[ImageJ-devel] Status and API of ROIs in ImageJ2 ?

Mon Aug 24 16:22:15 CDT 2015

Hi Adrian,

Glad to hear you found a working solution!

The short answer about ROIs is that they have not been a focus of ImageJ2
or ImgLib2 development in recent years. Support for labelings (highly
related to ROIs) was rewritten this January [1], but a rewrite of the core
ImgLib2 ROI library [2] is still pending. And there is a substantial
pending redesign of the ImageJ Common data model planned as well -- though
it is unlikely anyone will work on it this year.

At this juncture, the most effective balance for most plugin developers is
probably to use parameterized commands and/or scripts, but with the ImageJ1
data structures (ij.ImagePlus, etc.) -- unless you need access to a new
capability that ImageJ2 + ImgLib2 make possible (>5D images, very large
image planes, very large numbers of image planes, dynamically generated
images, images stored in places besides disk, cell-based image caching,
image types beyond uint8/uint16/float32, etc.).

That said, your feedback is very much appreciated.

And some issues will be ironed out in the next couple of weeks as we revamp
the tutorials for the upcoming ImageJ conference.

> The easiest way to give a plugin a (rectangular) roi is to ... just
> declare a net.imagej.overlay.RectangularOverlay as an input parameter.
> It is properly populated by the origin and extent of a rectangular
> selection drawn on the active image.

If all you care about is the bounding box of the active selection, you can
just do it the same way as the ImageJ2 CropImageJ command: by calling
OverlayService.getSelectionBounds [3]. Then you would avoid some of the
current weirdness associated with Overlay parameters.

> If I launch the default UI, then the ROI will not show, but the plugin
> can launch. If on the other hand I launch the "swing" UI as in the
> tutorial, I do see the ROI

Yes, that tutorial was written when the ImageJ2 Swing UI was still the
default. It is not tested/working with the Legacy UI (which is now the
default). I will try to remedy that very soon.

> (not until I call Image>Adjust>Brightness/Contrast..., but that's a
> minor detail),

Yes, that annoying bug has been around for quite a while. Many things that
refresh the display will do, such as pressing + then - to zoom in/out.

> but now the invocation of the plugin at the end of main() will throw a
> MethodCallException with the stackTrace pasted below. How can the
> choice of a UI make the plugin execution fail ?
...
> Caused by: java.lang.NullPointerException
>         at Goutte_pendante.initTitle(Goutte_pendante.java:94)

In 2014, we made a conscious decision to support the ImageJ 1.x classes
_only_ from the legacy UI. You cannot use them from the Swing UI. In your
case: the ActiveImagePlusPreprocessor cannot set the active ImagePlus
because WindowManager.getCurrentImage() returns null [4], because no ImageJ
1.x user interface exists. So it stays null and then your initializer
throws the NPE.

Regards,
Curtis

[1]
https://github.com/imglib/imglib2-roi/tree/imglib2-roi-0.3.2/src/main/java/net/imglib2/labeling

[2] https://github.com/imglib/imglib2-roi

[3]
https://github.com/imagej/imagej-plugins-commands/blob/imagej-plugins-commands-0.5.1/src/main/java/net/imagej/plugins/commands/imglib/CropImage.java#L104

[4]
https://github.com/imagej/imagej-legacy/blob/imagej-legacy-0.17.1/src/main/java/net/imagej/legacy/plugin/ActiveImagePlusPreprocessor.java#L49-L52

On Sun, Aug 23, 2015 at 6:30 AM, Adrian Daerr <
adrian.daerr at univ-paris-diderot.fr> wrote:

> Hello,
>
> While I am still interested in answers concerning the status/API/roadmap
> for ROIs and overlays beyond what's on http://imagej.net/ROIs, I have
> solved the problem at hand which was keeping me from making progress, so I
> post the (rather obvious, once I found the net.imagej.overlay package)
> solution here for the record and to close this thread.
>
> The easiest way to give a plugin a (rectangular) roi is to ...
> just declare a net.imagej.overlay.RectangularOverlay as an input
> parameter. It is properly populated by the origin and extent of a
> rectangular selection drawn on the active image.
>
> cheers,
> Adrian
>
>
> On Wed, 19 Aug 2015 17:10:06 +0200
>
>  "Adrian Daerr" <adrian.daerr at univ-paris-diderot.fr> wrote:
>
>>
>> Dear ImageJ developers,
>>
>> I have included code from the AddROIs tutorial into the main()
>> method of my plugin (for the moment essentially one of Curtis'
>> commands-with-preview example), to select a Rectangle before
>> calling the plugin. The source is available here:
>>
>> https://gitlab.com/pendant-drop/pendant-drop
>> (in Goutte_pendante.java)
>>
>> If I launch the default UI, then the ROI will not show, but the
>> plugin can launch. If on the other hand I launch the "swing" UI
>> as in the tutorial, I do see the ROI (not until I call
>> Image>Adjust>Brightness/Contrast..., but that's a minor detail),
>> but now the invocation of the plugin at the end of main() will
>> throw a MethodCallException with the stackTrace pasted below. How
>> can the choice of a UI make the plugin execution fail ?
>>
>> Is there any other way that main can set a ROI on a loaded image
>> that the plugin, which still uses an ImagePlus as input
>> parameter, will see when calling imp.getProcessor().getRoi() ?
>>
>> TIA
>> Adrian
>>
>>
>> $> mvn package
>> $> fiji --class-path target/pendant_drop-2.0.0-SNAPSHOT.jar
>> Goutte_pendante.class
>> [INFO] Overriding About Pendant Drop; identifier:
>> command:About_Pendant_Drop; jar:
>> file:/home/adrian/Programmes/plugins_ImageJ_src/Traitement_Gouttes/target/pendant_drop-2.0.0-SNAPSHOT.jar
>> [INFO] Overriding Pendant Drop; identifier: command:Goutte_pendante; jar:
>> file:/home/adrian/Programmes/plugins_ImageJ_src/Traitement_Gouttes/target/pendant_drop-2.0.0-SNAPSHOT.jar
>> [INFO] Populating metadata
>> [INFO] Populating metadata
>> [INFO] Found 10 JHotDraw adapters.
>> org.scijava.module.MethodCallException: Error executing method:
>> Goutte_pendante#initTitle
>>         at org.scijava.module.MethodRef.execute(MethodRef.java:73)
>>         at
>> org.scijava.module.AbstractModuleItem.initialize(AbstractModuleItem.java:199)
>>         at
>> org.scijava.module.AbstractModule.initialize(AbstractModule.java:86)
>>         at
>> org.scijava.command.CommandModule.initialize(CommandModule.java:147)
>>         at
>> org.scijava.module.process.InitPreprocessor.process(InitPreprocessor.java:60)
>>         at
>> org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)
>>         at org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)
>>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
>>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
>>         at
>> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
>>         at
>> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>>         at
>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
>>         at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
>>         at java.lang.Thread.run(Thread.java:662)
>> Caused by: java.lang.reflect.InvocationTargetException
>>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>         at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>         at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>         at org.scijava.module.MethodRef.execute(MethodRef.java:69)
>>         ... 14 more
>> Caused by: java.lang.NullPointerException
>>         at Goutte_pendante.initTitle(Goutte_pendante.java:94)
>>         ... 19 more
>> [ERROR] Module threw exception
>> java.lang.NullPointerException
>>         at Goutte_pendante.cancel(Goutte_pendante.java:87)
>>         at
>> org.scijava.command.CommandModule.cancel(CommandModule.java:140)
>>         at
>> org.scijava.module.ModuleRunner.cleanupAndBroadcastCancelation(ModuleRunner.java:189)
>>         at org.scijava.module.ModuleRunner.run(ModuleRunner.java:161)
>>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
>>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
>>         at
>> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
>>         at
>> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>>         at
>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
>>         at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
>>         at java.lang.Thread.run(Thread.java:662)
>>
>>
>>
>> On Sat, 15 Aug 2015 13:14:13 +0200
>>  Adrian Daerr <adrian.daerr at univ-paris-diderot.fr> wrote:
>>
>>> Hello,
>>>
>>> I am seizing a major rewrite of a plugin as an opportunity to switch
>>> from ImageJ1 to ImageJ2, also to avoid concurrency issues[*], and now
>>> lots of questions come up. Some concern the way ROIs are handled. What
>>> has happened in this regard since
>>>   http://imagej.net/ROIs
>>> was last updated ?
>>>
>>> [*] cf discussion on the ImageJ list archived at
>>>
>>> http://imagej.1557.x6.nabble.com/ExtendedPlugInFilter-GenericDialog-and-synchronization-td5013333.html
>>>
>>> Here are two concrete questions:
>>>
>>> 1) My plugin relies on a rectangular ROI being drawn on the image to
>>> know which area to include in the computation. How do I draw this ROI
>>> once I have loaded the image as a dataset in the main() method that is
>>> used for testing purposes ?
>>>
>>> public static void main(final String... args) throws Exception {
>>>     final String testImagePath = "testImage.jpg";
>>>
>>>     // Launch ImageJ as usual.
>>>     final ImageJ ij = net.imagej.Main.launch(args);
>>>
>>>     // Open test image.
>>>     final Dataset dataset = ij.dataset().open(testImagePath);
>>>
>>>     // display the dataset
>>>     ij.ui().show(dataset);
>>>
>>>     // create rectangular ROI
>>>     //imp.setRoi(120,60,340,420);// How to do this on a dataset ?
>>>
>>>     // Launch the "Foo_Bar" command.
>>>     ij.command().run(Foo_Bar.class, true);
>>> }
>>>
>>> (alternatively, how would I generate a new dataset, or I guess something
>>> like a "View" in ImageJ2 terminology, of the ROI sub-image of the original
>>> dataset ? I could then substitute the original dataset with this sub-image
>>> and have the plugin operate on the whole image by default)
>>>
>>> 2) The plugin preview generates overlays using java.awt.geom.Path2D,
>>> java.awt.geom.Area and java.awt.Shape, which are then converted via
>>> ij.gui.ShapeRoi() and ij.gui.Overlay(), assembled with overlay.add(),
>>> and drawn using imp.setOverlay(). Is there a new IJ2-way to do this
>>> (especially since the cited web page (rightly) insists on separation
>>> of selection and visualisation shapes) ?
>>>
>>> TIA,
>>> Adrian
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel at imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>
>> --
>> http://www.msc.univ-paris-diderot.fr/~daerr/
>>
>> _______________________________________________
>> ImageJ-devel mailing list
>> ImageJ-devel at imagej.net
>> http://imagej.net/mailman/listinfo/imagej-devel
>>
>
> --
> http://www.msc.univ-paris-diderot.fr/~daerr/
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel at imagej.net
> http://imagej.net/mailman/listinfo/imagej-devel
>
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