misalignment - converted to true rotations (b5d06bab) · Commits · Elphel / imagej-elphel

src/main/java/AlignmentCorrection.java

+50 −10

Original line number	Original line	Diff line number	Diff line
	@@ -612,11 +612,13 @@ public class AlignmentCorrection {
	mdata = new double [8][samples_list.size()][3];		mdata = new double [8][samples_list.size()][3];
	}		}
	int indx = 0;		int indx = 0;
			final Matrix [] corr_rots = qc.geometryCorrection.getCorrVector().getRotMatrices(); // get array of per-sensor rotation matrices
	for (Sample s: samples_list){		for (Sample s: samples_list){
	int tileX = s.tile % tilesX;		int tileX = s.tile % tilesX;
	int tileY = s.tile / tilesX;		int tileY = s.tile / tilesX;
	double centerX = tileX * qc.tp.getTileSize() + qc.tp.getTileSize()/2;// - shiftX;		double centerX = tileX * qc.tp.getTileSize() + qc.tp.getTileSize()/2;// - shiftX;
	double centerY = tileY * qc.tp.getTileSize() + qc.tp.getTileSize()/2;//- shiftY;		double centerY = tileY * qc.tp.getTileSize() + qc.tp.getTileSize()/2;//- shiftY;
			/*
	double [][] centersXY_disp = qc.geometryCorrection.getPortsCoordinates(		double [][] centersXY_disp = qc.geometryCorrection.getPortsCoordinates(
	centerX,		centerX,
	centerY,		centerY,
	@@ -625,6 +627,22 @@ public class AlignmentCorrection {
	centerX,		centerX,
	centerY,		centerY,
	0.0); // disparity		0.0); // disparity
			*/
			double [][] centersXY_disp = qc.geometryCorrection.getPortsCoordinatesAndDerivatives(
			corr_rots, // Matrix [] rots,
			null, // Matrix [][] deriv_rots,
			null, // double [][] pXYderiv, // if not null, should be double[8][]
			centerX,
			centerY,
			disp_strength[2 * s.series + 0][s.tile]/magic_coeff); // disparity
			double [][] centersXY_inf = qc.geometryCorrection.getPortsCoordinatesAndDerivatives(
			corr_rots, // Matrix [] rots,
			null, // Matrix [][] deriv_rots,
			null, // double [][] pXYderiv, // if not null, should be double[8][]
			centerX,
			centerY,
			0.0); // disparity

	for (int i = 0; i < centersXY_disp.length;i++){		for (int i = 0; i < centersXY_disp.length;i++){
	centersXY_disp[i][0] -= centersXY_inf[i][0];		centersXY_disp[i][0] -= centersXY_inf[i][0];
	centersXY_disp[i][1] -= centersXY_inf[i][1];		centersXY_disp[i][1] -= centersXY_inf[i][1];
	@@ -2077,7 +2095,7 @@ B = \|+dy0 -dy1 -2*dy3 \|
	qc.geometryCorrection, // GeometryCorrection geometryCorrection,		qc.geometryCorrection, // GeometryCorrection geometryCorrection,
	qc.geometryCorrection.getCorrVector(), // GeometryCorrection.CorrVector corr_vector,		qc.geometryCorrection.getCorrVector(), // GeometryCorrection.CorrVector corr_vector,
	old_new_rms, // double [] old_new_rms, // should be double[2]		old_new_rms, // double [] old_new_rms, // should be double[2]
	debugLevel); // 2); // 1); // int debugLevel)		2); // debugLevel); // 2); // 1); // int debugLevel)
	if (debugLevel > -1){		if (debugLevel > -1){
	System.out.println("Old extrinsic corrections:");		System.out.println("Old extrinsic corrections:");
	System.out.println(qc.geometryCorrection.getCorrVector().toString());		System.out.println(qc.geometryCorrection.getCorrVector().toString());
	@@ -2218,20 +2236,31 @@ B = \|+dy0 -dy1 -2*dy3 \|
	jt_dbg = new double [num_pars][2 * NUM_SENSORS * mismatch_list.size()];		jt_dbg = new double [num_pars][2 * NUM_SENSORS * mismatch_list.size()];
	}		}

