Repo deprecated in favor of multiview-reconstruction?

[NicoKiaru]

I think this repo needs to be removed from the Java-8 update site. It has conflicts with multiview-reconstruction. This leads to weird bugs.

[ctrueden]

@NicoKiaru Can you be more specific about what "weird bugs"? How to reproduce?

@StephanPreibisch On which of update site(s) does this project belong? There are three targets:

1. The current Java-8 update site.
2. The new standalone Fiji update site for Java 21.
3. The old Fiji-Legacy update site for very old stuff.

If I don't hear from you, I'll leave this project on Java-8, but remove it from Java-21.

See also https://forum.image.sc/t/housecleaning-fiji-for-the-java-21-update/107452

[NicoKiaru]

Yes, sure, sorry, I experienced it and filed a bug in order not to forget about it. Thought I was going to add more info and got into something else.

I obtain a NPE when:

• both the multiview-reconstruction jar and the SPIM_registration jars are present
• I try to run the Apply Transformation command:

here's the stack trace:

java.lang.NullPointerException
    at spim.fiji.plugin.queryXML.GenericLoadParseQueryXML.queryDetails(GenericLoadParseQueryXML.java:621)
    at spim.fiji.plugin.queryXML.GenericLoadParseQueryXML.queryXML(GenericLoadParseQueryXML.java:334)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:104)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:95)
    at spim.fiji.plugin.Apply_Transformation.run(Apply_Transformation.java:96)
    at ij.IJ.runUserPlugIn(IJ.java:244)
    at ij.IJ.runPlugIn(IJ.java:210)
    at ij.Executer.runCommand(Executer.java:152)
    at ij.Executer.run(Executer.java:70)
    at ij.IJ.run(IJ.java:326)

/C:/Fiji.app/plugins/SPIM_Registration-5.0.25.jar
legacy:spim.fiji.plugin.Apply_Transformation

/C:/Fiji.app/plugins/multiview_reconstruction-4.3.6.jar
legacy:net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

What I understand now is that the apply transformation plugin was moved from SPIM_Registration to multiview_reconstruction, thus from the Java 8 update site to the BigStitcher update site. I see that the BigStitcher update site now shadows SPIM_Registration with a stub file named SPIM_Registration-0.0.1.jar that contains (almost) nothing. For some reasons I ended up with a SPIM_Registration jar which was not a STUB and a new multiview reconstruction jar which also contained the Apply Transformation plugin.

Maybe that's a mistake on my side and it won't happen somewhere else. But still from what I understand this means that this repo should be abandoned / archived.

[NicoKiaru]

Note: since this repo is most likely phased out, the documentation will need to be updated, and probably removed: https://imagej.net/plugins/spim-registration/

[ctrueden]

I would favor instead trying to fix this incompatibility. Otherwise, old scripts and macros that use this functionality would break. I'm in favor of clearing marking obsolete documentation, but probably not deleting it unless the maintenance burden becomes substantial.

I'll try to investigate as part of (or very shortly after) the impending Java 21 rollout; this issue is listed on the Fiji Fit project board.

[NicoKiaru]

Ok, I can't reproduce since the pom scijava 40 update. I think I have done something wrong. I close it for now. Please re-open if you think there's something to dig

[StephanPreibisch]

Hi, yes, let's remove it ... but other projects might depend on it. Should we try again moving BigStitcher to the Java8 site @ctrueden? Should be easier now I guess ...