Refactored 2 GPU-related classes, adding CPU-only (GPU code requires

deeper updates for 16 sensors) methods for interscene accumulation.

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

@@ -7161,6 +7161,7 @@ List calibration
     	imp.setProperty("focalLength", ""+subCam.focalLength);
     	imp.setProperty("focalLength_units", "mm");
     	imp.setProperty("pixelSize", ""+subCam.pixelSize);
+    	imp.setProperty("lineTime",  ""+subCam.lineTime);
     	imp.setProperty("pixelSize_units", "um");
     	imp.setProperty("distortionA8", ""+subCam.distortionA8);
     	imp.setProperty("distortionA7", ""+subCam.distortionA7);
@@ -7380,6 +7381,17 @@ List calibration
         	subCam.distortionRadius=        Double.parseDouble((String) imp.getProperty("distortionRadius"));
         	subCam.focalLength=             Double.parseDouble((String) imp.getProperty("focalLength"));
         	subCam.pixelSize=               Double.parseDouble((String) imp.getProperty("pixelSize"));
+        	if (imp.getProperty("lineTime") != null) {
+            	subCam.pixelSize=               Double.parseDouble((String) imp.getProperty("lineTime"));
+        	} else { // fix older saved files
+        		if (subCam.pixelSize < 5.0) {
+        			subCam.pixelSize=3.638E-5;
+	        	} else if (distortionCalibrationData.eyesisCameraParameters.getSensorWidth(numSensor) == 640){ // Boson
+	        		subCam.lineTime = 2.7778e-05; // 12um pixel, Boson
+	        	} else {
+	        		subCam.lineTime = 7.8e-05; // 12um pixel, Lepton (may7 be wrong)
+	        	}
+        	}
         	if (imp.getProperty("distortionA8")!=null) {
         		subCam.distortionA8=            Double.parseDouble((String) imp.getProperty("distortionA8"));
         	} else subCam.distortionA8=0.0;

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

@@ -15706,6 +15706,11 @@ public class PixelMapping {
     	public double psi;     // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target roll
 		public double focalLength=4.5;
 		public double pixelSize=  2.2; //um
+		public double lineTime =  3.638E-5; // 2.7778e-05 for Boson
+		
+		public boolean monochrome = false;
+		public boolean lwir =       false;
+		
 		public double distortionRadius=  2.8512; // mm - half width of the sensor
 		public double distortionA8=0.0; //r^8 (normalized to focal length or to sensor half width?)
 		public double distortionA7=0.0; //r^7 (normalized to focal length or to sensor half width?)
@@ -16301,6 +16306,9 @@ public class PixelMapping {
 
