Before trying to fix GEO output

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

@@ -1609,6 +1609,7 @@ public class EyesisCorrectionParameters {
     			e.printStackTrace();
     			return null;
     		}
+    		System.out.println("First line: "+lines.get(0)+"\n");
     		Path base_path = seq_path.getParent();
     		// first - scan all file and set sourceDirectory, x3dDirectory, linkedModels,videoDirectory,resultsDirectory
     		HashMap<String,String> dir_map = new HashMap<String,String>();

src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java

@@ -177,7 +177,7 @@ public class ComboMatch {
 		
 		
 		boolean use_saved_collection = true; // false;
-		boolean save_collection =     false; // true;
+		boolean save_collection =      true;
 		boolean process_correlation = true; // use false to save new version of data
 		int     num_tries_fit =       10;
 		boolean update_match =        true; // use false to save new version of data

src/main/java/com/elphel/imagej/orthomosaic/FloatImageData.java

@@ -26,6 +26,23 @@ public class FloatImageData {
 		this.data = data;
 	}
 
+	public double [] getDData() {
+		final double [] ddata = new double [data.length];
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+        for (int ithread = 0; ithread < threads.length; ithread++) {
+            threads[ithread] = new Thread() {
+                public void run() {
+                    for (int ipix = ai.getAndIncrement(); ipix < data.length; ipix = ai.getAndIncrement()) {
+                    	ddata[ipix] = data[ipix];
+                    }
+                }
+            };
+        }		      
+        ImageDtt.startAndJoin(threads);
+		return ddata;
+	}
+	
 	public static int getZoomLevel(
 			double pix_in_meters) {
 		return getZoomLevel (pix_in_meters, null, null);

src/main/java/com/elphel/imagej/orthomosaic/OrientationSceneLMA.java

@@ -52,6 +52,15 @@ public class OrientationSceneLMA {
 	public int                debug_width =     12;
 	public int                debug_decimals =  9;
 
+	public double [][] getOrientationQuaternions(){
+		double [][] qorient = new double [num_scenes][4];
+		for (int nscene = 0; nscene < num_scenes; nscene++) {
+			for (int i = 0; i < 4; i++) {
+				qorient[nscene][i] = parameters_vector[4*nscene + i];
+			}
+		}
+		return qorient;
+	}
 	
 	public int prepareLMA(
 			int    []     indices, // should all be used
@@ -81,7 +90,7 @@ public class OrientationSceneLMA {
 		double [] pull4 =    {pull_scales,  pull_tilts/2,  pull_tilts/2,  pull_rots};
 		
 		double sum_pull4 = 0;
-		for (double w: weights4) sum_pull4+= w;
+		for (double w: pull4) sum_pull4+= w;
 		if (sum_pull4 <= 0) {
 			pull = 0;
 		}

src/main/java/com/elphel/imagej/orthomosaic/OrthoAltitudeMatch.java

@@ -76,7 +76,7 @@ public class OrthoAltitudeMatch {
 		boolean invert_y =    true; // only for tilts->affines
         boolean show_details =false;
         
-        boolean do_not_save = true;
+        boolean do_not_save = false;
 
 //        OrientationSceneLMA.testGetPairErrQuaternion ();
 //        OrientationSceneLMA.testGetPairPairScaleDirError();
@@ -890,7 +890,7 @@ public class OrthoAltitudeMatch {
 		}
 //		double tilt_err_threshold = 0.01; // reduce weight if larger
 //overlop_pow = 2.0		
-
+        /*
 		for (int npair = 0; npair <quat_pairs.length; npair++ ) {
 			System.out.println("quat_pairs["+npair+"]="+QuatUtils.toString(quat_pairs[npair],use_degrees));
 		}
@@ -923,7 +923,7 @@ public class OrthoAltitudeMatch {
 		    SingularValueDecomposition svd =  SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine_pairs[npair], y_down_ccw); // boolean y_down_ccw)
 		    System.out.println("svd_affine["+npair+"]=" + svd.toString(use_degrees));
 		}
-		
+		*/
 		
