Implemented LWIR grids calculation (6733a12d) · Commits · Elphel / imagej-elphel

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

+69 −62

Original line number	Original line	Diff line number	Diff line
	@@ -361,12 +361,15 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene

	public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSimulatedPattern.DistortionParameters(		public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSimulatedPattern.DistortionParameters(
	64, //32, // use 64 for less artifacts, // correlationSize		64, //32, // use 64 for less artifacts, // correlationSize
	64, // Maximal correlation size		16, // int correlationSizeLwir,
			128, // 64, // Maximal correlation size
			16, // int maximalCorrelationSizeLwir,
	0.75,// reduce to 0.5 when correlationSize==64 // correlationGaussWidth		0.75,// reduce to 0.5 when correlationSize==64 // correlationGaussWidth
	false, // boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased		false, // boolean absoluteCorrelationGaussWidth=false; // do not scale correlationGaussWidth when the FFT size is increased
	0, //zeros - // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will		0, //zeros - // leave this number of zeros on the margins of the window (toatal from both sides). If correlationGaussWidth>0 will
	// additionally multiply by Hamming		// additionally multiply by Hamming
	128, // FFT size		256, // FFTSize (was 128)
			32, // FFTSize_lwir
	0.5, //fftGaussWidth		0.5, //fftGaussWidth
	0.0, //phaseCorrelationFraction		0.0, //phaseCorrelationFraction
	1.5, // 2.5, //6.0, // 2.0, // 0.0, // correlationHighPassSigma, - pixels in frequency domain		1.5, // 2.5, //6.0, // 2.0, // 0.0, // correlationHighPassSigma, - pixels in frequency domain
	@@ -385,7 +388,8 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
	0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1		0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
	0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5		0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5

