/*
 * BeadGeometry.java
 *
 * Created on April 28, 2008, 3:56 PM
 */
import java.io.*;
import java.text.*;
import java.util.regex.*;
import java.lang.Math.*;
import javax.swing.*;

/**
 *
 * @author  Tyler
 */
public class BeadGeometry extends javax.swing.JFrame {
    
    /** Creates new form BeadGeometry */
    public BeadGeometry() {
        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() {

        jLabel1 = new javax.swing.JLabel();
        jLabel2 = new javax.swing.JLabel();
        jTextField1 = new javax.swing.JTextField();
        jTextField2 = new javax.swing.JTextField();
        jTextField3 = new javax.swing.JTextField();
        jLabel3 = new javax.swing.JLabel();
        jLabel4 = new javax.swing.JLabel();
        jLabel5 = new javax.swing.JLabel();
        jTextField4 = new javax.swing.JTextField();
        jLabel6 = new javax.swing.JLabel();
        jTextField5 = new javax.swing.JTextField();
        jTextField6 = new javax.swing.JTextField();
        jLabel7 = new javax.swing.JLabel();
        jLabel8 = new javax.swing.JLabel();
        jLabel9 = new javax.swing.JLabel();
        jLabel10 = new javax.swing.JLabel();
        jLabel11 = new javax.swing.JLabel();
        jTextField7 = new javax.swing.JTextField();
        jTextField9 = new javax.swing.JTextField();
        jTextField10 = new javax.swing.JTextField();
        jLabel12 = new javax.swing.JLabel();
        jTextField11 = new javax.swing.JTextField();
        jLabel13 = new javax.swing.JLabel();
        jLabel14 = new javax.swing.JLabel();
        jLabel15 = new javax.swing.JLabel();
        jTextField12 = new javax.swing.JTextField();
        jTextField13 = new javax.swing.JTextField();
        jTextField14 = new javax.swing.JTextField();
        jTextField15 = new javax.swing.JTextField();
        jLabel16 = new javax.swing.JLabel();
        jLabel17 = new javax.swing.JLabel();
        jLabel18 = new javax.swing.JLabel();
        jLabel19 = new javax.swing.JLabel();
        jTextField16 = new javax.swing.JTextField();
        jTextField17 = new javax.swing.JTextField();
        jTextField18 = new javax.swing.JTextField();
        jTextField19 = new javax.swing.JTextField();
        jLabel21 = new javax.swing.JLabel();
        jLabel22 = new javax.swing.JLabel();
        jButton1 = new javax.swing.JButton();
        jLabel20 = new javax.swing.JLabel();
        jLabel23 = new javax.swing.JLabel();
        jLabel24 = new javax.swing.JLabel();
        jScrollPane1 = new javax.swing.JScrollPane();
        jTextArea1 = new javax.swing.JTextArea();

        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

        jLabel1.setText("Filenames");

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

        jTextField2.setText(".txt");

        jTextField3.setText(".xeo");

        jLabel3.setText("Stretched bead coordinates filename");

        jLabel4.setText("Filename of geometry file to be created");

        jLabel5.setText("Scaling parameters");

        jLabel6.setText("Image pixel spacing (microns)");

        jTextField5.setText("4413.0434783");

        jTextField6.setText("0");

        jLabel7.setText("Slide well spacing (microns), default");

        jLabel8.setText("Orientation difference (degrees)");

        jLabel9.setText("Common points");

        jLabel10.setText("Note: if using less than 3 common points, the remaining points should have duplicate values.");

        jLabel11.setFont(new java.awt.Font("Tahoma", 1, 11));
        jLabel11.setText("BeadGeometry program to create custom Bruker geometry files");

        jLabel12.setText("X1 (pixels)");

        jLabel13.setText("Y1 (pixels)");

        jLabel14.setText("X1 (fractional distance)");

        jLabel15.setText("Y1 (fractional distance)");

        jLabel16.setText("X2 (pixels)");

        jLabel17.setText("Y2 (pixels)");

        jLabel18.setText("X2 (fractional distance)");

        jLabel19.setText("Y2 (fractional distance)");

        jLabel21.setText("Y3 (pixels)");

        jLabel22.setText("X3 (fractional distance)");

