import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.gui.NonBlockingGenericDialog;
import ij.gui.Plot;
import ij.gui.Roi;
import ij.gui.TextRoi;
import ij.gui.WaitForUserDialog;
import ij.ImagePlus;
import ij.ImageStack;
import ij.measure.Calibration;
import ij.measure.Measurements;
import ij.measure.ResultsTable;
import ij.plugin.Colors;
import ij.plugin.Concatenator;
import ij.plugin.Duplicator;
import ij.plugin.filter.Analyzer;
import ij.plugin.frame.RoiManager;
import ij.plugin.frame.ThresholdAdjuster;
import ij.plugin.HyperStackConverter;
import ij.plugin.ImageCalculator;
import ij.plugin.PlugIn;
import ij.plugin.StackEditor;
import ij.plugin.SubstackMaker;
import ij.plugin.SubHyperstackMaker;
import ij.plugin.ZProjector;
import ij.process.Blitter;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import ij.process.ImageStatistics;
import ij.text.TextPanel;
import ij.text.TextWindow;
import ij.util.Tools;
import ij.WindowManager; 

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Image;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.Window;
import java.awt.geom.Rectangle2D;

import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;

import java.net.URL;

import java.text.DecimalFormat;
import java.text.DateFormat;
import java.text.SimpleDateFormat;

import java.util.Arrays;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.TimeZone;

import org.apache.commons.math3.linear.MatrixUtils;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.SingularValueDecomposition;

/**
	JEasyTFM version 2.1

	JEasyTFM is an open-source ImageJ plugins package aimed for the automatic analysis of large Traction Force Microscopy kinetic images data.
	This package able the automatic analysis of TFM data in time lapse with:
		- 1 to 2 beads channels (i.e. with two different beads colors)
		- 1 to 3 cells channels (for example with Bright Field, GFP and Hoechst channels)
		- multi-positions (i.e. several sample positions within a given experiment)
		- calculation of the traction forces
		- automatic cells segmentation carried out from their BF images
		- integration of the forces over the cells
		- tracking of the beads
		- focal adhesion segmentations
		- calculation of the traction forces applied on the focal adhesions
		- batch-processing using jobs creation, launching and tracking

	This plugin generates the "JEasyTFM.txt".
	i.e. the configuration file needed to launch traction force analysis methods.

	Author:     Philippe Carl (Philippe DOT Carl AT unistra DOT fr)

	Requires:   ImageJ 1.53d47 or later

	History:
		2020/07/31: Version 1.0 - First released version: The analysis package is made available for the community.
		2023/01/23: Version 2.0 - Extension of the code to allow the calculation of the traction forces applied on the focal adhesions.
		2023/02/23: Version 2.1 - For the particle_tracker feature JEasyTFM uses now the 1.0.25 version of the MosaicSuite code released on 20 September 2022
		                          (instead of the 1.5. version of the Particle_Tracker code released September 2006)
**/

/**
	Copyright (C) 2020 Philippe Carl.

	Permission is hereby granted, free of charge, to any person obtaining a copy
	of this software and associated documentation files (the "Software"), to deal
	in the Software without restriction, including without limitation the rights
	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	copies of the Software, and to permit persons to whom the Software is
	furnished to do so, subject to the following conditions:

	The above copyright notice and this permission notice shall be included in all
	copies or substantial portions of the Software.

	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
	SOFTWARE.
**/

public class launch_job implements PlugIn
{
	int					unitIndex				= 0;				// index corresponding to the force calculated in pN
	int					FTTC_max_vector_length	= 24;				// 24
	int					vs3						= 16;				// PIV window size
	double				length_scale;	//		= 6.5 / 60.0;		// 6.5µm is the size of the Hamamatsu ORCA-Flash4.0 V2 cell size (https://www.hamamatsu.com/resources/pdf/sys/SCAS0081E_C11440-22CU.pdf) and 60 corresponds to an 60x objective magnification
	double				window_area;	//		= Math.pow(vs3 * length_scale, 2);
	String				length_unit				= "micron";
	String				lut						= "multitxt";

	String				config_file;

	boolean				underscrore		= true;
	boolean				error			= false;
	String				link			= underscrore ? "_-_" : " - ";

	boolean				dupli, debug;

	String				folder  , file1  , file2;

	int					objective_magnification, job_index, channels, slices, frames, frames_begin, cells_number, beads, ch, numberCh, image_chosen, E;
//	double				camera_pixel_size, precisionForLambda, lambda;
	double				camera_pixel_size, precisionForLambda;
	double			[]	lambda_values = null;
	boolean				beads1, beads2;
	boolean				 ch1,  ch2,  ch3;
	boolean				mod1, mod2, mod3;
	int				[]	format					= { 0x1, 0x2, 0x4, 0x10, 0x20, 0x40 };

	boolean				cells_images                              , beads_reference_images                                        , beads_sequence_images                                       , traction_force                                  , cells_analysis                                              , traction_high_force                                       , FA_segmentation                                               , traction_force_applied_on_FA;
	boolean				                                            beads_reference_images_find_focused_slices                    , beads_sequence_images_find_focused_slices                                                                                                                                   , traction_high_enhance_constrast;
	int					cells_starting_folder, cells_ending_folder, beads_reference_starting_folder, beads_reference_ending_folder, beads_sequence_starting_folder, beads_sequence_ending_folder, traction_starting_folder, traction_ending_folder, cells_analysis_starting_folder, cells_analysis_ending_folder, traction_high_starting_folder, traction_high_ending_folder, FA_segmentation_starting_folder, FA_segmentation_ending_folder, traction_applied_on_FA_starting_folder, traction_applied_on_FA_ending_folder;

	boolean				traction_force_alignment, traction_force_alignment_make, traction_force_alignment_crop, traction_force_calculation, piv_calculation, lambda_calculation, force_calculation, force_superposition;
	boolean				high_piv_calculation, particle_tracker;
	boolean				cells_segmentation, cells_selection, force_integration;

	int					val;
	File				file;

//	ResultsTable		rt;
	String				str;
	int					counter, col;
	double				value;

	long				startTime;
	long				stopTime;
	long				elapsedTime;
//	SimpleDateFormat	sdf = new SimpleDateFormat("MMM dd,yyyy HH:mm");    
	SimpleDateFormat	sdf = new SimpleDateFormat("HH:mm:ss.SSS");
	Date				resultdate;
	URL					url;
	Image				icon	= null;

	public void run(String arg)
	{
		try
		{
			url		= getClass().getResource("/image/JEasyTFM.ico");
			icon	= Toolkit.getDefaultToolkit().getImage(url);
		}
		catch (Exception e)
		{
			IJ.showMessage("Loading the icon image", "The icon image \"/image/JEasyTFM.ico\" could not be found!");
		}

		sdf				.setTimeZone(TimeZone.getTimeZone("UTC"));
		startTime		= System.currentTimeMillis();
		config_file		= IJ.getDirectory("plugins") + "JEasyTFM.txt";
		setData			( readData(config_file) );
		if(!saveBeginJob())
			return;
		showData();

		if( cells_images					) cells_images					();
		if( beads_reference_images			) beads_reference_images		();
		if( beads_sequence_images			) beads_sequence_images			();
		if( traction_force					) traction_force				();
		if( cells_analysis					) cells_analysis				();
		if( traction_high_force				) traction_high_force			();
		if( FA_segmentation					) FA_segmentation				();
		if( traction_force_applied_on_FA	) traction_force_applied_on_FA	();

		stopTime	= System.currentTimeMillis();
		elapsedTime	= stopTime - startTime;
		resultdate	= new Date(elapsedTime);
		showDialogWithCustomOkAndNoCancel("Traction Force Microscopy Analysis", "The analysis took " + sdf.format(resultdate), "The analysis has been completed!!!");
	}

	private String [] readData(String parameters_file)
	{
		String [] data = {"false"};
		String [] columns;

		file = new File(parameters_file);
		if (!file.exists())
			IJ.log("File not found");
		try
		{
			String    config = IJ.openAsString(parameters_file);
			String [] lines  = Tools.split(config  ,"\n");
			data             = new String[lines.length];
			for(int i = 0; i != lines.length; i++)
			{
				columns = Tools.split(lines[i],"\t");
				data[i] = columns[1];
			}
		}
		catch (Exception e)
		{
			IJ.log("File open error \n\"" + e.getMessage() + "\"\n");
		}

		return data;
	}

	private void setData(String [] str_config_data)
	{
		int i;

		if(str_config_data.length == 56)
		{
			i = 0;
			camera_pixel_size								= Double.valueOf		(	str_config_data[i++] );
			objective_magnification							= Integer.parseInt		(	str_config_data[i++] );
			debug											= Boolean.parseBoolean	(	str_config_data[i++] );
			folder											=							str_config_data[i++]  ;
			file1											=							str_config_data[i++]  ;
			file2											=							str_config_data[i++]  ;
			cells_number									= Integer.parseInt		(	str_config_data[i++] );
			slices											= Integer.parseInt		(	str_config_data[i++] );
			frames											= Integer.parseInt		(	str_config_data[i++] );
			frames_begin									= Integer.parseInt		(	str_config_data[i++] );
			beads											= Integer.parseInt		(	str_config_data[i++] );
			ch												= Integer.parseInt		(	str_config_data[i++] );
			numberCh										= Integer.parseInt		(	str_config_data[i++] );
			E												= Integer.parseInt		(	str_config_data[i++].trim() );
			precisionForLambda								= Double.valueOf		(	str_config_data[i++] );
			cells_images									= Boolean.parseBoolean	(	str_config_data[i++] );
			image_chosen									= Integer.parseInt		(	str_config_data[i++] );
			cells_starting_folder							= Integer.parseInt		(	str_config_data[i++] );
			cells_ending_folder								= Integer.parseInt		(	str_config_data[i++] );
			beads_reference_images							= Boolean.parseBoolean	(	str_config_data[i++] );
			beads_reference_images_find_focused_slices		= Boolean.parseBoolean	(	str_config_data[i++] );
			beads_reference_starting_folder					= Integer.parseInt		(	str_config_data[i++] );
			beads_reference_ending_folder					= Integer.parseInt		(	str_config_data[i++] );
			beads_sequence_images							= Boolean.parseBoolean	(	str_config_data[i++] );
			beads_sequence_images_find_focused_slices		= Boolean.parseBoolean	(	str_config_data[i++] );
			beads_sequence_starting_folder					= Integer.parseInt		(	str_config_data[i++] );
			beads_sequence_ending_folder					= Integer.parseInt		(	str_config_data[i++] );
			traction_force									= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_starting_folder						= Integer.parseInt		(	str_config_data[i++] );
			traction_ending_folder							= Integer.parseInt		(	str_config_data[i++] );
			traction_force_alignment						= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_force_alignment_make					= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_force_alignment_crop					= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_force_calculation						= Boolean.parseBoolean	(	str_config_data[i++] );
			piv_calculation									= Boolean.parseBoolean	(	str_config_data[i++] );
			lambda_calculation								= Boolean.parseBoolean	(	str_config_data[i++] );
			force_calculation								= Boolean.parseBoolean	(	str_config_data[i++] );
			force_superposition								= Boolean.parseBoolean	(	str_config_data[i++] );
//			force_superposition								= Boolean.parseBoolean	(	str_config_data[i++] ) != 0;
			cells_analysis									= Boolean.parseBoolean	(	str_config_data[i++] );
			cells_analysis_starting_folder					= Integer.parseInt		(	str_config_data[i++] );
			cells_analysis_ending_folder					= Integer.parseInt		(	str_config_data[i++] );
			cells_segmentation								= Boolean.parseBoolean	(	str_config_data[i++] );
			cells_selection									= Boolean.parseBoolean	(	str_config_data[i++] );
			force_integration								= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_high_force								= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_high_enhance_constrast					= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_high_starting_folder					= Integer.parseInt		(	str_config_data[i++] );
			traction_high_ending_folder						= Integer.parseInt		(	str_config_data[i++] );
			high_piv_calculation							= Boolean.parseBoolean	(	str_config_data[i++] );
			particle_tracker								= Boolean.parseBoolean	(	str_config_data[i++] );
			FA_segmentation									= Boolean.parseBoolean	(	str_config_data[i++] );
			FA_segmentation_starting_folder					= Integer.parseInt		(	str_config_data[i++] );
			FA_segmentation_ending_folder					= Integer.parseInt		(	str_config_data[i++] );
			traction_force_applied_on_FA					= Boolean.parseBoolean	(	str_config_data[i++] );
			traction_applied_on_FA_starting_folder			= Integer.parseInt		(	str_config_data[i++] );
			traction_applied_on_FA_ending_folder			= Integer.parseInt		(	str_config_data[i++] );
			length_scale									= camera_pixel_size / objective_magnification;
			window_area										= Math.pow(vs3 * length_scale, 2);
			beads1											= (beads & 0x1 )	!= 0;
			beads2											= (beads & 0x2 )	!= 0;
			ch1												= (ch    & 0x1 )	!= 0;
			ch2												= (ch    & 0x2 )	!= 0;
			ch3												= (ch    & 0x4 )	!= 0;
			mod1											= (ch    & 0x10)	!= 0;
			mod2											= (ch    & 0x20)	!= 0;
			mod3											= (ch    & 0x40)	!= 0;
		}
		else
		{
			IJ.log("The configuration file is empty");
			return;
		}
	}

	private boolean saveBeginJob()
	{
		if (!checkAndCreateFolder(folder + "Jobs"))
			return false;
		job_index		= 0;
		dupli			= true;
		while (dupli)
		{
			job_index++;
//			file		= new File(folder + "Jobs" + File.separator + "job_" + IJ.pad(job_index, 2) + "_begin.txt");
			file		= new File(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_begin.txt");
			dupli		= file.exists();
		}
		saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_begin.txt");
		return true;
	}

	private void saveJob(String path)
	{
		beads								= beads1 ?         0x1 : 0;
		beads								= beads2 ? beads + 0x2 : beads;

		ch									= ch1    ?         0x1  : 0;
		ch									= ch2    ? ch    + 0x2  : ch;
		ch									= ch3    ? ch    + 0x4  : ch;
		ch									= mod1   ? ch    + 0x10 : ch;
		ch									= mod2   ? ch    + 0x20 : ch;
		ch									= mod3   ? ch    + 0x40 : ch;

		try
		{
			FileOutputStream		fos		= new FileOutputStream		(path);
			BufferedOutputStream	bos		= new BufferedOutputStream	(fos);
			PrintWriter				writer	= new PrintWriter			(bos);

			writer.println("camera_pixel_size\t"							+ camera_pixel_size);
			writer.println("objective_magnification\t"						+ objective_magnification);
			writer.println("debug\t"										+ debug);
			writer.println("folder\t"										+ folder);
			writer.println("file1\t"										+ file1);
			writer.println("file2\t"										+ file2);
			writer.println("cells_number\t"									+ cells_number);
			writer.println("slices\t"										+ slices);
			writer.println("frames\t"										+ frames);
			writer.println("frames_begin\t"									+ frames_begin);
			writer.println("beads\t"										+ beads);
			writer.println("channel\t"										+ ch);
			writer.println("number of acquired channels\t"					+ numberCh);
			writer.println("Young's_modulus_(in_Pascal)\t"					+ E);
			writer.println("precision for regularization_factor\t"			+ precisionForLambda);
			writer.println("cells_images\t"									+ cells_images);
			writer.println("image_chosen\t"									+ image_chosen);
			writer.println("cells_starting_folder\t"						+ cells_starting_folder);
			writer.println("cells_ending_folder\t"							+ cells_ending_folder);
			writer.println("beads_reference_images\t"						+ beads_reference_images);
			writer.println("beads_reference_images_find_focused_slices\t"	+ beads_reference_images_find_focused_slices);
			writer.println("beads_reference_starting_folder\t"				+ beads_reference_starting_folder);
			writer.println("beads_reference_ending_folder\t"				+ beads_reference_ending_folder);
			writer.println("beads_sequence_images\t"						+ beads_sequence_images);
			writer.println("beads_sequence_images_find_focused_slices\t"	+ beads_sequence_images_find_focused_slices);
			writer.println("beads_sequence_starting_folder\t"				+ beads_sequence_starting_folder);
			writer.println("beads_sequence_ending_folder\t"					+ beads_sequence_ending_folder);
			writer.println("traction_force\t"								+ traction_force);
			writer.println("traction_starting_folder\t"						+ traction_starting_folder);
			writer.println("traction_ending_folder\t"						+ traction_ending_folder);
			writer.println("traction_force_alignment\t"						+ traction_force_alignment);
			writer.println("traction_force_alignment_make\t"				+ traction_force_alignment_make);
			writer.println("traction_force_alignment_crop\t"				+ traction_force_alignment_crop);
			writer.println("traction_force_calculation\t"					+ traction_force_calculation);
			writer.println("piv_calculation\t"								+ piv_calculation);
			writer.println("lambda_calculation\t"							+ lambda_calculation);
			writer.println("force_calculation\t"							+ force_calculation);
			writer.println("force_superposition\t"							+ force_superposition);
			writer.println("cells_analysis\t"								+ cells_analysis);
			writer.println("cells_analysis_starting_folder\t"				+ cells_analysis_starting_folder);
			writer.println("cells_analysis_ending_folder\t"					+ cells_analysis_ending_folder);
			writer.println("cells_segmentation\t"							+ cells_segmentation);
			writer.println("cells_selection\t"								+ cells_selection);
			writer.println("force_integration\t"							+ force_integration);
			writer.println("traction_high_force\t"							+ traction_high_force);
			writer.println("traction_high_enhance_constrast\t"				+ traction_high_enhance_constrast);
			writer.println("traction_high_starting_folder\t"				+ traction_high_starting_folder);
			writer.println("traction_high_ending_folder\t"					+ traction_high_ending_folder);
			writer.println("high_piv_calculation\t"							+ high_piv_calculation);
			writer.println("particle_tracker\t"								+ particle_tracker);
			writer.println("FA_segmentation\t"								+ FA_segmentation);
			writer.println("FA_segmentation_starting_folder\t"				+ FA_segmentation_starting_folder);
			writer.println("FA_segmentation_ending_folder\t"				+ FA_segmentation_ending_folder);
			writer.println("traction_force_applied_on_FA\t"					+ traction_force_applied_on_FA);
			writer.println("traction_applied_on_FA_starting_folder\t"		+ traction_applied_on_FA_starting_folder);
			writer.println("traction_applied_on_FA_ending_folder\t"			+ traction_applied_on_FA_ending_folder);

			writer.close();
		}
		catch (IOException e)
		{
			showDialogWithImageAndCustomOkAndNoCancel("Job saving", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + path, "The job file couldn't be saved");
		}
	}

	private void showData()
	{
		String		title;
		Window		window;
		TextWindow	tw;
		TextPanel	tp;

		title		= "Analysis settings";
		window	= WindowManager.getWindow(title);
		if (!(window instanceof TextWindow))
		{
			IJ.run	("New... ", "name=[" + title + "] type=Table");
			window	= WindowManager.getWindow(title);
			window	.setIconImage(icon);
		}
		tw			= (TextWindow) window;
		tw			.setSize	(900, 1000);
		tw			.setLocation( 10,   10);
		tp			= tw.getTextPanel();

		tp.clear				();
		tp.setColumnHeadings	("Parameter\tValue");
		tp.appendLine			("Folder\t"											+ folder);
		tp.appendLine			("File1\t"											+ file1);
		tp.appendLine			("File2\t"											+ file2);
		tp.appendLine			("Slices\t"											+ slices);
		tp.appendLine			("Frames\t"											+ frames);
		tp.appendLine			("Frames_begin\t"									+ frames_begin);
		tp.appendLine			("Beads_color_1\t"									+ beads1);
		tp.appendLine			("Beads_color_2\t"									+ beads2);
		tp.appendLine			("Ch1\t"											+ ch1);
		tp.appendLine			("Ch2\t"											+ ch2);
		tp.appendLine			("Ch3\t"											+ ch3);
		tp.appendLine			("Model1\t"											+ mod1);
		tp.appendLine			("Model2\t"											+ mod2);
		tp.appendLine			("Model3\t"											+ mod3);
		tp.appendLine			("Number of acquired channels\t"					+ numberCh);
		tp.appendLine			("Young's_modulus_(in_Pascal)\t"					+ E);
		tp.appendLine			("Precision_for_regularization_factor\t"			+ precisionForLambda);
		tp.appendLine			("Cells_images\t"									+ cells_images);
		tp.appendLine			("Image_chosen\t"									+ image_chosen);
		tp.appendLine			("Cells_starting_folder\t"							+ cells_starting_folder);
		tp.appendLine			("Cells_ending_folder\t"							+ cells_ending_folder);
		tp.appendLine			("Beads_reference_images\t"							+ beads_reference_images);
		tp.appendLine			("Beads_reference_images_find_focused_slices\t"		+ beads_reference_images_find_focused_slices);
		tp.appendLine			("Beads_reference_starting_folder\t"				+ beads_reference_starting_folder);
		tp.appendLine			("Beads_reference_ending_folder\t"					+ beads_reference_ending_folder);
		tp.appendLine			("Beads_sequence_images\t"							+ beads_sequence_images);
		tp.appendLine			("Beads_sequence_images_find_focused_slices\t"		+ beads_sequence_images_find_focused_slices);
		tp.appendLine			("Beads_sequence_starting_folder\t"					+ beads_sequence_starting_folder);
		tp.appendLine			("Beads_sequence_ending_folder\t"					+ beads_sequence_ending_folder);
		tp.appendLine			("Traction_force\t"									+ traction_force);
		tp.appendLine			("Traction_starting_folder\t"						+ traction_starting_folder);
		tp.appendLine			("Traction_ending_folder\t"							+ traction_ending_folder);
		tp.appendLine			("Traction_force_alignment\t"						+ traction_force_alignment);
		tp.appendLine			("Traction_force_alignment_make\t"					+ traction_force_alignment_make);
		tp.appendLine			("Traction_force_alignment_crop\t"					+ traction_force_alignment_crop);
		tp.appendLine			("Traction_force_calculation\t"						+ traction_force_calculation);
		tp.appendLine			("PIV_calculation\t"								+ piv_calculation);
		tp.appendLine			("Lambda_calculation\t"								+ lambda_calculation);
		tp.appendLine			("Force_calculation\t"								+ force_calculation);
		tp.appendLine			("Force_superposition\t"							+ force_superposition);
		tp.appendLine			("Cells_analysis\t"									+ cells_analysis);
		tp.appendLine			("Cells_analysis_starting_folder\t"					+ cells_analysis_starting_folder);
		tp.appendLine			("Cells_analysis_ending_folder\t"					+ cells_analysis_ending_folder);
		tp.appendLine			("Cells_segmentation\t"								+ cells_segmentation);
		tp.appendLine			("Cells_selection\t"								+ cells_selection);
		tp.appendLine			("Force_integration\t"								+ force_integration);
		tp.appendLine			("Traction_high_force\t"							+ traction_high_force);
		tp.appendLine			("Traction_high_enhance_constrast\t"				+ traction_high_enhance_constrast);
		tp.appendLine			("Traction_high_starting_folder\t"					+ traction_high_starting_folder);
		tp.appendLine			("Traction_high_ending_folder  \t"					+ traction_high_ending_folder);
		tp.appendLine			("High_piv_calculation\t"							+ high_piv_calculation);
		tp.appendLine			("Particle_tracker\t"								+ particle_tracker);
		tp.appendLine			("FA_segmentation\t"								+ FA_segmentation);
		tp.appendLine			("FA_segmentation_starting_folder\t"				+ FA_segmentation_starting_folder);
		tp.appendLine			("FA_segmentation_ending_folder\t"					+ FA_segmentation_ending_folder);
		tp.appendLine			("traction_force_applied_on_FA\t"					+ traction_force_applied_on_FA);
		tp.appendLine			("traction_applied_on_FA_starting_folder\t"			+ traction_applied_on_FA_starting_folder);
		tp.appendLine			("traction_applied_on_FA_ending_folder\t"			+ traction_applied_on_FA_ending_folder);
	}

	private void cells_images()
	{
		ImagePlus		imp, imp2, impout;
		int				cells_folder, channel, frame;
		int			[]	bestFocus;
		String			folder_begin, folder_cell;

		for(channel = 1; channel <= numberCh && channel != 0; channel++)
		{
//			if(ch == 0) channel = 0;
			if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel = 0;
			else if((ch & format[channel - 1]) == 0) continue;
			for(cells_folder = cells_starting_folder; cells_folder <= cells_ending_folder; cells_folder++)
			{
				folder_cell  = folder + "Cell " + cells_folder + File.separator;
				checkAndCreateFolder(folder_cell);
				imp	= imp2 = null;

				if(frames == 1)
				{
					if(debug)
					{
						if(channel == 0)
							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif");
						else
							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif");
//							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 1, 2) + ".tif");		// ch2
//							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 2, 2) + ".tif");		// ch1
//							imp = IJ.openImage(folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 1, 2) + ".tif");
//							imp = IJ.openImage(folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 2, 2) + ".tif");
//							imp.show();
					}
					else
					{
						if(channel == 0)
							imp = openStealth (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif");
						else
							imp = openStealth (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif");
//						imp.show();
					}

					if(imp == null)
					{
						if(!error)
						{
							error = true;
							if(channel == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 1          , 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad(2 * cells_folder - 3 + channel, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
						}
						return;
					}

					if(imp.isHyperStack())
					{
						frames = imp.getNFrames();
						slices = imp.getNSlices();
						imp = HyperStackConverter.toHyperStack(imp, 1, slices, frames, "default", "Grayscale");
					}

					if(image_chosen == 0)
						bestFocus = KurtFocus(imp);
//						bestFocus = MaxFocus(imp);
//						IJ.run(imp, "Find focused slices", "select=100 variance=0.000 edge");
					else
						bestFocus = new int[] { image_chosen };

					imp2 = new Duplicator().run(imp, bestFocus[0], bestFocus[0]);
//					IJ.run("Make Substack...", "  slices=" + bestFocus);
//					IJ.run("Make Substack...", "  slices=" + 1);

