Putting all together, adding generation of thumbnails, KML, etc.

src/main/java/BiQuadParameters.java

@@ -226,16 +226,19 @@ public class BiQuadParameters {
 
 
 
+	public boolean ml_generate =               false;  // Generate ML data automatically when running ground truth
+	public boolean ml_poles =                  true;   // Generate ML data from the DSI that includes extracted poles
+	public boolean ml_copyJP4 =                true;   // Copy source jp4 files when running "Ground truth" command
 
-	public int     ml_hwidth =                 2;      // Half-width of the ML tiles to export (0-> 1x1, 1->3x3, 2 -> 5x5)
-	public double  ml_disparity_sweep  =       2.0;    // Disparity sweep around ground truth, each side
-	public int     ml_sweep_steps =            5;      // Number of disparity sweep steps
+	public int     ml_hwidth =                 4;      // Half-width of the ML tiles to export (0-> 1x1, 1->3x3, 2 -> 5x5)
+	public double  ml_disparity_sweep  =       1.0;    // Disparity sweep around ground truth, each side
+	public int     ml_sweep_steps =            21;      // Number of disparity sweep steps
 
-	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_aux =               false; // true; // include auxiliary camera data in the ML output
+	public boolean ml_keep_inter =             false; // 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_keep_tbrl =              false; // true; // include individual top, bottom, right, left pairs
+	public boolean ml_keep_debug=              false; // 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
 	public boolean ml_show_ml =                true; // show each generated MLoutput file
@@ -311,7 +314,7 @@ public class BiQuadParameters {
 		gd.addNumericField("Minimal RMS improvement after short cycle to exit",                                   this.rig_adjust_short_threshold,  3,6,"",
 				"Short cycle iteration finish after relative RMS improvement is less than this of maximal number of steps is exceeded");
 		gd.addCheckbox    ("Adjust orientation (azimuth, tilt, roll) of the auxiliary camera",                    this.rig_adjust_orientation,"3 angles, most basic adjustment");
-		gd.addCheckbox    ("Adjust orientation relative zoom of the auxiliary camera",                            this.rig_adjust_zoom,"Not likely to change, may be frozen");
+		gd.addCheckbox    ("Adjust relative zoom of the auxiliary camera",                                        this.rig_adjust_zoom,"Not likely to change, may be frozen");
 		gd.addCheckbox    ("Adjust position of the aux camera in the main camera pricipal plane",                 this.rig_adjust_angle,"0 - exactly  to the right, positive - higher than main");
 		gd.addCheckbox    ("Adjust aux camera distance from the main",                                            this.rig_adjust_distance,"Normally not practical, rely on direct measurement");
 		gd.addCheckbox    ("Adjust aux camera distance from the main principal plane",                            this.rig_adjust_forward,"Not implemented, assumed zero");
@@ -600,6 +603,13 @@ public class BiQuadParameters {
 
         gd.addTab("ML","Parameters related to the ML files generation for the dual-quad camera rig");
 
+		gd.addCheckbox    ("Generate ML data automatically",                                                       this.ml_generate,
+				"Generate ML data automatically when running ground truth (may run separately from a command button)");
+		gd.addCheckbox    ("Generate ML data from the DSI that includes extracted poles",                          this.ml_poles,
+				"If unchecked - use DSI w/o poles data");
+		gd.addCheckbox    ("Copy JP4 source images when generating ML data",                                       this.ml_copyJP4,
+				"Possible to run by a command button");
+
 		gd.addNumericField("Half-width of the ML tiles to export (0-> 1x1, 1->3x3, 2 -> 5x5)",                    this.ml_hwidth,  0,3,"",
 				"Amount of data to export to the ML system");
 		gd.addNumericField("Disparity sweep around ground truth, each side",                                      this.ml_disparity_sweep,  3,6,"",
@@ -802,6 +812,10 @@ public class BiQuadParameters {
 		this.rf_min_disp=                   gd.getNextNumber();
 		this.rf_remove_unselected=          gd.getNextBoolean();
 
+		this.ml_generate=                   gd.getNextBoolean();
+		this.ml_poles=                      gd.getNextBoolean();
+		this.ml_copyJP4=                    gd.getNextBoolean();
+
 		this.ml_hwidth=               (int) gd.getNextNumber();
 		this.ml_disparity_sweep=            gd.getNextNumber();
 		this.ml_sweep_steps=          (int) gd.getNextNumber();
@@ -995,6 +1009,9 @@ public class BiQuadParameters {
 		properties.setProperty(prefix+"rf_min_disp",               this.rf_min_disp+"");
 		properties.setProperty(prefix+"rf_remove_unselected",      this.rf_remove_unselected+"");
 
+		properties.setProperty(prefix+"ml_generate",               this.ml_generate+"");
+		properties.setProperty(prefix+"ml_poles",                  this.ml_poles+"");
+		properties.setProperty(prefix+"ml_copyJP4",                this.ml_copyJP4+"");
 		properties.setProperty(prefix+"ml_hwidth",                 this.ml_hwidth+"");
 		properties.setProperty(prefix+"ml_disparity_sweep",        this.ml_disparity_sweep+"");
 		properties.setProperty(prefix+"ml_sweep_steps",            this.ml_sweep_steps+"");
@@ -1185,6 +1202,9 @@ public class BiQuadParameters {
 		if (properties.getProperty(prefix+"rf_min_disp")!=null)             this.rf_min_disp=Double.parseDouble(properties.getProperty(prefix+"rf_min_disp"));
 		if (properties.getProperty(prefix+"rf_remove_unselected")!=null)    this.rf_remove_unselected=Boolean.parseBoolean(properties.getProperty(prefix+"rf_remove_unselected"));
 