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

        jLabel20.setText("X3 (pixels)");

        jLabel23.setText("Y3 (fractional distance)");

        jLabel24.setText("Messages during run:");

        jTextArea1.setColumns(20);
        jTextArea1.setRows(5);
        jTextArea1.setText("Currently no messages");
        jScrollPane1.setViewportView(jTextArea1);

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
        getContentPane().setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                    .addComponent(jTextField6)
                    .addComponent(jTextField5)
                    .addComponent(jTextField4)
                    .addComponent(jTextField2, javax.swing.GroupLayout.DEFAULT_SIZE, 107, Short.MAX_VALUE)
                    .addComponent(jTextField3))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel11)
                    .addComponent(jLabel3)
                    .addComponent(jLabel4)
                    .addComponent(jLabel7)
                    .addComponent(jLabel8)
                    .addComponent(jLabel6))
                .addGap(86, 86, 86))
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                .addContainerGap(10, Short.MAX_VALUE)
                .addComponent(jLabel10)
                .addGap(118, 118, 118))
            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                .addContainerGap(10, Short.MAX_VALUE)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jScrollPane1, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 356, Short.MAX_VALUE)
                    .addGroup(layout.createSequentialGroup()
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                            .addComponent(jLabel24, javax.swing.GroupLayout.Alignment.LEADING)
                            .addGroup(javax.swing.GroupLayout.Alignment.LEADING, layout.createSequentialGroup()
                                .addComponent(jTextField11, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addComponent(jLabel15)
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addComponent(jTextField15, javax.swing.GroupLayout.DEFAULT_SIZE, 61, Short.MAX_VALUE))
                            .addGroup(javax.swing.GroupLayout.Alignment.LEADING, layout.createSequentialGroup()
                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                                    .addComponent(jTextField9)
                                    .addComponent(jTextField7, javax.swing.GroupLayout.Alignment.TRAILING)
                                    .addComponent(jTextField10, javax.swing.GroupLayout.PREFERRED_SIZE, 61, javax.swing.GroupLayout.PREFERRED_SIZE))
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                        .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                            .addComponent(jLabel14))
                                        .addGroup(layout.createSequentialGroup()
                                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                            .addComponent(jLabel13)))
                                    .addComponent(jLabel12))
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                                    .addComponent(jTextField14, javax.swing.GroupLayout.Alignment.TRAILING)
                                    .addComponent(jTextField12)
                                    .addComponent(jTextField13, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))))
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addGroup(layout.createSequentialGroup()
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                    .addComponent(jLabel16)
                                    .addComponent(jLabel17)))
                            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                    .addComponent(jLabel19)
                                    .addComponent(jLabel18)
                                    .addGroup(layout.createSequentialGroup()
                                        .addGap(10, 10, 10)
                                        .addComponent(jButton1)))))))
                .addGap(18, 18, 18)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                    .addComponent(jTextField19, javax.swing.GroupLayout.Alignment.TRAILING)
                    .addComponent(jTextField16)
                    .addComponent(jTextField17)
                    .addComponent(jTextField18))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel22)
                    .addComponent(jLabel20)
                    .addComponent(jLabel23)
                    .addComponent(jLabel21))
                .addGap(10, 10, 10))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jTextField1, javax.swing.GroupLayout.PREFERRED_SIZE, 385, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addContainerGap(175, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel2)
                .addContainerGap(420, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel9)
                .addContainerGap(487, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel5)
                .addContainerGap(469, Short.MAX_VALUE))
            .addGroup(layout.createSequentialGroup()
                .addGap(10, 10, 10)
                .addComponent(jLabel1)
                .addContainerGap(513, Short.MAX_VALUE))
        );

        layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jTextField10, jTextField11, jTextField12, jTextField13, jTextField16});

        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addComponent(jLabel11)
                .addGap(11, 11, 11)
                .addComponent(jLabel2)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jTextField1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel1)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .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(jTextField3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel4))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel5)
                .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(jLabel6))
                .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(jLabel7))
                .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(jLabel8))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel9)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel10)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(layout.createSequentialGroup()
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jTextField7, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(jLabel12))
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel13)
                            .addComponent(jTextField9, 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(jLabel14)
                            .addComponent(jTextField10, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                    .addGroup(layout.createSequentialGroup()
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jTextField12, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(jLabel16))
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel17)
                            .addComponent(jTextField13, 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(jLabel18)
                            .addComponent(jTextField14, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                    .addGroup(layout.createSequentialGroup()
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jTextField16, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(jLabel20))
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jTextField17, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(jLabel21))
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                            .addComponent(jLabel22)
                            .addComponent(jTextField18, 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(jTextField11, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel15)
                    .addComponent(jTextField19, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jTextField15, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jLabel23)
                    .addComponent(jLabel19))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addComponent(jButton1)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jLabel24)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 42, 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{
                String WorkingPath = jTextField1.getText();

                if (WorkingPath.endsWith("\\") == false | WorkingPath.endsWith("/") == false )
		{
		WorkingPath = WorkingPath + "\\";
		}
                    
		String OutGeoFilename = jTextField3.getText();


		BufferedReader inIN = new BufferedReader(new FileReader(WorkingPath + jTextField2.getText()));

		int INlineCount = 0;

		do
		{
		  	String lineIN = inIN.readLine();
			if (lineIN == null) break;
	        	INlineCount++;		
		} while (true);
                
                jTextArea1.setText("Currently running");

		double PhysicalPixelSpacing = Double.valueOf(jTextField4.getText()).doubleValue();
		double PhysicalWellSpacing = Double.valueOf(jTextField5.getText()).doubleValue();
		double PlateOriginXa = Double.valueOf(jTextField7.getText()).doubleValue();
		double PlateOriginYa = Double.valueOf(jTextField9.getText()).doubleValue();
		double PlateOriginXb = Double.valueOf(jTextField12.getText()).doubleValue();
		double PlateOriginYb = Double.valueOf(jTextField13.getText()).doubleValue();
		double PlateOriginXc = Double.valueOf(jTextField16.getText()).doubleValue();
		double PlateOriginYc = Double.valueOf(jTextField17.getText()).doubleValue();

		double BrukerOriginXa = Double.valueOf(jTextField10.getText()).doubleValue();
		double BrukerOriginYa = Double.valueOf(jTextField11.getText()).doubleValue();
		double BrukerOriginXb = Double.valueOf(jTextField14.getText()).doubleValue();
		double BrukerOriginYb = Double.valueOf(jTextField15.getText()).doubleValue();
		double BrukerOriginXc = Double.valueOf(jTextField18.getText()).doubleValue();
		double BrukerOriginYc = Double.valueOf(jTextField19.getText()).doubleValue();

		double DegRot = Math.toRadians(Double.valueOf(jTextField6.getText()).doubleValue());		

		int rownum = -1;

		double[][] INCoord = new double[INlineCount][2];

	    	LineNumberReader lnr = new LineNumberReader(new FileReader(WorkingPath + jTextField2.getText()));
	    	lnr.setLineNumber(1);
	    	StreamTokenizer stok = new StreamTokenizer(lnr);
	    	stok.parseNumbers();
	    	stok.eolIsSignificant(true);
	    	stok.nextToken();

				while (stok.ttype != StreamTokenizer.TT_EOF)
				{
					double x=0;
					double y=0;

					while (stok.ttype != StreamTokenizer.TT_EOF)
					{

						for (int colnum=1; colnum<=3; colnum++)
						{
								if (colnum==1) {x=stok.nval;
										}

								if (colnum==2) {y=stok.nval;
										}

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

								stok.nextToken();
						}

					double[] Coord = new double[2];

					Coord[0]=x;
					Coord[1]=y;

					for (int col=0; col<=1; col++)
					{
					INCoord[rownum][col] = Coord[col];
					}


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

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

				}

	
		double[][] PhysicalINCoord = new double[INCoord.length][2];
		

		double PlateOriginX = 0;
		double PlateOriginY = 0;

		for (int i = 0; i <= INCoord.length-1; i++)
		{
			Double DistA =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXa), 2) + Math.pow((PlateOriginYa - INCoord[i][1]), 2) );
			Double DistB =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXb), 2) + Math.pow((PlateOriginYb - INCoord[i][1]), 2) );
			Double DistC =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXc), 2) + Math.pow((PlateOriginYc - INCoord[i][1]), 2) );


			if (DistA <= DistB && DistA <= DistC)
			{
			PlateOriginX = PlateOriginXa;
			PlateOriginY = PlateOriginYa;
			} 

			if (DistB <= DistA &&  DistB <= DistC)
			{
			PlateOriginX = PlateOriginXb;
			PlateOriginY = PlateOriginYb;
			} 


			if (DistC <= DistA &&  DistC <= DistB)
			{
			PlateOriginX = PlateOriginXc;
			PlateOriginY = PlateOriginYc;
			} 

