void NeighbourJoining::configure(const MatrixXf& D, MatrixXf& currentD, MatrixXi& rowsID, int numOccupiedNodes) {
numObservableNodes = rowsID.rows();
numCurrentNodes = numObservableNodes;
//allocates memory for the latent nodes
rowsID.conservativeResize((2 * numObservableNodes - 2), 1);
//gives latent nodes IDs
for (int i = numObservableNodes; i < 2 * numObservableNodes - 2; ++i) {
rowsID(i) = i + numOccupiedNodes;
}
sort(rowsID.data(), rowsID.data() + rowsID.size());
//cout << "rowsID after sort:" << rowsID.transpose(); cout << endl;
//copies distances of selected Nodes
int offseti = 0; int offsetj = 0;
for (int i = 0; i < numObservableNodes; ++i) {
while (rowsID(i) != i + offseti)
++offseti;
offsetj = 0;
for (int j = 0; j < numObservableNodes; ++j) {
while (rowsID(j) != j + offsetj)
++offsetj;
currentD(i, j) = D(i + offseti, j + offsetj);
currentD(j, i) = currentD(i, j);
}
}
//cout << "copied matrix: " << endl; printMatrix(currentD);
}
MatrixXf CharacterController::GenerateXapv(const std::vector<int> &activeParts)
{
// pvDim without
auto& allClipinfo = m_cpxClipinfo;
auto& pvFacade = allClipinfo.PvFacade;
int pvDim = pvFacade.GetAllPartDimension();
assert(pvDim > 0);
MatrixXf Xabpv(allClipinfo.ClipFrames(), size(activeParts) * pvDim);
ArrayXi incX(pvDim);
incX.setLinSpaced(0, pvDim - 1);
MatrixXi apMask = VectorXi::Map(activeParts.data(), activeParts.size()).replicate(1, pvDim).transpose();
apMask.array() = apMask.array() * pvDim + incX.replicate(1, apMask.cols());
auto maskVec = VectorXi::Map(apMask.data(), apMask.size());
selectCols(pvFacade.GetAllPartsSequence(), maskVec, &Xabpv);
Pca<MatrixXf> pcaXabpv(Xabpv);
int dXabpv = pcaXabpv.reducedRank(g_CharacterPcaCutoff);
Xabpv = pcaXabpv.coordinates(dXabpv);
XabpvT = pcaXabpv.components(dXabpv);
uXabpv = pcaXabpv.mean();
if (g_EnableDebugLogging)
{
ofstream fout(g_CharacterAnalyzeDir / (m_pCharacter->Name + "_Xabpv.pd.csv"));
fout << Xabpv.format(CSVFormat);
fout.close();
}
return Xabpv;
}
void read_SparseMatrix(SparseMatrix<double,0,int>& M, string path,string name){
FILE * pFile;
pFile = fopen((path + name+"i.bin").c_str(), "rb");
if (pFile==NULL) {fputs ("File error",stderr); exit (1);}
int n,m,ni;
if(1 != fread(&n,sizeof(int),1,pFile)){
fputs ("Read error\n",stderr); exit (1);
}
if(1 != fread(&m,sizeof(int),1,pFile)){
fputs ("Read error\n",stderr); exit (1);
}
if(1 != fread(&ni,sizeof(int),1,pFile)){
fputs ("Read error\n",stderr); exit (1);
}
M.resize(n,m);
MatrixXi ij;
ij.setZero(ni,2);
if(ni*2 != fread(ij.data(),sizeof(int),ni*2,pFile)){
fputs ("Read error\n",stderr); exit (1);
}
fclose(pFile);
VectorXd v;
v.setZero(ni);
pFile = fopen((path + name+"v.bin").c_str(), "rb");
if (pFile==NULL) {fputs ("File error",stderr); exit (1);}
if(ni != fread(v.data(),sizeof(double),ni,pFile)){
fputs ("Read error\n",stderr); exit (1);
}
fclose(pFile);
vector<T> coef;
for(int i=0;i<ni;i++){
coef.push_back(T(ij(i,0),ij(i,1),v(i)));
}
M.setFromTriplets(coef.begin(), coef.end());
}
void Mesh::CreateSimpleMesh() {
int c = 0;
MatrixXi g(n_node_x, n_node_y);
for (size_t i=0; i<n_node_x; i++) {
for (size_t j=0; j<n_node_y; j++) {
g(i,j) = c;
c++;
}
}
MatrixXi gg(n_node_p_elem, n_elem);
size_t xi = 0;
size_t xj = 0;
for (size_t i=0; i<n_elem; i++) {
size_t xi_min = xi;
size_t xj_min = xj;
size_t xi_max = xi + n_node_p_dim;
size_t xj_max = xj + n_node_p_dim;
MatrixXi block =
g.block(xi_min, xj_min, n_node_p_dim, n_node_p_dim);
Map<VectorXi> gv(block.data(), block.size());
gg.col(i) = gv;
if (xi_max == n_node_x) {
xi = 0;
xj = xj_max - 1;
} else {
xi = xi_max - 1;
}
}
c = 0;
MatrixXi nf(eqn_p_node, n_node);
for (size_t i=0; i<n_node; i++) {
nf(0,i) = c;
nf(1,i) = c+1;
c += 2;
}
imap.resize(n_dof_p_elem, n_elem);
for (size_t i=0; i<n_elem; i++) {
c = 0;
while (c+eqn_p_node <= n_dof_p_elem) {
imap.block(c, i, eqn_p_node, 1) =
nf.block(
0, gg(c/eqn_p_node, i), eqn_p_node, 1);
c += eqn_p_node;
}
}
valen.resize(n_dof_p_elem, n_elem);
valen.setZero();
for (size_t i=0; i<n_elem; i++) {
for (size_t j=0; j<n_dof_p_elem; j++) {
valen(j, i) += 1;
}
}
size_t k = 0;
size_t e = 0;
size_t n_node_x_vis {n_elem_x + 1};
connec.resize(4*n_elem);
for (size_t j=0; j<n_elem_y; j++) {
for (size_t i=0; i<n_elem_x; i++) {
connec(k+0) = (i+0) + (j+0) * n_node_x_vis;
connec(k+1) = (i+1) + (j+0) * n_node_x_vis;
connec(k+2) = (i+1) + (j+1) * n_node_x_vis;
connec(k+3) = (i+0) + (j+1) * n_node_x_vis;
k+=4;
e++;
}
}
connec = connec.array() + 1;
n_vis_node = connec.maxCoeff();
k = 0;
ex.resize(n_vis_node);
ey.resize(n_vis_node);
m_node_n.resize(n_vis_node);
for (size_t j=0; j<=n_elem_y; j++) {
for (size_t i=0; i<=n_elem_x; i++) {
ex(k) = i * s_elem_x;
ey(k) = j * s_elem_y;
m_node_n(k) = k;
k++;
}
}
m_node_n = m_node_n.array() + 1;
ctr_elem_x.resize(n_elem);
ctr_elem_y.resize(n_elem);
k = 0;
for (size_t j=0; j<n_elem_y; j++) {
for (size_t i=0; i<n_elem_x; i++) {
ctr_elem_x(k) = (1/2.) * (ex(k) + ex(k+1));
ctr_elem_y(k) = (1/2.) * (ey(k) + ey(k+1));
k++;
}
}
}