 	    public void setSensorDataFromImageStack(ImagePlus imp){
 //	    	int corrX=0,corrY=1,corrMask=2;
+	    	boolean need_lineTime_fix =   false; // will use sensor default if not provided, 3.638E-5 for RGB and 2.7778e-05 for Boson
+	    	boolean need_monochrome_fix = false; // will use sensor default if not provided, 3.638E-5 for RGB and 2.7778e-05 for Boson
+	    	boolean need_lwir_fix =       false; // will use sensor default if not provided, 3.638E-5 for RGB and 2.7778e-05 for Boson
 	    	if (imp == null){
 	    		String msg="Sensor Calibration image is null";
 	    		IJ.showMessage("Error",msg);
@@ -16325,10 +16333,29 @@ public class PixelMapping {
 	    	        "heading",
 	    	        "elevation",
 	    	        "roll",
-	    	        "channel"
+	    	        "channel",
+	        		"lineTime",   // optional
+	        		"monochrome", // optional
+	        		"lwir"        // optional
 	        		};
 	        for (int i=0; i<requiredProperties.length;i++) if (imp.getProperty(requiredProperties[i])==null){
 	    		String msg="Required property "+requiredProperties[i]+" is not defined in "+imp.getTitle();
+	    		// is it 
+	    		if (requiredProperties[i].equals("lineTime")) {
+	    			System.out.println(requiredProperties[i]+" is not provided, will use default");
+	    			need_lineTime_fix = true;
+	    			continue;
+	    		}
+	    		if (requiredProperties[i].equals("monochrome")) {
+	    			System.out.println(requiredProperties[i]+" is not provided, will use default");
+	    			need_monochrome_fix = true;
+	    			continue;
+	    		}
+	    		if (requiredProperties[i].equals("lwir")) {
+	    			System.out.println(requiredProperties[i]+" is not provided, will use default");
+	    			need_lwir_fix = true;
+	    			continue;
+	    		}
 	    		IJ.showMessage("Error",msg);
 	    		throw new IllegalArgumentException (msg);
 	        }
@@ -16352,6 +16379,43 @@ public class PixelMapping {
 	        this.distortionRadius= Double.parseDouble((String) imp.getProperty("distortionRadius"));
 	        this.focalLength=      Double.parseDouble((String) imp.getProperty("focalLength"));
 	        this.pixelSize=        Double.parseDouble((String) imp.getProperty("pixelSize"));
+	        if (need_lineTime_fix) {
+	        	if (this.pixelSize < 5.0) {
+	        		this.lineTime = 3.638E-5;
+	        	} else if (this.pixelCorrectionWidth == 640){ // Boson
+	        		this.lineTime = 2.7778e-05; // 12um pixel, Boson
+	        	} else {
+	        		this.lineTime = 7.8e-05; // 12um pixel, Lepton (may7 be wrong)
+	        	}
+	        } else {
+		        this.lineTime=        Double.parseDouble((String) imp.getProperty("lineTime"));
+	        }
+
+	        if (need_monochrome_fix) {
+	        	if (this.pixelSize < 5.0) {
+	        		this.monochrome = false;
+	        	} else if (this.pixelCorrectionWidth == 640){ // Boson
+	        		this.monochrome = true; // 12um pixel, Boson
+	        	} else {
+	        		this.monochrome = true; // 12um pixel, Lepton (may7 be wrong)
+	        	}
+	        } else {
+		        this.monochrome=        Boolean.parseBoolean((String) imp.getProperty("monochrome"));
+	        }
+	        
+	        
+	        if (need_lwir_fix) {
+	        	if (this.pixelSize < 5.0) {
+	        		this.lwir = false;
+	        	} else if (this.pixelCorrectionWidth == 640){ // Boson
+	        		this.lwir = true; // 12um pixel, Boson
+	        	} else {
+	        		this.lwir = true; // 12um pixel, Lepton (may7 be wrong)
+	        	}
+	        } else {
+		        this.lwir=        Boolean.parseBoolean((String) imp.getProperty("lwir"));
+	        }
+	        
 	        if (imp.getProperty("distortionA8")!=null)	this.distortionA8=     Double.parseDouble((String) imp.getProperty("distortionA8"));
 	        else this.distortionA8= 0.0;
 	        if (imp.getProperty("distortionA7")!=null)	this.distortionA7=     Double.parseDouble((String) imp.getProperty("distortionA7"));

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

@@ -44,6 +44,7 @@ import java.util.Properties;
     	public double psi;     // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target
 		public double focalLength=4.5;
 		public double pixelSize=  2.2; //um
+		public double lineTime =  3.638E-5; // 2.7778e-05 for Boson
 		public double distortionRadius=  2.8512; // mm - half width of the sensor
 		public double distortionA8=0.0; //r^8 (normalized to focal length or to sensor half width?)
 		public double distortionA7=0.0; //r^7 (normalized to focal length or to sensor half width?)
@@ -100,6 +101,7 @@ import java.util.Properties;
     			double psi,      // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target
     			double focalLength,
     			double pixelSize,//um
+    			double lineTime, //  =  3.638E-5; // 2.7778e-05 for Boson
     			double distortionRadius, //mm - half width of the sensor
     			double distortionA8, // r^8
     			double distortionA7, // r^7
@@ -183,6 +185,7 @@ import java.util.Properties;
     				this.psi,
     	    		this.focalLength,
     	    		this.pixelSize,
+    	    		this.lineTime,
     	    		this.distortionRadius,
     	    		this.distortionA8,
     	    		this.distortionA7,
@@ -227,6 +230,7 @@ import java.util.Properties;
     		properties.setProperty(prefix+"psi",                 this.psi+"");
 			properties.setProperty(prefix+"focalLength",         this.focalLength+"");
 			properties.setProperty(prefix+"pixelSize",           this.pixelSize+"");
+			properties.setProperty(prefix+"lineTime",            this.lineTime+"");
 			properties.setProperty(prefix+"distortionRadius",    this.distortionRadius+"");
 			properties.setProperty(prefix+"distortionA8",        this.distortionA8+"");
 			properties.setProperty(prefix+"distortionA7",        this.distortionA7+"");
@@ -288,6 +292,8 @@ import java.util.Properties;
 				this.focalLength=Double.parseDouble(properties.getProperty(prefix+"focalLength"));
 			if (properties.getProperty(prefix+"pixelSize")!=null)
 				this.pixelSize=Double.parseDouble(properties.getProperty(prefix+"pixelSize"));
+			if (properties.getProperty(prefix+"lineTime")!=null)
+				this.lineTime=Double.parseDouble(properties.getProperty(prefix+"lineTime"));
 			if (properties.getProperty(prefix+"distortionRadius")!=null)
 				this.distortionRadius=Double.parseDouble(properties.getProperty(prefix+"distortionRadius"));
 			if (properties.getProperty(prefix+"distortionA8")!=null)

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

@@ -104,7 +104,11 @@ import ij.process.ImageProcessor;
 	    	  not_empty = true;
 	    	  fpixels=new float[pixels[i].length];
 	    	  for (j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
-	    	  array_stack.addSlice(titles[i], fpixels);
+	    	  if (i < titles.length) {
+	    		  array_stack.addSlice(titles[i], fpixels);
+	    	  } else {
+	    		  array_stack.addSlice("slice-"+i, fpixels);
+	    	  }
 	      }
 	      if (not_empty) {
 	    	  ImagePlus imp_stack = new ImagePlus(title, array_stack);

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

@@ -1223,7 +1223,8 @@ public class EyesisDCT {
 			  ImageDtt image_dtt = new ImageDtt(
 					  4, // 4 sensors, will not be used here
 					  dctParameters.dct_size,
-					  null, // FIXME: needs ImageDttParameters (clt_parameters.img_dtt), 
+					  null, // FIXME: needs ImageDttParameters (clt_parameters.img_dtt),
+					  false, // aux
 					  false, // mono
 					  false, // lwir
 					  1.0); // Bayer( not monochrome), scale correlation strengths

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

+package com.elphel.imagej.gpu;
+
+public class TpTask {
+	public int   task; // [0](+1) - generate 4 images, [4..9]+16..+512 - correlation pairs, 2 - generate texture tiles
+	public float target_disparity;
+    public int num_sensors = 4;
+	public int ty;
+	public int tx;
+	public float[][] xy = null;
+	public float[][] xy_aux = null;
+	public float [][] disp_dist = null;
+	public TpTask() {}
+
+	public TpTask(int num_sensors, int tx, int ty, float target_disparity, int task ) {
+		this.tx = tx;
+		this.ty = ty;
+		this.target_disparity = target_disparity;
+		this.task = task;
+		this.num_sensors = num_sensors; // will not be encoded
+		this.disp_dist = new float [num_sensors][4];
+	}
+	/**
+	 * Initialize from the float array (read from the GPU)
+	 * @param flt float array containing tasks data
+	 * @param indx task number to use
+	 */
+	public TpTask(float [] flt, int indx, boolean use_aux)
+	{
+		task =    Float.floatToIntBits(flt[indx++]);
+		int txy = Float.floatToIntBits(flt[indx++]);
+		ty = txy >> 16;
+		tx = txy & 0xffff;
+		if (use_aux) {
+			xy_aux = new float[num_sensors][2];
+    		for (int i = 0; i < num_sensors; i++) {
+    			xy_aux[i][0] = flt[indx++];
+    			xy_aux[i][1] = flt[indx++];
+    		}
+		} else {
+			xy = new float[num_sensors][2];
+    		for (int i = 0; i < num_sensors; i++) {
+    			xy[i][0] = flt[indx++];
+    			xy[i][1] = flt[indx++];
+    		}
+		}
+		target_disparity = flt[indx++];
+		disp_dist = new float [num_sensors][4];
+		for (int i = 0; i < num_sensors; i++) {
+			for (int j = 0; j < 4; j++) {
+				disp_dist[i][j] = flt[indx++];
+			}
+		}
+	}
+	public float [][] getDispDist(){
+		return disp_dist;
+	}
+	public double [][] getDoubleDispDist(){
+		if (disp_dist == null) { // can it happen?
+			return null;
+		}
+		double [][] ddisp_dist = new double [disp_dist.length][disp_dist[0].length];
+		for (int nsens = 0; nsens < disp_dist.length; nsens++) {
+			for (int i = 0; i < disp_dist[nsens].length; i++) {
+				ddisp_dist[nsens][i] = disp_dist[nsens][i]; 
+			}
+		}
+		return ddisp_dist;
+	}
+	
+	public float [][] getXY(boolean use_aux){
+		return use_aux? xy_aux : xy;
+	}
+	public double [][] getDoubleXY(boolean use_aux){
+		float [][] fXY = getXY(use_aux);
+		if (fXY == null) {
+			return null;
+		}
+		double [][] dXY = new double [fXY.length][fXY[0].length];
+		for (int nsens = 0; nsens < fXY.length; nsens++) {
+			for (int i = 0; i < fXY[nsens].length; i++) {
+				dXY[nsens][i] = fXY[nsens][i]; 
+			}
+		}
+		return dXY;
+	}
+	
+	
+	
+	public int getTileY(){
+		return ty;
+	}
+	public int getTileX(){
+		return tx;
+	}
+	public int getTask() {
+		return task;
+	}
+	public double getTargetDisparity() {
+		return target_disparity;
+	}
+
+	// convert this class instance to float array to match layout of the C struct
+	public float [] asFloatArray(boolean use_aux) {
+		float [] flt = new float [GPUTileProcessor.TPTASK_SIZE];
+		return asFloatArray(flt, 0, use_aux);
+	}
+	// convert this class instance to float array to match layout of the C struct,
+	// fill existing float array from the specified index
+	public float [] asFloatArray(float [] flt, int indx, boolean use_aux) {
+		flt[indx++] = Float.intBitsToFloat(task);
+		flt[indx++] = Float.intBitsToFloat(tx + (ty << 16));
+		float [][] offsets = use_aux? this.xy_aux: this.xy;
+		for (int i = 0; i < num_sensors; i++) {
+			if (offsets != null) {
+				flt[indx++] = offsets[i][0];
+				flt[indx++] = offsets[i][1];
+			} else {
+				indx+= 2;
+			}
+		}
+		flt[indx++] = this.target_disparity;
+		/*
+		for (int i = 0; i < NUM_CAMS; i++) { // actually disp_dist will be initialized by the GPU
+			indx+= 4;
+			flt[indx++] = disp_dist[i][0];
+			flt[indx++] = disp_dist[i][1];
+			flt[indx++] = disp_dist[i][2];
+			flt[indx++] = disp_dist[i][3];
+		}
+		*/
+		return flt;
+	}
+}
\ No newline at end of file

