creating terrain 3d (removing vegetation)

src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java

@@ -3122,7 +3122,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 
 		double avg_all = getMaskedAverage (
 				elev, // final double [] data,
-				null); // final boolean [] mask)
+				null, // final boolean [] mask)
+				null); // final double []  stdp);
 		double abs_high= avg_all + initial_above;
 		double abs_low=  avg_all - initial_below;
 		boolean [] mask = 	removeAbsoluteLowHigh (
@@ -3236,15 +3237,18 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 * Calculate average of a double array, ignore masked out (!mask[i] and NaNs in the data)
 	 * @param data double data array
 	 * @param mask optional (may be null) boolean mask - ignore data items that have corresponding mask element false
+	 * @param stdp null or double[1] standard deviation
 	 * @return average value of the non-NaN and not disabled by mask elements of data[] 
 	 */
-	private static double getMaskedAverage (
+	public static double getMaskedAverage (
 			final double []  data,
-			final boolean [] mask) {
+			final boolean [] mask,
+			final double []  stdp) {
 		final Thread[] threads = ImageDtt.newThreadArray();
 		final AtomicInteger ai = new AtomicInteger(0);
 		final AtomicInteger ati = new AtomicInteger(0);
 		final double [] avg_arr = new double [threads.length];
+		final double [] std_arr = new double [threads.length];
 		final double [] npix_arr = new double [threads.length];
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
@@ -3252,18 +3256,25 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 					int thread_num = ati.getAndIncrement();
 					for (int iPix = ai.getAndIncrement(); iPix < data.length; iPix = ai.getAndIncrement()) if (!Double.isNaN(data[iPix]) && ((mask == null) || (mask[iPix]))){
 						avg_arr[thread_num] += data[iPix];
+						std_arr[thread_num] += data[iPix]*data[iPix];
 						npix_arr[thread_num] += 1.0;
 					}
 				}
 			};
 		}		      
 		ImageDtt.startAndJoin(threads);
-		double avg=0, num=0;
+		double avg=0, num=0,sum2=0;
 		for (int i = 0; i < avg_arr.length; i++) {
 			avg+=avg_arr[i];
 			num+=npix_arr[i];
+			sum2+=std_arr[i];
 		}
-		return avg/num;
+		avg /= num;
+		sum2 /= num;
+		if (stdp != null) {
+			stdp[0] = Math.sqrt(sum2- avg*avg);
+		}
+		return avg;
 	}
 
 	/**
@@ -3310,7 +3321,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 * @param threshold_low remove lower elements () and NaNs in the data
 	 * @return updated mask (same instance if not null) that disables (makes false) filtered out data [] elements
 	 */
-	private static boolean [] removeAbsoluteLowHigh (
+	public static boolean [] removeAbsoluteLowHigh (
 			final double [] data,
 			final boolean [] mask,
 			final double threshold_high,
@@ -3386,7 +3397,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 * @param num_bins number of the histogram bins
 	 * @return boolean array of the remaining data elements. Input mask_in array (if not null) is modified too.
 	 */
-	private static boolean [] removeRelativeLowHigh (
+	public static boolean [] removeRelativeLowHigh (
 			final double [] data,
 			final boolean [] mask_in,
 			final double abs_high,

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

@@ -320,8 +320,13 @@ public class IntersceneMatchParameters {
 	public  double  range_max =       5000.0;
 	// Export 3D model
 	public  boolean export3d =           false; // true;
-	
-	
+	public  boolean export3dterrain =    false; // true;	
+	// Generate CT scan
+	public  boolean export_CT =          false; // true;
+	public  double  ct_min =             3.7; //
+	public  double  ct_max =             4.5; //
+	public  double  ct_step =            0.02;  // pix
+	public  int     ct_expand =          2;    // pix // expand section area by 1 pixel in 8 directions
 	
 	// Debug and visualization
 	public  boolean scene_is_ref_test=              false; // correlate ref-2-ref for testing
@@ -1149,6 +1154,15 @@ min_str_neib_fpn	0.35
 		gd.addMessage  ("3D model generation");
 		gd.addCheckbox ("Generate 3D model",                         this.export3d,
 				"Generate textures and model.");
+		gd.addCheckbox ("Generate 3D model of terrain",              this.export3dterrain,
+				"Generate textures and model, remove vegetation.");
+		
+		gd.addMessage  ("CT scan generation");
+		gd.addCheckbox ("Generate ST scan",                          this.export_CT,	"Generate \"CT scan\" of the vegetation.");
+		gd.addNumericField("Minimal CT scan disparity",              this.ct_min, 5,7,"pix","Start disparity (lowest altitude).");
+		gd.addNumericField("Maximal CT scan disparity",              this.ct_max, 5,7,"pix","End disparity (highest altitude).");
+		gd.addNumericField("CT scan step",                           this.ct_step, 5,7,"pix","Scan step.");
+		gd.addNumericField("CT scan expand section",                 this.ct_expand, 0,3,"tiles","expand section area, 2 - a tile in 8 directions.");
 
 		gd.addMessage  ("Debug and visialization parameters");
 		gd.addCheckbox ("Replace scene with reference scene",        this.scene_is_ref_test,
@@ -2075,6 +2089,13 @@ min_str_neib_fpn	0.35
 		this.range_max =                      gd.getNextNumber();
 		
 		this.export3d =                       gd.getNextBoolean();
+		this.export3dterrain =                gd.getNextBoolean();
+		
+		this.export_CT =                      gd.getNextBoolean();
+		this.ct_min =                         gd.getNextNumber();
+		this.ct_max =                         gd.getNextNumber();
+		this.ct_step =                        gd.getNextNumber();
+		this.ct_expand =                (int) gd.getNextNumber();
 
 		this.scene_is_ref_test =              gd.getNextBoolean();
 		this.render_ref =                     gd.getNextBoolean();
@@ -2684,6 +2705,13 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"range_min_strength",            this.range_min_strength+"");            // double
 		properties.setProperty(prefix+"range_max",                     this.range_max+"");                     // double
 		properties.setProperty(prefix+"export3d",                      this.export3d+"");                      // boolean
+		properties.setProperty(prefix+"export3dterrain",               this.export3dterrain+"");               // boolean
+		
+		properties.setProperty(prefix+"export_CT",                     this.export_CT+"");                     // boolean
+		properties.setProperty(prefix+"ct_min",                        this.ct_min+"");                        // double
+		properties.setProperty(prefix+"ct_max",                        this.ct_max+"");                        // double
+		properties.setProperty(prefix+"ct_step",                       this.ct_step+"");                       // double
+		properties.setProperty(prefix+"ct_expand",                     this.ct_expand+"");                     // int
 		
 		properties.setProperty(prefix+"scene_is_ref_test",    this.scene_is_ref_test+"");   // boolean
 		properties.setProperty(prefix+"render_ref",           this.render_ref+"");          // boolean
@@ -3256,7 +3284,13 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"range_max")!=null)            this.range_max=Double.parseDouble(properties.getProperty(prefix+"range_max"));
 
 		if (properties.getProperty(prefix+"export3d")!=null)             this.export3d=Boolean.parseBoolean(properties.getProperty(prefix+"export3d"));		
+		if (properties.getProperty(prefix+"export3dterrain")!=null)      this.export3dterrain=Boolean.parseBoolean(properties.getProperty(prefix+"export3dterrain"));		
 		
