Commit ada64adb authored by Andrey Filippov's avatar Andrey Filippov
Browse files

implementing non-radial corrections to lens polynomial model

parent ab077ab1

src/main/java/Aberration_Calibration.java

+3 −1
Original line number Diff line number Diff line
@@ -403,7 +403,9 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi 
    		2360,// double distance// distance from the lens input pupil to the pattern plane along the camera axis, mm 

    		1296.0, // double px0     // lens axis from sensor, horizontal, from left (pixels)

    		968.0, // double py0     // lens axis from sensor, vertical, from top (pixels)

    		true//  boolean flipVertical // acquired image is mirrored vertically (mirror used)

    		true, //  boolean flipVertical // acquired image is mirrored vertically (mirror used)

    		null, //  double [][] r_xy,

    		null  //  double [][] r_od

    		);

//    public static double [] defaultGoniometerPosition={0.0, 0.0, 2360};

    public static EyesisCameraParameters EYESIS_CAMERA_PARAMETERS=new EyesisCameraParameters(

src/main/java/DistortionCalibrationData.java

+45 −5
Original line number Diff line number Diff line
@@ -264,7 +264,7 @@ import org.apache.commons.configuration.XMLConfiguration; 
        	}

    	}

    	public class GridImageSet{

    		private int numPars=27;

    		private int numPars=53; // 27;

    		private int thisParsStartIndex=6;



    		public int         stationNumber=0; // changes when camera/goniometer is moved to new position
@@ -465,12 +465,48 @@ import org.apache.commons.configuration.XMLConfiguration; 
    			{"subcamDistortionA5",   "Distortion A5(r^5)","relative","S","I"},                                                              //23 (21)

    			{"subcamDistortionA",    "Distortion A (r^4)","relative","S","I"},                                                              //24 (22)

    			{"subcamDistortionB",    "Distortion B (r^3)","relative","S","I"},                                                              //25 (23)

    			{"subcamDistortionC",    "Distortion C (r^2)","relative","S","I"}                                                               //26 (24)

    			{"subcamDistortionC",    "Distortion C (r^2)","relative","S","I"},                                                               //26 (24)

    			

        		{"subcamElong_C_o",      "Orthogonal elongation for r^2","relative","S","I"},     // 27 39 (37)

        		{"subcamElong_C_d",      "Diagonal   elongation for r^2","relative","S","I"},     // 28 40 (38)



        		{"subcamEccen_B_x",      "Distortion center shift X for r^3","relative","S","I"}, // 29 27 (25)

        		{"subcamEccen_B_y",      "Distortion center shift Y for r^3","relative","S","I"}, // 30 28 (26)

        		{"subcamElong_B_o",      "Orthogonal elongation for r^3","relative","S","I"},     // 31 41 (39)

        		{"subcamElong_B_d",      "Diagonal   elongation for r^3","relative","S","I"},     // 32 42 (40)



        		{"subcamEccen_A_x",      "Distortion center shift X for r^4","relative","S","I"}, // 33 29 (27)

        		{"subcamEccen_A_y",      "Distortion center shift Y for r^4","relative","S","I"}, // 34 30 (28)

        		{"subcamElong_A_o",      "Orthogonal elongation for r^4","relative","S","I"},     // 35 43 (41)

        		{"subcamElong_A_d",      "Diagonal   elongation for r^4","relative","S","I"},     // 36 44 (42)



        		{"subcamEccen_A5_x",     "Distortion center shift X for r^5","relative","S","I"}, // 37 31 (29)

        		{"subcamEccen_A5_y",     "Distortion center shift Y for r^5","relative","S","I"}, // 38 32 (30)

        		{"subcamElong_A5_o",     "Orthogonal elongation for r^5","relative","S","I"},     // 39 45 (43)

        		{"subcamElong_A5_d",     "Diagonal   elongation for r^5","relative","S","I"},     // 40 46 (44)



        		{"subcamEccen_A6_x",     "Distortion center shift X for r^6","relative","S","I"}, // 41 33 (31)

        		{"subcamEccen_A6_y",     "Distortion center shift Y for r^6","relative","S","I"}, // 42 34 (32)

