ENH: surfaceFeatureExtract now builds with CGAL support for curvature

extendedFeatureEdgeMesh: Add function to find all feature points within a sphere
treeDataPoint: Add support for point overlap test
This commit is contained in:
laurence
2012-03-16 11:21:43 +00:00
parent 23470c19ae
commit dbc7526abb
13 changed files with 1138 additions and 236 deletions

View File

@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011 OpenFOAM Foundation
\\ / A nd | Copyright (C) 2012 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@ -46,10 +46,263 @@ Description
#include "unitConversion.H"
#include "plane.H"
#ifdef ENABLE_CURVATURE
#include "buildCGALPolyhedron.H"
#include "CGALPolyhedronRings.H"
#include <CGAL/Monge_via_jet_fitting.h>
#include <CGAL/Lapack/Linear_algebra_lapack.h>
#include <CGAL/property_map.h>
#endif
using namespace Foam;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#ifdef ENABLE_CURVATURE
scalarField calcCurvature(const triSurface& surf)
{
scalarField k(surf.points().size(), 0);
Polyhedron P;
buildCGALPolyhedron convert(surf);
P.delegate(convert);
// Info<< "Created CGAL Polyhedron with " << label(P.size_of_vertices())
// << " vertices and " << label(P.size_of_facets())
// << " facets. " << endl;
// The rest of this function adapted from
// CGAL-3.7/examples/Jet_fitting_3/Mesh_estimation.cpp
// Licensed under CGAL-3.7/LICENSE.FREE_USE
// Copyright (c) 1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007
// Utrecht University (The Netherlands), ETH Zurich (Switzerland), Freie
// Universitaet Berlin (Germany), INRIA Sophia-Antipolis (France),
// Martin-Luther-University Halle-Wittenberg (Germany), Max-Planck-Institute
// Saarbruecken (Germany), RISC Linz (Austria), and Tel-Aviv University
// (Israel). All rights reserved.
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to permit
// persons to whom the Software is furnished to do so, subject to the
// following conditions:
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
// IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
// CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT
// OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
// THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//Vertex property map, with std::map
typedef std::map<Vertex*, int> Vertex2int_map_type;
typedef boost::associative_property_map< Vertex2int_map_type >
Vertex_PM_type;
typedef T_PolyhedralSurf_rings<Polyhedron, Vertex_PM_type > Poly_rings;
typedef CGAL::Monge_via_jet_fitting<Kernel> Monge_via_jet_fitting;
typedef Monge_via_jet_fitting::Monge_form Monge_form;
std::vector<Point_3> in_points; //container for data points
// default parameter values and global variables
unsigned int d_fitting = 2;
unsigned int d_monge = 2;
unsigned int min_nb_points = (d_fitting + 1)*(d_fitting + 2)/2;
//initialize the tag of all vertices to -1
Vertex_iterator vitb = P.vertices_begin();
Vertex_iterator vite = P.vertices_end();
Vertex2int_map_type vertex2props;
Vertex_PM_type vpm(vertex2props);
CGAL_For_all(vitb, vite)
{
put(vpm, &(*vitb), -1);
}
vite = P.vertices_end();
label vertI = 0;
for (vitb = P.vertices_begin(); vitb != vite; vitb++)
{
//initialize
Vertex* v = &(*vitb);
//gather points around the vertex using rings
// From: gather_fitting_points(v, in_points, vpm);
{
std::vector<Vertex*> gathered;
in_points.clear();
Poly_rings::collect_enough_rings(v, min_nb_points, gathered, vpm);
//store the gathered points
std::vector<Vertex*>::iterator itb = gathered.begin();
std::vector<Vertex*>::iterator ite = gathered.end();
CGAL_For_all(itb, ite)
{
in_points.push_back((*itb)->point());
}
}
//skip if the nb of points is to small
if ( in_points.size() < min_nb_points )
{
std::cerr
<< "not enough pts for fitting this vertex"
<< in_points.size()
<< std::endl;
continue;
}
// perform the fitting
Monge_via_jet_fitting monge_fit;
Monge_form monge_form = monge_fit
(
in_points.begin(),
in_points.end(),
d_fitting,
d_monge
);
// std::cout<< monge_form;;
// std::cout<< "condition number : "
// << monge_fit.condition_number() << nl << std::endl;
// Use the maximum curvature to give smaller cell sizes later.
