debugging texture generation in GPU, fixed old NaN bug, similar to noticed in the GPU code

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

@@ -4536,7 +4536,7 @@ public class MatchSimulatedPattern {
 			final int debugLevel
 			){
 		final int debugThreshold=2; // -1; // 1; ** Restore 1
-		if (debugThreshold < 0) {
+		if ((debugThreshold < 0) || (debugLevel < -10000)) {
 			System.out.println("findPatternCandidates(): debugThreshold < 0 - restore when done");
 		}
 		if ((debugLevel>debugThreshold) && ((debugLevel>1) || (startScanIndex>3))) {

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

@@ -112,6 +112,7 @@ public class CLTParameters {
 	public boolean    show_overlap =      true;  // show result RGBA (first channels, then RGBA combined?)
 	public boolean    show_rgba_color =   true;  // show combined color image
 	public boolean    show_map =          true;  // show disparity maps
+	public boolean    show_corr =         true;  // show GPU correlation
 
 	public double     disp_scan_start =   0.0;   // disparity scan start value
 	public double     disp_scan_step =    1.0;   // disparity scan step
@@ -768,10 +769,10 @@ public class CLTParameters {
 	public int        gpu_corr_rad =        7;  // size of the correlation to save - initially only 15x15
 	public double     gpu_weight_r =      0.25;
 	public double     gpu_weight_b =      0.25; // weight g = 1.0 - gpu_weight_r - gpu_weight_b
-	public double     gpu_sigma_r =       1.1;
-	public double     gpu_sigma_b =       1.1;
-	public double     gpu_sigma_g =       0.7;
-	public double     gpu_sigma_m =       0.7;
+	public double     gpu_sigma_r =       0.9; // 1.1;
+	public double     gpu_sigma_b =       0.9; // 1.1;
+	public double     gpu_sigma_g =       0.6; // 0.7;
+	public double     gpu_sigma_m =       0.4; // 0.7;
 	public double     gpu_sigma_rb_corr = 0.5; // apply LPF after accumulating R and B correlation before G,
 	public double     gpu_sigma_corr =    0.9;
 	public double     gpu_sigma_corr_m =  0.15;
@@ -946,6 +947,7 @@ public class CLTParameters {
 		properties.setProperty(prefix+"show_overlap",               this.show_overlap+"");
 		properties.setProperty(prefix+"show_rgba_color",            this.show_rgba_color+"");
 		properties.setProperty(prefix+"show_map",                   this.show_map+"");
+		properties.setProperty(prefix+"show_corr",                  this.show_corr+"");
 		properties.setProperty(prefix+"disp_scan_start",            this.disp_scan_start +"");
 		properties.setProperty(prefix+"disp_scan_step",             this.disp_scan_step +"");
 		properties.setProperty(prefix+"disp_scan_count",            this.disp_scan_count+"");
@@ -1693,6 +1695,8 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"show_overlap")!=null)                  this.show_overlap=Boolean.parseBoolean(properties.getProperty(prefix+"show_overlap"));
 		if (properties.getProperty(prefix+"show_rgba_color")!=null)               this.show_rgba_color=Boolean.parseBoolean(properties.getProperty(prefix+"show_rgba_color"));
 		if (properties.getProperty(prefix+"show_map")!=null)                      this.show_map=Boolean.parseBoolean(properties.getProperty(prefix+"show_map"));
+		if (properties.getProperty(prefix+"show_corr")!=null)                     this.show_corr=Boolean.parseBoolean(properties.getProperty(prefix+"show_corr"));
+
 		if (properties.getProperty(prefix+"disp_scan_start")!=null)               this.disp_scan_start=Double.parseDouble(properties.getProperty(prefix+"disp_scan_start"));
 		if (properties.getProperty(prefix+"disp_scan_step")!=null)                this.disp_scan_step=Double.parseDouble(properties.getProperty(prefix+"disp_scan_step"));
 		if (properties.getProperty(prefix+"disp_scan_count")!=null)               this.disp_scan_count=Integer.parseInt(properties.getProperty(prefix+"disp_scan_count"));
@@ -2473,11 +2477,13 @@ public class CLTParameters {
 		gd.addNumericField("Alpha channel 1.0 threshold (higher - opaque)",                                     this.alpha1,   3);
 		gd.addCheckbox    ("Generate shifted channel linear RGB stacks",                                        this.gen_chn_stacks);
 		gd.addCheckbox    ("Generate shifted channel color image stack",                                        this.gen_chn_img);
-		gd.addCheckbox    ("Generate shifted channel images and save with the model 'CLT process corr'",          this.gen_4_img);
+		gd.addCheckbox    ("Generate shifted channel images and save with the model 'CLT process corr'",        this.gen_4_img);
 		gd.addCheckbox    ("Show result RGBA before overlap combined",                                          this.show_nonoverlap);
 		gd.addCheckbox    ("Show result RGBA",                                                                  this.show_overlap);
 		gd.addCheckbox    ("Show result color",                                                                 this.show_rgba_color);
 		gd.addCheckbox    ("Show disparity maps",                                                               this.show_map);
+		gd.addCheckbox    ("Show correlation tiles",                                                            this.show_corr);
+
 		gd.addNumericField("Disparity scan start value",                                                        this.disp_scan_start,  2);
 		gd.addNumericField("Disparity scan step",                                                               this.disp_scan_step,  2);
 		gd.addNumericField("Disparity scan number of disparity values to scan",                                 this.disp_scan_count,            0);
@@ -3374,6 +3380,7 @@ public class CLTParameters {
 		this.show_overlap=          gd.getNextBoolean();
 		this.show_rgba_color=       gd.getNextBoolean();
 		this.show_map=              gd.getNextBoolean();
+		this.show_corr=             gd.getNextBoolean();
 		this.disp_scan_start=       gd.getNextNumber();
 		this.disp_scan_step=        gd.getNextNumber();
 		this.disp_scan_count= (int) gd.getNextNumber();

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

@@ -1220,7 +1220,11 @@ public class EyesisDCT {
 		  }
 
 		  if (this.correctionsParameters.deconvolve) { // process with DCT, otherwise use simple debayer
-			  ImageDtt image_dtt = new ImageDtt(dctParameters.dct_size, false, 1.0); // Bayer( not monochrome), scale correlation strengths
+			  ImageDtt image_dtt = new ImageDtt(
+					  dctParameters.dct_size,
+					  false, // mono
+					  false, // lwir
+					  1.0); // Bayer( not monochrome), scale correlation strengths
 			  double [][][][] dct_data = image_dtt.mdctStack(
 					  stack,
 					  channel,

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

@@ -3075,7 +3075,11 @@ private Panel panel1,
            	}
 
            }
-		  ImageDtt image_dtt = new ImageDtt(DCT_PARAMETERS.dct_size, false, 1.0); // Bayer( not monochrome), scale correlation strengths
+		  ImageDtt image_dtt = new ImageDtt(
+				  DCT_PARAMETERS.dct_size,
+				  false, // mono
+				  false, // lwir
+				  1.0); // Bayer( not monochrome), scale correlation strengths
            double [][][][] dctdc_data = image_dtt.mdctScale(
            		DBG_IMP.getStack(),
            		DCT_PARAMETERS.kernel_chn,
@@ -3173,7 +3177,11 @@ private Panel panel1,
         	}
 
         }
-        ImageDtt image_dtt = new ImageDtt(DCT_PARAMETERS.dct_size,false, 1.0); // Bayer( not monochrome), scale correlation strengths
+        ImageDtt image_dtt = new ImageDtt(
+        		DCT_PARAMETERS.dct_size,
+				  false, // mono
+				  false, // lwir
+				  1.0); // Bayer( not monochrome), scale correlation strengths
         double [][][][] dctdc_data = image_dtt.mdctStack(
         		DBG_IMP.getStack(),
         		DCT_PARAMETERS.kernel_chn,
@@ -7052,8 +7060,9 @@ private Panel panel1,
 
 		ImageDtt image_dtt = new ImageDtt(
 				CLT_PARAMETERS.transform_size,
-				false,
-				1.0); // Bayer( not monochrome), scale correlation strengths
+				  false, // mono
+				  false, // lwir
+				  1.0); // Bayer( not monochrome), scale correlation strengths
 		double [][][][][] clt_data = image_dtt.cltStack(
 				DBG_IMP.getStack(),
 				0, // CLT_PARAMETERS.kernel_chn,
@@ -7186,6 +7195,7 @@ private Panel panel1,
         ImageDtt image_dtt = new ImageDtt(
         		CLT_PARAMETERS.transform_size,
         		COLOR_PROC_PARAMETERS.isMonochrome(),
+        		COLOR_PROC_PARAMETERS.isLwir(),
         		CLT_PARAMETERS.getScaleStrength(false)); // Bayer, not monochrome
         String [] titles = {
         		"redCC",  "redSC",  "redCS",  "redSS",

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

@@ -63,6 +63,7 @@ public class MacroCorrelation {
 					tileSize,  // int tileSize,
 					tp.superTileSize, // int superTileSize,
 					tp.isMonochrome(),
+					tp.isLwir(),
 					tp.isAux(),
 					tp.getMagicScale(), // double scale,
 					trusted_correlation, // double trustedCorrelation,
@@ -309,6 +310,7 @@ public class MacroCorrelation {
 		ImageDtt image_dtt = new ImageDtt(
 				clt_parameters.transform_size,
 				this.mtp.isMonochrome(),
+				this.mtp.isLwir(),
 				clt_parameters.getScaleStrength(this.mtp.isAux()));
 		image_dtt.clt_aberrations_quad_corr(
 			    clt_parameters.img_dtt,       // final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others

