HiReconstruction.cpp

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#include "moab/DiscreteGeometry/HiReconstruction.hpp"
#include "moab/DiscreteGeometry/DGMSolver.hpp"
#include "moab/HalfFacetRep.hpp"

#ifdef MOAB_HAVE_MPI
#include "moab/ParallelComm.hpp"
#endif
#include "MBTagConventions.hpp"

#define HIREC_USE_AHF

#include 
#include 
#include 

namespace moab
{
HiReconstruction::HiReconstruction( Core* impl, ParallelComm* comm, EntityHandle meshIn, int minpnts, bool recwhole )
    : mbImpl( impl ), pcomm( comm ), _mesh2rec( meshIn ), _MINPNTS( minpnts )
{
    assert( NULL != impl );
    ErrorCode error;
    _MINEPS      = 1e-12;
    _dim         = 0;
    _hasfittings = false;
    _hasderiv    = false;
#ifdef MOAB_HAVE_MPI
    if( !pcomm )
    {
        pcomm = moab::ParallelComm::get_pcomm( mbImpl, 0 );
    }
#endif

    error = initialize( recwhole );
    if( MB_SUCCESS != error )
    {
        std::cout << "Error initializing HiReconstruction\n" << std::endl;
        exit( 1 );
    }
}

HiReconstruction::~HiReconstruction()
{
#ifdef MOAB_HAVE_AHF
    ahf = NULL;
#else
    delete ahf;
#endif
}

ErrorCode HiReconstruction::initialize( bool recwhole )
{
    ErrorCode error;

#ifdef HIREC_USE_AHF
    std::cout << "HIREC_USE_AHF: Initializing" << std::endl;
    ahf = new HalfFacetRep( mbImpl, pcomm, _mesh2rec, false );
    if( !ahf )
    {
        return MB_MEMORY_ALLOCATION_FAILED;
    }
    error = ahf->initialize();MB_CHK_ERR( error );
#else
    ahf        = NULL;
#endif

    // error = ahf->get_entity_ranges(_inverts,_inedges,_infaces,_incells); MB_CHK_ERR(error);
    error = mbImpl->get_entities_by_dimension( _mesh2rec, 0, _inverts );MB_CHK_ERR( error );
    error = mbImpl->get_entities_by_dimension( _mesh2rec, 1, _inedges );MB_CHK_ERR( error );
    error = mbImpl->get_entities_by_dimension( _mesh2rec, 2, _infaces );MB_CHK_ERR( error );
    error = mbImpl->get_entities_by_dimension( _mesh2rec, 3, _incells );MB_CHK_ERR( error );
    if( _inedges.size() && _infaces.empty() && _incells.empty() )
    {
        _dim     = 1;
        _MAXPNTS = 13;
    }
    else if( _infaces.size() && _incells.empty() )
    {
        _dim     = 2;
        _MAXPNTS = 128;
    }
    else
    {
        MB_SET_ERR( MB_FAILURE, "Encountered a non-manifold mesh or a mesh with volume elements" );
    }

    // get locally hosted vertices by filtering pstatus
#ifdef MOAB_HAVE_MPI
    if( pcomm )
    {
        error = pcomm->filter_pstatus( _inverts, PSTATUS_GHOST, PSTATUS_NOT, -1, &_verts2rec );MB_CHK_ERR( error );
    }
    else
    {
        _verts2rec = _inverts;
    }
#else
    _verts2rec = _inverts;
#endif
    _nv2rec = _verts2rec.size();

    if( recwhole )
    {
        // compute normals(surface) or tangent vector(curve) for all locally hosted vertices
        if( 2 == _dim )
        {
            compute_average_vertex_normals_surf();
        }
        else if( 1 == _dim )
        {
            compute_average_vertex_tangents_curve();
        }
        else
        {
            MB_SET_ERR( MB_FAILURE, "Unknow space dimension" );
        }
        _hasderiv = true;
    }
    return error;
}

/***************************************************
 *  User Interface for Reconstruction of Geometry  *
 ***************************************************/

ErrorCode HiReconstruction::reconstruct3D_surf_geom( int degree, bool interp, bool safeguard, bool reset )
{
    assert( 2 == _dim );
    if( _hasfittings && !reset )
    {
        // This object has precomputed fitting results and user don't want to reset
        return MB_SUCCESS;
    }
    else
    {
        _initfittings = _hasfittings = false;
    }
    // initialize for geometric information
    initialize_surf_geom( degree );
    ErrorCode error;
    double *coeffs, *coords;
    int* degree_out;
    int ncoeffs = ( degree + 2 ) * ( degree + 1 ) / 2;

    // DBG
    int dcount = 0;

    for( Range::iterator ivert = _verts2rec.begin(); ivert != _verts2rec.end(); ++ivert )
    {
        int index = _verts2rec.index( *ivert );
        // for debug
        /*if(index==70){
            EntityHandle vid = *ivert;
            double vertcoords[3];
            error = mbImpl->get_coords(&vid,1,vertcoords);
        }*/

        size_t istr     = _vertID2coeffID[index];
        coords          = &( _local_coords[9 * index] );
        coeffs          = &( _local_fit_coeffs[istr] );
        degree_out      = &( _degrees_out[index] );
        _interps[index] = interp;
        error = polyfit3d_walf_surf_vertex( *ivert, interp, degree, _MINPNTS, safeguard, 9, coords, degree_out, ncoeffs,
                                            coeffs );MB_CHK_ERR( error );

