working version

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

@@ -1598,7 +1598,7 @@ public class ErsCorrection extends GeometryCorrection {
 			
 		}
 	}
-	
+	@Deprecated
 	public void compareDSItoWorldDerivatives(
 			QuadCLT   scene_QuadClt,
 			double    max_inf_disparity, // absolute value

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

@@ -13256,6 +13256,7 @@ public class OpticalFlow {
 					param_regweights,                               // final double []   param_regweights,
 					vector_XYS,                                     // final double [][] vector_XYS, // optical flow X,Y, confidence obtained from the correlate2DIterate()
 					reference_tiles_macro,                          // final double [][] centers,    // macrotile centers (in pixels and average disparities
+					false,                                          // final boolean     same_weights,
 					(nlma == 0),                                    // boolean           first_run,
 					clt_parameters.ilp.ilma_debug_level);           // final int         debug_level)
 			
@@ -13392,6 +13393,7 @@ public class OpticalFlow {
 				null,          // final double []   param_regweights,
 				null,          // final double [][] vector_XYS, // optical flow X,Y, confidence obtained from the correlate2DIterate()
 				ref_pXpYD,     // final double [][] centers,    // macrotile centers (in pixels and average disparities
+				false,         // final boolean     same_weights,
 				false,         // boolean           first_run,
 				debug_level);  // final int         debug_level)
 		final double [][] last_jt = intersceneLma. getLastJT(); // alternating x,y for each selected parameters
@@ -13716,6 +13718,7 @@ public class OpticalFlow {
 					clt_parameters.ilp.ilma_regularization_weights, //  final double []   param_regweights,
 					vector_XYS,                                     // final double [][] vector_XYS, // optical flow X,Y, confidence obtained from the correlate2DIterate()
 					reference_tiles_macro,                          // final double [][] centers,    // macrotile centers (in pixels and average disparities
+					false,                                          // final boolean     same_weights,
 					(nlma == 0),                                    // boolean           first_run,
 					debug_level);                                   // final int         debug_level)
 			int lmaResult = intersceneLma.runLma(

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

@@ -2630,6 +2630,62 @@ public class QuadCLTCPU {
     }
 
 
+    public double [] smoothDisparity(
+    		double [] disparity_in,
+    		boolean [] reliable_ref, // optional
+    		double     sigma,
+    		double     max_diff,
+    		boolean    apply_nan) {
+    	final int tilesX =   tp.getTilesX();	
+    	double [] disparity = disparity_in.clone();
+    	if (reliable_ref != null) {
+    		for (int i = 0; i < reliable_ref.length; i++) {
+    			if (!reliable_ref[i]) {
+    				disparity[i] = Double.NaN;
+    			}
+    		}
+    	}
+    	boolean [] good_tiles = new boolean [disparity.length];
+    	for (int i = 0; i < disparity.length; i++) {
+    		good_tiles[i] = !Double.isNaN(disparity[i]);
+    	}
+
+    	double scale_sigma = 5.0; // non-NaN - 5 pixels from original NaN for each sigma
+    	int grow = 2* Math.min((int) Math.ceil(sigma * scale_sigma), tilesX);
+    	disparity = TileProcessor.fillNaNs(
+    			disparity,    // final double [] data,
+    			null,                     // final boolean [] prohibit,
+    			tilesX,          // int       width,
+    			// CAREFUL ! Remaining NaN is grown by unsharp mask filter ************* !
+    			grow,           // 100, // 2*width, // 16,           // final int grow,
+    			0.7,            // double    diagonal_weight, // relative to ortho
+    			100,            // int       num_passes,
+    			0.03);          // final double     max_rchange, //  = 0.01 - does not need to be accurate
+
+    	(new DoubleGaussianBlur()).blurDouble(
+    			disparity,          //
+    			tilesX,
+    			disparity.length/tilesX,
+    			sigma,              // double sigmaX,
+    			sigma,              // double sigmaY,
+    			0.01);              // double accuracy)
+    	if (max_diff > 0) {
+    		for (int i = 0; i < disparity.length; i++) if (good_tiles[i]){
+    			if (Math.abs(disparity[i] - disparity_in[i]) > max_diff) {
+    				good_tiles[i] = false;
+    			}
+    		} 
+    	}
+    	if (apply_nan) {
+    		for (int i = 0; i < disparity.length; i++) if (!good_tiles[i]){
+    			disparity[i] = Double.NaN;
+    		}
+    	}
+    	if (reliable_ref != null) {
+    		System.arraycopy(good_tiles, 0, reliable_ref, 0, disparity.length);
+    	}
+    	return disparity;
+    }
 
 
     public double [][] getDLS(){ // get disparity, disparity_lma, strength, sfm_gain

src/main/java/com/elphel/imagej/tileprocessor/sfm/StructureFromMotion.java

@@ -2278,6 +2278,7 @@ public class StructureFromMotion {
 						null,             // final double []   param_regweights,
 						null,             // final double [][] vector_XYS, // optical flow X,Y, confidence obtained from the correlate2DIterate()
 						ref_pXpYD,        // final double [][] centers,    // macrotile centers (in pixels and average disparities
+						false,            // final boolean     same_weights,
 						false,            // boolean           first_run,
 						debug_level);     // final int         debug_level)
 				last_jts[nscene] = intersceneLma. getLastJT(); // alternating x,y for each selected parameters

