/***************************************************************************
 *   Copyright (c) 2005 Imetric 3D GmbH                                    *
 *                                                                         *
 *   This file is part of the FreeCAD CAx development system.              *
 *                                                                         *
 *   This library is free software; you can redistribute it and/or         *
 *   modify it under the terms of the GNU Library General Public           *
 *   License as published by the Free Software Foundation; either          *
 *   version 2 of the License, or (at your option) any later version.      *
 *                                                                         *
 *   This library  is distributed in the hope that it will be useful,      *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU Library General Public License for more details.                  *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this library; see the file COPYING.LIB. If not,    *
 *   write to the Free Software Foundation, Inc., 59 Temple Place,         *
 *   Suite 330, Boston, MA  02111-1307, USA                                *
 *                                                                         *
 ***************************************************************************/


#include "PreCompiled.h"

#ifndef _PreComp_
# include <algorithm>
# include <vector>
#endif

#include <Mod/Mesh/App/WildMagic4/Wm4Matrix3.h>
#include <Mod/Mesh/App/WildMagic4/Wm4Vector3.h>

#include "Evaluation.h"
#include "Iterator.h"
#include "Algorithm.h"
#include "Approximation.h"
#include "MeshIO.h"
#include "Helpers.h"
#include "Grid.h"
#include "TopoAlgorithm.h"
#include <Base/Matrix.h>

#include <Base/Sequencer.h>

using namespace MeshCore;


MeshOrientationVisitor::MeshOrientationVisitor() : _nonuniformOrientation(false)
{
}

bool MeshOrientationVisitor::Visit (const MeshFacet &rclFacet, const MeshFacet &rclFrom, 
                                    unsigned long ulFInd, unsigned long ulLevel)
{
    if (!rclFrom.HasSameOrientation(rclFacet)) {
        _nonuniformOrientation = true;
        return false;
    }

    return true;
}

bool MeshOrientationVisitor::HasNonUnifomOrientedFacets() const
{
    return _nonuniformOrientation;
}

MeshOrientationCollector::MeshOrientationCollector(std::vector<unsigned long>& aulIndices, std::vector<unsigned long>& aulComplement)
 : _aulIndices(aulIndices), _aulComplement(aulComplement)
{
}

bool MeshOrientationCollector::Visit (const MeshFacet &rclFacet, const MeshFacet &rclFrom, 
                                      unsigned long ulFInd, unsigned long ulLevel)
{
    // different orientation of rclFacet and rclFrom
    if (!rclFacet.HasSameOrientation(rclFrom)) {
        // is not marked as false oriented
        if (!rclFrom.IsFlag(MeshFacet::TMP0)) {
            // mark this facet as false oriented
            rclFacet.SetFlag(MeshFacet::TMP0);
            _aulIndices.push_back( ulFInd );
        }
        else
            _aulComplement.push_back( ulFInd );
    }
    else {
        // same orientation but if the neighbour rclFrom is false oriented
        // then rclFrom is also false oriented
        if (rclFrom.IsFlag(MeshFacet::TMP0)) {
            // mark this facet as false oriented
            rclFacet.SetFlag(MeshFacet::TMP0);
            _aulIndices.push_back(ulFInd);
        }
        else
            _aulComplement.push_back( ulFInd );
    }

    return true;
}

MeshSameOrientationCollector::MeshSameOrientationCollector(std::vector<unsigned long>& aulIndices)
  : _aulIndices(aulIndices)
{
}

bool MeshSameOrientationCollector::Visit (const MeshFacet &rclFacet, const MeshFacet &rclFrom, 
                                          unsigned long ulFInd, unsigned long ulLevel)
{
    // different orientation of rclFacet and rclFrom
    if (rclFacet.HasSameOrientation(rclFrom)) {
        _aulIndices.push_back(ulFInd);
    }

    return true;
}

// ----------------------------------------------------

MeshEvalOrientation::MeshEvalOrientation (const MeshKernel& rclM)
  : MeshEvaluation( rclM )
{
}

MeshEvalOrientation::~MeshEvalOrientation()
{
}

bool MeshEvalOrientation::Evaluate ()
{
    const MeshFacetArray& rFAry = _rclMesh.GetFacets();
    MeshFacetArray::_TConstIterator iBeg = rFAry.begin();
    MeshFacetArray::_TConstIterator iEnd = rFAry.end();
    for (MeshFacetArray::_TConstIterator it = iBeg; it != iEnd; ++it) {
        for (int i = 0; i < 3; i++) {
            if (it->_aulNeighbours[i] != ULONG_MAX) {
                const MeshFacet& rclFacet = iBeg[it->_aulNeighbours[i]];
                for (int j = 0; j < 3; j++) {
                    if (it->_aulPoints[i] == rclFacet._aulPoints[j]) {
                        if ((it->_aulPoints[(i+1)%3] == rclFacet._aulPoints[(j+1)%3]) ||
                            (it->_aulPoints[(i+2)%3] == rclFacet._aulPoints[(j+2)%3])) {
                            return false; // adjacent face with wrong orientation
                        } 
                    }
                }
            }
        }
    }

