implemented 'neck' parameters (rotating/shifting camera as a whole), old bug fixes

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

@@ -109,7 +109,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
 	private Panel panelGoniometer;
 	private Panel panelPixelMapping, panelStereo,panelStereo1;
 	private Panel panelLWIR;
-	private Panel panelLWIR16;
+//	private Panel panelLWIR16;
 
 	private ShowDoubleFloatArrays SDFA_INSTANCE; // just for debugging?
 	JP46_Reader_camera JP4_INSTANCE;
@@ -508,6 +508,9 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
 	    	0.0,
 	    	0.0,
 	    	0.0, 0.0, 2360, //double [] GXYZ // coordinates (in mm) of the goniometer horizontal axis closest to the moving one in target system
+	    	0.0,
+	    	0.0,
+	    	0.0, 0.0,
 	       	2592, // int sensorWidth=      2592;
 	    	1936, //int sensorHeight=     1936;
 	    	2,    //int    shrinkGridForMask=2; //shrink detected grids by one point for/vert this number of times before calculating masks
@@ -692,14 +695,15 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
 		panelRun = new Panel();
 		panelRun.setLayout(new GridLayout(1, 0, 5, 5));
 		addButton("Process Calibration Files",panelRun);
-		addButton("Save",panelRun);
-		addButton("Save Selected",panelRun);
-		addButton("Restore",panelRun,color_restore);
+		addButton("Save",               panelRun);
+		addButton("Save Selected",      panelRun);
+		addButton("Restore",            panelRun,color_restore);
 		addButton("Restore no autoload",panelRun);
-		addButton("Restore SFE Latest",panelRun,color_restore);
-		addButton("List SFE",panelRun,color_report);
-		addButton("Stop",panelRun,color_stop);
-		addButton("Abort",panelRun,color_stop);
+		addButton("Properties clear",   panelRun, color_stop);
+		addButton("Restore SFE Latest", panelRun, color_restore);
+		addButton("List SFE",           panelRun,color_report);
+		addButton("Stop",               panelRun,color_stop);
+		addButton("Abort",              panelRun,color_stop);
 
 		add(panelRun);
 
@@ -1257,6 +1261,10 @@ if (MORE_BUTTONS) {
 	    } else if (label.equals("Restore") || label.equals("Restore no autoload")) {
 	    	restore(label.equals("Restore no autoload"));
 	    	return;
+/* ======================================================================== */
+	    } else if (label.equals("Properties clear")) {
+	    	PROPERTIES=new Properties();
+	    	return;
 /* ======================================================================== */
 		} else if (label.equals("Process Calibration Files")) {
 			processCalibrationFiles();
@@ -5977,7 +5985,7 @@ if (MORE_BUTTONS) {
 				return;
 			}
 			GenericDialog gd=new GenericDialog ("Select list mode");
-    		gd.addNumericField("Mode 0 - pointers, 1 - shift/Rots, 2 - points/extra, 3 - rms", 3, 0);
+    		gd.addNumericField("Mode 0 - pointers, 1 - shift/Rots, 2 - points/extra, 3 - rms, 4 - image numbers", 3, 0);
     		gd.showDialog();
     		if (gd.wasCanceled()) return;
     		int listMode=          (int) gd.getNextNumber();

