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  • Feb 18 21:45
    kant commented #196
  • Feb 18 19:55

    ctrueden on master

    Add JFreeSVG library to the Fij… (compare)

  • Feb 18 19:54

    ctrueden on jfreesvg

    WIP: Add JFreeSVG library to th… (compare)

  • Feb 18 19:53

    ctrueden on master

    Travis: fix uploading of compon… (compare)

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  • Feb 18 19:49

    ctrueden on master

    Add forum.image.sc badge to REA… Merge pull request #212 from fi… (compare)

  • Feb 18 19:49
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    ctrueden on add-forum-badge

    Add forum.image.sc badge to REA… (compare)

  • Feb 18 19:47
    ctrueden commented #196
  • Feb 18 19:46

    ctrueden on master

    Format Image.sh command in back… Merge pull request #196 from ka… (compare)

  • Feb 18 19:46
    ctrueden closed #196
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  • Feb 18 16:45
    cooketho closed #241
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  • Feb 18 03:22
    rasband commented #241
  • Feb 17 17:09
    imagejan commented #241
  • Feb 17 16:41
    cooketho commented #241
  • Feb 14 20:48

    ctrueden on fiji-2.0.0-pre-11

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

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.
Curtis Rueden
@ctrueden

@FreyaGoetz

If there is a more preferred way to share these errors, I'm happy to try that.

It would be great if you could post on the ImageJ Forum: http://forum.imagej.net/

Before you do that... to troubleshoot very quickly here:
If you are using the Java-6 version of Fiji, try enabling the Fiji-Legacy update site.
Otherwise, try switching to the Java-8 version. You can do that easily by simply downloading Fiji again.
More information available at: https://imagej.net/Java_8
I suspect you are using the Java-6 version of Fiji, and so enabling Fiji-Legacy will solve it for you.