void DeepCopy(BigMatrix *pInMat, BigMatrix *pOutMat, SEXP rowInds, SEXP colInds)
{
in_BMAccessorType inMat( *pInMat );
out_BMAccessorType outMat( *pOutMat );
double *pRows = NUMERIC_DATA(rowInds);
double *pCols = NUMERIC_DATA(colInds);
index_type nRows = GET_LENGTH(rowInds);
index_type nCols = GET_LENGTH(colInds);
if (nRows != pOutMat->nrow())
Rf_error("length of row indices does not equal # of rows in new matrix");
if (nCols != pOutMat->ncol())
Rf_error("length of col indices does not equal # of cols in new matrix");
index_type i = 0;
index_type j = 0;
in_CType *pInColumn;
out_CType *pOutColumn;
for (i = 0; i < nCols; ++i) {
pInColumn = inMat[static_cast<index_type>(pCols[i])-1];
pOutColumn = outMat[i];
for (j = 0; j < nRows; ++j) {
pOutColumn[j] = static_cast<out_CType>(
pInColumn[static_cast<index_type>(pRows[j])-1]);
}
}
return;
}
SEXP CombineSubMapsTransSimple(BigMatrix *oneVox_allSubs, SEXP allVoxs_allSubs, index_type seed, double *pVoxs, index_type nvoxs, index_type nsubs) {
//using namespace Rcpp;
BMAccessorType outMat( *oneVox_allSubs );
if (nvoxs != oneVox_allSubs->ncol())
::Rf_error("nvoxs must equal oneVox_allSubs->ncol");
if (nsubs != oneVox_allSubs->nrow())
::Rf_error("nsubs must equal oneVox_allSubs->nrow");
// loop through each subject's map
index_type s = 0;
index_type v = 0;
index_type vv = 0;
LDOUBLE x = 0;
LDOUBLE delta = 0;
LDOUBLE mean = 0;
LDOUBLE M2 = 0;
LDOUBLE stdev = 0;
// CType *inCol;
CType *outCol;
LDOUBLE scaled_x;
BigMatrix *allVoxs_oneSub;
SEXP Rp;
SEXP tmp;
//RObject RallVoxs_oneSub;
for (s=0; s < nsubs; ++s) {
PROTECT(tmp = VECTOR_ELT(allVoxs_allSubs, s));
//RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
PROTECT(Rp = GET_SLOT(tmp, install("address")));
//tmp = allVoxs_allSubs[s];
//RObject RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
allVoxs_oneSub = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(Rp));
UNPROTECT(2);
BMAccessorType inMat( *allVoxs_oneSub );
for (v=0; v < nvoxs; ++v) {
vv = static_cast<index_type>(pVoxs[v]-1);
outMat[v][s] = static_cast<CType>(inMat[vv][seed]);
}
}
return R_NilValue;
}
void densCalc(NcVar * inVar,
DataMatrix<double> & outMat){
int tLen,latLen,lonLen;
double invtLen;
double selfDiv;
tLen = inVar->get_dim(0)->size();
invtLen = 1.0/((double) tLen);
latLen = inVar->get_dim(1)->size();
lonLen = inVar->get_dim(2)->size();
DataMatrix3D<double> inMat(tLen,latLen,lonLen);
inVar->set_cur(0,0,0);
inVar->get((&inMat[0][0][0]), tLen,latLen,lonLen);
//DataMatrix<double> outMat(latLen,lonLen);
for (int i=0; i<latLen; i++){
for (int j=0; j<lonLen; j++){
outMat[i][j] = 0.0;
}
}
//Divide all cells by self and average over time
for (int t=0; t<tLen; t++){
for (int i=0; i<latLen; i++){
for (int j=0; j<lonLen; j++){
if (std::fabs(inMat[t][i][j])>0.0){
outMat[i][j]+=1.0;
}
}
}
}
for (int i=0; i<latLen; i++){
for (int j=0; j<lonLen; j++){
outMat[i][j]*=invtLen;
}
}
// outVar->set_cur(0,0);
//outVar->put((&outMat[0][0]),latLen,lonLen);
}
bool floodShouldPushPoint(const cv::Point &np, const cv::Mat &mat) {
return inMat(np, mat.rows, mat.cols);
}
SEXP CombineSubMaps(BigMatrix *oneVox_allSubs, SEXP allVoxs_allSubs, index_type seed, double *pVoxs, index_type nvoxs, index_type nsubs) {
//using namespace Rcpp;
BMAccessorType outMat( *oneVox_allSubs );
if (nsubs != oneVox_allSubs->ncol())
Rf_error("nsubs must equal oneVox_allSubs->ncol");
if (nvoxs != oneVox_allSubs->nrow())
Rf_error("nsubs must equal oneVox_allSubs->nrow");
// loop through each subject's map
index_type s = 0;
index_type v = 0;
index_type vv = 0;
LDOUBLE x = 0;
LDOUBLE delta = 0;
LDOUBLE mean = 0;
LDOUBLE M2 = 0;
LDOUBLE stdev = 0;
// CType *inCol;
CType *outCol;
LDOUBLE scaled_x;
BigMatrix *allVoxs_oneSub;
SEXP Rp;
SEXP tmp;
//RObject RallVoxs_oneSub;
for (s=0; s < nsubs; ++s) {
PROTECT(tmp = VECTOR_ELT(allVoxs_allSubs, s));
//RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
PROTECT(Rp = GET_SLOT(tmp, install("address")));
//tmp = allVoxs_allSubs[s];
//RObject RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
allVoxs_oneSub = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(Rp));
UNPROTECT(2);
BMAccessorType inMat( *allVoxs_oneSub );
// inCol = inMat[seed];
delta = mean = M2 = stdev = 0;
for (v=0; v < nvoxs; ++v) {
// todo: add checking for NaN...but shouldn't really have any!
// maybe can also pass the exact list of voxs to loop through!
// if (!ISNAN(pColumn[curj]))
// NA_REAL
vv = static_cast<index_type>(pVoxs[v]-1);
x = static_cast<LDOUBLE>(inMat[vv][seed]);
delta = x - mean;
mean = mean + delta/static_cast<LDOUBLE>(v+1);
M2 = M2 + delta*(x - mean);
}
stdev = sqrt(M2/(static_cast<LDOUBLE>(nvoxs-1)));
//printf("mean: %f; stdev: %f\n", mean, stdev);
outCol = outMat[s];
for (v=0; v < nvoxs; ++v) {
vv = static_cast<index_type>(pVoxs[v]-1);
scaled_x = (static_cast<LDOUBLE>(inMat[vv][seed])-mean)/stdev;
outCol[v] = static_cast<CType>(scaled_x);
}
}
return R_NilValue;
}
void expm_eigen(int n, double *rz, double *out)
{
Eigen::Map< Eigen::MatrixXd > inMat(rz, n, n);
Eigen::Map< Eigen::MatrixXd > outMat(out, n, n);
outMat = inMat.exp();
}
