TEST(H5Handle_Test, WriteReadTest) {
float data[12];
for (size_t i = 0; i < ArraySize(data); i++) {
data[i] = i;
}
{
H5File file;
file.SetFile("tmp.h5");
file.Open(true);
hsize_t dims[] = {3,4};
hsize_t chunking[] = {3,4};
H5DataSet *ds = file.CreateDataSet("/tmp/here/testdata", 2, dims, chunking, 2, H5T_NATIVE_FLOAT);
size_t starts[] = {0,0};
size_t ends[] = {3,4};
//ds->WriteRangeData(starts, ends, ArraySize(data), data);
ds->WriteRangeData(starts, ends, data);
ds->Close();
}
{
H5File file;
file.SetFile("tmp.h5");
file.Open();
H5DataSet *ds = file.OpenDataSet("/tmp/here/testdata");
float query[12];
size_t starts[] = {0,0};
size_t ends[] = {3,4};
ds->ReadRangeData(starts, ends, ArraySize(query), query);
for (size_t i = 0; i < ArraySize(data); i++) {
if (data[i] != query[i]) {
EXPECT_EQ(query[i], data[i]);
}
}
{
float update[4];
size_t starts[] = {1,2};
size_t ends[] = {3,4};
size_t count = 0;
for (size_t i = 11; i >= 8; i--) {
update[count++] = i;
}
//ds->WriteRangeData(starts, ends, ArraySize(update), update);
ds->WriteRangeData(starts, ends, update);
float query[12];
size_t rstarts[] = {0,0};
size_t rends[] = {3,4};
float gold[12] = {0,1,2,3,4,5,11,10,8,9,9,8};
ds->ReadRangeData(rstarts, rends, ArraySize(query), query);
for (size_t i = 0; i < 1; i++) {
EXPECT_EQ(gold[i], query[i]);
}
}
// ds->Close();
ds = file.OpenDataSet("shouldbenull");
EXPECT_EQ(NULL,ds);
}
}
void BkgParamH5::ConstructOneFile ( H5File &h5_local_ref, string &hgLocalFile, string &local_results, const char *my_name )
{
hgLocalFile = local_results;
if ( hgLocalFile[hgLocalFile.length()-1] != '/' )
hgLocalFile += '/';
hgLocalFile += my_name;
cout << "H5File for params:" << hgLocalFile << endl;
h5_local_ref.Init();
h5_local_ref.SetFile ( hgLocalFile );
h5_local_ref.Open ( true );
}
TEST(H5Handle_Test, MatrixTest) {
Mat<float> mymat = ones<Mat<float> >(5,3);
Mat<float>::iterator i;
int count = 0;
for (i = mymat.begin(); i != mymat.end(); i++) {
*i = count++;
}
// mymat.raw_print(cout);
{
H5File file;
file.SetFile("tmp.h5");
file.Open(true);
H5DataSet *ds = file.CreateDataSet("/tmp/fun/mat", mymat, 0);
//H5DataSet *ds = file.CreateDataSet("mat", mymat, 0);
ds->WriteMatrix(mymat);
ds->Close();
}
{
H5File file;
file.SetFile("tmp.h5");
file.Open();
H5DataSet *ds = file.OpenDataSet("/tmp/fun/mat");
// H5DataSet *ds = file.OpenDataSet("mat");
Mat<float> m;
ds->ReadMatrix(m);
// m.raw_print(cout);
Mat<float>::iterator gold, test;
for (gold = mymat.begin(), test = m.begin(); gold != mymat.end(); gold++, test++) {
float g = *gold;
float t = *test;
EXPECT_EQ(t, g);
}
ds->Close();
}
}
// 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);
//RcppStringVector 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();
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;
ends[1] = maxRow;
ends[2] = maxFlow;
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] = 3;
beadInitDS->ReadRangeData(starts,ends,sizeof(tbeadInit),tbeadInit);
beadParam.Close();
RcppMatrix< double > resErrMat(nRow*nCol,nFlow);
RcppMatrix< double > amplMulMat(nRow*nCol,nFlow);
RcppMatrix< double > krateMulMat(nRow*nCol,nFlow);
RcppMatrix< double > beadInitMat(nRow*nCol,4);
RcppMatrix< double > 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++;
}
RcppResultSet rs;
rs.add("beadParamFile", beadParamFile);
rs.add("nCol", (int)nCol);
rs.add("nRow", (int)nRow);
rs.add("minFlow",minFlow);
rs.add("maxFlow",maxFlow);
rs.add("nFlow", (int)nFlow);
rs.add("col", colOutInt);
rs.add("row",rowOutInt);
rs.add("res_error",resErrMat);
rs.add("ampl_multiplier",amplMulMat);
rs.add("krate_multiplier",krateMulMat);
rs.add("bead_init",beadInitMat);
rs.add("bead_dc",beadDCMat);
ret = rs.getReturnList();
free(tresErr);
free(tamplMul);
free(tkrateMul);
free(tbeadInit);
free(tbeadDC);
}
catch(exception& ex) {
exceptionMesg = copyMessageToR(ex.what());
} catch (...) {
exceptionMesg = copyMessageToR("Unknown reason");
}
if ( exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
