quadratic photometric equalization (3abbfc39) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

+2 −3

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

+428 −455

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

+2 −0

Original line number	Original line	Diff line number	Diff line
	@@ -4666,6 +4666,8 @@ public class OpticalFlow {
	threadsMax,		threadsMax,
	debugLevel-2);		debugLevel-2);
	}		}
			} else {
			System.out.println("Using photometric calibration from scene "+quadCLTs[ref_index].getPhotometricScene());
	}		}

	if (test_ers) { // only debug feature		if (test_ers) { // only debug feature

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

+69 −71

Original line number	Original line	Diff line number	Diff line
	@@ -2276,8 +2276,8 @@ public class QuadCLT extends QuadCLTCPU {
	System.out.println("processCLTQuadCorrs(): processing "+getTotalFiles(set_channels)+" files ("+set_channels.length+" file sets) finished at "+		System.out.println("processCLTQuadCorrs(): processing "+getTotalFiles(set_channels)+" files ("+set_channels.length+" file sets) finished at "+
	IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory3="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory3="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	}		}
			@Deprecated
	public static boolean calibratePhotometric(		public static boolean calibratePhotometric( // not used
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	final QuadCLT ref_scene, // now - may be null - for testing if scene is rotated ref		final QuadCLT ref_scene, // now - may be null - for testing if scene is rotated ref
	final double min_strength,		final double min_strength,
	@@ -2505,6 +2505,7 @@ public class QuadCLT extends QuadCLTCPU {
	double [] avg_pix = new double [len];		double [] avg_pix = new double [len];
	double [] offsets = new double[dpixels.length];		double [] offsets = new double[dpixels.length];
	double [] scales = new double[dpixels.length];		double [] scales = new double[dpixels.length];
			double [] scales2 = new double[dpixels.length];
	double s0 = 0.0;		double s0 = 0.0;
	double sx= 0.0;		double sx= 0.0;
	double sx2 = 0.0;		double sx2 = 0.0;
	@@ -2512,7 +2513,17 @@ public class QuadCLT extends QuadCLTCPU {
	double [] sxy = new double[num_sens];		double [] sxy = new double[num_sens];
	boolean [] good_pix = new boolean[len];		boolean [] good_pix = new boolean[len];
	double [][] pa_coeff = new double[num_sens][];		double [][] pa_coeff = new double[num_sens][];
			double min_abs_a = 1E-9;
	Arrays.fill(good_pix, true);		Arrays.fill(good_pix, true);

			double [] offs_old = ref_scene.getLwirOffsets();
			double [] scales_old = ref_scene.getLwirScales();
			double [] scales2_old = ref_scene.getLwirScales2();

			double [] offs_new = new double [num_sens];
			double [] scales_new = new double [num_sens];
			double [] scales2_new = new double [num_sens];

	for (int nref = 0; nref < num_refines; nref++) {		for (int nref = 0; nref < num_refines; nref++) {
	Arrays.fill(avg_pix, 0.0);		Arrays.fill(avg_pix, 0.0);
	int num_good = 0;		int num_good = 0;
	@@ -2527,77 +2538,74 @@ public class QuadCLT extends QuadCLTCPU {
	}		}
	}		}
	double [][] pa_data = new double [num_good][2];		double [][] pa_data = new double [num_good][2];
			double [][] raw = new double [num_sens][len];
	for (int nsens = 0; nsens < num_sens; nsens++) {		for (int nsens = 0; nsens < num_sens; nsens++) {
			Arrays.fill(raw[nsens],Double.NaN); // debug only