        // DBG
        if( degree_out[0] < degree ) dcount += 1;
    }

    // DBG
    // std::cout<<"Total #points ="<<_verts2rec.size()<<", #degraded points = "<get_coords( ngbvs, ngbcoords );MB_CHK_ERR( error );
    // get normals
    double* ngbnrms = new double[nverts * 3];
    error           = get_normals_surf( ngbvs, ngbnrms );MB_CHK_ERR( error );
    // switch vid to first one
    int index = ngbvs.index( vid );
    assert( index != -1 );
    std::swap( ngbcoords[0], ngbcoords[3 * index] );
    std::swap( ngbcoords[1], ngbcoords[3 * index + 1] );
    std::swap( ngbcoords[2], ngbcoords[3 * index + 2] );
    std::swap( ngbnrms[0], ngbnrms[3 * index] );
    std::swap( ngbnrms[1], ngbnrms[3 * index + 1] );
    std::swap( ngbnrms[2], ngbnrms[3 * index + 2] );
    // local WLS fitting
    int degree_pnt, degree_qr;
    polyfit3d_surf_get_coeff( nverts, ngbcoords, ngbnrms, degree, interp, safeguard, ncoords, coords, ncoeffs, coeffs,
                              degree_out, °ree_pnt, °ree_qr );
    delete[] ngbcoords;
    delete[] ngbnrms;
    return error;
}

ErrorCode HiReconstruction::polyfit3d_walf_curve_vertex( const EntityHandle vid,
                                                         const bool interp,
                                                         int degree,
                                                         int minpnts,
                                                         const bool safeguard,
                                                         const int ncoords,
                                                         double* coords,
                                                         int* degree_out,
                                                         const int ncoeffs,
                                                         double* coeffs )
{
    ErrorCode error;
    int ring = estimate_num_rings( degree, interp );
    // get n-ring neighbors
    Range ngbvs;
    error = obtain_nring_ngbvs( vid, ring, minpnts, ngbvs );MB_CHK_ERR( error );
    // get coordinates
    size_t nverts = ngbvs.size();
    assert( nverts );
    double* ngbcoords = new double[nverts * 3];
    error             = mbImpl->get_coords( ngbvs, ngbcoords );MB_CHK_ERR( error );
    // get tangent vectors
    double* ngbtangs = new double[nverts * 3];
    error            = get_tangents_curve( ngbvs, ngbtangs );MB_CHK_ERR( error );
    // switch vid to first one
    int index = ngbvs.index( vid );
    assert( index != -1 );
    std::swap( ngbcoords[0], ngbcoords[3 * index] );
    std::swap( ngbcoords[1], ngbcoords[3 * index + 1] );
    std::swap( ngbcoords[2], ngbcoords[3 * index + 2] );
    std::swap( ngbtangs[0], ngbtangs[3 * index] );
    std::swap( ngbtangs[1], ngbtangs[3 * index + 1] );
    std::swap( ngbtangs[2], ngbtangs[3 * index + 2] );
    // local WLS fittings
    polyfit3d_curve_get_coeff( nverts, ngbcoords, ngbtangs, degree, interp, safeguard, ncoords, coords, ncoeffs, coeffs,
                               degree_out );
    delete[] ngbcoords;
    delete[] ngbtangs;
    return error;
}

/**************************************************************
 *  User Interface for Evaluation via Reconstructed Geometry  *
 **************************************************************/

ErrorCode HiReconstruction::hiproj_walf_in_element( EntityHandle elem,
                                                    const int nvpe,
                                                    const int npts2fit,
                                                    const double* naturalcoords2fit,
                                                    double* newcoords )
{
    assert( newcoords );
    ErrorCode error;
    // get connectivity table
    std::vector< EntityHandle > elemconn;
    error = mbImpl->get_connectivity( &elem, 1, elemconn );MB_CHK_ERR( error );
    if( nvpe != (int)elemconn.size() )
    {
        MB_SET_ERR( MB_FAILURE, "element connectivity table size doesn't match input size" );
    }

    if( !_hasfittings )
    {
        MB_SET_ERR( MB_FAILURE, "There is no existing fitting results" );
    }
    else
    {
        std::ostringstream convert;
        convert << elem;
        std::string ID = convert.str();
        for( int i = 0; i < nvpe; ++i )
        {
            if( -1 == _verts2rec.index( elemconn[i] ) )
            {
                MB_SET_ERR( MB_FAILURE, "There is no existing fitting results for element " + ID );
            }
        }
    }
    // check correctness of input
    for( int i = 0; i < npts2fit; ++i )
    {
        if( !check_barycentric_coords( nvpe, naturalcoords2fit + i * nvpe ) )
        {
            MB_SET_ERR( MB_FAILURE, "Wrong barycentric coordinates" );
        }
    }

    double* elemcoords = new double[nvpe * 3];
    error              = mbImpl->get_coords( &( elemconn[0] ), nvpe, elemcoords );MB_CHK_ERR( error );

    double* coords2fit = new double[3 * npts2fit]();
    for( int i = 0; i < npts2fit; ++i )
    {
        for( int j = 0; j < nvpe; ++j )
        {
            coords2fit[3 * i] += naturalcoords2fit[i * nvpe + j] * elemcoords[3 * j];
            coords2fit[3 * i + 1] += naturalcoords2fit[i * nvpe + j] * elemcoords[3 * j + 1];
            coords2fit[3 * i + 2] += naturalcoords2fit[i * nvpe + j] * elemcoords[3 * j + 2];
        }
    }

    double* hiproj_new = new double[3 * npts2fit];
    // initialize output
    for( int i = 0; i < npts2fit; ++i )
    {
        newcoords[3 * i] = newcoords[3 * i + 1] = newcoords[3 * i + 2] = 0;
    }
    // for each input vertex, call nvpe fittings and take average
    for( int j = 0; j < nvpe; ++j )
    {
        error = hiproj_walf_around_vertex( elemconn[j], npts2fit, coords2fit, hiproj_new );MB_CHK_ERR( error );
        for( int i = 0; i < npts2fit; ++i )
        {
            newcoords[3 * i] += naturalcoords2fit[i * nvpe + j] * hiproj_new[3 * i];
            newcoords[3 * i + 1] += naturalcoords2fit[i * nvpe + j] * hiproj_new[3 * i + 1];
            newcoords[3 * i + 2] += naturalcoords2fit[i * nvpe + j] * hiproj_new[3 * i + 2];
        }
    }
    delete[] elemcoords;
    delete[] coords2fit;
    delete[] hiproj_new;
    return error;
}

