Added filtering, improved center DSI near margins

src/main/java/com/elphel/imagej/cuas/Cuas.java

@@ -9,7 +9,6 @@ import java.util.concurrent.atomic.AtomicInteger;
 import com.elphel.imagej.cameras.CLTParameters;
 import com.elphel.imagej.common.PolynomialApproximation;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
-import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.tileprocessor.ErsCorrection;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.OpticalFlow;
@@ -456,6 +455,7 @@ public class Cuas {
 		double [] cuas_atr = new double [] { center_ATR[0][0], center_ATR[0][1], center_ATR[0][2]};
 		double [][] cuas_xyzatr = {cuas_xyz, cuas_atr};
 		String center_name = QuadCLT.getCenterDirName(quadCLTs[quadCLTs.length - 1].getImageName());
+		
 		QuadCLT center_CLT = changeReference(
 				quadCLTs, // QuadCLT [] quadCLTs,
 				ref_scene, // QuadCLT    ref_old,
@@ -490,32 +490,75 @@ public class Cuas {
         		ds[0],             // double []      ref_disparity,			
         		ref_scene,         // QuadCLT        refCLT, // should be the same instance if one of quadCLTs
         		debugLevel);       // int            debugLevel)
+        //Filter ref_pXpYD from folds in pX, pY and other
+        boolean show_debug = false;
+        int     discard_border = clt_parameters.imp.cuas_discard_border;
+		double  max_fold =       clt_parameters.imp.cuas_max_fold;
+		int     min_in_row_col = clt_parameters.imp.cuas_min_in_row_col;
+        if (debugLevel > -3) {
+        	System.out.println("createCenterClt(): filtering ref_pXpYD: discard_border="+discard_border+
+        			" pix, max_fold="+max_fold+" pix, min_in_row_col="+min_in_row_col+" tiles");
+        }
+        int width =  ref_scene.getTilesX()*ref_scene.getTileSize();
+        int height = ref_scene.getTilesY()*ref_scene.getTileSize();
+        boolean apply_window_filter = (discard_border > 0) || (max_fold > 0) || (min_in_row_col > 0);
+        final Rectangle window = apply_window_filter ? (new Rectangle(discard_border,discard_border,width-2*discard_border,height-2*discard_border)): null; 
+        if (window != null) {
+            if (show_debug) {
+            	String debug_suffix="-center-disparity-pre-filtered";
+            	center_CLT.show_pXpYD(
+            			ref_pXpYD, // double [][] pXpYD,
+            			debug_suffix, // String      suffix,
+            			true);// boolean     show)
+            }
+        	ref_scene.windowPsPyD(	
+        			ref_pXpYD,           // final double [][] pXpYD,	
+        			window,          // final Rectangle window) // window in pixels!
+        			max_fold,        // final double max_fold)
+        			min_in_row_col); // final int         min_in_row_col,   // Minimal number of defined tiles in a row/column
+        }
         
         double [] disparity_center = new double [ref_pXpYD.length];
         Arrays.fill(disparity_center, Double.NaN);
         for (int i = 0; i < ref_pXpYD.length; i++) if (ref_pXpYD[i] != null) {
         	disparity_center[i] = ref_pXpYD[i][2];
         }
-        // TODO: extrapolate, fill gaps in disparity_center
+        // TODO: extra/interpolate, fill gaps in disparity_center
+        int grow_width = Math.max(center_CLT.getTilesX(), center_CLT.getTilesY());
+        int       num_passes = 20;
+        double [][] debug_disparity_center = show_debug? (new double [2][]): null;
+        if (debug_disparity_center != null) {
+        	debug_disparity_center[0] = disparity_center.clone();
+        }
         
+        disparity_center = TileProcessor.fillNaNs(
+        		disparity_center,  // final double [] data,
+    			null,            // final boolean [] prohibit,
+    			center_CLT.getTilesX(),       // int       width,
+    			2 * grow_width,  // 100, // 2*width, // 16,           // final int grow,
+    			0.7,             // double    diagonal_weight, // relative to ortho
+    			num_passes,      // int       num_passes,
+    			0.03);           // final double     max_rchange, //  = 0.01 - does not need to be accurate
+        if (debug_disparity_center != null) {
+        	debug_disparity_center[1] = disparity_center.clone();
+        }
+
+        if (show_debug) {
+        	String debug_suffix="-center-disparity-filtered";
+        	center_CLT.show_pXpYD(
+        			ref_pXpYD, // double [][] pXpYD,
+        			debug_suffix, // String      suffix,
+        			true);// boolean     show)
+        	ShowDoubleFloatArrays.showArrays(
+        			debug_disparity_center,
+        			center_CLT.getTilesX(),
+        			center_CLT.getTilesY(),
+        			true,
+        			center_CLT.getImageName()+"-center-disparity-filtering",
+        			new String[] {"before","after"});
+        }
         