			PhysicalINCoord[i][0] = (INCoord[i][0] - PlateOriginX) * PhysicalPixelSpacing;
			PhysicalINCoord[i][1] = (PlateOriginY - INCoord[i][1]) * PhysicalPixelSpacing;
		}
		
		double[][] OutCoordTemp = new double[PhysicalINCoord.length][2];

		for (int i = 0; i <= INCoord.length-1; i++)
		{
			OutCoordTemp[i][0] = PhysicalINCoord[i][0] / PhysicalWellSpacing * 0.086956454545454545;
			OutCoordTemp[i][1] = PhysicalINCoord[i][1] / PhysicalWellSpacing * 0.086956454545454545;
		}

		double[][] OutCoord = new double[PhysicalINCoord.length][2];

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

			Double DistA =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXa), 2) + Math.pow((PlateOriginYa - INCoord[i][1]), 2) );
			Double DistB =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXb), 2) + Math.pow((PlateOriginYb - INCoord[i][1]), 2) );
			Double DistC =  Math.sqrt( Math.pow((INCoord[i][0] - PlateOriginXc), 2) + Math.pow((PlateOriginYc - INCoord[i][1]), 2) );

			if (DistA <= DistB && DistA <= DistC)
			{
			OutCoord[i][0] = OutCoordTemp[i][0]*Math.cos(DegRot) + OutCoordTemp[i][1]*Math.sin(DegRot) + BrukerOriginXa;
			OutCoord[i][1] = -1*OutCoordTemp[i][0]*Math.sin(DegRot) + OutCoordTemp[i][1]*Math.cos(DegRot) + BrukerOriginYa;
			}

			if (DistB <= DistA &&  DistB <= DistC)
			{
			OutCoord[i][0] = OutCoordTemp[i][0]*Math.cos(DegRot) + OutCoordTemp[i][1]*Math.sin(DegRot) + BrukerOriginXb;
			OutCoord[i][1] = -1*OutCoordTemp[i][0]*Math.sin(DegRot) + OutCoordTemp[i][1]*Math.cos(DegRot) + BrukerOriginYb;
			}

			if (DistC <= DistA &&  DistC <= DistB)
			{
			OutCoord[i][0] = OutCoordTemp[i][0]*Math.cos(DegRot) + OutCoordTemp[i][1]*Math.sin(DegRot) + BrukerOriginXc;
			OutCoord[i][1] = -1*OutCoordTemp[i][0]*Math.sin(DegRot) + OutCoordTemp[i][1]*Math.cos(DegRot) + BrukerOriginYc;
			}

		}

		System.out.println(OutCoordTemp[0][0]);
		System.out.println(OutCoordTemp[0][1]);

		
		BufferedWriter outFile = new BufferedWriter(new FileWriter(WorkingPath + OutGeoFilename));
		PrintWriter out = new PrintWriter(outFile);

		out.println("<!-- $Revision: 1.5 $-->");

		out.println("<PlateType>");

		out.println("	<GlobalParameters PlateTypeName=\"MTP Slide Adapter II\" ProbeType=\"MTP\"");
		out.println("	                  RowsNumber=\"100\" ChipNumber=\"1\" ChipsInRow=\"1\"");
		out.println("	                  X_ChipOffsetSize=\"0\" Y_ChipOffsetSize=\"0\"");
		out.println("	                  HasDirectLabels=\"false\" HasColRowLabels=\"true\"");
		out.println("	                  HasNearNeighbourCalibrants=\"false\"");
		out.println("	                  ProbeDiameterX=\"103.5\" SampleDiameter=\"2\"");
		out.println("	                  SamplePixelRadius=\"5\" ZoomFactor=\"1\"");
		out.println("	                  FirstCalibrant=\"TPX1\" SecondCalibrant=\"TPX2\" ThirdCalibrant=\"TPX3\"");
		out.println("	                  />");

		out.print("	<MappingParameters mox=\"56.239998\" moy=\"42.635009\" sinphi=\"0.000000\" cosphi=\"1.000000\"");
		out.println(" alpha=\"51.750000\" beta=\"51.750000\" tansigma=\"0.000000\"/>");

		out.print("	<PlateSpots PositionNumber=\"");
		out.print(INCoord.length);
		out.println("\">");

