/*
 * MSIReconstructor.java
 *
 * Created on April 29, 2008, 5:17 PM
 */
import java.io.*;
import javax.imageio.*;
import java.awt.image.*;
import java.awt.*;
import java.lang.*;
import java.lang.Math.*;
import java.util.*;
import java.util.Arrays.*;
import javax.swing.*;



/**
 *
 * @author  Tyler
 */
public class MSIReconstructor extends javax.swing.JFrame {
    
    /** Creates new form MSIReconstructor */
    public MSIReconstructor() {
        initComponents();
    }
    
    /** This method is called from within the constructor to
     * initialize the form.
     * WARNING: Do NOT modify this code. The content of this method is
     * always regenerated by the Form Editor.
     */
    // <editor-fold defaultstate="collapsed" desc="Generated Code">
    private void initComponents() {

        buttonGroup1 = new javax.swing.ButtonGroup();
        jLabel1 = new javax.swing.JLabel();
        jTextField1 = new javax.swing.JTextField();
        jLabel2 = new javax.swing.JLabel();
        jTextField2 = new javax.swing.JTextField();
        jLabel3 = new javax.swing.JLabel();
        jTextField3 = new javax.swing.JTextField();
        jLabel4 = new javax.swing.JLabel();
        jLabel5 = new javax.swing.JLabel();
        jRadioButton1 = new javax.swing.JRadioButton();
        jRadioButton2 = new javax.swing.JRadioButton();
        jLabel6 = new javax.swing.JLabel();
        jLabel7 = new javax.swing.JLabel();
        jTextField4 = new javax.swing.JTextField();
        jLabel8 = new javax.swing.JLabel();
        jTextField5 = new javax.swing.JTextField();
        jLabel9 = new javax.swing.JLabel();
        jLabel10 = new javax.swing.JLabel();
        jLabel11 = new javax.swing.JLabel();
        jTextField6 = new javax.swing.JTextField();
        jLabel12 = new javax.swing.JLabel();
        jButton1 = new javax.swing.JButton();
        jCheckBox1 = new javax.swing.JCheckBox();
        jLabel13 = new javax.swing.JLabel();
        jScrollPane2 = new javax.swing.JScrollPane();
        jTextArea2 = new javax.swing.JTextArea();

        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

        jLabel1.setFont(new java.awt.Font("Tahoma", 1, 11));
        jLabel1.setText("MSIReconstructor for creating ion images from MSI on stretched tissues");

        jLabel2.setText("Full path of working directory");

        jLabel3.setText("Analyte nominal mass (daltons)");

        jTextField3.setText("5");

        jLabel4.setText("Mass window (daltons)");

        jLabel5.setText("Image intensity scale");

        buttonGroup1.add(jRadioButton1);
        jRadioButton1.setText("Relative to average intensity");

        buttonGroup1.add(jRadioButton2);
        jRadioButton2.setText("Relative to maximum intensity (Absolute scale)");

        jLabel6.setText("Input data");

        jLabel7.setText("Note: subfolder \"Spectra\\\" containing MS data in text files must also exist in the working directory");

        jTextField4.setText(".txt");

        jLabel8.setText("Initial positions filename");

        jTextField5.setText(".txt");

        jLabel9.setText("Free transform parameters filename");

        jLabel10.setText("Output image filename");

        jLabel11.setText("Note: text files of transformed coordinates and stretched coordinates are automatically ouputted");

        jLabel12.setText("(Choose only .bmp, .png, or .jpg extensions)");

        jButton1.setText("Go!");
        jButton1.addMouseListener(new java.awt.event.MouseAdapter() {
            public void mouseClicked(java.awt.event.MouseEvent evt) {
                jButton1MouseClicked(evt);
            }
        });

        jCheckBox1.setText("Double match reassignment (optional)");

        jLabel13.setText("Messages during run:");

        jTextArea2.setColumns(20);
        jTextArea2.setRows(5);
        jTextArea2.setText("Currently no messages");
        jScrollPane2.setViewportView(jTextArea2);

