removing blanks in the LWIR kernel corners

src/main/java/com/elphel/imagej/calibration/Distortions.java

@@ -65,7 +65,8 @@ import ij.text.TextWindow;
 // 1 - put commons-configuration-1.7.jar under ImageJ plugins directory (I used ImageJ-Elphel)
 // 2 - in Eclipse project properties -> Build Path -> Libraries -> Add External jar
 public class Distortions {
-	final public double hintedMaxRelativeRadius=1.2; // make adjustable?
+//	final public double hintedMaxRelativeRadius=1.2; // make adjustable?
+	final public double hintedMaxRelativeRadiusToDiagonal= 1.1; // 0.96; // make adjustable?
 	private ShowDoubleFloatArrays SDFA_INSTANCE=new ShowDoubleFloatArrays(); // just for debugging?
 //    int numInputs=27; // with A8...// 24;   // parameters in subcamera+...
 //    int numOutputs=16; // with A8...//13;  // parameters in a single camera
@@ -3331,7 +3332,7 @@ For each point in the image
 			int global_debug_level, // DEBUG_LEVEL
 			int debug_level // debug level used inside loops
 	){
-
+		boolean invert = false;
 		int debugThreshold0=0;
 		int debugThreshold=2;
 		MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern(64); // new instance, all reset, FFTSize=64 will not be used
@@ -3481,11 +3482,12 @@ For each point in the image
 					int rslt= matchSimulatedPattern.combineGridCalibration(
 							laserPointer, // LaserPointer object or null
 							ignoreLaserPointers?null:dcd.gIP[numGridImage].laserPixelCoordinates, //pointersXY,
-									removeOutOfGridPointers, //
-									hintGrid, // predicted grid array (or null)
-									hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
-									global_debug_level, // DEBUG_LEVEL
-									noMessageBoxes );
+							removeOutOfGridPointers, //
+							hintGrid, // predicted grid array (or null)
+							hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
+							invert,
+							global_debug_level, // DEBUG_LEVEL
+							noMessageBoxes );
 					if (global_debug_level>0){
 						System.out.println("applyHintedGrids(): rslt="+rslt);
 					}
@@ -4040,7 +4042,14 @@ For each point in the image
 			int numImg,
 			int u, // grid signed u,v
 			int v){
-		double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
+
+		
+		int subCamera=   this.fittingStrategy.distortionCalibrationData.gIP[numImg].channel;
+		int sensorWidth=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(subCamera);
+		int sensorHeight=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(subCamera);
+//		double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
+		double maxRelativeRadius=hintedMaxRelativeRadiusToDiagonal * Math.sqrt(sensorWidth * sensorWidth + sensorHeight*sensorHeight)/ sensorWidth;
+		
 		return  reprojectGridNode(
 				lensDistortionParameters,
 				numImg,
@@ -4134,7 +4143,12 @@ For each point in the image
 			double goniometerInterAxis,     // interAxisAngle
 			int  imageSet,
 			boolean filterBorder){
-		double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
+		int sensorWidth=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(subCamera);
+		int sensorHeight=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(subCamera);
+//		double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
+		double maxRelativeRadius=hintedMaxRelativeRadiusToDiagonal * Math.sqrt(sensorWidth * sensorWidth + sensorHeight*sensorHeight)/ sensorWidth;
+		// 1.1 is sufficient
+//		double maxRelativeRadius= 2.0*Math.sqrt(sensorWidth * sensorWidth + sensorHeight*sensorHeight)/ sensorWidth;
 		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);
@@ -4156,8 +4170,6 @@ For each point in the image
 			parVector[goniometerInterAxisAngleIndex]=  goniometerInterAxis;
 		}
 //		/interAxis
-		int sensorWidth=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(subCamera);
-		int sensorHeight=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(subCamera);
 		System.out.println("estimateGridOnSensor(): subCamera="+subCamera+", goniometerHorizontal="+goniometerHorizontal+", goniometerAxial="+goniometerAxial);
 		this.lensDistortionParameters.lensCalcInterParamers(
 				this.lensDistortionParameters, // 22-long parameter vector for the image
@@ -4187,43 +4199,45 @@ For each point in the image
 		// simple fix - remove pixels with too few neighbors (maybe just all border pixels?
 
