void Threads::FnBac(const Complex & cpx, int *res) const
{
int iter =0;
Complex tmpp;
Complex tmp;
Complex tmpn(cpx);
for (iter = 0; tmpn.Abs2() < 4 && iter < maxIter ;iter++){
tmp = tmpn;
tmpn = tmp * tmp + tmpp.Re() + tmpp.Im() + julia_c;
tmpp = tmp;
}
*res = iter;
}
void Threads::FnPhoenix(const Complex & cpx, int *res) const
{
int iter =0;
Complex tmpp;
Complex tmp;
Complex tmpn(cpx);
for (iter = 0; tmpn.Abs2() < 4 && iter < maxIter ;iter++){
tmp = tmpn;
tmpn = tmp * tmp + julia_c.Re() + Complex(0,julia_c.Im()) * tmpp;
tmpp = tmp;
}
*res = iter;
}
List log_EMx(const arma::mat& transition_, const arma::cube& emission_,
const arma::vec& init_, const arma::ucube& obs, const arma::uvec& nSymbols,
const arma::mat& coef_, const arma::mat& X, const arma::uvec& numberOfStates,
int itermax, double tol, int trace, unsigned int threads) {
// Make sure we don't alter the original vec/mat/cube
// needed for cube, in future maybe in other cases as well
arma::cube emission = log(emission_);
arma::mat transition = log(transition_);
arma::vec init = log(init_);
arma::mat coef(coef_);
coef.col(0).zeros();
arma::mat weights = exp(X * coef).t();
if (!weights.is_finite()) {
return List::create(Named("error") = 3);
}
weights.each_row() /= sum(weights, 0);
weights = log(weights);
arma::mat initk(emission.n_rows, obs.n_slices);
for (unsigned int k = 0; k < obs.n_slices; k++) {
initk.col(k) = init + reparma(weights.col(k), numberOfStates);
}
arma::cube alpha(emission.n_rows, obs.n_cols, obs.n_slices); //m,n,k
arma::cube beta(emission.n_rows, obs.n_cols, obs.n_slices); //m,n,k
log_internalForwardx(transition, emission, initk, obs, alpha, threads);
log_internalBackward(transition, emission, obs, beta, threads);
arma::vec ll(obs.n_slices);
#pragma omp parallel for if(obs.n_slices >= threads) schedule(static) num_threads(threads) \
default(none) shared(obs, alpha, ll)
for (unsigned int k = 0; k < obs.n_slices; k++) {
ll(k) = logSumExp(alpha.slice(k).col(obs.n_cols - 1));
}
double sumlogLik = sum(ll);
if (trace > 0) {
Rcout << "Log-likelihood of initial model: " << sumlogLik << std::endl;
}
//
// //EM-algorithm begins
//
double change = tol + 1.0;
int iter = 0;
arma::uvec cumsumstate = cumsum(numberOfStates);
while ((change > tol) & (iter < itermax)) {
iter++;
arma::mat ksii(emission.n_rows, emission.n_rows, arma::fill::zeros);
arma::cube gamma(emission.n_rows, emission.n_cols, emission.n_slices, arma::fill::zeros);
arma::vec delta(emission.n_rows, arma::fill::zeros);
for (unsigned int k = 0; k < obs.n_slices; k++) {
delta += exp(alpha.slice(k).col(0) + beta.slice(k).col(0) - ll(k));
}
#pragma omp parallel for if(obs.n_slices>=threads) schedule(static) num_threads(threads) \
default(none) shared(transition, obs, ll, alpha, beta, emission, ksii, gamma, nSymbols)
for (unsigned int k = 0; k < obs.n_slices; k++) {
if (obs.n_cols > 1) {
for (unsigned int j = 0; j < emission.n_rows; j++) {
for (unsigned int i = 0; i < emission.n_rows; i++) {
if (transition(i, j) > -arma::datum::inf) {
arma::vec tmpnm1(obs.n_cols - 1);
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
tmpnm1(t) = alpha(i, t, k) + transition(i, j) + beta(j, t + 1, k);
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmpnm1(t) += emission(j, obs(r, t + 1, k), r);
}
}
#pragma omp atomic
ksii(i, j) += exp(logSumExp(tmpnm1) - ll(k));
}
}
}
}
for (unsigned int r = 0; r < emission.n_slices; r++) {
for (unsigned int l = 0; l < nSymbols[r]; l++) {
for (unsigned int i = 0; i < emission.n_rows; i++) {