        		{"subcamElong_A6_o",     "Orthogonal elongation for r^6","relative","S","I"},     // 43 47 (45)

        		{"subcamElong_A6_d",     "Diagonal   elongation for r^6","relative","S","I"},     // 44 48 (46)



        		{"subcamEccen_A7_x",     "Distortion center shift X for r^7","relative","S","I"}, // 45 35 (33)

        		{"subcamEccen_A7_y",     "Distortion center shift Y for r^7","relative","S","I"}, // 46 36 (34)

        		{"subcamElong_A7_o",     "Orthogonal elongation for r^7","relative","S","I"},     // 47 49 (47)

        		{"subcamElong_A7_d",     "Diagonal   elongation for r^7","relative","S","I"},     // 48 50 (48)



        		{"subcamEccen_A8_x",     "Distortion center shift X for r^8","relative","S","I"}, // 49 37 (35)

        		{"subcamEccen_A8_y",     "Distortion center shift Y for r^8","relative","S","I"}, // 50 38 (36)

        		{"subcamElong_A8_o",     "Orthogonal elongation for r^8","relative","S","I"},     // 51 51 (49)

        		{"subcamElong_A8_d",     "Diagonal   elongation for r^8","relative","S","I"}      // 52 52 (50)

        };

        public String [] channelSuffixes={ // natural order (same as array indices, may be modified to camera/subcamera

        		"00","01","02","03","04","05","06","07","08","09",

        		"10","11","12","13","14","15","16","17","18","19",

        		"20","21","22","23","24","25","26","27","28","29"};

        public boolean isNonRadial(int index){

        	return parameterDescriptions[index][0].startsWith("subcamEccen_") || parameterDescriptions[index][0].startsWith("subcamElong_");

        }

        public int getParameterIndexByName(String name){

        	for (int i=0;i<this.parameterDescriptions.length;i++) if (this.parameterDescriptions[i][0].equals(name)){

        		return i;
@@ -1550,7 +1586,7 @@ import org.apache.commons.configuration.XMLConfiguration; 
                	int minIndex=       this.gIS[index].getMinIndex();

                	int maxIndexPlusOne=this.gIS[index].getMaxIndexPlusOne();

                	for (int j=minIndex;j<maxIndexPlusOne;j++) if (sub.getString(parameterDescriptions[j][0])!=null) {

                		this.gIS[index].setParameterValue(j,Double.parseDouble((sub.getString(parameterDescriptions[j][0]))), false);

                		this.gIS[index].setParameterValue(j,Double.parseDouble(sub.getString(parameterDescriptions[j][0])), false);

                	}

            		if (sub.getString("orientationEstimated")!=null) {

            			this.gIS[i].orientationEstimated=Boolean.parseBoolean(sub.getString("orientationEstimated"));
@@ -1590,9 +1626,13 @@ import org.apache.commons.configuration.XMLConfiguration; 
        			if (sub.getString(parameterDescriptions[j][0])!=null)

        				this.pars[i][j] = Double.parseDouble(sub.getString(parameterDescriptions[j][0]));

        			else

        				if (isNonRadial(j)){

        					this.pars[i][j] = 0.0; // old calibration files without non-radial parameters

        				} else {

        					this.pars[i][j] = Double.NaN;

        				}

        		}

        	}

        	if (this.gIS!=null){

            	System.out.println("Using stored image set data");

        		for (int is=0;is<this.gIS.length;is++){

src/main/java/Distortions.java

+65 −13
Original line number Diff line number Diff line
@@ -30,8 +30,10 @@ import ij.io.Opener; 
import ij.process.FloatProcessor;

import ij.process.ImageProcessor;

import ij.text.TextWindow;



import java.awt.Rectangle;

import java.awt.geom.Point2D;

import java.util.Arrays;

//import java.io.StringWriter;

import java.util.List;

import java.util.ArrayList;
@@ -3299,7 +3301,7 @@ For each point in the image 
		double [] vectorFX=new double[doubleNumAllPoints];

//		this.fX=new double[doubleNumAllPoints];

		if (this.debugLevel>2) {

			System.out.println("calculateFxAndJacobian(), calcJacobian="+calcJacobian);