+		if (properties.getProperty(prefix+"export_CT")!=null)            this.export_CT=Boolean.parseBoolean(properties.getProperty(prefix+"export_CT"));		
+		if (properties.getProperty(prefix+"ct_min")!=null)               this.ct_min=Double.parseDouble(properties.getProperty(prefix+"ct_min"));
+		if (properties.getProperty(prefix+"ct_max")!=null)               this.ct_max=Double.parseDouble(properties.getProperty(prefix+"ct_max"));
+		if (properties.getProperty(prefix+"ct_step")!=null)              this.ct_step=Double.parseDouble(properties.getProperty(prefix+"ct_step"));
+		if (properties.getProperty(prefix+"ct_expand")!=null)            this.ct_expand=Integer.parseInt(properties.getProperty(prefix+"ct_expand"));
 		
 		if (properties.getProperty(prefix+"scene_is_ref_test")!=null)    this.scene_is_ref_test=Boolean.parseBoolean(properties.getProperty(prefix+"scene_is_ref_test"));		
 		if (properties.getProperty(prefix+"render_ref")!=null)           this.render_ref=Boolean.parseBoolean(properties.getProperty(prefix+"render_ref"));		
@@ -3834,8 +3868,13 @@ min_str_neib_fpn	0.35
 		imp.range_min_strength            = this.range_min_strength;
 		imp.range_max                     = this.range_max;
 		imp.export3d                      = this.export3d;
+		imp.export3dterrain               = this.export3dterrain;
 		
-		
+		imp.export_CT                     = this.export_CT;
+		imp.ct_min                        = this.ct_min;
+		imp.ct_max                        = this.ct_max;
+		imp.ct_step                       = this.ct_step;
+		imp.ct_expand                     = this.ct_expand;
 		
 		imp.scene_is_ref_test     = this.scene_is_ref_test;
 		imp.render_ref            = this.render_ref;

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

@@ -4673,6 +4673,13 @@ public class OpticalFlow {
 		boolean generate_mapped =            clt_parameters.imp.generate_mapped &&
 				(gen_seq_mono_color[0] || gen_seq_mono_color[1]);   // generate sequences - Tiff and/or video
 		boolean export3d =                   clt_parameters.imp.export3d; //  true;
+		boolean export3dterrain =            clt_parameters.imp.export3dterrain; //  true;
+
+		boolean export_CT =                  clt_parameters.imp.export_CT; //  false;
+		double  ct_min =                     clt_parameters.imp.ct_min ;
+		double  ct_max =                     clt_parameters.imp.ct_max ;
+		double  ct_step =                    clt_parameters.imp.ct_step ;
+		int     ct_expand =                  clt_parameters.imp.ct_expand ;
 		
 		boolean [] annotate_mono_color = {clt_parameters.imp.annotate_mono,clt_parameters.imp.annotate_color}; 
 		boolean annotate_transparent_mono = clt_parameters.imp.annotate_transparent_mono;
@@ -6176,9 +6183,60 @@ public class OpticalFlow {
 	        }
 		}
 		
+		if (export_CT) {
+			double [][][] ct_scans = new double [(int) Math.ceil((ct_max-ct_min)/ct_step) + 1][][];
+			boolean ok_ct = TexturedModel.output3d( // quadCLTs have same image name, and everything else
+					clt_parameters,      // CLTParameters                            clt_parameters,
+					colorProcParameters, // ColorProcParameters                      colorProcParameters,
+					rgbParameters,       // EyesisCorrectionParameters.RGBParameters rgbParameters,
+					quadCLTs[ref_index], // quadCLTs.length-1], // quadCLT_main,        // final QuadCLT                            parameter_scene, // to use for rendering parameters in multi-series sequences
+		            // if null - use reference scene 
+					quadCLTs,            // QuadCLT []                               scenes,
+					ref_index,           // final int                                ref_index,
+					combo_dsn_final,     //double [][]                              combo_dsn_final, // null OK, will read file
+					ct_scans,            // final double [][]                        ct_scans,
+					ct_min,              // final double                             ct_min,
+					ct_step,             // final double                             ct_step,
+					ct_expand,           // final int                                ct_expand,
+					false,               // final boolean                            terrain_mode,
+					null, // final double [][]                        hdr_render_size, // { hdr_whs[3],hdr_x0y0[2]}; save/use rendering parameters
+					false, // final boolean                            hdr_render_slave,// use rendering parameters (to match other mode)
+					updateStatus,        // final boolean                            updateStatus,
+					debugLevel); //  + 1);         // final int                                debugLevel)
+			System.out.println ("CT scan-> "+ok_ct);
+			String [] titles = new String[ct_scans.length];
+			for (int i = 0; i < titles.length; i++) {
+				titles[i] = String.format("disparity=%.3f pix",ct_min+ct_step*i);
+			}
+			String suffix = String.format("-CT_SCAN_%.3f_%.3f_%.3f_%d",ct_min,ct_max,ct_step,ct_expand);
+			final int transform_size=           quadCLTs[ref_index].getTileProcessor().getTileSize();
+	 		final int tilesX =                  quadCLTs[ref_index].getTileProcessor().getTilesX();
+			final int tilesY =                  quadCLTs[ref_index].getTileProcessor().getTilesY();
+			int nslices = 0;
+			for (int n = 0; n < ct_scans.length; n++) {
+				nslices = Math.max(nslices,  ct_scans[n].length);
+			}
+			for (int nslice = 0; nslice < nslices; nslice++) {
+				double [][] ct_scan_slice = new double [ct_scans.length][];
+				for (int n = 0; n < ct_scan_slice.length; n++) {
+//					int i = Math.min(nslice, ct_scans[n].length);
+					if (nslice < ct_scans[n].length) {
+						ct_scan_slice[n] = ct_scans[n][nslice];
+					}
+				}
+				quadCLTs[ref_index].saveDoubleArrayInModelDirectory(
+						suffix+"-SLICE"+nslice,   // String      suffix,
+						titles,                   // String []   labels, // or null
+						ct_scan_slice,         // double [][] data,
+						tilesX * transform_size,  // int            width, // int tilesX,
+						tilesY * transform_size); // int            height, // int tilesY,
+			}
+		}
+		
 		// debugging 3D model
 		int [] whs = new int[3];
 		double [] x0y0 = new double[2];
+		double [][] hdr_render_size = new double[2][];
 		if (export3d) { //combo_dsn_final had strength 1.0e-4 where it should not? Reset it?
 			boolean ok_3d = TexturedModel.output3d( // quadCLTs have same image name, and everything else
 					clt_parameters,      // CLTParameters                            clt_parameters,
@@ -6189,9 +6247,38 @@ public class OpticalFlow {
 					quadCLTs,            // QuadCLT []                               scenes,
 					ref_index,           // final int                                ref_index,
 					combo_dsn_final,     //double [][]                              combo_dsn_final, // null OK, will read file
+					null,                // final double [][]                        ct_scans,
+					0,                   // final double                             ct_min,
+					0,                   // final double                             ct_step,
+					0,                   // final int                                ct_expand,
+					false,               // final boolean                            terrain_mode,
+					hdr_render_size,     // final double [][]                        hdr_render_size, // { hdr_whs[3],hdr_x0y0[2]}; save/use rendering parameters
+					false,               // final boolean                            hdr_render_slave,// use rendering parameters (to match other mode)
+					updateStatus,        // final boolean                            updateStatus,
+					debugLevel); //  + 1);         // final int                                debugLevel)
+			System.out.println ("TexturedModel.output3d() -> "+ok_3d+" (full, with vegetation)");
+		}
+		if (export3dterrain) { //combo_dsn_final had strength 1.0e-4 where it should not? Reset it?
+			boolean  hdr_render_slave= true;
+			boolean ok_3d = TexturedModel.output3d( // quadCLTs have same image name, and everything else
+					clt_parameters,      // CLTParameters                            clt_parameters,
+					colorProcParameters, // ColorProcParameters                      colorProcParameters,
+					rgbParameters,       // EyesisCorrectionParameters.RGBParameters rgbParameters,
+					quadCLTs[ref_index], // quadCLTs.length-1], // quadCLT_main,        // final QuadCLT                            parameter_scene, // to use for rendering parameters in multi-series sequences
+		            // if null - use reference scene 
+					quadCLTs,            // QuadCLT []                               scenes,
+					ref_index,           // final int                                ref_index,
+					combo_dsn_final,     //double [][]                              combo_dsn_final, // null OK, will read file
+					null,                // final double [][]                        ct_scans,
+					0,                   // final double                             ct_min,
+					0,                   // final double                             ct_step,
+					0,                   // final int                                ct_expand,
+					true,        // final boolean                            terrain_mode,
+					hdr_render_size,     // final double [][]                        hdr_render_size, // { hdr_whs[3],hdr_x0y0[2]}; save/use rendering parameters
+					hdr_render_slave,    // final boolean                            hdr_render_slave,// use rendering parameters (to match other mode)
 					updateStatus,        // final boolean                            updateStatus,
 					debugLevel); //  + 1);         // final int                                debugLevel)
-			System.out.println ("TexturedModel.output3d() -> "+ok_3d);
+			System.out.println ("TexturedModel.output3d() -> "+ok_3d+" (terrain only, no vegetation)");
 		}
 		