+		if (properties.getProperty(prefix+"ml_generate")!=null)             this.ml_generate=Boolean.parseBoolean(properties.getProperty(prefix+"ml_generate"));
+		if (properties.getProperty(prefix+"ml_poles")!=null)                this.ml_poles=Boolean.parseBoolean(properties.getProperty(prefix+"ml_poles"));
+		if (properties.getProperty(prefix+"ml_copyJP4")!=null)              this.ml_copyJP4=Boolean.parseBoolean(properties.getProperty(prefix+"ml_copyJP4"));
 		if (properties.getProperty(prefix+"ml_hwidth")!=null)               this.ml_hwidth=Integer.parseInt(properties.getProperty(prefix+"ml_hwidth"));
 		if (properties.getProperty(prefix+"ml_disparity_sweep")!=null)      this.ml_disparity_sweep=Double.parseDouble(properties.getProperty(prefix+"ml_disparity_sweep"));
 		if (properties.getProperty(prefix+"ml_sweep_steps")!=null)          this.ml_sweep_steps=Integer.parseInt(properties.getProperty(prefix+"ml_sweep_steps"));
@@ -1376,6 +1396,9 @@ public class BiQuadParameters {
 		bqp.rf_min_disp=                this.rf_min_disp;
 		bqp.rf_remove_unselected=       this.rf_remove_unselected;
 
+		bqp.ml_generate=                this.ml_generate;
+		bqp.ml_poles=                   this.ml_poles;
+		bqp.ml_copyJP4=                 this.ml_copyJP4;
 		bqp.ml_hwidth=                  this.ml_hwidth;
 		bqp.ml_disparity_sweep=         this.ml_disparity_sweep;
 		bqp.ml_sweep_steps=             this.ml_sweep_steps;

src/main/java/BiScan.java

@@ -871,10 +871,10 @@ public class BiScan {
 									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
 									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
 								}
-								if (nTile == 66945) {
-									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
-									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
-								}
+//								if (nTile == 66945) {
+//									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
+//									System.out.println("suggestNewScan(): nTile="+nTile+" w="+w);
+//								}
 
 							}
 						}

src/main/java/EyesisCorrections.java

@@ -2443,7 +2443,7 @@ public class EyesisCorrections {
 				   }
 			   }
 
-			   if (hasAlphaHighByte){
+			   if (hasAlphaHighByte && (jpegQuality <= 0)){
 				   if (png){
 					   if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
 					   (new EyesisTiff()).savePNG_ARGB32(

src/main/java/Eyesis_Correction.java

@@ -552,7 +552,7 @@ private Panel panel1,
 			addButton("CLT infinity corr",         panelClt2, color_conf_process);
 			addButton("CLT ext infinity corr",     panelClt2, color_conf_process);
 			addButton("CLT reset 3D",              panelClt2, color_stop);
-			addButton("CLT Extrinsics",            panelClt2, color_process);
+			addButton("MAIN extrinsics",           panelClt2, color_process);
 			addButton("CLT Poly corr",             panelClt2, color_process);
 			addButton("CLT 3D",                    panelClt2, color_process);
 			addButton("CLT planes",                panelClt2, color_conf_process);
@@ -583,19 +583,21 @@ private Panel panel1,
 //			addButton("CLT 2*4 images",             panelClt4, color_conf_process);
 //			addButton("CLT 2*4 images - 2",         panelClt4, color_conf_process);
 //			addButton("CLT 2*4 images - 3",         panelClt4, color_conf_process);
+			addButton("SHOW extrinsics",              panelClt4, color_configure);
+			addButton("MAIN extrinsics",            panelClt4, color_process);
+			addButton("RIG extrinsics",             panelClt4, color_conf_process);
+			addButton("AUX extrinsics",             panelClt4, color_process);
 			addButton("Rig8 images",                panelClt4, color_conf_process);
-			addButton("Rig infinity calibration",   panelClt4, color_conf_process);
-			addButton("AUX Extrinsics",             panelClt4, color_process);
-			addButton("AUX show fine",              panelClt4, color_configure);
-//			addButton("Rig enhance",                panelClt4, color_conf_process);
+
+			//			addButton("Rig enhance",                panelClt4, color_conf_process);
 //			/"Reset GT"
 			addButton("Reset GT",                   panelClt4, color_stop);
-			addButton("Ground truth 0",             panelClt4, color_configure);
+//			addButton("Ground truth 0",             panelClt4, color_configure);
 			addButton("Ground truth",               panelClt4, color_conf_process);
 			addButton("Show biscan",                panelClt4, color_configure);
 			addButton("Poles GT",                   panelClt4, color_process);
 			addButton("ML export",                  panelClt4, color_conf_process);
-			addButton("Rig planes",                 panelClt4, color_conf_process);
+			addButton("JP4 copy",                   panelClt4, color_conf_process);
 
 
 			add(panelClt4);
@@ -4253,9 +4255,9 @@ private Panel panel1,
 
 /// ============================================
 
-    } else if (label.equals("CLT 3D") || label.equals("CLT Extrinsics") || label.equals("CLT Poly corr")) {
+    } else if (label.equals("CLT 3D") || label.equals("MAIN extrinsics") || label.equals("CLT Poly corr")) {
 
