Package sc.fiji.snt.gui.cmds

Class SNTLinkHandler

java.lang.Object
org.scijava.AbstractContextual
org.scijava.plugin.AbstractRichPlugin
org.scijava.plugin.AbstractTypedPlugin<URI>
org.scijava.plugin.AbstractHandlerPlugin<URI>
org.scijava.desktop.links.AbstractLinkHandler
sc.fiji.snt.gui.cmds.SNTLinkHandler
All Implemented Interfaces:
Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.desktop.links.LinkHandler, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HandlerPlugin<URI>, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.plugin.SingletonPlugin, org.scijava.plugin.TypedPlugin<URI>, org.scijava.Prioritized, org.scijava.Typed<URI>, org.scijava.Versioned
public class SNTLinkHandler extends org.scijava.desktop.links.AbstractLinkHandler
Handles snt:// links, allowing SNT to be launched (or driven) from outside Fiji, e.g., from a browser, a paper's supplementary HTML, or another SciJava application, via scijava-desktop's LinkHandler mechanism.

The canonical form is fiji://snt/<operation>?<parameters>, which works on all platforms. snt://<operation>?<parameters> is also accepted where the OS allows registering it (see Links). Parameter values must be percent-encoded. Images and tracings must be given as URLs or as absolute local paths/ file: URIs (local ones only work on the machine hosting them). 

 Operations:
   open (default)  Opens image (SNT Stream for streamed data), loads tracings and flies to view. If image is already
   open, only the latter two are applied
   fly             As open, but view is mandatory
   demo            Loads a demo (see id), or a demo reconstruction (see tree)

 Parameters of open/fly:
   image     URL, path, file: URI, or demo:name for a bundled image (as in SNTService#initialize(String, boolean)).
             If omitted, acts on what is open
   stream    true|false. Inferred from image (.zarr, .n5, .ims, .xml, s3:, gs: mean stream)
   viewer    bvv (default)|bdv. Streamed launches only
   tracer    true (default)|false. false opens a plain viewer with no SNT session. Streamed launches only
   tracings  URL, path, file: URI, or demo:name for a bundled reconstruction. Streamed launches also accept a folder
             or .zip archive (but not demos). Not loaded into an already-open
             standalone viewer
   mode      add (default)|replace. Whether tracings replace existing paths (TRACES files always do). Ignored when
             launching a stream
   view      x,y,z[,t]: world coordinates and optional 1-based timepoint. ig viewers only (ignored by traditional
             launches)

 Parameters of demo:
   id        Stable id of a DemoRunner scenario, e.g., 4 (image, tracings, notes, etc.). Takes precedence over tree
   tree      Name of a bundled reconstruction (default: AA0001)

Examples: 

   fiji://snt/open?image=https%3A%2F%2Fhost%2Fdata.ome.zarr&view=82.9,-239,-65
   fiji://snt/open?image=file%3A%2F%2F%2FUsers%2Fme%2Fimg.tif
   fiji://snt/open?tracings=https%3A%2F%2Fhost%2Frec.swc&mode=replace
   fiji://snt/fly?view=10,20,30,2
   fiji://snt/open?image=demo:OP1&tracings=demo:OP1
   fiji://snt/demo?id=4
   fiji://snt/demo?tree=OP_1

NB: channel and ui are not supported yet, and are ignored

Links are pre-flighted against the current state of SNT (see SNTLink#preflight) before anything is changed. view (world coordinates, optionally followed by a 1-based timepoint) is only supported in SNT Stream/big viewers. Streamed links launch SNT Stream (see BigDataLoaderCmd.open(java.lang.String, java.lang.String, boolean, boolean)), closing a conflicting session first.

NB: handle(URI) may be called off the EDT (e.g., by LinkArgument while processing command-line/launch arguments), so all SNT/UI calls are marshaled onto the EDT.

Author:
Tiago Ferreira

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    SCHEME
    The URI scheme handled by this plugin.

  • Constructor Summary

    Constructors
    Constructor
    Description
    SNTLinkHandler()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    List<String>
    getSchemes()
     
    void
    handle(URI uri)
     
    boolean
    supports(URI uri)
     

    Methods inherited from class org.scijava.plugin.AbstractRichPlugin

    getInfo, getPriority, setInfo, setPriority, toString

    Methods inherited from class org.scijava.AbstractContextual

    context, getContext

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    Methods inherited from interface org.scijava.Contextual

    context, getContext, setContext

    Methods inherited from interface org.scijava.plugin.HasPluginInfo

    getInfo, setInfo

    Methods inherited from interface org.scijava.desktop.links.LinkHandler

    getType

    Methods inherited from interface org.scijava.Locatable

    getLocation

    Methods inherited from interface org.scijava.Prioritized

    compareTo, getPriority, setPriority

    Methods inherited from interface org.scijava.plugin.RichPlugin

    getIdentifier, log

    Methods inherited from interface org.scijava.Versioned

    getVersion

  • Field Details

  • Constructor Details

    • SNTLinkHandler

      public SNTLinkHandler()

  • Method Details

    • supports

      public boolean supports(URI uri)
      Specified by:
      supports in interface org.scijava.Typed<URI>
      Overrides:
      supports in class org.scijava.plugin.AbstractTypedPlugin<URI>

    • getSchemes

      public List<String> getSchemes()

    • handle

      public void handle(URI uri)