Updated/tested with center reference

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

@@ -484,7 +484,7 @@ public class CLTParameters {
 
 	
 	
-
+	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
 	// not used anywhere so far
@@ -1624,6 +1624,7 @@ 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+"generate_bg",                this.generate_bg+"");
 		properties.setProperty(prefix+"show_textures",              this.show_textures+"");
 		properties.setProperty(prefix+"debug_filters",              this.debug_filters+"");
 
@@ -2639,6 +2640,7 @@ 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+"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"));
 		if (properties.getProperty(prefix+"debug_filters")!=null)                 this.debug_filters=Boolean.parseBoolean(properties.getProperty(prefix+"debug_filters"));
 
@@ -3900,6 +3902,7 @@ public class CLTParameters {
 		
 		
 		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);
 		gd.addCheckbox    ("show intermediate results of filtering",                                                 this.debug_filters);
 
@@ -5112,6 +5115,7 @@ public class CLTParameters {
 		
 		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();
 		this.min_smth=              gd.getNextNumber();

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

@@ -237,6 +237,10 @@ public class ErsCorrection extends GeometryCorrection {
 	public double [] getCameraATR() {
 		return camera_atr;
 	}
+	
+	public double [][] getErsXYZATR_dt() {
+		return new double[][] {ers_wxyz_center_dt,ers_watr_center_dt};
+	}
 	public double [] getErsXYZ_dt() {
 		return ers_wxyz_center_dt;
 	}
@@ -378,7 +382,7 @@ public class ErsCorrection extends GeometryCorrection {
 		scenes_poses = new HashMap <String, XyzAtr>();
 	}
 
-	public void removeScene(String timestamp) {
+	public void removeScene(String timestamp) { // not used
 		scenes_poses.remove(timestamp);
 	}
 
@@ -393,20 +397,45 @@ public class ErsCorrection extends GeometryCorrection {
 		return scenes;
 	}
 
-	public void addScene(String timestamp, XyzAtr scene) {
-		scenes_poses.put(timestamp, scene);
+	public void addScene(String timestamp) { // will it work?
+//		scenes_poses.put(timestamp, null);
+		scenes_poses.remove(timestamp);
+	}
+	
+	public void addScene(String timestamp, XyzAtr scene) { // will it work?
+		if (scene != null) {
+			scenes_poses.put(timestamp, scene);
+		} else {
+			scenes_poses.remove(timestamp);
+		}
 	}
+
 	public void addScene(String timestamp, double [] xyz, double [] atr) {
 		scenes_poses.put(timestamp, new XyzAtr(xyz, atr));
 	}
+	public void addScene(String timestamp, double [][] xyzatr) {
+		scenes_poses.put(timestamp, new XyzAtr(xyzatr[0], xyzatr[1]));
+	}
 	
 	public void addScene(String timestamp, double [] xyz, double [] atr, double [] ers_xyz_dt, double [] ers_atr_dt) {
 		scenes_poses.put(timestamp, new XyzAtr(xyz, atr, ers_xyz_dt, ers_atr_dt));
 	}
+	
+	public void addScene(String timestamp, double [][] xyzatr, double [][] ers_xyzatr_dt) {
+		scenes_poses.put(timestamp, new XyzAtr(xyzatr[0], xyzatr[1], ers_xyzatr_dt[0], ers_xyzatr_dt[1]));
+	}
+	
 	//not used
 	public void addScene(String timestamp, double [] xyz, double [] atr, double [] ers_xyz_dt, double [] ers_atr_dt, double [] ers_xyz_d2t, double [] ers_atr_d2t) {
 		scenes_poses.put(timestamp, new XyzAtr(xyz, atr, ers_xyz_dt, ers_atr_dt, ers_xyz_d2t, ers_atr_d2t));
 	}
+
+	public void addScene(String timestamp, double [][] xyzatr, double [][] ers_xyzatr_dt, double [][] ers_xyzatr_d2t) {
+		scenes_poses.put(timestamp, new XyzAtr(
+				xyzatr[0], xyzatr[1],
+				ers_xyzatr_dt[0], ers_xyzatr_dt[1],
+				ers_xyzatr_d2t[0], ers_xyzatr_d2t[1]));
+	}
 	
 	public String getEarliestScene() {
 		return Collections.min(scenes_poses.keySet());
@@ -419,7 +448,10 @@ public class ErsCorrection extends GeometryCorrection {
 	
 	public double[][] getSceneXYZATR(String timestamp) {
 		XyzAtr scene = scenes_poses.get(timestamp);
-		if (scene == null) return null;
+		if (scene == null) {
+//			if timestamp.equals()
+			return null;
+		}
 		return scene.getXYZATR();
 	}
 	public double[] getSceneXYZ(String timestamp) {
@@ -432,6 +464,14 @@ public class ErsCorrection extends GeometryCorrection {
 		if (scene == null) return null;
 		return scene.getATR();
 	}
+
+	public double[][] getSceneErsXYZATR_dt(String timestamp) {
+		XyzAtr scene = scenes_poses.get(timestamp);
+		if (scene == null) return null;
+		return scene.getErsXYZATR_dt();
+	}
+	
+	
 	public double[] getSceneErsXYZ_dt(String timestamp) {
 		XyzAtr scene = scenes_poses.get(timestamp);
 		if (scene == null) return null;

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

@@ -763,7 +763,7 @@ public class IntersceneLma {
 		final double [] full_vector = getFullVector(vector);
 		final ErsCorrection ers_ref =   reference_QuadClt.getErsCorrection();
 		final ErsCorrection ers_scene = scene_QuadClt.getErsCorrection();
-		final double [] scene_xyz =     new double[3];;
+		final double [] scene_xyz =     new double[3];
 		final double [] scene_atr  =    new double[3];
 		final double [] reference_xyz = new double[3]; // will stay 0
 		final double [] reference_atr = new double[3]; // will stay 0
@@ -786,6 +786,10 @@ public class IntersceneLma {
 			scene_atr[i] =     full_vector[ErsCorrection.DP_DSAZ +  i];
 			scene_xyz[i] =     full_vector[ErsCorrection.DP_DSX +  i];
 		}
+		if (Double.isNaN(scene_xyz[0])) {
+			System.out.println("getFxDerivs(): scene_xyz[0]=NaN");
+			System.out.println();
+		}
 		ers_scene.setupERS();
 		ers_ref.setupERS();
 		final Matrix [] reference_matrices_inverse = ErsCorrection.getInterRotDeriveMatrices(

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

@@ -52,6 +52,7 @@ public class IntersceneMatchParameters {
 				ims_mount_atr[1] * Math.PI/180,
 				ims_mount_atr[2] * Math.PI/180};
 	}
+	public  boolean center_reference =   false;
 	public  boolean force_ref_dsi =      false; // true;
 	public  boolean force_orientations = false;
 	public  boolean run_ly =             false; // will return just after LY adjustments, skipping all output generation
@@ -161,7 +162,8 @@ public class IntersceneMatchParameters {
 	//------------	
 	
 	// Sky detection/filtering
-	public  boolean sky_recalc =                    false; // force blue sky recalculation even if it exists
+	public  boolean sky_extract =                    true;  // do not try to extract blue sky
+	public  boolean sky_recalc =                     false; // force blue sky recalculation even if it exists
 	public  double  sky_highest_min =                -50; // lowest absolute value should not be higher (requires photometric) 
 	public  double  cold_frac =                        0.005; // this and lower will scale fom by  cold_scale
 	public  double  hot_frac =                         0.9;    // this and above will scale fom by 1.0
@@ -444,6 +446,8 @@ public class IntersceneMatchParameters {
 		gd.addTab         ("Scene Series", "Processing series of scenes and multi-series sets");
 		gd.addMessage  ("Build series options");
 		
