Added option to deconvolve patterns using projected (not extracted) grid

src/main/java/Distortions.java

@@ -2486,7 +2486,8 @@ For each point in the image
 				subCam,
 				goniometerTilt, // Tilt, goniometerHorizontal
 				goniometerAxial,  // Axial,goniometerAxial
-				-1 // use camera parameters, not imageSet
+				-1, // use camera parameters, not imageSet
+				true // filter border
 		);
 		if (hintGrid==null){
 			String msg="Grid is not visible for subcamera="+subCam+",  tilt="+goniometerTilt+", axial="+goniometerAxial;
@@ -2664,7 +2665,8 @@ For each point in the image
 							dcd.gIP[numGridImage].channel,
 							goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 							goniometerTiltAxial[1],  // Axial,goniometerAxial
-							setNumber // -1 or specific image set
+							setNumber, // -1 or specific image set
+							true // filter border
 					);
 					if (global_debug_level>0){
 						System.out.println("\n**** applyHintedGrids(): processing grid image # "+numGridImage+", path="+dcd.gIP[numGridImage].path);
@@ -2859,7 +2861,6 @@ For each point in the image
 			pixels[4][index]=1000.0;
 		}
 		(new showDoubleFloatArrays()).showArrays(pixels, width, height,  true, "grid-"+numGridImage, titles);
-
 	}
 	public void showGridAndHint(){
 		GenericDialog gd=new GenericDialog("Show selected grid and/or hint grid");
@@ -2903,7 +2904,8 @@ For each point in the image
 				fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel,
 				goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 				goniometerTiltAxial[1],  // Axial,goniometerAxial
-				useSetData?fittingStrategy.distortionCalibrationData.gIP[numGridImage].setNumber:-1
+				(useSetData?fittingStrategy.distortionCalibrationData.gIP[numGridImage].setNumber:-1),
+				true // filter border
 				);
 		showHintGrid(hintGrid,"hint-"+numGridImage);
 
@@ -3061,7 +3063,8 @@ For each point in the image
 			int subCamera,
 			double goniometerHorizontal, // Tilt 
 			double goniometerAxial,     // Axial
-			int  imageSet){
+			int  imageSet,
+			boolean filterBorder){
 		int debugThreshold=2;
 		// Get parameter vector (22) for the selected sensor, current Eyesisparameters and specified orientation angles 		
 		double [] parVector=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getParametersVector(stationNumber,subCamera);
@@ -3139,6 +3142,7 @@ For each point in the image
 				}
 			}
 		}
+		if (filterBorder){
 			// now filter border nodes
 			boolean [] mask= new boolean [patternGeometry.length*patternGeometry[0].length];
 			int index=0;
@@ -3153,7 +3157,7 @@ For each point in the image
 			for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){
 				if (!mask[index++]) result[v][u]=null;
 			}
-		
+		}
 		if (this.debugLevel>debugThreshold){
 			for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){
 				int uv=u+v*result[v].length;

