More untested mapping code, bug fix in variable DSI average disparity

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

@@ -509,6 +509,8 @@ public class CLTParameters {
 	public int        gmap_crop_extra =      20;
 	public int []     gmap_tex_pals =        {0,1,2};
 
+	public boolean    gmap_gnss_vert =       true;  // reference ll to the point below (false - top left corner)
+	// use Tiff XPosition, YPosition to specify offset to the vertical in the image
 	public boolean    gmap_save_alt =        true;  // save height map (meters ASL)  
 	public boolean    gmap_save_tiff32 =     true;  // save float TIFF (NaN for transparency) with geo metadata (top left corner)
 	public boolean    gmap_save_tiff =       true;  // save transparent TIFF with geo metadata (top left corner)
@@ -1687,6 +1689,7 @@ public class CLTParameters {
 		properties.setProperty(prefix+"gmap_crop_extra",            this.gmap_crop_extra+"");            // int     
 		properties.setProperty(prefix+"gmap_tex_pals",              CLTParameters.arr_to_str(this.gmap_tex_pals)); // int[]
 		
+		properties.setProperty(prefix+"gmap_gnss_vert",             this.gmap_gnss_vert+"");             // boolean 
 		properties.setProperty(prefix+"gmap_save_alt",              this.gmap_save_alt+"");              // boolean 
 		properties.setProperty(prefix+"gmap_save_tiff32",           this.gmap_save_tiff32+"");           // boolean 
 		properties.setProperty(prefix+"gmap_save_tiff",             this.gmap_save_tiff+"");             // boolean 
@@ -2737,6 +2740,7 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"gmap_crop_extra")!=null)      this.gmap_crop_extra=Integer.parseInt(properties.getProperty(prefix+       "gmap_crop_extra"));// int     
 		if (properties.getProperty(prefix+"gmap_tex_pals")!=null)        this.gmap_tex_pals=CLTParameters.str_to_iarr(properties.getProperty(prefix+"gmap_tex_pals"));
 
+   		if (properties.getProperty(prefix+"gmap_gnss_vert")!=null)       this.gmap_gnss_vert=Boolean.parseBoolean(properties.getProperty(prefix+     "gmap_gnss_vert"));
    		if (properties.getProperty(prefix+"gmap_save_alt")!=null)        this.gmap_save_alt=Boolean.parseBoolean(properties.getProperty(prefix+     "gmap_save_alt"));
    		if (properties.getProperty(prefix+"gmap_save_tiff32")!=null)     this.gmap_save_tiff32=Boolean.parseBoolean(properties.getProperty(prefix+  "gmap_save_tiff32"));
    		if (properties.getProperty(prefix+"gmap_save_tiff")!=null)       this.gmap_save_tiff=Boolean.parseBoolean(properties.getProperty(prefix+    "gmap_save_tiff"));
@@ -4055,6 +4059,8 @@ public class CLTParameters {
 		gd.addStringField ("LWIR palettes to render the maps",     CLTParameters.arr_to_str(this.gmap_tex_pals), 40,
 				"Enter space-separated list of the palette numbers, such as, such as '0 1 2'");
 
+		gd.addCheckbox ("Reference GNSS LLA to below the camera",  this.gmap_gnss_vert, // true; // enable change FG pixel to opaque from transparent
+				"If false - to the top left image corner(NW). Use Tiff XPosition, YPosition for the offset to the vertical.");
 		gd.addCheckbox ("Save height map (meters ASL)",            this.gmap_save_alt, // true; // enable change FG pixel to opaque from transparent
 				"Save height map (meters Above Seal Level) as a floating-point single-slice TIFF (NAN for transparency).");
 		gd.addCheckbox ("Save float Tiff with transparency and Geo",this.gmap_save_tiff32, // true; // enable change FG pixel to opaque from transparent
@@ -5315,6 +5321,7 @@ public class CLTParameters {
 		this.gmap_crop_extra= (int) gd.getNextNumber();
 		this.gmap_tex_pals =        CLTParameters.str_to_iarr(gd.getNextString());
 		
+		this.gmap_gnss_vert=        gd.getNextBoolean();
 		this.gmap_save_alt=         gd.getNextBoolean();
 		this.gmap_save_tiff32=      gd.getNextBoolean();
 		this.gmap_save_tiff=        gd.getNextBoolean();

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

@@ -112,6 +112,7 @@ import com.elphel.imagej.lwir.LwirReader;
 import com.elphel.imagej.orthomosaic.ComboMatch;
 import com.elphel.imagej.readers.ChangeImageResolution;
 import com.elphel.imagej.readers.DumpImageMetadata;
+import com.elphel.imagej.readers.ElphelTiffReader;
 import com.elphel.imagej.readers.EyesisTiff;
 import com.elphel.imagej.tensorflow.TensorflowInferModel;
 import com.elphel.imagej.tileprocessor.Clt1d;
@@ -844,6 +845,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Show mice", panelLWIRWorld, color_process);
 			addButton("Set pair",  panelLWIRWorld, color_process);
 			addButton("Warp pair",  panelLWIRWorld, color_process);
+			addButton("Read Tiff",  panelLWIRWorld, color_process);
+			addButton("Set pair GPS",  panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5683,9 +5686,166 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
 			ComboMatch.testPair();
+		} else if (label.equals("Read Tiff")) {
+			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+			ImagePlus imp_sel = WindowManager.getCurrentImage();
+			if (imp_sel == null) {
+				IJ.showMessage("Error", "No images selected");
+				return;
+			}
+			String orig_path = imp_sel.getOriginalFileInfo().getFilePath();
+			try {
+				ElphelTiffReader.getTiffMeta(orig_path);				
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+//			ComboMatch.testReadTiff();
+		} else if (label.equals("Set pair GPS")) {
+			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+			/*
+			boolean run_pre = true; // false;
+			if (run_pre) {
+				String path = loadProperties(null, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES);
+				if (path != null) {
+					getAllProperties(PROPERTIES);
+					if (DEBUG_LEVEL > -3)
+						System.out.println("Configuration parameters are restored from " + path);
+				} else {
+					if (DEBUG_LEVEL > -10)
+						System.out.println("Failed to restore configuration parameters");
+					return;
+				}
+			}
+			*/
+			if (GPU_TILE_PROCESSOR == null) {
+				try {
+					GPU_TILE_PROCESSOR = new GPUTileProcessor(CORRECTION_PARAMETERS.tile_processor_gpu);
+				} catch (Exception e) {
+					System.out.println("Failed to initialize GPU class");
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+					return;
+				} // final int debugLevel);
+			}
+			/*
+			if (!run_pre) {
+				String path = loadProperties(null, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES);
+				if (path != null) {
+					getAllProperties(PROPERTIES);
+					if (DEBUG_LEVEL > -3)
+						System.out.println("Configuration parameters are restored from " + path);
+				} else {
+					if (DEBUG_LEVEL > -10)
+						System.out.println("Failed to restore configuration parameters");
+					return;
+				}
+			}
+			*/
+			
+//////////////////////
+// Temporarily initialize on scene GPU
+			
+			boolean init_scene = false; // true;
+			if (init_scene) {
+				debugInitOneScene();
+			}
+			ComboMatch.openTestPairGps(
+					CLT_PARAMETERS,     // CLTParameters    clt_parameters,
+					GPU_TILE_PROCESSOR,
+					DEBUG_LEVEL);
 		}
+		
 	}
 
