Convex hull method not found and GetMask null value

[Eddie Iannuccelli]

Hello,
I am trying to translate a macro into plugin but I encounter some problems
;)
Basically, I browse a particle analyser result table (ran on a stack
z-projection image) to extract each particle from the source stack into
dedicated image.

For each particle :
        {
        use Wand class to get outline -> OK
        transform outline to roi -> OK
        run a convex hull to enlarge this roi -> did not find any hull
method except
                                                             using the macro
launcher IJ.run which throws following  error:
                                                            Convex Hull:
Polygonal or point selection required -> ?
        create a mask for current particle    -> getMask return null ->
still don't understand the null/not null
                                                                for
irregular/regular shapes-> :(
        }

Thanks for your help.


Here is my code
////////////////////////////////////////////////
//ipProcess is the
for (int i=0;i<resTable.getCounter();i++)
        {
      Wand myWand = new Wand(ipProcess);    
      myWand.autoOutline((int)x,(int)y);
      PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
      ipProcess.setRoi(myROI);
      IJ.run("Convex Hull");
      ipMask=myROI.getMask();
        }
////////////////////////////////////////////////

----------------------------------------
Eddie Iannuccelli
Laboratoire de génétique cellulaire
INRA - Castanet Tolosan
Tel: [phone] / Fax: [phone]

[Thomas Boudier-2]

Eddie Iannuccelli a écrit :

> Hello,
> I am trying to translate a macro into plugin but I encounter some problems
> ;)
> Basically, I browse a particle analyser result table (ran on a stack
> z-projection image) to extract each particle from the source stack into
> dedicated image.
>
> For each particle :
> {
> use Wand class to get outline -> OK
> transform outline to roi -> OK
> run a convex hull to enlarge this roi -> did not find any hull
> method except
>  

Hi Eddie,

Ca va ?

Maybe you can use the dilate operation on the mask of the roi using the
methods getMask() in Roi and then dilate() in imageProcessor.

a+

Thomas

>     using the macro
> launcher IJ.run which throws following  error:
>    Convex Hull:
> Polygonal or point selection required -> ?
> create a mask for current particle    -> getMask return null ->
> still don't understand the null/not null
> for
> irregular/regular shapes-> :(
> }
>
> Thanks for your help.
>
>
> Here is my code
> ////////////////////////////////////////////////
> //ipProcess is the
> for (int i=0;i<resTable.getCounter();i++)
> {
>       Wand myWand = new Wand(ipProcess);    
>       myWand.autoOutline((int)x,(int)y);
>       PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
> myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
>       ipProcess.setRoi(myROI);
>       IJ.run("Convex Hull");
>       ipMask=myROI.getMask();
> }
> ////////////////////////////////////////////////
>
> ----------------------------------------
> Eddie Iannuccelli
> Laboratoire de génétique cellulaire
> INRA - Castanet Tolosan
> Tel: [phone] / Fax: [phone]
>
> .
>
>  

--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 Imagerie Intégrative,Institut Curie - INSERM U759.
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Wayne Rasband]

ImageJ commands invoked using the IJ.run() method operate on the
current image so you need to use code something like this:

     IJ.doWand(x,y);
     IJ.run("Convex Hull");
     mask = IJ.getImage().getMask();

-wayne

On Jul 12, 2006, at 4:46 AM, Eddie Iannuccelli wrote:

> Hello,
> I am trying to translate a macro into plugin but I encounter some
> problems
> ;)
> Basically, I browse a particle analyser result table (ran on a stack
> z-projection image) to extract each particle from the source stack into
> dedicated image.
>
> For each particle :
> {
> use Wand class to get outline -> OK
> transform outline to roi -> OK
> run a convex hull to enlarge this roi -> did not find any hull
> method except
>     using the macro
> launcher IJ.run which throws following  error:
>    Convex Hull:
> Polygonal or point selection required -> ?
> create a mask for current particle    -> getMask return null ->
> still don't understand the null/not null
> for
> irregular/regular shapes-> :(
> }
>
> Thanks for your help.
>
>
> Here is my code
> ////////////////////////////////////////////////
> //ipProcess is the
> for (int i=0;i<resTable.getCounter();i++)
> {
>       Wand myWand = new Wand(ipProcess);
>       myWand.autoOutline((int)x,(int)y);
>       PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
> myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
>       ipProcess.setRoi(myROI);
>       IJ.run("Convex Hull");
>       ipMask=myROI.getMask();
> }
> ////////////////////////////////////////////////
>
> ----------------------------------------
> Eddie Iannuccelli
> Laboratoire de génétique cellulaire
> INRA - Castanet Tolosan
> Tel: [phone] / Fax: [phone]
>