fixing projected grid used for aberrations kernels generation

src/main/java/Aberration_Calibration.java

@@ -1094,6 +1094,7 @@ if (MORE_BUTTONS) {
 	    	boolean noAuto=label.equals("Restore no autoload");
 	    	ABERRATIONS_PARAMETERS.autoRestore=false;
 	    	loadProperties(null,PROCESS_PARAMETERS.kernelsDirectory,PROCESS_PARAMETERS.useXML, PROPERTIES);
+			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 	    	if (ABERRATIONS_PARAMETERS.autoRestore && !noAuto){
 	    		if (DEBUG_LEVEL>0)System.out.println("Auto-loading configuration files");
 	    		if (LENS_DISTORTIONS==null) {
@@ -1141,6 +1142,27 @@ if (MORE_BUTTONS) {
 
 		    		
 		    	}
+				if (LENS_DISTORTIONS.fittingStrategy != null) { // trying to fix restore
+	    			if (DEBUG_LEVEL>0) System.out.println("LENS_DISTORTIONS.fittingStrategy != null -> Extra after loading");
+	    			int minGridsNoPointer=1000;
+	        		int [] numImages=DISTORTION_CALIBRATION_DATA.filterImages(
+	        				false, // resetHinted,
+	        				2, // minPointers,
+	        				0.4, // minGridPeriod,
+	        				true, // disableNoVignetting,
+	        				minGridsNoPointer); //minGridsNoPointer);
+	        		System.out.println("Number of enabled grid images: "+numImages[0]+
+	        				", of them new: "+numImages[1]+
+	        				", disabled without vignetting info: "+numImages[2]+
+	        				", disabled having less than "+minGridsNoPointer+" nodes and no matched pointers: "+numImages[3]);
+	    			
+		    		if (DISTORTION_CALIBRATION_DATA.gIS==null) {
+		    			int numImageSets=DISTORTION_CALIBRATION_DATA.buildImageSets(false); // from scratch
+		    			if (DEBUG_LEVEL>0) System.out.println("Image set was empty, built a new one with "+numImageSets+" image sets (\"panoramas\"): ");
+		    			DISTORTION_CALIBRATION_DATA.updateSetOrientation(null); // restore orientation from (enabled) image files
+		    			if (DEBUG_LEVEL>0) System.out.println("Setting sets orientation from per-grid image data");
+		    		}
+				}
 		    	restoreFocusingHistory(false);
 	    	}
 	    	return;

src/main/java/Distortions.java

@@ -3073,12 +3073,16 @@ For each point in the image
 				(this.fittingStrategy.distortionCalibrationData.gIS[imageSet]!=null)){
 			this.fittingStrategy.distortionCalibrationData.gIS[imageSet].updateParameterVectorFromSet(parVector);
 		}
-		int goniometerHorizontalIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getGoniometerHorizontalIndex();
-		int goniometerAxialIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getGoniometerAxialIndex();
+		if (!Double.isNaN(goniometerHorizontal)) {
+			int goniometerHorizontalIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getGoniometerHorizontalIndex();
+			parVector[goniometerHorizontalIndex]=goniometerHorizontal;
+		}
+		if (!Double.isNaN(goniometerAxial)) {
+			int goniometerAxialIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getGoniometerAxialIndex();
+			parVector[goniometerAxialIndex]=     goniometerAxial;
+		}
 		int sensorWidth=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(subCamera);
 		int sensorHeight=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(subCamera);
-		parVector[goniometerHorizontalIndex]=goniometerHorizontal;
-		parVector[goniometerAxialIndex]=     goniometerAxial;
 		System.out.println("estimateGridOnSensor(): subCamera="+subCamera+", goniometerHorizontal="+goniometerHorizontal+", goniometerAxial="+goniometerAxial);
 		calcInterParamers(
 				this.lensDistortionParameters, // 22-long parameter vector for the image

src/main/java/EyesisAberrations.java

@@ -1116,7 +1116,7 @@ public class EyesisAberrations {
     	} else if (debugLevel>2){
     		System.out.println("Skipping disabled image "+imgNum);
     	}
-    	if (debugLevel>0)System.out.println("Enabled "+numSelected+" source files ("+numDeselected+") were removed by channel selection");
+    	if (debugLevel>0)System.out.println("Enabled "+numSelected+" source files ("+numDeselected+") were removed by channel selection. partialToReprojected="+partialToReprojected);
 