    return true;
}

unsigned long MeshEvalOrientation::HasFalsePositives(const std::vector<unsigned long>& inds) const
{
    // All faces with wrong orientation (i.e. adjacent faces with a normal flip and their neighbours)
    // build a segment and are marked as TMP0. Now we check all border faces of the segments with 
    // their correct neighbours if there was really a normal flip. If there is no normal flip we have
    // a false positive.
    // False-positives can occur if the mesh structure has some defects which let the region-grow
    // algorithm fail to detect the faces with wrong orientation.
    const MeshFacetArray& rFAry = _rclMesh.GetFacets();
    MeshFacetArray::_TConstIterator iBeg = rFAry.begin();
    for (std::vector<unsigned long>::const_iterator it = inds.begin(); it != inds.end(); ++it) {
        const MeshFacet& f = iBeg[*it];
        for (int i = 0; i < 3; i++) {
            if (f._aulNeighbours[i] != ULONG_MAX) {
                const MeshFacet& n = iBeg[f._aulNeighbours[i]];
                if (f.IsFlag(MeshFacet::TMP0) && !n.IsFlag(MeshFacet::TMP0)) {
                    for (int j = 0; j < 3; j++) {
                        if (f.HasSameOrientation(n)) {
                            // adjacent face with same orientation => false positive
                            return f._aulNeighbours[i];
                        }
                    }
                }
            }
        }
    }

    return ULONG_MAX;
}

std::vector<unsigned long> MeshEvalOrientation::GetIndices() const
{
    unsigned long ulStartFacet, ulVisited;

    if (_rclMesh.CountFacets() == 0)
        return std::vector<unsigned long>();

    // reset VISIT flags
    MeshAlgorithm cAlg(_rclMesh);
    cAlg.ResetFacetFlag(MeshFacet::VISIT);
    cAlg.ResetFacetFlag(MeshFacet::TMP0);

    const MeshFacetArray& rFAry = _rclMesh.GetFacets();
    MeshFacetArray::_TConstIterator iTri = rFAry.begin();
    MeshFacetArray::_TConstIterator iBeg = rFAry.begin();
    MeshFacetArray::_TConstIterator iEnd = rFAry.end();

    ulVisited = 0;
    ulStartFacet = 0;

    std::vector<unsigned long> uIndices, uComplement;
    MeshOrientationCollector clHarmonizer(uIndices, uComplement);

    while (ulStartFacet !=  ULONG_MAX) {
        unsigned long wrongFacets = uIndices.size();

        uComplement.clear();
        uComplement.push_back( ulStartFacet );
        ulVisited = _rclMesh.VisitNeighbourFacets(clHarmonizer, ulStartFacet) + 1;

        // In the currently visited component we have found less than 40% as correct
        // oriented and the rest as false oriented. So, we decide that it should be the other
        // way round and swap the indices of this component.
        if (uComplement.size() < (unsigned long)(0.4f*(float)ulVisited)) {
            uIndices.erase(uIndices.begin()+wrongFacets, uIndices.end());
            uIndices.insert(uIndices.end(), uComplement.begin(), uComplement.end());
        }

        // if the mesh consists of several topologic independent components
        // We can search from position 'iTri' on because all elements _before_ are already visited
        // what we know from the previous iteration.
        iTri = std::find_if(iTri, iEnd, std::bind2nd(MeshIsNotFlag<MeshFacet>(), MeshFacet::VISIT));

        if (iTri < iEnd)
            ulStartFacet = iTri - iBeg;
        else
            ulStartFacet = ULONG_MAX;
    }

    // in some very rare cases where we have some strange artefacts in the mesh structure
    // we get false-positives. If we find some we check all 'invalid' faces again
    cAlg.ResetFacetFlag(MeshFacet::TMP0);
    cAlg.SetFacetsFlag(uIndices, MeshFacet::TMP0);
    ulStartFacet = HasFalsePositives(uIndices);
    while (ulStartFacet != ULONG_MAX) {
        cAlg.ResetFacetsFlag(uIndices, MeshFacet::VISIT);
        std::vector<unsigned long> falsePos;
        MeshSameOrientationCollector coll(falsePos);
        _rclMesh.VisitNeighbourFacets(coll, ulStartFacet);

        std::sort(uIndices.begin(), uIndices.end());
        std::sort(falsePos.begin(), falsePos.end());

        std::vector<unsigned long> diff;
        std::back_insert_iterator<std::vector<unsigned long> > biit(diff);
        std::set_difference(uIndices.begin(), uIndices.end(), falsePos.begin(), falsePos.end(), biit);
        uIndices = diff;

        cAlg.ResetFacetFlag(MeshFacet::TMP0);
        cAlg.SetFacetsFlag(uIndices, MeshFacet::TMP0);
        unsigned long current = ulStartFacet;
        ulStartFacet = HasFalsePositives(uIndices);
        if (current == ulStartFacet)
            break; // avoid an endless loop
    }

    return uIndices;
}

MeshFixOrientation::MeshFixOrientation (MeshKernel& rclM)
  : MeshValidation( rclM )
{
}

MeshFixOrientation::~MeshFixOrientation()
{
}

bool MeshFixOrientation::Fixup ()
{
    MeshTopoAlgorithm(_rclMesh).HarmonizeNormals();
    return MeshEvalOrientation(_rclMesh).Evaluate();
}

