Incorporated blue_sky into dsi as a slice

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

@@ -847,7 +847,6 @@ public class QuadCLT extends QuadCLTCPU {
 			final int         num_refines, // 2
 			final int         min_good,     // minimal number of "good" pixels
 			final double [][] combo_dsn_final,     // double [][]    combo_dsn_final, // dls,
-			final boolean[]   blue_sky,
 			int               threadsMax,
 			final boolean     debug)
 	{
@@ -862,8 +861,8 @@ public class QuadCLT extends QuadCLTCPU {
 					disparity_ref[i] = Double.NaN;
 				}
 			}
-			if (blue_sky != null) {
-				for (int i = 0; i < blue_sky.length; i++) if (blue_sky[i]) {
+			if (combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY] != null) {
+				for (int i = 0; i < disparity_ref.length; i++) if (combo_dsn_final[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY][i] > 0.0) {
 						disparity_ref[i] = 0.0;
 				}
 			}

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

@@ -167,7 +167,9 @@ public class QuadCLTCPU {
     public int                                             num_orient = 0; 
     //number of times scenes are accumulated: 0 - none, 1 - after first orientation, 2 - after second orientation
     public int                                             num_accum =  0;
-    public boolean[] blue_sky =                            null;
+    // TODO: Use dsi[] instead
+//    @Deprecated
+//    public boolean[] blue_sky =                            null;
     public void inc_orient()        {num_orient++;}
     public void inc_accum()         {num_accum++;}
     public void set_orient(int num) {num_orient = num;}
@@ -720,15 +722,53 @@ public class QuadCLTCPU {
 		}
 		return sky_tiles;
 	}
+//	@Deprecated
+//	public boolean [] getBlueSky () {
+//		return this.blue_sky;
+//	}
+	public double [] getDoubleBlueSky() {
+		if (this.dsi == null) {
+			return null;
+		}
+		return this.dsi[is_aux?TwoQuadCLT.DSI_BLUE_SKY_AUX:TwoQuadCLT.DSI_BLUE_SKY_MAIN];
+	}
+	public boolean[] getBooleanBlueSky() {
+		double [] double_blue_sky = getDoubleBlueSky();
+		if (double_blue_sky == null) {
+			return null;
+		}
+		boolean [] blue_sky = new boolean[double_blue_sky.length];
+		for (int i = 0; i < blue_sky.length; i++) {
+			blue_sky[i] = double_blue_sky[i] > 0;
+		}
+		return blue_sky;
+	}
 	
-	public boolean [] getBlueSky () {
-		return this.blue_sky;
+	public boolean hasBlueSky() {
+		return (getDoubleBlueSky() != null);
+		
 	}
+	
 
+//	@Deprecated
 	public void setBlueSky (boolean [] blue_sky) {
-		this.blue_sky = blue_sky;
+		double [] double_blue_sky = new double [blue_sky.length];
+		for (int i = 0; i < blue_sky.length; i++) {
+			double_blue_sky[i] = blue_sky[i]? 1.0 : 0.0;
+		}
+		setBlueSky (double_blue_sky);
+	}
+	
+
+	public void setBlueSky (double [] double_blue_sky) {
+		if (dsi == null) {	
+			dsi = new double [TwoQuadCLT.DSI_SLICES.length][]; // will not have DSI_SPREAD_AUX
+		}
+		int bs_index = is_aux?TwoQuadCLT.DSI_BLUE_SKY_AUX:TwoQuadCLT.DSI_BLUE_SKY_MAIN;
+		dsi[bs_index] = double_blue_sky;
 	}
 	
+	
 	public void setBlueSky (
 			double sky_seed, //  =       7.0;  // start with product of strength by diff_second below this
 			double lma_seed, //          2.0;  // seed - disparity_lma limit
@@ -755,7 +795,8 @@ public class QuadCLTCPU {
 			double [] avg_val,
 			int debugLevel) {
 		int width = tp.getTilesX();
-		this.blue_sky = getBlueSky  (
+//		this.blue_sky = getBlueSky  (
+		setBlueSky(getBlueSky  (
 				sky_seed, //  =       7.0;  // start with product of strength by diff_second below this
 				lma_seed, //          2.0;  // seed - disparity_lma limit
 				sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
@@ -780,13 +821,10 @@ public class QuadCLTCPU {
 				spread,
 				disp_lma,
 				avg_val,
-				debugLevel);
+				debugLevel));
 	}
-	
-	
-	public void setDSI(
-			double [][] dsi) {
-		this.dsi = dsi;
+	public void setDSI(	double [][] dsi) {
+		this.dsi = dsi; // make sure available blue sky is not erased
 	}
 
 	public void setDSIFromCombo(
@@ -798,6 +836,8 @@ public class QuadCLTCPU {
 				combo_dsi[OpticalFlow.COMBO_DSN_INDX_STRENGTH];
 		this.dsi[is_aux?TwoQuadCLT.DSI_DISPARITY_AUX_LMA:TwoQuadCLT.DSI_DISPARITY_MAIN_LMA] =
 				combo_dsi[OpticalFlow.COMBO_DSN_INDX_LMA];
+		this.dsi[is_aux?TwoQuadCLT.DSI_BLUE_SKY_AUX:TwoQuadCLT.DSI_BLUE_SKY_MAIN] =
+				combo_dsi[OpticalFlow.COMBO_DSN_INDX_BLUE_SKY];
 	}
 	
