Commit c190e536 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

fixing conflict

parent ab7fc3e7

src/main/java/Eyesis_Correction.java

+515 −487
Original line number Original line Diff line number Diff line
@@ -25,18 +25,16 @@ 
**

**

*/

*/





import ij.*;

import java.awt.Button;

import ij.process.*;

import java.awt.Color;

import ij.gui.*;

import java.awt.Frame;

import ij.io.FileInfo;

import java.awt.GraphicsEnvironment;

import ij.io.FileSaver;

import java.awt.GridLayout;

import ij.io.OpenDialog;

import java.awt.Panel;

import ij.io.Opener;

import java.awt.Rectangle;

import ij.plugin.frame.*;

import java.awt.event.ActionEvent;

import ij.plugin.PlugIn;

import java.awt.event.ActionListener;



import java.awt.event.WindowEvent;

import java.awt.*;

import java.awt.event.*;

import java.io.File;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileInputStream;

import java.io.FileNotFoundException;

import java.io.FileNotFoundException;
@@ -54,6 +52,28 @@ import java.util.concurrent.atomic.AtomicInteger; 
import javax.swing.JFileChooser;

import javax.swing.JFileChooser;

import javax.swing.filechooser.FileFilter;

import javax.swing.filechooser.FileFilter;





import ij.CompositeImage;

import ij.IJ;

import ij.ImageJ;

import ij.ImagePlus;

import ij.ImageStack;

import ij.Macro;

import ij.Prefs;

import ij.WindowManager;

import ij.gui.GUI;

import ij.gui.GenericDialog;

import ij.gui.Plot;

import ij.gui.PlotWindow;

import ij.gui.Roi;

import ij.io.FileInfo;

import ij.io.FileSaver;

import ij.io.OpenDialog;

import ij.io.Opener;

import ij.plugin.PlugIn;

import ij.plugin.frame.PlugInFrame;

import ij.process.ColorProcessor;

import ij.process.FloatProcessor;

import ij.process.ImageProcessor;

import loci.common.services.DependencyException;

import loci.common.services.DependencyException;

import loci.common.services.ServiceException;

import loci.common.services.ServiceException;

import loci.formats.FormatException;

import loci.formats.FormatException;
@@ -346,6 +366,7 @@ private Panel panel1, 
	    public String  buttonLabel="";

	    public String  buttonLabel="";

	}

	}





	@Override

	public void run(String arg) {

	public void run(String arg) {

		String options=Macro.getOptions();

		String options=Macro.getOptions();

		try {

		try {
@@ -378,7 +399,7 @@ private Panel panel1, 
		Color color_conf_process=  new Color(180, 240, 240);

		Color color_conf_process=  new Color(180, 240, 240);

		Color color_restore=       new Color(180, 240, 180);

		Color color_restore=       new Color(180, 240, 180);

		Color color_stop=          new Color(255, 160, 160);

		Color color_stop=          new Color(255, 160, 160);

<<<<<<< HEAD

//<<<<<<< HEAD

		plugInFrame=new PlugInFrame("Eyesis_Correction") {

		plugInFrame=new PlugInFrame("Eyesis_Correction") {

			private static final long serialVersionUID = -4138832568507690332L;

			private static final long serialVersionUID = -4138832568507690332L;

			@Override

			@Override
@@ -389,11 +410,11 @@ private Panel panel1, 
				}

				}

			}

			}

		};

		};

		instance=(Frame)plugInFrame;

		instance=plugInFrame;

		plugInFrame.addKeyListener(IJ.getInstance());

		plugInFrame.addKeyListener(IJ.getInstance());

		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0);

		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0);

		plugInFrame.setLayout(new GridLayout(menuRows, 1));

		plugInFrame.setLayout(new GridLayout(menuRows, 1));

=======

/*=======









		instance = this;

		instance = this;
@@ -402,6 +423,7 @@ private Panel panel1, 
		setLayout(new GridLayout(menuRows, 1));

		setLayout(new GridLayout(menuRows, 1));





>>>>>>> origin/dct

>>>>>>> origin/dct

*/

		panel6 = new Panel();

		panel6 = new Panel();

		panel6.setLayout(new GridLayout(1, 0, 5, 5));

		panel6.setLayout(new GridLayout(1, 0, 5, 5));

		addButton("Save",panel6);

		addButton("Save",panel6);
@@ -497,9 +519,9 @@ private Panel panel1, 
			addButton("Plane Likely", panelPostProcessing3);

			addButton("Plane Likely", panelPostProcessing3);

			plugInFrame.add(panelPostProcessing3);

			plugInFrame.add(panelPostProcessing3);

		}

		}

<<<<<<< HEAD

// <<<<<<< HEAD

		plugInFrame.pack();

		plugInFrame.pack();

=======

/* =======

		if (DCT_MODE) {

		if (DCT_MODE) {

			panelDct1 = new Panel();

			panelDct1 = new Panel();

			panelDct1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap

			panelDct1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
@@ -534,7 +556,7 @@ private Panel panel1, 
		}

		}

		pack();

		pack();

>>>>>>> origin/dct

>>>>>>> origin/dct



*/

		GUI.center(plugInFrame);

		GUI.center(plugInFrame);

		plugInFrame.setVisible(true);

		plugInFrame.setVisible(true);

		FHT_INSTANCE=       new DoubleFHT();

		FHT_INSTANCE=       new DoubleFHT();
@@ -647,6 +669,7 @@ private Panel panel1, 
		b.addKeyListener(IJ.getInstance());

		b.addKeyListener(IJ.getInstance());

		panel.add(b);

		panel.add(b);

	}

	}

	@Override

	public void actionPerformed(ActionEvent e) {

	public void actionPerformed(ActionEvent e) {

		String label = e.getActionCommand();

		String label = e.getActionCommand();

		if        (label.equals("Abort")) {

		if        (label.equals("Abort")) {
@@ -2612,7 +2635,7 @@ private Panel panel1, 








    	for (int ii = 0; ii<n; ii++) {

    	for (int ii = 0; ii<n; ii++) {

    		dindex[ii] = (double) ii;

    		dindex[ii] = ii;

    		x[ii] = 0.0;

    		x[ii] = 0.0;

    	}

    	}

//    	x[1] = 1.0;

//    	x[1] = 1.0;
@@ -4306,6 +4329,7 @@ private Panel panel1, 
	  public MultipleExtensionsFileFilter (String [] patterns) {

	  public MultipleExtensionsFileFilter (String [] patterns) {

		  this.patterns=patterns.clone();

		  this.patterns=patterns.clone();

	  }

	  }

	  @Override

	public boolean accept (File file) {

	public boolean accept (File file) {

		  int i;

		  int i;

		  String name=file.getName();

		  String name=file.getName();
@@ -4315,6 +4339,7 @@ private Panel panel1, 
		  }

		  }

		  return false;

		  return false;

	  }

	  }

	  @Override

	public String getDescription() {

	public String getDescription() {

		  return description;

		  return description;

	  }

	  }
@@ -5613,6 +5638,7 @@ private Panel panel1, 
	  final long startTime = System.nanoTime();

	  final long startTime = System.nanoTime();

	  for (int ithread = 0; ithread < threads.length; ithread++) {

	  for (int ithread = 0; ithread < threads.length; ithread++) {

		  threads[ithread] = new Thread() {

		  threads[ithread] = new Thread() {

			  @Override

			public void run() {

			public void run() {

				  float [] pixels=null;       // will be initialized at first use

				  float [] pixels=null;       // will be initialized at first use

				  float [] kernelPixels=null; // will be initialized at first use

				  float [] kernelPixels=null; // will be initialized at first use
@@ -5755,6 +5781,7 @@ private Panel panel1, 
	  final long startTime = System.nanoTime();

	  final long startTime = System.nanoTime();

	  for (int ithread = 0; ithread < threads.length; ithread++) {

	  for (int ithread = 0; ithread < threads.length; ithread++) {

		  threads[ithread] = new Thread() {

		  threads[ithread] = new Thread() {

			  @Override

			public void run() {

			public void run() {

				  double [][] tile=        new double[nChn][debayerParameters.size * debayerParameters.size ];

				  double [][] tile=        new double[nChn][debayerParameters.size * debayerParameters.size ];

				  double [][] both_masks;

				  double [][] both_masks;
@@ -6002,6 +6029,7 @@ private Panel panel1, 
	  final long startTime = System.nanoTime();

	  final long startTime = System.nanoTime();

	  for (int ithread = 0; ithread < threads.length; ithread++) {

	  for (int ithread = 0; ithread < threads.length; ithread++) {

		  threads[ithread] = new Thread() {

		  threads[ithread] = new Thread() {

			  @Override

			public void run() {

			public void run() {

				  double [] tile=        new double[size * size ];

				  double [] tile=        new double[size * size ];

				  int tileY,tileX;

				  int tileY,tileX;