Object classification problems with plugin version ilastik4ij-1.8.3-SNAPSHOT.jar

[k-dominik]

Currently I cannot run the object classification bit of the plugin (on osx) but get the following error (this is before the dialog to choose images and stuff even shows up):

traceback

(Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Mac OS X 10.16; 54MB of 12407MB (<1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304)
	... 5 more
Caused by: java.lang.RuntimeException: Module threw exception
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Stack argument out of range: 1
	at net.imglib2.img.VirtualStackAdapter$ImagePlusLoader.get(VirtualStackAdapter.java:194)
	at net.imglib2.img.VirtualStackAdapter$ImagePlusLoader.get(VirtualStackAdapter.java:170)
	at net.imglib2.img.planar.PlanarImg.update(PlanarImg.java:118)
	at net.imglib2.img.planar.PlanarImg.update(PlanarImg.java:66)
	at net.imglib2.type.numeric.integer.GenericByteType.updateContainer(GenericByteType.java:100)
	at net.imglib2.img.planar.PlanarCursor.reset(PlanarCursor.java:167)
	at net.imglib2.img.planar.PlanarCursor.<init>(PlanarCursor.java:95)
	at net.imglib2.img.planar.PlanarCursor2D.<init>(PlanarCursor2D.java:50)
	at net.imglib2.img.planar.PlanarImg.cursor(PlanarImg.java:217)
	at net.imglib2.img.planar.PlanarImg.cursor(PlanarImg.java:66)
	at net.imglib2.img.AbstractImg.firstElement(AbstractImg.java:81)
	at net.imagej.ImgPlus.firstElement(ImgPlus.java:274)
	at net.imagej.DefaultDatasetService.create(DefaultDatasetService.java:206)
	at net.imagej.legacy.translate.DisplayCreator.makeDataset(DisplayCreator.java:139)
	at net.imagej.legacy.translate.DisplayCreator.getDataset(DisplayCreator.java:101)
	at net.imagej.legacy.translate.DisplayCreator.makeDisplay(DisplayCreator.java:179)
	at net.imagej.legacy.translate.DisplayCreator.createDisplay(DisplayCreator.java:93)
	at net.imagej.legacy.translate.ImageTranslator.createDisplay(ImageTranslator.java:64)
	at net.imagej.legacy.LegacyImageMap.registerLegacyImage(LegacyImageMap.java:288)
	at net.imagej.legacy.convert.ImagePlusToDatasetConverter.convert(ImagePlusToDatasetConverter.java:80)
	at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
	at org.ilastik.ilastik4ij.util.StringToDatasetConverter.convert(StringToDatasetConverter.java:42)
	at org.scijava.convert.AbstractConvertService.convert(AbstractConvertService.java:125)
	at org.scijava.module.DefaultModuleService.load(DefaultModuleService.java:316)
	at org.scijava.module.DefaultModuleService.loadInput(DefaultModuleService.java:544)
	at org.scijava.module.DefaultModuleService.lambda$loadInputs$1(DefaultModuleService.java:346)
	at java.util.ArrayList.forEach(ArrayList.java:1259)
	at java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1082)
	at org.scijava.module.DefaultModuleService.loadInputs(DefaultModuleService.java:346)
	at org.scijava.module.process.LoadInputsPreprocessor.process(LoadInputsPreprocessor.java:58)
	at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:152)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	... 6 more
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Stack argument out of range: 1
	at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:145)
	at net.imglib2.cache.util.LoaderCacheAsCacheAdapter.get(LoaderCacheAsCacheAdapter.java:76)
	at net.imglib2.img.VirtualStackAdapter$ImagePlusLoader.get(VirtualStackAdapter.java:190)
	... 38 more
Caused by: java.lang.IllegalArgumentException: Stack argument out of range: 1
	at ij.ImageStack.getPixels(ImageStack.java:216)
	at net.imglib2.img.VirtualStackAdapter$ImagePlusLoader.load(VirtualStackAdapter.java:200)
	at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:135)
	... 40 more

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/ilastik4ij-plugin-only-imports-back-object-predictions/82359/2

[emilmelnikov]

imagej/imagej-legacy#246 was closed about a year ago, so we probably can remove our own converter and let ImageJ handle the conversion.

[k-dominik]

Hi @emilmelnikov, thank you for looking into this! Would you mind removing the converter?

[emilmelnikov]

I tried to run an Object Classification Workflow, both manually by clicking through the dialog, and by executing a macro, and it worked for me. This is the macro I've used:

run("Run Object Classification Prediction", "projectfilename=/Users/em/MyProject.ilp inputimage=blobs.gif inputproborsegimage=blobs.gif secondinputtype=Probabilities");

I ran ImageJ from within the project:

ImageJ ij = new ImageJ();
ij.ui().showUI();

[k-dominik]

hm that's sorta good, and also bad news ;). Did you run it from the source here? Then doing a new release might fix it. I'm just wondering if you build here, if the scijava version that is being pulled i is to slow. I'll check #99 and merge it once tests are fixed.

[emilmelnikov]

Did you run it from the source here?

Yes, from the current main, but I used just a simple cube.gif image, both as the input data and "probabilities". I've also just tried the same procedure on the "Organ of Corti" sample dataset because it is a 4D stack: it also works.