<div dir="ltr">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...".<div><br></div><div>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.</div><div><br></div><div>Note that there is still a known issue if overwriting multi-dot files (like .ome.tif) with JFileChooser enabled[1].</div><div><br></div><div>Thanks again for your help identifying these issues!</div><div><br></div><div>Best,</div><div>Mark</div><div><br></div><div>[1] <a href="https://github.com/imagej/imagej-legacy/issues/102">https://github.com/imagej/imagej-legacy/issues/102</a></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 21, 2015 at 6:24 PM, Hadrien Mary <span dir="ltr"><<a href="mailto:hadrien.mary@gmail.com" target="_blank">hadrien.mary@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Ok thanks. However even if I enable JFileChoose I still have an error<br>
which prevent me to save the file. See below.<br>
<br>
------------------------------------------<br>
(Fiji Is Just) ImageJ 2.0.0-rc-22/1.49m; Java 1.7.0_65 [64-bit]; Linux<br>
3.13.0-44-generic; 80MB of 4362MB (1%)<br>
<div><div class="h5"><br>
java.lang.RuntimeException: java.util.concurrent.ExecutionException:<br>
java.lang.IllegalArgumentException<br>
at net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:256)<br>
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160)<br>
at ij.IJ.runPlugIn(IJ.java)<br>
at ij.Executer.runCommand(Executer.java:131)<br>
at ij.Executer.run(Executer.java:64)<br>
at java.lang.Thread.run(Thread.java:745)<br>
Caused by: java.util.concurrent.ExecutionException:<br>
java.lang.IllegalArgumentException<br>
at java.util.concurrent.FutureTask.report(FutureTask.java:122)<br>
at java.util.concurrent.FutureTask.get(FutureTask.java:188)<br>
at net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:252)<br>
... 5 more<br>
Caused by: java.lang.IllegalArgumentException<br>
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br>
at java.lang.reflect.Method.invoke(Method.java:606)<br>
at org.scijava.util.ReflectedUniverse.exec(ReflectedUniverse.java:314)<br>
at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:327)<br>
at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:310)<br>
at net.imagej.plugins.commands.io.SaveAsImage.run(SaveAsImage.java:101)<br>
at org.scijava.command.CommandModule.run(CommandModule.java:201)<br>
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)<br>
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)<br>
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)<br>
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)<br>
at java.util.concurrent.FutureTask.run(FutureTask.java:262)<br>
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)<br>
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)<br>
... 1 more<br>
</div></div>-------------------------------------------<br>
<br>
I can't tell if it's related or another bug...<br>
<span class="im HOEnZb"><br>
--<br>
Hadrien Mary<br>
<br>
Ph.D student in Biology<br>
Tournier-Gachet Team<br>
CNRS - LBCMCP - UMR 5088<br>
<br>
Université de Toulouse - Bât. 4R3B1<br>
118, route de Narbonne - 31062 Toulouse<br>
<br>
<br>
</span><div class="HOEnZb"><div class="h5">On Wed, Jan 21, 2015 at 8:04 PM, Mark Hiner <<a href="mailto:hiner@wisc.edu">hiner@wisc.edu</a>> wrote:<br>
> Hi Hadrien,<br>
><br>
> Thanks for reporting this. I finally tracked it down when working on<br>
> updating File > Export > Image... and File > Import > Image... to use the<br>
> fixes to OME-TIFF writing[1].<br>
><br>
> The issue has to do with whether or not the JFileChooser is enabled[2]. A<br>
> temporary workaround should be just to enable the use of the JFileChooser.<br>
> I'm hoping to have an actual fix soon though.<br>
><br>
> Thanks again!<br>
> - Mark<br>
><br>
> [1] <a href="http://imagej.net/pipermail/imagej-devel/2015-January/002407.html" target="_blank">http://imagej.net/pipermail/imagej-devel/2015-January/002407.html</a><br>
