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--- documents:101105ij_r_jython [2011/05/27 14:31] – kota
+++ documents:101105ij_r_jython [2020/11/26 09:11] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Jython <- (ImageJ, R) ======
+======= 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.
+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.
-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.
+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.
@@ Line 66: / Line 131: @@
 </sxh>