Tiff writer, fixed bug in Z interpolation in plane render

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

@@ -480,7 +480,8 @@ public class CLTParameters {
 	public double     gmap_discard_adisp =   0.2;   // discard above/below this fraction of average height 
 	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 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/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!