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

@@ -378,10 +378,22 @@ public class CLTPass3d{
 			}
 			return has_lma;
 		}
+
 		public void setLMA(boolean [] has_lma) {// use for combo tiles
 			this.has_lma = has_lma;
 		}
 
+		public void resetLMA() {
+			this.has_lma = null;
+		}
+		public void setLMA(double [] disparity_lma) {// use for combo tiles
+			this.has_lma = new boolean [disparity_lma.length];
+			for (int i = 0; i < disparity_lma.length; i++) {
+				this.has_lma[i] = !Double.isNaN(disparity_lma[i]);
+			}
+		}
+		
+		
 		public void fixNaNDisparity()
 		{
 			fixNaNDisparity(

src/main/java/com/elphel/imagej/tileprocessor/Clt1d.java

@@ -50,6 +50,7 @@ public class Clt1d {
 				nSens,
 				transform_size,
 				null, // FIXME: needs ImageDttParameters (clt_parameters.img_dtt), 
+				false, // aux
 				false,
 				false,
 				1.0);

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

@@ -1285,6 +1285,7 @@ public class Correlation2d {
      * @param col_weights RBG color weights
      * @return [pair][quadrant][index]
      */
+    @Deprecated
     public double [][][]  correlateCompositeTD(
     		double [][][][][][] clt_data,
     		int                 tileX,
@@ -1310,14 +1311,50 @@ public class Correlation2d {
 
     /**
      * Calculate all required image pairs phase correlation, stay in Transform Domain
-     * @param clt_data_tile aberration-corrected FD CLT data for one tile [camera][color][quadrant][index]
+     * @param clt_data aberration-corrected FD CLT data [camera][color][tileY][tileX][quadrant][index]
+     * @param tileX tile to extract X index
+     * @param tileY tile to extract Y index
      * @param pairs_mask bimask of required pairs
+     * @param lpf_rb optional low-pass filter - extra LPF for red and blue
+     * @param scale_value   scale correlation results to compensate for lpf changes and other factors
+     * @param col_weights RBG color weights
+     * @return [pair][quadrant][index]
+     */
+    public double [][][]  correlateCompositeTD(
+    		double [][][][][][] clt_data,
+    		int                 tileX,
+    		int                 tileY,
+    		boolean []          pairs_mask,
+    		double []           lpf_rb, // extra lpf for red and blue (unused for mono) or null
+    		double              scale_value, // scale correlation value
+    		double []           col_weights) {
+    	double [][][][]     clt_data_tile = new double[clt_data.length][][][]; // [camera][color][quadrant][index]
+    	for (int ncam = 0; ncam < clt_data.length; ncam++) if (clt_data[ncam] != null){
+    		clt_data_tile[ncam] = new double[clt_data[ncam].length][][];
+        	for (int ncol = 0; ncol < clt_data[ncam].length; ncol++) if ((clt_data[ncam][ncol] != null) && (clt_data[ncam][ncol][tileY] != null)){
+        		clt_data_tile[ncam][ncol] = clt_data[ncam][ncol][tileY][tileX];
+        	}
+    	}
+    	return correlateCompositeTD(
+    		    		clt_data_tile,
+    		    		pairs_mask, // already decoded so bit 0 - pair 0
+    		    		lpf_rb,
+    		    		scale_value,
+    		    		col_weights);
+    }
+    
+    
+    /**
+     * Calculate all required image pairs phase correlation, stay in Transform Domain
+     * @param clt_data_tile aberration-corrected FD CLT data for one tile [camera][color][quadrant][index]
+     * @param pairs_mask bimask of required pairs NOW USE boolean array and new pairs
      * @param lpf optional final low-pass filter 
      * @param lpf_rb optional low-pass filter (extra) for R,B components
      * @param scale_value   scale correlation results to compensate for lpf changes and other factors
      * @param col_weights RBG color weights
      * @return [pair][quadrant][index]
      */
+    @Deprecated
     public double [][][]  correlateCompositeTD(
     		double [][][][]     clt_data_tile,
     		int                 pairs_mask, // already decoded so bit 0 - pair 0
@@ -1341,6 +1378,42 @@ public class Correlation2d {
     	return pairs_corr;
     }
 