// ----------------------------------------------------

MeshEvalSolid::MeshEvalSolid (const MeshKernel& rclM)
  :MeshEvaluation( rclM )
{
}

MeshEvalSolid::~MeshEvalSolid()
{
}

bool MeshEvalSolid::Evaluate ()
{
  std::vector<MeshGeomEdge> edges;
  _rclMesh.GetEdges( edges );
  for (std::vector<MeshGeomEdge>::iterator it = edges.begin(); it != edges.end(); it++)
  {
    if (it->_bBorder)
      return false;
  }

  return true;
}

// ----------------------------------------------------

namespace MeshCore {

struct Edge_Index
{
    unsigned long p0, p1, f;
};

struct Edge_Less  : public std::binary_function<const Edge_Index&, 
                                                const Edge_Index&, bool>
{
    bool operator()(const Edge_Index& x, const Edge_Index& y) const
    {
        if (x.p0 < y.p0)
            return true;
        else if (x.p0 > y.p0)
            return false;
        else if (x.p1 < y.p1)
            return true;
        else if (x.p1 > y.p1)
            return false;
        return false;
    }
};

}

bool MeshEvalTopology::Evaluate ()
{
    // Using and sorting a vector seems to be faster and more memory-efficient
    // than a map.
    const MeshFacetArray& rclFAry = _rclMesh.GetFacets();
    std::vector<Edge_Index> edges;
    edges.reserve(3*rclFAry.size());

    // build up an array of edges
    MeshFacetArray::_TConstIterator pI;
    Base::SequencerLauncher seq("Checking topology...", rclFAry.size());
    for (pI = rclFAry.begin(); pI != rclFAry.end(); pI++) {
        for (int i = 0; i < 3; i++) {
            Edge_Index item;
            item.p0 = std::min<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.p1 = std::max<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.f  = pI - rclFAry.begin();
            edges.push_back(item);
        }

        seq.next();
    }

    // sort the edges
    std::sort(edges.begin(), edges.end(), Edge_Less());

    // search for non-manifold edges
    unsigned long p0 = ULONG_MAX, p1 = ULONG_MAX;
    nonManifoldList.clear();
    nonManifoldFacets.clear();

    int count = 0;
    std::vector<unsigned long> facets;
    std::vector<Edge_Index>::iterator pE;
    for (pE = edges.begin(); pE != edges.end(); pE++) {
        if (p0 == pE->p0 && p1 == pE->p1) {
            count++;
            facets.push_back(pE->f);
        }
        else {
            if (count > 2) {
                // Edge that is shared by more than 2 facets
                nonManifoldList.push_back(std::make_pair
                    <unsigned long, unsigned long>(p0, p1));
                nonManifoldFacets.push_back(facets);
            }

            p0 = pE->p0;
            p1 = pE->p1;
            facets.clear();
            facets.push_back(pE->f);
            count = 1;
        }
    }

    return nonManifoldList.empty();
}

// generate indexed edge list which tangents non-manifolds
void MeshEvalTopology::GetFacetManifolds (std::vector<unsigned long> &raclFacetIndList) const
{
    raclFacetIndList.clear();
    const MeshFacetArray& rclFAry = _rclMesh.GetFacets();
    MeshFacetArray::_TConstIterator pI;

    for (pI = rclFAry.begin(); pI != rclFAry.end(); pI++) {
        for (int i = 0; i < 3; i++) {
            unsigned long ulPt0 = std::min<unsigned long>(pI->_aulPoints[i],  pI->_aulPoints[(i+1)%3]);
            unsigned long ulPt1 = std::max<unsigned long>(pI->_aulPoints[i],  pI->_aulPoints[(i+1)%3]);
            std::pair<unsigned long, unsigned long> edge = std::make_pair<unsigned long, unsigned long>(ulPt0, ulPt1);

            if (std::find(nonManifoldList.begin(), nonManifoldList.end(), edge) != nonManifoldList.end())
                raclFacetIndList.push_back(pI - rclFAry.begin());
        }
    }
}

unsigned long MeshEvalTopology::CountManifolds() const
{
    return nonManifoldList.size();
}

bool MeshFixTopology::Fixup ()
{
    std::vector<unsigned long> indices;
#if 0
    MeshEvalTopology eval(_rclMesh);
    if (!eval.Evaluate()) {
        eval.GetFacetManifolds(indices);

        // remove duplicates
        std::sort(indices.begin(), indices.end());
        indices.erase(std::unique(indices.begin(), indices.end()), indices.end());

        _rclMesh.DeleteFacets(indices);
    }
#else
    const MeshFacetArray& rFaces = _rclMesh.GetFacets();
    indices.reserve(3 * nonManifoldList.size()); // allocate some memory
    std::list<std::vector<unsigned long> >::const_iterator it;
    for (it = nonManifoldList.begin(); it != nonManifoldList.end(); ++it) {
        std::vector<unsigned long> non_mf;
        non_mf.reserve(it->size());
        for (std::vector<unsigned long>::const_iterator jt = it->begin(); jt != it->end(); ++jt) {
            // fscet is only connected with one edge and there causes a non-manifold
            unsigned short numOpenEdges = rFaces[*jt].CountOpenEdges();
            if (numOpenEdges == 2)
                non_mf.push_back(*jt);
            else if (rFaces[*jt].IsDegenerated())
                non_mf.push_back(*jt);
        }

