SupportRenumbering reverse(const SupportRenumbering& numbering)
{
SupportRenumbering ret = reverseRows(numbering);
assert(ret.checkValidity());
ret = transpose(ret);
ret = reverseRows(ret);
assert(ret.checkValidity());
ret = transpose(ret);
return ret;
}
void rotate(vector< vector<int> >& matrix)
{
const int rowSize = matrix.size();
const int colSize = matrix[0].size();
//assert(rowSize == colSize);
if (rowSize == 0)
{
return;
}
transpose(matrix);
reverseRows(matrix);
}
loos::RealMatrix rsv(std::vector<loos::AtomicGroup>& ensemble, ExtractPolicy& extractor) {
loos::RealMatrix M = extractor(ensemble);
loos::RealMatrix C = loos::Math::MMMultiply(M, M, false, true);
// Compute [U,D] = eig(C)
char jobz = 'V';
char uplo = 'L';
f77int n = M.rows();
f77int lda = n;
float dummy;
loos::RealMatrix W(n, 1);
f77int lwork = -1;
f77int info;
ssyev_(&jobz, &uplo, &n, C.get(), &lda, W.get(), &dummy, &lwork, &info);
if (info != 0)
throw(loos::NumericalError("ssyev failed in loos::pca()", info));
lwork = static_cast<f77int>(dummy);
float *work = new float[lwork+1];
ssyev_(&jobz, &uplo, &n, C.get(), &lda, W.get(), work, &lwork, &info);
if (info != 0)
throw(loos::NumericalError("ssyev failed in loos::pca()", info));
reverseColumns(C);
reverseRows(W);
// Correctly scale the eigenvalues
for (uint j=0; j<W.rows(); ++j)
W[j] = W[j] < 0 ? 0.0 : sqrt(W[j]);
// Multiply eigenvectors by inverse eigenvalues
for (uint i=0; i<C.cols(); ++i) {
double konst = (W[i] > 0.0) ? (1.0/W[i]) : 0.0;
for (uint j=0; j<C.rows(); ++j)
C(j, i) *= konst;
}
W.reset();
loos::RealMatrix Vt = loos::Math::MMMultiply(C, M, true, false);
loos::RealMatrix V = loos::Math::transpose(Vt);
return(V);
}
boost::tuple<loos::RealMatrix, loos::RealMatrix> pca(std::vector<loos::AtomicGroup>& ensemble, ExtractPolicy& extractor) {
loos::RealMatrix M = extractor(ensemble);
loos::RealMatrix C = loos::Math::MMMultiply(M, M, false, true);
// Compute [U,D] = eig(C)
char jobz = 'V';
char uplo = 'L';
f77int n = M.rows();
f77int lda = n;
float dummy;
loos::RealMatrix W(n, 1);
f77int lwork = -1;
f77int info;
ssyev_(&jobz, &uplo, &n, C.get(), &lda, W.get(), &dummy, &lwork, &info);
if (info != 0)
throw(loos::NumericalError("ssyev failed in loos::pca()", info));
lwork = static_cast<f77int>(dummy);
float *work = new float[lwork+1];
ssyev_(&jobz, &uplo, &n, C.get(), &lda, W.get(), work, &lwork, &info);
if (info != 0)
throw(loos::NumericalError("ssyev failed in loos::pca()", info));
reverseColumns(C);
reverseRows(W);
// Zap negative eigenvalues...
for (uint j=0; j<W.rows(); ++j)
if (W[j] < 0.0)
W[j] = 0.0;
boost::tuple<loos::RealMatrix, loos::RealMatrix> result(W, C);
return(result);
}