			Matrix [] corr_rots = corr_vector.getRotMatrices(); // get array of per-sensor rotation matrices
			Matrix [][] deriv_rots = corr_vector.getRotDeriveMatrices();
	for (int indx = 0; indx<mismatch_list.size(); indx++){ // need indx value		for (int indx = 0; indx<mismatch_list.size(); indx++){ // need indx value
	Mismatch mm = mismatch_list.get(indx);		Mismatch mm = mismatch_list.get(indx);
	double [] pXY = mm.getPXY();		double [] pXY = mm.getPXY();
	double [][] deriv = new double [2 * NUM_SENSORS][];		double [][] deriv = new double [2 * NUM_SENSORS][];
	int dbg_index =dbg_index (pXY, dbg_decimate);		int dbg_index =dbg_index (pXY, dbg_decimate);
	// double [][] f =		// double [][] f =
	geometryCorrection.getPortsCoordinatesAndDerivatives(		/*
			geometryCorrection.getPortsCoordinatesAndDerivatives_old(
	corr_vector, // CorrVector corr_vector,		corr_vector, // CorrVector corr_vector,
	deriv, // boolean calc_deriv,		deriv, // boolean calc_deriv,
	pXY[0], // double px,		pXY[0], // double px,
	pXY[1], // double py,		pXY[1], // double py,
	mm.getDisparityMeas()); // getDisparityTask()); // double disparity)		mm.getDisparityMeas()); // getDisparityTask()); // double disparity)
	// convert to symmetrical coordianets		*/
			geometryCorrection.getPortsCoordinatesAndDerivatives(
			corr_rots, // Matrix [] rots,
			deriv_rots, // Matrix [][] deriv_rots,
			deriv, // boolean calc_deriv,
			pXY[0], // double px,
			pXY[1], // double py,
			mm.getDisparityMeas()); // getDisparityTask()); // double disparity)

			// convert to symmetrical coordinates

	double [][] jt_partial = corr_vector.getJtPartial(		double [][] jt_partial = corr_vector.getJtPartial(
	deriv, // double [][] port_coord_deriv,		deriv, // double [][] port_coord_deriv,
	@@ -2381,17 +2410,27 @@ B = \|+dy0 -dy1 -2*dy3 \|
	{		{
	double [][] dMismatch_dXY = (new Mismatch()).get_dMismatch_dXY(); // just a static array		double [][] dMismatch_dXY = (new Mismatch()).get_dMismatch_dXY(); // just a static array
	double [] mv = new double [2 * NUM_SENSORS * mismatch_list.size()];		double [] mv = new double [2 * NUM_SENSORS * mismatch_list.size()];
			Matrix [] corr_rots = corr_vector.getRotMatrices(); // get array of per-sensor rotation matrices
	for (int indx = 0; indx<mismatch_list.size(); indx++){ // need indx value		for (int indx = 0; indx<mismatch_list.size(); indx++){ // need indx value
	Mismatch mm = mismatch_list.get(indx);		Mismatch mm = mismatch_list.get(indx);
	double [] pXY = mm.getPXY();		double [] pXY = mm.getPXY();
	double [][] f = geometryCorrection.getPortsCoordinatesAndDerivatives( // 4x2		/*
			double [][] f = geometryCorrection.getPortsCoordinatesAndDerivatives_old( // 4x2
	corr_vector, // CorrVector corr_vector,		corr_vector, // CorrVector corr_vector,
	null, // boolean calc_deriv,		null, // boolean calc_deriv,
	pXY[0], // double px,		pXY[0], // double px,
	pXY[1], // double py,		pXY[1], // double py,
	mm.getDisparityMeas()); // getDisparityTask()); // double disparity)		mm.getDisparityMeas()); // getDisparityTask()); // double disparity)
	// convert to symmetrical coordianets		*/
			double [][] f = geometryCorrection.getPortsCoordinatesAndDerivatives( // 4x2
			corr_rots, // Matrix [] rots,
			null, // Matrix [][] deriv_rots,
			null, // boolean calc_deriv,
			pXY[0], // double px,
			pXY[1], // double py,
			mm.getDisparityMeas()); // getDisparityTask()); // double disparity)

			// convert to symmetrical coordinates
	// f is [4][2] array of port x,y coordinates - convert them to mv (linear array)		// f is [4][2] array of port x,y coordinates - convert them to mv (linear array)

	double [] mv_partial = new double [dMismatch_dXY.length];		double [] mv_partial = new double [dMismatch_dXY.length];
	@@ -2588,6 +2627,7 @@ B = \|+dy0 -dy1 -2*dy3 \|
	mismatch_list, // ArrayList<Mismatch> mismatch_list,		mismatch_list, // ArrayList<Mismatch> mismatch_list,
	geometryCorrection, // GeometryCorrection geometryCorrection,		geometryCorrection, // GeometryCorrection geometryCorrection,
	corr_vector, // GeometryCorrection.CorrVector corr_vector)		corr_vector, // GeometryCorrection.CorrVector corr_vector)
			// debugLevel); // int debugLevel)
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)

	// convert Jacobian outputs to symmetrical measurement vectors (last one is non-zero only if disparity should be adjusted)		// convert Jacobian outputs to symmetrical measurement vectors (last one is non-zero only if disparity should be adjusted)

src/main/java/EyesisCorrectionParameters.java

+41 −21

Original line number	Original line	Diff line number	Diff line
	@@ -114,13 +114,15 @@ public class EyesisCorrectionParameters {

	// CLT 3d batch parameters		// CLT 3d batch parameters

	public boolean clt_batch_4img = true; // Create a set of 4 images, usually for disparity = 0		public boolean clt_batch_apply_man = true; // Apply (and disable) manual pixel shift
	public boolean clt_batch_extrinsic = false; // Calibrate extrinsic parameters for each set		public boolean clt_batch_extrinsic = false; // Calibrate extrinsic parameters for each set
	public boolean clt_batch_poly = false; // Calculate fine polynomial correction for each set		public boolean clt_batch_poly = false; // Calculate fine polynomial correction for each set
			public boolean clt_batch_4img = true; // Create a set of 4 images, usually for disparity = 0
	public boolean clt_batch_explore = true; // 1-st step of 3d reconstruction - explore disparities for each tile		public boolean clt_batch_explore = true; // 1-st step of 3d reconstruction - explore disparities for each tile
	public boolean clt_batch_surf = true; // Create super-tile 2.5d surfaces		public boolean clt_batch_surf = true; // Create super-tile 2.5d surfaces
	public boolean clt_batch_assign = true; // Assign tiles to surfaces		public boolean clt_batch_assign = true; // Assign tiles to surfaces
	public boolean clt_batch_gen3d = true; // Generate 3d output: x3d and/or obj+mtl		public boolean clt_batch_gen3d = true; // Generate 3d output: x3d and/or obj+mtl
			public boolean clt_batch_dbg1 = true; // Generate debug images if a single set is selected



	@@ -215,13 +217,15 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"x3dDirectory", this.x3dDirectory);		properties.setProperty(prefix+"x3dDirectory", this.x3dDirectory);
	properties.setProperty(prefix+"use_x3d_subdirs", this.use_x3d_subdirs+"");		properties.setProperty(prefix+"use_x3d_subdirs", this.use_x3d_subdirs+"");

	properties.setProperty(prefix+"clt_batch_4img", this.clt_batch_4img+"");		properties.setProperty(prefix+"clt_batch_apply_man", this.clt_batch_apply_man+"");
	properties.setProperty(prefix+"clt_batch_extrinsic", this.clt_batch_extrinsic+"");		properties.setProperty(prefix+"clt_batch_extrinsic", this.clt_batch_extrinsic+"");
	properties.setProperty(prefix+"clt_batch_poly", this.clt_batch_poly+"");		properties.setProperty(prefix+"clt_batch_poly", this.clt_batch_poly+"");
			properties.setProperty(prefix+"clt_batch_4img", this.clt_batch_4img+"");
	properties.setProperty(prefix+"clt_batch_explore", this.clt_batch_explore+"");		properties.setProperty(prefix+"clt_batch_explore", this.clt_batch_explore+"");
	properties.setProperty(prefix+"clt_batch_surf", this.clt_batch_surf+"");		properties.setProperty(prefix+"clt_batch_surf", this.clt_batch_surf+"");
	properties.setProperty(prefix+"clt_batch_assign", this.clt_batch_assign+"");		properties.setProperty(prefix+"clt_batch_assign", this.clt_batch_assign+"");
	properties.setProperty(prefix+"clt_batch_gen3d", this.clt_batch_gen3d+"");		properties.setProperty(prefix+"clt_batch_gen3d", this.clt_batch_gen3d+"");
			properties.setProperty(prefix+"clt_batch_dbg1", this.clt_batch_dbg1+"");
	}		}