        // are we able to repair the non-manifold edge by not removing all facets?
        if (it->size() - non_mf.size() == 2)
            indices.insert(indices.end(), non_mf.begin(), non_mf.end());
        else
            indices.insert(indices.end(), it->begin(), it->end());
    }

    if (!indices.empty()) {
        // remove duplicates
        std::sort(indices.begin(), indices.end());
        indices.erase(std::unique(indices.begin(), indices.end()), indices.end());

        _rclMesh.DeleteFacets(indices);
        _rclMesh.RebuildNeighbours();
    }
#endif

    return true;
}

// ---------------------------------------------------------

bool MeshEvalSingleFacet::Evaluate ()
{
  // get all non-manifolds
  MeshEvalTopology::Evaluate();
/*
  // for each (multiple) single linked facet there should
  // exist two valid facets sharing the same edge 
  // so make facet 1 neighbour of facet 2 and vice versa
  const std::vector<MeshFacet>& rclFAry = _rclMesh.GetFacets();
  std::vector<MeshFacet>::const_iterator pI;

  std::vector<std::list<unsigned long> > aclMf = _aclManifoldList;
  _aclManifoldList.clear();

  std::map<std::pair<unsigned long, unsigned long>, std::list<unsigned long> > aclHits;
  std::map<std::pair<unsigned long, unsigned long>, std::list<unsigned long> >::iterator pEdge;

  // search for single links (a non-manifold edge and two open edges)
  //
  //
  // build edge <=> facet map
  for (pI = rclFAry.begin(); pI != rclFAry.end(); pI++)
  {
    for (int i = 0; i < 3; i++)
    {
      unsigned long ulPt0 = std::min<unsigned long>(pI->_aulPoints[i],  pI->_aulPoints[(i+1)%3]);
      unsigned long ulPt1 = std::max<unsigned long>(pI->_aulPoints[i],  pI->_aulPoints[(i+1)%3]);
      aclHits[std::pair<unsigned long, unsigned long>(ulPt0, ulPt1)].push_front(pI - rclFAry.begin());
    }
  }

  // now search for single links
  for (std::vector<std::list<unsigned long> >::const_iterator pMF = aclMf.begin(); pMF != aclMf.end(); pMF++)
  {
    std::list<unsigned long> aulManifolds;
    for (std::list<unsigned long>::const_iterator pF = pMF->begin(); pF != pMF->end(); ++pF)
    {
      const MeshFacet& rclF = rclFAry[*pF];

      unsigned long ulCtNeighbours=0;
      for (int i = 0; i < 3; i++)
      {
        unsigned long ulPt0 = std::min<unsigned long>(rclF._aulPoints[i],  rclF._aulPoints[(i+1)%3]);
        unsigned long ulPt1 = std::max<unsigned long>(rclF._aulPoints[i],  rclF._aulPoints[(i+1)%3]);
        std::pair<unsigned long, unsigned long> clEdge(ulPt0, ulPt1); 

        // number of facets sharing this edge
        ulCtNeighbours += aclHits[clEdge].size();
      }

      // single linked found
      if (ulCtNeighbours == pMF->size() + 2)
        aulManifolds.push_front(*pF);
    }

    if ( aulManifolds.size() > 0 )
      _aclManifoldList.push_back(aulManifolds);
  }
*/
  return (nonManifoldList.size() == 0);
}

bool MeshFixSingleFacet::Fixup ()
{
  std::vector<unsigned long> aulInvalids;
//  MeshFacetArray& raFacets = _rclMesh._aclFacetArray;
  for ( std::vector<std::list<unsigned long> >::const_iterator it=_raclManifoldList.begin();it!=_raclManifoldList.end();++it )
  {
    for ( std::list<unsigned long>::const_iterator it2 = it->begin(); it2 != it->end(); ++it2 )
    {
      aulInvalids.push_back(*it2);
//      MeshFacet& rF = raFacets[*it2];
    }
  }
  
  _rclMesh.DeleteFacets(aulInvalids);
  return true;
}

// ----------------------------------------------------------------

bool MeshEvalSelfIntersection::Evaluate ()
{
    // Contains bounding boxes for every facet 
    std::vector<Base::BoundBox3f> boxes;

    // Splits the mesh using grid for speeding up the calculation
    MeshFacetGrid cMeshFacetGrid(_rclMesh);
    const MeshFacetArray& rFaces = _rclMesh.GetFacets();
    MeshGridIterator clGridIter(cMeshFacetGrid);
    unsigned long ulGridX, ulGridY, ulGridZ;
    cMeshFacetGrid.GetCtGrids(ulGridX, ulGridY, ulGridZ);

    MeshFacetIterator cMFI(_rclMesh);
    for (cMFI.Begin(); cMFI.More(); cMFI.Next()) {
        boxes.push_back((*cMFI).GetBoundBox());
    }

    // Calculates the intersections
    Base::SequencerLauncher seq("Checking for self-intersections...", ulGridX*ulGridY*ulGridZ);
    for (clGridIter.Init(); clGridIter.More(); clGridIter.Next()) {
        //Get the facet indices, belonging to the current grid unit
        std::vector<unsigned long> aulGridElements;
        clGridIter.GetElements(aulGridElements);

        seq.next();
        if (aulGridElements.size()==0)
            continue;

