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Merged
merged 11 commits into from
Jun 18, 2017
Merged

Add conversion & unit tests for dgT, dtT & dsTMatrix #136

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214a686
Add support for dtCMatrix&dsCMatrix
binxiangni Jun 14, 2017
409c2f0
Indentation
binxiangni Jun 16, 2017
c74a0b8
Add unit test for dtc2dgc
binxiangni Jun 16, 2017
04faf58
Fix bug
binxiangni Jun 17, 2017
ba58bd2
Add unit tests for dtCMatrix & dsCMatrix
binxiangni Jun 17, 2017
ecbb0d0
Add conversion and unit tests for dtCMatrix & dsCMatrix
binxiangni Jun 17, 2017
f5d2f74
Update ChangeLog
binxiangni Jun 17, 2017
457c6c2
Add unit test for low triangle dsCMatrix
binxiangni Jun 17, 2017
4017720
Add conversion for dgT, dtT& dsT
binxiangni Jun 17, 2017
58c3f88
Add unit tests for dgT, dtT& dsT
binxiangni Jun 17, 2017
13653c1
Merge branch 'master' into Tsparse
binxiangni Jun 18, 2017
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86 changes: 84 additions & 2 deletions inst/include/RcppArmadilloAs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,6 @@ namespace traits {
std::copy(x.begin(), x.end(), arma::access::rwp(res.values));
}
else if (type == "dtCMatrix") {
// The following 3 lines might be duplicate, but when the type == dgT or dgR, we have to include the lines inside the conditional statements rather than outside.
IntegerVector i = mat.slot("i");
IntegerVector p = mat.slot("p");
Vector<RTYPE> x = mat.slot("x");
Expand All @@ -130,7 +129,6 @@ namespace traits {
}
}
else if (type == "dsCMatrix") {
// The following 3 lines might be duplicate, but when the type == dgT or dgR, we have to include the lines inside the conditional statements rather than outside.
IntegerVector i = mat.slot("i");
IntegerVector p = mat.slot("p");
Vector<RTYPE> x = mat.slot("x");
Expand All @@ -150,6 +148,90 @@ namespace traits {
res = symmatl(res);
}
}
else if (type == "dgTMatrix") {
IntegerVector tj = mat.slot("j");
IntegerVector i = mat.slot("i");
Vector<RTYPE> x = mat.slot("x");
IntegerVector p = IntegerVector(ncol + 1);

int nnz = x.size();
// Count the number of nnz in each column
for(int idx = 0; idx < nnz; idx++){
int col = tj[idx];
p[col + 1]++;
}

// Cumsum p
for(int col = 0, cumsum = 0; col < ncol + 1; col++){
cumsum += p[col];
p[col] = cumsum;
}

res.mem_resize(static_cast<unsigned>(x.size()));
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 if (type == "dtTMatrix") {
IntegerVector tj = mat.slot("j");
IntegerVector i = mat.slot("i");
Vector<RTYPE> x = mat.slot("x");
IntegerVector p = IntegerVector(ncol + 1);
std::string diag = Rcpp::as<std::string>(mat.slot("diag"));

int nnz = x.size();
// Count the number of nnz in each column
for(int idx = 0; idx < nnz; idx++){
int col = tj[idx];
p[col + 1]++;
}

// Cumsum p
for(int col = 0, cumsum = 0; col < ncol + 1; col++){
cumsum += p[col];
p[col] = cumsum;
}

res.mem_resize(static_cast<unsigned>(x.size()));
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));

if (diag == "U"){
res.diag().ones();
}
}
else if (type == "dsTMatrix") {
IntegerVector tj = mat.slot("j");
IntegerVector i = mat.slot("i");
Vector<RTYPE> x = mat.slot("x");
IntegerVector p = IntegerVector(ncol + 1);
std::string uplo = Rcpp::as<std::string>(mat.slot("uplo"));

int nnz = x.size();
// Count the number of nnz in each column
for(int idx = 0; idx < nnz; idx++){
int col = tj[idx];
p[col + 1]++;
}

// Cumsum p
for(int col = 0, cumsum = 0; col < ncol + 1; col++){
cumsum += p[col];
p[col] = cumsum;
}

res.mem_resize(static_cast<unsigned>(x.size()));
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));

if (uplo == "U") {
res = symmatu(res);
} else {
res = symmatl(res);
}
}

// Setting the sentinel
arma::access::rw(res.col_ptrs[static_cast<unsigned>(ncol + 1)]) =
Expand Down
57 changes: 49 additions & 8 deletions inst/unitTests/runit.sparse.R
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Original file line number Diff line number Diff line change
Expand Up @@ -100,12 +100,11 @@ if (.runThisTest) {
M <- as.matrix(read.table(textConnection(mtxt)))
dimnames(M) <- NULL
dtc <- Matrix(M, sparse=TRUE)
dgc <- as(dtc, "dgCMatrix")

dgc <- methods::as(dtc, "dgCMatrix")
checkEquals(dgc, asSpMat(dtc), msg="asSpMat")

dtc@diag <- "U"
dgc <- as(dtc, "dgCMatrix")
dgc <- methods::as(dtc, "dgCMatrix")
checkEquals(dgc, asSpMat(dtc), msg="asSpMat")
}

Expand All @@ -118,13 +117,55 @@ if (.runThisTest) {
M <- as.matrix(read.table(textConnection(mtxt)))
dimnames(M) <- NULL
dsc <- Matrix(M, sparse=TRUE)
dgc <- as(dsc, "dgCMatrix")

dgc <- methods::as(dsc, "dgCMatrix")
checkEquals(dgc, asSpMat(dsc), msg="asSpMat")

dsc <- t(dsc)
dgc <- as(dsc, "dgCMatrix")

dgc <- methods::as(dsc, "dgCMatrix")
checkEquals(dgc, asSpMat(dsc), msg="asSpMat")
}
}

test.dgt2dgc <- function() {
dgt <- methods::as(SM, "dgTMatrix")
checkEquals(SM, asSpMat(dgt), msg="asSpMat")
}

test.dtt2dgc <- function() {
mtxt <- c("0 0 0 3",
"0 0 7 0",
"0 0 0 0",
"0 0 0 0")
M <- as.matrix(read.table(textConnection(mtxt)))
dimnames(M) <- NULL
dtc <- Matrix(M, sparse=TRUE)
dgc <- methods::as(dtc, "dgCMatrix")
dtt <- methods::as(dtc, "dtTMatrix")
checkEquals(dgc, asSpMat(dtt), msg="asSpMat")

dtc@diag <- "U"
dgc <- methods::as(dtc, "dgCMatrix")
dtt <- methods::as(dtc, "dtTMatrix")
checkEquals(dgc, asSpMat(dtt), msg="asSpMat")
}

test.dst2dgc <- function() {
mtxt <- c("10 0 1 0 3",
"0 10 0 1 0",
"1 0 10 0 1",
"0 1 0 10 0",
"3 0 1 0 10")
M <- as.matrix(read.table(textConnection(mtxt)))
dimnames(M) <- NULL
dsc <- Matrix(M, sparse=TRUE)
dgc <- methods::as(dsc, "dgCMatrix")
dst <- methods::as(dsc, "dsTMatrix")
checkEquals(dgc, asSpMat(dst), msg="asSpMat")

dsc <- t(dsc)
dgc <- methods::as(dsc, "dgCMatrix")
dst <- methods::as(dsc, "dsTMatrix")
checkEquals(dgc, asSpMat(dst), msg="asSpMat")
}
}