			System.out.println("calculateFxAndJacobian(), calcJacobian="+calcJacobian+" D3304 + this.debugLevel="+this.debugLevel);

			if (vector!=null) {

			  for (int ii=0;ii<vector.length;ii++) System.out.println(ii+": "+vector[ii]);

			} else {
@@ -3331,8 +3333,9 @@ For each point in the image 
// and this.interParameterDerivatives

//			if (this.debugLevel>1) {

			if (this.debugLevel>2) {

				System.out.println("calculateFxAndJacobian(), imgNum="+imgNum+" calcInterParamers():");

				System.out.println("calculateFxAndJacobian(), imgNum="+imgNum+" calcInterParamers(): (D3336)");

			}

			this.lensDistortionParameters.debugLevel=this.debugLevel;

			this.lensDistortionParameters.lensCalcInterParamers(

					this.lensDistortionParameters,

					this.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.isTripod,
@@ -3359,7 +3362,7 @@ For each point in the image 
	    					IJ.d2s(targetXYZ[fullIndex][1],2)+","+

	    					IJ.d2s(targetXYZ[fullIndex][2],2)+" ("+calcJacobian+") -> "+

	    					IJ.d2s(derivatives15[0][0],2)+"/"+IJ.d2s(derivatives15[0][1],2));

	    			String all="derivatives15:";

	    			String all="derivatives15: D3365";

	    			for (int ii=0;ii<derivatives15.length;ii++) all+=" "+ii+":"+IJ.d2s(derivatives15[ii][0],3)+"/"+IJ.d2s(derivatives15[ii][1],3);

	    			System.out.println(all);

	    		}
@@ -3470,7 +3473,7 @@ For each point in the image 
						IJ.d2s(patternXYZ[fullIndex][1],2)+","+

						IJ.d2s(patternXYZ[fullIndex][2],2)+" ("+calcJacobian+") -> "+

						IJ.d2s(derivatives15[0][0],2)+"/"+IJ.d2s(derivatives15[0][1],2));

				String all="derivatives15:";

				String all="derivatives15: D3476";

				for (int ii=0;ii<derivatives15.length;ii++) all+=" "+ii+":"+IJ.d2s(derivatives15[ii][0],3)+"/"+IJ.d2s(derivatives15[ii][1],3);

				System.out.println(all);

			}
@@ -3557,7 +3560,7 @@ For each point in the image 
									IJ.d2s(targetXYZ[fullIndex][1],2)+","+

									IJ.d2s(targetXYZ[fullIndex][2],2)+" -> "+

									IJ.d2s(derivatives15[0][0],2)+"/"+IJ.d2s(derivatives15[0][1],2));

							String all="derivatives15:";

							String all="derivatives15: D3563";

							for (int ii=0;ii<derivatives15.length;ii++) all+=" "+ii+":"+IJ.d2s(derivatives15[ii][0],3)+"/"+IJ.d2s(derivatives15[ii][1],3);

							System.out.println(all);

						}
@@ -5916,6 +5919,14 @@ List calibration 
    	imp.setProperty("comment_entrancePupilForward",  "entrance pupil distance from the azimuth/radius/height, outwards in mm");

    	imp.setProperty("entrancePupilForward",  ""+entrancePupilForward); // currently global, decoders will use per-sensor

       	imp.setProperty("comment_defects", "Sensor hot/cold pixels list as x:y:difference");

		for (int i=0;i<subCam.r_xy.length;i++){

			imp.setProperty("r_xy_"+i+"_x",subCam.r_xy[i][0]+"");

			imp.setProperty("r_xy_"+i+"_y",subCam.r_xy[i][1]+"");

		}

		for (int i=0;i<subCam.r_od.length;i++){

			imp.setProperty("r_od_"+i+"_o",subCam.r_od[i][0]+"");

			imp.setProperty("r_od_"+i+"_d",subCam.r_od[i][1]+"");

		}

       	if (subCam.defectsXY!=null){

    		StringBuffer sb = new StringBuffer();

    		for (int i=0;i<subCam.defectsXY.length;i++){
@@ -6076,6 +6087,16 @@ List calibration 
        		subCam.defectsXY=null;

        		subCam.defectsDiff=null;