+	public boolean debugInitOneScene() {
+		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+		if (EYESIS_CORRECTIONS_AUX == null) {
+			EYESIS_CORRECTIONS_AUX = new EyesisCorrections(SYNC_COMMAND.stopRequested,
+					CORRECTION_PARAMETERS.getAux());
+		}
+		EYESIS_CORRECTIONS_AUX.setDebug(DEBUG_LEVEL);
+		if (QUAD_CLT_AUX == null) {
+			QUAD_CLT_AUX = new QuadCLT(QuadCLT.PREFIX_AUX, PROPERTIES, EYESIS_CORRECTIONS_AUX,
+					CORRECTION_PARAMETERS.getAux());
+			if (DEBUG_LEVEL > 0) {
+				System.out.println("Created new QuadCLT AUX instance, will need to read CLT kernels");
+			}
+		}
+		String configPath = getSaveCongigPath();
+		if (configPath.equals("ABORT"))
+			return false;
+
+		EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL, false, // boolean missing_ok,
+				true, // boolean all_sensors, Otherwise - Eyesis
+				COLOR_PROC_PARAMETERS_AUX.correct_vignetting); // boolean correct_vignetting
+
+		int numChannels = EYESIS_CORRECTIONS_AUX.getNumChannels();
+//    NONLIN_PARAMETERS.modifyNumChannels(numChannels);
+		CHANNEL_GAINS_PARAMETERS_AUX.modifyNumChannels(numChannels);
+
+		if (!QUAD_CLT_AUX.CLTKernelsAvailable()) {
+			if (DEBUG_LEVEL > 0) {
+				System.out.println("Reading AUX CLT kernels");
+			}
+			QUAD_CLT_AUX.readCLTKernels(CLT_PARAMETERS, THREADS_MAX, UPDATE_STATUS, // update status info
+					DEBUG_LEVEL);
+
+			if (DEBUG_LEVEL > 1) {
+				QUAD_CLT_AUX.showCLTKernels(THREADS_MAX, UPDATE_STATUS, // update status info
+						DEBUG_LEVEL);
+			}
+		}
+
+		if (!QUAD_CLT_AUX.geometryCorrectionAvailable()) {
+			if (DEBUG_LEVEL > 0) {
+				System.out.println("Calculating geometryCorrection");
+			}
+			if (!QUAD_CLT_AUX.initGeometryCorrection(DEBUG_LEVEL + 2)) {
+				return false;
+			}
+		}
+		// After kernels and GeometryCorrection
+		if (CLT_PARAMETERS.useGPU()) { // only init GPU instances if it is used
+			if (GPU_TILE_PROCESSOR == null) {
+				try {
+					GPU_TILE_PROCESSOR = new GPUTileProcessor(CORRECTION_PARAMETERS.tile_processor_gpu);
+				} catch (Exception e) {
+					System.out.println("Failed to initialize GPU class");
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+					return false;
+				} // final int debugLevel);
+			}
+			/*
+			 * if (CLT_PARAMETERS.useGPU(false) && (QUAD_CLT != null) && (GPU_QUAD == null))
+			 * { // if GPU main is needed try { GPU_QUAD = new GpuQuad( GPU_TILE_PROCESSOR,
+			 * QUAD_CLT); } catch (Exception e) {
+			 * System.out.println("Failed to initialize GpuQuad class"); // TODO
+			 * Auto-generated catch block e.printStackTrace(); return; // false; } //final
+			 * int debugLevel); QUAD_CLT.setGPU(GPU_QUAD); }
+			 */
+			if (CLT_PARAMETERS.useGPU(true) && (QUAD_CLT_AUX != null) && (GPU_QUAD_AUX == null)) { // if GPU AUX is
+				try {
+					GPU_QUAD_AUX = new GpuQuad(//
+							GPU_TILE_PROCESSOR, QUAD_CLT_AUX, CLT_PARAMETERS.gpu_debug_level);
+				} catch (Exception e) {
+					System.out.println("Failed to initialize GpuQuad class");
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+					return false; // false;
+				} // final int debugLevel);
+				QUAD_CLT_AUX.setGPU(GPU_QUAD_AUX);
+			}
+		}
+		
+		
+		return true;
+	}
+	
+	
 	/* ======================================================================== */
 	public boolean editIMU(boolean aux) {
 		if (aux) {

src/main/java/com/elphel/imagej/orthomosaic/FloatImageData.java

+package com.elphel.imagej.orthomosaic;
+
+public class FloatImageData {
+	public int       width;
+	public int       height;
+	public int       zoom_lev;
+	public double [] vert = new double[2]; // x,y offset (in meters) of the point under the camera
+	public float[]   data;
+	public FloatImageData (
+			int       width,
+			int       height,
+			int       zoom_lev,
+			double [] vert, // x,y pixel offset of the point under the camera
+			float[]   data) {
+		this.width = width;
+		this.height = height;
+		this.zoom_lev = zoom_lev;
+		this.vert = vert.clone();
+		this.data = data;
+	}
+
+	public static int getZoomLevel(
+			double pix_in_meters) {
+		return getZoomLevel (pix_in_meters, null, null);
+	}
+	
+	public static boolean isZoomValid(double pix_in_meters) {
+		boolean [] is_zoom_valid = new boolean[1];
+		getZoomLevel(pix_in_meters,is_zoom_valid, null);
+		return is_zoom_valid[0];
+	}
+	
+	public static double needZoomIn(double pix_in_meters) {
+		double  [] extra_zoom = new double[1];
+		getZoomLevel(pix_in_meters,null, extra_zoom);
+		return extra_zoom[0];
+	}
+	
+	/**
+	 * Find scale level (0: 1pix/cm, 1 - 2pix/cm, -1 - 0.5 pix/cm) from pixel size in meters
+	 * If scale does not match, provide false in optional valid_zoom[0]
+	 * zoom_in_extra  
+	 * @param pix_size_in_meters pixel size in meters (e.g. 0.02 means 2cm/pix)
+	 * @param valid_zoom if provided boolean[1] will return true for valid scale
+	 * @param zoom_in_extra enlarge (1.0x..2.0x) (reduce pixel size) to get to the standard scale 
+	 * @return zoom level (the higher - the more detailed) 0: - 1cm/pix,-1: 2cm/pix, 1: 0.5 cm/pix 
+	 */
+	
+	public static int getZoomLevel(
+			double pix_size_in_meters, // pixel size in meters
+			boolean [] valid_zoom,
+			double []  zoom_in_extra) {
+		int zl = 0;
+		double e = 1E-6;
+		double pix_size_in_cm = 100 * pix_size_in_meters; // pixel size in cm
+		boolean vz = true;
+		double ze = 1.0;
+		if (pix_size_in_cm > (1.0-e)) { // low resolution, pixel size > 1cm
+			zl++;
+			while (pix_size_in_cm > (1.0-e)) {
+				zl--;		
+				pix_size_in_cm /= 2;
+			} // exits with (1-e) >= pix_in_cm > 0.5 - e/2
+			vz = pix_size_in_cm < (0.5+e);
+			if (!vz) {
+				ze = 2.0 * pix_size_in_cm;
+			}
+		} else { // high resolution, pixel size < 1 
+			zl--;
+			while (pix_size_in_cm <= (1.0-e)) {
+				zl++;		
+				pix_size_in_cm *= 2;
+			}// exits with (2-2*e) >= pix_in_cm > (1-e)
+			vz = pix_size_in_cm > (2.0 - e);
+			if (!vz) {
+				ze = pix_size_in_cm;
+			}
+		}
+		if (valid_zoom != null) {
+			valid_zoom[0] = vz; 
+		}
+		if (zoom_in_extra != null) {
+			zoom_in_extra[0] = ze;
+		}
+
+
+		return zl;
+	}
+	
+}

