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bigmemory.cpp
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bigmemory.cpp
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#include <fstream>
//#include <typeinfo>
#include <Rcpp.h>
#include "bigmemory/BigMatrix.h"
#include "bigmemory/MatrixAccessor.hpp"
#include "bigmemory/isna.hpp"
#include "bigmemory/util.h"
#define R_BYTE_MIN (0)
#define R_BYTE_MAX (255)
#define NA_BYTE (0)
using namespace Rcpp;
/* Notes
* R does not natively contain float type objects
* Therefore, every time you pass object to see they will initially be
* double unless they are already within a C/C++ object.
*
* For example, the SetMatrixElements function
* Normally the function looks like this:
* SetMatrixElements<double, double, MatrixAccessor<double> >(...
* Where both the CType and RType are double but with float
* types R is still passing only double. Trying to pass RType
* as float will result in all NA values. So the function ultimately
* must still pass double like so:
* SetMatrixElements<float, double, MatrixAccessor<float> >(...
*/
template<typename T>
string ttos(T i)
{
stringstream s;
s.precision(16);
s << i;
return s.str();
}
template<>
string ttos<unsigned char>(unsigned char i)
{
stringstream s;
s << static_cast<short>(i);
return s.str();
}
template<>
string ttos<char>(char i)
{
stringstream s;
s << static_cast<short>(i);
return s.str();
}
bool TooManyRIndices( index_type val )
{
return double(val) > pow(2.0, 31.0)-1.0;
}
template<typename CType, typename RType, typename BMAccessorType>
void SetMatrixElements( BigMatrix *pMat, SEXP col, SEXP row, SEXP values,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
double *pCols = REAL(col);
index_type numCols = Rf_length(col);
double *pRows = REAL(row);
index_type numRows = Rf_length(row);
VecPtr<RType> vec_ptr;
RType *pVals = vec_ptr(values);
index_type valLength = Rf_length(values);
index_type i=0;
index_type j=0;
index_type k=0;
CType *pColumn;
index_type kIndex;
for (i=0; i < numCols; ++i)
{
pColumn = mat[static_cast<index_type>(pCols[i])-1];
for (j=0; j < numRows; ++j)
{
kIndex = k++%valLength;
pColumn[static_cast<index_type>(pRows[j])-1] =
((pVals[kIndex] < C_MIN || pVals[kIndex] > C_MAX) ?
static_cast<CType>(NA_C) : static_cast<CType>(pVals[kIndex]));
}
}
}
// Function contributed by Peter Haverty at Genentech.
template<typename CType, typename RType, typename BMAccessorType, typename RcppType>
SEXP
GetIndivMatrixElements(
BigMatrix *pMat, double NA_C, double NA_R,
NumericVector col, NumericVector row)
{
BMAccessorType mat(*pMat);
index_type numCols = col.size();
RcppType retVec(numCols);
index_type i;
for (i=0; i < numCols; ++i)
{
CType element = mat[static_cast<index_type>(col[i])-1][static_cast<index_type>(row[i])-1];
retVec[i] = element == static_cast<CType>(NA_C) ? static_cast<RType>(NA_R) : element;
}
return(retVec);
}
// Function contributed by Charles Detemran Jr.
template<typename CType, typename RType, typename BMAccessorType, typename RcppType>
SEXP
GetIndivVectorMatrixElements(
BigMatrix *pMat, double NA_C, double NA_R,
NumericVector elems)
{
BMAccessorType mat(*pMat);
index_type numElems = elems.size();
RcppType retVec(numElems);
index_type i = 0;
int idx = 0;
for (index_type j = 0; j < elems.size(); j++){
CType element = mat[i][static_cast<index_type>(elems[j])-1];
retVec[idx] = element == static_cast<CType>(NA_C) ? static_cast<RType>(NA_R) : element;
idx += 1;
}
return(retVec);
}
// Function contributed by Charles Detemran Jr.
template<typename CType, typename RType, typename BMAccessorType, typename RcppType>
void
SetIndivVectorMatrixElements(
BigMatrix *pMat, double NA_C, double NA_R,
NumericVector elems, NumericVector inVec)
{
BMAccessorType mat(*pMat);
index_type i = 0;
for (index_type j = 0; j < elems.size(); j++){
mat[i][static_cast<index_type>(elems[j])-1] = inVec[j];
}
}
// Function contributed by Peter Haverty at Genentech.
template<typename CType, typename RType, typename BMAccessorType>
void SetIndivMatrixElements( BigMatrix *pMat, SEXP col, SEXP row, SEXP values,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
double *pCols = REAL(col);
index_type numCols = Rf_length(col);
double *pRows = REAL(row);
VecPtr<RType> vec_ptr;
RType *pVals = vec_ptr(values);
index_type i=0;
CType *pColumn;
for (i=0; i < numCols; ++i)
{
pColumn = mat[static_cast<index_type>(pCols[i])-1];
pColumn[static_cast<index_type>(pRows[i])-1] =
((pVals[i] < C_MIN || pVals[i] > C_MAX) ?
static_cast<CType>(NA_C) :
static_cast<CType>(pVals[i]));
}
}
template<typename CType, typename RType, typename BMAccessorType>
void SetMatrixAll( BigMatrix *pMat, SEXP values,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
index_type numCols = pMat->ncol();
index_type numRows = pMat->nrow();
VecPtr<RType> vec_ptr;
RType *pVals = vec_ptr(values);
index_type valLength = Rf_length(values);
index_type i=0;
index_type j=0;
index_type k=0;
CType *pColumn;
index_type kIndex;
for (i=0; i < numCols; ++i)
{
pColumn = mat[i];
for (j=0; j < numRows; ++j)
{
kIndex = k++%valLength;
pColumn[j] = ((pVals[kIndex] < C_MIN || pVals[kIndex] > C_MAX) ?
static_cast<CType>(NA_C) :
static_cast<CType>(pVals[kIndex]));
}
}
}
template<typename CType, typename RType, typename BMAccessorType>
void SetMatrixCols( BigMatrix *pMat, SEXP col, SEXP values,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
double *pCols = REAL(col);
index_type numCols = Rf_length(col);
index_type numRows = pMat->nrow();
VecPtr<RType> vec_ptr;
RType *pVals = vec_ptr(values);
index_type valLength = Rf_length(values);
index_type i=0;
index_type j=0;
index_type k=0;
CType *pColumn;
index_type kIndex;
for (i=0; i < numCols; ++i)
{
pColumn = mat[static_cast<index_type>(pCols[i])-1];
for (j=0; j < numRows; ++j)
{
kIndex = k++%valLength;
pColumn[j] = ((pVals[kIndex] < C_MIN || pVals[kIndex] > C_MAX) ?
static_cast<CType>(NA_C) :
static_cast<CType>(pVals[kIndex]));
}
}
}
template<typename CType, typename RType, typename BMAccessorType>
void SetMatrixRows( BigMatrix *pMat, SEXP row, SEXP values,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
index_type numCols = pMat->ncol();
double *pRows = REAL(row);
index_type numRows = Rf_length(row);
VecPtr<RType> vec_ptr;
RType *pVals = vec_ptr(values);
index_type valLength = Rf_length(values);
index_type i=0;
index_type j=0;
index_type k=0;
CType *pColumn;
index_type kIndex;
for (i=0; i < numCols; ++i)
{
pColumn = mat[i];
for (j=0; j < numRows; ++j)
{
kIndex = k++%valLength;
pColumn[static_cast<index_type>(pRows[j])-1] =
((pVals[kIndex] < C_MIN || pVals[kIndex] > C_MAX) ?
