[ImageJ-devel] Save OME Tiff with File > Export > Image

Thu Jan 22 06:27:36 CST 2015

Very nice. Thanks Mark!
Le 22 janv. 2015 11:51, "Mark Hiner" <hiner at wisc.edu> a écrit :

> 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.mary at 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 <hiner at 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.mary at 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 at imagej.net
>> >> http://imagej.net/mailman/listinfo/imagej-devel
>> >
>> >
>>
>
>
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