// Read the file and print out summary
void ReadSummary(RString& rFilename, vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),false);
HDF5OutputConverter oc;
string fileSummary;
vector<string> gpsummary, dasummary, attsummary;
string detail = ExtractAttribute(inAttributes,FULLDETAIL);
gpsummary=da.GetGroupNamesFullPathDetails();
// print detail which includes the data type and size
if(StringUtils::CompareNoCase(detail,"true"))
{
dasummary=da.GetDatasetNamesFullPathDetails();
attsummary=da.GetAttributeNamesFullPathDetails();
}
else
{
dasummary=da.GetDatasetNamesFullPath();
attsummary=da.GetAttributeNamesFullPath();
}
fileSummary=da.ToString();
results=oc.ConvertSummaryOutput(fileSummary,gpsummary, dasummary, attsummary).Object();
}
// read attribute
void ReadAttribute( RString& rFilename,
RString& rPath,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),false);
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
vector<string> attsummary=da.GetAttributeNamesFullPath();
bool isAtt = (find( attsummary.begin( ), attsummary.end( ), strPath)!=attsummary.end( ));
if(!isAtt)
throw RException("path - "+strPath+" is not attribute.");
// get the data type of the attribute
attsummary=da.GetAttributeNamesFullPathDetails();
vector<string> attLine;
string attDataType;
for(size_t i=0; i<attsummary.size(); i++)
{
std::vector<std::string> attLine;
StringUtils::Parse(attsummary[i],' ',attLine);
if(attLine[0]==strPath)
{
attDataType=attLine[attLine.size()-1];
break;
}
}
switch (HDF5DataType::MapHDF5TypeFromString(attDataType))
{
case HDF5DataType::CHAR:{
Matrix<char> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT:{
Matrix<int> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT64:{
Matrix<__int64> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::FLOAT:{
Matrix<float> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::DOUBLE:{
Matrix<double> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::STRING:{
Matrix<string> data;
DoReadAttribute(da,strPath,data);
results=oc.ConvertStrMatrix(data);
break;}
default:
throw RException("Unknown data type");
}
}
// 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);
}
}
// Read data from file
void ReadData( RString& rFilename,
RString& rPath,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),false);
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
// check if this is a valid dataset
vector<string> dasummary=da.GetDatasetNamesFullPath();
bool isDataset = (find( dasummary.begin( ), dasummary.end( ), strPath)!=dasummary.end( ));
if(!isDataset)
throw RException("path - "+strPath+" is not dataset.");
HDF5Dataset ds = da.OpenDatasetByFullPath(strPath);
string startStr = ExtractAttribute(inAttributes,STARTINDEX);
string nrowsStr = ExtractAttribute(inAttributes,NROWS);
size_t start=0;
size_t nRows=ds.NumberOfRows();
// if only start index is supplied, we need to figure out the nrows.
if ((startStr.size()>0))
{
start = atoi(startStr.c_str());
nRows = nRows-start;
}
// nrows is supplied as well
if (nrowsStr.size()>0)
nRows = atoi(nrowsStr.c_str());
switch (ds.GetDataType())
{
case HDF5DataType::CHAR:{
Matrix<char> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT:{
Matrix<int> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT64:{
Matrix<__int64> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::FLOAT:{
Matrix<float> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::DOUBLE:{
Matrix<double> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::STRING:{
Matrix<string> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertStrMatrix(data);
break;}
case HDF5DataType::COMPOUND:{
HDF5CompoundType data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertCompoundType(data);
break;}
default:
throw RException("Unknown data type");
}
}