        	}

 // non-radial

        	subCam.setDefaultNonRadial();

			for (int i=0;i<subCam.r_xy.length;i++) {

				if (imp.getProperty("r_xy_"+i+"_x")  !=null) subCam.r_xy[i][0]= Double.parseDouble((String) imp.getProperty("r_xy_"+i+"_x"));

				if (imp.getProperty("r_xy_"+i+"_y")  !=null) subCam.r_xy[i][1]= Double.parseDouble((String) imp.getProperty("r_xy_"+i+"_y"));

			}

			for (int i=0;i<subCam.r_od.length;i++) {

				if (imp.getProperty("r_od_"+i+"_o")  !=null) subCam.r_od[i][0]= Double.parseDouble((String) imp.getProperty("r_od_"+i+"_o"));

				if (imp.getProperty("r_od_"+i+"_d")  !=null) subCam.r_od[i][1]= Double.parseDouble((String) imp.getProperty("r_od_"+i+"_d"));

			}

        }

        for (int imgNum=0;imgNum<fittingStrategy.distortionCalibrationData.getNumImages();imgNum++){

        	int imageSubCam=  fittingStrategy.distortionCalibrationData.getImageSubcamera(imgNum);
@@ -9289,7 +9310,7 @@ M * V = B 
			gd.addNumericField("Select parameter number (0.."+(parameterNames.length-1)+") from above", 0, 0);



	    }

		if (debugDerivatives) gd.addNumericField("Select delta to increment selected parameter", .01, 5);

		if (debugDerivatives) gd.addNumericField("Select delta to increment selected parameter", .001, 5);

		if (debugDerivatives) gd.addCheckbox("Show inter-parameter derivatives matrix", true);

	    gd.showDialog();

	    if (gd.wasCanceled()) return;
@@ -9304,7 +9325,7 @@ M * V = B 
	    String title;

	    if (useActualParameters) {

	    	this_currentfX=calculateFxAndJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)

	    	d_derivative=this.jacobian[selectedParameter].clone();

	    	d_derivative=this.jacobian[selectedParameter].clone(); //  wrong?

	    	if (debugDerivatives) {

	    		double[] modVector=this.currentVector.clone();

	    		modVector[selectedParameter]+=delta;
@@ -9354,13 +9375,17 @@ M * V = B 
	 * @return rms 

	 */

	public double showCompareDerivatives(int imgNumber, double [] d_derivative, double [] d_delta, boolean applySensorMask, String title ){

		String [] titlesDebug={"dX-derivative","dY-derivative","abs-derivative","diff-X (should be 0)","diff-Y (should be 0)","dX-delta/delta","dY-delta/delta"};

		String [] titlesDebug={"dX-derivative","dY-derivative","abs-derivative","diff-X (should be 0)","diff-Y (should be 0)","dX-delta/delta","dY-delta/delta","dX-delta","dY-delta"};

		String [] titlesNoDebug={"dX-derivative","dY-derivative","abs-derivative"};

		String [] titles= (d_delta==null)? titlesNoDebug:titlesDebug;

		double [] d_diff=new double [d_derivative.length];

		double [] r_diff=new double [d_derivative.length];

		double [] aDeriv=new double [d_derivative.length/2];

		

		if (d_delta!=null) for (int i=0;i<d_diff.length;i++) d_diff[i]=d_derivative[i]-d_delta[i];

		if (d_delta!=null) for (int i=0;i<d_diff.length;i++){

			d_diff[i]=d_derivative[i]-d_delta[i];

			r_diff[i]=d_diff[i]/d_delta[i];

		}

// find data range for the selected image

		int index=0;

		int numImg=fittingStrategy.distortionCalibrationData.getNumImages();
@@ -9396,8 +9421,10 @@ M * V = B 
			if (d_delta!=null) {

				imgData[3][vu]=   d_diff[2*(index+i)];

				imgData[4][vu]=   d_diff[2*(index+i)+1];

				imgData[5][vu]=   d_delta[2*(index+i)];

				imgData[6][vu]=   d_delta[2*(index+i)+1];

				imgData[5][vu]=   r_diff[2*(index+i)];

				imgData[6][vu]=   r_diff[2*(index+i)+1];

				imgData[7][vu]=   d_delta[2*(index+i)];

				imgData[8][vu]=   d_delta[2*(index+i)+1];