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

@@ -27,6 +27,7 @@ import java.awt.Point;
 import java.awt.Rectangle;
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
+import java.util.Arrays;
 //import java.util.Arrays;
 //import java.io.StringWriter;
 import java.util.List;
@@ -3321,10 +3322,12 @@ For each point in the image
 		int numSuccess=0;
 		DistortionCalibrationData dcd=fittingStrategy.distortionCalibrationData;
 		for (int numGridImage=0;numGridImage<dcd.gIP.length;numGridImage++) {
+			/*
 			if (numGridImage >= 1680)	{
 				System.out.println("Processing debug image "+numGridImage);
 				System.out.println("Processing debug image "+numGridImage);
 			}
+			*/
 			int set_number = dcd.gIP[numGridImage].getSetNumber();
 			if ((set_number >= start_set) &&
 					(set_number <= end_set) &&
@@ -10747,17 +10750,31 @@ M * V = B
     		EyesisCameraParameters eyesisCameraParameters
     ){
     	boolean resetParametersToZero=false;
+    	boolean updateAllSubcameras = false;
     	boolean [] parameterMask= new boolean[distortionCalibrationData.getNumParameters()];
     	boolean [] channelMask=   new boolean[distortionCalibrationData.getNumSubCameras()];
     	boolean [] stationMask=   new boolean[distortionCalibrationData.getNumStations()];
+    	String [] source_stations = new String[stationMask.length+1];
+    	source_stations[0] = "---";
+    	for (int i = 0; i < stationMask.length; i++) {
+    		source_stations[i+1]=""+i;
+    	}
     	for (int i=0;i<parameterMask.length;i++) parameterMask[i]=false;
     	for (int i=0;i<channelMask.length;i++)   channelMask[i]=  true;
     	for (int i=0;i<stationMask.length;i++)   stationMask[i]=  true;
     	GenericDialog gd=new GenericDialog("Update (new) image settings from known data");
     	//
     	gd.addCheckbox("Reset selected parameters to zero (false - update from camera parameters)", resetParametersToZero);
+    	if (stationMask.length > 1) {
+    		gd.addChoice("Copy selected parameters from tis station to all other stations" , source_stations, source_stations[0]);
+    	}
     	gd.addMessage("Select which individual image parameters to be updated from the camera parameters (or reset to 0)");
-    	for (int i=0;i<parameterMask.length;i++) gd.addCheckbox(i+": "+distortionCalibrationData.getParameterName(i), parameterMask[i]);
+    	
+    	gd.addCheckbox("Update all subcamera parameters", updateAllSubcameras);
+    	
+    	for (int i=0;i<parameterMask.length;i++) {
+    		gd.addCheckbox(i+": "+distortionCalibrationData.getParameterName(i), parameterMask[i]);
+    	}
     	gd.addMessage("----------");
     	gd.addMessage("Select which channels (sub-cameras) to update");
     	for (int i=0;i<channelMask.length;i++) gd.addCheckbox("Subcamera "+i, channelMask[i]);
@@ -10776,6 +10793,12 @@ M * V = B
     	gd.showDialog();
     	if (gd.wasCanceled()) return false;
     	resetParametersToZero=gd.getNextBoolean();
+    	int source_station = -1;
+    	if (stationMask.length > 1) {
+    		source_station = gd.getNextChoiceIndex() - 1;
+    	}
+
+    	updateAllSubcameras = gd.getNextBoolean();
     	for (int i=0;i<parameterMask.length;i++) parameterMask[i]= gd.getNextBoolean();
     	for (int i=0;i<channelMask.length;i++)   channelMask[i]=   gd.getNextBoolean();
     	if (stationMask.length>1) {
@@ -10784,6 +10807,25 @@ M * V = B
     	boolean updateFromTimestamps= gd.getNextBoolean();
     	boolean allowClosest=         gd.getNextBoolean();
     	boolean reCenterVertically=   gd.getNextBoolean();
+
+    	if (updateAllSubcameras) {
+    		resetParametersToZero = false; // just for safety
+        	for (int i=0;i<parameterMask.length;i++) {
+        		parameterMask[i] |= distortionCalibrationData.isSubcameraParameter(i);
+        	}
+    	}
+    	
+    	if (source_station >= 0) {
+    		updateOtherStations(
+    	    		eyesisCameraParameters,
+    	    		source_station,
+    	    		parameterMask,
+    	    		channelMask,
+    	    		stationMask);    		
+    	}
+    	
+    	
+    	
     	if (reCenterVertically){
     		eyesisCameraParameters.recenterVertically(channelMask, stationMask);
     		for (int i=0;i<channelMask.length;i++) channelMask[i]= true;
@@ -10904,6 +10946,38 @@ M * V = B
     }
 