ErrorCode HiReconstruction::hiproj_walf_around_vertex( EntityHandle vid,
                                                       const int npts2fit,
                                                       const double* coords2fit,
                                                       double* hiproj_new )
{
    if( !_hasfittings )
    {
        MB_SET_ERR( MB_FAILURE, "There is no existing fitting results" );
    }
    else if( -1 == _verts2rec.index( vid ) )
    {
        std::ostringstream convert;
        convert << vid;
        std::string VID = convert.str();
        MB_SET_ERR( MB_FAILURE, "There is no existing fitting results for vertex " + VID );
    }
    ErrorCode error;
    // get center of local coordinates system
    double local_origin[3];
    error = mbImpl->get_coords( &vid, 1, local_origin );MB_CHK_ERR( error );
    // get local fitting parameters
    int index     = _verts2rec.index( vid );
    bool interp   = _interps[index];
    int local_deg = _degrees_out[index];
    double *uvw_coords, *local_coeffs;
    if( _geom == HISURFACE )
    {
        uvw_coords = &( _local_coords[9 * index] );
        // int ncoeffs = (local_deg+2)*(local_deg+1)>>1;
        size_t istr  = _vertID2coeffID[index];
        local_coeffs = &( _local_fit_coeffs[istr] );
        walf3d_surf_vertex_eval( local_origin, uvw_coords, local_deg, local_coeffs, interp, npts2fit, coords2fit,
                                 hiproj_new );
    }
    else if( _geom == HI3DCURVE )
    {
        uvw_coords   = &( _local_coords[3 * index] );
        size_t istr  = _vertID2coeffID[index];
        local_coeffs = &( _local_fit_coeffs[istr] );
        walf3d_curve_vertex_eval( local_origin, uvw_coords, local_deg, local_coeffs, interp, npts2fit, coords2fit,
                                  hiproj_new );
    }
    return error;
}

void HiReconstruction::walf3d_surf_vertex_eval( const double* local_origin,
                                                const double* local_coords,
                                                const int local_deg,
                                                const double* local_coeffs,
                                                const bool interp,
                                                const int npts2fit,
                                                const double* coords2fit,
                                                double* hiproj_new )
{
    double xaxis[3], yaxis[3], zaxis[3];
    for( int i = 0; i < 3; ++i )
    {
        xaxis[i] = local_coords[i];
        yaxis[i] = local_coords[3 + i];
        zaxis[i] = local_coords[6 + i];
    }
    // double *basis = new double[(local_deg+2)*(local_deg+1)/2-1];
    std::vector< double > basis( ( local_deg + 2 ) * ( local_deg + 1 ) / 2 - 1 );
    for( int i = 0; i < npts2fit; ++i )
    {
        double local_pos[3];
        for( int j = 0; j < 3; ++j )
        {
            local_pos[j] = coords2fit[3 * i + j] - local_origin[j];
        }
        double u, v, height = 0;
        u        = DGMSolver::vec_innerprod( 3, local_pos, xaxis );
        v        = DGMSolver::vec_innerprod( 3, local_pos, yaxis );
        basis[0] = u;
        basis[1] = v;
        int l    = 1;
        for( int k = 2; k <= local_deg; ++k )
        {
            ++l;
            basis[l] = u * basis[l - k];
            for( int id = 0; id < k; ++id )
            {
                ++l;
                basis[l] = basis[l - k - 1] * v;
            }
        }
        if( !interp )
        {
            height = local_coeffs[0];
        }
        for( int p = 0; p <= l; ++p )
        {
            height += local_coeffs[p + 1] * basis[p];
        }
        hiproj_new[3 * i]     = local_origin[0] + u * xaxis[0] + v * yaxis[0] + height * zaxis[0];
        hiproj_new[3 * i + 1] = local_origin[1] + u * xaxis[1] + v * yaxis[1] + height * zaxis[1];
        hiproj_new[3 * i + 2] = local_origin[2] + u * xaxis[2] + v * yaxis[2] + height * zaxis[2];
    }
    // delete [] basis;
}

void HiReconstruction::walf3d_curve_vertex_eval( const double* local_origin,
                                                 const double* local_coords,
                                                 const int local_deg,
                                                 const double* local_coeffs,
                                                 const bool interp,
                                                 const int npts2fit,
                                                 const double* coords2fit,
                                                 double* hiproj_new )
{
    assert( local_origin && local_coords && local_coeffs );
    int ncoeffspvpd = local_deg + 1;
    for( int i = 0; i < npts2fit; ++i )
    {
        // get the vector from center to current point, project to tangent line
        double vec[3], ans[3] = { 0, 0, 0 };
        DGMSolver::vec_linear_operation( 3, 1, coords2fit + 3 * i, -1, local_origin, vec );
        double u = DGMSolver::vec_innerprod( 3, local_coords, vec );
        // evaluate polynomials
        if( !interp )
        {
            ans[0] = local_coeffs[0];
            ans[1] = local_coeffs[ncoeffspvpd];
            ans[2] = local_coeffs[2 * ncoeffspvpd];
        }
        double uk = 1;  // degree_out and degree different, stored in columnwise contiguously
        for( int j = 1; j < ncoeffspvpd; ++j )
        {
            uk *= u;
            ans[0] += uk * local_coeffs[j];
            ans[1] += uk * local_coeffs[j + ncoeffspvpd];
            ans[2] += uk * local_coeffs[j + 2 * ncoeffspvpd];
        }
        hiproj_new[3 * i]     = ans[0] + local_origin[0];
        hiproj_new[3 * i + 1] = ans[1] + local_origin[1];
        hiproj_new[3 * i + 2] = ans[2] + local_origin[2];
    }
}

bool HiReconstruction::get_fittings_data( EntityHandle vid,
                                          GEOMTYPE& geomtype,
                                          std::vector< double >& coords,
                                          int& degree_out,
                                          std::vector< double >& coeffs,
                                          bool& interp )
{
    if( !_hasfittings )
    {
        return false;
    }
    else
    {
        int index = _verts2rec.index( vid );
        if( -1 == index )
        {
            std::cout << "Input vertex is not locally hosted vertex in this mesh set" << std::endl;
            return false;
        }
        geomtype = _geom;
        if( HISURFACE == _geom )
        {
            coords.insert( coords.end(), _local_coords.begin() + 9 * index, _local_coords.begin() + 9 * index + 9 );
            degree_out  = _degrees_out[index];
            interp      = _interps[index];
            int ncoeffs = ( degree_out + 2 ) * ( degree_out + 1 ) >> 1;
            size_t istr = _vertID2coeffID[index];
            coeffs.insert( coeffs.end(), _local_fit_coeffs.begin() + istr, _local_fit_coeffs.begin() + istr + ncoeffs );
        }
        else if( HI3DCURVE == _geom )
        {
            coords.insert( coords.end(), _local_coords.begin() + 3 * index, _local_coords.begin() + 3 * index + 3 );
            degree_out  = _degrees_out[index];
            interp      = _interps[index];
            int ncoeffs = 3 * ( degree_out + 1 );
            size_t istr = _vertID2coeffID[index];
            coeffs.insert( coeffs.end(), _local_fit_coeffs.begin() + istr, _local_fit_coeffs.begin() + istr + ncoeffs );
        }
        return true;
    }
}

/****************************************************************
 *  Basic Internal Routines to initialize and set fitting data  *
 ****************************************************************/

int HiReconstruction::estimate_num_rings( int degree, bool interp )
{
    return interp ? ( ( degree + 1 ) >> 1 ) + ( ( degree + 1 ) & 1 ) : ( ( degree + 2 ) >> 1 ) + ( ( degree + 2 ) & 1 );
}

ErrorCode HiReconstruction::vertex_get_incident_elements( const EntityHandle& vid,
                                                          const int elemdim,
                                                          std::vector< EntityHandle >& adjents )
{
    ErrorCode error;
    assert( elemdim == _dim );
#ifdef HIREC_USE_AHF
    error = ahf->get_up_adjacencies( vid, elemdim, adjents );MB_CHK_ERR( error );
#else
    error      = mbImpl->get_adjacencies( &vid, 1, elemdim, false, adjents );MB_CHK_ERR( error );
#endif
    return error;
}

ErrorCode HiReconstruction::obtain_nring_ngbvs( const EntityHandle vid, int ring, const int minpnts, Range& ngbvs )
{
    ErrorCode error;
    std::deque< EntityHandle > todo;
    todo.push_back( vid );
    ngbvs.insert( vid );
    EntityHandle pre, nxt;
    for( int i = 1; i <= ring; ++i )
    {
        int count = todo.size();
        while( count )
        {
            EntityHandle center = todo.front();
            todo.pop_front();
            --count;
            std::vector< EntityHandle > adjents;
            error = vertex_get_incident_elements( center, _dim, adjents );MB_CHK_ERR( error );
            for( size_t j = 0; j < adjents.size(); ++j )
            {
                std::vector< EntityHandle > elemconn;
                error = mbImpl->get_connectivity( &adjents[j], 1, elemconn );MB_CHK_ERR( error );
                int nvpe = elemconn.size();
                for( int k = 0; k < nvpe; ++k )
                {
                    if( elemconn[k] == center )
                    {
                        pre = k == 0 ? elemconn[nvpe - 1] : elemconn[k - 1];
                        nxt = elemconn[( k + 1 ) % nvpe];
                        if( ngbvs.find( pre ) == ngbvs.end() )
                        {
                            ngbvs.insert( pre );
                            todo.push_back( pre );
                        }
                        if( ngbvs.find( nxt ) == ngbvs.end() )
                        {
                            ngbvs.insert( nxt );
                            todo.push_back( nxt );
                        }
                        break;
                    }
                }
            }
        }
        if( _MAXPNTS <= (int)ngbvs.size() )
        {
            // obtain enough points
            return error;
        }
        if( !todo.size() )
        {
            // current ring cannot introduce any points, return incase deadlock
            return error;
        }
        if( ( i == ring ) && ( minpnts > (int)ngbvs.size() ) )
        {
            // reach maximum ring but not enough points
            ++ring;
        }
    }
    return error;
}

void HiReconstruction::initialize_surf_geom( const int degree )
{
    if( !_hasderiv )
    {
        compute_average_vertex_normals_surf();
        _hasderiv = true;
    }
    if( !_initfittings )
    {
        int ncoeffspv = ( degree + 2 ) * ( degree + 1 ) / 2;
        _degrees_out.assign( _nv2rec, 0 );
        _interps.assign( _nv2rec, false );
        _vertID2coeffID.resize( _nv2rec );
        _local_fit_coeffs.assign( _nv2rec * ncoeffspv, 0 );
        for( size_t i = 0; i < _nv2rec; ++i )
        {
            _vertID2coeffID[i] = i * ncoeffspv;
        }
        _initfittings = true;
    }
}

void HiReconstruction::initialize_surf_geom( const size_t npts, const int* degrees )
{
    if( !_hasderiv )
    {
        compute_average_vertex_normals_surf();
        _hasderiv = true;
    }
    if( !_initfittings )
    {
        assert( _nv2rec == npts );
        _degrees_out.assign( _nv2rec, 0 );
        _interps.assign( _nv2rec, false );
        _vertID2coeffID.resize( _nv2rec );
        size_t index = 0;
        for( size_t i = 0; i < _nv2rec; ++i )
        {
            _vertID2coeffID[i] = index;
            index += ( degrees[i] + 2 ) * ( degrees[i] + 1 ) / 2;
        }
        _local_fit_coeffs.assign( index, 0 );
        _initfittings = true;
    }
}

void HiReconstruction::initialize_3Dcurve_geom( const int degree )
{
    if( !_hasderiv )
    {
        compute_average_vertex_tangents_curve();
        _hasderiv = true;
    }
    if( !_initfittings )
    {
        int ncoeffspvpd = degree + 1;
        _degrees_out.assign( _nv2rec, 0 );
        _interps.assign( _nv2rec, false );
        _vertID2coeffID.resize( _nv2rec );
        _local_fit_coeffs.assign( _nv2rec * ncoeffspvpd * 3, 0 );
        for( size_t i = 0; i < _nv2rec; ++i )
        {
            _vertID2coeffID[i] = i * ncoeffspvpd * 3;
        }
        _initfittings = true;
    }
}

void HiReconstruction::initialize_3Dcurve_geom( const size_t npts, const int* degrees )
{
    if( !_hasderiv )
    {
        compute_average_vertex_tangents_curve();
        _hasderiv = true;
    }
    if( !_hasfittings )
    {
        assert( _nv2rec == npts );
        _degrees_out.assign( _nv2rec, 0 );
        _interps.assign( _nv2rec, false );
        _vertID2coeffID.reserve( _nv2rec );
        size_t index = 0;
        for( size_t i = 0; i < _nv2rec; ++i )
        {
            _vertID2coeffID[i] = index;
            index += 3 * ( degrees[i] + 1 );
        }
        _local_fit_coeffs.assign( index, 0 );
        _initfittings = true;
    }
}

