implementing non-radial corrections to lens polynomial model

src/main/java/Aberration_Calibration.java

@@ -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

@@ -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"));
@@ -1589,8 +1625,12 @@ import org.apache.commons.configuration.XMLConfiguration;
         		for (int j=0;j<this.parameterDescriptions.length;j++){
         			if (sub.getString(parameterDescriptions[j][0])!=null)
         				this.pars[i][j] = Double.parseDouble(sub.getString(parameterDescriptions[j][0]));
-        			else 
-        				this.pars[i][j] = Double.NaN;
+        			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){

src/main/java/EyesisSubCameraParameters.java

@@ -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){
@@ -175,9 +217,19 @@ 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;
+				this.channelWeightCurrent=this.channelWeightDefault;
 			}
     	}
     	public void setChannelWeightCurrent(
@@ -190,5 +242,4 @@ import java.util.Properties;
     	public double getChannelWeightDefault(){
     		return this.channelWeightDefault;
     	}
-
     }

src/main/java/FittingStrategy.java

@@ -422,6 +422,34 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 			this.pathName=pathname;
         	return true;
         }
+        public int findLastValidSeries(int numSeries){
+        	for (;numSeries>=0;numSeries--) if (isSeriesValid(numSeries)) return numSeries;
+        	return -1; // none valid
+        }
+        public boolean copySeries(int sourceSeries, int numSeries){
+     		if (isSeriesValid(sourceSeries)){
+    				invalidateSelectedImages(numSeries); // just in case -= will be recalculated
+    				for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
+    					this.selectedImages[numSeries][i]=this.selectedImages[sourceSeries][i]; // copy for all, not only enabled
+    				}
+    				for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i]){
+    					this.parameterMode[numSeries][i]=this.parameterMode[sourceSeries][i];
+    					this.parameterGroups[numSeries][i]=(this.parameterGroups[sourceSeries][i]==null)?null:this.parameterGroups[sourceSeries][i].clone();
+    				}
+    				this.masterImages[numSeries]=this.masterImages[sourceSeries];
+    				this.lambdas[numSeries]=this.lambdas[sourceSeries];
+    				this.stepDone[numSeries]=this.stepDone[sourceSeries];
+    				this.stopAfterThis[numSeries]=this.stopAfterThis[sourceSeries];
+    				this.varianceModes[numSeries]=this.varianceModes[sourceSeries];
+    				this.zGroups[numSeries]=(this.zGroups[sourceSeries]!=null)?this.zGroups[sourceSeries].clone():null;
+    				return true;
+    		} else {
+    			return false;
+    		}
+        }
+        
+        
+        
         /**
          * Verifies that series exists and is not empty (valid for LMA)
          * @param num - series to verify
@@ -1406,31 +1434,13 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     			sNumNewEnabledPerStation+=numNewEnabledPerStation[i];
     		}
      		if (!isSeriesValid(numSeries)){
-    			int sourceSeries=-1;
-    			for (int i=numSeries-1;i>=0;i--) if (isSeriesValid(i)){
-    				sourceSeries=i;
-    				break;
-    			}
-    			if (sourceSeries>=0){
-    				invalidateSelectedImages(numSeries); // just in case -= will be recalculated
-    				for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
-    					this.selectedImages[numSeries][i]=this.selectedImages[sourceSeries][i]; // copy for all, not only enabled
-    				}
-    				for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i]){
-    					this.parameterMode[numSeries][i]=this.parameterMode[sourceSeries][i];
-    					this.parameterGroups[numSeries][i]=(this.parameterGroups[sourceSeries][i]==null)?null:this.parameterGroups[sourceSeries][i].clone();
-    				}
-    				this.masterImages[numSeries]=this.masterImages[sourceSeries];
-    				this.lambdas[numSeries]=this.lambdas[sourceSeries];
-    				this.stepDone[numSeries]=this.stepDone[sourceSeries];
-    				this.stopAfterThis[numSeries]=this.stopAfterThis[sourceSeries];
-    				this.varianceModes[numSeries]=this.varianceModes[sourceSeries];
-    				this.zGroups[numSeries]=(this.zGroups[sourceSeries]!=null)?this.zGroups[sourceSeries].clone():null;
-    			}
+    			int sourceSeries= findLastValidSeries(numSeries);
+    			if (sourceSeries>=0)  copySeries(sourceSeries, numSeries);
     		}
     		
 			GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+" number of enabled images="+this.distortionCalibrationData.getNumEnabled());
-			gd.addCheckbox("Copy all from previous series (ignore all other fields)", false);
+			gd.addCheckbox("Copy all from the series below, ignore all other fields", false);
+			gd.addNumericField("Source series to copy from", (numSeries>0)?(numSeries-1):(numSeries+1), 0, 3, "");
 			gd.addCheckbox("Remove all (but first) images, reopen dialog", false); // remove all will be invalid, copied from the previous
 			gd.addCheckbox("Select all images, reopen dialog", false);
 			if (numEstimated>0){
@@ -1571,6 +1581,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 			gd.showDialog();
 			if (gd.wasCanceled()) return -2;
 			boolean copyFromPrevious=gd.getNextBoolean();
+			int sourceStrategy= (int) gd.getNextNumber();
 			boolean removeAllImages=gd.getNextBoolean();
 			boolean selectAllImages=gd.getNextBoolean();
 			boolean selectEstimated=false;
@@ -1595,7 +1606,17 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 				return numSeries; // caller will repeat with the same series
 			}
 			
-			if (copyFromPrevious || removeAllImages || selectAllImages) {
+			if (copyFromPrevious){
+    			int sourceSeries= findLastValidSeries(sourceStrategy);
+    			if (sourceSeries>=0) {
+    				copySeries(sourceSeries, numSeries);
+    			} else {
+    				System.out.println("Could not copy from invalid series "+sourceSeries);
+    			}
+				return numSeries; // caller will repeat with the same series
+			}
+			if (removeAllImages || selectAllImages) {
+//				
 				for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
 //					this.selectedImages[numSeries][i]=false; // invalidate - all, regardless of .enabled
 					this.selectedImages[numSeries][i]=selectAllImages || ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled
@@ -1777,7 +1798,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 
 		}
     	public boolean selectStrategy(int startSerNumber){
-    		int defaultLength=20;
+    		int defaultLength=30;
     		boolean selectImages=    false;
     		boolean allImages=       false;
     		boolean selectParameters=true;