     
+    /**
+     * Update selected parameters from sourceStation to selected (stationMask) stations, filtered by channelMask
+     * @param eyesisCameraParameters
+     * @param sourceStation
+     * @param parameterMask
+     * @param channelMask
+     * @param stationMask
+     */
+    public void updateOtherStations(
+    		EyesisCameraParameters eyesisCameraParameters,
+    		int                    sourceStation,
+    		boolean []             parameterMask,
+    		boolean []             channelMask,
+    		boolean []             stationMask
+    		) {
+    	for (int stationNumber = 0; stationNumber <  stationMask.length; stationNumber++) if (stationMask[stationNumber]) {
+    		for (int subCam=0; subCam < channelMask.length; subCam++) if (channelMask[subCam]) {
+        		double [] oldVector=eyesisCameraParameters.getParametersVector(stationNumber,subCam);
+        		double [] newVector=eyesisCameraParameters.getParametersVector(sourceStation,subCam);
+        		for (int j=0;j<oldVector.length;j++) if (parameterMask[j]){
+        			oldVector[j]=newVector[j];
+        		}
+    			eyesisCameraParameters.setParametersVector(
+    					newVector,
+    					parameterMask,
+    					stationNumber,
+    					subCam);
+    		}
+    	}
+    }
+    
+
     /**
      * Copies selected parameters from the camera parameters to per-image parameters (i.e. for new/previously disabled images)
      * @param distortionCalibrationData grid distortionCalibrationData
@@ -11078,6 +11152,10 @@ M * V = B
     	int numSeries=allImages?(-1):this.fittingStrategy.currentSeriesNumber;
 		boolean [] selectedImages=fittingStrategy.selectedImages(numSeries); // all enabled
 		boolean [] selectedImagesDebug=null;
+		boolean include_disabled = allImages;
+		if (include_disabled) {
+			Arrays.fill(selectedImages, true);
+		}
 		boolean debugThis=false;
 		int maxDebugImages=10;
 		if (this.debugLevel>0) System.out.println("updateCameraParametersFromCalculated("+allImages+")");
@@ -11108,6 +11186,7 @@ M * V = B
 					System.out.println(i+": "+fittingStrategy.distortionCalibrationData.getParameterName(i)+" = "+par[i]);
 				}
 			}
+//			System.out.println(numImg+"[21]: "+fittingStrategy.distortionCalibrationData.getParameterName(21)+" = "+par[21]);
 		}
 		if (this.debugLevel>1) System.out.println("updateCameraParametersFromCalculated("+allImages+") for series="+numSeries);
 		// Next line is not needed anymore (will harm as will set orientationEstimated for all unselected sets)

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

@@ -669,6 +669,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     	 */
 
     	public int  buildParameterMap (int numSeries){
+    		return buildParameterMap (numSeries, true);
+    	}
+       	public int  buildParameterMap (int numSeries, boolean mark_disabled){
     		int numPars=this.distortionCalibrationData.getNumParameters();
     		int numImg=this.distortionCalibrationData.getNumImages();
     		int numTPars=this.parameterMode[numSeries].length;
@@ -681,7 +684,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 //    		int [][] tmpMap=new int[numTPars][3]; // temporary array parameterMap[][] (will be truncated)
     		int [][] tmpMap=new int[numPars*numImg][3]; // temporary array parameterMap[][] (will be truncated)
 			double masterTS=this.distortionCalibrationData.getImageTimestamp(this.masterImages[numSeries]); // timestamp of the master image
-			int [] masterVectorIndices = new int [numTPars];
+			int [] masterVectorIndices = new int [numTPars]; //[855] 
+			// all but [4][21] are 0,[4][21] is 2 (modeSupercommon),
+			// [4][63,105,147,189,231,273,315,357,399,441,483,525,567,609,651,]=10
+			// [4][693]= 2 EO(==16)?
+			// [4][733,777,819]= 26
 // iterate through all global/subcamera parameters
     		for (int numTPar=0;numTPar<numTPars;numTPar++) if (this.parameterMode[numSeries][numTPar]!=modeFixed){ // skip "fixed"
     			boolean isCommon=
@@ -695,7 +702,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     			int numPar=this.parameterList[numTPar][1]; // number of per-image parameter for this total parameter index
     			boolean isSubCamera=this.distortionCalibrationData.isSubcameraParameter(numPar);
     			// is it "same as" ?
-    			int sameAs = this.parameterMode[numSeries][numTPar] - this.definedModesAll.length; // number of subcamera to use
+    			int sameAs = this.parameterMode[numSeries][numTPar] - this.definedModesAll.length; // number of subcamera to use (this.definedModesAll.length==10)
     			int numTParMaster = -1;
     			int vectorIndexMaster = -1;
     			if (sameAs < 0  ) {
@@ -713,20 +720,26 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     				vectorIndexMaster = masterVectorIndices[numTParMaster]; // use as vectorIndex for slaves
     			}
 