 		double max_flat_err = 0; // tilt_err_threshold
 		for (int npair = 0; npair < num_pairs; npair++) {
@@ -964,17 +964,23 @@ public class OrthoAltitudeMatch {
 				last_run,         // boolean last_run,
 				null, // String dbg_prefix,
 				debugLevel);      // int    debug_level)
-		System.out.println("LMA -> "+lma_rslt);
 		if (lma_rslt >= 0) {
-			if (debugLevel > -3) {
-				//ersTiltLMA.printSceneResults(use_degrees, use_percents);
-				//ersTiltLMA.printPairsResults(use_degrees, use_percents);				
+			System.out.println("LMA -> "+lma_rslt);
+			double [][] qorients = orientationSceneLMA.getOrientationQuaternions();
+			for (int nscene = 0; nscene < indices.length; nscene++) {
+				ortho_maps[indices[nscene]].setQOrient(qorients[nscene]);
+				
+			}
+			for (int npair = 0; npair < quat_pairs.length; npair++) {
+				int [] cpair = condensed_pairs[npair]; // index alt_multi
+				int [] ipair = {indices[cpair[0]], indices[cpair[1]]};
+				PairwiseOrthoMatch pairwiseOrthoMatch = ortho_maps[ipair[0]].getMatch(ortho_maps[ipair[1]].getName(), true); // ?
+				pairwiseOrthoMatch.setQuaternion(quat_pairs[npair]);
 			}
 		}
-		System.out.println();
-		
 		
 		
+		/*
 		
 		ERSTiltLMA ersTiltLMA = new  ERSTiltLMA();
 		ersTiltLMA.prepareLMA(
@@ -986,15 +992,6 @@ public class OrthoAltitudeMatch {
 				scene_tilts_pairs, // double [][][] tilts,      // [pair][scene(2)][tilt(2)]
 				affine_pairs,      // double [][][] affine_pairs,
 				debugLevel);       // int           debug_level)
-		/*
-		double  lambda =            0.1;
-		double  lambda_scale_good = 0.5;
-		double  lambda_scale_bad =  8.0;
-		double  lambda_max =      1000;
-		boolean last_run =       false;
-		double  rms_diff =          0.0001;
-		int     num_iter = 100;
-		*/
 		lma_rslt=ersTiltLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)
 				lambda, // double lambda,           // 0.1
 				lambda_scale_good,// double lambda_scale_good,// 0.5
@@ -1027,6 +1024,8 @@ public class OrthoAltitudeMatch {
 
 		}
 		
+		*/
+		
 		//printResults(boolean degrees)
 		if (orthoMapsCollection_path != null) {
         	try {

src/main/java/com/elphel/imagej/orthomosaic/OrthoEqualizeLMA.java

@@ -135,7 +135,7 @@ public class OrthoEqualizeLMA {
 
 
 		int [] indices = maps_collection.getScenesSelection(
-				null, // boolean select_all,
+				clt_parameters, // CLTParameters       clt_parameters,				
 				" to build a map"); // String purpose)
 		OrthoEqualizeLMA oel = new OrthoEqualizeLMA();
 		oel.prepareLMA (

src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java

@@ -160,6 +160,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		oos.writeObject(num_scenes);
 		oos.writeObject(sfm_gain);
 		oos.writeObject(equalize);
+		oos.writeObject(qorient);
 	}
 	
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
@@ -185,6 +186,11 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		sfm_gain = (double) ois.readObject();
 //		equalize = new double[] {1,0};
 		equalize = (double []) ois.readObject();
+		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
+			qorient = (double[]) ois.readObject();
+		}
+		
+		
 		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
 		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
 		

src/main/java/com/elphel/imagej/orthomosaic/PairwiseOrthoMatch.java

@@ -308,6 +308,8 @@ public class PairwiseOrthoMatch implements Serializable {
 		oos.writeObject(overlap);
 		oos.writeObject(equalize1to0);
 		oos.writeObject(alt_data);
+		oos.writeObject(quat);
+		oos.writeObject(qaffine);
 		
 	}
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
@@ -327,6 +329,11 @@ public class PairwiseOrthoMatch implements Serializable {
 		if (!READ_NO_ALT) {
 			alt_data = (double[]) ois.readObject();
 		}
+		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
+			quat= (double[]) ois.readObject();
+			qaffine = (double[][]) ois.readObject();
+		}		
+		
 	}
 	//private void readObjectNoData() throws ObjectStreamException; // used to modify default values
 }

src/main/java/com/elphel/imagej/orthomosaic/QuatUtils.java

@@ -1840,5 +1840,43 @@ q11 - q22 = c3
 		return;
 	}
 	
+	public static void applyTo(
+			final double [] q,
+			final double [] in,
+			final double [] out) {
+		final double q0= q[0];
+		final double q1= q[1];
+		final double q2= q[2];
+		final double q3= q[3];
+
+		final double x = in[0];
+		final double y = in[1];
+		final double z = in[2];
+
+		final double s = q1 * x + q2 * y + q3 * z;
+		out[0] = 2 * (q0 * (x * q0 - (q2 * z - q3 * y)) + s * q1) - x;
+		out[1] = 2 * (q0 * (y * q0 - (q3 * x - q1 * z)) + s * q2) - y;
+		out[2] = 2 * (q0 * (z * q0 - (q1 * y - q2 * x)) + s * q3) - z;
+	}
+
+	public static void applyTo(
+			final double    k, // scale
+			final double [] q,
+			final double [] in,
+			final double [] out) {
+		final double q0= q[0];
+		final double q1= q[1];
+		final double q2= q[2];
+		final double q3= q[3];
+
+		final double x = in[0];
+		final double y = in[1];
+		final double z = in[2];
+
+		final double s = q1 * x + q2 * y + q3 * z;
+		out[0] = k * (2 * (q0 * (x * q0 - (q2 * z - q3 * y)) + s * q1) - x);
+		out[1] = k * (2 * (q0 * (y * q0 - (q3 * x - q1 * z)) + s * q2) - y);
+		out[2] = k * (2 * (q0 * (z * q0 - (q1 * y - q2 * x)) + s * q3) - z);
+	}
 	
 }

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

@@ -35,6 +35,7 @@ public class IntersceneMatchParameters {
 	public static String [] MODES3D = {"RAW", "INF", "FG", "BG"}; // RAW:-1
 	public static String [] MODES_AVI = {"RAW", "JPEG", "PNG"};
 	public static String [] FLT_ALT_MODES = {"--- (no ALT filter)", "ALT only", "no ALT only"};
+	public static String [] FLT_ORIENT_MODES = {"--- (no ORIENT filter)", "ORIENT only", "no ORIENT only"};
 	
 	// Maybe add parameters to make sure there is enough data? Enough in each zone? Enough spread?
 	public  boolean ims_use =            true;   // use IMS data
@@ -223,6 +224,7 @@ public class IntersceneMatchParameters {
     public double   flt_min_sfm =         0.0;  // minimal minimal SfM gain of a pair
     public double   flt_max_sfm =      1000.0; // maximal minimal SfM gain of a pair
 	public	int     flt_alt =             0; // 0 - do not filter, 1 - keep only with alt data, 2 - keep only without alt data
+	public	int     flt_orient =          0; // 0 - do not filter, 1 - keep only with orientation data, 2 - keep only without orientation data
     
     public boolean  flt_show_names =      true;
     public boolean  flt_show_overlaps =   true;
@@ -987,6 +989,7 @@ min_str_neib_fpn	0.35
 		gd.addNumericField("Minimal SfM gain",            this.flt_min_sfm,  3,7,"","Minimal SfM gain of the minimum in the scene pair.");
 		gd.addNumericField("Maximal SfM gain",            this.flt_max_sfm,  3,7,"","Maximal SfM gain of the minimum in the scene pair.");
 		gd. addChoice("Filter by pairwise ALT availability",FLT_ALT_MODES, FLT_ALT_MODES[this.flt_alt],"Filter by pairwise ALT availability.");
+		gd. addChoice("Filter by orientation availability",FLT_ORIENT_MODES, FLT_ORIENT_MODES[this.flt_orient],"Filter by the scene orientation availability.");
 		
