#@ File image_dir1 ( label="First directory", style="directory" )
#@ File image_dir2 ( label="Second directory", style="directory" )
#@ Boolean save_plot ( label="Save plot?" )
#@ Boolean save_data ( label="Save Data points?" )
#@ String threshold_method (label="Threshold method", choices={"Fixed 1/7", "Half-bit", "Three sigma"})


import ch.epfl.biop.frc.FRC
import ch.epfl.biop.frc.FRC.ThresholdMethod
import ij.IJ
import ij.ImagePlus
import java.io.FilenameFilter
import ij.gui.Plot
import ij.measure.ResultsTable

def rt = new ResultsTable()
def tm = FRC.ThresholdMethod.values().find{ it.toString() == threshold_method} 
batchFolders( image_dir1, image_dir2, tm, rt, save_plot, save_data )


def batchFolders(File directory1, File directory2, ThresholdMethod method, ResultsTable rt, boolean is_save_plot, boolean is_save_data) {
	def frc = new FRC()
	// Navigate folder for tiffs
	String[] the_files = directory1.list(new FilenameFilter() {
		
		@Override
		public boolean accept(File dir, String name) {
			// check extensions
			return true;				
		}
	});
	
	// Prepare saving if necessary
	File save_dir = new File(directory1.getParentFile(), "Graphs");
	save_dir.mkdir();
	
	// For each file, open one in each directory
	for(String the_file : the_files) {
		File f1 = new File(directory1.getAbsolutePath()+File.separator+the_file);
		File f2 = new File(directory2.getAbsolutePath()+File.separator+the_file);
		
		if(f2.exists()) {
			ImagePlus i1 = IJ.openImage(f1.getAbsolutePath());
			ImagePlus i2 = IJ.openImage(f2.getAbsolutePath());
			
			// Finally calculate FRC
			double[][] frc_curve = frc.calculateFrcCurve(i1.getProcessor(), i2.getProcessor());
			
			double[][] smooth_frc = frc.getSmoothedCurve(frc_curve);

			// Fourier Image REsolution number ("FIRE")
			double fire = frc.calculateFireNumber(smooth_frc, method);
			
			rt.incrementCounter();
			rt.addLabel(i1.getTitle());
			rt.addValue("FRC ["+method+"]", fire);
			rt.addValue("FRC ["+method+"] Calibrated ["+i1.getCalibration().getUnit()+"]", fire*i1.getCalibration().pixelHeight);
			rt.show("FRC Results");
			
			if(is_save_plot) {
				Plot p = frc.doPlot(frc_curve, smooth_frc, method, fire, i1.getTitle());
				plotWindow = p.show()
				ImagePlus plot_image = p.makeHighResolution("FRC", 3, true, false);
				String plot_name = save_dir.getAbsolutePath()+File.separator+f1.getName().substring(0,f1.getName().lastIndexOf("."));
				plot_name += "_"+method.toString().replaceAll("/", " over ")+".tif";
				IJ.save(plot_image, plot_name);
				
				if( is_save_data ) {
					def rt2 = p.getResultsTableWithLabels()
					String res_name = save_dir.getAbsolutePath()+File.separator+f1.getName().substring(0,f1.getName().lastIndexOf("."));
					res_name += "_"+method.toString().replaceAll("/", " over ")+".csv";
					rt2.saveAs( res_name )
				}
				plotWindow.close()		
			}
		}
	}
}