-    			if (this.debugLevel>2) System.out.println("numTPar="+numTPar+" numSub="+numSub+" numPar="+numPar+" numTParMaster="+numTParMaster);
+    			if (this.debugLevel > 2) System.out.println("numTPa = "+numTPar+" numSub="+numSub+" numPar="+numPar+" numTParMaster="+numTParMaster);
 // iterate through available images
     			for (int numThisImg=0;numThisImg<numImg;numThisImg++) {
-    				if ((selectedEnabledImages[numThisImg]) &&
-    						(!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numThisImg))) &&
+//    				if ((selectedEnabledImages[numThisImg]) &&
+//    						(!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numThisImg))) &&
+//    						(this.reverseParameterMap[numThisImg][numPar]<0)){ // image used, this cell is not (yet) defined
+    					
+        			if((!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numThisImg))) &&
         						(this.reverseParameterMap[numThisImg][numPar]<0)){ // image used, this cell is not (yet) defined
     					if (this.debugLevel>2){
     						System.out.println("buildParameterMap("+numSeries+"): numThisImg="+numThisImg+", numPar="+numPar+", vectorIndex="+vectorIndex);
     					}
-// is it "same as" ?
+// is it "same as" ? // "same as" is only applicable to subcamera parameters
     					if (vectorIndexMaster >= 0){
+    						if (mark_disabled || selectedEnabledImages[numThisImg]) {
     							this.reverseParameterMap[numThisImg][numPar] = vectorIndexMaster;
+    						}
     						// does not look for same parameter in later images - leave it for the master?
     					} else {
+    						if (selectedEnabledImages[numThisImg]) {
 // assign it a new parameter
     							this.reverseParameterMap[numThisImg][numPar]=vectorIndex;
     							masterVectorIndices[numTPar] = vectorIndex;
@@ -739,9 +752,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     							double minDist=Math.abs(this.distortionCalibrationData.getImageTimestamp(numThisImg)-masterTS);
     							if (this.debugLevel>2) System.out.println("vectorIndex="+vectorIndex+" numThisImg="+numThisImg);
 // see if same parameter in some other (later) image(s) is shared
-    						for (int numOtherImg=numThisImg + 1; numOtherImg < numImg; numOtherImg++)
-    							if ((selectedEnabledImages[numOtherImg]) && // OOB 1
-    									(!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numOtherImg))) &&
+//    							for (int numOtherImg=numThisImg + 1; numOtherImg < numImg; numOtherImg++) {
+    							boolean proc_disabled = mark_disabled && (isCommon || isStation || isGroup);
+       							for (int numOtherImg=0; numOtherImg < numImg; numOtherImg++) {
+       								// 06.03.2021: old way for enabled images - only assign to later images
+       								// disabled or unselected images - assign to even earlier ones
+   								    if ((selectedEnabledImages[numOtherImg] && (numOtherImg > numThisImg)) || (proc_disabled && !selectedEnabledImages[numOtherImg])) {
+//   								    	if ((selectedEnabledImages[numOtherImg]) && // OOB 1
+							    		if ((!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numOtherImg))) &&
    								    			(this.reverseParameterMap[numOtherImg][numPar]<0)){ // image used, this cell is not (yet) defined
    								    		if ((this.distortionCalibrationData.getImageTimestamp(numOtherImg)==thisTS) ||  // same parameter same timestamp - same group even if is set differently
    								    				(isStation && (this.distortionCalibrationData.gIP[numOtherImg].getStationNumber()==thisStation)) || // new
@@ -757,10 +775,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
    								    			}
    								    		}
    								    	}
+   								    }
+       							}
     							vectorIndex++;
     						}
     					}
     				}
+    			}
+// second pass    			
+    			
 
