void save_current_iteration(List& trace_x, List& trace_pi, List& trace_A, List& trace_B, List& log_posterior, List& trace_switching_prob,
arma::ivec x, NumericVector pi, NumericMatrix A, NumericMatrix B, double& loglik, NumericVector switching_prob,
int index){
IntegerVector xx(x.begin(), x.end());
trace_x[index] = clone(xx);
trace_pi[index] = clone(pi);
trace_A[index] = clone(A);
trace_B[index] = clone(B);
log_posterior[index] = clone(wrap(loglik));
trace_switching_prob[index] = clone(switching_prob);
}
arma::mat exact_trans2(arma::cube joint_means_trans, Rcpp::List eigen_decomp, double time_int, arma::ivec absorb_states, int start_state, int end_state, int exact_time_index){
arma::mat rate_matrix=Rcpp::as<arma::mat>(eigen_decomp["rate"]);
arma::mat out=arma::zeros<arma::mat>(rate_matrix.n_rows,rate_matrix.n_rows);
arma::mat temp=arma::zeros<arma::mat>(rate_matrix.n_rows,rate_matrix.n_rows);
int i=start_state-1;
int j=end_state-1;
int k=0;
bool i_in_A=0;
bool j_in_A=0;
//std::cout<<absorb_states;
while(i_in_A==0 && k<absorb_states.size()){
int test=absorb_states[k]-1;
if(test==i){
i_in_A=1;
}
k++;
}
k=0;
while(j_in_A==0 && k<absorb_states.size()){
int test=absorb_states[k]-1;
if(test==j){
j_in_A=1;
}
k++;
}
int in_either=i_in_A+j_in_A;
if(in_either==0){
for(int l=0;l<absorb_states.size();l++){
int absorb_state=absorb_states[l]-1;
temp.col(absorb_state)=rate_matrix.col(absorb_state);
}
out=joint_means_trans.slice(exact_time_index)*temp;
}
if(i_in_A==0 && j_in_A==1){
arma::mat prob_mat=mat_exp_eigen_cpp(eigen_decomp,time_int);
out.col(j)=prob_mat.col(i)*rate_matrix(i,j);
}
return(out);
}
arma::mat joint_dur_dur_exact_time(int i,int j, double interval_len, arma::ivec absorb_states,Rcpp::List eigen_decomp){
arma::cx_mat Q=Rcpp::as<arma::cx_mat>(eigen_decomp["rate"]);
double t=interval_len;
arma::mat joint_dur=joint_duration_2moment(i, j,eigen_decomp,t);
arma::cx_mat temp=arma::zeros<arma::cx_mat>(Q.n_rows,Q.n_rows);
bool i_in_A=0;
bool j_in_A=0;
int k=0;
//std::cout<<absorb_states;
while(i_in_A==0 && k<absorb_states.size()){
int test=absorb_states[k];
if(test==i){
i_in_A=1;
}
k++;
}
k=0;
while(j_in_A==0 && k<absorb_states.size()){
int test=absorb_states[k];
if(test==j){
j_in_A=1;
}
k++;
}
int in_either=i_in_A+j_in_A;
if(i_in_A+j_in_A==0){
for(int l=0;l<absorb_states.size();l++){
int absorb_state=absorb_states[l];
temp.col(absorb_state)=Q.col(absorb_state);
}
temp=joint_dur*temp;
}else{
temp=arma::zeros<arma::cx_mat>(Q.n_rows,Q.n_rows);
}
arma::mat out=arma::real(temp);
return(out);
}
// [[Rcpp::export]]
arma::mat sgd(arma::mat& coords,
arma::ivec& targets_i, // vary randomly
arma::ivec& sources_j, // ordered
arma::ivec& ps, // N+1 length vector of indices to start of each row j in vector is
arma::vec& weights, // w{ij}
const double& gamma,
const double& rho,
const arma::uword& n_samples,
const int& M,
const double& alpha,
const Rcpp::Nullable<Rcpp::NumericVector> momentum,
const bool& useDegree,
const Rcpp::Nullable<Rcpp::NumericVector> seed,
const Rcpp::Nullable<Rcpp::NumericVector> threads,
const bool verbose) {
#ifdef _OPENMP
checkCRAN(threads);
#endif
const dimidxtype D = coords.n_rows;
const vertexidxtype N = coords.n_cols;
const edgeidxtype E = targets_i.n_elem;
Visualizer* v;
if (momentum.isNull()) v = new Visualizer(
sources_j.memptr(), targets_i.memptr(), coords.memptr(),
D, N, E,
rho, n_samples,
M, alpha, gamma);
else {
float moment = NumericVector(momentum)[0];
