correcting extrinsics after being changed (c8348852) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+80 −8

Original line number	Original line	Diff line number	Diff line
	@@ -55,7 +55,7 @@ public class EyesisCorrectionParameters {
	public boolean blueProc = true;		public boolean blueProc = true;
	public boolean toRGB = true;		public boolean toRGB = true;
	public boolean rotate = true;		public boolean rotate = true;
	public boolean crop = true; // crop to the sennor size		public boolean crop = true; // crop to the sensor size
	public int equirectangularFormat= 0; // 0 - 8 bit RGBA, 1 - 16 bit RGBA, 2 (32 int or 16 float!) ?, 3 - 32-bit FP RGBA. only 0, 1 and 3 currently supported		public int equirectangularFormat= 0; // 0 - 8 bit RGBA, 1 - 16 bit RGBA, 2 (32 int or 16 float!) ?, 3 - 32-bit FP RGBA. only 0, 1 and 3 currently supported
	public double outputRangeInt= 0.25; // 1.0 intensity will be mapped to 65535*0.25		public double outputRangeInt= 0.25; // 1.0 intensity will be mapped to 65535*0.25
	public double outputRangeFP= 255.0; // 1.0 intensity will be saved as 255.0 (in float 32-bit mode)		public double outputRangeFP= 255.0; // 1.0 intensity will be saved as 255.0 (in float 32-bit mode)
	@@ -2004,11 +2004,24 @@ public class EyesisCorrectionParameters {
	public double fine_corr_x_3 = 0.0; // additionally shift image in port 3 in x direction		public double fine_corr_x_3 = 0.0; // additionally shift image in port 3 in x direction
	public double fine_corr_y_3 = 0.0; // additionally shift image in port 3 in y direction		public double fine_corr_y_3 = 0.0; // additionally shift image in port 3 in y direction

	public double fcorr_min_stength = 0.005; // minimal correlation strength to apply fine correction		public double fcorr_min_strength = 0.15 ; // 0.005 minimal correlation strength to apply fine correction
	public double fcorr_disp_diff = 3.0; // consider only tiles with absolute residual disparity lower than		public double fcorr_disp_diff = 1.5; // consider only tiles with absolute residual disparity lower than
	public boolean fcorr_quadratic = true; // Use quadratic polynomial for fine correction (false - only linear)		public boolean fcorr_quadratic = true; // Use quadratic polynomial for fine correction (false - only linear)
	public boolean fcorr_ignore = false; // Ignore currently calculated fine correction		public boolean fcorr_ignore = false; // Ignore currently calculated fine correction

			public double fcorr_inf_strength = 0.20 ; // Minimal correlation strength to use for infinity correction
			public double fcorr_inf_diff = 0.2; // Disparity half-range for infinity
			public boolean fcorr_inf_quad = true; // Use quadratic polynomial for infinity correction (false - only linear)
			public boolean fcorr_inf_vert = false; // Correct infinity in vertical direction (false - only horizontal)

			public int fcorr_sample_size = 32; // Use square this size side to detect outliers
			public int fcorr_mintiles = 8; // Keep tiles only if there are more in each square
			public double fcorr_reloutliers = 0.5; // Remove this fraction of tiles from each sample
			public double fcorr_sigma = 20.0; // Gaussian blur channel mismatch data




	public double corr_magic_scale = 0.85; // reported correlation offset vs. actual one (not yet understood)		public double corr_magic_scale = 0.85; // reported correlation offset vs. actual one (not yet understood)

	// 3d reconstruction		// 3d reconstruction
	@@ -2366,6 +2379,9 @@ public class EyesisCorrectionParameters {
	public double taDiffPwr = 0.25; // Strength power when calculating disparity error		public double taDiffPwr = 0.25; // Strength power when calculating disparity error
	public double taBestPwr = 0.0; // Strength power when calculating disparity error over best		public double taBestPwr = 0.0; // Strength power when calculating disparity error over best
	public double taDiff9Pwr = 0.5; // Strength power when calculating disparity error for group of 9		public double taDiff9Pwr = 0.5; // Strength power when calculating disparity error for group of 9
			public double taColSigma = 1.5; // Gaussian sigma to blur color difference between tiles along each direction
			public double taColFraction = 0.3; // Relative amount of the blurred color difference in the mixture


