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

[Agustin Lobo]

ok, thanks. I did not know that there was another class raster in
another package.

This means that we cannot convert from RImageJ objects to
raster::raster objects.
But we can use RImageJ to process, save to disk and read back as raster:raster:

logo <- system.file( "images", "R.jpg", package = "RImageJ" )
image = IJ$openImage( logo )
image$show()
IJ$run( "8-bit" )
IJ$run( "Invert" )
IJ$save( "bw-google.gif" )
image$close()

r4 <- raster("bw-google.gif")
plot(r4)
summary(r4)
extent(r4)

Hopefully I'll be able to use RImageJ for applying smoothing filters
and other image processing
methods that are too slow within R, without having to leave the R
scripting environment.

Agus

On Fri, Jan 17, 2014 at 9:26 AM, Michael Sumner <mdsumner at gmail.com> wrote:
> 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
>
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