Starting cuas series combining

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -7893,6 +7893,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		
 		try {
 			TwoQuadCLT.buildSeriesTQ(
+		    		0, // int                                                  cuas_proc_mode, // 0 - old, 1 combine scene series
 					quadCLT, // QUAD_CLT, // QuadCLT quadCLT_main,
 					-1, // int  ref_index,
 					0,  // int  ref_step, 

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

@@ -1825,7 +1825,7 @@ public class CuasMotion {
 		for (int i = 0; i < CuasMotionLMA.LMA_TITLES.length; i++) {
 			frame_titles[i] = CuasMotionLMA.LMA_TITLES[i];
 		}
-		frame_titles[CuasMotionLMA.LMA_TITLES.length] = "Targets";
+		frame_titles[CuasMotionLMA.LMA_TITLES.length] = CuasMotionLMA.EXTRA_SLICE_DISCARD_ON_LOAD; // "Targets"; // will be discarded
 		double [][][] img_data = new double [num_fields+1][num_scenes][num_tiles];
 		for (int nscene = 0; nscene < num_scenes; nscene++) {
 			for (int nfield = 0; nfield < img_data.length; nfield++) {
@@ -1837,6 +1837,7 @@ public class CuasMotion {
 					for (int nfield = 0; nfield < num_fields; nfield++) {
 						img_data[nfield][nscene][ntile] = target[nfield];
 					}
+					// dangerous - saves and then loads (on reuse)
 					img_data[num_fields][nscene][ntile] = ((target[CuasMotionLMA.RSLT_FAIL]==CuasMotionLMA.FAIL_NONE) &&
 							Double.isNaN(target[CuasMotionLMA.RSLT_STRONGER]))? 1:0;
 				}
@@ -1913,7 +1914,8 @@ public class CuasMotion {
 		return vf;
 	}
 	
-	public static double [][][] getTargetsFromHyperAugment(String path){ // add empty fields to the end of each target if shorter than CuasMotionLMA.RSLT_LEN
+	public static double [][][] getTargetsFromHyperAugment(
+			String path){ // add empty fields to the end of each target if shorter than CuasMotionLMA.RSLT_LEN
 		int [] wh = new int [2];
 		String [][] pvf_top_titles = new String[1][];
 		String [][] pvf_titles = new String[1][];
@@ -1926,6 +1928,11 @@ public class CuasMotion {
 			return null;
 		}
 		int num_fields = targets_file.length;
+		// fix - discarding last slice if it is called CuasMotionLMA.EXTRA_SLICE_DISCARD_ON_LOAD ("Targets")
+		if (pvf_top_titles[0][pvf_top_titles[0].length-1].equals(CuasMotionLMA.EXTRA_SLICE_DISCARD_ON_LOAD)) {
+			System.out.println("getTargetsFromHyperAugment(): removing last slice called "+ pvf_top_titles[0][pvf_top_titles[0].length-1]);
+			num_fields--;
+		}
 		int num_fields_augmented = Math.max(num_fields, CuasMotionLMA.RSLT_LEN);
 		int num_seq = targets_file[0].length;
 		int num_tiles = targets_file[0][0].length;
@@ -3167,7 +3174,7 @@ public class CuasMotion {
 	 * @param mask_blur        mask transition width    
 	 * @param round            false - square (no blur), true - round
 	 * @param target_keyframes accumulated target images (centered to the tiles if center is true)
-	 * @param vector_field     [scene][tile][] first two elements - targets vX, vY in pixels per frame. Empty are nulls, same velocities for 5x5  
+	 * @param target_sequence  [scene][tile][] first two elements - targets vX, vY in pixels per frame. Empty are nulls, same velocities for 5x5  
 	 * @param target_positions [scene][tile][] target positions of the targets relative to the tile center
 	 * @param background       static scenes to be overlaid by the targets
 	 * @param frame0           frame number of the background corresponding to the first keyframe 

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

@@ -93,7 +93,13 @@ public class CuasMotionLMA {
 	public static final int RSLT_GDISP_DIFF=       51;
 	public static final int RSLT_GDISP_STR =       52;
 	public static final int RSLT_GRANGE =          53;
-	public static final int RSLT_LEN = RSLT_GRANGE+1;
+	public static final int RSLT_FL_PX =           54; // flight log px
+	public static final int RSLT_FL_PY =           55; // flight log py
+	public static final int RSLT_FL_DISP =         56; // flight log true disparity
+	public static final int RSLT_FL_RANGE =        57; // flight log range (meters)
+	public static final int RSLT_INFINITY =        58; // disparity at infinity used for range calculation
+	
+	public static final int RSLT_LEN = RSLT_INFINITY + 1;
 	
 	public static final String [] LMA_TITLES = 
 		{"X-OFFS","Y-OFFS", "AMPLITUDE", "RADIUS","RAD_POS", "OVERSHOOT","OFFSET","RMSE","RMSE/A","MAX2A","ITERATIONS",
@@ -110,8 +116,9 @@ public class CuasMotionLMA {
 				"Stronger","Slow",
 				"WHEN", "FAILURE",
 				"Disparity","Disparity-Diff","Strength","Range","Global-index",
-				"segment-length","segment-disparity","segment_disp-diff", "segment-strength", "segment-range"};
-	
+				"segment-length","segment-disparity","segment_disp-diff", "segment-strength", "segment-range",
+				"FLOG-px","FLOG-pY","FLOG-DISP","FLOG-range","infinity"};
+	public static final String EXTRA_SLICE_DISCARD_ON_LOAD = "Targets"; 
 	public static final int FAIL_NONE =      0;
 	public static final int FAIL_MOTION =    1;  // motion strength/fraction too low
 	public static final int FAIL_NO_MAX =    2;  // no suitable local maximum 
@@ -133,6 +140,7 @@ public class CuasMotionLMA {
 	public static final int FAIL_NEIGHBOR = 18;  // failed because some neighbor is stronger   
 	public static final int FAIL_DUPLICATE= 19;  // coordinate are (almost) the same as those of a stronger tile   
 	public static final int FAIL_USED=      20;  // non-centered used to generate centered, remove this   
+	public static final int FAIL_FL_ONLY=   21;  // Flight log data only, no target detected here   
 	
 	public static final int CENTERED_NO =    0; 
 	public static final int CENTERED_YES =   1; 

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

@@ -238,7 +238,8 @@ public class CuasRanging {
 					System.out.println("processMovingTargetsMulti(): re-using target disparities from "+disparity_path);
 				}
 			}
-			if ((disparity_targets == null) || rng_glob) { // for now - always recalculate if 
+//			if ((disparity_targets == null) || rng_glob) { // for now - always recalculate if 
+			if (disparity_targets == null) { 
 				if (debugLevel > -4) {
 					System.out.println("detectTargets(): Generating target disparities");
 				}
@@ -264,14 +265,6 @@ public class CuasRanging {
 						System.out.println ("Skipping omegas recalculation omegas.");
 					}
 				}
-				/*
-	public double [][] rangeSingleTargets(
-			final double [][][] targets,   // centers
-			final boolean       log_ranging,
-			final boolean       rng_vfy, // Generate/save ranging verification images (per-sensor and combined rendering from the same data) NOT implemented
-			final int           debugLevel) {
-
-				 */
 				//	String model_prefix = center_CLT.getImageName()+CuasMotion.getParametersSuffix(clt_parameters,null);
 				if (rng_glob) {
 					// glob_stats =  
@@ -290,24 +283,36 @@ public class CuasRanging {
 							rng_vfy,          // final boolean       rng_vfy, // Generate/save ranging verification images (per-sensor and combined rendering from the same data)
 							debugLevel);      // final int           debugLevel)
 				}
-				ImagePlus imp_with_range = CuasMotion.showTargetSequence(
-						targets,          // double [][][] vector_fields_sequence,
-						cuasMotion.getSliceTitles(),         // String []     titles, // all slices*frames titles or just slice titles or null
-//						model_prefix+TARGET_DISPARITIES_SUFFIX, // "-TARGET_DISPARITIES",// String        title,
-						center_CLT.getImageName()+CuasMotion.getParametersSuffixRanging(clt_parameters,TARGET_DISPARITIES_SUFFIX),
-						!batch_mode,          // boolean       show,
-						cuasMotion.getTilesX());   //  int           tilesX) {
-				center_CLT.saveImagePlusInModelDirectory(imp_with_range);  // ImagePlus   imp)
+				if (!generate_csv) { // if csv is generated, data will be saved later
+					ImagePlus imp_with_range = CuasMotion.showTargetSequence(
+							targets,          // double [][][] vector_fields_sequence,
+							cuasMotion.getSliceTitles(),         // String []     titles, // all slices*frames titles or just slice titles or null
+							center_CLT.getImageName()+CuasMotion.getParametersSuffixRanging(clt_parameters,TARGET_DISPARITIES_SUFFIX),
+							!batch_mode,          // boolean       show,
+							cuasMotion.getTilesX());   //  int           tilesX) {
+					center_CLT.saveImagePlusInModelDirectory(imp_with_range);  // ImagePlus   imp)
+				}
 			}
 		}
 		// calculate range from disparity
-		getRangeFromDisparity(targets);
-		// generate results video (move from earlier)
-		
+		{ // always save after calculating ranges and adding UAS data. Later may be moved to after rangeTargets() above, only when calculated
+			getRangeFromDisparity(targets); // adds RSLT_INFINITY field
+			// generate results video (move from earlier)
+			addUasData(targets); // add flight log data to the nearest tiles, either existing or new
+			// re-saving data with flight log (ground truth) additions
+			ImagePlus imp_with_range = CuasMotion.showTargetSequence(
+					targets,          // double [][][] vector_fields_sequence,
+					cuasMotion.getSliceTitles(),         // String []     titles, // all slices*frames titles or just slice titles or null
+					center_CLT.getImageName()+CuasMotion.getParametersSuffixRanging(clt_parameters,TARGET_DISPARITIES_SUFFIX),
+					!batch_mode,          // boolean       show,
+					cuasMotion.getTilesX());   //  int           tilesX) {
+			center_CLT.saveImagePlusInModelDirectory(imp_with_range);  // ImagePlus   imp)
+		}
 		if (generate_csv) {
 			saveTargetStats(targets); // final double [][][] targets_single) {
 		}
 		
+		
 		if (generate_output) {
 			cuasMotion.generateExtractFilterMovingTargets( // move parameters to clt_parameters
 					false, // final boolean       video_pass, // if clt_parameters.cuas_clean_video=true, video_pass=0 - output TIFFS, but no video. If video_pass==1 - only video with no debug
@@ -380,6 +385,7 @@ public class CuasRanging {
 				public void run() {
 					for (int nSeq = ai.getAndIncrement(); nSeq < targets.length; nSeq = ai.getAndIncrement()) {
 						for (int ntile = 0; ntile < targets[nSeq].length; ntile++) if (targets[nSeq][ntile] != null){
+							targets[nSeq][ntile][CuasMotionLMA.RSLT_INFINITY] = cuas_infinity;
 							if (!Double.isNaN(targets[nSeq][ntile][CuasMotionLMA.RSLT_DISPARITY]) && (targets[nSeq][ntile][CuasMotionLMA.RSLT_DISPARITY] != 0.0)) {
 								double disparity =      targets[nSeq][ntile][CuasMotionLMA.RSLT_DISPARITY] - cuas_infinity; // corrected disparity
 								double disparity_diff = targets[nSeq][ntile][CuasMotionLMA.RSLT_DISP_DIFF];
@@ -2636,6 +2642,38 @@ public class CuasRanging {
 		return masked_img;
 	}
 	
+	public void addUasData(
+			final double [][][] targets_single) {
+		int num_seq = targets_single.length;
+		UasLogReader  uasLogReader = cuasMotion.getUasLogReader();
+		String [] slice_titles = 	cuasMotion.getSliceTitles(); // timestamps
+		int tilesX =     cuasMotion.getTilesX();
+		int tilesY =    targets_single[0].length / tilesX;
+		for (int nseq = 0; nseq < num_seq; nseq++) {
+			String timestamp = slice_titles[nseq];
+			double [] uas_pXpYDRange = uasLogReader.getUasPxPyDRange(timestamp); // px, py, d-  cuas_infinity (true disparity), range
+			if (uas_pXpYDRange != null) {
+				double px =        uas_pXpYDRange[0];
+				double py =        uas_pXpYDRange[1];
+				double disparity = uas_pXpYDRange[2]; // true disparity, w/o infinity offset
+				double range =     uas_pXpYDRange[3];
+				int tileX = (int) (px/GPUTileProcessor.DTT_SIZE);
+				int tileY = (int) (py/GPUTileProcessor.DTT_SIZE);
+				if ((tileX>=0) && (tileY>=0) && (tileX < tilesX)  && (tileY < tilesY)) {
+					int ntile = tileX + tileY * tilesX;
+					if (targets_single[nseq][ntile] == null) {
+						targets_single[nseq][ntile] = CuasMotionLMA.getEmpty(); // all fields NaN
+						targets_single[nseq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_FL_ONLY; // should be enough not to treat as a target
+					}
+					double [] tile = targets_single[nseq][ntile];
+					tile[CuasMotionLMA.RSLT_FL_PX] =    px;
+					tile[CuasMotionLMA.RSLT_FL_PY] =    py;
+					tile[CuasMotionLMA.RSLT_FL_DISP] =  disparity;
+					tile[CuasMotionLMA.RSLT_FL_RANGE] = range;
+				}
+			}
+		}		
+	}
 	
 	// relies on calcMatchingTargetsLengths(.., true,...) called from recalcOmegas() to set [RSLT_GLOBAL] 
 	public void saveTargetStats(
@@ -2680,7 +2718,7 @@ public class CuasRanging {
 			String timestamp = slice_titles[nseq];
 			sb.append(nseq+"\t"+timestamp+"\t");
 			// get azimuth, elevation, target disparity from the log plus infinity, log range
-			double [] uas_pXpYDRange = uasLogReader.getUasPxPyDRange(timestamp); // px, py, d, range + cuas_infinity
+			double [] uas_pXpYDRange = uasLogReader.getUasPxPyDRange(timestamp); // px, py, d-  cuas_infinity (true disparity), range
 			double [][] az_el_oaz_oel= 	CuasMotion.getPixToAzElev(
 					clt_parameters,     // CLTParameters  clt_parameters,
 					uas_pXpYDRange[0],  // double         target_x,

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

@@ -8561,6 +8561,7 @@ if (debugLevel > -100) return true; // temporarily !
 	 * @throws Exception
 	 */
     public static void buildSeriesTQ(
+    		int                                                  cuas_proc_mode, // 0 - old, 1 combine scene series
 			QuadCLT                                              quadCLT_main, // tiles should be set
 			int                                                  ref_index_unused, // -1 - last
 			int                                                  ref_step_unused, // not used here