static_cast<CType>(NA_C) : static_cast<CType>(pVals[kIndex]));
}
}
}
template<typename CType, typename BMAccessorType>
void SetAllMatrixElements( BigMatrix *pMat, SEXP value,
double NA_C, double C_MIN, double C_MAX, double NA_R)
{
BMAccessorType mat( *pMat );
double val = REAL(value)[0];
index_type i=0;
index_type j=0;
index_type ncol = pMat->ncol();
index_type nrow = pMat->nrow();
//bool outOfRange=false;
if (val < C_MIN || val > C_MAX || isna(val))
{
if (!isna(val))
{
//outOfRange=true;
Rf_warning("The value given is out of range, elements will be set to NA.");
}
val = NA_C;
}
for (i=0; i < ncol; ++i)
{
CType *pColumn = mat[i];
for (j=0; j < nrow; ++j)
{
pColumn[j] = static_cast<CType>(val);
}
}
}
template<typename CType, typename RType, typename BMAccessorType>
SEXP GetMatrixElements( BigMatrix *pMat, double NA_C, double NA_R,
SEXP col, SEXP row, SEXPTYPE sxpType)
{
VecPtr<RType> vec_ptr;
BMAccessorType mat(*pMat);
double *pCols = REAL(col);
double *pRows = REAL(row);
index_type numCols = Rf_length(col);
index_type numRows = Rf_length(row);
/*
if (TooManyRIndices(numCols*numRows))
{
Rf_error("Too many indices (>2^31-1) for extraction.");
return R_NilValue;
}
*/
SEXP ret = Rf_protect(Rf_allocVector(VECSXP, 3));
int protectCount = 1;
SET_VECTOR_ELT( ret, 1, R_NilValue );
SET_VECTOR_ELT( ret, 2, R_NilValue );
SEXP retMat;
if (numCols == 1 || numRows == 1) {
retMat = Rf_protect( Rf_allocVector(sxpType, numRows * numCols) );
} else {
retMat = Rf_protect( Rf_allocMatrix(sxpType, numRows, numCols) );
}
++protectCount;
SET_VECTOR_ELT(ret, 0, retMat);
//SEXP ret = Rf_protect( new_vec(numCols*numRows) );
RType *pRet = vec_ptr(retMat);
CType *pColumn;
index_type k=0;
index_type i,j;
for (i=0; i < numCols; ++i)
{
if (isna(pCols[i]))
{
for (j=0; j < numRows; ++j)
{
pRet[k] = static_cast<RType>(NA_R);
}
}
else
{
pColumn = mat[static_cast<index_type>(pCols[i])-1];
for (j=0; j < numRows; ++j)
{
if (isna(pRows[j]))
{
pRet[k] = static_cast<RType>(NA_R);
}
else
{
pRet[k] = (pColumn[static_cast<index_type>(pRows[j])-1] ==
static_cast<CType>(NA_C)) ? static_cast<RType>(NA_R) :
(static_cast<RType>(pColumn[static_cast<index_type>(pRows[j])-1]));
}
++k;
}
}
}
Names colNames = pMat->column_names();
if (!colNames.empty())
{
++protectCount;
SEXP rCNames = Rf_protect(Rf_allocVector(STRSXP, numCols));
for (i=0; i < numCols; ++i)
{
if (!isna(pCols[i]))
SET_STRING_ELT( rCNames, i,
Rf_mkChar(colNames[static_cast<index_type>(pCols[i])-1].c_str()) );
}
SET_VECTOR_ELT(ret, 2, rCNames);
}
Names rowNames = pMat->row_names();
if (!rowNames.empty())
{
++protectCount;
SEXP rRNames = Rf_protect(Rf_allocVector(STRSXP, numRows));
for (i=0; i < numRows; ++i)
{
if (!isna(pRows[i]))
{
SET_STRING_ELT( rRNames, i,
Rf_mkChar(rowNames[static_cast<index_type>(pRows[i])-1].c_str()) );
}
}
SET_VECTOR_ELT(ret, 1, rRNames);
}
Rf_unprotect(protectCount);
return ret;
}
// Function by Florian Prive
// [[Rcpp::export]]
SEXP to_int_checked(SEXP x) {
if (TYPEOF(x) == INTSXP) return x;
NumericVector nv(x);
int i, n = nv.size();
IntegerVector res(n);
for (i = 0; i < n; i++) {
res[i] = nv[i];
if (nv[i] != res[i]) {
warning("Value changed when converting to integer type.");
break;
}
}
for (; i < n; i++) res[i] = nv[i];
return res;
}
// Function contributed by Peter Haverty at Genentech.
