Debugging/fixing with Codex

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

@@ -269,6 +269,19 @@ public class CuasMotion {
 			CLTParameters  clt_parameters) {
 		return clt_parameters.imp.cuas_half_step ? (clt_parameters.imp.cuas_corr_offset/2) : clt_parameters.imp.cuas_corr_offset;
 	}
+
+	/**
+	 * Geometric separation between adjacent keyframes in scene units.
+	 *
+	 * When {@code cuas_half_step} is enabled and {@code cuas_corr_offset} is odd, the
+	 * actual scan index advance returned by {@link #getCorrInc(CLTParameters)} is truncated
+	 * to an integer scene step. For chaining targets between neighboring keyframes we need
+	 * the intended half-offset geometry rather than the truncated array index increment.
+	 */
+	public static double getCorrIncExact(
+			CLTParameters clt_parameters) {
+		return clt_parameters.imp.cuas_half_step ? (0.5 * clt_parameters.imp.cuas_corr_offset) : clt_parameters.imp.cuas_corr_offset;
+	}
 	
 	public int getCorrInc() { // == frame_step;
 		return getCorrInc(clt_parameters);
@@ -285,17 +298,12 @@ public class CuasMotion {
 	}
 	
 	public double getInterseqScale() {   // multiply target velocity to get offset in the middle between the key frames
-//		double inter_scale = 0.5* getCorrInc()/corr_offset;
-		double inter_scale = 0.5*1.25 * getCorrInc()/corr_offset;
-		System.out.println("getInterseqScale(): getCorrInc()="+getCorrInc()+" corr_offset="+corr_offset+
-				" clt_parameters.imp.cuas_half_step="+clt_parameters.imp.cuas_half_step+
-				" clt_parameters.imp.cuas_corr_offset="+clt_parameters.imp.cuas_corr_offset+
-				" inter_scale="+inter_scale);
-		return inter_scale; // 0.5* getCorrInc()/corr_offset;
+		return 0.5 * getCorrIncExact(clt_parameters) / corr_offset;
 	}
 	
 	/**
-	 * Multiply RESULT_VX,RESULT_VX to get pixel offset per scene (at ~60Hz) 
+	 * Multiply raw {@code RSLT_VX}/{@code RSLT_VY} pair displacement by this factor
+	 * to get pixel offset per scene (at ~60Hz).
 	 * @param clt_parameters
 	 * @return coefficient for VX, VY
 	 */
@@ -304,12 +312,13 @@ public class CuasMotion {
 	}
 
 	/**
-	 * Multiply RESULT_VX,RESULT_VX to get pixel offset per key frame (now ~6Hz) 
+	 * Multiply raw {@code RSLT_VX}/{@code RSLT_VY} pair displacement by this factor
+	 * to get pixel offset between neighboring keyframe centers.
 	 * @param clt_parameters
 	 * @return coefficient for VX, VY
 	 */
 	public static double getKeyFrameVelocityScale(CLTParameters  clt_parameters) {
-		return getCorrInc(clt_parameters)/clt_parameters.imp.cuas_corr_offset;
+		return getCorrIncExact(clt_parameters)/clt_parameters.imp.cuas_corr_offset;
 	}
 	
 	
@@ -1451,6 +1460,9 @@ public class CuasMotion {
 					true);            // final boolean     calc_fraction	){ // calculate fraction inside center circle
 			for (int ntile = 0; ntile < num_tiles; ntile++) if (vector_field[ntile] != null){
 				double [] target =  CuasMotionLMA.getEmpty();
+				// Store the raw displacement over one correlation-pair separation
+				// (cuas_corr_offset scenes). Convert later with getFrameVelocityScale()
+				// or getKeyFrameVelocityScale() depending on the consumer.
 				target[CuasMotionLMA.RSLT_VX] =    vector_field[ntile][INDX_VX];
 				target[CuasMotionLMA.RSLT_VY] =    vector_field[ntile][INDX_VY];
 				target[CuasMotionLMA.RSLT_VSTR] =  vector_field[ntile][INDX_STRENGTH];
@@ -2820,7 +2832,15 @@ public class CuasMotion {
 		}
 		ImageDtt.startAndJoin(threads);
 
-		final int [][] ltargets_first_last = new int [amax.get()][]; // correct
+		final int max_ltarg_all = amax.get();
+		if (max_ltarg_all < 0) {
+			System.out.println(
+					"convertToRgbAnnotateTargets(): no detected targets or UAS-log targets available for annotation in \"" +
+					title + "\"; returning RGB stack without target overlays.");
+			return imp;
+		}
+
+		final int [][] ltargets_first_last = new int [max_ltarg_all][]; // correct
 		
 		for (int nseq = 0; nseq < num_seq; nseq++) if ((local_tiles[nseq] != null) && (local_tiles[nseq].length > 0)){ // no if is not needed - bug fixed
 			uas_tiles[nseq] = local_tiles[nseq][0];
@@ -2925,7 +2945,10 @@ public class CuasMotion {
 						final int [] targets_order = Arrays.stream(targets_order_integer).mapToInt(Integer::intValue).toArray();
 						
 						// plot targets
-						// now target_coord is ordered from highest priority to the lowest
+						// now target_coord is ordered from highest priority to the lowest  java.lang.NegativeArraySizeException: -1
+						if (local_tiles[nSeq].length == 0) {
+							continue;
+						}
 						double [][][] target_coord = new double [local_tiles[nSeq].length-1][][]; // save centers of targets and text coordinates
 						Rectangle [][] annot_boxes = new Rectangle[local_tiles[nSeq].length-1][]; // order will match target_coord order
 						String [][]    annots =      new String [local_tiles[nSeq].length-1][];
@@ -3706,6 +3729,7 @@ public class CuasMotion {
 		boolean  show_inf_gt =   clt_parameters.imp.cuas_show_inf_gt;     // false; // Use ">max" instead of infinity symbol
 		double   max_annot_range = clt_parameters.imp.cuas_rng_limit; // 5000, maybe make a separate parameter
 		double   max_axial_range = clt_parameters.imp.cuas_radar_range; // may be a separate - maximal range for axial velocity/heading
+		double velocity_scale = getFrameVelocityScale(clt_parameters);
 		double ifov = ersCorrection.getIFOV();
 		int sensor_width =  ersCorrection.getSensorWH()[0];
 		int sensor_height = ersCorrection.getSensorWH()[1];
@@ -3767,9 +3791,10 @@ public class CuasMotion {
 		while (el < -Math.PI) el += 2* Math.PI;
 		double az_deg = az * 180/Math.PI;
 		double el_deg = el * 180/Math.PI;
-		
-		double omega_az =  interpolate (target0[CuasMotionLMA.RSLT_VX],target1[CuasMotionLMA.RSLT_VX],k) * ifov * fps;
-		double omega_el = -interpolate (target0[CuasMotionLMA.RSLT_VY],target1[CuasMotionLMA.RSLT_VY],k) * ifov * fps;
+		double vx = interpolate (target0[CuasMotionLMA.RSLT_VX],target1[CuasMotionLMA.RSLT_VX],k) * velocity_scale;
+		double vy = interpolate (target0[CuasMotionLMA.RSLT_VY],target1[CuasMotionLMA.RSLT_VY],k) * velocity_scale;
+		double omega_az =  vx * ifov * fps;
+		double omega_el = -vy * ifov * fps;
 		double omega_az_degs = omega_az * 180/Math.PI;
 		double omega_el_degs = omega_el * 180/Math.PI;
 		
@@ -3924,8 +3949,8 @@ public class CuasMotion {
 	 * @param fps
 	 * @param px
 	 * @param py
-	 * @param vx
-	 * @param vy
+	 * @param vx target velocity in pixels per frame
+	 * @param vy target velocity in pixels per frame
 	 * @return
 	 */
 	public static double [][] getPixToAzElev(
@@ -4898,7 +4923,7 @@ public class CuasMotion {
 		// final int min_keep = 2; // Keep at least this number of (preliminary) best candidates
 		final int tile1 = GPUTileProcessor.DTT_SIZE;
 		final int tile2 = 2 * tile1;
-		final int dbg_tile=12 + 23*80;
+		final int dbg_tile=-(12 + 23*80);
 		final double [] mask_centered = (centered && (centered_radius > 0)) ? new double [tile2* tile2]: null;
 		final boolean [] disabled_centered = (mask_centered != null) ? (new boolean [mask_centered.length]) : null;
 		if (mask_centered != null) {
@@ -4955,7 +4980,7 @@ public class CuasMotion {
 		param_select[CuasMotionLMA.INDX_RR0] = lma_fit_r;
 		param_select[CuasMotionLMA.INDX_K] =   lma_fit_k;
 //		final int dbg_tile = -(38 + 45 * 80); //(38 + 45 * 80);
-		final int dbg_seq = 48;
+		final int dbg_seq = -48;
 		boolean show_dbg = (dbg_tile >= 0) && (parentCLT != null);
 		final String [] dbg_titles = {"mask","tile","masked","limited","blured","um","um-blured","um-blured-scaled",
 				"centroid","lma-Y","fX","ymfx","weights"};
@@ -7380,7 +7405,7 @@ public class CuasMotion {
 			final int             debugLevel){
 		final boolean  use_motion = (motion_sequence != null) ? use_motion_in : false;
 		final boolean  select_new = (motion_sequence != null) ? select_new_in : false;
-		boolean debug_now = (debugLevel>-5);
+		boolean debug_now = (debugLevel>5);
 		final int num_seq = target_sequence_multi.length;
 		final int num_tiles = target_sequence_multi[0].length;
 		final int tilesY = num_tiles/ tilesX;

