Debugging preExpandCLTQuad3d() with 16-sensor LWIR setup

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

@@ -126,14 +126,14 @@ public class CLTParameters {
 
 	public double     diff_sigma =        5.0;   // RMS difference from average to reduce weights (~ 1.0 - 1/255 full scale image)
 	public double     diff_threshold =    1.5;   // RMS difference from average to discard channel (~ 1.0 - 1/255 full scale image)
-	public boolean    diff_gauss =        true;  // when averaging images, use gaussian around average as weight (false - sharp all/nothing)
+	public boolean    diff_gauss =        true;  // when averaging images, use Gaussian around average as weight (false - sharp all/nothing)
 	public double     min_agree =         3.0;   // minimal number of channels to agree on a point (real number to work with fuzzy averages)
 	public boolean    dust_remove =       true;  // Do not reduce average weight when only one image differes much from the average
 
 	public boolean    black_back =        true;  // use Black for backdrop outside of the FOV
 	public boolean    keep_weights =      true;  // add port weights to RGBA stack (debug feature)
 	public boolean    sharp_alpha =       false; // combining mode for alpha channel: false - treat as RGB, true - apply center 8x8 only
-	public double     alpha0 = 	          0.6; // > .525 Alpha channel 0.0 thereshold (lower - transparent) (watch for far objects)
+	public double     alpha0 = 	          0.6; // > .525 Alpha channel 0.0 threshold (lower - transparent) (watch for far objects)
 	public double     alpha1 = 	          0.8; // Alpha channel 1.0 threshold (higher - opaque) (watch for window dust)
 
 	public boolean    gen_chn_stacks =    false; // generate shifted channel rgb stacks
@@ -345,7 +345,7 @@ public class CLTParameters {
 	public int        min_clstr_seed   = 4; //2;     // number of tiles in a cluster to seed (just background?)
 	public int        min_clstr_lone   = 4;     // number of tiles in a cluster not close to other clusters (more than 2 tiles apart)
 	public double     min_clstr_weight = 0.0;   // Minimal total strength of the cluster
-	public double     min_clstr_max    = 0.25;  // Minimal maximal strength of the cluster
+	public double     min_clstr_max    = 0.18;  // Minimal maximal strength of the cluster
 
 	public int        fill_gaps        = 4;     // same as in grow - 1:  4 directions by 1 step, 2: 8 directions by 1 step. +2*n - alternating hor/vert
 	public int        fill_final       = 50;    // same as fill_gaps, on the final pass

src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java

@@ -57,8 +57,8 @@ public class CLTPass3d{
 		                                                     // exceeds minBgFract, otherwise proceed to the next one (and accumulate strength)
 		private double []       bgTileDisparity =      null;
 		private double []       bgTileStrength =       null;
-		public  boolean []      border_tiles =         null; // these are border tiles, zero out alpha
-		public  boolean []      selected =             null; // which tiles are selected for this layer
+		private  boolean []     border_tiles =         null; // these are border tiles, zero out alpha
+		private  boolean []     selected =             null; // which tiles are selected for this layer
 		public  double [][][][] texture_tiles;
 		// texture_selection is only used for the GPU and if not null means it is for the GPU
 		public boolean []       texture_selection =    null; // use by the GPU to set texture to generate

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

@@ -455,10 +455,10 @@ public class Correlation2d {
 					HashSet<Integer> contrib_set = new HashSet<Integer>();
 					Iterator<Integer> contrib_itr;
 					for (int num_pair = ai.getAndIncrement(); num_pair < corr_pairs.length; num_pair = ai.getAndIncrement()) {
-						if (num_pair == 62) {
-							System.out.println("num_pair="+num_pair);
-							System.out.println("num_pair="+num_pair);
-						}
+//						if (num_pair == 62) {
+//							System.out.println("num_pair="+num_pair);
+//							System.out.println("num_pair="+num_pair);
+//						}
 						if (corr_pairs[num_pair]) {
 							resample_indices[num_pair] = new int    [mcorr_comb_width * mcorr_comb_height][];
 							resample_weights[num_pair] = new double [mcorr_comb_width * mcorr_comb_height][];
@@ -485,10 +485,10 @@ public class Correlation2d {
 									int ix = j - mcorr_comb_width/2;
 									Arrays.fill(contrib, 0.0);
 									contrib_set.clear();
-									if ((num_pair == 62) && (i==7) && (j==7)) {
-										System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
-										System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
-									}
+//									if ((num_pair == 62) && (i==7) && (j==7)) {
+//										System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+//										System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+//									}
 									
 									for (int idy = 0; idy < weights_size; idy++) {
 										mxy.set(1, 0,  iy+ (idy - SUB_SAMPLE + 1) * ksub); //idy == (SUB_SAMPLE -1) - no fractional pixel
@@ -564,10 +564,10 @@ public class Correlation2d {
  					ArrayList<Integer> contrib_list = new ArrayList<Integer>();
  					ArrayList<Double>  contrib_weights_list = new ArrayList<Double>();
  					for (int num_pair = ai.getAndIncrement(); num_pair < corr_pairs.length; num_pair = ai.getAndIncrement()) {
- 						if (num_pair == 62) {
- 							System.out.println("num_pair="+num_pair);
- 							System.out.println("num_pair="+num_pair);
- 						}
+// 						if (num_pair == 62) {
+// 							System.out.println("num_pair="+num_pair);
+// 							System.out.println("num_pair="+num_pair);
+// 						}
  						if (corr_pairs[num_pair]) {
  							resample_indices[num_pair] = new int    [mcorr_comb_width * mcorr_comb_height][];
  							resample_weights[num_pair] = new double [mcorr_comb_width * mcorr_comb_height][];
@@ -596,10 +596,10 @@ public class Correlation2d {
  									int iy = i + mcorr_comb_offset - mcorr_comb_height/2;
  									for (int j = 0; j < mcorr_comb_width; j++) {
  										int ix = j - mcorr_comb_width/2;
- 										if ((num_pair == 62) && (i==7) && (j==7)) {
- 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
- 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
- 										}
+// 										if ((num_pair == 62) && (i==7) && (j==7)) {
+// 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+// 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+// 										}
  		 								// convert +/- 1 pixel to pair
  										double minXPair = Double.NaN,minYPair = Double.NaN, maxXPair = Double.NaN, maxYPair = Double.NaN;
  										for (int d = 0; d < four_corners.length; d++) {
@@ -676,10 +676,10 @@ public class Correlation2d {
  										mxy.set(0, 0,  ix);
  										mxy.set(1, 0,  iy);
  										double [] xy_pair = toPair.times(mxy).getColumnPackedCopy();
- 										if ((num_pair == 62) && (i==7) && (j==7)) {
- 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
- 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
- 										}
+// 										if ((num_pair == 62) && (i==7) && (j==7)) {
+// 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+// 											System.out.println("num_pair="+num_pair+", i="+i+", j="+j);
+// 										}
  										// find 4 corners in the pair array
  										if (    (xy_pair[0] >= (1 - transform_size)) &&
  												(xy_pair[0] <= (transform_size - 1)) &&

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

@@ -114,8 +114,9 @@ public class ImageDtt extends ImageDttCPU {
 //gpuQuad
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 
@@ -929,8 +930,9 @@ public class ImageDtt extends ImageDttCPU {
 //gpuQuad
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 
@@ -1617,8 +1619,9 @@ public class ImageDtt extends ImageDttCPU {
 //gpuQuad
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 //dbg_pair_mask
@@ -1967,8 +1970,9 @@ public class ImageDtt extends ImageDttCPU {
 //gpuQuad
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 //dbg_pair_mask

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

@@ -1705,8 +1705,9 @@ public class ImageDttCPU {
 		final boolean debug_distort= (globalDebugLevel >0); // .false; // true;
 //		final double [][] debug_offsets = null;
 		//lma_dbg_scale
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 
@@ -2563,8 +2564,9 @@ public class ImageDttCPU {
 			final int                 globalDebugLevel)
 	{
 		final boolean debug_distort= (globalDebugLevel >0); // .false; // true;
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 
@@ -3205,8 +3207,10 @@ public class ImageDttCPU {
 			final double [][][][]     clt_combo_dbg,  // generate sparse  partial rotated/scaled pairs
 			// When clt_mismatch is non-zero, no far objects extraction will be attempted
 			// clt_mismatch is used in older code, not supported in GPU - there is cltMeasureLazyEye for that purpose
+			// this.correlation2d should be not null if disparity_map != null
 			final double [][]         disparity_map,   // [8][tilesY][tilesX], only [6][] is needed on input or null - do not calculate
 			                                           // last 2 - contrast, avg/ "geometric average)
+			
 			final double [][][][]     texture_tiles,   // [tilesY][tilesX]["RGBA".length()][];  null - will skip images combining
 			final int                 width,
 			final double              corr_fat_zero,    // add to denominator to modify phase correlation (same units as data1, data2). <0 - pure sum
@@ -3322,8 +3326,9 @@ public class ImageDttCPU {
 		}
 		final boolean [][] combo_sels = pcombo_sels; 
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 		
@@ -4112,12 +4117,16 @@ public class ImageDttCPU {
 								}
 							}
 							// iclt here: [quad][color][256]
-							if ((globalDebugLevel > 0) && debugTile) {
+							if ((globalDebugLevel > 0) && debugTile0) {
 								ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
-								String [] titles = {"red0","blue0","green0","red1","blue1","green1","red2","blue2","green2","red3","blue3","green3"};
+								String [] col_names= {"red","blue","green"};
+								String [] titles = new String[numSensors * numcol];
+//								String [] titles = {"red0","blue0","green0","red1","blue1","green1","red2","blue2","green2","red3","blue3","green3"};
 								double [][] dbg_tile = new double [numSensors*numcol][];
 								for (int i = 0; i < numSensors; i++) {
 									for (int ncol = 0; ncol <numcol; ncol++) if (iclt_tile[i][ncol] != null) { // color
+										String col_name = (ncol < col_names.length)?col_names[ncol]:("c<"+ncol+">");
+										titles[i * numcol + ncol] = col_name + i; 
 										dbg_tile[i * numcol + ncol] = iclt_tile[i][ncol];
 									}
 								}
@@ -4145,12 +4154,16 @@ public class ImageDttCPU {
 									}
 								}
 							}
-							if ((globalDebugLevel > 0) && debugTile) {
+							if ((globalDebugLevel > 0) && debugTile0) {
 								ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
-								String [] titles = {"red0","blue0","green0","red1","blue1","green1","red2","blue2","green2","red3","blue3","green3"};
+								String [] col_names= {"red","blue","green"};
+								String [] titles = new String[numSensors * numcol];
+								
 								double [][] dbg_tile = new double [numSensors*numcol][];
 								for (int i = 0; i < numSensors; i++) {
 									for (int chn = 0; chn <numcol; chn++) { // color
+										String col_name = (chn< col_names.length)?col_names[chn]:("c<"+chn+">");
+										titles[i * numcol + chn] = col_name + i; 
 										dbg_tile[i * numcol + chn] = tiles_debayered[i][chn];
 									}
 								}
@@ -4182,7 +4195,10 @@ public class ImageDttCPU {
 									(globalDebugLevel > 0) && debugTile,
 									false);          // boolean       debug_gpu)      // generate output fro matching with GPU processing
 