 
-		for (int v=0;v<result.length;v++) for (int u=0;u<result[v].length;u++){
-			int [] iUV=this.patternParameters.uvIndicesToUV (u, v);
-			if (iUV==null) {
-				result[v][u]=null;
-			} else {
-				double [] XYZM=this.patternParameters.getXYZM(iUV[0],iUV[1],stationNumber);
-// project the target point to this sensor
-				double [][]pXY=  this.lensDistortionParameters.calcPartialDerivatives(
-						XYZM[0], // target point horizontal, positive - right,  mm
-						XYZM[1], // target point vertical,   positive - down,  mm
-						XYZM[2], // target point horizontal, positive - away from camera,  mm
-						maxRelativeRadius,
-						false); // calculate derivatives, false - values only (NaN for behind points - only when false here)
-// verify the grid is inside the sensor area (may use sensor mask later too? probably not needed)
-				// Now NaN if point is behind the sensor
-				if (Double.isNaN(pXY[0][0]) || (pXY[0][0]<0) || (pXY[0][0]>=sensorWidth) || (pXY[0][1]<0) || (pXY[0][1]>=sensorHeight)){
-					if (this.debugLevel>debugThreshold){
-						System.out.println("--- estimateGridOnSensor():v="+v+" u="+u+" X="+XYZM[0]+" Y="+XYZM[1]+" Z="+XYZM[2]+" M="+XYZM[3]+
-								" pXY[0][0]="+pXY[0][0]+", pXY[0][1]="+pXY[0][1]+", iUV[0]="+iUV[0]+", iUV[1]="+iUV[1]);
-					}
+		for (int v=0;v<result.length;v++) {
+			for (int u=0;u<result[v].length;u++){
+				int [] iUV=this.patternParameters.uvIndicesToUV (u, v);
+				if (iUV==null) {
 					result[v][u]=null;
 				} else {
-					double [] resultCell={pXY[0][0],pXY[0][1],iUV[0],iUV[1]};
-					result[v][u]=resultCell;
+					double [] XYZM=this.patternParameters.getXYZM(iUV[0],iUV[1],stationNumber);
+					// project the target point to this sensor
+					double [][]pXY=  this.lensDistortionParameters.calcPartialDerivatives(
+							XYZM[0], // target point horizontal, positive - right,  mm
+							XYZM[1], // target point vertical,   positive - down,  mm
+							XYZM[2], // target point horizontal, positive - away from camera,  mm
+							maxRelativeRadius,
+							false); // calculate derivatives, false - values only (NaN for behind points - only when false here)
+					// verify the grid is inside the sensor area (may use sensor mask later too? probably not needed)
+					// Now NaN if point is behind the sensor
+					if (Double.isNaN(pXY[0][0]) || (pXY[0][0]<0) || (pXY[0][0]>=sensorWidth) || (pXY[0][1]<0) || (pXY[0][1]>=sensorHeight)){
+						if (this.debugLevel>debugThreshold){
+							System.out.println("--- estimateGridOnSensor():v="+v+" u="+u+" X="+XYZM[0]+" Y="+XYZM[1]+" Z="+XYZM[2]+" M="+XYZM[3]+
+									" pXY[0][0]="+pXY[0][0]+", pXY[0][1]="+pXY[0][1]+", iUV[0]="+iUV[0]+", iUV[1]="+iUV[1]);
+						}
+						result[v][u]=null;
+					} else {
+						double [] resultCell={pXY[0][0],pXY[0][1],iUV[0],iUV[1]};
+						result[v][u]=resultCell;
+						if (this.debugLevel>debugThreshold){
+							System.out.println("+++ estimateGridOnSensor():v="+v+" u="+u+" X="+XYZM[0]+" Y="+XYZM[1]+" Z="+XYZM[2]+" M="+XYZM[3]+
+									" pXY[0][0]="+pXY[0][0]+", pXY[0][1]="+pXY[0][1]+", iUV[0]="+iUV[0]+", iUV[1]="+iUV[1]);
+						}
+						visibleCells++;
+					}
 					if (this.debugLevel>debugThreshold){
-						System.out.println("+++ estimateGridOnSensor():v="+v+" u="+u+" X="+XYZM[0]+" Y="+XYZM[1]+" Z="+XYZM[2]+" M="+XYZM[3]+
-								" pXY[0][0]="+pXY[0][0]+", pXY[0][1]="+pXY[0][1]+", iUV[0]="+iUV[0]+", iUV[1]="+iUV[1]);
+						int uv=u+v*result[v].length;
+						debugPixels[0][uv]=pXY[0][0];
+						debugPixels[1][uv]=pXY[0][1];
+						debugPixels[2][uv]=XYZM[0];
+						debugPixels[3][uv]=XYZM[1];
+						debugPixels[4][uv]=XYZM[2];
 					}
-					visibleCells++;
-				}
-				if (this.debugLevel>debugThreshold){
-					int uv=u+v*result[v].length;
-					debugPixels[0][uv]=pXY[0][0];
-					debugPixels[1][uv]=pXY[0][1];
-					debugPixels[2][uv]=XYZM[0];
-					debugPixels[3][uv]=XYZM[1];
-					debugPixels[4][uv]=XYZM[2];
 				}
 			}
 		}