src/main/java/EyesisAberrations.java

@@ -1073,6 +1073,8 @@ public class EyesisAberrations {
 			int debugLevel
 			){
     	Distortions.DistortionCalibrationData distortionCalibrationData= distortions.fittingStrategy.distortionCalibrationData;
+    	boolean partialToReprojected=this.aberrationParameters.partialToReprojected;
+    	// this.distortions is set to top level LENS_DISTORTIONS
 		if (distortions==null){
     		String msg="Distortions instance does not exist, exiting";
     		IJ.showMessage("Error",msg);
@@ -1212,7 +1214,7 @@ public class EyesisAberrations {
     	}
     	// reorder in the ascending channel number order
     	String [][] files=new String [numFiles][2]; // 0 - source, 1 - result
-    	int [] fileIndices =new int [numFiles]; // needed to mark bad kernels
+    	int [] fileIndices =new int [numFiles]; // needed to mark bad kernels (and also to reference grid parameters to replace extracted)
     	int numListedFiles=0;
     	int numChannel=0;
     	while (numListedFiles<numFiles) {
@@ -1239,6 +1241,22 @@ public class EyesisAberrations {
         	int iRetry=0;
         	for (iRetry=0;iRetry<MaxRetries;iRetry++){ // is this retry needed?
         		try {
+        			
+        			double [][][] projectedGrid=null;
+        			double hintTolerance=0.0; 
+        			if (partialToReprojected){ // replace px, py with projected values form the grid
+        				// this.distortions is set to the global LENS_DISTORTIONS
+        				int numGridImage=fileIndices[imgNum];
+        				projectedGrid=distortions.estimateGridOnSensor( // return grid array [v][u][0- x,  1 - y, 2 - u, 3 - v] 
+        						distortions.fittingStrategy.distortionCalibrationData.getImageStation(numGridImage), // station number,
+        						distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel, // subCamera,
+        						Double.NaN, // goniometerHorizontal, - not used
+        						Double.NaN, // goniometerAxial, - not used
+        						distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getSetNumber(), //imageSet,
+        						true); //filterBorder)
+        				hintTolerance=5.0; // TODO:set from configurable parameter
+        			}
+        			
         			int rslt=matchSimulatedPattern.calculateDistortions(
         					distortionParameters, //
         					patternDetectParameters,
@@ -1247,9 +1265,8 @@ public class EyesisAberrations {
         					imp,
         					null, // LaserPointer laserPointer, // LaserPointer object or null
         					true, // don't care -removeOutOfGridPointers
-        					null, //   double [][][] hintGrid, // predicted grid array (or null)
-        					0,    //   double  hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
-
+        					projectedGrid, // null, //   double [][][] hintGrid, // predicted grid array (or null)
+        					hintTolerance, // 0,    //   double  hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
         					threadsMax,
         					updateStatus,
         					debugLevel,
@@ -1259,6 +1276,11 @@ public class EyesisAberrations {
             			if (debugLevel>0) System.out.println("calculateDistortions failed, returned error code "+rslt+" iRetry="+iRetry+" (of "+MaxRetries+")");
             			continue;
         			}
+        			// now replace extracted grid X,Y with projected:
+        			if (projectedGrid!=null){
+        				int numReplaced= matchSimulatedPattern.replaceGridXYWithProjected(projectedGrid);
+            			if (debugLevel>0) System.out.println("Replaced extracted XY with projected ones for "+numReplaced+" nodes");
+        			}
         			correlationSizesUsed=matchSimulatedPattern.getCorrelationSizesUsed();
         			simArray=	(new SimulationPattern(simulParameters)).simulateGridAll (
         					imp.getWidth(),
@@ -4428,6 +4450,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
 		public boolean autoReCalibrateIgnoreLaser=false; // "Ignore laser pointers on recalibrate"
     	public boolean noMessageBoxes=true;
     	public boolean overwriteResultFiles=false;
+    	public boolean partialToReprojected=true; // Use reprojected grid for partial kernel calculation (false - use extracted)
     	public int     seriesNumber=0;
     	public boolean allImages;
     	public String sourcePrefix="";
@@ -4460,6 +4483,8 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
 			properties.setProperty(prefix+"autoReCalibrateIgnoreLaser",this.autoReCalibrateIgnoreLaser+"");
 			properties.setProperty(prefix+"noMessageBoxes",this.noMessageBoxes+"");
 			properties.setProperty(prefix+"overwriteResultFiles",this.overwriteResultFiles+"");
+			properties.setProperty(prefix+"partialToReprojected",this.partialToReprojected+"");
+			
 			properties.setProperty(prefix+"seriesNumber",this.seriesNumber+"");
 			properties.setProperty(prefix+"allImages",this.allImages+"");
 
