// writing attribute to the file
void WriteAttribute( RString& rFilename,
RString& rPath,
RVector<int> rIntdata,
RVector<double> rDoubledata,
RString rStrdata,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),StringUtils::CompareNoCase(ExtractAttribute(inAttributes,NEWFILE),"true"));
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
// read the compress level
string compressStr = ExtractAttribute(inAttributes,COMPRESSLEVEL);
int compressedLevel = 0;
if ((compressStr.size()>0))
compressedLevel = atoi(compressStr.c_str());
// the dimension of the data to be read
string strRow = ExtractAttribute(inAttributes,ROW);
string strCol = ExtractAttribute(inAttributes,COL);
size_t row=0;
size_t col=0;
if ((strRow.size()>0) && (strCol.size()>0))
{
row = atoi(strRow.c_str());
col = atoi(strCol.c_str());
}
string::size_type index = strPath.find_last_of('/');
if((index == string::npos )||(index==0))
throw RException("Attribute can only be directly under an existing dataset or group.");
string parent = strPath.substr(0,index);
string attr = strPath.substr(index+1,string::npos);
// are we going to overwrite an existing attribute
bool overwrite = StringUtils::CompareNoCase(ExtractAttribute(inAttributes,OVERWRITE),"true");
if(rIntdata.Size()>0)
{
// obtain the data from input
rIntdata.Dimensions(row,col);
Matrix<int> intdata;
rIntdata.Extract(intdata);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,intdata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,intdata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
else if(rDoubledata.Size()>0)
{
// obtain the data from input
rDoubledata.Dimensions(row,col);
Matrix<double> doubledata;
rDoubledata.Extract(doubledata);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,doubledata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,doubledata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
else if(rStrdata.Size()>0)
{
// obtain the data from input
rStrdata.Dimensions(row,col);
Matrix<string> strdata;
rStrdata.Extract(strdata,row,col);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,strdata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,strdata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
}
// write data to file
void WriteData( RString& rFilename,
RString& rPath,
RVector<int> rIntdata,
RVector<double> rDoubledata,
RString rStrdata,
RDataFrame rDataframedata,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),StringUtils::CompareNoCase(ExtractAttribute(inAttributes,NEWFILE),"true"));
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
string compressStr = ExtractAttribute(inAttributes,COMPRESSLEVEL);
int compressedLevel = 0;
if ((compressStr.size()>0))
compressedLevel = atoi(compressStr.c_str());
// the dimension of the data to be written
string strRow = ExtractAttribute(inAttributes,ROW);
string strCol = ExtractAttribute(inAttributes,COL);
size_t row=0;
size_t col=0;
if ((strRow.size()>0) && (strCol.size()>0))
{
row = atoi(strRow.c_str());
col = atoi(strCol.c_str());
}
// if start index and nRows =0, it means user has not specified a subset to write,
// therefore we will read the whole data set
string startStr = ExtractAttribute(inAttributes,STARTINDEX);
string nrowsStr = ExtractAttribute(inAttributes,NROWS);
size_t start=0;
size_t nRows=0;
bool writeAll=true;
if (rIntdata.Size()>0) nRows=row;
if (rDoubledata.Size()>0) nRows=row;
if (rStrdata.Size()>0) nRows=row;
if ((startStr.size()>0))
{
start = atoi(startStr.c_str());
writeAll=false;
}
if (nrowsStr.size()>0)
{
nRows = atoi(nrowsStr.c_str());
writeAll=false;
}
// delete the dataset first if it already exists
string overwrite = ExtractAttribute(inAttributes,OVERWRITE);
if(rIntdata.Size()>0)
{
// obtain the data from input
rIntdata.Dimensions(row,col);
Matrix<int> intdata;
rIntdata.Extract(intdata);
if(writeAll)
{
if(StringUtils::CompareNoCase(overwrite,"true"))
{
if(da.DatasetFullPathExist(strPath))
da.DeleteDataByFullPath(strPath);
}
da.WriteDataByFullPath(strPath, intdata, compressedLevel);
}
else
da.WriteDataByFullPath(strPath, start, nRows, intdata, compressedLevel);
}
else if(rDoubledata.Size()>0)
{
// obtain the data from input
rDoubledata.Dimensions(row,col);
Matrix<double> doubledata;
rDoubledata.Extract(doubledata);
if(writeAll)
{
if(StringUtils::CompareNoCase(overwrite,"true"))
{
if(da.DatasetFullPathExist(strPath))
da.DeleteDataByFullPath(strPath);
}
da.WriteDataByFullPath(strPath, doubledata, compressedLevel);
}
else
da.WriteDataByFullPath(strPath, start, nRows, doubledata, compressedLevel);
}
else if(rStrdata.Size()>0)
{
// obtain the data from input
rStrdata.Dimensions(row,col);
Matrix<string> strdata;
rStrdata.Extract(strdata,row,col);
if(writeAll)
{
if(StringUtils::CompareNoCase(overwrite,"true"))
{
if(da.DatasetFullPathExist(strPath))
da.DeleteDataByFullPath(strPath);
}
da.WriteDataByFullPath(strPath, strdata, compressedLevel);
}
else
da.WriteDataByFullPath(strPath, start, nRows, strdata, compressedLevel);
}
else if(rDataframedata.Size()>0)
{
if(writeAll)
{
if(StringUtils::CompareNoCase(overwrite,"true"))
{
if(da.DatasetFullPathExist(strPath))
da.DeleteDataByFullPath(strPath);
}
da.WriteDataByFullPath(strPath, rDataframedata.CompoundType(), compressedLevel);
}
else
da.WriteDataByFullPath(strPath, start, nRows, rDataframedata.CompoundType(), compressedLevel);
}
}
