add c_ListofMatrixRows()

.github/workflows/R-CMD-check.yaml

@@ -61,7 +61,7 @@ jobs:
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          done < <(Rscript -e 'writeLines(c(remotes::system_requirements("ubuntu", "20.04"), remotes::system_requirements("ubuntu", "20.04", package="curl")))')
 
       - name: Install dependencies
         run: |

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: natcpp
 Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
-Version: 0.1.0.9000
+Version: 0.1.1
 Authors@R: 
     person(given = "Gregory",
            family = "Jefferis",

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(c_EdgeListFromSegList)
+export(c_ListofMatrixRows)
 export(c_listlengths)
 export(c_seglengths)
 export(c_topntail)

NEWS.md

@@ -1,5 +1,9 @@
 # natcpp (development version)
 
+# natcpp 0.1.1
+
+* adds `c_ListofMatrixRows()`
+
 # natcpp 0.1.0
 
 * First version of the package with basic functions for manipulating segment

R/RcppExports.R

@@ -20,6 +20,30 @@ c_total_cable <- function(sl, x, y, z) {
     .Call(`_natcpp_c_total_cable`, sl, x, y, z)
 }
 
+#' Convert a matrix into list of row vectors
+#'
+#' @details Typically this will be for 3D coordinates but there are no limits
+#'   on row length.
+#' @param object An integer, numeric, character or logical matrix of N rows and
+#'   M columns
+#' @return a list containing N vectors of length M corresponding to the rows of
+#'   \code{object}.
+#' @export
+#' @examples
+#' \dontrun{
+#' library(nat)
+#' xyz=xyzmatrix(Cell07PNs)
+#' mat2list = function(m) {
+#' um=unname(m)
+#' lapply(1:nrow(um), function(i) um[i,])
+#' }
+#' bench::mark(rcpp=c_ListofMatrixRows(xyz), r=mat2list(xyz))
+#' }
+#' @export
+c_ListofMatrixRows <- function(object) {
+    .Call(`_natcpp_c_ListofMatrixRows`, object)
+}
+
 #' A simple function to compute the lengths of the elements of an R list
 #'
 #' @details This is equivalent to the \code{base::lengths} however it it much

src/RcppExports.cpp

@@ -38,6 +38,17 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// c_ListofMatrixRows
+List c_ListofMatrixRows(const SEXP& object);
+RcppExport SEXP _natcpp_c_ListofMatrixRows(SEXP objectSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const SEXP& >::type object(objectSEXP);
+    rcpp_result_gen = Rcpp::wrap(c_ListofMatrixRows(object));
+    return rcpp_result_gen;
+END_RCPP
+}
 // c_listlengths
 IntegerVector c_listlengths(const List& L);
 RcppExport SEXP _natcpp_c_listlengths(SEXP LSEXP) {
@@ -86,6 +97,7 @@ END_RCPP
 static const R_CallMethodDef CallEntries[] = {
     {"_natcpp_c_seglengths", (DL_FUNC) &_natcpp_c_seglengths, 4},
     {"_natcpp_c_total_cable", (DL_FUNC) &_natcpp_c_total_cable, 4},
+    {"_natcpp_c_ListofMatrixRows", (DL_FUNC) &_natcpp_c_ListofMatrixRows, 1},
     {"_natcpp_c_listlengths", (DL_FUNC) &_natcpp_c_listlengths, 1},
     {"_natcpp_c_topntail", (DL_FUNC) &_natcpp_c_topntail, 1},
     {"_natcpp_c_topntail_list", (DL_FUNC) &_natcpp_c_topntail_list, 1},

src/matrix.cpp

@@ -0,0 +1,48 @@
+#include "natcpp.h"
+
+template <typename T>
+List c_ListofMatrixRowsT(const T &m) {
+  List L(m.nrow());
+
+  for(int i=0; i<(m.nrow()); i++) {
+    // NumericVector v = m( 0 , _ );
+    L[i]=m.row(i);
+  }
+  return L;
+}
+
+
+//' Convert a matrix into list of row vectors
+//'
+//' @details Typically this will be for 3D coordinates but there are no limits
+//'   on row length.
+//' @param object An integer, numeric, character or logical matrix of N rows and
+//'   M columns
+//' @return a list containing N vectors of length M corresponding to the rows of
+//'   \code{object}.
+//' @export
+//' @examples
+//' \dontrun{
+//' library(nat)
+//' xyz=xyzmatrix(Cell07PNs)
+//' mat2list = function(m) {
+//' um=unname(m)
+//' lapply(1:nrow(um), function(i) um[i,])
+//' }
+//' bench::mark(rcpp=c_ListofMatrixRows(xyz), r=mat2list(xyz))
+//' }
+//' @export
+// [[Rcpp::export]]
+List c_ListofMatrixRows(const SEXP &object) {
+  if (!Rf_isMatrix(object))
+    stop("Please provide a matrix!");
+
+  switch (TYPEOF(object))
+  {
+  case INTSXP: return c_ListofMatrixRowsT<IntegerMatrix>(object);
+  case REALSXP: return c_ListofMatrixRowsT<NumericMatrix>(object);
+  case CHARSXP: return c_ListofMatrixRowsT<CharacterMatrix>(object);
+  case LGLSXP: return c_ListofMatrixRowsT<LogicalMatrix>(object);
+  }
+  stop("Unimplemented matrix type!");
+}

tests/testthat/test-matrix.R

@@ -0,0 +1,20 @@
+test_that("multiplication works", {
+  m=matrix(1:6, ncol=3, byrow = T)
+  l=list(1:3, 4:6)
+  colnames(m)=c("X","Y","Z")
+  expect_equal(c_ListofMatrixRows(m), l)
+
+  nm=matrix(rnorm(n = 300), ncol=3)
+
+  expect_equal(c_ListofMatrixRows(nm),
+               lapply(seq_len(nrow(nm)), function(i) nm[i,]))
+
+  expect_equal(c_ListofMatrixRows(matrix(1L, nrow=2, ncol=0)),
+               list(integer(), integer()))
+  expect_equal(c_ListofMatrixRows(matrix(1L, nrow=0, ncol=2)),
+               list())
+  expect_error(c_ListofMatrixRows(l))
+  # matrix of lists
+  ml=matrix(rep(list(1), 4), ncol = 2)
+  expect_error(c_ListofMatrixRows(ml))
+})