-    	boolean adjust_extrinsics = label.equals("CLT Extrinsics") || label.equals("CLT Poly corr");
+    	boolean adjust_extrinsics = label.equals("MAIN extrinsics") || label.equals("CLT Poly corr");
     	boolean adjust_poly = label.equals("CLT Poly corr");
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
@@ -4333,8 +4335,8 @@ private Panel panel1,
         }
 */
         return;
-    } else if (label.equals("AUX Extrinsics") || label.equals("AUX Poly corr")) {
-    	boolean adjust_extrinsics = label.equals("AUX Extrinsics") || label.equals("AUX Poly corr");
+    } else if (label.equals("AUX extrinsics") || label.equals("AUX Poly corr")) {
+    	boolean adjust_extrinsics = label.equals("AUX extrinsics") || label.equals("AUX Poly corr");
     	boolean adjust_poly = label.equals("AUX Poly corr");
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
@@ -4567,13 +4569,13 @@ private Panel panel1,
     	getPairImages2(true);
     	return;
 /* ======================================================================== */
-    } else if (label.equals("Rig infinity calibration")) {
+    } else if (label.equals("RIG extrinsics")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
     	infinityRig();
     	return;
 /* ======================================================================== */
-    } else if (label.equals("AUX show fine")) {
+    } else if (label.equals("SHOW extrinsics")) {
         if (QUAD_CLT == null){
         	QUAD_CLT = new  QuadCLT (
         			QuadCLT.PREFIX,
@@ -4599,6 +4601,8 @@ private Panel panel1,
         	}
         }
         QUAD_CLT_AUX.showExtrinsicCorr("aux");// show_fine_corr("aux");
+        QUAD_CLT_AUX.geometryCorrection.showRig();// show_fine_corr("aux");
+
         QuadCLT dbg_QUAD_CLT = QUAD_CLT;
         QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;
 
@@ -4649,6 +4653,12 @@ private Panel panel1,
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
     	exportMLData();
     	return;
+/* ======================================================================== */
+    } else if (label.equals("JP4 copy")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+    	copyJP4src();
+    	return;
 
 /* ======================================================================== */
     } else if (label.equals("CLT rig edit")) {
@@ -5163,7 +5173,7 @@ private Panel panel1,
 		return true;
 	}
 
-//	boolean adjust_extrinsics = label.equals("CLT Extrinsics") || label.equals("CLT Poly corr");
+//	boolean adjust_extrinsics = label.equals("MAIN extrinsics") || label.equals("CLT Poly corr");
 //	boolean adjust_poly = label.equals("CLT Poly corr");
 	public boolean clt3d(
 			boolean adjust_extrinsics,
@@ -5285,8 +5295,8 @@ private Panel panel1,
 
 	public boolean exportMLData() {
 		long startTime=System.nanoTime();
-		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)) {
-			String msg = "DSI data is not available. Please run \"CLT 3D\" first";
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.rig_pre_poles_ds == null)) {
+			String msg = "DSI data is not available. Please run \"Ground truth\" first";
 			IJ.showMessage("Error",msg);
 			System.out.println(msg);
 			return false;
@@ -5325,6 +5335,94 @@ private Panel panel1,
     	return true;
 	}
 
+	public boolean copyJP4src() {
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)) {
+			if (QUAD_CLT == null){
+				QUAD_CLT = new  QuadCLT (
+						QuadCLT.PREFIX,
+						PROPERTIES,
+						EYESIS_CORRECTIONS,
+						CORRECTION_PARAMETERS);
+				if (DEBUG_LEVEL > 0){
+					System.out.println("Created new QuadCLT instance, will need to read CLT kernels");
+				}
+			}
+			String configPath=getSaveCongigPath();
+			if (configPath.equals("ABORT")) return false;
+
+			EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
+			int numChannels=EYESIS_CORRECTIONS.getNumChannels();
+			CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
+
+			if (!QUAD_CLT.CLTKernelsAvailable()){
+				if (DEBUG_LEVEL > 0){
+					System.out.println("Reading CLT kernels");
+				}
+				QUAD_CLT.readCLTKernels(
+						CLT_PARAMETERS,
+						THREADS_MAX,
+						UPDATE_STATUS, // update status info
+						DEBUG_LEVEL);
+
+				if (DEBUG_LEVEL > 1){
+					QUAD_CLT.showCLTKernels(
+							THREADS_MAX,
+							UPDATE_STATUS, // update status info
+							DEBUG_LEVEL);
+				}
+			}
+
+			if (!QUAD_CLT.geometryCorrectionAvailable()){
+				if (DEBUG_LEVEL > 0){
+					System.out.println("Calculating geometryCorrection");
+				}
+				if (!QUAD_CLT.initGeometryCorrection(DEBUG_LEVEL+2)){
+					return false;
+				}
+			}
+/*
+			boolean OK = clt3d(
+					false, // boolean adjust_extrinsics,
+					false); // boolean adjust_poly);
+			if (! OK) {
+				String msg = "DSI data is not available and \"CLT 3D\" failed";
+				IJ.showMessage("Error",msg);
+				System.out.println(msg);
+				return false;
+			}
+*/
+		}
+		if (!prepareRigImages()) return false;
+    	String configPath=getSaveCongigPath();
+    	if (configPath.equals("ABORT")) return false;
+
+    	if (DEBUG_LEVEL > -2){
+    		System.out.println("++++++++++++++ Copying JP4 source files ++++++++++++++");
+    	}
+    	try {
+    		TWO_QUAD_CLT.copyJP4src( // actually there is no sense to process multiple image sets. Combine with other processing?
+    				QUAD_CLT, // QuadCLT quadCLT_main,
+    				QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
+    				CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
+    				DEBUG_LEVEL);
+    	} catch (Exception e) {
+    		// TODO Auto-generated catch block
+    		e.printStackTrace();
+    	} //final int        debugLevel);
+
+    	if (configPath!=null) {
+    		saveTimestampedProperties( // save config again
+    				configPath,      // full path or null
+    				null, // use as default directory if path==null
+    				true,
+    				PROPERTIES);
+    	}
+
+		return true;
+	}
+
+
+
 	public boolean infinityRig() {
 		if (!prepareRigImages()) return false;
     	String configPath=getSaveCongigPath();