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

@@ -487,6 +487,7 @@ public class VegetationLMA {
 				max_warp,           // final double       max_warp,
 				valid_pixels_in,    // final boolean [] valid_pixels_in, // should be initialized to woi, normally set to all true 
 				max_offset,         // final int        max_offset,
+				elev_radius,        // final double []    elev_radius, // this.elevation_radius
 				max_sacrifice,      // final int        max_sacrifice,
 				valid_stats,        // final int []       stats,
 				max_warp_scene_pix, // final int []       max_warp_scene_pix, 
@@ -5200,12 +5201,14 @@ public class VegetationLMA {
 			final double       max_warp,
 			final boolean []   valid_pixels_in, // should be initialized to woi, normally set to all true 
 			final int          max_offset,
+			final double []    elev_radius, // this.elevation_radius
 			final int          max_sacrifice,
 			final int []       stats,
 			final int []       max_warp_scene_pix, 
 			final Rectangle    woi, 
 			final Rectangle    woi_veg // should be initialized, will be modified
 			) {
+		final int dbg_pix = 801; // 918;
 		final int woi_length = woi.width*woi.height;
 		final boolean [] valid_pixels = (valid_pixels_in != null) ? valid_pixels_in : (new boolean [woi_length]);
 		if (valid_pixels_in == null) {
@@ -5255,6 +5258,9 @@ public class VegetationLMA {
 						int y = indx / woi_ext.width  + woi_ext.y;
 						int x = indx % woi_ext.width  + woi_ext.x;
 						int npix = x + y * full.width;
+						double radius = elev_radius[npix];
+						double radius2 = radius*radius;
+						int iradius = (int) Math.ceil (radius);
 						double elevation =  tvao[TVAO_ELEVATION][npix];
 						double vegetation = tvao[TVAO_VEGETATION][npix];
 						if (!Double.isNaN(elevation) && !Double.isNaN(vegetation)) {
@@ -5267,6 +5273,37 @@ public class VegetationLMA {
 								if (scales != null) {
 									double dx = scales[0] * elevation;
 									double dy = scales[1] * elevation;
+									int ax0 = (int) Math.floor(x + dx - radius);
+									int ax1 = (int) Math.ceil (x + dx + radius);
+									int ay0 = (int) Math.floor(y + dy - radius);
+									int ay1 = (int) Math.ceil (y + dy + radius);
+									Rectangle ar = new Rectangle(ax0, ay0, ax1-ax0 +1, ay1-ay0 +1);
+									if (woi.intersects(ar)) {
+										boolean has_valid_dependent = false;
+										for (int ay = ay0; ay <= ay1; ay++) {
+											double ddy = ay - (y + dy);
+											double ddy2 = ddy*ddy;
+											for (int ax = ax0; ax <= ax1; ax++) {
+												if (woi.contains(ax,ay)) {
+													double ddx = ax - (x + dx);
+													double ddr2 = ddy2 + ddx*ddx;
+													if (ddr2 <= radius2) {
+														int wx = ax - woi.x;
+														int wy = ay - woi.y;
+														int wpix =wx + wy*woi.width; 
+														if (valid_pixels[wpix]) {
+															has_veg_thread[nthread][nscene][wpix] = true;
+															has_valid_dependent = true;
+														}
+													}
+												}
+											}
+										}
+										if (has_valid_dependent) {
+											veg_scene_used_prefilter[indx] = true;
+										}
+									}
+									/*
 									int px05 = (int) Math.floor(x + dx); // TODO: check sign! // ELEV-SIGN
 									int py05 = (int) Math.floor(y + dy); // TODO: check sign! // ELEV-SIGN
 									if (woi_plus1.contains(px05,py05)) { // up to 1 pixel to the nearest
@@ -5291,6 +5328,7 @@ public class VegetationLMA {
 											veg_scene_used_prefilter[indx] = true;
 										}
 									}
+									*/
 								}
 							}
 						}
@@ -5338,6 +5376,9 @@ public class VegetationLMA {
 			threads[ithread] = new Thread() {
 				public void run() {
 					for (int wPix = ai.getAndIncrement(); wPix < woi_length; wPix = ai.getAndIncrement()) { // if (valid_pixels[wPix]){
+						if (wPix == dbg_pix) {
+							System.out.println ("getValidScenesPixels() 1 : wpix = "+wPix);
+						}
 						boolean has_offset_middle = true;
 						for (int nscene = first_scene + max_sacrifice; nscene <= last_scene-max_sacrifice; nscene++) if (valid_scenes[nscene]){
 							if (!has_veg[nscene][wPix]) {

