gv.clear(); |
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*/ |
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Alpha_shape_3::NT alpha_solid = ashape.find_alpha_solid(); |
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Alpha_iterator opt = ashape.find_optimal_alpha(1); |
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std::cout << "Smallest alpha value to get a solid through data points is " |
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<< alpha_solid << std::endl; |
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std::cout << "Optimal alpha value to get one connected component is " |
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<< *opt << std::endl; |
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ashape.set_alpha(*opt); |
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assert(ashape.number_of_solid_components() == 1); |
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std::list<Cell_handle> cells; |
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std::list<Facet> facets; |
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std::list<Edge> edges; |
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std::list<Vertex_handle> vertices; |
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|
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ashape.get_alpha_shape_cells(std::back_inserter(cells), |
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Alpha_shape_3::INTERIOR); |
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ashape.get_alpha_shape_facets(std::back_inserter(facets), |
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Alpha_shape_3::REGULAR); |
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ashape.get_alpha_shape_facets(std::back_inserter(facets), |
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Alpha_shape_3::SINGULAR); |
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ashape.get_alpha_shape_edges(std::back_inserter(edges), |
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Alpha_shape_3::SINGULAR); |
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ashape.get_alpha_shape_vertices(std::back_inserter(vertices), |
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Alpha_shape_3::REGULAR); |
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std::cout << " The 0-shape has : " << std::endl; |
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std::cout << cells.size() << " interior tetrahedra" << std::endl; |
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std::cout << facets.size() << " boundary facets" << std::endl; |
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std::cout << edges.size() << " singular edges" << std::endl; |
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std::cout << vertices.size() << " singular vertices" << std::endl; |
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|
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RealType volume_; |
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std::list<Cell_handle>::iterator thiscell; |
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|
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for(Alpha_shape_3::Cell_iterator c_it = ashape.cells_begin(); c_it != ashape.cells_end(); ++c_it) |
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{ |
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volume_ += ashape.tetrahedron(c_it).volume(); |
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} |
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|
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//gv << (Delaunay) ashape; |
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//std::cout << ashape; |
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|
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} |
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|
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RealType AlphaShape::getVolume() |
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{ |
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/* |
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std::list<Point> L; |
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L.push_front(Point(0,0,0)); |
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L.push_front(Point(1,0,0)); |
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L.push_front(Point(0,1,0)); |
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|
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Triangulation T(L.begin(), L.end()); |
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|
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int n = T.number_of_vertices(); |
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|
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// insertion from a vector : |
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std::vector<Point> V(3); |
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V[0] = Point(0,0,1); |
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V[1] = Point(1,1,1); |
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V[2] = Point(2,2,2); |
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|
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n = n + T.insert(V.begin(), V.end()); |
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|
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assert( n == 6 ); // 6 points have been inserted |
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assert( T.is_valid() ); // checking validity of T |
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|
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double sum_v = 0; |
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for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it) |
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{ |
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sum_v += T.tetrahedron(c_it).volume(); |
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} |
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std::cout << "sum_v " << sum_v << std::endl; |
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*/ |
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return 0.0; |
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} |
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|
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void AlphaShape::geomviewHull(const std::string& geomFileName) |
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{ |
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/* |
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std::ofstream newGeomFile; |
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|
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//create new .md file based on old .md file |
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newGeomFile.open(geomFileName.c_str()); |
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// Write polyhedron in Object File Format (OFF). |
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CGAL::set_ascii_mode( std::cout); |
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newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' ' |
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<< ch_polyhedron.size_of_facets() << " 0" << std::endl; |
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std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(), |
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std::ostream_iterator<Point_3>( newGeomFile, "\n")); |
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for ( Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i) |
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{ |
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Halfedge_facet_circulator j = i->facet_begin(); |
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// Facets in polyhedral surfaces are at least triangles. |
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CGAL_assertion( CGAL::circulator_size(j) >= 3); |
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newGeomFile << CGAL::circulator_size(j) << ' '; |
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do |
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{ |
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newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex()); |
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} |
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while ( ++j != i->facet_begin()); |
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newGeomFile << std::endl; |
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} |
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|
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newGeomFile.close(); |
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*/ |
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|
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} |
