Posted by
Jirka on
Jun 03, 2013; 10:29am
URL: http://imagej.273.s1.nabble.com/Re-how-to-load-label-data-in-trainable-weka-segmentation-GUI-tp5003142p5003186.html
Dear Shahab,
I am not sure how much HW memory you have, but have you tried to allow Fiji
to use more memory?
Edit -> Options -> Memory & Threads
Regards, JB
On 30 May 2013 14:43, Ignacio Arganda-Carreras <ignacio.arganda@gmail.com>wrote:
> Dear Shahab,
>
>
> > Thank you for your reply. it worked for me :)
> > would you please let me know if I can join the group to access all the
> other comments.
>
> No problem. You can join the ImageJ list if you follow these
> instructions:
http://rsbweb.nih.gov/ij/list.html>
>
> >
> > Actually now I have another problem:
> > when I want to open the weka GUI on my image stack consists of 100
> images of EM data (ISBI 2013 challenge)
> > it gives me the following error:
> >
> > (Fiji Is Just) ImageJ 1.47q; Java 1.6.0_24 [64-bit]; Linux
> 2.6.32-47-generic; 927MB of 934MB (99%)
> >
> > java.lang.reflect.InvocationTargetException
> > at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
> > at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at ij.Command.runPlugIn(Command.java:148)
> > at ij.Command.runCommand(Command.java:97)
> > at ij.Executer.run(Executer.java:64)
> > at java.lang.Thread.run(Thread.java:662)
> > Caused by: java.lang.OutOfMemoryError: Java heap space
> > at
> ij.process.TypeConverter.convertByteToFloat(TypeConverter.java:202)
> > at
> ij.process.TypeConverter.convertToFloat(TypeConverter.java:177)
> > at
> ij.process.ImageProcessor.convertToFloat(ImageProcessor.java:2101)
> > at
> trainableSegmentation.FeatureStack.<init>(FeatureStack.java:258)
> > at
> trainableSegmentation.WekaSegmentation.setTrainingImage(WekaSegmentation.java:321)
> > at
> trainableSegmentation.Weka_Segmentation.run(Weka_Segmentation.java:1228)
> > at ij.IJ.runUserPlugIn(IJ.java:194)
> > at ij.IJ.runPlugIn(IJ.java:160)
> > ... 7 more
> >
> > would you please let me know how I can handle that?
> > how can I increase my heap space?
>
> It seems you have only 1GB of RAM of that you're only reserving 1GB
> for Fiji, is that correct?
>
> The 2013 ISBI dataset is 100MB, so as soon as you add a large set of
> features, you will run out of memory.
>
> Solution: if you have access to a machine with more RAM, run the
> experiments in that machine. If you already have more RAM memory but
> don't know how to reserve it, have a look at how we do it in TrakEM2:
>
>
http://fiji.sc/TrakEM2#Running_fiji_for_heavy-duty.2C_memory-intensive.2C_high-performance_TrakEM2_tasks>
> I hope this helps!
>
> ignacio
>
> >
> > Best regards,
> >
> > ________________________________________
> > From: iargandacarreras@gmail.com [iargandacarreras@gmail.com] On Behalf
> Of Ignacio Arganda-Carreras [ignacio.arganda@gmail.com]
> > Sent: Wednesday, May 29, 2013 3:18 PM
> > To: Shahab Ensafi
> > Cc: ImageJ Interest Group
> > Subject: Re: how to load label data in trainable weka segmentation GUI?
> >
> > Dear Shahab,
> >
> > Thanks for your interest in the plugin. Let me answer you with copy to
> > the ImageJ list, so anybody else with the same question can find the
> > answer here.
> >
> >> I am using the weka segmentation GUI in Fiji.
> >> would you please let me know how I can add my labels file (which is a
> binary image of my 2 class labels) in the software?
> >> now I can just add labels manually using the 'add to' button. I have
> found out that in the java we can add it but it is not provided in the GUI
> if I am not wrong.
> >
> > There is no option to add directly the labels from the binary image
> > because the GUI is designed for interactive learning. However, there's
> > a workaround you can use:
> >
> > 1) click on your binary image and then on Edit > Selection > Create
> Selection.
> > 2) click on the Trainable Weka Segmentation GUI and then on Edit >
> > Selection > Restore Selection.
> > 3) add that ROI to one of the classes.
> > 4) click on your binary image and then on Edit > Selection > Make
> Inverse.
> > 5) click on the Trainable Weka Segmentation GUI and then on Edit >
> > Selection > Restore Selection.
> > 6) add that ROI to the other class
> >
> > Then you'll be ready to train.
> >
> > Just a warning: adding the ROIs like may make things slow at the
> > beginning of the training, since the program needs to check for every
> > pixel if it's inside or outside the ROI.
> >
> > Let me know what you think.
> >
> > Best,
> >
> > ignacio
>
> --
> Ignacio Arganda-Carreras, Ph.D.
>
--
Best regards and wishes of a nice day, Jiří Borovec
----------------------------------------------------------------------------------------------------
Jiří Borovec <jiri.borovec@fel.cvut.cz>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3--
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