	public double taCostEmpty = 1.0; // Cost of a tile that is not assigned		public double taCostEmpty = 1.0; // Cost of a tile that is not assigned
	public double taCostNoLink = 1.0; // Cost of a tile not having any neighbor in particular direction		public double taCostNoLink = 1.0; // Cost of a tile not having any neighbor in particular direction
	@@ -2499,11 +2515,21 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"fine_corr_x_3", this.fine_corr_x_3 +"");		properties.setProperty(prefix+"fine_corr_x_3", this.fine_corr_x_3 +"");
	properties.setProperty(prefix+"fine_corr_y_3", this.fine_corr_y_3 +"");		properties.setProperty(prefix+"fine_corr_y_3", this.fine_corr_y_3 +"");

	properties.setProperty(prefix+"fcorr_min_stength",this.fcorr_min_stength +"");		properties.setProperty(prefix+"fcorr_min_strength",this.fcorr_min_strength +"");
	properties.setProperty(prefix+"fcorr_disp_diff", this.fcorr_disp_diff +"");		properties.setProperty(prefix+"fcorr_disp_diff", this.fcorr_disp_diff +"");
	properties.setProperty(prefix+"fcorr_quadratic", this.fcorr_quadratic+"");		properties.setProperty(prefix+"fcorr_quadratic", this.fcorr_quadratic+"");
	properties.setProperty(prefix+"fcorr_ignore", this.fcorr_ignore+"");		properties.setProperty(prefix+"fcorr_ignore", this.fcorr_ignore+"");

			properties.setProperty(prefix+"fcorr_inf_strength",this.fcorr_inf_strength +"");
			properties.setProperty(prefix+"fcorr_inf_diff", this.fcorr_inf_diff +"");
			properties.setProperty(prefix+"fcorr_inf_quad", this.fcorr_inf_quad+"");
			properties.setProperty(prefix+"fcorr_inf_vert", this.fcorr_inf_vert+"");

			properties.setProperty(prefix+"fcorr_sample_size",this.fcorr_sample_size+"");
			properties.setProperty(prefix+"fcorr_mintiles", this.fcorr_mintiles+"");
			properties.setProperty(prefix+"fcorr_reloutliers",this.fcorr_reloutliers +"");
			properties.setProperty(prefix+"fcorr_sigma", this.fcorr_sigma +"");

	properties.setProperty(prefix+"corr_magic_scale", this.corr_magic_scale +"");		properties.setProperty(prefix+"corr_magic_scale", this.corr_magic_scale +"");

	properties.setProperty(prefix+"show_textures", this.show_textures+"");		properties.setProperty(prefix+"show_textures", this.show_textures+"");
	@@ -2830,6 +2856,8 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"taDiffPwr", this.taDiffPwr +"");		properties.setProperty(prefix+"taDiffPwr", this.taDiffPwr +"");
	properties.setProperty(prefix+"taBestPwr", this.taBestPwr +"");		properties.setProperty(prefix+"taBestPwr", this.taBestPwr +"");
	properties.setProperty(prefix+"taDiff9Pwr", this.taDiff9Pwr +"");		properties.setProperty(prefix+"taDiff9Pwr", this.taDiff9Pwr +"");
			properties.setProperty(prefix+"taColSigma", this.taColSigma +"");
			properties.setProperty(prefix+"taColFraction", this.taColFraction +"");

	properties.setProperty(prefix+"taCostEmpty", this.taCostEmpty +"");		properties.setProperty(prefix+"taCostEmpty", this.taCostEmpty +"");
	properties.setProperty(prefix+"taCostNoLink", this.taCostNoLink +"");		properties.setProperty(prefix+"taCostNoLink", this.taCostNoLink +"");
	@@ -2957,10 +2985,21 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"fine_corr_x_3")!=null) this.fine_corr_x_3=Double.parseDouble(properties.getProperty(prefix+"fine_corr_x_3"));		if (properties.getProperty(prefix+"fine_corr_x_3")!=null) this.fine_corr_x_3=Double.parseDouble(properties.getProperty(prefix+"fine_corr_x_3"));
	if (properties.getProperty(prefix+"fine_corr_y_3")!=null) this.fine_corr_y_3=Double.parseDouble(properties.getProperty(prefix+"fine_corr_y_3"));		if (properties.getProperty(prefix+"fine_corr_y_3")!=null) this.fine_corr_y_3=Double.parseDouble(properties.getProperty(prefix+"fine_corr_y_3"));

