/*
import the different Classes needed
	- Icy is needed to use getSequence() and Icy.addSequence()
	- Package thresholder is needed to do the threshold with 
	  Thresholder and KMeans classes.
*/
importClass(Packages.icy.image.IcyBufferedImage)
importClass(Packages.plugins.tprovoost.bestthreshold.BestThreshold)

importPackage(Packages.plugins.adufour.thresholder)

/* 
Get the focused Sequence. This is a shortcut for:
	Icy.getMainInterface().getFocusedSequence()
*/
seq = getSequence()
img = getImage()

// working on first channel
channel = 0

// Check if sequence is null, as we cannot perform a threshold on 
// something that does not exist.
if (img != null) {

	data2 = BestThreshold.getHistogramBins(img, channel)

	threshold = BestThreshold.Otsu(data2)
	
	// performs the threshold and put the result (a sequence) inside a variable
	result = Thresholder["threshold(icy.sequence.Sequence,int,double[],boolean)"](seq, 1, [threshold], false)

	// display the result of the threshold
	result.setName(seq.getName() + "thresholded")
	gui.addSequence(result)	
}