			}

		}

		this.SDFA_INSTANCE.showArrays(imgData, width, getGridHeight(),  true, title, titles);
@@ -9456,6 +9483,14 @@ M * V = B 
        	System.out.println("this.lensDistortionParameters.distortionA="+IJ.d2s(this.lensDistortionParameters.distortionA, 5));

        	System.out.println("this.lensDistortionParameters.distortionB="+IJ.d2s(this.lensDistortionParameters.distortionB, 5));

        	System.out.println("this.lensDistortionParameters.distortionC="+IJ.d2s(this.lensDistortionParameters.distortionC, 5));

        	for (int i=0;i<this.lensDistortionParameters.r_xy.length;i++){

            	System.out.println("this.lensDistortionParameters.r_xy["+i+"][0]="+IJ.d2s(this.lensDistortionParameters.r_xy[i][0], 5));

            	System.out.println("this.lensDistortionParameters.r_xy["+i+"][1]="+IJ.d2s(this.lensDistortionParameters.r_xy[i][1], 5));

        	}

        	for (int i=0;i<this.lensDistortionParameters.r_od.length;i++){

            	System.out.println("this.lensDistortionParameters.r_od["+i+"][0]="+IJ.d2s(this.lensDistortionParameters.r_od[i][0], 5));

            	System.out.println("this.lensDistortionParameters.r_od["+i+"][1]="+IJ.d2s(this.lensDistortionParameters.r_od[i][1], 5));

        	}

        }

        LensDistortionParameters ldp=this.lensDistortionParameters.clone();

//		public void setLensDistortionParameters(LensDistortionParameters ldp
@@ -9612,6 +9647,7 @@ M * V = B 
    		DistortionCalibrationData distortionCalibrationData,

    		EyesisCameraParameters eyesisCameraParameters

    ){

    	boolean resetParametersToZero=false;

    	boolean [] parameterMask= new boolean[distortionCalibrationData.getNumParameters()];

    	boolean [] channelMask=   new boolean[distortionCalibrationData.getNumSubCameras()];

    	boolean [] stationMask=   new boolean[distortionCalibrationData.getNumStations()];
@@ -9619,7 +9655,9 @@ M * V = B 
    	for (int i=0;i<channelMask.length;i++)   channelMask[i]=  true;

    	for (int i=0;i<stationMask.length;i++)   stationMask[i]=  true;

    	GenericDialog gd=new GenericDialog("Update (new) image settings from known data");

    	gd.addMessage("Select which individual image parameters to be updated from the camera parameters");

    	//

    	gd.addCheckbox("Reset selected parameters to zero (false - update from camera parameters)", resetParametersToZero);

    	gd.addMessage("Select which individual image parameters to be updated from the camera parameters (or reset to 0)");

    	for (int i=0;i<parameterMask.length;i++) gd.addCheckbox(i+": "+distortionCalibrationData.getParameterName(i), parameterMask[i]);

    	gd.addMessage("----------");

    	gd.addMessage("Select which channels (sub-cameras) to update");
@@ -9637,6 +9675,7 @@ M * V = B 
	    WindowTools.addScrollBars(gd);

    	gd.showDialog();

    	if (gd.wasCanceled()) return false;

    	resetParametersToZero=gd.getNextBoolean();

    	for (int i=0;i<parameterMask.length;i++) parameterMask[i]= gd.getNextBoolean();

    	for (int i=0;i<channelMask.length;i++)   channelMask[i]=   gd.getNextBoolean();

    	if (stationMask.length>1) {
@@ -9653,6 +9692,7 @@ M * V = B 
		

//		boolean updateDisabled=       gd.getNextBoolean();

    	updateImageSetFromCamera(

    			resetParametersToZero,

    			distortionCalibrationData,

    			eyesisCameraParameters,

    			parameterMask, //boolean [] parameterMask,
@@ -9741,6 +9781,7 @@ M * V = B 
    	}

