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

[Brian Northan]

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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