 		

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

@@ -75,6 +75,7 @@ import com.elphel.imagej.ims.Did_ins_2;
 import com.elphel.imagej.ims.Did_pimu;
 import com.elphel.imagej.ims.EventLogger;
 import com.elphel.imagej.ims.Imx5;
+import com.elphel.imagej.orthomosaic.OrthoMap;
 import com.elphel.imagej.readers.ElphelTiffWriter;
 import com.elphel.imagej.readers.ImagejJp4Tiff;
 import com.elphel.imagej.x3d.export.TriMesh;
@@ -1706,6 +1707,85 @@ public class QuadCLTCPU {
 				tilesY);               // int         height)
     }
     
+    public double [] getFlatGround(
+    		double [] disparity,
+			double    rmse_above, // from average
+			double    rmse_below, // from average, // positive value
+			int       num_refine,
+			double    frac_above,
+			double    frac_below,
+			String    debug_title) {
+    	final double [] plane_disparity = new double [disparity.length];
+		final int     num_bins = 1024;
+    	final int tilesX =   tp.getTilesX();	
+    	final int tilesY =   tp.getTilesY();
+    	final double [] center_xy= {0.5*tilesX, 0.5*tilesY};
+    	final double [] stdp = new double[1];
+		double avg_all = OrthoMap.getMaskedAverage (
+				disparity, // final double [] data,
+				null, // final boolean [] mask)
+				stdp); // final double []  stdp);
+		double initial_above = rmse_above*stdp[0];
+		double initial_below = rmse_below*stdp[0];
+		double abs_high= avg_all + initial_below;
+		double abs_low=  avg_all - rmse_below*stdp[0];
+		boolean [] mask = 	OrthoMap.removeAbsoluteLowHigh (
+				disparity,     // final double [] data,
+				null,     // final boolean [] mask,
+				abs_high, // final double threshold_high,
+				abs_low); // final double threshold_low),
+		double [] plane_tiles = {0,0,avg_all,center_xy[0], center_xy[1]}; // 5 elements here
+		for (int ntry = 0; ntry < num_refine; ntry++) {
+			if (ntry > 0) {
+				// remove relatives, start from new mask
+				mask = OrthoMap.removeRelativeLowHigh (
+						disparity,       // final double [] data,
+						null,       // final boolean [] mask_in,
+						initial_above,   //  final double abs_high,
+						-initial_below,    // final double abs_low,
+						frac_above, // final double rhigh,
+						frac_below, // final double rlow,
+						plane_tiles,  // final double []  ground_plane, // tiltx,tilty, offs, x0(pix), y0(pix) or null
+						tilesX,      // final int     width, // only used with ground_plane != null;
+						num_bins);  // final int    num_bins) 				
+				
+			}
+			plane_tiles=  OrthoMap.getPlane(
+					disparity,     // final double []   data,
+					mask ,         // final boolean [] mask,
+					null,          // final double []  weight,
+					tilesX,        // final int        width,
+					center_xy);    // final double []  xy0)
+		}
+    	
+		for (int nTile = 0; nTile < disparity.length; nTile++) {
+			int tileX = nTile % tilesX;
+			int tileY = nTile / tilesX;
+			double x = tileX - plane_tiles[3];
+			double y = tileY - plane_tiles[4];
+			plane_disparity[nTile] = plane_tiles[2]+ x *plane_tiles[0] +y * plane_tiles[1];
+		}
+		if (debug_title != null) {
+			String [] dbg_titles = {"disparity", "plane", "diff"};
+			double [][] dbg_img = new double [dbg_titles.length][disparity.length];
+			dbg_img[0] = disparity;
+			dbg_img[1] = plane_disparity;
+			for (int i = 0; i < disparity.length; i++) {
+				dbg_img[2][i] = disparity[i] - plane_disparity[i];
+			}
+    		ShowDoubleFloatArrays.showArrays(
+    				dbg_img,
+    				tilesX,
+    				tilesY,
+    				true,
+    				debug_title,
+    				dbg_titles);
+		}
+    	return plane_disparity;
+    	
+    }
+    
+    
     
     public double [] getSmoothGround(
     		CLTParameters clt_parameters,

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

@@ -43,6 +43,7 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.gpu.TpTask;
 import com.elphel.imagej.ims.Imx5;
+import com.elphel.imagej.orthomosaic.OrthoMap;
 import com.elphel.imagej.x3d.export.GlTfExport;
 import com.elphel.imagej.x3d.export.Render3D;
 import com.elphel.imagej.x3d.export.TriMesh;
@@ -2430,6 +2431,116 @@ public class TexturedModel {
 				titles);
 	}
 	
