Re: Can't automate copying of polygon ROIs

Posted by Andy-92 on Jun 12, 2008; 9:52pm
URL: http://imagej.273.s1.nabble.com/Can-t-automate-copying-of-polygon-ROIs-tp3695935p3695939.html

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