Using TrainableWeka objects in scripts

[Marcello DiStasio]

Hello,

I am trying to write a python script using the trainable weka plugin for
Fiji.  I am using the two libraries, imported like so:

from trainableSegmentation import WekaSegmentation
from trainableSegmentation import Weka_Segmentation


My question is, how do I get the object for the learner (class
WekaSegmentation) I create and populate with my script to be "loaded
into"/used by the GUI I create with an object of class Weka_Segmentation.

Or, alternatively, is there a way to get a handle for the WekaSegmentation
object (I am guessing might be) a member of the Weka_Segmentation class?
 This way I could just populate the images+ROIs in that.

The goal here is to get my Images and ROIs to appear in the Plugin GUI.
 For now.  But with the possibility of doing all the processing headless
if/when the time comes...

Sorry about the confusing use of underscores, but those are the class
names...

Thanks in advance
-Marcello

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Hello Marcello,

Thanks for your interest in the Trainable Weka Segmentation. Let me try to
address your questions between your lines:


 I am trying to write a python script using the trainable weka plugin for
> Fiji.  I am using the two libraries, imported like so:
>
> from trainableSegmentation import WekaSegmentation
> from trainableSegmentation import Weka_Segmentation
>
>
What do you exactly want to do? WekaSegmentation is the back-end class,
where all the methods are stored in a library fashion. Weka_Segmentation is
the plugin class, which contains the GUI and calls the library methods to
perform learning and segmentation.


>
> My question is, how do I get the object for the learner (class
> WekaSegmentation) I create and populate with my script to be "loaded
> into"/used by the GUI I create with an object of class Weka_Segmentation


If you already trained a classifier, you can get it from your
WekaSegmentation object using the method:

AbstractClassifier<http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true>
*getClassifier
<http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#getClassifier()>*
()
Returns the current classifier.

Equivalently you can set a new classifier to your WekaSegmentation object
using the method:

void *setClassifier
<http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#setClassifier(weka.classifiers.AbstractClassifier)>*
(AbstractClassifier<http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true>
 cls)
Set current classifier

If what you want is to load a new classifier into the GUI
(Weka_Segmentation object) then you have to do it from file using the
following method:

static void *loadClassifier
<http://fiji.sc/javadoc/trainableSegmentation/Weka_Segmentation.html#loadClassifier(java.lang.String)>*
(String<http://docs.oracle.com/javase/6/docs/api/java/lang/String.html?is-external=true>
 newClassifierPathName)
Load a new classifier

For encapsulation reasons there's no easy way to access the
WekaSegmentation object from the GUI. There's a workaround if you need it
by getting the object from the CustomWindow:

final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
if( iw instanceof CustomWindow )
{
final CustomWindow win = (CustomWindow) iw;
 final WekaSegmentation wekaSegmentation = win.getWekaSegmentation();
}


> .
>
> Or, alternatively, is there a way to get a handle for the WekaSegmentation
> object (I am guessing might be) a member of the Weka_Segmentation class?
>  This way I could just populate the images+ROIs in that.
>
>
Just the way I just explained.



> The goal here is to get my Images and ROIs to appear in the Plugin GUI.
>  For now.  But with the possibility of doing all the processing headless
> if/when the time comes...
>

I see. That's a bit tricky. The idea behind the library + plugin (GUI)
structure is that you can call all the library methods from any script or
plugin without the need of the GUI. If you then need to go back to the GUI,
you're supposed to load the classifier and/or data using the corresponding
buttons or macro commands. Why is that strategy not working for you?

Best,

ignacio


--
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://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Marcello DiStasio]

Thank you very much for the clarifications, Ignacio. I really appreciate
the help!   Using only the WekaSegmentation object to save the classifier
model object there and then loading in the GUI later seems quite
reasonable.   I primarily want the ability to run my WEKA training script
in headless mode on a cluster. The script now appears to work on my
desktop, with the GUI in place, but no overt calls to display any windows,
just saving outputs.   I am having a bit of trouble doing so, however,
since a couple of of the plugins I call seem not to be working in headless
mode.  I am making a couple calls like this in python:

IJ.run(imp_h, "Auto Threshold", "method=Li white")   # imp_h is an
imagePlus object

and getting java.lang.NullPointerException.  This does not happen when I
run fiji from the command line, but on a computer that has X11.


I am also getting java.awt.HeadlessException when I try creating an ROI
Manager, e.g.  with

roim = RoiManager(True) # I thought "True" was supposed to make the thing
run without a GUI window?

I am invoking fiji with the following:

~/Programs/fiji/fiji -Xms6400m -Xmx6400m -Xincgc -XX:MaxPermSize=256m
-XX:PermSize=256m -XX:NewRatio=5 -XX:CMSTriggerRatio=50
-XX:+UseCompressedOops -- --classpath ~/Programs/fiji/plugins
--headlessmyscript.py


Any ideas on what is going on?  Will the headless.java plugin help with
this?

