Implemented/tested full resolution interscene fitting

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

@@ -37,11 +37,13 @@ import java.util.Set;
 
 import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.common.WindowTools;
+import com.elphel.imagej.correction.CorrectionColorProc;
 import com.elphel.imagej.lwir.LwirReaderParameters;
 import com.elphel.imagej.tileprocessor.BiQuadParameters;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.ImageDttParameters;
 import com.elphel.imagej.tileprocessor.IntersceneLmaParameters;
+import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
 import com.elphel.imagej.tileprocessor.MeasuredLayersFilterParameters;
 import com.elphel.imagej.tileprocessor.OpticalFlowParameters;
 import com.elphel.imagej.tileprocessor.PoleProcessorParameters;
@@ -884,8 +886,10 @@ public class CLTParameters {
 	public double     gpu_sigma_corr_m =     0.15;
 	public double     gpu_sigma_log_corr =   3.0; // fill in after testing
 	public double     gpu_sigma_log_corr_m = 3.0; // fill in after testing
-	public double     gpu_fatz =           500.0; // was 30
-	public double     gpu_fatz_m =         500.0; // was 30
+	public double     gpu_fatz =          2000.0; //  500.0; // was 30
+	public double     gpu_fatz_m =        2000.0; //  500.0; // was 30
+	public double     gpu_fatz_inter =   10000.0; // There is some artifact (bug or float precision)
+	public double     gpu_fatz_inter_m = 10000.0; //
 
 	public boolean    gpu_woi =             false; // if true - use gpu_woi_tx, ...
 	public int        gpu_woi_tx =              0;
@@ -946,6 +950,7 @@ public class CLTParameters {
 	public MeasuredLayersFilterParameters mlfp =    new MeasuredLayersFilterParameters();
 	public LwirReaderParameters           lwir =    new LwirReaderParameters();
 	public OpticalFlowParameters          ofp =     new OpticalFlowParameters();
+	public IntersceneMatchParameters      imp =     new IntersceneMatchParameters();
 	public IntersceneLmaParameters        ilp =     new IntersceneLmaParameters();
 	public InterNoiseParameters           inp =     new InterNoiseParameters();
 			
@@ -953,9 +958,30 @@ public class CLTParameters {
 	public HashMap<String,Double> infinity_distace_map = new HashMap<String,Double>(); //new one
 	public static String Z_CORR_PREFIX = "z_corr.";
 	public static String INFINITY_DISTANCE_PREFIX = "infinity_distance.";
-
 	public boolean   batch_run =               false; // turned on only while running in batch mode
 
+	// Quick fix to pass these parameters
+	public ColorProcParameters                             colorProcParameters;
+	public ColorProcParameters                             colorProcParametersAux;
+	public EyesisCorrectionParameters.RGBParameters        rgbParameters;
+
+	public void setColorProcParameters(ColorProcParameters colorProcParameters, boolean aux) {
+		if (aux) {
+			this.colorProcParametersAux = colorProcParameters;
+		}else {
+			this.colorProcParameters = colorProcParameters;
+		}
+	}
+	public void setRGBParameters (EyesisCorrectionParameters.RGBParameters rgbParameters) {
+		this.rgbParameters =rgbParameters;
+	}
+	public EyesisCorrectionParameters.RGBParameters getRGBParameters(){
+		return rgbParameters;
+	}
+	public ColorProcParameters getColorProcParameters(boolean aux) {
+		return aux? colorProcParametersAux:colorProcParameters;
+	}
+	
 	public boolean useGPU() {
 		return  useGPU(false) || useGPU(true);
 	
@@ -981,6 +1007,10 @@ public class CLTParameters {
 		return monochrome ? gpu_fatz_m : gpu_fatz;
 	}
 
+	public double getGpuFatZeroInter(boolean monochrome) {
+		return monochrome ? gpu_fatz_inter_m : gpu_fatz_inter;
+	}
+	
 	public double getGpuCorrSigma(boolean monochrome) {
 		return monochrome ? gpu_sigma_corr_m : gpu_sigma_corr;
 	}
@@ -1765,6 +1795,8 @@ public class CLTParameters {
 		properties.setProperty(prefix+"gpu_sigma_log_corr_m",       this.gpu_sigma_log_corr_m +"");
 		properties.setProperty(prefix+"gpu_fatz",                   this.gpu_fatz +"");
 		properties.setProperty(prefix+"gpu_fatz_m",                 this.gpu_fatz_m +"");
+		properties.setProperty(prefix+"gpu_fatz_inter",             this.gpu_fatz_inter +"");
+		properties.setProperty(prefix+"gpu_fatz_inter_m",           this.gpu_fatz_inter_m +"");
 