@@ -4498,6 +4523,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
 			if (properties.getProperty(prefix+"autoReCalibrateIgnoreLaser")!=null) this.autoReCalibrateIgnoreLaser=Boolean.parseBoolean(properties.getProperty(prefix+"autoReCalibrateIgnoreLaser"));
 			if (properties.getProperty(prefix+"noMessageBoxes")!=null)             this.noMessageBoxes=Boolean.parseBoolean(properties.getProperty(prefix+"noMessageBoxes"));
 			if (properties.getProperty(prefix+"overwriteResultFiles")!=null)       this.overwriteResultFiles=Boolean.parseBoolean(properties.getProperty(prefix+"overwriteResultFiles"));
+			if (properties.getProperty(prefix+"partialToReprojected")!=null)       this.partialToReprojected=Boolean.parseBoolean(properties.getProperty(prefix+"partialToReprojected"));
 			if (properties.getProperty(prefix+"seriesNumber")!=null)               this.seriesNumber=Integer.parseInt(properties.getProperty(prefix+"seriesNumber"));
 			if (properties.getProperty(prefix+"allImages")!=null)                  this.allImages=Boolean.parseBoolean(properties.getProperty(prefix+"allImages"));
 			if (properties.getProperty(prefix+"sourcePrefix")!=null)	      this.sourcePrefix=properties.getProperty(prefix+"sourcePrefix");
@@ -4629,6 +4655,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     		gd.addCheckbox("Select aberrations kernels directory", false);
     		gd.addCheckbox("Supress non-essential message boxes", this.noMessageBoxes);
     		gd.addCheckbox("Overwrite result files if they exist", this.overwriteResultFiles);
+    		gd.addCheckbox("Use reprojected grids for partial kernel calculation (false - extracted grids)", this.partialToReprojected);
     		gd.addNumericField("Fitting series number to use for image selection", this.seriesNumber,0);
     		gd.addCheckbox("Process all enabled image files (false - use selected fitting series)", this.allImages);
     		gd.addMessage("===== Autoload options (when restoring configuration) =====");
@@ -4673,6 +4700,7 @@ if (globalDebugLevel>2)globalDebugLevel=0; //***********************************
     		if (gd.getNextBoolean()) selectAberrationsKernelDirectory(false, this.aberrationsKernelDirectory, false);
     		this.noMessageBoxes=        gd.getNextBoolean();
     		this.overwriteResultFiles=  gd.getNextBoolean();
+    		this.partialToReprojected=  gd.getNextBoolean();
     		this.seriesNumber=    (int) gd.getNextNumber();
     		this.allImages=             gd.getNextBoolean();
     		this.autoRestore=           gd.getNextBoolean();

src/main/java/Goniometer.java

@@ -598,7 +598,8 @@ horizontal axis:
 				subCam,
 				goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 				goniometerTiltAxial[1],  // Axial,goniometerAxial
-				-1 // use camera parameters, not imageSet
+				-1, // use camera parameters, not imageSet
+				true // filter border
 				);
 		if (hintGrid==null){
 			String msg= "Target is not visible";

src/main/java/MatchSimulatedPattern.java

@@ -6983,6 +6983,51 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
         	   
            }
            
+           public int replaceGridXYWithProjected(double [][][] projectedGrid){
+        	   int minU=0,minV=0,maxU=0,maxV=0;
+        	   boolean notYetSet=true;
+        	   for (double [][]row:projectedGrid) for (double [] cell:row) if (cell!=null){
+        		   int u = (int) cell[2];
+        		   int v = (int) cell[3];
+        		   if (notYetSet){
+        			   minU=u;
+        			   maxU=u;
+        			   minV=v;
+        			   maxV=v;
+        			   notYetSet=false;
+        		   } else {
+        			   if (minU>u) minU=u;
+        			   if (maxU<u) maxU=u;
+        			   if (minV>v) minV=v;
+        			   if (maxV<v) maxV=v;
+        		   }
+        	   }
+        	   double [][][] grid=new double [maxV-minV+1][maxU-minU+1][];
+//        	   for (double [][]row:grid) for (double [] cell:row) cell=null; // See if this works with "enhanced for loop"
+        	   for (double [][]row:grid) for (int u=0;u<row.length;u++) row[u]=null; // See if this works with "enhanced for loop"
+        	   
+        	   for (double [][] row:projectedGrid) for (double [] cell:row) if (cell!=null){
+        		   int u = (int) cell[2];
+        		   int v = (int) cell[3];
+        		   double [] xy={cell[0],cell[1]};
+        		   grid[v-minV][u-minU]=xy;
+        	   }
+        	   int numNewDefined=0;
+        	   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
+        			   } else {
+        				   numNewDefined++;
+        			   }
+        		   }
+        	   }
+        	   return numNewDefined;
+           }
+           
            /* Get calibrated pattern as a 8-slice image (can be saved as TIFF)
             * first   slice - pixel X or -1 for undefined
             * second  slice - pixel Y or -1 for undefined