src/main/java/com/elphel/imagej/readers/DumpImageMetadata.java

@@ -28,7 +28,8 @@ import javax.imageio.ImageIO;
 import javax.imageio.ImageReader;
 import javax.imageio.metadata.IIOMetadata;
 import javax.imageio.stream.ImageInputStream;
-
+import javax.imageio.plugins.tiff.TIFFDirectory;
+import javax.imageio.plugins.tiff.TIFFField;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 
@@ -136,6 +137,9 @@ public class DumpImageMetadata
 			IIOMetadata metadata = reader.getImageMetadata(0);
 			indent(1);
 			System.out.println("Image metadata");
+			TIFFDirectory ifd = TIFFDirectory.createFromMetadata(metadata);
+			TIFFField [] tf = ifd.getTIFFFields();
+//			TIFFField f1 = ifd.get​TIFFField(286);
 			dumpMetadata(metadata);
 			IIOMetadata smetadata = reader.getStreamMetadata();
 			if (smetadata != null)

src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java

@@ -32,9 +32,22 @@ import java.io.InputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLConnection;
+import java.time.LocalDateTime;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.Set;
+
+import javax.imageio.ImageIO;
+import javax.imageio.ImageReader;
+import javax.imageio.metadata.IIOMetadata;
+import javax.imageio.plugins.tiff.TIFFDirectory;
+import javax.imageio.plugins.tiff.TIFFField;
+import javax.imageio.plugins.tiff.TIFFTag;
+import javax.imageio.stream.ImageInputStream;
+import javax.imageio.plugins.tiff.ExifGPSTagSet;
 
 import org.apache.commons.compress.utils.IOUtils;
 import org.joda.time.DateTime;
@@ -588,4 +601,170 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		return comment != null && comment.startsWith("ImageJ=");
 	}
 
+	private static String getFileExtension(File file)
+	{
+		String fileName = file.getName();
+		int lastDot = fileName.lastIndexOf('.');
+		return fileName.substring(lastDot + 1);
+	}
+
+	public static Properties getTiffMeta(String path)  throws IOException {
+		Properties properties = new Properties();
+		File file = new File(path);
+		String extension = getFileExtension(file);
+//		System.out.println("\nProcessing " + file.getName() + ":\n");
+		Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(extension);
+		ImageInputStream stream = null;
+		while (readers.hasNext())
+		{
+			ImageReader reader = readers.next();
+			stream = ImageIO.createImageInputStream(file);
+			reader.setInput(stream, true);
+			IIOMetadata metadata = reader.getImageMetadata(0);
+			TIFFDirectory ifd = TIFFDirectory.createFromMetadata(metadata);
+			TIFFField [] tfs = ifd.getTIFFFields();
+			for (TIFFField tf: tfs) {
+				parseField(tf, properties);
+			}				
+			stream.close();
+		}
+//		Set<String> pnames = properties.stringPropertyNames();
+//		for (String pn:pnames) {
+//			System.out.println(pn+": "+properties.getProperty(pn));
+//		}
+		return properties;
+	}
+	private static void parseField(TIFFField tf, Properties properties) {
+		if (tf.hasDirectory()) {
+			TIFFField [] stfs = tf.getDirectory().getTIFFFields();
+			if ("GPSInfoIFDPointer".equals(tf.getTag().getName())) {
+				TIFFDirectory gifd = tf.getDirectory();
+				long [][] lat = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_LATITUDE).getAsRationals();
+				double dlat = 1.0*lat[0][0]/lat[0][1]+1.0/60*lat[1][0]/lat[1][1]+1.0/3600*lat[2][0]/lat[2][1];
+				String lat_ref = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_LATITUDE_REF).getValueAsString(0);
+				if (!lat_ref.equals("N")) {
+					dlat =- dlat;
+				}
+				long [][] lon = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_LONGITUDE).getAsRationals();
+				double dlon = 1.0*lon[0][0]/lon[0][1]+1.0/60*lon[1][0]/lon[1][1]+1.0/3600*lon[2][0]/lon[2][1];
+				String lon_ref = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_LONGITUDE_REF).getValueAsString(0);
+				if (!lon_ref.equals("E")) {
+					dlon =- dlon;
+				}
+				long [] alt =  gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_ALTITUDE).getAsRational(0);
+				double dalt = 1.0 *alt[0]/alt[1];
+				String alt_ref = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_ALTITUDE_REF).getValueAsString(0);
+				if (!alt_ref.equals("0")) {
+					dalt =- dalt;
+				}
+				String [] date_stamp = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_DATE_STAMP).getValueAsString(0).split(":");
+				long [][] gts = gifd.getTIFFField(ExifGPSTagSet.TAG_GPS_TIME_STAMP).getAsRationals();
+				double secs = 3600.0*gts[0][0]/gts[0][1]+60.0*gts[1][0]/gts[1][1]+1.0*gts[2][0]/gts[2][1];
+				int isecs = (int) Math.floor(secs);
+				int nanos = (int) Math.round((secs - isecs)*1E9);
+				LocalDateTime dt = LocalDateTime.of(
+						Integer.parseInt(date_stamp[0]), // year
+						Integer.parseInt(date_stamp[1]), // month
+						Integer.parseInt(date_stamp[2]), // day
+						0,0,0);
+				dt = dt.plusSeconds(isecs);
+				dt = dt.plusNanos(nanos);
+				properties.setProperty	("GPSLatitude",  ""+dlat);	
+				properties.setProperty	("GPSLongitude", ""+dlon);	
+				properties.setProperty	("GPSAltitude",  ""+dalt);	
+				properties.setProperty	("GPSDateTime",  ""+dt.toString());	
+			} else {
+				for (TIFFField stf: stfs) {
+					parseField(stf, properties);
+				}
+			}
+		} else { // will not parse long tags (>3)
+			if (tf.getCount() == 1) {
+				switch (tf.getType()) {
+				case TIFFTag.TIFF_RATIONAL:
+				{
+					long [] ndn = tf.getAsRational(0);
+					double v = 1.0*ndn[0]/ndn[1];
+					properties.setProperty(tf.getTag().getName(), ""+v);
+				}
+				break;
+				case TIFFTag.TIFF_SRATIONAL:
+				{
+					int [] ndn = tf.getAsSRational(0);
+					double v = 1.0*ndn[0]/ndn[1];
+					properties.setProperty(tf.getTag().getName(), ""+v);
+				}
+				break;
+				case TIFFTag.TIFF_ASCII:
+				case TIFFTag.TIFF_BYTE:
+				case TIFFTag.TIFF_DOUBLE:
+				case TIFFTag.TIFF_FLOAT:
+				case TIFFTag.TIFF_LONG:
+				case TIFFTag.TIFF_SHORT:
+				case TIFFTag.TIFF_SBYTE:
+				case TIFFTag.TIFF_SLONG:
+				case TIFFTag.TIFF_SSHORT:
+					properties.setProperty(tf.getTag().getName(), tf.getValueAsString(0));
+					break;
+				default:
+					System.out.println("not processed: "+tf.getTag().getName());
+				}
+			}
+		}
+	}
+	
+	public static double [] getLLA(Properties properties) {
+		double [] lla = new double [3];
+		lla[0] = Double.parseDouble(properties.getProperty("GPSLatitude"));
+		lla[1] = Double.parseDouble(properties.getProperty("GPSLongitude"));
+		lla[2] = Double.parseDouble(properties.getProperty("GPSAltitude"));
+		return lla;
+	}
+	
+	public static LocalDateTime getLocalDateTime(Properties properties) {
+		LocalDateTime dt = LocalDateTime.parse(properties.getProperty("GPSDateTime"));
+		return dt;
+	}
+	
+	
+	public static double [] getPixelSize(Properties properties) {
+		int res_unit = Integer.parseInt(properties.getProperty("ResolutionUnit"));
+		double unit_size = 0;
+		switch(res_unit) {
+		case 2: unit_size = 0.0254; break;
+		case 3: unit_size = 0.01; break;
+		default:
+			System.out.println("Wrong ResolutionUnit="+res_unit);
+			return null;
+		}
+		double [] xy_pixel_in_meters = new double[2];
+		xy_pixel_in_meters[0] = unit_size/Double.parseDouble(properties.getProperty("XResolution"));
+		xy_pixel_in_meters[1] = unit_size/Double.parseDouble(properties.getProperty("YResolution"));
+		return xy_pixel_in_meters; 
+	}
+
+	public static double [] getXYOffsetMeters(Properties properties) {
+		int res_unit = Integer.parseInt(properties.getProperty("ResolutionUnit"));
+		double unit_size = 0;
+		switch(res_unit) {
+		case 2: unit_size = 0.0254; break;
+		case 3: unit_size = 0.01; break;
+		default:
+			System.out.println("Wrong ResolutionUnit="+res_unit);
+			return null;
+		}
+		double [] xy_offset_meters = new double[2];
+		xy_offset_meters[0] = unit_size * Double.parseDouble(properties.getProperty("XPosition"));
+		xy_offset_meters[1] = unit_size * Double.parseDouble(properties.getProperty("YPosition"));
+		return xy_offset_meters; 
+		
+	}
+	
+	public static double [] getXYOffsetPixels(Properties properties) {
+		double [] xy_offset_pixels = new double[2];
+		xy_offset_pixels[0] = Double.parseDouble(properties.getProperty("XPosition")) * Double.parseDouble(properties.getProperty("XResolution"));
+		xy_offset_pixels[1] = Double.parseDouble(properties.getProperty("YPosition")) * Double.parseDouble(properties.getProperty("YResolution"));
+		return xy_offset_pixels; 
+	}
+	
 }

src/main/java/com/elphel/imagej/readers/ElphelTiffWriter.java

@@ -79,6 +79,7 @@ public class ElphelTiffWriter {
 			ImagePlus     imp,
 			String        path, // full path to save image
 			double []     lla,  // latitude, longitude, altitude (or null)
+			double []     xy_center, // X,Y of top left to vertical (negative meters)
 			LocalDateTime dt,   // local date/time or null
 			double        pix_in_meters, // resolution or Double.NaN
 			boolean       imageJTags, // later will use it to encode from properties
@@ -149,7 +150,7 @@ public class ElphelTiffWriter {
 	    	ifd.appendChild(gpsRootNode);
 	    }
 	    addResolutionMetadata(ifd,pix_in_meters,cm_dig_after); // NOP if pix_in_meters is NaN 
-	    
+	    addXYPositionMetadata(ifd,xy_center,3);
 	    if (debugLevel > 0) {
 	    	System.out.println("\n=== ifd ===:");DumpImageMetadata.displayMetadataNode(ifd, 1);
 	    	System.out.println("\n=== root_new ===:"); DumpImageMetadata.displayMetadataNode(root_new, 1);
@@ -447,6 +448,42 @@ public class ElphelTiffWriter {
     	ifd.appendChild(node_y_resolution);
 	}
 	
+	private static void addXYPositionMetadata(
+			IIOMetadataNode ifd,
+			double []       xy_position, // both should be negative
+			int             digits_after) {
+		if (xy_position == null) {
+			return;
+		}
+		double xpos = Math.max(-xy_position[0] * 100, 0); // cm, prevent negative rationals, use 0 if negative 
+		double ypos = Math.max(-xy_position[1] * 100, 0); // cm, prevent negative rationals, use 0 if negative 
+		int denom = 1;
+		for (int i = 0; i < digits_after; i++) denom *= 10;
+		int ixpos = (int) Math.round(denom * xpos); // XPosition numerator
+		int iypos = (int) Math.round(denom * ypos); // YPosition numerator
+    	
+	    IIOMetadataNode node_x_position = new IIOMetadataNode(TIFF_FIELD_TAG);
+	    node_x_position.setAttribute("number", "286");
+	    node_x_position.setAttribute("name", "XPosition");
+    	IIOMetadataNode node_x_rationals = new IIOMetadataNode(TIFF_RATIONALS_TAG);
+    	IIOMetadataNode node_x_rational =  new IIOMetadataNode(TIFF_RATIONAL_TAG);
+    	node_x_rational.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, ixpos+"/"+denom);
+    	node_x_rationals.appendChild(node_x_rational);
+    	node_x_position.appendChild(node_x_rationals);
+    	ifd.appendChild(node_x_position);
+    	
+	    IIOMetadataNode node_y_position = new IIOMetadataNode(TIFF_FIELD_TAG);
+	    node_y_position.setAttribute("number", "287");
+	    node_y_position.setAttribute("name", "YPosition");
+    	IIOMetadataNode node_y_rationals = new IIOMetadataNode(TIFF_RATIONALS_TAG);
+    	IIOMetadataNode node_y_rational =  new IIOMetadataNode(TIFF_RATIONAL_TAG);
+    	node_y_rational.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, iypos+"/"+denom);
+    	node_y_rationals.appendChild(node_y_rational);
+    	node_y_position.appendChild(node_y_rationals);
+    	ifd.appendChild(node_y_position);
+	}
+	
+	
 	/*
 	 * 
 	FileImageOutputStream outputStream = new FileImageOutputStream(outputFile);