	public void getProperties(String prefix,Properties properties){		public void getProperties(String prefix,Properties properties){
	@@ -317,13 +321,15 @@ public class EyesisCorrectionParameters {

	if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean((String) properties.getProperty(prefix+"use_x3d_subdirs"));		if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean((String) properties.getProperty(prefix+"use_x3d_subdirs"));

	if (properties.getProperty(prefix+"clt_batch_4img")!= null) this.clt_batch_4img=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_4img"));		if (properties.getProperty(prefix+"clt_batch_apply_man")!= null) this.clt_batch_apply_man=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_apply_man"));
	if (properties.getProperty(prefix+"clt_batch_extrinsic")!= null) this.clt_batch_extrinsic=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_extrinsic"));		if (properties.getProperty(prefix+"clt_batch_extrinsic")!= null) this.clt_batch_extrinsic=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_extrinsic"));
	if (properties.getProperty(prefix+"clt_batch_poly")!= null) this.clt_batch_poly=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_poly"));		if (properties.getProperty(prefix+"clt_batch_poly")!= null) this.clt_batch_poly=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_poly"));
			if (properties.getProperty(prefix+"clt_batch_4img")!= null) this.clt_batch_4img=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_4img"));
	if (properties.getProperty(prefix+"clt_batch_explore")!= null) this.clt_batch_explore=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_explore"));		if (properties.getProperty(prefix+"clt_batch_explore")!= null) this.clt_batch_explore=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_explore"));
	if (properties.getProperty(prefix+"clt_batch_surf")!= null) this.clt_batch_surf=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_surf"));		if (properties.getProperty(prefix+"clt_batch_surf")!= null) this.clt_batch_surf=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_surf"));
	if (properties.getProperty(prefix+"clt_batch_assign")!= null) this.clt_batch_assign=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_assign"));		if (properties.getProperty(prefix+"clt_batch_assign")!= null) this.clt_batch_assign=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_assign"));
	if (properties.getProperty(prefix+"clt_batch_gen3d")!= null) this.clt_batch_gen3d=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_gen3d"));		if (properties.getProperty(prefix+"clt_batch_gen3d")!= null) this.clt_batch_gen3d=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_gen3d"));
			if (properties.getProperty(prefix+"clt_batch_dbg1")!= null) this.clt_batch_dbg1=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_dbg1"));
	}		}

	public boolean showDialog(String title) {		public boolean showDialog(String title) {
	@@ -536,13 +542,15 @@ public class EyesisCorrectionParameters {
	gd.addStringField("CLT symmetical kernel files", this.cltSuffix, 40); // 19		gd.addStringField("CLT symmetical kernel files", this.cltSuffix, 40); // 19

	gd.addMessage ("============ batch parameters ============");		gd.addMessage ("============ batch parameters ============");
	gd.addCheckbox ("Create a set of 4 images, usually for disparity = 0", this.clt_batch_4img); // 20		gd.addCheckbox ("Apply (and disable) manual pixel shift", this.clt_batch_apply_man); // 20
	gd.addCheckbox ("Calibrate extrinsic parameters for each set", this.clt_batch_extrinsic); // 21		gd.addCheckbox ("Calibrate extrinsic parameters for each set", this.clt_batch_extrinsic); // 21
	gd.addCheckbox ("Calculate fine polynomial correction for each set", this.clt_batch_poly); // 22		gd.addCheckbox ("Calculate fine polynomial correction for each set", this.clt_batch_poly); // 22
	gd.addCheckbox ("1-st step of 3d reconstruction - explore disparities for each tile", this.clt_batch_explore); // 23		gd.addCheckbox ("Create a set of 4 images, usually for disparity = 0", this.clt_batch_4img); // 23
	gd.addCheckbox ("Create super-tile 2.5d surfaces", this.clt_batch_surf); // 24		gd.addCheckbox ("1-st step of 3d reconstruction - explore disparities for each tile", this.clt_batch_explore); // 24
	gd.addCheckbox ("Assign tiles to surfaces", this.clt_batch_assign); // 25		gd.addCheckbox ("Create super-tile 2.5d surfaces", this.clt_batch_surf); // 25
	gd.addCheckbox ("Generate 3d output: x3d and/or obj+mtl", this.clt_batch_gen3d); // 26		gd.addCheckbox ("Assign tiles to surfaces", this.clt_batch_assign); // 26
			gd.addCheckbox ("Generate 3d output: x3d and/or obj+mtl", this.clt_batch_gen3d); // 27
			gd.addCheckbox ("Generate debug images if a single set is selected", this.clt_batch_dbg1); // 28