/* ErrorCode HiReconstruction::set_geom_data_surf(const EntityHandle vid, const double* coords,
 const double degree_out, const double* coeffs, bool interp)
 {
   return MB_SUCCESS;
 }

 ErrorCode HiReconstruction::set_geom_data_3Dcurve(const EntityHandle vid, const double* coords,
 const double degree_out, const double* coeffs, bool interp)
 {
   return MB_SUCCESS;
 } */

/*********************************************************
 * Routines for vertex normal/tangent vector estimation *
 *********************************************************/
ErrorCode HiReconstruction::average_vertex_normal( const EntityHandle vid, double* nrm )
{
    ErrorCode error;
    std::vector< EntityHandle > adjfaces;
    error = vertex_get_incident_elements( vid, 2, adjfaces );MB_CHK_ERR( error );
    int npolys = adjfaces.size();
    if( !npolys )
    {
        MB_SET_ERR( MB_FAILURE, "Vertex has no incident 2D entities" );
    }
    else
    {
        double v1[3], v2[3], v3[3], a[3], b[3], c[3];
        nrm[0] = nrm[1] = nrm[2] = 0;
        for( int i = 0; i < npolys; ++i )
        {
            // get incident "triangles"
            std::vector< EntityHandle > elemconn;
            error = mbImpl->get_connectivity( &adjfaces[i], 1, elemconn );MB_CHK_ERR( error );
            EntityHandle pre, nxt;
            int nvpe = elemconn.size();
            for( int j = 0; j < nvpe; ++j )
            {
                if( vid == elemconn[j] )
                {
                    pre = j == 0 ? elemconn[nvpe - 1] : elemconn[j - 1];
                    nxt = elemconn[( j + 1 ) % nvpe];
                    break;
                }
            }
            // compute area weighted normals
            error = mbImpl->get_coords( &pre, 1, a );MB_CHK_ERR( error );
            error = mbImpl->get_coords( &vid, 1, b );MB_CHK_ERR( error );
            error = mbImpl->get_coords( &nxt, 1, c );MB_CHK_ERR( error );
            DGMSolver::vec_linear_operation( 3, 1, c, -1, b, v1 );
            DGMSolver::vec_linear_operation( 3, 1, a, -1, b, v2 );
            DGMSolver::vec_crossprod( v1, v2, v3 );
            DGMSolver::vec_linear_operation( 3, 1, nrm, 1, v3, nrm );
        }
#ifndef NDEBUG
        assert( DGMSolver::vec_normalize( 3, nrm, nrm ) );
#endif
    }
    return error;
}

ErrorCode HiReconstruction::compute_average_vertex_normals_surf()
{
    if( _hasderiv )
    {
        return MB_SUCCESS;
    }
    ErrorCode error;
    _local_coords.assign( 9 * _nv2rec, 0 );
    size_t index = 0;
    for( Range::iterator ivert = _verts2rec.begin(); ivert != _verts2rec.end(); ++ivert, ++index )
    {
        error = average_vertex_normal( *ivert, &( _local_coords[9 * index + 6] ) );MB_CHK_ERR( error );
    }
    return error;
}

ErrorCode HiReconstruction::get_normals_surf( const Range& vertsh, double* nrms )
{
    ErrorCode error = MB_SUCCESS;
    if( _hasderiv )
    {
        size_t id = 0;
        for( Range::iterator ivert = vertsh.begin(); ivert != vertsh.end(); ++ivert, ++id )
        {
            int index = _verts2rec.index( *ivert );
#ifdef MOAB_HAVE_MPI
            if( -1 == index )
            {
                // ghost vertex
                error = average_vertex_normal( *ivert, nrms + 3 * id );MB_CHK_ERR( error );
            }
            else
            {
                nrms[3 * id]     = _local_coords[9 * index + 6];
                nrms[3 * id + 1] = _local_coords[9 * index + 7];
                nrms[3 * id + 2] = _local_coords[9 * index + 8];
            }
#else
            assert( -1 != index );
            nrms[3 * id]     = _local_coords[9 * index + 6];
            nrms[3 * id + 1] = _local_coords[9 * index + 7];
            nrms[3 * id + 2] = _local_coords[9 * index + 8];
#endif
        }
    }
    else
    {
        size_t id = 0;
        for( Range::iterator ivert = vertsh.begin(); ivert != vertsh.end(); ++ivert, ++id )
        {
            error = average_vertex_normal( *ivert, nrms + 3 * id );MB_CHK_ERR( error );
        }
    }
    return error;
}

ErrorCode HiReconstruction::average_vertex_tangent( const EntityHandle vid, double* tang )
{
    ErrorCode error;
    std::vector< EntityHandle > adjedges;
    error = vertex_get_incident_elements( vid, 1, adjedges );MB_CHK_ERR( error );
    int nedges = adjedges.size();
    if( !nedges )
    {
        MB_SET_ERR( MB_FAILURE, "Vertex has no incident edges" );
    }
    else
    {
        assert( nedges <= 2 );
        tang[0] = tang[1] = tang[2] = 0;
        for( int i = 0; i < nedges; ++i )
        {
            std::vector< EntityHandle > edgeconn;
            error = mbImpl->get_connectivity( &adjedges[i], 1, edgeconn );
            double istr[3], iend[3], t[3];
            error = mbImpl->get_coords( &( edgeconn[0] ), 1, istr );
            error = mbImpl->get_coords( &( edgeconn[1] ), 1, iend );
            DGMSolver::vec_linear_operation( 3, 1, iend, -1, istr, t );
            DGMSolver::vec_linear_operation( 3, 1, tang, 1, t, tang );
        }
#ifndef NDEBUG
        assert( DGMSolver::vec_normalize( 3, tang, tang ) );
#endif
    }
    return error;
}

