Extracting parameters

src/main/java/com/elphel/imagej/cuas/CuasMotion.java

@@ -4389,6 +4389,14 @@ public class CuasMotion {
 		int height = image.length/width;
 		int xl = xc - icon_width/2;
 		int yt = yc - icon_height/2;
+		int xr = xc + icon_width/2;
+		int yb = yc + icon_height/2;
+		
+		if ((xl < 0) || (yt < 0) || (xr >= width) || (yb >= height)) {
+			System.out.println("imprintPixelIcon(): outside of the window: xc="+xc+", yc="+yc+", width="+width+", height="+height);
+			return;
+		}
+		
 		for (int y = 0; y < icon_height; y++) {
 			int py = yt + y;
 			if ((py >= 0) && (py < height)) {
@@ -4469,8 +4477,7 @@ public class CuasMotion {
 		final double ifov = scene.getGeometryCorrection().getIFOV();
 		final double radar_range =        clt_parameters.imp.cuas_radar_range;
 		final String font_name =          clt_parameters.imp.cuas_font_name;
-//		final int    font_size_radar =  clt_parameters.imp.cuas_font_size;
-		final int    font_size_radar =  7; // clt_parameters.imp.cuas_font_size;
+		final int    font_size_radar =    clt_parameters.imp.cuas_font_size; // 7; // 
 		final double font_ratio_radar = 1.2; // if 0 - will use default spacing ( ~=1.5)
 		final int    font_type =          clt_parameters.imp.cuas_font_type;
 		final Color   text_color =        clt_parameters.imp.cuas_text_color;
@@ -4480,7 +4487,6 @@ public class CuasMotion {
 		final int     target_type =       clt_parameters.imp.cuas_target_type;     //  0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
 		final int     uas_type =          clt_parameters.imp.cuas_known_type;      //  2; // Target location matching UAS flight log: 0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
 		
-		
 		final boolean reserve_missing_fields = false; // make a parameter.Reserve a line for requested but missing parameters
 		final boolean scale2x = true;
 		final int     image_scale = 2; // here always 2
@@ -4559,6 +4565,7 @@ public class CuasMotion {
 		final AtomicInteger ai =    new AtomicInteger(0);
 		final AtomicInteger amax =  new AtomicInteger(-1);
 		final int [] uas_tiles = new int[num_seq];
+		Arrays.fill(uas_tiles, -1);
 		final int [][] local_tiles = new int [num_seq][];
 		
 		for (int ithread = 0; ithread < threads.length; ithread++) {
@@ -4576,6 +4583,7 @@ public class CuasMotion {
 							if (target != null) {
 								if (!Double.isNaN(target[CuasMotionLMA.RSLT_FL_PX])) {
 									local_tiles_map.put(0, ntile); // flight log data
+									max_ltarg = Math.max(max_ltarg, 0);
 								}
 								if (!Double.isNaN(target[CuasMotionLMA.RSLT_GLOBAL])) {
 									int ltarg = (int) target[CuasMotionLMA.RSLT_GLOBAL];
@@ -4596,10 +4604,9 @@ public class CuasMotion {
 		}
 		ImageDtt.startAndJoin(threads);
 		
-		
 		final int [][] ltargets_first_last = new int [amax.get()][]; // correct
 		
-		for (int nseq = 0; nseq < num_seq; nseq++) {
+		for (int nseq = 0; nseq < num_seq; nseq++) if (local_tiles[nseq].length > 0){ // no if is not needed - bug fixed
 			uas_tiles[nseq] = local_tiles[nseq][0];
 		}
 		
@@ -5177,6 +5184,8 @@ public class CuasMotion {
 			double xc,
 			double yc,
 			double radius) {
+		int width =  colorProcessor.getWidth();
+		int height = colorProcessor.getHeight();
 		double radius2 = radius*radius;
 		int icolor = color.getRGB() | 0xff000000; // needed?
 		if (color != null) colorProcessor.setColor(color);
@@ -5184,7 +5193,11 @@ public class CuasMotion {
 		int y0 = (int) Math.floor(yc - radius);
 		int x1 = (int) Math.ceil (xc + radius);
 		int y1 = (int) Math.ceil (yc + radius);
-		int width = colorProcessor.getWidth();
+		if ((x0 < 0) || (y0 < 0) || (x1 >= width) || (y1 >= height)) {
+			System.out.println("drawCircle(): outside of the window: xc="+xc+", yc="+yc+", width="+width+", height="+height+
+					", color="+ color.toString());
+			return;
+		}
 		int [] pixels = (int[]) colorProcessor.getPixels();
 		for (int y = y0; y <= y1; y++) {
 			double dy = y-yc;
@@ -5193,7 +5206,8 @@ public class CuasMotion {
 				double dx = x-xc;
 				double r2 = dx*dx + dy2;
 				if (r2 <= radius2) {
-					pixels[x+y*width] = icolor;
+					pixels[x+y*width] = icolor; // java.lang.ArrayIndexOutOfBoundsException: Index -144985 out of bounds for length 552960 	at com.elphel.imagej.cuas.CuasMotion.drawCircle(CuasMotion.java:5197) at com.elphel.imagej.cuas.CuasMotion$33.run(CuasMotion.java:4662)
+
 				}
 			}
 		}
@@ -6903,7 +6917,7 @@ public class CuasMotion {
 	 */
 	public static int [][][] calcMatchingTargetsLengths( // calculate number of consecutive keyframes connected to each target
 			final double [][][][] targets_multi,
-			final boolean         calc_linked,
+			final boolean         calc_linked, // needed to calculate indices in the order of lengths. But only when there are few targets
 			final double          max_mismatch,     // if <=0, do not calculate  mismatch_ba and filter
 			final double          slow_fast_mismatch,
 			final double          match_len_pwr, // 0.5; // raise matching length to this power for calculating score
@@ -9783,6 +9797,7 @@ public class CuasMotion {
 	}
 	
 	final void recalcOmegas(
+			boolean       recalc,
 			double [][][] target_single,
 			boolean       batch_mode,
 			int           debugLevel){
@@ -9806,9 +9821,11 @@ public class CuasMotion {
 				targets_multi,        // final double [][][][]  targets_multi,
 				true,                 // final boolean          good_only,
 				tilesX);              //  int           tilesX) {
+		if (recalc) {
 			recalcOmegas(
 					targets_multi,        // double [][][][] targets_multi,
 					debugLevel);          // int           debugLevel){
+		}
 		getHalfBeforeAfterPixXY(
 				targets_multi,        // final double [][][][] targets_multi,
 				true,                 // final boolean       good_only,

src/main/java/com/elphel/imagej/cuas/CuasMultiSeries.java

@@ -78,12 +78,17 @@ public class CuasMultiSeries {
 		model_dirs =           new File[num_series];
 		model_names =          new String[num_series];
 		this.uasLogReader =    uasLogReader;
+		int dbg_nser = 45;
 		for (int nser = 0; nser < num_series; nser++) {
 			model_names[nser] =  scene_dirs[nser].getName(); // 1747803230_276111-CENTER
 			model_dirs[nser] = new File(scene_dirs[nser], version);  
 			String target_file_name = model_names[nser]+ CuasMotion.getParametersSuffixRanging(clt_parameters,CuasRanging.TARGET_DISPARITIES_SUFFIX)+".tiff";
 			File target_file=new File(model_dirs[nser], target_file_name);
 			String [][] scen_titles_w = new String[1][];
+			if (nser==dbg_nser) {
+				System.out.println("-nser="+nser);
+			}
+
 			targets_multi_series[nser] = CuasMotion.getTargetsFromHyperAugment(
 					null,          // String [][] pvf_top_titles,
 					scen_titles_w, // String [][] pvf_titles,
@@ -106,14 +111,23 @@ public class CuasMultiSeries {
 						break;
 					}
 				}
+				if (i >= linked_targets_multi[nser][ntarg].length) {
+					targets_start_end[nser][ntarg] = new int[0];
+				} else {
 					for ( i++; i < linked_targets_multi[nser][ntarg].length; i++) {
 						if (linked_targets_multi[nser][ntarg][i] == null) {
 							break;
 						}
 					}
 					targets_start_end[nser][ntarg][1] = i-1;
+					// targets_start_end[nser][ntarg][1] = i-1;
+//					p.y = i-1;
+//					tlist.add(p);
 				}
 			}
+			
+			
+		}
 		recalculateAllRanges(
 				targets_multi_series,                // final double [][][][] targets_multi_series, // [nser][nseq][ntile][nfield]
 				infinity,                            // final double new_infinity,
@@ -209,14 +223,17 @@ public class CuasMultiSeries {
 		double pts_scale = clt_parameters.imp.video_fps/clt_parameters.imp.sensor_fps;
 		pts_scale = 1.0;
 		String shellCommand;
-		//ffmpeg -i input_file.mkv -c copy -metadata:s:v:0 stereo_mode=1 output_file.mkv
 		//https://ffmpeg.org/ffmpeg-formats.html
-		//ffmpeg -i sample_left_right_clip.mpg -an -c:v libvpx -metadata stereo_mode=left_right -y stereo_clip.webm
-		//anaglyph_cyan_red
-		shellCommand = String.format("ffmpeg -y -f concat -safe 0 -i %s -r 60 -vf setpts=%f*PTS -b:v %fM -crf %d -c %s %s",
-				list_to_concat.toString(), pts_scale, video_bitrate_m,  video_crf_combo, video_codec_combo, video_out.toString());
 		
+		/*
+		 when called from java, ffmpeg terminated in ~5min and 848MB, but java continued to wait 
+		 
+		 For now - just run command manually by copying the shellCommand
+		 */
 		
+
+		shellCommand = String.format("ffmpeg -y -f concat -safe 0 -i %s -r 60 -vf setpts=%f*PTS -b:v %fM -crf %d -c %s %s",
+				list_to_concat.toString(), pts_scale, video_bitrate_m,  video_crf_combo, video_codec_combo, video_out.toString());
 		Process p = null;
 		int exit_code = -1;
 		System.out.println("Will run shell command: \""+shellCommand+"\"");
@@ -280,7 +297,7 @@ public class CuasMultiSeries {
 		//
 		ImagePlus imp_radar = testGenerateRadarImage(
 				clt_parameters, // CLTParameters       clt_parameters,
-				3, // 15, // int                 nser,
+				45, // 3, // 15, // int                 nser,
 				uasLogReader, // UasLogReader        uasLogReader, // contains camera orientation (getCameraATR())
 				debugLevel); // int                 debugLevel) {
 		return;
@@ -403,10 +420,15 @@ public class CuasMultiSeries {
 		final Thread[] threads =    ImageDtt.newThreadArray();
 		final AtomicInteger ai =    new AtomicInteger(0);
 		final AtomicInteger amiss = new AtomicInteger(0);
+		final int dbg_nser = 45;
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
 				public void run() {
 					for (int nSer = ai.getAndIncrement(); nSer < targets_multi_series.length; nSer = ai.getAndIncrement()) {
+						if (nSer==dbg_nser) {
+							System.out.println("-nser="+nSer);
+						}
+						
 						for (int nseq = 0; nseq < targets_multi_series[nSer].length; nseq++) {
 							for (int ntile = 0; ntile < targets_multi_series[nSer][nseq].length; ntile++) { 
 								double [] target = targets_multi_series[nSer][nseq][ntile];
@@ -441,10 +463,14 @@ public class CuasMultiSeries {
 		final Thread[] threads =    ImageDtt.newThreadArray();
 		final AtomicInteger ai =    new AtomicInteger(0);
 		final AtomicInteger aglob = new AtomicInteger(0);
+		final int dbg_nser = 45;
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
 				public void run() {
 					for (int nSer = ai.getAndIncrement(); nSer < targets_multi_series.length; nSer = ai.getAndIncrement()) {
+						if (nSer==dbg_nser) {
+							System.out.println("-nser="+nSer);
+						}
 						int [][][] ltargets = linked_targets_multi[nSer];
 						double [][][] mtargets = targets_multi_series[nSer];
 						int [] utiles = uas_tiles[nSer];
@@ -557,7 +583,9 @@ public class CuasMultiSeries {
 						}
 						// skip pairs that have global target_id >0 (at least skip UAS 
 						for (int ntarg = 0; ntarg < num_targ; ntarg++) if (!skip_assigned ||(target_map[nSer][ntarg] <= 0)) { // no globally assigned
+							if (targets_start_end[nSer][ntarg].length > 0) { // now, start,end pair may be [] if all were NaN
 								for (int ntarg1 = ntarg+1; ntarg1 < num_targ; ntarg1++)  if (!skip_assigned || (target_map[nSer][ntarg1] <= 0)) {  // no globally assigned
+									if (targets_start_end[nSer][ntarg1].length > 0) {
 										if (targets_start_end[nSer][ntarg][1] < targets_start_end[nSer][ntarg1][0]) {
 											if ((targets_start_end[nSer][ntarg1][0] - targets_start_end[nSer][ntarg][1]) <= tmtch_gaps) {
 												after[ntarg][ntarg1] = true; // ntarg1 is after ntarg
@@ -572,6 +600,8 @@ public class CuasMultiSeries {
 										}
 									}
 								}
+							}
+						}
 						local_map[nSer] = new int [num_targ];  // [nser][ntarg]
 						local_imap[nSer]= new int [num_targ][1];  // [nser][ntarg]
 						for (int i = 0; i < num_targ; i++) {
@@ -735,6 +765,7 @@ public class CuasMultiSeries {
 							if (targs0.length > 0){
 								int ntarg0 = targs0[targs0.length -1]; // last if several are connected
 								if (!skip_assigned || (target_map[prev_ser][ntarg0] <= 0)) { // not globally assigned
+									if (targets_start_end[prev_ser][ntarg0].length > 0) { // now, start,end pair may be [] if all were NaN
 										int nseq0 =  targets_start_end[prev_ser][ntarg0][1]; // end of the last segment in previous series
 										int end_gap = linked_targets_multi[prev_ser][ntarg0].length -1 - nseq0;
 										if (end_gap <= tmtch_ends) {
@@ -746,6 +777,7 @@ public class CuasMultiSeries {
 												if (targs1.length > 0){
 													int ntarg1 = targs1[0]; // first if several are connected
 													if (!skip_assigned || (target_map[nSer][ntarg1] <= 0)) { // no globally assigned
+														if (targets_start_end[nSer][ntarg1].length > 0) { // now, start,end pair may be [] if all were NaN
 															int nseq1 =  targets_start_end[nSer][ntarg1][0]; // start of the first segment in this series
 															if (nseq1 <= tmtch_ends) {
 																int ntile1 = linked_targets_multi[nSer][ntarg1][nseq1][0];
@@ -839,6 +871,8 @@ public class CuasMultiSeries {
 											}
 										}
 									}
+								}								
+							}
 						} // for (int ntgrp0 = 0; ntgrp0 < local_imap[prev_ser].length; ntgrp0++) {
 						// find and resolve conflicts between pairs
 						// pair.x is in previous segment (prev_seg), and in case of a chain - the last one

src/main/java/com/elphel/imagej/cuas/CuasRanging.java

@@ -69,6 +69,8 @@ public class CuasRanging {
 		boolean rng_img =            clt_parameters.imp.cuas_rng_img;
 		boolean rng_glob =           clt_parameters.imp.cuas_rng_glob;
 		boolean rng_disp =           clt_parameters.imp.cuas_rng_disp;
+		boolean recalc_target_id = true; // temporalily bug fixing, may be removed later
+		
 		boolean rng_vfy =            clt_parameters.imp.cuas_rng_vfy; // Generate/save ranging verification images (per-sensor and combined rendering from the same data)
 		boolean reset_disparity =    clt_parameters.imp.cuas_reset_disparity;
 		
@@ -282,13 +284,19 @@ public class CuasRanging {
         					System.out.println ("Recalculating omegas to better fit target positions in consecutive key frames.");
         				}
         				cuasMotion.recalcOmegas(
+        						true, // boolean       recalc,
         						targets,     // final double [][][] target_single_in,
         						batch_mode,  // boolean       batch_mode,
         						debugLevel); // final int             debugLevel){
 
         			} else {
+        				cuasMotion.recalcOmegas(
+        						false, // boolean       recalc,
+        						targets,     // final double [][][] target_single_in,
+        						batch_mode,  // boolean       batch_mode,
+        						debugLevel); // final int             debugLevel){
         				if (debugLevel > -4) {
-        					System.out.println ("Skipping omegas recalculation omegas.");
+        					System.out.println ("Skipping omegas recalculation omegas, still calculating local target index (called GLOBAL_INDEX).");
         				}
         			}
         			//	String model_prefix = center_CLT.getImageName()+CuasMotion.getParametersSuffix(clt_parameters,null);
@@ -318,6 +326,15 @@ public class CuasRanging {
         						cuasMotion.getTilesX());   //  int           tilesX) {
         				center_CLT.saveImagePlusInModelDirectory(imp_with_range);  // ImagePlus   imp)
         			}
+        		} else if (recalc_target_id){// if (disparity_targets == null) {
+    				cuasMotion.recalcOmegas(
+    						false, // boolean       recalc,
+    						targets,     // final double [][][] target_single_in,
+    						batch_mode,  // boolean       batch_mode,
+    						debugLevel); // final int             debugLevel){
+    				if (debugLevel > -4) {
+    					System.out.println ("(Re)calculating local target index (called GLOBAL_INDEX). May be remolved later");
+    				}
         		}
         	}
         	// calculate range from disparity