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

@@ -2788,6 +2788,7 @@ public class CuasRanging {
 		sb.append("\n"); // there will be 1 extra blank column
 		String [] slice_titles = 	cuasMotion.getSliceTitles(); // timestamps
 		ErsCorrection ersCorrection = center_CLT.getErsCorrection();
+		double velocity_scale = CuasMotion.getFrameVelocityScale(clt_parameters);
 		for (int nseq = 0; nseq < num_seq; nseq++) {
 			String timestamp = slice_titles[nseq];
 			sb.append(nseq+"\t"+timestamp+"\t");
@@ -2820,8 +2821,8 @@ public class CuasRanging {
 						int tileY = ntile / tilesX;
 					    double xc = tileSize * tileX + tileSize/2 + target[CuasMotionLMA.RSLT_X];  
 					    double yc = tileSize * tileY + tileSize/2 + target[CuasMotionLMA.RSLT_Y];
-						double vx = target[CuasMotionLMA.RSLT_VX];
-						double vy = target[CuasMotionLMA.RSLT_VY];
+						double vx = target[CuasMotionLMA.RSLT_VX] * velocity_scale;
+						double vy = target[CuasMotionLMA.RSLT_VY] * velocity_scale;
 						// calculate and output target azimuth, elevation, disparity (full) and range
 						az_el_oaz_oel= 	CuasMotion.getPixToAzElev(
 								ersCorrection, // ErsCorrection ersCorrection,

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

@@ -5782,6 +5782,11 @@ public class OpticalFlow {
 				OK = earliest_scene >=0;
 			}
 			if (!OK) {
+				if (use_cuas) {
+					System.out.println(
+							"buildSeries(): aborting CUAS sequence after failed initial orientations. " +
+							"Input IMS/orientation data appear inconsistent, so no automatic recovery will be attempted.");
+				}
 				return null;
 			}
 			// export csv
@@ -7233,7 +7238,7 @@ java.lang.NullPointerException
 		// Moved to the very end, after 3D
 //		boolean test_vegetation = true;
 		
-		if (master_CLT.hasCenterClt()) { // cuas mode
+		if (master_CLT.hasCenterClt() && clt_parameters.imp.cuas_targets_en) { // cuas mode
 			if (debugLevel >-3) {
 				System.out.println("===== Running CUAS ranging. =====");
 			}

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

@@ -549,6 +549,7 @@ public class QuadCLTCPU {
 				dts =     center_CLT.getTimeStamp();
 			}
 		}
+		CuasData localCuasData = cuasData;
 		// Read parent (cumulative if possible) data if full_path is provided
 		CuasData parentCuasData = null;
 		if (center_CLT == null) {
@@ -650,6 +651,38 @@ public class QuadCLTCPU {
 		if (full_path != null) { // set/update parent directory where to look for cumulative data
 			center_CLT.setCenterParentDir(full_path); // is not in cuasData, only in center_CLT instance
 		}
+		String centerBasePath = center_CLT.getImagePath()+Prefs.getFileSeparator()+center_CLT.getImageName();
+		String centerSinglePath = centerBasePath + CuasData.getCuasSuffix();
+		String centerCumulPath = centerBasePath + CuasData.getCuasCumulativeSuffix();
+		File centerSingleFile = new File(centerSinglePath);
+		File centerCumulFile = new File(centerCumulPath);
+		if (!centerSingleFile.exists() || !centerCumulFile.exists()) {
+			System.out.println(
+					"restoreCenterClt(): WARNING reused center data in "+center_CLT.getImagePath()+
+					", but serialized CuasData files are incomplete: single="+centerSingleFile.exists()+
+					", cumulative="+centerCumulFile.exists()+
+					". Backfilling from restored data.");
+			try {
+				if (!centerSingleFile.exists()) {
+					CuasData singleCuasData = (localCuasData != null) ? localCuasData : cuasData;
+					singleCuasData.writeCuasData(centerSinglePath);
+					if (debugLevel > -3) {
+						String source = (localCuasData != null) ? "local single-sequence data" : "effective restored data";
+						System.out.println("restoreCenterClt(): wrote missing single-scene CuasData to "+centerSinglePath+
+								" using "+source);
+					}
+				}
+				if (!centerCumulFile.exists()) {
+					cuasData.writeCuasData(centerCumulPath);
+					if (debugLevel > -3) {
+						System.out.println("restoreCenterClt(): wrote missing cumulative CuasData to "+centerCumulPath);
+					}
+				}
+			} catch (IOException e) {
+				System.out.println("restoreCenterClt(): ERROR backfilling serialized CuasData files for "+center_CLT.getImagePath());
+				e.printStackTrace();
+			}
+		}
 		
 		return center_CLT;
 	}
@@ -2400,20 +2433,44 @@ public class QuadCLTCPU {
     	int xr = (int) Math.round((offset[0] + (s+1)*width)/tile_size);  
     	int yt = (int) Math.round((offset[1] - s*    height)/tile_size);  
     	int yb = (int) Math.round((offset[1] + (s+1)*height)/tile_size);
-    	if (yt > 0)  {
-    		Arrays.fill(relable_scene_tiles, 0,           tilesX * yt,                false);
+    	int x0 = Math.max(0, Math.min(tilesX, xl));
+    	int x1 = Math.max(0, Math.min(tilesX, xr));
+    	int y0 = Math.max(0, Math.min(tilesY, yt));
+    	int y1 = Math.max(0, Math.min(tilesY, yb));
+    	boolean clipped = (x0 != xl) || (x1 != xr) || (y0 != yt) || (y1 != yb);
+    	if ((x0 >= x1) || (y0 >= y1)) {
+    		System.out.println(
+    				"maskByOverlap(): no overlap after clipping, offset=(" + offset[0] + ", " + offset[1] +
+    				"), raw x=[" + xl + ", " + xr + "), y=[" + yt + ", " + yb +
+    				"), clipped x=[" + x0 + ", " + x1 + "), y=[" + y0 + ", " + y1 +
+    				"), tiles=" + tilesX + "x" + tilesY + ", image=" + width + "x" + height);
+    		Arrays.fill(relable_scene_tiles, false);
+    		return relable_scene_tiles;
     	}
-    	if (yb < tilesY) {
-    		Arrays.fill(relable_scene_tiles, tilesX * yb, relable_scene_tiles.length, false);
+    	if (clipped) {
+    		System.out.println(
+    				"maskByOverlap(): clipped overlap bounds, offset=(" + offset[0] + ", " + offset[1] +
+    				"), raw x=[" + xl + ", " + xr + "), y=[" + yt + ", " + yb +
+    				"), clipped x=[" + x0 + ", " + x1 + "), y=[" + y0 + ", " + y1 +
+    				"), tiles=" + tilesX + "x" + tilesY + ", image=" + width + "x" + height);
     	}
-    	if (xl > 0) {
-    		for (int i = 0; i < tilesY; i++) {
-    			Arrays.fill(relable_scene_tiles, tilesX * i, tilesX * i + xl, false);
-    		}
+    	if (y0 > 0)  {
+    		Arrays.fill(relable_scene_tiles, 0, Math.min(relable_scene_tiles.length, tilesX * y0), false);
+    	}
+    	if (y1 < tilesY) {
+    		Arrays.fill(relable_scene_tiles, Math.min(relable_scene_tiles.length, tilesX * y1), relable_scene_tiles.length, false);
     	}
-    	if (xr < tilesX) {
-    		for (int i = 0; i < tilesY; i++) {
-    			Arrays.fill(relable_scene_tiles, tilesX * i + xr, tilesX  * (i + 1), false); //java.lang.IllegalArgumentException: fromIndex(9) > toIndex(0)
+    	for (int i = 0; i < tilesY; i++) {
+    		int rowStart = tilesX * i;
+    		if (rowStart >= relable_scene_tiles.length) {
+    			break;
+    		}
+    		int rowEnd = Math.min(relable_scene_tiles.length, tilesX * (i + 1));
+    		if (x0 > 0) {
+    			Arrays.fill(relable_scene_tiles, rowStart, Math.min(rowEnd, rowStart + x0), false);
+    		}
+    		if (x1 < tilesX) {
+    			Arrays.fill(relable_scene_tiles, Math.min(rowEnd, rowStart + x1), rowEnd, false);
     		}
     	}
     	return relable_scene_tiles;