package emblcmci;

/** Bleach Correction with three different methods, for 2D and 3D time series.
 * 	contact: Kota Miura (miura@embl.de)
 *
 * 	Simple Ratio Method:
 * 		Plugin version of Jens Rietdorf's macro, additionally with 3D time series
 * 			see http://www.embl.de/eamnet/html/bleach_correction.html
 *
 *  Exponential Fitting Method:
 *  	Similar to MBF-ImageJ method, additionally with 3D time series.
 *  		See http://www.macbiophotonics.ca/imagej/t.htm#t_bleach
 *  	MBF-ImageJ suggests to use "Exponential" equation for fitting,
 *  	whereas this plugin uses "Exponential with Offset"
 *
 *  HIstogram Matching Method:
 *  	This method does much better restoration of bleaching sequence
 *  	for segmentation but might not good for intensity quantification.
 *  	See documentation at http://cmci.embl.de
 *
 *
 * Copyright © 2010 Kota Miura
 * License: GPL 2
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 2
 * as published by the Free Software Foundation.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.gui.Roi;
import ij.plugin.Duplicator;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;


public class BleachCorrection implements PlugInFilter {
		ImagePlus imp;

		String[] CorrectionMethods =  { "Simple Ratio", "Exponential Fit", "Histogram Matching" };

		/**Correction Method  0: simple ratio 1: exponential fit 2: histogramMatch
		*/
		private static int CorrectionMethod = 0;

		@Override
		public int setup(String arg, ImagePlus imp) {
			this.imp = imp;
			if (!showDialog()){
					return 0;
			}
			return DOES_8G+DOES_16+STACK_REQUIRED;
		}

		@Override
		public void run(ImageProcessor ip) {
			Roi curROI = imp.getRoi();
			//System.out.println("in the method");
			if (curROI != null) {
				java.awt.Rectangle rect = curROI.getBounds();
				System.out.println("(x,y)=(" + rect.x + ","	+ rect.y);
				System.out.println("Width="+ rect.width);
				System.out.println("Height="+ rect.height);
			} else {
				System.out.println("No ROI");
			}
			imp.killRoi();
			ImagePlus impdup = new Duplicator().run(imp);
			if (curROI != null) impdup.setRoi(curROI);
			if 		(CorrectionMethod == 0){			//Simple Ratio Method
				BleachCorrection_SimpleRatio BCSR = null;
				if (curROI == null) {
					BCSR = new BleachCorrection_SimpleRatio(impdup);
				} else {
					BCSR = new BleachCorrection_SimpleRatio(impdup, curROI);
				}
				BCSR.showDialogAskBaseline();
				BCSR.correctBleach();
			}
			else if (CorrectionMethod == 1){	//Exponential Fitting Method
				BleachCorrection_ExpoFit BCEF;
				if (curROI == null) {
					BCEF = new BleachCorrection_ExpoFit(impdup);
				} else {
					BCEF = new BleachCorrection_ExpoFit(impdup, curROI);
				}

				BCEF.core();
			}
			else if (CorrectionMethod == 2){	//HIstogram Matching Method
				BleachCorrection_MH BCMH = null;
				//if (curROI == null) {
					BCMH = new BleachCorrection_MH(impdup);
				//} else {
				//	BCMH = new BleachCorrection_MH(impdup, curROI);
				//}
				BCMH.doCorrection();
			}
			impdup.show();
		}

		/**Dialog to ask which method to be used for Bleach Correction
		 *
		 * @return
		 */
		public boolean showDialog()	{
			GenericDialog gd = new GenericDialog("Bleach Correction");
			gd.addChoice("Correction Method :", CorrectionMethods , CorrectionMethods[CorrectionMethod]);
			gd.showDialog();
			if (gd.wasCanceled())
				return false;
			BleachCorrection.setCorrectionMethod(gd.getNextChoiceIndex());
			return true;

		}

		public static int getCorrectionMethod() {
			return CorrectionMethod;
		}

		public static void setCorrectionMethod(int correctionMethod) {
			CorrectionMethod = correctionMethod;
		}

}