if (emission(i, l, r) > -arma::datum::inf) {
arma::vec tmpn(obs.n_cols);
for (unsigned int t = 0; t < obs.n_cols; t++) {
if (l == (obs(r, t, k))) {
tmpn(t) = alpha(i, t, k) + beta(i, t, k);
} else
tmpn(t) = -arma::datum::inf;
}
#pragma omp atomic
gamma(i, l, r) += exp(logSumExp(tmpn) - ll(k));
}
}
}
}
}
unsigned int error = log_optCoef(weights, obs, emission, initk, beta, ll, coef, X, cumsumstate,
numberOfStates, trace);
if (error != 0) {
return List::create(Named("error") = error);
}
if (obs.n_cols > 1) {
ksii.each_col() /= sum(ksii, 1);
transition = log(ksii);
}
for (unsigned int r = 0; r < emission.n_slices; r++) {
gamma.slice(r).cols(0, nSymbols(r) - 1).each_col() /= sum(
gamma.slice(r).cols(0, nSymbols(r) - 1), 1);
emission.slice(r).cols(0, nSymbols(r) - 1) = log(gamma.slice(r).cols(0, nSymbols(r) - 1));
}
for (unsigned int i = 0; i < numberOfStates.n_elem; i++) {
delta.subvec(cumsumstate(i) - numberOfStates(i), cumsumstate(i) - 1) /= arma::as_scalar(
arma::accu(delta.subvec(cumsumstate(i) - numberOfStates(i), cumsumstate(i) - 1)));
}
init = log(delta);
for (unsigned int k = 0; k < obs.n_slices; k++) {
initk.col(k) = init + reparma(weights.col(k), numberOfStates);
}
log_internalForwardx(transition, emission, initk, obs, alpha, threads);
log_internalBackward(transition, emission, obs, beta, threads);
for (unsigned int k = 0; k < obs.n_slices; k++) {
ll(k) = logSumExp(alpha.slice(k).col(obs.n_cols - 1));
}
double tmp = sum(ll);
change = (tmp - sumlogLik) / (std::abs(sumlogLik) + 0.1);
sumlogLik = tmp;
if (!arma::is_finite(sumlogLik)) {
return List::create(Named("error") = 6);
}
if (trace > 1) {
Rcout << "iter: " << iter;
Rcout << " logLik: " << sumlogLik;
Rcout << " relative change: " << change << std::endl;
}
}
if (trace > 0) {
if (iter == itermax) {
Rcpp::Rcout << "EM algorithm stopped after reaching the maximum number of " << iter
<< " iterations." << std::endl;
} else {
Rcpp::Rcout << "EM algorithm stopped after reaching the relative change of " << change;
Rcpp::Rcout << " after " << iter << " iterations." << std::endl;
}
Rcpp::Rcout << "Final log-likelihood: " << sumlogLik << std::endl;
}
return List::create(Named("coefficients") = wrap(coef), Named("initialProbs") = wrap(exp(init)),
Named("transitionMatrix") = wrap(exp(transition)),
Named("emissionArray") = wrap(exp(emission)), Named("logLik") = sumlogLik,
Named("iterations") = iter, Named("change") = change, Named("error") = 0);
}
void TriangleType::draw(RenderMode::WhichColorMode& wcm, RenderMode::RenderType& r,const Matrix44& adjust_matrix, const Vec3& bias)
{
if (!visible_)
{
return;
}
// std::vector<Vertex*>& vs = sample_.vertices_;
//r = RenderMode::PointMode;
switch(r)
{
case RenderMode::PointMode:{
break;
}
case RenderMode::FlatMode:{
glBegin(GL_TRIANGLES);
for( int i = 0 ;i <3 ;++i)
{
if(this->i_norm[i]!=-1)
{
Vec4 tmpn( sample_[this->i_norm[i]].nx() , sample_[this->i_norm[i]].ny() ,sample_[this->i_norm[i]].nz() ,1.);
Vec4 normal_to_show = tmpn;//adjust_matrix * tmpn;
glNormal3f(
normal_to_show(0),
normal_to_show(1),
normal_to_show(2));
//Logger<<"NORMAL: "<<(float)vs[this->i_norm[i]]->nx()<<" "<<
// (float)vs[this->i_norm[i]]->ny()<<" "<<
// (float)vs[this->i_norm[i]]->nz()<<std::endl;
}
ColorType color2 = Color_Utility::span_color_from_table(sample_[this->i_vertex[i]].label());
glColor3f( color2(0) ,color2(1) ,color2(2)
/* (GLfloat) vs[this->i_vertex[i]]->r(),
(GLfloat) vs[this->i_vertex[i]]->g(),
(GLfloat) vs[this->i_vertex[i]]->b()*/ );
//Logger<<"COLOR: "<<vs[this->i_vertex[i]]->r()<<" "<<
