improving target detection

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

@@ -91,20 +91,23 @@ public class CuasMotionLMA {
 				"WHEN", "FAILURE"};
 	
 	public static final int FAIL_NONE =      0;
-	public static final int FAIL_CENT_STR =  1;  // centroid amplitude is too low
-	public static final int FAIL_CENT_FRAC = 2;  // Centroid fraction (energy in the peak fraction of all) is too low
-	public static final int FAIL_LMA =       3;  // LMA fail to converge
-	public static final int FAIL_A_LOW =     4;  // amplitude is too low
-	public static final int FAIL_ACENT =     5;  // ratio of maximal pixel to amplitude is too low
-	public static final int FAIL_RMSE =      6;  // RMSE is too high
-	public static final int FAIL_RMSE_R =    7;  // BOTH RMSE is not sufficient and RMSE/A is too high
-	public static final int FAIL_R0_HIGH =   8;  // Full radius (including negative overshoot) is too high
-	public static final int FAIL_R1_LOW =    9;  // Inner (positive) peak radius is too low
-	public static final int FAIL_K_LOW =    10;  // Overshoot is too low (not used, it can be down to 0)
-	public static final int FAIL_K_HIGH =   11;  // Overshoot is too high
-	public static final int FAIL_FAR =      12;  // Peak is too far from the center 
-	public static final int FAIL_HORIZON =  13;  // Peak is below horizon 
-	public static final int FAIL_MISMATCH = 14;  // Mismatch on both ends is too high 
+	public static final int FAIL_MOTION =    1;  // motion strength/fraction too low
+	public static final int FAIL_NO_MAX =    2;  // no suitable local maximum 
+	public static final int FAIL_CENT_STR =  3;  // centroid amplitude is too low
+	public static final int FAIL_CENT_FRAC = 4;  // centroid fraction (energy in the peak fraction of all) is too low
+	public static final int FAIL_LMA =       5;  // LMA fail to converge
+	public static final int FAIL_A_LOW =     6;  // amplitude is too low
+	public static final int FAIL_ACENT =     7;  // ratio of maximal pixel to amplitude is too low
+	public static final int FAIL_RMSE =      8;  // RMSE is too high
+	public static final int FAIL_RMSE_R =    9;  // BOTH RMSE is not sufficient and RMSE/A is too high
+	public static final int FAIL_R0_HIGH =  10;  // Full radius (including negative overshoot) is too high
+	public static final int FAIL_R1_LOW =   11;  // Inner (positive) peak radius is too low
+	public static final int FAIL_K_LOW =    12;  // Overshoot is too low (not used, it can be down to 0)
+	public static final int FAIL_K_HIGH =   13;  // Overshoot is too high
+	public static final int FAIL_FAR =      14;  // Peak is too far from the center 
+	public static final int FAIL_HORIZON =  15;  // Peak is below horizon 
+	public static final int FAIL_MISMATCH = 16;  // Mismatch on both ends is too high 
+	public static final int FAIL_NEIGHBOR = 17;  // failed because some neighbor is stronger   
 	
 	private int          width;
 	private double [][]  window;

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

@@ -4728,6 +4728,7 @@ public class GpuQuad{ // quad camera description
 	 * @param offset_scale multiply all vectors by this value when calculating pixel offsets
 	 * @param magnitude_scale Scale data for accumulation (here positive, will be negated). If 0 - will use scale=1.0 (no accumulation)
 	 * @param index_vx - index of vx in the targets_array[tile] array
+	 * @param index_xc - index of xc in the targets_array[tile] array to center target or <0 to render as is
 	 * @param image_width image width in tiles (80 for 640-wide images).
 	 * @return condensed array of TpTask
 	 */
@@ -4736,6 +4737,7 @@ public class GpuQuad{ // quad camera description
 			final double      offset_scale,
 			final double      magnitude_scale,
 			final int         index_vx, 
+			final int         index_xc,
 			final int         tilesX) {
 		final float fmagnitude_scale = (magnitude_scale==0)? 1.0f : ((float) -magnitude_scale);
 		final int tiles = targets_array.length;
@@ -4754,6 +4756,10 @@ public class GpuQuad{ // quad camera description
 						int tileX = nTile % tilesX;;
 						double dx = targets_array[nTile][index_vx + 0]*offset_scale; 
 						double dy = targets_array[nTile][index_vx + 1]*offset_scale; 
+						if ((index_xc >= 0) && !Double.isNaN( targets_array[nTile][index_xc])) {
+							dx += targets_array[nTile][index_xc + 0];
+							dy += targets_array[nTile][index_xc + 1];
+						}
 						double [] cxy0 = { // uniform coordinates for the center scene
 								(tileX + 0.5) * GPUTileProcessor.DTT_SIZE,
 								(tileY + 0.5) * GPUTileProcessor.DTT_SIZE};