     		}
     		// reverseParameterMap built,   vectorIndex equals to the total number of parameters needed for fitting
@@ -1140,7 +1163,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     									" nSub="+nSub+" distortionCalibrationData.getImageSubcamera("+numImg+")="+distortionCalibrationData.getImageSubcamera(numImg)+
     									" vector["+vPar+"]="+vector[vPar]);
     						}
-    						if ((!isSubCamera) || (nSub==this.distortionCalibrationData.getImageSubcamera(numImg))) {
+//    						if ((!isSubCamera) || (nSub==this.distortionCalibrationData.getImageSubcamera(numImg))) {
+    						if ((!isSubCamera) || (nSub==this.distortionCalibrationData.getImageSubcamera(numImg)) ||
+    								(this.reverseParameterMap[numImg][nPar] == vPar)) { // 06.03.2021
 //    							this.distortionCalibrationData.pars[numImg][nPar]=vector[vPar];
     							this.distortionCalibrationData.setParameterValue(numImg,nPar,vector[vPar],true);
     						}
@@ -1170,7 +1195,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     		return vector;
     	}
     	/**
-    	 * Calculates which of all parameters for the particular sensor are to be adjusted (to reduce calcualtions)
+    	 * Calculates which of all parameters for the particular sensor are to be adjusted (to reduce calculations)
     	 * @param numImg number of image
     	 * @param vector parameters vector
     	 * @return mask vector to be used with the results of getImageParametersVector()
@@ -2334,7 +2359,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 
 
 						thisChoice = theseChoices[indx];
-						System.out.println("selectStrategyStep(): this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]+" indx = "+indx);
+//						System.out.println("selectStrategyStep(): this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]+" indx = "+indx);
 					}
 					gd.addChoice( // ArrayIndexOutOfBoundsException: 9
 							(this.distortionCalibrationData.isSubcameraParameter(parIndex)?"":"* ") +

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

@@ -483,12 +483,19 @@ import ij.io.Opener;
         		index++;
         	}
         	for (int n=0;n<getNumGeometricChannels();n++) titles[n]=geometricTitles[n];
-        	for (int numStation=0;numStation<this.numStations;numStation++) {
+        	for (int numStation = 0; numStation < this.numStations; numStation++) {
+        		int numStationSrc = numStation;
+        		if (numStationSrc >= this.photometricByView.length) {
+        			System.out.println("Station"+numStationSrc+" >= this.photometricByView.length, saving from the last known station");
+        			numStationSrc = this.photometricByView.length-1;
+        		}
         		for (int nView=0;nView<getNumViews();nView++) {
         			for (int chn=0;chn<getNumPhotometricChannels();chn++){
         				//        		int pixIndex=getNumGeometricChannels()+chn*this.getNumPhotometricChannels()();
         				int pixIndex=getNumGeometricChannels()+numZCorr+(nView + numStation*getNumViews()) *getNumPhotometricChannels()+chn;
-        				for (int i=0;i<length;i++) pixels[pixIndex][i]= (float) this.photometricByView[numStation][nView][chn][i]; //OOB 8 //oob 12
+        				for (int i=0;i<length;i++) {
+        					pixels[pixIndex][i]= (float) this.photometricByView[numStationSrc][nView][chn][i]; //OOB 8 //oob 12
+        				}
         				titles[pixIndex]=photometricTitles[chn]+nView;
         			}
         		}