if (moment < 0) throw Rcpp::exception("Momentum cannot be negative.");
if (moment > 0.95) throw Rcpp::exception("Bad things happen when momentum is > 0.95.");
v = new MomentumVisualizer(
sources_j.memptr(), targets_i.memptr(), coords.memptr(),
D, N, E,
rho, n_samples, moment,
M, alpha, gamma);
}
distancetype* negweights = new distancetype[N];
std::fill(negweights, negweights + N, 0);
if (useDegree) {
std::for_each(targets_i.begin(), targets_i.end(), [&negweights](const sword& e) {negweights[e]++;});
} else {
for (vertexidxtype p = 0; p < N; ++p) {
for (edgeidxtype e = ps[p]; e != ps[p + 1]; ++e) {
negweights[p] += weights[e];
}
}
}
std::for_each(negweights, negweights + N, [](distancetype& weight) {weight = pow(weight, 0.75);});
v -> initAlias(weights.memptr(), negweights, seed);
delete[] negweights;
const uword batchSize = BATCHSIZE;
#ifdef _OPENMP
const unsigned int ts = omp_get_max_threads();
#else
const unsigned int ts = 2;
#endif
Progress progress(max((uword) ts, n_samples / BATCHSIZE), verbose);
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (unsigned int t = 0; t < ts; ++t) {
v->thread(progress, batchSize);
}
delete v;
return coords;
}
Rcpp::NumericMatrix rcpp_segIBDandN(std::string pathThisBreed, std::string pathNative, int NFileC, int NFileN, const arma::ivec& ArmaIndexC, const arma::ivec& ArmaIndexN, int NC, int minSNP, double minL, const arma::vec& ArmaPos, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
/* ***** initialize variables ****** */
int m, i, j, r, r2, rK, endoffile, gleich;
double L;
char str1[100];
FILE *fC, *fN;
char symB = stdsymB.at(0);
Rcpp::NumericMatrix confROH(NC, NC);
int K = (minSNP<=60)?(minSNP/2):(30);
int M = Armakb.n_elem - 1;
size_t bufsize = 2*(NFileC+NFileN);
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
int** Nat = (int**)calloc(M,sizeof(int*)); /* M xNC - matrix */
double** fROH = (double**)calloc(NC,sizeof(double*)); /* NCxNC - matrix */
int** thisROH = (int**)calloc(NC,sizeof(int*)); /* NCxNC - matrix */
double** lSEG = (double**)calloc(NC,sizeof(double*)); /* NCxNC - matrix */
int* currAllelesC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* prevAllelesC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* indexC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* indexN = (int*)calloc(NC,sizeof(int)); /* NC - vector */
double* Pos = (double*)calloc(ArmaPos.n_elem, sizeof(double)); /* M+1 - vector */
double* kb = (double*)calloc(Armakb.n_elem, sizeof(double)); /* M+1 - vector */
if(fROH == NULL){error_return("Memory allocation failed.");};
if(Nat == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(lSEG == NULL){error_return("Memory allocation failed.");};
if(currAllelesC== NULL){error_return("Memory allocation failed.");};
if(prevAllelesC== NULL){error_return("Memory allocation failed.");};
if(indexC == NULL){error_return("Memory allocation failed.");};
if(indexN == NULL){error_return("Memory allocation failed.");};
if(Pos == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
for(m=0;m<M+1;m++){
Pos[m] = ArmaPos.at(m);
kb[m] = Armakb.at(m);
}
for(i=0; i<NC;i++){
indexC[i] = ArmaIndexC.at(i);
indexN[i] = ArmaIndexN.at(i);
fROH[i] = (double*)calloc(i+1,sizeof(double));
thisROH[i]= (int*)calloc(i+1,sizeof(int));
lSEG[i] = (double*)calloc(i+1,sizeof(double));
if(fROH[i] == NULL){error_return("Memory allocation failed.");};
if(thisROH[i]== NULL){error_return("Memory allocation failed.");};