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
        getContentPane().setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel13)
                .addContainerGap(385, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jTextField6, javax.swing.GroupLayout.PREFERRED_SIZE, 132, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel12)
                .addGap(135, 135, 135))
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                    .addComponent(jTextField2)
                    .addComponent(jTextField3, javax.swing.GroupLayout.DEFAULT_SIZE, 59, Short.MAX_VALUE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel4)
                    .addComponent(jLabel3))
                .addContainerGap(276, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel2)
                .addContainerGap(348, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(79, 79, 79)
                .addComponent(jLabel1)
                .addContainerGap())
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel6)
                .addContainerGap(437, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel7)
                .addContainerGap(21, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                    .addComponent(jTextField5, javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jTextField4, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.PREFERRED_SIZE, 132, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel9)
                    .addComponent(jLabel8))
                .addContainerGap(179, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel10)
                .addContainerGap(380, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel11)
                .addContainerGap(21, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(layout.createSequentialGroup()
                        .addGap(10, 10, 10)
                        .addComponent(jLabel5))
                    .addGroup(layout.createSequentialGroup()
                        .addContainerGap()
                        .addComponent(jRadioButton1)))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 110, Short.MAX_VALUE)
                .addComponent(jCheckBox1)
                .addContainerGap(10, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jButton1, javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jRadioButton2, javax.swing.GroupLayout.Alignment.TRAILING))
                .addContainerGap())
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                    .addComponent(jTextField1)
                    .addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 336, Short.MAX_VALUE))
                .addContainerGap(152, Short.MAX_VALUE))
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addComponent(jLabel1)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(jLabel2)
                .addGap(4, 4, 4)
                .addComponent(jTextField1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jLabel3)
                    .addComponent(jTextField2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel4)
                    .addComponent(jTextField3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(layout.createSequentialGroup()
                        .addComponent(jLabel5)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(jRadioButton1)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(jRadioButton2)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(jLabel6))
                    .addComponent(jCheckBox1))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel7)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jTextField4, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel8))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jTextField5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel9))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel10)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel11)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jTextField6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel12))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jButton1, javax.swing.GroupLayout.PREFERRED_SIZE, 23, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(jLabel13)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 38, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        pack();
    }// </editor-fold>

    private void jButton1MouseClicked(java.awt.event.MouseEvent evt) {
              try {
        
                
                	
                int Validate = 0;
                int Double = 0;
                
                String WorkingPath = jTextField1.getText();                
                
                if (WorkingPath.endsWith("\\") == false | WorkingPath.endsWith("/") == false )
		{
		WorkingPath = WorkingPath + "\\";
		}
                
                BufferedReader inO = new BufferedReader(new FileReader(WorkingPath + jTextField4.getText()));
               
                if (jCheckBox1.isSelected() == true)
                {Double = 1;}
                if (jCheckBox1.isSelected() == false)
                {Double = 0;}             

                jTextArea2.setText("Currently running");
                
                
		int MassCenter = Integer.valueOf(jTextField2.getText());
		int MassWindow = Integer.valueOf(jTextField3.getText());
		int MassLow = MassCenter - MassWindow;
		int MassHigh = MassCenter + MassWindow;

		if (!(jTextField6.getText().toLowerCase().endsWith(".bmp")) && !(jTextField6.getText().toLowerCase().endsWith(".png")) 
			&& !(jTextField6.getText().toLowerCase().endsWith(".jpg")))
			{System.out.println("Error: ouput image can only end in .jpg, .png, or .bmp");}


		int OlineCount = 0;
			
		do
		{
	                String lineO = inO.readLine();
			if (lineO == null) break;
	        	OlineCount++;	
		} while (true);



		String userDir = WorkingPath + "Spectra";
		
    		File dir = new File(userDir);

		String[] childrenTemp = dir.list();

		String[] children = new String[childrenTemp.length];

		for (int i = 0; i <= childrenTemp.length-1; i++)
		{
			children[i] = WorkingPath + "Spectra\\" + childrenTemp[i];
		}
    

		double[] Intensity = new double[children.length];
		

		String[] SplitName = new String[5];


		double[][] SCoordUncentered = new double[children.length][2];

		for (int i = 0; i <= children.length-1; i ++)
		{
			SplitName = children[i].split("_");

			SCoordUncentered[i][0] = Integer.valueOf(SplitName[2].substring(0, SplitName[2].length()-1)).intValue();
			SCoordUncentered[i][1] = Integer.valueOf(SplitName[3].substring(0, SplitName[3].length()-4)).intValue();
		}

		int SlineCount = children.length;