ErrorCode HiReconstruction::compute_average_vertex_tangents_curve()
{
    if( _hasderiv )
    {
        return MB_SUCCESS;
    }
    ErrorCode error;
    _local_coords.assign( 3 * _nv2rec, 0 );
    size_t index = 0;
    for( Range::iterator ivert = _verts2rec.begin(); ivert != _verts2rec.end(); ++ivert, ++index )
    {
        error = average_vertex_tangent( *ivert, &( _local_coords[3 * index] ) );MB_CHK_ERR( error );
    }
    return error;
}

ErrorCode HiReconstruction::get_tangents_curve( const Range& vertsh, double* tangs )
{
    ErrorCode error = MB_SUCCESS;
    if( _hasderiv )
    {
        size_t id = 0;
        for( Range::iterator ivert = vertsh.begin(); ivert != vertsh.end(); ++ivert, ++id )
        {
            int index = _verts2rec.index( *ivert );
#ifdef MOAB_HAVE_MPI
            if( -1 != index )
            {
                tangs[3 * id]     = _local_coords[3 * index];
                tangs[3 * id + 1] = _local_coords[3 * index + 1];
                tangs[3 * id + 2] = _local_coords[3 * index + 2];
            }
            else
            {
                error = average_vertex_tangent( *ivert, tangs + 3 * id );MB_CHK_ERR( error );
            }
#else
            assert( -1 != index );
            tangs[3 * id]     = _local_coords[3 * index];
            tangs[3 * id + 1] = _local_coords[3 * index + 1];
            tangs[3 * id + 2] = _local_coords[3 * index + 2];
#endif
        }
    }
    else
    {
        size_t id = 0;
        for( Range::iterator ivert = vertsh.begin(); ivert != vertsh.end(); ++ivert, ++id )
        {
            error = average_vertex_tangent( *ivert, tangs + 3 * id );MB_CHK_ERR( error );
        }
    }
    return error;
}

/************************************************
 *  Internal Routines for local WLS fittings    *
 *************************************************/

void HiReconstruction::polyfit3d_surf_get_coeff( const int nverts,
                                                 const double* ngbcoords,
                                                 const double* ngbnrms,
                                                 int degree,
                                                 const bool interp,
                                                 const bool safeguard,
                                                 const int ncoords,
                                                 double* coords,
                                                 const int ncoeffs,
                                                 double* coeffs,
                                                 int* degree_out,
                                                 int* degree_pnt,
                                                 int* degree_qr )
{
    if( nverts <= 0 )
    {
        return;
    }

    // std::cout << "npnts in initial stencil = " << nverts << std::endl;
    // std::cout << "centered at (" << ngbcoords[0] << "," << ngbcoords[1] << "," << ngbcoords[2] <<
    // ")" << std::endl;

    // step 1. copmute local coordinate system
    double nrm[3] = { ngbnrms[0], ngbnrms[1], ngbnrms[2] }, tang1[3] = { 0, 0, 0 }, tang2[3] = { 0, 0, 0 };
    if( fabs( nrm[0] ) > fabs( nrm[1] ) && fabs( nrm[0] ) > fabs( nrm[2] ) )
    {
        tang1[1] = 1.0;
    }
    else
    {
        tang1[0] = 1.0;
    }

    DGMSolver::vec_projoff( 3, tang1, nrm, tang1 );
#ifndef NDEBUG
    assert( DGMSolver::vec_normalize( 3, tang1, tang1 ) );
#endif
    DGMSolver::vec_crossprod( nrm, tang1, tang2 );
    if( 9 <= ncoords && coords )
    {
        coords[0] = tang1[0];
        coords[1] = tang1[1];
        coords[2] = tang1[2];
        coords[3] = tang2[0];
        coords[4] = tang2[1];
        coords[5] = tang2[2];
        coords[6] = nrm[0];
        coords[7] = nrm[1];
        coords[8] = nrm[2];
    }
    if( !ncoeffs || !coeffs )
    {
        return;
    }
    else
    {
        assert( ncoeffs >= ( degree + 2 ) * ( degree + 1 ) / 2 );
    }

    // step 2. project onto local coordinates system
    int npts2fit = nverts - interp;
    if( 0 == npts2fit )
    {
        *degree_out = *degree_pnt = *degree_qr = 0;
        for( int i = 0; i < ncoeffs; ++i )
        {
            coeffs[i] = 0;
        }
        // coeffs[0] = 0;
        return;
    }
    std::vector< double > us( npts2fit * 2 );  // double *us = new double[npts2fit*2];
    std::vector< double > bs( npts2fit );      // double *bs = new double[npts2fit];
    for( int i = interp; i < nverts; ++i )
    {
        int k = i - interp;
        double uu[3];
        DGMSolver::vec_linear_operation( 3, 1, ngbcoords + 3 * i, -1, ngbcoords, uu );
        us[k * 2]     = DGMSolver::vec_innerprod( 3, tang1, uu );
        us[k * 2 + 1] = DGMSolver::vec_innerprod( 3, tang2, uu );
        bs[k]         = DGMSolver::vec_innerprod( 3, nrm, uu );
    }

    // step 3. compute weights
    std::vector< double > ws( npts2fit );  // double *ws = new double[npts2fit];
    int nzeros = compute_weights( npts2fit, 2, &( us[0] ), nverts, ngbnrms, degree, _MINEPS, &( ws[0] ) );

