These are chat archives for fiji/fiji

19th
Apr 2016
Nico Stuurman
@nicost
Apr 19 2016 03:33
Running Windows 10 and using the Fiji updater. Found that it continuously complains about "being in a protected environment', meaning that it is in "Program Files". Funny thing is that the updater otherwise works fine (because I have myself full permissions in the Security section of the Fiji folder's properties). It is much nicer to have Fiji in the appropriate location rather than a random place. Is there anyway to suppress those warnings (or better, have them check if the directory is writable)?
Brian Northan
@bnorthan
Apr 19 2016 12:15
@ctrueden those notebooks are really nice. What is the intended audience?? Are you considering using KNIME as well??
Curtis Rueden
@ctrueden
Apr 19 2016 12:31
@nicost You would have to patch the imagej-updater code. Add an environment variable that tells the updater to behave differently. PRs warmly accepted.
@bnorthan We would love to show KNIME at AQLM but Ellen and I do not feel qualified. :-(
I would love to see more notebooks like Lee's and Kevin's in a public & central location.
The challenge, just like the wiki and any docs, is: 1) to organize them well; and 2) to keep them working and correct over time.
Brian Northan
@bnorthan
Apr 19 2016 13:40
@ctrueden it would be really awesome to have notebooks in a central location. I have taught a beginner data analysis course the last couple of years, and have a lot of simple examples that I think could be useful for people learning.
I'd be happy to contribute them to a central repository.
Nico Stuurman
@nicost
Apr 19 2016 16:52
@ctrueden OK, I'll get on it.
Curtis Rueden
@ctrueden
Apr 19 2016 16:54
@nicost The initial update check's logic is here.
When you say "protected environment" do you mean "protected location"? Because I don't think the ImageJ updater component uses the exact term "protected environment"—if you are seeing that, it might be caused by something else.
Nico Stuurman
@nicost
Apr 19 2016 16:57
@ctrueden Not at that machine right now, but I may not have copied that message precisely. It sure looked like it came from the updater. Will pick this up as my night time project;)
Curtis Rueden
@ctrueden
Apr 19 2016 16:59
Thank you! I think it would be a worthwhile enhancement to add some customizability for that.
BTW: when we switch how ImageJ is deployed—stop using the ImageJ Launcher component in favor of a JavaFX-based launcher, later this year—we will also be looking at solving imagej/imagej#72, which would largely eliminate the need for the Program Files case logic.
@bnorthan How about https://github.com/imagej/imagej-notebooks ? Should I create it now?
Or without the imagej- prefix. I am not sure which way is better for such things.
Nico Stuurman
@nicost
Apr 19 2016 17:12
@ctrueden imagej/imagej#72 looks like a much better, and possibly simpler solution to me. Years ago I setup the Inno installer in Micro-Manager and it should not be too hard to build one for Fiji. Is that more useful, or will there be other aspects of the distribution model that would need to accommodate such a change?
Brian Northan
@bnorthan
Apr 19 2016 17:23
@ctrueden I think either way would be fine. I would envision some notebooks being imagej related (that is how to use imagej/scijava components in a notebook) and some generic (tutorials on how to use note books and perform common analysis tasks with python/r/etc).
Also what about KNIME examples?? There are a lot of great KNIME examples on the KNIME public server. A lot of the image processing ones seem to be geared towards people who have a working knowledge of KNIME. The examples contain a lot of meta nodes. If you don't know what a meta node is you might get confused.
Brian Northan
@bnorthan
Apr 19 2016 17:29
So I think there is a place for some simpler examples aimed at ImageJers interested in learning about KNIME. I have a few examples that are a bit simpler (3-10 nodes, no meta nodes) that may be useful.