		

		int Rownum = -1;

		for (int i = 0; i <= children.length-1; i++)
		{

		LineNumberReader lnr = new LineNumberReader(new FileReader(children[i]));
	    	lnr.setLineNumber(1);
	    	StreamTokenizer stokCurrentData = new StreamTokenizer(lnr);
	    	stokCurrentData.parseNumbers();
	    	stokCurrentData.eolIsSignificant(true);
	    	stokCurrentData.nextToken();

			while (stokCurrentData.ttype != StreamTokenizer.TT_EOF)
			{
				double intensMax = 0;

				while (stokCurrentData.ttype != StreamTokenizer.TT_EOF)
				{
					double mz = 0;					
				
					for (int colnum=1; colnum<=3; colnum++)
						{
							if (colnum==1) {mz=stokCurrentData.nval;
									}

							if (colnum==2) {
									if (mz >= MassLow && mz <= MassHigh)
										{
										if (stokCurrentData.nval > intensMax)
											{
											intensMax = stokCurrentData.nval;
											}
										}
									}

							if (colnum==3) {stokCurrentData.nextToken();
									Rownum++;
									break;}

							stokCurrentData.nextToken();
						}
				}

			Intensity[i] = intensMax;

			if (stokCurrentData.ttype == StreamTokenizer.TT_EOF) {break;}

			}

		}




		double[][] OCoordUncentered = new double [OlineCount][2];

		BufferedReader Par = new BufferedReader(new FileReader(WorkingPath + jTextField5.getText()));
		StreamTokenizer stokPar = new StreamTokenizer(Par);
		stokPar.eolIsSignificant(true);
		stokPar.nextToken();

		Double[] par = new Double[15];
		int a = 0;

		Rownum = 0;

				while (stokPar.ttype != StreamTokenizer.TT_EOF)
				{
					for (int colnum=1; colnum<=3; colnum++)
					{
						if (colnum==1) {a=1;
								}

						if (colnum==2) {par[Rownum]=stokPar.nval;
								}

						if (colnum==3) {Rownum++;
								stokPar.nextToken();
								break;
								}
						
						stokPar.nextToken();
					}

					
				}

		Double XCenStretched = par[0];
		Double YCenStretched = par[1];
		Double XCenTransformed = par[2];
		Double YCenTransformed = par[3];
		Double XCenOriginal = par [4];
		Double YCenOriginal = par [5];
		Double DeltaADeg = Math.toRadians(par[6]);
		Double WOriginal = par[7];
		Double HOriginal = par[8];
		Double WTransformed = par[9];
		Double HTransformed = par [10];
		Double XCenAloneStretched = par [11];
		Double YCenAloneStretched = par [12];
		Double XCenAloneOriginal = par [13];
		Double YCenAloneOriginal = par [14];

		Double deltaXcen = XCenTransformed - XCenOriginal;
		Double deltaYcen = YCenTransformed - YCenOriginal;
				
		int rownum = -1;

	
		LineNumberReader lnrO = new LineNumberReader(new FileReader(WorkingPath + jTextField4.getText()));
	    	lnrO.setLineNumber(1);
	    	StreamTokenizer stokO = new StreamTokenizer(lnrO);
	    	stokO.parseNumbers();
	    	stokO.eolIsSignificant(true);
	    	stokO.nextToken();	

		StreamTokenizer stok = new StreamTokenizer(lnrO);



				while (stokO.ttype != StreamTokenizer.TT_EOF)
				{
					double xS=0;
					double xO=0;
					double yS=0;
					double yO=0;

					while (stokO.ttype != StreamTokenizer.TT_EOF)
					{
						for (int colnum=1; colnum<=3; colnum++)
							{
								if (colnum==1) {xO=stokO.nval;}

								if (colnum==2) {yO=stokO.nval;}

								if (colnum==3) {stokO.nextToken();
										rownum++;
										break;}

								stokO.nextToken();
							}


					double[] Coord = new double[2];

					Coord[0]=xO;
					Coord[1]=yO;

					if (rownum <= OlineCount-1)
					{
						for (int coll=0; coll<=1; coll++)
						{
						OCoordUncentered[rownum][coll]= Coord[coll];
						}
					}

					if (stokO.ttype == StreamTokenizer.TT_EOF) {break;}

					}
				
				
				if (stokO.ttype == StreamTokenizer.TT_EOF) {break;}

				}


	double[][] SCoord = new double [SlineCount][2];
	double[][] OCoord = new double [OlineCount][2];

	for (int i = 0; i <= SCoord.length-1; i++)
	{
		SCoord[i][0] = SCoordUncentered[i][0] + (XCenStretched - XCenAloneStretched) + 100;
		SCoord[i][1] = SCoordUncentered[i][1] + (YCenStretched - YCenAloneStretched) + 60;
	}

	for (int i = 0; i <= OCoord.length-1; i++)
	{
		OCoord[i][0] = OCoordUncentered[i][0] + (XCenOriginal - XCenAloneOriginal);
		OCoord[i][1] = OCoordUncentered[i][1] + (YCenOriginal - YCenAloneOriginal);
	}



	double[][] TCoord = new double[OCoord.length][2];
	double[][] Dummy1 = new double[OCoord.length][2];
	double[][] Dummy2 = new double[OCoord.length][2];
	double[][] Dummy3 = new double[OCoord.length][2];
	
	for (int i = 0; i <= OCoord.length-1; i++)
	{
		Dummy1[i][0] = OCoord[i][0] + deltaXcen;
		Dummy1[i][1] = OCoord[i][1] + deltaYcen;

		Dummy2[i][0] = -1*(XCenTransformed - ((Dummy1[i][0] - XCenTransformed)*Math.cos(DeltaADeg) - (Dummy1[i][1] - YCenTransformed)*Math.sin(DeltaADeg) + XCenTransformed));
		Dummy2[i][1] = -1*(YCenTransformed - ((Dummy1[i][1] - YCenTransformed)*Math.cos(DeltaADeg) + (Dummy1[i][0] - XCenTransformed)*Math.sin(DeltaADeg) + YCenTransformed));

		Dummy3[i][0] = (Dummy2[i][0]*Math.cos(DeltaADeg) + Dummy2[i][1]*Math.sin(DeltaADeg)) * WTransformed/WOriginal;
		Dummy3[i][1] = (Dummy2[i][1]*Math.cos(DeltaADeg) - Dummy2[i][0]*Math.sin(DeltaADeg)) * HTransformed/HOriginal;

		TCoord[i][0] = Dummy3[i][0]*Math.cos(DeltaADeg) - Dummy3[i][1]*Math.sin(DeltaADeg) + XCenTransformed - 10;
		TCoord[i][1] = Dummy3[i][0]*Math.sin(DeltaADeg) + Dummy3[i][1]*Math.cos(DeltaADeg) + YCenTransformed - 10;
	}

	

	double TMatchCoord[][] = new double[TCoord.length][2];
	double[] IntensityMap = new double[TCoord.length];
	
	for (int i = 0; i <= OCoord.length-1; i++)
		{
		double Dist[] = new double[SCoord.length];

		double TCoordDummy[][] = new double[TCoord.length][2];
			for (int j = 0; j <= TCoord.length-1; j++)
			{
			TCoordDummy[j] = TCoord[j];
			}


		double IntensityDummy[] = new double[SCoord.length];
			for (int j = 0; j <= SCoord.length-1; j++)
			{
			IntensityDummy[j] = Intensity[j];
			}

	
		for (int l = 0; l <= SCoord.length-1; l++)
			{
				Dist[l] = Math.sqrt(Math.pow(TCoordDummy[i][0] - SCoord[l][0], 2) + Math.pow(TCoordDummy[i][1] - SCoord[l][1], 2));
			}

			
		for (int lastPlace = Dist.length-1; lastPlace > 0; lastPlace--)
			{
	          	int maxLoc = 0;
	
				for (int k = 0; k <= lastPlace; k++) 
				{
				if (Dist[k] > Dist[maxLoc])
				{
					maxLoc = k;
				}
				}	

			double Temp = Dist[maxLoc];
			Dist[maxLoc] = Dist[lastPlace];
			Dist[lastPlace] = Temp;	

			//double Temp1[] = TCoordDummy[maxLoc];
			//TCoordDummy[maxLoc] = TCoordDummy[lastPlace];
			//TCoordDummy[lastPlace] = Temp1;

			double Temp2 = IntensityDummy[maxLoc];
			IntensityDummy[maxLoc] = IntensityDummy[lastPlace];
			IntensityDummy[lastPlace] = Temp2;
			}

		//TMatchCoord[i] = TCoordDummy[0];
		IntensityMap[i] = IntensityDummy[0];
		



			if (Double == 1)
			{
				int DoubleInd = 0;
				int DoubleCount = 0;
				double DoubleTCoord[][] = new double[2][2];

				for (int e = 0; e <= i-1; e++)
				{
					if (TMatchCoord[i][0] == TMatchCoord[e][0] && TMatchCoord[i][1] == TMatchCoord[e][1])
					{
					DoubleCount++;
					DoubleInd=e;
					DoubleTCoord[1] = TMatchCoord[e];
					}
				}


				DoubleTCoord[0] = TMatchCoord[i];

				if (DoubleCount > 0)
				{
				
					double DistTCoord[] = new double[TCoord.length-1];
					double DistTCoordO[] = new double[2];


					double TCoordMinus1[][] = new double[TCoord.length-1][5];
					int RemoveInd = 0;

						for (int z = 0; z <= TCoord.length-1; z++)
						{
						if (TCoord[z] == TCoordDummy[0])
							{
							RemoveInd = z;
							break;
							}
						}

					for (int b = 0; b <= RemoveInd-1; b++)
						{
						TCoordMinus1[b] = TCoord[b];
						}
		
					for (int c = RemoveInd+1; c <= TCoordMinus1.length-1; c++)
						{
						TCoordMinus1[c] = TCoord[c];
						}

					for (int f = 0; f <= TCoord.length-2; f++)
					{
					DistTCoord[f] = Math.sqrt(Math.pow(TCoordMinus1[f][0] - TMatchCoord[i][0], 2) + Math.pow(TCoordMinus1[f][1] - TMatchCoord[i][1], 2));
					}

					for (int lastPlace = DistTCoord.length-1; lastPlace > 0; lastPlace--) 
					{
              					int maxLoc = 0;
		
						for (int k = 0; k <= lastPlace; k++) 
						{
						if (DistTCoord[k] > DistTCoord[maxLoc])
						{
							maxLoc = k;
						}
						}	

					double Temp = DistTCoord[maxLoc];
					DistTCoord[maxLoc] = DistTCoord[lastPlace];
					DistTCoord[lastPlace] = Temp;	

					double Temp1[] = TCoordMinus1[maxLoc];
					TCoordMinus1[maxLoc] = TCoordMinus1[lastPlace];
					TCoordMinus1[lastPlace] = Temp1;
					}

					double TCoordClosest[] = new double[2];

					for (int h = 0; h <=1; h++)
					{
					TCoordClosest[h] = TCoordMinus1[0][h];
					}

					double IntensitySub = 0;

					for (int y = 0; y <= TMatchCoord.length-1; y++)
					{
						if (TCoordClosest[0] == TMatchCoord[y][0] && TCoordClosest[1] == TMatchCoord[y][1])
						{
							IntensitySub = IntensityMap[y];
						}
					}



					DistTCoordO[0] = Math.sqrt(Math.pow(OCoord[i][0] - TCoordClosest[0], 2) + Math.pow(OCoord[i][1] - TCoordClosest[1], 2));
					DistTCoordO[1] = Math.sqrt(Math.pow(OCoord[DoubleInd][0] - TCoordClosest[0], 2) + Math.pow(OCoord[DoubleInd][1] - TCoordClosest[1], 2));

					if (DistTCoordO[0] < DistTCoordO[1])
					{
					TMatchCoord[i] = TCoordClosest;
					IntensityMap[i] = IntensitySub;
					}

					if (DistTCoordO[1] < DistTCoordO[0])
					{
					TMatchCoord[DoubleInd] = TCoordClosest;
					IntensityMap[DoubleInd] = IntensitySub;
					}
				}
			}
		
		}

		
		



		if (Validate == 1)
		{
			double PointCount = TCoord.length;
			double CorrectPointCount = 0;
		

			for (int j = 0; j <= TCoord.length-1; j++)
				{
				if (TMatchCoord[j][0] == TCoord[j][0] && TMatchCoord[j][1] == TCoord[j][1])
				{
					CorrectPointCount++;
				}
				}

			double ClassificationRate = (CorrectPointCount/PointCount) * 100;

			System.out.println("CorrectPointCount " + CorrectPointCount);
			System.out.println("PointCount " + PointCount);
			System.out.println("ClassificationRate " + ClassificationRate);	
		}


		double MaxX = 0;
		double MaxY = 0;

		for (int i = 0; i <= OCoord.length-1; i++)
		{
			if (OCoordUncentered[i][0] > MaxX)
			{
				MaxX = OCoordUncentered[i][0];
			}

			if (OCoordUncentered[i][1] > MaxY)
			{
				MaxY = OCoordUncentered[i][1];
			}
		}

		int width = (int)MaxX;
		int height = (int)MaxY;

		
		BufferedImage image = new BufferedImage(width + 10, height + 10, BufferedImage.TYPE_INT_RGB);

