Status of the (fiji?) Overlay Manager

[Adrian Custer]

Hello all,

In the fiji distribution (on ImageJ 1.51q), there is an Overlay Manager

   Image > Overlay > Overlay Manager

Unfortunately, selecting that menu entry throws with:

The module "net.imagej.ui.swing.commands.OverlayManager" is invalid:
  - Invalid duplicate paramter: private org.scijava.Context
net.imagej.ui.swing.commands.OverlayManager.context

There is also remarkably little documentation on this Overlay Manager
and its relation to the Roi Manager. I was hoping to learn more.


Is this part of ImageJ or specific to Fiji only?
Is this a work in progress, fully functional, or abandoned?
Where could I look for more information?


thanks for any pointers about this,
   ~adrian

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

[Stefan Helfrich-2]

Dear Adrian,

> There is also remarkably little documentation on this Overlay Manager
> and its relation to the Roi Manager. I was hoping to learn more.
The Overlay Manager is an ImageJ2 feature and is very likely to change
substantially in future, mostly due to changes in how we will represent
and handle selections/ROIs. My guess is, that the Overlay Manager was/is
supposed to supersede the ROI Manger in ImageJ2. Currently, the best
place to get "documentation" would be the source code ([1] and [2]).

> The module "net.imagej.ui.swing.commands.OverlayManager" is invalid:
>  - Invalid duplicate paramter: private org.scijava.Context
> net.imagej.ui.swing.commands.OverlayManager.context
That's an issue that has been recently introduced. I have filed a pull
request [3] for the imagej-ui-swing component.

Best,
Stefan

[1]
https://github.com/imagej/imagej-ui-swing/blob/master/src/main/java/net/imagej/ui/swing/commands/OverlayManager.java
[2]
https://github.com/imagej/imagej-ui-swing/blob/master/src/main/java/net/imagej/ui/swing/overlay/SwingOverlayManager.java
[3] https://github.com/imagej/imagej-ui-swing/pull/77

On 09/29/2017 12:56 PM, Adrian Custer wrote:

> Hello all,
>
> In the fiji distribution (on ImageJ 1.51q), there is an Overlay Manager
>
>   Image > Overlay > Overlay Manager
>
> Unfortunately, selecting that menu entry throws with:
>
> The module "net.imagej.ui.swing.commands.OverlayManager" is invalid:
>  - Invalid duplicate paramter: private org.scijava.Context
> net.imagej.ui.swing.commands.OverlayManager.context
>
> There is also remarkably little documentation on this Overlay Manager
> and its relation to the Roi Manager. I was hoping to learn more.
>
>
> Is this part of ImageJ or specific to Fiji only?
> Is this a work in progress, fully functional, or abandoned?
> Where could I look for more information?
>
>
> thanks for any pointers about this,
>   ~adrian
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Dr. Stefan Helfrich
Bioimaging Center (L931)
University of Konstanz

PO Box 604
78457 Konstanz
Germany

Tel [phone]
Fax [phone]

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

[ctrueden]

Hi Adrian & everyone,

As Stefan says, the "Overlay Manager" is an ImageJ2 command written to work
with ImageJ2 Overlay objects, which are (confusingly) not the same thing as
ImageJ1 overlays. Those ImageJ2 Overlay objects were the first attempt at
generalizing ImageJ ROIs to N dimensions, but we are now taking a different
tack [1]. This "Overlay Manager" command should be considered both
experimental and deprecated. It is an oversight that it is even included in
the ImageJ 1.x user interface; it will be hidden after the next update [2].

Regards,
Curtis

[1] http://forum.imagej.net/t/implementation-plan-for-imglib2-rois-2d/2531
[2]
https://github.com/imagej/imagej-ui-swing/commit/6f12f4896e9f3cd2d12e12b4adae4087bb17f8bc

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Oct 5, 2017 at 1:07 AM, Stefan Helfrich <
[hidden email]> wrote:

> Dear Adrian,
>
> There is also remarkably little documentation on this Overlay Manager and
>> its relation to the Roi Manager. I was hoping to learn more.
>>
> The Overlay Manager is an ImageJ2 feature and is very likely to change
> substantially in future, mostly due to changes in how we will represent and
> handle selections/ROIs. My guess is, that the Overlay Manager was/is
> supposed to supersede the ROI Manger in ImageJ2. Currently, the best place
> to get "documentation" would be the source code ([1] and [2]).
>
> The module "net.imagej.ui.swing.commands.OverlayManager" is invalid:
>>  - Invalid duplicate paramter: private org.scijava.Context
>> net.imagej.ui.swing.commands.OverlayManager.context
>>
> That's an issue that has been recently introduced. I have filed a pull
> request [3] for the imagej-ui-swing component.
>
> Best,
> Stefan
>
> [1] https://github.com/imagej/imagej-ui-swing/blob/master/src/
> main/java/net/imagej/ui/swing/commands/OverlayManager.java
> [2] https://github.com/imagej/imagej-ui-swing/blob/master/src/
> main/java/net/imagej/ui/swing/overlay/SwingOverlayManager.java
> [3] https://github.com/imagej/imagej-ui-swing/pull/77
>
>
> On 09/29/2017 12:56 PM, Adrian Custer wrote:
>
>> Hello all,
>>
>> In the fiji distribution (on ImageJ 1.51q), there is an Overlay Manager
>>
>>   Image > Overlay > Overlay Manager
>>
>> Unfortunately, selecting that menu entry throws with:
>>
>> The module "net.imagej.ui.swing.commands.OverlayManager" is invalid:
>>  - Invalid duplicate paramter: private org.scijava.Context
>> net.imagej.ui.swing.commands.OverlayManager.context
>>
>> There is also remarkably little documentation on this Overlay Manager and
>> its relation to the Roi Manager. I was hoping to learn more.
>>
>>
>> Is this part of ImageJ or specific to Fiji only?
>> Is this a work in progress, fully functional, or abandoned?
>> Where could I look for more information?
>>
>>
>> thanks for any pointers about this,
>>   ~adrian
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> Dr. Stefan Helfrich
> Bioimaging Center (L931)
> University of Konstanz
>
> PO Box 604
> 78457 Konstanz
> Germany
>
> Tel [phone]
> Fax [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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