     	String [] sourcePaths=new String [selectedImages.length];
     	// Set/verify source paths
@@ -1254,7 +1254,7 @@ public class EyesisAberrations {
         						Double.NaN, // goniometerAxial, - not used
         						distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getSetNumber(), //imageSet,
         						true); //filterBorder)
-        				hintTolerance=5.0; // TODO:set from configurable parameter
+        				hintTolerance=5.0; // TO DO:set from configurable parameter
         			}
         			
         			int rslt=matchSimulatedPattern.calculateDistortions(
@@ -2095,14 +2095,17 @@ public class EyesisAberrations {
 			PSFParameters psfParameters,
 			boolean [] correlationSizesUsed
 	){
-		int numDifferentFFT=0;
-		for (int i=0;i<correlationSizesUsed.length;i++) if (correlationSizesUsed[i]) {
-			numDifferentFFT++;
-		}
-		int [] corrSizes=new int [numDifferentFFT];
-		int index=0;
-		for (int i=0;i<correlationSizesUsed.length;i++) if (correlationSizesUsed[i]) {
-			corrSizes[index++]=1<<i;
+		int [] corrSizes={};
+		if (correlationSizesUsed!=null) {
+			int numDifferentFFT=0;
+			for (int i=0;i<correlationSizesUsed.length;i++) if (correlationSizesUsed[i]) {
+				numDifferentFFT++;
+			}
+			corrSizes=new int [numDifferentFFT];
+			int index=0;
+			for (int i=0;i<correlationSizesUsed.length;i++) if (correlationSizesUsed[i]) {
+				corrSizes[index++]=1<<i;
+			}
 		}
 		ImagePlus impPsf = new ImagePlus(path, stack);
 

src/main/java/MatchSimulatedPattern.java

@@ -7013,15 +7013,25 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         		   grid[v-minV][u-minU]=xy;
         	   }
         	   int numNewDefined=0;
+//        	   System.out.println("this.PATTERN_GRID.length="+this.PATTERN_GRID.length+"this.PATTERN_GRID[0.length="+this.PATTERN_GRID[0].length);
+//        	   System.out.println("this.targetUV.length="+this.targetUV.length+"this.targetUV[0.length="+this.targetUV[0].length);
         	   for (int v=0;v<this.PATTERN_GRID.length;v++) for (int u=0;u<this.PATTERN_GRID[v].length;u++) {
         		   double [][] cell=this.PATTERN_GRID[v][u];
         		   if ((cell !=null) && (cell.length>0) &&(cell[0] !=null) && (cell[0].length>1)){
-        			   cell[0][0]=grid[this.targetUV[v][u][1]+minV][this.targetUV[v][u][0]+minU][0];
-        			   cell[0][1]=grid[this.targetUV[v][u][1]+minV][this.targetUV[v][u][0]+minU][1];
-        			   if (Double.isNaN(cell[0][0]) || Double.isNaN(cell[0][1])){
-        				   this.PATTERN_GRID[v][u]=null; // make it undefined
+//                	   System.out.print("v="+v+" u="+u);
+        			   int tu=this.targetUV[v][u][0]-minU;
+        			   int tv=this.targetUV[v][u][1]-minV;
+//                	   System.out.println("  tv="+tv+" tu="+tu);
+        			   if ((tu>=0) && (tv>=0) && (tv<grid.length) && (tu<grid[tv].length) && (grid[tv][tu]!=null)) {
+        				   cell[0][0]=grid[tv][tu][0]; // -81 -.-1
+        				   cell[0][1]=grid[tv][tu][1];
+        				   if (Double.isNaN(cell[0][0]) || Double.isNaN(cell[0][1])){
+        					   this.PATTERN_GRID[v][u]=null; // make it undefined
+        				   } else {
+        					   numNewDefined++;
+        				   }
         			   } else {
-        				   numNewDefined++;
+        				   this.PATTERN_GRID[v][u]=null; // make it undefined
         			   }
         		   }
         	   }
@@ -7294,7 +7304,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         	   }
 // Now remove pointers that are not on white cells        	   
         	   
