std::string JtagShiftedData::GetASCIIString(const std::vector<U8>& bits) { std::string ret_val; // Check if the value of the number represented by bits is less than 0x100. // If it is, we can make an ASCII out of it, otherwise use GetDecimalString() std::vector<U8>::const_iterator srch_hi(std::find(bits.begin(), bits.end(), BIT_HIGH)); if (bits.end() - srch_hi <= 8) { // Get the numerical value from the bits. U64 val; // Only get the 8 least significant bits std::vector<U8>::const_iterator bsi(bits.end() - 8); for (val = 0; bsi != bits.end(); ++bsi) val = (val << 1) | (*bsi == BIT_HIGH ? 1 : 0); // make a string out of that value char number_str[32]; AnalyzerHelpers::GetNumberString(val, ASCII, 8, number_str, sizeof(number_str)); ret_val = number_str; } else { ret_val = '\'' + GetDecimalString(bits) + '\''; } return ret_val; }
std::string JtagShiftedData::GetHexOrBinaryString(const std::vector<U8>& bits, DisplayBase display_base) { std::string ret_val; std::vector<U8>::const_iterator bsi(bits.begin()); U64 val; size_t remain_bits = bits.size(), chunk_bits, bit_cnt; char number_str[128]; while (bsi != bits.end()) { chunk_bits = remain_bits % 64; if (chunk_bits == 0) chunk_bits = 64; // make a 64 bit value for (bit_cnt = chunk_bits, val = 0; bsi != bits.end() && bit_cnt > 0; ++bsi, --bit_cnt) { val = (val << 1) | (*bsi == BIT_HIGH ? 1 : 0); } // make a string out of that value AnalyzerHelpers::GetNumberString(val, display_base, (U32) chunk_bits, number_str, sizeof(number_str)); // concat the 64bit chunks but chop off all but the first 0x or 0b if (ret_val.empty()) ret_val = number_str; else ret_val += (number_str + 2); remain_bits -= chunk_bits; } return ret_val; }
std::string JtagShiftedData::GetStringFromBitStates(const std::vector<U8>& bits, DisplayBase display_base) { std::string ret_val; if (bits.size() > 64) { if (display_base == Hexadecimal || display_base == Binary) ret_val = GetHexOrBinaryString(bits, display_base); else if (display_base == Decimal) ret_val = GetDecimalString(bits); else if (display_base == ASCII) ret_val = GetASCIIString(bits); else if (display_base == AsciiHex) ret_val = GetASCIIString(bits) + " (" + GetHexOrBinaryString(bits, Hexadecimal) + ')'; } else { // get the numerical value from the bits std::vector<U8>::const_iterator bsi(bits.begin()); U64 val; // make a 64 bit value for (val = 0; bsi != bits.end(); ++bsi) val = (val << 1) | (*bsi == BIT_HIGH ? 1 : 0); // make a string out of that value char number_str[128]; AnalyzerHelpers::GetNumberString(val, display_base, (U32) bits.size(), number_str, sizeof(number_str)); ret_val = number_str; } return ret_val; }
// [[Rcpp::export]] Rcpp::List 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(emission_); arma::mat transition(transition_); arma::vec init(init_); arma::mat coef(coef_); coef.col(0).zeros(); arma::mat weights = exp(X * coef).t(); if (!weights.is_finite()) { return Rcpp::List::create(Rcpp::Named("error") = 3); } weights.each_row() /= sum(weights, 0); 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); } // // //EM-algorithm begins // double change = tol + 1.0; int iter = 0; arma::uvec cumsumstate = arma::cumsum(numberOfStates); double sumlogLik_new = 0; double sumlogLik = -1e150; 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); arma::mat bsi(emission.n_rows, obs.n_slices); sumlogLik_new = 0; double max_sf = 1; unsigned int error_code = 0; #pragma omp parallel for if(obs.n_slices >= threads) schedule(static) reduction(+:sumlogLik_new) num_threads(threads) \ default(shared) //shared(bsi, initk, transition, obs, emission, delta, ksii, gamma, nSymbols, error_code, max_sf, arma::fill::zeros) for (unsigned int k = 0; k < obs.n_slices; k++) { if (error_code == 0) { arma::mat alpha(emission.n_rows, obs.n_cols); //m,n,k arma::vec scales(obs.n_cols); arma::sp_mat sp_trans(transition); uvForward(sp_trans.t(), emission, initk.col(k), obs.slice(k), alpha, scales); arma::mat beta(emission.n_rows, obs.n_cols); //m,n,k uvBackward(sp_trans, emission, obs.slice(k), beta, scales); sumlogLik_new -= arma::sum(log(scales)); arma::mat ksii_k(emission.n_rows, emission.n_rows, arma::fill::zeros); arma::cube gamma_k(emission.n_rows, emission.n_cols, emission.n_slices, arma::fill::zeros); arma::vec delta_k(emission.n_rows); delta_k = alpha.col(0) % beta.col(0) / scales(0); for (unsigned int i = 0; i < emission.n_rows; i++) { for (unsigned int j = 0; j < emission.n_rows; j++) { if (transition(i, j) > 0.0) { for (unsigned int t = 0; t < (obs.n_cols - 1); t++) { double tmp = alpha(i, t) * transition(i, j) * beta(j, t + 1); for (unsigned int r = 0; r < obs.n_rows; r++) { tmp *= emission(j, obs(r, t + 1, k), r); } ksii_k(i, j) += tmp; } } } } 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) > 0.0) { for (unsigned int t = 0; t < obs.n_cols; t++) { if (l == (obs(r, t, k))) { double tmp = alpha(i, t) * beta(i, t) / scales(t); gamma_k(i, l, r) += tmp; } } } } } } for (unsigned int j = 0; j < emission.n_rows; j++) { bsi(j, k) = beta(j, 0) * initk(j, k); } #pragma omp critical { if(!scales.is_finite()) { error_code = 1; } if(!beta.is_finite()) { error_code = 2; } max_sf = std::min(max_sf, scales.max()); delta += delta_k; ksii += ksii_k; gamma += gamma_k; } } } if(error_code == 1) { return Rcpp::List::create(Rcpp::Named("error") = 1); } if(error_code == 2) { return Rcpp::List::create(Rcpp::Named("error") = 2); } if (max_sf > 1e150) { Rcpp::warning("Largest scaling factor was %e, results can be numerically unstable.", max_sf); } change = (sumlogLik_new - sumlogLik) / (std::abs(sumlogLik) + 0.1); sumlogLik = sumlogLik_new; if (trace > 0) { if(iter == 0) { Rcpp::Rcout << "Log-likelihood of initial model: " << sumlogLik << std::endl; } else { if (trace > 1) { Rcpp::Rcout << "iter: " << iter; Rcpp::Rcout << " logLik: " << sumlogLik; Rcpp::Rcout << " relative change: " << change << std::endl; } } } if (change > tol) { unsigned int error = optCoef(weights, obs, emission, bsi, coef, X, cumsumstate, numberOfStates, trace); if (error != 0) { return Rcpp::List::create(Rcpp::Named("error") = error); } if (obs.n_cols > 1) { ksii.each_col() /= sum(ksii, 1); transition = 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) = 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 = delta; for (unsigned int k = 0; k < obs.n_slices; k++) { initk.col(k) = init % reparma(weights.col(k), numberOfStates); } } } 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 Rcpp::List::create(Rcpp::Named("coefficients") = Rcpp::wrap(coef), Rcpp::Named("initialProbs") = Rcpp::wrap(init), Rcpp::Named("transitionMatrix") = Rcpp::wrap(transition), Rcpp::Named("emissionArray") = Rcpp::wrap(emission), Rcpp::Named("logLik") = sumlogLik, Rcpp::Named("iterations") = iter, Rcpp::Named("change") = change, Rcpp::Named("error") = 0); }