Anisotropy fail on Fiji 1.52g about bonej2 HOT 6 CLOSED

It looks like the latest BoneJ2 build was uploaded to the BoneJ update site, but the corresponding latest ImageJ Ops release that BoneJ2 depends on has not yet been uploaded to the core update site.

This is partially my fault for being slow in pushing out the new ImageJ Ops release. But it is also a problem with how BoneJ is currently being deployed—there is nothing safeguarding against such skews.

from bonej2.

Thanks for your help! So what could I do now? e.g. Change my Fiji version? Otherwise, considering the Anisotropy module, could you upload a currently available version of both Fiji and BoneJ? Many thanks!

from bonej2.

Hi @kld123509945 I added the missing dependency to the update site, and I tested it's working now. Try running Help > Update... again, and it should show imagej-ops:0.42.0 available from the BoneJ update site. If not, then:

1. Disable the update site and let Fiji uninstall BoneJ
2. Restart Fiji
3. Enable the BoneJ update site gain, and let Fiji install
4. Restart Fiji again

Let me know if this solves the problem. Apologies for the bother, and thank you for reporting the issue!

@ctrueden So the lesson here is that if we depend on newer artefacts then declared in the pom-scijava BOM, we need to have them "shadowed" on the BoneJ update site?

from bonej2.

@rimadoma Thanks so much for your help! The imagej-ops:0.42.0 didn't show, so I do the 4 steps as you told me. This method works! Shown as:

http://imglf5.nosdn0.126.net/img/M3B0VGdGQVdIRGowRzJQeGlnYWlqOURnMFZiR0pqd0cyNjR0ZnVlb0pkSVIwRVVGdlFyV3VnPT0.png?imageView&thumbnail=1680x0&quality=96&stripmeta=0

BTW, may I ask that how could I save the results in the BoneJ results window? e.g. save it as a .csv or .txt in the hard disk? I cannot see any button or command to save the result like:

http://imglf6.nosdn0.126.net/img/M3B0VGdGQVdIRGowRzJQeGlnYWlqL0VoWjhNZkZ0eWU1T05UTlQ0SjJoNVlrbjEwR0ZQWERBPT0.png?imageView&thumbnail=2264y726&type=png&quality=96&stripmeta=0

Many thanks!

from bonej2.

@kld123509945 If you click to select a row, you can use the common hot keys for copy-pasting, i.e. Ctrl + C for copying, and then Ctrl + V to paste it, e.g. to your favourite text editor. You can select multiple rows by holding down Ctrl, or key Ctrl + A to select them all.

from bonej2.

@ctrueden So the lesson here is that if we depend on newer artefacts then declared in the pom-scijava BOM, we need to have them "shadowed" on the BoneJ update site?

Unfortunately, the lesson is more complicated than that. Yes, if you depend on a newer imagej-ops, and you want to release your new BoneJ with that dependency before the core update sites are shipping the new imagej-ops, then yes, you need to upload imagej-ops to your site as well.

However, you then have the responsibility of removing that version of imagej-ops once it (or a newer version) gets uploaded to the core update site. Otherwise, your shadowed now-older version will continue to take precedence, and break core ImageJ features that might depend on the newer imagej-ops.

Best practice here is not to shadow imagej-ops at all, and instead push for the core update site to get the newest versions deployed as soon as possible. I have been slow about this, but this week I am working on deploying a new version of the whole Fiji software stack. I will try to remember to ping you once the latest imagej-ops has been deployed, so that we can mark the version on BoneJ as obsolete.

One (usually) easy way to avoid these sorts of issues is to depend on the same version of pom-scijava that fiji/fiji is using, and do not override any version properties of dependencies. Of course, if you need a bug-fix or new feature from a dependency, like you did with imagej-ops here, then we need to push to get that version of imagej-ops released and included in pom-scijava and utilized by fiji/fiji in as timely a manner as possible.

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