done refactoring, starting debugging

src/main/java/com/elphel/imagej/orthomosaic/Affine2Import.java

+package com.elphel.imagej.orthomosaic;
+
+public class Affine2Import {
+	public static final String AFFINE2_TAG = "AFFINE2";	
+	public static final int    AFFINE2_LEN = 10;
+	public String name1;
+	public String name2;
+	public double overlap;
+	public double [][] affine;
+	public static boolean matches(String [] tokens) {
+		return ((tokens.length == AFFINE2_LEN) && AFFINE2_TAG.equals(tokens[0]));
+	}
+	public Affine2Import(
+			String [] tokens) {
+		if (!matches(tokens)) {
+			throw new IllegalArgumentException ("Not Affine2Import tokens");
+		}
+		int indx = 1;
+		name1 = tokens[indx++];
+		name2 = tokens[indx++];
+		overlap = Double.parseDouble(tokens[indx++]);
+		affine = new double [2][3];
+		for (int i = 0; i < affine.length; i++) {
+			for (int j = 0; j < affine[i].length; j++) {
+				affine[i][j] = Double.parseDouble(tokens[indx++]);
+			}
+		}
+	}
+}

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

+package com.elphel.imagej.orthomosaic;
+
+public class AffineImport {
+	public static final String AFFINE_TAG = "AFFINE";
+	public static final int    AFFINE_LEN = 8;
+	public String name;
+	public double [][] affine;
+	public static boolean matches(String [] tokens) {
+		return ((tokens.length == AFFINE_LEN) && AFFINE_TAG.equals(tokens[0]));
+	}
+	public AffineImport(
+			String [] tokens) {
+		if (!matches(tokens)) {
+			throw new IllegalArgumentException ("Not AffineImport tokens");
+		}
+		int indx = 1;
+		name = tokens[indx++];
+		affine = new double [2][3];
+		for (int i = 0; i < affine.length; i++) {
+			for (int j = 0; j < affine[i].length; j++) {
+				affine[i][j] = Double.parseDouble(tokens[indx++]);
+			}
+		}
+	}
+	
+// String[] tokens	
+}

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

@@ -238,6 +238,10 @@ public class FloatImageData implements Serializable  {
 		return extra_zoom[0];
 	}
 	
+	public double needZoomIn() {
+		return needZoomIn(pix_meters);
+	}
+	
 	public int getZoomLevel() {
 		return zoom_lev;
 	}

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

@@ -106,54 +106,57 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	
 	
 	public static final String ALT_SUFFIX = "-ALT";
-	public transient String                     name;  // timestamp
-	public transient double                     ts;
-	public transient String                     path;        // full path to the model directory (including /vXX?)
-	public double []                            lla;      // lat/long/alt
-	public LocalDateTime                        dt;
+	public           String                       path;        // full path to the model directory (including /vXX?)
+//	public  double []                  lla;      // lat/long/alt
+//	public LocalDateTime                        dt;
 	// affine convert (input) rectified coordinates (meters) relative to vert_meters to source image
 	// coordinates relative to vert_meters
-	public double [][]                          affine = new double[][] {{1,0,0},{0,1,0}}; // relative to vert_meters[], positive Y is down (as in images)
-	public transient double [][]                ers_affine = new double[][] {{1,0},{0,1}}; // orientation only for remaining ERS, positive Y is down (as in images)
-	public transient FloatImageData             orig_image;
-	public transient FloatImageData             alt_image;
-	public int                                  orig_zoom_level;
-	public boolean                              orig_zoom_valid;
-	public double                               need_extra_zoom;
-	public double                               averageRawPixel = Double.NaN; // measure of scene temperature
+	public           double [][]                  affine = new double[][] {{1,0,0},{0,1,0}}; // relative to vert_meters[], positive Y is down (as in images)
+	public           double [][]                  ers_affine = new double[][] {{1,0},{0,1}}; // orientation only for remaining ERS, positive Y is down (as in images)
+	public           FloatImageData               orig_image;
+	public           FloatImageData               alt_image;
+//	public int                                  orig_zoom_level;
+//	public boolean                              orig_zoom_valid;
+//	public double                               need_extra_zoom;
+	public           double                       averageRawPixel = Double.NaN; // measure of scene temperature
+	HashMap          <String, PairwiseOrthoMatch> pairwise_matches;
+	public           SensorTemperatureData[]      temp_data;
+	public           double                       agl = Double.NaN;
+	public           int                          num_scenes = -1;;   // number of scenes that made up this image
+	public           double                       sfm_gain = Double.NaN;     // maximal SfM gain of this map
+	public           double []                    equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]
+	public           double []                    qorient = null; // quternion representing orientation+scale of the scene
+// really transient	
 	transient HashMap <Integer, FloatImageData> images;
-	HashMap <String, PairwiseOrthoMatch>        pairwise_matches;
-	public transient SensorTemperatureData[]    temp_data;
-	public transient double                     agl = Double.NaN;
-	public transient int                        num_scenes = -1;;   // number of scenes that made up this image
-	public transient double                     sfm_gain = Double.NaN;     // maximal SfM gain of this map
-	public transient double []                  equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]
-	public transient double []                  qorient = null; // quternion representing orientation+scale of the scene
+	public transient String                     name;  // timestamp
+	public transient double                       ts;
+
+	
 
