added preliminary inter-camera correlation, but it is not working yet

src/main/java/BiQuadParameters.java

@@ -78,6 +78,7 @@ public class BiQuadParameters {
 	public boolean ml_keep_aux =               true; // include auxiliary camera data in the ML output
 	public boolean ml_keep_inter =             true; // include inter-camera correlation data in the ML output
 	public boolean ml_keep_hor_vert =          true; // include combined horizontal and vertical pairs data in the ML output
+	public boolean ml_keep_tbrl =              true; // include individual top, bottom, right, left pairs
 	public boolean ml_keep_debug=              true; // include debug layer(s) data in the ML output
 	public boolean ml_8bit=                    true; // output in 8-bit format (default - 32-bit TIFF
 	public double  ml_limit_extrim =           0.00001; // ignore lowest and highest values when converting to 8 bpp
@@ -180,8 +181,11 @@ public class BiQuadParameters {
 				"ML output will have the second set of the layers for the auxiliary camera. Disparity values should be scaled for the camera baseline");
 		gd.addCheckbox    ("Keep inter-camera correlation data",                                                  this.ml_keep_inter,
 				"Inter-camera correlation data has only one layer (and one correlation pair). It is used to generate ground truth data. Usable disparity range (measured in the main camera pixels) is ~1/5 of teh main camera");
-		gd.addCheckbox    ("Keep combine horizonta/vertical pairs",                                               this.ml_keep_hor_vert,
+		gd.addCheckbox    ("Keep individual top, bottom, right, and left pairs",                                  this.ml_keep_tbrl,
 				"Each of these two layers per camera are calculated from a pair of top/bottom and left/right pairs. Can possibly be used instead of originals to reduce amount of input data");
+		gd.addCheckbox    ("Keep combined horizonta/vertical pairs",                                              this.ml_keep_hor_vert,
+				"Individual horizontal and vertical pairs (4 total). Can be replaced by two combined (horizontal+vertical) ones");
+
 		gd.addCheckbox    ("Keep debug layer(s)",                                                                 this.ml_keep_debug,
 				"Keep additional (debug) layers that may change for different file versions");
 		gd.addCheckbox    ("Use 8 bpp TIFF (default - 32 bpp)",                                                   this.ml_8bit,
@@ -241,6 +245,7 @@ public class BiQuadParameters {
 		this.ml_sweep_steps=          (int) gd.getNextNumber();
 		this.ml_keep_aux=                   gd.getNextBoolean();
 		this.ml_keep_inter=                 gd.getNextBoolean();
+		this.ml_keep_tbrl=                  gd.getNextBoolean();
 		this.ml_keep_hor_vert=              gd.getNextBoolean();
 		this.ml_keep_debug=                 gd.getNextBoolean();
 		this.ml_8bit=                       gd.getNextBoolean();
@@ -299,6 +304,7 @@ public class BiQuadParameters {
 		properties.setProperty(prefix+"ml_sweep_steps",            this.ml_sweep_steps+"");
 		properties.setProperty(prefix+"ml_keep_aux",               this.ml_keep_aux+"");
 		properties.setProperty(prefix+"ml_keep_inter",             this.ml_keep_inter+"");
+		properties.setProperty(prefix+"ml_keep_tbrl",              this.ml_keep_tbrl+"");
 		properties.setProperty(prefix+"ml_keep_hor_vert",          this.ml_keep_hor_vert+"");
 		properties.setProperty(prefix+"ml_keep_debug",             this.ml_keep_debug+"");
 		properties.setProperty(prefix+"ml_8bit",                   this.ml_8bit+"");
@@ -355,6 +361,7 @@ public class BiQuadParameters {
 		if (properties.getProperty(prefix+"ml_sweep_steps")!=null)          this.ml_sweep_steps=Integer.parseInt(properties.getProperty(prefix+"ml_sweep_steps"));
 		if (properties.getProperty(prefix+"ml_keep_aux")!=null)             this.ml_keep_aux=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_aux"));
 		if (properties.getProperty(prefix+"ml_keep_inter")!=null)           this.ml_keep_inter=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_inter"));
+		if (properties.getProperty(prefix+"ml_keep_tbrl")!=null)            this.ml_keep_tbrl=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_tbrl"));
 		if (properties.getProperty(prefix+"ml_keep_hor_vert")!=null)        this.ml_keep_hor_vert=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_hor_vert"));
 		if (properties.getProperty(prefix+"ml_keep_debug")!=null)           this.ml_keep_debug=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_debug"));
 		if (properties.getProperty(prefix+"ml_8bit")!=null)                 this.ml_8bit=Boolean.parseBoolean(properties.getProperty(prefix+"ml_8bit"));
@@ -411,6 +418,7 @@ public class BiQuadParameters {
 		bqp.ml_sweep_steps=             this.ml_sweep_steps;
 		bqp.ml_keep_aux=                this.ml_keep_aux;
 		bqp.ml_keep_inter=              this.ml_keep_inter;
+		bqp.ml_keep_tbrl=               this.ml_keep_tbrl;
 		bqp.ml_keep_hor_vert=           this.ml_keep_hor_vert;
 		bqp.ml_keep_debug=              this.ml_keep_debug;
 		bqp.ml_8bit=                    this.ml_8bit;

