#@ File    (label = "Input directory", style = "directory") srcFile
#@ File    (label = "Output directory", style = "directory") dstFile
#@ String  (label = "File extension", value=".tif") ext
#@ String  (label = "File name contains", value = "") containString
#@ Boolean (label = "Keep directory structure when saving", value = true) keepDirectories
#@ double (label = "Spot radius", stepSize=0.1) radius
#@ double (label = "Quality threshold") threshold
#@ int (label = "Max frame gap") frameGap
#@ double (label = "Linking max distance") linkingMax
#@ double (label = "Gap-closing max distance") closingMax


import ij.IJ
import fiji.plugin.trackmate.Model
import fiji.plugin.trackmate.Settings
import fiji.plugin.trackmate.TrackMate
import fiji.plugin.trackmate.detection.LogDetectorFactory
import fiji.plugin.trackmate.tracking.LAPUtils
import fiji.plugin.trackmate.tracking.sparselap.SparseLAPTrackerFactory
import fiji.plugin.trackmate.action.ExportTracksToXML

def main() {
	srcFile.eachFileRecurse {
		name = it.getName()
		if (name.endsWith(ext) && name.contains(containString)) {
			process(it, srcFile, dstFile, keepDirectories)
		}
	}
}

def process(file, src, dst, keep) {
	println "Processing $file"

	// Opening the image
	imp = IJ.openImage(file.getAbsolutePath())

	// Put your processing steps here
	// Swap Z and T dimensions if T=1
	dims = imp.getDimensions() // default order: XYCZT
	if (dims[4] == 1) {
		imp.setDimensions( dims[2,4,3] )
	}

	// Setup settings for TrackMate
	settings = new Settings()
	settings.setFrom(imp)
	settings.dt = 0.05
	settings.detectorFactory = new LogDetectorFactory()
	settings.detectorSettings = settings.detectorFactory.getDefaultSettings()
	println settings.detectorSettings

	settings.detectorSettings['RADIUS'] = radius
	settings.detectorSettings['THRESHOLD'] = threshold
	println settings.detectorSettings

	settings.trackerFactory = new SparseLAPTrackerFactory()
	settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap()
	
	settings.trackerSettings['MAX_FRAME_GAP']  = frameGap
	settings.trackerSettings['LINKING_MAX_DISTANCE']  = linkingMax
	settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE']  = closingMax
	
	// Run TrackMate and store data into Model
	model = new Model()
	trackmate = new TrackMate(model, settings)
	
	println trackmate.checkInput()
	println trackmate.process()
	println trackmate.getErrorMessage()
	
	println model.getSpots().getNSpots(true)
	println model.getTrackModel().nTracks(true)

	// Saving the result
	filename = file.getName()
	if (!filename.endsWith(".xml")) {
	filename += ".xml"
	}
	relativePath = keep ?
			src.toPath().relativize(file.getParentFile().toPath()).toString()
			: "" // no relative path
	saveDir = new File(dst.toPath().toString(), relativePath)
	if (!saveDir.exists()) saveDir.mkdirs()
	outFile = new File(saveDir, filename) // customize name if needed
	ExportTracksToXML.export(model, settings, outFile);

	// Clean up
	imp.close()
	}

main()