implemented/tested terrain layer in *-INTER-INTRA-LMA.tiff

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

@@ -76,7 +76,7 @@ import ij.plugin.filter.GaussianBlur;
 
 public class OpticalFlow {
 	public static String [] COMBO_DSN_TITLES = {"disp", "strength","disp_lma","num_valid","change",
-			"disp_bg", "strength_bg","disp_lma_bg","change_bg","disp_fg","disp_bg_all","blue_sky","sfm_gain", "ground"};
+			"disp_bg", "strength_bg","disp_lma_bg","change_bg","disp_fg","disp_bg_all","blue_sky","sfm_gain", "ground","terrain"};
 	public static int COMBO_DSN_INDX_DISP =        0; // cumulative disparity (from CM or POLY), FG
 	public static int COMBO_DSN_INDX_STRENGTH =    1; // strength, FG
 	public static int COMBO_DSN_INDX_LMA =         2; // masked copy from 0 - cumulative disparity
@@ -91,6 +91,7 @@ public class OpticalFlow {
 	public static int COMBO_DSN_INDX_BLUE_SKY =   11; // Detected featureless infinity (sky)
 	public static int COMBO_DSN_INDX_SFM_GAIN =   12; // SfM disparity gain pixel/pixel
 	public static int COMBO_DSN_INDX_GROUND =     13; // Smooth ground surface w/o vegetation
+	public static int COMBO_DSN_INDX_TERRAIN =    14; // Smooth ground surface w/o vegetation
 	
 // move to Interscene class?	
 	// interscene adjustments failure reasons.
@@ -5858,6 +5859,7 @@ public class OpticalFlow {
 		        				}
 	        					imp_scenes_pair[nstereo]= renderSceneSequence(
 	        							clt_parameters,     // CLTParameters clt_parameters,
+	        							clt_parameters.imp.um_mono, // boolean        um_mono,
 	        							fov_tiles,          // Rectangle     fov_tiles,
 	        							mode3d,             // int           mode3d,
 	        							toRGB,              // boolean       toRGB,
@@ -6285,7 +6287,33 @@ public class OpticalFlow {
 			System.out.println ("TexturedModel.output3d() -> "+ok_3d+" (terrain only, no vegetation)");
 		}
 		
-		
+		boolean export_terrain_sequence = true;
+		if (export_terrain_sequence) {
+			combo_dsn_final =quadCLTs[ref_index].restoreComboDSI(true);
+			if ((combo_dsn_final.length <= COMBO_DSN_INDX_TERRAIN) || (combo_dsn_final[COMBO_DSN_INDX_TERRAIN] == null)) {
+				System.out.println ("No terrain data available");
+			} else {
+				double [] terrain_disparity = combo_dsn_final[COMBO_DSN_INDX_TERRAIN];
+				String scenes_suffix = quadCLTs[quadCLTs.length-1].getImageName()+"-TERRAIN";
+				ImagePlus imp_terrain = renderSceneSequence(
+						clt_parameters,     // CLTParameters clt_parameters,
+						false,              // boolean        um_mono,
+						null,               // Rectangle     fov_tiles,
+						1,                  // int           mode3d,
+						false,              // boolean       toRGB,
+						ZERO3,              // double []     stereo_offset, // offset reference camera {x,y,z}
+						1,                  // int           sensor_mask,
+						scenes_suffix,      // String        suffix,
+						terrain_disparity,  // selected_disparity, // double []     ref_disparity,			
+						quadCLTs,           // QuadCLT []    quadCLTs,
+						ref_index,          // int           ref_index,
+						threadsMax,         // int           threadsMax,
+						debugLevel);        // int           debugLevel);
+				quadCLTs[ref_index].saveImagePlusInModelDirectory(
+						null,               // "GPU-SHIFTED-D"+clt_parameters.disparity, // String      suffix,
+						imp_terrain);       // imp_scenes); // ImagePlus   imp)
+			}
+		}
 		
 		if (export_images) {
 			if (combo_dsn_final == null) {
@@ -7320,6 +7348,7 @@ public class OpticalFlow {
     
     public static ImagePlus renderSceneSequence(
     		CLTParameters  clt_parameters,
+    		boolean        um_mono,
     		Rectangle      fov_tiles,
     		int            mode3d, // for older compatibility mode3d = -1 for RAW, 0 - INF, 1 - FG, 2 BG
     		boolean        toRGB,
@@ -7333,7 +7362,7 @@ public class OpticalFlow {
     		int            debugLevel) {
     	boolean corr_raw_ers = true;
     	double [] stereo_atr = ZERO3; // maybe later play with rotated camera
-		boolean um_mono =            clt_parameters.imp.um_mono;
+//		boolean um_mono =            clt_parameters.imp.um_mono;
 		double  um_sigma =           clt_parameters.imp.um_sigma;
 		double  um_weight =          clt_parameters.imp.um_weight;
 		boolean mb_en =       clt_parameters.imp.mb_en && (fov_tiles==null) && (mode3d > 0);
@@ -7342,7 +7371,7 @@ public class OpticalFlow {
 		
     	final float fum_weight = (float)  um_weight; 
     	
-    	boolean merge_all = clt_parameters.imp.merge_all;
+    	boolean merge_all = clt_parameters.imp.merge_all || !um_mono; // no unsharp mask -> terrain->merge_all
     	if (mode3d < 1) {
     		merge_all = false;
     	}

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

@@ -1706,6 +1706,26 @@ public class QuadCLTCPU {
 				tilesX,                // int         width,
 				tilesY);               // int         height)
     }
+
+    public void setTerrain(
+    		CLTParameters clt_parameters,
+    		double []     terrain,
+    		int           debugLevel) {
+    	double [][] combo_dsn_final = restoreComboDSI(true); // also sets quadCLTs[ref_index].dsi and blue sky    	
+    	combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_TERRAIN] = terrain;
+		String rslt_suffix = "-INTER-INTRA";
+		rslt_suffix += (clt_parameters.correlate_lma?"-LMA":"-NOLMA");
+    	final int tilesX =   tp.getTilesX();	
+    	final int tilesY =   tp.getTilesY();	
+		saveDoubleArrayInModelDirectory( // error
+				rslt_suffix,           // String      suffix,
+				OpticalFlow.COMBO_DSN_TITLES, // combo_dsn_titles_full, // null,          // String []   labels, // or null
+				combo_dsn_final,       // dbg_data,         // double [][] data,
+				tilesX,                // int         width,
+				tilesY);               // int         height)
+    }
+    
+    
     
     public double [] getFlatGround(
     		double [] disparity,
@@ -2617,12 +2637,14 @@ public class QuadCLTCPU {
     		//    		System.out.println("dsi== null, use spawnQuadCLT(), restoreFromModel(), ... to set it");
     		return null;
     	}
-    	double [][] dls = new double[5][];
+//    	double [][] dls = new double[5][];
+    	double [][] dls = new double[6][];
     	dls[0] = dsi[isAux()? TwoQuadCLT.DSI_DISPARITY_AUX :     TwoQuadCLT.DSI_DISPARITY_MAIN];
     	dls[1] = dsi[isAux()? TwoQuadCLT.DSI_DISPARITY_AUX_LMA : TwoQuadCLT.DSI_DISPARITY_MAIN_LMA];
     	dls[2] = dsi[isAux()? TwoQuadCLT.DSI_STRENGTH_AUX :      TwoQuadCLT.DSI_STRENGTH_MAIN];
     	dls[3] = dsi[isAux()? TwoQuadCLT.DSI_SFM_GAIN_AUX :      TwoQuadCLT.DSI_SFM_GAIN_MAIN];
-    	dls[4] = dsi[isAux()? TwoQuadCLT.DSI_GROUND_AUX :      TwoQuadCLT.DSI_GROUND_MAIN];
+    	dls[4] = dsi[isAux()? TwoQuadCLT.DSI_GROUND_AUX :        TwoQuadCLT.DSI_GROUND_MAIN];
+    	dls[5] = dsi[isAux()? TwoQuadCLT.DSI_TERRAIN_AUX :       TwoQuadCLT.DSI_TERRAIN_MAIN];
     	return dls;
     }
 