+    
+    /**
+     * Calculate all required image pairs phase correlation, stay in Transform Domain
+     * @param clt_data_tile aberration-corrected FD CLT data for one tile [camera][color][quadrant][index]
+     * @param pairs_mask bimask of required pairs
+     * @param lpf optional final low-pass filter 
+     * @param lpf_rb optional low-pass filter (extra) for R,B components
+     * @param scale_value   scale correlation results to compensate for lpf changes and other factors
+     * @param col_weights RBG color weights
+     * @return [pair][quadrant][index]
+     */
+    public double [][][]  correlateCompositeTD(
+    		double [][][][]     clt_data_tile,
+    		boolean[]           pairs_mask, // already decoded so bit 0 - pair 0
+    		double []           lpf_rb, // extra lpf for red and blue (unused for mono) or null
+    		double              scale_value, // scale correlation value
+    		double []           col_weights) {
+    	if (clt_data_tile == null) return null;
+    	double [][][] pairs_corr = new double [getNumPairs()][][];
+    	for (int npair = 0; npair < pairs_corr.length; npair++) if (pairs_mask[npair]) {
+    		int [] pair = getPair(npair);
+    		int ncam1 = pair[0]; // start 
+    		int ncam2 = pair[1]; // end
+    		if ((ncam1 < clt_data_tile.length) && (clt_data_tile[ncam1] != null) && (ncam2 < clt_data_tile.length) && (clt_data_tile[ncam2] != null)) {
+    			pairs_corr[npair] =  correlateCompositeTD(
+    					clt_data_tile[ncam1], // double [][][] clt_data1,
+    					clt_data_tile[ncam2], // double [][][] clt_data2,
+    		    		lpf_rb,               // double []     lpf_rb,
+    		    		scale_value,
+    		    		col_weights);         // double []     col_weights,
+    		}
+    	}
+    	return pairs_corr;
+    }
+    
+    
     /**
      * Calculate color channels FD phase correlations, mix results with weights, apply optional low-pass filter
      * No transposing or rotation

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

@@ -639,6 +639,8 @@ public class ErsCorrection extends GeometryCorrection {
 	public ErsCorrection(GeometryCorrection gc, boolean deep) {
 		debugLevel =           gc.debugLevel;
 		line_time =            gc.line_time;            // 36.38! //26.5E-6; // duration of sensor scan line (for ERS)
+		monochrome =           gc.monochrome;
+		lwir =                 gc.lwir;
 		pixelCorrectionWidth=  gc.pixelCorrectionWidth; // 2592;   // virtual camera center is at (pixelCorrectionWidth/2, pixelCorrectionHeight/2)
 		pixelCorrectionHeight= gc.pixelCorrectionHeight; // 1936;
 		focalLength =          gc.focalLength; // =FOCAL_LENGTH;

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

@@ -64,6 +64,9 @@ public class GeometryCorrection {
 */	
 	public int    debugLevel = 0;
 	public double line_time =  36.38E-6; // 26.5E-6; // duration of sensor scan line (for ERS) Wrong, 36.38us (change and re-run ERS
+	// Boson - 27.7778E-6 (750/27E6)
+	public boolean monochrome = false;
+	public boolean lwir =       false;
 	public int    pixelCorrectionWidth=2592;   // virtual camera center is at (pixelCorrectionWidth/2, pixelCorrectionHeight/2)
 	public int    pixelCorrectionHeight=1936;
 