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

@@ -2572,7 +2572,8 @@ public class Correlation2d {
 				System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+"), frac = " + rslt[3]);
 			}
 			if (Double.isNaN(rslt[0]) || Double.isNaN(rslt[1]) || Double.isNaN(rslt[2])) {
-				System.out.println("getMaxXYCm():NaN");
+//				System.out.println("getMaxXYCm():NaN");
+				return null;
 			}
 			return rslt;
 		} else {
@@ -2581,7 +2582,8 @@ public class Correlation2d {
 				System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+")");
 			}
 			if (Double.isNaN(rslt[0]) || Double.isNaN(rslt[1]) || Double.isNaN(rslt[2])) {
-				System.out.println("getMaxXYCm():NaN");
+//				System.out.println("getMaxXYCm():NaN");
+				return null;
 			}
 			return rslt;
 		}

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

@@ -4851,22 +4851,15 @@ public class OpticalFlow {
 		double min_ref_frac=         clt_parameters.imp.min_ref_frac;
 		
 		boolean cuas_subtract_fpn =  clt_parameters.imp.cuas_subtract_fpn;
-///		boolean cuas_calc_fpn =      clt_parameters.imp.cuas_calc_fpn;
-///		double  cuas_rot_period =    clt_parameters.imp.cuas_rot_period;
 		
 		boolean cuas_subtract_rowcol=clt_parameters.imp.cuas_subtract_rowcol;// Subtract row/column noise
-///		boolean cuas_calc_rowcol=    clt_parameters.imp.cuas_calc_rowcol;    // Recalculate+save  row/column noise, if false - try to read saved one first
-///		double  cuas_um_sigma =      clt_parameters.imp.cuas_um_sigma;       // Apply Unsharp Mask filter sigma when calculating row/column noise
-///		double  cuas_max_abs_rowcol= clt_parameters.imp.cuas_max_abs_rowcol; // consider pixels with abs(UM difference) does not exceed this value 
-///		double  cuas_outliers_rowcol=clt_parameters.imp.cuas_outliers_rowcol;// scale weight of the outliers with high difference (to prevent undefined values 
 		
 		boolean cuas_debug =         clt_parameters.imp.cuas_debug;  // save debug images (and show them if not in batch mode)
 		boolean cuas_step_debug =    clt_parameters.imp.cuas_step_debug;
 		boolean cuas_reset_first=    clt_parameters.imp.cuas_reset_first && first_in_series;
-///		int     cuas_invert_margins =    clt_parameters.imp.cuas_invert_margins;  // 1     Expand image each side when inverting tasks 	
-///		int     cuas_invert_iters =      clt_parameters.imp.cuas_invert_iters;    // 4     Enhance inversion iterations 
-///		double  cuas_invert_tolerance =  clt_parameters.imp.cuas_invert_tolerance;// 0.001 Finish enhancing when last change was lower than 		
-///		int     cuas_invert_gap2 =       clt_parameters.imp.cuas_invert_gap2;     // 10    Maximal dual gap size for inversion (depends on scanning radius in tiles)   
+		
+		boolean combine_clt =        clt_parameters.imp.cuas_rotation; // (cuas_atr[0] != 0) || (cuas_atr[1] != 0) || (cuas_atr[2] != 0);
+		boolean update_existing =    clt_parameters.imp.cuas_update_existing; // re-create center_CLT if it exists (FIXME: accumulates errors - need fixing)
 		
 		double [] ref_blue_sky = null; // turn off "lma" in the ML output  
 		if (reuse_video) { // disable all other options
@@ -5252,7 +5245,7 @@ public class OpticalFlow {
 			// use master_clt? - where to look for stage. in CUAS mode build directory name and look there
 			if (center_CLT != null) {
 				if (center_CLT.getNumOrient() == 0) {
-					if (debugLevel >-3) {
+					if (debugLevel >-4) {
 						System.out.println("center_CLT exists, but does not have egomotion data. Forcing its calculation.");
 					}
 					force_initial_orientations = true;
@@ -5480,7 +5473,7 @@ public class OpticalFlow {
 			if (combo_dsn_final == null) {
 				combo_dsn_final =quadCLTs[ref_index].restoreComboDSI(true); // also sets quadCLTs[ref_index].dsi and blue sky
 			}
-			if (debugLevel > -3) {
+			if (debugLevel > -4) {
 				System.out.println("Creating center_CLT from the reference one (ref_index="+ref_index);
 			}
 			center_CLT = Cuas.createCenterClt( // assuming cuas_rotation is true
@@ -5493,7 +5486,7 @@ public class OpticalFlow {
 					sensor_mask_clt, // int            sensor_mask, // -1 - all;
 		    		true,            // boolean          // new_average,
 					debugLevel);     // int            debugLevel)
-			if (debugLevel > -3) {
+			if (debugLevel > -4) {
 				System.out.println("Cuas.createCenterClt() done, center_CLT="+((center_CLT==null)? "null":center_CLT.toString()));
 			}			
 		}
@@ -6040,7 +6033,6 @@ public class OpticalFlow {
 			System.out.println ("Omegas ATR: "+center_ATR[2][0]+", "+center_ATR[2][1]+", "+center_ATR[2][2]);
 		}
 		
-		boolean combine_clt = clt_parameters.imp.cuas_rotation; // (cuas_atr[0] != 0) || (cuas_atr[1] != 0) || (cuas_atr[2] != 0);
 		// TODO: Refine center_CLT if it exists, not create
 		
 		
@@ -6071,13 +6063,13 @@ public class OpticalFlow {
 				if (cuas_centers != null) {
 					cuas_centers[1] = center_CLT.getImagePath();
 				}
-				if (debugLevel > -3) {
+				if (debugLevel > -4) {
 					System.out.println("Created/saved center CLT "+center_CLT.getImagePath());
 				}
 				dbg_created=true;
-			} else {
-				if (debugLevel > -3) {
-					System.out.println("Updating CLT");
+			} else if (update_existing) {
+				if (debugLevel > -4) {
+					System.out.println("Updating existing CLT (FIXME: accumulates errors - needs fixing)");
 				}
 				boolean  condition_dsi = true;
 				if (combo_dsn_final == null) {
@@ -6096,12 +6088,15 @@ public class OpticalFlow {
 				if (cuas_centers != null) {
 					cuas_centers[1] = center_CLT.getImagePath();
 				}
-				if (debugLevel > -3) {
+				if (debugLevel > -4) {
 					System.out.println("Updated/saved center CLT "+center_CLT.getImagePath());
 				}
 
+			} else {
+				if (debugLevel > -4) {
+					System.out.println("Spipping update of center CLT (it is reaed from "+center_CLT.getImagePath()+").");
+				}
 			}
-			
 			//		setCenterAverage();
 			ImagePlus imp_center_clt= center_CLT.showCenterClt(
     				null, // float [][] fclt, // may be null
@@ -7287,7 +7282,8 @@ public class OpticalFlow {
 		String [] bkp_sourcePaths =   quadCLT_main.correctionsParameters.sourcePaths;
 		boolean bkp_use_set_dirs = quadCLT_main.correctionsParameters.use_set_dirs;
 		