// [[Rcpp::export]]
SEXP GetIndivMatrixElements(SEXP bigMatAddr, SEXP col, SEXP row)
{
BigMatrix *pMat =
reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(bigMatAddr));
if (pMat->separated_columns())
{
switch(pMat->matrix_type())
{
case 1:
return GetIndivMatrixElements<char, int, SepMatrixAccessor<char>, IntegerVector >(
pMat, NA_CHAR, NA_INTEGER, col, row);
case 2:
return GetIndivMatrixElements<short,int, SepMatrixAccessor<short>, IntegerVector >(
pMat, NA_SHORT, NA_INTEGER, col, row);
case 3:
return GetIndivMatrixElements<unsigned char, unsigned char, SepMatrixAccessor<unsigned char>, IntegerVector >(
pMat, NA_BYTE, NA_INTEGER, col, row);
case 4:
return GetIndivMatrixElements<int, int, SepMatrixAccessor<int>, IntegerVector >(
pMat, NA_INTEGER, NA_INTEGER, col, row);
case 6:
return GetIndivMatrixElements<float, double, SepMatrixAccessor<float>, NumericVector >(
pMat, NA_FLOAT, NA_FLOAT, col, row);
case 8:
return GetIndivMatrixElements<double,double,SepMatrixAccessor<double>, NumericVector >(
pMat, NA_REAL, NA_REAL, col, row);
}
}
else
{
switch(pMat->matrix_type())
{
case 1:
return GetIndivMatrixElements<char, int, MatrixAccessor<char>, IntegerVector >(
pMat, NA_CHAR, NA_INTEGER, col, row);
case 2:
return GetIndivMatrixElements<short, int, MatrixAccessor<short>, IntegerVector >(
pMat, NA_SHORT, NA_INTEGER, col, row);
case 3:
return GetIndivMatrixElements<unsigned char, unsigned char, MatrixAccessor<unsigned char>, IntegerVector >(
pMat, NA_BYTE, NA_INTEGER, col, row);
case 4:
return GetIndivMatrixElements<int, int, MatrixAccessor<int>, IntegerVector >(
pMat, NA_INTEGER, NA_INTEGER, col, row);
case 6:
return GetIndivMatrixElements<float, double, MatrixAccessor<float>, NumericVector >(
pMat, NA_FLOAT, NA_FLOAT, col, row);
case 8:
return GetIndivMatrixElements<double, double, MatrixAccessor<double>, NumericVector >(
pMat, NA_REAL, NA_REAL, col, row);
}
}
return R_NilValue;
}
// Function contributed by Charles Determan Jr.
