// DataSet_Modes::SetAvgCoords()
void DataSet_Modes::SetAvgCoords(DataSet_2D const& mIn) {
avgcrd_.clear();
mass_.clear();
if (mIn.Type() == DataSet::MATRIX_DBL && mIn.Meta().ScalarType() != MetaData::UNDEFINED)
{ // May have avg coords
DataSet_MatrixDbl const& mat = static_cast<DataSet_MatrixDbl const&>( mIn );
avgcrd_ = mat.Vect();
mass_ = mat.Mass();
}
}
/** Assume input matrix contains all distances beween sets A and B.
* The directed Hausdorff distance from A to B will be the maximum of all
* minimums in each row.
* The directed Hausdorff distance from B to A will be the maximum of all
* minimums in each column.
* The symmetric Hausdorff distance is the max of the two directed distances.
* \param m1 The matrix containing distances from A to B.
* \param hd_ab The directed Hausdorff distance from A to B.
* \param hd_ba The directed Hausdorff distance from B to A.
* \return the symmetric Hausdorff distance.
*/
double Analysis_HausdorffDistance::CalcHausdorffFromMatrix(DataSet_2D const& m1,
double& hd_ab, double& hd_ba)
{
// if (m1 == 0) {
// mprinterr("Internal Error: Analysis_HausdorffDistance::(): Matrix set is null.\n");
// return -1.0;
// }
if (m1.Size() < 1) {
mprinterr("Error: '%s' is empty.\n", m1.legend());
return -1.0;
}
// Hausdorff distance from A to B.
hd_ab = 0.0;
for (unsigned int row = 0; row != m1.Nrows(); row++)
{
double minRow = m1.GetElement(0, row);
for (unsigned int col = 1; col != m1.Ncols(); col++)
minRow = std::min( minRow, m1.GetElement(col, row) );
//mprintf("DEBUG: Min row %6u is %12.4f\n", row, minRow);
hd_ab = std::max( hd_ab, minRow );
}
//mprintf("DEBUG: Hausdorff A to B= %12.4f\n", hd_ab);
// Hausdorff distance from B to A.
hd_ba = 0.0;
for (unsigned int col = 0; col != m1.Ncols(); col++)
{
double minCol = m1.GetElement(col, 0);
for (unsigned int row = 1; row != m1.Nrows(); row++)
minCol = std::min( minCol, m1.GetElement(col, row) );
//mprintf("DEBUG: Min col %6u is %12.4f\n", col, minCol);
hd_ba = std::max( hd_ba, minCol);
}
//mprintf("DEBUG: Hausdorff B to A= %12.4f\n", hd_ba);
// Symmetric Hausdorff distance
double hd = std::max( hd_ab, hd_ba );
return hd;
}
/** Get eigenvectors and eigenvalues. They will be stored in descending
* order (largest eigenvalue first).
*/
int DataSet_Modes::CalcEigen(DataSet_2D const& mIn, int n_to_calc) {
#ifdef NO_MATHLIB
mprinterr("Error: modes: Compiled without ARPACK/LAPACK/BLAS routines.\n");
return 1;
#else
bool eigenvaluesOnly = false;
int info = 0;
if (mIn.MatrixKind() != DataSet_2D::HALF) {
mprinterr("Error: DataSet_Modes: Eigenvector/value calc only for symmetric matrices.\n");
return 1;
}
// If number to calc is 0, assume we want eigenvalues only
if (n_to_calc < 1) {
if (n_to_calc == 0) eigenvaluesOnly = true;
nmodes_ = (int)mIn.Ncols();
} else
nmodes_ = n_to_calc;
if (nmodes_ > (int)mIn.Ncols()) {
mprintf("Warning: Specified # of eigenvalues to calc (%i) > matrix dimension (%i).\n",
nmodes_, mIn.Ncols());
nmodes_ = mIn.Ncols();
mprintf("Warning: Only calculating %i eigenvalues.\n", nmodes_);
}
if (eigenvaluesOnly)
mprintf("\tCalculating %i eigenvalues only.\n", nmodes_);
else
mprintf("\tCalculating %i eigenvectors and eigenvalues.\n", nmodes_);
// -----------------------------------------------------------------
if (nmodes_ == (int)mIn.Ncols()) {
// Calculate all eigenvalues (and optionally eigenvectors).
char jobz = 'V'; // Default: Calc both eigenvectors and eigenvalues
vecsize_ = mIn.Ncols();
// Check if only calculating eigenvalues
if (eigenvaluesOnly) {
jobz = 'N';
vecsize_ = 1;
}
// Set up space to hold eigenvectors
if (evectors_ != 0) delete[] evectors_;
if (!eigenvaluesOnly)
evectors_ = new double[ nmodes_ * vecsize_ ];
else
evectors_ = 0;
// Set up space to hold eigenvalues
if (evalues_ != 0) delete[] evalues_;
evalues_ = new double[ nmodes_ ];
// Create copy of matrix since call to dspev destroys it
double* mat = mIn.MatrixArray();
// Lower triangle; not upper since fortran array layout is inverted w.r.t. C/C++
char uplo = 'L';
// Allocate temporary workspace
double* work = new double[ 3 * nmodes_ ];
// NOTE: The call to dspev is supposed to store eigenvectors in columns.
// However as mentioned above fortran array layout is inverted
// w.r.t. C/C++ so eigenvectors end up in rows.