src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java

@@ -1455,6 +1455,7 @@ public class EyesisAberrations {
 					multiFilePSF ,         // MULTIFILE_PSF = new EyesisAberrations.MultiFilePSF(
 					fileList[nChn],
 					resultPaths[nChn],
+					nChn, // int                    sensor_channel,       // just for debugging
 					sdfa_instance,        // SDFA_INSTANCE
 					impShow, // just to show in the same window?
 					saveResult,
@@ -1478,6 +1479,7 @@ public class EyesisAberrations {
 			EyesisAberrations.MultiFilePSF           multiFilePSF ,         // MULTIFILE_PSF = new EyesisAberrations.MultiFilePSF(
 			String []              filenames,
 			String                 resultPath,
+			int                    sensor_channel,       // just for debugging
 			ShowDoubleFloatArrays  sdfa_instance,        // SDFA_INSTANCE
 			ImagePlus              imp_sel, // just to show in the same window?
 			boolean                saveResult,
@@ -1819,7 +1821,7 @@ public class EyesisAberrations {
 			}
 
 		}
-		if (multiFilePSF.showWeights) sdfa_instance.showArrays(weights, kWidth, kHeight,  true, "weights");
+		if (multiFilePSF.showWeights) sdfa_instance.showArrays(weights, kWidth, kHeight,  true, "weights-"+sensor_channel);
 		//    	double [][] weights=new double[nFiles+1][kLength];
 		for (int i=0;i<kLength;i++) weights[0][i]=0.0;
 		psfKernelMap=new double [kHeight][kWidth][nChn][];
@@ -2299,6 +2301,15 @@ public class EyesisAberrations {
 		final int full_fft_size = fft_size * PSF_subpixel / (is_mono? 2: 1); // for LWIR - 64, 5MPix: 1024. fft_size = 32/256
 
 
+		if (debug_level>3) {
+			double [] dbg_index = new double [commonMatchSimulatedPattern.UV_INDEX.length];
+			for (int i = 0; i < dbg_index.length; i++) {
+				dbg_index[i] = commonMatchSimulatedPattern.UV_INDEX[i];
+			}
+			SDFA_INSTANCE.showArrays(dbg_index, imp_sel.getWidth(), dbg_index.length/imp_sel.getWidth(), "UV_INDEX");
+		}
+		
+		
 		final boolean debugLateralShifts=(globalDebugLevel>1);
 		System.out.println("createPSFMap(): masterDebugLevel="+masterDebugLevel+" globalDebugLevel="+globalDebugLevel+" debug_level="+debug_level); // 2 2 0
 		final long startTime = System.nanoTime();

src/main/java/com/elphel/imagej/calibration/LensDistortionParameters.java

@@ -960,6 +960,7 @@ dPXmmc/dphi=
         		double zp, // target point horizontal, positive - away from camera,  mm
             	double maxRelativeRadius, // make configurable?
         		boolean calculateAll){ // calculate derivatives, false - values only
+//        	maxRelativeRadius *= 1.3; // REMOVE me!
         	switch (this.lensDistortionModelType){
         	case 0:
         	case 1:

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

@@ -6720,6 +6720,7 @@ public class MatchSimulatedPattern {
 			int threadsMax, boolean updateStatus, int global_debug_level, // DEBUG_LEVEL
 			int debug_level, // debug level used inside loops
 			boolean noMessageBoxes) {
+		
 		if (imp == null) {
 			IJ.showMessage("Error", "There are no images open\nProcess canceled");
 			return 0;
@@ -6733,6 +6734,8 @@ public class MatchSimulatedPattern {
 		int minimal_pattern_cluster = is_lwir ? distortionParameters.minimalPatternClusterLwir
 				: distortionParameters.minimalPatternCluster;
 
+		boolean invert = false; // is_lwir;
+
 		int fft_size = is_lwir ? distortionParameters.FFTSize_lwir : distortionParameters.FFTSize;
 
 		long startTime = System.nanoTime();
@@ -6991,6 +6994,7 @@ public class MatchSimulatedPattern {
 				pointersXY, removeOutOfGridPointers, //
 				hintGrid, // predicted grid array (or null)
 				hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
+				invert, // b/w
 				global_debug_level, // DEBUG_LEVEL
 				noMessageBoxes);
 	}
@@ -7738,7 +7742,7 @@ public class MatchSimulatedPattern {
 		return flipsToRot(flips[0], flips[1], flips[2]);
 	}
 
-	public int[][] gridMatrixApproximate(double[][] coeff) {
+	public int[][] gridMatrixApproximate(double[][] coeff, boolean invert) {
 		int rot = matrixToRot(coeff);
 		boolean[] flips = rotToFlips(rot);
 		double[][] aI = { { 1, 0 }, { 0, 1 } };
@@ -7755,7 +7759,8 @@ public class MatchSimulatedPattern {
 		// now M reconstructs coeff
 		double[][] aM = M.getArray();
 		// Black/white cells have to be flipped if flipU XOR flipW, regardless of swapUV
-		int flipForWhite = (flips[1] ^ flips[2]) ? 1 : 0;
+		
+		int flipForWhite = (invert ^ flips[1] ^ flips[2]) ? 1 : 0;
 		int[][] shifts = {
 				{ 2 * ((int) Math.round(0.5 * (coeff[0][2] + 0))),
 						2 * ((int) Math.round(0.5 * (coeff[1][2] + flipForWhite))) - flipForWhite },
@@ -7774,10 +7779,6 @@ public class MatchSimulatedPattern {
 					+ " d1=" + d1 + " d2=" + d2);
 		}
 		int[][] iCoeff = {
-				// {(int) Math.round(aM[0][0]), (int) Math.round(aM[0][1]),(int)
-				// Math.round(coeff[0][2])},
-				// {(int) Math.round(aM[1][0]), (int) Math.round(aM[1][1]),(int)
-				// Math.round(coeff[1][2])}};
 				{ (int) Math.round(aM[0][0]), (int) Math.round(aM[0][1]), shifts[shiftSelect][0] },
 				{ (int) Math.round(aM[1][0]), (int) Math.round(aM[1][1]), shifts[shiftSelect][1] } };
 		return iCoeff;
@@ -7805,8 +7806,17 @@ public class MatchSimulatedPattern {
 		return iCoeff;
 	}
 
-	public double worstGridMatchRotSkew(double[][] coeff) {
-		int[][] iCoeff = gridMatrixApproximate(coeff);
+	public double worstGridMatchRotSkew(
+			double[][] coeff) {
+		return worstGridMatchRotSkew(coeff, false);
+	}
+	
+	
+	public double worstGridMatchRotSkew(
+			double[][] coeff,
+			boolean invert
+			) {
+		int[][] iCoeff = gridMatrixApproximate(coeff, invert);
 		double worst = 0;
 		for (int i = 0; i < 2; i++)
 			for (int j = 0; j < 2; j++) {
@@ -7817,8 +7827,15 @@ public class MatchSimulatedPattern {
 		return worst;
 	}
 
