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  • May 25 09:10
    xulman commented #120
  • May 25 06:59

    tpietzsch on master

    ADD: MamutViewBdv.getViewerPane… (compare)

  • May 25 06:59
    tpietzsch closed #120
  • May 23 02:08
    xulman opened #120
  • May 21 22:51
    acardona opened #250
  • May 11 15:36
    acardona commented #247
  • May 11 12:39
    imagejan commented #230
  • May 11 12:32
    imagejan closed #247
  • May 11 12:32
    imagejan commented #247
  • May 08 19:13
    ctrueden commented #155
  • May 08 19:12

    ctrueden on master

    Bump to next development cycle … (compare)

  • May 08 19:12

    ctrueden on TrackMate_-6.0.0

    [maven-release-plugin] prepare … (compare)

  • May 07 22:36
    ctrueden commented #155
  • May 07 22:36

    ctrueden on master

    Bump imglib2 version to 5.9.2 … (compare)

  • May 07 22:24
    tinevez commented #155
  • May 07 22:23
    ctrueden commented #155
  • May 07 22:23
    ctrueden commented #155
  • May 07 22:22

    ctrueden on update-jgraphx

    (compare)

  • May 07 22:22

    ctrueden on master

    Update to jgraphx 4.1.0 And us… Merge pull request #155 from fi… (compare)