if(lSEG[i] == NULL){error_return("Memory allocation failed.");};
}
/* ******* Main part ******** */
fC = fopen(pathThisBreed.c_str(),"r");
fN = fopen(pathNative.c_str(),"r");
if(fC == NULL){error_return("File opening failed.");};
if(fN == NULL){error_return("File opening failed.");};
while(fgetc(fN)!='\n'){}
for(i=0;i<skip+1;i++){
while(fgetc(fC)!='\n'){}
}
endoffile=0;
m=0;
while(!endoffile){
/* *** Determine previous alleles and current alleles (K at a time) *** */
/* *** and native alleles for candidates *** */
for(i=0; i<NC;i++){
prevAllelesC[i] = currAllelesC[i];
currAllelesC[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(fC, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fscanf(fN, "%s ", str1)<1;
if(endoffile){break;}
endoffile = fgets(Line,2*NFileC,fC)==NULL;
if(endoffile){break;}
for(i=0; i<NC;i++){
if(Line[2*indexC[i]]==symB){currAllelesC[i]= currAllelesC[i] | (1u<<rK);}
}
endoffile = fgets(Line, 2*NFileN, fN)==NULL;
if(endoffile){break;}
Nat[m+rK] = (int*)calloc(NC,sizeof(int));
for(i=0; i<NC;i++){
Nat[m+rK][i] = ((Line[2*indexN[i]]=='1')?1:0);
}
rK++;
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i=0; i<NC;i++){
for(j=0; j<i+1; j++){
if(currAllelesC[i]==currAllelesC[j]){
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH verlängern */
thisROH[i][j] += rK;
for(r2=0;r2<rK;r2++){if(Nat[m+r2][i]*Nat[m+r2][j]>0){lSEG[i][j] += kb[m+r2+1]-kb[m+r2];}} /* !!!!! */
}else{ /* neuer ROH */
thisROH[i][j] = rK;
for(r2=0;r2<rK;r2++){if(Nat[m+r2][i]*Nat[m+r2][j]>0){lSEG[i][j] += kb[m+r2+1]-kb[m+r2];}} /* !!!!! */
if(m>0){
gleich = ~(prevAllelesC[i] ^ prevAllelesC[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
if(Nat[m-K+r][i]*Nat[m-K+r][j]>0){lSEG[i][j] += kb[m-K+r+1]-kb[m-K+r];} /* !!!!! */
r--;
}
}
}
}else{
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH beenden */
gleich = ~(currAllelesC[i] ^ currAllelesC[j]);
r = 0;
while(r<K && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
if(Nat[m+r][i]*Nat[m+r][j]>0){lSEG[i][j] += kb[m+r+1]-kb[m+r];} /* !!!!! */
r++;
}
if(thisROH[i][j]>=minSNP){
L = Pos[m+r]-Pos[m+r-thisROH[i][j]];
if(L>=minL){
fROH[i][j] += (L*L/(a+L*L))*lSEG[i][j];
}
}
thisROH[i][j] = 0;
lSEG[i][j] = 0.0;
}
}
}
Rcpp::NumericVector rcpp_segInbreeding(std::string path1, std::string path2, int NFile1, int NFile2, const arma::ivec& ArmaIndex1, const arma::ivec& ArmaIndex2, int N1, int N2, int M, int minSNP, double minL, const arma::vec& ArmacM, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
int m, i, i0, j, rK, r, endoffile, gleich;
double L;
char str1[100];
char symB = stdsymB.at(0);
FILE *f1, *f2;
int N = N1 + N2;
int K = (minSNP<=60)?(minSNP/2):(30);
Rcpp::NumericVector ArmasegInbr(N/2);
size_t bufsize = 2*(NFile1+NFile2);
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
double* fROH = (double*)calloc(N/2,sizeof(double));
int* thisROH = (int*)calloc(N/2,sizeof(int));
int* thisAllel = (int*)calloc(N,sizeof(int));
int* prevAllel = (int*)calloc(N,sizeof(int));
double* cM = (double*)calloc(M+1,sizeof(double));
double* kb = (double*)calloc(M+1,sizeof(double));
int* index1 = (int*)calloc(N1,sizeof(int)); /* N1 - vector */
int* index2 = (int*)calloc(N2,sizeof(int)); /* N2 - vector */
if(fROH == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(thisAllel == NULL){error_return("Memory allocation failed.");};
if(prevAllel == NULL){error_return("Memory allocation failed.");};
if(cM == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
