next working snapshot (85bebb08) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java

+135 −50

Original line number	Diff line number	Diff line
		@@ -100,7 +100,7 @@ public class VegetationLMA {

		//[2][image_length] - alpha, [3][num_scenes] - per-scene offset (mostly for vignetting. MAYBE add per-scene pair of tilts
		private int [][] par_index; // indices - [0..4][full_pixel] - same as for tvao, value - parameter index
		private int [][] par_rindex; // parameter -> pair of type (0..3) and full window pixel index
		private int [][] par_rindex; // parameter -> pair of type (0..4) and full window pixel index
		private int num_pars_terrain;
		private int num_pars_vegetation;
		private int num_pars_alpha; //== num_pars_vegetation
		@@ -186,6 +186,8 @@ public class VegetationLMA {
		private boolean alpha_en_holes = true; // Search for small semi-transparent holes, disable diffusion of local alpha minimums
		private double alpha_diff_hole = 0.01; // minimal alpha difference between min and max neighbor to be considered a hole

		private double w_alpha_neib = 0.7; // weight of each of the neighbors relative to the center when calculating average alpha
		private double holes_pwr = 2.0; // Raise alpha (0..1) to this power when replacing vegetation cold spots with holes

		private boolean from_file = false;

		@@ -2535,8 +2537,6 @@ public class VegetationLMA {
		// No need here to add contributors as this should not depend on any other parameters
		if (samples_pointers[SAMPLES_ALPHA_PULL][1] > 0) { // fits[TVAO_ALPHA] && ((alpha_loss > 0) \|\| (alpha_push > 0))) {
		int dbg_nx = -76340;
		// final int ind_y_alpha_loss = samples_pointers[SAMPLES_ALPHA_PULL][0]; // ind_next;
		// ind_next += num_pars_alpha;
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@@ -2563,41 +2563,7 @@ public class VegetationLMA {
		}
		}
		}
		double avg = 0;
		int nn = 0;
		// removing all dependence on neighbors!
		/*
		double neib_min = Double.POSITIVE_INFINITY, neib_max = Double.NEGATIVE_INFINITY;
		for (int i = 0; i < alpha_neibs[n].length; i++) { // now 4, may be increased
		int di = alpha_neibs[n][i];
		d=0;
		if (di >= 0) {
		d = vector[di]; // d - full parameter index
		avg+=d;
		if (d < neib_min) neib_min = d;
		if (d > neib_max) neib_max = d;
		nn++;
		} else if (di < -1) {
		d = tvao[TVAO_ALPHA][-di - 2];
		avg+=d;
		if (d < neib_min) neib_min = d;
		if (d > neib_max) neib_max = d;
		nn++;
		}
		}
		avg /= nn; // average
		*/
		if (alpha_push > 0) {
		/*
		* p = alpha_push
		* n = alpha_push_neutral
		* a0 = p/(2 * n)
		* a1 = p/(2 * (1 - n))
		* f1(x) = p/(2 * n)* x * (1 - x/(2*n))
		* f2(x) = p * (x - 2n + 1) (1 - x) / (4 * (1-n)*(1-n)
		* df1(x)/dx = p/(2 * n^2 )*( n - x)
		* df2(x)/dx = p* (n-x)/(2*(1-n)^2)
		*/
		// average including center:
		/// double sum_w = (nn + alpha_push_center);
		/// double avg_c = (avg * nn + vector[np] * alpha_push_center) / sum_w;
		@@ -2622,14 +2588,6 @@ public class VegetationLMA {
		dd = alpha_push / (sum_w * 2 * one_minus_n * one_minus_n) * (alpha_push_neutral - avg_c);
		}
		jt[np][nx] += dd * alpha_push_center; // 2 * alpha_loss * d; // d/dalpha[i]
		/*
		for (int i = 0; i < alpha_neibs[n].length; i++) { // now 4, may be increased
		int di = alpha_neibs[n][i];
		if (di >= 0) {
		jt[di][nx] += dd; // 2 * alpha_loss * d; // d/dalpha[i]
		}
		}
		*/
		}
		}
		}
		@@ -2834,10 +2792,8 @@ public class VegetationLMA {
		ImageDtt.startAndJoin(threads);
		}