 		properties.setProperty(prefix+"gpu_woi",                    this.gpu_woi +"");
 		properties.setProperty(prefix+"gpu_woi_tx",                 this.gpu_woi_tx +"");
@@ -1836,6 +1868,7 @@ public class CLTParameters {
 		poles.setProperties   (prefix+"_poles",   properties);
 		lwir.setProperties    (prefix+"_lwir",    properties);
 		ofp.setProperties     (prefix+"_ofp_",    properties);
+		imp.setProperties     (prefix+"_imp_",    properties);
 		ilp.setProperties     (prefix+"_ilp_",    properties);
 		inp.setProperties     (prefix+"_inp_",    properties);
 
@@ -2617,6 +2650,8 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"gpu_sigma_log_corr_m")!=null)        this.gpu_sigma_log_corr_m=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_log_corr_m"));
 		if (properties.getProperty(prefix+"gpu_fatz")!=null)                    this.gpu_fatz=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz"));
 		if (properties.getProperty(prefix+"gpu_fatz_m")!=null)                  this.gpu_fatz_m=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz_m"));
+		if (properties.getProperty(prefix+"gpu_fatz_inter")!=null)              this.gpu_fatz_inter=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz_inter"));
+		if (properties.getProperty(prefix+"gpu_fatz_inter_m")!=null)            this.gpu_fatz_inter_m=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz_inter_m"));
 
 		if (properties.getProperty(prefix+"gpu_woi")!=null)                     this.gpu_woi=Boolean.parseBoolean(properties.getProperty(prefix+"gpu_woi"));
 		if (properties.getProperty(prefix+"gpu_woi_tx")!=null)                  this.gpu_woi_tx=Integer.parseInt(properties.getProperty(prefix+"gpu_woi_tx"));
@@ -2692,6 +2727,7 @@ public class CLTParameters {
 		poles.getProperties   (prefix+"_poles",   properties);
 		lwir.getProperties    (prefix+"_lwir",    properties);
 		ofp.getProperties     (prefix+"_ofp_",    properties);
+		imp.getProperties     (prefix+"_imp_",    properties);
 		ilp.getProperties     (prefix+"_ilp_",    properties);
 		inp.getProperties     (prefix+"_inp_",    properties);
 	}
@@ -3695,10 +3731,14 @@ public class CLTParameters {
 		gd.addNumericField("LoG sigma for correlation, mono",                                                           this.gpu_sigma_log_corr_m, 4, 6,"pix",
 				"Use LoG filter to reduce dynamic range of the correlation input to fit into float range");
 		
-		gd.addNumericField("Fat zero (absolute) for phase correlation of color images",                                 this.gpu_fatz, 4, 6,"",
-				"Add squared fat zero to the sum of squared amplitudes, color images");
-		gd.addNumericField("Fat zero (absolute) for phase correlation of monochrome images",                            this.gpu_fatz_m, 4, 6,"",
-				"Add squared fat zero to the sum of squared amplitudes, monochrome images");
+		gd.addNumericField("Fat zero (absolute) for intrascene phase correlation of color images",                                 this.gpu_fatz, 4, 6,"",
+				"Add squared fat zero to the sum of squared amplitudes in intrascene mode, color images");
+		gd.addNumericField("Fat zero (absolute) for intrascene phase correlation of monochrome images",                            this.gpu_fatz_m, 4, 6,"",
+				"Add squared fat zero to the sum of squared amplitudes in intrascene mode, monochrome images");
+		gd.addNumericField("Fat zero (absolute) for interscene phase correlation of color images",                                 this.gpu_fatz_inter, 4, 6,"",
+				"Add squared fat zero to the sum of squared amplitudes in interscene mode, color images");
+		gd.addNumericField("Fat zero (absolute) for interscene phase correlation of monochrome images",                            this.gpu_fatz_inter_m, 4, 6,"",
+				"Add squared fat zero to the sum of squared amplitudes in interscene mode, monochrome images");
 		gd.addMessage     ("--- GPU WOI selection ---");
 
 		gd.addCheckbox    ("Use following WOI for GPU processing (unchecked - ignore WOI dimensions)",                  this.gpu_woi);
@@ -3734,6 +3774,9 @@ public class CLTParameters {
 		gd.addTab         ("O-Flow", "parameters for the interscene Optical FLow calculations");
 		this.ofp.dialogQuestions(gd);
 
