Closed k-dominik closed 1 year ago
imagesc-bot
commented
1 year ago 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
commented
1 year ago https://github.com/imagej/imagej-legacy/issues/246 was closed about a year ago, so we probably can remove our own converter and let ImageJ handle the conversion.
k-dominik
commented
1 year ago Hi @emilmelnikov, thank you for looking into this! Would you mind removing the converter?
emilmelnikov
commented
1 year ago 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();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
commented
1 year ago 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.
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.