src/main/java/com/elphel/imagej/readers/EyesisTiff.java

@@ -318,6 +318,7 @@ the type of pixel data in this file 	getPixelType()
 					imp,
 					path,
 					lla,  // double []     lla,  // latitude, longitude, altitude (or null)
+					null, //double []            xy_center, // X,Y of top left to vertical (negative meters)
 					dt,   // LocalDateTime dt,   // local date/time or null
 					pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
 					imageJTags,
@@ -337,6 +338,7 @@ the type of pixel data in this file 	getPixelType()
 						imp,
 						path,
 						lla,  // double []     lla,  // latitude, longitude, altitude (or null)
+						null,     //double []            xy_center, // X,Y of top left to vertical (negative meters)
 						dt,   // LocalDateTime dt,   // local date/time or null
 						pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
 						imageJTags,
@@ -371,6 +373,7 @@ the type of pixel data in this file 	getPixelType()
 						imp_rgb,
 						path,
 						lla,  // double []     lla,  // latitude, longitude, altitude (or null)
+						null,     //double []            xy_center, // X,Y of top left to vertical (negative meters)
 						dt,   // LocalDateTime dt,   // local date/time or null
 						pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
 						imageJTags,

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

@@ -353,7 +353,7 @@ public class Interscene {
 		}
 		
 		
-		invertInitialOrientation(
+		int n_unresolved = invertInitialOrientation(
 				clt_parameters, // final CLTParameters          clt_parameters,
 				batch_mode,     // final boolean                batch_mode,
 				readjust,       // final boolean                readjust,
@@ -381,6 +381,12 @@ public class Interscene {
 				System.out.println("Egomotion table saved to "+ego_path);
 			}
         }
+		if (n_unresolved != 0) {
+			earliest_scene2 = -1;
+			System.out.println("invertInitialOrientation(). Consider more graceful bail out.");
+			start_ref_pointers[0] = start_ref_pointers1[0];
+			return earliest_scene2; // cent_index;
+		}
 		
 		
 		String cent_ts = quadCLTs[cent_index].getImageName();
@@ -442,7 +448,8 @@ public class Interscene {
 			final int                    earliest_index, // only used with readjust
 			final int                    debugLevel
 			) {
-		
+//Readjust may be needed similar to compensateDSI() - top DSI was calculated for wider scene 
+// range and be offset from the single-scene DSI		
 		if (debugLevel > -3) {
 			System.out.println("\ninvertInitialOrientation(): earliest_index "+earliest_index+", ref_index="+
 					ref_index+", last_index="+last_index+". readjust="+readjust+"\n");
@@ -700,6 +707,12 @@ public class Interscene {
 						avg_z,             // double             avg_z,
 						last_index, // ref_index,         // int                ref_index, // >= earliest_scene 
 						earliest_index);   // int                earliest_scene)
+				if (getFPNUnResolved(fpn_pairs) > 0) {
+					System.out.println("Unresolved FPN pairs:"+getFPNUnResolved(fpn_pairs));
+					return getFPNUnResolved(fpn_pairs);
+				}
+				
+				
 				// mitigating problem, that in the process of adjusting offset can fall below
 				// the minimum and coordinates will be NaN:
 				/*
@@ -788,10 +801,6 @@ public class Interscene {
 	    	sb.append("Maximal RMSE=   "+maximal_series_rms+"\n");
 	    	sb.append("------------------------\n\n");
 			quadCLTs[ref_index].saveStringInModelDirectory(sb.toString(), QuadCLT.ORIENTATION_LOGS_SUFFIX); // String  suffix)
-
-			
-			
-			
 		}
 		return 0;
 	}
@@ -1408,7 +1417,13 @@ public class Interscene {
 		return fpn_pairs;
 	}
 	
-	
+	public static int getFPNUnResolved(int [][] pairs) {
+		int n = 0;
+		for (int [] pair:pairs) {
+			if (pair[1] < 0) n++;
+		}
+		return n;
+	}
 	
 	public static int setInitialOrientations(
 			final CLTParameters          clt_parameters,
@@ -2170,77 +2185,6 @@ public class Interscene {
     					scenes_xyzatr_pull[nscene][0], // double []   new_xyz,
     					avg_z);                        // double      avg_z
     		}
-        	
-        	
-        	/*
-        	
-			double [][][] pimu_xyzatr = QuadCLT.integratePIMU(
-					clt_parameters, // final CLTParameters clt_parameters,
-					quadCLTs,       // final QuadCLT[]     quadCLTs,
-					ref_index,      // final int           ref_index,
-					null,           // double [][][]       dxyzatr,
-					earliest_scene, // final int           early_index,
-					last_scene      //(quadCLTs.length -1) // int           last_index,
-		    		);
-	    	double [] rms = new double[5];
-	    	double [] quat = new double[4];
-//	    	int quat_lma_mode = QuaternionLma.MODE_COMBO_LOCAL; // 2; // 1; // 2;
-	    	int quat_lma_mode = QuaternionLma.MODE_XYZQ; // MODE_XYZ4Q3; // MODE_XYZQ; // MODE_XYZQ_LOCAL; // 4; // 3; //  2; // 1;
-	    	int debug_lev = debugLevel; // 3;
-//	        double avg_z = quadCLTs[ref_index].getAverageZ(true); // in meters		
-	    	double  translation_weight =   1.0 / (avg_z + 1.0);
-			
-			//scenes_xyzatr
-        	
-	    	double [][][] rotated_xyzatr = QuadCLT.rotateImsToCameraXYZ(
-	    			clt_parameters,     // CLTParameters clt_parameters,
-	    			quat_lma_mode,      // int quat_lma_mode,
-	    			avg_z,              // double        avg_height,
-	    			translation_weight, // double        translation_weight,
-	    			quadCLTs,           // QuadCLT[]     quadCLTs,
-	    			scenes_xyzatr,      // double [][][] xyzatr,
-	    			pimu_xyzatr,        // double [][][] ims_xyzatr,
-	    			ref_index,          // int           ref_index,
-	    			earliest_scene,     // int           early_index,
-	    			last_scene,         // int           last_index,
-	    			rms,                // double []     rms, // null or double[5];
-	    			quat,               // double []     quaternion, // null or double[4]       
-	    			debug_lev);         // int           debugLevel
-	    	if (rotated_xyzatr == null) {
-	    		System.out.println("reAdjustPairsLMAInterscene(): QuadCLT.rotateImsToCameraXYZ() failed");
-	    	}  else {
-	    		System.out.println("reAdjustPairsLMAInterscene(): QuadCLT.rotateImsToCameraXYZ() finished in "+((int) rms[4])+ "iterations.");
-	    		System.out.println("rms="+rms[0]+" ("+rms[2]+"), pure rms="+rms[1]+" ("+rms[3]+")");
-	    		if (debug_lev > -3) {
-	    	    	Rotation rot = new Rotation(quat[0],quat[1],quat[2],quat[3], false); // no normalization - see if can be scaled
-	    			double []  angles = rot.getAngles(RotationOrder.YXZ, ErsCorrection.ROT_CONV);
-	    			double []  degrees = new double[3];
-	    			for (int i = 0; i < 3; i++) degrees[i]=angles[i]*180/Math.PI;
-	    			System.out.println("quat=["+quat[0]+", "+quat[1]+", "+quat[2]+", "+quat[3]+"]");
-	    			System.out.println("ATR(rad)=["+angles[0]+", "+angles[1]+", "+angles[2]+"]");
-	    			System.out.println("ATR(deg)=["+degrees[0]+", "+degrees[1]+", "+degrees[2]+"]");
-	    		}
-	    		
-	    		// TODO: Use quat[] to update corrections of the IMU relative to the camera?
-	    		for (int nscene = earliest_scene; nscene <= last_scene; nscene++) if (scenes_xyzatr[nscene] != null) {
-	    			scenes_xyzatr_pull[nscene] =  modifyATRtoXYZ(
-	    					scenes_xyzatr[nscene],     // double [][] cur_xyzatr, // careful with Z - using the new one
-	    					rotated_xyzatr[nscene][0], // double []   new_xyz,
-	    					avg_z);                    // double      avg_z
-	    		}
-	    	}
-	    	*/
-	    	// old version
-        	/*
-        	scenes_xyzatr_pull = QuadCLT.refineFromImsVelocities(
-        			clt_parameters, // CLTParameters clt_parameters,
-        			quadCLTs,       // QuadCLT[]     quadCLTs,
-        			scenes_xyzatr,  // double [][][] xyzatr,
-        			dxyzatr_dt,     // double [][][] dxyzatr,
-            		ref_index,      // int           ref_index,
-            		earliest_scene, // int           early_index,
-            		last_scene);    // int           last_index)
-            		*/
         }
         if (copy_pull_current) { // freeze_xy_pull) {
         	System.out.println("reAdjustPairsLMAInterscene(): freezing X,Y to X,Y pull values");