// vs[this->i_vertex[i]]->g()<<" "<<
// vs[this->i_vertex[i]]->b()<<std::endl;
Vec4 tmpv( sample_[this->i_vertex[i]].x() , sample_[this->i_vertex[i]].y() ,sample_[this->i_vertex[i]].z() ,1.);
Vec4 point_to_show = adjust_matrix * tmpv;
glVertex3f(
point_to_show(0)+ bias(0),
point_to_show(1)+ bias(1),
point_to_show(2)+ bias(2) );
//Logger<<"VERTEX: "<<vs[this->i_vertex[i]]->x()<<" "<<
// vs[this->i_vertex[i]]->y()<<" "<<
// vs[this->i_vertex[i]]->z()<<std::endl;
}
glEnd();
break;
}
case RenderMode::WireMode:{
glLineWidth(2.0f);
glBegin(GL_LINE_LOOP);
for( int i = 0 ;i <3 ;++i)
{
if(this->i_norm[i]!=-1)
{
Vec4 tmpn( sample_[this->i_norm[i]].nx() , sample_[this->i_norm[i]].ny() ,sample_[this->i_norm[i]].nz() ,1.);
Vec4 normal_to_show = adjust_matrix * tmpn;
glNormal3f(
normal_to_show(0),
normal_to_show(1),
normal_to_show(2));
}
ColorType color2 = Color_Utility::span_color_from_table(sample_[this->i_vertex[i]].label());
glColor3f( color2(0) ,color2(1) ,color2(2)
/*(GLfloat) vs[this->i_vertex[i]]->r(),
(GLfloat) vs[this->i_vertex[i]]->g(),
(GLfloat) vs[this->i_vertex[i]]->b() */);
Vec4 tmpv( sample_[this->i_vertex[i]].x() , sample_[this->i_vertex[i]].y() ,sample_[this->i_vertex[i]].z() ,1.);
Vec4 point_to_show = adjust_matrix * tmpv;
glVertex3f(
point_to_show(0)+ bias(0),
point_to_show(1)+ bias(1),
point_to_show(2)+ bias(2) );
}
glEnd();
break;
}
case RenderMode::FlatWireMode:{
glBegin(GL_TRIANGLES);
for( int i = 0 ;i <3 ;++i)
{
if(this->i_norm[i]!=-1)
{
Vec4 tmpn( sample_[this->i_norm[i]].nx() , sample_[this->i_norm[i]].ny() ,sample_[this->i_norm[i]].nz() ,1.);
Vec4 normal_to_show = tmpn;//adjust_matrix * tmpn;
glNormal3f(
normal_to_show(0),
normal_to_show(1),
normal_to_show(2));
//Logger<<"NORMAL: "<<(float)vs[this->i_norm[i]]->nx()<<" "<<
// (float)vs[this->i_norm[i]]->ny()<<" "<<
// (float)vs[this->i_norm[i]]->nz()<<std::endl;
}
ColorType color2 = Color_Utility::span_color_from_table(sample_[this->i_vertex[i]].label());
glColor3f( color2(0) ,color2(1) ,color2(2)
/* (GLfloat) vs[this->i_vertex[i]]->r(),
(GLfloat) vs[this->i_vertex[i]]->g(),
(GLfloat) vs[this->i_vertex[i]]->b()*/ );
//Logger<<"COLOR: "<<vs[this->i_vertex[i]]->r()<<" "<<
// vs[this->i_vertex[i]]->g()<<" "<<
// vs[this->i_vertex[i]]->b()<<std::endl;
Vec4 tmpv( sample_[this->i_vertex[i]].x() , sample_[this->i_vertex[i]].y() ,sample_[this->i_vertex[i]].z() ,1.);
Vec4 point_to_show = adjust_matrix * tmpv;
glVertex3f(
point_to_show(0)+ bias(0),
point_to_show(1)+ bias(1),
point_to_show(2)+ bias(2) );
//Logger<<"VERTEX: "<<vs[this->i_vertex[i]]->x()<<" "<<
// vs[this->i_vertex[i]]->y()<<" "<<
// vs[this->i_vertex[i]]->z()<<std::endl;
}
glEnd();
glLineWidth(2.0f);
glBegin(GL_LINE_LOOP);
for( int i = 0 ;i <3 ;++i)
{
if(this->i_norm[i]!=-1)
{
Vec4 tmpn( sample_[this->i_norm[i]].nx() , sample_[this->i_norm[i]].ny() ,sample_[this->i_norm[i]].nz() ,1.);
Vec4 normal_to_show = adjust_matrix * tmpn;
glNormal3f(
normal_to_show(0),
normal_to_show(1),
normal_to_show(2));
}
glColor3f( 0.5f,0.5f,0.5f
/*(GLfloat) vs[this->i_vertex[i]]->r(),
(GLfloat) vs[this->i_vertex[i]]->g(),
(GLfloat) vs[this->i_vertex[i]]->b() */);
Vec4 tmpv( sample_[this->i_vertex[i]].x() , sample_[this->i_vertex[i]].y() ,sample_[this->i_vertex[i]].z() ,1.);
Vec4 point_to_show = adjust_matrix * tmpv;
glVertex3f(
point_to_show(0)+ bias(0),
point_to_show(1)+ bias(1),
point_to_show(2)+ bias(2) );
}
glEnd();
break;
}
case RenderMode::SmoothMode:{ break;}
case RenderMode::TextureMode:{ break;}
case RenderMode::SelectMode:{ break;}
default:{}
}
}
