more debugging

src/main/java/EyesisAberrations.java

@@ -1066,7 +1066,7 @@ public class EyesisAberrations {
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
 			SimulationPattern.SimulParameters  simulParameters,
 			ColorComponents colorComponents,
-			boolean resetBadKernels, // ignore and reset noUsefulKernels mark for seleccted channel
+			boolean resetBadKernels, // ignore and reset noUsefulKernels mark for selected channel
 			int threadsMax,
 			boolean updateStatus,
 			int loopDebugLevel, // debug level used inside loops
@@ -1094,14 +1094,14 @@ public class EyesisAberrations {
     	boolean [] selectedChannels=this.aberrationParameters.getChannelSelection(distortions);
     	int numSelected=0;
     	int numDeselected=0;
-    	if (debugLevel>1){
+    	if (debugLevel>2){
     		for (int i=0;i<selectedChannels.length;i++){
     			System.out.println("Channel "+i+" is "+(selectedChannels[i]?"Enabled":"Disabled"));
     		}
     	}
     	for (int imgNum=0;imgNum<selectedImages.length;imgNum++) if (selectedImages[imgNum]) {
     		int numChannel=distortionCalibrationData.gIP[imgNum].channel;
-        	if (debugLevel>1){
+        	if (debugLevel>2){
         		System.out.println("Image "+imgNum+" channel "+numChannel+" is "+(selectedChannels[numChannel]?"ENABLED":"DISABLED"));
         	}    		
     		if (!selectedChannels[numChannel]){
@@ -1111,7 +1111,7 @@ public class EyesisAberrations {
     			distortions.fittingStrategy.setNoUsefulPSFKernels(imgNum,false); // reset noUsefulKernels mark (if it was not set - OK)
     			numSelected++;
     		}
-    	} else if (debugLevel>1){
+    	} 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");
@@ -1237,9 +1237,9 @@ public class EyesisAberrations {
 
         	int MaxRetries=4;
         	int iRetry=0;
-        	for (iRetry=0;iRetry<MaxRetries;iRetry++){
+        	for (iRetry=0;iRetry<MaxRetries;iRetry++){ // is this retry needed?
         		try {
-        			matchSimulatedPattern.calculateDistortions(
+        			int rslt=matchSimulatedPattern.calculateDistortions(
         					distortionParameters, //
         					patternDetectParameters,
         					simulParameters,
@@ -1255,7 +1255,10 @@ public class EyesisAberrations {
         					debugLevel,
         					loopDebugLevel, // debug level
         					aberrationParameters.noMessageBoxes);
-        			
+        			if (rslt<0){
+            			if (debugLevel>0) System.out.println("calculateDistortions failed, returned error code "+rslt+" riRetry="+iRetry+" (of "+MaxRetries+")");
+            			continue;
+        			}
         			correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed();
         			simArray=	(new SimulationPattern(simulParameters)).simulateGridAll (
         					imp.getWidth(),
@@ -1299,7 +1302,10 @@ public class EyesisAberrations {
         			continue;
         		}
         	}
-        	if (iRetry==MaxRetries) continue;
+        	if (iRetry==MaxRetries) {
+				System.out.println("File "+files[imgNum][1]+ " has problems - finished at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)); 
+        		continue;
+        	}
         	
 			
 			ImageStack stack=mergeKernelsToStack(this.pdfKernelMap);

src/main/java/MatchSimulatedPattern.java

@@ -3282,7 +3282,7 @@ public class MatchSimulatedPattern {
 						   triedIndices[numTries]=true; // all tried
 					   } else {
 //						   if (debugLevel>1) System.out.println("Found "+nodes.length+" candidates");
-						   if (debugLevel>1) System.out.println("Found "+nodeQueue.size()+" candidates");
+						   if (debugLevel>1) System.out.println("distortions: Found "+nodeQueue.size()+" candidates");
 					   }
 				   } else {
 					   if (debugLevel>1) System.out.println("All start points tried before - should not get here");
@@ -3330,15 +3330,23 @@ public class MatchSimulatedPattern {
 			   nodeQueue.add(new GridNode(node)); // will not be used, any element
 		   }
 		   int numDefinedCells=0;
-		   for (GridNode gn:nodeQueue){
+		   int debug_left=nodeQueue.size();
+		   for (GridNode gn:nodeQueue){ // trying candidates as grid seeds - until found or nothing left
+			   if (global_debug_level>1) {
+				   System.out.println("distortions: nodeQueue has "+(debug_left--)+" candidates left (including this one)");
+			   }
+			   
 			   if (!updating){
 				   double [][] node=gn.getNode();
 				   double [] centerXY=node[0];
+				   if (global_debug_level>1) {
+					   System.out.println("distortions: node X/Y are "+centerXY[0]+"/"+centerXY[1]);
+				   }
 				   //				   if (debugLevel>1) {
 				   if (global_debug_level>1) {
 					   System.out.println("*** distortions: Center x="+IJ.d2s(centerXY[0],3)+" y="+ 	IJ.d2s(centerXY[1],3));
 					   System.out.println("*** distortions: setting debugX="+IJ.d2s(centerXY[0],3)+" debugY="+ 	IJ.d2s(centerXY[1],3));
-					   patternDetectParameters.debugX=centerXY[0]; //
+					   patternDetectParameters.debugX=centerXY[0]; // Change debug coordinates to the initial node
 					   patternDetectParameters.debugY=centerXY[1]; //patternDetectParameters.debugRadius);
 				   }
 				   debugLevel=debug_level;
@@ -3352,7 +3360,9 @@ public class MatchSimulatedPattern {
 						   node[2]);
 				   waveFrontList.clear();
 				   putInWaveList(waveFrontList, centerUV, 0);
-				   
+				   if (global_debug_level>1) {
+					   System.out.println("putInWaveList(waveFrontList, {"+centerUV[0]+","+centerUV[1]+"}, 0);");
+				   }
 				   