if(index1 == NULL){error_return("Memory allocation failed.");};
if(index2 == NULL){error_return("Memory allocation failed.");};
for(i=0;i<N1;i++){index1[i]=ArmaIndex1.at(i);}
for(i=0;i<N2;i++){index2[i]=ArmaIndex2.at(i);}
for(m=0;m<M+1;m++){
cM[m]=ArmacM.at(m);
kb[m]=Armakb.at(m);
}
f1 = fopen(path1.c_str(),"r");
if(f1 == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(f1)!='\n'){}
}
if(N2>0){
f2 = fopen(path2.c_str(),"r");
if(f2 == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(f2)!='\n'){}
}
}else{f2 = f1; /* avoid warnings */}
endoffile=0;
m=0;
while(!endoffile){
for(i=0; i<N;i++){
prevAllel[i] = thisAllel[i];
thisAllel[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(f1, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line, 2*NFile1, f1)==NULL;
if(endoffile){break;}
for(i=0; i<N1;i++){
if(Line[2*index1[i]]==symB){thisAllel[i]= thisAllel[i] | (1u<<rK);}
}
rK++;
}
if(N2>0){
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(f2, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line,2*NFile2,f2)==NULL;
if(endoffile){break;}
for(i=0; i<N2;i++){
if(Line[2*index2[i]]==symB){thisAllel[i+N1]= thisAllel[i+N1] | (1u<<rK);}
}
rK++;
}
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i0=0; i0<N/2;i0++){
i = 2*i0;
j = 2*i0+1;
if(thisAllel[i]==thisAllel[j]){
if(prevAllel[i]==prevAllel[j] && m>0){ /* ROH verlängern */
thisROH[i0] += rK;
}else{ /* neuer ROH */
thisROH[i0] = rK;
if(m>0){
gleich = ~(prevAllel[i] ^ prevAllel[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i0] += 1;
r--;
}
}
}
}else{
if(prevAllel[i]==prevAllel[j] && m>0){ /* ROH beenden */
gleich = ~(thisAllel[i] ^ thisAllel[j]);
r = 0;
while(r<rK && ((gleich>>r)&1u)){
thisROH[i0] += 1;
r++;
}
if(thisROH[i0]>=minSNP){
L = cM[m+r]-cM[m+r-thisROH[i0]];
if(L>=minL){fROH[i0] += (L*L/(a+L*L))*(kb[m+r]-kb[m+r-thisROH[i0]]);}
}
thisROH[i0] = 0;
}
}
Rcpp::NumericMatrix rcpp_segIBDandNVersion2(std::string pathThisBreed, int NFileC, int NC, const arma::ivec& ArmaIndexC, const arma::mat& ArmaNat, int minSNP, double minL, const arma::vec& ArmaPos, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
int m, m2, i, j, r, rK, endoffile, gleich;
double L, w, lSEG ;
char str1[100];
char symB = stdsymB.at(0);
FILE *fC;
Rcpp::NumericMatrix confROH(NC, NC);
int K = (minSNP<=60)?(minSNP/2):(30);
int M = Armakb.n_elem - 1;
size_t bufsize = 2*NFileC;
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
int** Nat = (int**)calloc(NC,sizeof(int*));
double** fROH = (double**)calloc(NC,sizeof(double*));
int** thisROH = (int**)calloc(NC,sizeof(int*));
int* currAllelesC = (int*)calloc(NC,sizeof(int));
int* prevAllelesC = (int*)calloc(NC,sizeof(int));
int* indexC = (int*)calloc(NC,sizeof(int));
double* Pos = (double*)calloc(ArmaPos.n_elem, sizeof(double));
double* kb = (double*)calloc(Armakb.n_elem, sizeof(double));
if(Nat == NULL){error_return("Memory allocation failed.");};
if(fROH == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(currAllelesC == NULL){error_return("Memory allocation failed.");};
if(prevAllelesC == NULL){error_return("Memory allocation failed.");};
if(indexC == NULL){error_return("Memory allocation failed.");};
if(Pos == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
for(m=0;m<M+1;m++){
Pos[m] = ArmaPos.at(m);
kb[m] = Armakb.at(m);
}
for(i=0; i<NC;i++){
indexC[i] = ArmaIndexC.at(i);
fROH[i] = (double*)calloc(i+1, sizeof(double));
thisROH[i]= (int*)calloc(i+1, sizeof(int));
