Minor changes here and there during program use/debugging

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

@@ -28,8 +28,8 @@ public class ThermalColor {
 		double k = out_range/PALETTE_RANGE;
 		double value = (v-min)/(max-min) * (this.palette.length - 1);
 		int ivalue = (int) (value);
-		if (ivalue < 0) return this.palette[0];
-		if (ivalue >= (this.palette.length -1)) return this.palette[this.palette.length -1];
+		if (value < 0) return this.palette[0];
+		if (value >= (this.palette.length -1)) return this.palette[this.palette.length -1];
 		double a = (value-ivalue); // 0..1
 		double [] rslt = {
 				k*((1 - a) * this.palette[ivalue][0] + a * this.palette[ivalue+1][0]),

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

@@ -116,7 +116,7 @@ public class IntersceneLmaParameters {
 		gd.addMessage("Interframe LMA parameters selection");
 	    gd.addCheckbox    ("3D mode (use disparity)",                     this.ilma_3d,
 	    		"Use disparity for interscene matching (as for UAS imagery)" );
-		gd.addNumericField("Disp[arity weight",                           this.ilma_disparity_weight, 6,8,"",
+		gd.addNumericField("Disparity weight",                           this.ilma_disparity_weight, 6,8,"",
 				"Disparity component weight compared to dX and dY");
 	    gd.addCheckbox    ("LMA in 3D mode",                              this.ilma_3d_lma,
 	    		"Use LMA disparity  for interscene matching (as for UAS imagery)" );

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

@@ -223,6 +223,7 @@ public class QuadCLTCPU {
     // cac 
     public double [][] getGround(
     		boolean use_lma,
+    		double disparity_offset,    		
     		double discard_low,    // fraction of all pixels
     		double discard_high,   // fraction of all pixels
     		double discard_adisp,  // discard above/below this fraction of average height 
@@ -234,22 +235,24 @@ public class QuadCLTCPU {
     		int debug_level
     		) {
     	double [] z_tilts = null;
-    	final int tilesX=getTileProcessor().getTilesX();
-    	final int tilesY=getTileProcessor().getTilesY();
-    	double hist_rlow =    0.4;
+    	double normal_damping = 0.001; // pull to horizontal if not enough data 
+//    	final int tilesX=getTileProcessor().getTilesX();
+//    	final int tilesY=getTileProcessor().getTilesY();
+    	double hist_rlow =    0.5;
     	double hist_rhigh =   2.0;
     	int min_good =       20; //number of good tiles
-    	int min_good_quad =  20; // number of good tiles per quadrantto calculate tilts
-    	int gap_frac2=       20;
+///    	int min_good_quad =  20; // number of good tiles per quadrant to calculate tilts
+///    	int gap_frac2=       20;
     	double rel_hight =  0.2; // when calculating scale, ignore objects far from plane 
     	int num_bins = 1000;
     	double [][] dls = getDLS();
     	if (dls==null) {
     		return null;
     	}
-    	double [][] ds = new double [][] {dls[use_lma?1:0], dls[2]};
+    	double [][] ds = new double [][] {dls[use_lma?1:0].clone(), dls[2]};
     	double sw=0, swd=0;
     	for (int i = 0; i < ds[0].length; i++) if (!Double.isNaN(ds[0][i])){
+    		ds[0][i] -= disparity_offset;
     		sw +=   ds[1][i];
     		swd +=  ds[0][i] * ds[1][i];
     	}
@@ -318,7 +321,9 @@ public class QuadCLTCPU {
     		}
     		return null; // too few good 
     	}
-    	double z_avg= getGeometryCorrection().getZFromDisparity(swd/sw);
+    	
+//    	double z_avg= getGeometryCorrection().getZFromDisparity(swd/sw);
+    	/*
     	int gap_x_0 = tilesX/2 - tilesX/gap_frac2; 
     	int gap_x_1 = tilesX/2 + tilesX/gap_frac2; 
     	int gap_y_0 = tilesY/2 - tilesY/gap_frac2; 
@@ -348,9 +353,11 @@ public class QuadCLTCPU {
     			System.out.println("There are less than 3 quadrants ("+num_good_quads+") having more than "+min_good_quad+" tiles");
     			System.out.println("Using only level "+z_avg+", ignoring tilt."); 
     		}
-    		z_tilts = new double[] {z_avg, 0.0, 0.0}; // no tilts
+    		z_tilts = new double[] {-z_avg, 0.0, 0.0}; // no tilts
     		//    		return new double[] {z_avg, 0.0, 0.0}; // no tilts
     	} else {
+    		
+    	*/	
     		// fit plane
     		double [] ref_disparity = ds[0].clone();
     		for (int i = 0; i < ref_disparity.length; i++) {
@@ -381,17 +388,18 @@ public class QuadCLTCPU {
     			mindx++;
     		}    	
     		PolynomialApproximation pa = new PolynomialApproximation();
+    		double [] damping = new double [] {normal_damping, normal_damping};
     		double[][] approx2d = pa.quadraticApproximation(
     				mdata,
     				true,       // boolean forceLinear,  // use linear approximation
-    				null,       // double [] damping, null OK
+    				damping,    // double [] damping, null OK
     				-1);        // debug level
     		z_tilts= new double [] { approx2d[0][2], approx2d[0][0], approx2d[0][1]};
     		if (debug_level > -3) {
     			System.out.println("Found ground plane: level="+z_tilts[0]+", tiltX="+z_tilts[1]+", tiltY="+z_tilts[2]);
     		}
     		
-    	}
+ /*   	} */
 //    	ground - negative Z. picture right - positive X, picture up - positive Y
 //      positive tiltX - to the right higher ground (lower altitude above it) or camera tilted left
 //      positive tiltY - picture up - higher ground (or camera tilted back)
@@ -402,11 +410,16 @@ public class QuadCLTCPU {
 // It is approximate for small angles. OK for now    		
     	double [][] to_ground_xyxatr = ErsCorrection.invertXYZATR(ground_xyxatr);
     	// recalculate coordinates for all pixels including weak ones
-    	double [] ref_disparity = dls[0].clone();
+//    	double [] 
+    	ref_disparity = dls[0].clone();
     	for (int i = 0; i < ref_disparity.length; i++) {
     		if (Double.isNaN(ref_disparity[i])) ref_disparity[i] = 0.0;
+    		else {
+    			ref_disparity[i] -= disparity_offset;
     		}
-		double [][] wxyz = OpticalFlow.transformToWorldXYZ(
+    	}
+//		double [][] 
+    	wxyz = OpticalFlow.transformToWorldXYZ(
 				ref_disparity,          // final double []   disparity_ref, // invalid tiles - NaN in disparity
 				(QuadCLT) this, // final QuadCLT     quadClt, // now - may be null - for testing if scene is rotated ref
 				THREADS_MAX);   // int               threadsMax)
@@ -432,8 +445,11 @@ public class QuadCLTCPU {
     		if      (y < y_min_max[0]) y_min_max[0] = y;
     		else if (y > y_min_max[1]) y_min_max[1] = y;
     	}
+    	if ((x_min_max == null) || (y_min_max == null)) {
+    		return null; // no points at all?
+    	}
     	if (x0y0!=null) {
-    		x0y0[0] = x_min_max[0];
+    		x0y0[0] = x_min_max[0]; // null
     		x0y0[1] = y_min_max[0];
     	}
     	int scale = 0;
@@ -8387,6 +8403,9 @@ public class QuadCLTCPU {
 					  double [][] rgba = new double [num_slices][];
 					  for (int i = 0; i < 3; i++) rgba[i] = new double [texture_data[main_color_index].length];
 					  for (int i = 0; i < rbg_in[main_color_index].length; i++) {
+						  if (i==160000) {
+							  System.out.println ("i="+i);
+						  }
 						  double [] rgb = tc.getRGB(texture_data[main_color_index][i]);
 						  rgba[0][i] = rgb[0]; // red
 						  rgba[1][i] = rgb[1]; // green
@@ -15421,6 +15440,7 @@ public class QuadCLTCPU {
 	  public boolean writeLwirPreview(
 			  final CLTParameters  clt_parameters,
 			  double []            data,
+			  double []            minmax, // null for auto
 			  QuadCLT              scene,
 			  int                  tex_palette,
 			  String               suffix,
@@ -15429,6 +15449,7 @@ public class QuadCLTCPU {
 				  clt_parameters,
 				  data,
 				  getTileProcessor().getTilesX() *getTileProcessor().getTileSize(),
+				  minmax, // 			  double []            minmax, // null for auto
 				  scene,
 				  tex_palette,
 				  suffix,
@@ -15438,6 +15459,7 @@ public class QuadCLTCPU {
 			  final CLTParameters  clt_parameters,
 			  double []            data,
 			  int                  width,
+			  double []            minmax, // null for auto
 			  QuadCLT              scene,
 			  int                  tex_palette,
 			  String               suffix,
@@ -15449,7 +15471,15 @@ public class QuadCLTCPU {
 		  for (int i = 0; i < rendered_texture[0].length; i++) {
 			  rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
 		  }
-		  double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
+//		  double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
+		  if (!suffix.equals("")) {
+			  if (minmax == null) { // to replace standard preview file name
+				  minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
+				  suffix +="-AUTORANGE";
+			  } else {
+				  suffix +="-RANGE"+(minmax[1]-minmax[0]);
+			  }
+		  }
 //		  int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize(); 
 		  int height = data.length/width;
 		  String set_name = getImageName();