	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	@@ -567,13 +575,15 @@ public class EyesisCorrectionParameters {
	this.cltKernelPrefix= gd.getNextString(); // 18		this.cltKernelPrefix= gd.getNextString(); // 18
	this.cltSuffix= gd.getNextString(); // 19		this.cltSuffix= gd.getNextString(); // 19

	this.clt_batch_4img= gd.getNextBoolean(); // 20		this.clt_batch_apply_man= gd.getNextBoolean(); // 20
	this.clt_batch_extrinsic= gd.getNextBoolean(); // 21		this.clt_batch_extrinsic= gd.getNextBoolean(); // 21
	this.clt_batch_poly= gd.getNextBoolean(); // 22		this.clt_batch_poly= gd.getNextBoolean(); // 22
	this.clt_batch_explore= gd.getNextBoolean(); // 23		this.clt_batch_4img= gd.getNextBoolean(); // 23
	this.clt_batch_surf= gd.getNextBoolean(); // 24		this.clt_batch_explore= gd.getNextBoolean(); // 24
	this.clt_batch_assign= gd.getNextBoolean(); // 25		this.clt_batch_surf= gd.getNextBoolean(); // 25
	this.clt_batch_gen3d= gd.getNextBoolean(); // 26		this.clt_batch_assign= gd.getNextBoolean(); // 26
			this.clt_batch_gen3d= gd.getNextBoolean(); // 27
			this.clt_batch_dbg1= gd.getNextBoolean(); // 28
	return true;		return true;
	}		}

	@@ -2131,6 +2141,8 @@ public class EyesisCorrectionParameters {
	public double fine_corr_y_2 = 0.0; // additionally shift image in port 2 in y direction		public double fine_corr_y_2 = 0.0; // additionally shift image in port 2 in y direction
	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 boolean fine_corr_ignore = false; // Ignore manual pixel correction
			public boolean fine_corr_apply = true; // Apply and set to ignore manual pixel correction after extrinsics correction

	public double fcorr_radius = 0.75 ; // Do not try to correct outside this fraction of width/hight		public double fcorr_radius = 0.75 ; // Do not try to correct outside this fraction of width/hight
	public double fcorr_min_strength = 0.15 ; // 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
	@@ -2786,6 +2798,8 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"fine_corr_y_2", this.fine_corr_y_2 +"");		properties.setProperty(prefix+"fine_corr_y_2", this.fine_corr_y_2 +"");
	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+"fine_corr_ignore", this.fine_corr_ignore+"");
			properties.setProperty(prefix+"fine_corr_apply", this.fine_corr_apply+"");

	properties.setProperty(prefix+"fcorr_radius", this.fcorr_radius +"");		properties.setProperty(prefix+"fcorr_radius", this.fcorr_radius +"");
	properties.setProperty(prefix+"fcorr_min_strength",this.fcorr_min_strength +"");		properties.setProperty(prefix+"fcorr_min_strength",this.fcorr_min_strength +"");
	@@ -3385,6 +3399,8 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"fine_corr_y_2")!=null) this.fine_corr_y_2=Double.parseDouble(properties.getProperty(prefix+"fine_corr_y_2"));		if (properties.getProperty(prefix+"fine_corr_y_2")!=null) this.fine_corr_y_2=Double.parseDouble(properties.getProperty(prefix+"fine_corr_y_2"));
	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+"fine_corr_ignore")!=null) this.fine_corr_ignore=Boolean.parseBoolean(properties.getProperty(prefix+"fine_corr_ignore"));
			if (properties.getProperty(prefix+"fine_corr_apply")!=null) this.fine_corr_apply=Boolean.parseBoolean(properties.getProperty(prefix+"fine_corr_apply"));

