Re: Overlays from Java (2nd try)

Posted by Wayne Rasband-2 on Nov 06, 2018; 5:59pm
URL: http://imagej.273.s1.nabble.com/Overlays-from-Java-2nd-try-tp5021416p5021420.html

> On Nov 6, 2018, at 8:44 AM, Kenneth Sloan <[hidden email]> wrote:
>
> I'm trying to control Overlays from Java.  What I *think* I need is:
>
> a) initialize Overlay from an image (that's easy enough)
> b) EDIT the Overlay (preferably using one of the two Brush tools)
> c) extract the edited Overlay as an Image


You could create a custom version of the PlugInTool that implements the Paintbrush Tool.

  https://github.com/imagej/imagej1/blob/master/ij/plugin/tool/BrushTool.java

The Paintbrush Tool draws on an RGB ImageRoi in an Overlay when “Paint on overlay” is checked in the options dialog. I do not see a need to extend StackWindow.

-wayne

> All of this over an (extended) ImageStackWindow.
>
> I *think* I see a way forward - but I can't find documentation.  I'll start experimenting
> today.  Any clues that will speed that up will be welcome.
>
> My other option is to select a single (grey) image from the Stack, form a Composite with the
> (binary) overlay) and use the Brush Tool to draw in RED (to draw) and GREEN (to "erase").  The major
> issue here is that the drawing is destructive.  I would fix that by iterating on the editing process,
> periodically refreshing the binary overlay and re-constructing the composite image.  This has worked
> for me in the past, but feels clunky.  
>
> Most likely, my problem has to do with ignorance of ROI processing, and the details of how to get at the
> results of the Overlay created/modified by the two brush tools.
>
> While I'm at it - is my best bet the Overlay Brush tool, or the normal Brush tool with the "draw in overlay" box checked?
> What are the practical differences?
>
> My current plan is to assume that the Brush Tools leave behind a record of what they do in *some* ROI attached to the image (or the ImageStackWindow).  I already have a few purely graphic overlays in use - but presumably I can go through all the overlays
> associated with the StackWindow and pay attention to the "image" overlays.  I'm confused about whether to expect many of these, or just one.  I can find out by doing experiments, but I hate to base an application on empirically derived information - I'd prefer authoritative documentation.  
>
> What should I read?
>
> Does anyone have sample (Java) code for the three basic operations above?
>
> I am always impressed by the speed and usefullness of replies - the silence greeting my first plea for help is a but puzzling.
> Perhaps my message did not go through; perhaps it's just hard?
>
> Hoping against hope - does anyone have an "Edit Mask" plugin (in Java, preferably).  This task feels fairly generic - given a maxk, allow the user to edit it.  I can live with editing while referencing a SINGLE image - or modify two work with a Stack.
>
> My last resort is to further extend the StackWindow to include mask editing.  I really prefer to use the standard tools whenever possible.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html