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

@@ -5241,9 +5241,11 @@ public class OpticalFlow {
 					}
 				} 
 				if (!done_sfm) { // first pass or sfm failed
+					boolean              compensate_dsi = true;
 					// should skip scenes w/o orientation 06/29/2022
 					combo_dsn_final = intersceneExport( // result indexed by COMBO_DSN_TITLES, COMBO_DSN_INDX_***
 							clt_parameters,      // CLTParameters        clt_parameters,
+							compensate_dsi,      // boolean              compensate_dsi,
 							ref_index,           // int                  ref_index,							
 							quadCLTs,            // QuadCLT []           scenes,
 							colorProcParameters, // ColorProcParameters  colorProcParameters,
@@ -5259,6 +5261,9 @@ public class OpticalFlow {
 								updateStatus,		 // final boolean       updateStatus,
 								debugLevel);         // int            debugLevel)
 					}
+					
+					
+					
 				}
 				quadCLTs[ref_index].inc_accum();
 				// save with updated num_accum
@@ -8733,8 +8738,51 @@ public class OpticalFlow {
 		return imp_stack;
 	}
 	
+	public static double compensateDSI(
+			CLTParameters        clt_parameters,
+			boolean              compensate_dsi, // false - do not apply, just calculate
+			QuadCLT              ref_scene,
+			double []            disparity,      // new disparity          
+			int                  debug_level
+			) {
+		double [] disparity_dsi = ref_scene.getDLS()[1]; // null
+		double [] strength = ref_scene.getDLS()[2];
+		double sw=0,swd=0, swdi=0; // old, new-old
+		for (int i = 0; i < disparity.length; i++) {
+			if (!Double.isNaN(disparity[i]) && !Double.isNaN(disparity_dsi[i])) {
+				sw   += strength[i];
+				swd  += strength[i]*disparity_dsi[i];
+				swdi += strength[i]*disparity[i];
+			}
+		}
+		double avg_zold = ref_scene.getGeometryCorrection().getZFromDisparity(swd/sw);
+		double avg_znew = ref_scene.getGeometryCorrection().getZFromDisparity(swdi/sw);
+		double zdiff = avg_znew- avg_zold; // negative in the case
+		double scale =avg_znew/avg_zold;
+		System.out.println("Scale = "+scale);
+		if (compensate_dsi) {
+			ErsCorrection  ers_reference = ref_scene.getErsCorrection();
+			String [] timestamps = ers_reference.getScenes();
+			for (String ts:timestamps) {
+				double [][] xyzatr = ers_reference.getSceneXYZATR(ts);
+				for (int i = 0; i < xyzatr[0].length; i++) {
+					xyzatr[0][i] *= scale;
+				}
+//				xyzatr[0][2] -= zdiff;
+				ers_reference.addScene(ts,xyzatr);
+			}
+			ref_scene.saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
+					null, // String path,             // full name with extension or w/o path to use x3d directory
+					debug_level+1);
+			
+		}
+		return zdiff;
+	}
+	
+	
 	public static double [][] intersceneExport(
 			CLTParameters        clt_parameters,
+			boolean              compensate_dsi,
 //			ErsCorrection        ers_reference,
 			int                  ref_index,
 			QuadCLT []           scenes_in,
@@ -9506,7 +9554,19 @@ public class OpticalFlow {
 		//noise_sigma_level
 		String rslt_suffix = "-INTER-INTRA-HISTORIC";
 		rslt_suffix += (clt_parameters.correlate_lma?"-LMA":"-NOLMA");
+		// ref_index from the center is moved to the very end (indx_ref)
+		if (compensate_dsi && !scenes[ref_index].interDsiExists()) {
+			System.out.println("Will compensate pose Z as average disparity may change");
+			double z_corr = compensateDSI(
+					clt_parameters,    // CLTParameters        clt_parameters,
+					compensate_dsi,    // boolean              compensate_dsi, // false - do not apply, just calculate
+					scenes[indx_ref], // ref_index], // QuadCLT              ref_scene,
+					combo_dsn_final[COMBO_DSN_INDX_LMA], // double []            disparity,      // new disparity          
+					debug_level); // int                  debug_level
+			System.out.println("Z correction = "+z_corr);
+			
 
+		}
 		ref_scene.saveDoubleArrayInModelDirectory(
 				rslt_suffix,         // String      suffix,
 				refine_titles,       // null,          // String []   labels, // or null