 			   }
 
@@ -3382,6 +3392,7 @@ public class MatchSimulatedPattern {
 
 			   final AtomicInteger debugCellSet= new AtomicInteger(0); // cells added at cleanup stage
 			   // special case (most common, actually) when initial wave has 1  node. Remove it after processing
+			   //first cell(s) will need large correction and so may fail during "refine", so trying to recalculate it right after the first layer)
 			   ArrayList<Integer> initialWave=new ArrayList<Integer>();
 			   for (Integer I:waveFrontList) initialWave.add(I); 
 			   while (waveFrontList.size()>0) {
@@ -3430,7 +3441,8 @@ public class MatchSimulatedPattern {
 				   if (waveFrontList.size()==0) break; // not really needed?
 				   layer++;
 				   if (updateStatus) IJ.showStatus("Correlating patterns, layer "+layer+(cleanup.get()?"(cleanup)":"")+", length "+waveFrontList.size());
-				   if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
+//				   if (debugLevel>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
+				   if (global_debug_level>1) System.out.println("Correlating patterns, layer "+layer+", length "+waveFrontList.size());
 				   // starting layer
 				   cellNum.set(0);
 				   for (int ithread = 0; ithread < threads.length; ithread++) {
@@ -3453,7 +3465,8 @@ public class MatchSimulatedPattern {
 
 								   double [][] refCell=PATTERN_GRID[iUVRef[1]][iUVRef[0]]; // should never be null as it is an old one
 								   if (refCell==null){ 
-									   System.out.println("**** refCell==null - what does it mean?**** u="+iUVRef[0]+" v="+iUVRef[1]);
+									   System.out.println("**** refCell==null - what does it mean?**** u="+iUVRef[0]+" v="+iUVRef[1]+
+											   " current="+iUVdir[0]+"/"+iUVdir[1]+" len="+iUVdir.length);
 									   continue;
 								   } else if ((refCell[0]!=null) && (refCell[0].length>3)){
 									   System.out.println("**** refCell was deleted ****");
@@ -3678,7 +3691,7 @@ public class MatchSimulatedPattern {
 					   }
 					   if (global_debug_level>1) System.out.println("***** Starting cleanup, wave length="+waveFrontList.size());
 				   }
-				   // end of layer	
+				   // end of layer - it is a hack below, marking initial wave to recalculate it from neighbors	
 				   if (initialWave!=null){ // just after the first layer (usually one cell) - delete it and add next time - otherwise first one needs large correction
 					   if (global_debug_level>0)
 						   System.out.println("Removing "+initialWave.size()+" initial wave cells");
@@ -5415,6 +5428,7 @@ public class MatchSimulatedPattern {
 				   int [] uv){
 			   grid[uv[1]][uv[0]]=null;
 		   }
+
 		   private void markDeletedPatternGridCell(
 				   double [][][][] grid,
 				   int [] uv){
@@ -5426,8 +5440,10 @@ public class MatchSimulatedPattern {
 					   else
 						   newXYC[i]=Double.NaN;
 				   }
+				   grid[uv[1]][uv[0]][0]=newXYC;
 			   }
-			   grid[uv[1]][uv[0]]=null;
+//			   grid[uv[1]][uv[0]]=null;
+
 		   }
 		   private boolean isCellNew( //modified, for invalid uv will return "not new"
 				   double [][][][] grid,
@@ -5565,7 +5581,7 @@ public class MatchSimulatedPattern {
 		   public int gridUVHeight(){return ((this.PATTERN_GRID==null) || (this.PATTERN_GRID.length==0l) ||(this.PATTERN_GRID[0]==null))?0:this.PATTERN_GRID.length;}		   
 /* ======================================================================== */
 		   /**
-		    * returns number of laser pointers matched
+		    * returns number of laser pointers matched (or negative error)
 		    * if (this.flatFieldForGrid!=null) it should already be applied !!
 		    */
 		   public int calculateDistortions(