-    	String bkp_cuasUasLogs =            quadCLT_main.correctionsParameters.cuasUasLogs;      // json file path containing UAS logs
+    	String bkp_cuasUasLogs =            quadCLT_main.correctionsParameters.cuasSkyMask;      // TIFF image 640x512 where 1.0 - sky, 0.0 - ground, blurred with GB (now sigma==2.0)
+    	String bkp_cuasSkyMask =            quadCLT_main.correctionsParameters.cuasUasLogs;      // json file path containing UAS logs
     	double bkp_cuasUasTimeStamp =       quadCLT_main.correctionsParameters.cuasUasTimeStamp; // 0.0; // timestamp corresponding to the UAS time 0.0
     	double [] bkp_cuasCameraATR =       quadCLT_main.correctionsParameters.cuasCameraATR;    //{0, 0, 0};
     	double [] bkp_cuasUASHome =       quadCLT_main.correctionsParameters.cuasUASHome;    //{0, 0, 0};
@@ -7301,7 +7297,6 @@ public class OpticalFlow {
 		}
 		quadCLT_main.correctionsParameters.linkedModels =     bkp_linkedModels;
 		quadCLT_main.correctionsParameters.linkedCenters =    bkp_linkedCenters;
-///		quadCLT_main.correctionsParameters.cuasSeed =        bkp_cuasSeed;
 		quadCLT_main.correctionsParameters.cuasSeedDir =      bkp_cuasSeedDir;
 		quadCLT_main.correctionsParameters.videoDirectory =   bkp_videoDirectory;
 		quadCLT_main.correctionsParameters.x3dDirectory =     bkp_x3dDirectory;
@@ -7315,6 +7310,7 @@ public class OpticalFlow {
 		quadCLT_main.correctionsParameters.cuasCameraATR =    bkp_cuasCameraATR;
     	quadCLT_main.correctionsParameters.cuasUASHome =      bkp_cuasUASHome;
 		quadCLT_main.correctionsParameters.cuasSetHome =      bkp_cuasSetHome;
+		quadCLT_main.correctionsParameters.cuasSkyMask =      bkp_cuasSkyMask;
 		
 		System.out.println("buildSeries(): DONE"); //
 //		String top_dir0=quadCLTs[ref_index].getX3dTopDirectory();

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

@@ -8645,6 +8645,9 @@ if (debugLevel > -100) return true; // temporarily !
 			cuas_centers = new String [] {quadCLT_main.correctionsParameters.getCuasDir(),""};
 		}
 		*/
+		
+		String uas_sky_mask_path = quadCLT_main.correctionsParameters.getUasSkyMask();
+		
 		for (int nseq = 0; nseq < num_seq; nseq++) {
 	    	long start_time_seq = System.nanoTime();
 	    	System.out.println("\nSTARTED PROCESSING SCENE SEQUENCE "+nseq+" (last is "+(num_seq-1)+")\n");
@@ -8668,6 +8671,10 @@ if (debugLevel > -100) return true; // temporarily !
 								clt_parameters.imp.mov_max_len+" tiles.");
 					}
 				}
+				clt_parameters.imp.cuas_sky_path = uas_sky_mask_path;
+				if (clt_parameters.imp.cuas_sky_path != null) {
+					clt_parameters.imp.cuas_sky_offset = new double[] {pathFirstLast[nseq].mask_x,pathFirstLast[nseq].mask_y};
+				}
 			}
 			
 			String [][] video_list = new String[1][];
@@ -8676,9 +8683,6 @@ if (debugLevel > -100) return true; // temporarily !
 			int [] start_ref_pointers = new int[2]; //{earlist, reference} - reference may be center
 			boolean     first_in_series = true;
 			// Process UAS logs 
-//			quadCLT_main.correctionsParameters.cuasUasLogs,      // String                                               cuasUasLogs,
-//			quadCLT_main.correctionsParameters.cuasUasTimeStamp, // double                                               cuasUasTimeStamp,
-//			quadCLT_main.correctionsParameters.cuasCameraATR,    // double []                                            cuasCameraATR,
 			UasLogReader uasLogReader = null;
 			String uas_log_path = quadCLT_main.correctionsParameters.getUasLogsPath();
 			if ((uas_log_path != null) && (uas_log_path.length() > 0)) {
@@ -8686,6 +8690,8 @@ if (debugLevel > -100) return true; // temporarily !
 				uasLogReader.setCameraATR(quadCLT_main.correctionsParameters.cuasCameraATR);
 				uasLogReader.setUASHomeNed(quadCLT_main.correctionsParameters.cuasSetHome? quadCLT_main.correctionsParameters.cuasUASHome : null);
 			}
+			
+			
 			while ((ref_index < 0) || ((ref_index + 1) >= min_num_scenes)) {
 				String model_directory = opticalFlow.buildSeries(
 						(pathFirstLast != null),   //boolean                                              batch_mode,