	if (properties.getProperty(prefix+"fcorr_min_stength")!=null) this.fcorr_min_stength=Double.parseDouble(properties.getProperty(prefix+"fcorr_min_stength"));		if (properties.getProperty(prefix+"fcorr_min_strength")!=null) this.fcorr_min_strength=Double.parseDouble(properties.getProperty(prefix+"fcorr_min_strength"));
	if (properties.getProperty(prefix+"fcorr_disp_diff")!=null) this.fcorr_disp_diff=Double.parseDouble(properties.getProperty(prefix+"fcorr_disp_diff"));		if (properties.getProperty(prefix+"fcorr_disp_diff")!=null) this.fcorr_disp_diff=Double.parseDouble(properties.getProperty(prefix+"fcorr_disp_diff"));
	if (properties.getProperty(prefix+"fcorr_quadratic")!=null) this.fcorr_quadratic=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_quadratic"));		if (properties.getProperty(prefix+"fcorr_quadratic")!=null) this.fcorr_quadratic=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_quadratic"));
	if (properties.getProperty(prefix+"fcorr_ignore")!=null) this.fcorr_ignore=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_ignore"));		if (properties.getProperty(prefix+"fcorr_ignore")!=null) this.fcorr_ignore=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_ignore"));

			if (properties.getProperty(prefix+"fcorr_inf_strength")!=null) this.fcorr_inf_strength=Double.parseDouble(properties.getProperty(prefix+"fcorr_inf_strength"));
			if (properties.getProperty(prefix+"fcorr_inf_diff")!=null) this.fcorr_inf_diff=Double.parseDouble(properties.getProperty(prefix+"fcorr_inf_diff"));
			if (properties.getProperty(prefix+"fcorr_inf_quad")!=null) this.fcorr_inf_quad=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_inf_quad"));
			if (properties.getProperty(prefix+"fcorr_inf_vert")!=null) this.fcorr_inf_vert=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_inf_vert"));

			if (properties.getProperty(prefix+"fcorr_sample_size")!=null) this.fcorr_sample_size=Integer.parseInt(properties.getProperty(prefix+"fcorr_sample_size"));
			if (properties.getProperty(prefix+"fcorr_mintiles")!=null) this.fcorr_mintiles=Integer.parseInt(properties.getProperty(prefix+"fcorr_mintiles"));
			if (properties.getProperty(prefix+"fcorr_reloutliers")!=null) this.fcorr_reloutliers=Double.parseDouble(properties.getProperty(prefix+"fcorr_reloutliers"));
			if (properties.getProperty(prefix+"fcorr_sigma")!=null) this.fcorr_sigma=Double.parseDouble(properties.getProperty(prefix+"fcorr_sigma"));

	if (properties.getProperty(prefix+"corr_magic_scale")!=null) this.corr_magic_scale=Double.parseDouble(properties.getProperty(prefix+"corr_magic_scale"));		if (properties.getProperty(prefix+"corr_magic_scale")!=null) this.corr_magic_scale=Double.parseDouble(properties.getProperty(prefix+"corr_magic_scale"));

	if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));		if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
	@@ -3287,6 +3326,8 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"taDiffPwr")!=null) this.taDiffPwr=Double.parseDouble(properties.getProperty(prefix+"taDiffPwr"));		if (properties.getProperty(prefix+"taDiffPwr")!=null) this.taDiffPwr=Double.parseDouble(properties.getProperty(prefix+"taDiffPwr"));
	if (properties.getProperty(prefix+"taBestPwr")!=null) this.taBestPwr=Double.parseDouble(properties.getProperty(prefix+"taBestPwr"));		if (properties.getProperty(prefix+"taBestPwr")!=null) this.taBestPwr=Double.parseDouble(properties.getProperty(prefix+"taBestPwr"));
	if (properties.getProperty(prefix+"taDiff9Pwr")!=null) this.taDiff9Pwr=Double.parseDouble(properties.getProperty(prefix+"taDiff9Pwr"));		if (properties.getProperty(prefix+"taDiff9Pwr")!=null) this.taDiff9Pwr=Double.parseDouble(properties.getProperty(prefix+"taDiff9Pwr"));
			if (properties.getProperty(prefix+"taColSigma")!=null) this.taDiff9Pwr=Double.parseDouble(properties.getProperty(prefix+"taColSigma"));
			if (properties.getProperty(prefix+"taColFraction")!=null) this.taColFraction=Double.parseDouble(properties.getProperty(prefix+"taColFraction"));

