[ImageJ-devel] [ImgLib2] The img-metadata branch

[Mark Hiner]

Hi Brian,

 Ahhh.. I'm sorry! I misunderstood. If that's the actual stack trace then
no, I don't think you are having any problems with the dependency tree, and
all your pom settings should be fine given that stack trace.

 Sidetrack: the pom-scijava doesn't actually have snapshot versions. It's
basically just versioning glue - it defines a version properties to help
ensure consistent versions of the various SciJava libraries (like SCIFIO)
are consumed. Using 1.111 is fine, as we want to use the latest version of
everything since SCIFIO-0.7.4/0.7.5 are quite new. Let me know if that's
not clear...

  Anyway, since we know it worked in 0.7.3, I would like to
bisect<https://www.kernel.org/pub/software/scm/git/docs/git-bisect.html>and
figure out what happened. However, I currently can't reproduce the
issue. When I open a float dataset with SCIFIO 0.7.5 in IJ2 I'm able to
write it as a .tif. So you're probably exposing a bug with other commands
interacting with SCIFIO.

 Can you share your custom commands? If not, could you let me know which
commands you're calling?

Thanks,
- Mark




On Fri, Dec 13, 2013 at 1:49 PM, Brian Northan <bnorthan at gmail.com> wrote:

> Hi Mark
>
> I am using IJ2 in headless mode with some custom commands I wrote.  So it
> is always possible that I still have old references somewhere.  However
> that stack trace was actually generated with 0.7.4.  When I had noted that
> 0.7.5-SNAPSHOT threw an exception, I went back to 0.7.4 to make sure that
> worked but it also had the same exception.  Then I went back to 0.7.3 which
> worked (other than the floating point problem).
>
> Below is the stack trace using 0.7.5-SNAPSHOT.   (btw since I am using IJ2
> maybe there is something else wrong in the dependency tree??  One of the
> IJ2 components??  Should I set the sci-java version to a SNAPSHOT version
> too??  It is 1.111 right now.
>
>      at org.scijava.Context.inject(Context.java:273)
>     at
> org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:241)
>     at
> org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:229)
>     at
> org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:220)
>     at
> org.scijava.plugin.AbstractSingletonService.createInstances(AbstractSingletonService.java:95)
>     at
> org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:73)
>     at
> org.scijava.plugin.AbstractSingletonService$1.get(AbstractSingletonService.java:87)
>     at
> org.scijava.plugin.AbstractSingletonService$1.get(AbstractSingletonService.java:83)
>     at org.scijava.object.ObjectIndex.resolvePending(ObjectIndex.java:391)
>     at org.scijava.object.ObjectIndex.get(ObjectIndex.java:136)
>     at
> org.scijava.object.DefaultObjectService.getObjects(DefaultObjectService.java:89)
>     at
> io.scif.codec.DefaultCodecService.getCodec(DefaultCodecService.java:65)
>     at
> io.scif.formats.tiff.TiffCompression.compress(TiffCompression.java:330)
>     at io.scif.formats.tiff.TiffSaver.writeImage(TiffSaver.java:391)
>     at io.scif.formats.tiff.TiffSaver.writeImage(TiffSaver.java:279)
>      at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1250)
>     at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1290)
>
>     at io.scif.AbstractWriter.savePlane(AbstractWriter.java:107)
>     at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:532)
>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:380)
>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:133)
>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:114)
>
>
>
> On Fri, Dec 13, 2013 at 1:40 PM, Mark Hiner <hinerm at gmail.com> wrote:
>
>>
>> Hi Brian,
>>
>>
>>>  I referenced the scifio 0.7.5-SNAPSHOT (would that be correct to get
>>> the absolute latest??)
>>>
>>
>> Yep this should be the latest snapshot.
>>
>>  in my POM and ran into an exception when executing my code.
>>>
>>
>> ...
>>
>>
>>>      at
>>> io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1255)
>>>     at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1295)
>>>     at io.scif.AbstractWriter.savePlane(AbstractWriter.java:107)
>>>     at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:532)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:380)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:133)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:114)
>>>
>>
>> That stack trace suggests that an older version of the TIFFFormat is
>> being used. It must be from prior commit 37953<https://github.com/scifio/scifio/commit/379530aab9a9848e59363d87dcbdb79c4842bfc3>(because the TiffSaver.writeImage call is now on line 1250, not 1255). I'm
>> assuming it's from the 0.7.4 release.
>>
>>  Are you just running the code snippet that Curtis posted a while back
>> (or your own similar snippet)? Or are you using SCIFIO in IJ2, or another
>> application?
>>
>>  Could you run "mvn dependency:tree", or check the "Maven Dependencies"
>> tab if you're using Eclipse? I'm assuming something must still have a 0.7.4
>> SCIFIO reference, which is being pulled in instead of 0.7.5...
>>
>> Sorry for the inconvenience.. let me know what you find!
>>
>> Thanks,
>> Mark
>>
>
>
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