Before row/col

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

@@ -1279,7 +1279,7 @@ public class GpuQuad{ // quad camera description
 		if (!force && this.gpuTileProcessor.bayer_set && !quadCLT.hasNewImageData()) {
 			return;
 		}
-		double [][][]       bayer_data = quadCLT.getImageData(); // resets hasNewImageData()
+		double [][][]       bayer_data = quadCLT.getResetImageData(); // resets hasNewImageData()
 		setBayerImages(
 				bayer_data,
 				true);

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

@@ -664,10 +664,14 @@ min_str_neib_fpn	0.35
 	public  double  cuas_decay_average =  100.0;   // Decay in seconds for cimulative CLT 
 	public  double  cuas_keep_fraction =    0.9;   // Filter CLT variants for tiles keeping at least this fraction of the total weight
 	public  boolean cuas_step =             true;  // recalculate template image after each fitting step
+
+	public  boolean cuas_subtract_fpn=      true;  // Subtract FPN
+	public  boolean cuas_calc_fpn =         false; // Recalculate+save FPN unconditionally, if false - try to read saved one
+	public  double  cuas_rot_period =       175.0; // rotation period of te gimbal mount (in scenes)
+	
 	public  boolean cuas_debug =            false; // save debug images (and show them if not in batch mode)
 	public  boolean cuas_step_debug =       false; // save debug images during per-step cuas recalculation (and show them if not in batch mode)
 	
-	
 	// TODO: move next parameters elsewhere - they are not the motion blur ones.
 	public  int     mb_gain_index_pose =    5;     // pose readjust pass to switch to full mb_max_gain from mb_max_gain_inter
 	public  int     mb_gain_index_depth =   5;     // depth map refine pass (SfM) to switch to full mb_max_gain from mb_max_gain_inter
@@ -731,6 +735,7 @@ min_str_neib_fpn	0.35
 	public  String  video_codec_combo =  "vp8"; // applies when combining videos
 	public  int     video_crf_combo =   40;    // lower - better, larger file size applies when combining videos
 	public  boolean add_average =        true;
+	public  boolean calculate_average =  false; // Calculate average from the slices. False - use CLT average if available.
 	public  boolean subtract_average =   false;
 	public  int     running_average =    0;
 	public  boolean extract_center_orientation = true; // in lock_position mode only - debug feature
@@ -1995,10 +2000,15 @@ min_str_neib_fpn	0.35
 				"Filter tile CLT variants that keep fraction of the total weight.");
 		gd.addCheckbox ("Recalculate after each tuning step",        this.cuas_step,
 				"Recalciulate correlation pattern after each position/orientation and disparity adjustment step.");
+		gd.addCheckbox ("Subtract FPN",                              this.cuas_subtract_fpn,
+				"Subtract FPN from the channel images.");
+		gd.addCheckbox ("(Re)calculate FPN",                         this.cuas_calc_fpn,
+				"Recalculate+save FPN unconditionally, if false - try to read saved one.");
+		gd.addNumericField("Rotation period",                        this.cuas_rot_period, 5,7,"scene periods",
+				"Used for averaging FPN for integer number of rotation periods. TODO: calculate from the actual rotation.");
+		gd.addMessage("=== Debug ===");
 		gd.addCheckbox ("Save/show debug images",                    this.cuas_debug,
 				"Save CUAS-related debug images and show them in non-batch mode.");
-		gd.addMessage("=== Debug ===");
-
 		gd.addCheckbox ("Save/show debug images for each tuning step",this.cuas_step_debug,
 				"Save CUAS-related debug images during per-step cuas recalculation and show them in non-batch mode.");
 
@@ -2127,8 +2137,10 @@ min_str_neib_fpn	0.35
 				"FFMPEG video encoder, such as \"VP8\" or \"VP9\". Applies when merging segments.");
 		gd.addNumericField("Video CRF for combining",                this.video_crf_combo, 0,3,"",
 				"Quality - the lower the better. 40 - OK.  Applies when merging segments.");		
-		gd.addCheckbox ("Average slice",                             this.add_average,
+		gd.addCheckbox ("Insert average slice",                      this.add_average,
 				"Insert average slice before scene slices");
+		gd.addCheckbox ("Calculate average from slices",             this.calculate_average,
+				"Calculate average slice from other slices. If false - try to use average CLT if available.");
 		gd.addCheckbox ("Subtract average",                          this.subtract_average,
 				"Subtract average slice from all scenes");
 		gd.addNumericField("Running average length",                 this.running_average, 0,3,"",
@@ -2896,6 +2908,10 @@ min_str_neib_fpn	0.35
 		this.cuas_decay_average =       gd.getNextNumber();
 		this.cuas_keep_fraction =       gd.getNextNumber();
 		this.cuas_step =                gd.getNextBoolean();
+		this.cuas_subtract_fpn =        gd.getNextBoolean();
+		this.cuas_calc_fpn =            gd.getNextBoolean();
+		this.cuas_rot_period =          gd.getNextNumber();
+		
 		this.cuas_debug =               gd.getNextBoolean();
 		this.cuas_step_debug =          gd.getNextBoolean();
 		
@@ -2961,6 +2977,7 @@ min_str_neib_fpn	0.35
 		this.video_codec_combo=         gd.getNextString();	
 		this.video_crf_combo =    (int) gd.getNextNumber();
 		this.add_average =              gd.getNextBoolean();
+		this.calculate_average =        gd.getNextBoolean();
 		this.subtract_average =         gd.getNextBoolean();
 		this.running_average =    (int) gd.getNextNumber();
 		this.extract_center_orientation=gd.getNextBoolean();
@@ -3723,6 +3740,11 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_decay_average",   this.cuas_decay_average+"");  // double
 		properties.setProperty(prefix+"cuas_keep_fraction",   this.cuas_keep_fraction+"");  // double
 		properties.setProperty(prefix+"cuas_step",            this.cuas_step+"");           // boolean
+
+		properties.setProperty(prefix+"cuas_subtract_fpn",    this.cuas_subtract_fpn+"");   // boolean
+		properties.setProperty(prefix+"cuas_calc_fpn",        this.cuas_calc_fpn+"");       // boolean
+		properties.setProperty(prefix+"cuas_rot_period",      this.cuas_rot_period+"");     // double
+		
 		properties.setProperty(prefix+"cuas_debug",           this.cuas_debug+"");          // boolean
 		properties.setProperty(prefix+"cuas_step_debug",      this.cuas_step_debug+"");     // boolean
 		
@@ -3780,6 +3802,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"video_codec_combo",    this.video_codec_combo+"");   // String
 		properties.setProperty(prefix+"video_crf_combo",      this.video_crf_combo+"");     // int
 		properties.setProperty(prefix+"add_average",          this.add_average+"");         // boolean
+		properties.setProperty(prefix+"calculate_average",    this.calculate_average+"");   // boolean
 		properties.setProperty(prefix+"subtract_average",     this.subtract_average+"");    // boolean
 		properties.setProperty(prefix+"running_average",      this.running_average+"");     // int
 		
@@ -4525,6 +4548,10 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_decay_average")!=null)   this.cuas_decay_average=Double.parseDouble(properties.getProperty(prefix+"cuas_decay_average"));
 		if (properties.getProperty(prefix+"cuas_keep_fraction")!=null)   this.cuas_keep_fraction=Double.parseDouble(properties.getProperty(prefix+"cuas_keep_fraction"));
 		if (properties.getProperty(prefix+"cuas_step")!=null)            this.cuas_step=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_step"));
+		if (properties.getProperty(prefix+"cuas_subtract_fpn")!=null)    this.cuas_subtract_fpn=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_subtract_fpn"));
+		if (properties.getProperty(prefix+"cuas_calc_fpn")!=null)        this.cuas_calc_fpn=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_calc_fpn"));
+		if (properties.getProperty(prefix+"cuas_rot_period")!=null)      this.cuas_rot_period=Double.parseDouble(properties.getProperty(prefix+"cuas_rot_period"));
+		
 		if (properties.getProperty(prefix+"cuas_debug")!=null)           this.cuas_debug=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_debug"));
 		if (properties.getProperty(prefix+"cuas_step_debug")!=null)      this.cuas_step_debug=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_step_debug"));
 
@@ -4583,6 +4610,8 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"video_codec_combo")!=null)    this.video_codec_combo=(String) properties.getProperty(prefix+"video_codec_combo");
 		if (properties.getProperty(prefix+"video_crf_combo")!=null)      this.video_crf_combo=Integer.parseInt(properties.getProperty(prefix+"video_crf_combo"));
 		if (properties.getProperty(prefix+"add_average")!=null)          this.add_average=Boolean.parseBoolean(properties.getProperty(prefix+"add_average"));
+		if (properties.getProperty(prefix+"calculate_average")!=null)    this.calculate_average=Boolean.parseBoolean(properties.getProperty(prefix+"calculate_average"));
+//		
 		if (properties.getProperty(prefix+"subtract_average")!=null)     this.subtract_average=Boolean.parseBoolean(properties.getProperty(prefix+"subtract_average"));
 		if (properties.getProperty(prefix+"running_average")!=null)      this.running_average=Integer.parseInt(properties.getProperty(prefix+"running_average"));
 		if (properties.getProperty(prefix+"extract_center_orientation")!=null)this.extract_center_orientation=Boolean.parseBoolean(properties.getProperty(prefix+"extract_center_orientation"));
@@ -5327,6 +5356,10 @@ min_str_neib_fpn	0.35
 		imp.cuas_decay_average =    this.cuas_decay_average;
 		imp.cuas_keep_fraction =    this.cuas_keep_fraction;
 		imp.cuas_step =             this.cuas_step;
+		imp.cuas_subtract_fpn =     this.cuas_subtract_fpn;
+		imp.cuas_calc_fpn =         this.cuas_calc_fpn;
+		imp.cuas_rot_period =       this.cuas_rot_period;
+		
 		imp.cuas_debug =            this.cuas_debug;
 		imp.cuas_step_debug =       this.cuas_step_debug;
 
@@ -5386,6 +5419,7 @@ min_str_neib_fpn	0.35
 		imp.video_codec_combo =     this.video_codec_combo;
 		imp.video_crf_combo =       this.video_crf_combo;
 		imp.add_average =           this.add_average;
+		imp.calculate_average =     this.calculate_average;
 		imp.subtract_average =      this.subtract_average;
 		imp.running_average =       this.running_average;
 		imp.extract_center_orientation=this.extract_center_orientation;

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

@@ -958,7 +958,7 @@ public class MultisceneLY {
 				image_dtt.getCorrelation2d();
 				double [][][][]     dcorr_td = new double[tp_tasks_scenes[nscene].length][][][];
 				image_dtt.quadCorrTD( // clt_data [task][sensor][color][][];
-						scene.getImageData(),                           // final double [][][]       image_data,      // first index - number of image in a quad
+						scene.getResetImageData(),                           // final double [][][]       image_data,      // first index - number of image in a quad
 						scene_gc.getSensorWH()[0], // final int                 width,
 						tp_tasks_scenes[nscene],                        // tp_tasks,                            // final TpTask []           tp_tasks,
 						clt_parameters.img_dtt,              // final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others