     	boolean save_weights = true; // always
-    	/*
-		float [][][] center_clt_w = getTDComboSceneSequence(
-				clt_parameters,      // CLTParameters  clt_parameters,
-        		ref_pXpYD,           // double [][]    ref_pXpYD,    		
-				save_weights,        // boolean        save_weights, // output corresponding weights for each data
-				true,                // boolean        merge_all,
-				sensor_mask,         // int            sensor_mask,
-	    		null,                // Rectangle      fov_tiles,
-	    		OpticalFlow.ZERO3,   // double []      stereo_xyz, // offset reference camera {x,y,z}
-	    		cuas_atr,            // double []      stereo_atr_in, // offset reference orientation (cuas)
-	    		null, // ds[0],      // double []      ref_disparity,	// may be null if ref_pXpYD != null	
-	    		quadCLTs,            // QuadCLT []     quadCLTs,
-	    		ref_scene,           // QuadCLT        refCLT, // should be the same instance if one of quadCLTs
-	    		debugLevel);         // int            debugLevel)
-
-    	 */
 		float [][][] center_clt_w = getTDComboSceneSequence(
 				clt_parameters,      // CLTParameters  clt_parameters,
         		null, // ref_pXpYD,           // double [][]    ref_pXpYD,    		
@@ -529,129 +572,81 @@ public class Cuas {
 	    		quadCLTs,            // QuadCLT []     quadCLTs,
 	    		center_CLT, // ref_scene,           // QuadCLT        refCLT, // should be the same instance if one of quadCLTs
 	    		debugLevel);         // int            debugLevel)
-		/*
-		String center_name =  QuadCLT.getCenterDirName(last_clt.getImageName()); // make name from last timestamp, not reference
-		String ref_dir_path = ref_scene.getX3dDirectory(center_name);
-		File cdir = new File(ref_dir_path);
-		QuadCLT center_CLT = new QuadCLT(ref_scene, center_name); //null
-		cdir.mkdirs();
-		center_CLT.setImagePath(cdir.getPath());
-		*/
 		center_CLT.setCenterClt( // only for merged sensors
-				center_clt_w[0][0], // float [] clt,
-				center_clt_w[1][0]); // int []   clt_num, // Index 1 out of bounds for length 1
+				center_clt_w[0][0],  // float [] clt, // per CLT sample (4x pixels)
+				center_clt_w[1][0]); // float [] clt_weights // per tile
 
 		final int transform_size = ref_scene.getTileSize();
 		final int tilesX =         ref_scene.getTilesX();
 		final int tilesY =         ref_scene.getTilesY();
 		final double [][] center_combo_dsi = interpolateDSI(
 				ref_pXpYD,      // final double [][] ref_pXpYD,
-				ref_combo_dsi, // combo_dsi_cli,  // final double [][] dsi_in,
+				ref_combo_dsi,  // combo_dsi_cli,  // final double [][] dsi_in,
 				transform_size, // final int         transform_size,
 				tilesX,         // final int         tilesX,
 				tilesY);        //final int         tilesY);
+		
+		int [] slices_to_fill = {
+				OpticalFlow.COMBO_DSN_INDX_DISP,
+				OpticalFlow.COMBO_DSN_INDX_STRENGTH
+//				OpticalFlow.COMBO_DSN_INDX_LMA, // keep as is
+//				OpticalFlow.COMBO_DSN_INDX_CHANGE, // may just relace nan with 0
+///				OpticalFlow.COMBO_DSN_INDX_DISP_FG,
+///				OpticalFlow.COMBO_DSN_INDX_DISP_BG_ALL
+				};
+		fillNanDsi(
+				ref_pXpYD,        // double [][] ref_pXpYD,
+				center_combo_dsi, // double [][] dsi,
+				center_CLT,       // QuadCLT     ref_clt,  // just for dimensions
+				slices_to_fill,   // int []      slices)
+				debugLevel);      // int         debugLevel)
+		
 		center_CLT.setDSIFromCombo(center_combo_dsi); // reformat
-//		center_CLT.setDSI(center_combo_dsi); // WRONG!
 		String rslt_suffix = "-INTER-INTRA";
 		rslt_suffix += (clt_parameters.correlate_lma?"-LMA":"-NOLMA");
-		/*
-		// fixing NaN in strengths. It is uses to return RMS in Not needed - NaN was from Arrays.fill(combo_dsn_final[i], Double.NaN);
-		// OpticalFlow:10348
-		for (int slice: OpticalFlow.COMBO_DSN_NONNAN) { // new int[] {COMBO_DSN_INDX_STRENGTH,COMBO_DSN_INDX_STRENGTH_BG}) {
-			if (center_combo_dsi[slice] != null) {
-				for (int i = 0; i <center_combo_dsi[slice].length; i++) {
-					if (Double.isNaN(center_combo_dsi[slice][i])) {
-						center_combo_dsi[slice][i] = 0.0;
-					}
-				}
-			}
-		}
-		*/
-
 		center_CLT.saveDoubleArrayInModelDirectory( // error
 				rslt_suffix,                  // String      suffix,
 				OpticalFlow.COMBO_DSN_TITLES, // combo_dsn_titles_full, // null,          // String []   labels, // or null
 				center_combo_dsi,             // dbg_data,         // double [][] data,
 				tilesX,                       // int         width,
 				tilesY);                      // int         height)
-//		center_CLT.saveDSI();
 		center_CLT.saveCenterClt();
 