	int indx = 0;		int indx = 0;
	for (int i = 0; i < len; i++) if (good_pix[i]){		for (int i = 0; i < len; i++) if (good_pix[i]){
	pa_data[indx][0] = dpixels[nsens][i];		double A0 = scales2_old[nsens];
			double B0 = scales_old[nsens];
			double C0 = offs_old[nsens];
			double a = A0;
			double b = (B0 - 2 * C0 * A0);
			double c = (C0C0A0 -C0 * B0 - dpixels[nsens][i]);
			double p = -c/b;
			if (Math.abs(a) >= min_abs_a) {
			p= (-b + Math.sqrt(bb - 4 a * c))/(2 * a);
			}
			raw[nsens][i] = p;
			pa_data[indx][0] = p; // dpixels[nsens][i];
	pa_data[indx][1] = avg_pix[i];		pa_data[indx][1] = avg_pix[i];
	indx++;		indx++;
	}		}
	// quadratic		// quadratic
	pa_coeff[nsens] =(new PolynomialApproximation(0)).polynomialApproximation1d(pa_data, quadratic ? 2 : 1);		pa_coeff[nsens] =(new PolynomialApproximation(0)).polynomialApproximation1d(pa_data, quadratic ? 2 : 1);
			double a = pa_coeff[nsens][2];
			double b = pa_coeff[nsens][1];
			double c = pa_coeff[nsens][0];
			double A = a;
			double C = -c/b;
			if (Math.abs(a) >= min_abs_a) {
			C = (-b + Math.sqrt(bb - 4ac))/(2 a);
	}		}
			double B = 2 * C * a + b;
			scales2_new[nsens] = A;
			scales_new [nsens] = B;
			offs_new[nsens] = C;
			}

	if (debug) {		if (debug) {
	System.out.println("calibratePhotometric() nref="+nref);		System.out.println("calibratePhotometric() nref="+nref);
			/*
			System.out.println(String.format("%3s %8s %8s %8s",
			"chn"," c "," b ", " 1e6*a "));
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	System.out.println(String.format("%2d: %8.4f %8.6f %8.6f", n,pa_coeff[n][0],pa_coeff[n][1], 1e6*pa_coeff[n][2]));		System.out.println(String.format("%2d: %8.4f %8.6f %8.6f", n,pa_coeff[n][0],pa_coeff[n][1], 1e6*pa_coeff[n][2]));
	}		}
	System.out.println();		System.out.println();
	double [][] diffs = new double [num_sens][len];		*/
	for (int n = 0; n < num_sens; n++) {		System.out.println(String.format("%3s %10s %8s %8s %10s %8s %8s",
	Arrays.fill(diffs[n], Double.NaN);		// "chn"," c "," b ", " 1e6*a "));
	}		"chn"," offs0 ","scale0 ", "scale20"," offs "," scale ", " scale2"));
	for (int i = 0; i < len; i++) if (good_pix[i]) { // if (!Double.isNaN(avg_pix[i])){
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	// diffs[n][i] = dpixels[n][i] - (scales[n] * avg_pix[i] + offsets[n]);		System.out.println(String.format("%2d: %10.4f %8.5f %8.5f %10.4f %8.5f %8.5f",
	diffs[n][i] = -(avg_pix[i] - pa_coeff[n][2] * dpixels[n][i] * dpixels[n][i] - pa_coeff[n][1] * dpixels[n][i] - pa_coeff[n][0]);		n,offs_old[n],scales_old[n], 1e6*scales2_old[n],
	}		offs_new[n],scales_new[n], 1e6*scales2_new[n]));
	}
	(new ShowDoubleFloatArrays()).showArrays( // out of boundary 15
	diffs,
	width,
	height,
	true,
	"photometric-quad-err"+nref);
	}		}
			System.out.println();


	Arrays.fill(offsets,0.0);
	Arrays.fill(scales,0.0);
	s0 = 0.0;
	sx= 0.0;
	sx2 = 0.0;
	Arrays.fill(sy,0.0);
	Arrays.fill(sxy,0.0);
	for (int i = 0; i < len; i++) if (good_pix[i]) { // !Double.isNaN(avg_pix[i])){
	s0 += 1.0;
	sx += avg_pix[i];
	sx2 += avg_pix[i] * avg_pix[i];
	for (int n = 0; n < num_sens; n++) {
	sy[n] += dpixels[n][i];
	sxy[n] += dpixels[n][i] * avg_pix[i];
	}
	}
	for (int n = 0; n < num_sens; n++) {
	double d = s0 * sx2 + sx * sy[n];
	scales[n] = (sxy[n] * s0 + sy[n] * sy[n]) / d;
	offsets[n] = (sy[n] * sx2 -sxy[n]*sx) / d;
	}


