[Rimagej-commits] r13 - in pkg/RImageJ: . R inst/java man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Oct 9 07:52:54 CEST 2010
Author: phgrosjean
Date: 2010-10-09 07:52:53 +0200 (Sat, 09 Oct 2010)
New Revision: 13
Modified:
pkg/RImageJ/DESCRIPTION
pkg/RImageJ/NAMESPACE
pkg/RImageJ/R/onLoad.R
pkg/RImageJ/R/raster.R
pkg/RImageJ/inst/java/ij.jar
pkg/RImageJ/man/IJ.Rd
pkg/RImageJ/man/RImageJ-package.Rd
pkg/RImageJ/man/as.raster.Rd
Log:
Upgrade to ImageJ 1.44i + eliminate headless starting in Mac OS X (must use R under JGR on Mac OS X snow leopard anyway)
Added a notice to RImageJ-package.Rd to use JGR for Mac OS X
Modified: pkg/RImageJ/DESCRIPTION
===================================================================
--- pkg/RImageJ/DESCRIPTION 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/DESCRIPTION 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,6 +1,6 @@
Package: RImageJ
-Version: 0.2-143
-Date: 2010-02-18
+Version: 0.2-144
+Date: 2010-10-09
Title: R bindings for ImageJ
Author: Romain Francois, Philippe Grosjean with contributions from Paul Murrell
Maintainer: Romain Francois <romain at r-enthusiasts.com>
Modified: pkg/RImageJ/NAMESPACE
===================================================================
--- pkg/RImageJ/NAMESPACE 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/NAMESPACE 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,6 +1,6 @@
import("rJava")
export(IJ)
-importFrom( "grDevices", "as.raster" )
-S3method( "as.raster", "jobjRef" )
+importFrom("grDevices", "as.raster")
+S3method("as.raster", "jobjRef")
Modified: pkg/RImageJ/R/onLoad.R
===================================================================
--- pkg/RImageJ/R/onLoad.R 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/R/onLoad.R 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,10 +1,13 @@
.onLoad <- function (libname, pkgname) {
- if (substring(R.Version()$os, 1, 6) == "darwin") {
- # There is a problem starting Java with AWT on Mac OS X (Snow) Leopard
- # This tries to correct it!
- options(java.parameters = paste(getOption("java.parameters"),
- "-Djava.awt.headless=true"))
- }
+ #if (substring(R.Version()$os, 1, 6) == "darwin") {
+ # # There is a problem starting Java with AWT on Mac OS X (Snow) Leopard
+ # # This tries to correct it!
+ # options(java.parameters = paste(getOption("java.parameters"),
+ # "-Djava.awt.headless=true"))
+ #}
+ # Note: this does not solve *all* the problem because methods in IJ that
+ # rely on genericDialog still do not work. The only solution I [PhG]
+ # have found until now is to start RImageJ from within JGR.
.jpackage(pkgname)
cat("ImageJ version: ", IJ$getVersion(), "\n", sep = "")
}
Modified: pkg/RImageJ/R/raster.R
===================================================================
--- pkg/RImageJ/R/raster.R 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/R/raster.R 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,31 +1,30 @@
-# based on a contribution by Paul Murell
+### Based on a contribution by Paul Murell
#setGeneric("as.raster" )
#
-#setMethod( "as.raster", "jobjRef", function(x){
-as.raster.jobjRef <- function(x, ...){
- # first check that this is an instance of ij.ImagePlus
+#setMethod( "as.raster", "jobjRef", function (x) {
+as.raster.jobjRef <- function (x, ...)
+{
+ ## First check that this is an instance of ij.ImagePlus
if (!x %instanceof% "ij.ImagePlus")
stop("'x' must be a reference to an \"ImagePlus\" object")
- # Image dimensions
+ ## Image dimensions
w <- x$getWidth()
h <- x$getHeight()
- # Force to RGB image
+ ## Force to RGB image
ijp <- x$getProcessor()
ijrgb <- ijp$convertToRGB()
- # Grab the pixels (which should now be integers)
+ ## Grab the pixels (which should now be integers)
pixels <- ijrgb$getPixels()
- # Convert the integers to R colours
+ ## Convert the integers to R colours
colourChars <- as.character(as.hexmode(pixels))
red <- substr(colourChars, 3, 4)
green <- substr(colourChars, 5, 6)
blue <- substr(colourChars, 7, 8)
- colours <- paste("#", red, green, blue, sep="")
+ colours <- paste("#", red, green, blue, sep = "")
r <- colours
dim(r) <- c(h, w)
class(r) <- "raster"
- r
+ return(r)
}
-# )
-
Modified: pkg/RImageJ/inst/java/ij.jar
===================================================================
(Binary files differ)
Modified: pkg/RImageJ/man/IJ.Rd
===================================================================
--- pkg/RImageJ/man/IJ.Rd 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/man/IJ.Rd 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,35 +1,41 @@
\name{IJ}
-\Rdversion{1.1}
\alias{IJ}
\docType{data}
+
\title{
IJ object
}
+
\description{
-This represents an object of class \code{ij.IJ} created when the
-RImageJ package is loaded
+ This represents an object of class \code{ij.IJ} created when the RImageJ
+ package is loaded.
}
+
\usage{IJ}
+
\format{
-This is a java object, instance of the class \code{ij.IJ}, that is created when the
-package is loaded.
+ This is a java object, instance of the class \code{ij.IJ}, that is created
+ when the package is loaded.
}
+
\details{
-The ImageJ macro language is basically made of calls to methods of
-the IJ class. This object allows to mimic the macro language by using
-the convenient dollar notation. See examples below.
