Working on the image sequences captured from the UAS

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

@@ -3573,7 +3573,7 @@ public class GpuQuad{ // quad camera description
 	 * @param threadsMax Maximal number of threads to run concurrently.
 	 * @return Array of TpTask instances (fully prepared) to be fed to the GPU
 	 */
-	public TpTask[]  setInterTasks(
+	public TpTask[]  setInterTasks( // not used 2023.08.04
 			final boolean             calcPortsCoordinatesAndDerivatives, // GPU can calculate them centreXY
 			final double [][]         pXpYD, // per-tile array of pX,pY,disparity triplets (or nulls)
 			final boolean []          selection, // may be null, if not null do not  process unselected tiles

src/main/java/com/elphel/imagej/ims/EventLogger.java

@@ -33,7 +33,8 @@ public class EventLogger {
 		}
 		Arrays.sort(logger_files); // increasing start time stamps
 		
-		String out_did_gps_path = "/home/elphel/lwir16-proc/office_04/did_gps";
+//		String out_did_gps_path = "/home/elphel/lwir16-proc/office_04/did_gps";
+		String out_did_gps_path = dir+"../did_gps";
 		int gps_mask = 7; // +1 - DID_GPS1_POS, +2 - DID_GPS2_POS, +4 - DID_GPS1_UBX_POS
 		for (int nf = 0; nf < logger_files.length; nf++) {
 			System.out.println("Printing all DID_INS_1 data in "+logger_files[nf].abs_path);

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

@@ -325,6 +325,10 @@ public class ErsCorrection extends GeometryCorrection {
 				properties.setProperty(prefix+SCENES_PREFIX+"_"+k+"_dt",  s_scenes[1]);
 				properties.setProperty(prefix+SCENES_PREFIX+"_"+k+"_d2t", s_scenes[2]);
 				//			properties.setProperty(prefix+SCENES_PREFIX+"_"+k, getScene(k).toString());
+			} else { // so it is important to scenes_poses.put(timestamp, null), not scenes_poses.remove(ts)
+				properties.remove(prefix+SCENES_PREFIX+"_"+k);
+				properties.remove(prefix+SCENES_PREFIX+"_"+k+"_dt");
+				properties.remove(prefix+SCENES_PREFIX+"_"+k+"_d2t");
 			}
 		}
 	}
@@ -408,6 +412,12 @@ public class ErsCorrection extends GeometryCorrection {
 		return scenes_poses.get(timestamp);
 	}
 
+	
+	public double[][] getSceneXYZATR(String timestamp) {
+		XyzAtr scene = scenes_poses.get(timestamp);
+		if (scene == null) return null;
+		return scene.getXYZATR();
+	}
 	public double[] getSceneXYZ(String timestamp) {
 		XyzAtr scene = scenes_poses.get(timestamp);
 		if (scene == null) return null;
@@ -2103,6 +2113,17 @@ public class ErsCorrection extends GeometryCorrection {
 				scene_xyz,          // double [] camera_xyz,       // camera center in world coordinates
 				scene_rot_matrix,   // Matrix    rot_matrix,      // 1-st of 4 matricesArray of 4 matrices - 
 				LINE_ERR);          // double    line_err) // threshold error in scan lines (1.0)
+		if (pXpYD_scene == null) {
+			System.out.println("getDPxSceneDParameters(): pXpYD_scene==null. Object too close to the lens?"); // not here
+			return null;
+		}
+		if (Double.isNaN(pXpYD_scene[2])) {
+			System.out.println("getDPxSceneDParameters(): pXpYD_scene[2]==NaN.");
+			System.out.println("xyz4=["+xyz4[0]+","+xyz4[1]+","+xyz4[2]+","+xyz4[3]+"]");
+			System.out.println("scene_xyz=["+scene_xyz[0]+","+scene_xyz[1]+","+scene_xyz[2]+"]");
+			System.out.println("pXpYD_reference=["+pXpYD_reference[0]+","+pXpYD_reference[1]+","+pXpYD_reference[2]+"]");
+			return null;
+		}
 