					IJ.resetMinAndMax(imp2);
					try
					{
						switch (channel)
						{
							case 0:	IJ.saveAsTiff(imp2, folder_cell + "Cells_01.tif");		break;
							case 1:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch1_01.tif");	break;
							case 2:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch2_01.tif");	break;
							case 3:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch3_01.tif");	break;
						}
					}
					catch (Exception e)
					{
						switch (channel)
						{
							case 0:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_01.tif"    , "The analysis is stopped at the step \"Cells images\"");	break;
							case 1:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch1_01.tif", "The analysis is stopped at the step \"Cells images\"");	break;
							case 2:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch2_01.tif", "The analysis is stopped at the step \"Cells images\"");	break;
							case 3:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch3_01.tif", "The analysis is stopped at the step \"Cells images\"");	break;
						}
						return;
					}
//					IJ.run("Close");
					imp2.close();
				}
				else
				{
					if(debug)
					{
						if(channel == 0)
//							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad(3 * cells_folder - 1          , 2) + ".tif");
							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif");
						else
						{
							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif");
//							imp = checkScale  (folder + file1 + cells_folder + "_" + IJ.pad(2 * cells_folder - 1          , 2) + ".tif");
						}

						if(imp == null)
						{
							if(!error)
							{
								error = true;
								if(channel == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
							}
							return;
						}
						if(imp.isHyperStack())
						{
							frames = imp.getNFrames();
							slices = imp.getNSlices();
						}
						try
						{
							imp = HyperStackConverter.toHyperStack(imp, 1, slices, frames, "default", "Grayscale");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Cells images", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     1\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + slices * frames + " images" , "The analysis is stopped at the step \"Cells images\"");
							return;
						}
						imp.show();
					}
					else
					{
						if(channel == 0)
							imp = openStealth (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif");
						else
							imp = openStealth (folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif");
						if(imp == null)
						{
							if(!error)
							{
								error = true;
								if(channel == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) *  cells_folder - 1           , 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Cells images", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_folder + "_" + IJ.pad((numberCh + 1) * (cells_folder - 1) + channel, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells images\"");
							}
							return;
						}
						if(imp.isHyperStack())
						{
							frames = imp.getNFrames();
							slices = imp.getNSlices();
						}
						try
						{
							imp = HyperStackConverter.toHyperStack(imp, 1, slices, frames, "default", "Grayscale");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Cells images", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     1\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + slices * frames + " images" , "The analysis is stopped at the step \"Cells images\"");
							return;
						}
//						imp.show();
					}

					if(channel != 0 && (ch & format[channel + 2]) == 0)			// corresponds to mod1, mod2, mod3
					{	// Analysis with EDF
						for(frame = frames_begin; frame <= frames; frame++)
						{
							imp2 = SubHyperstackMaker.makeSubhyperstack(imp, "1", "1-" + slices, "" + frame);
							if(beads_sequence_images_find_focused_slices)
								imp2 = Find_Focused_Slices.getAlignedSlices(imp2, 80, 0.00, true, true, false);
							imp2.show();
							IJ.run("EDF Easy mode", "quality='4' topology='0' show-topology='off' show-view='off'");
							while(WindowManager.getImage("Output") == null)
							{
								IJ.wait(10);
							}
							impout = WindowManager.getImage("Output");
							try
							{
								IJ.saveAs(impout, "Tiff", folder_cell + "Cells_Ch" + channel + "_" + IJ.pad(frame, 2) + ".tif");
							}
							catch (Exception e)
							{
								showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch" + channel + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Cells images\"");
								return;
							}
							impout.close();
							imp2  .close();
						}
					}
					else
					{	// Analysis with Kurtosis
						if(image_chosen == 0)
							bestFocus = KurtFocus(imp);
						else
						{
							bestFocus = new int[frames];
							for(frame = 0; frame < frames; frame++)
								bestFocus[frame] = image_chosen;
						}

						for(frame = frames_begin; frame <= frames; frame++)
						{
//							imp.setPosition(1, bestFocus, frame);
//							IJ.run(imp, "Reduce Dimensionality...", "keep");
							imp2 = new Duplicator().run(imp, 1, 1, bestFocus[frame - 1], bestFocus[frame - 1], frame, frame);
							IJ.resetMinAndMax(imp2);
//							imp2.show();
//							IJ.saveAs("Tiff", folder_cell + "Cells_" + IJ.pad(frame, 2) + ".tif");
							IJ.showStatus("Saving Cells_" + IJ.pad(frame, 2) + ".tif");
							try
							{
								switch (channel)
								{
									case 0:	IJ.saveAsTiff(imp2, folder_cell + "Cells_"     + IJ.pad(frame, 2) + ".tif");	break;
									case 1:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch1_" + IJ.pad(frame, 2) + ".tif");	break;
									case 2:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch2_" + IJ.pad(frame, 2) + ".tif");	break;
									case 3:	IJ.saveAsTiff(imp2, folder_cell + "Cells_Ch3_" + IJ.pad(frame, 2) + ".tif");	break;
								}
							}
							catch (Exception e)
							{
								switch (channel)
								{
									case 0:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_"     + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Cells images\"");			break;
									case 1:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch1_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Cells images\"");			break;
									case 2:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch2_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Cells images\"");			break;
									case 3:	showDialogWithImageAndCustomOkAndNoCancel("Cells images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Cells_Ch3_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Cells images\"");			break;
								}
								return;
							}
//							IJ.run("Close");
							imp2.close();
						}
					}
					if(debug)
						IJ.run("Close");
					else
						imp.close();
				}
				// updating and saving "JEasyTFM_x_end.txt" file
				if(channel == 0 || channel == 3)
				{
					if(cells_starting_folder < cells_ending_folder)
						cells_starting_folder++;
					else
					{
						cells_images			= false;
						cells_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
				///////////////////////////////////////////////////
			}
			if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel--;
		}
	}	// cells_images

	private void beads_reference_images()
	{
		ImagePlus	imp, imp2, impout;
		int			beads_reference_folder, bead;
		String		folder_begin, folder_cell;

//		for(bead = 1; bead <= format.length && bead != 0; bead++)
		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;
			for(beads_reference_folder = beads_reference_starting_folder; beads_reference_folder <= beads_reference_ending_folder; beads_reference_folder++)
			{
				folder_begin = folder.substring(0, folder.length() - 1) + link + "Reference" + File.separator;
				folder_cell  = folder + "Cell " + beads_reference_folder + File.separator;
				imp = null;

				if(beads == 0)
				{
					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(2 * beads_reference_folder, 2) + ".tif");
					if(imp == null)
					{
						if(!error)
						{
							error = true;
							showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "undo.png", "The following file:\n\t\n" + folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(2 * beads_reference_folder, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads reference images\"");
						}
						return;
					}
//					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(3 * beads_reference_folder, 2) + ".tif");
					if(beads_reference_images_find_focused_slices)
						imp = Find_Focused_Slices.getAlignedSlices(imp, 80, 0.00, true, true, false);
					imp.show();

					IJ.run("EDF Easy mode", "quality='4' topology='0' show-topology='off' show-view='off'");
					while(WindowManager.getImage("Output") == null)
					{
						IJ.wait(10);
					}
					impout = WindowManager.getImage("Output");
					try
					{
						IJ.saveAs(impout, "Tiff", folder_cell + "BeadsReference.tif");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "BeadsReference.tif", "The analysis is stopped at the step \"Beads reference images\"");
						return;
					}
					impout.close();
				}
				else
				{
//					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + beads_reference_folder + ".tif");
//					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(beads_reference_folder, 2) + ".tif");
//					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(3 * beads_reference_folder, 2) + ".tif");
					imp = IJ.openImage(folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(2 * beads_reference_folder, 2) + ".tif");
//					imp = HyperStackConverter.toHyperStack(imp, 3, slices, frames, "default", "Grayscale");
					if(imp == null)
					{
						if(!error)
						{
							error = true;
							showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "undo.png", "The following file:\n\t\n" + folder_begin + file2 + beads_reference_folder + "_" + IJ.pad(2 * beads_reference_folder, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads reference images\"");
						}
						return;
					}
					if(imp.isHyperStack())
					{
//						frames = imp.getNFrames();
						slices = imp.getNSlices();
					}
					try
					{
						imp = HyperStackConverter.toHyperStack(imp, 2, slices, 1     , "default", "Grayscale");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     2\nSlices            " + slices + "\nFrames         1\ni.e.                  " + 2 * slices + " images" , "The analysis is stopped at the step \"Beads reference images\"");
						return;
					}
//					imp.show();

					imp2 = SubHyperstackMaker.makeSubhyperstack(imp, "" + bead, "1-" + slices, "1");
					if(beads_reference_images_find_focused_slices)
						imp2 = Find_Focused_Slices.getAlignedSlices(imp2, 80, 0.00, true, true, false);
					imp2.show();
					IJ.run("EDF Easy mode", "quality='4' topology='0' show-topology='off' show-view='off'");
					while(WindowManager.getImage("Output") == null)
					{
						IJ.wait(10);
					}
					impout = WindowManager.getImage("Output");
					try
					{
						IJ.saveAs(impout, "Tiff", folder_cell + "BeadsReference_" + bead + ".tif");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "BeadsReference_" + bead + ".tif", "The analysis is stopped at the step \"Beads reference images\"");
						return;
					}
					impout.close();
					imp2  .close();
				}
				imp.close();
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(beads_reference_starting_folder < beads_reference_ending_folder)
						beads_reference_starting_folder++;
					else
					{
						beads_reference_images		= false;
						beads_reference_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
				///////////////////////////////////////////////////
			}
			if(beads == 0) bead--;
		}
	}	// beads_reference_images

	private void beads_sequence_images()
	{
		ImagePlus	imp			= null;
		ImagePlus	imp1		= null;
		ImagePlus	imp2		= null;
		ImagePlus	imp3		= null;
		ImagePlus	impout		= null;
		int			beads_sequence_folder, bead;
		int			frame;
		String		folder_begin, folder_cell;

//		for(bead = 1; bead <= format.length && bead != 0; bead++)
		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;

			for(beads_sequence_folder = beads_sequence_starting_folder; beads_sequence_folder <= beads_sequence_ending_folder; beads_sequence_folder++)
			{
				folder_cell  = folder + "Cell " + beads_sequence_folder + File.separator;

				if(beads == 0)
				{
//					imp = openStealth (folder + file1 + beads_sequence_folder + "_" + IJ.pad((numberCh + 1) * beads_sequence_folder - numberCh - 1 + u, 2) + ".tif");
					imp = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad((numberCh + 1) * beads_sequence_folder, 2) + ".tif");
//					imp = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + ".tif");
					if(imp == null)
					{
						imp1 = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad((numberCh + 1) * beads_sequence_folder, 2) + "_p1.tif");
						if(imp1 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "undo.png", "The following file:\n\t\n" + folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p1.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads sequence images\"");
							}
							return;
						}
						imp2 = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad((numberCh + 1) * beads_sequence_folder, 2) + "_p2.tif");
						imp3 = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad((numberCh + 1) * beads_sequence_folder, 2) + "_p3.tif");
						if(imp1 != null && imp2 != null)
						{
							if(imp3 != null)
							{
								imp	= Concatenator.run(imp1, imp2, imp3);
								imp3.close();
							}
							else
								imp	= Concatenator.run(imp1, imp2);
//							imp	.show();
							imp1.close();
							imp2.close();
						}
						else if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "undo.png", "The following file:\n\t\n" + folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p1.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads sequence images\"");
							}
							imp1.close();
							return;
						}
					}
					if(imp.isHyperStack())
					{
						frames = imp.getNFrames();
						slices = imp.getNSlices();
					}
					try
					{
						imp = HyperStackConverter.toHyperStack(imp, 1, slices, frames, "default", "Grayscale");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     1\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + slices * frames + " images" , "The analysis is stopped at the step \"Beads reference images\"");
						return;
					}
//					imp.show();
					for(frame = frames_begin; frame <= frames; frame++)
					{
						imp2 = SubHyperstackMaker.makeSubhyperstack(imp, "1", "1-" + slices, "" + frame);
						if(beads_sequence_images_find_focused_slices)
							imp2 = Find_Focused_Slices.getAlignedSlices(imp2, 80, 0.00, true, true, false);
						imp2.show();
						IJ.run("EDF Easy mode", "quality='4' topology='0' show-topology='off' show-view='off'");
						while(WindowManager.getImage("Output") == null)
						{
							IJ.wait(10);
						}
						impout = WindowManager.getImage("Output");
						try
						{
							IJ.saveAs(impout, "Tiff", folder_cell + "BeadsAfter_" + IJ.pad(frame, 2) + ".tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "BeadsAfter_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Beads sequence images\"");
							return;
						}
						impout.close();
						imp2  .close();
					}
				}
				else
				{
					imp = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + ".tif");
//					imp = IJ.openImage(folder + getFileName(folder, file1, beads_sequence_folder));
					if(imp == null)
					{
						imp1 = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p1.tif");
						if(imp1 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "undo.png", "The following file:\n\t\n" + folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p1.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads sequence images\"");
							}
							return;
						}
						imp2 = IJ.openImage(folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p2.tif");
						if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "undo.png", "The following file:\n\t\n" + folder + file1 + String.valueOf(beads_sequence_folder) + "_" + IJ.pad(2 * beads_sequence_folder, 2) + "_p2.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Beads sequence images\"");
							}
							imp1.close();
							return;
						}
						imp  = Concatenator.run(imp1, imp2);
						imp1 .close();
						imp2 .close();
					}
					if(imp.isHyperStack())
					{
						frames = imp.getNFrames();
						slices = imp.getNSlices();
					}
					try
					{
//						imp = HyperStackConverter.toHyperStack(imp, 3, slices, frames, "default", "Grayscale");
						imp = HyperStackConverter.toHyperStack(imp, 2, slices, frames, "default", "Grayscale");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Beads reference images", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     2\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + 2 * slices * frames + " images" , "The analysis is stopped at the step \"Beads reference images\"");
						return;
					}
//					imp.show();

					for(frame = frames_begin; frame <= frames; frame++)
					{
						imp2 = SubHyperstackMaker.makeSubhyperstack(imp, "" + bead, "1-" + slices, "" + frame);
						if(beads_sequence_images_find_focused_slices)
							imp2 = Find_Focused_Slices.getAlignedSlices(imp2, 80, 0.00, true, true, false);
						imp2.show();
						IJ.run("EDF Easy mode", "quality='4' topology='0' show-topology='off' show-view='off'");
						while(WindowManager.getImage("Output") == null)
						{
							IJ.wait(10);
						}
						impout = WindowManager.getImage("Output");
						try
						{
							IJ.saveAs(impout, "Tiff", folder_cell + "BeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Beads sequence images", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "BeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Beads sequence images\"");
							return;
						}
						impout.close();
						imp2  .close();
					}
//					imp2 = SubHyperstackMaker.makeSubhyperstack(imp, "" + 3, "" + slices, "1");
//					imp2.show();
//					IJ.saveAsTiff(imp2, folder_cell + "Cells_01.tif");
//					imp2.close();
				}
				imp.close();
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(beads_sequence_starting_folder < beads_sequence_ending_folder)
						beads_sequence_starting_folder++;
					else
					{
						beads_sequence_images			= false;
						beads_sequence_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
				///////////////////////////////////////////////////
			}
			if(beads == 0) bead--;
		}
	}	// beads_sequence_images

	private void traction_force()
	{
		ImagePlus				imp1, imp2, stackImp, impProj;
		ImageProcessor			ip1 , ip2 , stackIp, stackIp2;
		ImageStack				is;
		ImageConverter			converter;
		ZProjector				zproj;
		Roi						roi;
		String					folder_cell, str;
		int						traction_folder, bead, channel, frame;
		int						widthCorr	= 0;
		int						heightCorr	= 0;
		double					scaleMin;
		double					scaleMax;
		double					dx, dy;
		double					 x,  y, width, height;
		int		[]				delta, dim;
		double	[]				displacement;
		double	[]				scale;

		FileOutputStream		fos;
		BufferedOutputStream	bos;
		PrintWriter				writer;

//		for(bead = 1; bead <= format.length && bead != 0; bead++)
		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;
			for(traction_folder = traction_starting_folder; traction_folder <= traction_ending_folder; traction_folder++)
			{
				folder_cell = folder + "Cell " + traction_folder + File.separator;

				scale = new double[frames];
//				dx = dy = 0;
//				f = File.open(folder_cell + "table.txt");

				if(traction_force_alignment)
				{
					if(traction_force_alignment_make)
					{
						// Creating the aligned images
						for(frame = frames_begin; frame <= frames; frame++)
						{
							imp1 = imp2 = null;
							if(beads == 0)
							{
//								imp1 = IJ.openImage(folder_cell + "BeadsReference.tif");
//								imp1.show();
//								imp1 = IJ.openImage(folder_cell + "BeadsAfter_"           + IJ.pad(frame, 2) + ".tif");
//								imp1.show();
								imp1	= IJ.openImage(folder_cell + "BeadsReference.tif");
								if(imp1 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "BeadsReference.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");
									}
									return;
								}
								IJ.run	(imp1, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp1, "Enhance Contrast..."   , "saturated=0.4 normalize");
								is		= imp1.getStack();
								imp2	= IJ.openImage(folder_cell + "BeadsAfter_"           + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "BeadsAfter_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");
									}
									imp1.close();
									return;
								}
								IJ.run	(imp2, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp2, "Enhance Contrast..."   , "saturated=0.4 normalize");
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								stackImp	= new ImagePlus("Stack", is);
//								stackImp	.show();
								imp1	.close();
								imp2	.close();
							}
							else
							{
//								imp1 = IJ.openImage(folder_cell + "BeadsReference_" + bead + ".tif");
//								imp1.show();
//								imp1 = IJ.openImage(folder_cell + "BeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//								imp1.show();
								imp1 = IJ.openImage(folder_cell + "BeadsReference_" + bead + ".tif");
								if(imp1 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "BeadsReference_" + bead                      + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");
									}
									return;
								}
								is		= imp1.getStack();
								imp2 = IJ.openImage(folder_cell + "BeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "BeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");
									}
									imp1.close();
									return;
								}
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								stackImp	= new ImagePlus("Stack", is);
//								stackImp	.show();
								imp1	.close();
								imp2	.close();
							}
//							IJ.run("Images to Stack", "name=Stack title=[] use");
//							IJ.run("16-bit");
							converter	= new ImageConverter(stackImp);
							converter	.convertToGray16();
//							stackImp.show();
//							IJ.run("Align slices in stack...", "method=5 windowsizex=604 windowsizey=602 x0=200 y0=200 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=250 windowsizey=250 x0=16 y0=681 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=250 windowsizey=250 x0=370 y0=940 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=311 windowsizey=281 x0=34 y0=488 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=300 windowsizey=300 x0=35 y0=490 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=404 windowsizey=371 x0=613 y0=606 swindow=0 subpixel=false itpmethod=0 ref.slice=1 show=true");
//							IJ.run("Align slices in stack...", "method=5 windowsizex=404 windowsizey=371 x0=613 y0=606 swindow=0 subpixel=true itpmethod=1 ref.slice=1 show=true");
							displacement = TemplateMatching.Align_slices.getAlignSlicesDisplacement(stackImp, "Normalized correlation coefficient", 72, 137, 455, 341, 0, true, "Bicubic", 1, false);
//							displacement = TemplateMatching.Align_slices.getAlignSlicesDisplacement(stackImp, "Normalized correlation coefficient", 404, 371, 613, 606, 0, true, "Bicubic", 1, false);
//							displacement = TemplateMatching.Align_slices.getAlignSlicesDisplacement(stackImp, "Normalized correlation coefficient", stackImp.getWidth() / 8, stackImp.getHeight() / 8, stackImp.getWidth() * 3 / 4, stackImp.getHeight() * 3 / 4, 0, true, "Bicubic", 1, false);
//							stackImp.deleteRoi();
//							closeWindow("Log");
//							dx2 = getResult("dX", 0);
//							dy2 = getResult("dY", 0);
							dx = displacement[0];
							dy = displacement[1];
//							closeWindow("Results");

//							IJ.run("Stack to Images");
//							if(beads == 0)
//								IJ.selectWindow("BeadsReference");
//							else
//								IJ.selectWindow("BeadsReference_" + bead);
							if(frame == 1)
							{
								imp1 = new Duplicator().run(stackImp, 1, 1);
								try
								{
									if(beads == 0)
									{
										checkAndCreateFolder(						  folder_cell + "Analysis");
//										IJ.saveAs           ("Tiff"					, folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif");
										IJ.saveAsTiff		(imp1					, folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif");
										IJ.saveString       ("Displacement data\n"	, folder_cell + "Analysis"         + File.separator + "Transformation.txt");
									}
									else
									{
										checkAndCreateFolder(						  folder_cell + "Analysis_" + bead);
//										IJ.saveAs           ("Tiff"					, folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
										IJ.saveAsTiff		(imp1					, folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
										IJ.saveString       ("Displacement data\n"	, folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");
									}
									imp1.close();
								}
								catch (Exception e)
								{
									if(beads == 0)
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif"             , "The analysis is stopped at the step \"Traction force alignment make\"");
									else
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
									return;
								}
							}
//							IJ.run("Close");
//							if(beads == 0)
//								IJ.selectWindow("BeadsAfter_"              + IJ.pad(frame, 2));
//							else
//								IJ.selectWindow("BeadsAfter_" + bead + "_" + IJ.pad(frame, 2));
							imp2 = new Duplicator().run(stackImp, 2, 2);
							stackImp.close();

//							print(f, dx + "  \t" + dy + "  \t" + dx + "  \t" + dy + "  \t" + getPositionX1() + "  \t" + getPositionX2() + "  \t" + getPositionY1() + "  \t" + getPositionY2());
							if(frame == 1)
							{
								if(beads == 0)
								{
									checkAndCreateFolder(folder_cell + "CorrBeadsAfter");
									checkAndCreateFolder(folder_cell + "CorrCells");
								}
								else
								{
									checkAndCreateFolder(folder_cell + "CorrBeadsAfter_" + bead);
									checkAndCreateFolder(folder_cell + "CorrCells_"      + bead);
								}
							}
							try
							{
								if(beads == 0)
//									IJ.saveAs("Tiff"  , folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif");
									IJ.saveAsTiff(imp2, folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif");
								else
//									IJ.saveAs("Tiff"  , folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
									IJ.saveAsTiff(imp2, folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//								IJ.run("Close");
								imp2.close();
							}
							catch (Exception e)
							{
								if(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
								return;
							}

							for(channel = 1; channel <= numberCh && channel != 0; channel++)
							{
								imp1 = null;
								if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel = 0;
								else if((ch & format[channel - 1]) == 0) continue;
//								imp1 = IJ.openImage(folder_cell + "Cells_" + IJ.pad(frame, 2) + ".tif");
								switch (channel)
								{
									case 0:	imp1 = IJ.openImage(folder_cell + "Cells_"     + IJ.pad(frame, 2) + ".tif");		break;
									case 1:	imp1 = IJ.openImage(folder_cell + "Cells_Ch1_" + IJ.pad(frame, 2) + ".tif");		break;
									case 2:	imp1 = IJ.openImage(folder_cell + "Cells_Ch2_" + IJ.pad(frame, 2) + ".tif");		break;
									case 3:	imp1 = IJ.openImage(folder_cell + "Cells_Ch3_" + IJ.pad(frame, 2) + ".tif");		break;
								}
								if(imp1 == null)
								{
									switch (channel)
									{
										case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "Cells_"     + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
										case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "Cells_Ch1_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
										case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "Cells_Ch2_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
										case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "undo.png", "The following file:\n\t\n" + folder_cell + "Cells_Ch3_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
									}
									return;
								}
//								ip1  = imp1.getProcessor();

