Adding minimal sequence travel

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

@@ -799,6 +799,7 @@ min_str_neib_fpn	0.35
 	public boolean  cuas_isolated =      true;  // remove targets that do not have neighbors before/after 
 	public int      cuas_min_seq =       3;     // minimal number of consecutive key frames for the same target
 	public int      cuas_enough_seq =    5;     // number of consecutive key frames considered good regardless of individual scores (maybe add minimal travel in pixels)?
+	public double   cuas_seq_travel =    3.0;   // minimal diagonal of the bounding box that includes sequence to be considered "cuas_enough_seq". Filtering out atmospheric fluctuations
 	public int      cuas_min_seq_fl =    2;     // minimal number of consecutive key frames for the same target that includes first or last key frame
 //	public boolean  cuas_remove_2seq =   true;  // Remove 2-long target sequences consisting of 2 consecutive key frames 
 //	public boolean  cuas_remove_2seq_all=true;  // Remove 2-long first/last target sequences
@@ -836,6 +837,8 @@ min_str_neib_fpn	0.35
 	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_clean_video =   true; // save video without any debug information for targets, output in TIFF files. False - same output for video and TIFFs
+	
 	
 	public boolean  cuas_annotate =      true; // save color  rendered images (same as videos)
 	public boolean  cuas_annotate_uas =  true; // indicate uas from log if available
@@ -2442,6 +2445,9 @@ min_str_neib_fpn	0.35
 				"Minimal number of consecutive key frames for the target to be detected.");
 		gd.addNumericField("Sufficient consecutive key frames",     this.cuas_enough_seq, 0,3,"key frames",
 				"Number of consecutive key frames considered good regardless of their scores.");
+		gd.addNumericField("Minimal sequence travel",               this.cuas_seq_travel, 5,8,"pix",
+				"Minimal diagonal of the bounding box that includes sequence to be considered \"cuas_enough_seq\". Filtering out atmospheric fluctuations.");
+		
 		gd.addNumericField("Minimal end sequence length",           this.cuas_min_seq_fl, 0,3,"key frames",
 				"Minimal number of consecutive key frames for the target to be detected if the sequence includes first or last key frame.");
 		
@@ -2508,6 +2514,8 @@ min_str_neib_fpn	0.35
 				"Save color rendered images (same as videos), optionally scaled.");
 		gd.addCheckbox ("Save videos",                              this.cuas_save_video,
 				"Save video with moving targets.");
+		gd.addCheckbox ("Clean videos",                             this.cuas_clean_video,
+				"Save video without any debug information for targets, output in TIFF files. False - same output for video and TIFFs.");
 		
 		gd.addMessage("=== Target Annotation ===");
 		gd.addCheckbox ("Annotate targets",                         this.cuas_annotate,
@@ -3590,6 +3598,7 @@ min_str_neib_fpn	0.35
 //		this.cuas_remove_2seq_all =     gd.getNextBoolean();
 		this.cuas_min_seq=        (int) gd.getNextNumber();
 		this.cuas_enough_seq=     (int) gd.getNextNumber();
+		this.cuas_seq_travel=           gd.getNextNumber();
 		
 		this.cuas_min_seq_fl=     (int) gd.getNextNumber();
 		
@@ -3624,6 +3633,7 @@ min_str_neib_fpn	0.35
 		this.cuas_save_mono =           gd.getNextBoolean();
 		this.cuas_save_color =          gd.getNextBoolean();
 		this.cuas_save_video =          gd.getNextBoolean();
+		this.cuas_clean_video =         gd.getNextBoolean();
 		
 		this.cuas_annotate =            gd.getNextBoolean();
 		this.cuas_annotate_uas =        gd.getNextBoolean();
@@ -4624,6 +4634,7 @@ min_str_neib_fpn	0.35
 //		properties.setProperty(prefix+"cuas_remove_2seq_all", this.cuas_remove_2seq_all+"");// boolean
 		properties.setProperty(prefix+"cuas_min_seq",         this.cuas_min_seq+"");        // int
 		properties.setProperty(prefix+"cuas_enough_seq",      this.cuas_enough_seq+"");     // int
+		properties.setProperty(prefix+"cuas_seq_travel",      this.cuas_seq_travel+"");     // double
 		properties.setProperty(prefix+"cuas_min_seq_fl",      this.cuas_min_seq_fl+"");     // int
 		
 		properties.setProperty(prefix+"cuas_max_mismatch",    this.cuas_max_mismatch+"");   // double
@@ -4657,6 +4668,7 @@ min_str_neib_fpn	0.35
 		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_clean_video",     this.cuas_clean_video+"");    // boolean
 		
 		
 		properties.setProperty(prefix+"cuas_annotate",        this.cuas_annotate+"");       // boolean
@@ -5619,6 +5631,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_isolated")!=null)        this.cuas_isolated=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_isolated"));
 		if (properties.getProperty(prefix+"cuas_min_seq")!=null)         this.cuas_min_seq=Integer.parseInt(properties.getProperty(prefix+"cuas_min_seq"));
 		if (properties.getProperty(prefix+"cuas_enough_seq")!=null)      this.cuas_enough_seq=Integer.parseInt(properties.getProperty(prefix+"cuas_enough_seq"));
+		if (properties.getProperty(prefix+"cuas_seq_travel")!=null)      this.cuas_seq_travel=Double.parseDouble(properties.getProperty(prefix+"cuas_seq_travel"));
 
 		if (properties.getProperty(prefix+"cuas_min_seq_fl")!=null)      this.cuas_min_seq_fl=Integer.parseInt(properties.getProperty(prefix+"cuas_min_seq_fl"));
 		if (properties.getProperty(prefix+"cuas_max_mismatch")!=null)    this.cuas_max_mismatch=Double.parseDouble(properties.getProperty(prefix+"cuas_max_mismatch"));
@@ -5653,6 +5666,7 @@ min_str_neib_fpn	0.35
 		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_clean_video")!=null)     this.cuas_clean_video=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_clean_video"));
 		
 		if (properties.getProperty(prefix+"cuas_annotate")!=null)        this.cuas_annotate=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_annotate"));
 		if (properties.getProperty(prefix+"cuas_annotate_uas")!=null)    this.cuas_annotate_uas=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_annotate_uas"));
@@ -6617,7 +6631,7 @@ min_str_neib_fpn	0.35
 		imp.cuas_isolated =         this.cuas_isolated; 
 		imp.cuas_min_seq =          this.cuas_min_seq;
 		imp.cuas_enough_seq =       this.cuas_enough_seq;
-		
+		imp.cuas_seq_travel=        this.cuas_seq_travel;
 		imp.cuas_min_seq_fl =       this.cuas_min_seq_fl; 
 		
 		imp.cuas_max_mismatch =     this.cuas_max_mismatch; 
@@ -6650,7 +6664,8 @@ min_str_neib_fpn	0.35
 		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_clean_video =      this.cuas_clean_video;
+
 		imp.cuas_annotate =         this.cuas_annotate;
 		imp.cuas_annotate_uas =     this.cuas_annotate_uas;
 		imp.cuas_text_color=        this.cuas_text_color;