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  • Oct 21 15:59

    ctrueden on jfreesvg

    WIP: Add JFreeSVG library to th… (compare)

  • Oct 18 08:46

    tinevez on fix-no-tags-crash

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  • Oct 17 13:19
    yifnzhao commented #82
  • Oct 17 12:23

    tpietzsch on master

    Fix crash: assigning tags when … Merge pull request #108 from fi… (compare)

  • Oct 17 12:23
    tpietzsch closed #108
  • Oct 17 11:24
    tinevez opened #108
  • Oct 17 11:24

    tinevez on fix-no-tags-crash

    Fix crash: assigning tags when … (compare)

  • Oct 15 10:36
    DeboraOlivier closed #138
  • Oct 15 09:03
    DeboraOlivier opened #138
  • Oct 07 20:13
    ctrueden commented #7
  • Oct 07 20:11
    ctrueden closed #7
  • Oct 07 20:11

    ctrueden on master

    Fix packaging of "F div F0" scr… (compare)

  • Oct 07 15:52

    tinevez on master

    Make the SparseLAPFrameToFrameT… (compare)

  • Oct 02 12:55
    ctrueden closed #226
  • Oct 02 12:55
    ctrueden commented #226
  • Oct 02 11:28
    ctrueden commented #211
  • Sep 30 13:45

    ctrueden on master

    POM: update Kota Miura GitHub ID Comment out plugins.dir assignm… Remove the IJ_Alt_Key_Listener … (compare)

  • Sep 27 12:27
    ctrueden commented #234
  • Sep 26 19:17
    imagejan commented #234
  • Sep 26 19:17
    imagejan commented #234
Curtis Rueden
@ctrueden
@kapoorlab You want to make a 3D display then, it sounds like? TrackMate does it using the 3D Viewer, but the 3D Viewer is on its way out unfortunately.
Varun Kapoor
@kapoorlab
@ctrueden Ok then if I could link my program to trackmate visualization utilities that would be great, I want to come in with a graph or a model made from a graph and then call trackmate utilities to visualize, is that possible @tinevez, anz example on how an external java program can call trackmate visualization part of the library?
Jean-Yves Tinevez
@tinevez
@kapoorlab The best is to check the https://imagej.net/Scripting_TrackMate page.
Here I use a Model object programmatically to create some spots and links and then to show them.
matrixbot
@matrixbot
superusercode test
superusercode Does Fiji have an IRC room?
Varun Kapoor
@kapoorlab
@tinevez Merci beaucoup, it looks exactly what I was looking for, I will try to use this and let you know if I faced any issues.
Kabouik
@Kabouik
Hi, is there a way to reorder ROI according to y AND x coordinates ? Or manually with clicks? The Sort button seems to work only on y coordinates.
Kabouik
@Kabouik
Nevermind, my sample was not so big so I just worked around by exporting the measurement results one by one in the order I needed.
Curtis Rueden
@ctrueden
@matrixbot It does! But it's not very active. I usually see posts there after a few days, long after whoever asked the question has given up and left. -_- So I would not recommend using it.
You should use http://forum.imagej.net/, or here if you want to discuss code.
matrixbot
@matrixbot
superusercode I'll just keep accessing gitter through matrix then.
Kabouik
@Kabouik
Last year I used a folder batch .ijm script that I wrote based on that: https://imagej.net/Batch_Processing
Now I am trying to run it again, on the same folders, and I get an error because my script starts with "@" (the three lines defining input folder, output folder and suffix). I tried commenting them out with either "//" or "#", but of course then the following lines don't work because they do not know input.
Was there an update breaking this syntax, or is it possible that I edited the script in a wrong text editor that removed some important symbols due to wrong syntax highlighting?
Jan Eglinger
@imagejan
@Kabouik the syntax is explained here: https://imagej.net/Script_Parameters
// @ is legacy and works
#@ is current recommendation
independent of the script language you choose
Kabouik
@Kabouik
None of them work, I suppose there are other changes to apply to my script then
Jan Eglinger
@imagejan
If in doubt, please open a topic on the forum with some example code and your installation details
Kabouik
@Kabouik
But it that something that changed since last year? I wonder why my script was even starting with @ and not // if it didn't work back then (probably did a mistake with some alternate versions of the script)
For instance, with the current recommendation, I get an error from line 1: Statement cannot begin with "#" in line 1.
Curtis Rueden
@ctrueden
@Kabouik The script syntax was enhanced, but it is supposed to be backwards compatible. If not, it is a bug. If you post the first 10 lines of your script, it would be helpful for analysis.
Kabouik
@Kabouik