Nat[i] = (int*)calloc(M, sizeof(int));
if(fROH[i] == NULL){error_return("Memory allocation failed.");};
if(thisROH[i] == NULL){error_return("Memory allocation failed.");};
if(Nat[i] == NULL){error_return("Memory allocation failed.");};
for(m=0; m<M;m++){
Nat[i][m] = ArmaNat.at(m,i);
}
}
fC = fopen(pathThisBreed.c_str(),"r");
if(fC == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(fC)!='\n'){}
}
endoffile=0;
m=0;
while(!endoffile){
for(i=0; i<NC;i++){
prevAllelesC[i] = currAllelesC[i];
currAllelesC[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(fC, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line,2*NFileC,fC)==NULL;
if(endoffile){break;}
for(i=0; i<NC;i++){
if(Line[2*indexC[i]]==symB){currAllelesC[i]= currAllelesC[i] | (1u<<rK);}
}
rK++;
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i=0; i<NC;i++){
for(j=0; j<i+1; j++){
if(currAllelesC[i]==currAllelesC[j]){
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH verlängern */
thisROH[i][j] += rK;
}else{ /* neuer ROH */
thisROH[i][j] = rK;
if(m>0){
gleich = ~(prevAllelesC[i] ^ prevAllelesC[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
r--;
}
}
}
}else{
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH beenden */
gleich = ~(currAllelesC[i] ^ currAllelesC[j]);
r = 0;
while(r<K && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
r++;
}
if(thisROH[i][j]>=minSNP){
L = Pos[m+r]-Pos[m+r-thisROH[i][j]];
if(L>=minL){
w = L*L/(a+L*L);
lSEG = 0.0;
for(m2=m+r-thisROH[i][j];m2<m+r;m2++){
if(Nat[i][m2]*Nat[j][m2]>0){lSEG += kb[m2+1]-kb[m2];}
}
fROH[i][j] += w*lSEG;
}
}
thisROH[i][j] = 0;
}
}
}
void SampleGradHistogram(double *pt, double radius, typename TImage::Pointer image, arma::ivec& samples)
{
typedef TImage ImageType;
int radius_pix[3]; //radius in voxels, to be calculated
radius_pix[0] = std::ceil(radius / image->GetSpacing()[0]);
radius_pix[1] = std::ceil(radius / image->GetSpacing()[1]);
radius_pix[2] = std::ceil(radius / image->GetSpacing()[2]);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Requested point: " << pt[0] << ", " << pt[1] << ", " << pt[2] << std::endl;
std::cout << "Neighborhood size in mm: " << radius << std::endl;
std::cout << "Neighborhood size in pix: " << radius_pix[0] << ", " << radius_pix[1] << ", " << radius_pix[2] << std::endl;
#endif
if (radius_pix[0] == 0 || radius_pix[1] == 0 || radius_pix[2] == 0) {
std::cout << "One of the neighborhood dimensions is zero. Please correct the radius. Aborting." << std::endl;
return;
}
//transform the point from physical s1pace
typename ImageType::PointType point;
point[0] = pt[0];
point[1] = pt[1];
point[2] = pt[2];
typename ImageType::IndexType pt_pix;
image->TransformPhysicalPointToIndex(point, pt_pix);
//define the region around the point of interest
typename ImageType::IndexType rgn_idx = {
{pt_pix[0] - radius_pix[0], pt_pix[1] - radius_pix[1], pt_pix[2] - radius_pix[2]}};
typename ImageType::SizeType rgn_size = {
{2 * radius_pix[0] + 1, 2 * radius_pix[1] + 1, 2 * radius_pix[2] + 1}};
//crop the region so that it is inside
rgn_idx[0] = std::max(rgn_idx[0], image->GetLargestPossibleRegion().GetIndex(0));
rgn_idx[1] = std::max(rgn_idx[1], image->GetLargestPossibleRegion().GetIndex(1));
rgn_idx[2] = std::max(rgn_idx[2], image->GetLargestPossibleRegion().GetIndex(2));
//set it first as a corner for comparison and then undo that operation
rgn_size[0] = std::min(rgn_size[0]+rgn_idx[0], image->GetLargestPossibleRegion().GetSize(0))-rgn_idx[0];
