more cleanup

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

@@ -138,6 +138,9 @@ public class EyesisCorrectionParameters {
     	public String x3dSubdirSuffix=         "";
 
   		// CLT 3d batch parameters
+    	public boolean process_main_sources = false;
+    	public boolean process_aux_sources =  true;
+    	
     	public int     rig_batch_adjust_main = 0;
     	public int     rig_batch_adjust_aux =  0;
     	public int     rig_batch_adjust_rig =  0;
@@ -298,6 +301,10 @@ public class EyesisCorrectionParameters {
   			cp.x3dModelVersion=    		this.x3dModelVersion;
   			cp.jp4SubDir=    	     	this.jp4SubDir;
 
+
+  			cp.process_main_sources=    this.process_main_sources;
+  			cp.process_aux_sources=     this.process_aux_sources;
+  			
   			cp.rig_batch_adjust_main=   this.rig_batch_adjust_main;
   			cp.rig_batch_adjust_aux=	this.rig_batch_adjust_aux;
   			cp.rig_batch_adjust_rig=	this.rig_batch_adjust_rig;
@@ -498,6 +505,9 @@ public class EyesisCorrectionParameters {
 
     		properties.setProperty(prefix+"mlDirectory",           this.mlDirectory);
 
+    		properties.setProperty(prefix+"process_main_sources",  this.process_main_sources+"");
+    		properties.setProperty(prefix+"process_aux_sources",   this.process_aux_sources+"");
+
     		properties.setProperty(prefix+"rig_batch_adjust_main", this.rig_batch_adjust_main+"");
     		properties.setProperty(prefix+"rig_batch_adjust_aux",  this.rig_batch_adjust_aux+"");
     		properties.setProperty(prefix+"rig_batch_adjust_rig",  this.rig_batch_adjust_rig+"");
@@ -680,6 +690,9 @@ public class EyesisCorrectionParameters {
 
 			if (properties.getProperty(prefix+"mlDirectory")!=          null) this.mlDirectory=properties.getProperty(prefix+"mlDirectory");
 
+			if (properties.getProperty(prefix+"process_main_sources")!= null) this.process_main_sources=Boolean.parseBoolean(properties.getProperty(prefix+"process_main_sources"));
+			if (properties.getProperty(prefix+"process_aux_sources")!= null)  this.process_aux_sources=Boolean.parseBoolean(properties.getProperty(prefix+"process_aux_sources"));
+
   		    if (properties.getProperty(prefix+"rig_batch_adjust_main")!=null) this.rig_batch_adjust_main=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_main"));
   		    if (properties.getProperty(prefix+"rig_batch_adjust_aux")!=null)  this.rig_batch_adjust_aux=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_aux"));
   		    if (properties.getProperty(prefix+"rig_batch_adjust_rig")!=null)  this.rig_batch_adjust_rig=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_rig"));
@@ -1069,9 +1082,10 @@ public class EyesisCorrectionParameters {
     		gd.addStringField ("Aux x3d subdirectory suffix",                          this.aux_camera.x3dSubdirSuffix, 10,     // 20ba
     				"When using timestamp as a subdirectory, add this suffix");
 
-
-
   			gd.addTab         ("Batch", "Select Batch parameters");
+    		gd.addCheckbox    ("Process main camera source images (false - ignore)",   this.process_main_sources); // 20c
+    		gd.addCheckbox    ("Process AUX camera source images (false - ignore)",    this.process_aux_sources); // 20d
+  			
 			gd.addNumericField("Repeat main camera field adjustment (early, before rig)",                  this.rig_batch_adjust_main,  0);
 			gd.addNumericField("Repeat aux camera field adjustment  (early, before rig)",                  this.rig_batch_adjust_aux,   0);
 			gd.addNumericField("Repeat 2-quad camera rig field adjustment  (early, before late main/aux)", this.rig_batch_adjust_rig,   0);
@@ -1209,7 +1223,10 @@ public class EyesisCorrectionParameters {
     		this.aux_camera.cltSuffix=              gd.getNextString();  // 20b
     		this.aux_camera.x3dSubdirSuffix=        gd.getNextString();  // 20ba
 