		/*
		if (samples_pointers[SAMPLES_VEGETATION_LPF][1] > 0) { // fits[TVAO_VEGETATION] && (veget_lpf >= 0)) { // should be positive for pull0 and terr_pull_cold (difference between vegetation and terrain)
		// final int ind_y_veget = samples_pointers[SAMPLES_VEGETATION_LPF][0]; // ind_next;
		// ind_next += num_pars_vegetation;
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@@ -2881,6 +2837,135 @@ public class VegetationLMA {
		ImageDtt.startAndJoin(threads);
		}

		*/


		if (samples_pointers[SAMPLES_VEGETATION_LPF][1] > 0) { // should be positive for pull0 and terr_pull_cold (difference between vegetation and terrain)
		if (num_pars_alpha <= 0) {
		System.out.println("getFxDerivs(): BUG: Asjusting SAMPLES_VEGETATION_LPF requires alpha parameters aslo to be fitted");
		} else {
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int n = ai.getAndIncrement(); n < num_pars_vegetation; n = ai.getAndIncrement()) {
		int np = n + samples_pointers[SAMPLES_VEGETATION_LPF][2];
		int nx = n + samples_pointers[SAMPLES_VEGETATION_LPF][0];
		int findx = par_rindex[np][1];//
		int npa = par_index[TVAO_ALPHA][findx]; // parameter for same-pixel alpha
		int na = npa - ind_pars_alpha;
		if (npa < 0) {
		System.out.println("getFxDerivs(): BUG: no alpha for vegetation, n="+n+", np="+np+", nx ="+nx+
		" findx="+findx+", npa="+npa);
		continue;
		}
		double d = 0;
		if (veget_lpf > 0) {
		double veget_avg4 = 0;
		int veget_nn4 = 0;
		for (int i = 0; i < veget_neibs[n].length; i++) { // now 4, may be increased
		int di = veget_neibs[n][i];
		d=0;
		if (di >= 0) {
		d = vector[di]; // d - full parameter index
		veget_avg4+=d;
		veget_nn4++;
		} else if ((di < -1) && lpf_fixed[TVAO_VEGETATION]) {
		d = tvao[TVAO_VEGETATION][-di - 2];
		veget_avg4+=d;
		veget_nn4++;
		}
		}
		if (veget_nn4 <= 0) {
		System.out.println("getFxDerivs(): BUG: veget_nn4="+veget_nn4+", n="+n+", np="+np+", nx ="+nx+
		" findx="+findx+", npa="+npa);
		continue;
		}
		veget_avg4 /= veget_nn4; // average
		double veget_lap = vector[np] - veget_avg4;
		if (veget_lap >=0) { // only for cold spots
		continue;
		}
		// fX[nx] += veget_lpf * (vector[np] - veget_avg4); // + veget_pull0 * vector[np];
		// double w_alpha_neib = 0.7;
		// double holes_pwr = 2.0;
		d = vector[npa];
		double alpha_avg5;
		if (alpha_piece_linear) {
		alpha_avg5 = (d < 0)? 0: ((d > 1) ? 1.0: d);
		} else {
		alpha_avg5 = (d < 0)? 0: ((d > 1) ? 1.0: 0.5 * (1.0 - Math.cos(d*Math.PI)));
		}
		// double alpha_avg5 = vector[npa]; // center alpha, weight = 1.0;
		double alpha_w5 = 1.0;
		// double [] derivs_neibs = new double [ alpha_neibs[n].length];
		for (int i = 0; i < alpha_neibs[n].length; i++) { // now 4, may be increased
		int di = alpha_neibs[na][i];
		d=0;
		if (di >= 0) {
		d = vector[di]; // d - full parameter index
		} else if ((di < -1) && lpf_fixed[TVAO_ALPHA]) {
		d = tvao[TVAO_ALPHA][-di - 2];
		}
		double alpha;