	if (debug) {
	System.out.println("calibratePhotometric() nref="+nref);
	for (int n = 0; n < num_sens; n++) {
	System.out.println(String.format("%2d: %8.4f %8.6f", n,offsets[n],scales[n]));
	}
	System.out.println();
	double [][] diffs = new double [num_sens][len];		double [][] diffs = new double [num_sens][len];
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	Arrays.fill(diffs[n], Double.NaN);		Arrays.fill(diffs[n], Double.NaN);
	}		}
	for (int i = 0; i < len; i++) if (good_pix[i]) { // if (!Double.isNaN(avg_pix[i])){		for (int i = 0; i < len; i++) if (good_pix[i]) { // if (!Double.isNaN(avg_pix[i])){
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	diffs[n][i] = dpixels[n][i] - (scales[n] * avg_pix[i] + offsets[n]);		double poffs = raw[n][i] - offs_new[n];
			diffs[n][i] = -(avg_pix[i] -
			(poffs * scales_new[n] + poffspoffsscales2_new[n]));
	}		}
	}		}
	(new ShowDoubleFloatArrays()).showArrays( // out of boundary 15		(new ShowDoubleFloatArrays()).showArrays( // out of boundary 15
	@@ -2605,14 +2613,13 @@ public class QuadCLT extends QuadCLTCPU {
	width,		width,
	height,		height,
	true,		true,
	"photometric-err"+nref);		"photometric-quad-err"+nref);

	// dpix_orig[n] = dpixels[n].clone();
	double [][] corrected = new double [num_sens][len];		double [][] corrected = new double [num_sens][len];
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	Arrays.fill(corrected[n], Double.NaN);		Arrays.fill(corrected[n], Double.NaN);
	for (int i = 0; i < len; i++) if (!Double.isNaN(dpixels[n][i])){		for (int i = 0; i < len; i++) if (!Double.isNaN(dpixels[n][i])){
	corrected[n][i] = (dpixels[n][i] - offsets[n])/scales[n];		double poffs = raw[n][i] - offs_new[n];
			corrected[n][i] = (poffs * scales_new[n] + poffspoffsscales2_new[n]);
	}		}
	}		}

	@@ -2621,15 +2628,16 @@ public class QuadCLT extends QuadCLTCPU {
	width,		width,
	height,		height,
	true,		true,
	"photometric-corr"+nref);		"photometric-quad-corr"+nref);
	}		}
	//max_diff		//max_diff
	if (nref < (num_refines-1)) {		if (nref < (num_refines-1)) {
	for (int i = 0; i < len; i++) if (good_pix[i]) { // !Double.isNaN(avg_pix[i])){		for (int i = 0; i < len; i++) if (good_pix[i]) { // !Double.isNaN(avg_pix[i])){
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	double diff = Math.abs(dpixels[n][i] - (scales[n] * avg_pix[i] + offsets[n]));		double poffs = raw[n][i] - offs_new[n];
			double diff = Math.abs(avg_pix[i] -
			(poffs * scales_new[n] + poffspoffsscales2_new[n]));
	if (diff > max_diff) {		if (diff > max_diff) {
	// dpixels[n][i] = Double.NaN;
	good_pix[i] = false;		good_pix[i] = false;
	break;		break;
	}		}
	@@ -2637,22 +2645,12 @@ public class QuadCLT extends QuadCLTCPU {
	}		}
	}		}
	}		}
	double [] offsets_old = ref_scene.getLwirOffsets();
	double [] scales_old = ref_scene.getLwirScales();
	double [] scales2_old = ref_scene.getLwirScales2();
	double [] offsets_new = new double[num_sens];
	double [] scales_new = new double[num_sens];
	double [] scales2_new = new double[num_sens];
	for (int n = 0; n < num_sens; n++) {
	scales_new[n] = scales_old[n]/scales[n];
	offsets_new[n] = offsets_old[n] + offsets[n] / scales_old[n];
	}
	System.out.println("calibratePhotometric() Updated calibration:");		System.out.println("calibratePhotometric() Updated calibration:");
	for (int n = 0; n < num_sens; n++) {		for (int n = 0; n < num_sens; n++) {
	System.out.println(String.format("%2d: %8.4f %8.6f %8.6f", n,offsets_new[n],scales_new[n], scales2_new[n]));		System.out.println(String.format("%2d: %10.4f %8.6f %8.6f", n,offs_new[n],scales_new[n], 1E6*scales2_new[n]));
	}		}
	System.out.println();		System.out.println();
	ref_scene.setLwirOffsets (offsets_new);		ref_scene.setLwirOffsets (offs_new);
	ref_scene.setLwirScales (scales_new);		ref_scene.setLwirScales (scales_new);
	ref_scene.setLwirScales2 (scales2_new);		ref_scene.setLwirScales2 (scales2_new);
	return true;		return true;

