Initial commit

.Rbuildignore

+^vigratools\.Rproj$
+^\.Rproj\.user$

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store

DESCRIPTION

+Package: vigratools
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person(given = "First",
+           family = "Last",
+           role = c("aut", "cre"),
+           email = "first.last@example.com")
+Description: What the package does (one paragraph).
+License: What license it uses
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    vigRa,
+    Rcpp
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 6.1.0
+SystemRequirements: C++11
+LinkingTo: 
+    Rcpp,
+    vigRa

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+importFrom(Rcpp,sourceCpp)
+useDynLib(vigratools, .registration = TRUE)

R/RcppExports.R

+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' Gaussian smoothing
+#'
+#' Perform isotropic Gaussian convolution. The function uses BORDER_TREATMENT_REFLECT.
+#' @param x Numeric matrix
+#' @param sigma Scale of the Gaussian kernel
+#' @return Numeric matrix; smoothed version of x
+gaussian_smoothing <- function(x, sigma) {
+    .Call(`_vigratools_gaussian_smoothing`, x, sigma)
+}
+

R/useDynLib.R

+#' @useDynLib vigratools, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
+NULL

R/vigratools-package.R

+#' @keywords internal
+"_PACKAGE"

README.md

+# vigratools
+
+The goal of vigratools is to ...
+
+## Installation
+
+You can install the released version of vigratools from [CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("vigratools")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+## basic example code
+```
+

man/gaussian_smoothing.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{gaussian_smoothing}
+\alias{gaussian_smoothing}
+\title{Gaussian smoothing}
+\usage{
+gaussian_smoothing(x, sigma)
+}
+\arguments{
+\item{x}{Numeric matrix}
+
+\item{sigma}{Scale of the Gaussian kernel}
+}
+\value{
+Numeric matrix; smoothed version of x
+}
+\description{
+Perform isotropic Gaussian convolution. The function uses BORDER_TREATMENT_REFLECT.
+}

man/vigratools-package.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vigratools-package.R
+\docType{package}
+\name{vigratools-package}
+\alias{vigratools}
+\alias{vigratools-package}
+\title{vigratools: What the Package Does (One Line, Title Case)}
+\description{
+What the package does (one paragraph).
+}
+\author{
+\strong{Maintainer}: First Last \email{first.last@example.com}
+
+}
+\keyword{internal}

src/.gitignore

+*.o
+*.so
+*.dll

src/RcppExports.cpp

+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+// gaussian_smoothing
+NumericMatrix gaussian_smoothing(NumericMatrix x, double sigma);
+RcppExport SEXP _vigratools_gaussian_smoothing(SEXP xSEXP, SEXP sigmaSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericMatrix >::type x(xSEXP);
+    Rcpp::traits::input_parameter< double >::type sigma(sigmaSEXP);
+    rcpp_result_gen = Rcpp::wrap(gaussian_smoothing(x, sigma));
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_vigratools_gaussian_smoothing", (DL_FUNC) &_vigratools_gaussian_smoothing, 2},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_vigratools(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

src/gaussian_smoothing.cpp

+//[[Rcpp::depends(vigRa)]]
+#include <Rcpp.h>
+#include <vigra/multi_array.hxx>
+#include <vigra/convolution.hxx>
+// #include <vigra/tensorutilities.hxx>
+// #include <vigra/mathutil.hxx>
+// #include <vigra/multi_tensorutilities.hxx>
+using namespace Rcpp;
+using namespace vigra;
+
+
+//' Gaussian smoothing
+//'
+//' Perform isotropic Gaussian convolution. The function uses BORDER_TREATMENT_REFLECT.
+//' @param x Numeric matrix
+//' @param sigma Scale of the Gaussian kernel
+//' @return Numeric matrix; smoothed version of x
+// [[Rcpp::export]]
+NumericMatrix gaussian_smoothing(NumericMatrix x, double sigma) {
+  const int nrows = x.nrow();
+  const int ncols = x.ncol();
+  Shape2 shape(nrows, ncols);
+  MultiArrayView<2, double> input_image(shape, x.begin());
+  NumericMatrix result(nrows, ncols);
+  MultiArrayView<2, double> output_image(shape, result.begin());
+  gaussianSmoothing(input_image, output_image, sigma);
+  return(result);
+}

vigratools.Rproj

+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+Encoding: UTF-8
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace