Creating kernel and matching images from different altitude

src/main/java/com/elphel/imagej/common/DoubleFHT.java

@@ -346,7 +346,7 @@ public class DoubleFHT  {
     	 return phaseCorrelate(first, phaseCoeff, filter,fht_save);
      }
 
-     public double [] phaseCorrelate (
+     public double [] phaseCorrelate ( // never
     		 double [] first,
     		 double    phaseCoeff,
     		 double [] filter) {     //  high/low pass filtering
@@ -561,7 +561,7 @@ public class DoubleFHT  {
     	 if (debug) ShowDoubleFloatArrays.showArrays(this.translateFHT, "translateFHT-"+IJ.d2s(dx,3)+":"+IJ.d2s(dy,3));
      }
 
- 	private boolean updateMaxN(double [] data){
+ 	public boolean updateMaxN(double [] data){ // was private
  		if (data==null) return false; // do nothing
 		if (!powerOf2Size(data)) {
 			String msg="Image is not power of 2 size";
@@ -2146,6 +2146,41 @@ public class DoubleFHT  {
 		return result;
 	}
 
+	public double [] divide(double [] h1, double [] h2, double fat_zero) {
+		int rowMod, colMod;
+		double mag, h2e, h2o;
+		double fz2=fat_zero*fat_zero;
+		double[] result = new double[maxN*maxN];
+		for (int r=0; r<maxN; r++) {
+			rowMod = (maxN - r) % maxN;
+			for (int c=0; c<maxN; c++) {
+				colMod = (maxN - c) % maxN;
+				mag =h2[r*maxN+c] * h2[r*maxN+c] + h2[rowMod*maxN+colMod] * h2[rowMod*maxN+colMod]+fz2;
+				if (mag<1e-20)
+					mag = 1e-20;
+				h2e = (h2[r*maxN+c] + h2[rowMod*maxN+colMod]);
+				h2o = (h2[r*maxN+c] - h2[rowMod*maxN+colMod]);
+				double tmp = (h1[r*maxN+c] * h2e - h1[rowMod*maxN+colMod] * h2o);
+				result[r*maxN+c] = tmp/mag;
+			}
+		}
+		return result;
+	}
+	
+	public double []  setReal (double [] amp) { // only first half used
+		double[] result = new double[maxN*maxN];
+		int rowMod, colMod;
+		for (int r=0; r<maxN/2; r++) {
+			rowMod = (maxN - r) % maxN;
+			for (int c=0; c<maxN; c++) {
+				colMod = (maxN - c) % maxN;
+				result[r*maxN+c] =           amp[r*maxN+c];
+				result[rowMod*maxN+colMod] = amp[r*maxN+c];
+			}
+		}
+		return result;
+	}
+	
 
   public double [] calculateAmplitude(double [] fht) {
     int size=(int) Math.sqrt(fht.length);
@@ -2156,6 +2191,31 @@ public class DoubleFHT  {
     swapQuadrants(amp);
     return amp;
   }
+  public double [] calculateAmplitudeNoSwap(double [] fht) {
+	    int size=(int) Math.sqrt(fht.length);
+	    double[] amp = new double[size*size];
+	    for (int row=0; row<size; row++) {
+	      amplitude(row, size, fht, amp);
+	    }
+	    return amp;
+	  }
+  public static double [] calculatePhaseNoSwap(double [] fht) {
+	    int size=(int) Math.sqrt(fht.length);
+	    double[] phs = new double[size*size];
+	    for (int row=0; row<size; row++) {
+	      phase(row, size, fht, phs);
+	    }
+	    return phs;
+	  }
+  public double [] calculatePhase(double [] fht) {
+	    int size=(int) Math.sqrt(fht.length);
+	    double[] phs = new double[size*size];
+	    for (int row=0; row<size; row++) {
+	      phase(row, size, fht, phs);
+	    }
+	    swapQuadrants(phs);
+	    return phs;
+	  }
 
   public double [] calculateAmplitudeHalf(double [] fht) {
 	  int size=(int) Math.sqrt(fht.length);
@@ -2186,6 +2246,19 @@ public class DoubleFHT  {
     }
   }
 
+  static void phase(int row, int size, double[] fht, double[] phase) {
+	  int base = row*size;
+	  int l;
+	  for (int c=0; c<size; c++) {
+		  l = ((size-row)%size) * size + (size-c)%size;
+		  double re=0.5*(fht[base+c]+fht[l]);
+		  double im=0.5*(fht[base+c]-fht[l]);
+		  phase[base+c] = Math.atan2(im,re);;
+	  }
+  }
+
+  
+  
   /* Squared amplitude of one row from 2D Hartley Transform. */
   void amplitude2(int row, int size, double[] fht, double[] amplitude) {
     int base = row*size;

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -849,6 +849,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Read Tiff",  panelLWIRWorld, color_process);
 			addButton("Set pair GPS",  panelLWIRWorld, color_process);
 			addButton("Test video",  panelLWIRWorld, color_process);
+			addButton("Deconvolve Slices",  panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5733,8 +5734,22 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				return;
 			}
 			OrthoMap.testVideo(imp_sel);
+		} else if (label.equals("Deconvolve Slices")) {
+			ImagePlus imp_sel = WindowManager.getCurrentImage();
+			if (imp_sel == null) {
+				IJ.showMessage("Error", "No images selected");
+				return;
+			}
+			OrthoMap.testDeconvolveSlices(
+					imp_sel,          // ImagePlus imp,
+					512,              // int [] slices,
+					new int [] {1,2}, // int [] slices, deconvolve slice 2 with slice1
+					4,                // int kernel_radius,
+					true,             // boolean hor_sym,
+					true,             // boolean vert_sym,
+					true, // false,            // boolean all_sym,
+					DEBUG_LEVEL);     // int debugLevel) { // >0
 		}
-		
 	}
 
 	public boolean debugInitOneScene() {