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

@@ -2452,6 +2452,7 @@ public class TexturedModel {
 			final int                                debugLevel)
 	{
 		final boolean render_hdr =        true; //false; // true; // generate textures w/o normalization to generate undistorted
+		final double  range_disparity_offset = clt_parameters.imp.range_disparity_offset;// double  range_disparity_offset
 		final boolean batch_mode =        clt_parameters.multiseq_run; // batch_run;
 		final boolean gltf_emissive =     clt_parameters.gltf_emissive;
 		final boolean use_alpha_blend =   clt_parameters.gltf_alpha_blend;
@@ -2495,6 +2496,9 @@ public class TexturedModel {
 //		final int     show_slice_bitmap =   clt_parameters.lre_show_slice_bitmap;
 		final int sky_layer = 0; // source disparity layer that contains "blue sky" 
 
+		final boolean tex_um_fixed =        clt_parameters.tex_um_fixed;  // imp.mono_fixed; //  true; // normalize to fixed range when converting to 8 bits 
+		final double  tex_um_range =        clt_parameters.tex_um_range;  // imp.mono_range; // 500.0;  // monochrome full-scale range (+/- half)
+
 		final int           ref_index =  scenes.length - 1;
 		final QuadCLT       ref_scene =  scenes[ref_index];
 		final TileProcessor tp =         ref_scene.getTileProcessor();
@@ -2986,10 +2990,12 @@ public class TexturedModel {
     		double    discard_adisp =   0.2;   // discard above/below this fraction of average height 
     		double    discard_rdisp =   0.02;  // discard above/below this fraction of average height
     		double    pix_size =        0.005; // hdr_x0y0,       // in meters
-    		int       max_image_width = 3200;  // increase pixel size as a power of 2 until image fits
+    		int       max_image_width = 4000; // 3200;  // increase pixel size as a power of 2 until image fits
     		boolean   crop_empty =      true;
     		int       crop_extra =      20;
     		int [] tex_pals = {0,1,2};
+//    		boolean use_fixed_range =  true;
+//    		double  fixed_range =      250.0;
 
     		int tex_palette_start = 0; 
     		int tex_palette_end =  12; 
@@ -2997,6 +3003,7 @@ public class TexturedModel {
 			double [] hdr_x0y0 = new double[2];		
 			double [][] to_ground_xyxatr = scenes[ref_index].getGround(
 					use_lma,         // boolean use_lma,
+					range_disparity_offset,// double  range_disparity_offset
 					discard_low,     // double discard_low,    // fraction of all pixels
 					discard_high,    // double discard_high,   // fraction of all pixels
 					discard_adisp,   // double discard_adisp,  // discard above/below this fraction of average height 
@@ -3006,7 +3013,9 @@ public class TexturedModel {
 		    		hdr_x0y0,        // double [] x0y0,        // initialize to double[2] to return width, height
 		    		hdr_whs,         // int [] whs,            // initialize to int[3] to return {width, height, scale reduction}
 		    		debugLevel);     // int debug_level
-			
+			if (to_ground_xyxatr == null) {
+				System.out.println("***** Failed to detect flat ground surface, skipping rendering and output files generation *****");
+			} else {
 				Render3D render3D = new Render3D (
 						//x3d_dir,               // String x3d_dir,
 						//ref_scene.correctionsParameters.getModelName(ref_scene.getImageName()), // String model_name,
@@ -3022,7 +3031,7 @@ public class TexturedModel {
 						last_is_alpha,         // final boolean            last_is_alpha,
 						scenes[ref_index],     //final QuadCLT            ref_scene,    // all coordinates relative to this scene
 						debugLevel);           //int                      debugLevel)
-//			String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());
+				//			String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());
 				String suffix ="-RECT"; 
 				if (clt_parameters.tex_um) {
 					suffix+="-UM"+(clt_parameters.tex_um_sigma)+"_"+(clt_parameters.tex_um_weight);
@@ -3049,12 +3058,15 @@ public class TexturedModel {
 							img_cropped,    // double [][] data,
 							wh[0],          // int            width, // int tilesX,
 							wh[1]);         // int            height, // int tilesY,
-//				for (int tex_palette = tex_palette_start; tex_palette <= tex_palette_end; tex_palette++) {
+					//				for (int tex_palette = tex_palette_start; tex_palette <= tex_palette_end; tex_palette++) {
 					for (int tex_palette: tex_pals) {
+						// try with fixed range?
+						double [] minmax =  tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;				
 						scenes[ref_index].writeLwirPreview(
 								clt_parameters, // final CLTParameters  clt_parameters,
 								img_cropped[0], // double []            data,
 								wh[0],          // int            width, // int tilesX,
+								minmax, // 			  double []            minmax, // null for auto
 								null, // QuadCLT              scene,
 								tex_palette, // int                  tex_palette,
 								suffix+"-CROP"+"-PAL"+tex_palette, // +tex_palette, // String               suffix,
@@ -3062,6 +3074,7 @@ public class TexturedModel {
 					}
 				}
 			}
+		}
 		
