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/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)
 	
@@ -2238,6 +2253,38 @@ min_str_neib_fpn	0.35
 		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,
 				"Save CUAS-related debug images and show them in non-batch mode.");
@@ -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
 		
@@ -5032,6 +5107,20 @@ min_str_neib_fpn	0.35
 		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)