+		gd.addTab         ("Inter-Match", "Parameters for full-resolution (no decimation/macrotiles) scene matching");
+		this.imp.dialogQuestions(gd);
+		
 		gd.addTab         ("Inter-LMA", "parameters for the interscene LMA fitting");
 		this.ilp.dialogQuestions(gd);
 		
@@ -4541,6 +4584,8 @@ public class CLTParameters {
 		this.gpu_sigma_log_corr_m = gd.getNextNumber();
 		this.gpu_fatz =             gd.getNextNumber();
 		this.gpu_fatz_m =           gd.getNextNumber();
+		this.gpu_fatz_inter =       gd.getNextNumber();
+		this.gpu_fatz_inter_m =     gd.getNextNumber();
 
 		this.gpu_woi=               gd.getNextBoolean();
 		this.gpu_woi_tx =     (int) gd.getNextNumber();
@@ -4564,6 +4609,7 @@ public class CLTParameters {
 		
 		this.lwir.dialogAnswers(gd);
 		this.ofp.dialogAnswers(gd);
+		this.imp.dialogAnswers(gd);
 		this.ilp.dialogAnswers(gd);
 		this.inp.dialogAnswers(gd);
 

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

@@ -6621,6 +6621,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				QUAD_CLT_AUX.setGPU(GPU_QUAD_AUX);
 			}
 		}
+		CLT_PARAMETERS.setColorProcParameters(COLOR_PROC_PARAMETERS,     false);
+		CLT_PARAMETERS.setColorProcParameters(COLOR_PROC_PARAMETERS_AUX, true);
+		CLT_PARAMETERS.setRGBParameters(RGB_PARAMETERS);
 
 		try {
 			TWO_QUAD_CLT.batchLwirRig(QUAD_CLT, // QuadCLT quadCLT_main,

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

@@ -85,6 +85,7 @@ public class GPUTileProcessor {
 	static String GPU_CONVERT_DIRECT_NAME =        "convert_direct";      // name in C code
 	static String GPU_IMCLT_ALL_NAME =             "imclt_rbg_all";
 	static String GPU_CORRELATE2D_NAME =           "correlate2D";         // name in C code
+	static String GPU_CORRELATE2D_INTER_NAME =     "correlate2D_inter";   // name in C code
 	static String GPU_CORR2D_COMBINE_NAME =        "corr2D_combine";      // name in C code
 	static String GPU_CORR2D_NORMALIZE_NAME =      "corr2D_normalize";    // name in C code
 	static String GPU_TEXTURES_NAME =              "textures_nonoverlap"; // name in C code
@@ -163,6 +164,7 @@ public class GPUTileProcessor {
     CUfunction GPU_CONVERT_DIRECT_kernel =          null; // "convert_direct"
     CUfunction GPU_IMCLT_ALL_kernel =               null; // "imclt_rbg_all"
     CUfunction GPU_CORRELATE2D_kernel =             null; // "correlate2D"
+    CUfunction GPU_CORRELATE2D_INTER_kernel =       null; // "correlate2D_inter"
     CUfunction GPU_CORR2D_COMBINE_kernel =          null; // "corr2D_combine"
     CUfunction GPU_CORR2D_NORMALIZE_kernel =        null; // "corr2D_normalize";
     CUfunction GPU_TEXTURES_kernel =                null; // "textures_nonoverlap"
@@ -314,6 +316,7 @@ public class GPUTileProcessor {
         		GPU_CONVERT_DIRECT_NAME,
         		GPU_IMCLT_ALL_NAME,
         		GPU_CORRELATE2D_NAME,
+        		GPU_CORRELATE2D_INTER_NAME,
         		GPU_CORR2D_COMBINE_NAME,
         		GPU_CORR2D_NORMALIZE_NAME,
         		GPU_TEXTURES_NAME,
@@ -337,27 +340,29 @@ public class GPUTileProcessor {
         GPU_CONVERT_DIRECT_kernel =          functions[0];
         GPU_IMCLT_ALL_kernel =               functions[1];
         GPU_CORRELATE2D_kernel =             functions[2];
-        GPU_CORR2D_COMBINE_kernel =          functions[3];
-        GPU_CORR2D_NORMALIZE_kernel =        functions[4];
-        GPU_TEXTURES_kernel=                 functions[5];
-        GPU_RBGA_kernel=                     functions[6];
-        GPU_ROT_DERIV_kernel =               functions[7];
-        GPU_CALCULATE_TILES_OFFSETS_kernel = functions[8];
-        GPU_CALC_REVERSE_DISTORTION_kernel = functions[9];
+        GPU_CORRELATE2D_INTER_kernel =       functions[3];
+        GPU_CORR2D_COMBINE_kernel =          functions[4];
+        GPU_CORR2D_NORMALIZE_kernel =        functions[5];
+        GPU_TEXTURES_kernel=                 functions[6];
+        GPU_RBGA_kernel=                     functions[7];
+        GPU_ROT_DERIV_kernel =               functions[8];
+        GPU_CALCULATE_TILES_OFFSETS_kernel = functions[9];
+        GPU_CALC_REVERSE_DISTORTION_kernel = functions[10];
      // Kernels to use w/o Dynamic Parallelism    
-        GPU_CLEAR_TEXTURE_LIST_kernel =      functions[10];
-        GPU_MARK_TEXTURE_LIST_kernel =       functions[11];
-        GPU_MARK_TEXTURE_NEIGHBOR_kernel =   functions[12];
-        GPU_GEN_TEXTURE_LIST_kernel =        functions[13];
-        GPU_CLEAR_TEXTURE_RBGA_kernel =      functions[14];
-        GPU_TEXTURES_ACCUMULATE_kernel =     functions[15];
-        GPU_CREATE_NONOVERLAP_LIST_kernel =  functions[16];
+        GPU_CLEAR_TEXTURE_LIST_kernel =      functions[11];
+        GPU_MARK_TEXTURE_LIST_kernel =       functions[12];
+        GPU_MARK_TEXTURE_NEIGHBOR_kernel =   functions[13];
+        GPU_GEN_TEXTURE_LIST_kernel =        functions[14];
+        GPU_CLEAR_TEXTURE_RBGA_kernel =      functions[15];
+        GPU_TEXTURES_ACCUMULATE_kernel =     functions[16];
+        GPU_CREATE_NONOVERLAP_LIST_kernel =  functions[17];
         