-
+							if ((globalDebugLevel > 0) && debugTile0) {
+								ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
+								sdfa_instance.showArrays(texture_tiles[tileY][tileX], 2* transform_size, 2* transform_size, true, "tile_combine_rgba_x"+tileX+"_y"+tileY);
+							}
 							// mix RGB from iclt_tile, mix alpha with - what? correlation strength or 'don't care'? good correlation or all > min?
 							for (int i = 0; i < iclt_tile[0][first_color].length; i++ ) {
 								double sw = 0.0;
@@ -4197,6 +4213,10 @@ public class ImageDttCPU {
 									}
 								}
 							}
+							if ((globalDebugLevel > 0) && debugTile0) { // same as previous for mono
+								ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
+								sdfa_instance.showArrays(texture_tiles[tileY][tileX], 2* transform_size, 2* transform_size, true, "tile_mixed_rgba_x"+tileX+"_y"+tileY);
+							}
 							if ((disparity_map != null) && (disparity_map.length >= (IMG_DIFF0_INDEX + numSensors))){
 								for (int i = 0; i < max_diff.length; i++){
 									disparity_map[IMG_DIFF0_INDEX + i][tIndex] = max_diff[i];
@@ -6702,8 +6722,9 @@ public class ImageDttCPU {
 		final boolean [][] saturation_imp = quadCLT.saturation_imp;               // boolean [][] saturation_imp, // (near) saturated pixels or null
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[quadCLT.getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 		final int quad = 4;   // number of subcameras
@@ -12682,8 +12703,9 @@ public class ImageDttCPU {
 		
 		final boolean debug_distort= globalDebugLevel > 0; ///false; // true;
 
-		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
-		for (int i = 0; i < debug_offsets.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
+//		final double [][] debug_offsets = new double[imgdtt_params.lma_dbg_offset.length][2];
+		final double [][] debug_offsets = new double[getNumSensors()][2];  
+		for (int i = 0; i < imgdtt_params.lma_dbg_offset.length; i++) for (int j = 0; j < debug_offsets[i].length; j++) {
 			debug_offsets[i][j] = imgdtt_params.lma_dbg_offset[i][j]*imgdtt_params.lma_dbg_scale;
 		}
 		

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

@@ -220,7 +220,11 @@ public class ImageDttParameters {
 	public boolean corr_var_cam =           true;  // New correlation mode compatible with 8 subcameras 
 	public double  cm_max_normalization =   0.55; // fraction of correlation maximum radius, being squared multiplied by maximum to have the same total mass
 	public double  lma_dbg_scale =          0.0;  // scale lma_dbg_offset
-	public double  [][] lma_dbg_offset =    {{ 1.0, 0.0},{ -1.0, 0.0},{-1.0, 0.0},{ 1.0, 0.0}}; //  new double [4][2];
+	public double  [][] lma_dbg_offset =    {
+			                                 {  1.0, 0.0},
+			                                 { -1.0, 0.0},
+			                                 { -1.0, 0.0},
+			                                 {  1.0, 0.0}}; //  new double [4][2];
 
 	public double getCorrSigma(boolean monochrome) {
 		return monochrome ? pcorr_sigma_mono : pcorr_sigma;

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

@@ -2047,7 +2047,7 @@ public class QuadCLT extends QuadCLTCPU {
 				is_mono,
 				is_lwir,
 				clt_parameters.getScaleStrength(isAux())); // 1.0);
-		
+		image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		float [][] lpf_rgb = new float[][] {
 			image_dtt.floatGetCltLpfFd(clt_parameters.gpu_sigma_r),
 			image_dtt.floatGetCltLpfFd(clt_parameters.gpu_sigma_b),
@@ -2312,6 +2312,7 @@ public class QuadCLT extends QuadCLTCPU {
 				is_mono,
 				is_lwir,
 				1.0);
+		image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		float [][] lpf_rgb = new float[][] {
 			image_dtt.floatGetCltLpfFd(clt_parameters.gpu_sigma_r),
 			image_dtt.floatGetCltLpfFd(clt_parameters.gpu_sigma_b),
@@ -3034,6 +3035,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -3177,7 +3179,7 @@ public class QuadCLT extends QuadCLTCPU {
 		  final int tilesX = tp.getTilesX();
 		  final int tilesY = tp.getTilesY();
 		  CLTPass3d bgnd_data = tp.clt_3d_passes.get(0);
-		  boolean [] bgnd_tiles_grown2 = bgnd_data.selected.clone(); // only these have non 0 alpha
+		  boolean [] bgnd_tiles_grown2 = bgnd_data.getSelected().clone(); // only these have non 0 alpha
 		  tp.growTiles(
 				  2,      // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
 				  bgnd_tiles_grown2,
@@ -3291,6 +3293,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -3433,6 +3436,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 //		  double z_correction =  clt_parameters.z_correction;
 //		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 //			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -3561,6 +3565,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  GPUTileProcessor.TpTask[] tp_tasks =  gpuQuad.setInterTasks(
 				  pXpYD,              // final double [][]         pXpYD, // per-tile array of pX,pY,disparity triplets (or nulls)
 				  geometryCorrection, // final GeometryCorrection  geometryCorrection,
@@ -4162,6 +4167,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -4417,7 +4423,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  texture_woi_pix.y/transform_size,
 				  texture_woi_pix.width/transform_size,
 				  texture_woi_pix.height/transform_size);
-		  scan.selected = scan.getTextureSelection().clone(); // null
+		  scan.setSelected(scan.getTextureSelection().clone()); // null
 		  ImagePlus imp_texture_cluster = linearStackToColor(
 				  clt_parameters,
 				  colorProcParameters,
@@ -4624,6 +4630,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -4744,6 +4751,7 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);
@@ -4935,14 +4943,17 @@ public class QuadCLT extends QuadCLTCPU {
 			  }
 		  }
 		  double min_corr_selected = clt_parameters.min_corr;
-		  double [][] shiftXY = new double [4][2];
-		  if (!clt_parameters.fine_corr_ignore) {
+		  double [][] shiftXY = new double [getNumSensors()][2];
+		  if (!clt_parameters.fine_corr_ignore) {// invalid for AUX!
 			  double [][] shiftXY0 = {
 					  {clt_parameters.fine_corr_x_0,clt_parameters.fine_corr_y_0},
 					  {clt_parameters.fine_corr_x_1,clt_parameters.fine_corr_y_1},
 					  {clt_parameters.fine_corr_x_2,clt_parameters.fine_corr_y_2},
 					  {clt_parameters.fine_corr_x_3,clt_parameters.fine_corr_y_3}};
-			  shiftXY = shiftXY0;
+			  // FIXME - only first 4 sensors have correction. And is it the same for aux and main? 
+			  for (int i = 0; i < shiftXY0.length;i++) {
+				  shiftXY[i] = shiftXY0[i];
+			  }
 		  }
 
 		  ImageDtt image_dtt = new ImageDtt(
@@ -4953,6 +4964,8 @@ public class QuadCLT extends QuadCLTCPU {
 				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()),
 				  gpuQuad);
+		  image_dtt.getCorrelation2d(); // initiate image_dtt.correlation2d, needed if disparity_map != null  
+		  
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
 			  z_correction +=clt_parameters.z_corr_map.get(image_name);

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

@@ -9126,9 +9126,9 @@ if (debugLevel > -100) return true; // temporarily !
 			int [] channelFiles_main = set_channels_main[nSet].fileNumber();
 			int [] channelFiles_aux =  set_channels_aux[nSet].fileNumber();
 			boolean [][] saturation_imp_main = (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_main.length][] : null;
-			boolean [][] saturation_imp_aux =  (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_main.length][] : null;
+			boolean [][] saturation_imp_aux =  (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_aux.length][] : null;
 			double [] scaleExposures_main = new double[channelFiles_main.length];
-			double [] scaleExposures_aux =  new double[channelFiles_main.length];
+			double [] scaleExposures_aux =  new double[channelFiles_aux.length];
 			if (updateStatus) IJ.showStatus("Conditioning main camera image set for "+quadCLT_main.image_name);
 			ImagePlus [] imp_srcs_main = quadCLT_main.conditionImageSet(
 					clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
@@ -9437,14 +9437,15 @@ if (debugLevel > -100) return true; // temporarily !
 								properties,  // Properties properties,    // if null - will only save extrinsics)
 								debugLevel);
 					}
-					continue; // skipping to the next file
+					
+///					continue; // skipping to the next file
 				}
 			}
 
