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3 - Script

By using the SciJava framework to store BigDataViewer windows through its BdvHandle interface, it is possible to communicate bdv instances between scripts and commands (see script parameter page). This also facilitates the use of Fiji GUI because the commands of this repository can be chained easily. Any script or Command which declares a BdvHandle parameter can retrieve or provide reference to existing BigDataViewer instances.

In practice, Bdv windows created via the commands from this update site are put by default in the ObjectService. To get a reference to these windows:

  • In groovy, add this at the beginning of your script
#@BdvHandle bdvh
BdvHandle bdvh;

How to make your BigDataViewer workflow compatible with SciJava ?

Two options:

  • Use any command from bigdataviewer-playground which generates a BDV window. It corresponding BdvHandle will be registered and can be retrieved through a SciJava parameter annotation. This will make your Bdv Window accessible to other plugins / commands.

  • Create your own Bdv window, but declare the associated BdvHandle as an output of your Command:

    • in Java: @Parameter(type = ItemIO.OUTPUT); BdvHandle bdvh_out;

The type of the parameter annotation can also be ItemIO.BOTH if your command is modifying an existing BdvHandle

Example scripts


  • Display a recursive Fiji image:
// Input : provided by Single Input Preprocessor in case no widow is present
#@BdvHandle bdv_h 
// Output : allow to updates list of sources
#@output BdvHandle bdv_h
#@output SourceAndConverter source

// Simple Fiji Image stored as an array
fijiData =
			 [0,0,0,0,0,0,0,0,0]] as short[][];

// Declare a procedural image
def s = new Procedural3DImageShort({p -> getRecursiveFiji(p[1], p[0], p[2])}).getRRA();  

// Interval (mainly useless here, but required by BdvFunctions
Interval interval = new FinalInterval([ 0, 0, 0] as long[], [ 9, 9, 0 ] as long[]);

// Display the source in the bdv_h window
bss = s , interval, "Fiji", BdvOptions.options().addTo(bdv_h) );

// Display options
bss.setColor(new ARGBType(ARGBType.rgba(101,164,227,255)));

source = bss.getSources().get(0) // to register the created source

//------------- FUNCTION for recursive Fiji Image generation

int getRecursiveFiji(double x, double y, double level) {
	def valueLevel = (int) (fijiData[((int)x%9)][((int)y%9)])
	if (level<=0) {
		return valueLevel
	} else {
		if (valueLevel==1) {
			if (level>2) {
			return getRecursiveFiji(x*9,y*9,level-1)
		} else {
			return 0

import bdv.util.Procedural3DImageShort
import net.imglib2.RealRandomAccessible
import bdv.util.BdvFunctions
import bdv.util.BdvOptions
import bdv.util.BdvHandle
import net.imglib2.type.numeric.integer.UnsignedShortType
import net.imglib2.FinalInterval
import net.imglib2.Interval
import net.imglib2.type.numeric.ARGBType

ImageJ Macro Language


List of all commands

The list of commands of this repository is available in the git repository :