	if (properties.getProperty(prefix+"taCostEmpty")!=null) this.taCostEmpty=Double.parseDouble(properties.getProperty(prefix+"taCostEmpty"));		if (properties.getProperty(prefix+"taCostEmpty")!=null) this.taCostEmpty=Double.parseDouble(properties.getProperty(prefix+"taCostEmpty"));
	if (properties.getProperty(prefix+"taCostNoLink")!=null) this.taCostNoLink=Double.parseDouble(properties.getProperty(prefix+"taCostNoLink"));		if (properties.getProperty(prefix+"taCostNoLink")!=null) this.taCostNoLink=Double.parseDouble(properties.getProperty(prefix+"taCostNoLink"));
	@@ -3429,10 +3470,21 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("X 3", this.fine_corr_x_3, 3);		gd.addNumericField("X 3", this.fine_corr_x_3, 3);
	gd.addNumericField("Y 4", this.fine_corr_y_3, 3);		gd.addNumericField("Y 4", this.fine_corr_y_3, 3);

	gd.addNumericField("Minimal correlation strength to apply fine correction", this.fcorr_min_stength, 3);		gd.addNumericField("Minimal correlation strength to apply fine correction", this.fcorr_min_strength,3);
	gd.addNumericField("Consider only tiles with absolute residual disparity lower than", this.fcorr_disp_diff, 3);		gd.addNumericField("Consider only tiles with absolute residual disparity lower than", this.fcorr_disp_diff, 3);
	gd.addCheckbox ("Use quadratic polynomial for fine correction (false - only linear)", this.fcorr_quadratic);		gd.addCheckbox ("Use quadratic polynomial for fine correction (false - only linear)", this.fcorr_quadratic);
	gd.addCheckbox ("Ignore current calculated fine correction (use manual only)", this.fcorr_ignore);		gd.addCheckbox ("Ignore current calculated fine correction (use manual only)", this.fcorr_ignore);

			gd.addNumericField("Minimal correlation strength to use for infinity correction", this.fcorr_inf_strength,3);
			gd.addNumericField("Disparity half-range for infinity", this.fcorr_inf_diff, 3);
			gd.addCheckbox ("Use quadratic polynomial for infinity correction (false - only linear)", this.fcorr_inf_quad);
			gd.addCheckbox ("Correct infinity in vertical direction (false - only horizontal)", this.fcorr_inf_vert);

			gd.addNumericField("Use square this size side to detect outliers", this.fcorr_sample_size, 0);
			gd.addNumericField("Keep tiles only if there are more in each square", this.fcorr_mintiles, 0);
			gd.addNumericField("Remove this fraction of tiles from each sample", this.fcorr_reloutliers, 3);
			gd.addNumericField("Gaussian blur channel mismatch data", this.fcorr_sigma, 3);

	gd.addNumericField("Calculated from correlation offset vs. actual one (not yet understood)", this.corr_magic_scale, 3);		gd.addNumericField("Calculated from correlation offset vs. actual one (not yet understood)", this.corr_magic_scale, 3);

	gd.addMessage ("--- 3D reconstruction ---");		gd.addMessage ("--- 3D reconstruction ---");
	@@ -3776,6 +3828,8 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("Strength power when calculating disparity error", this.taDiffPwr, 6);		gd.addNumericField("Strength power when calculating disparity error", this.taDiffPwr, 6);
	gd.addNumericField("Strength power when calculating disparity error over best", this.taBestPwr, 6);		gd.addNumericField("Strength power when calculating disparity error over best", this.taBestPwr, 6);
	gd.addNumericField("Strength power when calculating disparity error for group of 9", this.taDiff9Pwr, 6);		gd.addNumericField("Strength power when calculating disparity error for group of 9", this.taDiff9Pwr, 6);
			gd.addNumericField("Gaussian sigma to blur color difference between tiles along each direction", this.taColSigma, 6);
			gd.addNumericField("Relative amount of the blurred color difference in the mixture", this.taColFraction, 6);