src/main/java/GeometryCorrection.java

@@ -890,6 +890,19 @@ public class GeometryCorrection {
 			recalcRXY();
 			return true;
 		}
+		public void showRigOffsets()
+		{
+			System.out.println("=== Inter-camera adjustments ===");
+			System.out.println("                                                           Baseline "+ this.baseline +"mm");
+			System.out.println("                              Angle to the aux camera from the main "+ (180.0/Math.PI*this.aux_angle)+"°");
+			System.out.println("Auxilliary camera forward from the plane of the main one (not used) "+ this.aux_z +"mm");
+			System.out.println("               Auxilliary camera azimuth  (positive - to the right) "+ (par_scales[AUX_AZIMUTH_INDEX] * this.aux_azimuth) + "pix");
+			System.out.println("                     Auxilliary camera tilt (positive - looking up) "+ (par_scales[AUX_TILT_INDEX] * this.aux_tilt)+"pix");
+			System.out.println("                      Auxilliary camera roll (positive - clockwise) "+ (par_scales[AUX_ROLL_INDEX] * this.aux_roll)+"pix");
+			System.out.println("      Relative zoom - difference from 1.0 in parts parts per 1/1000 "+ (par_scales[AUX_ZOOM_INDEX] * this.aux_zoom) +"pix");
+		}
+
+
 	}
 
 	public boolean editRig() {
@@ -899,6 +912,10 @@ public class GeometryCorrection {
 		return this.rigOffset.editOffsetsPixels();
 	}
 
+	public void showRig() {
+		this.rigOffset.showRigOffsets();
+	}
+
 	public boolean setRigOffsetFromProperies(String parent_prefix,Properties properties) {
 		RigOffset rigOffset = new RigOffset();
 		boolean gotit = rigOffset.getProperties(parent_prefix, properties);

src/main/java/JP46_Reader_camera.java

@@ -310,6 +310,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		boolean showDemux=showImage && demux;
 		if (demux) showImage=false;
 		double [] xtraExif=new double[1]; // ExposureTime
+		double [] lla = null;
 		try {
 			imp = openJpegOrGif(directory, fileName);
 			if (imp == null) {
@@ -320,6 +321,12 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 				if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 14,xtraExif); /* after or 8.0.8.32 */
 				if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 12,xtraExif); /* after or 8.0.7.3 */
 				if (ElphelMakerNote==null) ElphelMakerNote = readElphelMakerNote(directory, fileName, 8 ,xtraExif); /* before 8.0.7.3 */
+				lla = readGpsLLA(directory, fileName);
+				if (lla != null) {
+					imp.setProperty("LATITUDE",   String.format("%f",lla[0]));
+					imp.setProperty("LONGITUDE",  String.format("%f",lla[1]));
+					imp.setProperty("ALTITUDE",   String.format("%f",lla[2]));
+				}
 			}
 		} catch (IOException e) {
 			IJ.showStatus("");
@@ -850,6 +857,78 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		return note;
 	}
 
