Save OME Tiff with File > Export > Image

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Save OME Tiff with File > Export > Image

Hadrien Mary
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

_______________________________________________
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Re: Save OME Tiff with File > Export > Image

Mark Hiner
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


On Wed, Jan 14, 2015 at 12:57 PM, Hadrien Mary <[hidden email]> 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
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel


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[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel
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Re: Save OME Tiff with File > Export > Image

Hadrien Mary
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 <[hidden email]> 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 <[hidden email]>
> 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
>> [hidden email]
>> http://imagej.net/mailman/listinfo/imagej-devel
>
>

_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel
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Re: Save OME Tiff with File > Export > Image

Mark Hiner
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



On Wed, Jan 21, 2015 at 6:24 PM, Hadrien Mary <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
> 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
>> [hidden email]
>> http://imagej.net/mailman/listinfo/imagej-devel
>
>


_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel
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Re: Save OME Tiff with File > Export > Image

Hadrien Mary

Very nice. Thanks Mark!

Le 22 janv. 2015 11:51, "Mark Hiner" <[hidden email]> 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



On Wed, Jan 21, 2015 at 6:24 PM, Hadrien Mary <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
> 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
>> [hidden email]
>> http://imagej.net/mailman/listinfo/imagej-devel
>
>


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