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

@@ -774,7 +774,6 @@ public class QuadCLT extends QuadCLTCPU {
 					"****************************************\n");
 			clt_parameters.z_correction = 0.0;
 		}
-
 		this.startTime=System.nanoTime();
 		String [] sourceFiles=correctionsParameters.getSourcePaths();
 		SetChannels [] set_channels=setChannels(debugLevel);
@@ -2281,6 +2280,10 @@ public class QuadCLT extends QuadCLTCPU {
 			final int                                       threadsMax,  // maximal number of threads to launch
 			final boolean                                   updateStatus,
 			final int                                       debugLevel){
+		if (debugLevel >= 100) {
+			return null;
+		}
+
 		if (gpuQuad == null) {
 			System.out.println("GPU instance is not initialized, using CPU mode");
 			processCLTQuadCorrCPU(
@@ -2392,6 +2395,9 @@ public class QuadCLT extends QuadCLTCPU {
 				clt_parameters.img_dtt.gpu_verify); // boolean verify
 
 		gpuQuad.execSetTilesOffsets(true); // prepare tiles offsets in GPU memory // calculate tile centers
+		gpuQuad.updateTasks( // just for testing, not needed
+				tp_tasks,
+				false); // boolean use_aux    // while is it in class member? - just to be able to free
 
 		if (showCoord) {
 			double max_r_by_rdist_err = gpuQuad.maxRbyRDistErr();
@@ -2403,6 +2409,24 @@ public class QuadCLT extends QuadCLTCPU {
 		
 		
 		gpuQuad.execConvertDirect(-1); // boolean erase_clt
+		
+		float [][] fclt = gpuQuad.getCltData(
+				false);// boolean use_ref);
+		System.out.println("Got CLT ["+fclt.length+"]["+fclt[0].length+"]");
+		ShowDoubleFloatArrays.showArrays(
+				fclt,
+				gpuQuad.img_width*2,
+				gpuQuad.img_height*2,
+				true,
+				"fclt_raw"); // , dbg_titles);
+		float [][] pfclt = gpuQuad.presentCltData(false);
+		ShowDoubleFloatArrays.showArrays(
+				pfclt,
+				gpuQuad.img_width*2,
+				gpuQuad.img_height*2,
+				true,
+				"fclt"); // , dbg_titles);
+		
 		int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt, getNumSensors());
 
 		if (test_execCorr2D) {

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

@@ -18046,6 +18046,7 @@ public class QuadCLTCPU {
 			  final CLTParameters  clt_parameters,
 			  double []            data,
 			  double []            lla,  // latitude, longitude, altitude (or null)
+			  double []            xy_center, // X,Y of top left to vertical (negative meters)
 			  LocalDateTime        dt,   // local date/time or null
 			  double               pix_in_meters,
 			  int                  width,
@@ -18097,6 +18098,7 @@ public class QuadCLTCPU {
 				  imp,
 				  image_path,
 				  lla,           // double []     lla,  // latitude, longitude, altitude (or null)
+				  xy_center,     //double []            xy_center, // X,Y of top left to vertical (negative meters)
 				  dt,            // LocalDateTime dt,   // local date/time or null
 				  pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
 				  false,         // imageJTags,
@@ -18109,6 +18111,7 @@ public class QuadCLTCPU {
 			  final CLTParameters  clt_parameters,
 			  double []            data,
 			  double []            lla,  // latitude, longitude, altitude (or null)
+			  double []            xy_center, // X,Y of top left to vertical (negative meters)
 			  LocalDateTime        dt,   // local date/time or null
 			  double               pix_in_meters,
 			  int                  width,
@@ -18141,6 +18144,7 @@ public class QuadCLTCPU {
 				  imp,
 				  image_path,
 				  lla,           // double []     lla,  // latitude, longitude, altitude (or null)
+				  xy_center,     //double []            xy_center, // X,Y of top left to vertical (negative meters)
 				  dt,            // LocalDateTime dt,   // local date/time or null
 				  pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
 				  false,         // imageJTags,

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

@@ -261,7 +261,7 @@ public class TDCorrTile {
 	 * @param neib_too_strong discard stronger neighbors from accumulating.                      
 	 * @param process_all process tiles even if the center tile is null. False - process only
 	 *                    the tiles around non-null ones.           
-	 * @return
+	 * @return tile-mapped array of the combined transform-domain 2D correlations.
 	 */
 	public static TDCorrTile [] calcNeibs(
 			TDCorrTile [] tiles,
@@ -318,6 +318,64 @@ public class TDCorrTile {
 		return rslt;
 	}
 	
+	/**
+	 * Average neighbors in TD primarily for rectilinear image matching 
+	 * @param tiles tile-mapped array of transform-domain 2D correlations and tile weights
+	 *              needed for correct application of fat zero for phase correlation and
+	 *              transform to pixel domain.
+	 * @param tilesX number of tiles in a scan row.
+	 * @param radius radius (in X and Y direction) for averaging neighbors using cosine
+	 *               for weights. Radius corresponds to PI/2, accumulation happens for
+	 *               integer values
+	 * @param process_all process tiles even if the center tile is null. False - process only
+	 *                    the tiles around non-null ones.           
+	 * @return same format as input tiles
+	 */
+	public static TDCorrTile [] calcNeibs(
+			TDCorrTile [] tiles,
+			final int     tilesX,
+			final double  radius,
+			final boolean process_all			
+			) {
+		final int tilesY = tiles.length / tilesX;
+		final int irad = (int) Math.floor(radius);
+		final int size = 2*irad+1;
+		final double [][] wnd = new double [size][size];
+		for (int i = 0; i < size; i++) {
+			double wy = Math.cos((i-irad)*0.5*Math.PI/radius);
+			for (int j = 0; j < size; j++) {
+				wnd[i][j] =wy*Math.cos((j-irad)*0.5*Math.PI/radius);
+			}
+		}
+		final TDCorrTile [] rslt = new TDCorrTile [tiles.length];
+		final Thread[] threads = ImageDtt.newThreadArray(ImageDtt.THREADS_MAX);
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					TileNeibs tn = new TileNeibs(tilesX,tilesY);
+					for (int iTile = ai.getAndIncrement(); iTile < tiles.length; iTile = ai.getAndIncrement())  if (process_all || (tiles[iTile] != null)) {
+						for (int dy = -irad; dy <= irad; dy++) {
+							for (int dx = -irad; dx <= irad; dx++) {
+								int iTile1 = tn.getNeibIndex(iTile, dx, dy);
+								if ((iTile1 >= 0) && (tiles[iTile1] != null)) {
+									if (rslt[iTile] == null) {
+										rslt[iTile] = tiles[iTile1].clone();
+										rslt[iTile].scale(wnd[dy+irad][dx+irad]);
+									} else {
+										rslt[iTile].accumulate(tiles[iTile1], wnd[dy+irad][dx+irad]);
+									}
+								}
+							}
+						}
+					}
+				}
+			};
+		}
+		ImageDtt.startAndJoin(threads);
+		return rslt;
+	}
+	
 	
 	/**
 	 * Convert Transform-domain 2D correlation to phase correlation,
@@ -329,8 +387,7 @@ public class TDCorrTile {
 	 * @param corr_type
 	 * @param gpu_fat_zero
 	 * @param debug_level
-	 * @return
-	 * 
+	 * @return sparse array in line-scan order. Each element either null or double[225]
 	 */
 	public static double [][] convertTDtoPD(
 			final GpuQuad       gpuQuad,
@@ -401,6 +458,64 @@ public class TDCorrTile {
 		return mapped_corrs;
 	}
 	
