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

Thu Jan 22 04:51:03 CST 2015

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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