 		if (dbg_mesh_imgs != null) {
 			ShowDoubleFloatArrays.showArrays(
@@ -7112,7 +7125,7 @@ public class TexturedModel {
 		final double  mb_max_gain =         clt_parameters.imp.mb_max_gain; // 5.0;  // motion blur maximal gain (if more - move second point more than a pixel
 
 		final double  max_distortion =      clt_parameters.tex_distort;   // 0.5;  // Maximal texture distortion to accumulate multiple scenes (0 - any)
-		final double  tex_mb =              clt_parameters.tex_mb;        // 1.0;  // Reduce texture weight if motion blur exceeds this (as square of MB length)
+		final double  tex_mb =              clt_parameters.imp.mb_en? clt_parameters.tex_mb: 0.0;        // 1.0;  // Reduce texture weight if motion blur exceeds this (as square of MB length)
 		final boolean is_lwir =             ref_scene.isLwir();
 		final boolean tex_um =              clt_parameters.tex_um;        // imp.um_mono; // TODO: add own parameter
 		final double  tex_um_sigma =        clt_parameters.tex_um_sigma;  // imp.um_sigma;
@@ -7129,6 +7142,7 @@ public class TexturedModel {
 		final boolean save_um_texture0=     clt_parameters.tex_save_um_texture0;
 		final boolean save_preview=         clt_parameters.tex_save_preview;
 
+		
 //		final boolean show_sky_textures =   clt_parameters.lre_show_sky_textures && !clt_parameters.multiseq_run;
 //		final int     show_slice_bitmap =   clt_parameters.lre_show_slice_bitmap;
 //		final int     shrink_sky_tiles =    2 * (2 +clt_parameters.tex_sky_extra); // 4; // 2; sum of 2 +bg extend 
@@ -7639,14 +7653,38 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 			}
 			if (save_preview) {
+//				final boolean tex_um_fixed =        clt_parameters.tex_um_fixed;  // imp.mono_fixed; //  true; // normalize to fixed range when converting to 8 bits 
+//				final double  tex_um_range =        clt_parameters.tex_um_range;  // imp.mono_range; // 500.0;  // monochrome full-scale range (+/- half)
+				double [] minmax =  tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
+				/*
 				ref_scene.writePreview( // may move to different (earlier) stage of processing, (search for "-combined_textures")
 						dbg_textures[0], // double [] data,
 						debugLevel); // int debugLevel
+				*/
 // Trying different palettes				
-				int tex_palette = 2; // regular color
+				int tex_palette = 0; // regular mono white-hot
+				ref_scene.writeLwirPreview(
+						clt_parameters, // final CLTParameters  clt_parameters,
+						dbg_textures[0], // double []            data,
+						minmax, // 			  double []            minmax, // null for auto
+						null, // QuadCLT              scene,
+						tex_palette, // int                  tex_palette,
+						"", // +tex_palette, // String               suffix,
+						debugLevel); // int                  debugLevel)
+				tex_palette = 1; // regular color
+				ref_scene.writeLwirPreview(
+						clt_parameters, // final CLTParameters  clt_parameters,
+						dbg_textures[0], // double []            data,
+						minmax, // 			  double []            minmax, // null for auto
+						null, // QuadCLT              scene,
+						tex_palette, // int                  tex_palette,
+						"-black_hot", // +tex_palette, // String               suffix,
+						debugLevel); // int                  debugLevel)
+				tex_palette = 2; // regular color
 				ref_scene.writeLwirPreview(
 						clt_parameters, // final CLTParameters  clt_parameters,
 						dbg_textures[0], // double []            data,
+						minmax, // 			  double []            minmax, // null for auto
 						null, // QuadCLT              scene,
 						tex_palette, // int                  tex_palette,
 						"-color", // +tex_palette, // String               suffix,

src/main/java/com/elphel/imagej/x3d/export/Render3D.java

@@ -69,7 +69,7 @@ public class Render3D {
 		this.out_width =  out_width; 
 		this.out_height = out_height; 
 		this.toground = toground;
-		this.tocam = ErsCorrection.invertXYZATR(this.toground);
+		this.tocam = ErsCorrection.invertXYZATR(this.toground);  // null
 //		double [][] test1 = ErsCorrection.invertXYZATR(this.tocam); //OK
 //		double [][] test2 = ErsCorrection.invertXYZATR(test1); // OK
 		// ground plane x0, y0 in camera coordinates