[ImageJ-devel] Status and API of ROIs in ImageJ2 ?
Adrian Daerr
adrian.daerr at univ-paris-diderot.fr
Fri Sep 4 14:29:46 CDT 2015
Hi Curtis,
OverlayService.getSelectionBounds seems to behave stranger yet. Take
the Foo_Bar test plugin source from my previous post, compile it and
place it in ImageJ's plugins directory. Start ImageJ, create a new
image (say 400x400 8bpp), draw a rectangular selection inside and
invoke Foo_Bar: as reported in my last mail it will report a
getSelectionBounds of 399x399 instead of the expected dimension of
the rectangular selection. Now crop the image to the rectangular
selection via Image->Crop, and invoke Foo_Bar again. It will report
the same getSelectionBounds (width 399, height 399) although the
active image is now strictly smaller. It's as if the ImageDisplay
parameter was getting populated by the image before cropping (and of
course still without rectangular selection).
How is one supposed to use OverlayService.getSelectionBounds ?
What are those WARNINGs printed upon plugin invokation ?
[WARNING] ====> Roi class = ij.gui.Roi
[WARNING] ====> RECTANGLE: Roi[Rectangle, x=76, y=92, width=209,
height=160]
cheers,
Adrian
On Tue, 01 Sep 2015 20:41:30 +0200
"Adrian Daerr" <adrian.daerr at univ-paris-diderot.fr> wrote:
> Hi Curtis, hi all,
>
>> 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. Then you would
>> avoid some of the current weirdness associated with Overlay
>> parameters.
>
> This was working fine with a programmatically added rectangular
>overlay/selection, but when I call getSelectionBounds on an image
>with an interactively created rectangular selection it returns the
>whole image dimension. It does not seem to be aware of the ROI. Below
>is a MVCE to reproduce. After compiling and placing it in the plugins
>folder, I start imagej, create a new image, draw a rectangular
>selection using ImageJ's leftmost tool and then invoque the plugin.
>It logs the following to the console:
>
> [WARNING] ====> Roi class = ij.gui.Roi
> [WARNING] ====> RECTANGLE: Roi[Rectangle, x=100, y=163, width=196,
>height=112]
> [INFO] image: plugin:class net.imagej.display.DefaultImageDisplay:
>type=interface net.imagej.display.DataView, name=Untitled,
>objects={net.imagej.display.DefaultDatasetView at 757dbeaf,
>net.imagej.display.DefaultOverlayView at 2198a037}
> [INFO] region: +0.0 +0.0, 559.0 x 559.0
>
> I expected the region in the last line (that obtained through
>OverlayService.getSelectionBounds) to coincide with the Roi
>mentionned in the WARNING.
>
> The CropImage command you mentionned does not do anything either
>before calling getSelectionBounds, and cropping works fine. Do you
>understand what is going on ?
>
> Cheers,
> Adrian
>
>
> import net.imagej.display.ImageDisplay;
> import net.imagej.display.OverlayService;
>
> import org.scijava.command.Command;
> import org.scijava.log.LogService;
> import org.scijava.plugin.Parameter;
> import org.scijava.plugin.Plugin;
> import org.scijava.util.RealRect;
>
> @Plugin(type = Command.class, menuPath = "Plugins>Foo_Bar")
> public class Foo_Bar implements Command {
>
> @Parameter
> private ImageDisplay display;
>
> @Parameter
> private OverlayService overlayService;
>
> @Parameter
> private LogService log;
>
> @Override
> public void run() {
> RealRect r = overlayService.getSelectionBounds(display);
> log.info("image: "+display);
> log.info("region: +" + r.x + " +" + r.y
> + ", " + r.width + " x " + r.height);
> }
> }
>
>
>
>
> On Mon, 24 Aug 2015 16:22:15 -0500
> Curtis Rueden <ctrueden at wisc.edu> wrote:
>> 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
>>>
>
> --
> http://www.msc.univ-paris-diderot.fr/~daerr/
--
http://www.msc.univ-paris-diderot.fr/~daerr/
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