-		
-		/*
-		boolean save_clt = true;
-		boolean save_dsi = true;
-		boolean save_in_ref = true;
-		boolean save_in_last = true;
-		if (save_clt) {
-			final int height_clt = combo_seq_clt[0].length/width_clt;
-			String [] clt_titles = new String [combo_seq_clt_w.length];
-			for (int i = 0; i < combo_seq_clt.length; i++) {
-				clt_titles[i] = "chn-"+i;
-				if (save_weights) {
-					clt_titles[i+combo_seq_clt.length] = "weight-"+i;
-				}
-			}
-			String suffix_clt = "-clt_combo";
-			if (save_weights) {
-				suffix_clt+="_weights";
-			}
-			if (save_in_ref) {
-			ref_clt.saveFloatArrayInModelDirectory( // error
-					suffix_clt,     // String      suffix,
-					clt_titles,       // combo_dsn_titles_full, // null,          // String []   labels, // or null
-					combo_seq_clt_w,    // dbg_data,         // float [][] data,
-					width_clt,        // int         width,
-					height_clt);      // int         height)
-			}
-			if (save_in_last) {
-				quadCLTs[quadCLTs.length - 1].saveFloatArrayInModelDirectory( // error
-						suffix_clt,     // String      suffix,
-						clt_titles,       // combo_dsn_titles_full, // null,          // String []   labels, // or null
-						combo_seq_clt_w,    // dbg_data,         // float [][] data,
-						width_clt,        // int         width,
-						height_clt);      // int         height)
-			}
-		}
-		
-		if (save_dsi) {
-//			final double [][] combo_dsi_cli = ref_clt.restoreComboDSI (true);
-			TileProcessor tp =         quadCLTs[quadCLTs.length - 1].getTileProcessor();
-			final int transform_size = tp.getTileSize();
-			final int tilesX =         tp.getTilesX();
-			final int tilesY =         tp.getTilesY();
-			final double [][] center_dsi = interpolateDSI(
-					ref_pXpYD,      // final double [][] ref_pXpYD,
-					ref_dsi, // combo_dsi_cli,  // final double [][] dsi_in,
-					transform_size, // final int         transform_size,
-					tilesX,         // final int         tilesX,
-					tilesY);        //final int         tilesY);
-			
-			String rslt_suffix = "-CENTER-INTER-INTRA";
-			// use quadCLTs[quadCLTs.length - 1].restoreComboDSI ("-CENTER",true); to restore
-			
-			rslt_suffix += (clt_parameters.correlate_lma?"-LMA":"-NOLMA");
-	    	if (save_in_ref) {
-	    		ref_clt.saveDoubleArrayInModelDirectory( // error
-	    				rslt_suffix,           // String      suffix,
-	    				OpticalFlow.COMBO_DSN_TITLES, // combo_dsn_titles_full, // null,          // String []   labels, // or null
-	    				center_dsi,       // dbg_data,         // double [][] data,
-	    				tilesX,                // int         width,
-	    				tilesY);               // int         height)
-	    	}
-	    	if (save_in_last) {
-	    		quadCLTs[quadCLTs.length - 1].saveDoubleArrayInModelDirectory( // error
-	    				rslt_suffix,           // String      suffix,
-	    				OpticalFlow.COMBO_DSN_TITLES, // combo_dsn_titles_full, // null,          // String []   labels, // or null
-	    				center_dsi,       // dbg_data,         // double [][] data,
-	    				tilesX,                // int         width,
-	    				tilesY);               // int         height)
-	    	}
-		}
-		*/
 		return center_CLT;
     }
     