	150, // minimalPatternCluster minimal pattern cluster size (0 - disable retries)		40, // 150, // minimalPatternCluster minimal pattern cluster size (0 - disable retries)
			10, // 150, // minimalPatternClusterLwir minimal pattern cluster size (0 - disable retries)
	2.0, // scaleMinimalInitialContrast increase/decrease minimal contrast if initial cluster is >0 but less than minimalPatternCluster		2.0, // scaleMinimalInitialContrast increase/decrease minimal contrast if initial cluster is >0 but less than minimalPatternCluster
	0.5, // when searching for grid, step this amount of the FFTSize		0.5, // when searching for grid, step this amount of the FFTSize
	4, // public int patternSubdiv;		4, // public int patternSubdiv;
	@@ -1417,10 +1421,9 @@ if (MORE_BUTTONS) {
	// matchSimulatedPattern.invalidateFlatFieldForGrid(); //It is already reset, no need to do it again		// matchSimulatedPattern.invalidateFlatFieldForGrid(); //It is already reset, no need to do it again
	// matchSimulatedPattern.invalidateFocusMask();		// matchSimulatedPattern.invalidateFocusMask();
	matchSimulatedPattern.calculateDistortions(		matchSimulatedPattern.calculateDistortions(
			null, // LwirReaderParameters lwirReaderParameters,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	PATTERN_DETECT.minGridPeriod/2,
	PATTERN_DETECT.maxGridPeriod/2,
	SIMUL,		SIMUL,
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel,		imp_sel,
	@@ -1815,10 +1818,9 @@ if (MORE_BUTTONS) {
	// matchSimulatedPattern.invalidateFlatFieldForGrid(); //It is already reset, no need to do it again		// matchSimulatedPattern.invalidateFlatFieldForGrid(); //It is already reset, no need to do it again
	// matchSimulatedPattern.invalidateFocusMask();		// matchSimulatedPattern.invalidateFocusMask();
	int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
			null, // LwirReaderParameters lwirReaderParameters,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	PATTERN_DETECT.minGridPeriod/2,
	PATTERN_DETECT.maxGridPeriod/2,
	SIMUL,		SIMUL,
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel,		imp_sel,
	@@ -9416,10 +9418,6 @@ if (MORE_BUTTONS) {
	}		}
	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("LWIR grids")) {		if (label.equals("LWIR grids")) {
	// if ((LASER_POINTERS==null) \|\| (LASER_POINTERS.laserUVMap.length==0)){
	// IJ.showMessage("Laser pointer data needed for this function is not provided");
	// return;
	// }
	calculateLwirGrids();		calculateLwirGrids();
	return;		return;
	}		}
	@@ -9449,23 +9447,20 @@ if (MORE_BUTTONS) {
	matchSimulatedPattern.debugLevel=MASTER_DEBUG_LEVEL;		matchSimulatedPattern.debugLevel=MASTER_DEBUG_LEVEL;
	String [] sourceSetList = DISTORTION_PROCESS_CONFIGURATION.selectSourceSets();		String [] sourceSetList = DISTORTION_PROCESS_CONFIGURATION.selectSourceSets();
	LWIR_PARAMETERS.selectSourceChannels();		LWIR_PARAMETERS.selectSourceChannels();
	boolean [] sel_chn = LWIR_PARAMETERS.getSelectedVnir(); // start with regular cameras only		// boolean [] sel_chn = LWIR_PARAMETERS.getSelectedVnir(); // start with regular cameras only
			boolean [] sel_chn = LWIR_PARAMETERS.getSelected();
	int numFiles = LWIR_PARAMETERS.getSourceFilesFlat(sourceSetList, sel_chn).length; // just the number		int numFiles = LWIR_PARAMETERS.getSourceFilesFlat(sourceSetList, sel_chn).length; // just the number
	String [][] sourceFilesList=LWIR_PARAMETERS.getSourceFiles(sourceSetList, sel_chn);		String [][] sourceFilesList=LWIR_PARAMETERS.getSourceFiles(sourceSetList, sel_chn);
	// String [] sourceFilesList=DISTORTION_PROCESS_CONFIGURATION.selectSourceFiles(); // select files - with/without dialog
	boolean saveGrids=DISTORTION_PROCESS_CONFIGURATION.saveGridImages;		boolean saveGrids=DISTORTION_PROCESS_CONFIGURATION.saveGridImages;
	boolean overwriteGrids=DISTORTION_PROCESS_CONFIGURATION.overwriteResultFiles;		boolean overwriteGrids=DISTORTION_PROCESS_CONFIGURATION.overwriteResultFiles;
	if (sourceSetList==null) return;		if (sourceSetList==null) return;
	showPatternMinMaxPeriodDialog(PATTERN_DETECT, true);		showPatternMinMaxPeriodDialog(PATTERN_DETECT, true);
	int this_file = 0;		int saved_file = 0;
	// if (DEBUG_LEVEL <100) return;		int in_file = 0;
	String gridDir=DISTORTION_PROCESS_CONFIGURATION.selectGridFileDirectory(		String gridDir=DISTORTION_PROCESS_CONFIGURATION.selectGridFileDirectory(
	true,DISTORTION_PROCESS_CONFIGURATION.gridDirectory,true);		true,DISTORTION_PROCESS_CONFIGURATION.gridDirectory,true);
	if (gridDir == null) saveGrids=false; // do not ask about the next ones too		if (gridDir == null) saveGrids=false; // do not ask about the next ones too




	for (int nset = 0; nset < sourceFilesList.length; nset++){		for (int nset = 0; nset < sourceFilesList.length; nset++){
	String set_name = sourceSetList[nset];		String set_name = sourceSetList[nset];
	int i = set_name.lastIndexOf(Prefs.getFileSeparator());		int i = set_name.lastIndexOf(Prefs.getFileSeparator());
	@@ -9481,11 +9476,12 @@ if (MORE_BUTTONS) {
	}		}

	for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){		for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
			in_file++;
	long startFileTime=System.nanoTime();		long startFileTime=System.nanoTime();
	if (DEBUG_LEVEL>0){		if (DEBUG_LEVEL>0){
	System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+		System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+
	sourceFilesList.length+"), channel # "+(nfile + 1)+		sourceFilesList.length+"), channel # "+(nfile + 1)+
	" (of "+ sourceFilesList[nset].length+"), file " +(this_file + 1)+" (of "+ numFiles+ ") - "+sourceFilesList[nset][nfile]);		" (of "+ sourceFilesList[nset].length+"), file "+in_file+" (of "+ numFiles+ ") success in "+saved_file+" - "+sourceFilesList[nset][nfile]);
	}		}
	String grid_path = null;		String grid_path = null;
	if (saveGrids && !overwriteGrids){ // check if result already exists		if (saveGrids && !overwriteGrids){ // check if result already exists
	@@ -9506,11 +9502,11 @@ if (MORE_BUTTONS) {

	matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
	matchSimulatedPattern.invalidateFocusMask();		matchSimulatedPattern.invalidateFocusMask();
			boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel);
	int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
			LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	PATTERN_DETECT.minGridPeriod/2,
	PATTERN_DETECT.maxGridPeriod/2,
	SIMUL,		SIMUL,
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel,		imp_sel,
	@@ -9526,7 +9522,7 @@ if (MORE_BUTTONS) {

	if (DEBUG_LEVEL>1) System.out.println("numAbsolutePoints="+numAbsolutePoints);		if (DEBUG_LEVEL>1) System.out.println("numAbsolutePoints="+numAbsolutePoints);
	if ((numAbsolutePoints==DISTORTION.errPatternNotFound) \|\| (numAbsolutePoints==DISTORTION.errTooFewCells)) {		if ((numAbsolutePoints==DISTORTION.errPatternNotFound) \|\| (numAbsolutePoints==DISTORTION.errTooFewCells)) {
	if (DEBUG_LEVEL>0) System.out.println("Grid "+(this_file+1)+" not found or too small ("+numAbsolutePoints+"), wasted "+		if (DEBUG_LEVEL>0) System.out.println("Grid "+(in_file)+" not found or too small ("+numAbsolutePoints+"), wasted "+
	IJ.d2s(0.000000001*(System.nanoTime()-startFileTime),3)+" seconds )\n");		IJ.d2s(0.000000001*(System.nanoTime()-startFileTime),3)+" seconds )\n");
	if (this.SYNC_COMMAND.stopRequested.get()>0) {		if (this.SYNC_COMMAND.stopRequested.get()>0) {
	System.out.println("User requested stop");		System.out.println("User requested stop");
	@@ -9561,7 +9557,7 @@ if (MORE_BUTTONS) {
	}		}
	}		}
	}		}
	if (DEBUG_LEVEL>0) System.out.println("Grid "+(this_file+1)+" calculation done at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" (in "+		if (DEBUG_LEVEL>0) System.out.println("Grid "+(saved_file+1)+" calculation done at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" (in "+
	IJ.d2s(0.000000001*(System.nanoTime()-startFileTime),3)+"s )\n");		IJ.d2s(0.000000001*(System.nanoTime()-startFileTime),3)+"s )\n");

	//		//
	@@ -9569,7 +9565,7 @@ if (MORE_BUTTONS) {
	System.out.println("User requested stop");		System.out.println("User requested stop");
	break;		break;
	}		}
	this_file++;		saved_file++;
	}		}
	}		}
	if (DEBUG_LEVEL>0) System.out.println(((this.SYNC_COMMAND.stopRequested.get()>0)?"Partial (interrupted by user) set of grids":"All")+ " grids calculation done at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));		if (DEBUG_LEVEL>0) System.out.println(((this.SYNC_COMMAND.stopRequested.get()>0)?"Partial (interrupted by user) set of grids":"All")+ " grids calculation done at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	@@ -9628,10 +9624,9 @@ if (MORE_BUTTONS) {
	matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
	matchSimulatedPattern.invalidateFocusMask();		matchSimulatedPattern.invalidateFocusMask();
	int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
			LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	PATTERN_DETECT.minGridPeriod/2,
	PATTERN_DETECT.maxGridPeriod/2,
	SIMUL,		SIMUL,
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel,		imp_sel,
	@@ -9733,12 +9728,10 @@ if (MORE_BUTTONS) {
	imp_sel); // reuse the same image window		imp_sel); // reuse the same image window
	//Remove for old method?		//Remove for old method?
	matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize);		matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize);