 		gd.addCheckbox    ("Show scene names",            this.flt_show_names, "Show scene full names (timestamps) in selection drop-down list.");
 		gd.addCheckbox    ("Show scene overlaps",         this.flt_show_overlaps, "Show scene overlaps (in percents) in selection drop-down list.");
@@ -1997,6 +2000,7 @@ min_str_neib_fpn	0.35
         this.flt_max_sfm       =              gd.getNextNumber();
         
         this.flt_alt           =              gd.getNextChoiceIndex();
+        this.flt_orient        =              gd.getNextChoiceIndex();
         this.flt_show_names    =              gd.getNextBoolean();
         this.flt_show_overlaps =              gd.getNextBoolean();
         this.flt_show_rms      =              gd.getNextBoolean();        
@@ -2598,6 +2602,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"flt_min_sfm",                   this.flt_min_sfm + "");                 // double
 		properties.setProperty(prefix+"flt_max_sfm",                   this.flt_max_sfm + "");                 // double
 		properties.setProperty(prefix+"flt_alt",                       this.flt_alt + "");                     // int
+		properties.setProperty(prefix+"flt_orient",                    this.flt_orient + "");                  // int
 		properties.setProperty(prefix+"flt_show_names",                this.flt_show_names + "");              // boolean
 		properties.setProperty(prefix+"flt_show_overlaps",             this.flt_show_overlaps + "");           // boolean
 		properties.setProperty(prefix+"flt_show_rms",                  this.flt_show_rms + "");                // boolean
@@ -3165,6 +3170,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"flt_min_sfm")!=      null)   this.flt_min_sfm=      Double.parseDouble(properties.getProperty(prefix+  "flt_min_sfm"));
 		if (properties.getProperty(prefix+"flt_max_sfm")!=      null)   this.flt_max_sfm=      Double.parseDouble(properties.getProperty(prefix+  "flt_max_sfm"));
 		if (properties.getProperty(prefix+"flt_alt")!=          null)   this.flt_alt=          Integer.parseInt(properties.getProperty(prefix+    "flt_alt"));
+		if (properties.getProperty(prefix+"flt_orient")!=       null)   this.flt_orient=       Integer.parseInt(properties.getProperty(prefix+    "flt_orient"));
 		if (properties.getProperty(prefix+"flt_show_names")!=   null)   this.flt_show_names=   Boolean.parseBoolean(properties.getProperty(prefix+"flt_show_names"));		
 		if (properties.getProperty(prefix+"flt_show_overlaps")!=null)   this.flt_show_overlaps=Boolean.parseBoolean(properties.getProperty(prefix+"flt_show_overlaps"));		
 		if (properties.getProperty(prefix+"flt_show_rms")!=     null)   this.flt_show_rms=     Boolean.parseBoolean(properties.getProperty(prefix+"flt_show_rms"));		
@@ -3753,9 +3759,8 @@ min_str_neib_fpn	0.35
         imp.flt_min_sfm                   = this.flt_min_sfm;
         imp.flt_max_sfm                   = this.flt_max_sfm;
         
-        
-        
         imp.flt_alt                       = this.flt_alt;
+        imp.flt_orient                    = this.flt_orient;
         imp.flt_show_names                = this.flt_show_names;
         imp.flt_show_overlaps             = this.flt_show_overlaps;
         imp.flt_show_rms                  = this.flt_show_rms;

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

@@ -8556,6 +8556,7 @@ if (debugLevel > -100) return true; // temporarily !
 		EyesisCorrectionParameters.CorrectionParameters.PathFirstLast[] pathFirstLast = null;
 		int num_seq = 1;
 		if (quadCLT_main.correctionsParameters.useSourceList) {
+	    	System.out.println("\nReading source list from file: "+quadCLT_main.correctionsParameters.sourceSequencesList);
 			pathFirstLast = quadCLT_main.correctionsParameters.getSourceSets(
 					quadCLT_main.correctionsParameters.sourceSequencesList);
 			if (pathFirstLast != null) {