Convert SciPy sparse matrix to R

.travis.yml

@@ -13,7 +13,8 @@ before_install:
   - ./run.sh bootstrap
 
 install:
-  - ./run.sh install_aptget  r-cran-rcpp r-cran-runit r-cran-matrix r-cran-pkgkitten
+  - ./run.sh install_aptget  r-cran-rcpp r-cran-runit r-cran-matrix r-cran-pkgkitten r-cran-jsonlite python-scipy
+  - ./run.sh install_r reticulate
 
 script:
   - ./run.sh run_tests

ChangeLog

@@ -1,3 +1,15 @@
+2017-08-07  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/unitTests/runit.scipy2r.R: Whitespace edits
+	* R/SciPy2R.R: Idem; also renamed from py2R, removed one require()
+
+	* .travis.yml (install): Also install reticulate and (r-cran-)jsonlite
+
+2017-08-07  Binxiang Ni  <binxiangni@gmail.com>
+
+	* R/py2r.R: Python to R conversion
+	* inst/unitTests/runit.scipy2r.R: Unit tests
+
 2017-08-06  Dirk Eddelbuettel  <edd@debian.org>
 
 	* DESCRIPTION (Version, Date): Rolled to fictional pre-release

DESCRIPTION

@@ -22,7 +22,7 @@ Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
 License: GPL (>= 2)
 LazyLoad: yes
 LinkingTo: Rcpp
-Imports: Rcpp (>= 0.11.0), stats, utils
+Imports: Rcpp (>= 0.11.0), stats, utils, methods, reticulate
 Suggests: RUnit, Matrix, pkgKitten
 URL: http://dirk.eddelbuettel.com/code/rcpp.armadillo.html
 BugReports: https://github.com/RcppCore/RcppArmadillo/issues

NAMESPACE

@@ -1,8 +1,10 @@
 useDynLib("RcppArmadillo", .registration=TRUE)
 
 import("Rcpp")
+import("reticulate")
 importFrom("stats", "coef", "fitted", "model.frame", "model.matrix", "model.response", "printCoefmat", "pt")
 importFrom("utils", "packageDescription", "package.skeleton")
+importFrom("methods", "new")
 
 export("fastLmPure",
        "fastLm",

R/SciPy2R.R

@@ -0,0 +1,40 @@
+## .sciPy2R.R: Conversion of SciPy sparse matrix to R
+##
+## Copyright (C) 2017  Binxiang Ni and Dirk Eddelbuettel
+##
+## This file is part of RcppArmadillo.
+##
+## RcppArmadillo is free software: you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 2 of the License, or
+## (at your option) any later version.
+##
+## RcppArmadillo is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+.SciPy2R <- function(spmat) {
+    type <- spmat$getformat()
+    shape <- unlist(spmat$shape)
+    data <- as.vector(py_get_attr(spmat, "data"))
+    if (type == "csc") {
+        indices <- as.vector(py_get_attr(spmat, "indices"))
+        indptr <- as.vector(py_get_attr(spmat, "indptr"))
+        res <- new("dgCMatrix", i = indices, p = indptr, x = data, Dim = shape)
+    } else if (type == "coo") {
+        row <- as.vector(py_get_attr(spmat, "row"))
+        col <- as.vector(py_get_attr(spmat, "col"))
+        res <- new("dgTMatrix", i = row, j = col, x = data, Dim = shape)
+    } else if (type == "csr") {
+        indices <- as.vector(py_get_attr(spmat, "indices"))
+        indptr <- as.vector(py_get_attr(spmat, "indptr"))
+        res <- new("dgRMatrix", j = indices, p = indptr, x = data, Dim = shape)
+    } else {
+        stop("Only CSC, COO and CSR matrices from SciPy are supported.")
+    }
+    return(res)
+}

inst/unitTests/runit.scipy2r.R

@@ -0,0 +1,59 @@
+## py2r.R: Conversion of SciPy sparse matrix to R
+### Copyright (C) 2017  Binxiang Ni and Dirk Eddelbuettel
+##
+## This file is part of RcppArmadillo.
+##
+## RcppArmadillo is free software: you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 2 of the License, or
+## (at your option) any later version.
+##
+## RcppArmadillo is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+## Reference: https://docs.scipy.org/doc/scipy-0.19.1/reference/sparse.html
+
+suppressMessages(require(Matrix))
+suppressMessages(require(reticulate))
+
+np <- import("numpy")
+mat <- np$array(list(list(1, 0, 4), list(0, 0, 5), list(2, 3, 6)))
+sp <- import("scipy.sparse")
+
+mtxt <- c("1 0 4",
+          "0 0 5",
+          "2 3 6")
+M <- as.matrix(read.table(text=mtxt))
+dimnames(M) <- NULL
+
+test.csc2dgc <- function() {
+    csc <- sp$csc_matrix(mat)
+    dgC <- methods::as(M, "dgCMatrix")
+    checkEquals(dgC, RcppArmadillo:::.SciPy2R(csc), msg="csc2dgc")
+}
+
+test.coo2dgt <- function() {
+    coo <- sp$coo_matrix(mat)
+    dgT <- new("dgTMatrix",
+               i = c(0L, 0L, 1L, 2L, 2L, 2L),
+               j = c(0L, 2L, 2L, 0L, 1L, 2L),
+               x = c(1, 4, 5, 2, 3, 6),
+               Dim = c(3L, 3L))
+    checkEquals(dgT, RcppArmadillo:::.SciPy2R(coo), msg="coo2dgt")
+}
+
+test.csr2dgr <- function() {
+    csr <- sp$csr_matrix(mat)
+    dgR <- methods::as(M, "dgRMatrix")
+    checkEquals(dgR, RcppArmadillo:::.SciPy2R(csr), msg="csr2dgr")
+}
+
+test.other <- function() {
+    bsr <- sp$bsr_matrix(list(3, 4))
+    checkException(RcppArmadillo:::.SciPy2R(bsr))
+}