ROI and IJ.run()

[Eddie Iannuccelli]

Hello,
my plugin use a Wand method in order to get particles ROI for further
processing . Some of these processing are done using IJ.run () calls,
but it does not seem to be effective in results. Here is my code :

// ipProcess is my source ImageProcessor containing particles
// impProcess is my source ImagePlus containing particles
// x and y are coordinate of my first particle

WindowManager.setTempCurrentImage(impProcess);  //show nothing
Wand myWand = new Wand(ipProcess);  
myWand.autoOutline((int)x,(int)y);
PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);          
impProcess.setRoi(myROI);
IJ.run("Convex Hull");                          --> do nothing  !
IJ.run("Enlarge...", "enlarge=100");       --> do nothing  !

Thanks

[dscho]

Hi,

On Thu, 30 Nov 2006, Eddie Iannuccelli wrote:

> WindowManager.setTempCurrentImage(impProcess);  //show nothing
> Wand myWand = new Wand(ipProcess);   myWand.autoOutline((int)x,(int)y);
> PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
> myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
> impProcess.setRoi(myROI);
> IJ.run("Convex Hull");                          --> do nothing  !
> IJ.run("Enlarge...", "enlarge=100");       --> do nothing  !

I suspect that you need to call impProcess.updateAndDraw() after
IJ.run(...).

Hth,
Dscho

[Eddie Iannuccelli]

Thanks for your response,

impProcess.updateAndDraw() still do nothing .... but if I show
impProcess instead of masking it  (by replacing
WindowManager.setTempCurrentImage(impProcess)  by impProcess.show() at
the first line),  it's fine !
My processing become a bit "verbose" but it does the job, I am still
interested for a silent solution ...
Thanks


Johannes Schindelin a écrit :

> Hi,
>
> On Thu, 30 Nov 2006, Eddie Iannuccelli wrote:
>
>  
>> WindowManager.setTempCurrentImage(impProcess);  //show nothing
>> Wand myWand = new Wand(ipProcess);   myWand.autoOutline((int)x,(int)y);
>> PolygonRoi myROI= new PolygonRoi(myWand.xpoints,
>> myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
>> impProcess.setRoi(myROI);
>> IJ.run("Convex Hull");                          --> do nothing  !
>> IJ.run("Enlarge...", "enlarge=100");       --> do nothing  !
>>    
>
> I suspect that you need to call impProcess.updateAndDraw() after
> IJ.run(...).
>
> Hth,
> Dscho
>
>  

[Eddie Iannuccelli]

Wayne,
you are right  but it still does not "Convex Hull" or "enlarge" my roi
when using setTempCurrentImage. Everything is ok when ImagePlus is shown .
Here is there new snippet (ipProcess is impProcess imageProcessor):

                WindowManager.setTempCurrentImage(impProcess);
                //impProcess.show();
                IJ.doWand((int)x,(int)y);
                IJ.run("Convex Hull");
                IJ.run("Enlarge...", "enlarge=" + EXTENSION);
                PolygonRoi myROI= (PolygonRoi)
impProcess.getRoi();            
                ipProcess.setValue(128);
                ipProcess.fillPolygon(myROI.getPolygon());  
                ipMask=impProcess.getMask();
                ...        

Thanks


Rasband, Wayne (NIH/NIMH) [E] a écrit :

>> Hello,
>> my plugin use a Wand method in order to get particles ROI for further processing .
>> Some of these processing are done using IJ.run () calls, but it does not seem to be
>> effective in results. Here is my code :
>>    
>
>  
>> // ipProcess is my source ImageProcessor containing particles
>> // impProcess is my source ImagePlus containing particles
>> // x and y are coordinate of my first particle
>>    
>
>  
>> WindowManager.setTempCurrentImage(impProcess);  //show nothing
>> Wand myWand = new Wand(ipProcess);   myWand.autoOutline((int)x,(int)y);
>> PolygonRoi myROI= new PolygonRoi(myWand.xpoints, myWand.ypoints,myWand.npoints, Roi.TRACED_ROI);
>> impProcess.setRoi(myROI);
>> IJ.run("Convex Hull");                          --> do nothing  !
>> IJ.run("Enlarge...", "enlarge=100");       --> do nothing  !
>>    
>
> This code seems to work okay and is simpler and easier to understand.
>
>    IJ.doWand(x, y);
>    IJ.run("Convex Hull");
>    IJ.run("Enlarge...", "enlarge=100");
>
> -wayne
>