-			this.rig_batch_adjust_main =      (int) gd.getNextNumber();
+    		this.process_main_sources=              gd.getNextBoolean(); // 20c
+    		this.process_aux_sources=               gd.getNextBoolean(); // 20d
+
+    		this.rig_batch_adjust_main =      (int) gd.getNextNumber();
 			this.rig_batch_adjust_aux =       (int) gd.getNextNumber();
 			this.rig_batch_adjust_rig =       (int) gd.getNextNumber();
 

src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java

@@ -767,7 +767,9 @@ public class CLTPass3d{
 				double [] strength) {
 			this.calc_disparity = disparity;
 			this.strength =       strength;
-			calc_disparity_combo = calc_disparity.clone();
+			if (calc_disparity_combo != null) {
+				calc_disparity_combo = calc_disparity.clone();
+			}
 		}
 
 		/**

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

@@ -30,6 +30,18 @@ import com.elphel.imagej.common.GenericJTabbedDialog;
 
 public class IntersceneMatchParameters {
 	// Maybe add parameters to make sure there is enough data? Enough in each zone? Enough spread?
+	public  boolean force_ref_dsi =      false; // true;
+	public  boolean force_orientations = false;
+	public  boolean force_interscene =   false; // true;
+	public  boolean export_images =      true; // 16-slice images (same disparity, COMBO_DSN_INDX_DISP_FG and COMBO_DSN_INDX_DISP_BG_ALL,
+	public  boolean show_images =        false;
+	public  boolean show_ranges =        true;
+	
+	public  double  range_disparity_offset =   -0.08;
+	public  double  range_min_strength = 0.5;
+	public  double  range_max =       5000.0;
+	
+
 	// Some "AGC" to adjust how much to discard
 	public  int     margin =                       1;      // do not use tiles if their centers are closer to the image edge
 	public  int     sensor_mask_inter =           -1;      // bitmask of the sensors to use (-1 - all)
@@ -85,6 +97,28 @@ public class IntersceneMatchParameters {
 	public void dialogQuestions(GenericJTabbedDialog gd) {
 		//		gd.addMessage  ("Scene parameters selection");
 
+		gd.addMessage  ("Build series options");
+		gd.addCheckbox ("Force reference scene DSI calculation",     this.force_ref_dsi,
+				"Calculate reference scene DSI even if the file exists.");
+		gd.addCheckbox ("Force egomotion calculation",               this.force_orientations,
+				"Calculate relative poses of each scene camera relative to the reference scene even if the data exists.");
+		gd.addCheckbox ("Force interscene DSI accumulation",         this.force_interscene,
+				"Force interscene calculation (+ML export) even if it was performed before.");
+		gd.addCheckbox ("Export all-sensor images",                  this.export_images,
+				"Export multi-slice images: with constant disparity, with foreground disparity, and with background disparity");
+		gd.addCheckbox ("Show exported images",                      this.show_images,
+				"Display generated/saved images");
+		gd.addCheckbox ("Show distances in meters",                  this.show_ranges,
+				"Calculate strength, distance, X, and Y in meters");
+		
+		gd.addNumericField("Disparity at infinity",                  this.range_disparity_offset, 5,7,"pix",
+				"Disparity at infinity - subtract from measured disparity when converting to ranges.");
+		gd.addNumericField("Minimal strength for range calculation", this.range_min_strength, 5,7,"",
+				"Disregard weaker results when measuring range.");
+		gd.addNumericField("Maximal displayed range",                this.range_max, 5,7,"m",
+				"Do not display extremely far objects.");
+		
+		gd.addMessage  ("Interscene match parameters");
 		gd.addNumericField("Image margin",                           this.margin, 0,5,"pix",
 				"Do not use tiles if their centers are closer to the virtual image edge");
 		gd.addNumericField("Used sensors mask",                      this.sensor_mask_inter, 0,5,"",
@@ -112,7 +146,7 @@ public class IntersceneMatchParameters {
 		gd.addNumericField("Difference from neighbors average ",     this.half_avg_diff, 5,7,"",
 				"Reduce twice for high difference from neighbors average.");
 