		if (alpha_piece_linear) {
		alpha = (d < 0)? 0: ((d > 1) ? 1.0: d);
		} else {
		alpha = (d < 0)? 0: ((d > 1) ? 1.0: 0.5 * (1.0 - Math.cos(d*Math.PI)));
		}
		alpha_avg5 += alpha * w_alpha_neib;
		alpha_w5 += w_alpha_neib;
		// TODO: calculate derivatives
		}
		// limit to 0..1 and apply cos
		alpha_avg5 /= alpha_w5; // average
		double alpha_pwr = Math.pow(alpha_avg5, holes_pwr);
		double val = veget_lap * alpha_pwr;
		fX[nx] += veget_lpf * val;

		if (jt != null) {
		jt[np][nx] += veget_lpf * alpha_pwr;
		for (int i = 0; i < veget_neibs[n].length; i++) { // now 4, may be increased
		int di = veget_neibs[n][i];
		if (di >= 0) {
		jt[di][nx] -= veget_lpf* alpha_pwr/veget_nn4;
		}
		}
		/* dval_dai = dval_dalpha_pwr * dalpha_pwr_dalpha * dalpha_dfai * dfai_dai; */
		double dval_dalpha_pwr = veget_lpf * veget_lap;
		double dalpha_pwr_dalpha = holes_pwr* Math.pow(alpha_avg5, holes_pwr - 1);
		double dval_dalpha = dval_dalpha_pwr * dalpha_pwr_dalpha;
		double dalpha_dai = 1.0 / alpha_w5; // dval_dalpha / alpha_w5;
		if ((vector[npa] > 0) && (vector[npa] < 1.0)) {
		if (!alpha_piece_linear) {
		dalpha_dai = 0.5 Math.PI * Math.sin(vector[npa]*Math.PI);
		}
		jt[npa][nx] += dval_dalpha * dalpha_dai;
		}
		for (int i = 0; i < alpha_neibs[na].length; i++) { // now 4, may be increased
		int di = alpha_neibs[na][i];
		if (di >= 0) {
		if ((vector[di] > 0) && (vector[di] < 1.0)) {
		// dalpha_dai = dval_dalpha * w_alpha_neib / alpha_w5;
		dalpha_dai = w_alpha_neib / alpha_w5;
		if (!alpha_piece_linear) {
		dalpha_dai = 0.5 Math.PI * Math.sin(vector[di]*Math.PI);
		}
		jt[di][nx] += dval_dalpha * dalpha_dai;
		}
		}
		}
		}
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		}
		}

		if (samples_pointers[SAMPLES_ELEVATION_PULL][1]>0) { // fits[TVAO_ELEVATION] && (elevation_lpf >= 0)) { // should be positive for pull0 and terr_pull_cold (difference between vegetation and terrain)
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		@@ -4280,7 +4365,7 @@ public class VegetationLMA {
		int [] ti = par_rindex[n];
		if (Math.abs(jt_diff[n][w]) > max_err) {
		System.out.println("debugDerivs(): n="+n+" ("+ti[0]+":"+ti[1]+"), w = "+w +", diff="+jt_diff[n][w]+" jt="+jt[n][w]+" jt_delta="+jt_delta[n][w]);
		} else if (Math.abs(jt_diff[n][w]) > .1) {
		} else if (Math.abs(jt_diff[n][w]) > .001) {
		System.out.println("debugDerivs(): n="+n+" ("+ti[0]+":"+ti[1]+"), w = "+w +", diff="+jt_diff[n][w]+" jt="+jt[n][w]+" jt_delta="+jt_delta[n][w]);
		}
		max_err = Math.max(max_err, Math.abs(jt_diff[n][w]));

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