+    public static void fillNanDsi(
+			double [][] ref_pXpYD,
+			double [][] dsi,
+			QuadCLT     ref_clt, // just for dimensions
+			int []      slices,
+			int         debugLevel)  {
+        int grow_width = Math.max(ref_clt.getTilesX(), ref_clt.getTilesY());
+        int       num_passes = 20;
+        for (int slice:slices) {
+        	double [] data = dsi[slice]; // .clone(); // not needed to clone
+        	for (int i = 0; i < ref_pXpYD.length; i++) {
+        		if (ref_pXpYD[i] == null) {
+        			data[i] = Double.NaN; // for strength layers that are 0-s
+        		}
+        	}
+    		if (debugLevel > -3) {
+    			System.out.println("fillNanDsi(); starting for slice "+slice+" ("+OpticalFlow.COMBO_DSN_TITLES[slice]+")");
+    		}
+        	dsi[slice] = TileProcessor.fillNaNs(
+        			data,  // final double [] data,
+        			null,            // final boolean [] prohibit,
+        			ref_clt.getTilesX(),       // int       width,
+        			2 * grow_width,  // 100, // 2*width, // 16,           // final int grow,
+        			0.7,             // double    diagonal_weight, // relative to ortho
+        			num_passes,      // int       num_passes,
+        			0.03);           // final double     max_rchange, //  = 0.01 - does not need to be accurate
+        	if (debugLevel > -3) {
+        		System.out.println("fillNanDsi(); done for slice "+slice+" ("+OpticalFlow.COMBO_DSN_TITLES[slice]+")");
+        	}
+        }
+        return;
+    }
     
     public static double [][] interpolateDSI( // uses combo_dsi, not this.dsi
 			final double [][] ref_pXpYD,

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

@@ -5828,7 +5828,7 @@ public class OpticalFlow {
 				}
 			}
 			// just for verification
-			boolean show_clt = false;// true;
+			boolean show_clt = true; // false;// true;
 			if (show_clt) {
 				center_CLT.showCenterClt(
 						clt_parameters); // CLTParameters clt_parameters,			
@@ -15495,7 +15495,8 @@ public class OpticalFlow {
 		return mb_vectors;
 	}
 	
-	public static double[] fillGapsDouble(
+	// Use TileProcessor.fillNaNs
+	public static double[] fillGapsDouble( 
 			double []  data,
 			boolean [] mask_in, // do not process if false (may be null)
 			int       width,

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

@@ -1689,7 +1689,8 @@ public class QuadCLT extends QuadCLTCPU {
 		int width=ref_scene.getTilesX()*ref_scene.getTileSize();
 		int height=ref_scene.getTilesY()*ref_scene.getTileSize();
 		// window in pixels!
-		final Rectangle window = (discard_border > 0)? (new Rectangle(discard_border,discard_border,width-2*discard_border,height-2*discard_border)): null; 
+		boolean apply_window_filter = (discard_border > 0) || (max_fold > 0) || (min_in_row_col > 0);
+		final Rectangle window = apply_window_filter ? (new Rectangle(discard_border,discard_border,width-2*discard_border,height-2*discard_border)): null; 
 		if (ref_pXpYD != null) { // cuas mode, ref_pXpYD defines offset reference scene
 			pXpYD=OpticalFlow.transformToScenePxPyD(
 					ref_pXpYD, // final double [][] reference_pXpYD,   // invalid tiles - NaN in disparity. Should be no nulls, no NaN disparity

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

@@ -932,11 +932,7 @@ public class QuadCLTCPU {
             	}    			
     		}
     	}
-    	
-    	
-    	
     	return new double [] {coeffs[0][1],coeffs[1][1],coeffs[2][1]};
-
     }
     
     public static double [] getOmegaCorrections(
@@ -13889,7 +13885,8 @@ public class QuadCLTCPU {
 				  tp.getTilesX(),
 				  tp.getTilesY(),
 				  true,
-				  "filtered_bgnd_disp_strength",dbg_titles);
+				  "filtered_bgnd_disp_strength",
+				  dbg_titles);
 		  }
 		  int num_bg = tp.clt_3d_passes.get(bg_scan).setTileOpDisparity( // other minimal strength?
 				  bg_sel, // bg_use, // bg_sel, // bg_use, // boolean [] selection, measure all that can be bg

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

@@ -8835,7 +8835,7 @@ ImageDtt.startAndJoin(threads);
 	}
 
 	/**
-	 * Us this one when filling full frame and prohibit is not used. Faster as it first tries lower resolution, then full
+	 * Use this one when filling full frame and prohibit is not used. Faster as it first tries lower resolution, then full
 	 * @param data_in       input data array
 	 * @param width_full    width of the input dtata
 	 * @param decimate_step decimation step (such as 16)