//								ip1.translate(dx, dy);
								IJ.run(imp1, "Translate...", "x=" + dx + " y=" + dy + " interpolation=Bicubic");
								str = frame + "\t" + dx + "\t" + dy;

								try
								{
									if(beads == 0)
									{
//										IJ.saveAs(imp1, "Tiff", folder_cell + "CorrCells" + File.separator + "CorrCells_"                                       + IJ.pad(frame, 2) + ".tif");
										switch (channel)
										{
											case 0:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif");		break;
											case 1:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif");		break;
											case 2:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif");		break;
											case 3:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif");		break;
										}
										IJ.append(str, folder_cell + "Analysis" + File.separator + "Transformation.txt");
									}
									else
									{
//										IJ.saveAs(imp1, "Tiff", folder_cell + "CorrCells_"   + bead + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
										switch (channel)
										{
											case 0:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif");		break;
											case 1:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif");		break;
											case 2:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif");		break;
											case 3:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif");		break;
										}
										IJ.append(str, folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");
									}
									imp1.close();
								}
								catch (Exception e)
								{
									if(beads == 0)
									{
										switch (channel)
										{
											case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
										}
									}
									else
									{
										switch (channel)
										{
											case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
											case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");		break;
										}
									}
									return;
								}
								if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel--;
							}
						}
//						File.close(f);
						// updating and saving "JEasyTFM_x_end.txt" file
						if((bead == 0 || bead == 2) && traction_folder == traction_ending_folder)
						{
							traction_force_alignment_make	= false;
							saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
						}
					}	// traction_force_alignment_make

					if(traction_force_alignment_crop)
					{
						// generating the ROI
						frame	= 1;
						if(beads == 0)
						{
							imp1 = null;
							imp1 = IJ.openImage    (folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                        + IJ.pad(frame, 2) + ".tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");
								}
								return;
							}
							is		= imp1.getStack();
							for(frame = 2; frame <= frames; frame++)
							{
								imp2 = null;
								imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                     + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");
									}
									return;
								}
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								imp2	.close();
							}
						}
						else
						{
							imp1 = null;
							imp1	= IJ.openImage    (folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel    ("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");
								}
								return;
							}
							is		= imp1.getStack();
							for(frame = 2; frame <= frames; frame++)
							{
								imp2 = null;
								imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");
									}
									return;
								}
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								imp2	.close();
							}
						}
						stackImp	= new ImagePlus("Stack", is);
						imp1.close();
//						stackImp	.show();
//						IJ.run("Z Project...", "projection=[Min Intensity]");
						zproj = new ZProjector(stackImp);
						zproj.setStartSlice(1);
						zproj.setStopSlice (is.getSize());
						zproj.setMethod(ZProjector.MIN_METHOD);
						zproj.doProjection();
						impProj = zproj.getProjection();
//						impProj = ZProjector.run(stackImp, "min");
/*
						if(dx >= 0)
							hx = Math.round(dx / 2);
						else
							hx = IJ.getImage().getWidth() + Math.round(dx / 2);
						if(dy >= 0)
							hy = Math.round(dy / 2);
						else
							hy = IJ.getImage().getHeight() + Math.round(dy / 2);
						IJ.doWand(hx, hy);
						IJ.run("Make Inverse");
*/
						str = "Croping data\n" + getPositionX1(impProj) + "\t" + getPositionY1(impProj) + "\t" + (getPositionX2(impProj) - getPositionX1(impProj) + 1) + "\t" + (getPositionY2(impProj) - getPositionY1(impProj) + 1);
						if(beads == 0)
							IJ.append(str, folder_cell + "Analysis" + File.separator + "Transformation.txt");
						else
							IJ.append(str, folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");

//						IJ.makeRectangle(getPositionX1(), getPositionY1(), getPositionX2() - getPositionX1() + 1, getPositionY2() - getPositionY1() + 1);
						impProj.setRoi  (getPositionX1(impProj), getPositionY1(impProj), getPositionX2(impProj) - getPositionX1(impProj) + 1, getPositionY2(impProj) - getPositionY1(impProj) + 1);
						impProj.close();

						// getting the ROI position and size
//						IJ.run("Restore Selection");
						stackImp.restoreRoi();

						// getBoundingRect(x, y, width, height);
						roi = stackImp.getRoi();
						if(roi != null)
						{
							Rectangle2D.Double r	= roi.getFloatBounds();
							x						= r.x;
							y						= r.y;
							width					= r.width;
							height					= r.height;
						}
						else
							x = y = width = height = 0;

						// croping and saving the beads time images
//						stackIp  = stackImp.getProcessor();
//						stackIp2 = stackIp .crop();
						IJ.run(stackImp, "Crop", "");

						// getDimensions(widthCorr, heightCorr, channelsCorr, slicesCorr, framesCorr);
//						stackImp	= new ImagePlus("Croped stack", stackIp2);
//						stackImp.show();
						dim			= stackImp.getDimensions();
						widthCorr	= dim[0];
						heightCorr	= dim[1];

						// images cleaning - code from Mickael Schmid
//						IJ.run(stackImp, "Thresholded Blur", "radius=3 threshold=1000 softness=0.50 strength=1 stack");
//						IJ.run(stackImp, "Subtract Background...", "rolling=0.2 sliding stack");

						for(frame = frames_begin; frame <= frames; frame++)
						{
//							IJ.run("Make Substack...", "  slices=" + frame);
							imp1 = new Duplicator().run(stackImp, frame, frame);
							try
							{
								if(beads == 0)
									IJ.saveAsTiff(imp1, folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif");
								else
									IJ.saveAsTiff(imp1, folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//								IJ.run("Close");
								imp1.close();
							}
							catch (Exception e)
							{
								if(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
								return;
							}
						}
//						IJ.run("Close");
						stackImp.close();

						// croping and saving the beads reference image
						imp1 = null;
						if(beads == 0)
							imp1 = IJ.openImage(folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif");
						else
							imp1 = IJ.openImage(folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
						if(imp1 == null)
						{
							if(!error)
							{
								error = true;
								if(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif\n\t\ncould not be found"             , "The analysis is stopped at the step \"Traction force alignment crop\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");
							}
							return;
						}
						imp1.setRoi((int) x, (int) y, (int) width, (int) height);
						ip1	= imp1.getProcessor();
						ip2	= ip1 .crop();
						imp1.setProcessor(ip2);

						// Images cleaning - code from Mickael Schmid
//						IJ.run(imp1, "Thresholded Blur", "radius=3 threshold=1000 softness=0.50 strength=1");
//						IJ.run(imp1, "Subtract Background...", "rolling=0.2 sliding");

						try
						{
							if(beads == 0)
								IJ	.saveAs(imp1, "Tiff", folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif");
							else
								IJ	.saveAs(imp1, "Tiff", folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
							imp1.close();
						}
						catch (Exception e)
						{
							if(beads == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif"             , "The analysis is stopped at the step \"Traction force alignment make\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment make", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif", "The analysis is stopped at the step \"Traction force alignment make\"");
							return;
						}

						// croping and saving the Cells time images
						for(channel = 1; channel <= numberCh && channel != 0; channel++)
						{
							if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel = 0;
							else if((ch & format[channel - 1]) == 0) continue;
							for(frame = frames_begin; frame <= frames; frame++)
							{
								imp1 = null;
								if(beads == 0)
								{
									switch (channel)
									{
										case 0:	imp1 = IJ.openImage(folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif");		break;
										case 1:	imp1 = IJ.openImage(folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif");		break;
										case 2:	imp1 = IJ.openImage(folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif");		break;
										case 3:	imp1 = IJ.openImage(folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif");		break;
									}
								}
								else
								{
//									imp1 = IJ.openImage(folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
									switch (channel)
									{
										case 0:	imp1 = IJ.openImage(folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif");		break;
										case 1:	imp1 = IJ.openImage(folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif");		break;
										case 2:	imp1 = IJ.openImage(folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif");		break;
										case 3:	imp1 = IJ.openImage(folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif");		break;
									}
								}
								if(imp1 == null)
								{
									if(!error)
									{
										error = true;
										if(beads == 0)
										{
											switch (channel)
											{
												case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											}
										}
										else
										{
											switch (channel)
											{
												case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
												case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											}
										}
									}
									return;
								}

								imp1.setRoi((int) x, (int) y, (int) width, (int) height);
								ip1  = imp1.getProcessor();
								ip2  = ip1 .crop();
								imp1.setProcessor(ip2);
								try
								{
									if(beads == 0)
									{
//										IJ	.saveAs(imp1, "Tiff", folder_cell + "CorrCells" + File.separator + "CorrCells_"                     + IJ.pad(frame, 2) + ".tif");
										switch (channel)
										{
											case 0:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif");		break;
											case 1:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif");		break;
											case 2:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif");		break;
											case 3:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif");		break;
										}
									}
									else
									{
//										IJ	.saveAs(imp1, "Tiff", folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
										switch (channel)
										{
											case 0:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif");		break;
											case 1:	IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif");		break;
											case 2: IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif");		break;
											case 3: IJ.saveAsTiff(imp1, folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif");		break;
										}
									}
									imp1.close();
								}
								catch (Exception e)
								{
									if(beads == 0)
									{
										switch (channel)
										{
											case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
										}
									}
									else
									{
										switch (channel)
										{
											case 0:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_"     + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 1:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 2:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
											case 3:	showDialogWithImageAndCustomOkAndNoCancel("Traction force alignment crop", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "CorrCells_" + bead + File.separator + "CorrCells_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force alignment crop\"");		break;
										}
									}
									return;
								}
							}
							if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel--;
						}
						// updating and saving "JEasyTFM_x_end.txt" file
						if((bead == 0 || bead == 2) && traction_folder == traction_ending_folder)
						{
							traction_force_alignment		= false;
							traction_force_alignment_crop	= false;
							saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
						}
						///////////////////////////////////////////////////
					}	// traction_force_alignment_crop
				}	// traction_force_alignment

				if(traction_force_calculation)
				{
					if(piv_calculation)
					{
						for(frame = frames_begin; frame <= frames; frame++)
						{
							imp1 = imp2 = null;
							// Force 0
							if(beads == 0)
							{
								imp1	= IJ.openImage(folder_cell + "Analysis" + File.separator + "CorrBeadsReference.tif");
								if(imp1 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "CorrBeadsReference.tif\n\t\ncould not be found", "The analysis is stopped at the step \"PIV calculation\"");
									}
									return;
								}
								is		= imp1.getStack();
								imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                     + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                     + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"PIV calculation\"");
									}
									imp1.close();
									return;
								}
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								stackImp= new ImagePlus("Stack_" + IJ.pad(frame, 2) + ".tif", is);
							}
							else
							{
								imp1	= IJ.openImage(folder_cell + "Analysis_"       + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
								if(imp1 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_"       + bead + File.separator + "CorrBeadsReference_" + bead + ".tif\n\t\ncould not be found"                         , "The analysis is stopped at the step \"PIV calculation\"");
									}
									return;
								}
								is		= imp1.getStack();
								imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								if(imp2 == null)
								{
									if(!error)
									{
										error = true;
										showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"PIV calculation\"");
									}
									imp1.close();
									return;
								}
								ip2		= imp2.getProcessor();
								is		.addSlice(ip2);
								stackImp= new ImagePlus("Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", is);
							}
//							IJ.run("Images to Stack", "name=Stack title=[] use");
//							IJ.run("Translation Alignment");
//							IJ.saveAs("Tiff", folder_cell + "Stack" + IJ.pad(frame, 2) + ".tif");
//							IJ.selectWindow("Stack" + IJ.pad(frame, 2) + ".tif");

							// Force 1
							converter	= new ImageConverter(stackImp);
							converter	.convertToGray16();

							if(debug)
							{
								stackImp	.show();
//								IJ.run("Reverse");
								if(beads == 0)
									IJ.run(stackImp, "PIV Advanced", "  piv1=128 sw1=256 vs1=64 piv2=64 sw2=128 vs2=32 piv3=48 sw3=128 vs3=&vs3 correlation=0.60 debug_x=-1 debug_y=-1 path=/ what=[Normalized median test and replace invalid by median then Accept this PIV and output] noise=0.20 threshold=5 c1=3 c2=1 save=[" + folder_cell + "Analysis"         + File.separator + "Stack_"              + IJ.pad(frame, 2) + ".txt]");
								else
									IJ.run(stackImp, "PIV Advanced", "  piv1=128 sw1=256 vs1=64 piv2=64 sw2=128 vs2=32 piv3=48 sw3=128 vs3=&vs3 correlation=0.60 debug_x=-1 debug_y=-1 path=/ what=[Normalized median test and replace invalid by median then Accept this PIV and output] noise=0.20 threshold=5 c1=3 c2=1 save=[" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt]");
								IJ.run("Close");
								if(beads == 0)
								{
//									IJ.selectWindow("PIV3_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
//									IJ.saveAs("Tiff", folder_cell + "PIV3_" + "Stack_" + IJ.pad(frame, 2) + ".tif");
//									IJ.run("Close");
									closeWindow("PIV3_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
									closeWindow("PIV2_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
									closeWindow("PIV1_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
									closeWindow(          "Stack_"           + IJ.pad(frame, 2) + ".tif");
								}
								else
								{
//									IJ.selectWindow("PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//									IJ.saveAs("Tiff", folder_cell + "PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//									IJ.run("Close");
									closeWindow("PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
									closeWindow("PIV2_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
									closeWindow("PIV1_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
									closeWindow(          "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								}
							}
							else
							{
								if(beads == 0)
									PIV_iterative.generateAdvancedIterativePIV(stackImp, false, 128, 256, 64, 64, 128, 32, 48, 128, 16, 0.60, false, false, false, false, "", "Normalized median test and replace invalid by median then Accept this PIV and output", 0.20, 5, 3, 1, folder_cell + "Analysis"         + File.separator + "Stack_"              + IJ.pad(frame, 2) + ".txt");
								else
									PIV_iterative.generateAdvancedIterativePIV(stackImp, false, 128, 256, 64, 64, 128, 32, 48, 128, 16, 0.60, false, false, false, false, "", "Normalized median test and replace invalid by median then Accept this PIV and output", 0.20, 5, 3, 1, folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
							}
							imp1	.close();
							imp2	.close();
							stackImp.changes = false;
							stackImp.close();
							closeWindows();

							try
							{
								if(beads == 0)
								{
									PIV_plot.drawPlot(folder_cell + "Analysis"         + File.separator,       "Stack_"              + IJ.pad(frame, 2) + ".txt", true, 1, 50.0, 0, 0, false, false, false, true, false, false, lut);
									IJ.saveAs("Tiff", folder_cell + "Analysis"         + File.separator + "PIV3_Stack_"              + IJ.pad(frame, 2) + ".tif");
								}
								else
								{
									PIV_plot.drawPlot(folder_cell + "Analysis_" + bead + File.separator,       "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", true, 1, 50.0, 0, 0, false, false, false, true, false, false, lut);
									IJ.saveAs("Tiff", folder_cell + "Analysis_" + bead + File.separator + "PIV3_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								}
								IJ.run("Close");
							}
							catch (Exception e)
							{
								if	(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "PIV3_Stack_"                    + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"PIV calculation\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("PIV calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "PIV3_Stack_"       + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"PIV calculation\"");
								return;
							}
						}
						// updating and saving "JEasyTFM_x_end.txt" file
						if((bead == 0 || bead == 2) && traction_folder == traction_ending_folder)
						{
							piv_calculation				= false;
							saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
						}
						///////////////////////////////////////////////////
					}	// piv_calculation
					if(lambda_calculation)
					{
						try
						{
							if(beads == 0)
							{
								checkAndCreateFolder(						  folder_cell + "Analysis");
								IJ.saveString       ("Stack\tLambda\n"		, folder_cell + "Analysis"         + File.separator + "Lambda.txt");
							}
							else
							{
								checkAndCreateFolder(						  folder_cell + "Analysis_" + bead);
								IJ.saveString       ("Stack\tLambda\n"		, folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt");
							}
						}
						catch (Exception e)
						{
							if(beads == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Lambda value calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "Lambda.txt", "The analysis is stopped at the step \"Traction force Lambda calculation\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Lambda value calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt", "The analysis is stopped at the step \"Traction force Lambda calculation\"");
							return;
						}

						lambda_values = new double[frames];

						for(frame = frames_begin; frame <= frames; frame++)
						{
//							frame = 1;
/*
debut
							double min		= FTTC_main.getScaleValue(folder_cell + "Analysis" + File.separator, "Stack_" + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, 1.0e1  , unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
							double max		= FTTC_main.getScaleValue(folder_cell + "Analysis" + File.separator, "Stack_" + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, 1.0e-21, unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
							double goal		= (max - min) / 2.0;

							IJ.log("min    = " + min);
							IJ.log("max    = " + max);

							IJ.log("precisionForLambda = " + precisionForLambda);

							IJ.log("goal    = " + goal);
fin
*/
//							lambda						= Math.pow(10.0, -runBinarySearch(-1, 21, precisionForLambda, folder_cell, frame, widthCorr, heightCorr));
							lambda_values[frame - 1]	= Math.pow(10.0, -runBinarySearch(-1, 21, precisionForLambda, folder_cell, frame, widthCorr, heightCorr));

//							IJ.log("output = " + FTTC_main.getScaleValue(folder_cell + "Analysis" + File.separator, "Stack_" + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, lambda, unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut));

							try
							{
								if(beads == 0)
									IJ.append("Stack_" + IJ.pad(frame, 2) + "\t" + lambda_values[frame - 1]	, folder_cell + "Analysis"         + File.separator + "Lambda.txt");
								else
									IJ.append("Stack_" + IJ.pad(frame, 2) + "\t" + lambda_values[frame - 1]	, folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt");
							}
							catch (Exception e)
							{
								if(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Lambda value calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "Lambda.txt", "The analysis is stopped at the step \"Traction force Lambda calculation\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Lambda value calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt", "The analysis is stopped at the step \"Traction force Lambda calculation\"");
								return;
							}
						}
					}	// lambda_calculation
					if(force_calculation)
					{
						// In the case the lamda values haven't been generated they can be read from the Lambda.txt file
						if(lambda_values == null)
						{
							if(beads == 0)
								lambda_values = get_lambda_values(folder_cell + "Analysis"         + File.separator + "Lambda.txt");
							else
								lambda_values = get_lambda_values(folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt");
						}

						for(frame = frames_begin; frame <= frames; frame++)
						{
							// Force 2
							if(beads == 0)
							{
								file = new File(folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + ".txt");
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "undo.png", "The following file:\n\t\n" +	folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"Force calculation\"");
									return;
								}
								else
								{
									try
									{
										scale[frame - 1] = FTTC_main.getScaleValue(folder_cell + "Analysis" + File.separator, "Stack_" + IJ.pad(frame, 2) + ".txt",							length_scale, 0.5, E, lambda_values[frame - 1], unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis" + File.separator + "Stack_"	+ IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Force calculation\"");
										return;
									}
								}
							}
							else
							{
								file = new File(folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"Force calculation\"");
									return;
								}
								else
								{
									try
									{
										scale[frame - 1] = FTTC_main.getScaleValue(folder_cell + "Analysis_" + bead + File.separator, "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt",	length_scale, 0.5, E, lambda_values[frame - 1], unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Force calculation\"");
									}
								}
							}
						}

//						Array.getStatistics(Scale, Scalemin, Scalemax, Scalemean, ScalestdDev);
						scaleMin = scaleMax = scale[0];
						for(frame = 1; frame < scale.length; frame++)
						{
								if(scale[frame] > scaleMax)
										scaleMax = scale[frame];
								else if (scale[frame] < scaleMin)
										scaleMin = scale[frame];
						}
						if(debug)
							IJ.log("Scale   " + scaleMin + "   " + scaleMax);

						try
						{
							if(beads == 0)
								fos		= new FileOutputStream		(folder_cell + "Analysis"         + File.separator + "scale.txt");
							else
								fos		= new FileOutputStream		(folder_cell + "Analysis_" + bead + File.separator + "scale_" + bead + ".txt");
							bos		= new BufferedOutputStream	(fos);
							writer	= new PrintWriter			(bos, true);
							if(beads == 0)
							{
								for(frame = 1; frame < scale.length; frame++)
									writer	.println("Stack_"           + IJ.pad(frame, 2) + "\t" + String.valueOf(scale[frame - 1]));
							}
							else
							{
								for(frame = 1; frame < scale.length; frame++)
									writer	.println("Stack_" + bead + "_" + IJ.pad(frame, 2) + "\t" + String.valueOf(scale[frame - 1]));
							}
							writer	.println("Scale   " + scaleMin + "   " + scaleMax);
							writer	.close();
						}
						catch (IOException e)
						{
							if(beads == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "scale.txt"             , "The analysis is stopped at the step \"Force calculation\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "scale_" + bead + ".txt", "The analysis is stopped at the step \"Force calculation\"");
							return;
						}

						// Force 3
						if(beads == 0)
							checkAndCreateFolder(folder_cell + "Traction_Vector_Plot");
						else
							checkAndCreateFolder(folder_cell + "Traction_Vector_Plot_" + bead);
						for(frame = frames_begin; frame <= frames; frame++)
						{
							if(beads == 0)
							{
								file = new File(folder_cell + "Analysis" + File.separator + "Traction_Stack_" + IJ.pad(frame, 2) + ".txt");
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "Traction_Stack_"           + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"Force calculation\"");
									return;
								}
								else
								{
									try
									{
										FTTC_plot.drawPlot(folder_cell + "Analysis" + File.separator     , "Traction_Stack_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, false, true, true, false, false, false, lut);
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis" + File.separator + "Traction_Stack_"           + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Force calculation\"");
										return;
									}
								}
								imp1 = IJ.getImage();
								try
								{
									IJ.saveAsTiff(imp1, folder_cell + "Traction_Vector_Plot" + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + IJ.pad(frame, 2) + ".tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("force_integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_Vector_Plot"      + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp1.close();
								imp2 = IJ.getImage();
								try
								{
									IJ.saveAsTiff(imp2, folder_cell + "Traction_Vector_Plot" + File.separator + "Traction_Vector_Plot_Traction_Stack_"    + IJ.pad(frame, 2) + ".tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("force_integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_Vector_Plot"      + File.separator + "Traction_Vector_Plot_Traction_Stack_"    + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp2.close();
							}
							else
							{
								file = new File(folder_cell + "Analysis_" + bead + File.separator + "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"Force calculation\"");
									return;
								}
								else
								{
									try
									{
										FTTC_plot.drawPlot(folder_cell + "Analysis_" + bead + File.separator, "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, false, true, true, false, false, false, lut);
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Force calculation\"");
										return;
									}
								}
								imp1 = IJ.getImage();
								try
								{
									IJ.saveAsTiff(imp1, folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("force_integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp1.close();
								imp2 = IJ.getImage();
								try
								{
									IJ.saveAsTiff(imp2, folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("force_integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp2.close();

								try
								{
									IJ.saveAs("Tiff", folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force calculation", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_Vector_Plot_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Force calculation\"");
									return;
								}
							}
//							IJ.run("Close");
//							closeWindows();
						}
						// updating and saving "JEasyTFM_x_end.txt" file
						if((bead == 0 || bead == 2) && traction_folder == traction_ending_folder)
						{
							traction_force_calculation	= false;
							force_calculation			= false;
							saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
						}
						///////////////////////////////////////////////////
					}	// force_calculation

					if(force_superposition)
					{
						//	Force 4
						if(beads == 0)
							checkAndCreateFolder(folder_cell + "PicCells");
						else
							checkAndCreateFolder(folder_cell + "PicCells_" + bead);

						for(channel = 1; channel <= numberCh && channel != 0; channel++)
						{
							if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel = 0;
							else if((ch & format[channel - 1]) == 0) continue;
							for(frame = frames_begin; frame <= frames; frame++)
							{
								cellsAndForceImagesSuperposition(channel, traction_folder, bead, frame, folder_cell, "Traction_Vector_Plot", "PicCells", "Superposition", "Vector"   , Blitter.COPY_ZERO_TRANSPARENT, false, Double.NaN);
								cellsAndForceImagesSuperposition(channel, traction_folder, bead, frame, folder_cell, "Traction_Vector_Plot", "PicCells", "Superposition", "Magnitude", Blitter.ADD                  , false, Double.NaN);
							}
							if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel--;
						}
						Roi.setPasteMode(Blitter.COPY);
						// updating and saving "JEasyTFM_x_end.txt" file
						if((bead == 0 || bead == 2) && traction_folder == traction_ending_folder)
						{
							force_superposition			= false;
							force_calculation			= false;
							saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
						}
						///////////////////////////////////////////////////
					}	// force_superposition
				}	// traction_force_calculation
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(traction_starting_folder < traction_ending_folder)
						traction_starting_folder++;
					else
					{
						traction_force				= false;
						traction_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
				///////////////////////////////////////////////////
			}
			if(beads == 0) bead--;
		}	// traction_force_calculation
	}	// traction_force

	private void cells_analysis()
	{
		boolean					generate_scale = true;
//		double					regularization_factor = lambda;
//		double					regularization_factor = 1e-10;			// !!! Different from the lambda used in the rest of the analysis
//		double					regularization_factor = 0;

//		DecimalFormat			decimalFormat1 = new DecimalFormat("#0.00000");
//		DecimalFormat			decimalFormat2 = new DecimalFormat("#0.00");
//		DecimalFormat			decimalFormat3 = new DecimalFormat("0.00E0");
		ImagePlus				imp0, imp1, imp2, imp3, imp4, imp5;
		ImageConverter			converter;
		ImageCalculator			ic;
		Color					color;
		ResultsTable			rt;
//		Roi						roi;
		RoiManager				rm;
		WaitForUserDialog		waitForUserDialog;
		String					folder_cell;
		String					Name;
		String					str;
		String	[]				lines, columns;
		int						cells_analysis_folder, bead, channel, frame, slice;
		int						roi_x, roi_y;
		int						roi_width	= 0;
		int						roi_height	= 0;
		int						width, height;
//		int						channels, slices, frames;
		int		[]				dim;
		double	[]				shift_x, shift_y;

		int						widthCorr	= 0;
		int						heightCorr	= 0;
//		int						area, force;
		double					scaleMin;
		double					scaleMax;
//		int		[]				delta, dim;
		double	[]				scale;

		imp2					= null;
		imp5					= null;

//		for(bead = 1; bead <= format.length && bead != 0; bead++)
		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;

			for(cells_analysis_folder = cells_analysis_starting_folder; cells_analysis_folder <= cells_analysis_ending_folder; cells_analysis_folder++)
			{
				folder_cell = folder + "Cell " + cells_analysis_folder + File.separator;

				if(cells_segmentation)
				{
					if(beads == 0)
						str = IJ.openAsString(folder_cell + "Analysis"         + File.separator + "Transformation.txt");
					else
						str = IJ.openAsString(folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");
					if(str.startsWith("Error"))
					{
						if(!error)
						{
							error = true;
							if(beads == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"         + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"Cells segmentation\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"Cells segmentation\"");
						}
						return;
					}

					lines = split(str, "\n");
					if(lines.length <= 3)
					{
						if(beads == 0)
							showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "calculator.png", "The format of the data imported from the following file:\n \n" + folder_cell + "Analysis"         + File.separator + "Transformation.txt\n \n\nare not correct!\n \nPlease check the content of the file.", "The analysis is stopped at the step \"Cells segmentation\"");
						else
							showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "calculator.png", "The following file:\n\t\n"                                     + folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt\n \n\nare not correct!\n \nPlease check the content of the file.", "The analysis is stopped at the step \"Cells segmentation\"");
						return;
					}
					shift_x = new double[lines.length - 3];
					shift_y = new double[lines.length - 3];

					for (int line = 1; line < lines.length - 2; line++)
					{
						columns = split(lines[line], "\t");
						shift_x[line - 1] = Double.valueOf(columns[1]);
						shift_y[line - 1] = Double.valueOf(columns[2]);
					}

					columns		= split(lines[lines.length - 1], "\t");
					roi_x		= Integer.parseInt(columns[0]);
					roi_y		= Integer.parseInt(columns[1]);
					roi_width	= Integer.parseInt(columns[2]);
					roi_height	= Integer.parseInt(columns[3]);

