Cleaning up, preparing to the batch run

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

@@ -2549,7 +2549,7 @@ public class EyesisCorrectionParameters {
 
     	// select qualified (by 'name' - quad timestamp) x3d subdirectory
 
-    	public String selectX3dDirectory(String name, String version, boolean smart, boolean newAllowed) {
+    	public String selectX3dDirectory(String name, String version, boolean smart, boolean newAllowed) { // no trailing "/"
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
     				newAllowed, // save

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

@@ -5,11 +5,16 @@ import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.concurrent.atomic.AtomicInteger;
 import javax.imageio.ImageIO;
 import java.awt.image.BufferedImage;
+import java.nio.file.Paths;
+import java.nio.file.Path;
+import java.net.URISyntaxException;
+import java.net.URL;
 
 import com.elphel.imagej.cameras.CLTParameters;
 import com.elphel.imagej.common.GenericJTabbedDialog;
@@ -49,6 +54,17 @@ public class CuasMotion {
 	final static public int TARGET_VY =        3;
 	final static public int TARGET_STRENGTH =  4;
 	final static public int TARGET_LENGTH = TARGET_STRENGTH+1;
+	
+	public static String RESOURCE_GRAPICS_DIR ="graphics";
+	public static String ICON_TARGET_1X =      "TDbox_dashed21x21_bold.png";
+	public static String ICON_TARGET_2X =      "TDbox_dashed43x43_2px.png";
+	public static String [][] TARGET_ICONS = {
+			{"TDbox_dashed21x21_bold.png","TDbox_dashed43x43_2px.png"}, // unknown
+			{"TDbox21x21.png",            "TDbox43x43_2px.png"},        // selected 
+			{"Circle21x21.png",           "Circle43x43_2px.png"},       // friend
+			{"diamond21x17.png",          "diamond43x35_2px.png"}       // foe
+	};
+	
 
 	private final  GPUTileProcessor gpuTileProcessor;
 	private CLTParameters           clt_parameters=null;
@@ -114,7 +130,7 @@ public class CuasMotion {
 			int               debugLevel) {
 		int     framecent =         180;
 		int     corr_offset =       clt_parameters.imp.cuas_corr_offset;
-		int     corr_pairs =       clt_parameters.imp.cuas_corr_pairs;
+		int     corr_pairs =        clt_parameters.imp.cuas_corr_pairs;
 		double  cuas_fat_zero =     clt_parameters.imp.cuas_fat_zero;
 		double  cuas_cent_radius =  clt_parameters.imp.cuas_cent_radius;
 		int     cuas_n_recenter =   clt_parameters.imp.cuas_n_recenter;
@@ -246,6 +262,12 @@ public class CuasMotion {
 			CLTParameters     clt_parameters,
 			QuadCLT           parentCLT,
 			int               debugLevel) {
+		String image_name = imp_sel.getTitle().substring(0,17);
+		parentCLT.setImageName(image_name);
+		
+		String x3d_path = parentCLT.getX3dDirectory();
+		System.out.println ("Model directory = "+x3d_path);
+		
 		int     corr_offset =    clt_parameters.imp.cuas_corr_offset;
 		int     corr_pairs =     clt_parameters.imp.cuas_corr_pairs;
 		double  fat_zero =       clt_parameters.imp.cuas_fat_zero;
@@ -287,6 +309,26 @@ public class CuasMotion {
 	    double  lma_mink =       clt_parameters.imp.cuas_lma_mink; // =      0.0;  // Minimal K (overshoot)  <0.007
 	    double  lma_maxk =       clt_parameters.imp.cuas_lma_maxk; // =      5.0;  // Minimal K (overshoot) > 3.8
 		
+		double  mask_width =     clt_parameters.imp.cuas_mask_width;  // 9;
+		double  mask_blur =      clt_parameters.imp.cuas_mask_blur;   // 3;
+		boolean mask_round =     clt_parameters.imp.cuas_mask_round;  // false;
+	    
+		int     target_type =    clt_parameters.imp.cuas_target_type; //0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
+		double  input_range =    clt_parameters.imp.cuas_input_range; // 5;
+		boolean scale2x =        clt_parameters.imp.cuas_scale2x;      //true;
+		
+		boolean ra_background =  clt_parameters.imp.cuas_ra_background;   //true;
+
+		boolean intermed_low =   clt_parameters.imp.cuas_intermed_low;    //true;
+		boolean intermed_high =  clt_parameters.imp.cuas_intermed_high;   //true;
+		boolean save_mono =      clt_parameters.imp.cuas_save_mono;       //true;
+		boolean save_color =     clt_parameters.imp.cuas_save_color;      //true;
+		boolean save_video =     clt_parameters.imp.cuas_save_video;      //true;
+		
+	    
+		
+		
+	    
 		for (int i = 0; i < target_frac.length; i++) {
 			if (clt_parameters.imp.cuas_target_frac[i].length >= 2) {
 				target_frac[i][0] = clt_parameters.imp.cuas_target_frac[i][0];
@@ -372,6 +414,37 @@ public class CuasMotion {
 					"Maximal ratio of the overshoot radius to the first 0 radius (typical 3.0).");
 			
 			
+			gd.addNumericField("Mask diameter",                         mask_width, 5,8,"pix",
+					"Taget mask to replace static background with moving target.");
+			gd.addNumericField("Mask transition width",                 mask_blur, 5,8,"pix",
+					"Transition between opaque and transparent mask.");
+			gd.addCheckbox ("Mask round",                               mask_round,
+					"Use round mask. Unchesked - use sharp square mask without any transition.");
+			gd.addNumericField("Targets icon type",                     target_type, 0,3,"",
+					"0 - unknown (dashed square), 1 - known (square), 2 - friend (circle), 3 - foe (diamond).");
+			gd.addNumericField("Image range",                           input_range, 5,8,"10mK",
+					"Dispaly pixel values range (1.0 ~= 10 mK).");
+			gd.addCheckbox ("Scale images twice",                       scale2x,
+					"Scale imges to 1280x1024 for higher annotation quality.");
+			gd.addCheckbox ("Smooth background with runnong average",   ra_background,
+					"Apply running average to the background of the moving targets (false - use high-noise no-averaged images.");
+
+			gd.addMessage("=== Saving intermediate and final images and video ===");		
+			gd.addCheckbox ("Save tile-resolution intermediate images", intermed_low,
+					"Save intermediate vector fields and target coordinates from the LMA (80x64 layers).");
+			gd.addCheckbox ("Save pixel-resolution intermediate images",intermed_high,
+					"Save pixel-resolution accumulated images (640x512).");
+			gd.addCheckbox ("Save monochrome targets+background",       save_mono,
+					"Save 32-bit monochrome targets+background Tiffs (before optional scaling).");
+			gd.addCheckbox ("Save color targets+background",            save_color,
+					"Save color rendered images (same as videos), optionally scaled.");
+			gd.addCheckbox ("Save videos",                              save_video,
+					"Save video with moving targets.");
+
+			
+			
+			
+			
 			gd.addStringField("Data directory",       data_dir,100,"Intermediate results directory (to bypass first stages during debugging).");
 			