-        	   if (laserPointer.whiteOnly){
+        	   if ((laserPointer!=null) && laserPointer.whiteOnly){
         		   int numBad=0;
         		   for (int i=0;i<uv.length;i++) if (uv[i]!=null) {
         			   // Verify that laser spots are on the white cells (sum of uv is even)
@@ -7364,7 +7374,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         		   for (int i=0;i<uv.length;i++) if (uv[i]!=null) for (int j=i+1;j<uv.length;j++) if (uv[j]!=null) {
         			   pairMatch=false;
         			   allMatch=false;
-        			   diffUVTable[0]=(int) Math.round(laserPointer.laserUVMap[j][0]-laserPointer.laserUVMap[i][0]);
+        			   diffUVTable[0]=(int) Math.round(laserPointer.laserUVMap[j][0]-laserPointer.laserUVMap[i][0]); // should not get here if uv is {}
         			   diffUVTable[1]=(int) Math.round(laserPointer.laserUVMap[j][1]-laserPointer.laserUVMap[i][1]);
         			   diffUVMeas[0]= (int) Math.round(uv[j][0]-uv[i][0]);
         			   diffUVMeas[1]= (int) Math.round(uv[j][1]-uv[i][1]);
@@ -7450,7 +7460,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         		   }
         	   }
 //TODO: here at least some rotations match all points. If there ere more than two - try to use closest to the default/previous
-        	   int rotation=flipsToRot(laserPointer.swapUV,laserPointer.flipU,laserPointer.flipV);
+        	   int rotation=(laserPointer!=null)?(flipsToRot(laserPointer.swapUV,laserPointer.flipU,laserPointer.flipV)):0;
         	   if (!possibleRotations[rotation]) { // current rotation value defined by laserPointer.{swapUV,flipU,flipV} does not match
         		   // find a new one (first - without mirroring)
         		   for (int i=0; i<8;i++) if (possibleRotations[(((rotation ^ i) & 4)) | ((rotation+i) & 3)]) {
@@ -7466,12 +7476,14 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
             	   }
         	   }
 // now rotation is the correct one, update laserPointer.{swapUV,flipU,flipV};
-        	   laserPointer.swapUV=rotToFlips(rotation)[0];
-        	   laserPointer.flipU =rotToFlips(rotation)[1];
-        	   laserPointer.flipV =rotToFlips(rotation)[2];
+        	   if (laserPointer!=null){
+        		   laserPointer.swapUV=rotToFlips(rotation)[0];
+        		   laserPointer.flipU =rotToFlips(rotation)[1];
+        		   laserPointer.flipV =rotToFlips(rotation)[2];
+        	   }
 //calculate shift
         	   int [] uvShift=dfltShifts[rotation].clone(); //{0,0};
-        	   for (int i=0;i<uv.length;i++) if (uv[i]!=null) {
+        	   for (int i=0;i<uv.length;i++) if (uv[i]!=null) { // laserPointer -> uv=={}
         		   uvShift[0]=(int) Math.round(uv[i][0]-
         				   (rotations[rotation][0][0]*laserPointer.laserUVMap[i][0]+
         				    rotations[rotation][0][1]*laserPointer.laserUVMap[i][1]));
@@ -7480,6 +7492,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         				    rotations[rotation][1][1]*laserPointer.laserUVMap[i][1]));
         		   break;
         	   }
+        	   
 // Hinted shift will only be used if no laser pointers are available, otherwise - only verify/warn
         	   if (hintTranslateUV!=null) {
 //        		   if ((uv.length==0) || (numPointesLeft==0)){
@@ -7549,7 +7562,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         	   int numBad=0;
         	   double [] distUV=new double[2];
         	   double dist;
-        	   for (int i=0;i<uv.length;i++) if (uv[i]!=null) {
+        	   for (int i=0;i<uv.length;i++) if (uv[i]!=null) { //laserPointer == null > uv={}
         		// Verify that laser spots are inside specified distance from the cell centers        	   
         		   distUV[0]=reReMap[0][0]*uv[i][0]+reReMap[0][1]*uv[i][1]+reReMap[0][2]-laserPointer.laserUVMap[i][0];
         		   distUV[1]=reReMap[1][0]*uv[i][0]+reReMap[1][1]*uv[i][1]+reReMap[1][2]-laserPointer.laserUVMap[i][1];