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Accomodate upcoming change in package Matrix (fixes #415) #417

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merged 3 commits into from Jun 5, 2023
Merged

Accomodate upcoming change in package Matrix (fixes #415) #417

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321fe06
fixes #415
jaganmn Jun 4, 2023
33c90d4
thinko
jaganmn Jun 4, 2023
319eb57
ChangeLog entry for #415 patch
jaganmn Jun 4, 2023
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209 changes: 73 additions & 136 deletions inst/include/RcppArmadillo/interface/RcppArmadilloAs.h
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Expand Up @@ -123,38 +123,38 @@ namespace traits {

// Get the type of sparse matrix
std::string type = Rcpp::as<std::string>(mat.slot("class"));

if (type == "dgCMatrix" || mat.is("dgCMatrix")) {
IntegerVector i = mat.slot("i");
IntegerVector p = mat.slot("p");
Vector<RTYPE> x = mat.slot("x");

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
#define DO_RESULT \
do { \
/* Allocate: */ \
res.mem_resize(static_cast<unsigned>(x.size())); \
\
/* To access arrays internal to SpMat class: */ \
res.sync(); \
\
/* Copy: */ \
std::copy(i.begin(), i.end(), \
arma::access::rwp(res.row_indices)); \
std::copy(p.begin(), p.end(), \
arma::access::rwp(res.col_ptrs)); \
std::copy(x.begin(), x.end(), \
arma::access::rwp(res.values)); \
} while (0)

DO_RESULT;
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Old school :) Maybe we have too much C around R to not let go of macros.

}
else if (type == "dtCMatrix" || mat.is("dtCMatrix")) {
IntegerVector i = mat.slot("i");
IntegerVector p = mat.slot("p");
Vector<RTYPE> x = mat.slot("x");
std::string diag = Rcpp::as<std::string>(mat.slot("diag"));

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;

if (diag == "U") {
res.diag().ones();
Expand All @@ -166,16 +166,7 @@ namespace traits {
Vector<RTYPE> x = mat.slot("x");
std::string uplo = Rcpp::as<std::string>(mat.slot("uplo"));

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;

if (uplo == "U") {
res = symmatu(res);
Expand Down Expand Up @@ -250,16 +241,7 @@ namespace traits {
last = tmp;
}

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;
}
else if (type == "dtRMatrix" || mat.is("dtRMatrix")) {
IntegerVector rj = mat.slot("j");
Expand Down Expand Up @@ -304,16 +286,7 @@ namespace traits {
last = tmp;
}

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;

if (diag == "U"){
res.diag().ones();
Expand Down Expand Up @@ -362,16 +335,7 @@ namespace traits {
last = tmp;
}

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;

if (uplo == "U") {
res = symmatu(res);
Expand All @@ -380,82 +344,61 @@ namespace traits {
}
}
else if (type == "indMatrix" || mat.is("indMatrix")) {
std::vector<int> i;
IntegerVector p(ncol + 1);
IntegerVector x(nrow, 1);
IntegerVector perm = mat.slot("perm");

typedef std::pair<int, int> Key;
typedef std::set<Key> Set;
Set permiSet;

// Sort i;
int nnz = perm.size();
for(int tmp = 0; tmp < nnz; tmp++){
Key permi(perm[tmp], tmp);
permiSet.insert(permi);
}

for(Set::iterator tmp = permiSet.begin(); tmp != permiSet.end(); tmp++){
i.push_back(tmp -> second);
}

// Count the number of nnz in each column
for(int idx = 0; idx < nnz; idx++){
int col = perm[idx];
p[col]++;
}

// Cumsum p
for(int col = 0, cumsum = 0; col < ncol + 1; col++){
cumsum += p[col];
p[col] = cumsum;
IntegerVector p(ncol + 1);
IntegerVector i(perm.size());
IntegerVector x(perm.size());

if (!mat.hasSlot("margin") ||
as<IntegerVector>(mat.slot("margin"))[0] == 1) {
int *work = reinterpret_cast<int *>(
R_alloc((std::size_t) ncol, sizeof(int)));
std::memset(work, 0, ncol * sizeof(int));
for (int ii = 0; ii < nrow; ++ii)
work[perm[ii] - 1]++;
for (int jj = 0; jj < ncol; ++jj) {
p[jj + 1] = p[jj] + work[jj];
work[jj] = p[jj];
}
for (int ii = 0; ii < nrow; ++ii) {
i[work[perm[ii] - 1]++] = ii;
x[ii] = 1;
}
} else {
for (int jj = 0; jj < ncol; ++jj) {
p[jj] = jj;
i[jj] = perm[jj] - 1;
x[jj] = 1;
}
p[ncol] = ncol;
}

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;
}
else if (type == "pMatrix" || mat.is("pMatrix")) {
std::vector<int> i;
IntegerVector p(ncol + 1);
IntegerVector x(ncol, 1);
IntegerVector perm = mat.slot("perm");

// Sort the row number by the column number
typedef std::map <int, int> Map;
Map colrow;
for(int tmp = 0; tmp < perm.size(); tmp++){
colrow[perm[tmp]] = tmp;
}

// Calculate i
for(Map::iterator tmp = colrow.begin(); tmp != colrow.end(); tmp++){
i.push_back(tmp -> second);
}

// Calculate p
for(int tmp = 0; tmp < p.size(); tmp++){
p[tmp] = tmp;
IntegerVector p(ncol + 1);
IntegerVector i(ncol);
IntegerVector x(ncol);

if (!mat.hasSlot("margin") ||
as<IntegerVector>(mat.slot("margin"))[0] == 1) {
for (int jj = 0; jj < ncol; ++jj)
i[perm[jj] - 1] = jj;
for (int jj = 0; jj < ncol; ++jj) {
p[jj] = jj;
x[jj] = 1;
}
} else {
for (int jj = 0; jj < ncol; ++jj) {
p[jj] = jj;
i[jj] = perm[jj] - 1;
x[jj] = 1;
}
}
p[ncol] = ncol;

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));

// In order to access the internal arrays of the SpMat class
res.sync();

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
DO_RESULT;
}
else if (type == "ddiMatrix" || mat.is("ddiMatrix")) {
std::vector<int> i;
Expand Down Expand Up @@ -484,16 +427,10 @@ namespace traits {
p.push_back(tmpp);
}

// Making space for the elements
res.mem_resize(static_cast<unsigned>(x.size()));
DO_RESULT;

// In order to access the internal arrays of the SpMat class
res.sync();
#undef DO_RESULT

// Copying elements
std::copy(i.begin(), i.end(), arma::access::rwp(res.row_indices));
std::copy(p.begin(), p.end(), arma::access::rwp(res.col_ptrs));
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
}
else {
Rcpp::stop(type + " is not supported.");
Expand Down