 		Vector3D[]  scene_vectors = ers_scene.getDWorldDPixels( // [0] X,Y,Z, other ones [DW_D* + 1] 
 				correctDistortions,
@@ -2111,8 +2132,12 @@ public class ErsCorrection extends GeometryCorrection {
 				scene_xyz,
 				scene_matrices_inverse,
 				debug_level);
+		if (scene_vectors == null) {
+			System.out.println("getDPxSceneDParameters(): scene_vectors==null. Why?");
+			return null;
+		}
 		Matrix dx_dpscene = new Matrix(new double[][] {
-			scene_vectors[DW_DPX + 1].toArray(),
+			scene_vectors[DW_DPX + 1].toArray(), // null pointer?
 			scene_vectors[DW_DPY + 1].toArray(),
 			scene_vectors[DW_DD +  1].toArray()}).transpose();
 		// next variables are {x,y,z} * disparity
@@ -2153,8 +2178,10 @@ public class ErsCorrection extends GeometryCorrection {
 			dpscene_dxyz = dx_dpscene.inverse();
 		} catch (Exception e) {
 			// TODO Auto-generated catch block
-			System.out.println("dx_dpscene is singular");
+			if (debug_level > -1) {
+				System.out.println("dx_dpscene is singular, debug_level="+debug_level+"> -1");
 				e.printStackTrace();
+			}
 			return null;
 		}
 		Matrix dpscene_dxyz_minus = dpscene_dxyz.times(-1.0); // negated to calculate /d{pX,pY,D) for the scene parameters

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

@@ -1326,6 +1326,8 @@ public class ImageDtt extends ImageDttCPU {
 
 	public double [][][] clt_process_tl_interscene( // convert to pixel domain and process correlations already prepared in fcorr_td and/or fcorr_combo_td
 			final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
+			// only used here to keep extra array element for disparity difference
+			boolean                   use3D,         // generate disparity difference
 	        final float  [][][][]     fcorr_td,        // [tilesY][tilesX][pair][4*64] transform domain representation of all selected corr pairs
 	        float [][][]              num_acc,         // number of accumulated tiles [tilesY][tilesX][pair] (or null). Can be inner null if not used in tp_tasks
 	        double []                 dcorr_weight,    // alternative to num_acc, compatible with CPU processing (only one non-zero enough)
@@ -1601,9 +1603,10 @@ public class ImageDtt extends ImageDttCPU {
 							}
 						}
 						if ((mv_td != null) || (mv_pd != null)) {
-							double [] mv = new double[3];
+							double [] mv = new double[3 + (use3D? 2 :0)]; // keep for disparity/strength
 							if (mv_pd != null) {
-								mv = mv_pd;
+///								mv = mv_pd;
+								System.arraycopy(mv_pd, 0, mv, 0, 3); // keep [3] for optional disparities
 								// mv[2] *= pd_weight;
 								if ((mv_td != null) && !td_nopd_only) {  // mix
 									mv[0] = (mv[0] * pd_weight + mv_td[0] * td_weight)/ (pd_weight + td_weight);
@@ -1612,7 +1615,8 @@ public class ImageDtt extends ImageDttCPU {
 									mv[2] = (mv[2] * pd_weight + mv_td[2] * td_weight)/ (pd_weight + td_weight);
 								} // mix
 							} else { // (mv_pd == null) &&  (mv_td != null)  below
-								mv = mv_td;
+///								mv = mv_td;
+								System.arraycopy(mv_td, 0, mv, 0, 3); // keep [3] for optional disparities
 								//mv[2] *= td_weight;
 							}
 							if (mv != null) {

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

@@ -29,6 +29,10 @@ import java.util.Properties;
 import com.elphel.imagej.common.GenericJTabbedDialog;
 
 public class IntersceneLmaParameters {
+	public boolean    ilma_3d =                   false;  // use disparity for interscene matching (as for UAS imagery)
+	public double     ilma_disparity_weight =     2.0;    // disparity component weight compared to dX and dY
+	public boolean    ilma_3d_lma =               false;  // Use LMA for disparity in 3D pose matching mode
+	public boolean    ilma_3d_tilt_only =         true;   // remove disparity average, use tilts only
 	public boolean    ilma_thread_invariant =     true; // Do not use DoubleAdder, provide results not dependent on threads
 	public boolean [] ilma_lma_select =             new boolean [ErsCorrection.DP_NUM_PARS]; // first three will not be used
 	public double  [] ilma_regularization_weights = new double  [ErsCorrection.DP_NUM_PARS]; // first three will not be used
@@ -107,6 +111,15 @@ public class IntersceneLmaParameters {
 	
 	public void dialogQuestions(GenericJTabbedDialog gd) {
 		gd.addMessage("Interframe LMA parameters selection");
+	    gd.addCheckbox    ("3D mode (use disparity)",                     this.ilma_3d,
+	    		"Use disparity for interscene matching (as for UAS imagery)" );
+		gd.addNumericField("Disp[arity weight",                           this.ilma_disparity_weight, 6,8,"",
+				"Disparity component weight compared to dX and dY");
+	    gd.addCheckbox    ("LMA in 3D mode",                              this.ilma_3d_lma,
+	    		"Use LMA disparity  for interscene matching (as for UAS imagery)" );
+	    gd.addCheckbox    ("Remove average disparity, use tilts only",    this.ilma_3d_tilt_only,
+	    		"Calculate disparity for tilts only." );
+	    
 	    gd.addCheckbox    ("Thread-invariant execution",                  this.ilma_thread_invariant,
 	    		"Do not use DoubleAdder and provide results not dependent on threads" );
 		for (int i = ErsCorrection.DP_DVAZ; i < ErsCorrection.DP_NUM_PARS; i++) {
@@ -163,6 +176,10 @@ public class IntersceneLmaParameters {
 	}
 	
 	public void dialogAnswers(GenericJTabbedDialog gd) {
+		this.ilma_3d =                            gd.getNextBoolean();
+		this.ilma_disparity_weight =              gd.getNextNumber();
+		this.ilma_3d_lma =                        gd.getNextBoolean();
+		this.ilma_3d_tilt_only =                  gd.getNextBoolean();
 		this.ilma_thread_invariant =              gd.getNextBoolean();
 		for (int i = ErsCorrection.DP_DVAZ; i < ErsCorrection.DP_NUM_PARS; i++) {
 		    this.ilma_lma_select[i] =             gd.getNextBoolean();
@@ -191,6 +208,10 @@ public class IntersceneLmaParameters {
 		
 	}
 	public void setProperties(String prefix,Properties properties){
+		properties.setProperty(prefix+"ilma_3d",                this.ilma_3d+"");	
+		properties.setProperty(prefix+"ilma_disparity_weight",  this.ilma_disparity_weight+"");	
+		properties.setProperty(prefix+"ilma_3d_lma",            this.ilma_3d_lma+"");	
+		properties.setProperty(prefix+"ilma_3d_tilt_only",      this.ilma_3d_tilt_only+"");	
 		properties.setProperty(prefix+"ilma_thread_invariant",  this.ilma_thread_invariant+"");	
 		for (int i = ErsCorrection.DP_DVAZ; i < ErsCorrection.DP_NUM_PARS; i++) {
 			properties.setProperty(prefix+ErsCorrection.DP_DERIV_NAMES[i]+"_sel",           this.ilma_lma_select[i]+"");	
@@ -216,6 +237,10 @@ public class IntersceneLmaParameters {
 		properties.setProperty(prefix+"ilma_debug_ers",          this.ilma_debug_ers+"");	
 	}
 	public void getProperties(String prefix,Properties properties){
+		if (properties.getProperty(prefix+"ilma_3d")!=null)                 this.ilma_3d=Boolean.parseBoolean(properties.getProperty(prefix+"ilma_3d"));
+		if (properties.getProperty(prefix+"ilma_disparity_weight")!=null)   this.ilma_disparity_weight=Double.parseDouble(properties.getProperty(prefix+"ilma_disparity_weight"));
+		if (properties.getProperty(prefix+"ilma_3d_lma")!=null)             this.ilma_3d_lma=Boolean.parseBoolean(properties.getProperty(prefix+"ilma_3d_lma"));
+		if (properties.getProperty(prefix+"ilma_3d_tilt_only")!=null)       this.ilma_3d_tilt_only=Boolean.parseBoolean(properties.getProperty(prefix+"ilma_3d_tilt_only"));
 		if (properties.getProperty(prefix+"ilma_thread_invariant")!=null)   this.ilma_thread_invariant=Boolean.parseBoolean(properties.getProperty(prefix+"ilma_thread_invariant"));
 		for (int i = ErsCorrection.DP_DVAZ; i < ErsCorrection.DP_NUM_PARS; i++) {
 			String pn_sel = prefix+ErsCorrection.DP_DERIV_NAMES[i]+"_sel";
@@ -255,6 +280,10 @@ public class IntersceneLmaParameters {
 	@Override
 	public IntersceneLmaParameters clone() throws CloneNotSupportedException {
 		IntersceneLmaParameters ilp =     new IntersceneLmaParameters();
+		ilp.ilma_3d =                  this.ilma_3d;
+		ilp.ilma_disparity_weight =    this.ilma_disparity_weight;
+		ilp.ilma_3d_lma =              this.ilma_3d_lma;
+		ilp.ilma_3d_tilt_only =        this.ilma_3d_tilt_only;
 		ilp.ilma_thread_invariant =    this.ilma_thread_invariant;
 		System.arraycopy(this.ilma_lma_select,             0, ilp.ilma_lma_select,             0, ilma_lma_select.length);
 		System.arraycopy(this.ilma_regularization_weights, 0, ilp.ilma_regularization_weights, 0, ilma_regularization_weights.length);

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

@@ -67,7 +67,11 @@ public class IntersceneMatchParameters {
 	public  boolean [] generate_stereo_var = new boolean[stereo_views.length];
 
 	// Other parameters
+	public  double  scale_extrap_atr =    1.0; // scale angular extrapolation
+	public  double  scale_extrap_xyz =    0.0; // scale linear extrapolation (1.0 for drones)
+	public  int     avg_len =             1;   // average pose over number of previous scenes
 	public  int     min_num_scenes =     10;   // abandon series if there are less than this number of scenes in it 
+	public  int     max_num_scenes =    100;   // abandon series if longer than 
 	public  double  blur_egomotion =      2.0;
 	
 	
@@ -449,13 +453,23 @@ public class IntersceneMatchParameters {
 				"Display calculated depth map in meters");
 		
 		gd.addMessage  ("Additional parameters");
-
 		gd.addCheckbox ("Color NaN background",                      this.show_color_nan,
 				"Use NaN for undefined tiles (false - 0.0f). NaN produces sharp distinct result, 0.0f - blended");
 		gd.addCheckbox ("Mono NaN background",                       this.show_mono_nan,
 				"Use NaN for undefined tiles (false - 0.0f). NaN produces sharp distinct result, 0.0f - blended");
+
+		gd.addNumericField("Scale angular pose extrapolation",       this.scale_extrap_atr, 3,5,"",
+				"Scale angular extrapolation relative to the previous pair");
+		gd.addNumericField("Scale linear pose extrapolation",        this.scale_extrap_xyz, 3,5,"",
+				"Scale linear extrapolation relative to the previous pair (use 1.0 for a drone)");
+		gd.addNumericField("Number of previous scenes to extrapolate",this.avg_len, 0,3,"",
+				"Average this number of previous scenes movement for next scene prediction");
+
 		gd.addNumericField("Minimal number of scenes to keep series",this.min_num_scenes, 0,3,"",
 				"Scrap all seriest if less numer of scenes can be matched to the reference scene (including reference itself)");
+		gd.addNumericField("Cut longer series",                      this.max_num_scenes, 0,3,"",
+				"Cut longer series");
+		
 		gd.addNumericField("LPF egomotion sigma",                    this.blur_egomotion, 3,5,"scenes",
 				"LPF egomotion components with this sigma before using as ERS (not implemented).");
 
@@ -999,8 +1013,11 @@ public class IntersceneMatchParameters {
 		this.show_color_nan =                 gd.getNextBoolean();
 		this.show_mono_nan =                  gd.getNextBoolean();
 		
