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

Adrian Daerr adrian.daerr at univ-paris-diderot.fr
Sun Aug 23 06:30:17 CDT 2015 

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/
> 
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