					Name		= file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2);
					imp1		= imp2 = imp3 = null;
					imp1		= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + ".tif");
					if(imp1 == null)
					imp1		= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(3 * cells_analysis_folder - 2, 2) + ".tif");
					if(imp1 == null)
					{
						imp2	= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + "_p1.tif");
						if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + "_p1.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells segmentation\"");
							}
							return;
						}
						imp3	= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + "_p2.tif");
						if(imp3 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + "_p2.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells segmentation\"");
							}
							imp2.close();
							return;
						}
						imp1	= Concatenator.run(imp2, imp3);
						imp2	.close();
						imp3	.close();
					}
					if(imp1 == null)
					{
						imp2	= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(3 * cells_analysis_folder - 2, 2) + "_p1.tif");
						if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_analysis_folder + "_" + IJ.pad(3 * cells_analysis_folder - 2, 2) + "_p1.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells segmentation\"");
							}
							imp1.close();
							return;
						}
						imp3	= IJ.openImage(folder + file1 + cells_analysis_folder + "_" + IJ.pad(3 * cells_analysis_folder - 2, 2) + "_p2.tif");
						if(imp3 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "undo.png", "The following file:\n\t\n" + folder + file1 + cells_analysis_folder + "_" + IJ.pad(3 * cells_analysis_folder - 2, 2) + "_p2.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells segmentation\"");
							}
							imp1.close();
							imp2.close();
							return;
						}
						imp1	= Concatenator.run(imp2, imp3);
						imp2	.close();
						imp3	.close();
					}
					if(imp1.isHyperStack())
					{
						frames = imp1.getNFrames();
						slices = imp1.getNSlices();
					}
					try
					{
						imp1	= HyperStackConverter.toHyperStack(imp1, 1, slices, frames, "default", "Grayscale");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "calculator.png", "Error while trying to transform the stack image \n" + imp1.getTitle() + "\ncontaining    " + imp1.getStackSize() + " pictures into an hyperStack of\nChannels     1\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + slices * frames + " images" , "The analysis is stopped at the step \"Cells segmentation\"");
						return;
					}
//					imp1		.show();

					for(frame = frames_begin; frame <= frames; frame++)
					{
						for(slice = 1; slice <= slices; slice++)
						{
							imp1.setPosition(1, slice, frame);
							IJ.run(imp1, "Translate...", "x=" + shift_x[frame - 1] + " y=" + shift_y[frame - 1] + " interpolation=Bicubic slice");
						}
					}
					imp1.setRoi(roi_x, roi_y, roi_width, roi_height);
					IJ.run(imp1, "Crop", "");

//					IJ.saveAs(imp1, "Tiff", folder_cell + file1 + cells_analysis_folder + "_" + IJ.pad(2 * cells_analysis_folder - 1, 2) + "_aligned.tif");

					// * Préparation image
					dim		= imp1.getDimensions();
					width	= dim[0];
					height	= dim[1];
//					IJ.run("Set... ", "zoom=50 x=" + width + " y=" + height);

					// * Segmentation
//					IJ.log		("Focusing ...");
					if(frames > 1)
					{
						imp1		.setSlice(KurtFocus(imp1)[0]);
						IJ.run		(imp1, "Reduce Dimensionality...", "frames keep");
						imp2		= IJ.getImage();
					}
					else
						imp2 = SubstackMaker.run(imp1, String.valueOf(KurtFocus(imp1)[0]));
					converter	= new ImageConverter(imp2);
					converter	.convertToGray8();
					imp2		.show();
					imp2		.setTitle(Name + " focused");
//					IJ.run		("Set... ", "zoom=50 x=" + width + " y=" + height);

//					IJ.log		("Segmenting ...");
					IJ.run		(imp1, "Z Project...", "projection=[Standard Deviation] all");
					imp3		= IJ.getImage();
					converter	= new ImageConverter(imp3);
					converter	.convertToGray16();
//					imp3		.show();
//					imp3		.setTitle("SD_Project");
//					IJ.run		("Set... ", "zoom=50 x=" + width + " y=" + height);
					IJ.run		(imp3, "Enhance Contrast", "saturated=2");

					if(frames > 1)
					{
						IJ.run	(imp3, "Z Project...", "projection=[Min Intensity]");
						imp4	= IJ.getImage();
						ic		= new ImageCalculator();
						imp5	= ic.run("Subtract create stack", imp3, imp4);

						imp4		.close();
					}
					else
						imp5	= imp3.duplicate();
					imp5		.show();
					IJ.run		(imp5, "Mean...", "radius=1 stack");
					IJ.run		(imp5, "Mean 3D...", "x=0 y=0 z=1");
//					IJ.run		("Set... ", "zoom=50 x=" + width + " y=" + height);
					imp5		.setTitle("Binaries");

					imp1		.close();
					imp3		.close();

					IJ			.setTool("freehand");
					Brightness	(imp5, 5);

					if(!cells_selection)
					{
						try
						{
							IJ.saveAsTiff(imp2, folder_cell + "focused.tif");
							imp2.close();
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "focused.tif", "The analysis is stopped at the step \"Cells segmentation\"");
							return;
						}
						try
						{
							IJ.saveAsTiff(imp5, folder_cell + "binaries.tif");
							imp5.close();
						}
						catch (Exception e)
						{
							imp2.close();
							showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "binaries.tif", "The analysis is stopped at the step \"Cells segmentation\"");
							return;
						}
					}
					// updating and saving "JEasyTFM_x_end.txt" file
					if(!cells_selection && (bead == 0 || bead == 2) && cells_analysis_folder == cells_analysis_ending_folder)
					{
						cells_segmentation			= false;
						saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
					}
					///////////////////////////////////////////////////
				}	// cells_segmentation
				if(cells_selection)
				{
					if(!cells_segmentation)
					{
						imp2 = imp5 = null;
						imp2 = IJ.openImage(folder_cell + "focused.tif");
						if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells selection", "undo.png", "The following file:\n\t\n" + folder_cell + "focused.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells selection\"");
							}
							return;
						}
						imp5 = IJ.openImage(folder_cell + "binaries.tif");
						if(imp5 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Cells selection", "undo.png", "The following file:\n\t\n" + folder_cell + "binaries.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Cells selection\"");
							}
							imp2.close();
							return;
						}
						imp2 .show();
						imp5 .show();
					}

					waitForUserDialog = new WaitForUserDialog("Action Required", "Select Region of interest (or nothing if there is only one cell)");
					waitForUserDialog.show();

//					roi	= imp5.getRoi();
//					if(roi != null)
					if(imp5.getRoi() != null)
					{
						rm				= RoiManager.getInstance();
						if(rm == null)	rm = new RoiManager();
//						rm.addRoi		(roi);
						rm.addRoi		(imp5.getRoi());
						rm.select		(0);
						IJ.run			(imp5, "Make Inverse", "");
						IJ.run			(imp5, "Set...", "value=0 stack");
						rm.runCommand	(imp5, "Deselect");
						IJ.run			(imp5, "Select None", "");
					}
					IJ.run("Threshold...");
					IJ.setRawThreshold	(imp5, 1600, 65535, null);
					waitForUserDialog	= new WaitForUserDialog("Action Required", "Adjust Threshold");
					waitForUserDialog	.show();
					Prefs				.blackBackground = true;
					imp5				.hide();
					IJ.run				(imp5, "Make Binary", "method=Default background=Default black");

//					closeWindow			("Threshold");
					ThresholdAdjuster	thresholdAdjuster = (ThresholdAdjuster) WindowManager.getWindow("Threshold");
					thresholdAdjuster	.close();

					// Selection de la cellule
					IJ.run				(imp5, "Maximum 3D...", "x=5 y=5 z=1");
					IJ.run				(imp5, "Fill Holes",           "stack");
					IJ.run				(imp5, "Median..." , "radius=2  stack");
					IJ.run				(imp5, "Minimum...", "radius=4  stack");

					// Fermeture lissage 2D 
//					IJ.log				("Smooting 2D ...");
					IJ.run				(imp5, "Median..." , "radius=3  stack");
					IJ.run				(imp5, "Maximum...", "radius=8  stack");
					IJ.run				(imp5, "Fill Holes",           "stack");
					IJ.run				(imp5, "Minimum...", "radius=10 stack");
					IJ.run				(imp5, "Median..." , "radius=5  stack");

					imp5				.show();
					for(frame = frames_begin; frame <= frames; frame++)
					{
						imp5			.setSlice(frame);
						biggestParticule (imp5, 200);
					}
					imp5				.hide();

					// lissage temporel
//					IJ.log				("Smooting 3D ...");
					IJ.run				(imp5, "Gaussian Blur 3D..."	,	"x=4 y=4 z=1");
					IJ.setRawThreshold	(imp5, 75, 255, null);
					IJ.run				(imp5, "Convert to Mask"		, "method=Default background=Dark black");
					IJ.run				(imp5, "Fill Holes"				, "stack");
					IJ.run				(imp5, "Minimum 3D..."			, "x=1 y=1 z=1");
					IJ.run				(imp5, "Minimum..."				, "radius=3 stack");
					IJ.run				(imp5, "Median 3D..."			, "x=0 y=0 z=2");
					IJ.run				(imp5, "Median..."				, "radius=2 stack");
					IJ.run				(imp5, "Make Binary"			, "method=Default background=Default calculate black");
					IJ.run				(imp5, "Median..."				, "radius=2 stack");

					imp5				.show();
					for(frame = frames_begin; frame <= frames; frame++)
					{
						imp5			.setSlice(frame);
						biggestParticule(imp5, 200);
					}
					imp5				.hide();

					// Mesures
					IJ.run				("Set Measurements...", "area centroid shape redirect=None decimal=4");
					IJ.run				(imp5, "Analyze Particles...", "size=200-Infinity clear add stack");

					// Fichiers de sortie
					rm					= RoiManager.getInstance();
					if(beads == 0)
						rm.runCommand		("Save", folder_cell + "Analysis"         + File.separator + "RoiSet.zip");
					else
						rm.runCommand		("Save", folder_cell + "Analysis_" + bead + File.separator + "RoiSet.zip");

//					imp3				= FlatStack_old(imp2);
//					IJ.saveAs			(imp3, "Tiff", folder_cell + "segmentation.tif");
					FlatStack			(imp2);
					try
					{
						IJ.saveAsTiff		(imp2, folder_cell + "segmentation.tif");
					}
					catch (Exception e)
					{
						showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "segmentation.tif", "The analysis is stopped at the step \"Cells segmentation\"");
						return;
					}

					// Show
					imp2				.close();
/*
					imp5				.setSlice(1);
					IJ.run				("Set... ", "zoom=50 x=" + width + " y=" + height);
					rm.runCommand		(imp5,"Show None");
					IJ.run				(imp5, "Select None", "");
*/
					imp5				.close();

					if(!force_integration)
					{
//						closeWindow			("ROI Manager");
//						RoiManager rm		= RoiManager.getInstance();
						if(rm != null)
							rm.close();
					}

					// updating and saving "JEasyTFM_x_end.txt" file
					if((bead == 0 || bead == 2) && cells_analysis_folder == cells_analysis_ending_folder)
					{
						if(cells_segmentation)
						cells_segmentation			= false;
						cells_selection				= false;
						saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
					}
					///////////////////////////////////////////////////
				}	// cells_selection
				if(force_integration)
				{
					if(!cells_segmentation)
					{
						// Does the Roi file "RoiSet.zip" exist or not?
						if(beads == 0)
							file = new File(folder_cell + "Analysis"         + File.separator + "RoiSet.zip");
						else
							file = new File(folder_cell + "Analysis_" + bead + File.separator + "RoiSet.zip");
						if (!file.exists())
						{
							if(beads == 0)
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"         + File.separator + "RoiSet.zip\n\t\ncould not be found", "The analysis is stopped at the step \"Force integration\"");
							else
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "RoiSet.zip\n\t\ncould not be found", "The analysis is stopped at the step \"Force integration\"");
							return;
						}

						// Load the Roi file "RoiSet.zip" within the roiManager
						rm				= RoiManager.getInstance();
						if(rm == null)	rm = new RoiManager();
						if(beads == 0)
							rm.runCommand("Open", folder_cell + "Analysis"         + File.separator + "RoiSet.zip");
						else
							rm.runCommand("Open", folder_cell + "Analysis_" + bead + File.separator + "RoiSet.zip");

						// reading the Transformation.txt that is already read within cells_segmentation
						if(beads == 0)
							str = IJ.openAsString(folder_cell + "Analysis"         + File.separator + "Transformation.txt");
						else
							str = IJ.openAsString(folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");
						if(str.startsWith("Error"))
						{
							if(!error)
							{
								error = true;
								if(beads == 0)
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"         + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"force_integration\"");
								else
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"force_integration\"");
							}
							return;
						}

						lines = split(str, "\n");

						columns		= split(lines[lines.length - 1], "\t");
						roi_x		= Integer.parseInt(columns[0]);
						roi_y		= Integer.parseInt(columns[1]);
						roi_width	= Integer.parseInt(columns[2]);
						roi_height	= Integer.parseInt(columns[3]);
					}
					color		= Color.yellow;
					IJ			.setForegroundColor(color.getRed(), color.getGreen(), color.getBlue());
					rm			= RoiManager.getInstance();
					widthCorr	= roi_width;
					heightCorr	= roi_height;
					scale		= new double[frames];

					if(beads == 0)
					{
						checkAndCreateFolder(folder_cell + "Integration_calculation");
						checkAndCreateFolder(folder_cell + "Integration_results");
					}
					else
					{
						checkAndCreateFolder(folder_cell + "Integration_calculation_" + bead);
						checkAndCreateFolder(folder_cell + "Integration_results_"     + bead);
					}

					// In the case the lamda values haven't been generated they can be read from the Lambda.txt file
					if(lambda_values == null)
					{
						if(beads == 0)
							lambda_values = get_lambda_values(folder_cell + "Analysis"         + File.separator + "Lambda.txt");
						else
							lambda_values = get_lambda_values(folder_cell + "Analysis_" + bead + File.separator + "Lambda.txt");
					}

					for(frame = frames_begin; frame <= frames; frame++)
					{
						if(beads == 0)
						{
							try
							{
								copyFile(new File(folder_cell + "Analysis"         + File.separator + "Stack_"              + IJ.pad(frame, 2) + ".txt"), new File(folder_cell + "Integration_calculation" + File.separator + "Stack_"                      + IJ.pad(frame, 2) + ".txt"));
							}
							catch (Exception e)
							{
								IJ.log("File open error \n\"" + e.getMessage() + "\"\n");
							}
							scale[frame - 1] = FTTC_main.getScaleValue(folder_cell + "Integration_calculation"                 + File.separator, "Stack_"              + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, lambda_values[frame - 1], unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
						}
						else
						{
							try
							{
								copyFile(new File(folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt"), new File(folder_cell + "Integration_calculation_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt"));
							}
							catch (Exception e)
							{
								showDialogWithImageAndCustomOkAndNoCancel("force_integration"    , "write.png"     , "Error while trying to copy the file\n \n"                + folder_cell + "Analysis_"                + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n \n onto the\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n \none:\n \n" + e.getMessage(), "The analysis is stopped at the step \"force_integration\"");
								return;
							}

							file = new File(folder_cell + "Integration_calculation_" + bead + File.separator, "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
							if (!file.exists())
							{
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");
								return;
							}
							else
							{
								try
								{
									scale[frame - 1] = FTTC_main.getScaleValue(folder_cell + "Integration_calculation_" + bead + File.separator, "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, lambda_values[frame - 1], unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt"                                                                                                                                                                         , "The analysis is stopped at the step \"force_integration\"");
									return;
								}
							}
						}
//						closeWindows();
					}

					scaleMin = scaleMax = scale[0];
					for(slice = 1; slice < scale.length; slice++)
					{
							if(scale[slice] > scaleMax)
									scaleMax = scale[slice];
							else if (scale[slice] < scaleMin)
									scaleMin = scale[slice];
					}

//	IJ.log("" + scaleMax + "   " + niceNumber(scaleMax));
//	scaleMax = 3000.0;

					// Measure force and area
					IJ.run("Set Measurements...", "area integrated redirect=None decimal=4");
					for(frame = frames_begin; frame <= frames; frame++)
					{
						if(beads == 0)
						{
							file = new File(folder_cell + "Integration_calculation" + File.separator, "Traction_Stack_" + IJ.pad(frame, 2) + ".txt");
							if (!file.exists())
							{
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Integration_calculation" + File.separator + "Traction_Stack_"           + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");
								return;
							}
							else
							{
								try
								{
									if(frame == frames_begin && generate_scale)
										FTTC_plot.drawPlot(folder_cell + "Integration_calculation" + File.separator, "Traction_Stack_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, true, true, true, false, false, false, lut);
									else
										FTTC_plot.drawPlot(folder_cell + "Integration_calculation" + File.separator, "Traction_Stack_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, false, true, true, false, false, false, lut);
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation" + File.separator + "Traction_Stack_"           + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
							}

							if(frame == frames_begin && generate_scale)
							{
								imp0 = WindowManager.getImage("Traction_Scale_Graph_in_pN_Traction_Stack_" + IJ.pad(frame, 2) + ".txt");
								try
								{
									IJ.saveAsTiff(imp0, folder_cell + "Integration_calculation" + File.separator + "Traction_Vector_Scale.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation" + File.separator + "Traction_Vector_Scale.tif", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp0.close();
							}
							imp1 = WindowManager.getImage("Traction_Magnitude_Map_in_pN_Traction_Stack_" + IJ.pad(frame, 2) + ".txt");
							try
							{
								IJ.saveAsTiff(imp1, folder_cell + "Integration_calculation" + File.separator + "Traction_Magnitude_Plot_Traction_Stack_"                     + IJ.pad(frame, 2) + ".tif");
							}
							catch (Exception e)
							{
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation" + File.separator + "Traction_Magnitude_Plot_Traction_Stack_"                     + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
								return;
							}
							rm.select(frame - 1);
							IJ.run(imp1, "Measure", "");
							imp1.close();
							imp2 = WindowManager.getImage("Traction_Vector_Plot_in_pN_Traction_Stack_" + IJ.pad(frame, 2) + ".txt");
							try
							{
								IJ.saveAsTiff(imp2, folder_cell + "Integration_calculation" + File.separator + "Traction_Vector_Plot_Traction_Stack_"                        + IJ.pad(frame, 2) + ".tif");
							}
							catch (Exception e)
							{
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation" + File.separator + "Traction_Vector_Plot_Traction_Stack_"                        + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
								return;
							}
							imp2.close();
						}
						else
						{
							file = new File(folder_cell + "Integration_calculation_" + bead + File.separator, "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
							if (!file.exists())
							{
								showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");
								return;
							}
							else
							{
								try
								{
									if(frame == frames_begin && generate_scale)
										FTTC_plot.drawPlot(folder_cell + "Integration_calculation_" + bead + File.separator, "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, true, true, true, false, false, false, lut);
									else
										FTTC_plot.drawPlot(folder_cell + "Integration_calculation_" + bead + File.separator, "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", FTTC_max_vector_length, niceNumber(scaleMax), niceNumber(scaleMax * window_area), unitIndex, widthCorr, heightCorr, false, true, true, false, false, false, lut);
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"force_integration\"");
									return;
								}
							}

							if(frame == frames_begin && generate_scale)
							{
								imp0 = WindowManager.getImage("Traction_Scale_Graph_in_pN_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
								try
								{
									IJ.saveAsTiff(imp0, folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Vector_Scale.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Vector_Scale.tif"                                                       , "The analysis is stopped at the step \"force_integration\"");
									return;
								}
								imp0.close();
							}
							imp1 = WindowManager.getImage("Traction_Magnitude_Map_in_pN_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
							try
							{
								IJ.saveAsTiff(imp1, folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
							}
							catch (Exception e)
							{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Magnitude_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
							}
							rm.select(frame - 1);
							IJ.run(imp1, "Measure", "");
							imp1.close();
							imp2 = WindowManager.getImage("Traction_Vector_Plot_in_pN_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt");
							try
							{
								IJ.saveAsTiff(imp2, folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_"    + bead + "_" + IJ.pad(frame, 2) + ".tif");
							}
							catch (Exception e)
							{
									showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Integration_calculation_" + bead + File.separator + "Traction_Vector_Plot_Traction_Stack_"    + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"force_integration\"");
									return;
							}
							imp2.close();
						}
					}

					// Write measurements on the image
					for(channel = 1; channel <= numberCh && channel != 0; channel++)
					{
						if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel = 0;
						else if((ch & format[channel - 1]) == 0) continue;
						for(frame = frames_begin; frame <= frames; frame++)
						{
//							cellsAndForceImagesSuperposition(int light = channel, int cell = cells_analysis_folder, int bead = bead, int frame = frame, String folder = folder_cell, String folderIn, String folderOut, int pasteMode, boolean text, double scaleMax)
							cellsAndForceImagesSuperposition(channel, cells_analysis_folder, bead, frame, folder_cell, "Integration_calculation", "Integration_results", "Integration", "Vector"   , Blitter.COPY_ZERO_TRANSPARENT, true, scaleMax);
							cellsAndForceImagesSuperposition(channel, cells_analysis_folder, bead, frame, folder_cell, "Integration_calculation", "Integration_results", "Integration", "Magnitude", Blitter.ADD                  , true, scaleMax);
						}
						if((ch & 0x1) == 0 && (ch & 0x2) == 0 && (ch & 0x4) == 0) channel--;
					}
//					closeWindow("Results");
					TextWindow resultsWindow	= (TextWindow) WindowManager.getWindow("Results");
//					if (ResultsWindow != null)
//					{
						IJ.run("Clear Results");
						resultsWindow.close();
//					}
//					closeWindow("ROI Manager");
//					RoiManager rm				= RoiManager.getInstance();
					if(rm != null)
						rm.close();

					// updating and saving "JEasyTFM_x_end.txt" file
					if((bead == 0 || bead == 2) && cells_analysis_folder == cells_analysis_ending_folder)
					{
						force_integration			= false;
						saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
					}
					///////////////////////////////////////////////////
				}	// force_integration
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(cells_analysis_starting_folder < cells_analysis_ending_folder)
						cells_analysis_starting_folder++;
					else
					{
						cells_analysis					= false;
						cells_analysis_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
				///////////////////////////////////////////////////
			}
			if(beads == 0) bead--;
		}
	}	// cells_analysis

	private void traction_high_force()
	{
		ImagePlus				imp1, imp2, stackImp, impProj, prosImp;
		ImageProcessor			ip1 , ip2 , stackIp, stackIp2;
		ImageStack				is;
		ImageConverter			converter;
		Roi						roi;
		String					folder_cell;
		int						traction_high_folder, bead, frame;
		int						widthCorr	= 0;
		int						heightCorr	= 0;
		double					scaleMin;
		double					scaleMax;
		double					dx, dy, dx2, dy2;
		double					 x,  y, width, height;
		int		[]				delta, dim;
		double	[]				scale;

		FileOutputStream		fos;
		BufferedOutputStream	bos;
		PrintWriter				writer;

		double					startTime;
		double					stopTime;
		double					elapsedTime;
		double					neededTime;
		DecimalFormat			decimalFormat	= new DecimalFormat("#0.00");

/*		// Particle Tracking using the 1.5. version of the Particle_Tracker code released September 2006
		int						radius			= 5;
		int						cutoff			= 3;
//		int						percentile		= 10;
		int						percentile		= 7;
		int						displacement	= 5;
*/
		// Particle Tracking using the 1.0.25 version of the MosaicSuite code released on 20 September 2022
		int						radius			= 3;
		double					cutoff			= 0.0001;
		int						percentile		= 3;
		int						displacement	= 5;

//		for(bead = 1; bead <= format.length && bead != 0; bead++)
		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;
			for(traction_high_folder = traction_high_starting_folder; traction_high_folder <= traction_high_ending_folder; traction_high_folder++)
			{
				folder_cell = folder + "Cell " + traction_high_folder + File.separator;

				if(high_piv_calculation)
				{
					for(frame = frames_begin; frame <= frames; frame++)
					{
						startTime = System.currentTimeMillis();
						imp1 = imp2 = null;
						if(beads == 0)
						{
							imp1	= IJ.openImage(folder_cell + "Analysis" + File.separator + "CorrBeadsReference.tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "CorrBeadsReference.tif\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
								}
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp1, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp1, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							is		= imp1.getStack();
							imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                     + IJ.pad(frame, 2) + ".tif");
							if(imp2 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter" + File.separator + "CorrBeadsAfter_"                     + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
								}
								imp1.close();
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp2, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp2, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							ip2		= imp2.getProcessor();
							is		.addSlice(ip2);
							stackImp= new ImagePlus("Stack_" + IJ.pad(frame, 2) + ".tif", is);
						}
						else
						{
							imp1	= IJ.openImage(folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
								}
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp1, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp1, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							is		= imp1.getStack();
							imp2	= IJ.openImage(folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
							if(imp2 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
								}
								imp1.close();
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp2, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp2, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							ip2		= imp2.getProcessor();
							is		.addSlice(ip2);
							stackImp= new ImagePlus("Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", is);
						}

//						IJ.run("Images to Stack", "name=Stack title=[] use");
//						IJ.run("Translation Alignment");
//						IJ.saveAs("Tiff", folder_cell + "Stack" + IJ.pad(frame, 2) + ".tif");
//						IJ.selectWindow("Stack" + IJ.pad(frame, 2) + ".tif");

						converter	= new ImageConverter(stackImp);
						converter	.convertToGray16();
						if(debug)
						{
							stackImp	.show();
//							IJ.run("Reverse");
							file = new File(folder_cell + "Analysis" + File.separator + "Stack_"           + IJ.pad(frame, 2) + ".txt");
							if(beads == 0)
							{
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
									return;
								}
								else
								{
									try
									{
										IJ.run(stackImp, "PIV Advanced", "load piv1=48 sw1=128 vs1=16 piv2=36 sw2=64 vs2=16 piv3=24 sw3=32 vs3=" + vs3 / 2 + " correlation=2 debug_x=-1 debug_y=-1 path=/ select=[" + folder_cell + "Analysis"        + File.separator + "Stack_"              + IJ.pad(frame, 2) + ".txt] what=[Normalized median test and replace invalid by median then Accept this PIV and output] noise=0.20 threshold=5 c1=3 c2=1 save=[" + folder_cell + "Analysis"         + File.separator + "Stack_"              + IJ.pad(frame, 2) + "_2.txt]");
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis"         + File.separator + "Stack_"              + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"high PIV calculation\"");
										return;
									}
								}
							}
							else
							{
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
									return;
								}
								else
								{
									try
									{
										IJ.run(stackImp, "PIV Advanced", "load piv1=48 sw1=128 vs1=16 piv2=36 sw2=64 vs2=16 piv3=24 sw3=32 vs3=" + vs3 / 2 + " correlation=2 debug_x=-1 debug_y=-1 path=/ select=[" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt] what=[Normalized median test and replace invalid by median then Accept this PIV and output] noise=0.20 threshold=5 c1=3 c2=1 save=[" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt]");
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"high PIV calculation\"");
										return;
									}
								}
							}
							IJ.run("Close");
							if(beads == 0)
							{
//								IJ.selectWindow(                "PIV3_" + "Stack_" + IJ.pad(frame, 2) + ".tif");
//								IJ.saveAs("Tiff", folder_cell + "PIV3_" + "Stack_" + IJ.pad(frame, 2) + ".tif");
//								IJ.run("Close");
								closeWindow("PIV3_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
								closeWindow("PIV2_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
								closeWindow("PIV1_" + "Stack_"           + IJ.pad(frame, 2) + ".tif");
								closeWindow(          "Stack_"           + IJ.pad(frame, 2) + ".tif");
								closeWindow(          "Stack_"           + IJ.pad(frame, 2) + ".tif_PIV0");
							}
							else
							{
//								IJ.selectWindow("PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//								IJ.saveAs("Tiff", folder_cell + "PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
//								IJ.run("Close");
								closeWindow("PIV3_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								closeWindow("PIV2_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								closeWindow("PIV1_" + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								closeWindow(          "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
								closeWindow(          "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif_PIV0");
							}
						}
						else
						{
							if(beads == 0)
							{
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + "_2.txt\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
									return;
								}
								else
								{
									try
									{
//										PIV_iterative.generateAdvancedIterativePIV(stackImp, true, 64, 256, 32, 48, 128, 16, 24, 128, 8, 0.60, false, false, false, false, folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + ".txt", "Normalized median test and replace invalid by median then Accept this PIV and output", 0.20, 5, 3, 1, folder_cell + "Analysis" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_2.txt");
										PIV_iterative.generateAdvancedIterativePIV(stackImp, true, 48, 128, 16, 36, 64, 16, 24, 32, 8, 2, false, false, false, false, folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + ".txt", "Normalized median test and replace invalid by median then Accept this PIV and output"                                                          , 0.20, 5, 3, 1, folder_cell + "Analysis" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_2.txt");
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + "_2.txt", "The analysis is stopped at the step \"high PIV calculation\"");
									}
								}
							}
							else
							{
								if (!file.exists())
								{
									showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt\n\t\ncould not be found", "The analysis is stopped at the step \"high PIV calculation\"");
									return;
								}
								else
								{
									try
									{
//										PIV_iterative.generateAdvancedIterativePIV(stackImp, true, 64, 256, 32, 48, 128, 16, 24, 128, 8, 0.60, false, false, false, false, folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "Normalized median test and replace invalid by median then Accept this PIV and output", 0.20, 5, 3, 1, folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt");
										PIV_iterative.generateAdvancedIterativePIV(stackImp, true, 48, 128, 16, 36, 64, 16, 24, 32, 8, 2, false, false, false, false, folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "Normalized median test and replace invalid by median then Accept this PIV and output"                                                          , 0.20, 5, 3, 1, folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt");
									}
									catch (Exception e)
									{
										showDialogWithImageAndCustomOkAndNoCancel("high PIV calculation", "calculator.png", "Error while calculating\n \n" + e.getMessage() + "\n \n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"high PIV calculation\"");
										return;
									}
								}
							}
							stackImp.close();
						}
						imp1	.close();
						imp2	.close();
//						stackImp.close();
						closeWindows();
						stopTime	= System.currentTimeMillis();
						elapsedTime	= stopTime - startTime;
						neededTime	= (frames - frame) * elapsedTime / 60000;
						IJ.log("Performed calculation within the folder " + folder_cell + " on the image "				+ String.valueOf(frame));
						IJ.log("Time needed for the calculation of the last frame:                                 "	+ String.valueOf(decimalFormat.format(elapsedTime / 60000))											+ " min");
						IJ.log("Frames still needed to be calculated to terminate the next iterration:    "				+ String.valueOf(frames - frame)																			);
						if(neededTime / 60 > 1)
						{
							if(neededTime % 60 == 0)
								IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "	+ String.valueOf((int) (neededTime / 60)) + " hours");
							else
								IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "	+ String.valueOf((int) (neededTime / 60)) + " hours and " + String.valueOf((int) (neededTime % 60)) + " min");
						}
						else
							IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "		+ String.valueOf(decimalFormat.format(neededTime))													+ " min");
					}
					// updating and saving "JEasyTFM_x_end.txt" file
					if((bead == 0 || bead == 2) && traction_high_folder == traction_high_ending_folder)
					{
						high_piv_calculation		= false;
						saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
					}
					///////////////////////////////////////////////////
				}	// high_piv_calculation

				if(particle_tracker)
				{
					for(frame = frames_begin; frame <= frames; frame++)
					{
						startTime = System.currentTimeMillis();
						imp1 = imp2 = null;
						if(beads == 0)
						{
							imp1		= IJ.openImage(folder_cell + "Analysis"         + File.separator + "CorrBeadsReference.tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"       + File.separator + "CorrBeadsReference.tif\n\t\ncould not be found", "The analysis is stopped at the step \"Particle tracker\"");
								}
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp1, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp1, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							is			= imp1.getStack();
							imp2		= IJ.openImage(folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif");
							if(imp2 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter"         + File.separator + "CorrBeadsAfter_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Particle tracker\"");
								}
								imp1.close();
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp2, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp2, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							ip2			= imp2.getProcessor();
							is			.addSlice(ip2);
							stackImp	= new ImagePlus("Stack_"           + IJ.pad(frame, 2) + ".tif", is);
						}
						else
						{
							imp1		= IJ.openImage(folder_cell + "Analysis_" + bead + File.separator + "CorrBeadsReference_" + bead + ".tif");
							if(imp1 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_"       + bead + File.separator + "CorrBeadsReference_" + bead                          + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Particle tracker\"");
								}
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp1, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp1, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							is			= imp1.getStack();
							imp2		= IJ.openImage(folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
							if(imp2 == null)
							{
								if(!error)
								{
									error = true;
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "undo.png", "The following file:\n\t\n" + folder_cell + "CorrBeadsAfter_" + bead + File.separator + "CorrBeadsAfter_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Particle tracker\"");
								}
								imp1.close();
								return;
							}
							if(traction_high_enhance_constrast)
							{
								IJ.run	(imp2, "Subtract Background...", "rolling=10 sliding");
								IJ.run	(imp2, "Enhance Contrast..."   , "saturated=0.4 normalize");
							}
							ip2			= imp2.getProcessor();
							is			.addSlice(ip2);
							stackImp	= new ImagePlus("Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif", is);
						}

//						IJ.run("Images to Stack", "name=Stack title=[] use");
//						IJ.run("Translation Alignment");
//						IJ.saveAs("Tiff", folder_cell + "Stack" + IJ.pad(frame, 2) + ".tif");
//						IJ.selectWindow("Stack" + IJ.pad(frame, 2) + ".tif");

						converter	= new ImageConverter(stackImp);
						converter	.convertToGray8();
						IJ.run(stackImp, "Enhance Contrast", "saturated=0.35");

						if(debug)
						{
							stackImp	.show();

							if(beads == 0)
							{
/*
								// Particle Tracking using the 1.5. version of the Particle_Tracker code released September 2006
								IJ.run
									(
										stackImp, 
										"Particle Tracker PIV and Trajectories Inputs   ", 
										"radius=" + radius + 
										" cutoff=" + cutoff + 
										" percentile=" + percentile + 
										" link=1 displacement=" + displacement + 
										" use_piv_file piv_file=[" + folder_cell + "Analysis" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_2.txt]"
									);
*/
								// Particle Tracking using the 1.0.25 version of the MosaicSuite code released on 20 September 2022
								prosImp = mosaic.plugins.ParticleTracker3DModular_.trackParticlePIVInputs
									(
										stackImp,																						// ImagePlus	_iInputImage,
										"multi",																						// String		_trajectoryColor,
										radius,																							// int			_radius,
										cutoff,																							// double		_cutoff,
										percentile,																						// float		_percentile,
										false,																							// boolean		_absolute,
										false,																							// boolean		_useClij,
										false,																							// boolean		_force,							// _force = false & _straight_line = false => Brownian
										false,																							// boolean		_straight_line,					// _force = false & _straight_line = true  => Straight lines
										true,																							// boolean		_drawing_trajectory,			// _force = true  & _straight_line = false => Constant velocity
										true,																							// boolean		_drawing_particle,
										1,																								// int			_iLinkRange,
										displacement,																					// double		_displacement,
										true,																							// boolean		_usePivFile,
										folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + "_2.txt",				// String		_filePivDirectoryAndName
										folder_cell + "Analysis" + File.separator,														// String		_outputDirectory,
										"Stack_" + IJ.pad(frame, 2) + "_2_Trajectories.txt"												// String		_outputName
									);

								closeWindow("Stack_"           + IJ.pad(frame, 2) + ".tif");
							}
							else
							{
/*
								// Particle Tracking using the 1.5. version of the Particle_Tracker code released September 2006
								IJ.run
									(
										stackImp, 
										"Particle Tracker PIV and Trajectories Inputs   ", 
										"radius=" + radius + 
										" cutoff=" + cutoff + 
										" percentile=" + percentile + 
										" link=1 displacement=" + displacement + 
										" use_piv_file piv_file=[" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt]"
									);
*/
								// Particle Tracking using the 1.0.25 version of the MosaicSuite code released on 20 September 2022
								prosImp = mosaic.plugins.ParticleTracker3DModular_.trackParticlePIVInputs
									(
										stackImp,																									// ImagePlus	_iInputImage,
										"multi",																									// String		_trajectoryColor,
										radius,																										// int			_radius,
										cutoff,																										// double		_cutoff,
										percentile,																									// float		_percentile,
										false,																										// boolean		_absolute,
										false,																										// boolean		_useClij,
										false,																										// boolean		_force,							// _force = false & _straight_line = false => Brownian
										false,																										// boolean		_straight_line,					// _force = false & _straight_line = true  => Straight lines
										true,																										// boolean		_drawing_trajectory,			// _force = true  & _straight_line = false => Constant velocity
										true,																										// boolean		_drawing_particle,
										1,																											// int			_iLinkRange,
										displacement,																								// double		_displacement,
										true,																										// boolean		_usePivFile,
										folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt",	// String		_filePivDirectoryAndName
										folder_cell + "Analysis_" + bead + File.separator,															// String		_outputDirectory,
										"Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt"											// String		_outputName
									);

								closeWindow("Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
							}

							if(beads == 0)
							{
								if(frame == 1)
									checkAndCreateFolder(folder_cell + "Trajectories");
								try
								{
									IJ.saveAsTiff(prosImp, folder_cell + "Trajectories" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_Trajectories.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "Trajectories" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_Trajectories.tif", "The analysis is stopped at the step \"Particle tracker\"");
									return;
								}
							}
							else
							{
								if(frame == 1)
									checkAndCreateFolder(folder_cell + "Trajectories_" + bead);
								try
								{
									IJ.saveAsTiff(prosImp, folder_cell + "Trajectories_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_Trajectories.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "Trajectories_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_Trajectories.tif", "The analysis is stopped at the step \"Particle tracker\"");
									return;
								}
							}
							prosImp		.close();
						}
						else
						{
							if(beads == 0)
/*
								// Particle Tracking using the 1.5. version of the Particle_Tracker code released September 2006
								prosImp = Particle_Tracker_PIV_and_Trajectories_Inputs.trackParticlePIVInputs
									(
										stackImp,
										false,
										radius,
										cutoff,
										percentile,
										1,
										displacement,
										true,
										folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + "_2.txt"
									);
*/
								// Particle Tracking using the 1.0.25 version of the MosaicSuite code released on 20 September 2022
								prosImp = mosaic.plugins.ParticleTracker3DModular_.trackParticlePIVInputs
									(
										stackImp,																						// ImagePlus	_iInputImage,
										"multi",																						// String		_trajectoryColor,
										radius,																							// int			_radius,
										cutoff,																							// double		_cutoff,
										percentile,																						// float		_percentile,
										false,																							// boolean		_absolute,
										false,																							// boolean		_useClij,
										false,																							// boolean		_force,							// _force = false & _straight_line = false => Brownian
										false,																							// boolean		_straight_line,					// _force = false & _straight_line = true  => Straight lines
										true,																							// boolean		_drawing_trajectory,			// _force = true  & _straight_line = false => Constant velocity
										true,																							// boolean		_drawing_particle,
										1,																								// int			_iLinkRange,
										displacement,																					// double		_displacement,
										true,																							// boolean		_usePivFile,
										folder_cell + "Analysis" + File.separator + "Stack_" + IJ.pad(frame, 2) + "_2.txt",				// String		_filePivDirectoryAndName
										folder_cell + "Analysis" + File.separator,														// String		_outputDirectory,
										"Stack_" + IJ.pad(frame, 2) + "_2_Trajectories.txt"												// String		_outputName
									);
							else
/*
								// Particle Tracking using the 1.5. version of the Particle_Tracker code released September 2006
								prosImp = Particle_Tracker_PIV_and_Trajectories_Inputs.trackParticlePIVInputs
									(
										stackImp,
										false,
										radius,
										cutoff,
										percentile,
										1,
										displacement,
										true,
										folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt"
										);
*/
								// Particle Tracking using the 1.0.25 version of the MosaicSuite code released on 20 September 2022
								prosImp = mosaic.plugins.ParticleTracker3DModular_.trackParticlePIVInputs
									(
										stackImp,																									// ImagePlus	_iInputImage,
										"multi",																									// String		_trajectoryColor,
										radius,																										// int			_radius,
										cutoff,																										// double		_cutoff,
										percentile,																									// float		_percentile,
										false,																										// boolean		_absolute,
										false,																										// boolean		_useClij,
										false,																										// boolean		_force,							// _force = false & _straight_line = false => Brownian
										false,																										// boolean		_straight_line,					// _force = false & _straight_line = true  => Straight lines
										true,																										// boolean		_drawing_trajectory,			// _force = true  & _straight_line = false => Constant velocity
										true,																										// boolean		_drawing_particle,
										1,																											// int			_iLinkRange,
										displacement,																								// double		_displacement,
										true,																										// boolean		_usePivFile,
										folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2.txt",	// String		_filePivDirectoryAndName
										folder_cell + "Analysis_" + bead + File.separator,															// String		_outputDirectory,
										"Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt"											// String		_outputName
									);

							stackImp	.close();
							if(beads == 0)
							{
								if(frame == 1)
									checkAndCreateFolder(folder_cell + "Trajectories");
								try
								{
									IJ.saveAsTiff(prosImp, folder_cell + "Trajectories" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_Trajectories.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "Trajectories" + File.separator + "Stack_"                     + IJ.pad(frame, 2) + "_Trajectories.tif", "The analysis is stopped at the step \"Particle tracker\"");
									return;
								}
							}
							else
							{
								if(frame == 1)
									checkAndCreateFolder(folder_cell + "Trajectories_" + bead);
								try
								{
									IJ.saveAsTiff(prosImp, folder_cell + "Trajectories_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_Trajectories.tif");
								}
								catch (Exception e)
								{
									showDialogWithImageAndCustomOkAndNoCancel("Particle tracker", "write.png", "Error while saving\n \n" + e.getMessage() + "\n \n" + folder_cell + "Trajectories_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_Trajectories.tif", "The analysis is stopped at the step \"Particle tracker\"");
									return;
								}
							}
							prosImp		.close();
						}

//						closeWindow("Log");
						TextWindow logWindow = (TextWindow) WindowManager.getWindow("Log");
						logWindow	.close();

						stopTime	= System.currentTimeMillis();
						elapsedTime	= stopTime - startTime;
						neededTime	= (frames - frame) * elapsedTime / 60000;
						IJ.log("Performed calculation within the folder " + folder_cell + " on the image "				+ String.valueOf(frame)																						);
						IJ.log("Time needed for the calculation of the last frame:                                 "	+ String.valueOf(decimalFormat.format(elapsedTime / 60000))											+ " min");
						IJ.log("Frames still needed to be calculated to terminate the next iterration:    "				+ String.valueOf(frames - frame)																			);
						if(neededTime / 60 > 1)
						{
							if(neededTime % 60 == 0)
								IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "	+ String.valueOf((int) (neededTime / 60)) + " hours"														);
							else
								IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "	+ String.valueOf((int) (neededTime / 60)) + " hours and " + String.valueOf((int) (neededTime % 60)) + " min");
						}
						else
							IJ.log("Linearly extrapolated time still needed to terminate the next iterration:  "		+ String.valueOf(decimalFormat.format(neededTime))													+ " min");
					}
					// updating and saving "JEasyTFM_x_end.txt" file
					if((bead == 0 || bead == 2) && traction_high_folder == traction_high_ending_folder)
					{
						particle_tracker			= false;
						saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
					}
				}	// particle_tracker
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(traction_high_starting_folder < traction_high_ending_folder)
						traction_high_starting_folder++;
					else
					{
						traction_high_force				= false;
						traction_high_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
			}
			if(beads == 0) bead--;
		}
	}	// traction_high_force

	private void FA_segmentation()
	{
		int							FA_segmentation_folder, bead, frame;
		int							roi_x, roi_y;
		int							roi_width			= 0;
		int							roi_height			= 0;
		int							width, height;
		int							i, j;
		double						value;
		String						folder_cell;
		String	[]					lines, columns;
		double	[]					shift_x, shift_y;
		RoiManager					rm;
		ImagePlus					imp, imp2, imp3, imp4, imp5;
		ZProjector					zproj;
		ImageCalculator				ic;
		NonBlockingGenericDialog	nbgd;
		Prefs						.blackBackground	= true;

		for(bead = 1; bead <= 2 && bead != 0; bead++)
		{
			if(beads == 0) bead = 0;
			else if((beads & format[bead - 1]) == 0) continue;
			for(FA_segmentation_folder = FA_segmentation_starting_folder; FA_segmentation_folder <= FA_segmentation_ending_folder; FA_segmentation_folder++)
			{
				folder_cell = folder + "Cell " + FA_segmentation_folder + File.separator;
				checkAndCreateFolder(folder_cell + "FA_analysis");

				// Reading of the data within the Transformation file
				if(beads == 0)
					str = IJ.openAsString(folder_cell + "Analysis"         + File.separator + "Transformation.txt");
				else
					str = IJ.openAsString(folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt");
				if(str.startsWith("Error"))
				{
					if(!error)
					{
						error = true;
						if(beads == 0)
							showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis"         + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"force_integration\"");
						else
							showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Transformation.txt\n\t\ncould not be opened and generated the following error message:\n \n\"" + str + "\"", "The analysis is stopped at the step \"force_integration\"");
					}
					return;
				}

				lines = split(str, "\n");
				if(lines.length <= 3)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Cells segmentation", "calculator.png", "The format of the data imported from the following file:\n \n" + folder_cell + "Analysis" + File.separator + "Transformation.txt\n \n\nare not correct!\n \nPlease check the content of the file.", "The analysis is stopped at the step \"Cells segmentation\"");
					return;
				}
				shift_x = new double[lines.length - 3];
				shift_y = new double[lines.length - 3];

				for (int line = 1; line < lines.length - 2; line++)
				{
					columns = split(lines[line], "\t");
					shift_x[line - 1] = Double.valueOf(columns[1]);
					shift_y[line - 1] = Double.valueOf(columns[2]);
				}

				columns		= split(lines[lines.length - 1], "\t");
				roi_x		= Integer.parseInt(columns[0]);
				roi_y		= Integer.parseInt(columns[1]);
				roi_width	= Integer.parseInt(columns[2]);
				roi_height	= Integer.parseInt(columns[3]);

				// Reading of the raw hyperstack
				imp = openStealth (folder + file1 + FA_segmentation_folder + "_" + IJ.pad((numberCh + 1) * FA_segmentation_folder - numberCh + 1, 2) + ".tif");
				if(imp == null)
				{
					showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "undo.png", "The following file:\n\t\n" + folder + file1 + FA_segmentation_folder + "_" + IJ.pad((numberCh + 1) * FA_segmentation_folder - numberCh + 1, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"FA_segmentation\"");
					return;
				}

				try
				{
					imp = HyperStackConverter.toHyperStack(imp, 1, slices, frames, "default", "Grayscale");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "calculator.png", "Error while trying to transform the stack image \n" + imp.getTitle() + "\ncontaining    " + imp.getStackSize() + " images into an hyperStack of\nChannels     1\nSlices            " + slices + "\nFrames         " + frames + "\ni.e.                  " + slices * frames + " images" , "The analysis is stopped at the step \"FA_segmentation\"");
					return;
				}
//				imp.show();

//				frame = frames_begin;
				for(frame = frames_begin; frame <= frames; frame++)
				{
					imp2	= SubHyperstackMaker.makeSubhyperstack(imp, "1", "1-" + slices, "" + frame);

//					if(beads_sequence_images_find_focused_slices)
//						imp2 = Find_Focused_Slices.getAlignedSlices(imp2, 80, 0.00, true, true, false);
//					imp2	.show();

					imp3	= imp2.duplicate();
//					IJ		.run(imp3, "Enhance Contrast", "saturated=0.35");
					IJ		.run(imp3, "Gaussian Blur...", "sigma=1 stack");
					IJ		.run(imp3, "Subtract Background...", "rolling=3 stack");
					for(i = 1; i <= imp3.getNSlices(); i++)
					{
						imp3.setSlice(i);
						IJ	.run(imp3, "Find Maxima...", "prominence=75 output=Count");
					}
					ResultsTable rt = Analyzer.getResultsTable();
					j		= 0;
					value	= rt.getValue("Count" , 0);
					for(i = 1; i < rt.getCounter(); i++)
					{
						if(rt.getValue("Count" , i) > value)
						{
							value	= rt.getValue("Count" , i);
							j		= i;
						}
					}
/*
					imp2	.setSlice(j);
					imp2	.show();
					nbgd	= new NonBlockingGenericDialog	("Action Required");
					nbgd	.addMessage						("Please select the best focused image");
					nbgd	.hideCancelButton();
					nbgd	.setOKLabel("Continue");
					nbgd	.showDialog();
					imp3	= new Duplicator().run(imp2, imp2.getCurrentSlice(), imp2.getCurrentSlice());
*/
//					imp3	= new Duplicator().run(imp2, j, j);
					imp3	= new Duplicator().run(imp3, j, j);
					imp2	.close();
//					imp3	= IJ.openImage(folder_cell + "Cells_Ch1_" + IJ.pad(frame, 2) + ".tif");
//					imp3	.show();
					imp4	= imp3.duplicate();
					IJ		.run(imp4, "Mean...", "radius=20");
					ic		= new ImageCalculator();
					imp5	= ic.run("Subtract create", imp3, imp4);
					imp5	.show();
					IJ		.run(imp5, "Translate...", "x=" + shift_x[frame - 1] + " y=" + shift_y[frame - 1] + " interpolation=Bicubic slice");
					imp5	.setRoi(roi_x, roi_y, roi_width, roi_height);
					IJ		.run(imp5, "Crop", "");
					IJ		.run(imp5, "Enhance Contrast", "saturated=0.35");

					if(beads == 0)
					{
						try
						{
							IJ.saveAsTiff(imp5, folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + IJ.pad(frame, 2) + ".tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"FA_segmentation\"");
							return;
						}
					}
					else
					{
						try
						{
							IJ.saveAsTiff(imp5, folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"FA_segmentation\"");
							return;
						}
					}

