Tiff writer, fixed bug in Z interpolation in plane render

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

@@ -481,6 +481,7 @@ public class CLTParameters {
 	public double     gmap_discard_rdisp =   0.02;  // discard above/below this fraction of average height
 	public double     gmap_pix_size =        0.005; // hdr_x0y0,       // in meters
 	public int        gmap_max_image_width = 4000;  // 3200;  // increase pixel size as a power of 2 until image fits
+	public double     gmap_min_sfm =         10.0;  // minimal SfM gain to keep ground map
 	public boolean    gmap_crop_empty =      true;
 	public int        gmap_crop_extra =      20;
 	public int []     gmap_tex_pals =        {0,1,2};
@@ -1626,6 +1627,7 @@ public class CLTParameters {
 		properties.setProperty(prefix+"gmap_discard_rdisp",         this.gmap_discard_rdisp+"");         // double
 		properties.setProperty(prefix+"gmap_pix_size",              this.gmap_pix_size+"");              // double
 		properties.setProperty(prefix+"gmap_max_image_width",       this.gmap_max_image_width+"");       // int     
+		properties.setProperty(prefix+"gmap_min_sfm",               this.gmap_min_sfm+"");               // double
 		properties.setProperty(prefix+"gmap_crop_empty",            this.gmap_crop_empty+"");            // boolean 
 		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[]
@@ -2644,6 +2646,7 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"gmap_discard_rdisp")!=null)   this.gmap_discard_rdisp=Double.parseDouble(properties.getProperty(prefix+  "gmap_discard_rdisp"));
 		if (properties.getProperty(prefix+"gmap_pix_size")!=null)        this.gmap_pix_size=Double.parseDouble(properties.getProperty(prefix+       "gmap_pix_size"));
 		if (properties.getProperty(prefix+"gmap_max_image_width")!=null) this.gmap_max_image_width=Integer.parseInt(properties.getProperty(prefix+  "gmap_max_image_width"));
+		if (properties.getProperty(prefix+"gmap_min_sfm")!=null)         this.gmap_min_sfm=Double.parseDouble(properties.getProperty(prefix+       "gmap_min_sfm"));
    		if (properties.getProperty(prefix+"gmap_crop_empty")!=null)      this.gmap_crop_empty=Boolean.parseBoolean(properties.getProperty(prefix+   "gmap_crop_empty"));
 		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"));
@@ -3908,6 +3911,8 @@ public class CLTParameters {
 				"Rendered absolute pixel size in meters.");
 		gd.addNumericField("Maximal rendered image width",         this.gmap_max_image_width, 0,3,"",
 				"Maximal output image size in pixels. Increase pixel size in the power-of-two ratio if calculated image width exceeds this value.");
+		gd.addNumericField("Minimal SfM gain",                     this.gmap_min_sfm,  4,6,"x",
+				"Minimal SfM gain to keep ground map, lower makes texture transparent.");
 		gd.addCheckbox ("Crop empty map areas",                    this.gmap_crop_empty, // true; // enable change FG pixel to opaque from transparent
 				"Crop the map output from four directions while only undefined pixels are removed.");
 		gd.addNumericField("Crop maps extra",                      this.gmap_crop_extra, 0,3,"pix",  // minimal neighbors to keep alpha
@@ -3915,7 +3920,6 @@ 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.addMessage     ("Earlier 3D generation parameters");
 		gd.addCheckbox    ("Generate background (infinity) image for 3D (not needed for view down)",                 this.generate_bg);
 		gd.addCheckbox    ("Show generated textures",                                                                this.show_textures);
@@ -5125,13 +5129,12 @@ public class CLTParameters {
 		this.gmap_discard_high=     gd.getNextNumber();
 		this.gmap_discard_adisp=    gd.getNextNumber();
 		this.gmap_discard_rdisp=    gd.getNextNumber();
-		gmap_pix_size=              gd.getNextNumber();
+		this.gmap_pix_size=         gd.getNextNumber();
 		this.gmap_max_image_width= (int) gd.getNextNumber();
+		this.gmap_min_sfm=          gd.getNextNumber();
 		this.gmap_crop_empty=       gd.getNextBoolean();
 		this.gmap_crop_extra= (int) gd.getNextNumber();
-		
 		this.gmap_tex_pals =           CLTParameters.str_to_iarr(gd.getNextString());
-		
 		this.generate_bg=           gd.getNextBoolean();
 		this.show_textures=         gd.getNextBoolean();
 		this.debug_filters=         gd.getNextBoolean();

