refactoring for ranging

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

@@ -57,6 +57,8 @@ import com.elphel.imagej.correction.CorrectionColorProc;
 import com.elphel.imagej.cuas.CorrectionFPN;
 import com.elphel.imagej.cuas.Cuas;
 import com.elphel.imagej.cuas.CuasCenterLma;
+import com.elphel.imagej.cuas.CuasMotion;
+import com.elphel.imagej.cuas.CuasRanging;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.gpu.GpuQuad;
 import com.elphel.imagej.gpu.TpTask;
@@ -6221,6 +6223,20 @@ public class OpticalFlow {
 		// Moved to the very end, after 3D
 		boolean test_vegetation = true;
 		
+		if (master_CLT.hasCenterClt()) { // cuas mode
+			CuasRanging cuasRanging = new CuasRanging 	(
+					clt_parameters, // CLTParameters     clt_parameters,
+					master_CLT, // QuadCLT           center_CLT,
+					quadCLTs, // QuadCLT []        scenes,
+					debugLevel); // int               debugLevel) {
+			CuasMotion cuasMotion = cuasRanging.detectTargets(
+					uasLogReader, // UasLogReader    uasLogReader,
+					batch_mode);  // boolean         batch_mode)
+			if (debugLevel > -4) {
+				System.out.println("Target detection DONE");
+			}
+		}		
+		
 		if (generate_mapped || reuse_video) { // modifies combo_dsn_final ?
 			int tilesX =  master_CLT.getTileProcessor().getTilesX();
 	        int tilesY =  master_CLT.getTileProcessor().getTilesY();
@@ -6394,6 +6410,23 @@ public class OpticalFlow {
 	        				if (generate_mapped) {
 		        				double [][] ds_vantage = new double[][] {selected_disparity,selected_strength};
 		        				if ((views[ibase][0] != 0) || (views[ibase][1] != 0) || (views[ibase][2] != 0) || (master_CLT.hasCenterClt()) && (mode3d > 0)) {
+		        					boolean debug_vantage = true;
+		        					//dls
+		        			    	double [][] dbg_vantage = debug_vantage ? (new double[7][]): null;
+		        					if (dbg_vantage != null) {
+		        			        	double [][] dls = { 
+		        			        			combo_dsn_final[COMBO_DSN_INDX_DISP], // **** null on second scene sequence
+		        			        			combo_dsn_final[COMBO_DSN_INDX_LMA],
+		        			        			combo_dsn_final[COMBO_DSN_INDX_STRENGTH]
+		        			        	};
+		        						
+		        						for (int i = 0; i < 3; i++) {
+		        							dbg_vantage[i] = dls[i].clone();
+		        						}
+		        						for (int i = 0; i < 2; i++) {
+		        							dbg_vantage[i+3] = ds_vantage[i].clone();
+		        						}
+		        					}
 		        					ds_vantage = transformCameraVew(
 		        							null, // (debug_ds_fg_virt?"transformCameraVew":null),     // final String    title,
 		        							ds_vantage,                 // final double [][] dsrbg_camera_in,
@@ -6402,6 +6435,19 @@ public class OpticalFlow {
 		        							master_CLT, // quadCLTs[ref_index],      // final QuadCLT   scene_QuadClt,
 		        							master_CLT, // quadCLTs[ref_index],      // final QuadCLT   reference_QuadClt,
 		        							8); // iscale);                  // final int       iscale);
+		        					if (dbg_vantage != null) {
+		        						for (int i = 0; i < 2; i++) {
+		        							dbg_vantage[i+5] = ds_vantage[i].clone();
+		        						}
+		        			    		ShowDoubleFloatArrays.showArrays(
+		        			    				dbg_vantage,
+		        			    				master_CLT.getTileProcessor().getTilesX(),
+		        			    				master_CLT.getTileProcessor().getTilesY(),
+		        			    				true,
+		        			    				center_CLT.getImageName()+"-ds_vantage-old", // "-corr2d"+"-"+frame0+"-"+frame1+"-"+corr_pairs,
+		        			    				new String[] {"disp0","lma0", "str0", "disp","str","virt_disp", "virt_str"});
+		        					}
+		        					
 		        				}
 		        				if (master_CLT.getFPN() != null) {
 		        					scenes_suffix += "-FPN";
@@ -6447,30 +6493,37 @@ public class OpticalFlow {
 	        									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);
-	        										String s = imp_targets.getStack().getSliceLabel(nscene+first_corr+1);
-	        										if (s.indexOf("-0") >=0) {
-	        											s=s.substring(0, s.indexOf("-0"));
+	        								boolean new_cuas_mode = (debugLevel < 1000);
+	        								if (new_cuas_mode) {
+	        									System.out.println("CuasMotion should be already calculated, disabling old mode below.");
+	        								} else {
+	        									System.out.println("Detecting targets in old 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);
+	        											String s = imp_targets.getStack().getSliceLabel(nscene+first_corr+1);
+	        											if (s.indexOf("-0") >=0) {
+	        												s=s.substring(0, s.indexOf("-0"));
+	        											}
+	        											scene_titles[nscene] = s;// imp_targets.getStack().getSliceLabel(nscene+first_corr+1);
 	        										}
-	        										scene_titles[nscene] = s;// 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,
+	        												uasLogReader,  // UasLogReader          uasLogReader,	        											 
+	        												scene_titles,  // String []             scene_titles, // recreate slice_titles from scene titles?
+	        												debugLevel);   // final int             debugLevel) 
 	        									}
-	        									master_CLT.processMovingTargets(
-	        											clt_parameters, // CLTParameters         clt_parameters,
-	        											batch_mode,     // final boolean         batch_mode,
-	        											fpixels,       // final float [][]      fpixels,
-	        											uasLogReader,  // UasLogReader          uasLogReader,	        											 
-	        											scene_titles,  // String []             scene_titles, // recreate slice_titles from scene titles?
-	        											debugLevel);   // final int             debugLevel) 
 	        								}
 	        							}
 	        						}

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

@@ -5994,7 +5994,7 @@ if (debugLevel < -100) {
 					debugLevel);
 		}
 
-	  
+	    @Deprecated
 		public void processMovingTargets(
 				CLTParameters         clt_parameters,
 				final boolean         batch_mode,
@@ -6010,16 +6010,6 @@ if (debugLevel < -100) {
 					uasLogReader,  // UasLogReader          uasLogReader,					
 					scene_titles,   // String []             scene_titles, // recreate slice_titles from scene titles?
 					debugLevel);    // final int             debugLevel)
-/*			
-			CuasMotion.processMovingTargets(
-					clt_parameters, // CLTParameters         clt_parameters,
-					batch_mode,     // final boolean         batch_mode,
-					this,           // QuadCLT               parentCLT,          //
-					fpixels,        // final float [][]      fpixels,
-					uasLogReader,  // UasLogReader          uasLogReader,					
-					scene_titles,   // String []             scene_titles, // recreate slice_titles from scene titles?
-					debugLevel);    // final int             debugLevel)
-*/					
 		}
 		
 }

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

@@ -3089,7 +3089,11 @@ public class QuadCLTCPU {
     	dls[5] = dsi[isAux()? TwoQuadCLT.DSI_TERRAIN_AUX :       TwoQuadCLT.DSI_TERRAIN_MAIN];
     	return dls;
     }
+    public double [][] comboFromMain(){
+    	return comboFromMain(this.dsi);
+    }
 
+    
     public double [][] comboFromMain(double [][] dsi){
     	if (dsi == null) {
     		return null;