import ij.IJ;
import ij.gui.GenericDialog;
import ij.macro.Interpreter;

suffix = ".TIF";
prefix = "RAHOTEP";

east = new Point(1, 0);
north = new Point(0, -1);
west = new Point(-1, 0);
south = new Point(0, 1);
START_DIRECTION = north;
TURNLEFT = false;

GenericDialog gd = new GenericDialog("MRI - Spiral Image Reconstruction");
gd.addCheckbox("clockwise", !TURNLEFT);
startEast = true;
if (START_DIRECTION.equals(north)&&TURNLEFT) startEast=false; 
if (START_DIRECTION.equals(south)&&!TURNLEFT) startEast=false;
gd.addCheckbox("start to the east", startEast); 
gd.addCheckbox("step", false);
gd.pack();
gd.showDialog();

if (gd.wasCanceled()) return;

clockwise = gd.getNextBoolean();
startEast = gd.getNextBoolean();
step = gd.getNextBoolean();

directory = IJ.getDirectory("Please select the source directory!");
if (directory==null) return;
destDirectory = IJ.getDirectory("Please select the results directory!");
if (destDirectory==null) return;

files = new File(directory).listFiles();

fileNameExpressions = new ArrayList();
for (file : files) {
	name = file.getName();
	if (!name.endsWith(suffix) || !name.startsWith(prefix)) continue;
	name = name.replace(suffix, "");
	components = name.split("f");
	if (!(components.length==2)) continue;
	part1 = components[0];
	components2 = components[1].split("d");
	if (!(components2.length==2)) continue;
	expr = part1 + "f.*" + "d" + components2[1] + suffix;
	if (!fileNameExpressions.contains(expr)) fileNameExpressions.add(expr);
}

Interpreter.batchMode = true;

counter = 1;
number = fileNameExpressions.size();
for (expr : fileNameExpressions) {
	IJ.log("\\Update:Creating mosaic " + counter + " from " + number);
	targetFilename = expr.replace("f.*", "_");
	IJ.run("Image Sequence...", "open=" + directory + files[0].getName()+" number=999999 starting=1 increment=1 scale=100 file=[] or=" + expr + " sort");
	IJ.run("Create Spiral Image", "clockwise="+ clockwise + " startEast=" + startEast + " step=" + step);
	IJ.save(destDirectory + targetFilename);
	image = IJ.getImage();
	image.changes = false;
	image.close();
	image = IJ.getImage();
	image.close();
	IJ.showProgress(counter, number);
	counter++;
}
Interpreter.batchMode = false;
IJ.showStatus("Finished creatinging mosaics. Created " + (counter-1) + " from " + number + " mosaics");
IJ.log("Finished creatinging mosaics.");