        MeshGeomFacet facet1, facet2;
        Base::Vector3f pt1, pt2;
        for (std::vector<unsigned long>::iterator it = aulGridElements.begin(); it != aulGridElements.end(); ++it) {
            const Base::BoundBox3f& box1 = boxes[*it];
            cMFI.Set(*it);
            facet1 = *cMFI;
            const MeshFacet& rface1 = rFaces[*it];
            for (std::vector<unsigned long>::iterator jt = it; jt != aulGridElements.end(); ++jt) {
                if (jt == it) // the identical facet
                    continue;
                // If the facets share a common vertex we do not check for self-intersections because they 
                // could but usually do not intersect each other and the algorithm below would detect false-positives,
                // otherwise
                const MeshFacet& rface2 = rFaces[*jt];
                if (rface1._aulPoints[0] == rface2._aulPoints[0] || 
                    rface1._aulPoints[0] == rface2._aulPoints[1] ||
                    rface1._aulPoints[0] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex
                if (rface1._aulPoints[1] == rface2._aulPoints[0] || 
                    rface1._aulPoints[1] == rface2._aulPoints[1] ||
                    rface1._aulPoints[1] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex
                if (rface1._aulPoints[2] == rface2._aulPoints[0] || 
                    rface1._aulPoints[2] == rface2._aulPoints[1] ||
                    rface1._aulPoints[2] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex

                const Base::BoundBox3f& box2 = boxes[*jt];
                if (box1 && box2) {
                    cMFI.Set(*jt);
                    facet2 = *cMFI;
                    int ret = facet1.IntersectWithFacet(facet2, pt1, pt2);
                    if (ret == 2) {
                        // abort after the first detected self-intersection
                        return false;
                    }
                }
            }
        }
    }

    return true;
}

void MeshEvalSelfIntersection::GetIntersections(const std::vector<std::pair<unsigned long, unsigned long> >& indices,
                                                std::vector<std::pair<Base::Vector3f, Base::Vector3f> >& intersection) const
{
    intersection.reserve(indices.size());
    MeshFacetIterator cMF1(_rclMesh);
    MeshFacetIterator cMF2(_rclMesh);

    Base::Vector3f pt1, pt2;
    std::vector<std::pair<unsigned long, unsigned long> >::const_iterator it;
    for (it = indices.begin(); it != indices.end(); ++it) {
        cMF1.Set(it->first);
        cMF2.Set(it->second);

        Base::BoundBox3f box1 = cMF1->GetBoundBox();
        Base::BoundBox3f box2 = cMF2->GetBoundBox();
        if (box1 && box2) {
            int ret = cMF1->IntersectWithFacet(*cMF2, pt1, pt2);
            if (ret == 2) {
                intersection.push_back(std::make_pair(pt1, pt2));
            }
        }
    }
}

void MeshEvalSelfIntersection::GetIntersections(std::vector<std::pair<unsigned long, unsigned long> >& intersection) const
{
    // Contains bounding boxes for every facet 
    std::vector<Base::BoundBox3f> boxes;
    //intersection.clear();

    // Splits the mesh using grid for speeding up the calculation
    MeshFacetGrid cMeshFacetGrid(_rclMesh);
    const MeshFacetArray& rFaces = _rclMesh.GetFacets();
    MeshGridIterator clGridIter(cMeshFacetGrid);
    unsigned long ulGridX, ulGridY, ulGridZ;
    cMeshFacetGrid.GetCtGrids(ulGridX, ulGridY, ulGridZ);

    MeshFacetIterator cMFI(_rclMesh);
    for(cMFI.Begin(); cMFI.More(); cMFI.Next()) {
        boxes.push_back((*cMFI).GetBoundBox());
    }

    // Calculates the intersections
    Base::SequencerLauncher seq("Checking for self-intersections...", ulGridX*ulGridY*ulGridZ);
    for (clGridIter.Init(); clGridIter.More(); clGridIter.Next()) {
        //Get the facet indices, belonging to the current grid unit
        std::vector<unsigned long> aulGridElements;
        clGridIter.GetElements(aulGridElements);

        seq.next(true);
        if (aulGridElements.size()==0)
            continue;

        MeshGeomFacet facet1, facet2;
        Base::Vector3f pt1, pt2;
        for (std::vector<unsigned long>::iterator it = aulGridElements.begin(); it != aulGridElements.end(); ++it) {
            const Base::BoundBox3f& box1 = boxes[*it];
            cMFI.Set(*it);
            facet1 = *cMFI;
            const MeshFacet& rface1 = rFaces[*it];
            for (std::vector<unsigned long>::iterator jt = it; jt != aulGridElements.end(); ++jt) {
                if (jt == it) // the identical facet
                    continue;
                // If the facets share a common vertex we do not check for self-intersections because they 
                // could but usually do not intersect each other and the algorithm below would detect false-positives,
                // otherwise
                const MeshFacet& rface2 = rFaces[*jt];
                if (rface1._aulPoints[0] == rface2._aulPoints[0] || 
                    rface1._aulPoints[0] == rface2._aulPoints[1] ||
                    rface1._aulPoints[0] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex
                if (rface1._aulPoints[1] == rface2._aulPoints[0] || 
                    rface1._aulPoints[1] == rface2._aulPoints[1] ||
                    rface1._aulPoints[1] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex
                if (rface1._aulPoints[2] == rface2._aulPoints[0] || 
                    rface1._aulPoints[2] == rface2._aulPoints[1] ||
                    rface1._aulPoints[2] == rface2._aulPoints[2])
                    continue; // ignore facets sharing a common vertex

