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Repo info
Activity
    Jan Eglinger
    @imagejan
    I have a strange issue with tests passing locally (on Windows) but failing in CI , maybe someone here give me a quick hint (before I ask on the forum)...
    I tried to wrap ImageJ's "Subtract background" headlessly: https://github.com/fmi-basel/faim-ij2-ij/blob/main/src/main/java/ch/fmi/ij/BackgroundSubtraction.java
    and wrote a small test here: https://github.com/fmi-basel/faim-ij2-ij/blob/main/src/test/java/ch/fmi/ij/BackgroundSubtractionTest.java

    Interestingly, I get a HeadlessException in only one of the two tests, and the other one is failing:

      Error:  Failures: 
  Error:    BackgroundSubtractionTest.testEqualParameters:75 Pixel values differ on coordinate (0, 0, 0, 0, 0), expected: 1904 actual: 158
  Error:  Errors: 
  Error:    BackgroundSubtractionTest.testUnequalParameters:82 ยป Headless

    https://github.com/fmi-basel/faim-ij2-ij/runs/6423053171?check_suite_focus=true#step:5:101

    6 replies
    odinsbane
    @odinsbane
    I put this on the forum but maybe somebody knows how to access the origin value from properties?
    odinsbane
    @odinsbane
    When I scale an image, the origin doesn't change. It seems like it should though.
    9 replies
    Gabriel Selzer
    @gselzer

    What is the best way to resolve the fact that

    int myInt = 4
ij.convert().supports(myInt, IntegerType.class)

    returns false? Is it to add a new Converter in imagej-common?

    Curtis Rueden
    @ctrueden
    New converter in SciJava Common.
    I'm surprised that returns false.
    Oh wait.
    You said IntegerType! I misread as Integer.
    Yes, imagej-common is the right place, then.
    And there is an issue for it already.
    Which is closed and merged. @gselzer You actually reviewed that PR! imagej/imagej-common#82
    Should be part of imagej-common 0.35.0, not yet part of an imagej2 release unfortunately.
    Curtis Rueden
    @ctrueden
    @gselzer Getting closer now: scijava/pom-scijava@d58ce8a.
    Gabriel Selzer
    @gselzer

    Which is closed and merged. @gselzer You actually reviewed that PR! imagej/imagej-common#82

    Yeah, I thought it was fixed already. I just couldn't find the PR... :sweat_smile:

    But, with another look, I'm not sure that PR does enough
    We'd want to ensure that the IntegerToIntType converter could handle that conversion above
    Curtis Rueden
    @ctrueden
    Feel free to make additional converters!
    You have to be careful to set the priorities correctly.
    Gabriel Selzer
    @gselzer
    Right
    I'd actually think what is best is to make a converter that calls the others based on a switch
    That could then be HIGH priority
    swathi
    @springwindfall_twitter
    Hi there,I'm opening an RGB tiff image on imageJ with data in three separate channels -RBG, but when I open it the channels tool shows up both the blue and green in the green channel and I'm unable to separate the green only in a separate channel. Can anyone please help, much appreciate it !!
    N-itin
    @N-itin

    Hey Everyone, Can someone advise or give any lead to this problem?
    I want to extract the geometry of the crystals and matrix as can be seen in the image. I would like to import the crystal structure and matrix data in Abaqus software for doing FEM analysis. Can anybody please provide me an idea, of how to do that? Because this software accepts geometries only such as
    . dwg. dxg, .step. .stl, .iges, AutoCAD file, not an image file.

    I have posted on forum two weeks before but still not answers received. Here is the complete link to problem at the forum -

    https://forum.image.sc/t/digitalization-of-micrographs/66991

    Curtis Rueden
    @ctrueden
    @hinerm Just wanted to draw your attention to this forum post about ImageJ-OMERO sessions I made a couple of weeks ago. Check out Josh's answer. We probably don't need to change anything right now, but it's good to be aware of our design limitation of one session per server. Now isn't a bad time to think about if we can/should do better.
    Curtis Rueden
    @ctrueden
    Heads up: I have created a #ImageJ2 channel on the image.sc Zulip.