// [[Rcpp::export]]
SEXP GetIndivVectorMatrixElements(SEXP bigMatAddr, NumericVector elems)
{
BigMatrix *pMat =
reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(bigMatAddr));
if (pMat->separated_columns())
{
switch(pMat->matrix_type())
{
case 1:
return GetIndivVectorMatrixElements<char, int, SepMatrixAccessor<char>, IntegerVector >(
pMat, NA_CHAR, NA_INTEGER, elems);
case 2:
return GetIndivVectorMatrixElements<short,int, SepMatrixAccessor<short>, IntegerVector >(
pMat, NA_SHORT, NA_INTEGER, elems);
case 3:
return GetIndivVectorMatrixElements<unsigned char, unsigned char, SepMatrixAccessor<unsigned char>, IntegerVector >(
pMat, NA_BYTE, NA_INTEGER, elems);
case 4:
return GetIndivVectorMatrixElements<int, int, SepMatrixAccessor<int>, IntegerVector >(
pMat, NA_INTEGER, NA_INTEGER, elems);
case 6:
return GetIndivVectorMatrixElements<float, double, SepMatrixAccessor<float>, NumericVector >(
pMat, NA_FLOAT, NA_FLOAT, elems);
case 8:
return GetIndivVectorMatrixElements<double,double,SepMatrixAccessor<double>, NumericVector >(
pMat, NA_REAL, NA_REAL, elems);
}
}
else
{
switch(pMat->matrix_type())
{
case 1:
return GetIndivVectorMatrixElements<char, int, MatrixAccessor<char>, IntegerVector >(
pMat, NA_CHAR, NA_INTEGER, elems);
case 2:
return GetIndivVectorMatrixElements<short, int, MatrixAccessor<short>, IntegerVector >(
pMat, NA_SHORT, NA_INTEGER, elems);
case 3:
return GetIndivVectorMatrixElements<unsigned char, unsigned char, MatrixAccessor<unsigned char>, IntegerVector >(
pMat, NA_BYTE, NA_INTEGER, elems);
case 4:
return GetIndivVectorMatrixElements<int, int, MatrixAccessor<int>, IntegerVector >(
pMat, NA_INTEGER, NA_INTEGER, elems);
case 6:
return GetIndivVectorMatrixElements<float, double, MatrixAccessor<float>, NumericVector >(
pMat, NA_FLOAT, NA_FLOAT, elems);
case 8:
return GetIndivVectorMatrixElements<double, double, MatrixAccessor<double>, NumericVector >(
pMat, NA_REAL, NA_REAL, elems);
}
}
return R_NilValue;
}
template<typename CType, typename RType, typename BMAccessorType>
SEXP GetMatrixRows( BigMatrix *pMat, double NA_C, double NA_R,
SEXP row, SEXPTYPE sxpType)
{
VecPtr<RType> vec_ptr;
BMAccessorType mat(*pMat);
double *pRows=REAL(row);
index_type numRows = Rf_length(row);
index_type numCols = pMat->ncol();
/*
if (TooManyRIndices(numCols*numRows))
{
Rf_error("Too many indices (>2^31-1) for extraction.");
return R_NilValue;
}
*/
SEXP ret = Rf_protect(Rf_allocVector(VECSXP, 3));
int protectCount = 1;
SET_VECTOR_ELT( ret, 1, R_NilValue );
SET_VECTOR_ELT( ret, 2, R_NilValue );
SEXP retMat;
if (numCols == 1 || numRows == 1) {
retMat = Rf_protect( Rf_allocVector(sxpType, numCols*numRows) );
} else {
retMat = Rf_protect( Rf_allocMatrix(sxpType, numRows, numCols) );
}
++protectCount;
SET_VECTOR_ELT(ret, 0, retMat);
RType *pRet = vec_ptr(retMat);
CType *pColumn = NULL;
index_type k=0;
index_type i,j;
for (i=0; i < numCols; ++i)
{
pColumn = mat[i];
for (j=0; j < numRows; ++j)
{
if (isna(pRows[j]))
{
pRet[k] = static_cast<RType>(NA_R);
}
else
{
pRet[k] = (pColumn[static_cast<index_type>(pRows[j])-1] ==
static_cast<CType>(NA_C)) ? static_cast<RType>(NA_R) :
