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

Wed Aug 19 10:10:06 CDT 2015

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
> 
> _______________________________________________
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> ImageJ-devel at imagej.net
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-- 
http://www.msc.univ-paris-diderot.fr/~daerr/