src/main/java/EyesisCorrections.java

@@ -476,12 +476,14 @@ public class EyesisCorrections {
 						}
 						if (correctionsParameters.isJP4()) imp=JP4_INSTANCE.demuxImage(imp_composite, subChannel);
 						if (imp==null) imp=imp_composite; // not a composite image
-						int [] widthHeight={imp.getWidth(),imp.getHeight()};
-						this.channelWidthHeight[srcChannel]=widthHeight;
+
+//						int [] widthHeight={imp.getWidth(),imp.getHeight()};
+
+//						this.channelWidthHeight[srcChannel]=widthHeight;
 						this.channelVignettingCorrection[srcChannel]=this.pixelMapping.getBayerFlatFieldFloat(
 								srcChannel,
-								this.channelWidthHeight[srcChannel][0],
-								this.channelWidthHeight[srcChannel][1],
+//								this.channelWidthHeight[srcChannel][0],
+//								this.channelWidthHeight[srcChannel][1],
 								bayer);
 						if (this.debugLevel>0){
 							System.out.println("Created vignetting info for channel "+srcChannel+

src/main/java/GeometryCorrection.java

@@ -85,6 +85,11 @@ public class GeometryCorrection {
 	public RigOffset   rigOffset =    null;
 
 
+	public int [] getSensorWH() {
+		int [] wh = {this.pixelCorrectionWidth, this.pixelCorrectionHeight};
+		return wh;
+	}
+
 	public GeometryCorrection(double [] extrinsic_corr)
 	{
 		this.extrinsic_corr = 	new CorrVector(extrinsic_corr);
@@ -98,6 +103,11 @@ public class GeometryCorrection {
 		return (use_rig && (rigOffset != null)) ? rigOffset.rXY_aux: rXY ;
 	}
 
+//	public double [] getAuxOffset(boolean use_rig){
+//		double [] main_offset = {0.0,0.0};
+//		return (use_rig && (rigOffset != null)) ? rigOffset.getAuxOffset(): main_offset ;
+//	}
+
 	public Matrix getRotMatrix(boolean use_rig){
 		return (use_rig && (rigOffset != null)) ? rigOffset.getRotMatrix(): null ;
 	}
@@ -656,6 +666,10 @@ public class GeometryCorrection {
 			return vector;
 		}
 
+//		public double [] getAuxOffset() {
+//			double [] aux_offset= {baseline * Math.cos(aux_angle)/getDisparityRadius(), baseline * Math.sin(aux_angle)/getDisparityRadius()};
+//			return aux_offset;
+//		}
 		public void recalcRXY() {
 			if (rXY != null) {
 				//			rXY_aux = rXY; // FIXME: put real stuff !!!
@@ -695,10 +709,6 @@ public class GeometryCorrection {
 					{ xc_pix,      yc_pix},
 					{dxc_dangle,   dyc_dangle},
 					{dxc_baseline, dyc_baseline}};
-/*			double [][] rslt = {
-					{ -xc_pix,      -yc_pix},
-					{-dxc_dangle,   -dyc_dangle},
-					{-dxc_baseline, -dyc_baseline}}; */
 			return rslt;
 		}
 
