Exception in ImageJ 3D Suite after update to imagescience 3.0.0

[Jan Eglinger]

Dear Thomas, dear Erik,

after the recent update of the ImageScience library [1,2] within Fiji,
some plugins of the nice ImageJ 3D Suite seem to be broken: when I run
'Plugins > 3D > 3D Hysteresis Thresholding', the exception pasted below
gets thrown [3].

This is probably solved by changing the import statement in
mcib_plugins/processing/Thresholder.java from

     import imagescience.utility.ImageScience;
to
     import imagescience.ImageScience;

but there might be many other places that have to be changed. I noticed
that e.g. the imagescience.transform.Affine#run method had changed its
signature from
     run(Image, Transform, int, boolean, boolean)
to
     run(Image, Transform, int, boolean, boolean , boolean)

@Erik: I would have appreciated if the transition to imagescience 3.0.0
had been a bit smoother, e.g. by marking some methods as deprecated
before removing/changing them completely. That way, plugin developers
could have reacted ahead of time and avoided breakage of their plugins
for users.

That said, it would be great if you could make the mcib3d-core source
code available on github, so the community can contribute patches more
easily :)

Best regards,
Jan


[1]:
https://github.com/fiji/imagescience/commit/46f778a
(careful, the huge commit might stall your browser for a little while)
[2]:
http://imagej.1557.x6.nabble.com/TransformJ-Update-td5014108.html

[3]:
  java.lang.NoClassDefFoundError: imagescience/utility/ImageScience
at mcib_plugins.processing.Thresholder.hysteresis(Thresholder.java:79)
at
mcib_plugins.Hysteresis_Thresholding.hysteresis(Hysteresis_Thresholding.java:46)
at mcib_plugins.Hysteresis_Thresholding.run(Hysteresis_Thresholding.java:34)
at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
at ij.IJ.runUserPlugIn(IJ.java:214)
at ij.IJ.runPlugIn(IJ.java:176)
at ij.Executer.runCommand(Executer.java:132)
at ij.Executer.run(Executer.java:62)
at java.lang.Thread.run(Thread.java:619)

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[Thomas Boudier-3]

Dear Jan,

Thanks for your mail. I also discovered this problem when trying to
compile TANGO. There are just some minor changes, that should be fixed
soon. The source code of mcib3d and mcib3d-plugins are already available
on github, if you do not find them, send me a private email, I will send
you the link.

Best,

Thomas


On 28/08/2015 17:26, Jan Eglinger wrote:

> Dear Thomas, dear Erik,
>
> after the recent update of the ImageScience library [1,2] within Fiji,
> some plugins of the nice ImageJ 3D Suite seem to be broken: when I run
> 'Plugins > 3D > 3D Hysteresis Thresholding', the exception pasted
> below gets thrown [3].
>
> This is probably solved by changing the import statement in
> mcib_plugins/processing/Thresholder.java from
>
>     import imagescience.utility.ImageScience;
> to
>     import imagescience.ImageScience;
>
> but there might be many other places that have to be changed. I
> noticed that e.g. the imagescience.transform.Affine#run method had
> changed its signature from
>     run(Image, Transform, int, boolean, boolean)
> to
>     run(Image, Transform, int, boolean, boolean , boolean)
>
> @Erik: I would have appreciated if the transition to imagescience
> 3.0.0 had been a bit smoother, e.g. by marking some methods as
> deprecated before removing/changing them completely. That way, plugin
> developers could have reacted ahead of time and avoided breakage of
> their plugins for users.
>
> That said, it would be great if you could make the mcib3d-core source
> code available on github, so the community can contribute patches more
> easily :)
>
> Best regards,
> Jan
>
>
> [1]:
> https://github.com/fiji/imagescience/commit/46f778a
> (careful, the huge commit might stall your browser for a little while)
> [2]:
> http://imagej.1557.x6.nabble.com/TransformJ-Update-td5014108.html
>
> [3]:
>  java.lang.NoClassDefFoundError: imagescience/utility/ImageScience
> at mcib_plugins.processing.Thresholder.hysteresis(Thresholder.java:79)
> at
> mcib_plugins.Hysteresis_Thresholding.hysteresis(Hysteresis_Thresholding.java:46)
> at
> mcib_plugins.Hysteresis_Thresholding.run(Hysteresis_Thresholding.java:34)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
> at ij.IJ.runUserPlugIn(IJ.java:214)
> at ij.IJ.runPlugIn(IJ.java:176)
> at ij.Executer.runCommand(Executer.java:132)
> at ij.Executer.run(Executer.java:62)
> at java.lang.Thread.run(Thread.java:619)
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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