-	public double worstGridMatchTranslate(double[][] coeff) { // in grids half-periods, not pixels!
-		int[][] iCoeff = gridMatrixApproximate(coeff);
+	public double worstGridMatchTranslate(
+			double[][] coeff) { // in grids half-periods, not pixels!
+		return worstGridMatchTranslate(coeff, false);
+	}
+	
+	public double worstGridMatchTranslate(
+			double[][] coeff,
+			boolean invert) { // in grids half-periods, not pixels!
+		int[][] iCoeff = gridMatrixApproximate(coeff, invert);
 		double worst = 0;
 		for (int i = 0; i < 2; i++) {
 			double d = Math.abs(coeff[i][2] - iCoeff[i][2]);
@@ -8246,7 +8263,7 @@ public class MatchSimulatedPattern {
 			if (gridMatchCoeff != null) {
 				gridRotation = matrixToRot(gridMatchCoeff);
 				this.debugLevel = global_debug_level;
-				int[][] iGridMatchCoeff = gridMatrixApproximate(gridMatchCoeff);
+				int[][] iGridMatchCoeff = gridMatrixApproximate(gridMatchCoeff, false);
 				if (global_debug_level > 1) {
 					System.out.println("gridMatchCoeff[0]={" + IJ.d2s(gridMatchCoeff[0][0], 5) + ", "
 							+ IJ.d2s(gridMatchCoeff[0][1], 5) + ", " + IJ.d2s(gridMatchCoeff[0][2], 5) + "}");
@@ -8317,9 +8334,10 @@ public class MatchSimulatedPattern {
 // Modified 06/19 to move laser pointers to files
 	public int combineGridCalibration(LaserPointer lp, // Only for possible hint on rotations/ flips.LaserPointer object
 														// or null
-			double[][] pointersXYUV, boolean removeOutOfGridPointers, //
+			double[][]   pointersXYUV, boolean removeOutOfGridPointers, //
 			double[][][] hintGrid, // predicted grid array (or null)
-			double hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
+			double       hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
+			boolean      invert,            // for lwir
 			int global_debug_level, // DEBUG_LEVEL
 			boolean noMessageBoxes) {
 		boolean has_lasers = false;
@@ -8342,7 +8360,7 @@ public class MatchSimulatedPattern {
 			if (gridMatchCoeff != null) {
 				gridRotation = matrixToRot(gridMatchCoeff);
 				this.debugLevel = global_debug_level;
-				int[][] iGridMatchCoeff = gridMatrixApproximate(gridMatchCoeff);
+				int[][] iGridMatchCoeff = gridMatrixApproximate(gridMatchCoeff, invert);
 				if (global_debug_level > 0) {
 					System.out.println("gridMatchCoeff[0]={" + IJ.d2s(gridMatchCoeff[0][0], 5) + ", "
 							+ IJ.d2s(gridMatchCoeff[0][1], 5) + ", " + IJ.d2s(gridMatchCoeff[0][2], 5) + "}");
@@ -8353,9 +8371,8 @@ public class MatchSimulatedPattern {
 							+ ", " + iGridMatchCoeff[0][2] + "}");
 					System.out.println("iGridMatchCoeff[1]={" + iGridMatchCoeff[1][0] + ", " + iGridMatchCoeff[1][1]
 							+ ", " + iGridMatchCoeff[1][2] + "}");
-					System.out.println("worstGridMatchRotSkew()=" + IJ.d2s(worstGridMatchRotSkew(gridMatchCoeff), 5));
-					System.out
-							.println("worstGridMatchTranslate()=" + IJ.d2s(worstGridMatchTranslate(gridMatchCoeff), 5));
+					System.out.println("worstGridMatchRotSkew()=" + IJ.d2s(worstGridMatchRotSkew(gridMatchCoeff, invert), 5));
+					System.out.println("worstGridMatchTranslate()=" + IJ.d2s(worstGridMatchTranslate(gridMatchCoeff, invert), 5));
 				}
 				// hintGridTolerance==0 - do not try to determine shift from the hint (not
 				// reliable yet)