@@ -3687,11 +3709,24 @@ public class QuadCLTCPU {
     		this.dsi[is_aux?TwoQuadCLT.DSI_SFM_GAIN_AUX:TwoQuadCLT.DSI_SFM_GAIN_MAIN] =
     				combo_dsi[OpticalFlow.COMBO_DSN_INDX_SFM_GAIN];
     	}
-
+    	/*
+    	 * Was a BUG!
     	if ((combo_dsi.length > OpticalFlow.COMBO_DSN_INDX_GROUND) && (combo_dsi[OpticalFlow.COMBO_DSN_INDX_GROUND] != null)) {
     		this.dsi[is_aux?TwoQuadCLT.DSI_SFM_GAIN_AUX:TwoQuadCLT.DSI_SFM_GAIN_MAIN] =
     				combo_dsi[OpticalFlow.COMBO_DSN_INDX_GROUND];
     	}
+
+    	 */
+
+    	if ((combo_dsi.length > OpticalFlow.COMBO_DSN_INDX_GROUND) && (combo_dsi[OpticalFlow.COMBO_DSN_INDX_GROUND] != null)) {
+    		this.dsi[is_aux?TwoQuadCLT.DSI_GROUND_AUX:TwoQuadCLT.DSI_GROUND_MAIN] =
+    				combo_dsi[OpticalFlow.COMBO_DSN_INDX_GROUND];
+    	}
+
+    	if ((combo_dsi.length > OpticalFlow.COMBO_DSN_INDX_TERRAIN) && (combo_dsi[OpticalFlow.COMBO_DSN_INDX_TERRAIN] != null)) {
+    		this.dsi[is_aux?TwoQuadCLT.DSI_TERRAIN_AUX:TwoQuadCLT.DSI_TERRAIN_MAIN] =
+    				combo_dsi[OpticalFlow.COMBO_DSN_INDX_TERRAIN];
+    	}
     }
 
 

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

@@ -2927,7 +2927,11 @@ public class TexturedModel {
 					expand_above,     // final int       expand,
 					flat_border,      // final boolean   flat_border,
 					tilesX,           // final int       width) ;
-					terr_mask);        // boolean []      dbg_mask);
+					terr_mask);       // boolean []      dbg_mask);
+			scenes[ref_index].setTerrain( // will save terrain as the last slice in INTER-INTRA-LMA
+					clt_parameters,    // CLTParameters clt_parameters,
+					terrain_disparity, // double []     smooth_ground,
+					debugLevel);       // 			    		int debugLevel)
 			
 			if (save_terrain || show_bs_debug) {
 				String [] dbg_titles = {"FG","BG","FG_LMA", "BG_LMA", "GND", "FLAT", "SINGLE", "TERRAIN", "TERR-MASK", "FS", "BS"};

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

@@ -80,11 +80,14 @@ public class TwoQuadCLT {
 	public static  int DSI_AVGVAL_AUX =        12;
 	public static  int DSI_BLUE_SKY_MAIN =     13;
 	public static  int DSI_BLUE_SKY_AUX =      14;
-	public static  int DSI_GROUND_MAIN =       15; // ground surface ignoring vegetation
+	public static  int DSI_GROUND_MAIN =       15; // ground surface ignoring vegetation (smooth, has bumps where vegetation is)
 	public static  int DSI_GROUND_AUX =        16; // ground surface ignoring vegetation
 	public static  int DSI_SFM_GAIN_MAIN =     17; // SfM disparity gain pixel/pixel, RGB
 	public static  int DSI_SFM_GAIN_AUX =      18; // SfM disparity gain pixel/pixel, LWIR
-	public static  int DSI_LENGTH =            DSI_SFM_GAIN_AUX+1;
+	public static  int DSI_TERRAIN_MAIN =      19; // terrain with bumps (vegetation) completely cut off, RGB
+	public static  int DSI_TERRAIN_AUX =       20; // terrain with bumps (vegetation) completely cut off, LWIR
+///	public static  int DSI_LENGTH =            DSI_SFM_GAIN_AUX+1;
+	public static  int DSI_LENGTH =            DSI_TERRAIN_AUX+1;
 
 	public static String DSI_COMBO_SUFFIX = "-DSI_COMBO";
 	public static String DSI_MAIN_SUFFIX =  "-DSI_MAIN";
@@ -108,7 +111,10 @@ public class TwoQuadCLT {
 			    "ground_main",
 			    "ground_aux",
 			    "sfm_gain_main",
-			    "sfm_gain_aux"};
+			    "sfm_gain_aux",
+			    "terrain_main",
+			    "terrain_aux"
+			    };
 
 	public long                                            startTime;     // start of batch processing
 	public long                                            startSetTime;  // start of set processing