		String format = "JPG";
	
		if (jTextField6.getText().toLowerCase().endsWith(".png")) 
						{format = "PNG";}

		if (jTextField6.getText().toLowerCase().endsWith(".bmp")) 
						{format = "BMP";}

		double MaxIntensity = 0;
		double IntensitySum = 0;

		double MaxInd = 0;


		for (int i = 0; i <= IntensityMap.length-1; i++)
		{
			if (IntensityMap[i] > MaxIntensity)
			{
				MaxIntensity = IntensityMap[i];
				MaxInd = i;
			}

			IntensitySum += IntensityMap[i];
		}

		double IntensityAvg = IntensitySum / IntensityMap.length;

		System.out.println(Arrays.toString(IntensityMap));
		System.out.println(MaxInd);

		String[] SplitTemp = jTextField6.getText().split("\\.");

		String OutImageName = SplitTemp[0] + "_mz" + MassCenter + "+-" + MassWindow + "_Imax" + (int)MaxIntensity + "." + SplitTemp[1];

		double colorValue = 0;


		for (int i = 0; i <= IntensityMap.length-1; i++)
		{

			
			

			//colorValue = Math.log(IntensityMap[i] * 100 + 1) / Math.log(MaxIntensity * 100);
                        if (jRadioButton1.isSelected() == true)
                        {
			colorValue = IntensityMap[i] / (IntensityAvg);
                        }
                        
                        if (jRadioButton1.isSelected() == false)
                        {
			colorValue = IntensityMap[i] / (MaxIntensity);
                        }

			if (colorValue > 1)
			{
				colorValue = 1;
			}

			if (IntensityMap[i] < 10)
			{
				colorValue = 0;
			}

			Graphics graphics = image.getGraphics();
			Color color = new Color((int)(colorValue * 255), (int)(colorValue * 255), (int)(colorValue * 255));
			graphics.setColor(color);
			graphics.fillRect((int)OCoordUncentered[i][0] -7, (int)OCoordUncentered[i][1] - 7, 14, 14);
		}

		ImageIO.write(image, format, new File(WorkingPath + OutImageName));

		FileOutputStream out;
		PrintStream p; 
		out = new FileOutputStream(WorkingPath + "TCoord.txt");
		p = new PrintStream( out );

		for (int h = 0; h <= TCoord.length-1; h++)
		{			
    			p.print(TCoord[h][0] + "\t");
			p.println(TCoord[h][1]);			
		}
		p.close();


		FileOutputStream out1;
		PrintStream p1; 
		out1 = new FileOutputStream(WorkingPath + "SCoord.txt");
		p1 = new PrintStream( out1 );

		for (int h = 0; h <= SCoord.length-1; h++)
		{			
    			p1.print(SCoord[h][0] + "\t");
			p1.println(SCoord[h][1]);			
		}
		p.close();
                
                 jTextArea2.setText("Run has finished");
        }
               
       catch (IOException e) {System.out.println(e);
                            String er = e.toString();
                            jTextArea2.setText(er);}


    }
    
    /**
     * @param args the command line arguments
     */
    public static void main(String args[]) {
        java.awt.EventQueue.invokeLater(new Runnable() {
            public void run() {
                new MSIReconstructor().setVisible(true);
            }
        });
    }
    
    // Variables declaration - do not modify
    private javax.swing.ButtonGroup buttonGroup1;
    private javax.swing.JButton jButton1;
    private javax.swing.JCheckBox jCheckBox1;
    private javax.swing.JLabel jLabel1;
    private javax.swing.JLabel jLabel10;
    private javax.swing.JLabel jLabel11;
    private javax.swing.JLabel jLabel12;
    private javax.swing.JLabel jLabel13;
    private javax.swing.JLabel jLabel2;
    private javax.swing.JLabel jLabel3;
    private javax.swing.JLabel jLabel4;
    private javax.swing.JLabel jLabel5;
    private javax.swing.JLabel jLabel6;
    private javax.swing.JLabel jLabel7;
    private javax.swing.JLabel jLabel8;
    private javax.swing.JLabel jLabel9;
    private javax.swing.JRadioButton jRadioButton1;
    private javax.swing.JRadioButton jRadioButton2;
    private javax.swing.JScrollPane jScrollPane2;
    private javax.swing.JTextArea jTextArea2;
    private javax.swing.JTextField jTextField1;
    private javax.swing.JTextField jTextField2;
    private javax.swing.JTextField jTextField3;
    private javax.swing.JTextField jTextField4;
    private javax.swing.JTextField jTextField5;
    private javax.swing.JTextField jTextField6;
    // End of variables declaration
    
}