Nikon_NIS.Elements_Resave.brightfield.groovy

/*
 * Script written by Brenton Cavanagh 2018 brentoncavanagh@rcsi.ie
 * Purpose: To open and resave ND2 files from the Nikon Eclipse 90i
 * as single RGB TIF or PNG files with the correct colour order (BGR) 
 */
 
//Generate user input
#@File (label="Files to resave",style="directory") dirIN
#@File (label="Files to resave",style="directory") dirOUT

//Import libraries
import ij.IJ
import loci.plugins.BF
import loci.plugins.in.ImporterOptions
import java.awt.Color
import loci.common.DebugTools

//Count number of images processed
count = 0

//Recurse images in specified folders
dirIN.eachFileRecurse { file ->    
	filename =  dirIN.path+File.separator+file.name 
	savename =  dirOUT.path+File.separator+file.name
    //open if file type is ND2
    if (filename.endsWith(".nd2")){
    	//Bioformats options
    	options = new ImporterOptions();
		options.setId(filename);
		options.setAutoscale(false);
		options.setColorMode("Custom")
		options.setCustomColor(0,0,Color.BLUE)
		options.setCustomColor(0,1,Color.green)
		options.setCustomColor(0,2,Color.red)
    	//Open image
    	imp = BF.openImagePlus(options)
    	imp = imp[0]
		imp.setDisplayMode(IJ.COMPOSITE);
		imp.flattenStack();
		IJ.log("Resaving "+file.name);
		//Save image
		IJ.saveAs(imp, "Tiff", savename)
		imp.close()
		//add to number of images proccessed
		count++
		}
}
//Notify user that script is finished
IJ.log(" ");
IJ.log("Finished resaving "+count+" Images");
//Script updated by Brenton Cavanagh 20220120