added source image padding to match WOI in properties, making kernel

generation with large-cell calibration pattern

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

@@ -5949,6 +5949,16 @@ if (MORE_BUTTONS) {
 				IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set");
 				return;
 			}
+			DistortionCalibrationData dcd = LENS_DISTORTIONS.getDistortionCalibrationData();
+			if (dcd == null) {
+				dcd = DISTORTION_CALIBRATION_DATA;
+			}
+			if (dcd == null) {
+				System.out.println("dcd is null");
+				return;
+			}
+
+
 			GenericDialog gd=new GenericDialog ("Parameters of the filter by predicted grid");
     		gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", 0.5, 1,4,"fraction of grid half-period");
     		gd.addCheckbox    ("Calibrate by translation (false - orientation only)", true);
@@ -5957,6 +5967,8 @@ if (MORE_BUTTONS) {
     		gd.addCheckbox    ("Process images with estimated orientation and no matched laser pointers", false);
     		gd.addCheckbox    ("Use image sets data if available (false - use camera data)", true);
     		gd.addNumericField("Process only one specified image (<0 - all)", -1, 0);
+    		gd.addNumericField("Start image set", 0, 0);
+    		gd.addNumericField("End image set", dcd.getNumSets()-1, 0);
 
     		gd.showDialog();
     		if (gd.wasCanceled()) return;
@@ -5967,6 +5979,8 @@ if (MORE_BUTTONS) {
     		boolean processBlind=           gd.getNextBoolean();
     		boolean useSetsData=            gd.getNextBoolean();
     		int imageNumber=          (int) gd.getNextNumber();
+    		int start_set=            (int) gd.getNextNumber();
+    		int end_set=              (int) gd.getNextNumber();
     		if (imageNumber>=0) processAll=true; // no additional filtering
 
     		int numMatched=LENS_DISTORTIONS.applyHintedGrids(
@@ -5977,6 +5991,8 @@ if (MORE_BUTTONS) {
     				ignoreLaserPointers,
     				processBlind,
     				imageNumber,
+    				start_set,
+    				end_set,
     				useSetsData,
     				THREADS_MAX,                 //int threadsMax,
     				UPDATE_STATUS,               // boolean updateStatus,

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

@@ -1718,12 +1718,12 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
         		Arrays.fill(numMatchedPointersEnabledPerStation[n], 0);
     		}
 
-    		int []   numHintedMatch=        new int [matchedPointersIndex.length];
-    		int []   numHintedMatchSelected=new int [matchedPointersIndex.length];
-    		int []   numHintedMatchEnabled= new int [matchedPointersIndex.length];
-    		int [][] numHintedMatchPerStation=        new int [matchedPointersIndex.length][];
-    		int [][] numHintedMatchSelectedPerStation=new int [matchedPointersIndex.length][];
-    		int [][] numHintedMatchEnabledPerStation= new int [matchedPointersIndex.length][];
+    		int []   numHintedMatch=        new int [hintedMatchIndex.length];
+    		int []   numHintedMatchSelected=new int [hintedMatchIndex.length];
+    		int []   numHintedMatchEnabled= new int [hintedMatchIndex.length];
+    		int [][] numHintedMatchPerStation=        new int [hintedMatchIndex.length][];
+    		int [][] numHintedMatchSelectedPerStation=new int [hintedMatchIndex.length][];
+    		int [][] numHintedMatchEnabledPerStation= new int [hintedMatchIndex.length][];
     		for (int n=0;n<numHintedMatch.length;n++){
     			numHintedMatch[n]=0;
     			numHintedMatchSelected[n]=0;
@@ -1771,9 +1771,12 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
         			}
         			numMatchedPointersEnabledPerStation[mpi][imageStations[i]]++;
     				numMatchedPointersEnabled[mpi]++;
-
-        			numHintedMatchEnabledPerStation[hmi][imageStations[i]]++;
-    				numHintedMatchEnabled[hmi]++;
+    				if (hmi>=numHintedMatchEnabledPerStation.length) {
+    					System.out.println("*** Bug: hmi>=numHintedMatchEnabledPerStation.length");
+    				} else {
+    					numHintedMatchEnabledPerStation[hmi][imageStations[i]]++;
+    					numHintedMatchEnabled[hmi]++;
+    				}
 