 
         System.out.println("GPU kernel functions initialized");
         System.out.println(GPU_CONVERT_DIRECT_kernel.toString());
         System.out.println(GPU_IMCLT_ALL_kernel.toString());
         System.out.println(GPU_CORRELATE2D_kernel.toString());
+        System.out.println(GPU_CORRELATE2D_INTER_kernel.toString());
         System.out.println(GPU_CORR2D_COMBINE_kernel.toString());
         System.out.println(GPU_CORR2D_NORMALIZE_kernel.toString());
         System.out.println(GPU_TEXTURES_kernel.toString());

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

@@ -2384,7 +2384,7 @@ public class Correlation2d {
 	 * @return argmax() relative to the tile center
 	 */
 	
-	public double [] getMaxXYCm( // not used in lwir
+	public static double [] getMaxXYCm( // not used in lwir
 			double [] data,
 			int       data_width,      //  = 2 * transform_size - 1;
 			int       center_row,
@@ -2411,6 +2411,72 @@ public class Correlation2d {
 		return rslt;
 	}
 	
+	public static double [] getMaxXYCm(
+			double [] data,
+			int       data_width,      //  = 2 * transform_size - 1;
+			double    radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
+			int       refine, //  re-center window around new maximum. 0 -no refines (single-pass)
+			boolean   debug)
+	{
+		int data_height = data.length/data_width;
+		int center_xy = (data_width - 1)/2; //  = transform_size - 1;
+		double x0 = center_xy, y0 = center_xy;
+		int imax= 0;
+		for (int i= 1; i < data.length;i++) {
+			if (data[i] > data[imax]) {
+				imax = i;
+			}
+		}
+		double mx = data[imax];
+		x0 = imax % data_width;
+		y0 = imax / data_width;
+		//calculate as "center of mass"
+		if (radius == 0) {
+			double s0 = 0, sx=0,sy = 0;
+			for (int iy = 0; iy < data_height; iy++) {
+				double y = iy - y0;
+				for (int ix = 0; ix < data_width; ix++) {
+					double x = ix - x0;
+					double d =  data[iy * data_width + ix];
+					s0 += d;
+					sx += d * x;
+					sy += d * y;
+				}
+			}
+			x0 += sx / s0;
+			y0 += sy / s0;
+		} else {
+			double radius2 = radius*radius;
+			for (int nref = 0; nref <= refine; nref++) {
+				double s0 = 0, sx=0,sy = 0;
+				for (int iy = 0; iy < data_height; iy++) {
+					double y = iy - y0;
+					for (int ix = 0; ix < data_width; ix++) {
+						double x = ix - x0;
+						double r2= x*x + y*y;
+						if (r2 < radius2) {
+							double r = Math.sqrt(r2);	
+							double d =  data[iy * data_width + ix];
+							d *=  Math.cos(0.5*Math.PI*r/radius);
+							s0 += d;
+							sx += d * x;
+							sy += d * y;
+						}
+					}
+				}
+				x0 += sx / s0;
+				y0 += sy / s0;
+			}
+		}
+		double [] rslt = {x0 - center_xy, y0 - center_xy, mx};
+		if (debug){
+			System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1]);
+		}
+		return rslt;
+	}
+
+	
+	
 	/**
 	 * Analyze 1d correlation (single centerline of the 3D phase correlation combined output
 	 * from all pairs or only diameters to detect double maximum (simultaneous FG+BG)

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

@@ -89,33 +89,44 @@ public class IntersceneLma {
 	}
 
 	public String [] printOldNew(boolean allvectors) {
-		return printOldNew(allvectors, 8, 5);
+		return printOldNew(allvectors, 9, 6);
 	}
 
 	public String [] printOldNew(boolean allvectors, int w, int d) {
-		String fmt1 = String.format("%%%d.%df", w,d);
+		String fmt1 = String.format("%%%d.%df", w+2,d+2); // more for the differences
 		ArrayList<String> lines = new ArrayList<String>();
 		for (int n = ErsCorrection.DP_DVAZ; n < ErsCorrection.DP_NUM_PARS; n+=3) {
 			boolean adj = false;
 			for (int i = 0; i <3; i++) adj |= par_mask[n+i];
 			if (allvectors || adj) {
 				String line = printNameV3(n, false, w,d)+"  (was "+printNameV3(n, true, w,d)+")";
-				line += ", diff="+String.format(fmt1, getV3Diff(n));
+				line += ", diff_last="+String.format(fmt1, getV3Diff(n)[0]);
+				line += ", diff_first="+String.format(fmt1, getV3Diff(n)[1]);
 				lines.add(line);
 			}
 		}
 		return lines.toArray(new String[lines.size()]);
 	}
 	
-	public double getV3Diff(int indx) {
-		double [] v_new = new double[3], v_old = new double[3];
+	/**
+	 * Calculate L2 for 3-vector difference between the adjusted values, this LMA start values
+	 * and "backup" parameters - snapshot before the first adjustment (first calculation of 
+	 * the motion vectors+LMA iteration  
+	 * @param indx offset to the first element of the 3-vector in the full parameters array
+	 * @return a pair of L2 differences {diff_with_this_LMA_start, diff_with_first_lma_start}
+	 */
+	public double [] getV3Diff(int indx) {
+		double [] v_new = new double[3], v_backup = new double[3], v_start = new double[3];
 		System.arraycopy(getFullVector(parameters_vector), indx, v_new, 0, 3);
-		System.arraycopy(backup_parameters_full, indx, v_old, 0, 3);
-		double l2 = 0;
+		System.arraycopy(backup_parameters_full, indx, v_backup, 0, 3);
+		System.arraycopy(parameters_full, indx, v_start, 0, 3);
+		double l2_backup = 0;
+		double l2_start = 0;
 		for (int i = 0; i < 3; i++) {
-			l2 += (v_new[i]-v_old[i]) * (v_new[i]-v_old[i]); 
+			l2_backup += (v_new[i]-v_backup[i]) * (v_new[i]-v_backup[i]); 
+			l2_start +=  (v_new[i]-v_start[i]) *  (v_new[i]-v_start[i]); 
 		}
-		return Math.sqrt(l2);
+		return new double [] {Math.sqrt(l2_start), Math.sqrt(l2_backup)};
 	}
 	
 	public String printNameV3(int indx, boolean initial, int w, int d) {
@@ -129,7 +140,7 @@ public class IntersceneLma {
 	}
 	
 	public static String printNameV3(String name, double[] vector) {
-		return printNameV3(name, vector, 8, 5);
+		return printNameV3(name, vector, 10, 6);
 	}
 	
 	public static String printNameV3(String name, double[] vector, int w, int d) {
@@ -296,15 +307,17 @@ public class IntersceneLma {
 		if (show_intermediate && (debug_level > 0)) {
 			System.out.println("LMA: full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
 		}
-		String [] lines1 = printOldNew(false); // boolean allvectors)
-		System.out.print("iteration="+iter);
-		for (String line : lines1) {
-			System.out.println(line);
+		if (debug_level > 2){ 
+			String [] lines1 = printOldNew(false); // boolean allvectors)
+			System.out.println("iteration="+iter);
+			for (String line : lines1) {
+				System.out.println(line);
+			}
 		}
 		if (debug_level > 0) {
-			if ((debug_level > 1) || (iter == 1) || last_run) {
+			if ((debug_level > 1) ||  last_run) { // (iter == 1) || last_run) {
 				if (!show_intermediate) {
-					System.out.println("LMA: full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
+					System.out.println("LMA: iter="+iter+",   full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
 				}
 				String [] lines = printOldNew(false); // boolean allvectors)
 				for (String line : lines) {
@@ -676,7 +689,11 @@ public class IntersceneLma {
 	}
 	
 	
-	
+	/**
+	 * Combine unmodified parameters with these ones, using parameters mask
+	 * @param vector variable-length adjustable vector, corresponding to a parameter mask
+	 * @return full parameters vector combining adjusted and fixed parameters
+	 */
 	private double [] getFullVector(double [] vector) {
 		double [] full_vector = parameters_full.clone();
 		for (int i = 0; i < par_indices.length; i++) {

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

@@ -923,7 +923,7 @@ public class MultisceneLY {
 						clt_parameters.img_dtt,            // final ImageDttParameters imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 						tp_tasks_scenes[nscene],           // *** will be updated inside from GPU-calculated geometry
 						fcorr_td,                          // fcorrs_td[nscene],                 // [tilesY][tilesX][pair][4*64] transform domain representation of 6 corr pairs
-						scene_gc,     //
+//						scene_gc,     //
 						clt_parameters.gpu_sigma_r,        // 0.9, 1.1
 						clt_parameters.gpu_sigma_b,        // 0.9, 1.1
 						clt_parameters.gpu_sigma_g,        // 0.6, 0.7
@@ -1045,7 +1045,7 @@ public class MultisceneLY {
 					clt_parameters.tileY,          // final int                 debug_tileY,
 					threadsMax,                    // final int                 threadsMax,      // maximal number of threads to launch
 					debug_level + 2); // -1 );              // final int                 globalDebugLevel)
-			image_dtt.convertFcltCorr(
+			ImageDtt.convertFcltCorr(
 					dcorr_tiles, // double [][][] dcorr_tiles,// [tile][sparse, correlation pair][(2*transform_size-1)*(2*transform_size-1)] // if null - will not calculate
 					fclt_corr);  // float  [][][] fclt_corr) //  new float [tilesX * tilesY][][] or null
 

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

@@ -1869,6 +1869,89 @@ public class QuadCLT extends QuadCLTCPU {
 				IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
 	}
 	
