Getting Roi names from Roi Manager?

[Luciano Marpegan]

Dear List, I'm starting to write a macro that will need to get a
string with the name of an Roi selected from the Roi Manager but I
have no idea how to get the name. Could anyone give me a hint?
Cheers,

Luciano

 

[Albert Cardona]

Luciano,

Using jython and the Jython Interpreter, make sure the Roi Manager is
the last selected window and then simply type:

rm = WindowManager.getFrontWindow()
roi_names = rm.getComponents()[0].getItems()
for r in roi_names:
         print r

0160-0416
0211-0369

The last two lines of numbers are the two names of the rois in the Roi
Manager.


--
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
http://www.pensament.net/java/
http://www.mcdb.ucla.edu/Research/Hartenstein/

[Luciano Marpegan]

Dear Albert,
Many thanks for your answer on how to get the ROI names from
RoiManager, I'm new to Jython so it will take me a while to figure
out how it works but it is probably worth it. By the way, I tried to
install the Open Sequentially as Stack plugin but I couldn't make it
work in my system (Windows XP Pro SP2) with SPE files and some tiff files.

One of the error messages I got for the tiff files was:

java.lang.ArrayIndexOutOfBoundsException: -1
  at Open_sequentially_as_stack.run(Open_sequentially_as_stack.java:74)
  at ij.IJ.runUserPlugIn(IJ.java:271)
  at ij.IJ.runPlugIn(IJ.java:115)
  at ij.Executer.runPlugIn(Executer.java:169)
  at ij.Executer.runCommand(Executer.java:131)
  at ij.Executer.run(Executer.java:63)
  at java.lang.Thread.run(Thread.java:595)


For the SPE files I got a message box stating that it couldn't read
the first image and that it couldn't get the size of it. Is this
because the plugin doesn't work with SPE files?


Best,
Luciano



At 12:17 PM 11/15/2005, you wrote:

>Luciano,
>
>Using jython and the Jython Interpreter, make sure the Roi Manager is
>the last selected window and then simply type:
>
>rm = WindowManager.getFrontWindow()
>roi_names = rm.getComponents()[0].getItems()
>for r in roi_names:
>          print r
>
>0160-0416
>0211-0369
>
>The last two lines of numbers are the two names of the rois in the Roi
>Manager.
>
>--
>Albert Cardona
>Molecular Cell Developmental Biology
>University of California Los Angeles
>Tel [phone]
><http://www.pensament.net/java/>http://www.pensament.net/java/
>http://www.mcdb.ucla.edu/Research/Hartenstein/

[Albert Cardona]

Luciano,

The plugin "Open sequentially as stack" will only open the kind of
images that the Opener class can, which do not include the SPE files. I
don't know how your SPE files are opened; if it's a plugin, or even
some settings in the "Import/Raw...", you can call it from within a
customized version of the "Open sequentially as stack" plugin. Look for
the line:

     Opener o = new Opener();

and replace the

     ImagePlus imp = o.openImage(dir_name, first_item.name);

by whatever method opens the SPE file into an ImagePlus.


About jython, anything that can be done with it can also be done on the
Java side, but it would took much more code to acomplish the same
thing. For example in jython downcasting is automatic, so in the ROI
Manager example

> roi_names = rm.getComponents()[0].getItems()

one can call the method getItems() from class java.awt.List over a
java.awt.Component, because such Component instance is but a List that
has been stored as a Component. This is because python stores class
identity in the object itself, not in the name used to refer to it.

The main issue with using jython/python is that it becomes so
convenient one doesn't want to program in any clunky languages such as
java anymore. Good luck with that!

Albert