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

@@ -123,6 +123,7 @@ public class QuadCLT {
 
 // magic scale should be set before using  TileProcessor (calculated disparities depend on it)
     public boolean isMonochrome() {return is_mono;}  // USED in lwir
+
     public boolean isAux()        {return is_aux;} // USED in lwir
     public String  sAux()         {return isAux()?"-AUX":"";} // USED in lwir
     public boolean isLwir()       {return !Double.isNaN(lwir_offset);} // clt_kernels // USED in lwir
@@ -170,6 +171,7 @@ public class QuadCLT {
 					clt_parameters.transform_size,
 					clt_parameters.stSize,
 					isMonochrome(),
+					isLwir(),
 					isAux(),
 					clt_parameters.corr_magic_scale,
 					clt_parameters.grow_disp_trust,
@@ -583,6 +585,7 @@ public class QuadCLT {
 					  ImageDtt image_dtt = new ImageDtt(
 							  clt_parameters.transform_size,
 							  isMonochrome(),
+							  isLwir(),
 							  clt_parameters.getScaleStrength(isAux()));
 					  int chn,tileY,tileX;
 					  DttRad2 dtt = new DttRad2(dtt_size);
@@ -759,7 +762,11 @@ public class QuadCLT {
 		  if (globalDebugLevel > 1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
 		  System.out.println("1.Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
 		  // Calculate differential offsets to interpolate for tiles between kernel centers
-		  ImageDtt image_dtt = new ImageDtt(clt_parameters.transform_size,isMonochrome(),clt_parameters.getScaleStrength(isAux()));
+		  ImageDtt image_dtt = new ImageDtt(
+				  clt_parameters.transform_size,
+				  isMonochrome(),
+				  isLwir(),
+				  clt_parameters.getScaleStrength(isAux()));
 		  image_dtt.clt_fill_coord_corr(
 				  clt_parameters.kernel_step,  //  final int             kern_step, // distance between kernel centers, in pixels.
 				  clt_kernels,                 // final double [][][][] clt_data,
@@ -1722,6 +1729,7 @@ public class QuadCLT {
 			  ImageDtt image_dtt = new ImageDtt(
 					  clt_parameters.transform_size,
 					  isMonochrome(),
+					  isLwir(),
 					  clt_parameters.getScaleStrength(isAux()));
 			  for (int i =0 ; i < double_stack[0].length; i++){
 				  double_stack[2][i]*=0.5; // Scale blue twice to compensate less pixels than green
@@ -2327,6 +2335,7 @@ public class QuadCLT {
 			  ImageDtt image_dtt = new ImageDtt(
 					  clt_parameters.transform_size,
 					  isMonochrome(),
+					  isLwir(),
 					  clt_parameters.getScaleStrength(isAux()));
 			  for (int i =0 ; i < double_stack[0].length; i++){
 				  double_stack[2][i]*=0.5; // Scale blue twice to compensate less pixels than green
@@ -2895,6 +2904,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  for (int i = 0; i < double_stacks.length; i++){
 			  for (int j =0 ; j < double_stacks[i][0].length; j++){
@@ -4130,6 +4140,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  for (int i = 0; i < double_stacks.length; i++){
 			  if ( double_stacks[i].length > 2) {
@@ -4730,10 +4741,8 @@ public class QuadCLT {
 			  debugLevel = clt_parameters.ly_debug_level;
 		  }
 
-		  final boolean      batch_mode = clt_parameters.batch_run; //disable any debug images
-
-		  String name=this.correctionsParameters.getModelName((String) imp_quad[0].getProperty("name"));
-		  //		int channel= Integer.parseInt((String) imp_src.getProperty("channel"));
+///		  final boolean      batch_mode = clt_parameters.batch_run; //disable any debug images
+///		  String name=this.correctionsParameters.getModelName((String) imp_quad[0].getProperty("name"));
 		  String path= (String) imp_quad[0].getProperty("path");
 