 			gd.addCheckbox    ("Save_params",         save_params,    	"Save edited parameters");
@@ -400,7 +473,7 @@ public class CuasMotion {
 			target_radius =             gd.getNextNumber();
 			target_strength =           gd.getNextNumber();
 			target_frac =   IntersceneMatchParameters.stringToDouble2d(gd.getNextString());
-			no_border =           gd.getNextBoolean();   
+			no_border =                 gd.getNextBoolean();   
 			lma_sigma =                 gd.getNextNumber();
 			lma_r0 =                    gd.getNextNumber();
 			lma_ovrsht =                gd.getNextNumber();
@@ -422,6 +495,22 @@ public class CuasMotion {
 			lma_maxr =                  gd.getNextNumber();
 			lma_mink =                  gd.getNextNumber();
 			lma_maxk =                  gd.getNextNumber();
+			
+			mask_width =                gd.getNextNumber();
+			mask_blur =                 gd.getNextNumber();
+			mask_round =                gd.getNextBoolean();
+			target_type=          (int) gd.getNextNumber();
+			input_range =               gd.getNextNumber();
+			scale2x =                   gd.getNextBoolean();
+			ra_background =             gd.getNextBoolean();
+
+			intermed_low =              gd.getNextBoolean();
+			intermed_high =             gd.getNextBoolean();
+			save_mono =                 gd.getNextBoolean();
+			save_color =                gd.getNextBoolean();
+			save_video =                gd.getNextBoolean();
+			
+			
 			data_dir =                  gd.getNextString();
 			save_params =               gd.getNextBoolean();
 			
@@ -474,6 +563,20 @@ public class CuasMotion {
 				clt_parameters.imp.cuas_lma_maxr =    lma_maxr;
 				clt_parameters.imp.cuas_lma_mink =    lma_mink;
 				clt_parameters.imp.cuas_lma_maxk =    lma_maxk;
+				clt_parameters.imp.cuas_mask_width =   mask_width;
+				clt_parameters.imp.cuas_mask_blur =    mask_blur;
+				clt_parameters.imp.cuas_mask_round =   mask_round;
+				clt_parameters.imp.cuas_target_type	=  target_type;
+				clt_parameters.imp.cuas_input_range	=  input_range;
+				clt_parameters.imp.cuas_scale2x =      scale2x;
+				clt_parameters.imp.cuas_ra_background =ra_background;		
+				clt_parameters.imp.cuas_intermed_low = intermed_low; 
+				clt_parameters.imp.cuas_intermed_high =intermed_high;
+				clt_parameters.imp.cuas_save_mono =    save_mono;    
+				clt_parameters.imp.cuas_save_color =   save_color;   
+				clt_parameters.imp.cuas_save_video =   save_video;   
+				
+				
 			}
 
 			int start_frame = 0;
@@ -527,6 +630,24 @@ public class CuasMotion {
 				System.out.println("lma_maxr=	     "+lma_maxr);
 				System.out.println("lma_mink=        "+lma_mink);
 				System.out.println("lma_maxk=	     "+lma_maxk);
+				System.out.println("mask_width=	     "+mask_width);
+				System.out.println("mask_blur=	     "+mask_blur);
+				System.out.println("mask_round=	     "+mask_round);
+				System.out.println("target_type=     "+target_type);
+				System.out.println("input_range=     "+input_range);
+				System.out.println("scale2x=	     "+scale2x);
+				System.out.println("ra_background=   "+ra_background);
+				System.out.println("intermed_low=    "+intermed_low);
+				System.out.println("intermed_high=   "+intermed_high);
+				System.out.println("save_mono=	     "+save_mono);
+				System.out.println("save_color=	     "+save_color);
+				System.out.println("save_video=	     "+save_video);
+				System.out.println("ra_background=   "+ra_background);
+				System.out.println("intermed_low=    "+intermed_low);
+				System.out.println("intermed_high=   "+intermed_high);
+				System.out.println("save_mono=	     "+save_mono);
+				System.out.println("save_color=	     "+save_color);
+				System.out.println("save_video=	     "+save_video);
 			}
 			float [][] fpixels = new float[num_scenes][];
 			String [] scene_titles = new String [num_scenes];
@@ -551,7 +672,6 @@ public class CuasMotion {
 			String imp_name = imp_sel.getTitle();
 			imp_name = trimSuffix(imp_name,".tif");
 			imp_name = trimSuffix(imp_name,".tiff");
-//			String [] vf_top_titles = {"vX","vY","strength","fraction","speed", "confidence"};
 			String title_cor2d =        imp_name+"-corr2d"+suffix_param; // "-corr2d"+"-"+frame0+"-"+frame1+"-"+corr_pairs,
 			String title_vf_all =       imp_name+"-vector_field_all"+suffix_param; //
 			String title_vf =           imp_name+"-vector_field"+suffix_param; //
@@ -568,7 +688,7 @@ public class CuasMotion {
 
 			final int     frame0 = start_frame + seq_length/2;
 			final int     half_accum_range = corr_pairs/2;
-			final boolean smooth_accum = true;
+//			final boolean smooth_accum = true;
 			
 			double [][][] corr2d =               null; // to read it if bypassing calculations
 			double [][][] motion_scan =          null;
@@ -582,7 +702,7 @@ public class CuasMotion {
 			String vf_path = data_dir + "/" + title_vf+".tiff";
 //			motion_scan_filtered = getVectorFieldHyper(vf_filtered_path); // String path)
 			if (test_lma) {
-				String path_vf = "/media/elphel/NVME/lwir16-proc/eagle_mountain/linked/movement/selected/25_r1.5/I-1747803449_165687-vector_field_good-offs20-pairs50-rstr0.01-fz300.0-cr3.0-mr1-ms0.0-sp0.0-sb1.0-tr2.0-ts0.8-tf0.0,0.12:2.5,0.15:5.0,0.25.tiff";
+				String path_vf =  "/media/elphel/NVME/lwir16-proc/eagle_mountain/linked/movement/selected/25_r1.5/I-1747803449_165687-vector_field_good-offs20-pairs50-rstr0.01-fz300.0-cr3.0-mr1-ms0.0-sp0.0-sb1.0-tr2.0-ts0.8-tf0.0,0.12:2.5,0.15:5.0,0.25.tiff";
 				String path_acc = "/media/elphel/NVME/lwir16-proc/eagle_mountain/linked/movement/selected/25_r1.5/I-1747803449_165687-accumulated-offs20-pairs50-rstr0.01-fz300.0-cr3.0-mr1-ms0.0-sp0.0-sb1.0-tr2.0-ts0.8-tf0.0,0.12:2.5,0.15:5.0,0.25-n20.tiff";
 				double [][][] vf_sequence = getVectorFieldHyper(path_vf); // String path)
 				if (vf_sequence == null) {
@@ -600,6 +720,21 @@ public class CuasMotion {
 						0, // int         num_slices, // (0 - all)
 						wh); // int []      wh)
 				
+				boolean batch_mode = true;
+				
+				generateExtractFilterMovingTargets( // move parameters to clt_parameters
+					       clt_parameters, // CLTParameters       clt_parameters,
+					       batch_mode, // final boolean       batch_mode,
+					       parentCLT, // QuadCLT             parentCLT,          //
+					       fpixels, // final float [][]    fpixels,
+					       accum, // final float [][]    accum,        //
+					       vf_sequence, // final double [][][] vf_sequence,  // 
+					       frame0,      //final int           frame0,      // for vector_field[0] // source scene corresponding to the first sequence 
+					       cuasMotion, // final CuasMotion    cuasMotion,
+					       scene_titles, // String []           scene_titles, // recreate slice_titles from scene titles?
+					       slice_titles, // String []           slice_titles,
+					       debugLevel); // final int            debugLevel)
+				/*
                 double [][][][] coord_data2 = 	getAccumulatedCoordinates(
                 		vf_sequence,          // final double [][][] vector_fields, // centers
 						accum,                // final double [][]   accum_data,   // should be around 0, no low-freq
@@ -653,7 +788,8 @@ public class CuasMotion {
 						title_targets_filt+"-VF-TEST-FILTERED",   // String        title_targets_filt,
 						targets_remain,       // int []        targets_remain,
 						cuasMotion.tilesX,   // int           tilesX)
-						true); // show_vector_field);   // boolean       show)
+						true, // show_vector_field);   // boolean       show)
+						null); // do not save //QuadCLT       parentCLT)
 				int remained_total = printRemain(targets_remain, "Total good targets", true);
 
 				double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA(
@@ -669,7 +805,8 @@ public class CuasMotion {
 						title_targets_filt+"-LMA-TEST-FILTERED",   // String        title_targets_filt,
 						targets_remain,       // int []        targets_remain,
 						cuasMotion.tilesX,    // int           tilesX)
-						true); // show_vector_field);   // boolean       show)
+						true, // show_vector_field);   // boolean       show)
+						null); // do not save //QuadCLT       parentCLT)
 				remained_total = printRemain(targets_remain, "coord_data_filtered_lma: Total new targets LMA", true);
 				
 				// remove tiles that did not pass old vf filter
@@ -706,7 +843,7 @@ public class CuasMotion {
 						frame0,               // final int           frame0,      // for vector_field[0]
 						corr_step,            // final int           frame_step,
 						half_accum_range,     // final int           half_range,
-						smooth_accum,         // final boolean       smooth,
+						smooth,               // final boolean       smooth,
 						corr_offset,          // final int           corr_offset, // interframe distance for correlation
 						true);               // final boolean       batch_mode) {
 				// zero-fill undefined tiles
@@ -719,12 +856,9 @@ public class CuasMotion {
 						title_accumulated+"-TARGETS5x5", // "-corr2d"+"-"+frame0+"-"+frame1+"-"+corr_pairs,
 						slice_titles); // titles_accum);
 				
-				double  mask_width = 9;
-				double  mask_blur =  3;
-				boolean round =      false;
 				double  velocity_scale = 1.0/corr_offset;
 				double [][][] targets60hz = new double [fpixels.length][][];
-				boolean ra_background = true;
+//				boolean ra_background = true;
 				float  [][]  background = fpixels;
 				if (ra_background) {
 					background = runningAverage(
@@ -737,7 +871,7 @@ public class CuasMotion {
 						clt_parameters,          // CLTParameters       clt_parameters,
 						mask_width,              // final double        mask_width,
 						mask_blur,               // final double        mask_blur,
-						round,                   // final boolean       round,
+						mask_round,                   // final boolean       round,
 						fpixels_accumulated5x5,  // final float  [][]   target_keyframes,
 						extended_vf_sequence,    // final double [][][] vector_field,
 						targets_lma_combo,       // final double [][][] target_positions,
@@ -756,16 +890,15 @@ public class CuasMotion {
 						true,
 						title_accumulated+"-REPLACED-TARGETS", // "-corr2d"+"-"+frame0+"-"+frame1+"-"+corr_pairs,
 						scene_titles); // titles_accum);
-				double   input_range = 5;
-				boolean  scale2x = true;
-				String diamond_path_1x = "/media/elphel/NVME/lwir16-proc/eagle_mountain/graphics/diamond21x17.png";
+//				String diamond_path_1x = "/media/elphel/NVME/lwir16-proc/eagle_mountain/graphics/diamond21x17.png";
 //				String diamond_path_2x = "/media/elphel/NVME/lwir16-proc/eagle_mountain/graphics/diamond43x35_2px.png";
-				String diamond_path_2x = "/media/elphel/NVME/lwir16-proc/eagle_mountain/graphics/TDbox_dashed43x43_2px.png";
-				String diamond_path = scale2x? diamond_path_2x : diamond_path_1x;
+//				String diamond_path_2x = "/media/elphel/NVME/lwir16-proc/eagle_mountain/graphics/TDbox_dashed43x43_2px.png";
+//				String diamond_path = scale2x? diamond_path_2x : diamond_path_1x;
 				ImagePlus imp_color = convertToRgbAnnotateTargets(
 						clt_parameters,             // CLTParameters       clt_parameters,
 						input_range,                // final double        input_range, // 5
 						scale2x, // boolean       scale2x,
+						target_type,                // final int target_type, //  = 0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
 						replaced_targets,           // final float  [][]   fpixels,
 						targets60hz,                // final double [][][] targets60hz,
 						frame0,                     // final int           frame0,
@@ -773,39 +906,26 @@ public class CuasMotion {
 						cuasMotion.gpu_max_width,   // final int           width,
 						title_accumulated+"-COLOR", // String              title,
 						scene_titles,               // String []           titles,
-						diamond_path, // //String              diamond_path,
+						null, // diamond_path, // //String              diamond_path, null - use resources
 						debugLevel);                // final int           debugLevel) {
-				
+				// save tiff in model directory
 				if (imp_color != null) {
 					// temporary, will use model directory
 					String save_directory = "/media/elphel/NVME/lwir16-proc/eagle_mountain/linked/movement/selected/video/";
 					String video_path_tmp = save_directory + imp_name+"-TARGETS";
 					String video_path = saveAsVideo(
 							clt_parameters, // CLTParameters       clt_parameters,
-							video_path_tmp, // String              file_path,
+							parentCLT,      // QuadCLT             scene,     // if not null - use it's model directory
+							null, // video_path_tmp, // String              file_path,
 							imp_color,      // ImagePlus           imp_color,
 							debugLevel);    // int debugLevel) {
-
 					imp_color.show();
 				}
+				*/
 				continue;
 			}
-			
-			
 			motion_scan = getVectorFieldHyper(vf_path); // title_vf); // String path)
 			
-			
-			/*
-			
-			if (motion_scan_filtered != null) {
-				extended_scan = extendMotionScan(
-						motion_scan_filtered,  // final double [][][] motion_scan,
-						filter5,               // final boolean [][]  filtered, // centers, should be non-overlapped
-						cuasMotion.tilesX,     // final int           tilesX)
-						1,                     // final int           range, // 1 or 2
-						remain);               // final int     []    remain)
-			}
-			*/
 //			extended_scan = getVectorFieldHyper(vf_extended_path); // String path)
 //			if (extended_scan == null) {
 			boolean show_vector_field =     false; //true;
@@ -984,7 +1104,7 @@ public class CuasMotion {
 						frame0,           // final int           frame0,      // for vector_field[0]
 						corr_step,        // final int           frame_step,
 						half_accum_range, // final int           half_range,
-						smooth_accum, // final boolean       smooth,
+						smooth,           // final boolean       smooth,
 						corr_offset,      // final int           corr_offset, // interframe distance for correlation
 						true);            // final boolean       batch_mode) {
 				// show just fpixels_accumulated
@@ -1072,7 +1192,9 @@ public class CuasMotion {
 						title_targets_filt+"-n"+niter,   // String        title_targets_filt,
 						targets_remain,       // int []        targets_remain,
 						cuasMotion.tilesX,    // int           tilesX)
-						show_vector_field);   // boolean       show)
+						show_vector_field,   // boolean       show)
+						null); // do not save //QuadCLT       parentCLT)
+						
 				remained_total = printRemain(targets_remain, "coord_data_filtered: Total new targets", true);
 				if (remained_total == 0) {
 					break;
@@ -1090,7 +1212,9 @@ public class CuasMotion {
 						title_targets_filt+"-n"+niter,   // String        title_targets_filt,
 						targets_remain,       // int []        targets_remain,
 						cuasMotion.tilesX,    // int           tilesX)
-						show_vector_field);   // boolean       show)
+						show_vector_field,   // boolean       show)
+						null); // do not save //QuadCLT       parentCLT)
+
 				remained_total = printRemain(targets_remain, "coord_data_filtered: Total new targets", true);
 
 				
@@ -1216,7 +1340,7 @@ public class CuasMotion {
 					frame0,           // final int           frame0,      // for vector_field[0]
 					corr_step,        // final int           frame_step,
 					half_accum_range, // final int           half_range,
-					smooth_accum, // final boolean       smooth,
+					smooth,           // final boolean       smooth,
 					corr_offset,      // final int           corr_offset, // interframe distance for correlation
 					true);            // final boolean       batch_mode) {
 			if (show_full_images) {
@@ -1302,7 +1426,9 @@ public class CuasMotion {
 					title_targets_filt+"-n"+niter,   // String        title_targets_filt,
 					targets_remain,       // int []        targets_remain,
 					cuasMotion.tilesX,   // int           tilesX)
-					show_vector_field);   // boolean       show)
+					show_vector_field,   // boolean       show)
+					null); // do not save //QuadCLT       parentCLT)
+
 			int remained_total = printRemain(targets_remain, "Total good targets", true);
 
 			double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA(
@@ -1318,7 +1444,9 @@ public class CuasMotion {
 					title_targets_filt+"-n"+niter,   // String        title_targets_filt,
 					targets_remain,       // int []        targets_remain,
 					cuasMotion.tilesX,    // int           tilesX)
-					show_vector_field);   // boolean       show)
+					show_vector_field,   // boolean       show)
+					null); // do not save //QuadCLT       parentCLT)
+
 			remained_total = printRemain(targets_remain, "coord_data_filtered: Total new targets LMA", true);
 			
 			
@@ -1435,7 +1563,10 @@ public class CuasMotion {
 			String        title_targets_filt,
 			int []        targets_remain,
 			int           tilesX,
-			boolean       show) {
+			boolean       show,
+			QuadCLT       parentCLT) {
+		boolean save = (parentCLT != null);
+			
 		boolean [][] good_targets = filterTargets(
 				coord_data,         // final double [][][] target_coords,
 				target_strength,    // final double        target_strength,
@@ -1445,9 +1576,8 @@ public class CuasMotion {
 		double [][][] coord_data_filtered = applyFilter(
 				coord_data,         // double [][][] motion_scan,
 				good_targets);      // boolean [][] filter5)
-		if (show) {
-		///ImagePlus imp = 
-			showVectorFieldsSequence(
+		if (show || save) {
+			ImagePlus imp =	showVectorFieldsSequence(
 					coord_data_filtered,  // double [][][] vector_fields_sequence,
 					0.0,                  // double        speed_min,		
 					0.0,                  // double        speed_pref,		
@@ -1455,8 +1585,11 @@ public class CuasMotion {
 					slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
 					title_targets_filt,   // String        title,
 					false,                // boolean       nan_effective_strength,
-					true,                 // boolean       show,
+					show,                 // boolean       show,
 					tilesX);   //  int           tilesX) {
+			if (save) {
+				parentCLT.saveImagePlusInModelDirectory(imp);  // ImagePlus   imp)
+			}
 		}
 		return coord_data_filtered; // manually restart with different parameters
 	}
@@ -1474,7 +1607,9 @@ public class CuasMotion {
 			String        title_targets_filt,
 			int []        targets_remain,
 			int           tilesX,
-			boolean       show) {
+			boolean       show,
+			QuadCLT       parentCLT) {
+		boolean save = (parentCLT != null);
 		double lma_minxy = 0.8;
 		boolean [][] good_targets = filterTargetsLMA(
 				coord_data,         // final double [][][] target_coords,
@@ -1491,14 +1626,16 @@ public class CuasMotion {
 		double [][][] coord_data_filtered = applyFilter(
 				coord_data,         // double [][][] motion_scan,
 				good_targets);      // boolean [][] filter5)
-		if (show) {
-		///ImagePlus imp = 
-			showVectorFieldsSequenceLMA(
+		if (save || show) {
+			ImagePlus imp =	showVectorFieldsSequenceLMA(
 					coord_data_filtered,  // double [][][] target_scene_sequence,
 					slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
 					title_targets_filt,   // String        title,
-					true,                 // boolean       show,
+					show,                 // boolean       show,
 					tilesX);   //  int           tilesX) {
+			if (save) {
+					parentCLT.saveImagePlusInModelDirectory(imp);  // ImagePlus   imp)
+			}
 		}
 		return coord_data_filtered; // manually restart with different parameters
 	}
@@ -2936,6 +3073,7 @@ public class CuasMotion {
 			CLTParameters       clt_parameters,
 			final double        input_range, // 5
 			final boolean       scale2x,
+			final int           target_type, //  = 0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
 			final float  [][]   fpixels,
 			final double [][][] targets60hz,
 			final int           frame0,
@@ -2945,6 +3083,18 @@ public class CuasMotion {
 			String []           titles,
 			String              diamond_path,
 			final int           debugLevel) {
+		if (diamond_path == null) {
+			String resource_name = TARGET_ICONS[target_type][scale2x? 1 : 0];
+			URL resourceUrl = CuasMotion.class.getClassLoader().getResource("graphics/"+resource_name);
+			Path resourcePath = null;
+			try {
+				resourcePath = Paths.get(resourceUrl.toURI());
+			} catch (URISyntaxException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			diamond_path = resourcePath.toString();
+		}
 		final int scale = scale2x? 2 : 1;
 		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
 		final AtomicInteger ai = new AtomicInteger(0);
@@ -3152,13 +3302,14 @@ public class CuasMotion {
 			};
 		}		      
 		ImageDtt.startAndJoin(threads);
-		imp.show();
+//		imp.show();
 		return imp;
 	}
 	
 	public static String saveAsVideo(
 			CLTParameters       clt_parameters,
-			String              file_path,
+			QuadCLT             scene,     // if not null - use it's model directory
+			String              file_path, // if not null, use it regardless of scene
 			ImagePlus           imp_color,
 			int debugLevel) {
 		double  video_fps =          clt_parameters.imp.video_fps;
@@ -3172,18 +3323,35 @@ public class CuasMotion {
 		
 		boolean dry_run = false;
 		String avi_path = null;
-		try {
-			avi_path=QuadCLT.saveAVI(
-					file_path, // String      file_path, // forces avi, removes .tif, tiff, and .avi
-					dry_run, // !generate_mapped, // boolean     dry_run, 
-					mode_avi,         // int         avi_mode,
-					avi_JPEG_quality, // int         avi_JPEG_quality,
-					video_fps,        // double      fps,
-					imp_color); // imp_scenes_pair[nstereo]);      // ImagePlus   imp)
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return null;
+		
+		if (file_path != null) {
+			try {
+				avi_path=QuadCLT.saveAVI(
+						file_path, // String      file_path, // forces avi, removes .tif, tiff, and .avi
+						dry_run, // !generate_mapped, // boolean     dry_run, 
+						mode_avi,         // int         avi_mode,
+						avi_JPEG_quality, // int         avi_JPEG_quality,
+						video_fps,        // double      fps,
+						imp_color); // imp_scenes_pair[nstereo]);      // ImagePlus   imp)
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+				return null;
+			}
+		} else {
+			try {
+				avi_path=scene.saveAVIInModelDirectory(
+						dry_run,          // !generate_mapped, // boolean     dry_run, 
+						null,             // String      suffix, // null - use title from the imp
+						mode_avi,         // int         avi_mode,
+						avi_JPEG_quality, // int         avi_JPEG_quality,
+						video_fps,        // double      fps,
+						imp_color);       // imp_scenes_pair[nstereo]);      // ImagePlus   imp)
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+				return null;
+			}
 		}
 		if (avi_path == null) {
 			return null;
@@ -3231,6 +3399,315 @@ public class CuasMotion {
 		return webm_path;
 	}
 	
-	
+
+	public static void generateExtractFilterMovingTargets( // move parameters to clt_parameters
+			CLTParameters       clt_parameters,
+			final boolean       batch_mode,
+			QuadCLT             parentCLT,          //
+			final float [][]    fpixels,
+			final float [][]    accum,        //
+			final double [][][] vf_sequence,  // 
+			final int           frame0,      // for vector_field[0] // source scene corresponding to the first sequence 
+			final CuasMotion    cuasMotion,
+			String []           scene_titles, // recreate slice_titles from scene titles?
+			String []           slice_titles,
+			final int            debugLevel) {
+
+//		String x3d_path = parentCLT.getX3dDirectory();
+		String model_prefix = parentCLT.getImageName();
+		
+		boolean show_vector_field =     true;
+		boolean show_full_images =      true;
+		show_vector_field &= !batch_mode;
+		show_full_images &=  !batch_mode;
+		
+//		final String model_dir = 
+		
+		final int     corr_offset =       clt_parameters.imp.cuas_corr_offset;
+		final int     corr_pairs =        clt_parameters.imp.cuas_corr_pairs;
+		final boolean half_step =         clt_parameters.imp.cuas_half_step; // true;
+		final boolean smooth =            clt_parameters.imp.cuas_smooth; // true;
+		final int corr_step =             half_step ? (corr_offset/2) : corr_offset;
+		final int     half_accum_range =  corr_pairs/2;
+		final double target_radius =      clt_parameters.imp.cuas_target_radius;
+		final int     n_recenter =        clt_parameters.imp.cuas_n_recenter;
+		final boolean no_border=          clt_parameters.imp.cuas_no_border; // true;
+		
+		final double  mask_width =        clt_parameters.imp.cuas_mask_width;  // 9;
+		final double  mask_blur =         clt_parameters.imp.cuas_mask_blur;   // 3;
+		final boolean mask_round =        clt_parameters.imp.cuas_mask_round;  // false;
+		
+		final double target_strength = clt_parameters.imp.cuas_target_strength;
+		final double [][] target_frac = new double [clt_parameters.imp.cuas_target_frac.length][2];
+		
+		// Moving target LMA	
+	    double  lma_sigma =      clt_parameters.imp.cuas_lma_sigma; // =     3.0;
+	    double  lma_r0 =         clt_parameters.imp.cuas_lma_r0; // =        3.0;  //maximum with with overshoot
+	    double  lma_ovrsht =     clt_parameters.imp.cuas_lma_ovrsht; // =    2.0;
+	// CUAS Motion LMA parameters
+		boolean lma_fit_xy=      clt_parameters.imp.cuas_lma_fit_xy; // true;
+		boolean lma_fit_a=       clt_parameters.imp.cuas_lma_fit_a; // true;
+		boolean lma_fit_c=       clt_parameters.imp.cuas_lma_fit_c; // true;
+		boolean lma_fit_r=       clt_parameters.imp.cuas_lma_fit_r; // true;
+		boolean lma_fit_k=       clt_parameters.imp.cuas_lma_fit_k; // true;
+	    double  lambda =         clt_parameters.imp.cuas_lambda; // =        0.1;
+	    double  lambda_good =    clt_parameters.imp.cuas_lambda_good; // =   0.5;
+	    double  lambda_bad =     clt_parameters.imp.cuas_lambda_bad; // =    8;
+	    double  lambda_max =     clt_parameters.imp.cuas_lambda_max; // =  100;
+	    double  rms_diff =       clt_parameters.imp.cuas_rms_diff; // =      0.001; // relative RMS improvement
+	    int     num_iter =       clt_parameters.imp.cuas_num_iter; // =     20;
+		// CUAS Motion LMA filter parameters
+	    double  lma_rms =        clt_parameters.imp.cuas_lma_rms; // =       1.5;  // Maximal RMS, regardless of amplitude
+	    double  lma_arms =       clt_parameters.imp.cuas_lma_arms; // =      0.06; // Maximal absolute RMS, sufficient for any amplitude
+	    double  lma_rrms =       clt_parameters.imp.cuas_lma_rrms; // =      0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
+	    double  lma_mina =       clt_parameters.imp.cuas_lma_mina; // =      1.0;  // Minimal A (amplitude)
+	    double  lma_maxr =       clt_parameters.imp.cuas_lma_maxr; // =      5.0;  // Maximal radius (>3.8)
+	    double  lma_mink =       clt_parameters.imp.cuas_lma_mink; // =      0.0;  // Minimal K (overshoot)  <0.007
+	    double  lma_maxk =       clt_parameters.imp.cuas_lma_maxk; // =      5.0;  // Minimal K (overshoot) > 3.8
+		int     target_type =    clt_parameters.imp.cuas_target_type; //0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
+		double  input_range =    clt_parameters.imp.cuas_input_range; // 5;
+		boolean scale2x =        clt_parameters.imp.cuas_scale2x;      //true;
+		
+		boolean ra_background =  clt_parameters.imp.cuas_ra_background;   //true;
+		boolean intermed_low =   clt_parameters.imp.cuas_intermed_low;    //true;
+		boolean intermed_high =  clt_parameters.imp.cuas_intermed_high;   //true;
+		boolean save_mono =      clt_parameters.imp.cuas_save_mono;       //true;
+		boolean save_color =     clt_parameters.imp.cuas_save_color;      //true;
+		boolean save_video =     clt_parameters.imp.cuas_save_video;      //true;
+		
+		
+        double [][][][] coord_data2 = 	getAccumulatedCoordinates(
+        		vf_sequence,          // final double [][][] vector_fields, // centers
+				accum,                // final double [][]   accum_data,   // should be around 0, no low-freq
+				target_radius,        // final double        centroid_radius,
+				n_recenter,           // final int           n_recenter, //  re-center window around new maximum. 0 -no refines (single-pass)
+				cuasMotion.tilesX,               // final int           tilesX){
+				no_border,            // final boolean       no_border,
+				// Moving target LMA	
+			    lma_sigma,            // final double        lma_sigma,
+			    lma_r0,               // final double        lma_r0,
+			    lma_ovrsht,  // final double        lma_ovrsht,
+			// CUAS Motion LMA parameters
+			    lma_fit_xy,           // final boolean       lma_fit_xy,		
+			    lma_fit_a,            // final boolean       lma_fit_a,						
+			    lma_fit_c,            // final boolean       lma_fit_c,
+			    lma_fit_r,            // final boolean       lma_fit_r,
+			    lma_fit_k,            // final boolean       lma_fit_k,		
+			    lambda,               // final double        lambda,
+			    lambda_good,          // final double        lambda_good,
+			    lambda_bad,           // final double        lambda_bad,
+			    lambda_max,           // final double        lambda_max,
+			    rms_diff,             // final double        rms_diff,
+			    num_iter,             // final int           num_iter,
+			    debugLevel);          // final int           debugLevel);
+		double [][][] coord_data = 	coord_data2[0];	
+		double [][][] coord_lma = 	coord_data2[1];	
+		if (show_vector_field || intermed_low) {
+			ImagePlus imp_vf = showVectorFieldsSequence(
+					coord_data,          // double [][][] vector_fields_sequence,
+					0.0,                  // double        speed_min,		
+					0.0,                  // double        speed_pref,		
+					1.0,                  // double        speed_boost, 
+					slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
+					model_prefix+"-VF-UNFILTERED",    // String        title,
+					false,                // boolean       nan_effective_strength,
+					show_vector_field,                 // boolean       show,
+					cuasMotion.tilesX);   //  int           tilesX) {
+			if (intermed_low) {
+				parentCLT.saveImagePlusInModelDirectory(imp_vf);
+			}
+			ImagePlus imp_lma = showVectorFieldsSequenceLMA(
+					coord_lma,            // double [][][] target_scene_sequence, // rename
+					slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
+					model_prefix+"-LMA-UNFILTERED", // String        title,
+					show_vector_field,                 // boolean       show,
+					cuasMotion.tilesX);   //  int           tilesX) {
+			if (intermed_low) {
+				parentCLT.saveImagePlusInModelDirectory(imp_lma);
+			}
+		}
+		
+		int [] remain = new int [coord_data.length];
+		double [][][] coord_data_filtered = filterAndShowTargets(
+				coord_data,           // double [][][] coord_data,
+				target_strength,      // double        target_strength,
+				target_frac,          // double [][]   target_frac,
+				slice_titles,         // String []     slice_titles, //
+				model_prefix+"-VF-FILTERED",   // String        title_targets_filt,
+				remain,       // int []        targets_remain,
+				cuasMotion.tilesX,   // int           tilesX)
+				show_vector_field,   // boolean       show)
+				intermed_low?parentCLT:null); // parentCLT to save in model directory, null - do not save
+		if (debugLevel > -4) printRemain(remain, "Total good targets", true);
+
+		double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA(
+				coord_lma,// double [][][] coord_data,
+				lma_rms,  // double        lma_rms, // =       1.5;  // Maximal RMS (should always match, regardless if A)
+                lma_arms, // double  lma_arms, // =      0.03; // Maximal absolutre RMS
+                lma_rrms, // double  lma_rrms, // =      0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
+                lma_mina, // double  lma_mina, // =      1.0;  // Minimal A (amplitude)
+                lma_maxr, // double  lma_maxr, // =      5.0;  // Minimal K (overshoot) = 3.0
+                lma_mink, // double  lma_mink, // =      1.0;  // Minimal K (overshoot) = 1.0
+                lma_maxk, // double  lma_maxk, // =      1.0;  // Minimal K (overshoot) = 3.0
+				slice_titles,         // String []     slice_titles, //
+				model_prefix+"-LMA-FILTERED",   // String        title_targets_filt,
+				remain,       // int []        targets_remain,
+				cuasMotion.tilesX,    // int           tilesX)
+				show_vector_field, // show_vector_field);   // boolean       show)
+				intermed_low?parentCLT:null); // parentCLT to save in model directory, null - do not save
+		if (debugLevel > -4) printRemain(remain, "coord_data_filtered_lma: Total new targets LMA", true);
+		
+		// remove tiles that did not pass old vf filter
+		double [][][] targets_lma_combo  = filterMotionScans( // should keep LMA coordinates
+				coord_data_filtered_lma,  // double [][][] scan0,
+				coord_data_filtered, // double [][][] scan1)
+				remain);
+		// create vector field sequence by masking after the last filter
+		double [][][] targets_vf_combo  = filterMotionScans( // should keep LMA coordinates
+				vf_sequence,        // double [][][] scan0,
+				targets_lma_combo,  // double [][][] scan1)
+				remain);
+		
+		if (debugLevel > -4) printRemain(remain, "targets_lma_combo", true);
+		ImagePlus imp_filtered_combo= showVectorFieldsSequenceLMA(
+				targets_lma_combo,    // double [][][] target_scene_sequence,
+				slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
+				model_prefix+"-FILTERED-COMBO",   // String        title,
+				show_vector_field,    // boolean       show,
+				cuasMotion.tilesX);   //  int           tilesX) {
+		
+		if (intermed_low) {
+			parentCLT.saveImagePlusInModelDirectory(imp_filtered_combo);  // ImagePlus   imp)
+		}
+		
+		// create larger, 5x5 vector field for accumulation
+		double [][][] extended_vf_sequence = extendMotionScan(
+				targets_vf_combo,     // final double [][][] motion_scan,
+				null, // filter5,     // final boolean [][]  filtered, // centers, should be non-overlapped
+				cuasMotion.tilesX,    // final int           tilesX)
+				2,                    // final int           range, // 1 or 2
+				remain);              // final int     []    remain)
+		
+		ImagePlus imp_extended = showVectorFieldsSequence(
+				extended_vf_sequence, // double [][][] vector_fields_sequence,
+				0.0,                  // double        speed_min,		
+				0.0,                  // double        speed_pref,		
+				1.0,                  // double        speed_boost, 
+				slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
+				model_prefix+"-EXTENDED",    // String        title,
+				false,                // boolean       nan_effective_strength,
+				show_vector_field,                 // boolean       show,
+				cuasMotion.tilesX);   //  int           tilesX) {
+		if (intermed_low) {
+			parentCLT.saveImagePlusInModelDirectory(imp_extended);
+		}
+
+		
+		float [][] fpixels_accumulated5x5 = cuasMotion.shiftAndRenderAccumulate(
+				clt_parameters,       // CLTParameters       clt_parameters,
+				true, // final boolean       fill_zeros,
+				fpixels,              // final float [][]    fpixels,
+				extended_vf_sequence, // final double [][][] vector_field,
+				frame0,               // final int           frame0,      // for vector_field[0]
+				corr_step,            // final int           frame_step,
+				half_accum_range,     // final int           half_range,
+				smooth,               // final boolean       smooth,
+				corr_offset,          // final int           corr_offset, // interframe distance for correlation
+				true);                // final boolean       batch_mode) {
+		// zero-fill undefined tiles
+		
+		
+		ImagePlus imp_accumulated5x5 = ShowDoubleFloatArrays.makeArrays(
+				fpixels_accumulated5x5, // float[][] pixels,
+				cuasMotion.gpu_max_width, // int width,
+				cuasMotion.gpu_max_height, // int height,
+				model_prefix+"-TARGETS5x5", //String title,
+				slice_titles); //String [] titles)
+		if (show_full_images) {
+			imp_accumulated5x5.show();
+		}		
+		if (intermed_high) {
+			parentCLT.saveImagePlusInModelDirectory(imp_accumulated5x5);            // ImagePlus   imp)
+		}
+		
+		double  velocity_scale = 1.0/corr_offset;
+		double [][][] targets60hz = new double [fpixels.length][][];
+		float  [][]  background = fpixels;
+		
+		String ra_bg_suffix=(ra_background? "-RABG":"");
+		if (ra_background) {
+			background = runningAverage(
+					fpixels,                   // final float [][] fpixels,
+					corr_pairs,                // final int        ra_length,
+					cuasMotion.gpu_max_width); // final int        width)
+		}
+		
+		
+		float [][] replaced_targets = cuasMotion.shiftAndRenderTargets(
+				clt_parameters,          // CLTParameters       clt_parameters,
+				mask_width,              // final double        mask_width,
+				mask_blur,               // final double        mask_blur,
+				mask_round,                   // final boolean       round,
+				fpixels_accumulated5x5,  // final float  [][]   target_keyframes,
+				extended_vf_sequence,    // final double [][][] vector_field,
+				targets_lma_combo,       // final double [][][] target_positions,
+				background,              // final float  [][]   background, // background image
+				frame0,                  // final int           frame0,
+				corr_step,               // final int           frame_step,
+				velocity_scale,          // final double        velocity_scale, // 1.0/(disparity in frames)
+				targets60hz,             // final double [][][] targets60hz, 
+				batch_mode,              // final boolean       batch_mode,
+				debugLevel);             // final int debugLevel)
+		ImagePlus imp_replaced_targets = ShowDoubleFloatArrays.makeArrays(
+				replaced_targets, // float[][] pixels,
+				cuasMotion.gpu_max_width, // int width,
+				cuasMotion.gpu_max_height, // int height,
+				model_prefix+"-REPLACED-TARGETS"+(ra_background? "-RABG":""), //String title,
+				scene_titles); //String [] titles)
+		if (show_full_images) {
+			imp_replaced_targets.show();
+		}
+		if (save_mono) {
+			parentCLT.saveImagePlusInModelDirectory(imp_replaced_targets);            // ImagePlus   imp)
+
+		}
+		
+		ImagePlus imp_color = convertToRgbAnnotateTargets(
+				clt_parameters,             // CLTParameters       clt_parameters,
+				input_range,                // final double        input_range, // 5
+				scale2x, // boolean       scale2x,
+				target_type,                // final int target_type, //  = 0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
+				replaced_targets,           // final float  [][]   fpixels,
+				targets60hz,                // final double [][][] targets60hz,
+				frame0,                     // final int           frame0,
+				corr_step,                   // final int           frame_step,
+				cuasMotion.gpu_max_width,   // final int           width,
+				model_prefix+"-RGB"+ra_bg_suffix, // String              title,
+				scene_titles,               // String []           titles,
+				null, // diamond_path, // //String              diamond_path, null - use resources
+				debugLevel);                // final int           debugLevel) {
+		// save tiff in model directory
+		if (imp_color != null) {
+			if (show_full_images) {
+				imp_color.show();
+			}
+			if (save_color) {
+				parentCLT.saveImagePlusInModelDirectory(imp_color);      // ImagePlus   imp)
+			}
+			// temporary, will use model directory
+////		String save_directory = "/media/elphel/NVME/lwir16-proc/eagle_mountain/linked/movement/selected/video/";
+////		String video_path_tmp = save_directory + model_prefix+"-TARGETS";
+			if (save_video) {
+//			String video_path = 
+				saveAsVideo( // will take name from the image title
+						clt_parameters, // CLTParameters       clt_parameters,
+						parentCLT,      // QuadCLT             scene,     // if not null - use it's model directory
+						null, // video_path_tmp, // String              file_path,
+						imp_color,      // ImagePlus           imp_color,
+						debugLevel);    // int debugLevel) {
+			}
+		}
+		
+	}
 	
 }

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

@@ -743,6 +743,21 @@ min_str_neib_fpn	0.35
 	public double   cuas_lma_mink =      0.0;  // Minimal K (overshoot) = 0.0 (<0.007)
 	public double   cuas_lma_maxk =      5.0;  // Maximal K (overshoot) = 5.0 (>3.8)
 	
+	public double   cuas_mask_width =      9;
+	public double   cuas_mask_blur =       3;
+	public boolean  cuas_mask_round =  false;
+	
+	public int      cuas_target_type =     0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
+	public double   cuas_input_range =     5;
+	public boolean  cuas_scale2x =      true;
+	public boolean  cuas_ra_background = true; // apply running average to the background of the moving targets (false - use high-noise no-averaged images
+	// which files to save in the model directory:
+
+	public boolean  cuas_intermed_low =  true; // save intermediate vector fields and target coordinates from the LMA (80x64 layers) 
+	public boolean  cuas_intermed_high = true; // save pixel-resolution accumulated images (640x512) 
+	public boolean  cuas_save_mono =     true; // save 32-bit monochrome target+backgrounds Tiffs (before optional scaling)
+	public boolean  cuas_save_color =    true; // save color  rendered images (same as videos)
+	public boolean  cuas_save_video =    true; // save color  rendered images (same as videos)
 	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)
 	
@@ -2237,6 +2252,38 @@ min_str_neib_fpn	0.35
 				"Minimal ratio of the overshoot radius to the first 0 radius (typical 1.0).");
 		gd.addNumericField("Maximal overshoot ratio",                this.cuas_lma_maxk, 5,8,"",
 				"Maximal ratio of the overshoot radius to the first 0 radius (typical 3.0).");
+
+		gd.addMessage("=== Targets video generation (see also Vidoe/Stereo tab)  ===");
+		
+
+		gd.addNumericField("Mask diameter",                         this.cuas_mask_width, 5,8,"pix",
+				"Taget mask to replace static background with moving target.");
+		gd.addNumericField("Mask transition width",                 this.cuas_mask_blur, 5,8,"pix",
+				"Transition between opaque and transparent mask.");
+		gd.addCheckbox ("Mask round",                    this.cuas_mask_round,
+				"Use round mask. Unchesked - use sharp square mask without any transition.");
+		
+		gd.addNumericField("Targets icon type",                     this.cuas_target_type, 0,3,"",
+				"0 - unknown (dashed square), 1 - known (square), 2 - friend (circle), 3 - foe (diamond).");
+		
+		gd.addNumericField("Image range",                           this.cuas_input_range, 5,8,"10mK",
+				"Dispaly pixel values range (1.0 ~= 10 mK).");
+		gd.addCheckbox ("Scale images twice",                       this.cuas_scale2x,
+				"Scale imges to 1280x1024 for higher annotation quality.");
+		gd.addCheckbox ("Smooth background with runnong average",   this.cuas_ra_background,
+				"Apply running average to the background of the moving targets (false - use high-noise no-averaged images.");
+
+		gd.addMessage("=== Saving intermediate and final images and video ===");
+		gd.addCheckbox ("Save tile-resolution intermediate images", this.cuas_intermed_low,
+				"Save intermediate vector fields and target coordinates from the LMA (80x64 layers).");
+		gd.addCheckbox ("Save pixel-resolution intermediate images",this.cuas_intermed_high,
+				"Save pixel-resolution accumulated images (640x512).");
+		gd.addCheckbox ("Save monochrome targets+background",       this.cuas_save_mono,
+				"Save 32-bit monochrome targets+background Tiffs (before optional scaling).");
+		gd.addCheckbox ("Save color targets+background",            this.cuas_save_color,
+				"Save color rendered images (same as videos), optionally scaled.");
+		gd.addCheckbox ("Save videos",                              this.cuas_save_video,
+				"Save video with moving targets.");
 		
 		gd.addMessage("=== Debug ===");
 		gd.addCheckbox ("Save/show debug images",                    this.cuas_debug,
@@ -3227,6 +3274,20 @@ min_str_neib_fpn	0.35
 		this.cuas_lma_mink =            gd.getNextNumber();
 		this.cuas_lma_maxk =            gd.getNextNumber();
 		
+		this.cuas_mask_width =          gd.getNextNumber();
+		this.cuas_mask_blur =           gd.getNextNumber();
+		this.cuas_mask_round =          gd.getNextBoolean();
+		this.cuas_target_type=    (int) gd.getNextNumber();
+		this.cuas_input_range =         gd.getNextNumber();
+		this.cuas_scale2x =             gd.getNextBoolean();
+		this.cuas_ra_background =       gd.getNextBoolean();
+
+		this.cuas_intermed_low =        gd.getNextBoolean();
+		this.cuas_intermed_high =       gd.getNextBoolean();
+		this.cuas_save_mono =           gd.getNextBoolean();
+		this.cuas_save_color =          gd.getNextBoolean();
+		this.cuas_save_video =          gd.getNextBoolean();
+		
 		this.cuas_debug =               gd.getNextBoolean();
 		this.cuas_step_debug =          gd.getNextBoolean();
 		
@@ -4143,6 +4204,20 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_lma_mink",        this.cuas_lma_mink+"");       // double
 		properties.setProperty(prefix+"cuas_lma_maxk",        this.cuas_lma_maxk+"");       // double
 		
+		properties.setProperty(prefix+"cuas_mask_width",      this.cuas_mask_width+"");     // double
+		properties.setProperty(prefix+"cuas_mask_blur",       this.cuas_mask_blur+"");      // double
+		properties.setProperty(prefix+"cuas_mask_round",      this.cuas_mask_round+"");     // boolean
+		properties.setProperty(prefix+"cuas_target_type",     this.cuas_target_type+"");    // int
+		properties.setProperty(prefix+"cuas_input_range",     this.cuas_input_range+"");    // double
+		properties.setProperty(prefix+"cuas_scale2x",         this.cuas_scale2x+"");        // boolean
+		properties.setProperty(prefix+"cuas_ra_background",   this.cuas_ra_background+"");  // boolean
+
+		properties.setProperty(prefix+"cuas_intermed_low",    this.cuas_intermed_low+"");   // boolean
+		properties.setProperty(prefix+"cuas_intermed_high",   this.cuas_intermed_high+"");  // boolean
+		properties.setProperty(prefix+"cuas_save_mono",       this.cuas_save_mono+"");      // boolean
+		properties.setProperty(prefix+"cuas_save_color",      this.cuas_save_color+"");     // boolean
+		properties.setProperty(prefix+"cuas_save_video",      this.cuas_save_video+"");     // boolean
+		
 		properties.setProperty(prefix+"cuas_debug",           this.cuas_debug+"");          // boolean
 		properties.setProperty(prefix+"cuas_step_debug",      this.cuas_step_debug+"");     // boolean
 		
@@ -5031,6 +5106,20 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_lma_maxr")!=null)        this.cuas_lma_maxr=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxr"));
 		if (properties.getProperty(prefix+"cuas_lma_mink")!=null)        this.cuas_lma_mink=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_mink"));
 		if (properties.getProperty(prefix+"cuas_lma_maxk")!=null)        this.cuas_lma_maxk=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxk"));
+
+		if (properties.getProperty(prefix+"cuas_mask_width")!=null)      this.cuas_mask_width=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_width"));
+		if (properties.getProperty(prefix+"cuas_mask_blur")!=null)       this.cuas_mask_blur=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_blur"));
+		if (properties.getProperty(prefix+"cuas_mask_round")!=null)      this.cuas_mask_round=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_mask_round"));
+		if (properties.getProperty(prefix+"cuas_target_type")!=null)     this.cuas_target_type=Integer.parseInt(properties.getProperty(prefix+"cuas_target_type"));
+		if (properties.getProperty(prefix+"cuas_input_range")!=null)     this.cuas_input_range=Double.parseDouble(properties.getProperty(prefix+"cuas_input_range"));
+		if (properties.getProperty(prefix+"cuas_scale2x")!=null)         this.cuas_scale2x=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_scale2x"));
+		if (properties.getProperty(prefix+"cuas_ra_background")!=null)   this.cuas_ra_background=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_ra_background"));
+
+		if (properties.getProperty(prefix+"cuas_intermed_low")!=null)    this.cuas_intermed_low=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_intermed_low"));
+		if (properties.getProperty(prefix+"cuas_intermed_high")!=null)   this.cuas_intermed_high=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_intermed_high"));
+		if (properties.getProperty(prefix+"cuas_save_mono")!=null)       this.cuas_save_mono=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_save_mono"));
+		if (properties.getProperty(prefix+"cuas_save_color")!=null)      this.cuas_save_color=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_save_color"));
+		if (properties.getProperty(prefix+"cuas_save_video")!=null)      this.cuas_save_video=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_save_video"));
 		
 		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"));
@@ -5920,6 +6009,20 @@ min_str_neib_fpn	0.35
 		imp.cuas_lma_mink =         this.cuas_lma_mink;
 		imp.cuas_lma_maxk =         this.cuas_lma_maxk;
 		
+		imp.cuas_mask_width =       this.cuas_mask_width; 
+		imp.cuas_mask_blur =        this.cuas_mask_blur;  
+		imp.cuas_mask_round =       this.cuas_mask_round; 
+		imp.cuas_target_type=       this.cuas_target_type;
+		imp.cuas_input_range =		this.cuas_input_range;
+		imp.cuas_scale2x =    		this.cuas_scale2x;    
+		imp.cuas_ra_background =    this.cuas_ra_background;
+
+		imp.cuas_intermed_low =     this.cuas_intermed_low;
+		imp.cuas_intermed_high =    this.cuas_intermed_high;
+		imp.cuas_save_mono =        this.cuas_save_mono;
+		imp.cuas_save_color =       this.cuas_save_color;
+		imp.cuas_save_video =       this.cuas_save_video;
+		
 		imp.cuas_debug =            this.cuas_debug;
 		imp.cuas_step_debug =       this.cuas_step_debug;
 		

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

@@ -5847,6 +5847,13 @@ public class QuadCLTCPU {
 	}
 	
 	
+	public String saveImagePlusInModelDirectory( // use title as filename
+			ImagePlus   imp) {
+		return saveImagePlusInModelDirectory(
+				null, // String      suffix, // null - use title from the imp
+				imp); // ImagePlus   imp)
+	}
+	
 	public String saveImagePlusInModelDirectory(
 			String      suffix, // null - use title from the imp
 			ImagePlus   imp)