@@ -117,6 +120,15 @@ public class GeometryCorrection {
 	public int getNumSensors() {
 		return numSensors;
 	}
+	
+	public boolean isMonochrome() {
+		return monochrome;
+	}
+
+	public boolean isLwir() {
+		return lwir;
+	}
+	
 	protected double [][] get_rXY_ideal(){
 		if (rXY_ideal == null) {
 			if (numSensors == 4) {
@@ -798,7 +810,7 @@ public class GeometryCorrection {
 			ro.aux_tilt =       this.aux_tilt;
 			ro.aux_roll =       this.aux_roll;
 			ro.aux_zoom =       this.aux_zoom;
-			ro.full_par_index = this.full_par_index.clone();
+			ro.full_par_index = (this.full_par_index == null)?null:this.full_par_index.clone();
 			ro.par_scales =     this.par_scales.clone();
 			return ro;
 		}
@@ -1477,8 +1489,10 @@ public class GeometryCorrection {
 			double distortionRadius,
 			int    pixelCorrectionWidth,   // virtual camera center is at (pixelCorrectionWidth/2, pixelCorrectionHeight/2)
 			int    pixelCorrectionHeight,
-			double pixelSize
-
+			double pixelSize,
+			double line_time,
+			boolean monochrome,
+			boolean lwir
 			)	{
 		if (!Double.isNaN(focalLength))      this.focalLength = focalLength;
 		if (!Double.isNaN(distortionC))      this.distortionC = distortionC;
@@ -1492,6 +1506,9 @@ public class GeometryCorrection {
 		if (pixelCorrectionWidth >= 0)       this.pixelCorrectionWidth = pixelCorrectionWidth;
 		if (pixelCorrectionHeight >= 0)      this.pixelCorrectionHeight = pixelCorrectionHeight;
 		if (!Double.isNaN(pixelSize))        this.pixelSize = pixelSize;
+		if (!Double.isNaN(line_time))        this.line_time = line_time;
+		this.monochrome = monochrome;
+		this.lwir =       lwir;
 		//	imp.setProperty("distortion_formula",  "(normalized by distortionRadius in mm) Rdist/R=A8*R^7+A7*R^6+A6*R^5+A5*R^4+A*R^3+B*R^2+C*R+(1-A6-A7-A6-A5-A-B-C)");
 		//	imp.setProperty("distortionRadius", ""+subCam.distortionRadius);
 	}
@@ -1671,6 +1688,9 @@ public class GeometryCorrection {
 		System.out.println("pixelCorrectionWidth =\t"+  pixelCorrectionWidth+"\tpix");
 		System.out.println("pixelCorrectionHeight =\t"+ pixelCorrectionHeight+"\tpix");
 		System.out.println("pixelSize =\t"+             pixelSize+"\tum");
+		System.out.println("lineTime =\t"+             (1E6*line_time)+"\tus");
+		System.out.println("monochrome =\t"+            monochrome+"\t");
+		System.out.println("lwir =\t"+                  lwir+"\t");
 		System.out.println("distortionRadius =\t"+      distortionRadius+"\tmm");
 		System.out.println("'=== Common input parameters ===");
 		System.out.println("distortionA8 =\t"+ distortionA8);

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

@@ -5,24 +5,28 @@ import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.gpu.GPUTileProcessor;
+import com.elphel.imagej.gpu.GpuQuad;
+import com.elphel.imagej.gpu.TpTask;
 
 //import Jama.Matrix;
 
 public class ImageDtt extends ImageDttCPU {
 	public boolean debug_strengths = false; // true;
-	private final GPUTileProcessor.GpuQuad gpuQuad;
+	private final GpuQuad gpuQuad;
 
 	public ImageDtt(
 			int numSensors,
 			int transform_size,
 			ImageDttParameters imgdtt_params,
+			boolean aux,
 			boolean mono,
 			boolean lwir,
 			double scale_strengths,
-			GPUTileProcessor.GpuQuad gpuQuadIn){
+			GpuQuad gpuQuadIn){
 		super ( numSensors,
 				transform_size,
 				imgdtt_params,
+				aux,
 				mono,
 				lwir,
 				scale_strengths);
@@ -33,19 +37,21 @@ public class ImageDtt extends ImageDttCPU {
 			int numSensors,
 			int transform_size,
 			ImageDttParameters imgdtt_params,
+			boolean aux,
 			boolean mono,
 			boolean lwir,
 			double scale_strengths){
 		super ( numSensors,
 				transform_size,
 				imgdtt_params,
+				aux,
 				mono,
 				lwir,
 				scale_strengths);
 		gpuQuad = null;
 	}
 	
-	public GPUTileProcessor.GpuQuad getGPU() {
+	public GpuQuad getGPU() {
 		return this.gpuQuad;
 	}
 	