+	public static double [] getTerrainDisparity(
+			final double [] disparity, // maybe already filtered from smooth (combined, allow strong deviations)
+			final double [] flat,
+			final double    threshold_above,
+			final int       expand,
+			final int       width){
+		final int height = disparity.length/width;
+		double [] terrain_disparity = disparity.clone();
+		boolean [] above_terrain = new boolean [disparity.length];
+		for (int i = 0; i <disparity.length; i++) {
+			above_terrain[i] = (disparity[i]-flat[i]) > threshold_above;
+		}
+		TileNeibs tn = new TileNeibs (width,height);
+		tn.growSelection(
+				expand,           // int              grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+				above_terrain,    //final boolean [] tiles,
+				null);            // final boolean [] prohibit)
+		
+		for (int i = 0; i <above_terrain.length; i++) if (above_terrain[i]){
+			terrain_disparity[i] = Double.NaN;
+		}		
+		OrthoMap.fillNaNs(
+				terrain_disparity, // double [] data,
+				tn, // TileNeibs tn,
+				3); // int min_neibs)
+		return terrain_disparity;
+	}
+	
+	public static void mixDisparityWithSmooth(
+			double [][] ds_fg_bg, // modified inside
+			double [][] ss_fg_bg, // modified inside
+			double []   smooth_ground,
+			double []   sfm_gain,
+			double      gsmth_sfm_gain,
+			int         gsmth_sfm_rad,
+			double      lim_disparity, // 100
+			double      gsmth_str_bump,
+			double      gsmth_str_dip,
+			double      small_strength,
+			int         width,
+			String      dbg_title) {
+		double  [][] ds_fg_bg_bkp = (dbg_title != null) ? (new double [][] {ds_fg_bg[0].clone(), ds_fg_bg[1].clone()}): null;
+		double  [][] ss_fg_bg_bkp = (dbg_title != null) ? (new double [][] {ss_fg_bg[0].clone(), ss_fg_bg[1].clone()}): null;
+		TileNeibs tn = new TileNeibs(width, smooth_ground.length/width);
+		for (int ntile = 0; ntile < smooth_ground.length; ntile++) {
+			double disp = (ss_fg_bg[1][ntile] > ss_fg_bg[0][ntile]) ? ds_fg_bg[1][ntile] : ds_fg_bg[1][ntile]; // strongest
+			if (disp > lim_disparity) {
+				disp = lim_disparity;
+			}
+
+			double str =  Math.max(ss_fg_bg[1][ntile], ss_fg_bg[0][ntile]);
+			boolean strong = false;
+			if (disp > smooth_ground[ntile]) {
+				strong = str >= gsmth_str_bump;
+			} else {
+				strong = str >= gsmth_str_dip;
+			}
+			if (strong) {
+				check_neibs:
+				{
+					for (int dy = -gsmth_sfm_rad; dy <= gsmth_sfm_rad; dy++) {
+						for (int dx = -gsmth_sfm_rad; dx <= gsmth_sfm_rad; dx++) {
+							int ntile1 = tn.getNeibIndex(ntile, dx, dy);
+							if ((ntile1 < 0) || (sfm_gain[ntile1] < gsmth_sfm_gain)) {
+								strong = false;
+								break check_neibs;
+							}
+						}
+					}
+					if (disp > smooth_ground[ntile]) {
+						ds_fg_bg[0][ntile] = disp;
+						ss_fg_bg[0][ntile] = str;
+						ds_fg_bg[1][ntile] = smooth_ground[ntile];								
+						ss_fg_bg[1][ntile] = small_strength;
+					} else {
+						ds_fg_bg[0][ntile] = Double.NaN;
+						ss_fg_bg[0][ntile] = 0.0;
+						smooth_ground[ntile] = disp;
+						ds_fg_bg[1][ntile] = smooth_ground[ntile];								
+						ss_fg_bg[1][ntile] = str;
+					}
+				}
+			}
+			if (!strong) { // either was weak or broke check_neibs
+                ds_fg_bg[0][ntile] = Double.NaN;
+                ds_fg_bg[1][ntile] = smooth_ground[ntile];
+                ss_fg_bg[0][ntile] = 0.0;
+                ss_fg_bg[1][ntile] = str;
+			}
+		}
+		if (dbg_title != null) {
+			String [] dbg_titles = {"FG0","BG0","FG", "BG", "SG0", "SG1", "SG", "BG"};
+			double [][] dbg_img = {
+					ds_fg_bg_bkp[0], ds_fg_bg_bkp[1], ds_fg_bg[0], ds_fg_bg[1],
+					ss_fg_bg_bkp[0], ss_fg_bg_bkp[1], ss_fg_bg[0], ss_fg_bg[1],
+			};
+			ShowDoubleFloatArrays.showArrays(
+					dbg_img,
+					width,
+					dbg_img[0].length/width,
+					true,
+					dbg_title,
+					dbg_titles);
+		}
+		return;
+		
+	}
+	
+	
+	
 	
 
 	/**
@@ -2453,9 +2564,20 @@ public class TexturedModel {
 			QuadCLT []                               scenes,
 			final int                                ref_index,
 			double [][]                              combo_dsn_final, // null OK, will read file
+			final double [][][]                      ct_scans,
+			final double                             ct_min,
+			final double                             ct_step,
+			final int                                ct_expand_in,
+			final boolean                            terrain_mode,
+			final double [][]                        hdr_render_size, // { hdr_whs[3],hdr_x0y0[2]}; save/use rendering parameters
+			final boolean                            hdr_render_slave,// use rendering parameters (to match other mode)
 			final boolean                            updateStatus,
 			final int                                debugLevel)
 	{
+		final boolean       save_ct_disp = true;
+		final boolean       expand_bg = (ct_expand_in <0);
+		final int ct_expand = Math.abs(ct_expand_in);
+		
 		final boolean map_en =            clt_parameters.gmap_en;
 		final boolean render_hdr =        clt_parameters.gmap_render_hdr || map_en;// true; //false; // true; // generate textures w/o normalization to generate undistorted
 		final boolean use_parallel_proj = clt_parameters.gmap_parallel_proj; // Use parallel projection (map)\
@@ -2556,6 +2678,7 @@ public class TexturedModel {
 		ArrayList<TriMesh> tri_meshes = null; 
 		long startStepTime=System.nanoTime();
 		final int    tilesX = tp.getTilesX();
+		final int    tilesY = tp.getTilesY();
 		final int    transform_size = tp.getTileSize();
 
 		final int width = tilesX * transform_size;
@@ -2570,8 +2693,8 @@ public class TexturedModel {
 			combo_dsn_final =scenes[ref_index].restoreComboDSI(true);  // also sets quadCLTs[ref_index].dsi and blue sky
 		}
 		
-		double[][] ds_fg_bg = null;
-		double[][] ss_fg_bg = null;
+		double[][] ds_fg_bg_common = null;
+		double[][] ss_fg_bg_common = null;
 		double small_strength = 0.0001;
 		
 		/// normal conditioning
@@ -2607,6 +2730,7 @@ public class TexturedModel {
 				combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_LMA_BG].clone(),
 				combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_STRENGTH_BG].clone()
 		};
+		
 		for (int i = 0; i < dls_bg[0].length; i++) if (Double.isNaN(dls_bg[0][i])){
 			dls_bg[0][i] = dls_fg[0][i];
 			dls_bg[1][i] = dls_fg[1][i];
@@ -2643,52 +2767,246 @@ public class TexturedModel {
 			}
 		}
 		
-		ds_fg_bg = new double[][] {ds_fg[0], ds_bg[0].clone()};
-		ss_fg_bg = new double[][] {ds_fg[1], ds_bg[1]};
+		
+		
+		boolean mixed_flat = false;
+		double lim_disparity_noct=100;
+		int num_scans = (ct_scans==null)? 1 : ct_scans.length;
+		TileCluster [] tileClusters = null;
+		double[][][] faded_textures = null;
+		double [][][][] lin_text0 =   null;
+		double [][] ct_disparity = ((ct_scans!=null) && save_ct_disp)? new double [num_scans][]:null;
+		
 		if (show_bs_debug) {
-			String [] dbg_titles = {"FG","BG","BS"};
-			double [][] dbg_img = {ds_fg_bg[0], ds_fg_bg[1],combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY].clone()};
-			for (int i = 0; i < dbg_img[0].length; i++) {
-				dbg_img[2][i] = sky_tiles[i]? 20:0; // *= 20;
-			}
+			String [] dbg_titles = {"FG","BG","FS", "BS"};
+			double [][] dbg_img = {ds_fg[0], ds_bg[0],ds_fg[1], ds_bg[1]}; // here BG==FG
 			ShowDoubleFloatArrays.showArrays(
 					dbg_img,
 					tilesX,
 					dbg_img[0].length/tilesX,
 					true,
-					ref_scene.getImageName()+"-disparity_layers",
+					ref_scene.getImageName()+"-fg-bg-disparity_strength",
 					dbg_titles);
 		}
 		