@@ -2236,8 +2246,13 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 		double  ri_scale = 0.001 * gc_main.pixelSize / gc_main.distortionRadius;
 
 		// non-distorted XY relative to the auxiliary camera center if it was parallel to the main one
-		double pXci0 = pXc - disparity *  aux_offset_derivs[0][0]; // in pixels
-		double pYci0 = pYc - disparity *  aux_offset_derivs[0][1]; // in pixels
+		// Allow aux_offset_derivs null only if disparity == 0.0;
+		double pXci0 = pXc; //  - disparity *  aux_offset_derivs[0][0]; // in pixels
+		double pYci0 = pYc; // - disparity *  aux_offset_derivs[0][1]; // in pixels
+		if (disparity != 0.0) { // aux_offset_derivs != null)
+			pXci0 -= disparity *  aux_offset_derivs[0][0]; // in pixels
+			pYci0 -= disparity *  aux_offset_derivs[0][1]; // in pixels
+		}
 		// rectilinear here
 
 		// Convert a 2-d non-distorted vector to 3d at fl_pix distance in z direction
@@ -2246,7 +2261,7 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 
 		// Apply port-individual combined rotation/zoom matrix
 
-		Matrix rvi = aux_rot.times(vi);
+		Matrix rvi = (aux_rot == null) ? vi: aux_rot.times(vi);
 
 
 		// get back to the projection plane by normalizing vector
@@ -2480,6 +2495,51 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 		return pXY;
 	}
 
+	/*
+	public double [] getAuxCoordinatesRigIdeal( // used in macro mode
+			GeometryCorrection gc_main,
+			Matrix rots,
+			double px,
+			double py,
+			double disparity)
+	{
+		// reverse getPortsCoordinates
+		double c_roll = 1.0; // Math.cos(( - this.common_roll) * Math.PI/180.0);
+		double s_roll = 0.0; // Math.sin(( - this.common_roll) * Math.PI/180.0);
+		double pXcd0 = px -  0.5 * this.pixelCorrectionWidth;
+		double pYcd0 = py -  0.5 * this.pixelCorrectionWidth;
+		double pXcd = c_roll *  pXcd0 - s_roll* pYcd0;
+		double pYcd = s_roll *  pXcd0 + c_roll* pYcd0;
+		double rD = Math.sqrt(pXcd*pXcd + pYcd*pYcd)*0.001*this.pixelSize; // distorted radius in a virtual center camera
+		double rND2R=getRByRDist(rD/this.distortionRadius, (debugLevel > -1));
+		double pXc = pXcd * rND2R; // non-distorted coordinates relative to the (0.5 * this.pixelCorrectionWidth, 0.5 * this.pixelCorrectionHeight)
+		double pYc = pYcd * rND2R; // in pixels
+		double [] a={this.distortionC,this.distortionB,this.distortionA,this.distortionA5,this.distortionA6,this.distortionA7,this.distortionA8};
+		double [] pXY = new double[2];
+		// calculate for aux (this) camera
+		double [][] aux_offset = getAuxOffsetAndDerivatives(gc_main);
+			// non-distorted XY of the shifted location of the individual sensor
+			double pXci = pXc - disparity *  aux_offset[0][0]; // in pixels
+			double pYci = pYc - disparity *  aux_offset[0][1];
+
+			// calculate back to distorted
+			double rNDi = Math.sqrt(pXci*pXci + pYci*pYci); // in pixels
+			//		Rdist/R=A8*R^7+A7*R^6+A6*R^5+A5*R^4+A*R^3+B*R^2+C*R+(1-A8-A7-A6-A5-A-B-C)");
+			double ri = rNDi* 0.001 * this.pixelSize / this.distortionRadius; // relative to distortion radius
+			//    		double rD2rND = (1.0 - distortionA8 - distortionA7 - distortionA6 - distortionA5 - distortionA - distortionB - distortionC);
+			double rD2rND = 1.0;
+			double rri = 1.0;
+			for (int j = 0; j < a.length; j++){
+				rri *= ri;
+				rD2rND += a[j]*(rri - 1.0);
+			}
+			double pXid = pXci * rD2rND;
+			double pYid = pYci * rD2rND;
+			pXY[i][0] =  c_roll *  pXid + s_roll* pYid + 0.5 * this.pixelCorrectionWidth; // this.pXY0[i][0];
+			pXY[i][1] = -s_roll *  pXid + c_roll* pYid + 0.5 * this.pixelCorrectionWidth; // this.pXY0[i][1];
+		return pXY;
+	}
+*/
 