		String a = "		<PlateSpot PositionIndex=\"";
		String b = "\" PositionName=\"";
		String c = "\" UnitCoord_X=\"";
		String d = "\" UnitCoord_Y=\"";
		String e = "\"/>";

		DecimalFormat df = new DecimalFormat("#.######");
		
		for (int i=0; i <= INCoord.length-1; i++)
		{
			out.print(a);
			out.print(i);
			out.print(b);
			out.print("x_" + (int)INCoord[i][0] + "y_" + (int)INCoord[i][1]);
			out.print(c);
			out.print(df.format(OutCoord[i][0]));
			out.print(d);
			out.print(df.format(OutCoord[i][1]));
			out.println(e);
		}

		out.println("	</PlateSpots>");

		out.println("	<AutoTeachSpots>");
		out.println("		<PlateSpot PositionIndex=\"0\" PositionName=\"TPX1\" UnitCoord_X=\"-0.729469\" UnitCoord_Y=\"0.550725\"/>");
		out.println("		<PlateSpot PositionIndex=\"1\" PositionName=\"TPX2\" UnitCoord_X=\"0.729469\" UnitCoord_Y=\"0.550725\"/>");
		out.println("		<PlateSpot PositionIndex=\"2\" PositionName=\"TPX3\" UnitCoord_X=\"0.729469\" UnitCoord_Y=\"0.057971\"/>");
		out.println("		<PlateSpot PositionIndex=\"3\" PositionName=\"TPX4\" UnitCoord_X=\"-0.729469\" UnitCoord_Y=\"0.057971\"/>");
		out.println("		<PlateSpot PositionIndex=\"4\" PositionName=\"TPY1\" UnitCoord_X=\"-0.729469\" UnitCoord_Y=\"-0.057971\"/>");
		out.println("		<PlateSpot PositionIndex=\"5\" PositionName=\"TPY2\" UnitCoord_X=\"0.729469\" UnitCoord_Y=\"-0.057971\"/>");
		out.println("		<PlateSpot PositionIndex=\"6\" PositionName=\"TPY3\" UnitCoord_X=\"-0.729469\" UnitCoord_Y=\"-0.550725\"/>");
		out.println("		<PlateSpot PositionIndex=\"7\" PositionName=\"TPY4\" UnitCoord_X=\"0.729469\" UnitCoord_Y=\"-0.550725\"/>");
		out.println("	</AutoTeachSpots>");

		out.println("</PlateType>");

		out.close();    
                
                jTextArea1.setText("Run has finished");
        }
        catch (IOException e) {System.out.println("Error");
                                jTextArea1.setText(e.toString());}
            
        
                
    
    }
    
    /**
     * @param args the command line arguments
     */
    public static void main(String args[]) {
        java.awt.EventQueue.invokeLater(new Runnable() {
            public void run() {
                new BeadGeometry().setVisible(true);
            }
        });
    }
    
    // Variables declaration - do not modify
    private javax.swing.JButton jButton1;
    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 jLabel14;
    private javax.swing.JLabel jLabel15;
    private javax.swing.JLabel jLabel16;
    private javax.swing.JLabel jLabel17;
    private javax.swing.JLabel jLabel18;
    private javax.swing.JLabel jLabel19;
    private javax.swing.JLabel jLabel2;
    private javax.swing.JLabel jLabel20;
    private javax.swing.JLabel jLabel21;
    private javax.swing.JLabel jLabel22;
    private javax.swing.JLabel jLabel23;
    private javax.swing.JLabel jLabel24;
    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.JScrollPane jScrollPane1;
    private javax.swing.JTextArea jTextArea1;
    private javax.swing.JTextField jTextField1;
    private javax.swing.JTextField jTextField10;
    private javax.swing.JTextField jTextField11;
    private javax.swing.JTextField jTextField12;
    private javax.swing.JTextField jTextField13;
    private javax.swing.JTextField jTextField14;
    private javax.swing.JTextField jTextField15;
    private javax.swing.JTextField jTextField16;
    private javax.swing.JTextField jTextField17;
    private javax.swing.JTextField jTextField18;
    private javax.swing.JTextField jTextField19;
    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;
    private javax.swing.JTextField jTextField7;
    private javax.swing.JTextField jTextField9;
    // End of variables declaration
    
}