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

+20 −4

Original line number	Original line	Diff line number	Diff line
	@@ -151,6 +151,7 @@ public class QuadCLTCPU {
	boolean new_image_data = false;		boolean new_image_data = false;
	boolean [][] saturation_imp = null; // (near) saturated pixels or null		boolean [][] saturation_imp = null; // (near) saturated pixels or null
	boolean is_aux = false;		boolean is_aux = false;
			String photometric_scene = null;
	double [] lwir_offsets = null; // per image subtracted values		double [] lwir_offsets = null; // per image subtracted values
	double [] lwir_scales = null; // per image scales		double [] lwir_scales = null; // per image scales
	double [] lwir_scales2 = null; // per image quadratic scales		double [] lwir_scales2 = null; // per image quadratic scales
	@@ -264,6 +265,8 @@ public class QuadCLTCPU {
	if (qParent.saturation_imp != null) this.saturation_imp = qParent.saturation_imp.clone(); // each camera will be re-written, not just modified, so shallow copy		if (qParent.saturation_imp != null) this.saturation_imp = qParent.saturation_imp.clone(); // each camera will be re-written, not just modified, so shallow copy
	this.is_aux = qParent.is_aux;		this.is_aux = qParent.is_aux;
	// this.is_mono = qParent.is_mono;		// this.is_mono = qParent.is_mono;

			this.photometric_scene = qParent.photometric_scene;
	this.lwir_offsets = ErsCorrection.clone1d(qParent.lwir_offsets);		this.lwir_offsets = ErsCorrection.clone1d(qParent.lwir_offsets);
	this.lwir_scales = ErsCorrection.clone1d(qParent.lwir_scales);		this.lwir_scales = ErsCorrection.clone1d(qParent.lwir_scales);
	this.lwir_scales2 = ErsCorrection.clone1d(qParent.lwir_scales2);		this.lwir_scales2 = ErsCorrection.clone1d(qParent.lwir_scales2);
	@@ -1807,13 +1810,20 @@ public class QuadCLTCPU {
	} else {		} else {
	lwir_offset = Double.NaN;		lwir_offset = Double.NaN;
	}		}
			this.photometric_scene = getImageName();
			}

			public String getPhotometricScene() {
			return this.photometric_scene;
	}		}

	public void setLwirScales(double [] scales) {		public void setLwirScales(double [] scales) {
	lwir_scales = scales; // will need to update properties!		lwir_scales = scales; // will need to update properties!
			this.photometric_scene = getImageName();
	}		}
	public void setLwirScales2(double [] scales2) {		public void setLwirScales2(double [] scales2) {
	lwir_scales2 = scales2; // will need to update properties!		lwir_scales2 = scales2; // will need to update properties!
			this.photometric_scene = getImageName();
	}		}

	public double [] getColdHot() { // USED in lwir		public double [] getColdHot() { // USED in lwir
	@@ -2018,7 +2028,9 @@ public class QuadCLTCPU {
	properties.setProperty(prefix+"lwir_scales2",		properties.setProperty(prefix+"lwir_scales2",
	IntersceneMatchParameters.doublesToString(this.lwir_scales2));		IntersceneMatchParameters.doublesToString(this.lwir_scales2));
	}		}
			if (this.photometric_scene != null) {
			properties.setProperty(prefix+"photometric_scene", this.photometric_scene);
			}
	}		}


