Working on FOPEN

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

@@ -1672,7 +1672,7 @@ public class OrangeTest {
 						for (int ipix=0; ipix < num_pixels; ipix++) {
 							mask[nframe][ipix] = !(weights_in[nframe][ipix] > 0);
 						}
-						tn. growSelection(
+						tn.growSelection(
 								shrink, // 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
 								mask[nframe], // final boolean [] tiles,
 								null); // final boolean [] prohibit)

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

@@ -60,6 +60,7 @@ import com.elphel.imagej.ims.Did_ins_2;
 import com.elphel.imagej.ims.Did_pimu;
 import com.elphel.imagej.ims.Imx5;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
+import com.elphel.imagej.orthomosaic.VegetationModel;
 import com.elphel.imagej.tileprocessor.sfm.StructureFromMotion;
 
 import Jama.Matrix;
@@ -5685,6 +5686,23 @@ public class OpticalFlow {
 		
 		// generates 3-d modes, colors, stereos, tiffs/videos
 		
+		// Testing vegetation, for debugging supposing that terrain layer is already set in *-INTER-INTRA-LMA.tiff - normally it is only set during 3d model generation
+		boolean test_vegetation = true;
+		if (test_vegetation) { // limit start of the quadCLTs by reading start/end from the reference scene
+			VegetationModel.test_vegetation(
+					clt_parameters, // CLTParameters  clt_parameters,
+					quadCLTs,       // QuadCLT []     quadCLTs,
+					ref_index,      // int            ref_index,
+					debugLevel);    // int debugLevel)
+			if (videos != null) {
+				videos[0] = new String[0];
+			}
+			// temporarily - exiting now
+			return quadCLTs[ref_index].getX3dTopDirectory();
+		}
+		
+		
+		
 		if (generate_mapped || reuse_video) { // modifies combo_dsn_final ?
 			int tilesX =  quadCLTs[ref_index].getTileProcessor().getTilesX();
 	        int tilesY =  quadCLTs[ref_index].getTileProcessor().getTilesY();

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

@@ -3044,96 +3044,6 @@ public class TexturedModel {
 				
 			}
 			
-			/*
-			
-			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]; // 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
-//							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]);
-							ss_fg_bg[1][i] = Math.max(ss_fg_bg[1][i],small_strength);
-							ds_fg_bg[0][i] = Double.NaN;
-							ss_fg_bg[0][i] = 0.0;
-						}
-					}
-
-				}
-				
-				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
@@ -3248,10 +3158,9 @@ public class TexturedModel {
 					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
+					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
@@ -3266,15 +3175,6 @@ public class TexturedModel {
 					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(

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

@@ -8660,6 +8660,9 @@ if (debugLevel > -100) return true; // temporarily !
 				}
 				first_in_series = false; // at least once success in this series
 				System.out.println("adding to video_sets_list start="+start_ref_pointers[0]+", end="+ref_index); // start_ref_pointers[1]);
+//				if ((video_list != null) && (video_list.length>0) && (video_list[0] == null)) {
+//					video_list[0]= new String[0];
+//				}
 				for (int i= 0; i < video_list[0].length; i++) {
 					System.out.println(i+": "+video_list[0][i]+", "+widths_list[0][i]);
 				}