	gd.addNumericField("Cost of a tile that is not assigned", this.taCostEmpty, 6);		gd.addNumericField("Cost of a tile that is not assigned", this.taCostEmpty, 6);
	gd.addNumericField("Cost of a tile not having any neighbor in particular direction", this.taCostNoLink, 6);		gd.addNumericField("Cost of a tile not having any neighbor in particular direction", this.taCostNoLink, 6);
	@@ -3909,10 +3963,21 @@ public class EyesisCorrectionParameters {
	this.fine_corr_x_3= gd.getNextNumber();		this.fine_corr_x_3= gd.getNextNumber();
	this.fine_corr_y_3= gd.getNextNumber();		this.fine_corr_y_3= gd.getNextNumber();

	this.fcorr_min_stength= gd.getNextNumber();		this.fcorr_min_strength= gd.getNextNumber();
	this.fcorr_disp_diff= gd.getNextNumber();		this.fcorr_disp_diff= gd.getNextNumber();
	this.fcorr_quadratic= gd.getNextBoolean();		this.fcorr_quadratic= gd.getNextBoolean();
	this.fcorr_ignore= gd.getNextBoolean();		this.fcorr_ignore= gd.getNextBoolean();

			this.fcorr_inf_strength= gd.getNextNumber();
			this.fcorr_inf_diff= gd.getNextNumber();
			this.fcorr_inf_quad= gd.getNextBoolean();
			this.fcorr_inf_vert= gd.getNextBoolean();

			this.fcorr_sample_size= (int)gd.getNextNumber();
			this.fcorr_mintiles= (int) gd.getNextNumber();
			this.fcorr_reloutliers= gd.getNextNumber();
			this.fcorr_sigma= gd.getNextNumber();

	this.corr_magic_scale= gd.getNextNumber();		this.corr_magic_scale= gd.getNextNumber();

	this.show_textures= gd.getNextBoolean();		this.show_textures= gd.getNextBoolean();
	@@ -4240,6 +4305,9 @@ public class EyesisCorrectionParameters {
	this.taDiffPwr= gd.getNextNumber();		this.taDiffPwr= gd.getNextNumber();
	this.taBestPwr= gd.getNextNumber();		this.taBestPwr= gd.getNextNumber();
	this.taDiff9Pwr= gd.getNextNumber();		this.taDiff9Pwr= gd.getNextNumber();
			this.taColSigma= gd.getNextNumber();
			this.taColFraction= gd.getNextNumber();


	this.taCostEmpty= gd.getNextNumber();		this.taCostEmpty= gd.getNextNumber();
	this.taCostNoLink= gd.getNextNumber();		this.taCostNoLink= gd.getNextNumber();
	@@ -4335,6 +4403,8 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("Strength power when calculating disparity error", this.taDiffPwr, 6);		gd.addNumericField("Strength power when calculating disparity error", this.taDiffPwr, 6);
	gd.addNumericField("Strength power when calculating disparity error over best", this.taBestPwr, 6);		gd.addNumericField("Strength power when calculating disparity error over best", this.taBestPwr, 6);
	gd.addNumericField("Strength power when calculating disparity error for group of 9", this.taDiff9Pwr, 6);		gd.addNumericField("Strength power when calculating disparity error for group of 9", this.taDiff9Pwr, 6);
			gd.addNumericField("Gaussian sigma to blur color difference between tiles along each direction", this.taColSigma, 6);
			gd.addNumericField("Relative amount of the blurred color difference in the mixture", this.taColFraction, 6);

	gd.addNumericField("Cost of a tile that is not assigned", this.taCostEmpty, 6);		gd.addNumericField("Cost of a tile that is not assigned", this.taCostEmpty, 6);
	gd.addNumericField("Cost of a tile not having any neighbor in particular direction", this.taCostNoLink, 6);		gd.addNumericField("Cost of a tile not having any neighbor in particular direction", this.taCostNoLink, 6);
	@@ -4411,6 +4481,8 @@ public class EyesisCorrectionParameters {
	this.taDiffPwr= gd.getNextNumber();		this.taDiffPwr= gd.getNextNumber();
	this.taBestPwr= gd.getNextNumber();		this.taBestPwr= gd.getNextNumber();
	this.taDiff9Pwr= gd.getNextNumber();		this.taDiff9Pwr= gd.getNextNumber();
			this.taColSigma= gd.getNextNumber();
			this.taColFraction= gd.getNextNumber();

