Re: Working with stacks

Posted by Juanjo Vega on Jun 09, 2009; 2:47pm
URL: http://imagej.273.s1.nabble.com/Working-with-stacks-tp3692217p3692219.html

Hi Julian,

Finally I'm using part of the code from the duplicate plugin. I will
need to work withg a fourth dimension for the time soon and I find the
code approach more interesting.

Thanks a lot! :)

Sincerelly,
Juanjo.

Julian Cooper escribió:

> Hi Juanjo,
>
> If I understand you correctly you can achieve what you describe in your
> first paragraph by drawing your rectangle ROI, and then go to Image >
> Duplicate (or press Ctrl, Shift and D). Make sure the duplicate stack
> checkbox is selected and leave the range as it is if you want the whole
> stack of rectangles. A new stack will open with the stack of ROIs.
>
> Kind regards,
>
> Julian
>
>  
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On
>> Behalf Of Juanjo Vega
>> Sent: 09 June 2009 14:33
>> To: [hidden email]
>> Subject: Working with stacks
>>
>>
>> Hello everyone, I want to copy a ROI from a stack of images.
>>
>> The idea is to select a rectangle from the stack of images and then,
>> when a button is pressed, a new image containing the stack of ROIs is
>> created.
>>
>> I'm doing this, but it doesn't works (only the first image is
>> created).
>> The problem is that I don't know where to find some help about how to
>> work with stacks to get a slice, replace, add a new one, or whatever.
>>
>> Right now I'm doing this, but I tried many other stuff
>> without success:
>>  
>>        Roi roi = IJ.getImage().getRoi();
>>
>>         Point a = new Point(roi.getBounds().x, roi.getBounds().y);
>>         Point b = new Point(roi.getBounds().x +
>> roi.getBounds().width,
>> roi.getBounds().y + roi.getBounds().height);
>>
>>        short copy[][] = new short[IJ.getImage().getStackSize()][];
>>
>>        for (int i = 0; i < IJ.getImage().getStackSize(); i++) {
>>            copy[i] = AUXcopyArea(IJ.getImage().getProcessor(), a, b);
>>        }
>>
>>        ImageProcessor ipp = new ShortProcessor(roi.getBounds().width,
>> roi.getBounds().height, copy[0], null);
>>        ImagePlus processedImg = new ImagePlus("Processed", ipp);
>>
>>        for (int i = 0; i < IJ.getImage().getStackSize(); i++) {
>>            processedImg.getStack().setPixels(copy[i], i);
>>        }
>>
>>        processedImg.getProcessor().resetMinAndMax();
>>        processedImg.show();
>>
>>
>>
>> Sincerelly,
>>
>> Juanjo.
>>
>> --
>> Juanjo Vega ([hidden email])
>>
>> Unidad de Biocomputación. Laboratorio B-13.
>> Centro Nacional de Biotecnología. CNB-CSIC.
>> C\ Darwin, 3. Campus de Cantoblanco.
>> Universidad Autónoma de Madrid.
>> 28049, Madrid, Spain.
>>
>> http://www.cnb.csic.es
>> http://www.biocomp.cnb.uam.es
>>
>> [phone]
>>
>>
>> "Las mejores almas son capaces de los mayores vicios como de
>> las mayores virtudes, y aquellos que caminan despacio por el
>> camino recto pueden llegar más lejos que los que corren pero
>> se apartan de él." - Discurso del Método, René Descartes.
>>
>>    
>
>  

--
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.uam.es

[phone]


"Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes.