Recording geo-tagged float Tiff

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

@@ -487,10 +487,10 @@ public class CLTParameters {
 	public int []     gmap_tex_pals =        {0,1,2};
 
 	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)
 	public int        gmap_tiff_pal =        0;     // LWIR palette for TIFF  
 	
-	
 	public boolean    generate_bg =      true;  // Generate background image for 3dmodels
 	public boolean    show_textures    = true;  // show generated textures
 	public boolean    debug_filters    = false;// show intermediate results of filtering
@@ -1635,6 +1635,11 @@ 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_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 
+		properties.setProperty(prefix+"gmap_tiff_pal",              this.gmap_tiff_pal+"");              // int     
+		
 		properties.setProperty(prefix+"generate_bg",                this.generate_bg+"");
 		properties.setProperty(prefix+"show_textures",              this.show_textures+"");
 		properties.setProperty(prefix+"debug_filters",              this.debug_filters+"");
@@ -2649,10 +2654,15 @@ 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_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"));
+
+   		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"));
+		if (properties.getProperty(prefix+"gmap_tiff_pal")!=null)        this.gmap_tiff_pal=Integer.parseInt(properties.getProperty(prefix+         "gmap_tiff_pal"));// int     
 		
 		if (properties.getProperty(prefix+"generate_bg")!=null)                   this.generate_bg=Boolean.parseBoolean(properties.getProperty(prefix+"generate_bg"));
 		if (properties.getProperty(prefix+"show_textures")!=null)                 this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
@@ -3922,6 +3932,15 @@ public class CLTParameters {
 				"Additionally crop map by this number of pixels from each of the four directions.");
 		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 ("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
+				"Save float (32-bit) TIFF with geo and resolution metadata (coordinates correspond to the top left image corner), NAN for transparency.");
+		gd.addCheckbox ("Save ARGB Tiff with transparency and Geo",this.gmap_save_tiff, // true; // enable change FG pixel to opaque from transparent
+				"Save transparent TIFF with geo and resolution metadata (coordinates correspond to the top left image corner).");
+		gd.addNumericField("Crop maps extra",                      this.gmap_tiff_pal, 0,3,"",  // minimal neighbors to keep alpha
+				"LWIR palette for Geo/transparency TIFF output.");
 		
 		gd.addMessage     ("Earlier 3D generation parameters");
 		gd.addCheckbox    ("Generate background (infinity) image for 3D (not needed for view down)",                 this.generate_bg);
@@ -5137,7 +5156,13 @@ public class CLTParameters {
 		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.gmap_tex_pals =        CLTParameters.str_to_iarr(gd.getNextString());
+		
+		this.gmap_save_alt=         gd.getNextBoolean();
+		this.gmap_save_tiff32=        gd.getNextBoolean();
+		this.gmap_save_tiff=        gd.getNextBoolean();
+		this.gmap_tiff_pal=   (int) gd.getNextNumber();
+		
 		this.generate_bg=           gd.getNextBoolean();
 		this.show_textures=         gd.getNextBoolean();
 		this.debug_filters=         gd.getNextBoolean();

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

@@ -114,7 +114,7 @@ public class DumpImageMetadata
 		System.out.println(">");
 	}
 	
-	private static void dumpMetadata(IIOMetadata metadata)
+	static void dumpMetadata(IIOMetadata metadata)
 	{
 		String[] names = metadata.getMetadataFormatNames();
 		int length = names.length;

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

@@ -23,11 +23,18 @@
  */
 package com.elphel.imagej.readers;
 
+import java.awt.Transparency;
+import java.awt.color.ColorSpace;
 import java.awt.image.BufferedImage;
 import java.awt.image.ColorModel;
+import java.awt.image.ComponentColorModel;
+import java.awt.image.DataBuffer;
 import java.awt.image.DataBufferInt;
+import java.awt.image.DataBufferFloat;
 import java.awt.image.Raster;
 import java.awt.image.SampleModel;
+import java.awt.image.WritableRaster;
+import java.awt.image.PixelInterleavedSampleModel;
 import java.io.File;
 import java.io.IOException;
 import java.time.LocalDateTime;
@@ -68,7 +75,7 @@ public class ElphelTiffWriter {
 	public static String TIFF_FIELD_DESCRIPTION_ATTRIBUTE = "description";
 	
 	
-	public static void saveTiffARGB32(
+	public static void saveTiffARGBOrGray32(
 			ImagePlus     imp,
 			String        path, // full path to save image
 			double []     lla,  // latitude, longitude, altitude (or null)
@@ -87,19 +94,30 @@ public class ElphelTiffWriter {
 // 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);
-	    /* 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);
-	    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);
-	    
+	    BufferedImage bufferedImageAlpha;
+    	BufferedImage bufferedImage = (BufferedImage) imp.getImage(); // properties=null
+	    if (imp.getType()==ImagePlus.COLOR_RGB) {
+	    	/* ImagePlus image removes alpha, so we need to create a new ARGB BufferedImage
+	    	 * and copy data (it is correct in imp.getImage() */
+	    	bufferedImageAlpha = new BufferedImage(
+	    			bufferedImage.getWidth(),
+	    			bufferedImage.getHeight(),
+	    			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);
+	    } else {
+	    	bufferedImageAlpha = createFloatBufferedImage(
+	    			bufferedImage.getWidth(),
+	    			bufferedImage.getHeight()
+	    			);
+	    	float [] pixels = (float[]) imp.getProcessor().getPixels();
+	    	final float[] bia_as_arr = ( (DataBufferFloat) bufferedImageAlpha.getRaster().getDataBuffer() ).getData();
+	    	System.arraycopy(pixels, 0, bia_as_arr, 0, bia_as_arr.length);
+	    }
 	    ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImageAlpha);            
 	    IIOMetadata imageMetadata = tiffWriter.getDefaultImageMetadata(imageType, tiffWriteParam);
+	    if (debugLevel > 0) {System.out.println("\n=== imageMetadata ===:");DumpImageMetadata.dumpMetadata(imageMetadata);}
 // just for testing:
 	    int cm_dig_after = 9;
 	    // Here is a way adding tag sets through TIFFDirectory
@@ -166,6 +184,82 @@ public class ElphelTiffWriter {
 	    System.out.println();
 	}
 	
+	private static BufferedImage createFloatBufferedImage(
+			int width,
+			int height
+			) {
+		//https://stackoverflow.com/questions/26766751/java-create-bufferedimage-with-float-precision/26775056#26775056	
+//        int bands = 4; // 4 bands for ARGB, 3 for RGB etc
+//        int[] bandOffsets = {0, 1, 2, 3}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A
+        int bands = 1; // 4 bands for ARGB, 3 for RGB etc
+        int[] bandOffsets = {0}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A
+        // Create a TYPE_FLOAT sample model (specifying how the pixels are stored)
+        SampleModel sampleModel0 = new PixelInterleavedSampleModel(
+        		DataBuffer.TYPE_FLOAT,
+        		width,
+        		height,
+        		bands,
+        		width  * bands,
+        		bandOffsets);
+
+        // Create a color model compatible with this sample model/raster (TYPE_FLOAT)
+        // Note that the number of bands must equal the number of color components in the 
+        // color space (3 for RGB) + 1 extra band if the color model contains alpha 
+        ColorSpace colorSpace = ColorSpace.getInstance(ColorSpace.CS_GRAY); // CS_sRGB);
+//        ColorModel colorModel = new ComponentColorModel(colorSpace, true, false, Transparency.TRANSLUCENT, DataBuffer.TYPE_FLOAT);
+        ColorModel colorModel = new ComponentColorModel(
+        		colorSpace,
+        		false, // true,
+        		false,
+        		Transparency.TRANSLUCENT, // ?
+        		DataBuffer.TYPE_FLOAT);
+        SampleModel sampleModel = colorModel.createCompatibleSampleModel (width, height);       
+        // ...and data buffer (where the pixels are stored)
+        DataBuffer buffer = new DataBufferFloat(width * height * bands);
+        // Wrap it in a writable raster
+        WritableRaster raster = Raster.createWritableRaster(sampleModel, buffer, null);
+
+        // And finally create an image with this raster
+        BufferedImage image = new BufferedImage(colorModel, raster, colorModel.isAlphaPremultiplied(), null);
+        return image;
+        
+		
+/*
+ * color space (ColorSpace.CS_GRAY) and no transparency may make more sense.
+ public class FloatImage {
+    public static void main(String[] args) {
+        // Define dimensions and layout of the image
+        int w = 300;
+        int h = 200;
+        int bands = 4; // 4 bands for ARGB, 3 for RGB etc
+        int[] bandOffsets = {0, 1, 2, 3}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A
+
+        // Create a TYPE_FLOAT sample model (specifying how the pixels are stored)
+        SampleModel sampleModel = new PixelInterleavedSampleModel(DataBuffer.TYPE_FLOAT, w, h, bands, w  * bands, bandOffsets);
+        // ...and data buffer (where the pixels are stored)
+        DataBuffer buffer = new DataBufferFloat(w * h * bands);
+
+        // Wrap it in a writable raster
+        WritableRaster raster = Raster.createWritableRaster(sampleModel, buffer, null);
+
+        // Create a color model compatible with this sample model/raster (TYPE_FLOAT)
+        // Note that the number of bands must equal the number of color components in the 
+        // color space (3 for RGB) + 1 extra band if the color model contains alpha 
+        ColorSpace colorSpace = ColorSpace.getInstance(ColorSpace.CS_sRGB);
+        ColorModel colorModel = new ComponentColorModel(colorSpace, true, false, Transparency.TRANSLUCENT, DataBuffer.TYPE_FLOAT);
+
+        // And finally create an image with this raster
+        BufferedImage image = new BufferedImage(colorModel, raster, colorModel.isAlphaPremultiplied(), null);
+
+        System.out.println("image = " + image);
+    }
+}
+
+
+ */
+	}
+	
+	
 	private static IIOMetadataNode createRationalDegrees(double d, int digits_after) { // 8
 		int denom = 1;
 		for (int i = 0; i < digits_after; i++) denom *= 10;

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

@@ -314,7 +314,7 @@ the type of pixel data in this file 	getPixelType()
 		
 		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(
+			ElphelTiffWriter.saveTiffARGBOrGray32(
 					imp,
 					path,
 					lla,  // double []     lla,  // latitude, longitude, altitude (or null)
@@ -330,39 +330,53 @@ the type of pixel data in this file 	getPixelType()
 			return;
 
 		} else if (imp.getType()==ImagePlus.GRAY32) {
-			int            lwir_palette = 0;
-			double []      minmax = null;
-			String title = imp.getTitle();
-			float [] fpixels = (float[]) imp.getProcessor().getPixels();
-			double [] dpixels = new double [fpixels.length];
-			for (int i = 0; i < fpixels.length; i++) {
-				dpixels[i] = fpixels[i];
+			boolean save_float = true;
+			if (save_float) {
+				if (debugLevel>1) System.out.println("Saving GRAY32 TIFF (NaN for transparency): "+path); // is it possible to just add alpha to high bytes?
+				ElphelTiffWriter.saveTiffARGBOrGray32(
+						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);
+
+			} else {
+				int            lwir_palette = 0;
+				double []      minmax = null;
+				String title = imp.getTitle();
+				float [] fpixels = (float[]) imp.getProcessor().getPixels();
+				double [] dpixels = new double [fpixels.length];
+				for (int i = 0; i < fpixels.length; i++) {
+					dpixels[i] = fpixels[i];
+				}
+				ImagePlus imp_rgb =  	  QuadCLTCPU.linearStackToColorLWIR(
+						Eyesis_Correction.CLT_PARAMETERS, // clt_parameters, // CLTParameters  clt_parameters,
+						lwir_palette, // int            lwir_palette, // <0 - do not convert
+						minmax, // minmax, // double []      minmax,
+						title, // String         name,
+						"-rgba",              // String         suffix, // such as disparity=...
+						true,            // boolean        toRGB,
+						new double[][] {dpixels},         // faded_textures[nslice], // double [][]    texture_data,
+						imp.getWidth(),  // int            width, // int tilesX,
+						imp.getHeight(), // int            height, // int tilesY,
+						debugLevel);     // int            debugLevel )
+				//			File test_dump = new File("/home/elphel/Documents/DoD/Ukraine/photos/test/1694531940_120446-02-gps.tiff");
+				//			DumpImageMetadata.processFile(test_dump);
+
+
+				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.saveTiffARGBOrGray32(
+						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);
 			}
-			ImagePlus imp_rgb =  	  QuadCLTCPU.linearStackToColorLWIR(
-					Eyesis_Correction.CLT_PARAMETERS, // clt_parameters, // CLTParameters  clt_parameters,
-					lwir_palette, // int            lwir_palette, // <0 - do not convert
-					minmax, // minmax, // double []      minmax,
-					title, // String         name,
-					"-rgba",              // String         suffix, // such as disparity=...
-					true,            // boolean        toRGB,
-					new double[][] {dpixels},         // faded_textures[nslice], // double [][]    texture_data,
-					imp.getWidth(),  // int            width, // int tilesX,
-					imp.getHeight(), // int            height, // int tilesY,
-					debugLevel);     // int            debugLevel )
-//			File test_dump = new File("/home/elphel/Documents/DoD/Ukraine/photos/test/1694531940_120446-02-gps.tiff");
-//			DumpImageMetadata.processFile(test_dump);
-			
-			
-			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,
-					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;
 		}
 		IJ.showMessage("Not yet implemented for this image type");

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

@@ -16445,7 +16445,7 @@ public class QuadCLTCPU {
 				  height, // int            height, // int tilesY,
 				  debugLevel); // int            debugLevel )
 		  String image_path = model_dir +  Prefs.getFileSeparator() + title+".tiff";
-		  ElphelTiffWriter.saveTiffARGB32(
+		  ElphelTiffWriter.saveTiffARGBOrGray32(
 				  imp,
 				  image_path,
 				  lla,           // double []     lla,  // latitude, longitude, altitude (or null)

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

@@ -2466,7 +2466,7 @@ 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 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};