	this.taCostEmpty= gd.getNextNumber();		this.taCostEmpty= gd.getNextNumber();
	this.taCostNoLink= gd.getNextNumber();		this.taCostNoLink= gd.getNextNumber();

src/main/java/Eyesis_Correction.java

+93 −32

Original line number	Original line	Diff line number	Diff line
	@@ -77,7 +77,9 @@ private Panel panel1,
	panelPostProcessing2,		panelPostProcessing2,
	panelPostProcessing3,		panelPostProcessing3,
	panelDct1,		panelDct1,
	panelClt1;		panelClt1,
			panelClt2
			;
	JP46_Reader_camera JP4_INSTANCE=null;		JP46_Reader_camera JP4_INSTANCE=null;

	// private deBayerScissors debayer_instance;		// private deBayerScissors debayer_instance;
	@@ -368,7 +370,7 @@ private Panel panel1,

	instance = this;		instance = this;
	addKeyListener(IJ.getInstance());		addKeyListener(IJ.getInstance());
	int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?2:0);		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?3:0);
	setLayout(new GridLayout(menuRows, 1));		setLayout(new GridLayout(menuRows, 1));

	panel6 = new Panel();		panel6 = new Panel();
	@@ -488,7 +490,7 @@ private Panel panel1,
	if (DCT_MODE) {		if (DCT_MODE) {
	panelClt1 = new Panel();		panelClt1 = new Panel();
	panelClt1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap		panelClt1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
	addButton("Setup CLT parameters", panelClt1, color_configure);		// addButton("Setup CLT parameters", panelClt1, color_configure);
	addButton("Select CLT image", panelClt1, color_configure);		addButton("Select CLT image", panelClt1, color_configure);
	addButton("CLT stack", panelClt1, color_process);		addButton("CLT stack", panelClt1, color_process);
	addButton("Select second CLT image", panelClt1, color_configure);		addButton("Select second CLT image", panelClt1, color_configure);
	@@ -499,19 +501,48 @@ private Panel panel1,
	addButton("CLT process files", panelClt1, color_process);		addButton("CLT process files", panelClt1, color_process);
	addButton("CLT process sets", panelClt1, color_process);		addButton("CLT process sets", panelClt1, color_process);
	addButton("CLT process quads", panelClt1, color_process);		addButton("CLT process quads", panelClt1, color_process);
	addButton("CLT process corr", panelClt1, color_conf_process);		// addButton("CLT process corr", panelClt1, color_conf_process);
	addButton("CLT disparity scan", panelClt1, color_conf_process);		// addButton("CLT disparity scan", panelClt1, color_conf_process);
	addButton("CLT reset fine corr", panelClt1, color_stop);		// addButton("CLT reset fine corr", panelClt1, color_stop);
	addButton("CLT show fine corr", panelClt1, color_configure);		// addButton("CLT show fine corr", panelClt1, color_configure);
	addButton("CLT apply fine corr", panelClt1, color_process);		// addButton("CLT apply fine corr", panelClt1, color_process);
	addButton("CLT reset 3D", panelClt1, color_stop);		// addButton("CLT reset 3D", panelClt1, color_stop);
	addButton("CLT 3D", panelClt1, color_process);		// addButton("CLT 3D", panelClt1, color_process);
	addButton("CLT planes", panelClt1, color_conf_process);		// addButton("CLT planes", panelClt1, color_conf_process);
	addButton("CLT ASSIGN", panelClt1, color_process);		// addButton("CLT ASSIGN", panelClt1, color_process);
	addButton("CLT OUT 3D", panelClt1, color_process);		// addButton("CLT OUT 3D", panelClt1, color_process);

