// col, row, and flow are zero-based in this function, info read out include both borders.
RcppExport SEXP readBeadParamR(SEXP RbeadParamFile,SEXP RminCol, SEXP RmaxCol, SEXP RminRow, SEXP RmaxRow,SEXP RminFlow, SEXP RmaxFlow) {
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
//vector<string> beadParamFile = Rcpp::as< vector<string> > (RbeadParamFile);
//Rcpp::StringVector tBeadParamFile(RbeadParamFile);
string beadParamFile = Rcpp::as< string > (RbeadParamFile);
int minCol = Rcpp::as< int > (RminCol);
int maxCol = Rcpp::as< int > (RmaxCol);
int minRow = Rcpp::as< int > (RminRow);
int maxRow = Rcpp::as< int > (RmaxRow);
int minFlow = Rcpp::as< int > (RminFlow);
int maxFlow = Rcpp::as< int > (RmaxFlow);
// Outputs
unsigned int nCol = maxCol - minCol+1;
unsigned int nRow = maxRow - minRow+1;
unsigned int nFlow = maxFlow - minFlow+1;
vector<unsigned int> colOut,rowOut,flowOut;
vector< double > resErr;
colOut.reserve(nCol * nRow * nFlow);
rowOut.reserve(nCol * nRow * nFlow);
// Recast int to unsigned int
vector<unsigned int> col, row, flow;
col.resize(nCol);
for(unsigned int i=0;i<col.size();++i)
col[i] = (unsigned int)(i+minCol);
row.resize(nRow);
for(unsigned int i=0;i<row.size();++i)
row[i] = (unsigned int) (i+minRow);
flow.resize(nFlow);
for(unsigned int i=0;i<flow.size();++i)
flow[i] = (unsigned int) (i+minFlow);
H5File beadParam;
beadParam.SetFile(beadParamFile);
//beadParam.Open();
beadParam.OpenForReading();
H5DataSet *resErrDS = beadParam.OpenDataSet("/bead/res_error");
H5DataSet *ampMulDS = beadParam.OpenDataSet("bead/ampl_multiplier");
H5DataSet *krateMulDS = beadParam.OpenDataSet("bead/k_rate_multiplier");
H5DataSet *beadInitDS = beadParam.OpenDataSet("bead/bead_init_param");
H5DataSet *beadDCDS = beadParam.OpenDataSet("bead/fg_bead_DC");
//float tresErr[nCol * nRow * nFlow];
float *tresErr;
float *tamplMul;
float *tkrateMul;
float *tbeadInit;
float *tbeadDC;
tresErr = (float *) malloc ( sizeof(float) * nCol * nRow * nFlow);
tamplMul = (float *) malloc ( sizeof(float) * nCol * nRow * nFlow);
tkrateMul = (float *) malloc ( sizeof(float) * nCol * nRow * nFlow);
tbeadInit = (float *) malloc ( sizeof(float) * nCol * nRow * 4);
tbeadDC = (float *) malloc ( sizeof(float) * nCol * nRow * nFlow);
size_t starts[3];
size_t ends[3];
starts[0] = minCol;
starts[1] = minRow;
starts[2] = minFlow;
ends[0] = maxCol+1;
ends[1] = maxRow+1;
ends[2] = maxFlow+1;
resErrDS->ReadRangeData(starts, ends, sizeof(tresErr),tresErr);
ampMulDS->ReadRangeData(starts, ends, sizeof(tamplMul),tamplMul);
krateMulDS->ReadRangeData(starts, ends, sizeof(tkrateMul),tkrateMul);
beadDCDS->ReadRangeData(starts, ends, sizeof(tbeadDC),tbeadDC);
starts[2] = 0;
ends[2] = 4;
beadInitDS->ReadRangeData(starts,ends,sizeof(tbeadInit),tbeadInit);
beadParam.Close();
Rcpp::NumericMatrix resErrMat(nRow*nCol,nFlow);
Rcpp::NumericMatrix amplMulMat(nRow*nCol,nFlow);
Rcpp::NumericMatrix krateMulMat(nRow*nCol,nFlow);
Rcpp::NumericMatrix beadInitMat(nRow*nCol,4);
Rcpp::NumericMatrix beadDCMat(nRow*nCol,nFlow);
vector<int> colOutInt,rowOutInt,flowOutInt;
int count = 0;
for(size_t icol=0;icol<nCol;++icol)
for(size_t irow=0;irow<nRow;++irow) {
for(size_t iFlow=0;iFlow<nFlow;++iFlow)
{
amplMulMat(count,iFlow) = (double) tamplMul[icol * nRow * nFlow + irow * nFlow + iFlow] ;
krateMulMat(count,iFlow) = (double) tkrateMul[icol * nRow * nFlow + irow * nFlow + iFlow];
beadDCMat(count,iFlow) = (double) tbeadDC[icol * nRow *nFlow + irow * nFlow + iFlow];
}
for(size_t ip=0;ip<4;++ip)
beadInitMat(count,ip) = (double) tbeadInit[icol * nRow * ip + irow * 4 + ip];
colOutInt.push_back(minCol+icol);
rowOutInt.push_back(minRow+irow);
count++;
}
ret = Rcpp::List::create(Rcpp::Named("beadParamFile") = beadParamFile,
Rcpp::Named("nCol") = (int)nCol,
Rcpp::Named("nRow") = (int)nRow,
Rcpp::Named("minFlow") = minFlow,
Rcpp::Named("maxFlow") = maxFlow,
Rcpp::Named("nFlow") = (int)nFlow,
Rcpp::Named("col") = colOutInt,
Rcpp::Named("row") = rowOutInt,
Rcpp::Named("res_error") = resErrMat,
Rcpp::Named("ampl_multiplier") = amplMulMat,
Rcpp::Named("krate_multiplier") = krateMulMat,
Rcpp::Named("bead_init") = beadInitMat,
Rcpp::Named("bead_dc") = beadDCMat);
free(tresErr);
free(tamplMul);
free(tkrateMul);
free(tbeadInit);
free(tbeadDC);
}
catch(exception& ex) {
forward_exception_to_r(ex);
} catch (...) {
::Rf_error("c++ exception (unknown reason)");
}
if ( exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