+	public static double [][] getMismatchVector(
+			final double [][] tiles,
+			double            rmax, 
+			final double      centroid_radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
+			final int         n_recenter){ //  re-center window around new maximum. 0 -no refines (single-pass)
+		double [][] vector_field = new double [tiles.length][];
+		final int corr_size = 2 * GPUTileProcessor.DTT_SIZE - 1;
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		final AtomicInteger ati = new AtomicInteger(0);
+		final double [] th_max = new double [threads.length];
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					int thread_num = ati.getAndIncrement();
+					for (int iTile = ai.getAndIncrement(); iTile < tiles.length; iTile = ai.getAndIncrement()) if (tiles[iTile] != null) {
+						for (double d:tiles[iTile]) {
+							if (d > th_max[thread_num]) {
+								th_max[thread_num] = d;
+							}
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		double amax = th_max[0];
+		for (int i = 1; i < th_max.length; i++) {
+			if (th_max[i] > amax) {
+				amax = th_max[i];
+			}
+		}
+		final double min_str = rmax * amax;
+		ai.set(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int iTile = ai.getAndIncrement(); iTile < tiles.length; iTile = ai.getAndIncrement()) if (tiles[iTile] != null) {
+						double [] mv = Correlation2d.getMaxXYCm( // last, average
+								tiles[iTile],    // corrs.length-1], // double [] data,
+								corr_size,       // int       data_width,      //  = 2 * transform_size - 1;
+								centroid_radius, // double    radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
+								n_recenter,      // int       refine, //  re-center window around new maximum. 0 -no refines (single-pass)
+								null,            // boolean [] fpn_mask,
+								false,           // boolean    ignore_border, // only if fpn_mask != null - ignore tile if maximum touches fpn_mask
+								false);          // boolean   debug)
+						if (mv[2] > min_str) {
+							vector_field[iTile] = new double [] {mv[0], mv[1], mv[2]-min_str};
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		return vector_field;
+	}
+	
+	
 	/**
 	 * Get GPU TD data after interscene correlation of 2 scenes (only use
 	 * combo of all channels)  

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

@@ -2472,6 +2472,7 @@ public class TexturedModel {
 		final int       crop_extra =      clt_parameters.gmap_crop_extra ; //20;
 		final int []    tex_pals =        clt_parameters.gmap_tex_pals ; //{0,1,2};
 		final boolean   gmap_save_alt =   clt_parameters.gmap_save_alt;  // true;  // save height map (meters ASL)  
+		final boolean   gmap_gnss_vert =  clt_parameters.gmap_gnss_vert;  // true;  // reference ll to the point below (false - top left corner)  
 		final boolean   gmap_save_tiff32= clt_parameters.gmap_save_tiff32; // save float TIFF (NaN for transparency) with geo metadata (top left corner)
 		final boolean   gmap_save_tiff =  clt_parameters.gmap_save_tiff; // true;  // save transparent TIFF with geo metadata (top left corner)
 		final int       gmap_tiff_pal =   clt_parameters.gmap_tiff_pal;  // 0;     // LWIR palette for TIFF  
@@ -3240,11 +3241,16 @@ public class TexturedModel {
 							ref_lla = new double[3];
 						}
 						// correct GPS coordinates to top-left corner of the result (full) image
-						double [] top_left_lla_offset_ned = new double[] {
-							hdr_x0y0[1], // North // hdr_x0y0 - in meters !
-							hdr_x0y0[0], // East
-							0}; // no altitude offset here
-						double [] top_left_lla = Imx5.offsetLla(ref_lla,top_left_lla_offset_ned);
+						double [] top_left_lla_offset_ned = new double[3]; // use center
+						if (gmap_gnss_vert) {
+							suffix+="-VERT";
+						} else { // top left
+							top_left_lla_offset_ned = new double[] {
+									hdr_x0y0[1], // North // hdr_x0y0 - in meters !
+									hdr_x0y0[0], // East
+									0}; // no altitude offset here
+						}
+						double [] corrected_lla = Imx5.offsetLla(ref_lla,top_left_lla_offset_ned);
 						int num_pix = 0;
 						double sum_z = 0.0;
 						for (int i = 0; i < cropped_z[0].length; i++) {
@@ -3258,7 +3264,7 @@ public class TexturedModel {
 						}
 						double avg_z = sum_z/num_pix;
 						LocalDateTime dt = scenes[ref_index].getLocalDateTime(); 
-						top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
+						corrected_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
 						if (gmap_save_alt) {
 							/*
 							scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z
@@ -3271,7 +3277,8 @@ public class TexturedModel {
 							scenes[ref_index].writeLwirGeoTiff32( // Negative value supplied for TIFF_RATIONAL
 									clt_parameters,                     // final CLTParameters  clt_parameters,
 									cropped_z[0],                       // double []            data,
-									top_left_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+									corrected_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+									hdr_x0y0, // double []            xy_center, // X,Y of top left to vertical (negative meters)
 									dt,                                 // LocalDateTime        dt,   // local date/time or null
 									scaled_pixel_size,                  // double               pix_in_meters,
 									hdr_whs[0],                         // int     width,
@@ -3283,7 +3290,8 @@ public class TexturedModel {
 							scenes[ref_index].writeLwirGeoTiff32(
 									clt_parameters,                     // final CLTParameters  clt_parameters,
 									img_cropped[0],                       // double []            data,
-									top_left_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+									corrected_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+									hdr_x0y0, // double []            xy_center, // X,Y of top left to vertical (negative meters)
 									dt,                                 // LocalDateTime        dt,   // local date/time or null
 									scaled_pixel_size,                  // double               pix_in_meters,
 									hdr_whs[0],                         // int     width,
@@ -3338,7 +3346,8 @@ public class TexturedModel {
 								scenes[ref_index].writeLwirGeoTiffARGB(
 										clt_parameters,                     // final CLTParameters  clt_parameters,
 										img_cropped[0],                     // double []            data,
-										top_left_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+										corrected_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+										hdr_x0y0, // double []            xy_center, // X,Y of top left to vertical (negative meters)
 										dt,                                 // LocalDateTime        dt,   // local date/time or null
 										scaled_pixel_size,                  // double               pix_in_meters,
 										hdr_whs[0],                         // int     width,

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

@@ -9376,6 +9376,7 @@ if (debugLevel > -100) return true; // temporarily !
 			// Does not need to specify reference scene - it is always the last even if out of timestamp order
 			OpticalFlow.intersceneExport(
 					clt_parameters,            // CLTParameters       clt_parameters,
+					false, // boolean              compensate_dsi,
 //					ers_reference,       // ErsCorrection        ers_reference,
 					indx_ref, // ref_index,           // int                  ref_index,							
 					scenes,                    // QuadCLT []           scenes,