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  • Feb 24 20:22
    JoBoPo closed #284
  • Feb 24 20:20
    JoBoPo commented #284
  • Feb 24 19:50
    imagejan commented #284
  • Feb 24 16:59
    JoBoPo edited #284
  • Feb 24 16:30
    JoBoPo opened #284
  • Feb 23 16:53

    tinevez on gauss-fit

    Skip tracking when tracker is n… Merge branch 'master' into gaus… Make the tables easier to use i… and 2 more (compare)

  • Feb 23 16:53

    tinevez on master

    Skip tracking when tracker is n… Make the tables easier to use i… Make the table creation methd p… (compare)

  • Feb 23 10:46

    tinevez on gauss-fit

    An algorithm to refine spot pos… An example for the gaussian pea… Integrate the gauss fitter in T… and 1 more (compare)

  • Feb 20 12:00

    tinevez on draw-filled

    (compare)

  • Feb 20 12:00

    tinevez on master

    New display settings: paint the… Defend against min > max errors… Merge pull request #170 from fi… (compare)

  • Feb 20 12:00
    tinevez closed #170
  • Feb 20 11:59
    tinevez opened #170
  • Feb 20 11:56

    tinevez on draw-filled

    Defend against min > max errors… (compare)

  • Feb 20 11:50

    tinevez on draw-filled

    New display settings: paint the… (compare)

  • Feb 20 11:25

    tinevez on cancelable

    (compare)

  • Feb 20 11:25
    tinevez closed #169
  • Feb 19 19:21
    tinevez synchronize #169
  • Feb 19 19:21

    tinevez on cancelable

    Two new icons in the collection. (compare)

  • Feb 19 19:20

    tinevez on v7

    Acquaint the GUI changes in Tra… (compare)

  • Feb 19 17:06
    tinevez synchronize #169
Jan Eglinger
@imagejan
(in the future, please disclose when cross-posting on different communication channels, so that others can follow)
Christian Tischer
@tischi
Is it possible to add own example data to Fiji?
Mark Hiner
@hinerm
@tischi like sample images? There's the Samples repo... I think you could just submit a PR to add more links to this plugins.config. Given how many sample images there are, there must be other ways too..
Stephan Saalfeld
@axtimwalde
Want to link a 5TB N5 there?
Christian Tischer
@tischi
@hinerm Thanks a lot! @axtimwalde Why not :D but in this case it's just a small TIFF image.
Curtis Rueden
@ctrueden
The sample data itself is not in a git repo.
samples.fiji.sc is where it lives.
It's just a plain old Apache virtual host.
As for adding it to Fiji's menu: that would require a PR, yeah.
1 reply
We don't have 5TB of disk to host an N5 sample, but if you are already hosting it somewhere else @axtimwalde, we could just link to it. However, ImageJ's sample downloading mechanism is surely inadequate for that one??
Kyle I S Harrington
@kephale
n5 can lazy load from buckets tho
Curtis Rueden
@ctrueden
@kephale Sure, but then it wouldn't be using ImageJ1's "Open Samples" logic.
Christian Tischer
@tischi
Here: https://github.com/fiji/fiji/blob/master/pom.xml it says that it is using the parent pom 30.0.0
Can one always rely on the fact that all version that are currently shipped with Fiji are exactly the ones that are given in this parent pom?
Or are there sometimes exceptions?
Christian Tischer
@tischi
...probably I should rather look at the latest release? https://github.com/fiji/fiji/blob/fiji-2.2.0/pom.xml
Jan Eglinger
@imagejan
In theory, the latest release of fiji/fiji should reflect what’s on the update site, indeed. However, you can’t trust this currently, because people can manually upload to the Java-8 update site, and do so to quickly fix bugs, without having a new release every time.
Christian Tischer
@tischi
Indeed, I just figured out that several bigdataviewer and imglib2 libraries are a significantly higher version than what is specified in 30.0.0
Do you know how I could emulate this in my development environment, i.e. what do I have to put in my pom when I want to develop against what is currently shipped with Fiji?
Jan Eglinger
@imagejan

The proper way of having a consistent Fiji would be to 1) update the component versions in pom-scijava, 2) cut a new release of pom-scijava, 3) update fiji to inherit from that new pom-scijava release, 4) cut a new release of Fiji, and then finally 5) let the automated CI deploy everything and upload. We’re still a bit away from that scenario.

Developing against the same pom-scijava as the latest fiji release would be safest. Or if you can wait with deployment until other developers update their stuff as well (in case of breaking changes only, of course), develop against latest pom-scijava release, and then wait with deploying until fiji is updated to that pom-scijava version as well.
Or ship all updated dependencies on your own update site, and risk them breaking other update sites on a user’s system. In any case, within the bdv ecosystem (and as long as bdv-playground, bigstitcher, etc. all have their own update sites) there’s no way around concerted updates of all the components.