 
 	public double [][] getPortsCoordinatesIdeal(
@@ -2500,6 +2560,30 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 		return coords;
 	}
 
+	public double [] getRigAuxCoordinatesIdeal(
+			int                macro_scale, // 1 for pixels, 8 - for tiles when correlating tiles instead of the pixels
+			GeometryCorrection gc_main,
+			Matrix             aux_rot,
+			double             px,
+			double             py,
+			double             disparity)
+	{
+		double [] xy = getRigAuxCoordinatesAndDerivatives(
+				gc_main,           // GeometryCorrection gc_main,
+				aux_rot,           // Matrix      aux_rot,
+				null,              // Matrix []   aux_rot_derivs,
+				null,              // double [][] aux_offset_derivs,
+				null,              // double [][] pXYderiv, // if not null, should be double[6][]
+				px * macro_scale,  // double px,
+				py * macro_scale,  // double py,
+				disparity);        // double disparity);
+		double [] coords = {xy[0]/macro_scale,xy[1]/macro_scale};
+		return coords;
+	}
+
+
+
+
 
 	// Copied from PixelMapping
 	/**

src/main/java/PixelMapping.java

@@ -201,25 +201,26 @@ public class PixelMapping {
 
 	public float [] getBayerFlatFieldFloat(
 			int channel,
-			int width,
-			int height,
+//			int width,
+//			int height,
 			int [][] bayer){ //{{1,0},{2,1}} GR/BG
 		if ((this.sensors == null) || (channel<0)  && (channel>=this.sensors.length))return null;
+//		width = this.sensors[channel]
 		return this.sensors[channel].getBayerFlatFieldFloat(
-				width,
-				height,
+//				width,
+//				height,
 				bayer);
 	}
 
 	public double [] getBayerFlatField(
 			int channel,
-			int width,
-			int height,
+//			int width,
+//			int height,
 			int [][] bayer){ //{{1,0},{2,1}} GR/BG
 		if ((this.sensors == null) || (channel<0)  && (channel>=this.sensors.length))return null;
 		return this.sensors[channel].getBayerFlatField(
-				width,
-				height,
+//				width,
+//				height,
 				bayer);
 	}
 
@@ -15645,8 +15646,8 @@ public class PixelMapping {
 	    public double [][] pixelCorrection=      null; // x,y, alpha, add flat, color, etc.
 //	    public double []   sensorMask=           null;
 	    public int    pixelCorrectionDecimation= 1;
-	    public int    pixelCorrectionWidth=      2592;
-	    public int    pixelCorrectionHeight=     1936;
+	    public int    pixelCorrectionWidth=      -1; // 2592;
+	    public int    pixelCorrectionHeight=     -1; // 1936;
 	    public double entrancePupilForward=      0.0;
 
 
@@ -15673,6 +15674,11 @@ public class PixelMapping {
 
 		public double [][] r_xyod=null; //{x0,y0,ortho, diagonal}
 
+		public int [] getSensorWH() {
+			int [] wh = {this.pixelCorrectionWidth, this.pixelCorrectionHeight};
+			return wh;
+		}
+
 
 	    public SensorData (String channelPath , boolean ok ){
 	    	createEquirectangularMap(channelPath);
@@ -15880,9 +15886,11 @@ public class PixelMapping {
 		}
 
 		public double [] getBayerFlatField(
-				int width,
-				int height,
+//				int width,
+//				int height,
 				int [][] bayer){ //{{1,0},{2,1}} GR/BG
+			int width = this.pixelCorrectionWidth; //  width,
+			int height= this.pixelCorrectionHeight; // int height,
 