 	private void writeObject(ObjectOutputStream oos) throws IOException {
 		oos.defaultWriteObject();
-		oos.writeObject(path);
-		oos.writeObject(temp_data); // temporary, while transient
-		oos.writeObject(agl);
-		oos.writeObject(num_scenes);
-		oos.writeObject(sfm_gain);
-		oos.writeObject(equalize);
-		oos.writeObject(qorient);
+//		oos.writeObject(path);
+//		oos.writeObject(temp_data); // temporary, while transient
+//		oos.writeObject(agl);
+//		oos.writeObject(num_scenes);
+//		oos.writeObject(sfm_gain);
+//		oos.writeObject(equalize);
+//		oos.writeObject(qorient);
 	}
 	
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
 		ois.defaultReadObject();
-		path = (String) ois.readObject();
+//		path = (String) ois.readObject();
 		name = getNameFromPath(path);
 		ts= Double.parseDouble(name.replace("_", "."));
-		temp_data = (SensorTemperatureData[]) ois.readObject();
-		agl = (double)  ois.readObject();
-		num_scenes = (int) ois.readObject();
-		sfm_gain = (double) ois.readObject();
-		equalize = (double []) ois.readObject();
-		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
-			qorient = (double[]) ois.readObject();
-		}
+//		temp_data = (SensorTemperatureData[]) ois.readObject();
+//		agl = (double)  ois.readObject();
+//		num_scenes = (int) ois.readObject();
+//		sfm_gain = (double) ois.readObject();
+//		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)
 		
@@ -229,7 +232,16 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		if (with_undefined || match.isDefined()) return match;
 		return null;
 	}
-
+	public static boolean isAffineNonTrivial(double [][] affine) {
+		if (affine == null) {
+			return false;
+		}
+		return ( affine[0][0] != 1.0) || (affine[0][1] != 0.0)  || (affine[0][2] != 0.0) ||
+				(affine[1][0] != 0.0) || (affine[1][1] != 1.0)  || (affine[1][2] != 0.0);
+	}
+	public boolean isAffineNonTrivial() {
+		return isAffineNonTrivial(this.affine);
+	}
 	
 	
 	public PairwiseOrthoMatch getMatch(String name) {
@@ -252,7 +264,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	}
 	
 	public int getOriginalZoomLevel() {
-		return orig_zoom_level;
+		return getImage().getZoomLevel(); // image, not altitude!
+//		return orig_zoom_level;
 	}
 // Generate ALT image path from the GEO
 	public static String getAltPath(String path) {
@@ -285,7 +298,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 */
 	public int getNumberScenes() {
 		if (num_scenes < 0) {
-			String merged_path = getLatestFilePath(MERGED_SUFFIX);
+			String merged_path = getLatestFilePath(MERGED_SUFFIX); 
 			if (merged_path != null) {
 				ImagePlus imp_merged = new ImagePlus(merged_path);
 				if (imp_merged.getWidth() > 0) {
@@ -494,7 +507,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		
 		// initialize and read Exif for the images
 		orig_image = new FloatImageData(path);
-		dt = orig_image.getDT();
+//		dt = orig_image.getDT();
 		/*
 		
 		Properties imp_prop = null;
@@ -551,7 +564,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 				return false;
 			}
 			orig_image = new FloatImageData(path);
-			dt = orig_image.getDT();
+//			dt = orig_image.getDT();
 		}
 		if (alt_image != null) {
 			String alt_path = getAltPath(path);
@@ -577,7 +590,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 				return null;
 			}
 			orig_image = new FloatImageData(path);
-			dt = orig_image.getDT();
+//			dt = orig_image.getDT();
 		}
 		return orig_image;
 	}
@@ -654,7 +667,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return ts;
 	}
 	public LocalDateTime getLocalDateTime() {
-		return dt;
+		return getImage().getDT();
+//		return dt;
 	}
 	
 	public String getName() {
@@ -974,11 +988,11 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			return false;
 		}
 		if (!orig_image.isZoomValid()) {
-			System.out.println("Original zoom level is invalid, need_extra_zoom = "+need_extra_zoom);
+			System.out.println("Original zoom level is invalid, need_extra_zoom = "+orig_image.needZoomIn());
 			return false;
 		}
 		if (zoom_level > orig_image.getZoomLevel()) {
-			System.out.println("Requested zoom level is too high ("+zoom_level+" > "+orig_zoom_level+")");
+			System.out.println("Requested zoom level is too high ("+zoom_level+" > "+orig_image.getZoomLevel()+")");
 			return false;
 		}
 		if (images.get(zoom_level) != null) {
@@ -1085,7 +1099,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		final float [] felev = src_elev.readFData(); 
 		final double [] elev = new double [tilesX*tilesY];
 		Arrays.fill(elev, Double.NaN);
-		final int diff_zoom_lev = zoom_level-orig_zoom_level;
+		final int diff_zoom_lev = zoom_level-getAlt().getZoomLevel(); // orig_zoom_level;
 		final double scale = 1.0/getScale (diff_zoom_lev); //	int zoom_lev);
 		
 		final Thread[] threads = ImageDtt.newThreadArray();

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

@@ -32,20 +32,61 @@ import Jama.Matrix;
 
 public class PairwiseOrthoMatch implements Serializable {
 	private static final long serialVersionUID = 1L;
-	public static boolean  READ_NO_ALT = false; // to read old format w/o alt data ( not final!)
-	private double [][]           affine = new double[2][3];
+//	public static boolean  READ_NO_ALT = false; // to read old format w/o alt data ( not final!)
+	private          double [][] affine = new double[2][3];
+	public           int         zoom_lev;
+	public           double      rms = Double.NaN;
+	public           double      overlap = 0.0;
+	public           double []   alt_data = null;
+	public           double []   equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
+	public           double []   quat = null; // relative orientation of the second scene (ERS affine removed). Will be eventually saved 
+	public           double [][] qaffine = null; // affine relative to rotated scenes 
+	// real transient
 	public transient double [][] jtj =    new double [6][6];
-	public int                   zoom_lev;
-	public double                rms = Double.NaN;
-	public transient double      overlap = 0.0;
-	public transient double []   alt_data = null;
-	public transient double []   equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
-	public transient double []   quat = null; // relative orientation of the second scene (ERS affine removed). Will be eventually saved 
-	public transient double [][] qaffine = null; // affine relative to rotated scenes 
 	// below - not saved/restored
 	public transient boolean     ok = false; // not saved/restored
 	public transient int []      nxy = null; // not saved, just to communicate for logging
-
+	
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+		for (int i = 0; i < jtj.length; i++) {
+			for (int j = i; j < jtj[i].length; j++) {
+				oos.writeObject(jtj[i][j]);
+			}
+		}
+//		oos.writeObject(overlap);
+//		oos.writeObject(equalize1to0);
+//		oos.writeObject(alt_data);
+//		oos.writeObject(quat);
+//		oos.writeObject(qaffine);
+		
+	}
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+		jtj = new double [6][6]; // readObject does not use constructor!
+		for (int i = 0; i < jtj.length; i++) {
+			for (int j = i; j < jtj[i].length; j++) {
+				jtj[i][j] = (Double) ois.readObject();
+				if (j > i) {
+					jtj[j][i] = jtj[i][j];
+				}
+			}
+		}
+//		overlap = (Double) ois.readObject();
+//		equalize1to0 = new double[] {1,0};
+//		equalize1to0 = (double[]) ois.readObject();
+//		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();
+//		}		
+		
+	}
+	
+	
+	
 	public double [] getQuaternion() {
 		return quat;
 	}
@@ -95,6 +136,11 @@ public class PairwiseOrthoMatch implements Serializable {
 	public boolean isDefined() {
 		return affine != null;
 	}
+	
+	public boolean isAffineNonTrivial() {
+		return OrthoMap.isAffineNonTrivial(this.affine);
+	}
+
 	public double [] getEqualize2to1() {
 		return equalize1to0;
 	}
@@ -298,42 +344,5 @@ public class PairwiseOrthoMatch implements Serializable {
 		this.affine= affine;
 	}
 	
-	private void writeObject(ObjectOutputStream oos) throws IOException {
-		oos.defaultWriteObject();
-		for (int i = 0; i < jtj.length; i++) {
-			for (int j = i; j < jtj[i].length; j++) {
-				oos.writeObject(jtj[i][j]);
-			}
-		}
-		oos.writeObject(overlap);
-		oos.writeObject(equalize1to0);
-		oos.writeObject(alt_data);
-		oos.writeObject(quat);
-		oos.writeObject(qaffine);
-		
-	}
-	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
-		ois.defaultReadObject();
-		jtj = new double [6][6]; // readObject does not use constructor!
-		for (int i = 0; i < jtj.length; i++) {
-			for (int j = i; j < jtj[i].length; j++) {
-				jtj[i][j] = (Double) ois.readObject();
-				if (j > i) {
-					jtj[j][i] = jtj[i][j];
-				}
-			}
-		}
-		overlap = (Double) ois.readObject();
-//		equalize1to0 = new double[] {1,0};
-		equalize1to0 = (double[]) ois.readObject();
-		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
 }