	add(panelClt1);		add(panelClt1);
	}		}
			if (DCT_MODE) {
			panelClt2 = new Panel();
			panelClt2.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
			addButton("Setup CLT parameters", panelClt2, color_configure);
			// addButton("Select CLT image", panelClt2, color_configure);
			// addButton("CLT stack", panelClt2, color_process);
			// addButton("Select second CLT image", panelClt2, color_configure);
			// addButton("CLT correlate", panelClt2, color_process);
			// addButton("Create CLT kernels", panelClt2, color_process);
			// addButton("Read CLT kernels", panelClt2, color_process);
			// addButton("Reset CLT kernels", panelClt2, color_stop);
			// addButton("CLT process files", panelClt2, color_process);
			// addButton("CLT process sets", panelClt2, color_process);
			// addButton("CLT process quads", panelClt2, color_process);
			addButton("CLT process corr", panelClt2, color_conf_process);
			addButton("CLT disparity scan", panelClt2, color_conf_process);
			addButton("CLT reset fine corr", panelClt2, color_stop);
			addButton("CLT show fine corr", panelClt2, color_configure);
			addButton("CLT apply fine corr", panelClt2, color_process);
			addButton("CLT test fine corr", panelClt2, color_process);
			addButton("CLT process fine corr", panelClt2, color_conf_process);
			addButton("CLT reset 3D", panelClt2, color_stop);
			addButton("CLT 3D", panelClt2, color_process);
			addButton("CLT planes", panelClt2, color_conf_process);
			addButton("CLT ASSIGN", panelClt2, color_process);
			addButton("CLT OUT 3D", panelClt2, color_process);

			add(panelClt2);
			}
	pack();		pack();

	GUI.center(this);		GUI.center(this);
	@@ -2888,7 +2919,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -3490,7 +3521,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -3556,7 +3587,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -3606,7 +3637,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4082,7 +4113,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4132,7 +4163,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4187,7 +4218,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4273,7 +4304,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4368,7 +4399,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4465,7 +4496,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4562,6 +4593,24 @@ private Panel panel1,
	QUAD_CLT.show_fine_corr();		QUAD_CLT.show_fine_corr();
	return;		return;

			} else if (label.equals("CLT process fine corr") \|\| label.equals("CLT test fine corr")) {
			boolean dry_run = label.equals("CLT test fine corr");
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if (QUAD_CLT == null){
			QUAD_CLT = new QuadCLT (
			PROPERTIES,
			EYESIS_CORRECTIONS,
			CORRECTION_PARAMETERS);
			if (DEBUG_LEVEL > 0){
			System.out.println("Created new QuadCLT instance, will need to read CLT kernels");
			}
			}
			QUAD_CLT.process_fine_corr(
			dry_run, // boolean dry_run
			CLT_PARAMETERS,
			DEBUG_LEVEL);
			return;

	} else if (label.equals("CLT disparity scan")) {		} else if (label.equals("CLT disparity scan")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	@@ -4585,7 +4634,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4697,7 +4746,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -4823,7 +4872,7 @@ private Panel panel1,
	IJ.showMessage("Warning",msg);		IJ.showMessage("Warning",msg);
	return;		return;
	}		}
	configPath+=Prefs.getFileSeparator()+"autoconfig";		configPath+=Prefs.getFileSeparator()+"autoconfig"+Prefs.getFileSeparator()+"autoconfig";
	try {		try {
	saveTimestampedProperties(		saveTimestampedProperties(
	configPath, // full path or null		configPath, // full path or null
	@@ -5396,9 +5445,21 @@ private Panel panel1,
	try {		try {
	os = new FileOutputStream(path);		os = new FileOutputStream(path);
	} catch (FileNotFoundException e1) {		} catch (FileNotFoundException e1) {
			// missing config directory
			File dir = (new File(path)).getParentFile();
			if (!dir.exists()){
			dir.mkdirs();
			try {
			os = new FileOutputStream(path);
			} catch (FileNotFoundException e2) {
			IJ.showMessage("Error","Failed to create directory "+dir.getName()+" to save configuration file: "+path);
			return;
			}
			} else {
	IJ.showMessage("Error","Failed to open configuration file: "+path);		IJ.showMessage("Error","Failed to open configuration file: "+path);
	return;		return;
	}		}
			}
	if (useXML) {		if (useXML) {
	try {		try {
	properties.storeToXML(os,		properties.storeToXML(os,

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