+	public ImagePlus renderFromTD (
+			CLTParameters clt_parameters,
+			ColorProcParameters colorProcParameters,
+			EyesisCorrectionParameters.RGBParameters rgbParameters,
+			boolean toRGB,
+			boolean use_reference
+			) {
+        gpuQuad.execImcltRbgAll(isMonochrome(), use_reference); // add ref
+		// get data back from GPU
+		float [][][] iclt_fimg = new float [getNumSensors()][][];
+		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
+			iclt_fimg[ncam] = gpuQuad.getRBG(ncam);
+		}
+
+		int out_width =  gpuQuad.getImageWidth();//   + gpuQuad.getDttSize(); // 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
+		int out_height = gpuQuad.getImageHeight(); // + gpuQuad.getDttSize(); // 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
+		if (isLwir() && colorProcParameters.lwir_autorange) {
+			double rel_low =  colorProcParameters.lwir_low;
+			double rel_high = colorProcParameters.lwir_high;
+			if (!Double.isNaN(getLwirOffset())) {
+				rel_low -=  getLwirOffset();
+				rel_high -= getLwirOffset();
+			}
+			double [] cold_hot =  autorange(
+					iclt_fimg,                         // iclt_data, // double [][][] iclt_data, //  [iQuad][ncol][i] - normally only [][2][] is non-null
+					rel_low,                           // double hard_cold,// matches data, DC (this.lwir_offset)  subtracted
+					rel_high,                          // double hard_hot,   // matches data, DC (this.lwir_offset)  subtracted
+					colorProcParameters.lwir_too_cold, // double too_cold, // pixels per image
+					colorProcParameters.lwir_too_hot,  // double too_hot,  // pixels per image
+					1024); // int num_bins)
+			if (cold_hot != null) {
+				if (!Double.isNaN(getLwirOffset())) {
+					cold_hot[0] += getLwirOffset();
+					cold_hot[1] += getLwirOffset();
+				}
+			}
+			setColdHot(cold_hot); // will be used for shifted images and for texture tiles
+		}
+		/* Prepare 4-channel images*/
+		ImagePlus [] imps_RGB = new ImagePlus[iclt_fimg.length];
+		for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
+            String title=String.format("%s%s-%02d",image_name, sAux(), ncam);
+			imps_RGB[ncam] = linearStackToColor( // probably no need to separate and process the second half with quadCLT_aux (!)
+					clt_parameters,
+					colorProcParameters,
+					rgbParameters,
+					title, // String name,
+					"-D"+clt_parameters.disparity, //String suffix, // such as disparity=...
+					toRGB,
+					!correctionsParameters.jpeg, // boolean bpp16, // 16-bit per channel color mode for result
+					false, // true, // boolean saveShowIntermediate, // save/show if set globally
+					false, // boolean saveShowFinal,        // save/show result (color image?)
+					iclt_fimg[ncam],
+					out_width,
+					out_height,
+					1.0, // scaleExposures[iAux][iSubCam], // double scaleExposure, // is it needed?
+					-1); // debugLevel );
+		}
+
+		// combine to a sliced color image
+		int [] slice_seq = {0,1,3,2}; //clockwise
+		if (imps_RGB.length > 4) {
+			slice_seq = new int [imps_RGB.length];
+			for (int i = 0; i < slice_seq.length; i++) {
+				slice_seq[i] = i;
+			}
+		}
+		int width = imps_RGB[0].getWidth();
+		int height = imps_RGB[0].getHeight();
+		ImageStack array_stack=new ImageStack(width,height);
+		for (int i = 0; i<slice_seq.length; i++){
+			///				if (imps_RGB[slice_seq[i]] != null) {
+			array_stack.addSlice("port_"+slice_seq[i], imps_RGB[slice_seq[i]].getProcessor().getPixels());
+			///				} else {
+			///					array_stack.addSlice("port_"+slice_seq[i], results[slice_seq[i]].getProcessor().getPixels());
+			///				}
+		}
+		ImagePlus imp_stack = new ImagePlus(image_name+sAux()+"GPU-SHIFTED-D"+clt_parameters.disparity, array_stack);
+		imp_stack.getProcessor().resetMinAndMax();
+		return imp_stack;
+	}
+	
+	
 	
 	
 	public ImagePlus processCLTQuadCorrGPU(
@@ -2459,20 +2542,20 @@ public class QuadCLT extends QuadCLTCPU {
 		};
 		quadCLT_main.getGPU().setLpfRbg( // constants memory - same for all cameras
 				lpf_rgb,
-				debugLevel > -1); // -3
+				debugLevel > 2); // -3
 
 		float [] lpf_flat = image_dtt.floatGetCltLpfFd(clt_parameters.getGpuCorrSigma(is_mono));
 
 		quadCLT_main.getGPU().setLpfCorr(// constants memory - same for all cameras
 				"lpf_corr", // String const_name, // "lpf_corr"
 				lpf_flat,
-				debugLevel > -1); // -3
+				debugLevel > 2); // -3
 
 		float [] lpf_rb_flat = image_dtt.floatGetCltLpfFd(clt_parameters.getGpuCorrRBSigma(is_mono));
 		quadCLT_main.getGPU().setLpfCorr(// constants memory - same for all cameras
 				"lpf_rb_corr", // String const_name, // "lpf_corr"
 				lpf_rb_flat,
-				debugLevel > -1); // -3
+				debugLevel > 2); // -3
 
 		final boolean use_aux = false; // currently GPU is configured for a single quad camera
 