                const Base::BoundBox3f& box2 = boxes[*jt];
                if (box1 && box2) {
                    cMFI.Set(*jt);
                    facet2 = *cMFI;
                    int ret = facet1.IntersectWithFacet(facet2, pt1, pt2);
                    if (ret == 2) {
                        intersection.push_back(std::make_pair
                            <unsigned long, unsigned long>(*it,*jt));
                    }
                }
            }
        }
    }
}

bool MeshFixSelfIntersection::Fixup()
{
    std::vector<unsigned long> indices;
    const MeshFacetArray& rFaces = _rclMesh.GetFacets();
    for (std::vector<std::pair<unsigned long, unsigned long> >::const_iterator
        it = selfIntersectons.begin(); it != selfIntersectons.end(); ++it) {
        unsigned short numOpenEdges1 = rFaces[it->first].CountOpenEdges();
        unsigned short numOpenEdges2 = rFaces[it->second].CountOpenEdges();

        // often we have only single or border facets that intersect other facets
        // in this case remove only these facets and keep the other one
        if (numOpenEdges1 == 0 && numOpenEdges2 > 0) {
            indices.push_back(it->second);
        }
        else if (numOpenEdges1 > 0 && numOpenEdges2 == 0) {
            indices.push_back(it->first);
        }
        else {
            indices.push_back(it->first);
            indices.push_back(it->second);
        }
    }

    // remove duplicates
    std::sort(indices.begin(), indices.end());
    indices.erase(std::unique(indices.begin(), indices.end()), indices.end());

    _rclMesh.DeleteFacets(indices);

    return true;
}

// ----------------------------------------------------------------

bool MeshEvalNeighbourhood::Evaluate ()
{
    // Note: If more than two facets are attached to the edge then we have a 
    // non-manifold edge here. 
    // This means that the neighbourhood cannot be valid, for sure. But we just
    // want to check whether the neighbourhood is valid for topologic correctly
    // edges and thus we ignore this case.
    // Non-manifolds are an own category of errors and are handled by the class
    // MeshEvalTopology.
    //
    // Using and sorting a vector seems to be faster and more memory-efficient
    // than a map.
    const MeshFacetArray& rclFAry = _rclMesh.GetFacets();
    std::vector<Edge_Index> edges;
    edges.reserve(3*rclFAry.size());

    // build up an array of edges
    MeshFacetArray::_TConstIterator pI;
    Base::SequencerLauncher seq("Checking indices...", rclFAry.size());
    for (pI = rclFAry.begin(); pI != rclFAry.end(); pI++) {
        for (int i = 0; i < 3; i++) {
            Edge_Index item;
            item.p0 = std::min<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.p1 = std::max<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.f  = pI - rclFAry.begin();
            edges.push_back(item);
        }

        seq.next();
    }

    // sort the edges
    std::sort(edges.begin(), edges.end(), Edge_Less());

    unsigned long p0 = ULONG_MAX, p1 = ULONG_MAX;
    unsigned long f0 = ULONG_MAX, f1 = ULONG_MAX;
    int count = 0;
    std::vector<Edge_Index>::iterator pE;
    for (pE = edges.begin(); pE != edges.end(); pE++) {
        if (p0 == pE->p0 && p1 == pE->p1) {
            f1 = pE->f;
            count++;
        }
        else {
            // we handle only the cases for 1 and 2, for all higher
            // values we have a non-manifold that is ignorned here
            if (count == 2) {
                const MeshFacet& rFace0 = rclFAry[f0];
                const MeshFacet& rFace1 = rclFAry[f1];
                unsigned short side0 = rFace0.Side(p0,p1);
                unsigned short side1 = rFace1.Side(p0,p1);
                // Check whether rFace0 and rFace1 reference each other as
                // neighbours
                if (rFace0._aulNeighbours[side0]!=f1 ||
                    rFace1._aulNeighbours[side1]!=f0)
                    return false;
            }
            else if (count == 1) {
                const MeshFacet& rFace = rclFAry[f0];
                unsigned short side = rFace.Side(p0,p1);
                // should be "open edge" but isn't marked as such
                if (rFace._aulNeighbours[side] != ULONG_MAX)
                    return false;
            }

            p0 = pE->p0;
            p1 = pE->p1;
            f0 = pE->f;
            count = 1;
        }
    }

    return true;
}

std::vector<unsigned long> MeshEvalNeighbourhood::GetIndices() const
{
    std::vector<unsigned long> inds;
    const MeshFacetArray& rclFAry = _rclMesh.GetFacets();
    std::vector<Edge_Index> edges;
    edges.reserve(3*rclFAry.size());