	matchSimulatedPattern.calculateDistortions(		matchSimulatedPattern.calculateDistortions(
			LWIR_PARAMETERS,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	PATTERN_DETECT.minGridPeriod/2,
	PATTERN_DETECT.maxGridPeriod/2,
	SIMUL,		SIMUL,
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel,		imp_sel,
	@@ -17208,7 +17201,8 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	null, // no mesh distortion here		null, // no mesh distortion here
	thisSimulParameters.subdiv,// SIMUL.subdiv, - do not need high quality here		thisSimulParameters.subdiv,// SIMUL.subdiv, - do not need high quality here
	size,		size,
	true); // center for greens		true, // center for greens
			false);//boolean mono
	sim_pix= simulationPattern.extractSimulPatterns (		sim_pix= simulationPattern.extractSimulPatterns (
	thisSimulParameters,		thisSimulParameters,
	1,		1,
	@@ -17783,7 +17777,8 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	distortedPattern[2], //		distortedPattern[2], //
	simulParameters.subdiv,		simulParameters.subdiv,
	fft_size,		fft_size,
	simulParameters.center_for_g2);		simulParameters.center_for_g2,
			false);//boolean mono
	wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;		wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;
	wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;		wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;
	wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;		wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;
	@@ -17835,7 +17830,8 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	simCorr, //		simCorr, //
	simulParameters.subdiv,		simulParameters.subdiv,
	fft_size,		fft_size,
	simulParameters.center_for_g2);		simulParameters.center_for_g2,
			false);//boolean mono
	}		}
	simul_pixels= simulationPattern.extractSimulPatterns (		simul_pixels= simulationPattern.extractSimulPatterns (
	simulParameters,		simulParameters,
	@@ -20302,10 +20298,13 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	public boolean showDistortionDialog(MatchSimulatedPattern.DistortionParameters distortionParameters) {		public boolean showDistortionDialog(MatchSimulatedPattern.DistortionParameters distortionParameters) {
	int i;		int i;
	GenericDialog gd = new GenericDialog("Distrortion parameters");		GenericDialog gd = new GenericDialog("Distrortion parameters");
	gd.addNumericField("FFTSize (Initial pattern detection only):", distortionParameters.FFTSize, 0); // 128		gd.addNumericField("FFTSize (Initial pattern detection only):", distortionParameters.FFTSize, 0); // 256
			gd.addNumericField("FFTSize for LWIR sensors):", distortionParameters.FFTSize_lwir, 0); // 32
	gd.addNumericField("FFT Gaussian width (relative):", distortionParameters.fftGaussWidth, 3);		gd.addNumericField("FFT Gaussian width (relative):", distortionParameters.fftGaussWidth, 3);
	gd.addNumericField("Correlation size:", distortionParameters.correlationSize, 0); // 64		gd.addNumericField("Correlation size:", distortionParameters.correlationSize, 0); // 64
	gd.addNumericField("Maximal correlation size:", distortionParameters.maximalCorrelationSize, 0); // 64		gd.addNumericField("Correlation size LWIR:", distortionParameters.correlationSizeLwir, 0); // 16
			gd.addNumericField("Maximal correlation size:", distortionParameters.maximalCorrelationSize, 0); // 128
			gd.addNumericField("Maximal correlation size LWIR:", distortionParameters.maximalCorrelationSizeLwir, 0); // 16

	gd.addNumericField("Correlation Gauss width (relative):", distortionParameters.correlationGaussWidth, 3);		gd.addNumericField("Correlation Gauss width (relative):", distortionParameters.correlationGaussWidth, 3);
	gd.addCheckbox("Keep Gaussian width absolute when increasing FFT size",distortionParameters.absoluteCorrelationGaussWidth);		gd.addCheckbox("Keep Gaussian width absolute when increasing FFT size",distortionParameters.absoluteCorrelationGaussWidth);
	@@ -20330,20 +20329,21 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	gd.addNumericField("Gaussian sigma to select correlation off-centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);		gd.addNumericField("Gaussian sigma to select correlation off-centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);
	gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);		gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);

	gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);		gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0); // 40
			gd.addNumericField("Minimal initial LWIR pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternClusterLwir, 0); // 10
	gd.addNumericField("Scale minimal contrast if the initial cluster is nonzero but smaller", distortionParameters.scaleMinimalInitialContrast, 3);		gd.addNumericField("Scale minimal contrast if the initial cluster is nonzero but smaller", distortionParameters.scaleMinimalInitialContrast, 3);
	gd.addNumericField("Overlap of FFT areas when searching for pattern", distortionParameters.searchOverlap, 3);		gd.addNumericField("Overlap of FFT areas when searching for pattern", distortionParameters.searchOverlap, 3);

	gd.addNumericField("Pattern subdivision:", distortionParameters.patternSubdiv, 0);		gd.addNumericField("Pattern subdivision:", distortionParameters.patternSubdiv, 0); // 4
	gd.addNumericField("Blur pattern bitmap (sigma): ", distortionParameters.bPatternSigma, 3,5,"pattern cell");		gd.addNumericField("Blur pattern bitmap (sigma): ", distortionParameters.bPatternSigma, 3,5,"pattern cell"); // 0.02
	gd.addNumericField("Blur pattern (sigma): ", distortionParameters.barraySigma, 3,5,"sensor pix");		gd.addNumericField("Blur pattern (sigma): ", distortionParameters.barraySigma, 3,5,"sensor pix"); // 0.5
	gd.addNumericField("Correlation weights (around maximum):", distortionParameters.correlationWeightSigma, 3,5,"nodes");		gd.addNumericField("Correlation weights (around maximum):", distortionParameters.correlationWeightSigma, 3,5,"nodes"); // 2.5
	gd.addNumericField("Correlation radius scale (0 - sharp sigma)", distortionParameters.correlationRadiusScale, 1,3,"sigmas");		gd.addNumericField("Correlation radius scale (0 - sharp sigma)", distortionParameters.correlationRadiusScale, 1,3,"sigmas"); //2.0

	gd.addNumericField("Correlation maximal radius to use", distortionParameters.correlationRadius, 0,1,"pix");		gd.addNumericField("Correlation maximal radius to use", distortionParameters.correlationRadius, 0,1,"pix"); // 2.0
	gd.addNumericField("Correlation maximum calculation threshold", distortionParameters.correlationThreshold*100, 2,5,"%");		gd.addNumericField("Correlation maximum calculation threshold", distortionParameters.correlationThreshold*100, 2,5,"%"); // .8
	gd.addNumericField("Interpolate correlation (FFT*linear)", distortionParameters.correlationSubdiv, 0,1,"x");		gd.addNumericField("Interpolate correlation (FFT*linear)", distortionParameters.correlationSubdiv, 0,3,"x"); // 16
	gd.addNumericField("Interpolate correlation with FFT", distortionParameters.correlationFFTSubdiv, 0,1,"x");		gd.addNumericField("Interpolate correlation with FFT", distortionParameters.correlationFFTSubdiv, 0,3,"x"); // 4

	gd.addNumericField("Correlation dx (debug)", distortionParameters.correlationDx, 3);		gd.addNumericField("Correlation dx (debug)", distortionParameters.correlationDx, 3);
	gd.addNumericField("Correlation dy (debug)", distortionParameters.correlationDy, 3);		gd.addNumericField("Correlation dy (debug)", distortionParameters.correlationDy, 3);
	@@ -20386,14 +20386,13 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
			distortionParameters.FFTSize = makePowerOfTwo((int) gd.getNextNumber());
	distortionParameters.FFTSize=1;		distortionParameters.FFTSize_lwir = makePowerOfTwo((int) gd.getNextNumber());
	for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.FFTSize <<=1; /* make it to be power of 2 */
	distortionParameters.fftGaussWidth= gd.getNextNumber();		distortionParameters.fftGaussWidth= gd.getNextNumber();
	distortionParameters.correlationSize=1;		distortionParameters.correlationSize = makePowerOfTwo((int) gd.getNextNumber());
	for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.correlationSize <<=1; /* make it to be power of 2 */		distortionParameters.correlationSizeLwir = makePowerOfTwo((int) gd.getNextNumber());
	distortionParameters.maximalCorrelationSize=1;		distortionParameters.maximalCorrelationSize = makePowerOfTwo((int) gd.getNextNumber());
	for (i=(int) gd.getNextNumber(); i >1; i>>=1) distortionParameters.maximalCorrelationSize <<=1; /* make it to be power of 2 */		distortionParameters.maximalCorrelationSizeLwir = makePowerOfTwo((int) gd.getNextNumber());
	distortionParameters.correlationGaussWidth= gd.getNextNumber();		distortionParameters.correlationGaussWidth= gd.getNextNumber();
	distortionParameters.absoluteCorrelationGaussWidth=gd.getNextBoolean();		distortionParameters.absoluteCorrelationGaussWidth=gd.getNextBoolean();
	distortionParameters.zeros= (int) gd.getNextNumber();		distortionParameters.zeros= (int) gd.getNextNumber();
	@@ -20414,6 +20413,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	distortionParameters.contrastAverageSigma= gd.getNextNumber();		distortionParameters.contrastAverageSigma= gd.getNextNumber();