 
     			}
@@ -2013,6 +2016,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     			IJ.showMessage("Error",msg);
     			return;
     		}
+    		int numSubCams=this.distortionCalibrationData.getNumSubCameras();
     		int [] choice_offsets = new int [this.parameterEnable.length];
     		//
     	    String header="Strategy #\tType";
@@ -2061,12 +2065,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 				int subMaxNum = -1;
 				if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters
 					if (zeroAndOther) {
-						subMaxNum = this.distortionCalibrationData.firstInGroup(subCam)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
+//						subMaxNum = this.distortionCalibrationData.firstInGroup(subCam)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
+						subMaxNum = (this.distortionCalibrationData.sourceToCopy(subCam) < 0)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
 					} else {
 						subMaxNum =  subCam-1; // 0 will be -1 - this may be wrong to align to higher index
 					}
 				}
 
+
 	/*=========*/
 
 				String [] commonChoices = (isTilt?this.definedModesTiltEq:(noWeak?this.definedModesNoWeak:this.definedModes));
@@ -2080,24 +2086,33 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 						thisChoice = this.definedModesAll[this.parameterMode[numSeries][ipar]];
 					} else { // only can happen if (!isTilt) && (noWeak)
 						choice_offsets[ipar] = commonChoices.length;
-						theseChoices = new String [commonChoices.length + subMaxNum + 1];
+//						theseChoices = new String [commonChoices.length + subMaxNum + 1];
+						theseChoices = new String [commonChoices.length];
 						for (int ch = 0; ch < commonChoices.length; ch++) theseChoices[ch] = commonChoices[ch];
+/*
 						if (zeroAndOther) {
 							if (subMaxNum >=0) { // can only be 0
-								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.masterSub(subCam);
+//								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.masterSub(subCam);
+								// TODO: Make human-readable channel name?
+								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.sourceToCopy(subCam);
 							}
 						} else {
 							for (int ch = 0; ch <= subMaxNum; ch++)  {
 								theseChoices[ch + commonChoices.length] = "same as "+ch;
 							}
 						}
+*/
 						// choice index for "same as ..." starts with  this.definedModesAll.length, but in the listbox index is lower
 						int indx = this.parameterMode[numSeries][ipar];
 