    // build up an array of edges
    MeshFacetArray::_TConstIterator pI;
    Base::SequencerLauncher seq("Checking indices...", rclFAry.size());
    for (pI = rclFAry.begin(); pI != rclFAry.end(); pI++) {
        for (int i = 0; i < 3; i++) {
            Edge_Index item;
            item.p0 = std::min<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.p1 = std::max<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.f  = pI - rclFAry.begin();
            edges.push_back(item);
        }

        seq.next();
    }

    // sort the edges
    std::sort(edges.begin(), edges.end(), Edge_Less());

    unsigned long p0 = ULONG_MAX, p1 = ULONG_MAX;
    unsigned long f0 = ULONG_MAX, f1 = ULONG_MAX;
    int count = 0;
    std::vector<Edge_Index>::iterator pE;
    for (pE = edges.begin(); pE != edges.end(); pE++) {
        if (p0 == pE->p0 && p1 == pE->p1) {
            f1 = pE->f;
            count++;
        }
        else {
            // we handle only the cases for 1 and 2, for all higher
            // values we have a non-manifold that is ignorned here
            if (count == 2) {
                const MeshFacet& rFace0 = rclFAry[f0];
                const MeshFacet& rFace1 = rclFAry[f1];
                unsigned short side0 = rFace0.Side(p0,p1);
                unsigned short side1 = rFace1.Side(p0,p1);
                // Check whether rFace0 and rFace1 reference each other as
                // neighbours
                if (rFace0._aulNeighbours[side0]!=f1 ||
                    rFace1._aulNeighbours[side1]!=f0) {
                    inds.push_back(f0);
                    inds.push_back(f1);
                }
            }
            else if (count == 1) {
                const MeshFacet& rFace = rclFAry[f0];
                unsigned short side = rFace.Side(p0,p1);
                // should be "open edge" but isn't marked as such
                if (rFace._aulNeighbours[side] != ULONG_MAX)
                    inds.push_back(f0);
            }

            p0 = pE->p0;
            p1 = pE->p1;
            f0 = pE->f;
            count = 1;
        }
    }

    // remove duplicates
    std::sort(inds.begin(), inds.end());
    inds.erase(std::unique(inds.begin(), inds.end()), inds.end());

    return inds;
}

bool MeshFixNeighbourhood::Fixup()
{
    _rclMesh.RebuildNeighbours();
    return true;
}

void MeshKernel::RebuildNeighbours (unsigned long index)
{
    std::vector<Edge_Index> edges;
    edges.reserve(3 * (this->_aclFacetArray.size() - index));

    // build up an array of edges
    MeshFacetArray::_TConstIterator pI;
    MeshFacetArray::_TConstIterator pB = this->_aclFacetArray.begin();
    for (pI = pB + index; pI != this->_aclFacetArray.end(); pI++) {
        for (int i = 0; i < 3; i++) {
            Edge_Index item;
            item.p0 = std::min<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.p1 = std::max<unsigned long>(pI->_aulPoints[i], pI->_aulPoints[(i+1)%3]);
            item.f  = pI - pB;
            edges.push_back(item);
        }
    }

    // sort the edges
    std::sort(edges.begin(), edges.end(), Edge_Less());

    unsigned long p0 = ULONG_MAX, p1 = ULONG_MAX;
    unsigned long f0 = ULONG_MAX, f1 = ULONG_MAX;
    int count = 0;
    std::vector<Edge_Index>::iterator pE;
    for (pE = edges.begin(); pE != edges.end(); pE++) {
        if (p0 == pE->p0 && p1 == pE->p1) {
            f1 = pE->f;
            count++;
        }
        else {
            // we handle only the cases for 1 and 2, for all higher
            // values we have a non-manifold that is ignorned here
            if (count == 2) {
                MeshFacet& rFace0 = this->_aclFacetArray[f0];
                MeshFacet& rFace1 = this->_aclFacetArray[f1];
                unsigned short side0 = rFace0.Side(p0,p1);
                unsigned short side1 = rFace1.Side(p0,p1);
                rFace0._aulNeighbours[side0] = f1;
                rFace1._aulNeighbours[side1] = f0;
            }
            else if (count == 1) {
                MeshFacet& rFace = this->_aclFacetArray[f0];
                unsigned short side = rFace.Side(p0,p1);
                rFace._aulNeighbours[side] = ULONG_MAX;
            }

            p0 = pE->p0;
            p1 = pE->p1;
            f0 = pE->f;
            count = 1;
        }
    }

    // we handle only the cases for 1 and 2, for all higher
    // values we have a non-manifold that is ignorned here
    if (count == 2) {
        MeshFacet& rFace0 = this->_aclFacetArray[f0];
        MeshFacet& rFace1 = this->_aclFacetArray[f1];
        unsigned short side0 = rFace0.Side(p0,p1);
        unsigned short side1 = rFace1.Side(p0,p1);
        rFace0._aulNeighbours[side0] = f1;
        rFace1._aulNeighbours[side1] = f0;
    }
    else if (count == 1) {
        MeshFacet& rFace = this->_aclFacetArray[f0];
        unsigned short side = rFace.Side(p0,p1);
        rFace._aulNeighbours[side] = ULONG_MAX;
    }
}

void MeshKernel::RebuildNeighbours (void)
{
    // complete rebuild
    RebuildNeighbours(0);
}

