implementing averaging of multiple sequencing

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

@@ -54,8 +54,15 @@ import ij.gui.GenericDialog;
 
 public class EyesisCorrectionParameters {
     public static class CorrectionParameters{
-    	public static final String [] KEY_DIRS= {"rootDirectory",
-    			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory"};
+    	public static final String [] KEY_DIRS= {
+    			"rootDirectory",    // 0
+    			"sourceDirectory",  // 1
+    			"linkedModels",     // 2
+    			"linkedCenters",    // 3
+    			"videoDirectory",   // 4
+    			"x3dDirectory",     // 5
+    			"resultsDirectory", // 6
+    			"cuasSeed"};        // 7
     	public static final String AUX_PREFIX = "AUX-";
     	public boolean swapSubchannels01=      true; // false; // (false: 0-1-2, true - 1-0-2)
   		public boolean split=                  true;
@@ -213,9 +220,10 @@ public class EyesisCorrectionParameters {
     	
 
     	public String linkedModels="";   // linked models with reference scenes
+    	public String linkedCenters="";  // linked models with centers scene in CUAS mode
     	public String x3dDirectory="";
     	public String videoDirectory=""; // combined (with MPEG) from multiple scene sequences video files
-
+    	public String cuasSeed ="";
 
     	public String mlDirectory="ml";
 
@@ -332,6 +340,8 @@ public class EyesisCorrectionParameters {
   			cp.relativeExposure=    	this.relativeExposure;
   			cp.swapSubchannels01=    	this.swapSubchannels01;
   			cp.linkedModels=    		this.linkedModels;
+  			cp.linkedCenters=    		this.linkedCenters;
+  			cp.cuasSeed=    	    	this.cuasSeed;
   			cp.videoDirectory=    		this.videoDirectory;
   			cp.x3dDirectory=    		this.x3dDirectory;
   			cp.mlDirectory=    	     	this.mlDirectory;
@@ -547,6 +557,8 @@ public class EyesisCorrectionParameters {
     		properties.setProperty(prefix+"cltSuffix",             this.cltSuffix);
 
     		properties.setProperty(prefix+"linkedModels",          this.linkedModels);
+    		properties.setProperty(prefix+"linkedCenters",         this.linkedCenters);
+    		properties.setProperty(prefix+"cuasSeed",              this.cuasSeed);
     		properties.setProperty(prefix+"videoDirectory",        this.videoDirectory);
     		properties.setProperty(prefix+"x3dDirectory",          this.x3dDirectory);
     		properties.setProperty(prefix+"use_x3d_subdirs",       this.use_x3d_subdirs+"");
@@ -743,6 +755,8 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(prefix+"cltSuffix")!=            null) this.cltSuffix=properties.getProperty(prefix+"cltSuffix");
 
 			if (properties.getProperty(prefix+"linkedModels")!=         null) this.linkedModels=properties.getProperty(prefix+"linkedModels");
+			if (properties.getProperty(prefix+"linkedCenters")!=        null) this.linkedCenters=properties.getProperty(prefix+"linkedCenters");
+			if (properties.getProperty(prefix+"cuasSeed")!=             null) this.cuasSeed=properties.getProperty(prefix+"cuasSeed");
 			if (properties.getProperty(prefix+"videoDirectory")!=       null) this.videoDirectory=properties.getProperty(prefix+"videoDirectory");
 			if (properties.getProperty(prefix+"x3dDirectory")!=         null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");
 
@@ -928,6 +942,10 @@ public class EyesisCorrectionParameters {
     				"Directory where links to reference models directories will be created.");
     		gd.addCheckbox    ("Select linked reference models directory",         false);
     		
+    		gd.addStringField ("Linked centers",                                   this.linkedCenters, 80,
+    				"Directory where links to model centers directories will be created.");
+    		gd.addCheckbox    ("Select linked models centers directory",           false);
+    		
     		gd.addStringField ("Video directory",                                  this.videoDirectory, 80,
     				"Directory to store combined video files.");
     		gd.addCheckbox    ("Select video directory",                           false);
@@ -1064,6 +1082,7 @@ public class EyesisCorrectionParameters {
     		this.x3dModelVersion=        gd.getNextString(); // 10a
     		this.jp4SubDir=              gd.getNextString(); // 10b
     		this.linkedModels=           gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
+    		this.linkedCenters=          gd.getNextString(); if (gd.getNextBoolean()) selectLinkedCentersDirectory(false, true);
     		this.videoDirectory=         gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
     		this.x3dDirectory=           gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);
     		this.use_x3d_subdirs=        gd.getNextBoolean();
@@ -1150,6 +1169,10 @@ public class EyesisCorrectionParameters {
     				"Directory where links to reference models directories will be created.");
     		gd.addCheckbox    ("Select linked reference models directory",         false);
     		
+    		gd.addStringField ("Linked centers",                                   this.linkedCenters, 80,
+    				"Directory where links to model centers directories will be created.");
+    		gd.addCheckbox    ("Select linked models centers directory",           false);
+
     		gd.addStringField ("Video directory",                                  this.videoDirectory, 80,
     				"Directory to store combined video files.");
     		gd.addCheckbox    ("Select video directory",                           false);
@@ -1327,6 +1350,7 @@ public class EyesisCorrectionParameters {
     		this.x3dModelVersion=        gd.getNextString(); //  10a
     		this.jp4SubDir=              gd.getNextString(); //  10b
     		this.linkedModels=           gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
+    		this.linkedCenters=          gd.getNextString(); if (gd.getNextBoolean()) selectLinkedCentersDirectory(false, true);
     		this.videoDirectory=         gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
     		this.x3dDirectory=           gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);       // 9
     		this.use_x3d_subdirs=        gd.getNextBoolean(); // 10
@@ -1651,34 +1675,47 @@ public class EyesisCorrectionParameters {
 			if (!source_dir.exists()) {
 				source_dir.mkdirs();
 			}
+            if (dir_map.containsKey("cuasSeed")) {
+            	this.cuasSeed=(base_path.resolve(Paths.get(dir_map.get("cuasSeed")))).toString();
+            }
+			
+			
             // Set other directories (possibly relative to base_path)
-			for (int i = 2; i < KEY_DIRS.length; i++) { // skip "rootDirectory" and "sourceDirectory"
-	            if (dir_map.containsKey(KEY_DIRS[i])) {
-	            	Path dir_path=base_path.resolve(Paths.get(dir_map.get(KEY_DIRS[i])));
-	    			File dir_file = new File(dir_path.toString());
-	    			if (!dir_file.exists()) {
-	    				dir_file.mkdirs();
-	    			}
-	    			switch (i) {
-	    			case 2: 
-	    				this.linkedModels =     dir_path.toString();
-	    				System.out.println("this.linkedModels="+this.linkedModels);
-	    				break;
-	    			case 3: 
-	    				this.videoDirectory =   dir_path.toString();
-	    				System.out.println("this.videoDirectory="+this.videoDirectory);
-	    				break;
-	    			case 4: 
-	    				this.x3dDirectory =     dir_path.toString();
-	    				System.out.println("this.x3dDirectory="+this.x3dDirectory);
-	    				break;
-	    			case 5: 
-	    				this.resultsDirectory = dir_path.toString();
-	    				System.out.println("this.resultsDirectory="+this.resultsDirectory);
-	    				break;
-	    			}
-	            }
-			}
+            for (int i = 2; i < KEY_DIRS.length; i++) { // skip "rootDirectory" and "sourceDirectory"
+            	if (dir_map.containsKey(KEY_DIRS[i])) {
+            		Path dir_path=base_path.resolve(Paths.get(dir_map.get(KEY_DIRS[i])));
+            		File dir_file = new File(dir_path.toString());
+            		if (!dir_file.exists()) {
+            			dir_file.mkdirs();
+            		}
+            		switch (i) {
+            		case 2: 
+            			this.linkedModels =     dir_path.toString();
+            			System.out.println("this.linkedModels="+this.linkedModels);
+            			break;
+            		case 3: 
+            			this.linkedCenters =     dir_path.toString();
+            			System.out.println("this.linkedCenters="+this.linkedCenters);
+            			break;
+            		case 4: 
+            			this.videoDirectory =   dir_path.toString();
+            			System.out.println("this.videoDirectory="+this.videoDirectory);
+            			break;
+            		case 5: 
+            			this.x3dDirectory =     dir_path.toString();
+            			System.out.println("this.x3dDirectory="+this.x3dDirectory);
+            			break;
+            		case 6: 
+            			this.resultsDirectory = dir_path.toString();
+            			System.out.println("this.resultsDirectory="+this.resultsDirectory);
+            			break;
+            		case 7: 
+            			this.resultsDirectory = dir_path.toString();
+            			System.out.println("this.cuasSeed="+this.cuasSeed);
+            			break;
+            		}
+            	}
+            }
 			// process source sequence directories
     		ArrayList<PathFirstLast> path_list= new ArrayList<PathFirstLast>();
     		for (String line:lines){
@@ -2409,6 +2446,17 @@ public class EyesisCorrectionParameters {
     		if (dir!=null) this.linkedModels=dir;
     		return dir;
     	}
+    	public String selectLinkedCentersDirectory(boolean smart, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"linked centers directory", // title
+    				"Select linked centers directory", // button
+    				null, // filter
+    				this.linkedCenters); //this.sourceDirectory);
+    		if (dir!=null) this.linkedCenters=dir;
+    		return dir;
+    	}
 
     	public String selectVideoDirectory(boolean smart, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(

src/main/java/com/elphel/imagej/cuas/CuasTile.java

+package com.elphel.imagej.cuas;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+import com.elphel.imagej.gpu.GPUTileProcessor;
+
+public class CuasTile implements  Comparable<CuasTile>, Serializable {
+	private static final long serialVersionUID = 1L;
+	public final static int TILE_SIZE = GPUTileProcessor.DTT_SIZE; // 8
+	public final static int TILE_LENGTH = TILE_SIZE * TILE_SIZE;   // 64
+	public final static int CLT_TILE_LENGTH = 4 * TILE_LENGTH;     // 256
+	public float [] clt_data; //  = new float [CLT_TILE_LENGTH];
+	public double   dts =      0; // time stamp as double
+	public double   weight = 0;
+
+	/*
+	public int      parent_index = -1;
+	public void setParentIndex(int indx) {
+		parent_index = indx;
+	}
+	
+	public int getParentIndex() {
+		return parent_index;
+	}
+	*/
+	public CuasTile (
+			int num_colors,
+			double dts,
+			double weight,
+			float [] clt_data) {
+//		clt_data = new float [num_colors * CLT_TILE_LENGTH];
+		this.dts = dts;
+		this.weight = weight;
+		this.clt_data = clt_data;
+	}
+	public CuasTile (
+			int num_colors,
+			double dts,
+			double weight,
+			float [] clt_full,
+			int ntile) {
+		int tile_length = num_colors * CLT_TILE_LENGTH;
+		clt_data = new float [tile_length];
+		this.dts = dts;
+		this.weight = weight;
+		System.arraycopy(
+				clt_full,
+				ntile * tile_length,
+				clt_data,
+				0,
+				tile_length);
+	}
+	
+	public void getData (
+			float [] fclt,
+			int      ntile) {
+		if (isEmpty()) return; // do nothing
+		System.arraycopy(
+				clt_data,
+				0,
+				fclt,
+				ntile * clt_data.length,
+				clt_data.length);
+	}
+	
+	
+	public double getWeight() {
+		return weight;
+	}
+
+	public double getTimeStamp() {
+		return dts;
+	}
+	
+	public boolean isEmpty() {
+		return (clt_data == null) || (weight <= 0);
+	}
+	public float [] getData() {
+		return clt_data;
+	}
+
+	public double getWeight(
+			double decay,
+			double ts_now) {
+		if (isEmpty()) {
+			return 0;
+		}
+		if (decay > 0) {
+			return weight * Math.exp(-Math.max(ts_now-this.dts, 0)/decay);
+		}
+		return weight;
+	}
+	
+	public CuasTile cloneEmpty() {
+		int num_colors = clt_data.length/CLT_TILE_LENGTH;
+		return new CuasTile(num_colors, dts, 0, null);
+	}
+	
+	public double merge (CuasTile tile, double decay) {
+		if ((tile.clt_data == null) || (tile.weight == 0)) {
+			// do nothing
+		} else if ((clt_data == null) || (weight == 0)) {
+			clt_data = tile.clt_data;
+			weight =   tile.weight;
+			dts =      tile.dts;
+		} else {
+			double w = weight, wt = tile.weight;
+			if (decay > 0) {
+				if (dts < tile.dts) {
+					w = getWeight(
+							decay, // double decay,
+							tile.dts); // double ts_now)
+				} else if (dts > tile.dts) {
+					wt = tile.getWeight(
+							decay, // double decay,
+							dts); // double ts_now)
+				}
+			}
+			double sumw = w + wt;
+			w  /= sumw;
+			wt /= sumw;
+			for (int i = 0; i < clt_data.length; i++) {
+				clt_data[i] = (float)(clt_data[i] * w + tile.clt_data[i] * wt); 
+			}
+			dts = Math.max(dts, tile.dts);
+			weight = sumw;
+		}
+		return weight;
+		
+	}
+	
+	@Override
+	public CuasTile clone() {
+		int num_colors = clt_data.length/CLT_TILE_LENGTH;
+		return new CuasTile(num_colors, dts, weight, clt_data.clone());
+	}
+
+	@Override
+	public int compareTo(CuasTile otherTile) {
+		return Double.compare(dts, otherTile.dts);
+	}
+
+	public double diffTile2 (float [] clt_data_other) {
+		double d2 = 0;
+		for (int i = 0; i < clt_data.length; i++) {
+			double dd = clt_data_other[i] - clt_data[i];
+			d2 += dd * dd;
+		}
+		return d2/clt_data.length;
+	}
+
+	public double diffTile2 (CuasTile tile_other) {
+		return diffTile2(tile_other.clt_data);
+	}
+
+	@SuppressWarnings("static-method")
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+	}
+
+	@SuppressWarnings("static-method")
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+	}
+
+}

src/main/java/com/elphel/imagej/orthomosaic/OrthoMapsCollection.java

@@ -81,8 +81,8 @@ public class OrthoMapsCollection  implements Serializable{
 	*/  
 	
 	public static final String [] KEY_DIRS= {"rootDirectory", // from EyesisCorrectionParameters
-			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory","scenesDirectory",
-			"kernelsDirectory", "patternsDirectory"};
+			"sourceDirectory","linkedModels","linkedCenters","videoDirectory","x3dDirectory","resultsDirectory","scenesDirectory",
+			"kernelsDirectory", "patternsDirectory","cuasSeed"};
 	public static final String [] NAME_FH = {"full","half"};
 	public static final String [] NAME_MO = {"main","other"};
 	

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

@@ -158,7 +158,7 @@ public class Interscene {
 			QuadCLT                                      quadCLT_main, // tiles should be set			
 			final QuadCLT[]                              quadCLTs, //
 			final int                                    ref_index,
-			final QuadCLT.SetChannels []                 set_channels,
+			final SetChannels []                 set_channels,
 			final boolean                                batch_mode,
 			int                                          earliest_scene,
 			int []                                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index
@@ -170,7 +170,7 @@ public class Interscene {
 		// when going first - do not go beyond center (center by IMS coordinates) or just index?
 		// Index is easier, no need to change
 //		QuadCLT[]              quadCLTs_half = new QuadCLT[(quadCLTs.length+1)/2];
-//		QuadCLT.SetChannels [] set_channels_half;
+//		SetChannels [] set_channels_half;
 		// consider if it is using initial DSI from previous in overlap mode
     	boolean overlap_sequences =  clt_parameters.imp.overlap_sequences;
 		int [] start_ref_pointers1 = new int[2];
@@ -248,7 +248,7 @@ public class Interscene {
 					colorProcParameters, // final ColorProcParameters    colorProcParameters,
 					quadCLTs,            // final QuadCLT[]              quadCLTs, //
 					ref_index,           // final int                    ref_index,
-					set_channels,        // final QuadCLT.SetChannels [] set_channels,
+					set_channels,        // final SetChannels [] set_channels,
 					batch_mode,          // final boolean                batch_mode,
 					cent_index,     // int                          earliest_scene,
 					start_ref_pointers1, // int []                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index
@@ -324,7 +324,7 @@ public class Interscene {
 				colorProcParameters, // final ColorProcParameters    colorProcParameters,
 				quadCLTs,            // final QuadCLT[]              quadCLTs, //
 				cent_index,          // final int                    ref_index,
-				set_channels,        // final QuadCLT.SetChannels [] set_channels,
+				set_channels,        // final SetChannels [] set_channels,
 				batch_mode,          // final boolean                batch_mode,
 				earliest_scene,      // int                          earliest_scene,
 				start_ref_pointers2, // int []                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index
@@ -845,7 +845,7 @@ public class Interscene {
 			final ColorProcParameters    colorProcParameters,
 			final QuadCLT[]              quadCLTs, //
 			final int                    ref_index,
-			final QuadCLT.SetChannels [] set_channels,
+			final SetChannels [] set_channels,
 			final boolean                batch_mode,
 			int                          earliest_scene,
 			int []                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index
@@ -1444,7 +1444,7 @@ public class Interscene {
 			int                          min_num_scenes,
 			final ColorProcParameters    colorProcParameters,
 			final QuadCLT[]              quadCLTs, //
-			final QuadCLT.SetChannels [] set_channels,
+			final SetChannels [] set_channels,
 			final boolean                batch_mode,
 			int []                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index. Set if non-null
 			final boolean                updateStatus,
@@ -2047,7 +2047,7 @@ public class Interscene {
 			final ColorProcParameters    colorProcParameters,
 			final QuadCLT[]              quadCLTs, //
 			final int                    ref_index,
-			final QuadCLT.SetChannels [] set_channels,
+			final SetChannels [] set_channels,
 			final boolean                batch_mode,
 			int                          earliest_scene,
 			int []                       start_ref_pointers, // [0] - earliest valid scene, [1] ref_index

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

@@ -658,8 +658,15 @@ min_str_neib_fpn	0.35
 	public  int     cuas_discard_border =   8;     // Discard this number of pixels from each side when merging
 	public  double  cuas_max_fold =         50;
 	public  int     cuas_min_in_row_col =   4;     // Minimal number of defined tiles in a row/column
-	public  double  cuas_clt_threshold =    20;    // threshold for CLT tile difference from a template
+	public  double  cuas_clt_variant =      10;    // threshold from the nearest to create a variant for the tile
+	public  double  cuas_clt_threshold =    20;    // threshold for CLT tile difference not merged when selecting the best
 	public  double  cuas_clt_decrease =     0.01;  // Scale CLT outliers weight 
+	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_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
@@ -1975,10 +1982,24 @@ min_str_neib_fpn	0.35
 				"Maximal non-monotonic Px, Py in PxPyD (usually near image edges).");
 		gd.addNumericField("Minimal tiles in a row/column",          this.cuas_min_in_row_col, 0,3,"tiles",
 				"Discards rows then columns that have less defined tiles (noticed in a diagonal after folds removal).");
-		gd.addNumericField("CLT tile diff thershold",                this.cuas_clt_threshold, 5,7,"pix",
-				"Threshold to the CLT tile difference to a template (RMS).");
-		gd.addNumericField("CLT outliers scale",                     this.cuas_clt_decrease, 5,7,"pix",
+		gd.addNumericField("CLT tile variant thershold",             this.cuas_clt_variant, 5,7,"",
+				"Threshold from the nearest in teplate to create a variant for the tile (RMS).");
+		gd.addNumericField("CLT tile diff merge",                this.cuas_clt_threshold, 5,7,"",
+				"Threshold to the CLT tile difference to a template (RMS) when selectin a single best.");
+		gd.addNumericField("CLT outliers scale",                     this.cuas_clt_decrease, 5,7,"x",
 				"Scale CLT outliers tiles weight when averaging.");
+		gd.addNumericField("Decay of average",                       this.cuas_decay_average, 5,7,"s",
+				"Reduce weight of old scenes while averaging (in e times) after this time.");
+		gd.addNumericField("Keep weight fraction",                   this.cuas_keep_fraction, 5,7,"x",
+				"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 ("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.");
 
 		gd.addTab("LMA sequence","Interscene LMA sequence control");
 		gd.addMessage("Parameters for control of the LMA pose adjustment sequence");
@@ -2866,8 +2887,14 @@ min_str_neib_fpn	0.35
 		this.cuas_discard_border= (int) gd.getNextNumber();
 		this.cuas_max_fold =            gd.getNextNumber();
 		this.cuas_min_in_row_col= (int) gd.getNextNumber();
+		this.cuas_clt_variant =         gd.getNextNumber();
 		this.cuas_clt_threshold =       gd.getNextNumber();
 		this.cuas_clt_decrease =        gd.getNextNumber();
+		this.cuas_decay_average =       gd.getNextNumber();
+		this.cuas_keep_fraction =       gd.getNextNumber();
+		this.cuas_step =                gd.getNextBoolean();
+		this.cuas_debug =               gd.getNextBoolean();
+		this.cuas_step_debug =          gd.getNextBoolean();
 		
 		this.mb_gain_index_pose = (int) gd.getNextNumber();
 		this.mb_gain_index_depth =(int) gd.getNextNumber();
@@ -3686,8 +3713,14 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_discard_border",  this.cuas_discard_border+""); // int
 		properties.setProperty(prefix+"cuas_max_fold",        this.cuas_max_fold+"");       // double
 		properties.setProperty(prefix+"cuas_min_in_row_col",  this.cuas_min_in_row_col+""); // int
+		properties.setProperty(prefix+"cuas_clt_variant",     this.cuas_clt_variant+"");    // double
 		properties.setProperty(prefix+"cuas_clt_threshold",   this.cuas_clt_threshold+"");  // double
 		properties.setProperty(prefix+"cuas_clt_decrease",    this.cuas_clt_decrease+"");   // double
+		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_debug",           this.cuas_debug+"");          // boolean
+		properties.setProperty(prefix+"cuas_step_debug",      this.cuas_step_debug+"");     // boolean
 		
 		properties.setProperty(prefix+"mb_gain_index_pose",   this.mb_gain_index_pose+"");  // int
 		properties.setProperty(prefix+"mb_gain_index_depth",  this.mb_gain_index_depth+""); // int
@@ -4481,12 +4514,16 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_discard_border")!=null)  this.cuas_discard_border=Integer.parseInt(properties.getProperty(prefix+"cuas_discard_border"));
 		if (properties.getProperty(prefix+"cuas_max_fold")!=null)        this.cuas_max_fold=Double.parseDouble(properties.getProperty(prefix+"cuas_max_fold"));
 		if (properties.getProperty(prefix+"cuas_min_in_row_col")!=null)  this.cuas_min_in_row_col=Integer.parseInt(properties.getProperty(prefix+"cuas_min_in_row_col"));
+		if (properties.getProperty(prefix+"cuas_clt_variant")!=null)     this.cuas_clt_variant=Double.parseDouble(properties.getProperty(prefix+"cuas_clt_variant"));
 		if (properties.getProperty(prefix+"cuas_clt_threshold")!=null)   this.cuas_clt_threshold=Double.parseDouble(properties.getProperty(prefix+"cuas_clt_threshold"));
 		if (properties.getProperty(prefix+"cuas_clt_decrease")!=null)    this.cuas_clt_decrease=Double.parseDouble(properties.getProperty(prefix+"cuas_clt_decrease"));
-		
-		if (properties.getProperty(prefix+"mb_gain_index_pose")!=null)   this.mb_gain_index_pose=Integer.parseInt(properties.getProperty(prefix+"mb_gain_index_pose"));
-		if (properties.getProperty(prefix+"mb_gain_index_depth")!=null)  this.mb_gain_index_depth=Integer.parseInt(properties.getProperty(prefix+"mb_gain_index_depth"));
+		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_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"));
 
+		if (properties.getProperty(prefix+"mb_gain_index_pose")!=null)   this.mb_gain_index_pose=Integer.parseInt(properties.getProperty(prefix+"mb_gain_index_pose"));
 		if (properties.getProperty(prefix+"mb_ers_index")!=null)         this.mb_ers_index=Integer.parseInt(properties.getProperty(prefix+"mb_ers_index"));
 		if (properties.getProperty(prefix+"mb_ers_y_index")!=null)       this.mb_ers_y_index=Integer.parseInt(properties.getProperty(prefix+"mb_ers_y_index"));
 		if (properties.getProperty(prefix+"mb_ers_r_index")!=null)       this.mb_ers_r_index=Integer.parseInt(properties.getProperty(prefix+"mb_ers_r_index"));
@@ -5278,8 +5315,14 @@ min_str_neib_fpn	0.35
 		imp.cuas_discard_border =   this.cuas_discard_border;
 		imp.cuas_max_fold =         this.cuas_max_fold;
 		imp.cuas_min_in_row_col =   this.cuas_min_in_row_col;
+		imp.cuas_clt_variant =      this.cuas_clt_variant;
 		imp.cuas_clt_threshold =    this.cuas_clt_threshold;
 		imp.cuas_clt_decrease =     this.cuas_clt_decrease;
+		imp.cuas_decay_average =    this.cuas_decay_average;
+		imp.cuas_keep_fraction =    this.cuas_keep_fraction;
+		imp.cuas_step =             this.cuas_step;
+		imp.cuas_debug =            this.cuas_debug;
+		imp.cuas_step_debug =       this.cuas_step_debug;
 
 		imp.mb_gain_index_pose    = this.mb_gain_index_pose;
 		imp.mb_gain_index_depth   = this.mb_gain_index_depth;

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

@@ -52,7 +52,7 @@ import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.gpu.GpuQuad;
 import com.elphel.imagej.gpu.TpTask;
-//import com.elphel.imagej.tileprocessor.QuadCLTCPU.SetChannels;
+//import com.elphel.imagej.tileprocessor.SetChannels;
 
 import ij.IJ;
 import ij.ImagePlus;
@@ -124,16 +124,28 @@ public class QuadCLT extends QuadCLTCPU {
 	}
 	
 	public ImagePlus showCenterClt(
-			CLTParameters clt_parameters) {
+			float [][] fclt, // may be null 
+			CLTParameters clt_parameters,
+			boolean       show) {
 		if (getCenterClt() == null) {
 			System.out.println("showCenterClt(): not a center CLT");
 			return null;
 		}
 		int sensor_mask_clt = 1; // just one
 		setQuadClt();
+		int tilesX = getTilesX();
+		int tilesY = getTilesY();
+		int tile_size = getTileSize();
+		int [] wh = {tilesX*tile_size,tilesY*tile_size};
+		getGPUQuad().handleWH(
+				wh,     // int []  wh,
+				false); // boolean ref_scene)
+		getGPUQuad().handleWH(
+				wh,     // int []  wh,
+				true); // boolean ref_scene)
 		int [] whc = new int[3];
 		setComboToTD(
-				null, // new float [][] {center_CLT.getCenterClt()}, // ,combo_seq_clt,   // final float [][]  fclt,
+				fclt, // new float [][] {center_CLT.getCenterClt()}, // ,combo_seq_clt,   // final float [][]  fclt,
 				true,            // merge_clt,       // final boolean     merge_channels, // duplicate same data to all selected channels
 				sensor_mask_clt, // final int         sensor_mask, // only if merge_channels
 				whc,             // final int []      whc, // if int[2], will return width, height
@@ -149,10 +161,12 @@ public class QuadCLT extends QuadCLTCPU {
                 false, // toRGB,                                // boolean toRGB,
                 false, // use_reference,                        // boolean use_reference
                 suffix);                                        // String  suffix)
-		imp_virtual.show();
+		if (show) {
+			imp_virtual.show();
+		}
 		return imp_virtual;
 	}
-	
+	@Deprecated
 	public ImagePlus showCenterCltWeights(
 			CLTParameters clt_parameters) {
 		if (getCenterCltWeights() == null) {
@@ -2870,11 +2884,14 @@ public class QuadCLT extends QuadCLTCPU {
 		return gpuQuad.getCltTileLength();
 	}
 	
+	@Deprecated
 	public boolean saveCenterClt() {
 		if (!hasCenterClt()) {
 			System.out.println("saveCenterCli(): center CLT data is not set");
 			return false;
 		}
+		
+		
 		int fclt_tile_length = getCltTileLength(); 
 		float [] fcenter_clt_data_weights = new float [center_clt.length + center_clt_weights.length]; // to include weights
 		System.arraycopy(center_clt,         0, fcenter_clt_data_weights, 0,                 center_clt.length);
@@ -2885,21 +2902,6 @@ public class QuadCLT extends QuadCLTCPU {
 				new float [][] {fcenter_clt_data_weights},                // dbg_data,         // float [][] data,
 				(fclt_tile_length+1), // getCenterCltWH()[0],  // int         width,
 				center_clt.length / fclt_tile_length); // getCenterCltWH()[1]); // int         height)
-		
-		/*
-		float [] fcenter_clt_num = new float [center_clt_num.length];
-		for (int i = 0; i <center_clt_num.length; i++) {
-			fcenter_clt_num[i] = center_clt_num[i];
-		}
-		String [] clt_titles= {"CLT","num-acc"};
-		float [][] fdata = {center_clt, fcenter_clt_num};
-		saveFloatArrayInModelDirectory( // error
-				CENTER_CLT_SUFFIX,    // String      suffix,
-				clt_titles,           // String []   labels, // or null
-				fdata,                // dbg_data,         // float [][] data,
-				getCenterCltWH()[0],  // int         width,
-				getCenterCltWH()[1]); // int         height)
-		*/
 		return true;
 	}
 	
@@ -3041,6 +3043,7 @@ public class QuadCLT extends QuadCLTCPU {
 			fclt = new float[][] {getCenterClt()};
 			merge_channels = true;
 		}
+		
 		final int [] width_height = gpuQuad.getWH(use_reference);
 		final int num_colors = gpuQuad.getNumColors();
 		if (whc != null) {

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

+package com.elphel.imagej.tileprocessor;
+
+public class SetChannels{ // USED in lwir
+	  public String set_name;    // set name (timestamp)
+	  int [] file_number; // array of file numbers for channels
+	  public SetChannels(String name, int[] fn){ // USED in lwir
+		  set_name = name;
+		  file_number = fn;
+	  }
+	  public String name() { // USED in lwir
+		  return set_name;
+	  }
+	  public int [] fileNumber() { // USED in lwir
+		  return file_number;
+	  }
+	  public int fileNumber(int i) { // not used in lwir
+		  return file_number[i];
+	  }
+}

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

@@ -23,7 +23,6 @@ package com.elphel.imagej.tileprocessor;
  **
  */
 
-import java.awt.Rectangle;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Arrays;

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

@@ -38,6 +38,7 @@ import com.elphel.imagej.correction.CorrectionColorProc;
 import com.elphel.imagej.tileprocessor.CLTPass3d;
 import com.elphel.imagej.tileprocessor.OpticalFlow;
 import com.elphel.imagej.tileprocessor.QuadCLT;
+import com.elphel.imagej.tileprocessor.SetChannels;
 import com.elphel.imagej.tileprocessor.TileProcessor;
 import com.elphel.imagej.tileprocessor.TwoQuadCLT;
 
@@ -274,13 +275,13 @@ public class LwirWorld {
 		// final boolean    batch_mode = clt_parameters.batch_run;
 //		this.startTime=System.nanoTime();
 		String [] sourceFiles0=quadCLT_main.correctionsParameters.getSourcePaths();
-		QuadCLT.SetChannels [] set_channels_main = quadCLT_main.setChannels(debugLevel);
+		SetChannels [] set_channels_main = quadCLT_main.setChannels(debugLevel);
 		if ((set_channels_main == null) || (set_channels_main.length==0)) {
 			System.out.println("buildSeriesTQ(): No files to process (of "+sourceFiles0.length+")");
 			return null;
 		}
 		// set_channels will include all 99 scenes even as quadCLTs.length matches ref_index
-		QuadCLT.SetChannels [] set_channels=quadCLT_main.setChannels(debugLevel);
+		SetChannels [] set_channels=quadCLT_main.setChannels(debugLevel);
 		
 		// Each of (usually 99) set_channels entries has set name (timestamp) and an array of corresponding (16) file indices