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

@@ -401,14 +401,15 @@ public class VegetationModel {
 		double      min_above = 0.02; // 0.025; // .04;
 		int         patch_neib = 4; // 5;
 		double      neibs_pow =  0.5;
-	
+		final int   grow_vegetation = clt_parameters.imp.terr_veget_grow;
 		double [][] combo_dsn =quadCLTs[ref_index].restoreComboDSI(true);
 		double [][] terr_veg = getTerrainVegetation(
-				combo_dsn,   // double [][] combo_dsn);
-				tilesX,      // final int         tilesX,
-				min_above,   // final double      min_above, // absolute disparity difference
-				patch_neib,  // final int         patch_neib){
-				neibs_pow);  // final double      neibs_pow);
+				combo_dsn,        // double [][] combo_dsn);
+				tilesX,           // final int         tilesX,
+				min_above,        // final double      min_above, // absolute disparity difference
+				patch_neib,       // final int         patch_neib){
+				neibs_pow,        // final double      neibs_pow);
+				grow_vegetation); // final int grow_vegetation);
 				
 		if (show_debug) {
 			String [] titles_terr_veg = {"terrain","vegetation"};
@@ -725,7 +726,8 @@ public class VegetationModel {
 			final int         tilesX,
 			final double      min_above, // absolute disparity difference
 			final int         patch_neibs,
-			final double      neibs_pow){ // raise strength to this power when averaging neighbors 
+			final double      neibs_pow, // raise strength to this power when averaging neighbors
+			final int grow_vegetation){
 		final double [] terrain = combo_dsn[OpticalFlow.COMBO_DSN_INDX_TERRAIN]; 
 		final double [] ground =  combo_dsn[OpticalFlow.COMBO_DSN_INDX_GROUND]; 
 		final double [] disparity =  combo_dsn[OpticalFlow.COMBO_DSN_INDX_LMA]; 
@@ -733,7 +735,7 @@ public class VegetationModel {
 		final int num_pixels = disparity.length;
 		final double [] vegetation = new double [num_pixels];
 		Arrays.fill(vegetation, Double.NaN);
-		final int dbg_tile = -(22+17*80);
+		final int dbg_tile = (25+20*80);
 		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
 		final AtomicInteger ai = new AtomicInteger(0);
 		for (int ithread = 0; ithread < threads.length; ithread++) {
@@ -771,7 +773,20 @@ public class VegetationModel {
 			};
 		}		      
 		ImageDtt.startAndJoin(threads);
-		return new double [][] {terrain,vegetation};
+		double [] veget=vegetation;
+		if (grow_vegetation > 0) {
+			veget= TileProcessor.fillNaNs(
+					vegetation, // final double [] data,
+					null,                     // final boolean [] prohibit,
+					tilesX,          // int       width,
+					// CAREFUL ! Remaining NaN is grown by unsharp mask filter ************* !
+					grow_vegetation,           // 100, // 2*width, // 16,           // final int grow,
+					0.7,            // double    diagonal_weight, // relative to ortho
+					100,            // int       num_passes,
+					0.03);           // final double     max_rchange, //  = 0.01 - does not need to be accurate
+
+		}
+		return new double [][] {terrain,veget}; // ation};
 	}
 	
 	
@@ -819,14 +834,15 @@ public class VegetationModel {
 		double      min_above = 0.02; // 0.025; // .04;
 		int         patch_neib = 4; // 5;
 		double      neibs_pow =  0.5;
-	
+		final int   grow_vegetation = clt_parameters.imp.terr_veget_grow;
 		double [][] combo_dsn =quadCLTs[ref_index].restoreComboDSI(true);
 		double [][] terr_veg = getTerrainVegetation(
 				combo_dsn,   // double [][] combo_dsn);
 				tilesX,      // final int         tilesX,
 				min_above,   // final double      min_above, // absolute disparity difference
 				patch_neib,  // final int         patch_neib){
-				neibs_pow);  // final double      neibs_pow);
+				neibs_pow,        // final double      neibs_pow);
+				grow_vegetation); // final int grow_vegetation);
 				
 		String [] titles_terr_veg = {"terrain","vegetation"};
 		ShowDoubleFloatArrays.showArrays(
@@ -2089,7 +2105,7 @@ public class VegetationModel {
 					lambda_scale_bad, // double lambda_scale_bad, // 8.0
 					lambda_max,       // double lambda_max,       // 100
 					rms_diff,         // double rms_diff,         // 0.001
-					15, // num_iter,         //int    num_iter,         // 20
+					num_iter, // 15, // num_iter,         //int    num_iter,         // 20
 					last_run,         // boolean last_run,
 					null,             // String dbg_prefix,
 					debugLevel);      // int    debug_level)