+		
+		ds_fg_bg_common = new double[][] {ds_fg[0].clone(), ds_bg[0].clone()};
+		ss_fg_bg_common = new double[][] {ds_fg[1].clone(), ds_bg[1].clone()};
+		/*
+		if (ct_scans==null) {
+			for (int i = 0; i < ds_fg_bg[0].length; i++) {
+				if (ds_fg_bg[0][i] > lim_disparity) {
+					ds_fg_bg[0][i] = lim_disparity;
+				}
+				if (ds_fg_bg[1][i] > lim_disparity) {
+					ds_fg_bg[1][i] = lim_disparity;
+				}
+			}
+		}
+		*/
 		// Create data for consolidated textures (multiple texture segments combined in same "passes"
 		// now it will be able to modify ds_fg_bg and sky_tiles to improve around blue sky
 		if (require_lma) { // make non-LMA very weak;
-			for (int i = 0; i < ss_fg_bg.length; i++) {
-				ss_fg_bg[i]= ss_fg_bg[i].clone();
+			for (int i = 0; i < ss_fg_bg_common.length; i++) {
+				ss_fg_bg_common[i]= ss_fg_bg_common[i].clone();
 			}
-			for (int i = 0; i < ss_fg_bg[0].length; i++) {
-				if (Double.isNaN(dls_fg[1][i])){
-					ss_fg_bg[0][i] = Math.min(ss_fg_bg[0][i],small_strength); // do not increase if it was already 0
+			for (int i = 0; i < ss_fg_bg_common[0].length; i++) {
+				if (Double.isNaN(dls_fg[1][i])){ // no LMA
+					ss_fg_bg_common[0][i] = Math.min(ss_fg_bg_common[0][i],small_strength); // do not increase if it was already 0
 				}
 				if (Double.isNaN(dls_bg[1][i])){
-					ss_fg_bg[1][i] = Math.min(ss_fg_bg[1][i],small_strength); // do not increase if it was already 0
+					ss_fg_bg_common[1][i] = Math.min(ss_fg_bg_common[1][i],small_strength); // do not increase if it was already 0
 				}
 			}
+			
+			if (show_bs_debug) {
+				String [] dbg_titles = {"FG","BG","FG_LMA", "BG_LMA", "FS", "BS"};
+				double [][] dbg_img = {ds_fg_bg_common[0], ds_fg_bg_common[1], dls_fg[1], dls_bg[1], ss_fg_bg_common[0], ss_fg_bg_common[1]}; // here BG==FG
+				ShowDoubleFloatArrays.showArrays(
+						dbg_img,
+						tilesX,
+						dbg_img[0].length/tilesX,
+						true,
+						ref_scene.getImageName()+"-fg-bg-disparity_strength-LMA",
+						dbg_titles);
 			}
-		// -------
-		boolean mixed_flat = false;
+		}
+		double [] smooth_ground = null;
+		double    rmse_above = 1.0; // from average
+		double    rmse_below = 1.0; // from average, // positive value
+		int       num_refine = 5;
+		double    frac_above = 0.4;
+		double    frac_below = 0.3;
+		double [] flat_ground = null;
+		
+		final double    threshold_above = 0.05;
+		final int       expand_above = 4; // 2;
+		
 		if (gsmth_enable && (!has_sfm || gsmth_sfm_gnd)) {
-			double [] smooth_ground = scenes[ref_index].getSmoothGround(
+			smooth_ground = scenes[ref_index].getSmoothGround(
 					clt_parameters,
 					has_sfm, // boolean       sfm_mode,
 					debugLevel);
+			String title_flat = (show_bs_debug)? (ref_scene.getImageName()+"-dbg_flat"):null ;
+			flat_ground =  scenes[ref_index].getFlatGround(
+					smooth_ground, // double [] disparity,
+					rmse_above,    //double    rmse_above, // from average
+					rmse_below,    // double    rmse_below, // from average, // positive value
+					num_refine,    // int       num_refine,
+					frac_above,    // double    frac_above,
+					frac_below,    // double    frac_below,
+					title_flat);         // String    debug_title)
+			
+			if (smooth_ground != null) {
+				if (has_sfm && gsmth_sfm_deviate) {
+					mixed_flat = true;
+					String      dbg_title = show_bs_debug?(ref_scene.getImageName()+"-fg-bg-disparity_strength-LMA-GND-FLAT"):null;
+					mixDisparityWithSmooth(
+							ds_fg_bg_common, //double [][] ds_fg_bg, // modified inside
+							ss_fg_bg_common, //double [][] ss_fg_bg, // modified inside
+							smooth_ground,   // double []   smooth_ground,
+							sfm_gain,        // double []   sfm_gain,
+							gsmth_sfm_gain,  // double      gsmth_sfm_gain,
+							gsmth_sfm_rad,   // int         gsmth_sfm_rad,
+							100,             // double      lim_disparity, // 100
+							gsmth_str_bump,  // double      gsmth_str_bump,
+							gsmth_str_dip,   // double      gsmth_str_dip,
+							small_strength,  // double      small_strength,
+							tilesX,          // int         width)
+							dbg_title); // String      dbg_title);
+				} else { // smooth surface only: nothing in FG, surface - in BG
+					for (int i = 0; i < smooth_ground.length; i++) {
+						ds_fg_bg_common[1][i] = smooth_ground[i];
+						ss_fg_bg_common[1][i] = Math.max(ss_fg_bg_common[1][i],ss_fg_bg_common[0][i]);
+						ss_fg_bg_common[1][i] = Math.max(ss_fg_bg_common[1][i],small_strength);
+						ds_fg_bg_common[0][i] = Double.NaN;
+						ss_fg_bg_common[0][i] = 0.0;
+					}
+				}
+			}
+			double [] single_disparity = ds_fg_bg_common[0].clone();
+			for (int i = 0; i < single_disparity.length; i++) if (ss_fg_bg_common[1][i] > ss_fg_bg_common[0][i]) {
+				single_disparity[i] = ds_fg_bg_common[1][i];
+			}
+			double [] terrain_disparity = getTerrainDisparity(
+					single_disparity, // final double [] disparity, // maybe already filtered from smooth (combined, allow strong deviations)
+					flat_ground, // final double [] flat,
+					threshold_above, // final double    threshold_above,
+					expand_above, // final int       expand,
+					tilesX); // final int       width) ;
+			
+			if (show_bs_debug) {
+				String [] dbg_titles = {"FG","BG","FG_LMA", "BG_LMA", "GND", "FLAT", "SINGLE", "TERRAIN", "FS", "BS"};
+				double [][] dbg_img = {
+						ds_fg_bg_common[0], ds_fg_bg_common[1], dls_fg[1], dls_bg[1],
+						smooth_ground, flat_ground, single_disparity, terrain_disparity,
+						ss_fg_bg_common[0], ss_fg_bg_common[1]}; // here BG==FG
+				ShowDoubleFloatArrays.showArrays(
+						dbg_img,
+						tilesX,
+						dbg_img[0].length/tilesX,
+						true,
+						ref_scene.getImageName()+"-fg-bg-disparity_strength-LMA-GND-FLAT",
+						dbg_titles);
+			}
+			scenes[ref_index].setSmoothGround( // was in the end
+					clt_parameters, // CLTParameters clt_parameters,
+					smooth_ground,  // double []     smooth_ground,
+					debugLevel);    // 			    		int debugLevel)
+			if (terrain_mode) {
+//				ds_fg_bg_common[0] = terrain_disparity.clone();
+//				ds_fg_bg_common[1] = terrain_disparity.clone();
+				for (int i = 0; i < smooth_ground.length; i++) { // ~smooth terrain surface only: nothing in FG, surface - in BG
+					ds_fg_bg_common[1][i] = terrain_disparity[i];
+					ss_fg_bg_common[1][i] = Math.max(ss_fg_bg_common[1][i],ss_fg_bg_common[0][i]);
+					ss_fg_bg_common[1][i] = Math.max(ss_fg_bg_common[1][i],small_strength);
+					ds_fg_bg_common[0][i] = Double.NaN;
+					ss_fg_bg_common[0][i] = 0.0;
+				}
+			}
+		}		
+		
+		for (int nscan = 0; nscan < num_scans; nscan++) {
+			double [][] ds_fg_bg = new double[][] {ds_fg_bg_common[0].clone(), ds_fg_bg_common[1].clone()};
+			double [][] ss_fg_bg = new double[][] {ss_fg_bg_common[0].clone(), ss_fg_bg_common[1].clone()};
+			double lim_disparity = lim_disparity_noct;
+			boolean ct_mode = false;
+			if (ct_scans != null) {
+				if (nscan < (num_scans- 1)) { // last pass in ct mode - as if no CT, no limit
+					ct_mode = true;
+					lim_disparity = ct_min+ct_step*nscan;
+				}
+				String sstat = String.format("processing CT scan %d, disparity=%.3f",nscan,lim_disparity);
+		   		if (updateStatus) IJ.showStatus(sstat);
+		   		System.out.println(sstat);
+			}
+			boolean [][] ct_section_fgbg = new boolean[2][ ds_fg_bg[0].length]; // only FG!
+			for (int i = 0; i < ds_fg_bg[0].length; i++) {
+				if (ds_fg_bg[0][i] > lim_disparity) {
+					ds_fg_bg[0][i] = lim_disparity;
+					ct_section_fgbg[0][i] = true;
+				}
+				if (ds_fg_bg[1][i] > lim_disparity) {
+					ds_fg_bg[1][i] = lim_disparity;
+					ct_section_fgbg[1][i] = true;
+				}
+			}
+			
+			double [][] fg_bg_preexpand = null;
+			
+			if (ct_mode && (ct_expand > 0)) {
+				if (show_bs_debug) {
+					fg_bg_preexpand = new double[][] {ds_fg_bg[0].clone(),ds_fg_bg[0].clone()};
+				}
+				
+				TileNeibs tn = new TileNeibs(tilesX,tilesY);
+				int nexp = expand_bg? 2:1; // no need to expand bg
+				for (int n = 0; n < nexp; n++) {
+					tn.growSelection(
+							ct_expand,           // int              grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+							ct_section_fgbg[n], //final boolean [] tiles,
+							null);              // final boolean [] prohibit)
+					for (int i = 0; i < ct_section_fgbg[n].length; i++) if (ct_section_fgbg[n][i]) {
+						ds_fg_bg[n][i] = lim_disparity;
+					}
+				}
+				if (show_bs_debug) {
+					String [] dbg_titles = {"FG","BG","FG_preexp", "BG_preexp", "FG_full", "BG_full", "GND", "FS", "BS"};
+					double [][] dbg_img = {
+							ds_fg_bg[0],    ds_fg_bg[1],
+							fg_bg_preexpand[0],fg_bg_preexpand[1],
+							ds_fg_bg_common[0], ds_fg_bg_common[1],
+							smooth_ground,
+							ss_fg_bg_common[0], ss_fg_bg_common[1]}; // here BG==FG
+					ShowDoubleFloatArrays.showArrays(
+							dbg_img,
+							tilesX,
+							dbg_img[0].length/tilesX,
+							true,
+							ref_scene.getImageName()+"-fg-bg-expansion",
+							dbg_titles);
+				}
+				
+				
+			}
+			
+			/*
+			
+			if ((smooth_ground != null) && !ct_mode) { // no sense to use with CT? or compare with the common only?
+				
+				
+				
 				if (has_sfm && gsmth_sfm_deviate) {
 					mixed_flat = true;
 					// Change!
 					// Use FG for FG, and ground plane as BG?
 					TileNeibs tn = new TileNeibs(tilesX, smooth_ground.length/tilesX);
 					for (int ntile = 0; ntile < smooth_ground.length; ntile++) {
-					double disp = (ss_fg_bg[1][ntile] > ss_fg_bg[0][ntile]) ? ds_fg_bg[1][ntile] : ds_fg_bg[1][ntile];
+						double disp = (ss_fg_bg[1][ntile] > ss_fg_bg[0][ntile]) ? ds_fg_bg[1][ntile] : ds_fg_bg[1][ntile]; // strongest
+						if (disp > lim_disparity) {
+							disp = lim_disparity;
+						}
+
 						double str =  Math.max(ss_fg_bg[1][ntile], ss_fg_bg[0][ntile]);
 						boolean strong = false;
 						if (disp > smooth_ground[ntile]) {
@@ -2723,13 +3041,21 @@ public class TexturedModel {
 							}
 						}
 						if (!strong) { // either was weak or broke check_neibs
+//							if (ct_mode) {
+//								ds_fg_bg[0][ntile] = lim_disparity;
+//								ss_fg_bg[0][ntile] = str;
+//								ds_fg_bg[1][ntile] = smooth_ground[ntile];								
+//								ss_fg_bg[1][ntile] = small_strength;
+//							} else {
 								ds_fg_bg[0][ntile] = Double.NaN;
 								ds_fg_bg[1][ntile] = smooth_ground[ntile];
 								ss_fg_bg[0][ntile] = 0.0;
 								ss_fg_bg[1][ntile] = str;
+//							}
 						}
 					}
 				} else { // smooth surface only: nothing in FG, surface - in BG
+					if (!ct_mode) { // no sense to use smooth_ground in CT scan mode
 						for (int i = 0; i < smooth_ground.length; i++) {
 							ds_fg_bg[1][i] = smooth_ground[i];
 							ss_fg_bg[1][i] = Math.max(ss_fg_bg[1][i],ss_fg_bg[0][i]);
@@ -2737,25 +3063,36 @@ public class TexturedModel {
 							ds_fg_bg[0][i] = Double.NaN;
 							ss_fg_bg[0][i] = 0.0;
 						}
-				/*
-				for (int i = 0; i < smooth_ground.length; i++) {
-					ds_fg_bg[1][i] = Double.NaN;
-					ds_fg_bg[0][i] = smooth_ground[i];
-					ss_fg_bg[1][i] = 0.0;
-					ss_fg_bg[0][i] = Math.max(ss_fg_bg[0][i], small_strength); //???
 					}
-				 */
 