    	

    	if (updateFromCamera) updateImageSetFromCamera(

    			false, //resetParametersToZero

    			distortionCalibrationData,

    			eyesisCameraParameters,

    			parameterMask, //boolean [] parameterMask,
@@ -9771,6 +9812,7 @@ M * V = B 
     * @param copyOrientation copy 2 goniometer angles, normally should be false

     */

    public void updateImageSetFromCamera(

    		boolean resetParametersToZero, // reset to 0 instead of camera parameters

    		DistortionCalibrationData distortionCalibrationData,

    		EyesisCameraParameters eyesisCameraParameters,

    		boolean [] parameterMask,
@@ -9785,7 +9827,17 @@ M * V = B 
    		if ((stationMask!=null) && !stationMask[stationNumber]) continue;

    		double [] oldVector=distortionCalibrationData.getParameters(i);

    		double [] newVector=eyesisCameraParameters.getParametersVector(stationNumber,subCam);

    		for (int j=0;j<oldVector.length;j++) if (parameterMask[j]) oldVector[j]=newVector[j];

    		for (int j=0;j<oldVector.length;j++) if (parameterMask[j]){

    			if (resetParametersToZero) newVector[j]=0.0;

    			oldVector[j]=newVector[j];

    		}

    		if (resetParametersToZero){

    			eyesisCameraParameters.setParametersVector(

    					newVector,

    					parameterMask,

    					stationNumber,

    					subCam);

    		}

    		distortionCalibrationData.setParameters(oldVector, i);

    		this.lensDistortionParameters.pixelSize=eyesisCameraParameters.getPixelSize(subCam);

    		this.lensDistortionParameters.distortionRadius=eyesisCameraParameters.getDistortionRadius(subCam);

src/main/java/EyesisCameraParameters.java

+136 −5

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/EyesisSubCameraParameters.java

+54 −3
Original line number Diff line number Diff line
@@ -47,6 +47,24 @@ import java.util.Properties; 
		public double channelWeightCurrent=1.0;

		public int [][] defectsXY=null; // pixel defects coordinates list (starting with worst)

		public double [] defectsDiff=null; // pixel defects value (diff from average of neighbors), matching defectsXY

		

		final private double [][] r_xy_dflt={{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0}}; // only 6, as for the first term delta x, delta y ==0  

		final private double [][] r_od_dflt=   {{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0},{0.0,0.0}}; // ortho

		

		public double [][] r_xy=null; // only 6, as for the first term delta x, delta y ==0  

		public double [][] r_od=null; // ortho

		/*

		 Modifying to accommodate for eccentricity of different terms (2 parameters per term) and elliptical shape (another 2 terms). When all are

		 zeroes, the old parameters are in effect:

				Rdist/R=A8*R^7+A7*R^6+A6*R^5+A5*R^4+A*R^3+B*R^2+C*R+(1-A6-A7-A6-A5-A-B-C)");

				Rdist/R=A8*R6^7+A7*R5^6+A6*R4^5+A5*R3^4+A*R2^3+B*R1^2+C*R0+(1-A6-A7-A6-A5-A-B-C)");

				R[i] depends on px,py and r_xy[i][], r_o[i] (positive - "landscape", negative - "portrait"), r_d (positive - along y=x, negative - along y=-x)

				R[i] = r0[i]*(1+  (r_od[i][0]*(y[i]**2-x[i]**2)+ 2*r_od[i][1]*x[i]*y[i])/r0[i]**2;

				r0[i]=sqrt(x[i]**2+y[2]**2)

				x[i]=pixel_x-px0-((i>0)?r_xy[i-1][0]:0) 

				y[i]=pixel_y-py0-((i>0)?r_xy[i-1][1]:0)

		*/		

		

    	public EyesisSubCameraParameters(

    			double azimuth, // azimuth of the lens entrance pupil center, degrees, clockwise looking from top

    			double radius,  // mm, distance from the rotation axis
@@ -66,6 +84,8 @@ import java.util.Properties; 
    			double distortionC, // r^2

    			double px0,           // center of the lens on the sensor, pixels

    			double py0,           // center of the lens on the sensor, pixels

				double [][] r_xy,     // eccentricity for b,a,a5,a6,a7,a8

				double [][] r_od,     // elongation for c,b,a,a5,a6,a7,a8

    			double channelWeightDefault

    	){

    		this.azimuth=azimuth;
@@ -86,6 +106,12 @@ import java.util.Properties; 
    		this.distortionC=distortionC; // r^2