+		gd.addCheckbox ("Use center scene as a reference",           this.center_reference,
+				"True for mapping with post-processing. If false, use the last scene as a reference (driving).");
 		gd.addCheckbox ("Force reference scene DSI calculation",     this.force_ref_dsi,
 				"Calculate reference scene DSI even if the file exists.");
 		gd.addCheckbox ("Force egomotion calculation",               this.force_orientations,
@@ -657,6 +661,8 @@ public class IntersceneMatchParameters {
 		
 		gd.addTab("Sky","Featureless sky areas detection and filtering (LWIR only)");
 		gd.addMessage  ("Temperature-related filtering (requires photometric calibration)");
+		gd.addCheckbox ("Try blue sky calculation/use",              this.sky_extract,
+				"Disable if no sky will appear in the image (such as for down-pointed camera).");
 		gd.addCheckbox ("Force blue sky recalculation",              this.sky_recalc,
 				"Recalculate blue sky even if it already exists.");
 		gd.addNumericField("High limit of the scene coldest tile",   this.sky_highest_min, 5,7,"",
@@ -1108,6 +1114,7 @@ public class IntersceneMatchParameters {
 		this.ims_mount_xyz = IntersceneMatchParameters. StringToDoubles(gd.getNextString(), 3);
 		this.sfm_use =                        gd.getNextBoolean();
 		this.sfm_min_base =                   gd.getNextNumber();
+		this.center_reference =               gd.getNextBoolean();
 		this.force_ref_dsi =                  gd.getNextBoolean();
 		this.force_orientations =             gd.getNextBoolean();
 		this.run_ly =                         gd.getNextBoolean();
@@ -1203,6 +1210,7 @@ public class IntersceneMatchParameters {
 		this.strong_strength =                gd.getNextNumber();
 		this.weak_strength =                  gd.getNextNumber();
 		
+		this.sky_extract =              gd.getNextBoolean();
 		this.sky_recalc =               gd.getNextBoolean();
 		this.sky_highest_min =          gd.getNextNumber(); 	
 		this.cold_frac =                gd.getNextNumber();       	
@@ -1461,6 +1469,7 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"ims_mount_xyz",                 IntersceneMatchParameters.doublesToString(this.ims_mount_xyz));
 		properties.setProperty(prefix+"sfm_use",                       this.sfm_use + "");                     // boolean
 		properties.setProperty(prefix+"sfm_min_base",                  this.sfm_min_base+"");                  // double
+		properties.setProperty(prefix+"center_reference",              this.center_reference + "");               // boolean
 		properties.setProperty(prefix+"force_ref_dsi",                 this.force_ref_dsi + "");               // boolean
 		properties.setProperty(prefix+"force_orientations",            this.force_orientations + "");          // boolean
 		properties.setProperty(prefix+"run_ly",                        this.run_ly + "");                      // boolean
@@ -1563,6 +1572,7 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"strong_strength",               this.strong_strength+"");               // double
 		properties.setProperty(prefix+"weak_strength",                 this.weak_strength+"");                 // double
 
+		properties.setProperty(prefix+"sky_extract",          this.sky_extract+"");         // boolean
 		properties.setProperty(prefix+"sky_recalc",           this.sky_recalc+"");          // boolean
 		properties.setProperty(prefix+"sky_highest_min",      this.sky_highest_min+"");     // double
 		properties.setProperty(prefix+"cold_frac",            this.cold_frac+"");           // double
@@ -1774,6 +1784,7 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"ims_mount_xyz")!=null) 	   this.ims_mount_xyz= IntersceneMatchParameters.StringToDoubles(properties.getProperty(prefix+"ims_mount_xyz"),3);
 		if (properties.getProperty(prefix+"sfm_use")!=null)            this.sfm_use=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_use"));		
 		if (properties.getProperty(prefix+"sfm_min_base")!=null)       this.sfm_min_base=Double.parseDouble(properties.getProperty(prefix+"sfm_min_base"));
+		if (properties.getProperty(prefix+"center_reference")!=null)              this.center_reference=Boolean.parseBoolean(properties.getProperty(prefix+"center_reference"));		
 		if (properties.getProperty(prefix+"force_ref_dsi")!=null)                 this.force_ref_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"force_ref_dsi"));		
 		if (properties.getProperty(prefix+"force_orientations")!=null)            this.force_orientations=Boolean.parseBoolean(properties.getProperty(prefix+"force_orientations"));		
 		if (properties.getProperty(prefix+"run_ly")!=null)                        this.run_ly=Boolean.parseBoolean(properties.getProperty(prefix+"run_ly"));		
@@ -1881,6 +1892,7 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"strong_strength")!=null)               this.strong_strength=Double.parseDouble(properties.getProperty(prefix+"strong_strength"));
 		if (properties.getProperty(prefix+"weak_strength")!=null)                 this.weak_strength=Double.parseDouble(properties.getProperty(prefix+"weak_strength"));
 		
+		if (properties.getProperty(prefix+"sky_extract")!=null)          this.sky_extract=Boolean.parseBoolean(properties.getProperty(prefix+"sky_extract"));		
 		if (properties.getProperty(prefix+"sky_recalc")!=null)           this.sky_recalc=Boolean.parseBoolean(properties.getProperty(prefix+"sky_recalc"));		
 		if (properties.getProperty(prefix+"sky_highest_min")!=null)      this.sky_highest_min=Double.parseDouble(properties.getProperty(prefix+"sky_highest_min"));
 		if (properties.getProperty(prefix+"cold_frac")!=null)            this.cold_frac=Double.parseDouble(properties.getProperty(prefix+"cold_frac"));
@@ -2114,6 +2126,7 @@ public class IntersceneMatchParameters {
  		imp.ims_mount_xyz                 = this.ims_mount_xyz.clone();
  		imp.sfm_use                       = this.sfm_use;
  		imp.sfm_min_base                  = this.sfm_min_base;
+		imp.center_reference              = this.center_reference;
 		imp.force_ref_dsi                 = this.force_ref_dsi;
 		imp.force_orientations            = this.force_orientations;
 		imp.run_ly                        = this.run_ly;
@@ -2212,6 +2225,7 @@ public class IntersceneMatchParameters {
 		imp.strong_strength               = this.strong_strength;
 		imp.weak_strength                 = this.weak_strength;
 		
+		imp.sky_extract =           this.sky_extract;
 		imp.sky_recalc =            this.sky_recalc;
 		imp.sky_highest_min =       this.sky_highest_min;
 		imp.cold_frac =             this.cold_frac;

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

@@ -2447,6 +2447,7 @@ public class TexturedModel {
 			final QuadCLT                            parameter_scene, // to use for rendering parameters in multi-series sequences
 			// if null - use reference scene 
 			QuadCLT []                               scenes,
+			final int                                ref_index,
 			double [][]                              combo_dsn_final, // null OK, will read file
 			final boolean                            updateStatus,
 			final int                                debugLevel)
@@ -2512,7 +2513,7 @@ public class TexturedModel {
 		final boolean tex_um_fixed =        clt_parameters.tex_um_fixed;  // imp.mono_fixed; //  true; // normalize to fixed range when converting to 8 bits 
 		final double  tex_um_range =        clt_parameters.tex_um_range;  // imp.mono_range; // 500.0;  // monochrome full-scale range (+/- half)
 
-		final int           ref_index =  scenes.length - 1;
+//		final int           ref_index =  scenes.length - 1;
 		final QuadCLT       ref_scene =  scenes[ref_index];
 		final TileProcessor tp =         ref_scene.getTileProcessor();
 

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

@@ -144,6 +144,10 @@ public class XyzAtr {
 		atr[2] = d[2];
 	}
 	
+	public double [][] getErsXYZATR_dt() {
+		return new double [][] {ers_xyz_dt, ers_atr_dt};
+	}
+	
 	public double [] getErsXYZ_dt() {
 		return ers_xyz_dt;
 	}

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwirWorld.java

@@ -340,6 +340,13 @@ public class LwirWorld {
 				quadCLTs[ref_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
 				quadCLTs[ref_index].preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
 						clt_parameters,
+						// adding these parameters for more flexibility in accuracy/speed
+						clt_parameters.gr_max_clust_radius, //int      gr_max_clust_radius,			  
+						clt_parameters.disp_scan_start,     // double  disp_scan_start,
+						clt_parameters.disp_scan_step,      // double  disp_scan_step,
+						clt_parameters.disp_scan_count,     // double  disp_scan_count,
+						false,                              // boolean no_bg_generate,			  
+						false,                              // boolean no_lma,			  
 						debayerParameters,
 						colorProcParameters,
 						rgbParameters,

src/main/java/com/elphel/imagej/tileprocessor/sfm/SfmCorr.java

 package com.elphel.imagej.tileprocessor.sfm;
 
 class SfmCorr{
-	double sfm_gain;
-	double [] corr_ind = null;  // {disparity, strength}
+	double sfm_gain =     0;
+	double [] corr_ind =  null;  // {disparity, strength}
 	double [] corr_neib = null; // {disparity, strength}
 }

src/main/java/com/elphel/imagej/tileprocessor/sfm/StructureFromMotion.java

@@ -643,7 +643,7 @@ public class StructureFromMotion {
         				tilesY,
         				true,
         				"sfm_corr-"+scene_pairs[num_pairs-1][1].getImageName()+"-"+
-        						scene_pairs[0][0].getImageName()+"-"+num_pairs,
+        						scene_pairs[0][0].getImageName()+"-"+num_pairs+"-"+String.format("%02d", ntry),
         						dbg_titles);
         	}
         	
@@ -862,6 +862,9 @@ public class StructureFromMotion {
 			threads[ithread] = new Thread() {
 				public void run() {
 					for (int nTile = ai.getAndIncrement(); nTile < accum_PD.length; nTile = ai.getAndIncrement()) {
+//						if (nTile==4600) {
+//							System.out.println("getSfmCorr(): nTile="+nTile);
+//						}
 						if ((disp_corr[0][nTile] != null) || (use_neibs && (disp_corr[1][nTile] != null) )) {
 							sfmCorr[nTile] = new SfmCorr();
 							double [] sxy = dpXYddisp_avg[nTile];
@@ -1007,19 +1010,47 @@ public class StructureFromMotion {
 						debugLevel);                // int            debug_level)
 			}
 		}
+		// remove tiles from both that are null for any
+		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for	(int nTile = ai.getAndIncrement(); nTile < ref_pXpYD.length; nTile = ai.getAndIncrement())
+						if (ref_pXpYD[nTile] != null){
+							boolean undefined = false;
+							for (int nscene = 0; nscene < scenes.length; nscene++) {
+								if (scenes_pXpYD[nscene][nTile] == null) {
+									undefined=true;
+									break;
+								}
+							}
+							if (undefined) {
+								for (int nscene = 0; nscene < scenes.length; nscene++) {
+									scenes_pXpYD[nscene][nTile] = null;
+								}								
+							}
+						
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+
+		
 		tp_tasks_ref = // were used only for the FPN removal
 				Interscene.setReferenceGPU (
-				clt_parameters,            // CLTParameters      clt_parameters,			
-				ref_scene,                 // QuadCLT            ref_scene,
-				ref_disparity,             // double []          ref_disparity, // null or alternative reference disparity
-				ref_pXpYD,                 // double [][]        ref_pXpYD,
-				null, // reliable_ref,              // final boolean []   selection, // may be null, if not null do not  process unselected tiles
-				margin,                    // final int          margin,
+				clt_parameters,      // CLTParameters      clt_parameters,			
+				scenes[0],           // ref_scene,                 // QuadCLT            ref_scene,
+				null,                // ref_disparity,             // double []          ref_disparity, // null or alternative reference disparity
+				scenes_pXpYD[0],     // ref_pXpYD,                 // double [][]        ref_pXpYD,
+				null,                // reliable_ref,              // final boolean []   selection, // may be null, if not null do not  process unselected tiles
+				margin,              // final int          margin,
 				// motion blur compensation 
-				mb_tau,                    // double             mb_tau,      // 0.008; // time constant, sec
-				mb_max_gain,               // double             mb_max_gain, // 5.0;   // motion blur maximal gain (if more - move second point more than a pixel
-				mb_vectors_scenes[0], // mb_vectors_ref,            // double [][]        mb_vectors,  // now [2][ntiles];
-				debugLevel);               // int         debugLevel)
+				mb_tau,              // double             mb_tau,      // 0.008; // time constant, sec
+				mb_max_gain,         // double             mb_max_gain, // 5.0;   // motion blur maximal gain (if more - move second point more than a pixel
+				mb_vectors_scenes[0],// mb_vectors_ref,            // double [][]        mb_vectors,  // now [2][ntiles];
+				debugLevel);         // int         debugLevel)
 		// is it needed here?
 		scenes[0].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry