Before motion blur correction

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

@@ -1527,10 +1527,12 @@ public class EyesisCorrectionParameters {
     		public String path;
     		public int first = 0;
     		public int last = -1;
-    		PathFirstLast (String path, int first, int last){
+    		public int movement_size = -1;
+    		PathFirstLast (String path, int first, int last, int movement_size){
     			this.path = path;
     			this.first = first;
     			this.last =  last;
+    			this.movement_size = movement_size;
     		}
     	}
     	public PathFirstLast [] getSourceSets(
@@ -1623,7 +1625,8 @@ public class EyesisCorrectionParameters {
                 	path_list.add(new PathFirstLast(
                 			dir_path.toString(),
                 			((tokens.length > 1)? Integer.parseInt(tokens[1]):0),
-                			((tokens.length > 2)? Integer.parseInt(tokens[2]):-1)));
+                			((tokens.length > 2)? Integer.parseInt(tokens[2]):-1),
+                			((tokens.length > 3)? Integer.parseInt(tokens[3]):-1)));
                 }
             }
             return path_list.toArray(new PathFirstLast[0]);

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

@@ -26,6 +26,7 @@ package com.elphel.imagej.tileprocessor;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Properties;
@@ -398,6 +399,10 @@ public class ErsCorrection extends GeometryCorrection {
 		scenes_poses.put(timestamp, new XyzAtr(xyz, atr, ers_xyz_dt, ers_atr_dt, ers_xyz_d2t, ers_atr_d2t));
 	}
 	
+	public String getEarliestScene() {
+		return Collections.min(scenes_poses.keySet());
+	}
+	
 	public XyzAtr getScene(String timestamp) { // null if not found
 		return scenes_poses.get(timestamp);
 	}

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

@@ -146,6 +146,7 @@ public class IntersceneMatchParameters {
 	public  int     seed_rows =                        5; // sky should appear in this top rows 
 	public  double  sky_lim =                         15.0; // then expand to product of strength by diff_second below this
 	public  int     sky_expand_extra =                 0; // 1?
+	public  int     sky_bottleneck =                   5;
 	public  double  min_strength =                     0.08;
 	public  int     lowest_sky_row =                  50; // appears that low - invalid, remove completely
 	public  double  sky_bottom_override =           -300; // maximal average sky value to override lowest_sky_row test
@@ -530,6 +531,8 @@ public class IntersceneMatchParameters {
 				"Expand while FOM is below this value (usually to a high-contrast skyline).");
 		gd.addNumericField("Expand extra",                           this.sky_expand_extra, 0,3,"",
 				"Additionally expand sky area after reaching threshold in the previous step.");
+		gd.addNumericField("Bottleneck width",                       this.sky_bottleneck, 0,3,"",
+				"Shrink/reexpand from the seed detected sky to prevent \"leaks\" through narrow gaps in the high-contrast sky limit.");
 		gd.addNumericField("Modify strength to be at least this",    this.min_strength, 5,7,"",
 				"Input strength has some with zero values resulting in zero FOM. Make them at least this.");
 		gd.addNumericField("Lowest sky row",                         this.lowest_sky_row, 0,3,"",
@@ -910,6 +913,7 @@ public class IntersceneMatchParameters {
 		this.seed_rows =          (int) gd.getNextNumber();       	
 		this.sky_lim =                  gd.getNextNumber();         	
 		this.sky_expand_extra =   (int) gd.getNextNumber();	
+		this.sky_bottleneck =     (int) gd.getNextNumber();	
 		this.min_strength =             gd.getNextNumber();    
 		this.lowest_sky_row =     (int) gd.getNextNumber();
 		this.sky_bottom_override =      gd.getNextNumber();    
@@ -1182,6 +1186,7 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"seed_rows",            this.seed_rows+"");           // int
 		properties.setProperty(prefix+"sky_lim",              this.sky_lim+"");             // double
 		properties.setProperty(prefix+"sky_expand_extra",     this.sky_expand_extra+"");    // int
+		properties.setProperty(prefix+"sky_bottleneck",       this.sky_bottleneck+"");      // int
 		properties.setProperty(prefix+"min_strength",         this.min_strength+"");        // double
 		properties.setProperty(prefix+"lowest_sky_row",       this.lowest_sky_row+"");      // int
 		properties.setProperty(prefix+"sky_bottom_override",  this.sky_bottom_override+""); // double
@@ -1405,6 +1410,7 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"seed_rows")!=null)            this.seed_rows=Integer.parseInt(properties.getProperty(prefix+"seed_rows"));
 		if (properties.getProperty(prefix+"sky_lim")!=null)              this.sky_lim=Double.parseDouble(properties.getProperty(prefix+"sky_lim"));
 		if (properties.getProperty(prefix+"sky_expand_extra")!=null)     this.sky_expand_extra=Integer.parseInt(properties.getProperty(prefix+"sky_expand_extra"));
+		if (properties.getProperty(prefix+"sky_bottleneck")!=null)       this.sky_bottleneck=Integer.parseInt(properties.getProperty(prefix+"sky_bottleneck"));
 		if (properties.getProperty(prefix+"min_strength")!=null)         this.min_strength=Double.parseDouble(properties.getProperty(prefix+"min_strength"));
 		if (properties.getProperty(prefix+"lowest_sky_row")!=null)       this.lowest_sky_row=Integer.parseInt(properties.getProperty(prefix+"lowest_sky_row"));
 		if (properties.getProperty(prefix+"sky_bottom_override")!=null)  this.sky_bottom_override=Double.parseDouble(properties.getProperty(prefix+"sky_bottom_override"));
@@ -1645,6 +1651,7 @@ public class IntersceneMatchParameters {
 		imp.seed_rows =             this.seed_rows;
 		imp.sky_lim =               this.sky_lim;
 		imp.sky_expand_extra =      this.sky_expand_extra;
+		imp.sky_bottleneck =        this.sky_bottleneck;
 		imp.min_strength =          this.min_strength;
 		imp.lowest_sky_row =        this.lowest_sky_row;
 		imp.sky_bottom_override =   this.sky_bottom_override;

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

@@ -4131,6 +4131,7 @@ public class OpticalFlow {
  		double sky_seed =            clt_parameters.imp.sky_seed;
  		double lma_seed =            clt_parameters.imp.lma_seed;
  		int    sky_shrink =          clt_parameters.imp.sky_shrink;
+ 		int    sky_bottleneck =      clt_parameters.imp.sky_bottleneck;
  		int    seed_rows =           clt_parameters.imp.seed_rows;
  		double sky_lim =             clt_parameters.imp.sky_lim;
  		int    sky_expand_extra =    clt_parameters.imp.sky_expand_extra;
@@ -4268,6 +4269,7 @@ public class OpticalFlow {
 							sky_lim,            // double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 							sky_shrink,         // int    sky_shrink, //  =       4;
 							sky_expand_extra,   // int    sky_expand_extra, //  = 100; // 1?
+							sky_bottleneck,     //int    sky_bottleneck, // 
 							cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
 							cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
 							hot_frac, // =         0.9;    // this and above will scale fom by 1.0
@@ -4321,6 +4323,7 @@ public class OpticalFlow {
 							sky_lim,                               // double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 							sky_shrink,                            // int    sky_shrink, //  =       4;
 							sky_expand_extra,                      // int    sky_expand_extra, //  = 100; // 1?
+							sky_bottleneck,       //int    sky_bottleneck, // 
 							cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
 							cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
 							hot_frac, // =         0.9;    // this and above will scale fom by 1.0
@@ -4530,9 +4533,23 @@ public class OpticalFlow {
 							debugLevel-2);
 				}
 			}
+			for (int scene_index =  ref_index - 1; scene_index >= earliest_scene ; scene_index--) {
+				if (!quadCLTs[ref_index].tsExists(set_channels[scene_index].set_name)) {
+					earliest_scene = scene_index + 1;
+				}
+			}
+			if ((ref_index - earliest_scene + 1) < min_num_scenes) {
+				System.out.println("2.Total number of useful scenes = "+(ref_index - earliest_scene + 1)+
+						" < "+min_num_scenes+". Scrapping this series.");
+				if (start_ref_pointers != null) {
+					start_ref_pointers[0] = earliest_scene;
+				}
+				return null;
+			}
+
 		}
 		// just in case that orientations were calculated before:
-		earliest_scene = getEarliestScene(quadCLTs);
+//		earliest_scene = getEarliestScene(quadCLTs);
 		
 		double [][] combo_dsn_final = null;
 		while (!reuse_video && ((quadCLTs[ref_index].getNumOrient() < min_num_orient) || (quadCLTs[ref_index].getNumAccum() < min_num_interscene))) {
@@ -4852,18 +4869,18 @@ public class OpticalFlow {
 	        				if (views[ibase][2] != 0) {
 	        					scenes_suffix += "-Z"+String.format("%.0f",views[ibase][2]);
 	        				}
-	        				double [][] ds_vantage = new double[][] {selected_disparity,selected_strength};
-	        				if ((views[ibase][0] != 0) || (views[ibase][1] != 0) || (views[ibase][2] != 0)) {
-	        					ds_vantage = transformCameraVew(
-	        							null, // (debug_ds_fg_virt?"transformCameraVew":null),     // final String    title,
-	        							ds_vantage,                    // final double [][] dsrbg_camera_in,
-	        							xyz_offset, // _inverse[0], // final double [] scene_xyz, // camera center in world coordinates
-	        							ZERO3, // _inverse[1], // final double [] scene_atr, // camera orientation relative to world frame
-	        							quadCLTs[ref_index],      // final QuadCLT   scene_QuadClt,
-	        							quadCLTs[ref_index],      // final QuadCLT   reference_QuadClt,
-	        							8); // iscale);                  // final int       iscale);
-	        				}
 	        				if (generate_mapped) {
+		        				double [][] ds_vantage = new double[][] {selected_disparity,selected_strength};
+		        				if ((views[ibase][0] != 0) || (views[ibase][1] != 0) || (views[ibase][2] != 0)) {
+		        					ds_vantage = transformCameraVew(
+		        							null, // (debug_ds_fg_virt?"transformCameraVew":null),     // final String    title,
+		        							ds_vantage,                    // final double [][] dsrbg_camera_in,
+		        							xyz_offset, // _inverse[0], // final double [] scene_xyz, // camera center in world coordinates
+		        							ZERO3, // _inverse[1], // final double [] scene_atr, // camera orientation relative to world frame
+		        							quadCLTs[ref_index],      // final QuadCLT   scene_QuadClt,
+		        							quadCLTs[ref_index],      // final QuadCLT   reference_QuadClt,
+		        							8); // iscale);                  // final int       iscale);
+		        				}
 	        					imp_scenes_pair[nstereo]= renderSceneSequence(
 	        							clt_parameters,     // CLTParameters clt_parameters,
 	        							fov_tiles,          // Rectangle     fov_tiles,
@@ -10054,15 +10071,19 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 		ErsCorrection ers_reference = scenes[ref_index].getErsCorrection();
 		for (int nscene = ref_index-1; nscene >= 00; nscene--) {
 			String ts = scenes[nscene].getImageName();
-			double []   scene_xyz = ers_reference.getSceneXYZ(ts);
-			double []   scene_atr = ers_reference.getSceneATR(ts);
-			if ((scene_xyz == null) || (scene_atr == null)){
+			if (!scenes[ref_index].tsExists(ts) ) {
 				return nscene + 1; // scene is not matched
 			}
+//			double []   scene_xyz = ers_reference.getSceneXYZ(ts);
+//			double []   scene_atr = ers_reference.getSceneATR(ts);
+//			if ((scene_xyz == null) || (scene_atr == null)){
+//				return nscene + 1; // scene is not matched
+//			}
 		}
 		return 0;
 	}
 	
+	
 // Cleaned up and optimized version to reduce memory usage (on-the-fly integration, not saving full correlation data)
 	public double[][] correlateInterscene(
 			final CLTParameters  clt_parameters,
@@ -12723,7 +12744,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 								}
 								double target_str=Math.exp(
 										eq_level*Math.log(avg_stile_str) +
-										(1.0-eq_level)*stile_weight[sTile]);
+										(1.0-eq_level)*Math.log(stile_weight[sTile]));
 								Arrays.fill(mod_weights,0);
 								double sum_weights = 0.0;
 								int num_tiles = 0; // for partial stiles

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

@@ -432,6 +432,7 @@ public class QuadCLTCPU {
 	 *                        be expanded
 	 * @param sky_shrink shrink initial sky area to eliminate small non-sky areas. 
 	 * @param sky_expand_extra additionally expand
+	 * @param int sky_bottleneck - shrink/reexpand from the seed detected sky to prevent "leaks"
 	 * @param width number of tiles in a row 
 	 * @param strength 1d array of tile strengths in scanline order
 	 * @param spread 1d array of tile spreads (second maximal difference from
@@ -447,6 +448,7 @@ public class QuadCLTCPU {
 			double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 			int    sky_shrink, //  =       4;
 			int    sky_expand_extra, //  = 100; // 1?
+			int    sky_bottleneck, //            
 			double cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
 			double cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
 			double hot_frac, // =         0.9;    // this and above will scale fom by 1.0
@@ -465,6 +467,8 @@ public class QuadCLTCPU {
 		if ((strength == null) || (spread==null)) {
 			return null;
 		}
+//		int sky_bottleneck = 5; // shrink full selection, then re-expand from seed to disable
+		// small (narrow) leaks (or just disable leaks near margins)?
 //		int shrink_for_temp = 10;
 //		double sky_temp_override = -300;      // really cold average seed - ignore lowest_sky_row filter
 		double [] temp_scales = null;
@@ -485,7 +489,7 @@ public class QuadCLTCPU {
 					num_def++;
 				}
 			}
-			if (num_def > 00) {
+			if (num_def > 0) {
 				avg_temp/= num_def;
 				// build a histogram from min to max
 				double [] hist = new double [num_bins];
@@ -550,7 +554,7 @@ public class QuadCLTCPU {
 		