> [2] <a href="https://github.com/imagej/imagej-legacy/issues/101" target="_blank">https://github.com/imagej/imagej-legacy/issues/101</a><br>
><br>
> On Wed, Jan 14, 2015 at 12:57 PM, Hadrien Mary <<a href="mailto:hadrien.mary@gmail.com">hadrien.mary@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> I'd like to report a bug I noticed some time ago.<br>
>><br>
>> I have an error when I try to save an OME Tiff file with File > Export<br>
>> > Image (to save it as an OME Tiff format). Note that it works well<br>
>> when the saved image is not an OME Tiff file.<br>
>><br>
>> The bug is weird.<br>
>><br>
>> First when I click File > Export > Image, gtk file manager open to ask<br>
>> where I want to save the file. The default filename is test.ometif<br>
>> (instead of test.ome.tif, current filename). I change the filename to<br>
>> be test.ome.tif (same bug when I don't change it) and when I click<br>
>> "save", I have this message :<br>
>><br>
>> ------------------------------------<br>
>> (Fiji Is Just) ImageJ 2.0.0-rc-21/1.49m; Java 1.7.0_65 [64-bit]; Linux<br>
>> 3.13.0-44-generic; 80MB of 3600MB (2%)<br>
>><br>
>> java.lang.RuntimeException: java.util.concurrent.ExecutionException:<br>
>> java.lang.IllegalArgumentException<br>
>> at<br>
>> net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:256)<br>
>> at<br>
>> net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160)<br>
>> at ij.IJ.runPlugIn(IJ.java)<br>
>> at ij.Executer.runCommand(Executer.java:131)<br>
>> at ij.Executer.run(Executer.java:64)<br>
>> at java.lang.Thread.run(Thread.java:745)<br>
>> Caused by: java.util.concurrent.ExecutionException:<br>
>> java.lang.IllegalArgumentException<br>
>> at java.util.concurrent.FutureTask.report(FutureTask.java:122)<br>
>> at java.util.concurrent.FutureTask.get(FutureTask.java:188)<br>
>> at<br>
>> net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:252)<br>
>> ... 5 more<br>
>> Caused by: java.lang.IllegalArgumentException<br>
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
>> at<br>
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br>
>> at<br>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br>
>> at java.lang.reflect.Method.invoke(Method.java:606)<br>
>> at org.scijava.util.ReflectedUniverse.exec(ReflectedUniverse.java:314)<br>
>> at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:327)<br>
>> at net.imagej.DefaultDatasetService.save(DefaultDatasetService.java:310)<br>
>> at net.imagej.plugins.commands.io.SaveAsImage.run(SaveAsImage.java:101)<br>
>> at org.scijava.command.CommandModule.run(CommandModule.java:201)<br>
>> at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)<br>
>> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)<br>
>> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)<br>
>> at<br>
>> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)<br>
>> at java.util.concurrent.FutureTask.run(FutureTask.java:262)<br>
>> at<br>
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)<br>
>> at<br>
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)<br>
>> ... 1 more<br>
>> ------------------------------------<br>
>><br>
>> I currently use BF exporter function which is working well for my<br>
>> daily use. So don't rush on this.<br>
>><br>
>> Thank you<br>
>><br>
>> --<br>
>> Hadrien Mary<br>
>><br>
>> Ph.D student in Biology<br>
>> Tournier-Gachet Team<br>
>> CNRS - LBCMCP - UMR 5088<br>
>><br>
>> Université de Toulouse - Bât. 4R3B1<br>
>> 118, route de Narbonne - 31062 Toulouse<br>
>><br>
>> _______________________________________________<br>
>> ImageJ-devel mailing list<br>
>> <a href="mailto:ImageJ-devel@imagej.net">ImageJ-devel@imagej.net</a><br>
>> <a href="http://imagej.net/mailman/listinfo/imagej-devel" target="_blank">http://imagej.net/mailman/listinfo/imagej-devel</a><br>
><br>
><br>
</div></div></blockquote></div><br></div>