	@@ -2066,6 +2078,10 @@ public class QuadCLTCPU {
	properties.setProperty(this_prefix+"lwir_scales2",		properties.setProperty(this_prefix+"lwir_scales2",
	IntersceneMatchParameters.doublesToString(this.lwir_scales2));		IntersceneMatchParameters.doublesToString(this.lwir_scales2));
	}		}
			if (other_properties.getProperty(other_prefix+"photometric_scene")!=null) {
			this.photometric_scene= (String) other_properties.getProperty(other_prefix+"photometric_scene");
			properties.setProperty(this_prefix+"photometric_scene", this.photometric_scene);
			}


	/*		/*
	@@ -2190,9 +2206,9 @@ public class QuadCLTCPU {
	this.lwir_scales2= IntersceneMatchParameters.StringToDoubles(		this.lwir_scales2= IntersceneMatchParameters.StringToDoubles(
	properties.getProperty(prefix+"lwir_scales2"),0);		properties.getProperty(prefix+"lwir_scales2"),0);
	}		}
			if (properties.getProperty(prefix+"photometric_scene")!=null) {
			this.photometric_scene= (String) properties.getProperty(prefix+"photometric_scene");
			}
	}		}

	public void setKernelImageFile(ImagePlus img_kernels){ // not used in lwir		public void setKernelImageFile(ImagePlus img_kernels){ // not used in lwir

Original line number	Original line	Diff line number	Diff line
	@@ -3218,9 +3218,9 @@ public class CLTParameters {
	gd.addMessage ("It is applied when the source files are read.");		gd.addMessage ("It is applied when the source files are read.");
	gd.addCheckbox ("Enable photometric calibration", this.photo_en,		gd.addCheckbox ("Enable photometric calibration", this.photo_en,
	"Equalize per- sensor gains and offsets. Requires disparity map. Save to reference scene and with current scene (to .corr-zml).");		"Equalize per- sensor gains and offsets. Requires disparity map. Save to reference scene and with current scene (to .corr-zml).");
	gd.addNumericField("Full photometric (re)calibrations", this.photo_num_full, 0,3,"pix",		gd.addNumericField("Full photometric (re)calibrations", this.photo_num_full, 0,3,"",
	"Full recalibratrions include re-importing raw images with updated offsets/gains");		"Full recalibratrions include re-importing raw images with updated offsets/gains");
	gd.addNumericField("Refines", this.photo_num_refines, 0,3,"pix",		gd.addNumericField("Refines", this.photo_num_refines, 0,3,"",
	"Calculate calibration, remove outliers (e.g. FG/BG) and repeat");		"Calculate calibration, remove outliers (e.g. FG/BG) and repeat");
	gd.addNumericField("Minimal DSI strength", this.photo_min_strength, 5,7,"",		gd.addNumericField("Minimal DSI strength", this.photo_min_strength, 5,7,"",
	"Do not use weak tiles.");		"Do not use weak tiles.");
	@@ -3895,7 +3895,6 @@ public class CLTParameters {
	gd.addTab ("O-Flow", "parameters for the interscene Optical FLow calculations");		gd.addTab ("O-Flow", "parameters for the interscene Optical FLow calculations");
	this.ofp.dialogQuestions(gd);		this.ofp.dialogQuestions(gd);

	gd.addTab ("Inter-Match", "Parameters for full-resolution (no decimation/macrotiles) scene matching");
	this.imp.dialogQuestions(gd);		this.imp.dialogQuestions(gd);

	gd.addTab ("Inter-LMA", "parameters for the interscene LMA fitting");		gd.addTab ("Inter-LMA", "parameters for the interscene LMA fitting");

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