-		
+		this.scale_extrap_atr =               gd.getNextNumber();
+		this.scale_extrap_xyz =               gd.getNextNumber();
+		this.avg_len =                  (int) gd.getNextNumber();
 		this.min_num_scenes =           (int) gd.getNextNumber();
+		this.max_num_scenes =           (int) gd.getNextNumber();
 		this.blur_egomotion =                 gd.getNextNumber();
 		this.range_disparity_offset =         gd.getNextNumber();
 		this.range_min_strength =             gd.getNextNumber();
@@ -1008,9 +1025,6 @@ public class IntersceneMatchParameters {
 		
 		this.export3d =                       gd.getNextBoolean();
 		
-		
-		
-		
 		this.scene_is_ref_test =        gd.getNextBoolean();
 		this.render_ref =               gd.getNextBoolean();
 		this.render_scene =             gd.getNextBoolean();
@@ -1329,12 +1343,15 @@ public class IntersceneMatchParameters {
 		
 		properties.setProperty(prefix+"show_color_nan",                this.show_color_nan + "");              // boolean
 		properties.setProperty(prefix+"show_mono_nan",                 this.show_mono_nan + "");               // boolean
+		properties.setProperty(prefix+"scale_extrap_atr",              this.scale_extrap_atr+"");              // double
+		properties.setProperty(prefix+"scale_extrap_xyz",              this.scale_extrap_xyz+"");              // double
+		properties.setProperty(prefix+"avg_len",                       this.avg_len+"");                       // int
 		properties.setProperty(prefix+"min_num_scenes",                this.min_num_scenes+"");                // int
+		properties.setProperty(prefix+"max_num_scenes",                this.max_num_scenes+"");                // int
 		properties.setProperty(prefix+"blur_egomotion",                this.blur_egomotion+"");                // double
 		properties.setProperty(prefix+"range_disparity_offset",        this.range_disparity_offset+"");        // double
 		properties.setProperty(prefix+"range_min_strength",            this.range_min_strength+"");            // double
 		properties.setProperty(prefix+"range_max",                     this.range_max+"");                     // double
-		
 		properties.setProperty(prefix+"export3d",                      this.export3d+"");                      // boolean
 		
 		properties.setProperty(prefix+"scene_is_ref_test",    this.scene_is_ref_test+"");   // boolean
@@ -1606,7 +1623,13 @@ public class IntersceneMatchParameters {
 
 		if (properties.getProperty(prefix+"show_color_nan")!=null)       this.show_color_nan=Boolean.parseBoolean(properties.getProperty(prefix+"show_color_nan"));		
 		if (properties.getProperty(prefix+"show_mono_nan")!=null)        this.show_mono_nan=Boolean.parseBoolean(properties.getProperty(prefix+"show_mono_nan"));
+
+		if (properties.getProperty(prefix+"scale_extrap_atr")!=null)     this.scale_extrap_atr=Double.parseDouble(properties.getProperty(prefix+"scale_extrap_atr"));
+		if (properties.getProperty(prefix+"scale_extrap_xyz")!=null)     this.scale_extrap_xyz=Double.parseDouble(properties.getProperty(prefix+"scale_extrap_xyz"));
+		
+		if (properties.getProperty(prefix+"avg_len")!=null)              this.avg_len=Integer.parseInt(properties.getProperty(prefix+"avg_len"));
 		if (properties.getProperty(prefix+"min_num_scenes")!=null)       this.min_num_scenes=Integer.parseInt(properties.getProperty(prefix+"min_num_scenes"));
+		if (properties.getProperty(prefix+"max_num_scenes")!=null)       this.max_num_scenes=Integer.parseInt(properties.getProperty(prefix+"max_num_scenes"));
 		if (properties.getProperty(prefix+"blur_egomotion")!=null)       this.blur_egomotion=Double.parseDouble(properties.getProperty(prefix+"blur_egomotion"));
 		if (properties.getProperty(prefix+"range_disparity_offset")!=null)this.range_disparity_offset=Double.parseDouble(properties.getProperty(prefix+"range_disparity_offset"));
 		if (properties.getProperty(prefix+"range_min_strength")!=null)   this.range_min_strength=Double.parseDouble(properties.getProperty(prefix+"range_min_strength"));
@@ -1895,15 +1918,17 @@ public class IntersceneMatchParameters {
 		imp.debug_ranges                  = this.debug_ranges;		
 		imp.show_ranges                   = this.show_ranges;
 		imp.export_ml_files               = this.export_ml_files;
-
 		imp.show_color_nan                = this.show_color_nan;
 		imp.show_mono_nan                 = this.show_mono_nan;
+		imp.scale_extrap_atr              = this.scale_extrap_atr;
+		imp.scale_extrap_xyz              = this.scale_extrap_xyz;
+		imp.avg_len                       = this.avg_len;
 		imp.min_num_scenes                = this.min_num_scenes;
+		imp.max_num_scenes                = this.max_num_scenes;
 		imp.blur_egomotion                = this.blur_egomotion;
 		imp.range_disparity_offset        = this.range_disparity_offset;
 		imp.range_min_strength            = this.range_min_strength;
 		imp.range_max                     = this.range_max;
-
 		imp.export3d                      = this.export3d;
 		
 		

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

@@ -807,7 +807,7 @@ public class QuadCLT extends QuadCLTCPU {
 					debugLevel); // int                                       debugLevel);
 
 
-			// once per quad here
+			// once per quad here. "GPU not initialized, using CPU mode"
 			processCLTQuadCorrGPU(  // returns ImagePlus, but it already should be saved/shown
 					null,           // imp_srcs, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
 					saturation_imp, // boolean [][] saturation_imp, // (near) saturated pixels or null

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

@@ -189,6 +189,9 @@ public class QuadCLTCPU {
     		}
     		String ts = scenes[nscene].getImageName();
     		if (!ts.equals(ts_ref)) {
+    			if (ers_reference.getScene(ts) == null) {
+    				return nscene + 1;
+    			}
 				double []   scene_xyz = ers_reference.getSceneXYZ(ts);
 				double []   scene_atr = ers_reference.getSceneATR(ts);
 				if ((scene_xyz == null) || (scene_atr == null)){
@@ -15028,7 +15031,43 @@ public class QuadCLTCPU {
 		  return true;
 	  }
 
-
+	  public boolean writePreview(
+			  double [] data,
+//			  boolean   overwrite, // correctionsParameters.thumb_overwrite
+			  int debugLevel
+			  )
+	  {
+		  int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize(); 
+		  int height = data.length/width;
+		  String set_name = getImageName();
+		  if (set_name == null ) {
+			  QuadCLTCPU.SetChannels [] set_channels = setChannels(debugLevel);
+			  set_name = set_channels[0].set_name;
+		  }
+		  String model_dir= correctionsParameters.selectX3dDirectory(
+				  set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+				  null,
+				  true,  // smart,
+				  true);  //newAllowed, // save\
+		  String title = getImageName()+"-preview";
+		  ImagePlus imp= ShowDoubleFloatArrays.makeArrays(data, width, height, title);
+		  String preview_path = model_dir +  Prefs.getFileSeparator() + title+".jpeg";
+		  if (new File(preview_path).exists() && !correctionsParameters.thumb_overwrite) {
+			  System.out.println("file "+preview_path+" exists, skipping preview generation");
+			  return false;
+		  }
+		  if (debugLevel > -2) {
+			  System.out.println("Saving preview image to "+preview_path);
+		  }
+		  EyesisCorrections.saveAndShow(
+				  imp,
+				  model_dir,
+				  false,
+				  false,
+				  correctionsParameters.JPEG_quality, // jpegQuality); // jpegQuality){//  <0 - keep current, 0 - force Tiff, >0 use for JPEG
+				  (debugLevel > -2) ? debugLevel : 1); // int debugLevel (print what it saves)
+		  return true;
+	  }
 
 	  public boolean writeRatingFile( // USED in lwir
 			  int debugLevel

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

@@ -2691,7 +2691,7 @@ public class TexturedModel {
 		boolean [] scenes_sel = new boolean[scenes.length];
 		//		for (int i = scenes.length - 10; i <  scenes.length; i++) { // start with just one (reference) scene
 
-		for (int i = 0; i <  scenes.length; i++) { // start with just one (reference) scene
+		for (int i = 0; i <  scenes.length; i++) if (scenes[i] != null){ // start with just one (reference) scene
 			scenes_sel[i] = true;
 		}
 
@@ -7297,7 +7297,7 @@ public class TexturedModel {
 				min_trim_disparity,        // final double min_trim_disparity, // do not try to trim texture outlines with lower disparities
 				tp_tasks_ref,              // final TpTask[][][]   tp_tasks_ref,       // reference tasks for each slice to get offsets			
 				ref_scene.getImageName()); // null); // ref_scene.getImageName()); // final String         dbg_prefix);
-		if (debugLevel > -1) {
+		if (debugLevel > -20) {
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
 			String [] dbg_titles = new String[dbg_textures.length];
 			String [] dbg_subtitles = new String [faded_textures[0].length];
@@ -7309,14 +7309,22 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
+			String suffix = "-combined_textures-prenorm-pre_UM";
+			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,
 						tilesX * transform_size,
 						tilesY * transform_size,
 						true,
-					ref_scene.getImageName()+"-combined_textures-prenorm-pre_UM",
+						ref_scene.getImageName()+suffix,
 						dbg_titles);
-
+			}
+			ref_scene.saveDoubleArrayInModelDirectory(
+					suffix, // String      suffix,
+					null, // String []   labels, // or null
+					dbg_textures, // double [][] data,
+					tilesX * transform_size, // int            width, // int tilesX,
+					tilesY * transform_size); // int            height, // int tilesY,
 		}
 		// fix alpha
 		if (alphaOverlapFix) {
@@ -7342,7 +7350,7 @@ public class TexturedModel {
 					THREADS_MAX); // final int threadsMax)      // maximal number of threads to launch 
 		}
 
-		if (debugLevel > -1) {
+		if (debugLevel > -20) {
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
 			String [] dbg_titles = new String[dbg_textures.length];
 			String [] dbg_subtitles = new String [faded_textures[0].length];
@@ -7355,14 +7363,23 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
+			String suffix = "-combined_textures-filled-NaNs";
+			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,
 						tilesX * transform_size,
 						tilesY * transform_size,
 						true,
-					ref_scene.getImageName()+"-combined_textures-filled-NaNs",
+						ref_scene.getImageName()+suffix,
 						dbg_titles);
 			}
+			ref_scene.saveDoubleArrayInModelDirectory(
+					suffix, // String      suffix,
+					null, // String []   labels, // or null
+					dbg_textures, // double [][] data,
+					tilesX * transform_size, // int            width, // int tilesX,
+					tilesY * transform_size); // int            height, // int tilesY,
+		}		
 
 		// Optionally apply UM (before auto/manual range)
 		final boolean um_ignore_alpha =     true;
@@ -7376,7 +7393,7 @@ public class TexturedModel {
 					tex_um_weight);          // final double um_weight)
 		}
 
-		if (debugLevel > -1) {
+		if (debugLevel > -20) {
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
 			String [] dbg_titles = new String[dbg_textures.length];
 			String [] dbg_subtitles = new String [faded_textures[0].length];
@@ -7389,20 +7406,39 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
+			String suffix = "-combined_textures-prenorm";
+			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,
 						tilesX * transform_size,
 						tilesY * transform_size,
 						true,
-					ref_scene.getImageName()+"-combined_textures-prenorm",
+						ref_scene.getImageName()+suffix,
 						dbg_titles);
+			}
+			ref_scene.saveDoubleArrayInModelDirectory(
+					suffix, // String      suffix,
+					null, // String []   labels, // or null
+					dbg_textures, // double [][] data,
+					tilesX * transform_size, // int            width, // int tilesX,
+					tilesY * transform_size); // int            height, // int tilesY,
 			if (dbg_weights != null) {
+				suffix = "-texture_weights-prenorm";
+				if (!batch_run && (debugLevel > -1)) {
 					ShowDoubleFloatArrays.showArrays(
 							dbg_weights,
-						tilesX,
-						tilesY,
+							tilesX * transform_size,
+							tilesY * transform_size,
 							true,
-						ref_scene.getImageName()+"-texture_weights-prenorm");
+							ref_scene.getImageName()+suffix,
+							dbg_titles);
+				}
+				ref_scene.saveDoubleArrayInModelDirectory(
+						suffix, // String      suffix,
+						null, // String []   labels, // or null
+						dbg_weights, // double [][] data,
+						tilesX * transform_size, // int            width, // int tilesX,
+						tilesY * transform_size); // int            height, // int tilesY,
 			}
 		}
 
@@ -7471,7 +7507,7 @@ public class TexturedModel {
 		}
 
 
-		if (!batch_run && (debugLevel > -2)) {
+		if (debugLevel > -20) { // always
 			double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
 			String [] dbg_titles = new String[dbg_textures.length];
 			String [] dbg_subtitles = new String [faded_textures[0].length];
@@ -7484,21 +7520,47 @@ public class TexturedModel {
 				dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
 
 			}
+			ref_scene.writePreview( // may movbe to different (earlier) stage of processing, (search for "-combined_textures")
+					dbg_textures[0], // double [] data,
+					debugLevel); // int debugLevel
+
+			String suffix = "-combined_textures";
+			if (!batch_run && (debugLevel > -1)) {
 				ShowDoubleFloatArrays.showArrays(
 						dbg_textures,
 						tilesX * transform_size,
 						tilesY * transform_size,
 						true,
-					ref_scene.getImageName()+"-combined_textures",
+						ref_scene.getImageName()+suffix,
 						dbg_titles);
+			}
+			ref_scene.saveDoubleArrayInModelDirectory(
+					suffix, // String      suffix,
+					null, // String []   labels, // or null
+					dbg_textures, // double [][] data,
+					tilesX * transform_size, // int            width, // int tilesX,
+					tilesY * transform_size); // int            height, // int tilesY,
 			if (dbg_weights != null) {
+				suffix = "-texture_weights";
+				if (!batch_run && (debugLevel > -1)) {
 					ShowDoubleFloatArrays.showArrays(
 							dbg_weights,
-						tilesX,
-						tilesY,
+							tilesX * transform_size,
+							tilesY * transform_size,
 							true,
-						ref_scene.getImageName()+"-texture_weights");
+							ref_scene.getImageName()+suffix,
+							dbg_titles);
 				}
+				ref_scene.saveDoubleArrayInModelDirectory(
+						suffix, // String      suffix,
+						null, // String []   labels, // or null
+						dbg_weights, // double [][] data,
+						tilesX * transform_size, // int            width, // int tilesX,
+						tilesY * transform_size); // int            height, // int tilesY,
+			}
+			
+			
+			
 		}
 		return faded_textures;
 	}
@@ -7528,6 +7590,7 @@ public class TexturedModel {
 			int                  transform_size,
 			int                  debugLevel)
 	{
+		boolean save_tiff_texture = true;
 		if (debugLevel > -2) {
 			System.out.println("getInterCombinedTextures(): no_alpha=" + no_alpha); // true
 		}
@@ -7540,8 +7603,18 @@ public class TexturedModel {
 		double [] minmax = parameter_scene.getColdHot(); // used in linearStackToColor
 		ImagePlus [] imp_tex = new ImagePlus[num_slices];
 		for (int nslice = 0; nslice < num_slices; nslice++) {
+			String suffix=String.format("-combo%03d-texture",nslice);
 			String title=String.format("%s-combo%03d-texture",ref_scene.getImageName(), nslice);
 			double [][] rendered_texture = faded_textures[nslice].clone(); // shallow !
+			if (save_tiff_texture) {
+				ref_scene.saveDoubleArrayInModelDirectory(
+						suffix, // String      suffix,
+						null, // String []   labels, // or null
+						rendered_texture, // double [][] data,
+						tilesX * transform_size, // int            width, // int tilesX,
+						tilesY * transform_size); // int            height, // int tilesY,
+			}
+			
 			if (no_alpha) {
 				rendered_texture[1] = new double [rendered_texture[0].length];
 				for (int i = 0; i < rendered_texture[0].length; i++) {

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

@@ -124,7 +124,9 @@ public class XyzAtr {
 				String.format("%f,  %f, %f, %f, %f, %f",ers_xyz_d2t[0], ers_xyz_d2t[1], ers_xyz_d2t[2], ers_atr_d2t[0], ers_atr_d2t[1], ers_atr_d2t[2])};
 	}
 	
-	
+	public double [][] getXYZATR() {
+		return new double[][] {xyz,atr};
+	}
 	public double [] getXYZ() {
 		return xyz;
 	}