k[vertI++]
= max
(
mag(monge_form.principal_curvatures(0)),
mag(monge_form.principal_curvatures(1))
);
}
return k;
}
#endif
bool edgesConnected(const edge& e1, const edge& e2)
{
if
(
e1.start() == e2.start() || e1.start() == e2.end()
|| e1.end() == e2.start() || e1.end() == e2.end()
)
{
return true;
}
return false;
}
scalar calcProximityOfFeaturePoints
(
const List<pointIndexHit>& hitList,
const scalar defaultCellSize
)
{
scalar minDist = defaultCellSize;
for
(
label hI1 = 0;
hI1 < hitList.size() - 1;
++hI1
)
{
const pointIndexHit& pHit1 = hitList[hI1];
if (pHit1.hit())
{
for
(
label hI2 = hI1 + 1;
hI2 < hitList.size();
++hI2
)
{
const pointIndexHit& pHit2 = hitList[hI2];
if (pHit2.hit())
{
scalar curDist = mag(pHit1.hitPoint() - pHit2.hitPoint());
minDist = min(curDist, minDist);
}
}
}
}
return minDist;
}
scalar calcProximityOfFeatureEdges
(
const extendedFeatureEdgeMesh& efem,
const List<pointIndexHit>& hitList,
const scalar defaultCellSize
)
{
scalar minDist = defaultCellSize;
for
(
label hI1 = 0;
hI1 < hitList.size() - 1;
++hI1
)
{
const pointIndexHit& pHit1 = hitList[hI1];
if (pHit1.hit())
{
const edge& e1 = efem.edges()[pHit1.index()];
for
(
label hI2 = hI1 + 1;
hI2 < hitList.size();
++hI2
)
{
const pointIndexHit& pHit2 = hitList[hI2];
if (pHit2.hit())
{
const edge& e2 = efem.edges()[pHit2.index()];
// Don't refine if the edges are connected to each other
if (!edgesConnected(e1, e2))
{
scalar curDist
= mag(pHit1.hitPoint() - pHit2.hitPoint());
minDist = min(curDist, minDist);
}
}
}
}
}
return minDist;
}
void dumpBox(const treeBoundBox& bb, const fileName& fName)
{
OFstream str(fName);
@ -299,10 +552,9 @@ int main(int argc, char *argv[])
"writeVTK",
"write extendedFeatureEdgeMesh vtk files"
);
argList::addOption
argList::addBoolOption
(
"closeness",
"scalar",
"span to look for surface closeness"
);
argList::addOption
@ -331,7 +583,7 @@ int main(int argc, char *argv[])
# ifdef ENABLE_CURVATURE
argList::addBoolOption
(
"calcCurvature",
"curvature",
"calculate curvature and closeness fields"
);
# endif
@ -527,6 +779,7 @@ int main(int argc, char *argv[])
<< " will be included as feature edges."<< endl;
}
surfaceFeatures newSet(surf);
newSet.setFromStatus(edgeStat);
@ -564,7 +817,6 @@ int main(int argc, char *argv[])
feMesh.write();
// Write a featureEdgeMesh for backwards compatibility
{
featureEdgeMesh bfeMesh
@ -595,7 +847,7 @@ int main(int argc, char *argv[])
(
sFeatFileName + ".closeness",
runTime.constant(),
"extendedFeatureEdgeMesh",
"triSurface",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
@ -603,13 +855,6 @@ int main(int argc, char *argv[])
surf
);
if (!curvature)
{
Info<< "End\n" << endl;
return 0;
}
// Find close features
// // Dummy trim operation to mark features
@ -677,70 +922,56 @@ int main(int argc, char *argv[])
// )
// );
Info<< "Examine curvature, feature proximity and internal and "
<< "external closeness." << endl;
// Internal and external closeness
// Prepare start and end points for intersection tests
const vectorField& normals = searchSurf.faceNormals();
scalar span = searchSurf.bounds().mag();
args.optionReadIfPresent("closeness", span);
scalar externalAngleTolerance = 10;
scalar externalToleranceCosAngle = Foam::cos
(
degToRad(180 - externalAngleTolerance)
);
scalar internalAngleTolerance = 45;
scalar internalToleranceCosAngle = Foam::cos
(
degToRad(180 - internalAngleTolerance)
);
Info<< "externalToleranceCosAngle: " << externalToleranceCosAngle << nl
<< "internalToleranceCosAngle: " << internalToleranceCosAngle
<< endl;
// Info<< "span " << span << endl;
pointField start = searchSurf.faceCentres() - span*normals;
pointField end = searchSurf.faceCentres() + span*normals;
const pointField& faceCentres = searchSurf.faceCentres();
List<List<pointIndexHit> > allHitInfo;
// Find all intersections (in order)
searchSurf.findLineAll(start, end, allHitInfo);
scalarField internalCloseness(start.size(), GREAT);
scalarField externalCloseness(start.size(), GREAT);
forAll(allHitInfo, fI)
if (args.optionFound("closeness"))
{
const List<pointIndexHit>& hitInfo = allHitInfo[fI];
Info<< nl << "Extracting internal and external closeness of surface."
<< endl;
if (hitInfo.size() < 1)
{
drawHitProblem(fI, surf, start, faceCentres, end, hitInfo);
// Internal and external closeness
// FatalErrorIn(args.executable())
// << "findLineAll did not hit its own face."