Curtis Rueden
@ctrueden
Regarding pom-scijava matching Fiji: in order to reach the desired scenario, we'll have to lock down uploads to the update sites, and make updating pom-scijava the only path forward, and then get better at responding as quickly as possible to people when they file PRs.
I don't see any real showstoppers toward doing this, except for fear that: A) there will be a period of people being unhappy and complaining; and B) it will force us to spend time iterating on the mega-melt to get the new process working as smoothly as possible.
And maybe C) some people will be unsatisfied no matter how rapid we make the process work, since it will still be slower than the previous process of "I just upload it"—and then more DevOps work will be needed to add something like an "unstable" core update site on top of the current system.
Christian Tischer
@tischi
I think having a pom-scijava that reflects the actual state of the currently shipped Fiji including the Java8 update site would be important. Otherwise I would not know how to ensure that my update sites are compatible with current Fiji.
Christian Tischer
@tischi
What would be also great is that one could subscribe to something such that one gets an e-mail when the current-fiji-pom was modified.
Another idea that comes to my mind is to, in addition, have a mechanism that one could have a pom that uses current-fiji-pom <version>LATEST-RELEASE</version> as a parent pom, such that one would not have to manually go through all repositories to update to the latest.
NicoKiaru
@NicoKiaru

What would be also great is that one could subscribe to something such that one gets an e-mail when the current-fiji-pom was modified.

You can watch https://github.com/scijava/pom-scijava ?

5 replies
Christian Tischer
@tischi
@ctrueden If the Java8 Update site is the only source of versions that are different from the latest release, could we make another pom-java8-scijava that has the currently released pom-scijava as a parent and then just overrides the (few) dependencies that are shipped with the Java8 update site?
Jan Eglinger
@imagejan
@tischi I don’t see how that would solve the general issue of someone uploading to that update site without in parallel committing to pom-java8-scijava (or filing a PR). IMHO, the problem can only be solved by blocking direct uploads, and making the content of the update site synced with pom-scijava releases, as @ctrueden suggests.
Christian Tischer
@tischi
Of course one would have to in parallel commit to pom-java8-scijava, I took this as a given.
Jan Eglinger
@imagejan
You can’t guarantee that this will always happen, unless you enforce it by some automation
Christian Tischer
@tischi
Sure, if the pom-java8-scijava would be automatically in sync with the content of the update site that would of course be good.
I think my point is that right now pull request like this: scijava/pom-scijava#168
don't really help because the pom-scijava that they will be merged into is too new and thus cannot be used.
If they would instead by merged into a pom-java8-scijava then this would be usable, I think.
CellKai
@CellKai
Hi! I am trying to test a proposed fix in the java code for an issue with BigStitcher as described on image.sc. To change the java code, I have cloned the multiview-reconstruction repo , but when I try to build it with maven, compilation fails: javafx... does not exist.
Does someone have a pointer for me how I could move on?
Jan Eglinger
@imagejan
@CellKai you’re probably trying to build with a Java version that doesn’t have JavaFX. I can reproduce the failing build with AdoptOpenJDK 1.8.0_275 on Windows.
I see that on travis, the build uses this line to install javafx before building: https://github.com/PreibischLab/multiview-reconstruction/blob/bf2c20b425cb4ce5f934be441019a9ccc2a777e1/.travis.yml#L10
I’m not sure what's the right way forward here. @StephanPreibisch can you suggest which Java flavor to use for building mvrecon locally?
63 replies
NicoKiaru
@NicoKiaru
@CellKai @imagejan I just clicked install, and I manage to get a jar. Isn't that sufficient ? I'll continue and let you know
Ok, it doesn't work - I'll post on the forum what I get for now.
CellKai
@CellKai
Hi @imagejan, thank you for reproducing the issue and looking into it. @NicoKiaru thank you as well for testing! How did you install it, do you maybe use an IDE? What I did is I went into the locally cloned repo in a terminal and then just started the build using $ mvn
NicoKiaru
@NicoKiaru
Yes, I cloned the repo, imported it into intellij, modifed the file, and then clicked lifecycle > install, which creates the jar in the target folder of the repo
image.png
Then you can replace the jar within fiji
NicoKiaru
@NicoKiaru
I had good hope, but it doesn't work unfortunately...
CellKai
@CellKai
I saw, thats indeed unfortunate. thank you for trying, though! much appreciated!
Curtis Rueden
@ctrueden
@CellKai Use Zulu JDK FX 8.
It comes bundled with JavaFX, unlike other flavors of OpenJDK 8.