======= R + ImageJ =======

Analysis using several tools is a powerful way to deal with complex Image data. We often do this, and here is one small example of taking advantages of ImageJ and R at the same time. There are three ways:

  - Use R from ImageJ (Rserve)
  - Use ImageJ from R (no description yet)
  - Use ImageJ and R from Jython REPL

====== 1. Using R from ImageJ via Rserve ======

In this example, R functions are used from ImageJ via Rserve using Jython scripting. 

[[http://www.rforge.net/Rserve/doc.html|Rserve]] is a package that you could install from within R. In addition, you need two jar files in the plugin folder of ImageJ/Fiji. 

  * [[http://www.rforge.net/Rserve/files/|Rserve downloads]]

After the installation, Rserve is an independent program so you could directly start it from the commandline (Rserve is a server that waits for commands, exectutes them and return the output) by:
<code>
R CMD Rserve
</code>

Then in the Fiji script editor, try the following code:

<sxh python>
from org.rosuda.REngine.Rserve import RConnection
 
c = RConnection()
x = c.eval("R.version.string")
print x.asString()
c.close()
</sxh>

If you see the version number of R printed in the output field, then you are successfully communicating with R from ImageJ.

[[http://rforge.net/org/doc/|Here is the Javadoc of Rserve]].  

[[http://cmci.embl.de/documents/120206pyip_cooking/python_imagej_cookbook#rmulti-peak_fitting_using_r|Here is an example]] of using multi-peak fitting and shoing the peak positions within the current image. 

====== 2. Using ImageJ from R ======

One easy way is to execute a shell command to run ImageJ macro / scripts in R. Such example is well documented in the link below. 

http://stackoverflow.com/questions/18989725/how-can-i-call-execute-an-imagej-macro-with-r

I have not made any attempt to directly access ImageJ classes from R but here is my advice for an inquiry. There is an R-package "RImageJ" that allows you to use ImageJ commands. Problem is that this package has not been updated since 2010. 

<blockquote>
 RImageJ:

http://romainfrancois.blog.free.fr/index.php?category/R-package/RImageJ

This basically allows use of methods available in one of the classes in ImageJ called ij.IJ

http://rsbweb.nih.gov/ij/developer/api/ij/IJ.html

This class IJ is a kind of utility class with many static methods that allows user to operate on images like ImageJ macro (especially the **run()** method does sort of such). 

Access is limited, but depending on what you want to do, I could maybe advice more. 

Another option is to access at much lower level using rJava:

http://www.rforge.net/rJava/index.html

By adding ImageJ to your Java path, it's probably possible to write script in R like Rhino javascript or Jython. 

</blockquote>

====== 3. Using ImageJ and R from Jython Interactive Interpreter ======

ImageJ classes could be accessed by Jython, a python based java interface. R has rJava (JRI, Java - R Interface). For this reason, one way of using ImageJ functions and R functions in an integrated environment is to use these resources from Jython. 

Python-scripting environment is light enough to test many things. After these testings are done, then a serious Java code could be written. 

Here is a trial in win32. All commands will be done from command line. It should basically be similar in other environment.  

===== Setting Up Environment. =====

You should have done:

  * [[http://rosuda.org/rJava/|rJava]] package should be installed in R.  
  * [[http://www.jython.org/|jython.jar]] should be somewhere locally. 

**1. set CLASSPATH**

Following three jars should be in your classpath. 
  * JRI.jar
  * REngine.jar
  * JRIEngine.jar
  * ij.jar
... so in command line
<code>
set CLASSPATH=%CLASSPATH%;C:\Program Files\R\R-2.12.0\library\rJava\jri\JRI.jar;C:\Program Files\R\R-2.12.0\library\rJava\jri\REngine.jar;C:\Program Files\R\R-2.12.0\library\rJava\jri\JRIEngine.jar;C:\ImageJ2\ij.jar
</code>
**2.  set PATH**

R native libraries should be linked. Then the path should be added with bin, jri, R.dll and JVM.dll:
<code>
set PATH=%PATH%;C:\Program Files\R\R-2.12.0\bin;C:\Program Files\R\R-2.12.0\library\rJava\jri;C:\Program Files\R\R-2.12.0\bin\i386;C:\Program Files\Java\jre6\bin\client
</code>
===== Example Scripting =====
<sxh python>
C:\>java org.python.util.jython
Jython 2.5.1 (Release_2_5_1:6813, Sep 26 2009, 13:47:54)
[Java HotSpot(TM) Client VM (Sun Microsystems Inc.)] on java1.6.0_22
Type "help", "copyright", "credits" or "license" for more information.

#importing image using ImageJ

>>> import ij.IJ
>>> import org.rosuda.JRI.REXP
>>> import org.rosuda.JRI.Rengine as Rengine
>>> import ij.IJ as IJ
>>> imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/blobs.gif")
>>> imp.show()
>>> flA = imp.getProcessor().getFloatArray()
>>> intA = imp.getProcessor().getIntArray()
>>> intA3=intA[3]
>>> histA = imp.getProcessor().getHistogram()

# going into R, first instantiate
>>> engine = Rengine(['--no-save'], False, None)
>>> engine.assign("histR", histA)
>>> engine.eval("pixint <- {0:255}")
>>> engine.eval("histform <- data.frame(pixint, histR)")

>>> engine.eval("plot(histform$pixint, histform$histR)")
#.. will plot the graph but one cannot close it...

>>> engine.eval("graphics.off()")
#will close all the plots. 

</sxh>