	if (properties.getProperty(prefix+"fcorr_radius")!=null) this.fcorr_radius=Double.parseDouble(properties.getProperty(prefix+"fcorr_radius"));		if (properties.getProperty(prefix+"fcorr_radius")!=null) this.fcorr_radius=Double.parseDouble(properties.getProperty(prefix+"fcorr_radius"));
	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_min_strength")!=null) this.fcorr_min_strength=Double.parseDouble(properties.getProperty(prefix+"fcorr_min_strength"));
	@@ -4000,7 +4016,9 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("X 2", this.fine_corr_x_2, 3);		gd.addNumericField("X 2", this.fine_corr_x_2, 3);
	gd.addNumericField("Y 2", this.fine_corr_y_2, 3);		gd.addNumericField("Y 2", this.fine_corr_y_2, 3);
	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 3", this.fine_corr_y_3, 3);
			gd.addCheckbox ("Ignore manual pixel correction (set/reset automatically if enabled below)", this.fine_corr_ignore);
			gd.addCheckbox ("Apply and set to ignore manual pixel correction after extrinsics correction", this.fine_corr_apply);

	gd.addNumericField("fcorr_radius", this.fcorr_radius, 3);		gd.addNumericField("fcorr_radius", this.fcorr_radius, 3);
	gd.addNumericField("Do not try to correct outside this fraction of width/hight", this.fcorr_min_strength,3);		gd.addNumericField("Do not try to correct outside this fraction of width/hight", this.fcorr_min_strength,3);
	@@ -4647,6 +4665,8 @@ public class EyesisCorrectionParameters {
	this.fine_corr_y_2= gd.getNextNumber();		this.fine_corr_y_2= gd.getNextNumber();
	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.fine_corr_ignore= gd.getNextBoolean();
			this.fine_corr_apply= gd.getNextBoolean();

	this.fcorr_radius= gd.getNextNumber();		this.fcorr_radius= gd.getNextNumber();
	this.fcorr_min_strength= gd.getNextNumber();		this.fcorr_min_strength= gd.getNextNumber();

src/main/java/EyesisCorrections.java

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -2327,7 +2327,7 @@ public class EyesisCorrections {
	saveAndShowEnable( imp, correctionsParameters , true, true);		saveAndShowEnable( imp, correctionsParameters , true, true);
	}		}

	private void saveAndShowEnable(		public void saveAndShowEnable(
	ImagePlus imp,		ImagePlus imp,
	EyesisCorrectionParameters.CorrectionParameters correctionsParameters,		EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
	boolean enableSave,		boolean enableSave,

src/main/java/Eyesis_Correction.java

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -542,8 +542,8 @@ private Panel panel1,
	if (DCT_MODE) {		if (DCT_MODE) {
	panelClt3 = new Panel();		panelClt3 = new Panel();
	panelClt3.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap		panelClt3.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
	addButton("Setup CLT Batch parameters", panelClt3, color_configure);
	addButton("Setup CLT parameters", panelClt3, color_configure);		addButton("Setup CLT parameters", panelClt3, color_configure);
			addButton("Setup CLT Batch parameters", panelClt3, color_configure);
	addButton("CLT batch process", panelClt3, color_process);		addButton("CLT batch process", panelClt3, color_process);
	add(panelClt3);		add(panelClt3);
	}		}
	@@ -4604,7 +4604,7 @@ private Panel panel1,
	System.out.println("Created new QuadCLT instance, will need to read CLT kernels");		System.out.println("Created new QuadCLT instance, will need to read CLT kernels");
	}		}
	}		}
	QUAD_CLT.resetExtrinsicCorr();		QUAD_CLT.resetExtrinsicCorr(CLT_PARAMETERS);
	return;		return;
	} else if (label.equals("CLT show fine corr")) {		} else if (label.equals("CLT show fine corr")) {
	if (QUAD_CLT == null){		if (QUAD_CLT == null){

src/main/java/GeometryCorrection.java

+410 −36

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