rgn_size[1] = std::min(rgn_size[1]+rgn_idx[1], image->GetLargestPossibleRegion().GetSize(1))-rgn_idx[1];
rgn_size[2] = std::min(rgn_size[2]+rgn_idx[2], image->GetLargestPossibleRegion().GetSize(2))-rgn_idx[2];
typename ImageType::RegionType window(rgn_idx, rgn_size);
#ifdef DEBUG_MESSAGES_HOG
std::cout << "Region: " << window << std::endl;
#endif
samples.set_size(rgn_size[0]*rgn_size[1]*rgn_size[2]);
samples.zeros();
// itk::ImageRegionConstIterator<typename GradientFilterType::OutputImageType> imageIterator(gradient_filter->GetOutput(), window);
itk::ImageRegionConstIterator<ImageType> imageIterator(image, window);
imageIterator.GoToBegin();
int i=0;
while (!imageIterator.IsAtEnd()) {
// Get the value of the current pixel
typename ImageType::PixelType val = imageIterator.Get();
//std::cout << val << std::endl;
samples[i++] = val;
++imageIterator;
}
}
List objectivex(const arma::mat& transition, NumericVector emissionArray,
const arma::vec& init, IntegerVector obsArray, const arma::imat& ANZ,
IntegerVector emissNZ, const arma::ivec& INZ, const arma::ivec& nSymbols,
const arma::mat& coef, const arma::mat& X, arma::ivec& numberOfStates,
int threads) {
IntegerVector eDims = emissionArray.attr("dim"); //m,p,r
IntegerVector oDims = obsArray.attr("dim"); //k,n,r
arma::cube emission(emissionArray.begin(), eDims[0], eDims[1], eDims[2], false, true);
arma::icube obs(obsArray.begin(), oDims[0], oDims[1], oDims[2], false, true);
arma::icube BNZ(emissNZ.begin(), emission.n_rows, emission.n_cols - 1, emission.n_slices, false, true);
unsigned int q = coef.n_rows;
arma::vec grad(
arma::accu(ANZ) + arma::accu(BNZ) + arma::accu(INZ) + (numberOfStates.n_elem- 1) * q,
arma::fill::zeros);
arma::mat weights = exp(X * coef).t();
if (!weights.is_finite()) {
grad.fill(-arma::math::inf());
return List::create(Named("objective") = arma::math::inf(), Named("gradient") = wrap(grad));
}
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);
}
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
arma::mat scales(obs.n_cols, obs.n_slices); //m,n,k
arma::sp_mat sp_trans(transition);
internalForwardx(sp_trans.t(), emission, initk, obs, alpha, scales, threads);
if (!scales.is_finite()) {
grad.fill(-arma::math::inf());
return List::create(Named("objective") = arma::math::inf(), Named("gradient") = wrap(grad));
}
internalBackwardx(sp_trans, emission, obs, beta, scales, threads);
if (!beta.is_finite()) {
grad.fill(-arma::math::inf());
return List::create(Named("objective") = arma::math::inf(), Named("gradient") = wrap(grad));
}
arma::ivec cumsumstate = arma::cumsum(numberOfStates);
arma::mat gradmat(
arma::accu(ANZ) + arma::accu(BNZ) + arma::accu(INZ) + (numberOfStates.n_elem- 1) * q,
obs.n_slices, arma::fill::zeros);
#pragma omp parallel for if(obs.n_slices >= threads) schedule(static) num_threads(threads) \
default(none) shared(q, alpha, beta, scales, gradmat, nSymbols, ANZ, BNZ, INZ, \
numberOfStates, cumsumstate, obs, init, initk, X, weights, transition, emission)
for (int k = 0; k < obs.n_slices; k++) {
int countgrad = 0;
// transitionMatrix
if (arma::accu(ANZ) > 0) {
for (int jj = 0; jj < numberOfStates.n_elem; jj++) {
arma::vec gradArow(numberOfStates(jj));
arma::mat gradA(numberOfStates(jj), numberOfStates(jj));
int ind_jj = cumsumstate(jj) - numberOfStates(jj);
for (int i = 0; i < numberOfStates(jj); i++) {
arma::uvec ind = arma::find(ANZ.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1));