 			double [] corrScale = new double [width*height];
 			for (int y=0;y<height;y++) for (int x=0;x<width;x++){
@@ -15908,6 +15916,13 @@ public class PixelMapping {
 			return corrScale;
 		}
 		public float [] getBayerFlatFieldFloat(
+				int [][] bayer){ //{{1,0},{2,1}} GR/BG
+			return _getBayerFlatFieldFloat(
+					this.pixelCorrectionWidth, //  width,
+					this.pixelCorrectionHeight, // int height,
+					bayer);
+		}
+		private float [] _getBayerFlatFieldFloat(
 				int width,
 				int height,
 				int [][] bayer){ //{{1,0},{2,1}} GR/BG

src/main/java/QuadCLT.java

@@ -26,6 +26,7 @@
 import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Map;
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
@@ -38,6 +39,7 @@ import ij.WindowManager;
 //import ij.gui.Overlay;
 import ij.io.FileSaver;
 import ij.process.ColorProcessor;
+import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 
 
@@ -2629,6 +2631,10 @@ public class QuadCLT {
 						  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_srcs[srcChannel]); // decode existent properties from info
 						  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 					  }
+					  imp_srcs[srcChannel] =  padBayerToFullSize(
+							  imp_srcs[srcChannel], // ImagePlus imp_src,
+							  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
+							  true); // boolean replicate);
 					  scaleExposures[srcChannel] = 1.0;
 					  if (!Double.isNaN(referenceExposures[nFile]) && (imp_srcs[srcChannel].getProperty("EXPOSURE")!=null)){
 						  scaleExposures[srcChannel] = referenceExposures[nFile]/Double.parseDouble((String) imp_srcs[srcChannel].getProperty("EXPOSURE"));
@@ -3189,6 +3195,81 @@ public class QuadCLT {
 		  return nf;
 	  }
 
+	  /**
+	   * Pad acquired Bayer image to the full sensor width/height. Used when optical center pixel coordinates do not match for channels
+	   * and WOI is adjusted during image capture to avoid ERS mismatch between horizontal pairs
+	   * @param imp_src source image with WOI specified as properties (sizes and offsets should be even)
+	   * @param wh {sesnor_width, sensor_height} in pixels
+	   * @param replicate fill gaps by replicating existing pixels
+	   * @return full size image
+	   */
+
+	  ImagePlus padBayerToFullSize(
+			  ImagePlus imp_src,
+			  int [] wh,
+			  boolean replicate) {
+		  int woi_top =    Integer.parseInt((String) imp_src.getProperty("WOI_TOP")); // enforce even
+		  int woi_left =   Integer.parseInt((String) imp_src.getProperty("WOI_LEFT"));
+		  int woi_width =  imp_src.getWidth(); // Integer.parseInt((String) imp_src.getProperty("WOI_WIDTH"));
+		  int woi_height = imp_src.getHeight(); // Integer.parseInt((String) imp_src.getProperty("WOI_HEIGHT"));
+		  Properties properties = imp_src.getProperties();
+
+
+		  if ((woi_top == 0) && (woi_left == 0) && (woi_width == wh[0])  && (woi_height == wh[1])){
+			  return imp_src; // good as is
+		  }
+		  float [] full_pixels = new float [wh[0]*wh[1]];
+		  float [] pixels=(float []) imp_src.getProcessor().getPixels();
+		  int dst_col = woi_left;
+		  int copy_width = woi_width;
+		  if ((dst_col + copy_width) > wh[0]) {
+			  copy_width = wh[0] - dst_col;
+		  }
+		  for (int src_row = 0; src_row < woi_height; src_row++) {
+			  int dst_row = src_row + woi_top;
+			  if (dst_row < wh[1]) {
+				  System.arraycopy( pixels,   src_row * woi_width,  full_pixels, dst_row * wh[0] + dst_col,  copy_width);
+			  }
+		  }
+		  if (replicate) {
+			  // replicate top
+			  for (int dst_row = 0; dst_row < woi_top; dst_row++) {
+				  int src_row = woi_top + (dst_row & 1);
+				  System.arraycopy( full_pixels,   src_row * wh[0] + dst_col,  full_pixels, dst_row * wh[0] + dst_col,  copy_width);
+			  }
+			  // replicate bottom
+			  for (int dst_row = woi_top + woi_height; dst_row < wh[1]; dst_row++) {
+				  int src_row = woi_top + woi_height - 2 + (dst_row & 1);
+				  System.arraycopy( full_pixels,   src_row * wh[0] + dst_col,  full_pixels, dst_row * wh[0] + dst_col,  copy_width);
+			  }
+			  // right and left are not likely, as there is no need to use them - horizontal mismatch does not influence ERS
+			  for (int col = 0; col < woi_left; col++) {
+				  for (int row = 0; row < wh[1]; row++) {
+					  full_pixels[row*wh[0] + col] = full_pixels[row*wh[0] + woi_left + (col & 1)];
+				  }
+			  }
+
+			  for (int col = woi_left + woi_width; col < wh[0]; col++) {
+				  for (int row = 0; row < wh[1]; row++) {
+					  full_pixels[row*wh[0] + col] = full_pixels[row*wh[0] + woi_left + woi_width - 2 +(col & 1)];
+				  }
+			  }
+		  }
+		  ImageProcessor ip = new FloatProcessor(wh[0],wh[1]);
+		  ip.setPixels(full_pixels);
+		  ip.resetMinAndMax(); // is it needed here?
+		  ImagePlus imp = new ImagePlus(imp_src.getTitle(),ip); // OK to have the same name?
+		  for (Map.Entry<?, ?> entry: properties.entrySet()) {
+			  String key = (String) entry.getKey();
+			  String value = (String) entry.getValue();
+			  imp.setProperty(key, value);
+		  }
+		  imp.setProperty("WOI_WIDTH", wh[0]+"");
+		  imp.setProperty("WOI_HEIGHTH", wh[1]+"");
+		  imp.setProperty("WOI_TOP", "0");
+		  imp.setProperty("WOI_LEFT", "0");
+		  return imp;
+	  }
 
 	  /**
 	   * Conditions images for a single image set
@@ -3215,6 +3296,7 @@ public class QuadCLT {
 		  ImagePlus [] imp_srcs = new ImagePlus[channelFiles.length];
 //		  double [] scaleExposures = new double[channelFiles.length]; //
 		  double [][] dbg_dpixels = new double [channelFiles.length][];
+//		  int [] fullWindowWH = geometryCorrection.getSensorWH();
 
 		  for (int srcChannel=0; srcChannel < channelFiles.length; srcChannel++){
 			  int nFile=channelFiles[srcChannel]; // channelFiles[srcChannel];
@@ -3246,7 +3328,12 @@ public class QuadCLT {
 					  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_srcs[srcChannel]); // decode existent properties from info
 					  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 				  }
+// imp_srcs[srcChannel].show(); // REMOVE ME!
 
+				  imp_srcs[srcChannel] =  padBayerToFullSize(
+						  imp_srcs[srcChannel], // ImagePlus imp_src,
+						  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
+						  true); // boolean replicate);
 				  scaleExposures[srcChannel] = 1.0;
 				  if (!Double.isNaN(referenceExposures[nFile]) && (imp_srcs[srcChannel].getProperty("EXPOSURE")!=null)){
 					  scaleExposures[srcChannel] = referenceExposures[nFile]/Double.parseDouble((String) imp_srcs[srcChannel].getProperty("EXPOSURE"));
@@ -4736,6 +4823,10 @@ public class QuadCLT {
 						  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_srcs[srcChannel]); // decode existent properties from info
 						  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 					  }
+					  imp_srcs[srcChannel] =  padBayerToFullSize(
+							  imp_srcs[srcChannel], // ImagePlus imp_src,
+							  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
+							  true); // boolean replicate);
 					  scaleExposures[srcChannel] = 1.0;
 					  if (!Double.isNaN(referenceExposures[nFile]) && (imp_srcs[srcChannel].getProperty("EXPOSURE")!=null)){
 						  scaleExposures[srcChannel] = referenceExposures[nFile]/Double.parseDouble((String) imp_srcs[srcChannel].getProperty("EXPOSURE"));
@@ -8373,7 +8464,7 @@ public class QuadCLT {
 	  }
 
 
-	  public ImagePlus [] conditionImageSet(
+	  public ImagePlus [] conditionImageSetBatch( // used in batchCLT3d
 			  final int                           nSet, // index of the 4-image set
 			  final EyesisCorrectionParameters.CLTParameters           clt_parameters,
 			  final int [][]                      fileIndices, // =new int [numImagesToProcess][2]; // file index, channel number
@@ -8431,7 +8522,10 @@ public class QuadCLT {
 					  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_srcs[srcChannel]); // decode existent properties from info
 					  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 				  }
-
+				  imp_srcs[srcChannel] =  padBayerToFullSize(
+						  imp_srcs[srcChannel], // ImagePlus imp_src,
+						  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
+						  true); // boolean replicate);
 				  scaleExposures[srcChannel] = 1.0;
 				  if (!Double.isNaN(referenceExposures[nFile]) && (imp_srcs[srcChannel].getProperty("EXPOSURE")!=null)){
 					  scaleExposures[srcChannel] = referenceExposures[nFile]/Double.parseDouble((String) imp_srcs[srcChannel].getProperty("EXPOSURE"));
@@ -8712,7 +8806,7 @@ public class QuadCLT {
 			  this.startSetTime = System.nanoTime();
 			  boolean [][] saturation_imp = (clt_parameters.sat_level > 0.0)? new boolean[QUAD][] : null;
 			  double [] scaleExposures = new double[QUAD]; //
-			  ImagePlus [] imp_srcs = conditionImageSet(
+			  ImagePlus [] imp_srcs = conditionImageSetBatch(
 					  nSet,               // final int                           nSet, // index of the 4-image set
 					  clt_parameters,     // final EyesisCorrectionParameters.CLTParameters           clt_parameters,
 					  fileIndices,        // final int [][]                      fileIndices, // =new int [numImagesToProcess][2]; // file index, channel number

src/main/java/showDoubleFloatArrays.java

 import java.awt.Rectangle;
 
-import ij.*;
+import ij.IJ;
+import ij.ImagePlus;
+import ij.ImageStack;
 import ij.gui.GenericDialog;
 import ij.gui.Roi;
-import ij.process.*;
+import ij.process.ColorProcessor;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
 
   public class showDoubleFloatArrays {
 	  // defaults for color conversion
@@ -14,7 +18,7 @@ import ij.process.*;
 	  public double Kr=0.299;   // 0.299;
 	  public double Kb=0.114;   // 0.114;
 	  public double brightness=0.5;
-	  
+
 