+	double [] readGpsLLA(String directory, String fileName)  throws IOException
+	{
+		RandomAccessFile in = new RandomAccessFile(directory + fileName, "r");
+		byte[] head = new byte[4096]; /* just read the beginning of the file */
+		in.readFully(head);
+		in.close(); // was no close()! -? "too many open files"
+		if ((head[this.ExifOffset]!=0x4d) || (head[this.ExifOffset+1]!=0x4d)) {
+			IJ.showMessage("JP46 Reader", "Exif Header not found in " + directory + fileName);
+			return null;
+		}
+		// skip to gps header
+		byte [] sig = {0x2, 0x2, 0x0, 0x0};
+		int i = this.ExifOffset + 2;
+		boolean match=false;
+		for (i = this.ExifOffset + 2; i < (head.length - sig.length); i++ ) {
+			match=true;
+			for (int j=0;j<sig.length;j++)if (head[i+j]!=sig[j]){
+				match=false;
+				break;
+			}
+			if (match) break;
+		}
+		i += sig.length;
+		if (i >= (head.length-4)) {
+			/* IJ.showMessage("JP46 Reader", "MakerNote tag not found in "+directory + fileName+ ", finished at offset="+i); // re-enable with DEBUG_LEVEL*/
+			return null;
+		}
+//		System.out.println(String.format("offset=0x%04x", i));
+		double [] lla = new double[3];
+		boolean [] lla_sign = new boolean[3];
+		for (int ntag = 0; ntag < 10; ntag++) {
+			// read 2 big endian bytesof tag, and 2 - type
+			int tag =  ((head[i+0] << 8) & 0xff00) +     ((head[i+1] << 0) & 0x00ff);
+			int typ =  ((head[i+2] << 8) & 0xff00) +     ((head[i+3] << 0) & 0x00ff);
+			int len =  ((head[i+4] <<24) & 0xff000000) + ((head[i+5] <<16) & 0x00ff0000) + ((head[i+ 6] << 8) & 0x0000ff00) + ((head[i+ 7] << 0) & 0x000000ff);
+			int val =  ((head[i+8] <<24) & 0xff000000) + ((head[i+9] <<16) & 0x00ff0000) + ((head[i+10] << 8) & 0x0000ff00) + ((head[i+11] << 0) & 0x000000ff);
+//			System.out.println(String.format("ntag=%2d tag = 0x%04x type = 0x%04x len = 0x%08x value = 0x%08x", ntag, tag, typ, len, val));
+			i+=12;
+			switch (tag) {
+			case 1: lla_sign[0] = ((val >> 24) & 0xff) == 0x53; break; // S GPSLatitudeRef
+			case 2: int [] lat_arr = readExifBE(head, this.ExifOffset + val , 2 * len); //GPSLatitude
+			lla[0] = 1.0*lat_arr[0]/lat_arr[1] + (1.0/60)* lat_arr[2]/lat_arr[3] + (1.0/3600)* lat_arr[4]/lat_arr[5];
+			break;
+			case 3: lla_sign[1] = ((val >> 24) & 0xff) == 0x57; break; // W GPSLongitudeRef
+			case 4: int [] long_arr = readExifBE(head, this.ExifOffset + val , 2 * len); // GPSLongitude
+			lla[1] = 1.0*long_arr[0]/long_arr[1] + (1.0/60)* long_arr[2]/long_arr[3] + (1.0/3600)* long_arr[4]/long_arr[5];
+			break;
+			case 5: lla_sign[2] = ((val >> 24) & 0xff) != 0x0; break; // GPSAltitudeRef
+			case 6: int [] alt_arr = readExifBE(head, this.ExifOffset + val , 2 * len); // GPSLongitude
+			lla[2] = 1.0*alt_arr[0]/alt_arr[1];
+			break;
+			}
+		}
+		for (int j = 0; j < lla.length; j++) {
+			if (lla_sign[j]) lla[j] *= -1;
+		}
+//		System.out.println("Lat = "+lla[0]+" Long = "+lla[1]+ " alt = "+lla[2]+"m");
+		return lla;
+
+	}
+	int [] readExifBE(byte [] head, int offset, int len) {
+		int [] data = new int [len];
+		for (int i = 0; i < len; i++) {
+			int offs = offset + 4*i;
+			data[i] = ((head[offs + 0] << 24) & 0xff000000) +
+					  ((head[offs + 1] << 16) & 0x00ff0000) +
+					  ((head[offs + 2] <<  8) & 0x0000ff00) +
+					  ((head[offs + 3] <<  0) & 0x000000ff);
+		}
+		return data;
+	}
+
 	long[] readElphelMakerNoteURL(String url, int len, double [] xtraExif) throws IOException  {
 		URL camURL = null;
 		URLConnection urlConn = null;

src/main/java/MeasuredLayers.java

@@ -1261,7 +1261,8 @@ public class MeasuredLayers {
 										}
 										if (iworst < 0){
 											if (debugLevel > 0) {
-												System.out.println("**** this may be BUG in getDisparityStrengthML() can not find the worst sample  - all tiles fit perfectly ****");
+												System.out.println("**** this may be BUG in getDisparityStrengthML() can not find the worst sample  - all tiles fit perfectly ****, num_in_sample="+
+														num_in_sample+", stX="+stX+", stY="+stY);
 											}
 											// this can happen if some samples are the same and all the pixels fit exactly - use all of them
 											break;
@@ -1354,7 +1355,8 @@ public class MeasuredLayers {
 										//remove_far_only
 									}
 									if (iworst < 0){
-										System.out.println("**** this is a BUG2 in getDisparityStrengthML() ****"); // all smpl_d are NaNs
+										System.out.println("**** this may be BUG2 in getDisparityStrengthML() can not find the worst sample  - all tiles fit perfectly ****, num_in_sample="+
+												num_in_sample+", stX="+stX+", stY="+stY);
 										break;
 									}
 									// remove worst sample
@@ -1378,7 +1380,7 @@ public class MeasuredLayers {
 									}
 								} else {
 									num_in_sample = 0;
-									System.out.println("**** this is a BUG in getDisparityStrengthML(), shoud not happen ? ****");
+									System.out.println("**** this is a BUG in getDisparityStrengthML(), should not happen ? ****");
 								}
 							}
 							}
@@ -1453,6 +1455,12 @@ public class MeasuredLayers {
 										}
 										ds[0][indx] = sd;
 										ds[1][indx] = sw * lapWeight[dy][dx] /sum_wnd; // average weights, multiply by window //** TODO: change
+
+										if ((ds[0][indx] ==0.0) && (ds[0][indx] ==0.0)) {
+											System.out.println("**** this may be BUG5 in getDisparityStrengthML()  ****, num_in_sample="+
+													num_in_sample+", stX="+stX+", stY="+stY+" ds[0]["+indx+"]="+ds[0][indx]+", ds[1]["+indx+"]="+ds[1][indx]);
+											ds[1][indx] = 0.0;
+										}
 									}
 								} else {
 									num_in_sample = 0;

src/main/java/QuadCLT.java

@@ -24,10 +24,19 @@
 
 //import java.awt.Polygon;
 import java.awt.Rectangle;
+import java.io.File;
 import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+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;
 
 import ij.CompositeImage;
@@ -67,6 +76,7 @@ public class QuadCLT {
 	TileProcessor                                          tp = null;
 