@ctrueden The script is short so it pasted it full here: https://hastebin.com/iwexirecox.php
This is with the #@, but it doesn't work here. Last time I used it successfully was last year so I don't quite remember the details. When I opened it today, there was no // or # before the "@". Perhaps that was an error, this was my first ImageJ script so I am not familiar with the syntax, but is that possible that it worked like that anyway last year?

In any case, it doesn't work now, fails right from these parameters at the top.

I can open a thread on the forum if that is easier, but it looks like I just got the syntax wrong somwhere, might not be worth cluttering the forum for a simple typo in a script.
Kabouik
@Kabouik
Also, I get the same error if I do File/New/Script and Templates/ImageJ 1.x/Examples/Process folder (IJ1 macro), save the script, and execute it. FiJi says that the line 5 cannot start with #.
Kabouik
@Kabouik
Alright it seems to work with the button "RUN" from the script editor (and "#@"), but not from Plugins/Macros/Run (weird, because I have another script that works from there). And I needed to edit the first lines to replace "style" with "value" to prefill the window asking for input and output paths.
Kabouik
@Kabouik
Thanks @imagejan, @ctrueden, for pointing into the right direction.
amirffff
@amirffff
Hi everyone
does someone programming with imageJ/Jthon and can help me please?
Curtis Rueden
@ctrueden
@Kabouik The Plugins/Macros/Run is an ImageJ 1.x command, which has not been tested with ImageJ2 scripts. Sorry for the confusion there.
@Kabouik The syntax looks correct, apart from the style attribute being used incorrectly, yeah.
The script should work if you press Run in script editor, and it should work if you place it into $IMAGEJ_DIR/scripts/Foo/Bar. Then it will appear in the Foo > Bar menu and should work from the menus, as well.
Curtis Rueden
@ctrueden
NOTICE: The ImageJ server infrastructure will be going down within the next few minutes. Downtime should be short (less than 10 minutes).
Curtis Rueden
@ctrueden
Servers should all be back online; please ping if you notice otherwise.
li8
@liberium_li8_twitter
I have taken several microscopy images through a camera but I can't upload then to Image J unless I use bio-format importing. The problem is that in this way I can't apply the color threshold, as it doesn't work properly, with all 3 items (Hue, saturation and brightness) appearing blank. Any ideas?
Jan Eglinger
@imagejan
@liberium_li8_twitter bio-formats will import as multi-channel hyperstack. Try converting to RGB first before using color threshold.
li8
@liberium_li8_twitter
It worked! Thank you very much! Have a nice day!
Varun Kapoor
@kapoorlab
Hi, what do I have to write in my pom.xml so that I can write import fiji.plugin* in my java code?
Jan Eglinger
@imagejan
@kapoorlab you can search http://maven.imagej.net for the classname you want to import, it will give the the necessary xml snippet for your POM
(and you shouldn't use wildcard imports, of course ;-)
Varun Kapoor
@kapoorlab
@imagejan Thanks :) no wildcards, ok am getting an error which I do not understand:
Failure to transfer sc.fiji:TrackMate_:jar:3.6.1 from http://maven.imagej.net/content/groups/public was cached in the local repository, resolution will not be reattempted until the update interval of imagej.public has elapsed or updates are forced.
tpietzsch
@tpietzsch
That means maven tried to download sc.fiji:TrackMate_:jar:3.6.1 and failed for some reason
It will not reattempt to download for some period of time
instead remember that this failed
you can force it retry by running with -U option
(e.g. mvn clean package -U)
@kapoorlab
Varun Kapoor
@kapoorlab
@tpietzsch yeah it is the reason thats bugging me, i will try force, clean with/without wifi/ethernet. Thanks Tobias
Curtis Rueden
@ctrueden
@kapoorlab If you still have trouble, you can also rm -rf ~/.m2/repository/sc/fiji/TrackMate_. This is sometimes necessary if a JAR file is corrupted during download.
amirffff
@amirffff
HI can I ask a question the manager of this Chat?