debugging partial kernel generation

src/main/java/Aberration_Calibration.java

@@ -619,6 +619,8 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
 		addButton("Conf. Multifile",panelConf1,color_configure);
 		addButton("Conf. Simulation",panelConf1);
 		addButton("Conf. Pattern Detection",panelConf1);
+		addButton("Waves",panelConf1);
+		//WavePatternGenerator
 		add(panelConf1);
 
 		panelConf2 = new Panel();
@@ -1048,6 +1050,11 @@ if (MORE_BUTTONS) {
 		} else if (label.equals("Conf. Pattern Detection")) {
 			showPatternDetectParametersDialog(PATTERN_DETECT);
 			return;
+/* ======================================================================== */
+		} else if (label.equals("Waves")) {
+			WavePatternGenerator wpg=new WavePatternGenerator();
+			while(wpg.selectAndGenerate());
+			return;
 /* ======================================================================== */
 		} else if (label.equals("Conf. PSF")) {
 			showPSFParametersDialog(PSF_PARS);

src/main/java/FittingStrategy.java

@@ -1798,12 +1798,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 	    			500)) return -1; //perPage))
     		case 6: // start from current selection
     			selection=selected.clone();
+    			break;
     		case 5: // start from empty selection
     			if (!selectImageSets(
     	    			selection,
     	    			false, // allImages,
     	    			0, // star iIndex
     	    			500)) return -1; //perPage))
+    			break;
     		}
 			for (int i=0;i<selection.length;i++) selection[i] &= requiredMatchedPointers[mapMP.get(new Integer(matchedPointers[i]))]; 
 			for (int i=0;i<selection.length;i++) selection[i] &= requiredHintedMatch[mapHM.get(new Integer(hintedMatch[i]))]; 

src/main/java/MatchSimulatedPattern.java

@@ -5770,7 +5770,8 @@ public class MatchSimulatedPattern {
 			   double [] xyc={
 					   this.PATTERN_GRID[v][u][0][0],
 					   this.PATTERN_GRID[v][u][0][1],
-					   (this.gridContrastBrightness==null)?1.0:this.gridContrastBrightness[0][v][u]
+					   (this.PATTERN_GRID[v][u][0].length>2)?this.PATTERN_GRID[v][u][0][2]:
+					   ((this.gridContrastBrightness==null)?1.0:this.gridContrastBrightness[0][v][u])
 			   };
 			   return xyc; // this.PATTERN_GRID[uv[1]][uv[0]][0];
 		   }
@@ -5779,7 +5780,8 @@ public class MatchSimulatedPattern {
 			   double [] xyc={
 					   this.PATTERN_GRID[uv[1]][uv[0]][0][0],
 					   this.PATTERN_GRID[uv[1]][uv[0]][0][1],
-					   (this.gridContrastBrightness==null)?1.0:this.gridContrastBrightness[0][uv[1]][uv[0]]
+					   (this.PATTERN_GRID[uv[1]][uv[0]][0].length>2)?this.PATTERN_GRID[uv[1]][uv[0]][0][2]:
+					   ((this.gridContrastBrightness==null)?1.0:this.gridContrastBrightness[0][uv[1]][uv[0]])
 			   };
 			   return xyc; // this.PATTERN_GRID[uv[1]][uv[0]][0];
 		   }
@@ -6623,7 +6625,7 @@ public class MatchSimulatedPattern {
             * @return {{Au, Bu, Cu}.{Av, Bc, Cv}}; where Umeas=Au*Uhint+Bu*Vhint+Cu, Vmeas=Av*Uhint+Bv*Vhint+Cv
             */
            public double [][] calcGridMatchMatrix (double [][][] hintGrid, double searchAround){
-        	   double [][][] measuredUV=mapEstimatedToMeasured(hintGrid, searchAround);
+        	   double [][][] measuredUV=mapEstimatedToMeasured(hintGrid, searchAround); // contrast - minimal of the ones around
         	   if (this.debugLevel>2){
         		   double [][] pixels=new double[9][measuredUV.length*measuredUV[0].length];
         		   int index=0;
@@ -7247,6 +7249,31 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         	   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);
+        	   if (this.debugLevel>0){
+            	   double [][] debugReplace=null;
+            	   String [] debugTiltes={"deltaX","deltaY","Contrast", "measX","measY", "targetU","targetV"};
+        		   debugReplace=new double[7][this.PATTERN_GRID.length*this.PATTERN_GRID[0].length];
+        		   for (int i=0;i<debugReplace.length;i++) Arrays.fill(debugReplace[i],Double.NaN);
+        		   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)){
+        				   int tu=this.targetUV[v][u][0]-minU;
+        				   int tv=this.targetUV[v][u][1]-minV;
+        				   if ((tu>=0) && (tv>=0) && (tv<grid.length) && (tu<grid[tv].length) && (grid[tv][tu]!=null)) {
+        					   int index=v*this.PATTERN_GRID[0].length+u;
+        					   debugReplace[0][index]=grid[tv][tu][0]-this.PATTERN_GRID[v][u][0][0];
+        					   debugReplace[1][index]=grid[tv][tu][1]-this.PATTERN_GRID[v][u][0][1];
+        					   debugReplace[2][index]=this.PATTERN_GRID[v][u][0][2];
+        					   debugReplace[3][index]=this.PATTERN_GRID[v][u][0][0];
+        					   debugReplace[4][index]=this.PATTERN_GRID[v][u][0][1];
+        					   debugReplace[5][index]=tu;
+        					   debugReplace[6][index]=tu;
+        				   }
+        			   }
+        		   }
+        		   SDFA_INSTANCE.showArrays(debugReplace, this.PATTERN_GRID[0].length, this.PATTERN_GRID.length, true, "replaceGridXYWithProjected", debugTiltes);
+        	   }
+        	   
         	   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)){