// << exit(FatalError);
}
else if (hitInfo.size() == 1)
// Prepare start and end points for intersection tests
const vectorField& normals = searchSurf.faceNormals();
scalar span = searchSurf.bounds().mag();
//args.optionReadIfPresent("closeness", span);
scalar externalAngleTolerance = 10;
scalar externalToleranceCosAngle = Foam::cos
(
degToRad(180 - externalAngleTolerance)
);
scalar internalAngleTolerance = 45;
scalar internalToleranceCosAngle = Foam::cos
(
degToRad(180 - internalAngleTolerance)
);
Info<< "externalToleranceCosAngle: " << externalToleranceCosAngle << nl
<< "internalToleranceCosAngle: " << internalToleranceCosAngle
<< endl;
// Info<< "span " << span << endl;
pointField start = searchSurf.faceCentres() - span*normals;
pointField end = searchSurf.faceCentres() + span*normals;
const pointField& faceCentres = searchSurf.faceCentres();
List<List<pointIndexHit> > allHitInfo;
// Find all intersections (in order)
searchSurf.findLineAll(start, end, allHitInfo);
scalarField internalCloseness(start.size(), GREAT);
scalarField externalCloseness(start.size(), GREAT);
forAll(allHitInfo, fI)
{
if (!hitInfo[0].hit())
{
// FatalErrorIn(args.executable())
// << "findLineAll did not hit any face."
// << exit(FatalError);
}
else if (hitInfo[0].index() != fI)
const List<pointIndexHit>& hitInfo = allHitInfo[fI];
if (hitInfo.size() < 1)
{
drawHitProblem(fI, surf, start, faceCentres, end, hitInfo);
@ -748,202 +979,299 @@ int main(int argc, char *argv[])
// << "findLineAll did not hit its own face."
// << exit(FatalError);
}
}
else
{
label ownHitI = -1;
forAll(hitInfo, hI)
else if (hitInfo.size() == 1)
{
// Find the hit on the triangle that launched the ray
if (hitInfo[hI].index() == fI)
if (!hitInfo[0].hit())
{
ownHitI = hI;
break;
// FatalErrorIn(args.executable())
// << "findLineAll did not hit any face."
// << exit(FatalError);
}
}
if (ownHitI < 0)
{
drawHitProblem(fI, surf, start, faceCentres, end, hitInfo);
// FatalErrorIn(args.executable())
// << "findLineAll did not hit its own face."
// << exit(FatalError);
}
else if (ownHitI == 0)
{
// There are no internal hits, the first hit is the closest
// external hit
if
(
(normals[fI] & normals[hitInfo[ownHitI + 1].index()])
< externalToleranceCosAngle
)
else if (hitInfo[0].index() != fI)
{
externalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI + 1].hitPoint()
);
}
}
else if (ownHitI == hitInfo.size() - 1)
{
// There are no external hits, the last but one hit is the
// closest internal hit
drawHitProblem(fI, surf, start, faceCentres, end, hitInfo);
if
(
(normals[fI] & normals[hitInfo[ownHitI - 1].index()])
< internalToleranceCosAngle
)
{
internalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI - 1].hitPoint()
);
// FatalErrorIn(args.executable())
// << "findLineAll did not hit its own face."
// << exit(FatalError);
}
}
else
{
if
(
(normals[fI] & normals[hitInfo[ownHitI + 1].index()])
< externalToleranceCosAngle
)
label ownHitI = -1;
forAll(hitInfo, hI)
{
externalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI + 1].hitPoint()
);
// Find the hit on the triangle that launched the ray
if (hitInfo[hI].index() == fI)
{
ownHitI = hI;
break;
}
}
if
(
(normals[fI] & normals[hitInfo[ownHitI - 1].index()])
< internalToleranceCosAngle
)
if (ownHitI < 0)
{
internalCloseness[fI] = mag
drawHitProblem(fI, surf, start, faceCentres, end, hitInfo);
// FatalErrorIn(args.executable())
// << "findLineAll did not hit its own face."