 			// Process AUX (LWIR) camera data
 			// 1) Prepare DS for adjustments (just d/s, with ambiguous disparity tiles removed)
 			// 2) Prepare full D/S and FG/BG data to be embedded within the ML files
-			double [][] main_ds = {dsi[DSI_DISPARITY_MAIN], dsi[DSI_STRENGTH_MAIN]};
+			double [][] main_ds = {dsi[DSI_DISPARITY_MAIN], dsi[DSI_STRENGTH_MAIN]}; // {null, null}
 
 			if ((adjust_aux == 0) &&
 					!quadCLT_main.correctionsParameters.clt_batch_4img_aux &&
@@ -9455,7 +9456,7 @@ if (debugLevel > -100) return true; // temporarily !
 				continue; 
 			}
 			
-			
+			if (main_ds[0] != null) {
 				quadCLT_aux.ds_from_main = quadCLT_aux.depthMapMainToAux( // only 2 layers for adjustments
 						main_ds, // double [][] ds,
 						quadCLT_main.getGeometryCorrection(), //  GeometryCorrection geometryCorrection_main,
@@ -9473,6 +9474,7 @@ if (debugLevel > -100) return true; // temporarily !
 						true,                                 // split_fg_bg,
 						false,                                // for_adjust,
 						debugLevel);                          // int debug_level
+			}
 
 			ImagePlus [] imp_srcs_aux = quadCLT_aux.conditionImageSet(
 					clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
@@ -9485,14 +9487,13 @@ if (debugLevel > -100) return true; // temporarily !
 					saturation_imp_aux,            //output  // boolean [][]                              saturation_imp,
 					threadsMax,                 // int                                       threadsMax,
 					debugLevelInner); // int                                       debugLevel);
-
 			// optionally adjust AUX extrinsics (using quadCLT_aux.ds_from_main )
 			for (int num_adjust_aux = 0; num_adjust_aux < adjust_aux; num_adjust_aux++) {
 				if (updateStatus) IJ.showStatus("Building basic  DSI for the AUX camera image set "+quadCLT_main.image_name+
-						" using main camera DSI, pass "+(num_adjust_aux+1)+" of "+num_adjust_aux);
+						" using main camera DSI, pass "+(num_adjust_aux+1)+" of "+adjust_aux);
 				if (debugLevel > -5) {
 					System.out.println("Building basic  DSI for the AUX camera image set "+quadCLT_main.image_name+
-							" using main camera DSI, pass "+(num_adjust_aux+1)+" of "+num_adjust_aux);
+							" using main camera DSI, pass "+(num_adjust_aux+1)+" of "+adjust_aux);
 				}
 				quadCLT_aux.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
 						imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
@@ -9530,7 +9531,7 @@ if (debugLevel > -100) return true; // temporarily !
 							updateStatus,// final boolean    updateStatus,
 							debugLevelInner); // final int        debugLevel)
 					if (!ok) break;
-				}
+				} else {
 					boolean ok = quadCLT_aux.extrinsicsCLTfromGT(
 							null,
 							quadCLT_aux.ds_from_main, // gt_disp_strength,
@@ -9539,9 +9540,10 @@ if (debugLevel > -100) return true; // temporarily !
 							threadsMax,               // final int        threadsMax,  // maximal number of threads to launch
 							updateStatus,             // final boolean    updateStatus,
 							debugLevel + 2);          // final int        debugLevel)
+					if (!ok) break;
+				}
 // clear memory for AUX
 				quadCLT_aux.tp.resetCLTPasses();
-				if (!ok) break;
 			}
 			// Generate 4 AUX camera images and thumbnail
 			if (quadCLT_main.correctionsParameters.clt_batch_4img_aux){