src/math/AlphaShape.cpp

/* Copyright (c) 2007 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 *
 *  AlphaShape.cpp
 *
 *  Purpose: To calculate convexhull, hull volume and radius
 *  using the CGAL library.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: AlphaShape.cpp,v 1.1 2007-12-07 00:48:47 chuckv Exp $
 *
 */

#include "math/AlphaShape.hpp"

#include <iostream>
#include <list>
#include <fstream>
#include <CGAL/IO/alpha_shape_geomview_ostream_3.h>

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Delaunay_triangulation_3.h>
#include <CGAL/Triangulation_hierarchy_3.h>
#include <CGAL/Alpha_shape_3.h>


 struct K : CGAL::Exact_predicates_inexact_constructions_kernel {};

 typedef CGAL::Alpha_shape_vertex_base_3<K>               Vb;
 typedef CGAL::Triangulation_hierarchy_vertex_base_3<Vb>  Vbh;
 typedef CGAL::Alpha_shape_cell_base_3<K>                 Fb;
 typedef CGAL::Triangulation_data_structure_3<Vbh,Fb>     Tds;
 typedef CGAL::Delaunay_triangulation_3<K,Tds>            Delaunay;
 typedef CGAL::Triangulation_hierarchy_3<Delaunay>        Delaunay_hierarchy;
 typedef CGAL::Alpha_shape_3<Delaunay_hierarchy>          Alpha_shape_3;

 typedef K::Point_3                                  Point;
 typedef Alpha_shape_3::Alpha_iterator               Alpha_iterator;
 typedef Alpha_shape_3::NT                           NT;


using namespace oopse;

AlphaShape::AlphaShape(){}


bool AlphaShape::genHull(std::vector<Vector3d> pos)
{
  Delaunay_hierarchy dt;
  //points.reserve(pos.size());
  // Copy the positon vector into a points vector for cgal.
  for (int i = 0; i < pos.size(); ++i)
    {
      Point pt(pos[i][0],pos[i][1],pos[i][2]);
      dt.insert(pt);
    }

  /* Generate Alpha Shape */

  Alpha_shape_3 ashape(dt);
  
   
  /*CGAL::Geomview_stream gv(CGAL::Bbox_3(0,0,0, 2, 2, 2));
  gv.set_line_width(4);
  gv.set_trace(false);
  gv.set_bg_color(CGAL::Color(0, 200, 200));
  gv.clear();*/
  std::cout << ashape;
}

RealType AlphaShape::getVolume()
{
        /*
  std::list<Point> L;
  L.push_front(Point(0,0,0));
  L.push_front(Point(1,0,0));
  L.push_front(Point(0,1,0));

  Triangulation T(L.begin(), L.end());

  int n = T.number_of_vertices();

  // insertion from a vector :
  std::vector<Point> V(3);
  V[0] = Point(0,0,1);
  V[1] = Point(1,1,1);
  V[2] = Point(2,2,2);

  n = n + T.insert(V.begin(), V.end());

  assert( n == 6 );       // 6 points have been inserted
  assert( T.is_valid() ); // checking validity of T

  double sum_v = 0;
  for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
    {
      sum_v += T.tetrahedron(c_it).volume();
    }
  std::cout << "sum_v " << sum_v << std::endl;
*/
        return 0.0;
}

void AlphaShape::geomviewHull(const std::string& geomFileName)
{
/*
  std::ofstream newGeomFile;

  //create new .md file based on old .md file
  newGeomFile.open(geomFileName.c_str());

  // Write polyhedron in Object File Format (OFF).
  CGAL::set_ascii_mode( std::cout);
  newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
  << ch_polyhedron.size_of_facets() << " 0" << std::endl;
  std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
             std::ostream_iterator<Point_3>( newGeomFile, "\n"));
  for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
    {
      Halfedge_facet_circulator j = i->facet_begin();
      // Facets in polyhedral surfaces are at least triangles.
      CGAL_assertion( CGAL::circulator_size(j) >= 3);
      newGeomFile << CGAL::circulator_size(j) << ' ';
      do
        {
          newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
        }
      while ( ++j != i->facet_begin());
      newGeomFile << std::endl;
    }

  newGeomFile.close();
*/

}
Revision:	3293
Committed:	Fri Dec 7 00:48:47 2007 UTC (17 years, 11 months ago) by chuckv
File size:	5858 byte(s)
Log Message:	Initial code for AlphaShape.
#	User	Rev	Content
1	chuckv	3293	/* Copyright (c) 2007 The University of Notre Dame. All Rights Reserved.
2			*
3			* The University of Notre Dame grants you ("Licensee") a
4			* non-exclusive, royalty free, license to use, modify and
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8			* 1. Acknowledgement of the program authors must be made in any
9			* publication of scientific results based in part on use of the
10			* program. An acceptable form of acknowledgement is citation of
11			* the article in which the program was described (Matthew
12			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14			* Parallel Simulation Engine for Molecular Dynamics,"
15			* J. Comput. Chem. 26, pp. 252-271 (2005))
16			*
17			* 2. Redistributions of source code must retain the above copyright
18			* notice, this list of conditions and the following disclaimer.
19			*
20			* 3. Redistributions in binary form must reproduce the above copyright
21			* notice, this list of conditions and the following disclaimer in the
22			* documentation and/or other materials provided with the
23			* distribution.
24			*
25			* This software is provided "AS IS," without a warranty of any
26			* kind. All express or implied conditions, representations and
27			* warranties, including any implied warranty of merchantability,
28			* fitness for a particular purpose or non-infringement, are hereby
29			* excluded. The University of Notre Dame and its licensors shall not
30			* be liable for any damages suffered by licensee as a result of
31			* using, modifying or distributing the software or its
32			* derivatives. In no event will the University of Notre Dame or its
33			* licensors be liable for any lost revenue, profit or data, or for
34			* direct, indirect, special, consequential, incidental or punitive
35			* damages, however caused and regardless of the theory of liability,
36			* arising out of the use of or inability to use software, even if the
37			* University of Notre Dame has been advised of the possibility of
38			* such damages.
39			*
40			*
41			* AlphaShape.cpp
42			*
43			* Purpose: To calculate convexhull, hull volume and radius
44			* using the CGAL library.
45			*
46			* Created by Charles F. Vardeman II on 11 Dec 2006.
47			* @author Charles F. Vardeman II
48			* @version $Id: AlphaShape.cpp,v 1.1 2007-12-07 00:48:47 chuckv Exp $
49			*
50			*/
51
52			#include "math/AlphaShape.hpp"
53
54			#include <iostream>
55			#include <list>
56			#include <fstream>
57			#include <CGAL/IO/alpha_shape_geomview_ostream_3.h>
58
59			#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
60			#include <CGAL/Delaunay_triangulation_3.h>
61			#include <CGAL/Triangulation_hierarchy_3.h>
62			#include <CGAL/Alpha_shape_3.h>
63
64
65			struct K : CGAL::Exact_predicates_inexact_constructions_kernel {};
66
67			typedef CGAL::Alpha_shape_vertex_base_3<K> Vb;
68			typedef CGAL::Triangulation_hierarchy_vertex_base_3<Vb> Vbh;
69			typedef CGAL::Alpha_shape_cell_base_3<K> Fb;
70			typedef CGAL::Triangulation_data_structure_3<Vbh,Fb> Tds;
71			typedef CGAL::Delaunay_triangulation_3<K,Tds> Delaunay;
72			typedef CGAL::Triangulation_hierarchy_3<Delaunay> Delaunay_hierarchy;
73			typedef CGAL::Alpha_shape_3<Delaunay_hierarchy> Alpha_shape_3;
74
75			typedef K::Point_3 Point;
76			typedef Alpha_shape_3::Alpha_iterator Alpha_iterator;
77			typedef Alpha_shape_3::NT NT;
78
79
80
81
82
83			using namespace oopse;
84
85			AlphaShape::AlphaShape(){}
86
87
88			bool AlphaShape::genHull(std::vector<Vector3d> pos)
89			{
90			Delaunay_hierarchy dt;
91			//points.reserve(pos.size());
92			// Copy the positon vector into a points vector for cgal.
93			for (int i = 0; i < pos.size(); ++i)
94			{
95			Point pt(pos[i][0],pos[i][1],pos[i][2]);
96			dt.insert(pt);
97			}
98
99			/* Generate Alpha Shape */
100
101			Alpha_shape_3 ashape(dt);
102
103
104			/*CGAL::Geomview_stream gv(CGAL::Bbox_3(0,0,0, 2, 2, 2));
105			gv.set_line_width(4);
106			gv.set_trace(false);
107			gv.set_bg_color(CGAL::Color(0, 200, 200));
108			gv.clear();*/
109			std::cout << ashape;
110			}
111
112			RealType AlphaShape::getVolume()
113			{
114			/*
115			std::list<Point> L;
116			L.push_front(Point(0,0,0));
117			L.push_front(Point(1,0,0));
118			L.push_front(Point(0,1,0));
119
120			Triangulation T(L.begin(), L.end());
121
122			int n = T.number_of_vertices();
123
124			// insertion from a vector :
125			std::vector<Point> V(3);
126			V[0] = Point(0,0,1);
127			V[1] = Point(1,1,1);
128			V[2] = Point(2,2,2);
129
130			n = n + T.insert(V.begin(), V.end());
131
132			assert( n == 6 ); // 6 points have been inserted
133			assert( T.is_valid() ); // checking validity of T
134
135			double sum_v = 0;
136			for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
137			{
138			sum_v += T.tetrahedron(c_it).volume();
139			}
140			std::cout << "sum_v " << sum_v << std::endl;
141			*/
142			return 0.0;
143			}
144
145			void AlphaShape::geomviewHull(const std::string& geomFileName)
146			{
147			/*
148			std::ofstream newGeomFile;
149
150			//create new .md file based on old .md file
151			newGeomFile.open(geomFileName.c_str());
152
153			// Write polyhedron in Object File Format (OFF).
154			CGAL::set_ascii_mode( std::cout);
155			newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
156			<< ch_polyhedron.size_of_facets() << " 0" << std::endl;
157			std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
158			std::ostream_iterator<Point_3>( newGeomFile, "\n"));
159			for ( Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
160			{
161			Halfedge_facet_circulator j = i->facet_begin();
162			// Facets in polyhedral surfaces are at least triangles.
163			CGAL_assertion( CGAL::circulator_size(j) >= 3);
164			newGeomFile << CGAL::circulator_size(j) << ' ';
165			do
166			{
167			newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
168			}
169			while ( ++j != i->facet_begin());
170			newGeomFile << std::endl;
171			}
172
173			newGeomFile.close();
174			*/
175
176			}