-		gd.addMessage  ("Initial search for the intre-scene match");
+		gd.addMessage  ("Initial search for the inter-scene match");
 		gd.addNumericField("Azimuth/tilt step",                      this.pix_step, 0,3,"pix",
 				"Search in a spiral starting with no-shift with this step between probes, in approximate pixels");
 		gd.addNumericField("Search spiral radius",                   this.search_rad, 0,3,"steps",
@@ -173,6 +207,16 @@ public class IntersceneMatchParameters {
 	}
 
 	public void dialogAnswers(GenericJTabbedDialog gd) {
+		this.force_ref_dsi =            gd.getNextBoolean();
+		this.force_orientations =       gd.getNextBoolean();
+		this.force_interscene =         gd.getNextBoolean();
+		this.export_images =            gd.getNextBoolean();
+		this.show_images =              gd.getNextBoolean();
+		this.show_ranges =              gd.getNextBoolean();
+		this.range_disparity_offset =   gd.getNextNumber();
+		this.range_min_strength =       gd.getNextNumber();
+		this.range_max =                gd.getNextNumber();
+
 		this.margin =             (int) gd.getNextNumber();
 		this.sensor_mask_inter=   (int) gd.getNextNumber();
 		this.use_partial =              gd.getNextBoolean();
@@ -214,6 +258,17 @@ public class IntersceneMatchParameters {
 	}
 	
 	public void setProperties(String prefix,Properties properties){
+		properties.setProperty(prefix+"force_ref_dsi",        this.force_ref_dsi + "");     // boolean
+		properties.setProperty(prefix+"force_orientations",   this.force_orientations + "");// boolean
+		properties.setProperty(prefix+"force_interscene",     this.force_interscene + "");  // boolean
+		properties.setProperty(prefix+"export_images",        this.export_images + "");     // boolean
+		properties.setProperty(prefix+"show_images",          this.show_images + "");       // boolean
+		properties.setProperty(prefix+"show_ranges",          this.show_ranges + "");       // boolean
+
+		properties.setProperty(prefix+"range_disparity_offset",this.range_disparity_offset+""); // double
+		properties.setProperty(prefix+"range_min_strength",   this.range_min_strength+"");  // double
+		properties.setProperty(prefix+"range_max",            this.range_max+"");           // double
+		
 		properties.setProperty(prefix+"margin",               this.margin+"");              // int
 		properties.setProperty(prefix+"sensor_mask_inter",    this.sensor_mask_inter+"");   // int
 		properties.setProperty(prefix+"use_partial",          this.use_partial+"");         // boolean
@@ -253,12 +308,21 @@ public class IntersceneMatchParameters {
 	}
 	