(static_cast<RType>(pColumn[static_cast<index_type>(pRows[j])-1]));
}
++k;
}
}
Names colNames = pMat->column_names();
if (!colNames.empty())
{
++protectCount;
SEXP rCNames = Rf_protect(Rf_allocVector(STRSXP, numCols));
for (i=0; i < numCols; ++i)
{
SET_STRING_ELT( rCNames, i, Rf_mkChar(colNames[i].c_str()) );
}
SET_VECTOR_ELT(ret, 2, rCNames);
}
Names rowNames = pMat->row_names();
if (!rowNames.empty())
{
++protectCount;
SEXP rRNames = Rf_protect(Rf_allocVector(STRSXP, numRows));
for (i=0; i < numRows; ++i)
{
if (!isna(pRows[i]))
{
SET_STRING_ELT( rRNames, i,
Rf_mkChar(rowNames[static_cast<index_type>(pRows[i])-1].c_str()) );
}
}
SET_VECTOR_ELT(ret, 1, rRNames);
}
Rf_unprotect(protectCount);
return ret;
}
template<typename CType, typename RType, typename BMAccessorType>
SEXP GetMatrixCols( BigMatrix *pMat, double NA_C, double NA_R,
SEXP col, SEXPTYPE sxpType)
{
VecPtr<RType> vec_ptr;
BMAccessorType mat(*pMat);
double *pCols=REAL(col);
index_type numCols = Rf_length(col);
index_type numRows = pMat->nrow();
/*
if (TooManyRIndices(numCols*numRows))
{
Rf_error("Too many indices (>2^31-1) for extraction.");
return R_NilValue;
}
*/
SEXP ret = Rf_protect(Rf_allocVector(VECSXP, 3));
int protectCount = 1;
SET_VECTOR_ELT( ret, 1, R_NilValue );
SET_VECTOR_ELT( ret, 2, R_NilValue );
SEXP retMat;
if (numCols == 1 || numRows == 1) {
retMat = Rf_protect( Rf_allocVector(sxpType, numRows*numCols) );
} else {
retMat = Rf_protect( Rf_allocMatrix(sxpType, numRows, numCols) );
}
++protectCount;
SET_VECTOR_ELT(ret, 0, retMat);
//SEXP ret = Rf_protect( new_vec(numCols*numRows) );
RType *pRet = vec_ptr(retMat);
CType *pColumn = NULL;
index_type k=0;
index_type i,j;
for (i=0; i < numCols; ++i)
{
if (isna(pCols[i]))
{
for (j=0; j < numRows; ++j)
{
pRet[k] = static_cast<RType>(NA_R);
}
}
else
{
pColumn = mat[static_cast<index_type>(pCols[i])-1];
for (j=0; j < numRows; ++j)
{
pRet[k] = (pColumn[j] == static_cast<CType>(NA_C)) ? static_cast<RType>(NA_R) :
(static_cast<RType>(pColumn[j]));
++k;
}
}
}
Names colNames = pMat->column_names();
if (!colNames.empty())
{
++protectCount;
SEXP rCNames = Rf_protect(Rf_allocVector(STRSXP, numCols));
for (i=0; i < numCols; ++i)
{
if (!isna(pCols[i]))
SET_STRING_ELT( rCNames, i,
Rf_mkChar(colNames[static_cast<index_type>(pCols[i])-1].c_str()) );
}
SET_VECTOR_ELT(ret, 2, rCNames);
}
Names rowNames = pMat->row_names();
if (!rowNames.empty())
{
++protectCount;
SEXP rRNames = Rf_protect(Rf_allocVector(STRSXP, numRows));
for (i=0; i < numRows; ++i)
{
SET_STRING_ELT( rRNames, i, Rf_mkChar(rowNames[i].c_str()) );
}
SET_VECTOR_ELT(ret, 1, rRNames);
}
Rf_unprotect(protectCount);
return ret;
}
template<typename CType, typename RType, typename BMAccessorType>
SEXP GetMatrixAll( BigMatrix *pMat, double NA_C, double NA_R,
SEXPTYPE sxpType)
{
VecPtr<RType> vec_ptr;
BMAccessorType mat(*pMat);
index_type numCols = pMat->ncol();
index_type numRows = pMat->nrow();
/*
if (TooManyRIndices(numCols*numRows))
{
Rf_error("Too many indices (>2^31-1) for extraction.");
return R_NilValue;
}
*/
SEXP ret = Rf_protect(Rf_allocVector(VECSXP, 3));
int protectCount = 1;
SET_VECTOR_ELT( ret, 1, R_NilValue );
SET_VECTOR_ELT( ret, 2, R_NilValue );
SEXP retMat;
if (numCols == 1 || numRows == 1) {
retMat = Rf_protect( Rf_allocVector(sxpType, numRows * numCols) );
} else {
retMat = Rf_protect( Rf_allocMatrix(sxpType, numRows, numCols) );
}
++protectCount;
SET_VECTOR_ELT(ret, 0, retMat);
//SEXP ret = Rf_protect( new_vec(numCols*numRows) );
RType *pRet = vec_ptr(retMat);
CType *pColumn = NULL;
index_type k=0;
index_type i,j;
for (i=0; i < numCols; ++i)
{
pColumn = mat[i];
for (j=0; j < numRows; ++j)
{
pRet[k] = (pColumn[j] == static_cast<CType>(NA_C)) ? static_cast<RType>(NA_R) :
(static_cast<RType>(pColumn[j]));
++k;
}
}
Names colNames = pMat->column_names();
if (!colNames.empty())
{
++protectCount;
SEXP rCNames = Rf_protect(Rf_allocVector(STRSXP, numCols));
for (i=0; i < numCols; ++i)
{
SET_STRING_ELT( rCNames, i, Rf_mkChar(colNames[i].c_str()) );
}
SET_VECTOR_ELT(ret, 2, rCNames);
}
Names rowNames = pMat->row_names();
if (!rowNames.empty())
{
++protectCount;
SEXP rRNames = Rf_protect(Rf_allocVector(STRSXP, numRows));
for (i=0; i < numRows; ++i)
{
SET_STRING_ELT( rRNames, i, Rf_mkChar(rowNames[i].c_str()) );
}
SET_VECTOR_ELT(ret, 1, rRNames);
}
Rf_unprotect(protectCount);
return ret;
}
template<typename T, typename BMAccessorType>
SEXP ReadMatrix(SEXP fileName, BigMatrix *pMat,
SEXP firstLine, SEXP numLines, SEXP numCols, SEXP separator,
SEXP hasRowNames, SEXP useRowNames, double C_NA, double posInf,
double negInf, double notANumber)
{
BMAccessorType mat(*pMat);
SEXP ret = Rf_protect(Rf_allocVector(LGLSXP, 1));
LOGICAL(ret)[0] = (Rboolean)0;
index_type fl = static_cast<index_type>(REAL(firstLine)[0]);
index_type nl = static_cast<index_type>(REAL(numLines)[0]);
string sep(CHAR(STRING_ELT(separator,0)));
index_type i=0,j;
bool rowSizeReserved = false;
//double val;
ifstream file;
string lc, element;
file.open(CHAR(Rf_asChar(fileName)));
if (!file.is_open())
{
Rf_unprotect(1);
return ret;
}
for (i=0; i < fl; ++i)
{
std::getline(file, lc);
}
Names rn;
index_type offset = static_cast<index_type>(LOGICAL(hasRowNames)[0]);
double d;
int charRead;
char *pEnd;
for (i=0; i < nl; ++i)
{
// getline may be slow
std::getline(file, lc);
string::size_type first=0, last=0;
j=0;
while (first < lc.size() && last < lc.size())
{
last = lc.find_first_of(sep, first);
element = lc.substr(first, last-first);
if (LOGICAL(hasRowNames)[0] && 0==j)
{
if (LOGICAL(useRowNames)[0])
{
if (!rowSizeReserved)
{
rn.reserve(nl);
rowSizeReserved = true;
}
std::size_t pos;
while ( (pos = element.find("\"", 0)) != string::npos )
{
element = element.replace(pos, 1, "");
}
while ( (pos = element.find("'", 0)) != string::npos )
{
element = element.replace(pos, 1, "");
}
rn.push_back(element);
}
}
else
{
if (j-offset < pMat->ncol()+1)
{
d = strtod(element.c_str(), &pEnd);
if (pEnd != element.c_str())
{
if (isna(d))
{
mat[j-offset][i] = static_cast<T>(C_NA);
}
else if (std::isinf(d) && d > 0)
{
mat[j-offset][i] = static_cast<T>(posInf);
}
else if (std::isinf(d) && d < 0)
{
mat[j-offset][i] = static_cast<T>(negInf);
}
else
{
mat[j-offset][i] = static_cast<T>(d);
}
}
else
{
