Commit e2086aa9 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

more debugging

parent cbbac8c8

src/main/java/EyesisAberrations.java

+14 −8
Original line number Diff line number Diff line
@@ -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

+25 −9
Original line number Diff line number Diff line
@@ -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(