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  • 17:09
    imagejan commented #241
  • 16:41
    cooketho commented #241
  • Feb 14 20:48

    ctrueden on fiji-2.0.0-pre-11

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

  • Feb 14 20:48

    ctrueden on master

    Travis: improve imagej version … POM: update parent to pom-scija… (compare)

  • Feb 12 21:58
    cooketho opened #241
  • Feb 12 14:23
    ctrueden opened #240
  • Feb 12 14:19
    ctrueden reopened #235
  • Feb 12 14:19
    ctrueden closed #235
  • Feb 10 12:18
    tinevez labeled #152
  • Feb 09 04:38
    snownontrace edited #152
  • Feb 09 04:36
    snownontrace opened #152
  • Feb 06 20:43

    tinevez on no-new-contexts

    (compare)

  • Feb 06 20:43

    tinevez on master

    TMUtils: add utility method to … Use existing SciJava Context C… Merge pull request #151 from fi… (compare)

  • Feb 06 20:43
    tinevez closed #151
  • Feb 06 20:43
    tinevez closed #149
  • Feb 06 17:34
    ctrueden review_requested #151
  • Feb 06 17:34
    ctrueden review_requested #151
  • Feb 06 17:33
    ctrueden opened #151
  • Feb 06 17:33

    ctrueden on no-new-contexts

    TMUtils: add utility method to … Use existing SciJava Context C… (compare)

  • Feb 06 17:23
    ctrueden commented #150
Curtis Rueden
@ctrueden
@bogovicj One other thing: can you enable Travis for trakem2-tps?
John Bogovic
@bogovicj
@ctrueden enabled!
Curtis Rueden
@ctrueden
@iarganda I am trying to migrate all component builds away from the ImageJ Jenkins, with the hope that I can eventually shut it down, or at least scale it back to be extremely minimal. Would you be willing to change MorphoLibJ over to Travis CI?
If so, visit this URL: https://travis-ci.org/ijpb/MorphoLibJ
You'll need to give Travis some permissions, and click the + symbol in the left-hand column, and enable MorphoLibJ Travis builds. If you do that, I'll file a PR on the GitHub side that updates the code to use it.
Curtis Rueden
@ctrueden
@fjug Same for indago etc.—any chance you can switch those over to Travis soon? Perhaps we can take care of it when I am there in person.
Jan Eglinger
@imagejan
I just noticed that the FFMPEG update site ships a jna-3.2.7.jar that is shadowing the jna-4.2.2.jar from the Java-8 update site. As we keep recommending the FFMPEG site on https://imagej.net/Video I'd like to prevent running into some breaking version skew in the future... @ctrueden can we stop shadowing jna from the FFMPEG site, as it ships with the Java-8 site now??
Jan Eglinger
@imagejan
Well, I see that there's incompatible API, so FFMPEG doesn't work with jna 4.x...
Jan Eglinger
@imagejan
The JNA major version was bumped in this commit scijava/pom-scijava@8f423f1, but I'm unsure what other projects depend on it.
Florian Jug
@fjug
@ctrueden absolutely no problem. I think you are right, it would make the most sense to do that together once you are here...
Jan Eglinger
@imagejan
@ctrueden didn't you mention at some point that the original repo for Fiji's FFMPEG_IO was lost during the transition from the old fiji.sc server? The source is still available on a few locations (https://github.com/erisir/FIJI/tree/master/native/FFMPEG_IO and https://github.com/william-grimes/fiji/tree/master/native/FFMPEG_IO ), so we can maybe move it back to the Fiji org and put it on an imagej.net update site?
Curtis Rueden
@ctrueden
@imagejan The history for that update site is in scifio/scifio-javacv.
I am very reluctant to resurrect it. I already tried two times, and could not make it build reproducibly.
Curtis Rueden
@ctrueden
@imagejan As for which projects use jna:
$ grep '>jna<' */*/pom.xml
clearvolume/scenery/pom.xml:            <artifactId>jna</artifactId>
fiji/CPU_Meter/pom.xml:            <artifactId>jna</artifactId>
fiji/SPIM_Registration/pom.xml:            <artifactId>jna</artifactId>
loci/flow-cytometry/pom.xml:            <artifactId>jna</artifactId>
scijava/pom-scijava/pom.xml:                <artifactId>jna</artifactId>
slim/curve-fitter/pom.xml:            <artifactId>jna</artifactId>
I bet they hardcode version 3... let's see.
clearvolume/scenery/pom.xml:            <artifactId>jna</artifactId>
clearvolume/scenery/pom.xml-            <version>4.2.2</version>
--
fiji/CPU_Meter/pom.xml:            <artifactId>jna</artifactId>
fiji/CPU_Meter/pom.xml-        </dependency>
--
fiji/SPIM_Registration/pom.xml:            <artifactId>jna</artifactId>
fiji/SPIM_Registration/pom.xml-        </dependency>
--
loci/flow-cytometry/pom.xml:            <artifactId>jna</artifactId>
loci/flow-cytometry/pom.xml-            <version>3.0.9</version>
--
scijava/pom-scijava/pom.xml:                <artifactId>jna</artifactId>
scijava/pom-scijava/pom.xml-                <version>${jna.version}</version>
--
slim/curve-fitter/pom.xml:            <artifactId>jna</artifactId>
slim/curve-fitter/pom.xml-            <version>3.2.2</version>
Heh, I guess I'll have to update flow-cytometry and curve-fitter, eventually.
Curtis Rueden
@ctrueden
For those who use legacy Fiji plugins such as the old script interpreter plugins (e.g., BeanShell_Interpreter): they just moved to a separate update site called Fiji-Legacy.
I will explain in more detail soon in a news post and forum post, but I wanted to give you a heads up (particularly you @axtimwalde) because I didn't want you to get a rude shock thinking these plugins have been deleted. They haven't—they just moved. They never made the transition to stable releases, but I know they are still useful, so I put all that stuff onto a new Fiji-Legacy site.
Gotta run; please ping back if you see any huge problems with this.
Stephan Saalfeld
@axtimwalde
Thanks for the warning and for keeping things up @ctrueden!
caboosechief
@caboosechief
Hi I am using FIJI(IMAGEJ)
I want to open multiple oif files on mac but it cannot be opened, is there any plugin that i need to install . Please advise
Stefan Helfrich
@stelfrich
Hi @caboosechief. Could you please ask that question at http://forum.imagej.net? This way, it will be more visible for others with the same question..
Jan Eglinger
@imagejan