	distortionParameters.minimalPatternCluster=(int) gd.getNextNumber();		distortionParameters.minimalPatternCluster=(int) gd.getNextNumber();
			distortionParameters.minimalPatternClusterLwir=(int) gd.getNextNumber();

	distortionParameters.scaleMinimalInitialContrast=gd.getNextNumber();		distortionParameters.scaleMinimalInitialContrast=gd.getNextNumber();
	distortionParameters.searchOverlap= gd.getNextNumber();		distortionParameters.searchOverlap= gd.getNextNumber();

	@@ -20460,6 +20461,12 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();		MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
	return true;		return true;
	}		}
			private int makePowerOfTwo(int v) {
			int v2 = 1;
			for (int i=v; i > 1; i>>=1 ) v2 <<=1; /* make it to be power of 2 */
			return v2;

			}
	/* ======================================================================== */		/* ======================================================================== */
	/* ======================================================================== */		/* ======================================================================== */
	public boolean showGaussianStackDialog(EyesisAberrations.InverseParameters inverseParameters) {		public boolean showGaussianStackDialog(EyesisAberrations.InverseParameters inverseParameters) {

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

+7 −4

Original line number	Original line	Diff line number	Diff line
	@@ -1278,10 +1278,11 @@ public class EyesisAberrations {
	}		}

	int rslt=matchSimulatedPattern.calculateDistortions(		int rslt=matchSimulatedPattern.calculateDistortions(
			null, // LwirReaderParameters lwirReaderParameters, // null is OK
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
	patternDetectParameters.minGridPeriod/2,		// patternDetectParameters.minGridPeriod/2,
	patternDetectParameters.maxGridPeriod/2,		// patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	colorComponents.equalizeGreens,		colorComponents.equalizeGreens,
	imp,		imp,
	@@ -2709,7 +2710,8 @@ public class EyesisAberrations {
	distortedPattern[2], //		distortedPattern[2], //
	simulParameters.subdiv,		simulParameters.subdiv,
	fft_size,		fft_size,
	simulParameters.center_for_g2);		simulParameters.center_for_g2,
			false);//boolean mono
	wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;		wVectors[0][0]=2.0*distortedPattern[0][0]/subpixel;
	wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;		wVectors[0][1]=2.0*distortedPattern[0][1]/subpixel;
	wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;		wVectors[1][0]=2.0*distortedPattern[1][0]/subpixel;
	@@ -2752,7 +2754,8 @@ public class EyesisAberrations {
	simCorr, //		simCorr, //
	simulParameters.subdiv,		simulParameters.subdiv,
	fft_size,		fft_size,
	simulParameters.center_for_g2);		simulParameters.center_for_g2,
			false);//boolean mono
	}		}
	// simul_pixels= simulationPattern.extractSimulPatterns (		// simul_pixels= simulationPattern.extractSimulPatterns (
	simul_pixels= simulationPattern.extractSimulPatterns (		simul_pixels= simulationPattern.extractSimulPatterns (