 
 /* For square arrays */
@@ -75,7 +79,7 @@ import ij.process.*;
         for (j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
         array_stack.addSlice("chn-"+i,    fpixels);
         if (pixels[i].length!=(width*height)){
-        	
+
         }
       }
       ImagePlus imp_stack = new ImagePlus(title, array_stack);
@@ -92,14 +96,18 @@ import ij.process.*;
 	    if (asStack) {
 	      float [] fpixels;
 	      ImageStack array_stack=new ImageStack(width,height);
+	      boolean not_empty = false;
 	      for (i=0;i<pixels.length;i++) if (pixels[i]!=null) {
-	        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);
+	    	  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 (not_empty) {
+	    	  ImagePlus imp_stack = new ImagePlus(title, array_stack);
+	    	  imp_stack.getProcessor().resetMinAndMax();
+	    	  imp_stack.show();
 	      }
-	      ImagePlus imp_stack = new ImagePlus(title, array_stack);
-	      imp_stack.getProcessor().resetMinAndMax();
-	      imp_stack.show();
 	      return;
 	    } else showArrays(pixels, width, height, titles);
 	  }
@@ -111,7 +119,7 @@ import ij.process.*;
 	      ImageStack array_stack=new ImageStack(width,height);
 	      for (i=0;i<pixels.length;i++) if (pixels[i]!=null) {
 	        fpixels=new float[pixels[i].length];
-	        for (j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
+	        for (j=0;j<fpixels.length;j++) fpixels[j]=pixels[i][j];
 	        array_stack.addSlice(titles[i], fpixels);
 	      }
 	      ImagePlus imp_stack = new ImagePlus(title, array_stack);
@@ -242,7 +250,7 @@ import ij.process.*;
 	  ImagePlus[]      imp=new ImagePlus[pixels.length];
 	  for (i=0;i<pixels.length;i++) if (pixels[i]!=null) {
 		  fpixels=new float[pixels[i].length];
-		  for (j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
+		  for (j=0;j<fpixels.length;j++) fpixels[j]=pixels[i][j];
 		  ip[i]=new FloatProcessor(width,height);
 		  ip[i].setPixels(fpixels);
 		  ip[i].resetMinAndMax();
@@ -299,7 +307,7 @@ import ij.process.*;
 	  float [] fpixels;
 	  if (pixels!=null) {
 		  fpixels=new float[pixels.length];
-		  for (j=0;j<pixels.length;j++) fpixels[j]=(float)pixels[j];
+		  for (j=0;j<pixels.length;j++) fpixels[j]=pixels[j];
 		  ImageProcessor ip=new FloatProcessor(width,height);
 		  ip.setPixels(fpixels);
 		  ip.resetMinAndMax();
@@ -323,14 +331,14 @@ import ij.process.*;
 	  }
 	  return null;
   }
-  
-  
+
+
   public ImagePlus makeArrays(float[] pixels, int width, int height, String title) {
 	  int j;
 	  float [] fpixels;
 	  if (pixels!=null) {
 		  fpixels=new float[pixels.length];
-		  for (j=0;j<pixels.length;j++) fpixels[j]=(float)pixels[j];
+		  for (j=0;j<pixels.length;j++) fpixels[j]=pixels[j];
 		  ImageProcessor ip=new FloatProcessor(width,height);
 		  ip.setPixels(fpixels);
 		  ip.resetMinAndMax();
@@ -394,7 +402,7 @@ import ij.process.*;
       ImagePlus imp_stack = new ImagePlus(title, stack);
       imp_stack.getProcessor().resetMinAndMax();
       imp_stack.show();
-      return imp_stack; 
+      return imp_stack;
   }
   public void showImageStackThree(ImageStack stack, String title) {
 	  if (stack==null) return;
@@ -410,7 +418,7 @@ import ij.process.*;
       imp_stack.getProcessor().resetMinAndMax();
       imp_stack.show();
   }
-  
+
   // additional methods to show 2-d "flows" in color
   /*
   	  public int sliceRminusG=1;
@@ -436,7 +444,7 @@ import ij.process.*;
 		gd.addNumericField("Color conversion coefficient Kr (default =0.299) ", this.Kr, 3);
 		gd.addNumericField("Color conversion coefficient Kb (default =0.114) ", this.Kb, 3);
 		gd.addNumericField("Brightness (0..1.0)", this.brightness, 3);
-		
+
 	    gd.showDialog();
 	    if (gd.wasCanceled()) return null;
 	    this.sliceRminusG=     (int) gd.getNextNumber();
@@ -457,7 +465,7 @@ import ij.process.*;
 				  this.Kb);
   }
 	/**
-	 * 
+	 *
 	 * @param imp image containing at least 2 slices, rectangular selection will be used to find min/max
 	 * @param sliceRminusG slice number to be interpreted as R-G
 	 * @param sliceBminusG slice number to be interpreted as B-G
@@ -477,7 +485,7 @@ import ij.process.*;
 			  sliceBminusG,
 			  colorSpan,
 			  brightnessModulate,0.5,0.299,0.114);
-  
+
   }
   public ImagePlus showFlowFromSlices(
 		  ImagePlus imp,
@@ -519,7 +527,7 @@ import ij.process.*;
     	  if (maxB<Math.abs(pixels[1][index])) maxB=Math.abs(pixels[1][index]);
     	  double a=Math.sqrt(pixels[0][index]*pixels[0][index]+pixels[1][index]*pixels[1][index]);
     	  if (maxA<a) maxA=a;
-    	  
+
       }
       double maxRB=Math.max(maxR,maxB);
       double Kg=1.0-Kr-Kb;
@@ -572,7 +580,7 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 	  return imp_color;
 
   }
-	  
-  
+
+
 }