 				}
-			// Save matching DSI data to *-INTER-INTRA-LMA.tiff
-			scenes[ref_index].setSmoothGround(
-					clt_parameters, // CLTParameters clt_parameters,
-					smooth_ground,  // double []     smooth_ground,
-					debugLevel);    // 			    		int debugLevel)
-			if (debugLevel > -3) {
-				System.out.println("output3d(): Using smooth ground for 3D/maps generation.");
+				
+				if (show_bs_debug && (debugLevel>1)) {
+					String [] dbg_titles = {"FGC","BGC","FG", "BG", "GND", "FS", "BS"};
+					double [][] dbg_img = {ds_fg_bg_common[0], ds_fg_bg_common[1], ds_fg_bg[0], ds_fg_bg[1], smooth_ground, ss_fg_bg_common[0], ss_fg_bg_common[1]}; // here BG==FG
+					ShowDoubleFloatArrays.showArrays(
+							dbg_img,
+							tilesX,
+							dbg_img[0].length/tilesX,
+							true,
+							ref_scene.getImageName()+"-fgc-bgc-fg-bg-disparity_strength-LMA-GND",
+							dbg_titles);
 				}
 			}
+*/
+			if (show_bs_debug) {
+				String [] dbg_titles = {"FGC","BGC","FG", "BG", "GND", "FS", "BS"};
+				double [][] dbg_img = {ds_fg_bg_common[0], ds_fg_bg_common[1], ds_fg_bg[0], ds_fg_bg[1], smooth_ground, ss_fg_bg_common[0], ss_fg_bg_common[1]}; // here BG==FG
+				ShowDoubleFloatArrays.showArrays(
+						dbg_img,
+						tilesX,
+						dbg_img[0].length/tilesX,
+						true,
+						ref_scene.getImageName()+"-fgc-bgc-fg-bg-disparity_strength-LMA-GND-final",
+						dbg_titles);
+			}
+			
+			
 			
 			final ArrayList <TileCluster> cluster_list = new ArrayList<TileCluster>();
 			double [][] disparity_layers =buildSkyCluster(
@@ -2775,17 +3112,18 @@ public class TexturedModel {
 					tilesX,            // final int             tilesX,
 					debugLevel);       // final int             debugLevel)
 