if (ind.n_elem > 0) {
gradArow.zeros();
gradA.eye();
gradA.each_row() -= transition.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1);
gradA.each_col() %= transition.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1).t();
for (int j = 0; j < numberOfStates(jj); j++) {
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
double tmp = alpha(ind_jj + i, t, k);
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(ind_jj + j, obs(r, t + 1, k), r);
}
gradArow(j) += tmp * beta(ind_jj + j, t + 1, k) / scales(t + 1, k);
}
}
gradArow = gradA * gradArow;
gradmat.col(k).subvec(countgrad, countgrad + ind.n_elem - 1) = gradArow.rows(ind);
countgrad += ind.n_elem;
}
}
}
}
if (arma::accu(BNZ) > 0) {
// emissionMatrix
for (unsigned int r = 0; r < obs.n_rows; r++) {
arma::vec gradBrow(nSymbols(r));
arma::mat gradB(nSymbols(r), nSymbols(r));
for (unsigned int i = 0; i < emission.n_rows; i++) {
arma::uvec ind = arma::find(BNZ.slice(r).row(i));
if (ind.n_elem > 0) {
gradBrow.zeros();
gradB.eye();
gradB.each_row() -= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1);
gradB.each_col() %= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1).t();
for (int j = 0; j < nSymbols(r); j++) {
if (obs(r, 0, k) == j) {
double tmp = initk(i, k);
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, 0, k), r2);
}
}
gradBrow(j) += tmp * beta(i, 0, k) / scales(0, k);
}
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
if (obs(r, t + 1, k) == j) {
double tmp = beta(i, t + 1, k) / scales(t + 1, k);
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, t + 1, k), r2);
}
}
gradBrow(j) += arma::dot(alpha.slice(k).col(t), transition.col(i)) * tmp;
}
}
}
gradBrow = gradB * gradBrow;
gradmat.col(k).subvec(countgrad, countgrad + ind.n_elem - 1) = gradBrow.rows(ind);
countgrad += ind.n_elem;
}
}
}
}
if (arma::accu(INZ) > 0) {
for (int i = 0; i < numberOfStates.n_elem; i++) {
int ind_i = cumsumstate(i) - numberOfStates(i);
arma::uvec ind = arma::find(
INZ.subvec(ind_i, cumsumstate(i) - 1));
if (ind.n_elem > 0) {
arma::vec gradIrow(numberOfStates(i), arma::fill::zeros);
for (int j = 0; j < numberOfStates(i); j++) {
double tmp = weights(i, k);
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(ind_i + j, obs(r, 0, k), r);
}
gradIrow(j) += tmp * beta(ind_i + j, 0, k) / scales(0, k);
}
arma::mat gradI(numberOfStates(i), numberOfStates(i), arma::fill::zeros);
gradI.eye();
gradI.each_row() -= init.subvec(ind_i, cumsumstate(i) - 1).t();
gradI.each_col() %= init.subvec(ind_i, cumsumstate(i) - 1);
gradIrow = gradI * gradIrow;
gradmat.col(k).subvec(countgrad, countgrad + ind.n_elem - 1) = gradIrow.rows(ind);
countgrad += ind.n_elem;
}
}
}
for (int jj = 1; jj < numberOfStates.n_elem; jj++) {
int ind_jj = (cumsumstate(jj) - numberOfStates(jj));
for (int j = 0; j < emission.n_rows; j++) {
double tmp = 1.0;
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(j, obs(r, 0, k), r);
}
if ((j >= ind_jj) & (j < cumsumstate(jj))) {
gradmat.col(k).subvec(countgrad + q * (jj - 1), countgrad + q * jj - 1) += tmp
* beta(j, 0, k) / scales(0, k) * initk(j, k) * X.row(k).t() * (1.0 - weights(jj, k));
} else {
gradmat.col(k).subvec(countgrad + q * (jj - 1), countgrad + q * jj - 1) -= tmp
* beta(j, 0, k) / scales(0, k) * initk(j, k) * X.row(k).t() * weights(jj, k);
}
}
}
}
return List::create(Named("objective") = -arma::accu(log(scales)),
Named("gradient") = wrap(-sum(gradmat, 1)));
}
