Sorry Hadrien - I didn't go into much detail on my last e-mail. You would've needed development versions of several other libraries to fix the bugs in "File > Export > Image...".
Anyway, I just uploaded all my fixes to Fiji. If you update, exporting as .ome.tif should be working now, regardless of whether JFileChooser is enabled or not. Note that there is still a known issue if overwriting multi-dot files (like .ome.tif) with JFileChooser enabled[1]. Thanks again for your help identifying these issues! Best, Mark [1] https://github.com/imagej/imagej-legacy/issues/102 On Wed, Jan 21, 2015 at 6:24 PM, Hadrien Mary <hadrien.m...@gmail.com> wrote: > Ok thanks. However even if I enable JFileChoose I still have an error > which prevent me to save the file. See below. > > ------------------------------------------ > (Fiji Is Just) ImageJ 2.0.0-rc-22/1.49m; Java 1.7.0_65 [64-bit]; Linux > 3.13.0-44-generic; 80MB of 4362MB (1%) > > java.lang.RuntimeException: java.util.concurrent.ExecutionException: > java.lang.IllegalArgumentException > at > net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:256) > at > net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160) > at ij.IJ.runPlugIn(IJ.java) > at ij.Executer.runCommand(Executer.java:131) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Thread.java:745) > Caused by: java.util.concurrent.ExecutionException: > java.lang.IllegalArgumentException > at java.util.concurrent.FutureTask.report(FutureTask.java:122) > at java.util.concurrent.FutureTask.get(FutureTask.java:188) > at > net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:252) > ... 5 more > Caused by: java.lang.IllegalArgumentException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at org.scijava.util.ReflectedUniverse.exec(ReflectedUniverse.java:314) > at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:327) > at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:310) > at net.imagej.plugins.commands.io.SaveAsImage.run(SaveAsImage.java:101) > at org.scijava.command.CommandModule.run(CommandModule.java:201) > at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) > at > org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164) > at java.util.concurrent.FutureTask.run(FutureTask.java:262) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) > ... 1 more > ------------------------------------------- > > I can't tell if it's related or another bug... > > -- > Hadrien Mary > > Ph.D student in Biology > Tournier-Gachet Team > CNRS - LBCMCP - UMR 5088 > > Université de Toulouse - Bât. 4R3B1 > 118, route de Narbonne - 31062 Toulouse > > > On Wed, Jan 21, 2015 at 8:04 PM, Mark Hiner <hi...@wisc.edu> wrote: > > Hi Hadrien, > > > > Thanks for reporting this. I finally tracked it down when working on > > updating File > Export > Image... and File > Import > Image... to use the > > fixes to OME-TIFF writing[1]. > > > > The issue has to do with whether or not the JFileChooser is enabled[2]. > A > > temporary workaround should be just to enable the use of the > JFileChooser. > > I'm hoping to have an actual fix soon though. > > > > Thanks again! > > - Mark > > > > [1] http://imagej.net/pipermail/imagej-devel/2015-January/002407.html > > [2] https://github.com/imagej/imagej-legacy/issues/101 > > > > On Wed, Jan 14, 2015 at 12:57 PM, Hadrien Mary <hadrien.m...@gmail.com> > > wrote: > >> > >> Hi, > >> > >> I'd like to report a bug I noticed some time ago. > >> > >> I have an error when I try to save an OME Tiff file with File > Export > >> > Image (to save it as an OME Tiff format). Note that it works well > >> when the saved image is not an OME Tiff file. > >> > >> The bug is weird. > >> > >> First when I click File > Export > Image, gtk file manager open to ask > >> where I want to save the file. The default filename is test.ometif > >> (instead of test.ome.tif, current filename). I change the filename to > >> be test.ome.tif (same bug when I don't change it) and when I click > >> "save", I have this message : > >> > >> ------------------------------------ > >> (Fiji Is Just) ImageJ 2.0.0-rc-21/1.49m; Java 1.7.0_65 [64-bit]; Linux > >> 3.13.0-44-generic; 80MB of 3600MB (2%) > >> > >> java.lang.RuntimeException: java.util.concurrent.ExecutionException: > >> java.lang.IllegalArgumentException > >> at > >> > net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:256) > >> at > >> > net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160) > >> at ij.IJ.runPlugIn(IJ.java) > >> at ij.Executer.runCommand(Executer.java:131) > >> at ij.Executer.run(Executer.java:64) > >> at java.lang.Thread.run(Thread.java:745) > >> Caused by: java.util.concurrent.ExecutionException: > >> java.lang.IllegalArgumentException > >> at java.util.concurrent.FutureTask.report(FutureTask.java:122) > >> at java.util.concurrent.FutureTask.get(FutureTask.java:188) > >> at > >> > net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:252) > >> ... 5 more > >> Caused by: java.lang.IllegalArgumentException > >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > >> at > >> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > >> at > >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > >> at java.lang.reflect.Method.invoke(Method.java:606) > >> at org.scijava.util.ReflectedUniverse.exec(ReflectedUniverse.java:314) > >> at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:327) > >> at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:310) > >> at net.imagej.plugins.commands.io.SaveAsImage.run(SaveAsImage.java:101) > >> at org.scijava.command.CommandModule.run(CommandModule.java:201) > >> at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) > >> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) > >> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) > >> at > >> > org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164) > >> at java.util.concurrent.FutureTask.run(FutureTask.java:262) > >> at > >> > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) > >> at > >> > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) > >> ... 1 more > >> ------------------------------------ > >> > >> I currently use BF exporter function which is working well for my > >> daily use. So don't rush on this. > >> > >> Thank you > >> > >> -- > >> Hadrien Mary > >> > >> Ph.D student in Biology > >> Tournier-Gachet Team > >> CNRS - LBCMCP - UMR 5088 > >> > >> Université de Toulouse - Bât. 4R3B1 > >> 118, route de Narbonne - 31062 Toulouse > >> > >> _______________________________________________ > >> ImageJ-devel mailing list > >> ImageJ-devel@imagej.net > >> http://imagej.net/mailman/listinfo/imagej-devel > > > > >
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