Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    lorita
    @Lorita92_gitlab
    hello everyone! does anyone know how to open a psd file in image j? i already have downloaded jimi reader, jimi writer and jimi jar and pasted the files in the plugin area, but it doesn't work
    tibuch
    @tibuch
    Hi @Lorita92_gitlab
    Welcome to the imagej community! Did you try https://forum.image.sc/ ? Maybe someone else already had this question. If not it would be great if you could ask there. You can reach a larger audience and the answer will be discoverable by other users :)
    Christian "Tischi" Tischer
    @tischi
    @tibuch Could you point me ( again ) to the piece of code where you retrieve pixel values at the current mouse coordinate, to be shown in the Bdv window? I am using a pattern like this *.nonVolatile().getSource( t, 0 ).randomAccess(); but I feel it blocks other processes. Is there maybe any way to just get the pixel values that Bdv already loaded anyway in order to show the image (instead of requesting them a second time)?
    Regarding other options I would have to ask @tpietzsch :)
    Christian "Tischi" Tischer
    @tischi
    Christian "Tischi" Tischer
    @tischi
    @tibuch Do you have code for a scale bar in Bdv?
    tibuch
    @tibuch
    @tischi I don't.
    Florian Jug
    @fjug
    @tischi -- I'd check with Saalfeld or @tpietzsch
    tpietzsch
    @tpietzsch
    @tischi you can enable it by putting a file ~/.bdv/bigdataviewer.properties (or alternatively in the Fiji directory or something like that. I don't remember, you can check the code...)
    with content like this:
    show-scale-bar = true
    scale-bar-color = #ffffffff
    scale-bar-bg-color = #88000000
    show-scale-bar-in-movie = true
    Florian Jug
    @fjug
    Wooow… this is good to know! :)
    Christian "Tischi" Tischer
    @tischi
    @bogovicj thanks! Looks like what I need :-) @tpietzsch I guess I would only need to do what you suggested for it to be working in vanilla Fiji?! ...my current use-case is just that I need it within my java code...
    tpietzsch
    @tpietzsch
    @tischi yes
    the properties file is used to populate bdv.util.Prefs
    you can also programmatically do, e.g., Prefs.showScaleBar(true)
    tpietzsch
    @tpietzsch
    (note that this will not affect BDV windows that are already open, IIRC)
    Michal Krumnikl
    @MKrumnikl
    There is an interesting article on BBC regarding Kofola, most of you have drinked in Ostrava - http://www.bbc.com/travel/story/20190329-the-cold-war-era-drink-that-rivals-cola
    janaklimova
    @janaklimova
    There are a few words about Hackathon in our quarterly newsletter pp. 12-16. Unfortunately translated into Czech but at least you can have a look at the pictures :D https://www.it4i.cz/wp-content/uploads/2019/04/IT4I-Newsletter-Q1-2019-CZ.pdf
    John Bogovic
    @bogovicj
    :+1:
    Christian "Tischi" Tischer
    @tischi
    @tibuch @tpietzsch Is it possible to override keyboard short-cuts of the Bdv? It would also be OK for us to deactivate all default short-cuts such that we can add our own.
    tpietzsch
    @tpietzsch
    @tischi it's possible, I'll dig up an example
    tpietzsch
    @tpietzsch
    @tischi @tibuch
    "Standard" BDV reads key configurations from a file ~/.bdv/bdvkeyconfig.yaml if it exists
    You can dump a file with the default keys by uncommenting this line and running BigDataViewer.main(): https://github.com/bigdataviewer/bigdataviewer-core/blob/4d8a5e2f774942cbdb41b7ceff7c4e90bd8d102c/src/main/java/bdv/BigDataViewer.java#L722
    This is a yaml file which maps actions/behaviours to (sets of) shortcuts
    replace everything with "not mapped"
    tpietzsch
    @tpietzsch
    you cannot simply use an empty file, because if no shortcut is given for an action/behaviour, the built-in default will be used
    If you use BDV programmatically, through vistools etc, you can give a InputTriggerConfig in the BdvOptions
    Here is how you would load one from a file (e.g. the one above) and then use it:
    InputTriggerConfig config = new InputTriggerConfig( YamlConfigIO.read( "/Users/pietzsch/Desktop/bdvkeyconfig.yaml" ) );
    BdvFunctions.show( img, "img", Bdv.options().inputTriggerConfig( config ) );
    You can also temporarily deactivate action/behaviour maps
    tibuch
    @tibuch
    Thank you!
    tpietzsch
    @tpietzsch
    For example, in https://github.com/bigdataviewer/bigdataviewer-core/blob/4d8a5e2f77/src/main/java/bdv/tools/boundingbox/TransformedBoxEditor.java, a input map is constructed to block normal navigation when the mouse is over a control point and replace it with editing actions for that control point
    tibuch
    @tibuch
    If I load the not-mapped-yaml file, most of the actions are blocked. but I can still use the mouse and arrow-keys. Is that expected?
    ( I am in 2D mode)
    tibuch
    @tibuch
    Had to add the 2d actions too:
    - !mapping
      action: 2d drag translate
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d scroll zoom
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d drag rotate
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d scroll rotate
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d scroll translate
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d rotate left
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d rotate right
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d zoom in
      contexts: [bdv]
      triggers: [not mapped]
    - !mapping
      action: 2d zoom out
      contexts: [bdv]
      triggers: [not mapped]
    tpietzsch
    @tpietzsch
    :thumbsup:
    Christian "Tischi" Tischer
    @tischi
    What surprises me a bit is that below code does in fact not remove all triggers. I would have thought that setting an empty InputTriggerConfig() would remove all behaviors, but it seems not to change anything.
    BdvFunction.show( spimData, BdvOptions.options().inputTriggerConfig( new InputTriggerConfig(  ) ));
    tpietzsch
    @tpietzsch
    No, then the default triggers get installed
    Khawalah Munshi
    @KhawalahMunshi_twitter
    hello
    I am trying to install images on my Mac Pro but it won't because of protection safety
    how I can do it
    Michal Krumnikl
    @MKrumnikl
    Hi. I don't have MacOS, but have you tried to look at https://imagej.net/MacOSX_tips and https://imagej.net/Troubleshooting and maybe if the message is related to unidentified developer source try this https://www.youtube.com/watch?v=yJoSrBe7Tpg