These are chat archives for fiji/fiji

29th
Jan 2019
Hadrien Mary
@hadim
Jan 29 19:32
@ctrueden I still have conflicts when trying to upload a package to an update site from travis: https://travis-ci.org/hadim/Hadim_Scripts/builds/486067914#L1091
My Scijava version in the pom file is 24.2.0 the same has the last fiji release.
Curtis Rueden
@ctrueden
Jan 29 19:39
@kapoorlab Please file an issue at https://github.com/imagej/imagej/issues about the recent files skew. It may not be an easy problem to fix, though, since it relates to the boundary between ImageJ2 and ImageJ1.
@hadim I am looking now...
Hadrien Mary
@hadim
Jan 29 19:42
Thanks @ctrueden. It's not urgent and neither very important as I can still upload manually. But if you know an easy fix, I'll take it :-)
Curtis Rueden
@ctrueden
Jan 29 20:47
@hadim I think I see the problem. You are doing Upload only "jars/hadim-scripts.jar". which executes $IJ_LAUNCHER --update upload --update-site "$UPDATE_SITE_NAME" --force-shadow --forget-missing-dependencies "jars/$NAME.jar" but then there are changed dependencies, hence the conflicts. Better would be not to do the mvn clean install -Dimagej.app.directory=… at all then, because it just installs dependencies that you don’t intend to upload.
So, maybe the upload-update-site.sh script in fiji/fiji should, if $UPLOAD_WITH_DEPENDENCIES is set to false, not copy in anything except the main artifact in target during the “Install project to Fiji directory” step?
Hadrien Mary
@hadim
Jan 29 20:50
@ctrueden ok so then I would move mvn clean install in the else statement and use the JAR file inside the target directory?
Will make a PR within a few days.
Thanks!
Curtis Rueden
@ctrueden
Jan 29 20:53
@hadim I think so… would be good to do some local testing first if you can.
Hadrien Mary
@hadim
Jan 29 20:53
Of course.
Maybe a cleaner way would be to disable copying dependencies during mvn clean install?
Is that possible from the command line?
Curtis Rueden
@ctrueden
Jan 29 20:55
Just don’t pass the -Dimagej.app.directory.
Oh, you mean to still copy the main artifact.
Hadrien Mary
@hadim
Jan 29 20:55
Yes but I want my artifact to be copied.
yes :-)
Curtis Rueden
@ctrueden
Jan 29 20:55
Hmm… let me check the documentation of the scijava-maven-plugin.
Hadrien Mary
@hadim
Jan 29 20:55
I can do it manually if it's not possible.
It does not seem possible from the README and actually it makes sense since you always want to copy deps with your artifact...
Curtis Rueden
@ctrueden
Jan 29 20:58
Aha! You can do it. -Dscijava.ignoreDependencies=true.
Hadrien Mary
@hadim
Jan 29 20:59
!!!
Great.
I'll use that then.
Curtis Rueden
@ctrueden
Jan 29 21:01
🤞 that it works!
firewater334
@firewater334
Jan 29 21:06
Hi are there edgefinding macros/commands in fiji? If I want to detect the locations of edges of an image and summarize those locations in a pop-up window (GUI) are there commands or already built in macros for that? Thanks!
Curtis Rueden
@ctrueden
Jan 29 21:43
@firewater334 There are several things. Process > Find Edges is the simplest one.
You can use thresholding to select the highlighted edges. But if you want something more sophisticated like fiber analysis (lengths, thicknesses, orientation), that is a different thing.
Post to https://forum.image.sc with more details about what you are trying to achieve, and image analysts can comment in more detail.