charRead = sscanf(element.c_str(), "%lf", &d);
if (charRead == static_cast<int>(element.size()))
{
mat[j-offset][i] = static_cast<T>(d);
}
else if (element == "NA")
{
mat[j-offset][i] = static_cast<T>(C_NA);
}
else if (element == "inf" || element == "Inf")
{
mat[j-offset][i] = static_cast<T>(posInf);
}
else if (element == "-inf" || element == "-Inf")
{
mat[j-offset][i] = static_cast<T>(negInf);
}
else if (element == "NaN")
{
mat[j-offset][i] = static_cast<T>(notANumber);
}
else if (element =="")
{
mat[j-offset][i] = static_cast<T>(C_NA);
}
else
{
mat[j-offset][i] = static_cast<T>(C_NA);
}
}
}
else
{
Rf_warning(
(string("Incorrect number of entries in row ")+ttos(j)).c_str());
}
}
first = last+1;
++j;
}
if (j-offset < pMat->ncol())
{
// warning( (string("Incorrect number of entries in row ")+ttos(j)).c_str());
while (j-offset < pMat->ncol())
{
mat[j++ - offset][i] = static_cast<T>(C_NA);
}
}
}
pMat->row_names( rn );
file.close();
LOGICAL(ret)[0] = (Rboolean)1;
Rf_unprotect(1);
return ret;
}
template<typename T, typename BMAccessorType>
void WriteMatrix( BigMatrix *pMat, SEXP fileName, SEXP rowNames,
SEXP colNames, SEXP sep, double C_NA )
{
BMAccessorType mat(*pMat);
FILE *FP = fopen(CHAR(Rf_asChar(fileName)), "w");
index_type i,j;
string s;
string sepString = string(CHAR(STRING_ELT(sep, 0)));
Names cn = pMat->column_names();
Names rn = pMat->row_names();
if (LOGICAL(colNames)[0] == Rboolean(TRUE) && !cn.empty())
{
for (i=0; i < (int) cn.size(); ++i)
s += "\"" + cn[i] + "\"" + (((int)cn.size()-1 == i) ? "\n" : sepString);
}
fprintf(FP, "%s", s.c_str());
s.clear();
for (i=0; i < pMat->nrow(); ++i)
{
if ( LOGICAL(rowNames)[0] == Rboolean(TRUE) && !rn.empty())
{
s += "\"" + rn[i] + "\"" + sepString;
}
for (j=0; j < pMat->ncol(); ++j)
{
if ( isna(mat[j][i]) )
{
s += "NA";
}
else
{
s += ttos(mat[j][i]);
}
if (j < pMat->ncol()-1)
{
s += sepString;
}
else
{
s += "\n";
}
}
fprintf(FP, "%s", s.c_str());
s.clear();
}
fclose(FP);
}
template<typename T>
struct NAMaker;
template<>
struct NAMaker<unsigned char>
{unsigned char operator()() const {return NA_BYTE;}};
template<>
struct NAMaker<char>
{char operator()() const {return NA_CHAR;}};
template<>
struct NAMaker<short>
{short operator()() const {return NA_SHORT;}};
template<>
struct NAMaker<int>
{int operator()() const {return NA_INTEGER;}};
template<>
struct NAMaker<double>
{double operator()() const {return NA_REAL;}};
// Note: naLast should be passed as an integer.
template<typename PairType>
struct SecondLess : public std::binary_function<PairType, PairType, bool>
{
SecondLess( const bool naLast ) : _naLast(naLast) {}
bool operator()(const PairType &lhs, const PairType &rhs) const
{
if (_naLast)
{
if (isna(lhs.second) || isna(rhs.second)) return false;
return lhs.second < rhs.second;
}
else
{
if (isna(lhs.second)) return true;
if (isna(rhs.second)) return false;
return lhs.second < rhs.second;
}
}
bool _naLast;
};
template<typename PairType>
struct SecondGreater : public std::binary_function<PairType, PairType, bool>
{
SecondGreater(const bool naLast ) : _naLast(naLast) {}
bool operator()(const PairType &lhs, const PairType &rhs) const
{