    		this.px0=px0;

    		this.py0=py0;

			if (r_xy==null) r_xy=r_xy_dflt;

			if (r_od==null) r_od=r_od_dflt;

			this.r_xy=new double [r_xy.length][2];

			for (int i=0;i<r_xy.length;i++)this.r_xy[i]=r_xy[i].clone();

			this.r_od=new double [r_od.length][2];

			for (int i=0;i<r_od.length;i++)this.r_od[i]=r_od[i].clone();

    		this.channelWeightDefault=channelWeightDefault;

    		this.channelWeightCurrent=this.channelWeightDefault;

    		this.defectsXY=null; // pixel defects coordinates list (starting with worst)
@@ -113,10 +139,18 @@ import java.util.Properties; 
    	    		this.distortionC,

    	    		this.px0,

    	    		this.py0,

    				this.r_xy,

    				this.r_od,

    	    		this.channelWeightDefault

    				);

    	}



    	public void setDefaultNonRadial(){

			r_od=new double [r_od_dflt.length][2];

			for (int i=0;i<r_od.length;i++) r_od[i]=r_od_dflt[i].clone();

			r_xy=new double [r_xy_dflt.length][2];

			for (int i=0;i<r_xy.length;i++) r_xy[i]=r_xy_dflt[i].clone();

    	}

// TODO: add/restore new properties

    	public void setProperties(String prefix,Properties properties){

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

    		properties.setProperty(prefix+"radius",this.radius+"");
@@ -136,6 +170,14 @@ import java.util.Properties; 
			properties.setProperty(prefix+"distortionC",this.distortionC+"");

			properties.setProperty(prefix+"px0",this.px0+"");

			properties.setProperty(prefix+"py0",this.py0+"");

			for (int i=0;i<this.r_xy.length;i++){

				properties.setProperty(prefix+"r_xy_"+i+"_x",this.r_xy[i][0]+"");

				properties.setProperty(prefix+"r_xy_"+i+"_y",this.r_xy[i][1]+"");

			}

			for (int i=0;i<this.r_od.length;i++){

				properties.setProperty(prefix+"r_od_"+i+"_o",this.r_od[i][0]+"");

				properties.setProperty(prefix+"r_od_"+i+"_d",this.r_od[i][1]+"");

			}

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

    	}

    	public void getProperties(String prefix,Properties properties){
@@ -175,6 +217,16 @@ import java.util.Properties; 
				this.px0=Double.parseDouble(properties.getProperty(prefix+"px0"));

			if (properties.getProperty(prefix+"py0")!=null)

				this.py0=Double.parseDouble(properties.getProperty(prefix+"py0"));

			setDefaultNonRadial();

			for (int i=0;i<this.r_xy.length;i++){

				if (properties.getProperty(prefix+"r_xy_"+i+"_x")!=null) this.r_xy[i][0]=Double.parseDouble(properties.getProperty(prefix+"r_xy_"+i+"_x"));

				if (properties.getProperty(prefix+"r_xy_"+i+"_y")!=null) this.r_xy[i][1]=Double.parseDouble(properties.getProperty(prefix+"r_xy_"+i+"_y"));

			}

			for (int i=0;i<this.r_od.length;i++){

				if (properties.getProperty(prefix+"r_od_"+i+"_o")!=null) this.r_od[i][0]=Double.parseDouble(properties.getProperty(prefix+"r_od_"+i+"_o"));

				if (properties.getProperty(prefix+"r_od_"+i+"_d")!=null) this.r_od[i][1]=Double.parseDouble(properties.getProperty(prefix+"r_od_"+i+"_d"));

			}



			if (properties.getProperty(prefix+"channelWeightDefault")!=null) {

				this.channelWeightDefault=Double.parseDouble(properties.getProperty(prefix+"channelWeightDefault"));

				this.channelWeightCurrent=this.channelWeightDefault;
@@ -190,5 +242,4 @@ import java.util.Properties; 
    	public double getChannelWeightDefault(){

    		return this.channelWeightDefault;

    	}



    }