Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Jan Eglinger
    @imagejan
    I tried using an older imagej-updater to test, but it won’t let me because it always updates the updater first, before allowing any changes.
    Curtis Rueden
    @ctrueden
    Can you SFTP to the box from the command line on that machine? You're using an SSH keypair?
    Jan Eglinger
    @imagejan
    yes, sftp it is, I believe.
    I can ssh on it using user and password credentials
    Curtis Rueden
    @ctrueden
    From the message, it looks like JSch is somehow picking up on a public/private keypair and trying to use that?
    Jan Eglinger
    @imagejan
    And I usually was providing the same credentials in the Fiji updater as well.
    Curtis Rueden
    @ctrueden
    Do you run Pageant (from Putty)?
    Jan Eglinger
    @imagejan
    ok, maybe it’s trying to use that, how can I remove? In my home folder? .ssh?
    Curtis Rueden
    @ctrueden
    Usually Pageant has its own settings where things live, IIRC.
    You could try shutting down Pageant before connecting.
    Also, we should fix that exception message to not print a stringified byte array.
    Jan Eglinger
    @imagejan
    I’m not aware of using Pageant. I’m on Windows btw.
    Curtis Rueden
    @ctrueden
    Yeah, that's why I mentioned Pageant, because it's how I've used SSH keypairs on Windows in the past. There are probably other ways.
    It's possible that JSch is just grabbing it from a file somewhere, possibly ~/.ssh, possibly somewhere else.
    Jan Eglinger
    @imagejan
    I recently changed my way to work with GitHub, using ssh keys from Git Bash. Could it affect how Fiji works with the updater?
    Curtis Rueden
    @ctrueden
    I'd like to make some changes to the imagej-plugins-uploader-ssh to help you out.
    Jan Eglinger
    @imagejan
    I’ll try moving .ssh out of the way then.
    Curtis Rueden
    @ctrueden
    OK, let me know how it goes. There are probably at least two bugs here:
    1. Failure to gracefully proceed from keypairs (when they don't match) to passwords, when the remote allows passwords.
    2. Failure to give a decent error message when keypairs don't work.
    OK, it looks like the plugin only supports id_dsa and id_rsa in the ~/.ssh folder, indeed. Here
    Jan Eglinger
    @imagejan
    :tada: ok, mv .ssh .ssh-backup did the trick, although Fiji wanted to recreate the directory to add an entry to known-hosts then. It also complained that it was successfully creating it and I should check the permissions :-D 
    [INFO] C:\Users\eglijan\.ssh has been succesfully created.
Please check its access permission.
    Curtis Rueden
    @ctrueden
    This code is interesting.
    :laughing:
    Jan Eglinger
    @imagejan
    Thanks for the quick help, Curtis!
    I hope I didn’t distract you from more important (pyimagej) things ;-)
    Curtis Rueden
    @ctrueden
    No worries. To be honest, I have been very distracted with family obligations since I came back from vacation. My kids have been needing a lot of help staying focused on virtual school. I am looking forward to schools reopening (safely) so that I can focus better myself.
    This morning I was looking for a router with better parental controls, so that I can block YouTube more effectively. >_<
    Recommendations welcome, if you know of any good ones. It seems like I'm going to need to run an open source firmware on it, since the stock firmwares don't (in my experience, and based on reviews I've read) work well enough.
    Jan Eglinger
    @imagejan
    In Germany there are a lot of fans of the Fritz!Box product line: https://en.avm.de/
    As far as I can tell, they provide a lot of control over router configuration and do a good job there.
    Curtis Rueden
    @ctrueden
    Thanks!
    Cameron Lloyd
    @camlloyd
    @ctrueden Would pi-hole work for you?
    Curtis Rueden
    @ctrueden
    @camlloyd Pi-hole looks awesome, thanks a lot for the pointer!
    Isaac Silbert
    @isaac.silbert_gitlab
    Hi, is it possible to have lines as region of interests? If not, is there a way to export a freehand segment as x and y values as a table or csv of some sort? I'm trying to measure the thickness of a layer from an OCT image but I have to do it freehand since the layers are difficult to distinguish easily. Thanks
    Jean-Yves Tinevez
    @tinevez
    Hello.
    Could you point me to the repo where the code in charge of translating a script with IJ2 shabangs into a Swing UI is?
    Jan Eglinger
    @imagejan
    @tinevez the scijava-ui-swing repo contains all the widget implementations for Swing, e.g. SwingNumberWidget.
    Before that, the processing of the #@ parameters is achieved by ParameterScriptProcessor in scijava-common.
    Jean-Yves Tinevez
    @tinevez
    Grazie
    Fokatu
    @Fokatu
    what is the default ui of Fiji or imagej2?
    which class does it use?
    NicoKiaru
    @NicoKiaru
    @Fokatu : https://github.com/BIOP/ijp-template-ij2/blob/17bca6b6c5932e3a1c0fa5bfe0ea68b9ee88065a/src/main/java/ch/epfl/biop/ij2command/DummyCommand.java#L60-L65 is usually how FIJI can be started from an IDE. Does that help ?
    You can also look at the FIJI example plugin repo : https://github.com/imagej/example-imagej-command/blob/f75477fc8fce992cd2733b34283c2a49e1f2438e/src/main/java/com/mycompany/imagej/GaussFiltering.java#L83-L84
    Curtis Rueden
    @ctrueden
    @Fokatu The default UI of Fiji is the LegacyUI from imagej-legacy; it has higher priority than the SwingSDIUI from imagej-ui-swing. If you exclude imagej-legacy than imagej-ui-swing's takes precedence. If you have a barebones environment without those, then the HeadlessUI of scijava-common is picked up.
    Philipp Hanslovsky
    @hanslovsky
    I consider this a must read for anyone who likes imaging: https://ciechanow.ski/cameras-and-lenses/
    Jan Eglinger
    @imagejan
    @ctrueden @hinerm I need help regarding an imagej-legacy issue. I am looking at String => ImagePlus and String => Dataset conversion for opened images, and added a test (imagej/imagej-legacy@b13c8f9) that I am planning to flesh out to cover most use cases. JaCoCo tells me that this line in StringToImagePlusConverter is never executed.
    When I change the signature from canConvert(Object, Class) to canConvert(Object, Type), then it hangs in the test. I suspect some infinite loop, but can’t wrap my head around it. Do you have any ideas/pointers?
    Curtis Rueden
    @ctrueden
    @imagejan I don't have immediate insight, but I can certainly try to reproduce.
    Jan Eglinger
    @imagejan
    Hm, I cannot reproduce the hanging/blocking now, I don’t know what was different yesterday. Will dig deeper when it reoccurs. Anyhow, I’ll try to come up with a PR shortly, trying to improve (and test) the behavior with macro parameters for image inputs.
    Curtis Rueden
    @ctrueden
    @imagejan I also cannot reproduce.
    Jan Eglinger
    @imagejan
    sorry for stealing your time :-(
    Curtis Rueden
    @ctrueden
    However, there is a problem on my linux64 system with the use of ImagePlus fields. The legacy injector can't do its job early enough, so the context can't initialize with legacy support.
    No problem! It spurred me to finish setting up my new computer. :smile: