Getting measures from some ares in an image by a mask

[luckyluke]

Hi ImageJ developers,

I am trying to get some measures ( as specified and set measurements) on an color image however  on its specific area defined by another mask images.

I am trying to do that by java codes..actually, i try to do this in image J by doing particle analyzer on my mask image then adding this to ROI manger and then do measures in ROI manger when set measure are redirected to my main image.

I have written a piece  of code but the counter below returns me 0..I am new to imageJ so I appreciate any help so I can write this program..


This is the piece of my code but i don't get any result

==========
        File f = new File(Test.class.getResource("/IMD002.bmp").toURI());
        File f1 = new File(Test.class.getResource("/IMD002_R1_Label4.bmp").toURI());
        ColorProcessor image = new ColorProcessor(ImageIO.read(f));
        //ByteProcessor mask = new ByteProcessor(ImageIO.read(f1));
        ColorProcessor maskI=new ColorProcessor(ImageIO.read(f1));
        ImagePlus imP=new ImagePlus("tt",maskI);      
        IJ.run(imP,"8-bit", "");//conveting the mask ti 8 bit image
        ResultsTable rt=new ResultsTable();
       
        ParticleAnalyzer pt=new  ParticleAnalyzer
        (ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET,
        ij.measure.Measurements.AREA+ij.measure.Measurements.MEAN,
        rt, 1, 1000, 1, 1000);
       
         
        ImagePlus img=new ImagePlus();  
        img.setProcessor(image);      
        RoiManager roi=RoiManager.getInstance();
        pt.setRoiManager(roi);      
        ij.plugin.filter.Analyzer.setRedirectImage(img);      
        pt.analyze(imP);
        ResultsTable rt1 = ij.plugin.filter.Analyzer.getResultsTable();
        int counter = rt1.getCounter();  //number of results
        System.out.println(counter);
        //if (counter==0)
          //no results, handle that error here
        int col = rt1.getColumnIndex("Area");
        for (int row=0; row<counter; row++)
        {
          double value = rt1.getValueAsDouble(col, row);
          System.out.println(value);
        }

======


Thanks any one if has any tip?

Regards

[Michael Schmid]

Hi lukyluke,

it seems there are two bugs in your code:

(1) your call the ParticleAnalyzer with minCirc=1, maxCirc=1000
You will never find a particle with a circularity greater than 1.

(2) If you tell the ParticleAnalyzer to use the ResultsTable rt, you can't expect the results in ResultsTable rt1.

Michael
________________________________________________________________
On Nov 19, 2014, at 10:48, luckyluke wrote:

> Hi ImageJ developers,
>
> I am trying to get some measures ( as specified and set measurements) on an
> color image however  on its specific area defined by another mask images.
>
> I am trying to do that by java codes..actually, i try to do this in image J
> by doing particle analyzer on my mask image then adding this to ROI manger
> and then do measures in ROI manger when set measure are redirected to my
> main image.
>
> I have written a piece  of code but the counter below returns me 0..I am new
> to imageJ so I appreciate any help so I can write this program..
>
>
> This is the piece of my code but i don't get any result
>
> ==========
>        File f = new File(Test.class.getResource("/IMD002.bmp").toURI());
>        File f1 = new
> File(Test.class.getResource("/IMD002_R1_Label4.bmp").toURI());
>        ColorProcessor image = new ColorProcessor(ImageIO.read(f));
>        //ByteProcessor mask = new ByteProcessor(ImageIO.read(f1));
>        ColorProcessor maskI=new ColorProcessor(ImageIO.read(f1));
>        ImagePlus imP=new ImagePlus("tt",maskI);      
>        IJ.run(imP,"8-bit", "");//conveting the mask ti 8 bit image
>        ResultsTable rt=new ResultsTable();
>
>        ParticleAnalyzer pt=new  ParticleAnalyzer
>        (ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET,
>         ij.measure.Measurements.AREA+ij.measure.Measurements.MEAN,
>         rt, 1, 1000, 1, 1000);
>
>
>        ImagePlus img=new ImagePlus();  
>        img.setProcessor(image);      
>        RoiManager roi=RoiManager.getInstance();
>        pt.setRoiManager(roi);      
>        ij.plugin.filter.Analyzer.setRedirectImage(img);      
>        pt.analyze(imP);
>        ResultsTable rt1 = ij.plugin.filter.Analyzer.getResultsTable();
>        int counter = rt1.getCounter();  //number of results
>        System.out.println(counter);
>        //if (counter==0)
>          //no results, handle that error here
>        int col = rt1.getColumnIndex("Area");
>        for (int row=0; row<counter; row++)
>        {
>          double value = rt1.getValueAsDouble(col, row);
>          System.out.println(value);
>        }
>
> ======
>
>
> Thanks any one if has any tip?
>
> Regards
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Getting-measures-from-some-ares-in-an-image-by-a-mask-tp5010537.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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