Can't automate copying of polygon ROIs

[andrew bovill]

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?

Thanks in advance!
--Andrew

[Wayne Rasband]

> 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

[Andy-92]

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
>

[Wayne Rasband]

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
> >

[Andy-92]

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
>> >
>>
>

[Wayne Rasband]

> 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?

Exceptions thrown on the event dispatch thread are displayed in the  
console window. To get a console window on Windows you need to change  
"javaw.exe" in the second line of ImageJ/ImageJ.cfg to "java.exe" and  
restart ImageJ. You can view console error messages on Mac OS X by  
running the /Applications/Utilities/Console program.

There was a bug in the JavaScript example that caused the ROI in the  
source Image to move to the upper left corner. You can fix this by  
changing  the line

     roi = img.getRoi();

to

    roi = img.getRoi().clone();

In Java, you need to caste the object returned by the clone() method to  
an Roi:

     roi = (Roi)img.getRoi().clone();

The corrected script is at

     http://rsb.info.nih.gov/ij/macros/js/ShowClipboard.js

With the 1.41f daily build, you can open this script in the macro  
editor by pasting the URL into the File>Import>URL dialog box, and run  
it by pressing ctrl-r (Macros>Run Macro).

-wayne

>
> 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
>>>>
>>>
>>
>

[Andy-92]

I finally got it working (I think) I had to clone the Roi and duplicate the
ImageProcessor to get it to work properly (I am removing about 200 Roi's
from the image)

The weird thing though, it runs a LOT slower than my IJ.run("Copy")
IJ.run("Internal Clipboard") method... any ideas why?
I REALLY appreciate all the help sofar!
--Andrew

On Thu, Jun 12, 2008 at 1:17 PM, Wayne Rasband <[hidden email]> wrote:

> 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?
>>
>
> Exceptions thrown on the event dispatch thread are displayed in the console
> window. To get a console window on Windows you need to change "javaw.exe" in
> the second line of ImageJ/ImageJ.cfg to "java.exe" and restart ImageJ. You
> can view console error messages on Mac OS X by running the
> /Applications/Utilities/Console program.
>
> There was a bug in the JavaScript example that caused the ROI in the source
> Image to move to the upper left corner. You can fix this by changing  the
> line
>
>    roi = img.getRoi();
>
> to
>
>   roi = img.getRoi().clone();
>
> In Java, you need to caste the object returned by the clone() method to an
> Roi:
>
>    roi = (Roi)img.getRoi().clone();
>
> The corrected script is at
>
>    http://rsb.info.nih.gov/ij/macros/js/ShowClipboard.js
>
> With the 1.41f daily build, you can open this script in the macro editor by
> pasting the URL into the File>Import>URL dialog box, and run it by pressing
> ctrl-r (Macros>Run Macro).
>
> -wayne
>
>
>
>
>> 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
>>>>>
>>>>>
>>>>
>>>
>>