					IJ		.setAutoThreshold(imp, "Li dark");
					IJ		.run("Threshold...");
					nbgd	= new NonBlockingGenericDialog	("Action Required");
					nbgd	.addMessage						("Please adjust the threshold settings");
					nbgd	.hideCancelButton();
					nbgd	.setOKLabel("Continue");
					nbgd	.showDialog();
					IJ		.run(imp5, "Convert to Mask", "");
					IJ		.selectWindow("Threshold");
					IJ		.run("Close");

					if(beads == 0)
					{
						try
						{
							IJ.saveAsTiff(imp5, folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + IJ.pad(frame, 2) + "_binary.tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + IJ.pad(frame, 2) + "_binary.tif", "The analysis is stopped at the step \"FA_segmentation\"");
							return;
						}
					}
					else
					{
						try
						{
							IJ.saveAsTiff(imp5, folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + "_binary.tif");
						}
						catch (Exception e)
						{
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + "_binary.tif", "The analysis is stopped at the step \"FA_segmentation\"");
							return;
						}
					}

					IJ		.run(imp5, "Analyze Particles...", "size=10-Infinity clear add");
/*
					imp2 = null;
					if(beads == 0)
						imp2	= IJ.openImage(folder_cell + "FA_Analysis" + File.separator + "CorrCells_"              + IJ.pad(frame, 2) + ".tif");
					else
						imp2	= IJ.openImage(folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
					if(imp2 == null)
					{
						if(beads == 0)
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"FA_segmentation\"");
						else
							showDialogWithImageAndCustomOkAndNoCancel("FA_segmentation", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis" + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"FA_segmentation\"");
						return;
					}
					imp2	.show();
*/
					rm		= RoiManager.getInstance();
					if(rm == null)
						rm	= new RoiManager		();
//					rm		.runCommand(imp2, "Show All without labels");
					rm		.runCommand(imp5, "Show All without labels");
					if(beads == 0)
						rm		.runCommand("Save", folder_cell + "FA_Analysis" + File.separator + "ROI_set_"              + IJ.pad(frame, 2) + ".zip");
					else
						rm		.runCommand("Save", folder_cell + "FA_Analysis" + File.separator + "ROI_set_" + bead + "_" + IJ.pad(frame, 2) + ".zip");
					nbgd	= new NonBlockingGenericDialog	("Action Required");
					nbgd	.addMessage						("Visualize your results");
					nbgd	.hideCancelButton();
					nbgd	.setOKLabel("Continue");
					nbgd	.showDialog();
//					imp2	.close();
					imp5	.close();
					IJ		.selectWindow("ROI Manager");
					IJ		.run("Close");
				}	// FA_segmentation()
				imp.close();
				// updating and saving "JEasyTFM_x_end.txt" file
				if(bead == 0 || bead == 2)
				{
					if(FA_segmentation_starting_folder < FA_segmentation_ending_folder)
						FA_segmentation_starting_folder++;
					else
					{
						FA_segmentation					= false;
						FA_segmentation_starting_folder	= 1;
					}
					saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
				}
			}
			if(beads == 0) bead--;
		}
	}	// FA_segmentation

	private void traction_force_applied_on_FA()
	{
		ImagePlus					imp, imp1, imp2, beadsPlotImp, lambdaPlotImp, forcePlotImp;
		Plot						                 beadsPlot   , lambdaPlot   , forcePlot;
		RoiManager					rm;
		Roi						[]	rois;

		final char				[]	charLambda			= { ( char ) 955 };
		final String				symbolLambda		= new String( charLambda );
		final double				conversionFactor	= E * Math.pow(length_scale, 2);		// force[nN] = E[kPa] * [pixel/micron]^2 

		boolean						set_cero		= true;
		int							i, j, k;
		int							image_width, image_height;
		int							beads_size_initial, FA_size_initial;
		int							traction_force_applied_on_FA_folder, bead, channel, frame;
		int							displacement_maximum_index = 0;;
		int							offset					= 13;
		int							DF;											// Degrees of freedom
		int							delLines				= 0;
		int							iset					= 0;
		int							delta1					= 5;
		int							delta2					= 0;
		int							delta3					= 1000;
		int							lsMin					= -3;				// Minima of the logspace vector lambda_v
		int							lsMax					= 1;				// Maxima of the logspace vector lambda_v
		int							lsSize					= 30;				// Size   of the logspace vector lambda_v
		double						scale					= 2.0;				// scaling factore for the force plotting graph
		double						sigma					= 1.0;
		double						rhoMin					= 0.0;
		double						rhoMax					= 0.0;

		double						lambda;
		double						length, min_length;
		double						displacement_maximum	= 0.0;
		double						displacement_magnitude;
		double						rho_opt;
		double						rho_opt_plus;
		double						rho_opt_minus;
		double						mag;
		double						val1, val2;		// temporary double values;
//		double					[]	sf;

		ArrayList <Double> focalsX	= new ArrayList <Double> ();
		ArrayList <Double> focalsY	= new ArrayList <Double> ();
		ArrayList <Double> beads1X	= new ArrayList <Double> ();
		ArrayList <Double> beads1Y	= new ArrayList <Double> ();
		ArrayList <Double> beads2X	= new ArrayList <Double> ();
		ArrayList <Double> beads2Y	= new ArrayList <Double> ();
		ArrayList <Double> u		= new ArrayList <Double> ();
		ArrayList <Double> s		= new ArrayList <Double> ();
		ArrayList <Double> FX		= new ArrayList <Double> ();
		ArrayList <Double> FY		= new ArrayList <Double> ();
		ArrayList <Double> lambda_v	= new ArrayList <Double> ();
		ArrayList <Double> beta		= new ArrayList <Double> ();
		ArrayList <Double> zeta		= new ArrayList <Double> ();
		ArrayList <Double>  eta		= new ArrayList <Double> ();
		ArrayList <Double> rho		= new ArrayList <Double> ();

		double					[]	centroids;
//		String						folder_begin, folder_cell;
		String						folder_cell;
		String					[]	lines, columns;

		//  This plugin is the translation into an ImageJ plugin of the code
		//  developped under Matlab by Ulrich Schwarz, MPI Colloids and Interfaces
		//  http://www.thphys.uni-heidelberg.de/~biophys/index.php?lang=e&n1=research_elasticsubstrates
		//  for the Inverse problem for elastic substrate method
		//  that he had written May 2000, modified Feb 2003.
		//  
		//  INPUT:   lines.dat contains displacement data in form x1 y1 x2 y2
		//           focals.dat contains positions of focals in form x1 y1
		//  OUTPUT:  newlines.dat contains displacement data in form x1 y1 x2 y2
		//           force_(lambda value).dat contains the calculated forces in form x1 y1


		for(traction_force_applied_on_FA_folder = traction_applied_on_FA_starting_folder; traction_force_applied_on_FA_folder <= traction_applied_on_FA_ending_folder; traction_force_applied_on_FA_folder++)
		{
			folder_cell = folder + "Cell " + traction_force_applied_on_FA_folder + File.separator;
			checkAndCreateFolder(folder_cell + "Traction_force_on_FA");

			for(frame = frames_begin; frame <= frames; frame++)
			{
				// Opening of the cell image
				imp = null;
				if(beads == 0)
				{
					imp = IJ.openImage(folder_cell + "FA_Analysis"               + File.separator + "CorrCells_"             + IJ.pad(frame, 2) + ".tif");
					if (imp == null)
					{
						if(!error)
						{
							error = true;
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis"         + File.separator + "CorrCells_"  + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
						}
						return;
					}
				}
				else
				{
					imp1 = imp2 = null;

					bead = 1;
					if((beads & format[bead - 1]) != 0)
					{
						imp1 = IJ.openImage(folder_cell + "FA_Analysis_" + bead + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
						imp1.show();
					}

					bead = 2;
					if((beads & format[bead - 1]) != 0)
					{
						imp2 = IJ.openImage(folder_cell + "FA_Analysis_" + bead + File.separator + "CorrCells_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
						imp2.show();
					}

					if(imp1 == null)
					{
						if(imp2 == null)
						{
							if(!error)
							{
								error = true;
								showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following files:\n\t\n" + folder_cell + "FA_Analysis_1" + File.separator + "CorrCells_1_" + IJ.pad(frame, 2) + ".tif\n\t\nand\n\t\n" + folder_cell + "FA_Analysis_2" + File.separator + "CorrCells_2_" + IJ.pad(frame, 2) + ".tif\n\t\n could not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							}
							return;
						}
						else
						{
							imp = imp2.duplicate();
							imp2.close();
						}
					}
					else
					{
						if(imp2 == null)
						{
							imp = imp1.duplicate();
							imp1.close();
						}
						else
						{
							IJ.selectWindow(imp1.getTitle());
							IJ.run("Add Image...", "image=" + imp2.getTitle() + " x=0 y=0 opacity=50");
							imp = imp1.duplicate();
							imp1.close();
							imp2.close();
						}
					}
				}
//				imp.show();

				// Reading of the beads displacements data
				str		= null;
				lines	= null;
				if(beads == 0)
				{
					str = IJ.openAsString(folder_cell + "Analysis" + File.separator + "Stack_"                           + IJ.pad(frame, 2) + "_2_Trajectories.txt");
					if(str.startsWith("Error"))
					{
						if(!error)
						{
							error = true;
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis" + File.separator + "Stack_"                           + IJ.pad(frame, 2) + "_2_Trajectories.txt\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
						}
						return;
					}
					lines	= str.split("\n");
					lines = Arrays.copyOfRange(lines, offset, lines.length);
				}
				else
				{
					bead = 1;
					str = IJ.openAsString(folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt");
					if(str.startsWith("Error"))
					{
//						showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
					}
					else
					{
						lines	= str.split("\n");
						lines = Arrays.copyOfRange(lines, offset, lines.length);
					}

					columns = null;
					bead = 2;
					str = IJ.openAsString(folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt");
					if(str.startsWith("Error"))
					{
//						showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "Analysis_" + bead + File.separator + "Stack_" + bead + "_" + IJ.pad(frame, 2) + "_2_Trajectories.txt\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
					}
					else
					{
						columns	= str.split("\n");										// columns is used here as temporary String[] to avoid the need to define such a new array as temporary
						columns = Arrays.copyOfRange(columns, offset, columns.length);
					}

					if(lines == null)
					{
						if(columns == null)
						{
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following files:\n\t\n" + folder_cell + "Analysis_1" + File.separator + "Stack_1_" + IJ.pad(frame, 2) + "_2_Trajectories.txt\n\t\nand\n\t\n" + folder_cell + "Analysis_2" + File.separator + "Stack_2_" + IJ.pad(frame, 2) + "_2_Trajectories.txt\n\t\n could not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							return;
						}
						else
						{
							lines = Arrays.copyOfRange(columns, 0, columns.length);
							columns = null;
						}
					}
					else
					{
						if(columns == null)
						{
							// nothing to do given that String[] lines is already defined as needed
						}
						else
						{
							ArrayList<String> both = new ArrayList(Arrays.asList(lines));
							both.addAll(Arrays.asList(columns));
							lines = both.toArray(new String[0]);
							columns = null;
						}
					}
				}

				beads1X.clear();
				beads2X.clear();
				beads1Y.clear();
				beads2Y.clear();

				for(i = 0; i != lines.length; i++)
				{
					columns	= split(lines[i],"\t");

					beads1X	.add(					Double.valueOf(columns[0]));
					beads1Y	.add(imp.getHeight() -	Double.valueOf(columns[1]));
					beads2X	.add(					Double.valueOf(columns[2]));
					beads2Y	.add(imp.getHeight() -	Double.valueOf(columns[3]));
				}

				// Reading of the beads displacements data
				rm = RoiManager.getRoiManager();
//				if(rm == null)	rm = new RoiManager();

				for(bead = 1; bead <= 2 && bead != 0; bead++)
				{
					if(beads == 0) bead = 0;
					else if((beads & format[bead - 1]) == 0) continue;

					if(beads == 0)
					{
						file = new File(folder_cell + "FA_Analysis"         + File.separator + "ROI_set_"              + IJ.pad(frame, 2) + ".zip");
						if (!file.exists())
						{
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis"         + File.separator + "ROI_set_"              + IJ.pad(frame, 2) + ".zip\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							return;
						}
						else if(!rm.open(folder_cell + "FA_Analysis"         + File.separator + "ROI_set_"              + IJ.pad(frame, 2) + ".zip"))
						{
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis"         + File.separator + "ROI_set_"              + IJ.pad(frame, 2) + ".zip\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							return;
						}
					}
					else
					{
						file = new File(folder_cell + "FA_Analysis_" + bead + File.separator + "ROI_set_" + bead + "_" + IJ.pad(frame, 2) + ".zip");
						if (!file.exists())
						{
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis_" + bead + File.separator + "ROI_set_" + bead + "_" + IJ.pad(frame, 2) + ".zip\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							return;
						}
						else if(!rm.open(folder_cell + "FA_Analysis_" + bead + File.separator + "ROI_set_" + bead + "_" + IJ.pad(frame, 2) + ".zip"))
						{
							showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "undo.png", "The following file:\n\t\n" + folder_cell + "FA_Analysis_" + bead + File.separator + "ROI_set_" + bead + "_" + IJ.pad(frame, 2) + ".zip\n\t\ncould not be found", "The analysis is stopped at the step \"Traction force applied on FA\"");
							return;
						}
					}
					if(beads == 0) bead--;
				}
				rois	= rm.getRoisAsArray();
				rm		.close();

				focalsX.clear();
				focalsY.clear();

				for(i = 0; i != rois.length; i++)
				{
					centroids	= rois[i].getContourCentroid();
					focalsX		.add(centroids[0]);
//					focalsY		.add(centroids[1]);
					focalsY		.add(imp.getHeight() - centroids[1]);
				}

				// saveFocalsData
				try
				{
					FileWriter		fstream				= new FileWriter(folder_cell + "Traction_force_on_FA" + File.separator + "FA_positions_" + IJ.pad(frame, 2) + ".txt");
					BufferedWriter	fileOutputStream	= new BufferedWriter(fstream);
					for(i = 0; i < focalsX.size(); i++)
						fileOutputStream.write( String.valueOf(focalsX.get(i)) + "\t" +  String.valueOf(focalsY.get(i)) + "\n" );
					fileOutputStream.close();
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "FA_positions_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

				image_width				= imp.getWidth();
				image_height			= imp.getHeight();
				beads_size_initial		= beads1X.size();
				FA_size_initial			= focalsX.size();

				beadsPlot				= new Plot				("Data before correction", "X Axis", "Y Axis");
				beadsPlot				.setLimits				(0., image_width, 0., image_height);
//				beadsPlot				.show					();
				Rectangle				beadsPlotDrawingFrame	= beadsPlot.getDrawingFrame();
				Dimension				beadsPlotSize			= beadsPlot.getSize();

				beadsPlot				.setSize				(beadsPlotSize.width + (image_width - beadsPlotDrawingFrame.width), beadsPlotSize.height + (image_height - beadsPlotDrawingFrame.height));
//				beadsPlot				.update					();

				beadsPlot				.setColor				(Color.red);
				beadsPlot				.setLineWidth			(2);
				beadsPlot				.addPoints				(focalsX, focalsY, Plot.BOX);

				beadsPlot				.setColor				(Color.blue);
				beadsPlot				.setLineWidth			(1);
				beadsPlot				.drawVectors			(beads1X, beads1Y, beads2X, beads2Y);
				IJ						.run					(imp, "Enhance Contrast", "saturated=0.35");
				IJ						.run					(imp, "RGB Color", "");
//				IJ						.run					(imp, "Invert", "");
				beadsPlot				.show					();
				beadsPlotImp									= beadsPlot.getImagePlus();

				// plotScaleBar
				Calibration				beadsPlotCalibration	= new Calibration();
				beadsPlotCalibration	.pixelWidth				= length_scale;
				beadsPlotCalibration	.pixelHeight			= length_scale;
				beadsPlotCalibration	.setXUnit				( "\u00B5m" );
//				beadsPlotImp			.setGlobalCalibration	(beadsPlotCalibration);
				beadsPlotImp			.setCalibration			(beadsPlotCalibration);
//				IJ.run(beadsPlotImp, "Scale Bar...", "width=10 height=1 thickness=4 font=16 color=Blue background=None location=[Upper Right] bold overlay");
				IJ.run(beadsPlotImp, "Scale Bar...", "width=10 height=1 thickness=4 font=16 color=Blue background=None location=[Upper Right] horizontal bold overlay");
//				IJ.run(forcePlotImp, "Scale Bar...", "width=10 height=1 thickness=4 font=16 color=Blue background=None location=[Upper Right] horizontal vertical bold overlay");
				beadsPlot				.setFrozen				(true);

				try
				{
					IJ				.saveAsTiff				(beadsPlotImp, folder_cell + "Traction_force_on_FA"         + File.separator + "Beads_displacement_plot_"              + IJ.pad(frame, 2) + ".tif");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Beads_displacement_plot_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

				imp						.copy					();
//				beadsPlot				.setFrozen				(true);
				beadsPlotDrawingFrame							= beadsPlot.getDrawingFrame();
				beadsPlotImp			.paste					(beadsPlotDrawingFrame.x, beadsPlotDrawingFrame.y, "XOR");
				beadsPlot				.update					();

				try
				{
					IJ				.saveAsTiff				(beadsPlotImp, folder_cell + "Traction_force_on_FA"         + File.separator + "Beads_displacement_plot_with_image_"              + IJ.pad(frame, 2) + ".tif");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Beads_displacement_plot_with_image_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}
				beadsPlotImp			.close();
//				imp						.close();

				// reformatAndSaveCorrectedData()

				// Set displacements to zero which are smaller than delta2 ?
				// This feature I used a lot in the beginning, since I figured
				// that small displacements only represent noise and should not be used;
				// now I think that there is no reason to exclude them, the
				// method itself is able to handle the noise problem by itself
				// remove all displacements which are closer to any focal than delta1
				// This is important since we assume point-like forces which diverge at the origin;
				// it can be shown that this approximates distributed force well as long as 
				// the displacement is evaluated at distances to the ellipse which are larger
				// than the ellipse itself
				// Remove displacements which are farer away from any focal than delta3
				// This is not necessary, but reasonable, since for displacements far
				// way, the signal decays below the noise level

				displacement_maximum		= getDistance(beads1X.get(0), beads2X.get(0), beads1Y.get(0), beads2Y.get(0));
				for(j = 1; j < beads1X.size(); j++)
				{
					displacement_magnitude	= getDistance(beads1X.get(j), beads2X.get(j), beads1Y.get(j), beads2Y.get(j));

					if (displacement_magnitude > displacement_maximum)
					{
						displacement_maximum_index	= j;
						displacement_maximum		= displacement_magnitude;
					}

					min_length = getDistance(focalsX.get(0), beads1X.get(j), focalsY.get(0), beads1Y.get(j));
					for(i = 1; i < focalsX.size(); i++)
					{
						length = getDistance(focalsX.get(i), beads1X.get(j), focalsY.get(i), beads1Y.get(j));

						if(length < min_length)
							min_length = length;
					}
					if ((min_length < delta1) || (min_length > delta3))
					{
						delLines++;
						beads1X.remove(j);
						beads1Y.remove(j);
						beads2X.remove(j);
						beads2Y.remove(j);
					}
				}

				iset		= 0;
				if(set_cero)					// set small displacements to cero if requested
				{
					for(i = 0; i < beads1X.size(); i++)
					{
						if(getDistance(beads1X.get(i), beads2X.get(i), beads1Y.get(i), beads2Y.get(i)) < delta2)
						{
							beads2X.set(i, beads1X.get(i));
							beads2Y.set(i, beads1Y.get(i));
							iset++;
						}
					}
				}

				// saveBeadsData(getfileLinesDirectory(fileLinesFullName) + File.separator + fileNewLinesName);
				try
				{
					FileWriter		fstream				= new FileWriter(folder_cell + "Traction_force_on_FA" + File.separator + "Beads_displacements_" + IJ.pad(frame, 2) + ".txt");
					BufferedWriter	fileOutputStream	= new BufferedWriter(fstream);
					for(i = 0; i < beads1X.size(); i++)
						fileOutputStream.write( String.valueOf(beads1X.get(i)) + "\t" +  String.valueOf(beads1Y.get(i)) + "\t" +  String.valueOf(beads2X.get(i)) + "\t" +  String.valueOf(beads2Y.get(i)) + "\n" );
					fileOutputStream.close();
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Beads_displacements_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

				// Implementation of the inverse.m code

				// standard deviation for noise in displacement
				// from this we can calculate an estimate for the regularization parameter lambda

				// displacements is stored both as one large vector u
				u.clear();
				for(i = 0; i < 2 * beads1X.size(); i++)
					u.add(calcultateU(i, beads1X, beads1Y, beads2X, beads2Y));

				// Number of degrees of freedom
				DF = 2 * ( beads1X.size() - focalsX.size() );
/*
				// estimate for residual norm and its confidence interval
				rho_opt			=  Math.sqrt(DF)							* sigma;
				rho_opt_plus	= (Math.sqrt(DF) + Math.pow(2 * DF, 0.25))	* sigma;
				rho_opt_minus	= (Math.sqrt(DF) - Math.pow(2 * DF, 0.25))	* sigma;
*/
				IJ.showStatus("Done...");

				// calculateG()
				IJ.showStatus("Calculating G ...");

				// build Greens function between the two sets of positions
				RealMatrix G = MatrixUtils.createRealMatrix(2 * beads1X.size(), 2 * focalsX.size());
//				G = new Matrix(2 * beads1X.size(), 2 * focalsX.size());

				for(i = 0; i < 2 * beads1X.size(); i++)
					for(j = 0; j < 2 * focalsX.size(); j++)
						G.setEntry(i, j, Greens(i, j, focalsX, focalsY, beads1X, beads1Y));
//						G.set(i, j, Greens(i, j));

				// singular value decomposition for G
				SingularValueDecomposition S = new SingularValueDecomposition(G);
//				S = G.svd();

				RealMatrix	U	= (S.getU()).scalarMultiply		(-1);
				double[]	sf	=  S		.getSingularValues	();
				RealMatrix	V	= (S.getV()).scalarMultiply		(-1);
//				U  = (S.getU()).times(-1);
//				sf = S.getSingularValues();
//				V  = (S.getV()).times(-1);

				s.clear();
				for(i = 0; i < sf.length; i++)
					s.add( sf[i] );

				// logspace generation for lambda_v
				lambda_v.clear();
				val1 = (double) (lsMax - lsMin) / (lsSize - 1);

				for(i = 0; i < lsSize; i++)
					lambda_v.add( Math.pow(10, lsMin + (val1 * i)) );

//				[F_v,rho_v,eta_v]   = tikhonov(U,s,V,u,lambda_v);
				tikhonovVect(U, s, V, u, lambda_v, beta, zeta, eta, rho);
/*
				// Transformation of lambda_v into Log(lambda_v)
				for(i = 0; i < lsSize; i++)
					lambda_v.set(i, Math.log( lambda_v.get(i) ));
*/
				rhoMin			= getRhoMinima(rho);
				rhoMax			= getRhoMaxima(rho);

				sigma			= (rhoMax + rhoMin) / (2 * Math.sqrt(DF));

				// estimate for residual norm and its confidence interval
				rho_opt			=  Math.sqrt(DF)							* sigma;
				rho_opt_plus	= (Math.sqrt(DF) + Math.pow(2 * DF, 0.25))	* sigma;
				rho_opt_minus	= (Math.sqrt(DF) - Math.pow(2 * DF, 0.25))	* sigma;

				lambdaPlot		= new Plot		("Choice of regularization parameter", symbolLambda, "residual norm || A x - b ||_2");
				lambdaPlot		.setAxes		(true, false, true, true, true, true, 10, 5);
				lambdaPlot		.setXLabelFont	( new Font("Helvetica", Font.PLAIN, 18) );

				lambdaPlot		.setLimits		(lambda_v.get( 0 ), lambda_v.get( lambda_v.size() - 1 ), Math.floor(rhoMin), Math.ceil(rhoMax));
				lambdaPlot		.setSize		(1584, 765);

				lambdaPlot		.setColor		(Color.blue);
//				lambdaPlot		.setLineWidth	(1);
				lambdaPlot		.addPoints		(lambda_v, rho, Plot.LINE);

				lambdaPlot		.setColor		(Color.red);
				lambdaPlot		.drawLine		(lambda_v.get( 0 ), rho_opt      , lambda_v.get( lambda_v.size() - 1 ), rho_opt);
				lambdaPlot		.drawDottedLine	(lambda_v.get( 0 ), rho_opt_plus , lambda_v.get( lambda_v.size() - 1 ), rho_opt_plus, 2);
				lambdaPlot		.drawDottedLine	(lambda_v.get( 0 ), rho_opt_minus, lambda_v.get( lambda_v.size() - 1 ), rho_opt_minus, 2);

				lambdaPlot		.show			();
				lambdaPlotImp	= lambdaPlot.getImagePlus();

				try
				{
					IJ			.saveAsTiff		(lambdaPlotImp, folder_cell + "Traction_force_on_FA" + File.separator + "Regularization_parameter_plot_" + IJ.pad(frame, 2) + ".tif");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Regularization_parameter_plot_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

				lambdaPlotImp	.close();

				lambda			= lambda_v.get( calculateRhoOpt( rho ) );
//				IJ.log( "Value = " + lambda );

				// calculateAndPlotForces
				IJ.showStatus("Solving inverse problem...");

				tikhonovVal(lambda, V, zeta, s, FX, FY);