 		
 		String [] dbg_in_titles =    {"fom", "strength", "spread", "disparity", "avg_val", "tscale"};
-		String [] dbg_titles = {"sky", "seed", "max", "shrank","full_shrank"};
+		String [] dbg_titles = {"sky", "seed", "max", "shrank","full_shrank","neck_shrank","reexpand"};
 		
 		if (debugLevel>0) {
 			double [] fom = new double[strength.length];
@@ -595,15 +599,17 @@ public class QuadCLTCPU {
 		if (seed_rows > 0) {
 			Arrays.fill(sky_tiles, seed_rows * width, sky_tiles.length, false);
 		}
+		boolean [] seed_sky = sky_tiles.clone();
 		if (dbg_img != null) {
 			for (int i = 0; i < sky_tiles.length; i++) {
 				dbg_img[3][i] = sky_tiles[i]? 1 : 0;
 			}			
 		}
+		
 		// Calculate average seed "temperature"
 		
 		tn.growSelection(
-				2*width ,        // int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+				4*width ,        // int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
 				sky_tiles,       // boolean [] tiles,
 				prohibit_tiles); // boolean [] prohibit)
 		if (sky_expand_extra > 0) {
@@ -612,6 +618,36 @@ public class QuadCLTCPU {
 					sky_tiles,         // boolean [] tiles,
 					null);             // boolean [] prohibit)
 		}
+		//shrink_neck
+		// Remove leaks through small holes
+		if (sky_bottleneck > 0) {
+			tn.shrinkSelection(
+					sky_bottleneck, // int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+					sky_tiles,   // boolean [] tiles,
+					null);       // boolean [] prohibit)
+			boolean [] prohibit_neck = new boolean[sky_tiles.length];
+			for (int i = 0; i < prohibit_neck.length; i++) {
+				prohibit_neck[i] = !seed_sky[i] && !sky_tiles[i];
+			}
+			sky_tiles = seed_sky.clone();
+			tn.growSelection(
+					4*width , // int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+					sky_tiles,         // boolean [] tiles,
+					prohibit_neck);             // boolean [] prohibit)
+			tn.growSelection(
+					sky_bottleneck , // int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+					sky_tiles,         // boolean [] tiles,
+					prohibit_tiles);             // boolean [] prohibit)
+			if (dbg_img != null) {
+				for (int i = 0; i < sky_tiles.length; i++) {
+					dbg_img[5][i] = prohibit_neck[i]? 0 : 1;
+					dbg_img[6][i] = sky_tiles[i]?     1 : 0;
+				}
+			}
+			
+			//prohibit_tiles
+		}
+		
 		double sky_max_temp = Double.NaN;
 		if (avg_val != null) {
 			boolean [] shrank_sky = sky_tiles.clone();
@@ -678,6 +714,7 @@ public class QuadCLTCPU {
 			double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 			int    sky_shrink, //  =       4;
 			int    sky_expand_extra, //  = 100; // 1?
+			int    sky_bottleneck,        // 
 			double cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
 			double cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
 			double hot_frac, // =         0.9;    // this and above will scale fom by 1.0
@@ -699,6 +736,7 @@ public class QuadCLTCPU {
 				sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 				sky_shrink, //  =       4;
 				sky_expand_extra, //  = 100; // 1?
+				sky_bottleneck,        // 
 				cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
 				cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
 				hot_frac, // =         0.9;    // this and above will scale fom by 1.0
@@ -2158,6 +2196,12 @@ public class QuadCLTCPU {
 		}
 	}
 	
+	public boolean tsExists(String ts) {
+		ErsCorrection ers_reference = getErsCorrection();
+		return ((ers_reference.getSceneXYZ(ts) != null) && (ers_reference.getSceneATR(ts) != null));
+	}
+	
+	
 	
 	public double [][][][][][] getCLTKernels(){ // USED in lwir
 		return clt_kernels;

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

@@ -8650,6 +8650,20 @@ if (debugLevel > -100) return true; // temporarily !
 						scene_dirs, // File [] scene_dirs,
 						pathFirstLast[nseq].first, // int scene_first, // first scene to process
 						pathFirstLast[nseq].last); // int scene_last);  // last scene to process (negative - add length
+				
+				if (pathFirstLast[nseq].movement_size < 0) {
+					clt_parameters.imp.mov_en = false;
+					if (debugLevel > -4) {
+						System.out.println("Disabling movement detection for this scene.");
+					}
+				} else {
+					clt_parameters.imp.mov_en = true;
+					clt_parameters.imp.mov_max_len = pathFirstLast[nseq].movement_size;
+					if (debugLevel > -4) {
+						System.out.println("Enabling movement detection for this scene with maximum cluster linear size of "+
+								clt_parameters.imp.mov_max_len+" tiles.");
+					}
+				}
 			}
 			
 			String [][] video_list = new String[1][];