    // step 4. adjust according to zero-weights
    if( nzeros )
    {
        if( nzeros == npts2fit )
        {
            *degree_out = *degree_pnt = *degree_qr = 0;
            for( int i = 0; i < ncoeffs; ++i )
            {
                coeffs[i] = 0;
            }
            // coeffs[0] = 0;
            return;
        }
        int index = 0;
        for( int i = 0; i < npts2fit; ++i )
        {
            if( ws[i] )
            {
                if( i > index )
                {
                    us[index * 2]     = us[i * 2];
                    us[index * 2 + 1] = us[i * 2 + 1];
                    bs[index]         = bs[i];
                    ws[index]         = ws[i];
                }
                ++index;
            }
        }
        npts2fit -= nzeros;
        assert( index == npts2fit );
        us.resize( npts2fit * 2 );
        bs.resize( npts2fit );
        ws.resize( npts2fit );
        /*us = realloc(us,npts2fit*2*sizeof(double));
        bs = realloc(bs,npts2fit*sizeof(double));
        ws = realloc(ws,npts2fit*sizeof(double));*/
    }

    // std::cout<<"npnts after weighting = "<> 1 ) - interp;
    while( 1 < degree && npts2fit < ncols )
    {
        --degree;
        ncols = ( ( ( degree + 2 ) * ( degree + 1 ) ) >> 1 ) - interp;
    }
    *degree_pnt = degree;

    // std::cout << "degree_pnt: " << *degree_pnt << std::endl;

    // step 2. construct Vandermonde matrix, stored in columnwise
    std::vector< double > V;  // V(npts2fit*(ncols+interp)); //double *V_init = new double[npts2fit*(ncols+interp)];
    DGMSolver::gen_vander_multivar( npts2fit, 2, us, degree, V );
    // remove the first column of 1s if interpolation
    if( interp )
    {
        V.erase( V.begin(), V.begin() + npts2fit );
    }
    /*double* V;
    if(interp){
        V = new double[npts2fit*ncols];
        std::memcpy(V,V_init+npts2fit,ncols*npts2fit*sizeof(double));
        delete [] V_init; V_init = 0;
    }else{
        V = V_init;
    }*/

    // step 3. Scale rows to assign different weights to different points
    for( int i = 0; i < npts2fit; ++i )
    {
        for( int j = 0; j < ncols; ++j )
        {
            V[j * npts2fit + i] *= ws[i];
        }
        for( int k = 0; k < ndim; ++k )
        {
            bs[k * npts2fit + i] *= ws[i];
        }
    }

    // step 4. scale columns to reduce condition number
    std::vector< double > ts( ncols );  // double *ts = new double[ncols];
    DGMSolver::rescale_matrix( npts2fit, ncols, &( V[0] ), &( ts[0] ) );

    // step 5. Perform Householder QR factorization
    std::vector< double > D( ncols );  // double *D = new double[ncols];
    int rank;
    DGMSolver::qr_polyfit_safeguarded( npts2fit, ncols, &( V[0] ), &( D[0] ), &rank );

    // step 6. adjust degree of fitting according to rank of Vandermonde matrix
    int ncols_sub = ncols;
    while( rank < ncols_sub )
    {
        --degree;
        if( degree == 0 )
        {
            // surface is flat, return 0
            *degree_out = *degree_qr = degree;
            for( int i = 0; i < npts2fit; ++i )
            {
                for( int k = 0; k < ndim; ++k )
                {
                    bs[k * npts2fit + i] = 0;
                }
            }
            return;
        }
        else
        {
            ncols_sub = ( ( ( degree + 2 ) * ( degree + 1 ) ) >> 1 ) - interp;
        }
    }
    *degree_qr = degree;

    // std::cout << "degree_qr: " << *degree_qr << std::endl;

    /* DBG
     * std::cout<<"before Qtb"< 2 )
    {
        coords[0] = tang[0];
        coords[1] = tang[1];
        coords[2] = tang[2];
    }
    if( !coeffs || !ncoeffs )
    {
        return;
    }
    else
    {
        assert( ncoeffs >= 3 * ( degree + 1 ) );
    }
    // step 2. project onto local coordinate system
    int npts2fit = nverts - interp;
    if( !npts2fit )
    {
        *degree_out = 0;
        for( int i = 0; i < ncoeffs; ++i )
        {
            coeffs[0] = 0;
        }
        return;
    }
    std::vector< double > us( npts2fit );      // double *us = new double[npts2fit];
    std::vector< double > bs( npts2fit * 3 );  // double *bs = new double[npts2fit*3];
    double uu[3];
    for( int i = interp; i < nverts; ++i )
    {
        int k = i - interp;
        DGMSolver::vec_linear_operation( 3, 1, ngbcors + 3 * i, -1, ngbcors, uu );
        us[k]                = DGMSolver::vec_innerprod( 3, uu, tang );
        bs[k]                = uu[0];
        bs[npts2fit + k]     = uu[1];
        bs[2 * npts2fit + k] = uu[2];
    }

    // step 3. copmute weights
    std::vector< double > ws( npts2fit );
    int nzeros = compute_weights( npts2fit, 1, &( us[0] ), nverts, ngbtangs, degree, _MINEPS, &( ws[0] ) );
    assert( nzeros <= npts2fit );

    // step 4. adjust according to number of zero-weights
    if( nzeros )
    {
        if( nzeros == npts2fit )
        {
            // singular case
            *degree_out = 0;
            for( int i = 0; i < ncoeffs; ++i )
            {
                coeffs[i] = 0;
            }
            return;
        }
        int npts_new = npts2fit - nzeros;
        std::vector< double > bs_temp( 3 * npts_new );
        int index = 0;
        for( int i = 0; i < npts2fit; ++i )
        {
            if( ws[i] )
            {
                if( i > index )
                {
                    us[index] = us[i];
                    ws[index] = ws[i];
                }
                bs_temp[index]                = bs[i];
                bs_temp[index + npts_new]     = bs[i + npts2fit];
                bs_temp[index + 2 * npts_new] = bs[i + 2 * npts2fit];
                ++index;
            }
        }
        assert( index == npts_new );
        npts2fit = npts_new;
        us.resize( index );
        ws.resize( index );
        bs = bs_temp;
        // destroy bs_temp;
        std::vector< double >().swap( bs_temp );
    }

    // step 5. fitting
    eval_vander_univar_cmf( npts2fit, &( us[0] ), 3, &( bs[0] ), degree, &( ws[0] ), interp, safeguard, degree_out );
    // step 6. write results to output pointers
    int ncoeffs_out_pvpd = *degree_out + 1;
    assert( ncoeffs >= 3 * ncoeffs_out_pvpd );
    // write to coeffs consecutively, bs's size is not changed by eval_vander_univar_cmf
    coeffs[0] = coeffs[ncoeffs_out_pvpd] = coeffs[2 * ncoeffs_out_pvpd] = 0;
    for( int i = 0; i < ncoeffs_out_pvpd - interp; ++i )
    {
        coeffs[i + interp]                        = bs[i];
        coeffs[i + interp + ncoeffs_out_pvpd]     = bs[i + npts2fit];
        coeffs[i + interp + 2 * ncoeffs_out_pvpd] = bs[i + 2 * npts2fit];
    }
}

void HiReconstruction::eval_vander_univar_cmf( const int npts2fit,
                                               const double* us,
                                               const int ndim,
                                               double* bs,
                                               int degree,
                                               const double* ws,
                                               const bool interp,
                                               const bool safeguard,
                                               int* degree_out )
{
    // step 1. determine degree of polynomials to fit according to number of points
    int ncols = degree + 1 - interp;
    while( npts2fit < ncols && degree >= 1 )
    {
        --degree;
        ncols = degree + 1 - interp;
    }
    if( !degree )
    {
        if( interp )
        {
            for( int icol = 0; icol < ndim; ++icol )
            {
                bs[icol * npts2fit] = 0;
            }
        }
        for( int irow = 1; irow < npts2fit; ++irow )
        {
            for( int icol = 0; icol < ndim; ++icol )
            {
                bs[icol * npts2fit + irow] = 0;
            }
        }
        *degree_out = 0;
        return;
    }
    // step 2. construct Vandermonde matrix
    std::vector< double > V;  // V(npts2fit*(ncols+interp));
    DGMSolver::gen_vander_multivar( npts2fit, 1, us, degree, V );

    if( interp )
    {
        V.erase( V.begin(), V.begin() + npts2fit );
    }

    // step 3. scale rows with respect to weights
    for( int i = 0; i < npts2fit; ++i )
    {
        for( int j = 0; j < ncols; ++j )
        {
            V[j * npts2fit + i] *= ws[i];
        }
        for( int k = 0; k < ndim; ++k )
        {
            bs[k * npts2fit + i] *= ws[i];
        }
    }

    // step 4. scale columns to reduce condition number
    std::vector< double > ts( ncols );
    DGMSolver::rescale_matrix( npts2fit, ncols, &( V[0] ), &( ts[0] ) );

    // step 5. perform Householder QR factorization
    std::vector< double > D( ncols );
    int rank;
    DGMSolver::qr_polyfit_safeguarded( npts2fit, ncols, &( V[0] ), &( D[0] ), &rank );

    // step 6. adjust degree of fitting
    int ncols_sub = ncols;
    while( rank < ncols_sub )
    {
        --degree;
        if( !degree )
        {
            // matrix is singular, consider curve on flat plane passing center and orthogonal to
            // tangent line
            *degree_out = 0;
            for( int i = 0; i < npts2fit; ++i )
            {
                for( int k = 0; k < ndim; ++k )
                {
                    bs[k * npts2fit + i] = 0;
                }
            }
        }
        ncols_sub = degree + 1 - interp;
    }

    // step 7. compute Q'*bs
    DGMSolver::compute_qtransposeB( npts2fit, ncols_sub, &( V[0] ), ndim, bs );

    // step 8. perform backward substitution and scale solutions
    // assign diagonals of V
    for( int i = 0; i < ncols_sub; ++i )
    {
        V[i * npts2fit + i] = D[i];
    }
    // backsolve
    if( safeguard )
    {
        DGMSolver::backsolve_polyfit_safeguarded( 1, degree, interp, npts2fit, ncols, &( V[0] ), ndim, bs, ws,
                                                  degree_out );
    }
    else
    {
        DGMSolver::backsolve( npts2fit, ncols_sub, &( V[0] ), ndim, bs, &( ts[0] ) );
        *degree_out = degree;
    }
}

int HiReconstruction::compute_weights( const int nrows,
                                       const int ncols,
                                       const double* us,
                                       const int nngbs,
                                       const double* ngbnrms,
                                       const int degree,
                                       const double toler,
                                       double* ws )
{
    assert( nrows <= _MAXPNTS && ws );
    bool interp = false;
    if( nngbs != nrows )
    {
        assert( nngbs == nrows + 1 );
        interp = true;
    }
    double epsilon = 1e-2;

    // First, compute squared distance from each input piont to the center
    for( int i = 0; i < nrows; ++i )
    {
        ws[i] = DGMSolver::vec_innerprod( ncols, us + i * ncols, us + i * ncols );
    }

    // Second, compute a small correction termt o guard against zero
    double h = 0;
    for( int i = 0; i < nrows; ++i )
    {
        h += ws[i];
    }
    h /= (double)nrows;

    // Finally, compute the weights for each vertex
    int nzeros = 0;
    for( int i = 0; i < nrows; ++i )
    {
        double costheta = DGMSolver::vec_innerprod( 3, ngbnrms, ngbnrms + 3 * ( i + interp ) );
        if( costheta > toler )
        {
            ws[i] = costheta * pow( ws[i] / h + epsilon, -1 * (double)degree / 2.0 );
        }
        else
        {
            ws[i] = 0;
            ++nzeros;
        }
    }
    return nzeros;
}
bool HiReconstruction::check_barycentric_coords( const int nws, const double* naturalcoords )
{
    double sum = 0;
    for( int i = 0; i < nws; ++i )
    {
        if( naturalcoords[i] < -_MINEPS )
        {
            return false;
        }
        sum += naturalcoords[i];
    }
    if( fabs( 1 - sum ) > _MINEPS )
    {
        return false;
    }
    else
    {
        return true;
    }
}
}  // namespace moab