-		if (show_bs_debug) {
-			String [] dbg_titles = {"FG","BG", "SFG", "SBG","BS"};
-			double [][] dbg_img = new double [dbg_titles.length][];
-			dbg_img[0] = disparity_layers[0];
-			dbg_img[1] = disparity_layers[1];
-			dbg_img[2] = ss_fg_bg[0];
-			dbg_img[3] = ss_fg_bg[1];
-			dbg_img[4] = new double [sky_tiles.length];
+			if (show_bs_debug && (debugLevel>1)) {
+				String [] dbg_titles = {"FG","FG0","BG","BG0", "SFG", "SBG","BS"};
+				double [] dbg_blue = new double [sky_tiles.length];
 				for (int i = 0; i < sky_tiles.length; i++) {
-				dbg_img[4][i] = sky_tiles[i]? 20: 0;
+					dbg_blue[i] = sky_tiles[i]? 20: 0;
 				}
+
+				double [][] dbg_img = new double [dbg_titles.length][];
+				dbg_img = new double [][] {
+					disparity_layers[0], ds_fg_bg[0], disparity_layers[1],ds_fg_bg[1],
+					ss_fg_bg[0], ss_fg_bg[1],
+					dbg_blue};
 				ShowDoubleFloatArrays.showArrays(
 						dbg_img,
 						tilesX,
@@ -2795,12 +3133,16 @@ public class TexturedModel {
 						dbg_titles);
 
 			}
+			if (ct_disparity != null) {
+				ct_disparity[nscan] = disparity_layers[0].clone();
+			}
 
+//			double [][] ct_disparity = ((ct_scans!=null) && show_bs_debug)? new double [num_scans][]:null;
 			
 
 
-		TileCluster [] tileClusters = 
-				clusterizeFgBg( // wrong result type, not decided
+
+			tileClusters = clusterizeFgBg( // wrong result type, not decided
 							cluster_list, // final ArrayList <TileCluster> cluster_list,
 							tilesX,            // final int          tilesX,
 							disparity_layers,  // ds_fg_bg,          // final double [][]  disparities, // may have more layers
@@ -2836,9 +3178,9 @@ public class TexturedModel {
 				scenes_sel[i] = true;
 			}
 
-		double [][][][] lin_text0 = render_hdr ? new double [1][][][] : null;
+			lin_text0 = render_hdr ? new double [1][][][] : null;
 
-		double[][][] faded_textures = getInterCombinedTextures( // return ImagePlus[] matching tileClusters[], with alpha
+			faded_textures = getInterCombinedTextures( // return ImagePlus[] matching tileClusters[], with alpha
 					clt_parameters,      // final CLTParameters  clt_parameters,
 					colorProcParameters, // ColorProcParameters  colorProcParameters,
 					parameter_scene,     // final QuadCLT        parameter_scene, // to use for rendering parameters in multi-series sequences
@@ -2851,7 +3193,45 @@ public class TexturedModel {
 					max_disparity_lim,   // final double         max_disparity_lim,   //  100.0;  // do not allow stray disparities above this
 					min_trim_disparity,  // final double         min_trim_disparity,  //  2.0;  // do not try to trim texture outlines with lower disparities
 					lin_text0, // 			final double [][][][] lin_textures, // null or [1][][][] to return non-normalized textures
+					(ct_scans != null),  // ct_mode, // final boolean        ct_mode,
+					terrain_mode,        // final boolean        terrain_mode, Just for file name
 					debugLevel);         // final int            debug_level)
+			if (ct_scans != null) {
+//				ct_scans[nscan] = new double [][] {faded_textures[0][0].clone(),faded_textures[1][0].clone()}; // both slices, channel 0 
+				ct_scans[nscan] = new double [faded_textures.length][];
+				for (int i = 0; i < ct_scans[nscan].length; i++) {
+					ct_scans[nscan][i] = faded_textures[i][0].clone(); // channel 0 from each slice
+				}
+		   		if (updateStatus) IJ.showProgress((nscan+1.0)/num_scans);
+			}
+		}
+		if (ct_scans != null) {
+			if (ct_disparity != null) {
+				String [] titles = new String[ct_disparity.length];
+				for (int nscan = 0; nscan < titles.length-1; nscan++) {
+					titles[nscan] = String.format("D=%.3f", ct_min+ct_step*nscan);
+				}
+				titles[titles.length-1]="full";
+				/*
+				ShowDoubleFloatArrays.showArrays(
+						ct_disparity,
+						tilesX,
+						ct_disparity[0].length/tilesX,
+						true,
+						ref_scene.getImageName()+"-CT_scan_disparities",
+						titles);
+						*/
+				double ct_max = ct_min+ct_step* (ct_scans.length-1);
+				String suffix = String.format("-CT_SCAN_%.3f_%.3f_%.3f",ct_min,ct_max,ct_step);
+				scenes[ref_index].saveDoubleArrayInModelDirectory(
+						suffix,                   // String      suffix,
+						titles,                   // String []   labels, // or null
+						ct_disparity,             // double [][] data,
+						tilesX,                   // int            width, // int tilesX,
+						tilesY);                  // int            height, // int tilesY,
+			}
+			return true;
+		}
 		double [][][] lin_textures = (lin_text0 != null) ? lin_text0[0] : null;
 		if (no_alpha && (lin_textures!= null)){
 			for (int nslice = 0; nslice < lin_textures.length; nslice++) {
@@ -2938,7 +3318,7 @@ public class TexturedModel {
 				// do nothing, just keep
 			}
 		}
-		if ((clt_parameters.output_x3d || clt_parameters.output_glTF) && (x3d_dir != null)) {
+		if ((clt_parameters.output_x3d || clt_parameters.output_glTF || render_hdr) && (x3d_dir != null)) {
 			tri_meshes = new ArrayList<TriMesh>();
 		}		
 