 						if (indx >= this.definedModesAll.length) {
 							indx -= (this.definedModesAll.length - choice_offsets[ipar]);
 						}
-						thisChoice = theseChoices[indx];
+						if (indx < theseChoices.length) {
+							thisChoice = theseChoices[indx];
+						} else {
+							thisChoice = "same as "+ (indx - theseChoices.length);
+						}
 //						System.out.println("selectStrategyStep(): this.parameterMode["+numSeries+"]["+ipar+"]=" + this.parameterMode[numSeries][ipar]+" indx = "+indx);
 					}
 					if (thisChoice.equals("fixed")) thisChoice = "-";
@@ -2278,7 +2293,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 					int subMaxNum = -1;
 					if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters
 						if (zeroAndOther) {
-							subMaxNum = this.distortionCalibrationData.firstInGroup(subCam)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
+//							subMaxNum = this.distortionCalibrationData.firstInGroup(subCam)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
+							subMaxNum = (this.distortionCalibrationData.sourceToCopy(subCam) < 0)?-1:0; //this.distortionCalibrationData.getSubGroup(subCam);
 						} else {
 							subMaxNum =  subCam-1; // 0 will be -1 - this may be wrong to align to higher index
 						}
@@ -2297,7 +2313,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 						for (int ch = 0; ch < commonChoices.length; ch++) theseChoices[ch] = commonChoices[ch];
 						if (zeroAndOther) {
 							if (subMaxNum >=0) {
-								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.masterSub(subCam);
+//								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.masterSub(subCam);
+								// TODO: Make human-readable channel name?
+								theseChoices[commonChoices.length] = "same as "+this.distortionCalibrationData.sourceToCopy(subCam);
 							}
 						} else {
 							for (int ch = 0; ch <= subMaxNum; ch++)  {
@@ -2309,6 +2327,12 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 						if (indx >= this.definedModesAll.length) {
 							indx -= (this.definedModesAll.length - choice_offsets[i]);
 						}
+						// currently only out of limits can occur with a single choice, so
+						if (indx >= theseChoices.length) {
+							indx = theseChoices.length - 1;
+						}
+
+
 						thisChoice = theseChoices[indx];
 						System.out.println("selectStrategyStep(): this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]+" indx = "+indx);
 					}
@@ -2474,6 +2498,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 
 					// make adjustment for "same as (other lower numbered subcamera)"
 					if ((choice_offsets[i] > 0) && (this.parameterMode[numSeries][i] >= choice_offsets[i])){
+						if (zeroAndOther) { // add reference channel
+							int ref_chn = this.distortionCalibrationData.sourceToCopy(this.parameterList[i][0]);
+							this.parameterMode[numSeries][i] += ref_chn;
+						}
 						System.out.print("selectStrategyStep(): choice_offsets["+i+"]="+choice_offsets[i]+ " this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]);
 						this.parameterMode[numSeries][i] += (this.definedModesAll.length - choice_offsets[i]);
 						System.out.println(", corrected=" + this.parameterMode[numSeries][i]);
@@ -2485,12 +2513,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 						selectGroups(numSeries,i);
 					}
 				}
-				if (zeroAndOther){
+				if (zeroAndOther ){
 					for (int i =0; i<this.parameterEnable.length;i++) {
 //						if ((this.parameterList[i][0]>1) && (this.parameterList[i][0]!=24)){ // "other" subchannels - copy from subchannel1
 						if (!this.distortionCalibrationData.firstInGroup(this.parameterList[i][0])){ // "other" subchannels - copy from subchannel1
+///						if (this.distortionCalibrationData.sourceToCopy(this.parameterList[i][0]) >= 0){ // "other" subchannels - copy from subchannel1
 //							int refChannel=(this.parameterList[i][0]<24)?1:24;
 							int refChannel= this.distortionCalibrationData.masterSub(this.parameterList[i][0]);
+///							int refChannel= this.distortionCalibrationData.sourceToCopy(this.parameterList[i][0]);
 
 							int iSub1=getParameterNumber(refChannel, this.parameterList[i][1]);
 							if (this.parameterEnable[iSub1]){

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

@@ -6136,7 +6136,7 @@ public class MatchSimulatedPattern {
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
 			SimulationPattern.SimulParameters  simulParameters,
 			boolean equalizeGreens,
-			ImagePlus imp, // image to process
+			ImagePlus imp, // image to process // has WOI_TOP and possibly - WOI_COMPENSATED
 			LaserPointer laserPointer, // LaserPointer object or null
 			boolean removeOutOfGridPointers, //
 			double [][][] hintGrid, // predicted grid array (or null)

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

@@ -626,7 +626,7 @@ Cv=(Cy*x-Cx*y)+(-Cy*Dx+Cx*Dy)
 		float [][] simArray=new float [2][];
 		simArray[0]=(new SimulationPattern(simulParameters)).combineWithCanvas(0.0,  k*width, k*height, scaledWoi,simArray0[0]);
 		simArray[1]=(new SimulationPattern(simulParameters)).combineWithCanvas(0.0,  k*width, k*height, scaledWoi,simArray0[1]);
-		if (globalDebugLevel>1) SDFA_INSTANCE.showArrays(simArray,width*k,height*k,true, "full-simulation");
+		if (globalDebugLevel>0) SDFA_INSTANCE.showArrays(simArray,width*k,height*k,true, "full-simulation");
 		return simArray;
 	}
 