  • May 07 22:22
    ctrueden closed #155
NicoKiaru
@NicoKiaru
Indeed it's back. Thanks!
joebron
@joebron
Thanks again @ctrueden and sorry for disappearing. If you do get any time free, there's a post now on the forum at: https://forum.image.sc/t/map-recorded-pixel-greyscale-to-corrected-predicted-incident-intensity/34134
Curtis Rueden
@ctrueden
@joebron Thanks for circling back. I responded with some scripts.
joebron
@joebron
Thank you! I'll try it out today
Ulrik Günther
@skalarproduktraum
hi everyone! seems imagej.net is down today as well, can't reach the website, updater also doesnt work @ctrueden
Philipp Hanslovsky
@hanslovsky
Can confirm (US East Coast)
Kyle I S Harrington
@kephale
yeek this is becoming quite frequent
Philipp Hanslovsky
@hanslovsky
It's back online
Ulrik Günther
@skalarproduktraum
thanks @hanslovsky :+1:
Curtis Rueden
@ctrueden
Huh... it also seems to happen frequently around the same times now, doesn't it. I wonder if some infrastructure somewhere has some daily jobs. The last few times I checked into the cause, it's always that people somewhere are downloading 100s or 1000s of copies of ImageJ1 (generally the Windows version).
I'm sorry I'm not more of a sysadmin ninja, guys. We need to add some fail2ban rule(s) that block those sorts of attempts more proactively. Like: if you download more than 5-10 copies of a file from the same IP within a short timeframe, you get temporarily banned.
Does anyone here know fail2ban and/or iptables well enough to help with that?
Kyle I S Harrington
@kephale
@ctrueden what about moving downloads to github?
Curtis Rueden
@ctrueden
Does GitHub still host large binaries? I thought they discontinued that years ago? Or are they doing that again?
Anyway, as a first step, it makes sense to just isolate downloads.imagej.net to its own box.
It's ~70GB total right now, with 30GB of that being from the last 4 months since we started archiving Fiji snapshots.
Curtis Rueden
@ctrueden
I've enabled a DoS protection filter for LOCI servers. I'd appreciate it if you could try navigating to imagej.net, click around, see if it works for you—maybe even try updating an out-of-date Fiji and see if it hits the packet limit when doing updates. Hopefully all still works... if not, I'll revert the rule.
Rule is committed.
Curtis Rueden
@ctrueden
For those who didn't already notice: I released pom-scijava 28.0.0 a few days ago, along with imagej 2.0.0-rc-72 and fiji 2.0.0-pre-11. These releases have not been uploaded to the end-user update sites, but are usable as Maven coordinates e.g. from pyimagej. I am in the process of doing a more across-the-board upgrade of dependencies for pom-scijava 29.0.0. I am instituting a new "mega-melt" job that thoroughly tests all components in the SciJava bill of materials together. I'll make a forum post when there is more news about this.
Jean-Yves Tinevez
@tinevez
@ctrueden works for me.
Curtis Rueden
@ctrueden
@tinevez Glad to hear. Did you try a Fiji update? Or just websites?
Jean-Yves Tinevez
@tinevez
websites. All my Fijis are up to date :(
Curtis Rueden
@ctrueden
Hehe, OK. Thanks.
NicoKiaru
@NicoKiaru
Thanks @ctrueden. Looks good for me, website and update sites.
Eric Leroy
@ricounet67
With the change in the Oracle license, I want to know if it is possible to use OpenJDK instead of Oracle Java on Mac OS X . And if so, which distribution should I use: Correto, AdoptOpenJDK, Zulu or an other one? And is there a difference between them?Wich version should I use : 8, 9, 11, 12 or 13?
Curtis Rueden
@ctrueden
@ricounet67 All the different flavors of OpenJDK I have tested work. But there are three important considerations for Fiji right now: 1) Java 8 works best; 2) a JDK is preferred over a JRE if you want to develop Java code from within the Script Editor; and 3) a few plugins use JavaFX, so an OpenJDK including OpenJFX is needed for that, at least when using Java 8.
My favorite distros meeting these requirements right now are:
  1. Zulu JDK 8 + OpenJFX
  2. JBRSDK8 from JetBrains
We are planning to update the Fiji bundled Java very very soon to use JBRSDK8 across all platforms.
An advantage of JBRSDK8 over the Zulu OpenJDK is that the JetBrains runtime includes some backported fixes from later versions of Java, including some graphical improvements that make Scenery + SciView work better.
I hope that answers your question. :-)
Eric Leroy
@ricounet67
thank you it is very clear :-)
Ulrik Günther
@skalarproduktraum
hi everyone! i noticed an issue yesterday with jdk 8u242, stemming from this commit in the jdk: adoptOpenJDK/openjdk-jdk8u@0c0e7e4 -- this kinda screws up the popular fix of setting sys_paths to null via reflection in order to pick up a java.library.path set during runtime for use with System.loadLibrary. after this commit, this still works, but screws up all other native library loading. so when you get a Could not instantiate class: java.awt.Toolkit or something along these lines with 8u242, this is almost certainly the issue. the way to solve this problem is to use System.load with the full paths. scenery and spirvcrossj just got fixes for that, which will also improve compatibilitity with java 12, because then you can't fiddle with sys_paths anymore
Ulrik Günther
@skalarproduktraum
(another workaround, should the sys_paths fiddling still be necessary, is to call ClassLoader.initLibraryPaths after, but that's also a private method, so it has to be done via reflection etc, did not test that one)
oh and, thanks to the jprofiler people for pointing this out on stackoverflow (https://stackoverflow.com/questions/60190879/software-report-the-missing-awt-error-when-start-jprofiler)
Curtis Rueden
@ctrueden
I think we need to avoid the sys_paths fiddling at all costs—at least years ago, my understanding was that this does not even work on all platforms. Does it?
Ulrik Günther
@skalarproduktraum
@ctrueden it worked fine for me on win, osx and linux :+1:
but that code is gone now
and System.load() works just as fine
Jean-Yves Tinevez
@tinevez
The downloads of fiji.sc do not respond . Do you have the same on your side?
Curtis Rueden
@ctrueden
Discussing in the imagej channel now. I'm on it already. Might be fixed momentarily.
Jean-Yves Tinevez
@tinevez
Okay!
...
What is the imagej channel?
Curtis Rueden
@ctrueden
imagej/imagej
Curtis Rueden
@ctrueden
TIL: you can System.out.close();!
Stephan Preibisch
@StephanPreibisch
Hi @/all, I am trying to build a far-jar (https://imagej.net/Uber-JAR) using the shaded maven plugin. However, it still seems to overwrite the annotations from BigDataViewer which manifests in the error:
Loading input XML: dataset.hdf5.xml
Exception in thread "main" mpicbg.spim.data.SpimDataInstantiationException: could not find XmlIoBasicImgLoader implementation for format bdv.hdf5
If anyone has an idea would be great