 	String                                                 image_name = null;
+	double []                                              gps_lla =    null;
 	double [][][]                                          image_data = null;
     boolean [][]                                           saturation_imp = null; // (near) saturated pixels or null
     boolean                                                is_aux = false;
@@ -4730,7 +4740,7 @@ public class QuadCLT {
 	  public boolean editRig()
 	  {
 		  if (!is_aux) {
-			  System.out.println("Rig offsets can only be edited for the auxiliary camera, not for the amin one");
+			  System.out.println("Rig offsets can only be edited for the auxiliary camera, not for the main one");
 			  return false;
 		  }
 //		  GeometryCorrection gc = this.geometryCorrection;
@@ -7700,13 +7710,16 @@ public class QuadCLT {
 			  System.out.println("Wavefront object file saved to "+wfOutput.obj_path);
 			  System.out.println("Wavefront material file saved to "+wfOutput.mtl_path);
 		  }
+
+		  // Save KML and ratings files if they do not exist (so not to overwrite edited ones), make them world-writable
+		  writeKml        (debugLevel);
+		  writeRatingFile (debugLevel);
+
+
 		  Runtime.getRuntime().gc();
 		  System.out.println("output3d(): generating 3d output files  finished at "+
 				  IJ.d2s(0.000000001*(System.nanoTime()-this.startStepTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
-
-
 		  return true;
-//		  return imp_bgnd; // relative (to x3d directory) path - (String) imp_bgnd.getProperty("name");
 	  }
 
 
@@ -9079,5 +9092,160 @@ public class QuadCLT {
 				  IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
 	  }
 
+	  public void setGpsLla(
+			  String source_file)
+	  {
+		  ImagePlus imp=(new JP46_Reader_camera(false)).open(
+				  "", // path,
+				  source_file,
+				  "",  //arg - not used in JP46 reader
+				  true, // un-apply camera color gains
+				  null, // new window
+				  false); // do not show
+		  if (imp.getProperty("LATITUDE") != null){
+			  gps_lla = new double[3];
+			  for (int i = 0; i < 3; i++) {
+				  gps_lla[i] = Double.NaN;
+			  }
+				if (imp.getProperty("LATITUDE")  != null) gps_lla[0] =Double.parseDouble((String) imp.getProperty("LATITUDE"));
+				if (imp.getProperty("LONGITUDE") != null) gps_lla[1] =Double.parseDouble((String) imp.getProperty("LONGITUDE"));
+				if (imp.getProperty("ALTITUDE")  != null) gps_lla[2] =Double.parseDouble((String) imp.getProperty("ALTITUDE"));
+		  }
+	  }
+
+
+	  public boolean writeKml(
+			  int debugLevel )
+	  {
+		  String [] sourceFiles_main=correctionsParameters.getSourcePaths();
+		  //		  String [] sourceFiles_aux=quadCLT_main.correctionsParameters.getSourcePaths();
+		  setGpsLla(sourceFiles_main[0]);
+		  String set_name = image_name;
+		  if (set_name == null ) {
+			  QuadCLT.SetChannels [] set_channels=setChannels(debugLevel);
+			  set_name = set_channels[0].set_name;
+		  }
+		  if (gps_lla != null) {
+			  String kml_copy_dir= correctionsParameters.selectX3dDirectory(
+					  set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+					  null,
+					  true,  // smart,
+					  true);  //newAllowed, // save
+			  double ts = Double.parseDouble(set_name.replace('_', '.'));
+			  (new X3dOutput()).generateKML(
+					  kml_copy_dir+ Prefs.getFileSeparator()+set_name+".kml", // String path,
+					  false, // boolean overwrite,
+					  "", // String icon_path, //<href>x3d/1487451413_967079.x3d</href> ?
+					  ts, // double timestamp,
+					  gps_lla); // double [] lla)
+		  } else {
+			  if (debugLevel > -2) {
+				  System.out.println("GPS data not available, skipping KML file generation (TODO: maybe make some default LLA?)");
+			  }
+		  }
+		  return true;
+	  }
+
+	  public boolean createThumbNailImage(
+			  ImagePlus imp,
+			  String dir,
+			  String name,
+			  int debugLevel)
+	  {
+		  String thumb_path = dir +  Prefs.getFileSeparator() + name+".jpeg";
+			if (new File(thumb_path).exists()) {
+				System.out.println("file "+thumb_path+" exists, skipping thumbnail generation");
+				return false;
+			}
+
+		  int image_width = imp.getWidth();
+		  int image_height = imp.getHeight();
+		  double scale_h = 1.0 * correctionsParameters.thumb_width/image_width;
+		  double scale_v = 1.0 * correctionsParameters.thumb_height/image_height;
+//		  double scale = Math.min(scale_h,  scale_v) /correctionsParameters.thumb_size;
+		  double scale = scale_h / correctionsParameters.thumb_size;
+
+//		  ImageProcessor ip = imp.getChannelProcessor();
+		  ImageProcessor ip = imp.getProcessor().duplicate();
+
+		  ip.setInterpolationMethod(ImageProcessor.BICUBIC);
+//		  ip.setInterpolationMethod(ImageProcessor.BILINEAR);
+		  ip.blurGaussian(2.0);
+		  ip.scale(scale, scale);
+//		  Rectangle rs = new Rectangle(
+//				  (int)Math.round(0.5*image_width*(1.0-scale)),
+//				  (int)Math.round(0.5*image_height*(1.0-scale)),
+//				  (int)Math.round(image_width*scale),
+//				  (int)Math.round(image_height*scale));
+
+//		  int scaled_width = rs.width; // ip.getWidth();
+//		  int scaled_height = rs.height; // ip.getHeight();
+//		  int lm = (int) Math.round ((scaled_width-correctionsParameters.thumb_width)* correctionsParameters.thumb_h_center);
+//		  int tm = (int) Math.round ((scaled_height-correctionsParameters.thumb_height)* correctionsParameters.thumb_v_center);
+		  int lm = (int) Math.round (((image_width*scale)-correctionsParameters.thumb_width)* correctionsParameters.thumb_h_center + (0.5*image_width*(1.0-scale)));
+		  int tm = (int) Math.round (((image_height*scale)-correctionsParameters.thumb_height)* correctionsParameters.thumb_v_center + (0.5*image_height*(1.0-scale)));
+		  Rectangle r = new Rectangle(lm,tm,correctionsParameters.thumb_width,correctionsParameters.thumb_height);
+		  ip.setRoi(r);
+		  ImageProcessor ip2 = ip.crop();
+		  ImagePlus ip_thumb = new ImagePlus(name,ip2);
+		  eyesisCorrections.saveAndShow(
+				  ip_thumb,
+				  dir,
+				  false,
+				  false,
+				  correctionsParameters.JPEG_quality, // jpegQuality); // jpegQuality){//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
+				  (debugLevel > -2) ? debugLevel : 1); // int debugLevel (print what it saves)
+		  return true;
+	  }
+
+
+
+	  public boolean writeRatingFile(
+			  int debugLevel
+			  )
+	  {
+		  String set_name = image_name;
+		  if (set_name == null ) {
+			  QuadCLT.SetChannels [] set_channels = setChannels(debugLevel);
+			  set_name = set_channels[0].set_name;
+		  }
+
+		  String model_dir= correctionsParameters.selectX3dDirectory(
+				  set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+				  null,
+				  true,  // smart,
+				  true);  //newAllowed, // save
+		  String fname = model_dir+ Prefs.getFileSeparator()+"rating.txt";
+		  File rating_file = new File(fname);
+		  if (rating_file.exists()) {
+			  if (debugLevel > -2){
+				  System.out.println("file "+rating_file.getPath()+" exists, skipping overwrite");
+			  }
+			  return false;
+		  }
+		  List<String> lines = Arrays.asList(correctionsParameters.default_rating+"");
+		  Path path = Paths.get(fname);
+		  try {
+			  Files.write(path,lines, Charset.forName("UTF-8"));
+		  } catch (IOException e1) {
+			  // TODO Auto-generated catch block
+			  e1.printStackTrace();
+			  return false;
+		  }
+		  try {
+			  Path fpath = Paths.get(rating_file.getCanonicalPath());
+			  Set<PosixFilePermission> perms =  Files.getPosixFilePermissions(fpath);
+			  perms.add(PosixFilePermission.OTHERS_WRITE);
+			  Files.setPosixFilePermissions(fpath, perms);
+		  } catch (IOException e) {
+			  // TODO Auto-generated catch block
+			  e.printStackTrace();
+			  return false;
+		  }
+		  return true;
+	  }
+
+
+
 
 }

src/main/java/TilePlanes.java

@@ -1926,6 +1926,10 @@ public class TilePlanes {
 					for (int indx = 0; indx < disp_str[nl][0].length; indx++){
 						if (tile_sel[nl][indx]) {
 							double w = disp_str[nl][1][indx];
+							if ((w > 0.0) && !(disp_str[nl][0][indx] > 0.0)) {
+								System.out.println("BUG!!!: getPlaneFromMeas(): disp_str[nl][0]["+indx+"]="+disp_str[nl][0][indx]+", disp_str[nl][1]["+indx+"]="+disp_str[nl][1][indx]);
+								continue;
+							}
 							if (w > 0.0){
 								tiles_xyzw[nl][indx] = new double [4];
 								double d = disp_str[nl][0][indx];
@@ -2020,6 +2024,7 @@ public class TilePlanes {
 								acovar [2][2] += w * z * z;
 								if (Double.isNaN(acovar [0][0])) {
 									System.out.println("--*--BUG! acovar[0][0] is NaN");
+									return null;
 								}
 							}
 						}

src/main/java/X3dOutput.java

@@ -21,9 +21,15 @@
  ** -----------------------------------------------------------------------------**
  **
  */
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.attribute.PosixFilePermission;
 import java.util.ArrayList;
+import java.util.Set;
 
-import java.io.File;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -34,7 +40,6 @@ import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import org.w3c.dom.Attr;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
@@ -52,6 +57,8 @@ public class X3dOutput {
 	Element     el_TopGroup;
 	public int  max_line_length = 0; // 100; // 0 - no limit
 
+	public X3dOutput() {}
+
 	public X3dOutput(
 			EyesisCorrectionParameters.CLTParameters        clt_parameters,
 			EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
@@ -207,7 +214,7 @@ public class X3dOutput {
 			transformer.setOutputProperty(OutputKeys.INDENT, "yes");
 			transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
 			transformer.transform(source, result);
-			System.out.println("x3d file saved to "+path);
+			System.out.println("x3d file is saved to "+path);
 
 		} catch (TransformerException tfe) {
 			tfe.printStackTrace();
@@ -223,4 +230,156 @@ public class X3dOutput {
 		double [][] bbox = {{0, 0, -depth/2},{width,height,depth}};
 		return bbox;
 	}
+
+	public void generateKML(
+			String path,
+			boolean overwrite,
+			String icon_path, //<href>x3d/1487451413_967079.x3d</href> ?
+			double timestamp,
+			double [] lla)
+	{
+		if (!overwrite) {
+			if (new File(path).exists()) {
+				System.out.println("KML file "+path+" exists, skipping KML generation");
+				return;
+			}
+		}
+		Document kmlDoc;
+		try {
+
+			DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
+			DocumentBuilder docBuilder =        docFactory.newDocumentBuilder();
+			kmlDoc =                   docBuilder.newDocument();
+
+		} catch (ParserConfigurationException pce) {
+			pce.printStackTrace();
+			return;
+		}
+		// root elements
+		Element el_kml = kmlDoc.createElement("kml");
+		el_kml.setAttribute("xmlns","http://earth.google.com/kml/2.2");
+		kmlDoc.appendChild(el_kml);
+		Element el_Document = addElement(kmlDoc, el_kml,"Document");
+		Element el_PhotoOverlay = addElement(kmlDoc, el_Document, "PhotoOverlay"); // kmlDoc.createElement("PhotoOverlay");
+		addTextElement(kmlDoc, el_PhotoOverlay, "name", "test");
+		addTextElement(kmlDoc, el_PhotoOverlay, "description", "this kml description");
+		addTextElement(kmlDoc, el_PhotoOverlay, "visibility", "1");
+		addTextElement(kmlDoc, el_PhotoOverlay, "shape", "rectangle");
+
+
+		Element el_TimeStamp = addElement(kmlDoc, el_PhotoOverlay, "TimeStamp");
+		addTextElement(kmlDoc, el_TimeStamp, "when", String.format("%f",timestamp));
+
+		Element el_Camera = addElement(kmlDoc, el_PhotoOverlay, "Camera");
+		addTextElement(kmlDoc, el_Camera, "latitude",  String.format("%f",lla[0]));
+		addTextElement(kmlDoc, el_Camera, "longitude", String.format("%f",lla[1]));
+		addTextElement(kmlDoc, el_Camera, "altitude",  String.format("%f",lla[2]));
+		addTextElement(kmlDoc, el_Camera, "heading",   String.format("%f",0.0));
+		addTextElement(kmlDoc, el_Camera, "tilt",      String.format("%f",90.0));
+		addTextElement(kmlDoc, el_Camera, "roll",      String.format("%f",0.0));
+		if (icon_path != null) {
+			Element el_Icon = addElement(kmlDoc, el_PhotoOverlay, "Icon");
+			addTextElement(kmlDoc, el_Icon, "href",  icon_path);
+		}
+		Element el_ExtendedData = addElement(kmlDoc, el_PhotoOverlay, "ExtendedData");
+		Element el_OriginalData = addElement(kmlDoc, el_ExtendedData, "OriginalData");
+		addTextElement(kmlDoc, el_OriginalData, "latitude",  String.format("%f",lla[0]));
+		addTextElement(kmlDoc, el_OriginalData, "longitude", String.format("%f",lla[1]));
+		addTextElement(kmlDoc, el_OriginalData, "altitude",  String.format("%f",lla[2]));
+		addTextElement(kmlDoc, el_OriginalData, "heading",   String.format("%f",0.0));
+		addTextElement(kmlDoc, el_OriginalData, "tilt",      String.format("%f",90.0));
+		addTextElement(kmlDoc, el_OriginalData, "roll",      String.format("%f",0.0));
+
+		try {
+			// write the content into xml file
+			TransformerFactory transformerFactory = TransformerFactory.newInstance();
+			Transformer transformer = transformerFactory.newTransformer();
+			DOMSource source = new DOMSource(kmlDoc);
+			StreamResult result = new StreamResult(new File(path));
+			// Output to console for testing
+			// StreamResult result = new StreamResult(System.out);
+			transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+			transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
+			transformer.transform(source, result);
+			System.out.println("kml file is saved to "+path);
+
+		} catch (TransformerException tfe) {
+			tfe.printStackTrace();
+		}
+
+		try {
+			Path fpath = Paths.get((new File(path)).getCanonicalPath());
+			Set<PosixFilePermission> perms =  Files.getPosixFilePermissions(fpath);
+			perms.add(PosixFilePermission.OTHERS_WRITE);
+			Files.setPosixFilePermissions(fpath, perms);
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+
+
+
+	}
+
+
+	Element addTextElement(Document doc, Element parent, String name, String text)
+	{
+		Element child = doc.createElement(name);
+		child.setTextContent(text);
+		parent.appendChild(child);
+		return child;
+	}
+	Element addElement(Document doc, Element parent, String name)
+	{
+		Element child = doc.createElement(name);
+		parent.appendChild(child);
+		return child;
+
+	}
+
+
 }
+
+
+/*
+ * <?xml version="1.0" encoding="UTF-8"?>
+<kml xmlns="http://earth.google.com/kml/2.2">
+<Document>
+<PhotoOverlay>
+	<name>test</name>
+	<visibility>1</visibility>
+	<shape>rectangle</shape>
+	<TimeStamp>
+		<when>1487451413.967079</when>
+	</TimeStamp>
+	<Camera>
+		<longitude>-111.93292339</longitude>
+		<latitude>40.72350154</latitude>
+		<altitude>1305.1</altitude>
+		<heading>68.8186</heading>
+		<tilt>90</tilt>
+		<roll>0</roll>
+	</Camera>
+	<Icon>
+		<href>x3d/1487451413_967079.x3d</href>
+	</Icon>
+	<ExtendedData>
+		<OriginalData>
+			<longitude>-111.9328843</longitude>
+			<latitude>40.7233861</latitude>
+			<altitude>1305.1</altitude>
+			<heading>65</heading>
+			<tilt>90</tilt>
+			<roll>0</roll>
+		</OriginalData>
+	</ExtendedData>
+<description></description></PhotoOverlay>
+</Document>
+</kml>
+
+<?xml version="1.0" encoding="UTF-8"?>
+<x3d profile="Interchange" version="3.3">
+  <Scene>
+    <Group bboxCenter="0.000 0.000 -1419.899 " bboxSize="3704.001 2766.569 2839.798 " class="GroupTop" id="GroupTop"/>
+
+ */