Overlays from Java (2nd try)

[Kenneth Sloan-2]

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

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.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

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

[Wayne Rasband-2]

> 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.

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

[Kenneth Sloan-2]

Thanks for the reply.  I'll look at the code and see what makes sense.

The StackWindow is currently extended for other reasons - I agree that the
editing of the overlay is NOT a good reason to extend it further.

Question: given that the Paintbrush Tool draws on an RGB ImageRoi - is it feasible to *find* that Roi
attached to an image (or stack)?  The only distinguishing feature I would need is the information that
it is an *Image* ROI.  My *guess* is that there would be two ImageRoi's associated with the image - one
that I initialize from an existing mask, and one representing the edit

But...at least *reading* the BrushTool.java code will probably answer all of my questions.

I have resisted creating customized versions of tools that already exist - but this may be the time to revisit that
practice.

Again - thank you for the rapid reply.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On 6 Nov 2018, at 11:59 , Wayne Rasband <[hidden email]> wrote:
>
>> On Nov 6, 2018, at 8:44 AM, Kenneth Sloan <[hidden email] <mailto:[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 <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 <http://imagej.nih.gov/ij/list.html>

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