//				saveFittingParametersData
				try
				{
					FileWriter		fstream				= new FileWriter(folder_cell + "Traction_force_on_FA" + File.separator + "Fitting_parameters_data_" + IJ.pad(frame, 2) + ".txt");
					BufferedWriter	fileOutputStream	= new BufferedWriter(fstream);

					fileOutputStream.write( "Beads displacements\t"											+ "Beads_displacements_"					+ IJ.pad(frame, 2) + ".txt"	+ "\n" );
					fileOutputStream.write( "FA positions\t"												+ "FA_positions_"							+ IJ.pad(frame, 2) + ".txt"	+ "\n" );
					fileOutputStream.write( "image width\t"													+ image_width															+ "\n" );
					fileOutputStream.write( "image height\t"												+ image_height														+ "\n" );
					fileOutputStream.write( "Beads positions initial\t"										+ beads_size_initial													+ "\n" );
					fileOutputStream.write( "FA positions initial\t"										+ FA_size_initial														+ "\n" );
					fileOutputStream.write( "Displacements smaller than value set to zero\t"				+ delta2																+ "\n" );
					fileOutputStream.write( "Maximal displacement\t"										+ displacement_maximum													+ "\n" );
					fileOutputStream.write( "Found at position\t"											+ (displacement_maximum_index + 1)										+ "\n" );
					fileOutputStream.write( "Minimum distance focals - displacements required (pixels)\t"	+ delta1																+ "\n" );
					fileOutputStream.write( "Maximal distance focals - displacements allowed  (pixels)\t"	+ delta3																+ "\n" );
					fileOutputStream.write( "Displacements deleted\t"										+ delLines																+ "\n" );
					fileOutputStream.write( "Displacements left\t"											+ beads1X.size()														+ "\n" );
					fileOutputStream.write( "Displacements set to zero\t"									+ iset																	+ "\n" );
					fileOutputStream.write( "Displacements left unchanged\t"								+ (beads1X.size() - iset)												+ "\n" );
					fileOutputStream.write( "Number of degrees of freedom\t"								+ DF																	+ "\n" );
					fileOutputStream.write( "Sigma\t"														+ sigma																	+ "\n" );
					fileOutputStream.write( "Optimal rho\t"													+ rho_opt																+ "\n" );
					fileOutputStream.write( "Regularization parameter\t"									+ lambda																+ "\n\n\n" );

					fileOutputStream.write( "focalsX (pixel)\tfocalsY (pixel)\tFX (pixel)\tFY (pixel)\tFX (nN)\tFY (nN)\tForce (nN)\n" );
					for(i = 0; i < FX.size(); i++)
						fileOutputStream.write( String.valueOf(focalsX.get(i)) + "\t" +  String.valueOf(focalsY.get(i)) + "\t"  + String.valueOf(FX.get(i)) + "\t" +  String.valueOf(FY.get(i)) + "\t"  + String.valueOf(conversionFactor * FX.get(i)) + "\t" +  String.valueOf(conversionFactor * FY.get(i))  + "\t" +  String.valueOf(conversionFactor * Math.sqrt(Math.pow(FX.get(i), 2) + Math.pow(FY.get(i), 2)) ) + "\n" );

					fileOutputStream.close();
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Fitting_parameters_data_" + IJ.pad(frame, 2) + ".txt", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}


				for(i = 0; i < FX.size(); i++)
				{
					FX.set(i, scale * FX.get(i) + focalsX.get(i));
					FY.set(i, scale * FY.get(i) + focalsY.get(i));
				}

				forcePlot				= new Plot				("Calculated forces for a regularization parameter of " + lambda + " and scaling of " + scale, "X Axis", "Y Axis");
				forcePlot				.setLimits				(0., image_width, 0., image_height);
//				forcePlot				.show					();
				Rectangle				forcePlotDrawingFrame	= forcePlot.getDrawingFrame();
				Dimension				forcePlotSize			= forcePlot.getSize();

				forcePlot				.setSize				(forcePlotSize.width + (image_width - forcePlotDrawingFrame.width), forcePlotSize.height + (image_height - forcePlotDrawingFrame.height));
//				forcePlot				.update					();

				forcePlot				.setColor				(Color.red);
				forcePlot				.setLineWidth			(2);
				forcePlot				.addPoints				(focalsX, focalsY, Plot.BOX);

				forcePlot				.setColor				(Color.blue);
				forcePlot				.setLineWidth			(1);
				forcePlot				.drawVectors			(focalsX, focalsY, FX, FY);

				forcePlot				.show					();
				forcePlotImp									= forcePlot.getImagePlus();

				// plotScaleBar
				Calibration				forcePlotCalibration	= new Calibration();
				forcePlotCalibration	.pixelWidth				= length_scale;
				forcePlotCalibration	.pixelHeight			= scale / conversionFactor;
				forcePlotCalibration	.setXUnit				( "\u00B5m" );
				forcePlotCalibration	.setYUnit				( "nN" );
//				forcePlotImp			.setGlobalCalibration	(forcePlotCalibration);
				forcePlotImp			.setCalibration			(forcePlotCalibration);
				IJ.run(forcePlotImp, "Scale Bar...", "width=10 height=1 thickness=4 font=16 color=Blue background=None location=[Upper Right] horizontal vertical bold overlay");
/*
				forcePlotCalibration	.pixelWidth				= length_scale;
				forcePlotCalibration	.pixelHeight			= length_scale;
				forcePlotCalibration	.setXUnit				( "\u00B5m");
				forcePlotCalibration	.setYUnit				( "\u00B5m");
				forcePlotImp			.setCalibration			(forcePlotCalibration);
*/
				forcePlot				.setFrozen				(true);

				try
				{
					IJ				.saveAsTiff				(forcePlotImp, folder_cell + "Traction_force_on_FA" + File.separator + "Force_plot_" + IJ.pad(frame, 2) + ".tif");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Force_plot_"              + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

//				imp						.copy					();
//				forcePlot				.setFrozen				(true);
				forcePlotDrawingFrame							= forcePlot.getDrawingFrame();
				forcePlotImp			.paste					(forcePlotDrawingFrame.x, forcePlotDrawingFrame.y, "XOR");
				forcePlot				.update					();

				try
				{
					IJ				.saveAsTiff				(forcePlotImp, folder_cell + "Traction_force_on_FA"         + File.separator + "Force_plot_with_image_" + IJ.pad(frame, 2) + ".tif");
				}
				catch (Exception e)
				{
					showDialogWithImageAndCustomOkAndNoCancel("Traction force applied on FA", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folder_cell + "Traction_force_on_FA" + File.separator + "Force_plot_with_image_" + IJ.pad(frame, 2) + ".tif", "The analysis is stopped at the step \"Traction force applied on FA\"");
				}

//				beadsPlotImp			.close();
				forcePlotImp			.close();
				imp						.close();
/*
				plotData("Calculated forces for a regularization parameter of " + lambda + " and scaling of " + scale, focalsX, focalsY, FX, FY, focalsX, focalsY);
				plotScaleBar();
				plotForceScaleBar();
*/
				IJ.showStatus("Done...");
			}
		}

		// updating and saving "JEasyTFM_x_end.txt" file
		if(traction_applied_on_FA_starting_folder < traction_applied_on_FA_ending_folder)
			traction_applied_on_FA_starting_folder++;
		else
		{
			traction_force_applied_on_FA			= false;
			traction_applied_on_FA_starting_folder	= 1;
		}
		saveJob(folder + "Jobs" + File.separator + "JEasyTFM_" + job_index + "_end.txt");
	}	// traction_force_applied_on_FA

	/*****************************************************************************************************************************/
	/*                                                      FUNCTIONS                                                            */
	/*****************************************************************************************************************************/

	private ImagePlus checkScale(String path)
	{
		ImagePlus		imp			= null;
		ImagePlus		imp1		= null;
		ImagePlus		imp2		= null;
		Calibration		cal;
		String			metadata	= null;
		String[]		metadataSub;
		String[]		ImageDescription;
		double			nbDecimals = 10000000d;
		int				dimSlices, dimSlices1, dimSlices2, dimFrames1;
		int		[]		dim;
		int				i;

//		IJ.run("Bio-Formats Importer", "open=[" + path + "] color_mode=Default view=Hyperstack stack_order=XYCZT");
//		imp			= IJ.getImage();
		imp			= IJ.openImage(path);
		if(imp == null)
		{
			imp2		= IJ.openImage(path.substring(0, path.length() - 4) + "_p2.tif");
//			imp2		.show();
			if(imp2 == null)
				return null;
			else
			{
				dim			= imp2.getDimensions();
				dimSlices2	= dim[3];
//				IJ			.run("Bio-Formats Importer", "open=[" + path.substring(0, path.length() - 4) + "_p1.tif" + "] color_mode=Default view=[Standard ImageJ] stack_order=Default");
//				imp1		= IJ.getImage();
//				cal			= imp1.getCalibration();
				imp1		= IJ.openImage(path.substring(0, path.length() - 4) + "_p1.tif");
				if(imp1 == null)
				{
					imp2	.close();
					return null;
				}
				else
				{
					metadata	= (String)imp1.getProperty("Info");
					if(ch1 && ch2)
					{
						dim			= imp1.getDimensions();
						dimSlices1	= dim[3];
						dimFrames1	= dim[4];
						dimSlices	= (dimFrames1 * dimSlices1) - dimSlices2;
						IJ			.run("Make Substack...", "  slices=1-" + dimSlices);
						imp1		.close();
						imp1		= IJ.getImage();
					}
					imp			= Concatenator.run(imp1, imp2);
					imp			.show();
					imp1		.close();
					imp2		.close();
				}
			}
		}
		else
		{
			imp			.show();
			metadata	= (String) imp.getProperty("Info");
		}
//		cal			= imp.getCalibration();

		if(metadata != null)
		{
			metadataSub		 = metadata      .split("\t\n\r");
			ImageDescription = metadataSub[0].split(" ");
			for(i = 0; i != ImageDescription.length; i++)
			{
				if(ImageDescription[i].startsWith("PhysicalSizeX"))
				{
					if(Math.round(length_scale * nbDecimals) / nbDecimals != Double.valueOf(ImageDescription[i].substring(15, ImageDescription[i].length() - 1)) ) showDialog("Error on width scaling!!!" , "Beware!!! the width scaling value of the image is not "  + String.valueOf(Math.round(length_scale * nbDecimals) / nbDecimals) + ", but " + ImageDescription[i].substring(15, ImageDescription[i].length() - 1));
				}
				if(ImageDescription[i].startsWith("PhysicalSizeY"))
				{
					if(Math.round(length_scale * nbDecimals) / nbDecimals != Double.valueOf(ImageDescription[i].substring(15, ImageDescription[i].length() - 1)) ) showDialog("Error on width scaling!!!" , "Beware!!! the width scaling value of the image is not "  + String.valueOf(Math.round(length_scale * nbDecimals) / nbDecimals) + ", but " + ImageDescription[i].substring(15, ImageDescription[i].length() - 1));
					return imp;
				}
			}
		}
/*
		if(Math.round(length_scale * nbDecimals) / nbDecimals != cal.pixelHeight) showDialog("Error on width scaling!!!" , "Beware!!! the height scaling value of the image is not " + String.valueOf(Math.round(length_scale * nbDecimals) / nbDecimals) + ", but " + String.valueOf(cal.pixelWidth));
		if(Math.round(length_scale * nbDecimals) / nbDecimals != cal.pixelWidth ) showDialog("Error on width scaling!!!" , "Beware!!! the width scaling value of the image is not "  + String.valueOf(Math.round(length_scale * nbDecimals) / nbDecimals) + ", but " + String.valueOf(cal.pixelWidth));
		if(length_unit										  != cal.getUnit()  ) showDialog("Error on scaling unit!!!"  , "Beware!!! the scaling unit of the image is not "         + length_unit                                                        + ", but " + cal.getUnit());
*/
		return imp;
	}

	private ImagePlus openStealth(String path)
	{
		ImagePlus imp	= null;
		ImagePlus imp1	= null;
		ImagePlus imp2	= null;
		ImagePlus imp3	= null;

		imp	= IJ.openImage(path);
		if(imp == null)
		{
			imp1 = IJ.openImage(path.substring(0, path.length() - 4) + "_p1.tif");
			imp2 = IJ.openImage(path.substring(0, path.length() - 4) + "_p2.tif");
			imp3 = IJ.openImage(path.substring(0, path.length() - 4) + "_p3.tif");
			if(imp1 != null && imp2 != null)
			{
				if(imp3 != null)
				{
					imp	= Concatenator.run(imp1, imp2, imp3);
					imp3.close();
				}
				else
					imp	= Concatenator.run(imp1, imp2);
//				imp	.show();
				imp1.close();
				imp2.close();
			}
		}

		return imp;
	}

	private void showDialog(String title, String text)
	{
		GenericDialog gd;

		gd = new GenericDialog(title);
		gd.addMessage(text);
		gd.showDialog();
	}

	private void showDialogWithCustomOkAndNoCancel(String title, String text, String text_for_ok_button)
	{
		GenericDialog gd;

		gd = new GenericDialog(title);
		gd.addMessage(text);
		gd.setOKLabel(text_for_ok_button);
		gd.hideCancelButton();
		gd.showDialog();
	}

	private void showDialogWithImageAndCustomOkAndNoCancel(String title, String imagePath, String text, String text_for_ok_button)
//	private void showDialogWithImageAndCustomOkAndNoCancel(String title, String text     , String text_for_ok_button)
	{
		GenericDialog	gd;
		URL				url = null;
		Image			image;
		ImagePlus		icon;
		String			str;

		gd = new GenericDialog(title);
		try
		{
			url		= getClass().getResource("/image/" + imagePath);
			image	= Toolkit.getDefaultToolkit().getImage(url);
			icon	= new ImagePlus("Error message", image);
			gd		.addImage(icon);
		}
		catch (Exception e)
		{
			str = e.getMessage();
			if (str == null || str.equals(""))
				str = "" + e;
			IJ.showMessage("Loading the error message image", str + "\n \n" + url);
		}
		gd.addToSameRow();
		gd.addMessage(text);
		gd.setOKLabel(text_for_ok_button);
		gd.hideCancelButton();
		gd.showDialog();
	}

	private ImagePlus FlatStack_old(ImagePlus image)
	{
		ImagePlus		imp;
		ImageConverter	converter;
		Color			color;
		RoiManager		rm;
		int				i;

		color			= Color.yellow;
		IJ				.setForegroundColor(color.getRed(), color.getGreen(), color.getBlue());
		rm				= RoiManager.getInstance();
//		if(rm == null)	rm = new RoiManager();
		imp				= image;

		for (i = 0; i != rm.getCount(); i++)
		{
			rm.runCommand	(image, "Deselect");
			image			.setSlice(i + 1);
			IJ.run			(image, "Select None", "");
			imp				= image.crop();
			converter		= new ImageConverter(imp);
			converter		.convertToRGB();
			imp.show();
			rm.select		(i);
			IJ.run			(imp, "Draw", "slice");
			imp.setTitle	("Flat-" + i);
//			imp.show();
		}
		IJ.run(imp, "Images to Stack", "name=" + image.getTitle() + "_Overlay title=Flat");

		return IJ.getImage();
	}

	public void copyFile(File in, File out) throws Exception
	{
		FileInputStream  fis = new FileInputStream(in);
		FileOutputStream fos = new FileOutputStream(out);

		try
		{
			byte[] buf = new byte[1024];
			int i = 0;
			while((i = fis.read(buf)) != -1)
			{
				fos.write(buf, 0, i);
			}
		}
		catch (IOException e)
		{
			IJ.log("File open error \n\"" + e.getMessage() + "\"\n");
			return;
		}
		finally
		{
			if (fis != null) fis.close();
			if (fos != null) fos.close();
		}
	}

	private void FlatStack(ImagePlus image)
	{
		ImageConverter	converter;
		Color			color;
		RoiManager		rm;
		int				i;

		color			= Color.yellow;
		IJ				.setForegroundColor(color.getRed(), color.getGreen(), color.getBlue());
		IJ				.selectWindow(image.getTitle());
		converter		= new ImageConverter(image);
		converter		.convertToRGB();
		rm				= RoiManager.getInstance();
//		if(rm == null)	rm = new RoiManager();

		for (i = 0; i != rm.getCount(); i++)
		{
			image			.setSlice(i + 1);
			rm.select		(i);
			IJ.run			(image, "Draw", "slice");
		}
		image				.setSlice(1);
		IJ.run				(image, "Select None", "");
	}

	private boolean checkAndCreateFolder(String myDir)
	{
		File file = new File(myDir);
		if (!file.exists())
			file.mkdir();
		file = new File(myDir);
		if (!file.exists())
		{
			showDialogWithImageAndCustomOkAndNoCancel("Create directory", "writing.png", "Unable to create directory\n \n" + myDir, "The directoy was not created");
			return false;
		}
		else
			return true;
	}

	private void closeWindow(String window)
	{
		if (WindowManager.getWindow(window) != null)
		{
			IJ.selectWindow(window);
			IJ.run("Close");
		}
	}

	private void closeWindows()
	{
		int i;
		String [] windows = {"Log", "Threshold", "Exception", "B&C", "Channels", "Results"};

		for(i = 0; i != windows.length; i++)
		{
			if (WindowManager.getWindow(windows[i]) != null)
			{
				IJ.selectWindow(windows[i]);
				IJ.run("Close");
			}
		}
	}

	private void Brightness(ImagePlus image, int value)
	{
		int			i;
		int			dimWidth, dimHeight, dimChannels, dimSlices, dimFrames;
		int								 posChannel , posSlice , posFrame ;
		int		[]	dim;

		dim			= image.getDimensions();
		dimWidth	= dim[0];
		dimHeight	= dim[1];
		dimChannels	= dim[2];
		dimSlices	= dim[3];
		dimFrames	= dim[4];

		posChannel	= image.getChannel();
		posSlice	= image.getSlice();
		posFrame	= image.getFrame();

		if(dimChannels != 1)
		{
			for(i = 1; i <= dimChannels; i++)
			{
				image.setPosition(i, posSlice, posFrame);
				IJ.run(image, "Enhance Contrast", "saturated=" + value);
				image.setPosition(posChannel, posSlice, posFrame);
			}
		}
		else
			IJ.run(image, "Enhance Contrast", "saturated=" + value);
	}

	private void biggestParticule(ImagePlus image, int value)
	{
		RoiManager		rm;

		IJ.run(image, "Analyze Particles...", "size=" + value + "-Infinity pixel clear add");
		rm				= RoiManager.getInstance();
		if(rm == null)	rm = new RoiManager();
		if(rm.getCount() > 1)
			biggestROI(image, rm);
		rm.select		(0);
		IJ.run			(image, "Make Inverse"	, "");
		IJ.run			(image, "Set..."		, "value=0");
		rm.runCommand	(image, "Deselect");
		IJ.run			(image, "Select None"	, "");
	}

	private void biggestROI(ImagePlus image, RoiManager rm)
	{
		ImageStatistics	stats;
		ImageProcessor	ip;
		Roi				roi;
		int				i;
		int				ROISize, ROIcount, BigestROI, BigestOne;

		ROIcount		= rm.getCount();
		BigestROI		= 0;
		BigestOne		= 0;
		ip				= image.getProcessor();

		for(i = 0; i != ROIcount; i++)
		{
			rm.select	(i);
			roi			= image.getRoi();
			ip			.setRoi(roi);
			stats		= ImageStatistics.getStatistics(ip, Measurements.AREA, null);
			ROISize		= (int) Math.round(stats.area);
			if(ROISize > BigestROI)
			{
				BigestROI	= ROISize;
				BigestOne	= i;
			}
		}
		rm.select		(BigestOne);
		rm.reset		();
		rm.addRoi		(image.getRoi());
	}

	private String [] split(String s1, String s2)
	{
		String [] strings = null;
		if (s1.length() > 0 && s2 != null && (s2.equals(",") || s2.equals(";")))
			strings = s1.split(s2, -1);
		else if (s1.length() > 0 && s2 != null && s2.length() >= 3 && s2.startsWith("(") && s2.endsWith(")"))
		{
			s2 = s2.substring(1, s2.length() - 1);
			strings = s1.split(s2, -1);
		}
		else 
			strings = (s2 == null || s2.equals("")) ? Tools.split(s1) : Tools.split(s1, s2);

		return strings;
	}

	private int getPositionX1(ImagePlus image)
	{
		for(int j = 0; j != image.getWidth(); j++)
			if(image.getProcessor().getPixel(j, Math.round(image.getHeight() / 2)) != 0)
				return j;

		return 0;
	}

	private int getPositionX2(ImagePlus image)
	{
		for(int j = image.getWidth() - 1; j >= 0; j--)
			if(image.getProcessor().getPixel(j, Math.round(image.getHeight() / 2)) != 0)
				return j;

		return 0;
	}

	private int getPositionY1(ImagePlus image)
	{
		for(int j = 0; j != image.getHeight(); j++)
			if(image.getProcessor().getPixel(Math.round(image.getWidth() / 2), j) != 0)
				return j;

		return 0;
	}

	private int getPositionY2(ImagePlus image)
	{
		for(int j = image.getHeight() - 1; j >= 0; j--)
			if(image.getProcessor().getPixel(Math.round(image.getWidth() / 2), j) != 0)
				return j;

		return 0;
	}

	private int [] KurtFocus(ImagePlus image)
	{
		ImagePlus		image2;
		ResultsTable	rt;
		int				index;
		int				frame;
		int				bestFocus;
//		double			bestScore;
		int	[]			bestFocusArray;

		IJ.run("Set Measurements...", "kurtosis redirect=None decimal=4");
		rt = Analyzer.getResultsTable();

		bestFocusArray	= new int[frames];
		for (index = 0; index != bestFocusArray.length; index++)
			bestFocusArray[index] = 0;

		for(frame = frames_begin; frame <= frames; frame++)
		{
			IJ.run("Clear Results", "");
			image2 = new Duplicator().run(image, 1, 1, 1, slices, frame, frame);
			IJ.run(image2, "Measure Stack...", "slices order=czt(default)");
			rt.sort("Kurt");
//			bestScore =			rt.getValue("Kurt" , getBestScoreIndexFromPositifMin(rt));
//			bestScore =			rt.getValue("Kurt" , getBestScoreIndexfromAbs		(rt));
//			bestScore =			rt.getValue("Kurt" , rt.size() - 1);
//			bestFocus = (int)	rt.getValue("Slice", getBestScoreIndexFromPositifMin(rt));
//			bestFocus = (int)	rt.getValue("Slice", getBestScoreIndexfromAbs		(rt));
			bestFocus = (int)	rt.getValue("Slice", rt.size() - 1);
//			IJ.log("frame = " + frame + "       bestScore = " + bestScore + "       bestFocus = " + bestFocus);
			bestFocusArray[frame - 1] = bestFocus;
		}

		TextWindow resultsWindow	= (TextWindow) WindowManager.getWindow("Results");
//		if (ResultsWindow != null)
//		{
			IJ.run("Clear Results");
			resultsWindow.close();
//		}

		return bestFocusArray;
	}

	private int getBestScoreIndexFromPositifMin(ResultsTable resultsTable)
	{
		int				index;

		for (index = 0; index < resultsTable.size(); index++)
			if (resultsTable.getValue("Kurt" , index) > 0)
				return index;

		return resultsTable.size() - 1;
	}


	private int getBestScoreIndexfromAbs(ResultsTable resultsTable)
	{
		int				index, minIndex;
		double		[]	values;

		values		= resultsTable.getColumn("Kurt");
		minIndex	= 0;

		for (index = 1; index < values.length; index++)
			if (Math.abs(values[index]) < Math.abs(values[minIndex]))
				minIndex = index;

		return minIndex;
	}

	private int MaxFocus(ImagePlus image)
	{
		ResultsTable	rt;
		int				frame, slice;
		int				bestFocus;
		double			bestScore, val;
		double	[]		bestScoreArray;

