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  • Aug 22 17:44
    ctrueden commented #205
  • Aug 16 17:34
    acardona opened #231
  • Aug 07 13:48
    chalkie666 opened #230
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:32
    tinevez opened #107
  • Aug 02 13:30
    tinevez commented #106
  • Aug 02 13:29
    tinevez synchronize #106
  • Aug 02 13:29

    tinevez on serialize-feature-model2

    Avoid feature name inflation wh… Update the MaMuT exporter examp… (compare)

  • Jul 18 11:57
    tpietzsch commented #106
  • Jul 18 11:44
    tinevez commented #106
  • Jul 18 11:41
    tpietzsch commented #106
  • Jul 18 11:32
    tinevez commented #106
  • Jul 18 11:31
    tpietzsch commented #106
  • Jul 18 11:20
    tpietzsch synchronize #106
  • Jul 18 11:20

    tpietzsch on serialize-feature-model2

    formatting Demonstrate that feature names … Add TODO and 2 more (compare)

  • Jul 10 13:08
    tinevez closed #104
  • Jul 10 13:08
    tinevez commented #104
  • Jul 10 13:08
    tinevez opened #106
  • Jul 10 10:56

    tinevez on serialize-feature-model2

    Fix weird compile error with Op… Make some static methods of MaM… JUnit test for the TrackMate im… and 5 more (compare)

Ulrik Günther
@skalarproduktraum
the renderer can also pretty much take any number of lights, i tested it up to 256 (which is the uniform array limit of my notebook’s GPU :D)
Kyle I S Harrington
@kephale
oh awesome, not stuck with that low limit on lights from OpenGL!!
Ulrik Günther
@skalarproduktraum
deferred lighting rocks ^^
and as you can see in the video above, there is also ambient occlusion, for better depth perception… though the algorithm and it’s parameters still deserve a little bit of tuning :D
oh and i forgot curtis’ repl… that’s quite high up on the priority list. so with the stuff i mentioned, it’ll be ready for a spin in about 1-2 weeks
Brian Northan
@bnorthan
I just tried to run the latest 32 bit Fiji and got
Could not reserve enough space for 1572864KB object heap
Java HotSpot(TM) Client VM warning: ignoring option PermSize=128m; support was removed in 8.0
Anybody know what the problem could be?? I don't usually use the 32 bit version, but I'm helping someone who is still working on a 32 bit computer.
Richard Domander
@rimadoma
Well this is a stupid question, but how much physical memory is actually available for ImageJ? Even if the computer has the maximum addressable amount (4 GB), it might not be all free to use, e.g. a built-in video card might be using some of System RAM
Brian Northan
@bnorthan
OK got it working. I had to create ImageJ.cfg and make sure that the max memory was set <1500m
For some reason ImageJ1 cannot allocate more than about 1.5 GB of memory on 32-bit systems
Curtis Rueden
@ctrueden
@bnorthan I guess the IJ launcher is being too aggressive when it guesses how much RAM to allocate to Java. Some 32-bit systems max out as low as 1.3GB in my experience. :-(
The JavaFX launcher will behave differently so we can fix the problem as part of that work.
Brian Northan
@bnorthan
@ctrueden, @rimadoma thanks. I'm not sure what it uses for the initial guess, or how that works. I did not see a ImageJ.cfg file in the fresh installation... but as soon as I added one, and set the max memory to 1000m it worked fine.
Curtis Rueden
@ctrueden
It uses 2/3 of your system RAM IIRC. The code is somewhere in the imagej/imagej-launcher project.
Or it might be 3/4.
kephale @kephale just noticed drag-and-drop of scripts onto the toolbar doesn't seem to invoke the fancy scijava eval/parsing/annotation
Ignacio Arganda-Carreras
@iarganda
@ctrueden and @hinerm I just realized my MorphoLibJ pom has scijava-pom as parent (i guess because I copied the pom from the old minimal-ij1-plugin example). What is the policy now? using pom-imagej, right?
Jan Eglinger
@imagejan
@iarganda that depends on what bill of materials you want to use. Your dependency on Jama can use the managed version from pom-scijava, but to also profit from the managed versions for ImageJ components, you should use pom-imagej I guess.
( @ctrueden , @hinerm correct me if I'm wrong)
Curtis Rueden
@ctrueden
@imagejan Precisely. And if you need to depend on Fiji plugins then use pom-fiji as parent.
Depending on pom-imagej (or descendent thereof) also inherits the imagej-maven-plugin config and probably other goodies.
Ignacio Arganda-Carreras
@iarganda
OK, makes sense, thanks a lot @imagejan and @ctrueden !
Curtis Rueden
@ctrueden
@iarganda Be sure to check the <description> tag of the POM parent you are using, since it lists all the XML elements you should override. Otherwise, you might inherit some erroneous configuration (e.g., the wrong license declaration).
You can use mvn help:effective-pom on your project to verify that everything looks good.
Stefan Helfrich
@stelfrich
@tinevez: I just stumbled over a TrackMate_-3.0.0.jar in one my user’s Fiji installations. How did that happen?
Jean-Yves Tinevez
@tinevez
Automatic version changed when everything was updated with java8 and 3D.
I don't know what to do with it.
Stefan Helfrich
@stelfrich
Ah ok. So it’s TrackMate(2)-3.0.0 instead of TrackMate3-1.0.0?
Jean-Yves Tinevez
@tinevez
Yep.
Stefan Helfrich
@stelfrich
Hmm. That’s.. unfortunate.. but oke. I was just wondering
Jean-Yves Tinevez
@tinevez
@ctrueden Is it something I could do about the 3.0.0 version of TrackMate? Could I release a new version with a proper 2.9.0 (for instance) without breaking everything?
Curtis Rueden
@ctrueden
It comes down to the fact that SemVer is incompatible with "romantic versioning"
In other words: you cannot hold off on 3.0.0 forever—SemVer demands the major version bump whenever some backwards incompatible change occurs.
One way people get around this is to use four digits: with the leftmost being the "romantic" one.
I.e.: the marketing one: big huge change with everything new!
I apologize that a TrackMate 3.0.0 was necessary, but IIRC it was needed due to the Java 3D changes.
One option is not to use the numeral for the new version of TrackMate, but instead "TrackMateX" or something. Or: just don't worry about it, and rebrand the artifact as TrackMate again once it is ready, with the next major version digit.
I don't have all the answers here: otherwise we wouldn't have a thing called "ImageJ2" ... :worried:
Stefan Helfrich
@stelfrich
Thanks to you @ctrueden, I will never stop learning new things, like "sentimental versioning”. :clap:
Curtis Rueden
@ctrueden
Hehehe
tpietzsch
@tpietzsch
Speaking of TrackMate3: YEsterday, trying to demo it, I ran into the Java8-Fiji issue
I had told people to update Fiji beforehand, but that doesn't bring in the java8 updates.
Can someone point me to best practices or something on the wiki?
I guess: Reinstall Fiji?
Stefan Helfrich
@stelfrich
Had a similar issue today. Only solution: reinstall
tpietzsch
@tpietzsch
Ok
I thought so
...
Stefan Helfrich
@stelfrich
I couldn’t even get any error message..
tpietzsch
@tpietzsch
Oh... then you ran into something different