Error when applying opening/closing with an ellipsoid structuring element

[giocard]

Note: the error appears only when specifying the Ball element and for some combinations of radii (e.g. 4,4,1 or 8,8,2)
I suspect that this is due to some rounding error when adding and removing the borders, but I was not able to pinpoint the piece of code.

The error can be reproduced with these two macro commands

newImage("HyperStack", "8-bit grayscale-mode", 512, 512, 1, 32, 1);
run("Morphological Filters (3D)", "operation=Opening element=Ball x-radius=4 y-radius=4 z-radius=1");

The error message is

(Fiji Is Just) ImageJ 2.14.0/1.54f; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 858MB of 65386MB (1%)

java.lang.IllegalArgumentException: Crop bounds exceed image bounds
at inra.ijpb.shape.ImageShape.cropRect(ImageShape.java:208)
at inra.ijpb.morphology.strel.AbstractStrel3D.closing(AbstractStrel3D.java:341)
at inra.ijpb.morphology.filter.Closing.process(Closing.java:82)
at inra.ijpb.morphology.Morphology.closing(Morphology.java:507)
at inra.ijpb.morphology.Morphology$Operation.apply(Morphology.java:176)
at inra.ijpb.plugins.MorphologicalFilter3DPlugin.process(MorphologicalFilter3DPlugin.java:169)
at inra.ijpb.plugins.MorphologicalFilter3DPlugin.run(MorphologicalFilter3DPlugin.java:110)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:67)
at ij.IJ.run(IJ.java:326)
at ij.IJ.run(IJ.java:337)
at ij.macro.Functions.doRun(Functions.java:703)
at ij.macro.Functions.doFunction(Functions.java:99)
at ij.macro.Interpreter.doStatement(Interpreter.java:281)
at ij.macro.Interpreter.doStatements(Interpreter.java:267)
at ij.macro.Interpreter.run(Interpreter.java:163)
at ij.macro.Interpreter.run(Interpreter.java:93)
at ij.macro.Interpreter.run(Interpreter.java:107)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:164)
at ij.IJ.runMacro(IJ.java:165)
at ij.IJ.runMacro(IJ.java:154)
at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1186)
at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1182)
at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:1133)
at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1182)
at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:145)
at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)

[dlegland]

Hi,

thanks for reporting!

It looks like a rounding error indeed! Actually, I could not reproduce, but I'm pretty sure the problem simply comes from the control that throws the exception. I try to check this more in details soon!

[giocard]

Hi,

thank you for looking into it. If it is of any help, I tried on two different Windows machine and on a fresh installation of Fiji, and I always get the error.
I also tried previous versions of the plugin, and the error is present in 1.6.0 but not in 1.5.0 (as packaged in sites.imagej.net)

[dlegland]

Hi,

I found a mistake in the way the "offset" of the structuring element was computed. I fixed it in 355b6c8, this made the bug disappear for me (I could finally reproduce on another computer).

[giocard]

Great! Thank you very much.