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embl-cba / elastixWrapper

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Exception using mhd files #17

Open Maik-Lu opened 2 years ago

Maik-Lu commented 2 years ago

Greetings @tischi, since recently I get an exception when I try loading .mhd files as moving or fixed image (I tried it with .tif stacks and it worked). The image opens but afterwards I get the following message:

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 202MB of 1288137MB (<1%) java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307) 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:748) 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:303) ... 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.NullPointerException at de.embl.cba.elastixwrapper.elastix.ElastixWrapper.stageImageAsMhd(ElastixWrapper.java:508) at de.embl.cba.elastixwrapper.elastix.ElastixWrapper.stageImages(ElastixWrapper.java:384) at de.embl.cba.elastixwrapper.elastix.ElastixWrapper.runElastix(ElastixWrapper.java:71) at de.embl.cba.elastixwrapper.commands.ElastixCommand.runElastix(ElastixCommand.java:127) at de.embl.cba.elastixwrapper.commands.ElastixCommand.run(ElastixCommand.java:116) at org.scijava.command.CommandModule.run(CommandModule.java:196) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124) ... 6 more

In addition I get in the Console:

[INFO] Temporary directory is: ... [ERROR] The image could not be loaded: ...

Do you have a suggestion? Thanks a lot, Maik

tischi commented 2 years ago

Dear @Maik-Lu,

Thank you very much for reporting this issue!

Could you please provide me with

...such that I could test it here on my computer?