Pasting content from PolygonRoi to a new Image

[Thomas Kesper]

Hi,

i have several regions of interest as PolygonRoi  in an ImagePlus object
that i want to extract to extra ImagePlus objects.

My attempts with

ImagePlus plus = new ImagePlus(..) ;
plus.setRoi(polyRoi); //

plus.copy(true);

ImagePlus iplus= ImagePlus.getClipboard();
iplus.setTitle(polyRoi.getName());
iplus.show();

or just with  "iplus.paste()" resulted in the insertion of the content
of the bounding Rectangle of my PolygonRoi.

when I use manually the GUI with copying the current ROI selection and
using "File>> New >> Internal Clipboard"
i have only the desired content of the Polygon Roi.

How can i get this result with java code?

best regards

Thomas

[Albert Cardona]

Hi Thomas,

You have to use the mask of the non-rectangular ROI to do a proper
fill/draw/paste etc.

call getMask() or getMaskPixels() on your ImageProcessor that has a ROI,
and then use them as boolean variables to set the pixels of your new image.

Otherwise, follow the trail of java code in ImageJ's source code:


$~/fiji/ImageJA$ grep -rn "Internal Clipboard" *
IJ_Props.txt:28:new03="Internal Clipboard",ij.plugin.Clipboard("show")


Now we search for the "show" argument:


$~/fiji/ImageJA$ grep -n -A 2 "\"show\"" ij/plugin/Clipboard.java
35:             else if (arg.equals("show"))
36-                     showInternalClipboard();
37-     }


Now we search for the showInternalClipboard method:


$~/fiji/ImageJA$ grep -n -A 20 "showInternalClipboard() {"
ij/plugin/Clipboard.java
148:    void showInternalClipboard() {
149-            ImagePlus clipboard = ImagePlus.getClipboard();
150-            if (clipboard!=null) {
151-                    ImageProcessor ip = clipboard.getProcessor();
152-                    ImagePlus imp2 = new ImagePlus("Clipboard",
ip.duplicate());
153-                    Roi roi = clipboard.getRoi();
154-                    imp2.killRoi();
155-                    if (roi!=null && roi.isArea() &&
roi.getType()!=Roi.RECTANGLE) {
156-                            roi = (Roi)roi.clone();
157-                            roi.setLocation(0, 0);
158-                            imp2.setRoi(roi);
159-                            IJ.run(imp2, "Clear Outside", null);
160-                            imp2.killRoi();
161-                    }
162-                    WindowManager.checkForDuplicateName =
true;        
163-                    imp2.show();
164-            } else
165-                    IJ.error("The internal clipboard is empty.");
166-    }



Above is the answer to your question.


Hope that helps,

Albert

> Hi,
>
> i have several regions of interest as PolygonRoi  in an ImagePlus
> object that i want to extract to extra ImagePlus objects.
>
> My attempts with
>
> ImagePlus plus = new ImagePlus(..) ;
> plus.setRoi(polyRoi); //
>
> plus.copy(true);
>
> ImagePlus iplus= ImagePlus.getClipboard();
> iplus.setTitle(polyRoi.getName());
> iplus.show();
>
> or just with  "iplus.paste()" resulted in the insertion of the content
> of the bounding Rectangle of my PolygonRoi.
>
> when I use manually the GUI with copying the current ROI selection and
> using "File>> New >> Internal Clipboard"
> i have only the desired content of the Polygon Roi.
>
> How can i get this result with java code?
>
> best regards
>
> Thomas

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona