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  • 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
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    tinevez opened #107
  • Aug 02 13:30
    tinevez commented #106
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  • 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
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    tinevez commented #106
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    tpietzsch commented #106
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  • 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)

  • Jul 09 11:01

    tinevez on serialize-feature-model2

    Move test data to proper packag… WIP: Junit test for MaMuT expor… (compare)

Curtis Rueden
@ctrueden
If your data is large you can open it as a cell image using the SCIFIOConfig settings, and it will page in cells on demand.
Curtis Rueden
@ctrueden
@skalarproduktraum If you use the toplevel interface and the endianness still seems wrong, let us know—then I'll concede it's probably a bug.
Ulrik Günther
@skalarproduktraum
@ctrueden: yes, i actually need it quite low level, primarily for performance reasons
so i’d rather get around the imglib2 data structures
Curtis Rueden
@ctrueden
@skalarproduktraum But if the high level API is not performant, we need to fix that.
Fair enough.
You could:
Ulrik Günther
@skalarproduktraum
just fyi, i have the same code in c++, using libtiff, there it works
Curtis Rueden
@ctrueden
  • try high level anyway momentarily just to see if the endianness bug still occurs—if not, then dig in to find out how the calls are different than what you are doing
  • try Bio-Formats's TiffParser and see if it suffers the same.
Ulrik Günther
@skalarproduktraum
do you have a snippet somewhere how to use the inservice/datasetioservice? i got the openPlane, etc code from the scifio tutorials on github
Curtis Rueden
@ctrueden
Check this.
In your case, you could either A) reuse the existing SciJava context, if you have one already; or B) use new SCIFIO() instead of new ImageJ() since you are SCIFIO-focused here.
And lastly: I apologize that SCIFIO still sucks so much. The fact is that we have not had time to work on it much over the past 2 years. But it is a critical piece of ImageJ2, so we do need to work on it (eventually ;-)).
Ulrik Günther
@skalarproduktraum
no problem, big thanks for the hints :)
Jean-Yves Tinevez
@tinevez
@thorstenwagner just contributed a new detector to TrackMate:
https://github.com/thorstenwagner/ij-trackmate-findmaxima
Hadrien Mary
@hadim
Nice !
Curtis Rueden
@ctrueden
@/all Expect some Fiji server downtime in coming days, as we migrate services.
Curtis Rueden
@ctrueden
OK, @/all: bad news. The imagej.net wiki, and Fiji BugZilla, need to go down for extended maintenance now. They may be down for as long as several days. I will be pushing to get it fixed ASAP, but if you need to access those services, I suggest you do so imminently.
Stephan Saalfeld
@axtimwalde
Hi @ctrueden update.fiji.sc does not work since yesterday. Is that related?
Curtis Rueden
@ctrueden
@axtimwalde Yes, it is related. Thanks for the heads up. Although: does it work for you right now? It is working for me.
(You may not be able to upload right now... but downloading should work.)
The IP address changed—it is now 144.92.48.178. Maybe your DNS did not update yet.
Stefan Helfrich
@stelfrich
@ctrueden Got a time-out some minutes ago..
Curtis Rueden
@ctrueden
@stelfrich Probably a firewall issue. Looking.
Stefan Helfrich
@stelfrich
IP is resolved correctly
Stephan Saalfeld
@axtimwalde
still timing out, but don't bother and get the servers fixed first, I wasn't planning on downloading updates but to set up a new update site. I built Fiji from fiji/fiji master rather than updating through the updater since I am still paranoid about executing binaries that are delivered without encryption.
not the right time for setting up a new update site I guess.
Curtis Rueden
@ctrueden
@axtimwalde Getting the firewall straight is part of this whole process. I expect to have update.fiji.sc fixed in a few minutes. I am doing lots of firewall cleanup. That new IP address just needs to whitelist port 80. I will let you guys know when it is ready.
Yeah, sorry, I would not recommend trying to set up an update site this week. :-(
@axtimwalde @stelfrich Any luck now?
Stefan Helfrich
@stelfrich
@ctrueden works as expected! :+1:
Curtis Rueden
@ctrueden
Great, thanks for testing.
Stephan Saalfeld
@axtimwalde
yes, works, thanks!
Curtis Rueden
@ctrueden
@stelfrich Would you mind checking whether you can access wiki.imagej.net ? I am curious.
Stefan Helfrich
@stelfrich
@ctrueden Works as far as I can tell..
Curtis Rueden
@ctrueden
@stelfrich Thanks.
Curtis Rueden
@ctrueden
@stelfrich Are you sure? You are using wiki.imagej.net, right? NOT imagej.net?
@stelfrich Because I cannot for the life of me figure out how that could possibly be working from off campus.
Stefan Helfrich
@stelfrich
@ctrueden Now I get an “Under maintenance” site..
Curtis Rueden
@ctrueden
Yeah, I went ahead and changed it to that.
Thanks.
Stefan Helfrich
@stelfrich
wait
➜ ~ ping wiki.imagej.net PING wiki.imagej.net (144.92.48.177): 56 data bytes Request timeout for icmp_seq 0
Meaning that I get a timeout when pinging but can connect via http
tested with curl, no caching involved
Curtis Rueden
@ctrueden
@stelfrich It's too late now; I updated the DNS entry to point to a new IP.
It used to point to 144.92.48.154 which was firewalled—hence my confusion when you said you could connect.
My theory is that you tested imagej.net and not wiki.imagej.net earlier.
Otherwise, I am stumped how it was working for you.