@@ -272,7 +278,7 @@ public class ImageDtt extends ImageDttCPU {
 		final boolean use_main = geometryCorrection_main != null;
 		boolean [] used_corrs = new boolean[1];
 	    final int all_pairs = imgdtt_params.dbg_pair_mask; //TODO: use tile tasks
-		final GPUTileProcessor.TpTask[] tp_tasks =  gpuQuad.setTpTask(
+		final TpTask[] tp_tasks =  gpuQuad.setTpTask(
 				disparity_array, // final double [][]  disparity_array,  // [tilesY][tilesX] - individual per-tile expected disparity
 				disparity_corr,  // final double       disparity_corr,
 				used_corrs,      // final boolean []   need_corrs,       // should be initialized to boolean[1] or null
@@ -319,13 +325,13 @@ public class ImageDtt extends ImageDttCPU {
 		gpuQuad.execSetTilesOffsets(); // prepare tiles offsets in GPU memory
 
 		if ((fdisp_dist != null) || (fpxpy != null)) {
-			final GPUTileProcessor.TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main);
+			final TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main);
 			for (int ithread = 0; ithread < threads.length; ithread++) {
 				threads[ithread] = new Thread() {
 					@Override
 					public void run() {
 						for (int indx_tile = ai.getAndIncrement(); indx_tile < tp_tasks_full.length; indx_tile = ai.getAndIncrement()) {
-							GPUTileProcessor.TpTask task = tp_tasks_full[indx_tile];
+							TpTask task = tp_tasks_full[indx_tile];
 							if (fdisp_dist != null) {
 								fdisp_dist[task.getTileY()][task.getTileX()] = task.getDispDist();
 							}
@@ -688,7 +694,7 @@ public class ImageDtt extends ImageDttCPU {
 			final int                 globalDebugLevel)
 	{
 		// prepare tasks
-       	GPUTileProcessor.TpTask[] tp_tasks =  gpuQuad.setInterTasks(
+       	TpTask[] tp_tasks =  gpuQuad.setInterTasks(
        			pXpYD,              // final double [][]         pXpYD, // per-tile array of pX,pY,disparity triplets (or nulls)
        			geometryCorrection, // final GeometryCorrection  geometryCorrection,
        			disparity_corr,     // final double              disparity_corr,
@@ -701,7 +707,6 @@ public class ImageDtt extends ImageDttCPU {
     			fcorr_td,        // [tilesY][tilesX][pair][4*64] transform domain representation of 6 corr pairs
     			fcorr_combo_td,  // [4][tilesY][tilesX][pair][4*64] TD of combo corrs: quad, cross, hor,vert
     			geometryCorrection,
-//    			disparity_corr,   // disparity offset at infinity
     			margin,           // do not use tiles if their centers are closer to the edges
     			gpu_sigma_r,     // 0.9, 1.1
     			gpu_sigma_b,     // 0.9, 1.1
@@ -718,7 +723,7 @@ public class ImageDtt extends ImageDttCPU {
 
 	public void quadCorrTD(
 			final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
-			final GPUTileProcessor.TpTask[] tp_tasks,
+			final TpTask[] tp_tasks,
 			final float  [][][][]     fcorr_td,        // [tilesY][tilesX][pair][4*64] transform domain representation of 6 corr pairs
 			final float  [][][][]     fcorr_combo_td,  // [4][tilesY][tilesX][pair][4*64] TD of combo corrs: quad, cross, hor,vert
 			final GeometryCorrection  geometryCorrection,
@@ -865,7 +870,7 @@ public class ImageDtt extends ImageDttCPU {
 	
 	
 	
-	public GPUTileProcessor.TpTask[][] clt_aberrations_quad_corr_GPU_test(
+	public TpTask[][] clt_aberrations_quad_corr_GPU_test(
 			final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
 			final int                 macro_scale,     // to correlate tile data instead of the pixel data: 1 - pixels, 8 - tiles
 			final int [][]            tile_op,         // [tilesY][tilesX] - what to do - 0 - nothing for this tile
@@ -1105,7 +1110,7 @@ public class ImageDtt extends ImageDttCPU {
 		final boolean use_main = geometryCorrection_main != null;
 		boolean [] used_corrs = new boolean[1];
 	    final int all_pairs = imgdtt_params.dbg_pair_mask; //TODO: use tile tasks
-		final GPUTileProcessor.TpTask[] tp_tasks =  gpuQuad.setTpTask(
+		final TpTask[] tp_tasks =  gpuQuad.setTpTask(
 				disparity_array, // final double [][]  disparity_array,  // [tilesY][tilesX] - individual per-tile expected disparity
 				disparity_corr,  // final double       disparity_corr,
 				used_corrs,      // final boolean []   need_corrs,       // should be initialized to boolean[1] or null
@@ -1151,17 +1156,17 @@ public class ImageDtt extends ImageDttCPU {
 
 		gpuQuad.execSetTilesOffsets(); // prepare tiles offsets in GPU memory
 
-		GPUTileProcessor.TpTask[][] test_tasks = new GPUTileProcessor.TpTask[3][];
+		TpTask[][] test_tasks = new TpTask[3][];
 		test_tasks[2] = tp_tasks;
 		if ((fdisp_dist != null) || (fpxpy != null)) {
-			final GPUTileProcessor.TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main);
+			final TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main);
 			test_tasks[0] = tp_tasks_full;
 			for (int ithread = 0; ithread < threads.length; ithread++) {
 				threads[ithread] = new Thread() {
 					@Override
 					public void run() {
 						for (int indx_tile = ai.getAndIncrement(); indx_tile < tp_tasks_full.length; indx_tile = ai.getAndIncrement()) {
-							GPUTileProcessor.TpTask task = tp_tasks_full[indx_tile];
+							TpTask task = tp_tasks_full[indx_tile];
 							if (fdisp_dist != null) {
 								fdisp_dist[task.getTileY()][task.getTileX()] = task.getDispDist();
 							}
@@ -1179,14 +1184,14 @@ public class ImageDtt extends ImageDttCPU {
 
 			gpuQuad.execSetTilesOffsets(); // prepare tiles offsets in GPU memory
 			
-			final GPUTileProcessor.TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main); // reads the same
+			final TpTask[] tp_tasks_full = gpuQuad.getTasks(use_main); // reads the same
 			test_tasks[1] = tp_tasks_full;
 			for (int ithread = 0; ithread < threads.length; ithread++) {
 				threads[ithread] = new Thread() {
 					@Override
 					public void run() {
 						for (int indx_tile = ai.getAndIncrement(); indx_tile < tp_tasks_full.length; indx_tile = ai.getAndIncrement()) {
-							GPUTileProcessor.TpTask task = tp_tasks_full[indx_tile];
+							TpTask task = tp_tasks_full[indx_tile];
 							if (fpxpy != null) {
 								fpxpy_test[task.getTileY()][task.getTileX()] = task.getXY(use_main); // boolean use_aux);
 							}
@@ -1637,20 +1642,6 @@ public class ImageDtt extends ImageDttCPU {
 //		final double [] col_weights= new double [numcol]; // colors are RBG
 		final double [][] dbg_distort = debug_distort? (new double [4*quad][tilesX*tilesY]) : null;
 		// not yet used with GPU
-/**		
-		final double [][] corr_wnd = Corr2dLMA.getCorrWnd(
-				transform_size,
-				imgdtt_params.lma_wnd);
-		final double [] corr_wnd_inv_limited = (imgdtt_params.lma_min_wnd <= 1.0)?  new double [corr_wnd.length * corr_wnd[0].length]: null;
-		if (corr_wnd_inv_limited != null) {
-			double inv_pwr = imgdtt_params.lma_wnd_pwr - (imgdtt_params.lma_wnd - 1.0); // compensate for lma_wnd
-			for (int i = imgdtt_params.lma_hard_marg; i < (corr_wnd.length - imgdtt_params.lma_hard_marg); i++) {
-				for (int j = imgdtt_params.lma_hard_marg; j < (corr_wnd.length - imgdtt_params.lma_hard_marg); j++) {
-					corr_wnd_inv_limited[i * (corr_wnd.length) + j] = 1.0/Math.max(Math.pow(corr_wnd[i][j],inv_pwr), imgdtt_params.lma_min_wnd);
-				}
-			}
-		}
-*/
 		// keep for now for mono, find out  what do they mean for macro mode
 		
 		final int corr_size = transform_size * 2 - 1;

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

@@ -295,6 +295,7 @@ public class MacroCorrelation {
 				geometryCorrection.getNumSensors(),
 				clt_parameters.transform_size,
 				clt_parameters.img_dtt,
+				this.mtp.isAux(),
 				this.mtp.isMonochrome(),
 				this.mtp.isLwir(),
 				clt_parameters.getScaleStrength(this.mtp.isAux()));

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

@@ -6160,6 +6160,7 @@ ImageDtt.startAndJoin(threads);
 				geometryCorrection.getNumSensors(),
 				clt_parameters.transform_size,
 				clt_parameters.img_dtt,
+				isAux(),
 				isMonochrome(),
 				isLwir(),
 				clt_parameters.getScaleStrength(is_aux));