		IJ.run("Set Measurements...", "min redirect=None decimal=4");
		rt = Analyzer.getResultsTable();

		bestScoreArray	= new double[slices];
		for (slice = 0; slice != bestScoreArray.length; slice++)
			bestScoreArray[slice] = 0.0;

		for(frame = frames_begin; frame <= frames; frame++)
		{
			IJ.run("Clear Results", "");
			bestFocus = 1;
			bestScore = 0.0;

			for (slice = 1; slice <= slices; slice++)
			{
				image.setPosition(1, slice, frame);
				IJ.run(image, "Measure", "");
				val	= rt.getValue("Max", slice - 1);

				if(val > bestScore)
				{
					bestScore = val;
					bestFocus = slice;
				}
			}
			bestScoreArray[bestFocus - 1] += bestScore;
		}
		TextWindow resultsWindow	= (TextWindow) WindowManager.getWindow("Results");
//		if (ResultsWindow != null)
//		{
			IJ.run("Clear Results");
			resultsWindow.close();
//		}
		RoiManager rm				= RoiManager.getInstance();
		if(rm != null)
			rm.close();

		bestFocus = 0;
		bestScore = 0.0;
		for (slice = 0; slice != bestScoreArray.length; slice++)
		{
			if(bestScoreArray[slice] > bestScore)
			{
				bestScore = bestScoreArray[slice];
				bestFocus = slice;
			}
		}

		return bestFocus + 1;
	}

	private int [] displacementCalculation()
	{
		int [] delta = new int [2];
		int dx1 = getPositionX1(IJ.getImage());
		int dx2 = getPositionX2(IJ.getImage());
		int dy1 = getPositionY1(IJ.getImage());
		int dy2 = getPositionY2(IJ.getImage());

		if(dx1 != 0)
			delta[0] = dx1;
		else if(dx2 != IJ.getImage().getWidth() - 1)
			delta[0] = dx2 - IJ.getImage().getWidth() + 1;

		if(dy1 != 0)
//			delta[1] = - dy1;	!!! modifié du fait de prbs d'alignements pour le Ch1
			delta[1] = dy1;
		else if(dy2 != IJ.getImage().getHeight() - 1)
			delta[1] = dy2 - IJ.getImage().getHeight() + 1;

		return delta;
	}

	private double getResult(String column, int row)
	{
		ResultsTable	rt;

		rt		= Analyzer.getResultsTable();
		counter	= rt.getCounter();
		if (row == -1)
			row = counter - 1;
		if (row < 0 || row >= counter)
			IJ.log("Row (" + row + ") out of range");
		col = rt.getColumnIndex(column);
		if (!rt.columnExists(col))
			return Double.NaN;
		else
		{
			value = rt.getValueAsDouble(col, row);
			if (Double.isNaN(value))
			{
				str = rt.getStringValue(col, row);
				if (str != null && !str.equals("NaN"))
					value = Tools.parseDouble(str);
			}
		}
		return value;
	}

	private double niceNumber(double v)
	{	//the smallest "nice" number >= v. "Nice" numbers are .. 0.5, 1, 2, 5, 10, 20 ...
		double base = Math.pow(10, Math.floor(Math.log10(v) - 1.e-6));
		     if (v > 9.0000001 * base) return 10 * base;
		else if (v > 8.0000001 * base) return  9 * base;
		else if (v > 7.0000001 * base) return  8 * base;
		else if (v > 6.0000001 * base) return  7 * base;
		else if (v > 5.0000001 * base) return  6 * base;
		else if (v > 4.0000001 * base) return  5 * base;
		else if (v > 3.0000001 * base) return  4 * base;
		else if (v > 2.0000001 * base) return  3 * base;
		else                           return  2 * base;
	}

	private String getFileName(String dir, String file, int cell)
	{
		str = "_Cell " + String.valueOf(cell) + "_1.tif";
		String [] fileList = getFileList(dir);

		for(int i = 0; i != fileList.length; i ++)
		{
			if(fileList[i].startsWith(file) && fileList[i].endsWith(str))
				return fileList[i];
		}
		return "";
	}

	private String [] getFileList(String dir)
	{
		File f = new File(dir);
		if (!f.exists() || !f.isDirectory())
			return new String[0];
		String [] list = f.list();
		if (list == null)
			return new String[0];
		if (System.getProperty("os.name").indexOf("Linux") != -1)
			ij.util.StringSorter.sort(list);
		File f2;
		int hidden = 0;
		for (int i = 0; i < list.length; i++)
		{
			if (list[i].startsWith(".") || list[i].equals("Thumbs.db"))
			{
				list[i] = null;
				hidden++;
			}
			else
			{
				f2 = new File(dir, list[i]);
				if (f2.isDirectory())
				list[i] = list[i] + "/";
			}
		}
		int n = list.length - hidden;
		if (n <= 0)
			return new String[0];
		if (hidden > 0)
		{
			String [] list2 = new String[n];
			int j = 0;
			for (int i = 0; i < list.length; i++)
			{
				if (list[i]!=null)
					list2[j++] = list[i];
			}
			list = list2;
		}
        String [] array = new String[n];
		for (int i = 0; i < n; i++)
			array[i] = list[i];
		return array;
	}

	private double runBinarySearch(double xmin, double xmax, double error, String folder, int frame, int widthCorr, int heightCorr)
	{
		double min	= getScaleValue(xmin, folder, frame, widthCorr, heightCorr);
		double max	= getScaleValue(xmax, folder, frame, widthCorr, heightCorr);
		double goal	= (max - min) / 2.0;

		while (xmin <= xmax)
		{
			double xmid = (xmin + xmax) / 2;
				 if (Math.abs(getScaleValue(xmid, folder, frame, widthCorr, heightCorr) - goal) < error)
				return xmid;
			else if (getScaleValue(xmid, folder, frame, widthCorr, heightCorr) < goal)
				xmin = xmid;
			else if (getScaleValue(xmid, folder, frame, widthCorr, heightCorr) > goal)
				xmax = xmid;
		}

		return -1.0;
	}

	private double getScaleValue(double xpos, String folder, int frame, int widthCorr, int heightCorr)
	{
		return FTTC_main.getScaleValue(folder + "Analysis" + File.separator, "Stack_" + IJ.pad(frame, 2) + ".txt", length_scale, 0.5, E, Math.pow(10.0, -xpos), unitIndex, widthCorr, heightCorr, false, false, false, false, false, false, lut);
	}

	private double [] get_lambda_values(String lambda_values_file)
	{
		double [] values = null;
/*
		file = new File(lambda_values_file);
		if (!file.exists())
			showDialogWithImageAndCustomOkAndNoCancel("Lambda value reading", "writing.png", "Error while reading\n \n" + e.getMessage() + "\n \n" + lambda_values_file, "The analysis is stopped at the step \"Traction force Lambda reading\"");
*/
		try
		{
			String		str		= IJ.openAsString(lambda_values_file);
			String []	lines	= Tools.split(str  ,"\n");
			String []	columns;
			values				= new double[lines.length - 1];
			for(int i = 1; i != lines.length; i++)
			{
				columns			= Tools.split(lines[i],"\t");
				values[i - 1]	= Double.valueOf(columns[1]);
			}
		}
		catch (Exception e)
		{
			showDialogWithImageAndCustomOkAndNoCancel("Lambda value reading", "writing.png", "Error while reading the file\n\n" + lambda_values_file + "\n\nwith the error\n\n" + e.getMessage(), "The analysis is stopped at the step \"Traction force Lambda values reading\"");
		}

		return values;
	}

//	private void cellsAndForceImagesSuperposition(int light = u, int cell = v, int bead = w, int frame = i, String folderRoot = folder_cell, String folderIn, String folderOut, String fileType, String fileName, int pasteMode, boolean text, double scaleMax)
	private void cellsAndForceImagesSuperposition(int light, int cell, int bead, int frame, String folderRoot, String folderIn, String folderOut, String fileName, String fileType, int pasteMode, boolean text, double scaleMax)
	{
		DecimalFormat	numericFormat			= new DecimalFormat("###,###.#");
		DecimalFormat	decimalFormat1			= new DecimalFormat("#0.00000");
		DecimalFormat	decimalFormat2			= new DecimalFormat("#0.00");
		DecimalFormat	decimalFormat3			= new DecimalFormat("0.00E0");
		ImagePlus		imp1, imp2;
		int				area					= 0;
		double			force					= 0.0;
//		double			regularization_factor	= lambda;
		String			str;
//		Roi.setPasteMode(Blitter.COPY_ZERO_TRANSPARENT);
//		Roi.setPasteMode(Blitter.ADD);
		Roi.setPasteMode(pasteMode);

		imp1 = imp2 = null;
		if(beads == 0)
		{
			switch (light)
			{
				case 0 :	imp1 = IJ.openImage(folderRoot + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif");		break;
				case 1 :	imp1 = IJ.openImage(folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif");		break;
				case 2 :	imp1 = IJ.openImage(folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif");		break;
				case 3 :	imp1 = IJ.openImage(folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif");		break;
				default:	imp1 = null;																															break;
			}
		}
		else
		{
			switch (light)
			{
				case 0 :	imp1 = IJ.openImage(folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_"     + bead + "_" + IJ.pad(frame, 2) + ".tif");		break;
				case 1 :	imp1 = IJ.openImage(folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch1_" + bead + "_" + IJ.pad(frame, 2) + ".tif");		break;
				case 2 :	imp1 = IJ.openImage(folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch2_" + bead + "_" + IJ.pad(frame, 2) + ".tif");		break;
				case 3 :	imp1 = IJ.openImage(folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch3_" + bead + "_" + IJ.pad(frame, 2) + ".tif");		break;
				default:	imp1 = null;																															break;
			}
		}
		if (imp1 == null)
		{
			if(beads == 0)
			{
				switch (light)
				{
					case 0:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells"         + File.separator + "CorrCells_"                  + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 1:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch1_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 2:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch2_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 3:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells"         + File.separator + "CorrCells_Ch3_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
				}
			}
			else
			{
				switch (light)
				{
					case 0:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_"     + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 1:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch1_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 2:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch2_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
					case 3:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + "CorrCells_" + bead + File.separator + "CorrCells_Ch3_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");		break;
				}
			}
			return;
		}
//		imp1.show();
		IJ.run(imp1, "Enhance Contrast", "saturated=0.35");
		IJ.run(imp1, "RGB Color", "");
		if(beads == 0)
			imp2 = IJ.openImage(folderRoot + folderIn              + File.separator + "Traction_" + fileType + "_Plot_Traction_Stack_"              + IJ.pad(frame, 2) + ".tif");
		else
			imp2 = IJ.openImage(folderRoot + folderIn + "_" + bead + File.separator + "Traction_" + fileType + "_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif");
		if (imp2 == null)
		{
			if(beads == 0)
				showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + folderIn              + File.separator + "Traction_" + fileType + "_Plot_Traction_Stack_"              + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");
			else
				showDialogWithImageAndCustomOkAndNoCancel("Force integration", "undo.png", "The following file:\n\t\n" + folderRoot + folderIn + "_" + bead + File.separator + "Traction_" + fileType + "_Plot_Traction_Stack_" + bead + "_" + IJ.pad(frame, 2) + ".tif\n\t\ncould not be found", "The analysis is stopped at the step \"force_integration\"");
			return;
		}
//		imp2	.show();
//		imp2	.setDisplayRange(0, 1000);
		IJ		.run(imp2, "Select All", "");
		IJ		.run(imp2, "Copy", "");
		imp2	.close();
		IJ		.run(imp1, "Paste", "");
		IJ		.run(imp1, "Select None", "");
		imp1	.show();

		if(text)
		{
			Font			font			= new Font("SansSerif", Font.PLAIN, 20);
			Font			fExp			= new Font("SansSerif", Font.BOLD , 15);
			RoiManager		rm				= RoiManager.getInstance();
			if(rm == null)	rm				= new RoiManager();
			ResultsTable	rt				= Analyzer.getResultsTable();

			rm				.select(frame - 1);
			Color			color	= Color.yellow;
			IJ				.setForegroundColor(color.getRed(), color.getGreen(), color.getBlue());
			IJ				.run(imp1, "Draw", "slice");
			area							= (int) Math.round(	rt.getValue("Area"  , frame - 1));
			force							=					rt.getValue("IntDen", frame - 1);
			color							= Color.white;
			IJ				.setForegroundColor(color.getRed(), color.getGreen(), color.getBlue());
//			str								= "Area = " + Integer.toString(area) + " pixels";
//			str								= "Area = " + Double.toString(area * Math.pow(length_scale, 2.0)) + " \u00B5m^2";
//			str								= "Area = " + decimalFormat2.format(area * Math.pow(length_scale, 2.0)) + " \u00B5m^2";
			str								= "Area = " + decimalFormat2.format(area * Math.pow(length_scale, 2.0)) + " \u00B5m";
			imp1			.setRoi(new TextRoi( 34, 5, str, font));
			IJ				.run(imp1, "Draw", "slice");
			imp1			.setRoi(new TextRoi( 34 + 2 + imp1.getProcessor().getStringWidth(str), 2, "2", fExp));
			IJ				.run(imp1, "Draw", "slice");
			str								= "Force = " + decimalFormat2.format(force * 1.0e-6) + " \u00B5N";
			imp1			.setRoi(new TextRoi(280, 5, str, font));
			IJ				.run(imp1, "Draw", "slice");
//			str								= "Ratio = " + decimalFormat1.format((double) force / area) + " N/pixels";
//			str								= "Ratio = " + decimalFormat1.format((double) force / (area * Math.pow(length_scale, 2))) + " N/\u00B5m^2";
//			str								= "Ratio = " + decimalFormat2.format((double) force / (area * Math.pow(length_scale, 2))) + " N/\u00B5m^2";
			str								= "Force ratio = " + decimalFormat2.format((double) force / (1.0e3 * area * Math.pow(length_scale, 2))) + " nN/\u00B5m";
			imp1			.setRoi(new TextRoi(500, 5, str, font));
			IJ				.run(imp1, "Draw", "slice");
			imp1			.setRoi(new TextRoi(500 + 2 + imp1.getProcessor().getStringWidth(str), 2, "2", fExp));
			IJ				.run(imp1, "Draw", "slice");
			str								= "E = " + numericFormat.format(E) + " Pa";
//			imp1			.setRoi(new TextRoi(1000, 5, str, font));
			imp1			.setRoi(new TextRoi(800, 5, str, font));
			IJ				.run(imp1, "Draw", "slice");
//			str								= "lambda = " + decimalFormat3.format(regularization_factor);
//			str								= "\u03BB = " + decimalFormat3.format(regularization_factor);
			str								= "\u03BB = " + decimalFormat3.format(lambda_values[frame - 1]);
//			imp1			.setRoi(new TextRoi(1000, 5, str, font));
			imp1			.setRoi(new TextRoi(imp1.getWidth() - imp1.getProcessor().getStringWidth(str) - 58, 5, str, font));
			IJ				.run(imp1, "Draw", "slice");
		}
		str = fileType == "Vector" ? "_" + IJ.pad(String.valueOf(FTTC_max_vector_length), 3) : "";
		try
		{
			if(beads == 0)
			{
				switch (light)
				{
					case 0:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut              + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_"                  + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 1:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut              + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch1_"              + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 2:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut              + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch2_"              + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 3:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut              + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch3_"              + IJ.pad(frame, 2) + str + ".jpg");		break;
				}
			}
			else
			{
				switch (light)
				{
					case 0:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_"     + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 1:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch1_" + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 2:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch2_" + IJ.pad(frame, 2) + str + ".jpg");		break;
					case 3:	IJ.saveAs(imp1, "Jpeg", folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch3_" + IJ.pad(frame, 2) + str + ".jpg");		break;
				}
			}
		}
		catch (Exception e)
		{
			if(beads == 0)
			{
				switch (light)
				{
					case 0:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut +              File.separator + fileName + "_with_Traction_" + fileType + "_Plot_"                  + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 1:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut +              File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch1_"              + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 2:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut +              File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch2_"              + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 3:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut +              File.separator + fileName + "_with_Traction_" + fileType + "_Plot_Ch3_"              + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
				}
			}
			else
			{
				switch (light)
				{
					case 0:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_"     + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 1:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch1_" + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 2:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch2_" + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
					case 3:	showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut + "_" + bead + File.separator + fileName + "_with_Traction_" + fileType + "_Plot_" + bead + "_Ch3_" + IJ.pad(frame, 2) + ".jpg", "The analysis is stopped at the step \"force_integration\"");		break;
				}
			}
			return;
		}
		IJ.run("Close");
//		imp1.close();

		if(text)
		{
			file = new File(folderRoot + folderOut + ".txt");
			if (!file.exists())
			{
				try
				{
					FileOutputStream	 fos	= new FileOutputStream		(folderRoot + folderOut + ".txt");
					BufferedOutputStream bos	= new BufferedOutputStream	(fos);
					PrintWriter			 writer	= new PrintWriter			(bos, true);
					writer	.println("Cell\tFrame\tArea (pixel)\tArea (\u00B5m^2)\tForce (pN)\tForce ratio (pN/\u00B5m^2)\tForce (pPa)\tForce ratio (pPa/\u00B5m^2)\tLambda (-)\tscaleMax (pPa)");
					writer	.println("Cell " + Integer.toString(cell) + "\t" + Integer.toString(frame) + "\t" + Integer.toString(area) + "\t" + decimalFormat2.format(area * Math.pow(length_scale, 2.0)) + "\t" + decimalFormat2.format(force) + "\t" + decimalFormat2.format((double) force / (area * Math.pow(length_scale, 2))) + "\t" + decimalFormat2.format(force / window_area) + "\t" + decimalFormat2.format((double) force / (window_area * area * Math.pow(length_scale, 2))) + "\t" + decimalFormat3.format(lambda_values[frame - 1]) + "\t" + String.valueOf(scaleMax));
					writer	.close();
				}
				catch (IOException e)
				{
					IJ.log("File open error \n\"" + e.getMessage() + "\"\n");
					showDialogWithImageAndCustomOkAndNoCancel("Force integration", "writing.png", "Error while writing\n \n" + e.getMessage() + "\n \n" + folderRoot + folderOut + ".txt", "The analysis is stopped at the step \"force_integration\"");
					return;
				}
			}
			else
			{
				IJ.append("Cell " + Integer.toString(cell) + "\t" + Integer.toString(frame) + "\t" + Integer.toString(area) + "\t" + decimalFormat2.format(area * Math.pow(length_scale, 2.0)) + "\t" + decimalFormat2.format(force) + "\t" + decimalFormat2.format((double) force / (area * Math.pow(length_scale, 2))) + "\t" + decimalFormat2.format(force / window_area) + "\t" + decimalFormat2.format((double) force / (window_area * area * Math.pow(length_scale, 2))) + "\t" + decimalFormat3.format(lambda_values[frame - 1]) + "\t" + String.valueOf(scaleMax), folderRoot + folderOut + ".txt");
			}
		}
	}

	public double getDistance(double x1, double x2, double y1, double y2)
	{
		return Math.sqrt( Math.pow(x2 - x1, 2.0) + Math.pow(y2 - y1, 2.0) );
	}

	public double calcultateU(int index, ArrayList <Double> beads1X, ArrayList <Double> beads1Y, ArrayList <Double> beads2X, ArrayList <Double> beads2Y)
	{
		int index2 = index / 2;

		if(index == 2 * index2)
			return beads2X.get(index2) - beads1X.get(index2);
		else
			return beads2Y.get(index2) - beads1Y.get(index2);
	}

	public double Greens(int indexI, int indexJ, ArrayList <Double> focalsX, ArrayList <Double> focalsY, ArrayList <Double> beads1X, ArrayList <Double> beads1Y)
	{
		int		indexI2	= indexI / 2;
		int		indexJ2	= indexJ / 2;
		double	mag		= Math.sqrt( Math.pow(beads1X.get(indexI2) - focalsX.get(indexJ2), 2.0) + Math.pow(beads1Y.get(indexI2) - focalsY.get(indexJ2), 2.0) );

		if(indexI == 2 * indexI2)
			if(indexJ == 2 * indexJ2)
				return 3.0 / ( 4.0 * Math.PI *          mag       ) * ( 1.0 + Math.pow( ( beads1X.get(indexI2) - focalsX.get(indexJ2) ) / mag, 2.0) );
			else
				return 3.0 / ( 4.0 * Math.PI * Math.pow(mag, 3.0) ) * (                   beads1X.get(indexI2) - focalsX.get(indexJ2) ) * ( beads1Y.get(indexI2) - focalsY.get(indexJ2) );
		else
			if(indexJ == 2 * indexJ2)
				return 3.0 / ( 4.0 * Math.PI * Math.pow(mag, 3.0) ) * (                   beads1X.get(indexI2) - focalsX.get(indexJ2) ) * ( beads1Y.get(indexI2) - focalsY.get(indexJ2) );
			else
				return 3.0 / ( 4.0 * Math.PI *          mag       ) * ( 1.0 + Math.pow( ( beads1Y.get(indexI2) - focalsY.get(indexJ2) ) / mag, 2.0) );
	}

	public void tikhonovVect(RealMatrix U, ArrayList <Double> s, RealMatrix V, ArrayList <Double> b, ArrayList <Double> lambda, ArrayList <Double> beta, ArrayList <Double> zeta, ArrayList <Double> eta, ArrayList <Double> rho)
	{
		// TIKHONOV Tikhonov regularization.

		// [x_lambda,rho,eta] = tikhonov(U,s,V,b,lambda,x_0)
		// [x_lambda,rho,eta] = tikhonov(U,sm,X,b,lambda,x_0) ,  sm = [sigma,mu]

		// Computes the Tikhonov regularized solution x_lambda.  If the SVD
		// is used, i.e. if U, s, and V are specified, then standard-form
		// regularization is applied:
		//    min { || A x - b ||^2 + lambda^2 || x - x_0 ||^2 } .
		// If, on the other hand, the GSVD is used, i.e. if U, sm, and X are
		// specified, then general-form regularization is applied:
		//    min { || A x - b ||^2 + lambda^2 || L (x - x_0) ||^2 } .

		// If x_0 is not specified, then x_0 = 0 is used

		// Note that x_0 cannot be used if A is underdetermined and L ~= I.

		// If lambda is a vector, then x_lambda is a matrix such that
		//    x_lambda = [ x_lambda(1), x_lambda(2), ... ] .

		// The solution norm (standard-form case) or seminorm (general-form
		// case) and the residual norm are returned in eta and rho.

		// Per Christian Hansen, IMM, April 14, 2003.

		// Reference: A. N. Tikhonov & V. Y. Arsenin, "Solutions of
		// Ill-Posed Problems", Wiley, 1977.

		// Initialization.
		if (minima(lambda) < 0)
			IJ.showMessage("Illegal regularization parameter lambda");

		int		i, j, k;
//		int		m = U.getRowDimension();
//		int		n = V.getRowDimension();
//		int		p = s.size();
//		int		ps = 1;
		double	val1, val2;

//		beta = U(:,1:p)'*b;
		beta.clear();
		for(i = 0; i < U.getColumnDimension(); i++)
		{
			val1 = 0.0;
			for(j = 0; j < b.size(); j++)
				val1 += U.getEntry(j, i) * b.get(j);
			beta.add( val1 );
		}

//		zeta = s(:,1).*beta;
		zeta.clear();
		for(i = 0; i < s.size(); i++)
			zeta.add( s.get(i) * beta.get(i) );

//		int ll = lambda.size();
		RealMatrix x_lambda =  MatrixUtils.createRealMatrix( V.getRowDimension(), lambda.size() );
		rho.clear();
//		eta.clear();

 		// The standard-form case.
//		x_lambda(:,i) = V(:,1:p)*(zeta./(s.^2 + lambda(i)^2));
/*
		for(i = 0; i < x_lambda.getRowDimension(); i++)		// 64
		{
			for(j = 0; j < lambda.size(); j++)		// 30
			{
				val1 = 0.0;
				for(k = 0; k < s.size(); k++)		// 64
					val +=  V.getEntry(i, k) * zeta.get(k) / ( Math.pow( s.get(k), 2.0) + Math.pow( lambda.get(j), 2.0) );
				x_lambda.setEntry( i, j, val );
			}
		}
*/

		// rho(i) = lambda(i)^2*norm(beta./(s.^2 + lambda(i)^2));
		// eta(i) = norm(x_lambda(:,i));
		for(i = 0; i < lambda.size(); i++)		// 30
		{
			val1 = 0.0;
			for(j = 0; j < s.size(); j++)		// 64
				val1 +=  Math.pow( Math.pow( lambda.get(i), 2.0 ) *  beta.get(j) / ( Math.pow( s.get(j), 2.0) + Math.pow( lambda.get(i), 2.0) ), 2.0 );
			rho.add( Math.sqrt( val1 ) );
/*
			val1 = 0.0;
			for(j = 0; j < x_lambda.getRowDimension(); j++)		// 64
				val1 +=  Math.pow( x_lambda.getEntry(j, i), 2.0 );
			eta.add( Math.sqrt( val1 ) );
*/
		}

		if( U.getRowDimension() > s.size() )
		{
			// rho = sqrt(rho.^2 + norm(b - U(:,1:n)*[beta;U(:,p+1:n)'*b])^2);
			if(U.getColumnDimension() != V.getRowDimension())
				IJ.showMessage( "Modification of the code required to add U(:,p+1:n)'*b to [beta;U(:,p+1:n)'*b]" );

			val2 = 0.0;
			for(i = 0; i < U.getRowDimension(); i++)
			{
				val1 = 0.0;
				for(j = 0; j < V.getRowDimension(); j++)
					val1 += U.getEntry(i , j) * beta.get(j);
				val1  = b.get(i) - val1;
				val2 += Math.pow( val1, 2.0 );
			}

			for(i = 0; i < rho.size(); i++)
				rho.set(i , Math.sqrt( Math.pow(rho.get( i ), 2.0) + val2 ) );
		}
	}

	public void tikhonovVal(double lambda, RealMatrix V, ArrayList <Double> zeta, ArrayList <Double> s, ArrayList <Double> FX, ArrayList <Double> FY)
	{
		// Initialization.
		if (lambda < 0)
			IJ.showMessage("Illegal regularization parameter lambda");

 		// The standard-form case.
//		x_lambda(:,i) = V(:,1:p)*(zeta./(s.^2 + lambda(i)^2));
		FX.clear();
		FY.clear();
		for(int i = 0; i < V.getRowDimension(); i++)		// 64
		{
			double val = 0.0;
			for(int j = 0; j < s.size(); j++)				// 64
				val +=  V.getEntry(i, j) * zeta.get(j) / ( Math.pow( s.get(j), 2.0) + Math.pow( lambda, 2.0) );
			if( i == 2 * (i / 2) )
				FX.add( val );
			else
				FY.add( val );
		}
	}

	public double minima(ArrayList <Double> list)
	{
		double val = list.get(0);

		for(int i = 1; i < list.size(); i++)
			if(list.get(i) < val)
				val = list.get(i);

		return val;
	}

	public int calculateRhoOpt(ArrayList <Double> array)
	{
		int		i, j	= 0;
		double	val1	= ( array.get( array.size() - 1 ) + array.get( 0 ) ) / 2.0 ;
		double	val2	= Math.abs( val - array.get( 0 ) );

		for( i = 1; i < array.size(); i++ )
			if( Math.abs( val1 - array.get( i ) ) < val2 )
			{
				val2 = Math.abs( val1 - array.get( i ) );
				j = i;
			}

		return j;
	}

	public double getRhoMinima(ArrayList <Double> array)
	{
		if(array.size() == 0)
			return 0.0;
		else
		{
			double val = array.get(0);

			for(int i = 1; i != array.size(); i++)
			{
				if(array.get(i) < val)
					val = array.get(i);
			}
			return val;
		}
	}

	public double getRhoMaxima(ArrayList <Double> array)
	{
		if(array.size() == 0)
			return 0.0;
		else
		{
			double val = array.get(0);

			for(int i = 1; i != array.size(); i++)
			{
				if(array.get(i) > val)
					val = array.get(i);
			}
			return val;
		}
	}
}