Fixed bug - twice correcting because two disparity arrays were equal

(not clones), so they were modified twice

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

@@ -848,9 +848,9 @@ public class EstimateSceneRange {
 		}
 		// Set both DSI_DISPARITY_AUX/MAIN and DSI_DISPARITY_AUX/MAIN_LMA to the one adjusted
   		final double [] disparity_sfm = quadCLTs[cent_index].getDLS()[clt_parameters.imp.use_lma_dsi?1:0];  
-  		quadCLTs[cent_index].setDisparityDSI   (disparity_sfm);
-  		quadCLTs[cent_index].setDisparityLmaDSI(disparity_sfm);
-  		quadCLTs[cent_index].setStrengthDSI    (sfm_confidence);
+  		quadCLTs[cent_index].setDisparityDSI   (disparity_sfm.clone());
+  		quadCLTs[cent_index].setDisparityLmaDSI(disparity_sfm.clone());
+  		quadCLTs[cent_index].setStrengthDSI    (sfm_confidence.clone());
   		// TODO: Maintain (similar to sfm_gain2) and set strength??
   		// Do not yet set combo dsi - copy after disparity correction from IMS
   		quadCLTs[cent_index].setSFMGain2(sfm_gain2);
@@ -862,7 +862,9 @@ public class EstimateSceneRange {
 	    	double scale_img = OpticalFlow.getImgImsScale( // correctInfinityFromIMS(
 	    			quadCLTs, // QuadCLT []       quadCLTs,
 	    			quadCLTs[cent_index], // QuadCLT          master_CLT)
-	    			earliest); // estimateSceneRange.earliest_prescan);     // int              earliest_scene)
+	    			earliest, // estimateSceneRange.earliest_prescan);     // int              earliest_scene)
+	    			latest); // int              latest_scene) { // -1 will use quadCLTs.length -1;
+
 			
 			double inf_disp = OpticalFlow.getImsDisparityCorrection(
 					scale_img,                      // double           scale_img,
@@ -875,7 +877,7 @@ public class EstimateSceneRange {
 	    	
 	    	if (apply_disparity_ims) { // make sure - which DSI it adjusts when using SFM
 	    		// Update DSI_MAIN with disparity at infinity. Store it somewhere in quadCLTs[ref_index]
-	    		quadCLTs[cent_index].offsetDSI(  // applies to all disparity slices
+	    		quadCLTs[cent_index].offsetDSI(  // applies to all disparity slices INCREMENTS twice?
 	    				inf_disp); // double inf_disp)
 	    		quadCLTs[cent_index].setDispInfinityRef( // may use incDispInfinityRef() - was 0 before
 	    				inf_disp); // double disp)
@@ -902,6 +904,7 @@ public class EstimateSceneRange {
 	    	}
 		}
 		double [][] combo_dsn = quadCLTs[cent_index].comboFromMainFgBg(); // set FG/BG layers to avoid null pointers
+		QuadCLTCPU.cloneInner(combo_dsn); // separate data array from its source
 		
 		quadCLTs[cent_index].saveDoubleArrayInModelDirectory(
 				QuadCLTCPU.DSI_SUFFIXES[0],   // String      suffix, always with LMA

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

@@ -1715,9 +1715,11 @@ public class Interscene {
 		boolean apply_disparity_ims =  clt_parameters.imp.air_disp_corr;
 		if (adjust_disparity_ims) {
 	    	double scale_img = OpticalFlow.getImgImsScale( // correctInfinityFromIMS(
-	    			quadCLTs, // QuadCLT []       quadCLTs,
+	    			quadCLTs,            // QuadCLT []       quadCLTs,
 	    			quadCLTs[ref_index], // QuadCLT          master_CLT)
-	    			earliest_scene);     // int              earliest_scene)
+	    			earliest_scene,      // int              earliest_scene)
+	    			-1);                 // int              latest_scene) { // -1 will use quadCLTs.length -1;
+
 			
 			double inf_disp = OpticalFlow.getImsDisparityCorrection(
 					scale_img,           // double           scale_img,

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

@@ -5894,7 +5894,8 @@ public class OpticalFlow {
 						    	double scale_img = OpticalFlow.getImgImsScale( // correctInfinityFromIMS(
 						    			quadCLTs, // QuadCLT []       quadCLTs,
 						    			quadCLTs[ref_index], // QuadCLT          master_CLT)
-						    			earliest_scene);     // int              earliest_scene)
+						    			earliest_scene,     // int              earliest_scene)
+						    			-1);                 // int              latest_scene) { // -1 will use quadCLTs.length -1;
 								double inf_disp = OpticalFlow.getImsDisparityCorrection(
 										scale_img,           // double           scale_img,
 										quadCLTs[ref_index], // QuadCLT          master_CLT,
@@ -7634,7 +7635,9 @@ public class OpticalFlow {
     	double scale_img = getImgImsScale( // correctInfinityFromIMS(
     			quadCLTs, // QuadCLT []       quadCLTs,
     			master_CLT, // QuadCLT          master_CLT)
-    			earliest_scene);     // int              earliest_scene)
+    			earliest_scene,     // int              earliest_scene)
+    			-1);                 // int              latest_scene) { // -1 will use quadCLTs.length -1;
+
 		double [] disparity_dsi = master_CLT.getDLS()[1]; // null
 		double [] strength = master_CLT.getDLS()[2];
 		double sw=0,swd=0; // old, new-old
@@ -7687,7 +7690,8 @@ public class OpticalFlow {
     	double scale_img = getImgImsScale( // correctInfinityFromIMS(
     			quadCLTs, // QuadCLT []       quadCLTs,
     			master_CLT, // QuadCLT          master_CLT)
-    			earliest_scene);     // int              earliest_scene)
+    			earliest_scene,     // int              earliest_scene)
+    			-1);                 // int              latest_scene) { // -1 will use quadCLTs.length -1;
 		double [] disparity_dsi = master_CLT.getDLS()[1]; // null
 		double [] strength = master_CLT.getDLS()[2];
 		double sw=0,swd=0; // old, new-old
@@ -7740,7 +7744,11 @@ public class OpticalFlow {
     public static double getImgImsScale( // correctInfinityFromIMS(
 			QuadCLT []       quadCLTs,
 			QuadCLT          master_CLT,
-			int              earliest_scene) {
+			int              earliest_scene,
+			int              latest_scene) { // -1 will use quadCLTs.length -1;
+    	if (latest_scene < 0) {
+    		latest_scene += quadCLTs.length;
+    	}
 		ErsCorrection ers_reference = master_CLT.getErsCorrection();
 		// find first and last initialized scenes, assuming approximate moving in the same direction
 		double [] xyz0 = null, xyz1 = null;
@@ -8001,7 +8009,9 @@ public class OpticalFlow {
 		    	double scale_img = getImgImsScale( // correctInfinityFromIMS(
 		    			quadCLTs,              // QuadCLT []       quadCLTs,
 		    			ref_scene,             // QuadCLT          master_CLT)
-		    			0); // earliest_scene);       // int              earliest_scene)		    			
+		    			0, // earliest_scene);       // int              earliest_scene)
+		    			-1);                 // int              latest_scene) { // -1 will use quadCLTs.length -1;
+
 		    	inf_disp_ref = disp_avg * (1.0 - scale_img);
 		    	System.out.println("inf_disp_ref="+inf_disp_ref);
 				

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

@@ -3183,9 +3183,20 @@ public class QuadCLTCPU {
     	return disparity;
     }
 
+    public static void cloneInner(double [][] data){
+    	if (data != null) {
+    		for (int i = 0; i < data.length; i++) {
+    			if (data[i] != null) {
+    				data[i] = data[i].clone();
+    			}
+    		}
+    	}
+    }
+    
     public double [][] getDLS(){ // get disparity, disparity_lma, strength, sfm_gain
     	return getDLS(this.dsi);
     }
+    
     public double [][] getDLS(double [][] dsi){ // get disparity, disparity_lma, strength, sfm_gain
     	if (dsi == null) {
     		//    		System.out.println("dsi== null, use spawnQuadCLT(), restoreFromModel(), ... to set it");
@@ -3201,12 +3212,12 @@ public class QuadCLTCPU {
     	dls[5] = dsi[isAux()? TwoQuadCLT.DSI_TERRAIN_AUX :       TwoQuadCLT.DSI_TERRAIN_MAIN];
     	return dls;
     }
-    public double [][] comboFromMain(){
+    public double [][] comboFromMain(){  // may want to run cloneInner() to separate data from its source
     	return comboFromMain(this.dsi);
     }
 
     
-    public double [][] comboFromMain(double [][] dsi){
+    public double [][] comboFromMain(double [][] dsi){ // may want to run cloneInner() to separate data from its source
     	if (dsi == null) {
     		return null;
     	}
@@ -3220,6 +3231,8 @@ public class QuadCLTCPU {
     	combo_dsi[OpticalFlow.COMBO_DSN_INDX_TERRAIN] =  dsi[isAux()? TwoQuadCLT.DSI_TERRAIN_AUX :       TwoQuadCLT.DSI_TERRAIN_MAIN];
     	return combo_dsi;
     }
+    
+    
 
     // Duplicate disparity to FG/BG to make OpticalFLow happy
     /*
@@ -3227,11 +3240,11 @@ public class QuadCLTCPU {
 	        	double [] bg_lma = combo_dsn_final[COMBO_DSN_INDX_DISP_BG_ALL].clone();
 	        	double [] bg_str = combo_dsn_final[COMBO_DSN_INDX_STRENGTH].clone();
      */
-    public double [][] comboFromMainFgBg(){
+    public double [][] comboFromMainFgBg(){  // may want to run cloneInner() to separate data from its source
     	return comboFromMainFgBg(this.dsi);
     }
 
-    public double [][] comboFromMainFgBg(double [][] dsi){
+    public double [][] comboFromMainFgBg(double [][] dsi){  // may want to run cloneInner() to separate data from its source
     	double [][] combo_dsi = comboFromMain(dsi);
     	combo_dsi[OpticalFlow.COMBO_DSN_INDX_DISP_BG] =      combo_dsi[OpticalFlow.COMBO_DSN_INDX_DISP];
     	combo_dsi[OpticalFlow.COMBO_DSN_INDX_STRENGTH_BG] =  combo_dsi[OpticalFlow.COMBO_DSN_INDX_STRENGTH];