Thanks!!
-Marcello


On Thu, Nov 7, 2013 at 4:32 AM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> Hello Marcello,
>
> Thanks for your interest in the Trainable Weka Segmentation. Let me try to
> address your questions between your lines:
>
>
>  I am trying to write a python script using the trainable weka plugin for
> > Fiji.  I am using the two libraries, imported like so:
> >
> > from trainableSegmentation import WekaSegmentation
> > from trainableSegmentation import Weka_Segmentation
> >
> >
> What do you exactly want to do? WekaSegmentation is the back-end class,
> where all the methods are stored in a library fashion. Weka_Segmentation is
> the plugin class, which contains the GUI and calls the library methods to
> perform learning and segmentation.
>
>
> >
> > My question is, how do I get the object for the learner (class
> > WekaSegmentation) I create and populate with my script to be "loaded
> > into"/used by the GUI I create with an object of class Weka_Segmentation
>
>
> If you already trained a classifier, you can get it from your
> WekaSegmentation object using the method:
>
> AbstractClassifier<
> http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true
> >
> *getClassifier
> <
> http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#getClassifier()
> >*
> ()
> Returns the current classifier.
>
> Equivalently you can set a new classifier to your WekaSegmentation object
> using the method:
>
> void *setClassifier
> <
> http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#setClassifier(weka.classifiers.AbstractClassifier)
> >*
> (AbstractClassifier<
> http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true
> >
>  cls)
> Set current classifier
>
> If what you want is to load a new classifier into the GUI
> (Weka_Segmentation object) then you have to do it from file using the
> following method:
>
> static void *loadClassifier
> <
> http://fiji.sc/javadoc/trainableSegmentation/Weka_Segmentation.html#loadClassifier(java.lang.String)
> >*
> (String<
> http://docs.oracle.com/javase/6/docs/api/java/lang/String.html?is-external=true
> >
>  newClassifierPathName)
> Load a new classifier
>
> For encapsulation reasons there's no easy way to access the
> WekaSegmentation object from the GUI. There's a workaround if you need it
> by getting the object from the CustomWindow:
>
> final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
> if( iw instanceof CustomWindow )
> {
> final CustomWindow win = (CustomWindow) iw;
>  final WekaSegmentation wekaSegmentation = win.getWekaSegmentation();
> }
>
>
> > .
> >
> > Or, alternatively, is there a way to get a handle for the
> WekaSegmentation
> > object (I am guessing might be) a member of the Weka_Segmentation class?
> >  This way I could just populate the images+ROIs in that.
> >
> >
> Just the way I just explained.
>
>
>
> > The goal here is to get my Images and ROIs to appear in the Plugin GUI.
> >  For now.  But with the possibility of doing all the processing headless
> > if/when the time comes...
> >
>
> I see. That's a bit tricky. The idea behind the library + plugin (GUI)
> structure is that you can call all the library methods from any script or
> plugin without the need of the GUI. If you then need to go back to the GUI,
> you're supposed to load the classifier and/or data using the corresponding
> buttons or macro commands. Why is that strategy not working for you?
>
> Best,
>
> ignacio
>
>
> --
> 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://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

[Ignacio Arganda-Carreras]

Hello Marcello,

I'm afraid I cannot help you with those error but probably someone else in
the list could. Maybe you should write those questions in new e-mail with a
more topic-focused subject :)

Good luck!

ignacio


On Sat, Nov 23, 2013 at 9:09 PM, Marcello DiStasio <[hidden email]>wrote:

> Thank you very much for the clarifications, Ignacio. I really appreciate
> the help!   Using only the WekaSegmentation object to save the classifier
> model object there and then loading in the GUI later seems quite
> reasonable.   I primarily want the ability to run my WEKA training script
> in headless mode on a cluster. The script now appears to work on my
> desktop, with the GUI in place, but no overt calls to display any windows,
> just saving outputs.   I am having a bit of trouble doing so, however,
> since a couple of of the plugins I call seem not to be working in headless
> mode.  I am making a couple calls like this in python:
>
> IJ.run(imp_h, "Auto Threshold", "method=Li white")   # imp_h is an
> imagePlus object
>
> and getting java.lang.NullPointerException.  This does not happen when I
> run fiji from the command line, but on a computer that has X11.
>
>
> I am also getting java.awt.HeadlessException when I try creating an ROI
> Manager, e.g.  with
>
> roim = RoiManager(True) # I thought "True" was supposed to make the thing
> run without a GUI window?
>
> I am invoking fiji with the following:
>
> ~/Programs/fiji/fiji -Xms6400m -Xmx6400m -Xincgc -XX:MaxPermSize=256m
> -XX:PermSize=256m -XX:NewRatio=5 -XX:CMSTriggerRatio=50
> -XX:+UseCompressedOops -- --classpath ~/Programs/fiji/plugins
> --headlessmyscript.py
>
>
> Any ideas on what is going on?  Will the headless.java plugin help with
> this?
>
> Thanks!!
> -Marcello
>
>
> On Thu, Nov 7, 2013 at 4:32 AM, Ignacio Arganda-Carreras <
> [hidden email]> wrote:
>
> > Hello Marcello,
> >
> > Thanks for your interest in the Trainable Weka Segmentation. Let me try
> to
> > address your questions between your lines:
> >
> >
> >  I am trying to write a python script using the trainable weka plugin for
> > > Fiji.  I am using the two libraries, imported like so:
> > >
> > > from trainableSegmentation import WekaSegmentation
> > > from trainableSegmentation import Weka_Segmentation
> > >
> > >
> > What do you exactly want to do? WekaSegmentation is the back-end class,
> > where all the methods are stored in a library fashion. Weka_Segmentation
> is
> > the plugin class, which contains the GUI and calls the library methods to
> > perform learning and segmentation.
> >
> >
> > >
> > > My question is, how do I get the object for the learner (class
> > > WekaSegmentation) I create and populate with my script to be "loaded
> > > into"/used by the GUI I create with an object of class
> Weka_Segmentation
> >
> >
> > If you already trained a classifier, you can get it from your
> > WekaSegmentation object using the method:
> >
> > AbstractClassifier<
> >
> http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true
> > >
> > *getClassifier
> > <
> >
> http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#getClassifier()
> > >*
> > ()
> > Returns the current classifier.
> >
> > Equivalently you can set a new classifier to your WekaSegmentation object
> > using the method:
> >
> > void *setClassifier
> > <
> >
> http://fiji.sc/javadoc/trainableSegmentation/WekaSegmentation.html#setClassifier(weka.classifiers.AbstractClassifier)
> > >*
> > (AbstractClassifier<
> >
> http://weka.sourceforge.net/doc.dev/weka/classifiers/AbstractClassifier.html?is-external=true
> > >
> >  cls)
> > Set current classifier
> >
> > If what you want is to load a new classifier into the GUI
> > (Weka_Segmentation object) then you have to do it from file using the
> > following method:
> >
> > static void *loadClassifier
> > <
> >
> http://fiji.sc/javadoc/trainableSegmentation/Weka_Segmentation.html#loadClassifier(java.lang.String)
> > >*
> > (String<
> >
> http://docs.oracle.com/javase/6/docs/api/java/lang/String.html?is-external=true
> > >
> >  newClassifierPathName)
> > Load a new classifier
> >
> > For encapsulation reasons there's no easy way to access the
> > WekaSegmentation object from the GUI. There's a workaround if you need it
> > by getting the object from the CustomWindow:
> >
> > final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
> > if( iw instanceof CustomWindow )
> > {
> > final CustomWindow win = (CustomWindow) iw;
> >  final WekaSegmentation wekaSegmentation = win.getWekaSegmentation();
> > }
> >
> >
> > > .
> > >
> > > Or, alternatively, is there a way to get a handle for the
> > WekaSegmentation
> > > object (I am guessing might be) a member of the Weka_Segmentation
> class?
> > >  This way I could just populate the images+ROIs in that.
> > >
> > >
> > Just the way I just explained.
> >
> >
> >
> > > The goal here is to get my Images and ROIs to appear in the Plugin GUI.
> > >  For now.  But with the possibility of doing all the processing
> headless
> > > if/when the time comes...
> > >
> >
> > I see. That's a bit tricky. The idea behind the library + plugin (GUI)
> > structure is that you can call all the library methods from any script or
> > plugin without the need of the GUI. If you then need to go back to the
> GUI,
> > you're supposed to load the classifier and/or data using the
> corresponding
> > buttons or macro commands. Why is that strategy not working for you?
> >
> > Best,
> >
> > ignacio
> >
> >
> > --
> > 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://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
>

--
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://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

On Nov 23, 2013, at 21:09, Marcello DiStasio wrote:

> ... I am making a couple calls like this in python:
>
> IJ.run(imp_h, "Auto Threshold", "method=Li white")
>
> and getting java.lang.NullPointerException.  This does not happen when I
> run fiji from the command line, but on a computer that has X11.

Hi Marcello,

there should be a stack trace saying in which module and at which line the NullPointerException happens, and how it was called.
Without this information no one will have any clue what happens.

---
By the way, as this seems to be a topic unrelated to 'TrainableWeka', it would have been nice to start a new thread in the mailing list for it.

Michael

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html