removing blanks in the LWIR kernel corners (f35dc2de) · Commits · Elphel / imagej-elphel

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

+58 −44

Original line number	Diff line number	Diff line
		@@ -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
		@@ -3484,6 +3485,7 @@ For each point in the image
		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){
		@@ -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= 2.0Math.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
		@@ -4187,7 +4199,8 @@ 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++){
		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;
		@@ -4227,6 +4240,7 @@ For each point in the image
		}
		}
		}
		}
		if (filterBorder){
		// now filter border nodes
		boolean [] mask= new boolean [patternGeometry.length*patternGeometry[0].length];

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

+12 −1

Original line number	Diff line number	Diff line
		@@ -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

+1 −0

Original line number	Diff line number	Diff line
		@@ -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

+34 −17

Original line number	Diff line number	Diff line
		@@ -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) + "}");
		@@ -8320,6 +8337,7 @@ public class MatchSimulatedPattern {
		double[][] pointersXYUV, boolean removeOutOfGridPointers, //
		double[][][] hintGrid, // predicted grid array (or null)
		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)

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