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

+23 −21

Original line number	Original line	Diff line number	Diff line
	@@ -665,11 +665,12 @@ horizontal axis:

	boolean noMessageBoxes=true;		boolean noMessageBoxes=true;
	int numAbsolutePoints = matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints = matchSimulatedPattern.calculateDistortions(
			null, // LwirReaderParameters lwirReaderParameters, // null is OK
	// allow more of grid around pointers?		// allow more of grid around pointers?
	distortionParameters, //		distortionParameters, //
	this.patternDetectParameters,		this.patternDetectParameters,
	this.patternDetectParameters.minGridPeriod/2,		// this.patternDetectParameters.minGridPeriod/2,
	this.patternDetectParameters.maxGridPeriod/2,		// this.patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	equalizeGreens, imp_eq,		equalizeGreens, imp_eq,
	this.laserPointers, // null, //LASER_POINTERS, //		this.laserPointers, // null, //LASER_POINTERS, //
	@@ -840,11 +841,12 @@ horizontal axis:
	// matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");		// matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");

	int numAbsolutePoints = this.matchSimulatedPatterns[numSensor].calculateDistortions(		int numAbsolutePoints = this.matchSimulatedPatterns[numSensor].calculateDistortions(
			null, // LwirReaderParameters lwirReaderParameters, // null is OK
	// allow more of grid around pointers?		// allow more of grid around pointers?
	distortionParameters, //		distortionParameters, //
	this.patternDetectParameters,		this.patternDetectParameters,
	this.patternDetectParameters.minGridPeriod/2,		// this.patternDetectParameters.minGridPeriod/2,
	this.patternDetectParameters.maxGridPeriod/2,		// this.patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	equalizeGreens, imp_eq,		equalizeGreens, imp_eq,
	this.laserPointers, // null, //LASER_POINTERS, //		this.laserPointers, // null, //LASER_POINTERS, //

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

+6 −3

Original line number	Original line	Diff line number	Diff line
	@@ -99,6 +99,7 @@ public class LensAdjustment {
	ImagePlus imp_eq=matchSimulatedPattern.applyFlatField (imp); // will throw if image size mismatch		ImagePlus imp_eq=matchSimulatedPattern.applyFlatField (imp); // will throw if image size mismatch
	if (updating) {		if (updating) {
	double maxActualCorr= matchSimulatedPattern.refineDistortionCorrelation (		double maxActualCorr= matchSimulatedPattern.refineDistortionCorrelation (
			null, // LwirReaderParameters lwirReaderParameters, // null is OK
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
	simulParameters,		simulParameters,
	@@ -132,7 +133,8 @@ public class LensAdjustment {
	System.out.println("updateFocusGrid(), number of already defined grid cells (before distortions()) = "+matchSimulatedPattern.numDefinedCells());		System.out.println("updateFocusGrid(), number of already defined grid cells (before distortions()) = "+matchSimulatedPattern.numDefinedCells());
	}		}
	matchSimulatedPattern.distortions(		matchSimulatedPattern.distortions(
	null, // is not used in update mode		null, //LwirReaderParameters lwirReaderParameters, // null is OK
			null, // final boolean [] triedIndices, // is not used in update mode
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
	patternDetectParameters.minGridPeriod/2,		patternDetectParameters.minGridPeriod/2,
	@@ -157,10 +159,11 @@ public class LensAdjustment {
	// matchSimulatedPattern.invalidateFlatFieldForGrid(); //Keep these!		// matchSimulatedPattern.invalidateFlatFieldForGrid(); //Keep these!
	// matchSimulatedPattern.invalidateFocusMask();		// matchSimulatedPattern.invalidateFocusMask();
	numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // allow more of grid around pointers?		numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // allow more of grid around pointers?
			null, // LwirReaderParameters lwirReaderParameters, // null is OK
	distortionParameters, //		distortionParameters, //
	patternDetectParameters,		patternDetectParameters,
	patternDetectParameters.minGridPeriod/2,		// patternDetectParameters.minGridPeriod/2,
	patternDetectParameters.maxGridPeriod/2,		// patternDetectParameters.maxGridPeriod/2,
	simulParameters,		simulParameters,
	equalizeGreens,		equalizeGreens,
	imp_eq,		imp_eq,

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

+9270 −8975

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