Re: Can't automate copying of polygon ROIs

Posted by Andy-92 on Jun 12, 2008; 2:55pm
URL: http://imagej.273.s1.nabble.com/Can-t-automate-copying-of-polygon-ROIs-tp3695935p3695937.html

Sorry to sound ignorant, I'm having trouble with this (I think it has to do
with the setLocation commands or something) but ImageJ has a nasty habit of
swallowing errors silently.  Is there any way to disable this? or is there a
verbose logfile somewhere that would tell me where exceptions are being
thrown/caught?

Thanks!
--Andrew

On Wed, Jun 11, 2008 at 10:28 PM, Rasband Wayne <[hidden email]> wrote:

> Here is code that duplicates what the Edit>Copy and File>New>Internal
> Clipboard commands do except that it fills  with zero instead of the
> background color. You can test it using the Macros>Evaluate JavaScript
> command that was added to the macro editor in v1.41e.
>
>   img = IJ.getImage();
>   ip = img.getProcessor();
>   ip = ip.crop();
>   roi = img.getRoi();
>   roi.setLocation(0,0);
>   ip.setColor(0);
>   ip.snapshot()
>   ip.fill();
>   s1 = new ShapeRoi(roi);
>   s2 = new ShapeRoi(new Roi(0,0, ip.getWidth(), ip.getHeight()));
>   s3 = s1.xor(s2);
>   ip.reset(s3.getMask());
>   new ImagePlus("img", ip).show();
>
> -wayne
>
>
>
>  Thanks Wayne,
>> That has the intended effect (and fixes the problem), however, I am
>> performing this copy/paste hundreds of times on the same image.  So, every
>> time I call Internal Clipboard, a new image pops up on the screen, I have
>> to
>> save it, and then hide the image so I can work on the original image
>> again.
>> It's just messy and I'm wondering why my method of copying using
>> getClipboard() produces unintended effects.  Thanks!
>>
>> On Mon, Jun 9, 2008 at 5:15 PM, Wayne Rasband <[hidden email]> wrote:
>>
>> > I am having trouble copying ROIs that are based on polygons
>> >> (non-rectangular).  If I create a polygon ROI by hand, and do
>> Edit->Copy,
>> >> then File->New->Internal Clipboard, I get a new image the same size as
>> the
>> >> bounding box of the ROI, but anything NOT inside the ROI is white (or
>> >> whatever the background color is). This is the effect I want, but if I
>> do
>> >> it
>> >> in code:
>> >>
>> >> img.setRoi(p); //Where p is a polygon and img is an ImagePlus
>> >> img.copy(false);
>> >> ImagePlus newImg = new
>> >> ImagePlus("img",ImagePlus.getClipboard().getProcessor().duplicate());
>> >>
>> >> When I do that, I get a new image that contains EVERYTHING inside the
>> >> bounding box of the polygon. this includes a LOT of data that I do not
>> >> want
>> >> in the image. How can I obtain the same effect as edit->copy in my
>> code?
>> >>
>> >
>> > You can do this sort of thing easily in a macro:
>> >
>> >   makeOval(50, 50, 100, 100);
>> >   run("Copy");
>> >   run("Internal Clipboard");
>> >
>> > In a plugin, the code would look something like this:
>> >
>> >   img = IJ.getImage();
>> >   img.setRoi(p)
>> >   IJ.run("Copy");
>> >   IJ.run("Internal Clipboard");
>> >
>> > -wayne
>> >
>>
>