Optimizing pairs generation

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

@@ -216,9 +216,33 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		pairwise_matches.remove(name);
 	}
 
+	public PairwiseOrthoMatch getMatch(
+			String name,
+			boolean with_undefined) {
+		PairwiseOrthoMatch match = pairwise_matches.get(name);
+		if (match == null) return null;
+		if (with_undefined || match.isDefined()) return match;
+		return null;
+	}
+
+	
 	
 	public PairwiseOrthoMatch getMatch(String name) {
-		return pairwise_matches.get(name);
+		return getMatch(name, false); // old - do not count undefined
+//		return pairwise_matches.get(name);
+	}
+	
+	public void unsetMatches(boolean undefined_only) {
+		if (undefined_only) {
+			String [] matches = pairwise_matches.keySet().toArray(new String[0]);
+			for (String match:matches) {
+				if (!getMatch(match).isDefined()) {
+					unsetMatch(match);
+				}
+			}
+		} else {
+			pairwise_matches = new HashMap<String, PairwiseOrthoMatch>();
+		}
 	}
 	
 	public int getOriginalZoomLevel() {
@@ -480,7 +504,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
 	}
 	
-	
+	public double getTimeStamp() {
+		return ts;
+	}
 	public LocalDateTime getLocalDateTime() {
 		return dt;
 	}
@@ -5244,6 +5270,71 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return pattern;
 	}
 	
+	/**
+	 * Decomposing linear transform into rotation
+	 * R1={{cos(beta),sin(beta)},{-sin(beta), cos(beta)}} ,
+	 * non-uniform scale transform W={{w1,0}{0,w2}}, and rotation
+	 * R2={{cos(gamma),sin(gamma)},{-sin(gamma), cos(gamma)}}
+	 * A=R1*W*R2 using singular value decomposition
+	 * https://math.stackexchange.com/questions/861674/decompose-a-2d-arbitrary-transform-into-only-scaling-and-rotation   
+	 * @param A - input 2x2 matrix
+	 * @return {s,beta,w,gamma,beta+gamma}
+	 * A = B + C
+	 * b00= b11; c00=-c01
+	 * b10=-b01; c10= c01
+	 */
+	public static double [] singularValueDecompose(
+			double [][] A) {
+		double a00=A[0][0],a01=A[0][1],a10=A[1][0],a11=A[1][1];
+		double b00=(a00+a11)/2; // , b11 = b00;
+		double c00=(a00-a11)/2; //, c11 =-c00;
+		double b01=(a01-a10)/2; //, b10 =-b01;
+		double c01=(a01+a10)/2; //, c10 = c01;
+		double w1_p_w2_2= Math.sqrt(b00*b00+b01*b01);
+		double w1_m_w2_2= Math.sqrt(c00*c00+c01*c01);
+		double w1 = w1_p_w2_2 + w1_m_w2_2;
+		double w2 = w1_p_w2_2 - w1_m_w2_2;
+		double g_p_b = Math.atan2(b01, b00);
+		double g_m_b = Math.atan2(c01, c00);
+		double gamma = (g_p_b + g_m_b)/2; 
+		double beta =  (g_p_b - g_m_b)/2; 
+		return new double [] {beta,w1,w2,gamma,g_p_b};
+	}
+	/**
+	 * Use singular value decomposition and then split scaling {{w1,0},{0,w1}}
+	 * into overall scaling caused by zoom != 1.0 because of altitude error
+	 * and unidirectional scaling caused by tilted projection plane. As the
+	 * input linear transformation matrix converts ground coordinates to source
+	 * image coordinates, the scale in the tilt direction is > than scale in the
+	 * perpendicular direction (tilt axis).
+	 * Matrix R1 is additionally rotated by PI/2 if needed so W={{w1,0},{0,w2}}
+	 * has w2>=w1 and W={{s,0},{0,s/t}}, where t <= 1.0 and equals to cos(tilt) 
+	 * 
+	 * @param A - linear transformation matrix from rectified ground coordinates
+	 *        to source image coordinates. OK to use 2x3 affine matrix,extra
+	 *        components will be ignored. 
+	 * @return {beta, s, t, beta+gamma}, beta+gamma - total rotation
+	 */
+	public static double [] singularValueDecomposeScaleTilt(
+			double [][] A) {
+		double [] svd=singularValueDecompose(A);
+		double w1 = svd[1], w2 = svd[2], beta=svd[0], g_p_b=svd[4];
+		
+		// considering tilt in y direction, it should have higher scale
+		// (and source image coordinates), while X should correspond to
+		// the axis of rotation, and scale is just scale caused by error in
+		// altitude.
+		double s = Math.min(w1, w2);
+		double t = w1/w2; // <=1.0, ==cos(tilt)
+		if (w1 > w2) { // rotate tilt by PI/2
+			t = w2/w1;
+			beta += Math.PI/2;
+			if (beta > Math.PI) {
+				beta -= 2* Math.PI;
+			}
+		}
+		return new double [] {beta, s,t, g_p_b};
+	}
 	
 	
 	

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

@@ -311,7 +311,7 @@ public class OrthoMultiLMA {
 				clt_parameters,   // CLTParameters       clt_parameters,
 				maps_collection,  // OrthoMapsCollection maps_collection,
 				indices,          // int []              indices,
-				ignore_affines,  // boolean             ignore_affines,
+				ignore_affines,   // boolean             ignore_affines,
 				val_coord,        // double []           val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
 				position_pull,    // double              position_pull,
 				skew_pull,        // double              skew_pull,

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

@@ -9,7 +9,7 @@ import Jama.Matrix;
 
 public class PairwiseOrthoMatch implements Serializable {
 	private static final long serialVersionUID = 1L;
-	public double [][]           affine = new double[2][3];
+	private double [][]           affine = new double[2][3];
 	public transient double [][] jtj =    new double [6][6];
 	public int                   zoom_lev;
 	public double                rms = Double.NaN;
@@ -17,12 +17,14 @@ public class PairwiseOrthoMatch implements Serializable {
 	public transient double      overlap = 0.0;
 	public transient double []   equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
 
-	public PairwiseOrthoMatch() {
-		
-	}
+//	public PairwiseOrthoMatch() {}
 	public double getOverlap() {
 		return overlap;
 	}
+	public void setOverlap(double overlap) {
+		this.overlap =overlap;
+	}
+	
 	public PairwiseOrthoMatch(
 			double [][] affine,
 			double [][] jtj,
@@ -36,6 +38,9 @@ public class PairwiseOrthoMatch implements Serializable {
 		this.overlap = overlap;
 	}
 	
+	public boolean isDefined() {
+		return affine != null;
+	}
 	public double [] getEqualize2to1() {
 		return equalize1to0;
 	}
@@ -52,7 +57,7 @@ public class PairwiseOrthoMatch implements Serializable {
 	}
 	
 	public PairwiseOrthoMatch clone() {
-		double [][] affine = {this.affine[0].clone(),this.affine[1].clone()};
+		double [][] affine = (this.affine==null) ? null: (new double [][] {this.affine[0].clone(),this.affine[1].clone()});
 		double [][] jtj = new double [this.jtj.length][];
 		for (int i = 0; i < this.jtj.length; i++) {
 			jtj[i] = this.jtj[i].clone();
@@ -221,9 +226,16 @@ public class PairwiseOrthoMatch implements Serializable {
 	}	
 	
 	public double [][] getAffine(){
+		if (affine == null) {
+			return new double [][] {{1,0,0},{0,1,0}};
+		}
 		return affine;
 	}
 	
+	public void setAffine(double [][] affine) {
+		this.affine= affine;
+	}
+	
 	private void writeObject(ObjectOutputStream oos) throws IOException {
 		oos.defaultWriteObject();
 		for (int i = 0; i < jtj.length; i++) {

src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java

@@ -609,6 +609,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	}
 
 	public static Properties getTiffMeta(String path)  throws IOException {
+//		System.out.println("getTiffMeta(): "+path);
 		Properties properties = new Properties();
 		File file = new File(path);
 		String extension = getFileExtension(file);
@@ -620,7 +621,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 			ImageReader reader = readers.next();
 			stream = ImageIO.createImageInputStream(file);
 			reader.setInput(stream, true);
-			IIOMetadata metadata = reader.getImageMetadata(0);
+			IIOMetadata metadata = reader.getImageMetadata(0); //java.lang.IllegalStateException: Input not set!
 			TIFFDirectory ifd = TIFFDirectory.createFromMetadata(metadata);
 			TIFFField [] tfs = ifd.getTIFFFields();
 			for (TIFFField tf: tfs) {

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

@@ -11639,6 +11639,7 @@ public class ImageDttCPU {
 	 */
 	public static void startAndJoin(Thread[] threads) // USED in lwir
 	{
+//		System.out.println("startAndJoin()");
 		for (int ithread = 0; ithread < threads.length; ++ithread)
 		{
 			threads[ithread].setPriority(Thread.NORM_PRIORITY);

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

@@ -29,6 +29,7 @@ import java.util.Properties;
 import java.util.StringTokenizer;
 
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.orthomosaic.ComboMatch;
 
 public class IntersceneMatchParameters {
 	public static String [] MODES3D = {"RAW", "INF", "FG", "BG"}; // RAW:-1
@@ -93,7 +94,10 @@ public class IntersceneMatchParameters {
 	public boolean  sfm_show_corr_ind = false;   // Show SfM for each pairs group, each refinement run 
 	public boolean  sfm_show_corr =     false;   // Show combined SfM for each refinement run
 	
-	// rectilinear matching parameters 
+	// rectilinear matching parameters
+	public String   omtch_img_set =   ComboMatch.FILES_LISTS_PATHS[0];       // image s
+	
+	
 	public int      rln_gpu_width =     4096;    // horizontal GPU image size (applied during init)
 	public int      rln_gpu_height =    4096;    // vertical GPU image size (applied during init)
 	
@@ -172,6 +176,8 @@ public class IntersceneMatchParameters {
     public int      pequ_num_iter =     100;    //  50;
     public int      pequ_debugLevel =     2;
 	
+    public String   patt_save_top = "/media/elphel/NVME/lwir16-proc/ortho_videos/debug/sept12-13/pattern_match/";
+    public String   patt_save_subdir = "combo_maps";
 	
 	
 	public double [] getImsMountATR() {
@@ -737,11 +743,16 @@ public class IntersceneMatchParameters {
 				"Show combined SfM for each refinement run.");
 
 		gd.addTab      ("Mosaic", "Combining scene series into a composite map map");
+		
+		gd.addChoice      ("Files list/data path (w/o extension):", ComboMatch.FILES_LISTS_PATHS, omtch_img_set);
+		
 		gd.addNumericField("GPU window width",                       this.rln_gpu_width, 0,5,"pix",
 				"Horizontal GPU image size (applied during init.)");
 		gd.addNumericField("GPU window height",                      this.rln_gpu_height, 0,5,"pix",
 				"Vertical GPU image size (applied during init).");
 		
+		
+		
 		gd.addMessage  ("Rectilinear image matching");
 		gd.addNumericField("Phase correlation fat zero",             this.rln_fat_zero, 5,8,"",
 				"Phase correlation fat zero - was set to 10000.");
@@ -829,6 +840,10 @@ public class IntersceneMatchParameters {
 		gd.addNumericField("RMSE relative improvement",   this.pequ_rms_diff,     3,7,"",	"Relative RMSE improvement to exit LMA.");
 		gd.addNumericField("LMA iterations",              this.pequ_num_iter, 0,3,"",".Maximal number of the LMA iterations.");
 		gd.addNumericField("Debug level for equalization",this.pequ_debugLevel, 0,3,"","Debug level for global (LMA-based) intensity equalization.");
+
+		gd.addMessage  ("Pattern match parameters");
+		gd.addStringField ("Pattern match save directory",this.patt_save_top, 120, "Top directory to save combo maps");
+		gd.addStringField ("Save subdirectory",           this.patt_save_subdir, 80, "Subdirectory for versions of the same scene/pair of scenes");
 		
 //		
 
@@ -1663,6 +1678,8 @@ public class IntersceneMatchParameters {
 		this.sfm_show_corr_ind =              gd.getNextBoolean();
 		this.sfm_show_corr =                  gd.getNextBoolean();
 		
+		this.omtch_img_set = ComboMatch.FILES_LISTS_PATHS[gd.getNextChoiceIndex()];
+		
 		this.rln_gpu_width =            (int) gd.getNextNumber();
 		this.rln_gpu_height =           (int) gd.getNextNumber();
 		this.rln_fat_zero =                   gd.getNextNumber();
@@ -1737,6 +1754,9 @@ public class IntersceneMatchParameters {
         this.pequ_num_iter =            (int) gd.getNextNumber();
         this.pequ_debugLevel =          (int) gd.getNextNumber();
         
+        this.patt_save_top=                   gd.getNextString();
+        this.patt_save_subdir =               gd.getNextString();
+        
 		this.center_reference =               gd.getNextBoolean();
 		this.overlap_sequences =              gd.getNextBoolean();
 		this.reset_photometric =              gd.getNextBoolean();
@@ -2185,6 +2205,7 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"sfm_show_seq",                  this.sfm_show_seq + "");                // boolean
 		properties.setProperty(prefix+"sfm_show_corr_ind",             this.sfm_show_corr_ind + "");           // boolean
 		properties.setProperty(prefix+"sfm_show_corr",                 this.sfm_show_corr + "");               // boolean
+		properties.setProperty(prefix+"omtch_img_set",                 this.omtch_img_set + "");              // String
 
 		properties.setProperty(prefix+"rln_gpu_width",                 this.rln_gpu_width+"");                 // int
 		properties.setProperty(prefix+"rln_gpu_height",                this.rln_gpu_height+"");                // int
@@ -2261,6 +2282,9 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"pequ_num_iter",                 this.pequ_num_iter + "");               // int
 		properties.setProperty(prefix+"pequ_debugLevel",               this.pequ_debugLevel + "");             // int
 		
