Remove "ReadRootDataset"

bioturing · Apr 4, 2022 · dbf41f8 · dbf41f8
1 parent 5771cb9
commit dbf41f8
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diff --git a/NAMESPACE b/NAMESPACE
@@ -49,7 +49,6 @@ export(Read10XH5Content)
 export(ReadColSumSpMt)
 export(ReadDoubleVector)
 export(ReadIntegerVector)
-export(ReadRootDataset)
 export(ReadRowSumSpMt)
 export(ReadSpMt)
 export(ReadSpMtAsS4)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -165,17 +165,6 @@ WriteRootDataset <- function(filePath, datasetName, datasetVal) {
     invisible(.Call(`_Signac_WriteRootDataset`, filePath, datasetName, datasetVal))
 }
 
-#' ReadRootDataset
-#'
-#' Read a string vector from root group
-#'
-#' @param filePath A fiel path
-#' @param datasetName A dataset name
-#' @export
-ReadRootDataset <- function(filePath, datasetName) {
-    .Call(`_Signac_ReadRootDataset`, filePath, datasetName)
-}
-
 #' ReadIntegerVector
 #'
 #' This function is used to read a integer vector from hdf5 file

diff --git a/src/Hdf5Util.cpp b/src/Hdf5Util.cpp
@@ -234,23 +234,6 @@ void WriteRootDataset(const std::string &filePath, const std::string &datasetNam
     oHdf5Util.Close(file);
 }
 
-//' ReadRootDataset
-//'
-//' Read a string vector from root group
-//'
-//' @param filePath A fiel path
-//' @param datasetName A dataset name
-//' @export
-// [[Rcpp::export]]
-Rcpp::StringVector ReadRootDataset(const std::string &filePath, const std::string &datasetName) {
-    com::bioturing::Hdf5Util oHdf5Util(filePath);
-    HighFive::File *file = oHdf5Util.Open(1);
-    std::vector<std::string> dataVec;
-    oHdf5Util.ReadRootDataset(file, datasetName, dataVec);
-    oHdf5Util.Close(file);
-    return Rcpp::wrap(dataVec);
-}
-
 //' ReadIntegerVector
 //'
 //' This function is used to read a integer vector from hdf5 file

diff --git a/src/Hdf5Util.h b/src/Hdf5Util.h
@@ -282,73 +282,6 @@ class Hdf5Util {
         }
     }
 
-    template <typename T>
-    void ReadRootDataset(HighFive::File *file, const std::string &datasetName, std::vector<T> &datasetVal) {
-        if(file == nullptr) {
-            std::stringstream ostr;
-            ostr << "Can not read dataset, please open file :" << file_name;
-            ::Rf_error(ostr.str().c_str());
-            throw;
-        }
-
-        try {
-            if(file->exist(datasetName) == false) {
-                std::stringstream ostr;
-                ostr << "Can not exist dataset :" << datasetName;
-                ::Rf_error(ostr.str().c_str());
-                Close(file);
-                throw;
-            }
-
-            HighFive::DataSet datasetVec = file->getDataSet(datasetName);
-
-#ifdef DEBUG
-            HighFive::DataSpace dataSpace = datasetVec.getSpace();
-            auto dims = dataSpace.getDimensions();
-            HighFive::DataType dataType = datasetVec.getDataType();
-            size_t str_size = H5Tget_size(dataType.getId());
-            std::stringstream ostr;
-            ostr << "Read dataset (T) : [" << datasetName << "] with str_size=" << str_size << ", dims[0]=" << dims[0];
-            ::Rf_warning(ostr.str().c_str());
-#endif
-
-            datasetVec.read(datasetVal);
-        } catch (HighFive::Exception& err) {
-            std::stringstream ostr;
-            ostr << "ReadRootDataset HDF5 format, error=" << err.what() ;
-            ::Rf_error(ostr.str().c_str());
-            Close(file);
-            throw;
-        }
-    }
-
-    void ReadRootDataset(HighFive::File *file, const std::string &datasetName, std::vector<std::string> &datasetVal) {
-        if(file == nullptr) {
-            std::stringstream ostr;
-            ostr << "Can not read dataset, please open file :" << file_name;
-            ::Rf_error(ostr.str().c_str());
-            throw;
-        }
-
-        try {
-            if(file->exist(datasetName) == false) {
-                std::stringstream ostr;
-                ostr << "Can not exist dataset :" << datasetName;
-                ::Rf_error(ostr.str().c_str());
-                Close(file);
-                throw;
-            }
-            //TODO: Change this?
-            ReadDatasetVector<256>(file, "", datasetName, datasetVal);
-        } catch (HighFive::Exception& err) {
-            std::stringstream ostr;
-            ostr << "ReadRootDataset HDF5 format, error=" << err.what() ;
-            ::Rf_error(ostr.str().c_str());
-            Close(file);
-            throw;
-        }
-    }
-
     void GetListAttributes(HighFive::File *file, const std::string &groupName, const std::string &datasetName, std::vector<std::string> &arrList) {
         if(file == nullptr) {
             std::stringstream ostr;

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -173,18 +173,6 @@ BEGIN_RCPP
     return R_NilValue;
 END_RCPP
 }
-// ReadRootDataset
-Rcpp::StringVector ReadRootDataset(const std::string& filePath, const std::string& datasetName);
-RcppExport SEXP _Signac_ReadRootDataset(SEXP filePathSEXP, SEXP datasetNameSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const std::string& >::type filePath(filePathSEXP);
-    Rcpp::traits::input_parameter< const std::string& >::type datasetName(datasetNameSEXP);
-    rcpp_result_gen = Rcpp::wrap(ReadRootDataset(filePath, datasetName));
-    return rcpp_result_gen;
-END_RCPP
-}
 // ReadIntegerVector
 Rcpp::NumericVector ReadIntegerVector(const std::string& filePath, const std::string& groupName, const std::string& datasetName);
 RcppExport SEXP _Signac_ReadIntegerVector(SEXP filePathSEXP, SEXP groupNameSEXP, SEXP datasetNameSEXP) {
@@ -687,7 +675,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Signac_GetListRootObjectNames", (DL_FUNC) &_Signac_GetListRootObjectNames, 1},
     {"_Signac_Read10XH5Content", (DL_FUNC) &_Signac_Read10XH5Content, 3},
     {"_Signac_WriteRootDataset", (DL_FUNC) &_Signac_WriteRootDataset, 3},
-    {"_Signac_ReadRootDataset", (DL_FUNC) &_Signac_ReadRootDataset, 2},
     {"_Signac_ReadIntegerVector", (DL_FUNC) &_Signac_ReadIntegerVector, 3},
     {"_Signac_ReadDoubleVector", (DL_FUNC) &_Signac_ReadDoubleVector, 3},
     {"_Signac_FastMatMult", (DL_FUNC) &_Signac_FastMatMult, 2},