// ----------------------------------------------------------------

MeshEigensystem::MeshEigensystem (const MeshKernel &rclB)
  : MeshEvaluation(rclB), _cU(1.0f, 0.0f, 0.0f), _cV(0.0f, 1.0f, 0.0f), _cW(0.0f, 0.0f, 1.0f)
{
    // use the values of world coordinates as default
    Base::BoundBox3f box = _rclMesh.GetBoundBox();
    _fU = box.LengthX();
    _fV = box.LengthY();
    _fW = box.LengthZ();
}

Base::Matrix4D MeshEigensystem::Transform() const
{
    // x,y,c ... vectors
    // R,Q   ... matrices (R is orthonormal so its transposed(=inverse) is equal to Q)
    //
    // from local (x) to world (y,c) coordinates we have the equation
    // y = R * x  + c
    //     <==> 
    // x = Q * y - Q * c
    Base::Matrix4D clTMat;
    // rotation part
    clTMat[0][0] = _cU.x; clTMat[0][1] = _cU.y; clTMat[0][2] = _cU.z; clTMat[0][3] = 0.0f;
    clTMat[1][0] = _cV.x; clTMat[1][1] = _cV.y; clTMat[1][2] = _cV.z; clTMat[1][3] = 0.0f;
    clTMat[2][0] = _cW.x; clTMat[2][1] = _cW.y; clTMat[2][2] = _cW.z; clTMat[2][3] = 0.0f;
    clTMat[3][0] =  0.0f; clTMat[3][1] =  0.0f; clTMat[3][2] =  0.0f; clTMat[3][3] = 1.0f;

    Base::Vector3f c(_cC);
    c = clTMat * c;

    // translation part
    clTMat[0][3] = -c.x; clTMat[1][3] = -c.y; clTMat[2][3] = -c.z;

    return clTMat;
}

bool MeshEigensystem::Evaluate()
{
    CalculateLocalSystem();

    float xmin=0.0f, xmax=0.0f, ymin=0.0f, ymax=0.0f, zmin=0.0f, zmax=0.0f;

    Base::Vector3f clVect, clProj;
    float fH;

    const MeshPointArray& aclPoints = _rclMesh.GetPoints ();
    for (MeshPointArray::_TConstIterator it = aclPoints.begin(); it!=aclPoints.end(); ++it) {
        // u-Richtung
        clVect = *it - _cC;
        clProj.ProjToLine(clVect, _cU);
        clVect = clVect + clProj;
        fH = clVect.Length();
      
        // zeigen Vektoren in die gleiche Richtung ?
        if ((clVect * _cU) < 0.0f)
            fH = -fH;

        xmax = std::max<float>(xmax, fH);
        xmin = std::min<float>(xmin, fH);

        // v-Richtung
        clVect = *it - _cC;
        clProj.ProjToLine(clVect, _cV);
        clVect = clVect + clProj;
        fH = clVect.Length();
  
        // zeigen Vektoren in die gleiche Richtung ?
        if ((clVect * _cV) < 0.0f)
          fH = -fH;

        ymax = std::max<float>(ymax, fH);
        ymin = std::min<float>(ymin, fH);

        // w-Richtung
        clVect = *it - _cC;
        clProj.ProjToLine(clVect, _cW);
        clVect = clVect + clProj;
        fH = clVect.Length();
  
        // zeigen Vektoren in die gleiche Richtung ?
        if ((clVect * _cW) < 0.0f)
            fH = -fH;

        zmax = std::max<float>(zmax, fH);
        zmin = std::min<float>(zmin, fH);
    }

    _fU = xmax - xmin;
    _fV = ymax - ymin;
    _fW = zmax - zmin;

    return false; // to call Fixup() if needed
}

Base::Vector3f MeshEigensystem::GetBoundings() const
{
    return Base::Vector3f ( _fU, _fV, _fW );
}

void MeshEigensystem::CalculateLocalSystem()
{
    // at least one facet is needed
    if (_rclMesh.CountFacets() < 1)
        return; // cannot continue calculation

    const MeshPointArray& aclPoints = _rclMesh.GetPoints ();
    MeshPointArray::_TConstIterator it;

    PlaneFit planeFit;
    for (it = aclPoints.begin(); it!=aclPoints.end(); ++it)
        planeFit.AddPoint(*it);

    planeFit.Fit();
    _cC = planeFit.GetBase();
    _cU = planeFit.GetDirU();
    _cV = planeFit.GetDirV();
    _cW = planeFit.GetNormal();

    // set the sign for the vectors
    float fSumU, fSumV, fSumW;
    fSumU = fSumV = fSumW = 0.0f;
    for (it = aclPoints.begin(); it!=aclPoints.end(); ++it)
    {
        float fU = _cU * (*it - _cC);
        float fV = _cV * (*it - _cC);
        float fW = _cW * (*it - _cC);
        fSumU += (fU > 0 ? fU * fU : -fU * fU);
        fSumV += (fV > 0 ? fV * fV : -fV * fV);
        fSumW += (fW > 0 ? fW * fW : -fW * fW);
    }

    // avoid ambiguities concerning directions
    if (fSumU < 0.0f)
        _cU *= -1.0f;
    if (fSumV < 0.0f)
        _cV *= -1.0f;
    if (fSumW < 0.0f)
        _cW *= -1.0f;

    if ((_cU%_cV)*_cW < 0.0f)
        _cW = -_cW; // make a right-handed system
}