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

@@ -6914,7 +6914,7 @@ public class QuadCLTCPU {
 		  float []   alpha = null; // (0..1.0)
 		  if (iclt_data.length > 3) alpha = iclt_data[3];
 		  if (isLwir()) {
-			  if (colorProcParameters.lwir_pseudocolor) {
+			  if (!colorProcParameters.lwir_pseudocolor) {
 				  ImageProcessor ip= new FloatProcessor(width,height);
 				  ip.setPixels(iclt_data[0]);
 				  ip.resetMinAndMax();
@@ -7040,7 +7040,7 @@ public class QuadCLTCPU {
 			  }
 		  }
 		  if (isLwir()) {
-			  if (colorProcParameters.lwir_pseudocolor) {
+			  if (!colorProcParameters.lwir_pseudocolor) {
 				  ImageProcessor ip= new FloatProcessor(width,height);
 				  float [] pixels = new float [iclt_data[0].length];
 				  for (int i = 0; i < pixels.length; i++) {
@@ -12938,7 +12938,6 @@ public class QuadCLTCPU {
 		  int mcorr_sel = save_corr ? Correlation2d.corrSelEncode(clt_parameters.img_dtt, getNumSensors()) : 0;
 		  TpTask[] tp_tasks = GpuQuad.setTasks( // null on geometryCorrection 
 				  num_sensors,                  // final int                      num_cams,
-//				  image_dtt.getTransformSize(), // final int                      transform_size,
 				  disparity_array,              // final double [][]	           disparity_array,  // [tilesY][tilesX] - individual per-tile expected disparity
 				  disparity_corr,               // final double                   disparity_corr,
 				  tile_op,                      // final int [][]                 tile_op,          // [tilesY][tilesX] - what to do - 0 - nothing for this tile
@@ -12953,7 +12952,7 @@ public class QuadCLTCPU {
 		  
 		  double [][][][][] clt_data =  null;
 		  double [] tile_corr_weights = null;
-			double[][] dbg_tilts =       null;
+			double[][] dbg_tilts =      null;
 		  
 		  final double gpu_sigma_corr =     clt_parameters.getGpuCorrSigma(isMonochrome());
 		  final double gpu_sigma_rb_corr =  isMonochrome()? 1.0 : clt_parameters.gpu_sigma_rb_corr;
@@ -12967,7 +12966,6 @@ public class QuadCLTCPU {
 			  // set tasks for all non-NaN target disparities
 			  TpTask [] tp_tasks_target = GpuQuad.setTasks(
 					  num_sensors,                  // final int                      num_cams,
-//					  image_dtt.getTransformSize(), // final int                      transform_size,
 					  disparity_array,              // final double [][]	           disparity_array,  // [tilesY][tilesX] - individual per-tile expected disparity
 					  disparity_corr,               // final double                   disparity_corr,
 					  null, // tile_op,             // final int [][]                 tile_op,          // [tilesY][tilesX] - what to do - 0 - nothing for this tile
@@ -13025,7 +13023,7 @@ public class QuadCLTCPU {
 						  clt_parameters.img_dtt,            // final ImageDttParameters imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 						  tp_tasks, // *** will be updated inside from GPU-calculated geometry
 						  fcorr_td, // fcorrs_td[nscene],                 // [tilesY][tilesX][pair][4*64] transform domain representation of 6 corr pairs
-						  geometryCorrection, //
+//						  geometryCorrection, //
 						  clt_parameters.gpu_sigma_r,        // 0.9, 1.1
 						  clt_parameters.gpu_sigma_b,        // 0.9, 1.1
 						  clt_parameters.gpu_sigma_g,        // 0.6, 0.7
@@ -13208,7 +13206,7 @@ public class QuadCLTCPU {
 							new String[] {"tiltX","tiltY","center","weight"});
 			  }
 			  float  [][][] fclt_corr = new float [dcorr_tiles.length][][]; // dcorr_tiles== null
-				image_dtt.convertFcltCorr(
+			  ImageDtt.convertFcltCorr(
 						dcorr_tiles, // double [][][] dcorr_tiles,// [tile][sparse, correlation pair][(2*transform_size-1)*(2*transform_size-1)] // if null - will not calculate
 						fclt_corr);  // float  [][][] fclt_corr) //  new float [tilesX * tilesY][][] or null
 				float [][] dbg_corr_rslt_partial = ImageDtt.corr_partial_dbg( // not used in lwir
@@ -13222,7 +13220,6 @@ public class QuadCLTCPU {
 						threadsMax, // final int               threadsMax,     // maximal number of threads to launch
 						debugLevel); // final int               globalDebugLevel)
 				
-//				String [] titles_ind_corr = image_dtt.getCorrelation2d().getCorrTitles();
 				String [] titles = new String [dbg_corr_rslt_partial.length]; // dcorr_tiles[0].length];
 				int ind_length = image_dtt.getCorrelation2d().getCorrTitles().length;