+ The ImageJ macro language is basically made of calls to methods of the IJ
+ class. This object allows to mimic the macro language by using the convenient
+ dollar notation. See examples below.
}
+
\references{
-The java documentation of the class IJ:
-\url{http://rsbweb.nih.gov/ij/developer/api/ij/IJ.html}
+ The java documentation of the class IJ:
+ \url{http://rsbweb.nih.gov/ij/developer/api/ij/IJ.html}
+
+ ImageJ macro language:
+ \url{http://rsbweb.nih.gov/ij/developer/macro/macros.html}
+}
-ImageJ macro language
-\url{http://rsbweb.nih.gov/ij/developer/macro/macros.html}
-}
\examples{
\dontrun{
-logo <- system.file( "images", "R.jpg", package = "RImageJ" )
-image <- IJ$openImage( logo )
+logo <- system.file("images", "R.jpg", package = "RImageJ")
+image <- IJ$openImage(logo)
image$show()
IJ$run("8-bit")
IJ$run("Invert")
Modified: pkg/RImageJ/man/RImageJ-package.Rd
===================================================================
--- pkg/RImageJ/man/RImageJ-package.Rd 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/man/RImageJ-package.Rd 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,31 +1,41 @@
\name{RImageJ-package}
-\Rdversion{1.1}
\alias{RImageJ-package}
\docType{package}
-\title{
-R bindings for ImageJ
-}
+
+\title{ R bindings for ImageJ }
+
\description{
-bindings between R and the java based image processing
-and analysis platform ImageJ
+ Bindings between R and the java based image processing and analysis platform
+ ImageJ.
}
+
\details{
-\tabular{ll}{
-Package: \tab RImageJ\cr
-Type: \tab Package\cr
-Version: \tab 0.2-143\cr
-Date: \tab 2010-02-18\cr
-License: \tab GPL-3\cr
-LazyLoad: \tab yes\cr
+ \tabular{ll}{
+ Package: \tab RImageJ\cr
+ Type: \tab Package\cr
+ Version: \tab 0.2-144\cr
+ Date: \tab 2010-10-09\cr
+ License: \tab GPL-3\cr
+ LazyLoad: \tab yes\cr
+ }
}
+
+\details{
+ On certain Mac OS X systems (like Snow Leopard), it is impossible to start AWT
+ from rJava started from R.app or from the terminal. Since ImageJ depends on
+ AWT, it will not run. The solution is to use R and RImageJ from within JGR
+ \url{http://www.rforge.net/JGR/}.
}
+
\author{
-Romain Francois for the R package
-Wayne Rasband for ImageJ
+ Romain Francois & Philippe Grosjean for the R package
+ Wayne Rasband for ImageJ
-Maintainer: Romain Francois <romain at r-enthusiasts.com>
+ Maintainer: Romain Francois <romain at r-enthusiasts.com>
}
+
\references{
-ImageJ: \url{http://rsbweb.nih.gov/ij/index.html}
+ ImageJ: \url{http://rsbweb.nih.gov/ij/index.html}
}
+
\keyword{ package }
Modified: pkg/RImageJ/man/as.raster.Rd
===================================================================
--- pkg/RImageJ/man/as.raster.Rd 2010-04-16 15:30:38 UTC (rev 12)
+++ pkg/RImageJ/man/as.raster.Rd 2010-10-09 05:52:53 UTC (rev 13)
@@ -1,37 +1,42 @@
\name{as.raster.jobjRef}
\alias{as.raster.jobjRef}
-\title{
-Support for converting ImageJ images to raster images
-}
+
+\title{ Support for converting ImageJ images to raster images }
+
\description{
-Support for converting ImageJ images to raster images
+ Support for converting ImageJ images to raster images.
}
+
\usage{
-\S3method{as.raster}{jobjRef}(x, ...)
+\S3method{as.raster}{jobjRef}(x, \dots)
}
\arguments{
-\item{x}{A java reference of class \samp{ij.ImagePlus} }
-\item{...}{not used}
+ \item{x}{ A java reference of class \samp{ij.ImagePlus}. }
+ \item{\dots}{ Not used. }
}
+
\value{
-A raster object. See \link[grDevices]{as.raster}
+ A raster object. See \link[grDevices]{as.raster}.
}
+
\author{
-Contributed by Paul Murrell \url{http://www.stat.auckland.ac.nz/~paul/}
+ Contributed by Paul Murrell \url{http://www.stat.auckland.ac.nz/~paul/}
}
+
\seealso{
-\link[grDevices]{as.raster}, \link[graphics]{raster}
+ \link[grDevices]{as.raster}, \link[graphics]{raster}
}
+
\examples{
\dontrun{
-logo <- system.file( "images", "R.jpg", package = "RImageJ" )
-image = IJ$openImage( logo )
-plot(c(100, 250), c(300, 450), type = "n", xlab="", ylab="")
-raster(image, 100, 300, 150, 350, interpolate=FALSE)
+logo <- system.file("images", "R.jpg", package = "RImageJ")
+image <- IJ$openImage(logo)
+plot(c(100, 250), c(300, 450), type = "n", xlab = "", ylab = "")
+raster(image, 100, 300, 150, 350, interpolate = FALSE)
raster(image, 100, 400, 150, 450)
-raster(image, 200, 300, 200 + xinch(.5), 300 + yinch(.3),
- interpolate=FALSE)
-raster(image, 200, 400, 250, 450, angle=15, interpolate=FALSE)
+raster(image, 200, 300, 200 + xinch(.5), 300 + yinch(.3), interpolate = FALSE)
+raster(image, 200, 400, 250, 450, angle = 15, interpolate = FALSE)
}
}
+
\keyword{ graphics}
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