// NOTE: Eigenvalues/vectors are returned in ascending order.
dspev_(jobz, uplo, nmodes_, mat, evalues_, evectors_, vecsize_, work, info);
// If no eigenvectors calcd set vecsize to 0
if (evectors_==0)
vecsize_ = 0;
delete[] work;
delete[] mat;
if (info != 0) {
if (info < 0) {
mprinterr("Internal Error: from dspev: Argument %i had illegal value.\n", -info);
mprinterr("Args: %c %c %i matrix %x %x %i work %i\n", jobz, uplo, nmodes_,
evalues_, evectors_, vecsize_, info);
} else { // info > 0
mprinterr("Internal Error: from dspev: The algorithm failed to converge.\n");
mprinterr("%i off-diagonal elements of an intermediate tridiagonal form\n", info);
mprinterr("did not converge to zero.\n");
}
return 1;
}
// -----------------------------------------------------------------
} else {
// Calculate up to n-1 eigenvalues/vectors using the Implicitly Restarted
// Arnoldi iteration.
// FIXME: Eigenvectors obtained with this method appear to have signs
// flipped compared to full method - is dot product wrong?
int nelem = mIn.Ncols(); // Dimension of input matrix (N)
// Allocate memory to store eigenvectors
vecsize_ = mIn.Ncols();
int ncv; // # of columns of the matrix V (evectors_), <= N (mIn.Ncols())
if (evectors_!=0) delete[] evectors_;
if (nmodes_*2 <= nelem)
ncv = nmodes_*2;
else
ncv = nelem;
evectors_ = new double[ ncv * nelem ];
// Temporary storage for eigenvectors to avoid memory overlap in dseupd
double* eigenvectors = new double[ ncv * nelem ];
// Allocate memory to store eigenvalues
if ( evalues_ != 0) delete[] evalues_;
evalues_ = new double[ nelem ] ; // NOTE: Should this be nmodes?
// Allocate workspace
double* workd = new double[ 3 * nelem ];
int lworkl = ncv * (ncv+8); // NOTE: should this be ncv^2 * (ncv+8)
double* workl = new double[ lworkl ];
double* resid = new double[ nelem ];
// Set parameters for dsaupd (Arnolid)
int ido = 0; // Reverse comm. flag; 0 = first call
// The iparam array is used to set parameters for the calc.
int iparam[11];
std::fill( iparam, iparam + 11, 0 );
iparam[0] = 1; // Method for selecting implicit shifts; 1 = exact
iparam[2] = 300; // Max # of iterations allowed
iparam[3] = 1; // blocksize to be used in the recurrence (code works with only 1).
iparam[6] = 1; // Type of eigenproblem being solved; 1: A*x = lambda*x
double tol = 0; // Stopping criterion (tolerance); 0 = arpack default
char bmat = 'I'; // Type of matrix B that defines semi-inner product; I = identity
char which[2]; // Which of the Ritz values of OP to compute;
which[0] = 'L'; // 'LA' = compute the NEV largest eigenvalues
which[1] = 'A';
// The ipntr array will hold starting locations in workd and workl arrays
// for matrices/vectors used by the Lanczos iteration.
int ipntr[11];
std::fill( ipntr, ipntr + 11, 0 );
// Create copy of matrix since it will be modified
double* mat = mIn.MatrixArray();
// LOOP
bool loop = false;
do {
if (loop) {
// Dot products
double* target = workd + (ipntr[1] - 1); // -1 since fortran indexing starts at 1
double* vec = workd + (ipntr[0] - 1);
std::fill( target, target + nelem, 0 );
for(int i = 0; i < nelem; i++) {
for(int j = i; j < nelem; j++) {
int ind = nelem * i + j - (i * (i + 1)) / 2;
target[i] += mat[ind] * vec[j];
if(i != j)
target[j] += mat[ind] * vec[i];
}
}
}
dsaupd_(ido, bmat, nelem, which, nmodes_, tol, resid,
ncv, eigenvectors, nelem, iparam, ipntr, workd, workl,
lworkl, info);
loop = (ido == -1 || ido == 1);
} while ( loop ); // END LOOP
if (info != 0) {
mprinterr("Error: DataSet_Modes: dsaupd returned %i\n",info);
} else {
int rvec = 1;
char howmny = 'A';
double sigma = 0.0;
int* select = new int[ ncv ];
dseupd_(rvec, howmny, select, evalues_, evectors_, nelem, sigma,
bmat, nelem, which, nmodes_, tol, resid,
ncv, eigenvectors, nelem, iparam, ipntr, workd, workl,
lworkl, info);
delete[] select;
}
delete[] mat;
delete[] workl;
delete[] workd;
delete[] resid;
delete[] eigenvectors;
if (info != 0) {
mprinterr("Error: DataSet_Modes: dseupd returned %i\n",info);
return 1;
}
}
// Eigenvalues and eigenvectors are in ascending order. Resort so that
// they are in descending order (i.e. largest eigenvalue first).
int pivot = nmodes_ / 2;
int nmode = nmodes_ - 1;
double* vtmp = 0;
if (evectors_ != 0)
vtmp = new double[ vecsize_ ];
for (int mode = 0; mode < pivot; ++mode) {
// Swap eigenvalue
double eval = evalues_[mode];
evalues_[mode] = evalues_[nmode];
evalues_[nmode] = eval;
// Swap eigenvector
if (vtmp != 0) {
double* Vec0 = evectors_ + (mode * vecsize_);
double* Vec1 = evectors_ + (nmode * vecsize_);
std::copy( Vec0, Vec0 + vecsize_, vtmp );
std::copy( Vec1, Vec1 + vecsize_, Vec0 );
std::copy( vtmp, vtmp + vecsize_, Vec1 );
}
--nmode;
}
if (vtmp != 0) delete[] vtmp;
return 0;
#endif
}