 	
@@ -852,7 +892,7 @@ public class QuadCLTCPU {
 			reliable[i] = (strength[i] >= min_strength) &&
 					(!needs_lma || !Double.isNaN(disparity_lma[i]));
 		}
-		boolean [] blue_sky = getBlueSky();
+		boolean [] blue_sky = getBooleanBlueSky();
 		if (blue_sky != null) {
 			for (int i = 0; i < reliable.length; i++) {
 				reliable[i] &= !blue_sky[i];
@@ -1246,31 +1286,6 @@ public class QuadCLTCPU {
 			referenceExposures = eyesisCorrections.calcReferenceExposures(sourceFiles, debugLevel);
 		}
 		// move after restoring properties
-		/*
-		int [] channelFiles = set_channels[0].fileNumber();		
-		boolean [][] saturation_imp = (clt_parameters.sat_level > 0.0)? new boolean[channelFiles.length][] : null;
-		double []    scaleExposures = new double[channelFiles.length];
-		conditionImageSet(
-				clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
-				colorProcParameters,            //  ColorProcParameters                       colorProcParameters, //
-				sourceFiles,                    // String []                                 sourceFiles,
-				this.image_name,                       // String                                    set_name,
-				referenceExposures,             // double []                                 referenceExposures,
-				channelFiles,                   // int []                                    channelFiles,
-				scaleExposures,                 // output  // double [] scaleExposures
-				saturation_imp,                 // output  // boolean [][]                              saturation_imp,
-				threadsMax,                     // int                                       threadsMax,
-				debugLevelInner);               // int                                       debugLevel);
-		if (noise_sigma_level != null) {
-			generateAddNoise(
-					"-NOISE",
-					ref_scene, // final QuadCLTCPU ref_scene, // may be null if scale_fpn <= 0
-					noise_sigma_level,
-					noise_variant, //final int       noise_variant, // <0 - no-variants, compatible with old code
-					threadsMax,
-					1); // debugLevel); // final int       debug_level)
-		}
-		*/
 		// try to restore DSI generated from interscene if available, if not use single-scene -DSI_MAIN
 		int dsi_result = -1;
 		int max_length=OpticalFlow.COMBO_DSN_TITLES.length;
@@ -1297,7 +1312,7 @@ public class QuadCLTCPU {
 				System.out.println("No DSI data for the scene "+this.getImageName()+", setting this.dsi=null");
 				setDSI(null);
 		}
-		// WAS: resore only if (dsi_result < 0)...  else 
+		// WAS: restore only if (dsi_result < 0)...  else 
 		restoreInterProperties( // restore properties for interscene processing (extrinsics, ers, ...) // get relative poses (98)
 				null, // String path,             // full name with extension or null to use x3d directory
 				false, // boolean all_properties,//				null, // Properties properties,   // if null - will only save extrinsics)

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

@@ -78,7 +78,9 @@ public class TwoQuadCLT {
 	public static  int DSI_SPREAD_AUX =        10;
 	public static  int DSI_AVGVAL_MAIN =       11;
 	public static  int DSI_AVGVAL_AUX =        12;
-	public static  int DSI_LENGTH =            DSI_AVGVAL_AUX+1;
+	public static  int DSI_BLUE_SKY_MAIN =     13;
+	public static  int DSI_BLUE_SKY_AUX =      14;
+	public static  int DSI_LENGTH =            DSI_BLUE_SKY_AUX+1;
 
 	public static String DSI_COMBO_SUFFIX = "-DSI_COMBO";
 	public static String DSI_MAIN_SUFFIX =  "-DSI_MAIN";
@@ -96,7 +98,9 @@ public class TwoQuadCLT {
 			    "spread_main",
 			    "spread_aux",
 			    "avgval_main",
-			    "avgval_aux"};
+			    "avgval_aux",
+			    "blue_sky_main",
+			    "blue_sky_aux"};
 
 	public long                                            startTime;     // start of batch processing
 	public long                                            startSetTime;  // start of set processing

src/main/java/com/elphel/imagej/tileprocessor/lwoc/LwirWorld.java

@@ -280,7 +280,7 @@ public class LwirWorld {
 		
 		
 /* */
-		while ((quadCLTs[ref_index] == null) || (quadCLTs[ref_index].getBlueSky() == null)) { // null
+		while ((quadCLTs[ref_index] == null) || !quadCLTs[ref_index].hasBlueSky()) { // null
 			if (build_ref_dsi) {
 				TwoQuadCLT.copyJP4src( // actually there is no sense to process multiple image sets. Combine with other
 						// processing?
@@ -392,11 +392,9 @@ public class LwirWorld {
 						dsi[TwoQuadCLT.DSI_AVGVAL_AUX],//	double [] avg_val,
 						batch_mode? -1: 1); /// debugLevel);        // int debugLevel)
 				if (ran_photo_each) {
-					quadCLTs[ref_index].setBlueSky(null); // Reset blue sky - is it needed?
-					// see if blue sky was detected - rerun photoEach
-					boolean [] blue_sky = quadCLTs[ref_index].getBlueSky();
+					double []  blue_sky = quadCLTs[ref_index].getDoubleBlueSky();
 					boolean has_blue_sky = false;
-					for (int i = 0; i < blue_sky.length; i++) if (blue_sky[i]) {
+					for (int i = 0; i < blue_sky.length; i++) if (blue_sky[i] > 0) {
 						has_blue_sky = true;
 						break;
 					}