WekaSegmentation class use

[David Rueda]

Hi all,

I am trying to use the WekaSegmentation class available among fiji's plugins.
So, I use the addElement method to add examples to each of my two
classes, and then i run the classifier with the trainClassifier
method.
The problem is that I have the following error message: "Cannot train
without at least 2 sets of examples!".
(the examples exist, i can see the number of examples for each classes
with 'weka.getExamples(OTHER_CLASS, SLICE).size()')

Would you have any solution for my problem?

Sincerely,
Davd

[Ignacio Arganda-Carreras]

Hello David,

Can you please send me the piece of code you're using to reproduce your error?

thanks!

ignacio

On Thu, Mar 22, 2012 at 6:43 AM, David Rueda <[hidden email]> wrote:

> Hi all,
>
> I am trying to use the WekaSegmentation class available among fiji's plugins.
> So, I use the addElement method to add examples to each of my two
> classes, and then i run the classifier with the trainClassifier
> method.
> The problem is that I have the following error message: "Cannot train
> without at least 2 sets of examples!".
> (the examples exist, i can see the number of examples for each classes
> with 'weka.getExamples(OTHER_CLASS, SLICE).size()')
>
> Would you have any solution for my problem?
>
> Sincerely,
> Davd

--
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

[David Rueda]

Here is the code i am using:

>             ImagePlus imp = getImp();
>             WekaSegmentation weka = new WekaSegmentation();
>             weka.setTrainingImage(imp);
>             weka.setNumOfClasses(2);
>
>             if (imp.getProcessor().getNChannels() != 3)
>                 throw new ScriptException(Bundle.UI.getString("message_rgbonly"));
>
>             ColorProcessor cp = new ColorProcessor(imp.getImage());
>             for (int x = 0; x < imp.getWidth(); x++) {
>                 for (int y = 0; y < imp.getHeight(); y++) {
>                     int[] pixel = imp.getPixel(x, y);
>                     if (pixel[0] == 0 && pixel[1] == 255 && pixel[2] == 255) {
>                         cp.setColor(Color.BLACK);
>                     } else {
>                         cp.setColor(Color.WHITE);
>                     }
>                     cp.drawPixel(x, y);
>                 }
>             }
> //            weka.addExample(OTHER_CLASS, negSelection, SLICE);
>
>             imp.setImage(cp.convertToByte(true).createImage());
>
>             ResultsTable paResults = new ResultsTable();
>             ParticleAnalyzer particleAnalyzer = new ParticleAnalyzer(
>                     ParticleAnalyzer.SHOW_NONE,
>                     Measurements.RECT | Measurements.ELLIPSE,
>                     paResults,
>                     0.0,
>                     INFINITY
>             );
>             particleAnalyzer.analyze(imp);
>
>             // X    Y    Major    Minor    Angle
>             ImagePlus labelImp = imp.duplicate();
>             for (int row = 0; row < paResults.getCounter(); row++) {
>                 double  bX = paResults.getColumnAsDoubles(paResults.getColumnIndex("BX"))[row],
>                         bY = paResults.getColumnAsDoubles(paResults.getColumnIndex("BY"))[row],
>                         bWidth = paResults.getColumnAsDoubles(paResults.getColumnIndex("Width"))[row],
>                         bHeight = paResults.getColumnAsDoubles(paResults.getColumnIndex("Height"))[row],
>                         eAngle = paResults.getColumnAsDoubles(paResults.getColumnIndex("Angle"))[row];
>
>                 EllipseRoi posSelection = null;
>                 if (eAngle < 90) {
>                     posSelection = new EllipseRoi(bX + bWidth, bY, bX, bY + bHeight, 0.60);
>                 } else {
>                     posSelection = new EllipseRoi(bX, bY, bX + bWidth, bY + bHeight, 0.60);
>                 }
>
>                 posSelection.setFillColor(Color.BLACK);
>                 labelImp.getProcessor().fillPolygon(posSelection.getPolygon());
>                 weka.addExample(OSTEO_CLASS, posSelection, SLICE);
>             }
>
>             int[] xpoints = {928,897,800,756,627,462,372,233,238,149,159,441,502,586,622,661,680,710,701,498};
>             int[] ypoints = {727,571,664,852,800,702,700,811,892,959,910,927,842,748,664,556,399,302,229,149};
>             weka.addExample(OTHER_CLASS, new PolygonRoi(xpoints,ypoints,20,Roi.POLYLINE), SLICE);
>
>             System.out.println(weka.getExamples(OTHER_CLASS, SLICE).size());
>             System.out.println(weka.getExamples(OSTEO_CLASS, SLICE).size());
>
>             if (weka.trainClassifier()) {
>                 weka.applyClassifier(false);
>                 weka.getClassifiedImage().show();
>             }

Thanks,
Davd


Le 22 mars 2012 15:02, Ignacio Arganda-Carreras
<[hidden email]> a écrit :

> Hello David,
>
> Can you please send me the piece of code you're using to reproduce your error?
>
> thanks!
>
> ignacio
>
> On Thu, Mar 22, 2012 at 6:43 AM, David Rueda <[hidden email]> wrote:
>> Hi all,
>>
>> I am trying to use the WekaSegmentation class available among fiji's plugins.
>> So, I use the addElement method to add examples to each of my two
>> classes, and then i run the classifier with the trainClassifier
>> method.
>> The problem is that I have the following error message: "Cannot train
>> without at least 2 sets of examples!".
>> (the examples exist, i can see the number of examples for each classes
>> with 'weka.getExamples(OTHER_CLASS, SLICE).size()')
>>
>> Would you have any solution for my problem?
>>
>> Sincerely,
>> Davd
>
>
>
> --
> 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

[Ignacio Arganda-Carreras]

Hello again David,

The error comes from the fact that you don't add examples to (at
least) two classes. You need to have samples of of two classes to
start training.

If you have a binary image with the labels of one class in white and
the labels of the other class in black, I would recommend you to use
this method:

http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=src-plugins/Trainable_Segmentation/trainableSegmentation/WekaSegmentation.java;h=f3222f5c88e5e7514a16dea632f0f5c10087421a;hb=HEAD#l822

Cheers!

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

[David Rueda]

Ok thanks you, now the trainclassifier is launched. But also, the it
block the execution of the end of my script...
Of course the train classifier takes some seconds, but i can not
understand why the instructions after the trainClassifier method are
not executed. Do you have an idea?

thank you a lot!
Davd

Le 22 mars 2012 15:46, Ignacio Arganda-Carreras
<[hidden email]> a écrit :

> Hello again David,
>
> The error comes from the fact that you don't add examples to (at
> least) two classes. You need to have samples of of two classes to
> start training.
>
> If you have a binary image with the labels of one class in white and
> the labels of the other class in black, I would recommend you to use
> this method:
>
> http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=src-plugins/Trainable_Segmentation/trainableSegmentation/WekaSegmentation.java;h=f3222f5c88e5e7514a16dea632f0f5c10087421a;hb=HEAD#l822
>
> Cheers!
>
> 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