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

@@ -1325,6 +1325,11 @@ import ij.gui.GenericDialog;
 
         public int getSensorWidth(int subCam) { return this.eyesisSubCameras[0][subCam].getSensorWidth();} // for the future? different sensors
         public int getSensorHeight(int subCam) { return this.eyesisSubCameras[0][subCam].getSensorHeight();}// for the future? different sensors
+        public int [] getSensorWidthHeight(int subCam) {
+        	int [] wh = {getSensorWidth( subCam), getSensorHeight( subCam)};
+        	return wh;
+        }
+
         public int getDecimateMasks(int subCam) { return this.eyesisSubCameras[0][subCam].getDecimateMasks();}// for the future? different sensors
 
         public void setSensorWidth(int subCam, int v)   {

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

 package com.elphel.imagej.common;
 import java.awt.Rectangle;
+import java.util.Map;
+import java.util.Properties;
 
 import ij.IJ;
 import ij.ImagePlus;
@@ -654,5 +656,86 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
   }
 
 
+  /**
+   * 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
+   */
+
+  public static ImagePlus padBayerToFullSize(
+		  ImagePlus imp_src,
+		  int [] wh, // null OK - will use {woi_left+width, woi_top+height}
+		  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 (wh == null) {
+		  wh = new int [2];
+		  wh[0] = woi_left + woi_width;
+		  wh[1] = woi_top  + woi_height;
+	  }
+	  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;
+  }
+
+
 }
 

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

@@ -619,6 +619,7 @@ private Panel panel1,
 			addButton("CLT reset 3D",              panelClt2, color_stop);
 			addButton("MAIN extrinsics",           panelClt2, color_process);
 			addButton("CLT Poly corr",             panelClt2, color_process);
+			addButton("DRY RUN",                   panelClt2, color_configure);
 			addButton("CLT 3D",                    panelClt2, color_process);
 			addButton("CLT planes",                panelClt2, color_conf_process);
 			addButton("CLT ASSIGN",                panelClt2, color_process);
@@ -4407,14 +4408,16 @@ private Panel panel1,
 
 /// ============================================
 
-    } else if (label.equals("CLT 3D") || label.equals("MAIN extrinsics") || label.equals("CLT Poly corr")) {
+    } else if (label.equals("CLT 3D") || label.equals("MAIN extrinsics") || label.equals("CLT Poly corr") || label.equals("DRY RUN")) {
 
     	boolean adjust_extrinsics = label.equals("MAIN extrinsics") || label.equals("CLT Poly corr");
     	boolean adjust_poly = label.equals("CLT Poly corr");
+		boolean dry_run =  label.equals("DRY RUN");// init kernel/geometry only
+
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
 
-    	clt3d(adjust_extrinsics, adjust_poly);
+    	clt3d(adjust_extrinsics, adjust_poly, dry_run);
         return;
     } else if (label.equals("AUX extrinsics") || label.equals("AUX Poly corr")) {
     	boolean adjust_extrinsics = label.equals("AUX extrinsics") || label.equals("AUX Poly corr");
@@ -5562,7 +5565,8 @@ private Panel panel1,
 
 	public boolean clt3d(
 			boolean adjust_extrinsics,
-			boolean adjust_poly
+			boolean adjust_poly,
+			boolean dry_run // init kernel/geometry only
 			) {
 		if (QUAD_CLT == null){
 			QUAD_CLT = new  QuadCLT (
@@ -5607,7 +5611,9 @@ private Panel panel1,
 				return false;
 			}
 		}
-
+		if (dry_run) {
+			return true;
+		}
 		QUAD_CLT.processCLTQuads3d(
 				adjust_extrinsics, // boolean adjust_extrinsics,
 				adjust_poly,       // boolean adjust_poly,
@@ -5639,7 +5645,9 @@ private Panel panel1,
 		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)  || (QUAD_CLT.tp.clt_3d_passes.size() == 0)) {
 			boolean OK = clt3d(
 					false, // boolean adjust_extrinsics,
-					false); // boolean adjust_poly);
+					false, // boolean adjust_poly);
+					false); // boolean dry_run // init kernel/geometry only
+
 			if (! OK) {
 				String msg = "DSI data is not available and \"CLT 3D\" failed";
 				IJ.showMessage("Error",msg);
@@ -5680,7 +5688,8 @@ private Panel panel1,
 		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)  || (QUAD_CLT.tp.clt_3d_passes.size() == 0)) {
 			boolean OK = clt3d(
 					false, // boolean adjust_extrinsics,
-					false); // boolean adjust_poly);
+					false, // boolean adjust_poly);
+					false); // boolean dry_run // init kernel/geometry only
 			if (! OK) {
 				String msg = "DSI data is not available and \"CLT 3D\" failed";
 				IJ.showMessage("Error",msg);

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

@@ -1810,12 +1810,32 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 		System.out.println("heading =\t"+      heading+"\tdegrees");
 		System.out.println("numSensors =\t"+   numSensors);
 		System.out.println("'=== Individual input parameters ===");
-		System.out.print  ("forward = ");for (int i = 0; i < numSensors;i++) System.out.print("\t"+forward[i]); System.out.println("\tmm");
-		System.out.print  ("right = ");  for (int i = 0; i < numSensors;i++) System.out.print("\t"+right[i]);   System.out.println("\tmm");
-		System.out.print  ("height = "); for (int i = 0; i < numSensors;i++) System.out.print("\t"+height[i]);  System.out.println("\tmm");
-		System.out.print  ("roll = ");   for (int i = 0; i < numSensors;i++) System.out.print("\t"+roll[i]);      System.out.println("\tdegrees");
-		System.out.print  ("px0 = ");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][0]);  System.out.println("\tpix");
-		System.out.print  ("py0 = ");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][1]);  System.out.println("\tpix");
+
+		System.out.print  ("forward = ");
+		if (forward != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+forward[i]); System.out.println("\tmm");
+		} 	else System.out.println("\tnull");
+		System.out.print  ("right = ");
+
+		if (right != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+right[i]);   System.out.println("\tmm");
+		} 	else System.out.println("\tnull");
+		System.out.print  ("height = ");
+		if (height != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+height[i]);  System.out.println("\tmm");
+		} 	else System.out.println("\tnull");
+		System.out.print  ("roll = ");
+		if (roll != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+roll[i]);      System.out.println("\tdegrees");
+		} 	else System.out.println("\tnull");
+		System.out.print  ("px0 = ");
+		if (pXY0 != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][0]);  System.out.println("\tpix");
+		} 	else System.out.println("\tnull");
+		System.out.print  ("py0 = ");
+		if (pXY0 != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+pXY0[i][1]);  System.out.println("\tpix");
+		} 	else System.out.println("\tnull");
 
 		System.out.println("'=== Common calculated parameters ===");
 		System.out.println("common_right =\t"+common_right + "\tmm");
@@ -1827,19 +1847,35 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 
 		if (showAll){
 			System.out.println("'=== Intermediate data: coordinates corrected for common elevation and heading ===");
-			System.out.print  ("X_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][0]);  System.out.println("\tmm");
-			System.out.print  ("Y_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][1]);  System.out.println("\tmm");
-			System.out.print  ("Z_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][2]);  System.out.println("\tmm");
+			if (XYZ_he != null) {
+				System.out.print  ("X_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][0]);  System.out.println("\tmm");
+				System.out.print  ("Y_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][1]);  System.out.println("\tmm");
+				System.out.print  ("Z_he =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_he[i][2]);  System.out.println("\tmm");
+			} else {
+				System.out.println("X_he, Y_he and Z_he are null");
+			}
 			System.out.println("'=== Intermediate data: coordinates corrected for common elevation, heading and roll ===");
-			System.out.print  ("X_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][0]);  System.out.println("\tmm");
-			System.out.print  ("Y_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][1]);  System.out.println("\tmm");
-			System.out.print  ("Z_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][2]);  System.out.println("\tmm");
+			if (XYZ_her != null) {
+				System.out.print  ("X_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][0]);  System.out.println("\tmm");
+				System.out.print  ("Y_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][1]);  System.out.println("\tmm");
+				System.out.print  ("Z_her =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+XYZ_her[i][2]);  System.out.println("\tmm");
+			} else {
+				System.out.println("X_her, Y_her and Z_her are null");
+			}
 		}
 