// << exit(FatalError);
}
else if (ownHitI == 0)
{
// There are no internal hits, the first hit is the closest
// external hit
if
(
faceCentres[fI] - hitInfo[ownHitI - 1].hitPoint()
);
(normals[fI] & normals[hitInfo[ownHitI + 1].index()])
< externalToleranceCosAngle
)
{
externalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI + 1].hitPoint()
);
}
}
else if (ownHitI == hitInfo.size() - 1)
{
// There are no external hits, the last but one hit is the
// closest internal hit
if
(
(normals[fI] & normals[hitInfo[ownHitI - 1].index()])
< internalToleranceCosAngle
)
{
internalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI - 1].hitPoint()
);
}
}
else
{
if
(
(normals[fI] & normals[hitInfo[ownHitI + 1].index()])
< externalToleranceCosAngle
)
{
externalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI + 1].hitPoint()
);
}
if
(
(normals[fI] & normals[hitInfo[ownHitI - 1].index()])
< internalToleranceCosAngle
)
{
internalCloseness[fI] = mag
(
faceCentres[fI] - hitInfo[ownHitI - 1].hitPoint()
);
}
}
}
}
triSurfaceScalarField internalClosenessField
(
IOobject
(
sFeatFileName + ".internalCloseness",
runTime.constant(),
"triSurface",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
internalCloseness
);
internalClosenessField.write();
triSurfaceScalarField externalClosenessField
(
IOobject
(
sFeatFileName + ".externalCloseness",
runTime.constant(),
"triSurface",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
externalCloseness
);
externalClosenessField.write();
if (writeVTK)
{
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"internalCloseness", // fieldName
internalCloseness,
false, // isNodeValues
true // verbose
);
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"externalCloseness", // fieldName
externalCloseness,
false, // isNodeValues
true // verbose
);
}
}
triSurfaceScalarField internalClosenessField
(
IOobject
(
sFeatFileName + ".internalCloseness",
runTime.constant(),
"extendedFeatureEdgeMesh",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
internalCloseness
);
internalClosenessField.write();
triSurfaceScalarField externalClosenessField
(
IOobject
(
sFeatFileName + ".externalCloseness",
runTime.constant(),
"extendedFeatureEdgeMesh",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
externalCloseness
);
externalClosenessField.write();
#ifdef ENABLE_CURVATURE
scalarField k = calcCurvature(surf);
// Modify the curvature values on feature edges and points to be zero.
forAll(newSet.featureEdges(), fEI)
if (args.optionFound("curvature"))
{
const edge& e = surf.edges()[newSet.featureEdges()[fEI]];
Info<< nl << "Extracting curvature of surface at the points." << endl;
k[surf.meshPoints()[e.start()]] = 0.0;
k[surf.meshPoints()[e.end()]] = 0.0;
}
scalarField k = calcCurvature(surf);
triSurfacePointScalarField kField
(
IOobject
// Modify the curvature values on feature edges and points to be zero.
// forAll(newSet.featureEdges(), fEI)
// {
// const edge& e = surf.edges()[newSet.featureEdges()[fEI]];
//
// k[surf.meshPoints()[e.start()]] = 0.0;
// k[surf.meshPoints()[e.end()]] = 0.0;
// }
triSurfacePointScalarField kField
(
sFeatFileName + ".curvature",
runTime.constant(),
"extendedFeatureEdgeMesh",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
k
);
IOobject
(
sFeatFileName + ".curvature",
runTime.constant(),
"triSurface",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
k
);
kField.write();
kField.write();
if (writeVTK)
{
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"curvature", // fieldName
k,
true, // isNodeValues
true // verbose
);
}
}
#endif
if (writeVTK)
if (args.optionFound("featureProximity"))
{
vtkSurfaceWriter().write
Info<< nl << "Extracting proximity of close feature points and edges "
<< "to the surface" << endl;
const scalar searchDistance =
args.optionRead<scalar>("featureProximity");
const scalar radiusSqr = sqr(searchDistance);
scalarField featureProximity(surf.size(), searchDistance);
forAll(surf, fI)
{
const triPointRef& tri = surf[fI].tri(surf.points());
const point& triCentre = tri.circumCentre();
List<pointIndexHit> hitList;
feMesh.allNearestFeatureEdges(triCentre, radiusSqr, hitList);
featureProximity[fI] =
calcProximityOfFeatureEdges
(
feMesh,
hitList,
featureProximity[fI]
);
feMesh.allNearestFeaturePoints(triCentre, radiusSqr, hitList);
featureProximity[fI] =
calcProximityOfFeaturePoints
(
hitList,
featureProximity[fI]
);
}
triSurfaceScalarField featureProximityField
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"internalCloseness", // fieldName
internalCloseness,
false, // isNodeValues
true // verbose
IOobject
(
sFeatFileName + ".featureProximity",
runTime.constant(),
"triSurface",
runTime,
IOobject::NO_READ,
IOobject::NO_WRITE
),
surf,
dimLength,
featureProximity
);
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"externalCloseness", // fieldName
externalCloseness,
false, // isNodeValues
true // verbose
);
featureProximityField.write();
# ifdef ENABLE_CURVATURE
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"curvature", // fieldName
k,
true, // isNodeValues
true // verbose
);
# endif
if (writeVTK)
{
vtkSurfaceWriter().write
(
runTime.constant()/"triSurface", // outputDir
sFeatFileName, // surfaceName
surf.points(),
faces,
"featureProximity", // fieldName
featureProximity,
false, // isNodeValues
true // verbose
);
}
}
Info<< "End\n" << endl;