Can anybody tell me in which repository the Make_Screencast.bsh script is located? I discovered that

  • it causes the ScriptProcessor to output:

    [WARNING] Unknown script language: /bin/sh
  • trying to run it will throw a NoClassDefFoundError:

    java.lang.NoClassDefFoundError: Process (wrong name: imageware/Process)
      at java.lang.ClassLoader.defineClass1(Native Method)
      at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
      at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
      at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
      at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
      at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
      at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
      at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
      at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
      at java.lang.Class.forName0(Native Method)
      at java.lang.Class.forName(Class.java:348)
Jan Eglinger
@imagejan
(The latter is due a name collision between imageware from the BIG-EPFL update site and Java's own java.lang.Process)
We should get rid of that CLI hack. Johannes was fond of it, but I don't want to support it. It isn't necessary; you can use fiji --run Make_Screencast.bsh and in fact that is better anyway because SciJava will handle the parameters etc. properly.
I love the cleverness, but now it causes problems with the new #! processor, and I don't want to add a hack to SciJava just to ignore it.
Jean-Yves Tinevez
@tinevez
Hi @ctrueden. I would like to use Travis CI for another TrackMate module repo. This one: https://github.com/tinevez/TrackMate-TrackAnalysis.
Is it enough to follow the instructions of https://github.com/tinevez/TrackMate-TrackAnalysis and the copy/paste the keys we used for another repo?
Curtis Rueden
@ctrueden
@tinevez The tricky part is adding the encrypted env vars. IIRC, I pasted you the shell script I use here on gitter in the past. I cannot make it public because it has the two env var values embedded.
I could put the script in a private repo and then give trusted folks like yourself read access. The tokens/passwords in question let you 1. deploy anything to the ImageJ Maven repo; and 2. Trigger an ImageJ Jenkis job which reacts to Travis builds.
Simpler is for me to just file a PR against TrackAnalysis adding the Travis config.
Some day, perhaps everyone will deploy somewhere more general like bintray or OSS sonatype, using thr own credentials, and this problem will disappear.
Jean-Yves Tinevez
@tinevez
Ok!
Philipp Hanslovsky
@hanslovsky
@ctrueden I don't know if you remember: I recently started my own update site but wasn't able to upload anything and I didn't see any error messages. I just tried again after updating my FIJI and it worked. So that is not an issue anymore.
Curtis Rueden
@ctrueden
@hanslovsky Glad to hear it is working now.
Curtis Rueden
@ctrueden
@tinevez tinevez/TrackMate-TrackAnalysis#1
Jean-Yves Tinevez
@tinevez
Success! Thanks @ctrueden
Curtis Rueden
@ctrueden
:+1:
Fevzi Kafexhiu
@fevzikafexhiu_twitter
Hello there, I kindly as anyone who can tell me how to save my table results in form of tab-delimited csv file. It used to be like that before I updated the FIJI, now it saves the tables in form of comma-delimited csv file!
Thanks in advance!
Ignacio Arganda-Carreras
@iarganda
@ctrueden I have just read your message about MorphoLibJ and Travis. I have followed your instructions, so I hope everything is OK now.
Curtis Rueden
@ctrueden
@fevzikafexhiu_twitter This changed in ImageJ 1.x. There is a setting in the options now IIRC.
Or try putting tsv for extension.
FreyaGoetz
@FreyaGoetz
Hi all, I hope this is the right place to get some help. I'm working on aligning slices in a tiff stack using TrakEM2 and I hadn't restarted Fiji for a while. I just restarted Fiji and accepted all updates. Now when I try to start a new(blank) trakEM2 project I get a bunch of erros. I'm not sure how to paste screen shots but I'll try.
image.png
image.png
image.png
If there is a more preferred way to share these errors, I'm happy to try that.