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--- documents:101105ij_r_jython [2010/11/04 13:46] – created kota
+++ documents:101105ij_r_jython [2014/04/15 15:23] – [2. Using ImageJ from R] kota
@@ Line 1: / Line 1: @@
-====== Python <- (ImageJ, R) ======
-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.
-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.
-Do everything from Java is one way, but 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>