Re: weka segmentation in batch mode

Posted by William Menegas on Mar 21, 2014; 5:00pm
URL: http://imagej.273.s1.nabble.com/weka-segmentation-in-batch-mode-tp5007024p5007039.html

Thanks for all the suggestions!

I'll try the 'quick fix' which is based on Aryeh's suggestion:

call("trainableSegmentation.Weka_Segmentation.getProbability");
waiting = 0;
while (waiting == 0){
if (isOpen("Probability maps") == true)
waiting = 1;
else
wait(10000);
}
selectWindow("Probability maps");

If that doesn't work, I'll try rewriting everything to run as a beanshell
script, or just the weka part as a beanshell script - as Ignacio suggested.

And I was planning on running this on a cluster, so I'll check out Larry's
plugin as well...

Thanks again everybody!
Will


On Fri, Mar 21, 2014 at 12:14 PM, Larry Lindsey <[hidden email]>wrote:

> Hi List,
>
> I ran into a similar problem a little while ago. There's a plugin (full
> disclosure: I wrote it) for the 2D case [1]. It's intended to run on a
> networked cluster, but it would be simple to modify it for single computers
> as well. Let me know if that sounds like it would be useful.
>
> Larry
>
> 1: http://fiji.sc/FijiArchipelago#Batch_Weka_Segmentation
>
>
> On Fri, Mar 21, 2014 at 3:56 AM, Ignacio Arganda-Carreras <
> [hidden email]> wrote:
>
> > Hello Aryeh and Will,
> >
> > For the classification task I think it's a bit risky to use a delay
> anyway
> > because you don't know how long the classification will take. Have you
> > tried using a script instead of a macro? That allows you to have much
> more
> > control over the images and the commands are executed as in a regular
> > program, so you won't need any wait call.
> >
> > Have a look at:
> >
> > http://fiji.sc/Scripting_the_Trainable_Segmentation
> >
> > A simple Beanshell script equivalent to your macro code would be:
> >
> > import trainableSegmentation.*;
> >
> >  // input train image
> >  input  = IJ.openImage( "input-grayscale-or-color-image.tif" );
> >  // create Weka Segmentation object
> >  segmentator = new WekaSegmentation( input );
> >  // load classifier from file
> >  segmentator.loadClassifier( "my-cool-trained-classifier.model" );
> >
> >  // apply classifier to current training image and get label result
> >  // (set parameter to true to get probabilities)
> >  segmentator.applyClassifier( false );
> >  // get result (float image)
> >  result = segmentator.getClassifiedImage();
> > Let me know if you have questions about it!
> >
> > ignacio
> >
> >
> >
> > On Fri, Mar 21, 2014 at 7:11 AM, Aryeh Weiss <[hidden email]>
> wrote:
> >
> > > On 3/21/14, 7:52 AM, William Menegas wrote:
> > >
> > >> Hello,
> > >>
> > >> I was wondering if anyone could give me some advice on using "Weka
> > >> Segmentation" in headless mode or in a normal session of fiji in batch
> > >> mode. I am using:
> > >>
> > >> ...
> > >> run("Trainable Weka Segmentation");
> > >> call("trainableSegmentation.Weka_Segmentation.loadClassifier",
> > >> "/path/classifier.model");
> > >> call("trainableSegmentation.Weka_Segmentation.getProbability");
> > >> selectWindow("Probability maps");
> > >> ...
> > >>
> > >> The problem is that fiji doesn't seem to want to wait for the
> > >> classification. I tried inserting "wait(100000)" before
> > >> "selectWindow("Probability maps"), but it didn't help and I don't
> think
> > >> there was even a wait.
> > >>
> > >> Any help would be much appreciated!
> > >> Will
> > >>
> > >> --
> > >> ImageJ mailing list:http://imagej.nih.gov/ij/list.html
> > >>
> > >>  I had a similar problem with the EDF plugin. Here is a quote form
> that
> > > post:
> > >
> > >> The problem I have is that the macro does not wait for EDF to finish,
> > and
> > >> EDF can take a while.
> > >> My solution to this is based on the fact that EDF creates a window
> > called
> > >> "Output". so I did the following:
> > >>
> > >> initTime = getTime();
> > >> while ( !isOpen("Output") ) {
> > >>     elapsedTime = getTime() - initTime;
> > >>     if (elapsedTime%10000 == 0) {
> > >>         print(elapsedTime/1000, " seconds elapsed");
> > >>         wait(10);
> > >>     }
> > >>
> > >> which works (as  long as there is no other window called "Output"). I
> > >> print an occasional reminder that the macro is still alive within this
> > wait
> > >> loop.
> > >>
> > >
> > > I posted this as a question, wondering if there is a better way to do
> it.
> > > I did not receive any reply, so perhaps in a macro this is the way to
> go.
> > > You should replace "Output" with "Probability maps".
> > >
> > > --aryeh
> > >
> > > --
> > > Aryeh Weiss
> > > Faculty of Engineering
> > > Bar Ilan University
> > > Ramat Gan 52900 Israel
> > >
> > > Ph:  972-3-5317638
> > > FAX: [phone]
> > >
> > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > > --
> > > Ignacio Arganda-Carreras, Ph.D.
> > > Seung's lab, 46-5065
> > > Department of Brain and Cognitive Sciences
> > > Massachusetts Institute of Technology
> > > 43 Vassar St.
> > > Cambridge, MA 02139
> > > USA
> > >
> > > Phone: [phone]
> > > Website: <http://imagej.nih.gov/ij/list.html>
> > > http://bioweb.cnb.csic.es/~iarganda/index_EN.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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