[R-sig-Geo] as.raster() does not work for RImageJ objects

[Michael Sumner]

You are see a clash of the grDevices::as.raster with the raster
package. grDevices is loaded by default, and has a (S3) method for
whatever your image is (a matrix?).

It seems like the S4 raster::as.raster should allow these to "pass
through" to the underlying S3 method.

I can't look any closer right now





On Fri, Jan 17, 2014 at 7:09 PM, Agustin Lobo <alobolistas at gmail.com> wrote:
> Actually, in OSX, there is no error message at using as.raster(), but
> it does not work either:
>
> r <- as.raster(image)
> class(r)
>
> [1] "raster"
>> str(r)
> 'raster' chr [1:76, 1:100] "#ffffff" "#ffffff" "#ffffff" "#ffffff"
> "#ffffff" "#ffffff" "#ffffff" ...
>
> which is not the structure a raster object should have.
>
> Then:
>
> r <- as.raster.jobjRef(image)
> Error: could not find function "as.raster.jobjRef"
>
> while ?as.raster.jobjRef shows the help page
> the function as.raster.jobjRef" is not in the workspace (and this is
> also the case in linux):
>> search()
>  [1] ".GlobalEnv"        "package:RImageJ"   "package:rJava"
> "package:raster"    "package:sp"
>  [6] "tools:rstudio"     "package:stats"     "package:graphics"
> "package:grDevices" "package:utils"
> [11] "package:datasets"  "package:methods"   "Autoloads"
> "package:base"
>> ls(2)
> [1] "IJ"              "IJWindowManager" "ImageJ"
>
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
>   [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
>   [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] RImageJ_0.2-146 rJava_0.9-6     raster_2.1-66   sp_1.0-13
>
> loaded via a namespace (and not attached):
>   [1] grid_3.0.2      lattice_0.20-23 tools_3.0.2
>
>
> Agus
>
> On Thu, Jan 16, 2014 at 4:09 PM, Agustin Lobo <alobolistas at gmail.com> wrote:
>> Hi!
>>
>> While the following works fine:
>> install.packages("/home/alobo/Downloads/RImageJ_0.2-146.tar.gz", repos
>> = NULL, type="source")
>> require(RImageJ)
>> require(raster)
>> logo <- system.file( "images", "R.jpg", package = "RImageJ" )
>> image = IJ$openImage( logo )
>> class(image)
>> plot(c(100, 250), c(300, 450), type = "n", xlab="", ylab="")
>> rasterImage(image, 100, 300, 150, 350, interpolate=FALSE)
>>
>> (note that the example in
>> http://romainfrancois.blog.free.fr/index.php?category/R-package/RImageJ
>> is currently wrong, it must be rasterImage() and not raster()
>>
>> But as.raster() (the most important for me) does not work:
>>
>>> class(image)
>> [1] "jobjRef"
>> attr(,"package")
>> [1] "rJava"
>>> r <- as.raster(image)
>> Error in as.raster.jobjRef(image) : attempt to apply non-function
>>
>> see ?as.raster.jobjRef
>>
>> Any fix?
>>
>> Thanks
>> Agus
>
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-- 
Michael Sumner
Hobart, Australia
e-mail: mdsumner at gmail.com