 	public void getProperties(String prefix,Properties properties){
+		if (properties.getProperty(prefix+"force_ref_dsi")!=null)        this.force_ref_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"force_ref_dsi"));		
+		if (properties.getProperty(prefix+"force_orientations")!=null)   this.force_orientations=Boolean.parseBoolean(properties.getProperty(prefix+"force_orientations"));		
+		if (properties.getProperty(prefix+"force_interscene")!=null)     this.force_interscene=Boolean.parseBoolean(properties.getProperty(prefix+"force_interscene"));		
+		if (properties.getProperty(prefix+"export_images")!=null)        this.export_images=Boolean.parseBoolean(properties.getProperty(prefix+"export_images"));		
+		if (properties.getProperty(prefix+"show_images")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_images"));		
+		if (properties.getProperty(prefix+"show_ranges")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_ranges"));
+		if (properties.getProperty(prefix+"range_disparity_offset")!=null) this.range_disparity_offset=Double.parseDouble(properties.getProperty(prefix+"range_disparity_offset"));
+		if (properties.getProperty(prefix+"range_min_strength")!=null)   this.range_min_strength=Double.parseDouble(properties.getProperty(prefix+"range_min_strength"));
+		if (properties.getProperty(prefix+"range_max")!=null)            this.range_max=Double.parseDouble(properties.getProperty(prefix+"range_max"));
 		if (properties.getProperty(prefix+"margin")!=null)               this.margin=Integer.parseInt(properties.getProperty(prefix+"margin"));
 		if (properties.getProperty(prefix+"sensor_mask_inter")!=null)    this.sensor_mask_inter=Integer.parseInt(properties.getProperty(prefix+"sensor_mask_inter"));
 		if (properties.getProperty(prefix+"use_partial")!=null)          this.use_partial=Boolean.parseBoolean(properties.getProperty(prefix+"use_partial"));		
 		if (properties.getProperty(prefix+"run_poly")!=null)             this.run_poly=Boolean.parseBoolean(properties.getProperty(prefix+"run_poly"));
 		if (properties.getProperty(prefix+"centroid_radius")!=null)      this.centroid_radius=Double.parseDouble(properties.getProperty(prefix+"centroid_radius"));
-		if (properties.getProperty(prefix+"margin")!=null)               this.margin=Integer.parseInt(properties.getProperty(prefix+"margin"));
+		if (properties.getProperty(prefix+"n_recenter")!=null)           this.n_recenter=Integer.parseInt(properties.getProperty(prefix+"n_recenter"));
 		if (properties.getProperty(prefix+"min_str")!=null)              this.min_str=Double.parseDouble(properties.getProperty(prefix+"min_str"));
 		if (properties.getProperty(prefix+"min_str_sum")!=null)          this.min_str_sum=Double.parseDouble(properties.getProperty(prefix+"min_str_sum"));
 		if (properties.getProperty(prefix+"min_neibs")!=null)            this.min_neibs=Integer.parseInt(properties.getProperty(prefix+"min_neibs"));
@@ -294,6 +358,15 @@ public class IntersceneMatchParameters {
 	@Override
 	public IntersceneMatchParameters clone() throws CloneNotSupportedException {
 		IntersceneMatchParameters imp =     new IntersceneMatchParameters();
+ 		imp.force_ref_dsi         = this.force_ref_dsi;
+		imp.force_orientations    = this.force_orientations;
+		imp.force_interscene      = this.force_interscene;
+		imp.export_images         = this.export_images;
+		imp.show_images           = this.show_images;
+		imp.show_ranges           = this.show_ranges;
+		imp.range_disparity_offset = this.range_disparity_offset;
+		imp.range_min_strength    = this.range_min_strength;
+		imp.range_max             = this.range_max;
 		imp.margin                = this.margin;
 		imp.sensor_mask_inter     = this.sensor_mask_inter;
 		imp.use_partial           = this.use_partial;

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

@@ -238,7 +238,7 @@ public class QuadCLT extends QuadCLTCPU {
 		final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
 		final AtomicInteger ai = new AtomicInteger(0);
 		final AtomicInteger anum_updated = new AtomicInteger(0);
-		final int dbg_tile = 1066;
+		final int dbg_tile = 1235;
 		anum_updated.set(0);
 		for (int ithread = 0; ithread < threads.length; ithread++) {
 			threads[ithread] = new Thread() {
@@ -5847,7 +5847,7 @@ if (debugLevel < -100) {
 		{
 			QuadCLT quadCLT = new QuadCLT(this, set_name); //null
 			
-			quadCLT.restoreNoModel(
+			return (QuadCLT) quadCLT.restoreNoModel(
 					clt_parameters,
 					colorProcParameters,
 					null,                 // double []    noise_sigma_level,
@@ -5855,8 +5855,7 @@ if (debugLevel < -100) {
 					null,                 // final QuadCLTCPU     ref_scene, // may be null if scale_fpn <= 0
 					threadsMax,
 					debugLevel);
-			
-			return quadCLT;
+//			return quadCLT;
 		}
 
 	  

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

@@ -11311,7 +11311,7 @@ if (debugLevel > -100) return true; // temporarily !
 		