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

@@ -70,113 +70,41 @@ public class ElphelTiffWriter {
 	
 	public static void saveTiffARGB32(
 			ImagePlus     imp,
-			String path,
-			boolean imageJTags,
+			String        path, // full path to save image
+			double []     lla,  // latitude, longitude, altitude (or null)
+			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
 			int           debugLevel
 			) {
-//		ImageWriter     tiffWriter;
-//	    ImageWriteParam tiffWriteParam;
-	    IIOMetadata     tiffStreamMetadata;
-	    IIOMetadata     primaryIFD;
-	    BufferedImage   bufferedImage = (BufferedImage) imp.getImage(); // properties=null
-	    BufferedImage   thumbnail;		
 	    File outputFile = new File(path);
+	    if (debugLevel > 0) {
 	    	System.out.println("saveTiffARGB32(): will write to "+outputFile);
 	    	System.out.println("ElphelTiffWriter.saveTiffARGB32");
-	       // Write only the primary IFD and image data.
-	    // Specify uncompressed output.
+	    }
 	    ImageWriter tiffWriter = ImageIO.getImageWritersByFormatName("tiff").next();
 	    ImageWriteParam tiffWriteParam = tiffWriter.getDefaultWriteParam();
 //	    tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+// https://docs.oracle.com/en/java/javase/17/docs/api/java.desktop/javax/imageio/metadata/doc-files/tiff_metadata.html	    
+//	    tiffWriteParam.setCompressionType("Exif JPEG");
 	    tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
-//	    tiffWriteParam.setSourceSubsampling(param.getSourceXSubsampling(), param.getSourceYSubsampling(), param.getSubsamplingXOffset(), param.getSubsamplingYOffset());
-//	    tiffWriteParam.setSourceRegion(param.getSourceRegion());
-//	    tiffWriteParam.setSourceBands(param.getSourceBands());
-/*
- * https://docs.oracle.com/javase%2F9%2Fdocs%2Fapi%2F%2F/javax/imageio/metadata/doc-files/tiff_metadata.html
-    Setting up the image metadata to write to a TIFF stream may be simplified by using
-    the TIFFDirectory class which represents a TIFF IFD. A field in a TIFF IFD is represented
-    by an instance of TIFFField. For each field to be written a TIFFField may be added to
-    the TIFFDirectory and the latter converted to an IIOMetadata object by invoking
-    TIFFDirectory.getAsMetadata. The IIOMetadata object so obtained may then be passed to
-    the TIFF writer.
-    
-ImageTypeSpecifier
-ImageTypeSpecifier(ColorModel colorModel, SampleModel sampleModel)
-Constructs an ImageTypeSpecifier directly from a ColorModel and a SampleModel.
-    
-static long computeImageSize(RenderedImage image) {
-  long bits = 0;
-  final int bands = image.getSampleModel().getNumBands();
-  for (int i = 0; i < bands; i++) {
-    bits += image.getSampleModel().getSampleSize(i);
-  }
-  return (long) Math.ceil(bits / 8) * image.getWidth() * image.getHeight();
-}
-
-void 	setRGB(int startX, int startY, int w, int h, int[] rgbArray, int offset, int scansize)
-Sets an array of integer pixels in the default RGB color model (TYPE_INT_ARGB) and default sRGB color space, into a portion of the image data.
-    
- */
-//	    Raster 	raster = bufferedImage.getData(); // use pixels from IJ
+	    /* ImagePlus image removes alpha, so we need to create a new ARGB BufferedImage
+	     * and copy data (it is correct in imp.getImage() */
+	    BufferedImage   bufferedImage = (BufferedImage) imp.getImage(); // properties=null
 	    BufferedImage bufferedImageAlpha = new BufferedImage(
 	    		bufferedImage.getWidth(),
 	    		bufferedImage.getHeight(),
-	    		BufferedImage.TYPE_INT_ARGB
-	    		);
+	    		BufferedImage.TYPE_INT_ARGB);
 	    int [] ipixels = (int[])imp.getProcessor().getPixels();
 	    final int[] bia_as_arr = ( (DataBufferInt) bufferedImageAlpha.getRaster().getDataBuffer() ).getData();
 	    System.arraycopy(ipixels, 0, bia_as_arr, 0, bia_as_arr.length);
-	    /*
-	    bufferedImageAlpha.setRGB( // slow
-	    		0,                         // int startX,
-	    		0,                         // int startY,
-	    		bufferedImage.getWidth(),  // int w,
-	    		bufferedImage.getHeight(), // int h,
-	    		ipixels,                   // int[] rgbArray,
-	    		0,                         // int offset,
-	    		bufferedImage.getWidth()); // int scansize);
-	    */
-	    
-	    
 	    
-//	    bufferedImageAlpha.setData(raster);
-	    //BufferedImage.TYPE_INT_ARGB
-//	    ColorModel colorModel = ColorModel.getRGBdefault();
-//	    SampleModel samleModel = bufferedImage.getSampleModel();
-//	    ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImage);            
 	    ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImageAlpha);            
 	    IIOMetadata imageMetadata = tiffWriter.getDefaultImageMetadata(imageType, tiffWriteParam);
 // just for testing:
-	    double [] lla = {	49.9476514222895,28.5547846609957,323.750316821841};
-	    LocalDateTime dt =  Did_ins.getLocalDateTime(2286, 491072.634526699);
-	    double pix_in_meters = 0.01;
 	    int cm_dig_after = 9;
+	    // Here is a way adding tag sets through TIFFDirectory
 	    /*
-	    ExifGPSTagSet exif_tag_set = ExifGPSTagSet.getInstance();
-	    
-	    
-	    TIFFTagSet [] tag_sets = {ExifGPSTagSet.getInstance()} ;
-	    ExifParentTIFFTagSet eptts = ExifParentTIFFTagSet.getInstance();
-	    TIFFDirectory gps_directory = new TIFFDirectory(
-	    		tag_sets, eptts.getTag(
-				ExifParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER));
-	    
-	    TIFFTagSet tag_set = ExifGPSTagSet.getInstance();
-	    TIFFField gps_ifd = null;
-//	    int df = TIFFField.TIFF_IFD_POINTER; // 13
-	    gps_ifd = new TIFFField(
-	    		eptts.getTag(
-	    				ExifParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER), // 'ExifIFDPointer', // TIFFTag tag,
-	    		13,            // TIFFField.TIFF_IFD_POINTER, // int type,
-	    		(long)         0, // long offset,
-	    		(TIFFDirectory) gps_directory); // TIFFDirectory dir)
-	    directory.addTIFFField(gps_ifd);
-	    directory.addTagSet(tag_set); // ExifGPSTagSet.getInstance());
-	    
-	    */
-	    
-	    /* */
 	    TIFFDirectory directory = null;
 	    try {
 			directory = TIFFDirectory.createFromMetadata(imageMetadata);
@@ -191,122 +119,41 @@ Sets an array of integer pixels in the default RGB color model (TYPE_INT_ARGB) a
 	    directory.addTagSet(eptts);   // ExifParentTIFFTagSet.getInstance());
 	    //ExifGPSTagSet
 	    imageMetadata = directory.getAsMetadata();
-	    /* */
+	    */
 	    
 	    IIOMetadataNode root_new = (IIOMetadataNode) imageMetadata.getAsTree(TIFF_METADATA_FORMAT);//?
-	    
-	    System.out.println("\n=== root_new ===:");
-	    DumpImageMetadata.displayMetadataNode(root_new, 1);
-	    
-//	    createGpsMetadata(double [] lla, LocalDateTime dt)
-	    
-	    
+	    if (debugLevel > 0) {System.out.println("\n=== root_new ===:");DumpImageMetadata.displayMetadataNode(root_new, 1);}
 	    IIOMetadataNode ifd =    (IIOMetadataNode)  root_new.getFirstChild();
-	    String ifd_attr =        ifd.getAttribute("tagSets");
-	    // set it to ifd_attr	"javax.imageio.plugins.tiff.BaselineTIFFTagSet,javax.imageio.plugins.tiff.ExifGPSTagSet,javax.imageio.plugins.tiff.ExifParentTIFFTagSet" (id=187)
-	    // remove directory above and addTagSet
+	    ifd.setAttribute("tagSets",
+	    		"javax.imageio.plugins.tiff.BaselineTIFFTagSet,javax.imageio.plugins.tiff.ExifGPSTagSet,javax.imageio.plugins.tiff.ExifParentTIFFTagSet");
+	    if ((lla != null) || (dt!=null)) { 
 	    	IIOMetadataNode gpsRootNode = createGpsMetadata(lla, dt);
-	    /*
-	    IIOMetadataNode gpsRootNode = new IIOMetadataNode("TIFFIFD");
-	    gpsRootNode.setAttribute("parentTagNumber", "34853");
-	    gpsRootNode.setAttribute("parentTagName",   "GPSInfoIFDPointer");
-	    gpsRootNode.setAttribute("tagSets", "javax.imageio.plugins.tiff.ExifGPSTagSet");
-
-	    IIOMetadataNode childNode = new IIOMetadataNode(TIFF_FIELD_TAG);
-	    childNode.setAttribute("number", "1");
-	    childNode.setAttribute("name", "GPSLatitudeRef");
-	    IIOMetadataNode asciiNode = new IIOMetadataNode(TIFF_ASCIIS_TAG);
-	    IIOMetadataNode childAsciiNode = new IIOMetadataNode(TIFF_ASCII_TAG);
-	    childAsciiNode.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, "N");
-	    asciiNode.appendChild(childAsciiNode);
-	    childNode.appendChild(asciiNode);
-	    gpsRootNode.appendChild(childNode);
-	    */
-	    System.out.println("\n=== gpsRootNode ===:");
-	    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
-	    
-	    
-	    addResolutionMetadata(ifd,pix_in_meters,cm_dig_after);
+	    	if (debugLevel > 0) {System.out.println("\n=== gpsRootNode ===:");DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);}
 	    	ifd.appendChild(gpsRootNode);
+	    }
+	    addResolutionMetadata(ifd,pix_in_meters,cm_dig_after); // NOP if pix_in_meters is NaN 
 	    
-	    System.out.println("\n=== ifd ===:");
-	    DumpImageMetadata.displayMetadataNode(ifd, 1);
-
-	    /*
-IIOMetadataNode childNode = new IIOMetadataNode(FileConstants.TIFF_FIELD_TAG);
-childNode.setAttribute(FileConstants.TIFF_FIELD_NUMBER_ATTRIBUTE, "1");
-childNode.setAttribute(FileConstants.TIFF_FIELD_NAME_ATTRIBUTE, "GPSLatitudeRef");
-IIOMetadataNode asciiNode = new IIOMetadataNode("TIFFAsciis");
-IIOMetadataNode childAsciiNode = new IIOMetadataNode("TIFFAscii");
-childAsciiNode.setAttribute(FileConstants.TIFF_FIELD_VALUE_ATTRIBUTE, "N");
-asciiNode.appendChild(childAsciiNode);
-childNode.appendChild(asciiNode);
-gpsRootNode.appendChild(childNode);
-ifd.appendChild(gpsRootNode);
-//Update metadata with new tree
-metadata.setFromTree(FileConstants.TIFF_METADATA_FORMAT, root);
-ImageOutputStream outstr = ImageIO.createImageOutputStream(writeTarget);
-writer.setOutput(outstr);
-//Write the image
-IIOImage img = new IIOImage(renderedImage, Collections.<BufferedImage> emptyList(), metadata);
-writer.write(img);
-outstr.close();
-
-	public static String TIFF_METADATA_FORMAT = "javax_imageio_tiff_image_1.0";
-	public static String TIFF_FIELD_TAG =       "TIFFField";
-	public static String TIFF_ASCIIS_TAG =      "TIFFAsciis";
-	public static String TIFF_ASCII_TAG =       "TIFFAscii";
-	public static String TIFF_RATIONALS_TAG =   "TIFFRationals";
-	public static String TIFF_RATIONAL_TAG =    "TIFFRational";
-	public static String TIFF_FIELD_VALUE_ATTRIBUTE = "value";
-	     */
-	    
-	    
-	    
-//	    imageMetadata.appendChild(dimension);
-	    
-	    
-////		IIOMetadataNode root_dimension = new IIOMetadataNode(TIFF_METADATA_FORMAT); // IIOMetadataFormatImpl.standardMetadataFormatName);
-//		root_dimension.appendChild(dimension);
-////		root_dimension.appendChild(root_new);
-////	    System.out.println("\n=== root_new ===:"); // should have 2 tagSets, but has only baseline
-	    /*
-	    <javax_imageio_tiff_image_1.0>
-        <TIFFIFD tagSets='javax.imageio.plugins.tiff.BaselineTIFFTagSet,javax.imageio.plugins.tiff.GeoTIFFTagSet'>
-	    */
-	    System.out.println("\n=== root_new ===:");
-	    DumpImageMetadata.displayMetadataNode(root_new, 1);
-	    System.out.println("\n=== imageMetadata - before merge ===:");
-	    DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);
-		
-		// lost GPS data after merge
+	    if (debugLevel > 0) {
+	    	System.out.println("\n=== ifd ===:");DumpImageMetadata.displayMetadataNode(ifd, 1);
+	    	System.out.println("\n=== root_new ===:"); DumpImageMetadata.displayMetadataNode(root_new, 1);
+	    	System.out.println("\n=== imageMetadata - before merge ===:"); DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);
+	    }
 		try {
 			imageMetadata.mergeTree(TIFF_METADATA_FORMAT, root_new); // dimension); // Root must have "TIFFIFD" child
-//			imageMetadata.setFromTree(TIFF_METADATA_FORMAT, root_dimension); // dimension);
 		} catch (IIOInvalidTreeException e1) {
-			// TODO Auto-generated catch block
 			e1.printStackTrace();
 			return;
 		}
 	    
-	    System.out.println("\n=== imageMetadata - after merge ===:");
-	    DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);
-		
-		
-		
-		
-	    System.out.println();
+		if (debugLevel > 0) {System.out.println("\n=== imageMetadata - after merge ===:");DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);}
 	    FileImageOutputStream outputStream;
 	    try {
 			outputStream = new FileImageOutputStream(outputFile);
 		} catch (IOException e1) {
-			// TODO Auto-generated catch block
 			e1.printStackTrace();
 			return;
 		}		
 	    tiffWriter.setOutput(outputStream);
-//	    IIOImage image_with_metadata = new IIOImage(bufferedImage, null, primaryIFD);
-//	    IIOImage image_with_metadata = new IIOImage(bufferedImage, null, null);
 	    IIOImage image_with_metadata = new IIOImage(bufferedImageAlpha, null, imageMetadata);
 	    System.out.println();
         try {
@@ -315,12 +162,11 @@ outstr.close();
 					image_with_metadata,
 			        tiffWriteParam);
 		} catch (IOException e) {
-			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
 	    System.out.println();
-        
 	}
+	
 	private static IIOMetadataNode createRationalDegrees(double d, int digits_after) { // 8
 		int denom = 1;
 		for (int i = 0; i < digits_after; i++) denom *= 10;
@@ -380,7 +226,9 @@ outstr.close();
 	    return node_date;
 	}
 	
-	private static IIOMetadataNode createGpsMetadata(double [] lla, LocalDateTime dt) {
+	private static IIOMetadataNode createGpsMetadata(
+			double [] lla,
+			LocalDateTime dt) {
 		int ang_sec_after = 5;
 		int meters_after =  3;
 		int seconds_after = 3;
@@ -390,13 +238,15 @@ outstr.close();
 	    gpsRootNode.setAttribute("parentTagNumber", "34853");
 	    gpsRootNode.setAttribute("parentTagName",   "GPSInfoIFDPointer");
 	    gpsRootNode.setAttribute("tagSets", "javax.imageio.plugins.tiff.ExifGPSTagSet");
-        boolean lat_south = lla[0] < 0;
-        double lat_abs = Math.abs(lla[0]);
-        boolean long_west = lla[1] < 0;
-        double long_abs = Math.abs(lla[1]);
-        boolean alt_down = lla[2] < 0;
-        double alt_abs = Math.abs(lla[2]);
-        
+        boolean lat_south, long_west, alt_down;
+        double lat_abs, long_abs, alt_abs;
+        if (lla != null) {
+        	lat_south = lla[0] < 0;
+        	lat_abs = Math.abs(lla[0]);
+        	long_west = lla[1] < 0;
+        	long_abs = Math.abs(lla[1]);
+        	alt_down = lla[2] < 0;
+        	alt_abs = Math.abs(lla[2]);
         	// Latitude
         	IIOMetadataNode node_lat_ref = new IIOMetadataNode(TIFF_FIELD_TAG);
         	node_lat_ref.setAttribute("number", "1");
@@ -412,10 +262,6 @@ outstr.close();
         	node_lat.setAttribute("name", "GPSLatitude");
         	node_lat.appendChild(createRationalDegrees(lat_abs, ang_sec_after));
         	gpsRootNode.appendChild(node_lat);
-
-	    System.out.println("\n=== gpsRootNode after latitude ===:");
-	    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
-
         	// Longitude
         	IIOMetadataNode node_long_ref = new IIOMetadataNode(TIFF_FIELD_TAG);
         	node_long_ref.setAttribute("number", "3");
@@ -431,10 +277,6 @@ outstr.close();
         	node_long.setAttribute("name", "GPSLongitude");
         	node_long.appendChild(createRationalDegrees(long_abs, ang_sec_after));
         	gpsRootNode.appendChild(node_long);
-
-	    System.out.println("\n=== gpsRootNode after longitude ===:");
-	    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
-	    
         	// Altitude
         	IIOMetadataNode node_alt_ref = new IIOMetadataNode(TIFF_FIELD_TAG);
         	node_alt_ref.setAttribute("number", "5");
@@ -451,10 +293,7 @@ outstr.close();
         	node_alt.setAttribute("name", "GPSAltitude");
         	node_alt.appendChild(createRationalMeters(alt_abs, meters_after));
         	gpsRootNode.appendChild(node_alt);
-	    
-	    System.out.println("\n=== gpsRootNode after altitude ===:");
-	    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
-	    
+        }
 	    if (dt != null) {
 		    // Time
 		    IIOMetadataNode node_time = new IIOMetadataNode(TIFF_FIELD_TAG);
@@ -462,8 +301,6 @@ outstr.close();
 		    node_time.setAttribute("name", "GPSTimeStamp");
 		    node_time.appendChild(createTimeStamp(dt,seconds_after));
 		    gpsRootNode.appendChild(node_time);
-		    System.out.println("\n=== gpsRootNode after time ===:");
-		    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
 		    // Date
 		    IIOMetadataNode node_date = new IIOMetadataNode(TIFF_FIELD_TAG);
 		    node_date.setAttribute("number", "29");
@@ -471,31 +308,16 @@ outstr.close();
 		    node_date.appendChild(createDateStamp(dt));
 		    gpsRootNode.appendChild(node_date);
 	    }
-	    System.out.println("\n=== gpsRootNode after date ===:");
-	    DumpImageMetadata.displayMetadataNode(gpsRootNode, 1);
 	    return gpsRootNode;
 	}
 	
-	private static IIOMetadataNode createResolutionMetadataStd(double resolutionPixelInMeters) {
-//		String pixelSize = Double.toString(25.4 / resolutionDPI);
-		String pixelSize = Double.toString(1000*resolutionPixelInMeters); // millimeters
-		IIOMetadataNode horizontal = new IIOMetadataNode("HorizontalPixelSize");
-		horizontal.setAttribute("value", pixelSize);
-		IIOMetadataNode vertical = new IIOMetadataNode("VerticalPixelSize");
-		vertical.setAttribute("value", pixelSize);
-		IIOMetadataNode dimension = new IIOMetadataNode("Dimension");
-		dimension.appendChild(horizontal);
-		dimension.appendChild(vertical);
-		return dimension;
-//		IIOMetadataNode root = new IIOMetadataNode(IIOMetadataFormatImpl.standardMetadataFormatName);
-//		root.appendChild(dimension);
-//		return root;
-	}
-	
 	private static void addResolutionMetadata(
 			IIOMetadataNode ifd,
-			double          resolutionPixelInMeters,
+			double          resolutionPixelInMeters, // NaN for undefined
 			int             digits_after) {
+		if (Double.isNaN(resolutionPixelInMeters)) {
+			return;
+		}
 		int denom = 1;
 		for (int i = 0; i < digits_after; i++) denom *= 10;
 		int fppcm = (int) Math.round(denom * 0.01/resolutionPixelInMeters); // pixels per cm 
@@ -532,41 +354,6 @@ outstr.close();
     	ifd.appendChild(node_y_resolution);
 	}
 	
-/*
- * 
-    	IIOMetadataNode node_rationals = new IIOMetadataNode(TIFF_RATIONALS_TAG);
-	    IIOMetadataNode node_hrs =       new IIOMetadataNode(TIFF_RATIONAL_TAG);
-	    node_hrs.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, dt.getHour()+"/1");
-	    IIOMetadataNode node_mins =      new IIOMetadataNode(TIFF_RATIONAL_TAG);
-	    node_mins.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, dt.getMinute()+"/1");
-	    IIOMetadataNode node_secs =      new IIOMetadataNode(TIFF_RATIONAL_TAG);
-	    node_secs.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, fsec+"/"+denom);
-	    node_rationals.appendChild(node_hrs);
-	    node_rationals.appendChild(node_mins);
-	    node_rationals.appendChild(node_secs);
- * 
- * The number of pixels per ResolutionUnit in the ImageWidth direction.
-            <TIFFField number='282' name='XResolution'>
-                <TIFFRationals>
-                    <TIFFRational value='1/1'/>
-                </TIFFRationals>
-            </TIFFField>
-            <TIFFField number='283' name='YResolution'>
-                <TIFFRationals>
-                    <TIFFRational value='1/1'/>
-                </TIFFRationals>
-            </TIFFField>
-            <TIFFField number='296' name='ResolutionUnit'>
-                <TIFFShorts>
-                    <TIFFShort value='1' description='None'/>
-                </TIFFShorts>
-            </TIFFField>
-
-	public static String TIFF_SHORTS_TAG =                  "TIFFShorts";
-	public static String TIFF_SHORT_TAG =                   "TIFFShort";
-
- */
-	
 	/*
 	 * 
 	FileImageOutputStream outputStream = new FileImageOutputStream(outputFile);

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

@@ -39,6 +39,7 @@ import java.io.UnsupportedEncodingException;
 import java.lang.reflect.Array;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
+import java.time.LocalDateTime;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -58,6 +59,7 @@ import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import com.elphel.imagej.correction.Eyesis_Correction;
+import com.elphel.imagej.ims.Did_ins;
 import com.elphel.imagej.tileprocessor.QuadCLTCPU;
 
 //import org.apache.log4j.Logger;
@@ -306,9 +308,20 @@ the type of pixel data in this file 	getPixelType()
 			boolean imageJTags,
 			int debugLevel
 			) throws IOException, FormatException, ServiceException, DependencyException{
+	    double [] lla = {	49.9476514222895,28.5547846609957,323.750316821841};
+	    LocalDateTime dt =  Did_ins.getLocalDateTime(2286, 491072.634526699);
+	    double pix_in_meters = 0.01;
+		
 		if (imp.getType()==ImagePlus.COLOR_RGB) { // 4*8 bit - type = 0
 			if (debugLevel>1) System.out.println("Saving 8-bit TIFF with alpha-channel: "+path); // is it possible to just add alpha to high bytes?
-			ElphelTiffWriter.saveTiffARGB32(imp, path, imageJTags, debugLevel);
+			ElphelTiffWriter.saveTiffARGB32(
+					imp,
+					path,
+					lla,  // double []     lla,  // latitude, longitude, altitude (or null)
+					dt,   // LocalDateTime dt,   // local date/time or null
+					pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
+					imageJTags,
+					debugLevel);
 //			saveTiffARGB32(imp, path, imageJTags, debugLevel);
 			return;
 		} else if (imp.getStackSize()==4) {
@@ -341,7 +354,14 @@ the type of pixel data in this file 	getPixelType()
 			
 			
 			if (debugLevel>1) System.out.println("Saving 8-bit RGBA TIFF with alpha-channel: "+path); // is it possible to just add alpha to high bytes?
-			ElphelTiffWriter.saveTiffARGB32(imp_rgb, path, imageJTags, debugLevel);
+			ElphelTiffWriter.saveTiffARGB32(
+					imp_rgb,
+					path,
+					lla,  // double []     lla,  // latitude, longitude, altitude (or null)
+					dt,   // LocalDateTime dt,   // local date/time or null
+					pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
+					imageJTags,
+					debugLevel);
 //			saveTiffARGB32(imp_rgb, path, imageJTags, debugLevel);
 			return;
 		}

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

@@ -5351,6 +5351,11 @@ public class OpticalFlow {
 				quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
 						null, // String path,             // full name with extension or w/o path to use x3d directory
 						debugLevel+1);
+			} else {
+				if (debugLevel> -3) {
+					System.out.println("Failed to perform attitude correction with QuaternionLma.");
+				}
+				
 			}
 		}
 		
@@ -5946,7 +5951,6 @@ public class OpticalFlow {
 		int [] whs = new int[3];
 		double [] x0y0 = new double[2];		
 		if (export3d) { //combo_dsn_final had strength 1.0e-4 where it should not? Reset it?
-			
 			boolean ok_3d = TexturedModel.output3d( // quadCLTs have same image name, and everything else
 					clt_parameters,      // CLTParameters                            clt_parameters,
 					colorProcParameters, // ColorProcParameters                      colorProcParameters,

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

@@ -696,6 +696,7 @@ public class QuadCLTCPU {
     		System.out.println("getGroundIns(): no INS data available.");
     		return null;
     	}
+        double    min_sfm_gain =  clt_parameters.gmap_min_sfm ; //10.0 minimal SfM gain to keep ground map
 		double [] ims_ortho =     clt_parameters.imp.ims_ortho;
 		double [] ims_mount_atr = clt_parameters.imp.getImsMountATR(); // converts to radians
 		double [] ims_mount_xyz = clt_parameters.imp.ims_mount_xyz;    // not yet used
@@ -721,6 +722,14 @@ public class QuadCLTCPU {
 		}
 		double [] scene_abs_atr_enu = Imx5.quatToCamAtr(cam_quat_enu);
     	double [][] dls = getDLS();
+    	if ((min_sfm_gain> 0) && (dls[3] != null)) {
+    		dls[2]=dls[2].clone();
+    		for (int i = 0; i <dls[2].length; i++) {
+    			if (dls[3][i] < min_sfm_gain) {
+    				dls[2][i] = 0; // zero strength if low SfM gain
+    			}
+    		}
+    	}
     	if (dls==null) {
     		return null;
     	}
@@ -941,15 +950,16 @@ public class QuadCLTCPU {
     
   
     
-    public double [][] getDLS(){ // get disparity, disparity_lma, strength
+    public double [][] getDLS(){ // get disparity, disparity_lma, strength, sfm_gain
     	if (dsi == null) {
 //    		System.out.println("dsi== null, use spawnQuadCLT(), restoreFromModel(), ... to set it");
     		return null;
     	}
-    	double [][] dls = new double[3][];
+    	double [][] dls = new double[4][];
     	dls[0] = dsi[isAux()? TwoQuadCLT.DSI_DISPARITY_AUX :     TwoQuadCLT.DSI_DISPARITY_MAIN];
     	dls[1] = dsi[isAux()? TwoQuadCLT.DSI_DISPARITY_AUX_LMA : TwoQuadCLT.DSI_DISPARITY_MAIN_LMA];
     	dls[2] = dsi[isAux()? TwoQuadCLT.DSI_STRENGTH_AUX :      TwoQuadCLT.DSI_STRENGTH_MAIN];
+    	dls[3] = dsi[isAux()? TwoQuadCLT.DSI_SFM_GAIN_AUX :      TwoQuadCLT.DSI_SFM_GAIN_MAIN];
     	return dls;
     }
     

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

@@ -2464,6 +2464,7 @@ public class TexturedModel {
 		final double    discard_rdisp =   clt_parameters.gmap_discard_rdisp ; //0.02;  // discard above/below this fraction of average height
 		final double    pix_size =        clt_parameters.gmap_pix_size ; //0.005; // hdr_x0y0,       // in meters
 		final int       max_image_width = clt_parameters.gmap_max_image_width ; //4000; // 3200;  // increase pixel size as a power of 2 until image fits
+		final double    min_sfm_gain =         clt_parameters.gmap_min_sfm ; //10.0 minimal SfM gain to keep ground map
 		final boolean   crop_empty =      clt_parameters.gmap_crop_empty ; //true;
 		final int       crop_extra =      clt_parameters.gmap_crop_extra ; //20;
 		final int []    tex_pals =        clt_parameters.gmap_tex_pals ; //{0,1,2};
@@ -2559,7 +2560,7 @@ public class TexturedModel {
 				combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_LMA],
 				combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_STRENGTH]
 		};
-
+		double [] sfm_gain = (min_sfm_gain > 0.0) ? combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_SFM_GAIN] : null;
 		// currently conditionInitialDS() zeroes disparity for blue_sky. TODO: allow some FG over blue_sky?
 		// gets Blue Sky from scene.dsi , not from the file!
 		double [][] ds_fg = OpticalFlow.conditionInitialDS(
@@ -2584,9 +2585,17 @@ public class TexturedModel {
 				dls_bg,                 // double [][]    dls
 				scenes[ref_index], // QuadCLT        scene,
 				debugLevel);         // int debug_level)
+		if (sfm_gain != null) {
+			for (int i = 0; i < ds_fg[0].length; i++) if (sfm_gain[i] < min_sfm_gain){
+				ds_fg[0][i] = Double.NaN;
+				ds_bg[0][i] = Double.NaN;
+				ds_fg[1][i] = 0.0;
+				ds_bg[1][i] = 0.0;
+			}
+		}
+		
 		double[][] ds_fg_bg = {ds_fg[0], ds_bg[0].clone()};
 		double[][] ss_fg_bg = {ds_fg[1], ds_bg[1]};
-
 		if (show_bs_debug) {
 			String [] dbg_titles = {"FG","BG","BS"};
 			double [][] dbg_img = {ds_fg_bg[0], ds_fg_bg[1],combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY].clone()};
@@ -2612,10 +2621,10 @@ public class TexturedModel {
 			}
 			for (int i = 0; i < ss_fg_bg[0].length; i++) {
 				if (Double.isNaN(dls_fg[1][i])){
-					ss_fg_bg[0][i] = 0.0001;
+					ss_fg_bg[0][i] = Math.min(ss_fg_bg[0][i],0.0001); // do not increase if it was already 0
 				}
 				if (Double.isNaN(dls_bg[1][i])){
-					ss_fg_bg[1][i] = 0.0001;
+					ss_fg_bg[1][i] = Math.min(ss_fg_bg[1][i],0.0001); // do not increase if it was already 0
 				}
 			}
 		}
@@ -2979,7 +2988,7 @@ public class TexturedModel {
 			}
 			// if (imp_textures[nslice] != null)
 		} // for (int nslice = 0; nslice < tileClusters.length; nslice++){
-		if (render_hdr) {
+		if (render_hdr) { //
 			int []    hdr_whs = new int[3];
 			double [] hdr_x0y0 = new double[2];		
 			double [][] to_ground_xyzatr = scenes[ref_index].getGround(

src/main/java/com/elphel/imagej/x3d/export/Render3D.java

@@ -254,6 +254,7 @@ public class Render3D {
 		if ((tri_meshes == null) || tri_meshes.isEmpty() || (tri_meshes.get(0).getTexturePixels() == null)) {
 			return null;
 		}
+		final boolean export_z = true;
 		final int dbg_ipix=1673752;
 		// get total number of triangles
 		int num_tri=0;
@@ -276,7 +277,7 @@ public class Render3D {
 			System.out.println("Prepare to render "+num_tri+" triangles in "+num_mesh+" meshes");
 		}
 		final int z_index = tri_meshes.get(0).getTexturePixels().length;
-		final double [][] full_rendered = new double[z_index][out_width * out_height];
+		final double [][] full_rendered = new double[z_index+ (export_z? 1:0)][out_width * out_height];
 		int alpha_index = last_is_alpha ? (z_index - 1) : z_index;
 		for (int chn = 0; chn < alpha_index; chn++) {
 			Arrays.fill(full_rendered[chn], Double.NaN);
@@ -361,12 +362,12 @@ public class Render3D {
 								double kx = dot2(d0p, orto2[0]);
 								double ky = dot2(d0p, orto2[1]);
 								// interpolate z
-
-								double z_interp = tri_out2[0][2] + kx * (tri_out2[1][2]-tri_out2[0][2]) + ky*(tri_out2[1][2]-tri_out2[0][2]);
+								double z_interp = tri_out2[0][2] +
+										kx * (tri_out2[1][2]-tri_out2[0][2]) +
+										ky * (tri_out2[2][2]-tri_out2[0][2]);
 								if ((rend[ipix] != null ) && (rend[ipix][z_index] < z_interp)) {
 									continue;
 								}
-								
 								// Get corresponding texture coordinates
 								double text_x = tri_text2[0][0] + kx * t01[0] + ky*t02[0]; // texture relative coordinates (0,1)
 								double text_y = tri_text2[0][1] + kx * t01[1] + ky*t02[1]; // y - up!
@@ -426,7 +427,7 @@ public class Render3D {
 						for (int sub_render = 0; sub_render < rendered.length; sub_render++) if (rendered[sub_render][indx] != null){
 							if (!(rendered[sub_render][indx][z_index] <= z)) { // OK previous NaN
 								z = rendered[sub_render][indx][z_index];
-								for (int chn = 0; chn < z_index; chn++) {
+								for (int chn = 0; chn < full_rendered.length; chn++) { // z_index; chn++) {
 									full_rendered[chn][indx] = rendered[sub_render][indx][chn];
 								}
 							}
@@ -549,12 +550,12 @@ public class Render3D {
 								double kx = dot2(d0p, orto2[0]);
 								double ky = dot2(d0p, orto2[1]);
 								// interpolate z
-
-								double z_interp = tri_out2[0][2] + kx * (tri_out2[1][2]-tri_out2[0][2]) + ky*(tri_out2[1][2]-tri_out2[0][2]);
+								double z_interp = tri_out2[0][2] +
+										kx * (tri_out2[1][2]-tri_out2[0][2]) +
+										ky * (tri_out2[2][2]-tri_out2[0][2]);
 								if ((rend[ipix] != null ) && (rend[ipix][z_index] < z_interp)) {
 									continue;
 								}
-								
 								// Get corresponding texture coordinates
 								double text_x = tri_text2[0][0] + kx * t01[0] + ky*t02[0]; // texture relative coordinates (0,1)
 								double text_y = tri_text2[0][1] + kx * t01[1] + ky*t02[1]; // y - up!