Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Philipp Hanslovsky
    @hanslovsky
    I would assume that the imglib2-imglyb and imglib2-unsafe versions that imglyb requires and that are used in pyimagej are inconsistent with imglyb >= 0.4
    Or maybe within imglyb itself, but that seems less likely
    Philipp Hanslovsky
    @hanslovsky
    @ctrueden This is my last week at Janelia and I would like to know people who to contact for various projects. Should I give them your name/e-mail for jgo and imglyb or should I just give a link to image.sc?
    Curtis Rueden
    @ctrueden
    @hanslovsky Sure, please list me for jgo and imglyb. I'll maintain them. Thanks again for all your work, and best wishes in the future. I'll be in touch about coauthorship of related papers. I assume your JRC email will go away—what address should I use in future for you?
    Philipp Hanslovsky
    @hanslovsky

    Please use philipp.hanslovsky@gmail.com
    I will probably stop by every once in a while just to see how things are going but I do not know how regular this will be. Feel free to e-mail me with any pressing issues, though.

    It was a pleasure working with you.

    Jean-Yves Tinevez
    @tinevez
    May we ask what is next for you Philipp?
    Philipp Hanslovsky
    @hanslovsky
    I will start at Capital One, leaving the scientific world.
    As a software engineer for machine learning
    Jean-Yves Tinevez
    @tinevez
    You mean academic world I guess. :) I don't think they use pentagram and deamon invocation in Capital One.
    Good fortune and happiness to you there!
    Philipp Hanslovsky
    @hanslovsky
    Yes, that is correct
    :smile:
    Thank you!
    John Bogovic
    @bogovicj
    I don't think they use pentagram and deamon invocation in Capital One.
    lol. @hanslovsky will have to tell us if they do!
    Deborah Schmidt
    @frauzufall
    All the best @hanslovsky!
    I'm struggling with reading scijava tables with row headers... Why is this parameter set to false and how can I set it to true? Currently using ij.io().open("xyz.csv")
    Jan Eglinger
    @imagejan
    @frauzufall I don’t think there is a way of using the @Parameters with IOService. In the test class, it is done by directly editing the annoted fields: https://github.com/scijava/scijava-plugins-io-table/blob/e09a9e06c73dde23ef474df33fa090cdbdf59966/src/test/java/org/scijava/table/DefaultTableIOPluginTest.java#L297-L310
    @ctrueden @stelfrich do you a better idea?
    Deborah Schmidt
    @frauzufall
    @imagejan yess, thank you, looks terrible but the method you linked works! Would also be interested in simpler solutions.
    PluginInfo<SciJavaPlugin> pluginInfo = pluginService.getPlugin(DefaultTableIOPlugin.class);
    DefaultTableIOPlugin plugin = (DefaultTableIOPlugin) pluginService.createInstance(pluginInfo);
    setValues(plugin, new String[]{"readRowHeaders"}, new Object[]{true});
    Deborah Schmidt
    @frauzufall
    btw. what about the Inputs branch, @ctrueden? We discussed this during the hackathon in December - having something like a generic dialog for asking the user for a set of inputs and you made this. I like it a lot. I could include the tests which are currently in comments and make a PR.
    Philipp Hanslovsky
    @hanslovsky
    Thank you @frauzufall!!
    Curtis Rueden
    @ctrueden
    @imagejan @frauzufall Why not have a vanilla Java method which accepts parameters, and then make an IOPlugin that calls that method?
    Or, a service method. This is what services are for, after all: providing reusable API.
    IOPlugin implementations are not intended to be called directly.
    In the case of DefaultTableIOPlugin, the business logic needs to be extracted to a TableIOService.
    Jan Eglinger
    @imagejan
    :+1: I created scijava/scijava-table#11 to track this.
    Deborah Schmidt
    @frauzufall
    @ctrueden yes if course I don't want to call the plugin directly, but at least it let's me read the table correctly for now. Happy to contribute to make this available via service - I continued the discussion in @imagejan's issue.
    Jean-Yves Tinevez
    @tinevez
    Dear @ctrueden .
    Did I have a chance to thank you for Pasrsington already (https://github.com/scijava/parsington )?
    We used it in Mastodon for a parser that can generate selection (spots and links) from expressions:
    https://github.com/mastodon-sc/mastodon-selection-creator/blob/master/src/main/resources/org/mastodon/revised/ui/selection/creator/parser/plugin/settings/Help.md
    It works great! A user can type something like this:
    ( vertexFeature('Spot N links') == 3 ) + ( vertexFeature('Spot frame') == 25 )
    and get what they want.
    So thank you.
    Curtis Rueden
    @ctrueden
    @tinevez I'm really glad to hear that Parsington is useful. It's one of the very few things I've done that I'm actually proud of, and I feel is clean and relatively complete. ☺️
    Jan Eglinger
    @imagejan
    @ctrueden you should be proud of a lot of things you’ve done!
    Philipp Hanslovsky
    @hanslovsky
    :plus1:
    Deborah Schmidt
    @frauzufall
    What @imagejan said
    John Bogovic
    @bogovicj
    :+1:
    Philipp Hanslovsky
    @hanslovsky

