Connected targets to other processing

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

@@ -755,6 +755,8 @@ min_str_neib_fpn	0.35
 	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_targets =       true; // enable targets generation together with the source UM images
+
 	public int      cuas_iter_show =        1; // Maximal enhancement iteration to show intermediate result (0 - none) 
 	public boolean  cuas_2d_save_show =  true; // save/show 2D correlation  
 	public boolean  cuas_intermed_low =  true; // save intermediate vector fields and target coordinates from the LMA (80x64 layers) 
@@ -762,6 +764,9 @@ 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_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)
 	
@@ -2280,6 +2285,9 @@ min_str_neib_fpn	0.35
 				"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 ("Generate and save targets images/video",   this.cuas_targets,
+				"Genearte after differential images are output");
+		
 		gd.addNumericField("Maximal iteration to save/show",        this.cuas_iter_show, 0,3,"",
 				"Maximal enhancement iteration to save/ show intermediate result (0 - none).");
 		gd.addCheckbox ("Save/show 2D correlations",                this.cuas_2d_save_show,
@@ -3294,6 +3302,7 @@ min_str_neib_fpn	0.35
 		this.cuas_scale2x =             gd.getNextBoolean();
 		this.cuas_ra_background =       gd.getNextBoolean();
 
+		this.cuas_targets =             gd.getNextBoolean();
 		this.cuas_iter_show=      (int) gd.getNextNumber();
 		this.cuas_2d_save_show =        gd.getNextBoolean();
 		this.cuas_intermed_low =        gd.getNextBoolean();
@@ -4227,7 +4236,8 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_scale2x",         this.cuas_scale2x+"");        // boolean
 		properties.setProperty(prefix+"cuas_ra_background",   this.cuas_ra_background+"");  // boolean
 
-		properties.setProperty(prefix+"cuas_iter_show",       this.cuas_iter_show+"");       // int
+		properties.setProperty(prefix+"cuas_targets",         this.cuas_targets+"");        // boolean
+		properties.setProperty(prefix+"cuas_iter_show",       this.cuas_iter_show+"");      // int
 		properties.setProperty(prefix+"cuas_2d_save_show",    this.cuas_2d_save_show+"");   // boolean
 		properties.setProperty(prefix+"cuas_intermed_low",    this.cuas_intermed_low+"");   // boolean
 		properties.setProperty(prefix+"cuas_intermed_high",   this.cuas_intermed_high+"");  // boolean
@@ -5133,6 +5143,7 @@ min_str_neib_fpn	0.35
 		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_targets")!=null)         this.cuas_targets=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_targets"));
 		if (properties.getProperty(prefix+"cuas_iter_show")!=null)       this.cuas_iter_show=Integer.parseInt(properties.getProperty(prefix+"cuas_iter_show"));
 		if (properties.getProperty(prefix+"cuas_2d_save_show")!=null)    this.cuas_2d_save_show=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_2d_save_show"));
 		if (properties.getProperty(prefix+"cuas_intermed_low")!=null)    this.cuas_intermed_low=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_intermed_low"));
@@ -6038,6 +6049,7 @@ min_str_neib_fpn	0.35
 		imp.cuas_scale2x =    		this.cuas_scale2x;    
 		imp.cuas_ra_background =    this.cuas_ra_background;
 
+		imp.cuas_targets =          this.cuas_targets;
 		imp.cuas_iter_show=         this.cuas_iter_show;
 		imp.cuas_2d_save_show =     this.cuas_2d_save_show;
 		imp.cuas_intermed_low =     this.cuas_intermed_low;

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

@@ -6439,6 +6439,28 @@ public class OpticalFlow {
 	        							master_CLT.saveImagePlusInModelDirectory(
 	        									null, // "GPU-SHIFTED-D"+clt_parameters.disparity, // String      suffix,
 	        									imp_scenes_pair[nstereo]); // imp_scenes); // ImagePlus   imp)
+	        							if (master_CLT.hasCenterClt()) { // cuas mode
+	        								boolean insert_average = (master_CLT.getCenterAverage() != null) || clt_parameters.imp.calculate_average;
+	        								boolean subtract_average = clt_parameters.imp.subtract_average && insert_average;
+	        								if (subtract_average && clt_parameters.imp.cuas_targets && (mode3d > 0)) {
+	        									System.out.println("Will generate targets images/videos, mode3d="+mode3d);
+	        									ImagePlus imp_targets = imp_scenes_pair[nstereo];
+	        									int first_corr = insert_average? 1:0; // skip average
+	        									int num_scenes = imp_targets.getStack().getSize()- first_corr; // includes average
+	        									float [][] fpixels = new float[num_scenes][];
+	        									String [] scene_titles = new String [num_scenes];
+	        									for (int nscene = 0; nscene < fpixels.length; nscene++) {
+	        										fpixels[nscene] = (float[]) imp_targets.getStack().getPixels(nscene+first_corr+1);
+	        										scene_titles[nscene] = imp_targets.getStack().getSliceLabel(nscene+first_corr+1);
+	        									}
+	        									master_CLT.processMovingTargets(
+	        											clt_parameters, // CLTParameters         clt_parameters,
+	        											batch_mode,     // final boolean         batch_mode,
+	        											 fpixels,       // final float [][]      fpixels,
+	        											 scene_titles,  // String []             scene_titles, // recreate slice_titles from scene titles?
+	        											 debugLevel);   // final int             debugLevel) 
+	        								}
+	        							}
 	        						}
 	        					}
 	        				} else {