 		System.out.println("'=== Individual calculated parameters ===");
-		System.out.print  ("residual_roll = ");   for (int i = 0; i < numSensors;i++) System.out.print("\t"+(roll[i]-common_roll));System.out.println("\tdegrees");
+
+		System.out.print  ("residual_roll = ");
+		if (roll != null) {
+			for (int i = 0; i < numSensors;i++) System.out.print("\t"+(roll[i]-common_roll));System.out.println("\tdegrees");
+		} 	else System.out.println("\tnull");
+		if (rXY != null) {
 		System.out.print  ("X_rel =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+rXY[i][0]);  System.out.println("\trelative to disparityRadius");
 		System.out.print  ("Y_rel =");    for (int i = 0; i < numSensors;i++) System.out.print("\t"+rXY[i][1]);  System.out.println("\trelative to disparityRadius");
+		} else {
+			System.out.println("X_rel and Y_rel are null");
+		}
 	}
 
 	// return distance from disparity (in pixel units) for the current camera geometry

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

@@ -35,7 +35,6 @@ import java.nio.file.attribute.PosixFilePermission;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -59,7 +58,6 @@ import ij.WindowManager;
 //import ij.gui.Overlay;
 import ij.io.FileSaver;
 import ij.process.ColorProcessor;
-import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 
 
@@ -875,12 +873,12 @@ public class QuadCLT {
 		  for (int i=0;i<sharpKernelPaths.length;i++){
 			  System.out.println(i+":"+sharpKernelPaths[i]);
 		  }
-			if (clt_kernels == null){
-				clt_kernels = new double[eyesisCorrections.usedChannels.length][][][][][];
-				for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
-					clt_kernels[chn] = null;
-				}
-			}
+		  if (clt_kernels == null){
+			  clt_kernels = new double[eyesisCorrections.usedChannels.length][][][][][];
+			  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
+				  clt_kernels[chn] = null;
+			  }
+		  }
 		  ShowDoubleFloatArrays sdfa_instance = new ShowDoubleFloatArrays();
 
 		  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
@@ -2714,7 +2712,7 @@ 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] =  ShowDoubleFloatArrays.padBayerToFullSize(
 							  imp_srcs[srcChannel], // ImagePlus imp_src,
 							  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
 							  true); // boolean replicate);
@@ -3279,81 +3277,6 @@ 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
@@ -3417,7 +3340,7 @@ public class QuadCLT {
 // imp_srcs[srcChannel].show(); // REMOVE ME!
 
 				  this.geometryCorrection.woi_tops[srcChannel] = Integer.parseInt((String) imp_srcs[srcChannel].getProperty("WOI_TOP"));
-				  imp_srcs[srcChannel] =  padBayerToFullSize(
+				  imp_srcs[srcChannel] =  ShowDoubleFloatArrays.padBayerToFullSize(
 						  imp_srcs[srcChannel], // ImagePlus imp_src,
 						  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
 						  true); // boolean replicate);
@@ -5006,7 +4929,7 @@ 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] =  ShowDoubleFloatArrays.padBayerToFullSize(
 							  imp_srcs[srcChannel], // ImagePlus imp_src,
 							  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
 							  true); // boolean replicate);
@@ -8907,7 +8830,7 @@ 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] =  ShowDoubleFloatArrays.padBayerToFullSize(
 						  imp_srcs[srcChannel], // ImagePlus imp_src,
 						  eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
 						  true); // boolean replicate);