+		properties.setProperty(prefix+"patt_save_top",                 this.patt_save_top + "");               // String
+		properties.setProperty(prefix+"patt_save_subdir",              this.patt_save_subdir + "");            // String
+		
 		properties.setProperty(prefix+"center_reference",              this.center_reference + "");            // boolean
 		properties.setProperty(prefix+"overlap_sequences",             this.overlap_sequences + "");           // boolean
 		properties.setProperty(prefix+"reset_photometric",             this.reset_photometric + "");           // boolean
@@ -2671,7 +2695,9 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"sfm_save_seq")!=null)       this.sfm_save_seq=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_save_seq"));		
 		if (properties.getProperty(prefix+"sfm_show_seq")!=null)       this.sfm_show_seq=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_show_seq"));		
 		if (properties.getProperty(prefix+"sfm_show_corr_ind")!=null)  this.sfm_show_corr_ind=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_show_corr_ind"));		
-		if (properties.getProperty(prefix+"sfm_show_corr")!=null)      this.sfm_show_corr=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_show_corr"));		
+		if (properties.getProperty(prefix+"sfm_show_corr")!=null)      this.sfm_show_corr=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_show_corr"));
+		
+		if (properties.getProperty(prefix+"omtch_img_set")!=null)     this.omtch_img_set=(String) properties.getProperty(prefix+                "omtch_img_set");
 		
 		if (properties.getProperty(prefix+"rln_gpu_width")!=null)      this.rln_gpu_width=Integer.parseInt(properties.getProperty(prefix+"rln_gpu_width"));
 		if (properties.getProperty(prefix+"rln_gpu_height")!=null)     this.rln_gpu_height=Integer.parseInt(properties.getProperty(prefix+"rln_gpu_height"));
@@ -2747,6 +2773,9 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"pequ_num_iter")!=null)       this.pequ_num_iter=Integer.parseInt(properties.getProperty(prefix+           "pequ_num_iter"));
 		if (properties.getProperty(prefix+"pequ_debugLevel")!=null)     this.pequ_debugLevel=Integer.parseInt(properties.getProperty(prefix+         "pequ_debugLevel"));
 		
+		if (properties.getProperty(prefix+"patt_save_top")!=null)       this.patt_save_top=(String) properties.getProperty(prefix+                "patt_save_top");
+		if (properties.getProperty(prefix+"patt_save_subdir")!=null)    this.patt_save_subdir=(String) properties.getProperty(prefix+                "patt_save_subdir");
+		
 		if (properties.getProperty(prefix+"center_reference")!=null)              this.center_reference=Boolean.parseBoolean(properties.getProperty(prefix+"center_reference"));		
 		if (properties.getProperty(prefix+"overlap_sequences")!=null)             this.overlap_sequences=Boolean.parseBoolean(properties.getProperty(prefix+"overlap_sequences"));		
 		if (properties.getProperty(prefix+"reset_photometric")!=null)             this.reset_photometric=Boolean.parseBoolean(properties.getProperty(prefix+"reset_photometric"));		
@@ -3185,6 +3214,7 @@ public class IntersceneMatchParameters {
 		imp.sfm_show_seq                  = this.sfm_show_seq;
 		imp.sfm_show_corr_ind             = this.sfm_show_corr_ind;
 		imp.sfm_show_corr                 = this.sfm_show_corr;
+		imp.omtch_img_set                 = this.omtch_img_set;
 		
 		imp.rln_gpu_width                 = this.rln_gpu_width;
 		imp.rln_gpu_height                = this.rln_gpu_height;
@@ -3260,6 +3290,9 @@ public class IntersceneMatchParameters {
         imp.pequ_num_iter                 = this.pequ_num_iter;
         imp.pequ_debugLevel               = this.pequ_debugLevel;
         
+        imp.patt_save_top                 = this.patt_save_top;
+        imp.patt_save_subdir              = this.patt_save_subdir;
+        
 		imp.center_reference              = this.center_reference;
 		imp.overlap_sequences             = this.overlap_sequences;
 		imp.reset_photometric             = this.reset_photometric;

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

@@ -222,17 +222,7 @@ public class QuadCLTCPU {
     	enu_corr_metric = corr;
     }
     
-    
-    
-    @Deprecated
-    public double [][] getPimuOffsets() {
-    	return pimu_offsets;
-    }
-    @Deprecated
-    public void setPimuOffsets(double[][] offsets) { // never
-    	pimu_offsets = offsets;
-    }
-    
+     
     // find best rotation between IMU XYZ and camera XYZ
     /**
      * Refine scene poses (now only linear) from currently adjusted poses