Working on kernel factorization with LMA - larger symmetrical kernel and small...

Working on kernel factorization with LMA - larger symmetrical kernel and small asymmetrical for direct convolution with bayer

src/main/java/DttRad2.java

@@ -71,7 +71,7 @@ public class DttRad2 {
 		double [] xr= new double[x.length];
 		int j= x.length-1;
 		for (int i=0; i < x.length;i++) xr[i] = x[j--];		
-		double [] y=  _dctiv_recurs(x);
+		double [] y=  _dctiv_recurs(xr);
 		double scale = 1.0/Math.sqrt(x.length);
 		for (int i = 0; i < y.length ; i++) {
 			y[i] *= scale;
@@ -225,6 +225,30 @@ public class DttRad2 {
 		return y;
 	}
 	
+	public double [] dttt_ii(double [] x){
+		return dttt_iv(x, 0, 1 << (ilog2(x.length)/2)); 
+	}
+
+	public double [] dttt_ii(double [] x, int n){
+		double [] y = new double [n*n];
+		double [] line = new double[n];
+		// first (horizontal) pass
+		for (int i = 0; i<n; i++){
+			System.arraycopy(x, n*i, line, 0, n);
+			line = dctii_direct(line);
+			for (int j=0; j < n;j++) y[j*n+i] =line[j]; // transpose 
+		}
+		// second (vertical) pass
+		for (int i = 0; i<n; i++){
+			System.arraycopy(y, n*i, line, 0, n);
+			line = dctii_direct(line);
+			System.arraycopy(line, 0, y, n*i, n);
+		}
+		return y;
+	}
+
+	
+	
 	public void set_window(){
 		set_window(0);
 	}
@@ -401,7 +425,7 @@ public class DttRad2 {
 					SIV[t][j][k] = SIV[t][k][j];  
 				}
 				for (int k = j; k<n; k++){
-					SIV[t][j][k] = scale *  Math.cos((2*j+1)*(2*k+1)*pi_4n);
+					SIV[t][j][k] = scale *  Math.sin((2*j+1)*(2*k+1)*pi_4n);
 				}
 			}
 		}

src/main/java/EyesisCorrectionParameters.java

@@ -1648,30 +1648,61 @@ public class EyesisCorrectionParameters {
   		}
   	}
     public static class DCTParameters {
-  		public int dct_size =   32;
-  		public int dct_window =  0; // currently only 2 types of window - 0 and 1
+  		public int dct_size =    32; //
+  		public int asym_size =    6; //
+  		public int dct_window =   1; // currently only 3 types of windows - 0 (none), 1 and 2
+  		public int LMA_steps =  100;
+  		public double compactness = 1.0;
+  		public int dbg_x =0;
+  		public int dbg_y =0;
+  		public int dbg_x1 =0;
+  		public int dbg_y1 =0;
+  		public double dbg_sigma =2.0;
 
-  		public DCTParameters(int dct_size, int dct_window) {
-  			this.dct_size = dct_size;
+  		public DCTParameters(int dct_size, int asym_size, int dct_window, double compactness) {
+  			this.dct_size =   dct_size;
+  			this.asym_size =  asym_size;
   			this.dct_window = dct_window;
+  			this.compactness = compactness;
   		}
   		public void setProperties(String prefix,Properties properties){
   			properties.setProperty(prefix+"dct_size",this.dct_size+"");
+  			properties.setProperty(prefix+"asym_size",this.asym_size+"");
   			properties.setProperty(prefix+"dct_window",   this.dct_window+"");
+  			properties.setProperty(prefix+"compactness",  this.compactness+"");
   		}
   		public void getProperties(String prefix,Properties properties){
   			this.dct_size=Integer.parseInt(properties.getProperty(prefix+"dct_size"));
+  			this.asym_size=Integer.parseInt(properties.getProperty(prefix+"asym_size"));
   			this.dct_window=Integer.parseInt(properties.getProperty(prefix+"dct_window"));
+  			this.compactness=Integer.parseInt(properties.getProperty(prefix+"compactness"));
   		}
   		public boolean showDialog() {
   			GenericDialog gd = new GenericDialog("Set DCT parameters");
-  			gd.addNumericField("DCT size",                                   this.dct_size,     0); //2
-  			gd.addNumericField("MDCT window type (0,1,2)",                   this.dct_window,   0); //32
+  			gd.addNumericField("DCT size",                                   this.dct_size,     0); //32
+  			gd.addNumericField("Size of asymmetrical (non-DCT) kernel",      this.asym_size,    0); //6
+  			gd.addNumericField("MDCT window type (0,1,2)",                   this.dct_window,   0); //0..2
+  			gd.addNumericField("LMA_steps",                                  this.LMA_steps,    0); //0..2
+  			gd.addNumericField("compactness",                                this.compactness,  6); //0..2
+  			
+  			gd.addNumericField("dbg_x",                                      this.dbg_x,   0); //0..2
+  			gd.addNumericField("dbg_y",                                      this.dbg_y,   0); //0..2
+  			gd.addNumericField("dbg_x1",                                     this.dbg_x1,  0); //0..2
+  			gd.addNumericField("dbg_y1",                                     this.dbg_y1,  0); //0..2
+  			gd.addNumericField("dbg_sigma",                                  this.dbg_sigma, 3); //0..2
   			//  	    gd.addNumericField("Debug Level:",                          MASTER_DEBUG_LEVEL,      0);
   			gd.showDialog();
   			if (gd.wasCanceled()) return false;
-  			this.dct_size=   (int) gd.getNextNumber();
-  			this.dct_window=       (int) gd.getNextNumber();
+  			this.dct_size=        (int) gd.getNextNumber();
+  			this.asym_size=       (int) gd.getNextNumber();
+  			this.dct_window=      (int) gd.getNextNumber();
+  			this.LMA_steps =      (int) gd.getNextNumber();
+  			this.compactness =          gd.getNextNumber();
+  			this.dbg_x=           (int) gd.getNextNumber();
+  			this.dbg_y=           (int) gd.getNextNumber();
+  			this.dbg_x1=          (int) gd.getNextNumber();
+  			this.dbg_y1=          (int) gd.getNextNumber();
+  			this.dbg_sigma=             gd.getNextNumber();
   			//  	    MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
   			return true;
   		}  

src/main/java/ImageDtt.java

@@ -208,7 +208,7 @@ public class ImageDtt {
 	 * From Stephan Preibisch's Multithreading.java class. See:
 	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
 	 */
-	private Thread[] newThreadArray(int maxCPUs) {
+	static Thread[] newThreadArray(int maxCPUs) {
 		int n_cpus = Runtime.getRuntime().availableProcessors();
 		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
 		return new Thread[n_cpus];