    Today is my last day at HHMI Janelia and the world of Academia. It has been an incredible 6 years and I feel grateful and honored for the great times had experience I had in the Saalfeld lab (@axtimwalde). I will start a new position at Capital One on Monday and I am very excited for what lies ahead.

    Back in 2014, I was lucky enough to join an amazing research group at one of the best neuroscience research institutes in the world. I learned a lot and connected with many brilliant people at Janelia and visitors from all around the world. Many of these connections grew into friendships and—while I leave the world of Academia—I am looking forward to stay in touch and learn what is new at Janelia and image.sc every once in a while. I will not actively work on my former projects at Janelia anymore but they remain in good hands. Use the project-specific issue trackers or the image.sc forum for any questions that you might have.

    In particular, the following projects with point(s) of contact for each of the projects if you have any questions that cannot be answered through issue trackers or the image.sc forum. Please look up their email addresses on their respective institute websites.

    Thank you for six great years!!

    Jean-Yves Tinevez
    @tinevez
    Hey folks.
    We have a series of artifacts that are mavenized and travisified.
    All work well, but in all of them we get javadoc warnings like these ones:
    4 warnings
    [WARNING] Javadoc Warnings
    [WARNING] javadoc: warning - Error fetching URL: https://javadoc.scijava.org/ImageJ1/
    [WARNING] javadoc: warning - Error fetching URL: https://javadoc.scijava.org/Eclipse/
    [WARNING] javadoc: warning - Error fetching URL: https://javadoc.scijava.org/Javassist/
    Do you know what cause them?
    Jan Eglinger
    @imagejan
    I’ve seen the same in my builds of various components.
    Jean-Yves Tinevez
    @tinevez
    Jan Eglinger
    @imagejan
    hm, but that issue is marked as resolved since 2018. And with pom-scijava 28.0.0, we’re using maven-javadoc-plugin in version 3.1.0...
    Maybe these three URLs differ from the other javadoc.scijava.org URLs in how they redirect… @ctrueden ?
    NicoKiaru
    @NicoKiaru
    Are you using pom-scijava 28.0.0 @tinevez ? Because there is this issue: scijava/pom-scijava#110
    tpietzsch
    @tpietzsch
    @NicoKiaru yes, we are using 28.0.0
    Jan Eglinger
    @imagejan
    @NicoKiaru the linked issue is a build ERROR, whereas what @tinevez wrote above is just a WARNING and doesn’t break the build.
    And: scijava/pom-scijava#110 is about the copy-jars goal, not javadoc, right?
    NicoKiaru
    @NicoKiaru
    yep, oki doki
    Curtis Rueden
    @ctrueden
    @NicoKiaru et al: Regarding the copy-jars problems: know that I have been actively working this week on improving scijava-maven-plugin to fix all these problems. Work is currently on a branch fix-everything. Will keep y'all posted on progress.
    NicoKiaru
    @NicoKiaru
    :+1: thanks a lot @ctrueden !
    Curtis Rueden
    @ctrueden
    Regarding the javadoc issues: some of the links are proxy/reverse-proxy, others are directly served, and still others are redirects. So yeah, there might be issues with one or more of those modalities interacting with the maven-javadoc-plugin.
    @NicoKiaru FWIW, I think that scijava/pom-scijava#110 is fixed by scijava/scijava-maven-plugin@90ba934 on that branch. If you have time and interest to test it, I can send instructions on how to do so. But if you just wait, I'll have it released soon™.