 		  ImagePlus [] results = new ImagePlus[imp_quad.length];
@@ -4746,19 +4755,14 @@ public class QuadCLT {
 		  setTiles (imp_quad[0], // set global tp.tilesX, tp.tilesY
 				  clt_parameters,
 				  threadsMax);
-//		  double [][] disparity_array = tp.setSameDisparity(clt_parameters.disparity); // 0.0); // [tp.tilesY][tp.tilesX] - individual per-tile expected disparity
-		  ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays(); // just for debugging?
-		  //		  clt_parameters.tileStep,
 
 		  final int tilesX=tp.getTilesX(); // imp_quad[0].getWidth()/clt_parameters.transform_size;
 		  final int tilesY=tp.getTilesY(); // imp_quad[0].getHeight()/clt_parameters.transform_size;
 
 		  final int clustersX= (tilesX + clt_parameters.tileStep - 1) / clt_parameters.tileStep;
 		  final int clustersY= (tilesY + clt_parameters.tileStep - 1) / clt_parameters.tileStep;
-		  final double [][] lazy_eye_data = new double [clustersY*clustersX][];
-
-		  //			final int nTilesInChn=tilesX*tilesY;
-		  final int nClustersInChn=clustersX * clustersY;
+///		  final double [][] lazy_eye_data = new double [clustersY*clustersX][];
+///		  final int nClustersInChn=clustersX * clustersY;
 
 		  double [][] dsxy = new double[clustersX * clustersY][];
 		  ImagePlus imp_sel = WindowManager.getCurrentImage();
@@ -4895,7 +4899,11 @@ public class QuadCLT {
 					  this.is_mono);
 		  }
 
-		  ImageDtt image_dtt = new ImageDtt(clt_parameters.transform_size,isMonochrome(),clt_parameters.getScaleStrength(isAux()));
+		  ImageDtt image_dtt = new ImageDtt(
+				  clt_parameters.transform_size,
+				  isMonochrome(),
+				  isLwir(),
+				  clt_parameters.getScaleStrength(isAux()));
 		  for (int i = 0; i < double_stacks.length; i++){
 			  if ( double_stacks[i].length > 2) {
 				  for (int j =0 ; j < double_stacks[i][0].length; j++){
@@ -6065,6 +6073,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  for (int i = 0; i < double_stacks.length; i++){
 			  for (int j =0 ; j < double_stacks[i][0].length; j++){
@@ -9441,6 +9450,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double [][] texture_overlap = image_dtt.combineRBGATiles(
 				  texture_tiles_bgnd, // texture_tiles,               // array [tp.tilesY][tp.tilesX][4][4*transform_size] or [tp.tilesY][tp.tilesX]{null}
@@ -9542,6 +9552,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double [][]alphaFade = tp.getAlphaFade(image_dtt.transform_size);
 		  if ((debugLevel > 0) && (scanIndex == 1)) { // not used in lwir
@@ -9756,6 +9767,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
@@ -9994,6 +10006,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
@@ -10129,6 +10142,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir
@@ -10304,6 +10318,7 @@ public class QuadCLT {
 		  ImageDtt image_dtt = new ImageDtt(
 				  clt_parameters.transform_size,
 				  isMonochrome(),
+				  isLwir(),
 				  clt_parameters.getScaleStrength(isAux()));
 		  double z_correction =  clt_parameters.z_correction;
 		  if (clt_parameters.z_corr_map.containsKey(image_name)){ // not used in lwir

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

@@ -80,6 +80,7 @@ public class TileProcessor {
 	public double [][] main_ds_ml =              null; // main camera DSI restored from the COMBO-DSI file to generate ML test files
 
 	public boolean   monochrome =                false;   // these are monochrome images
+	public boolean   lwir =                      false;   // all monochrome are lwir
 	private boolean  is_aux =                    false;   // this camera is aux
 	public int       clt_3d_passes_size =     0; //clt_3d_passes size after initial processing
 	public int       clt_3d_passes_rig_size = 0; //clt_3d_passes size after initial processing and rig processing
@@ -110,6 +111,7 @@ public class TileProcessor {
 			int tileSize,
 			int superTileSize,
 			boolean monochrome,
+			boolean lwir,
 			boolean is_aux,
 			double scale,
 			double trustedCorrelation,
@@ -121,6 +123,7 @@ public class TileProcessor {
 		this.tileSize = tileSize;
 		this.superTileSize = superTileSize;
 		this.monochrome = monochrome;
+		this.lwir =       lwir;
 		this.is_aux = is_aux;
 		this.corr_magic_scale = scale;
 		this.trustedCorrelation = trustedCorrelation;
@@ -128,6 +131,7 @@ public class TileProcessor {
 		this.threadsMax = threadsMax;
 	}
 	public boolean isMonochrome() {return monochrome;}
+	public boolean isLwir()       {return lwir;}
 	public boolean isAux()        {return is_aux;}
 
 	public int getTilesX() {return tilesX;}
@@ -5809,6 +5813,7 @@ public class TileProcessor {
 		ImageDtt image_dtt = new ImageDtt(
 				clt_parameters.transform_size,
 				isMonochrome(),
+				isLwir(),
 				clt_parameters.getScaleStrength(is_aux));
 
 		double [][][]  dispStrength = st.getDisparityStrengths(