@@ -3163,9 +3543,37 @@ public class TexturedModel {
 
 					}
 				}
+				
 				if ((hdr_whs[0]<0) || (hdr_whs[1]<0)) {
 					System.out.println("**** BUG: hdr_whs[0]="+hdr_whs[0]+", hdr_whs[1]="+hdr_whs[1]);
 				} else {
+					
+					if (hdr_render_slave && (hdr_render_size!=null) && (hdr_render_size[0]!=null) && (hdr_render_size[0]!=null)) {
+						for (int i = 0; i < hdr_whs.length; i++) {
+							hdr_whs[i] = (int) Math.round(hdr_render_size[0][i]);
+						}
+						for (int i = 0; i < hdr_x0y0.length; i++) {
+							hdr_x0y0[i] =hdr_render_size[1][i];
+						}
+						scaled_pixel_size = pix_size * hdr_whs[2];
+
+						System.out.println("Using pre-defined rendering parameters:");
+						if (debugLevel > -2) {
+							System.out.println("Updated parameters for rendering:BOTTOM left corner=["+hdr_x0y0[0]+"m, "+hdr_x0y0[1]+"m]");
+							System.out.println("                                : width="+hdr_whs[0]+"pix, height="+hdr_whs[1]+"pix, scale level="+hdr_whs[2]);
+							System.out.println("                                             : pixel size: ="+(1000*scaled_pixel_size)+"mm");
+						}
+					}
+					
+					if (hdr_render_size!=null) { // set/update rendering size
+						hdr_render_size[0] = new double [hdr_whs.length];
+						for (int i = 0; i < hdr_whs.length; i++) {
+							hdr_render_size[0][i] =  hdr_whs[i];
+						}
+						hdr_render_size[1] = hdr_x0y0.clone();
+					}
+					
+					
 					Render3D render3D = new Render3D (
 							//x3d_dir,               // String x3d_dir,
 							//ref_scene.correctionsParameters.getModelName(ref_scene.getImageName()), // String model_name,
@@ -3197,7 +3605,7 @@ public class TexturedModel {
 								debugLevel);           //int                      debugLevel)
 					}
 					//			String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());
-					String suffix ="-RECT"; 
+					String suffix =(terrain_mode?"-TERR":"")+"-RECT"; 
 					suffix +="-PIX"+pix_size * hdr_whs[2];
 					suffix += bicubic ? "-BC":"-BL";
 					if (gsmth_enable) {
@@ -7430,6 +7838,8 @@ public class TexturedModel {
 			final double         max_disparity_lim,
 			final double         min_trim_disparity,
 			final double [][][][] lin_textures, // null or [1][][][] to return non-normalized textures
+			final boolean        ct_mode,
+			final boolean        terrain_mode,
 			final int            debugLevel)
 	{
 		// TODO: ***** scenes with high motion blur also have high ERS to be corrected ! *****
@@ -7739,7 +8149,7 @@ public class TexturedModel {
 				min_trim_disparity,        // final double min_trim_disparity, // do not try to trim texture outlines with lower disparities
 				tp_tasks_ref,              // final TpTask[][][]   tp_tasks_ref,       // reference tasks for each slice to get offsets			
 				ref_scene.getImageName()); // null); // ref_scene.getImageName()); // final String         dbg_prefix);
-		if (save_interm_textures) {
+		if (save_interm_textures && !ct_mode) {
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
 			String [] dbg_titles = new String[dbg_textures.length];
 			String [] dbg_subtitles = new String [faded_textures[0].length];
@@ -7751,7 +8161,7 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
-			String suffix = "-combined_textures-prenorm-pre_UM";
+			String suffix = (terrain_mode?"-TERR":"")+"-combined_textures-prenorm-pre_UM";
 			ref_scene.saveDoubleArrayInModelDirectory(
 					suffix, // String      suffix,
 					null, // String []   labels, // or null
@@ -7783,6 +8193,9 @@ public class TexturedModel {
 					0.03,         // final double     max_rchange, //  = 0.01 - does not need to be accurate
 					THREADS_MAX); // final int threadsMax)      // maximal number of threads to launch 
 		}
+		if (ct_mode) {
+			return faded_textures; // use faded_textures[0][0];
+		}
 		
 		if (save_interm_textures) {
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
@@ -7797,7 +8210,7 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
-			String suffix = "-combined_textures-filled-NaNs";
+			String suffix = (terrain_mode?"-TERR":"")+"-combined_textures-filled-NaNs";
 			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,
@@ -7829,6 +8242,7 @@ public class TexturedModel {
 				}
 			}
 		}
+		
 		// Optionally apply UM (before auto/manual range)
 		final boolean um_ignore_alpha =     true;
 		final boolean hist_ignore_alpha =   true; 
@@ -7853,7 +8267,7 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
-			String suffix = "-combined_textures-prenorm";
+			String suffix = (terrain_mode?"-TERR":"")+"-combined_textures-prenorm";
 			if (save_interm_textures) {
 				if (!batch_run && (debugLevel > -1)) {
 					ShowDoubleFloatArrays.showArrays(
@@ -7872,7 +8286,7 @@ public class TexturedModel {
 						tilesX * transform_size, // int            width, // int tilesX,
 						tilesY * transform_size); // int            height, // int tilesY,
 				if (dbg_weights != null) {
-					suffix = "-texture_weights-prenorm";
+					suffix = (terrain_mode?"-TERR":"")+"-texture_weights-prenorm";
 					if (!batch_run && (debugLevel > -1)) {
 						ShowDoubleFloatArrays.showArrays(
 								dbg_weights,
@@ -7892,7 +8306,7 @@ public class TexturedModel {
 			}
 			// here is the best full-range texture. For UAS just use slice 0
 			if (save_um_texture0) {
-				suffix = "-texture";
+				suffix = (terrain_mode?"-TERR":"")+"-texture";
 				if (tex_um) {
 					suffix+= "-UM"+tex_um_sigma+"_"+tex_um_weight;
 				}
@@ -7996,7 +8410,7 @@ public class TexturedModel {
 							minmax, // 			  double []            minmax, // null for auto
 							null, // QuadCLT              scene,
 							tex_palette, // int                  tex_palette,
-							"", // +tex_palette, // String               suffix,
+							(terrain_mode?"-TERR":"")+"", // +tex_palette, // String               suffix,
 							debugLevel); // int                  debugLevel)
 					tex_palette = 1; // regular color
 					ref_scene.writeLwirPreview(
@@ -8005,7 +8419,7 @@ public class TexturedModel {
 							minmax, // 			  double []            minmax, // null for auto
 							null, // QuadCLT              scene,
 							tex_palette, // int                  tex_palette,
-							"-black_hot", // +tex_palette, // String               suffix,
+							(terrain_mode?"-TERR":"")+"-black_hot", // +tex_palette, // String               suffix,
 							debugLevel); // int                  debugLevel)
 					tex_palette = 2; // regular color
 					ref_scene.writeLwirPreview(
@@ -8014,12 +8428,12 @@ public class TexturedModel {
 							minmax, // 			  double []            minmax, // null for auto
 							null, // QuadCLT              scene,
 							tex_palette, // int                  tex_palette,
-							"-color", // +tex_palette, // String               suffix,
+							(terrain_mode?"-TERR":"")+"-color", // +tex_palette, // String               suffix,
 							debugLevel); // int                  debugLevel)
 					
 				}
 			if (save_interm_textures) {
-			String suffix = "-combined_textures";
+			String suffix = (terrain_mode?"-TERR":"")+"-combined_textures";
 			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,

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

@@ -78,12 +78,19 @@ public class Render3D {
 		ground_normal = ground_origin.subtract(
 				ground_x.scalarMultiply(ground_origin.dotProduct(ground_x))).subtract(
 						ground_y.scalarMultiply(ground_origin.dotProduct(ground_y)));
-		ground_normal_unit = ground_normal.normalize(); // unitary vector normal and away from the ground plane
+		Vector3D gnu; 
+		try {
+			gnu = ground_normal.normalize(); // unitary vector normal and away from the ground plane
+		} catch (Exception e) {
+			System.out.println("Zero above ground");
+			gnu = ground_x.crossProduct(ground_y).normalize(); // sets to (0, 0, 1)
+		}
+		ground_normal_unit = gnu; // only used for center projection where ground_origin != 0;
 		above_ground = ground_normal.getNorm();
 		xy_offs = new double[] {ground_x.dotProduct(ground_origin), ground_y.dotProduct(ground_origin)};
 	}
 	
-	public double [] projectToPlaneLinear(Vector3D v3) { // get ground plane pixel coordinate from camera x,y,z
+	public double [] projectToPlaneLinear(Vector3D v3) { // get ground plane pixel coordinate from camera x,y,z - not used
 		double   z =        ground_normal_unit.dotProduct(v3);
 		Vector3D in_plane = v3.scalarMultiply(above_ground/z);
 		double [] xy = new double[3];
@@ -93,7 +100,7 @@ public class Render3D {
 		return xy;
 	}
 	
-	public double [] projectToPlanePixels(Vector3D v3) { // get ground plane pixel coordinate from camera x,y,z
+	public double [] projectToPlanePixels(Vector3D v3) { // get ground plane pixel coordinate from camera x,y,z used in center proj
 		double   z =        ground_normal_unit.dotProduct(v3);
 		Vector3D in_plane = v3.scalarMultiply(above_ground/z);
 		double [] xy = new double[3];