 //		QuadCLT last_scene = quadCLTs[last_scene_index];
 		QuadCLT ref_scene = quadCLTs[ref_scene_index];
-		String composite_suffix =    "-INTER-INTRA-LMA";
+		String composite_suffix =    "-INTER-INTRA-LMA"; // is already read if available!
 		String num_corr_max_suffix = "-NUM-CORR-MAX";
 		int [] wh = new int[2];
 		double [][] composite_ds = ref_scene.readDoubleArrayFromModelDirectory(
@@ -11337,7 +11337,7 @@ if (debugLevel > -100) return true; // temporarily !
 		//		int []     num_tiles =    new int [clusters]; // may be null;; // null;
 		//		boolean [] inf_cluster  = new boolean [clusters]; // null;		
 
-		boolean       debug      = debugLevel > -2; 
+		boolean       debug      = debugLevel > -3; 
 
 		if (proc_infinity) {
 			double [] inf_avg = new double[1];
@@ -11666,6 +11666,8 @@ if (debugLevel > -100) return true; // temporarily !
 			final boolean    updateStatus,
 			final int        debugLevel)  throws Exception
 	{
+		
+		
 		if ((quadCLT_main != null) && (quadCLT_main.getGPU() != null)) {
 			quadCLT_main.setQuadClt(); // ignore previous result,
 		}
@@ -11673,6 +11675,7 @@ if (debugLevel > -100) return true; // temporarily !
 			quadCLT_aux.setQuadClt();
 		}
 
+		//quadCLT_main.correctionsParameters.rig_batch_adjust_main_gt
 		
 		// final boolean    batch_mode = clt_parameters.batch_run;
 		// Reset dsi data (only 2 slices will be used)
@@ -11684,8 +11687,22 @@ if (debugLevel > -100) return true; // temporarily !
 		this.startTime=System.nanoTime();
 		
 		String [] sourceFiles=quadCLT_main.correctionsParameters.getSourcePaths();
-		QuadCLT.SetChannels [] set_channels_main = quadCLT_main.setChannels(debugLevel);
-		QuadCLT.SetChannels [] set_channels_aux =  quadCLT_aux.setChannels(debugLevel);
+		boolean process_main_sources = false;
+		boolean process_aux_sources = false;
+		// TODO: clean up - are there duplicates
+		if (quadCLT_main != null) {
+			process_main_sources |= quadCLT_main.correctionsParameters.process_main_sources;
+			process_aux_sources |=  quadCLT_main.correctionsParameters.process_aux_sources;
+		}
+		if (quadCLT_aux != null) {
+			process_aux_sources |= quadCLT_aux.correctionsParameters.process_main_sources;
+			process_aux_sources |= quadCLT_aux.correctionsParameters.process_aux_sources;
+		}
+		
+		//quadCLT_main.correctionsParameters.rig_batch_adjust_main_gt
+		
+		QuadCLT.SetChannels [] set_channels_main = process_main_sources? quadCLT_main.setChannels(debugLevel):null;
+		QuadCLT.SetChannels [] set_channels_aux =  process_aux_sources?  quadCLT_aux.setChannels(debugLevel):null;
 		QuadCLT.SetChannels [] set_channels = set_channels_main;
 		if ((set_channels == null) || ((set_channels_aux != null) && (set_channels_aux.length > set_channels.length))) {
 			set_channels = set_channels_aux;