added saving dct kernel files

src/main/java/EyesisCorrectionParameters.java

@@ -1767,36 +1767,36 @@ public class EyesisCorrectionParameters {
   		}
   	}
     public static class DCTParameters {
-  		public int dct_size =     32; //
-  		public int asym_size =     6; //
-  		public int asym_pixels =  10; // maximal number of non-zero pixels in direct convolution kernel
-  		public int asym_distance = 2; // how far to try a new asym kernel pixel from existing ones 
-  		public int dct_window =   1; // currently only 3 types of windows - 0 (none), 1 and 2
-  		public int LMA_steps =  100;
-  		public double fact_precision=0.003; // stop iterations if error rms less than this part of target kernel rms
-  		public double compactness =  0.02;
-  		public double sym_compactness = 0.01;
-  		public double dc_weight = 10; // importance of dc realtive to rms_pure
-  		public int asym_tax_free  = 5; // "compactness" does not apply to pixels with |x|<=asym_tax_free  and |y| <= asym_tax_free
-  		public int seed_size = 8; // number of initial cells in asym_kernel - should be 4*b + 1 (X around center cell) or 4*n + 0  (X around between cells)
-  		public double asym_random; // initialize asym_kernel with random numbers
-  		public double dbg_x =0;
-  		public double dbg_y =0;
-  		public double dbg_x1 =0;
-  		public double dbg_y1 =0;
-  		public double dbg_sigma =2.0;
+  		public int dct_size =            8; //
+  		public int asym_size =          15; //
+  		public int asym_pixels =         4; // maximal number of non-zero pixels in direct convolution kernel
+  		public int asym_distance =       1; // how far to try a new asym kernel pixel from existing ones 
+  		public int dct_window =          1; // currently only 3 types of windows - 0 (none), 1 and 2
+  		public int LMA_steps =         100;
+  		public double fact_precision=    0.003; // stop iterations if error rms less than this part of target kernel rms
+  		public double compactness =      0.0;
+  		public double sym_compactness =  0.5;
+  		public double dc_weight =        1.0;  // importance of dc realtive to rms_pure
+  		public int    asym_tax_free  =   0;    // "compactness" does not apply to pixels with |x|<=asym_tax_free  and |y| <= asym_tax_free
+  		public int    seed_size =        1;    // number of initial cells in asym_kernel - should be 4*b + 1 (X around center cell) or 4*n + 0  (X around between cells)
+  		public double asym_random  =    -1; // initialize asym_kernel with random numbers
+  		public double dbg_x =            2.7;
+  		public double dbg_y =            0.0;
+  		public double dbg_x1 =          -1.3;
+  		public double dbg_y1 =           2.0;
+  		public double dbg_sigma =        0.8;
   		public String dbg_mask = ".........:::::::::.........:::::::::......*..:::::*:::.........:::::::::.........";
-  		public int dbg_mode = 1; // 0 - old LMA, 1 - new LMA - *** not used anymore ***
-  		public int dbg_window_mode = 2; // 0 - none, 1 - square, 2 - sin 3 - sin^2
+  		public int dbg_mode =            1; // 0 - old LMA, 1 - new LMA - *** not used anymore ***
+  		public int dbg_window_mode =     1; // 0 - none, 1 - square, 2 - sin 3 - sin^2 Now _should_ be square !!!
   		public boolean centerWindowToTarget = true;
   		// parameters to extract a kernel from the kernel image file
   		public int    color_channel =    2; // green (<0 - use simulated kernel, also will use simulated if kernels are not set)
   		public int    decimation =       2; // decimate original kernel this much in each direction
-  		public double decimateSigma =    0.4; // what is the optimal value for each decimation? 
+  		public double decimateSigma =   -1.0; // special mode for 2:1 deciamtion 
   		public int    tileX =            82;  // number of kernel tile (0..163) 
   		public int    tileY =            62;  // number of kernel tile (0..122) 
   		public boolean subtract_dc =     false;//subtract/restore dc
-  		public int    kernel_chn =      -1; //camera channel calibration to use for aberration correction ( < 0 - no correction)
+  		public int    kernel_chn =      -1; // camera channel calibration to use for aberration correction ( < 0 - no correction)
   		public boolean normalize =       true; //normalize both sym and asym kernels (asym to have sum==1, sym to have sum = dct_size
   		public boolean skip_sym =        false; // do not apply symmetrical correction
   		public boolean convolve_direct = false; // do not apply symmetrical correction

src/main/java/EyesisDCT.java

@@ -29,6 +29,7 @@ import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.Prefs;
+import ij.io.FileSaver;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 
@@ -107,31 +108,10 @@ public class EyesisDCT {
 			}
 		}
 	    showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
-//	    String [] sensor_files = correctionsParameters.selectSensorFiles(eyesisCorrections.debugLevel);
 	    
 
 		for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
 			if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (kernels[chn]==null)){
-//				if ((sensor_files!= null) && (sensor_files.length > chn) && (sensor_files[chn]!=null)){
-				/*				
-				double [][] vignetting = null;
-				int vign_width =       0;
-				int vign_height =      0;
-				int vign_decimation =  1;
-				if ((pixelMapping != null) &&
-						(pixelMapping.sensors != null) &&
-						(pixelMapping.sensors[chn] != null) &&
-						(pixelMapping.sensors[chn].pixelCorrection != null) &&
-						(pixelMapping.sensors[chn].pixelCorrection.length >=6)){
-					vignetting = new double[3][];
-					vignetting[0] = pixelMapping.sensors[chn].pixelCorrection[3]; // red
-					vignetting[2] = pixelMapping.sensors[chn].pixelCorrection[4]; // green
-					vignetting[1] = pixelMapping.sensors[chn].pixelCorrection[5]; // blue
-					vign_width =      pixelMapping.sensors[chn].pixelCorrectionWidth;
-					vign_height =     pixelMapping.sensors[chn].pixelCorrectionHeight;
-					vign_decimation = pixelMapping.sensors[chn].pixelCorrectionDecimation;
-				}
-*/				
 				ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);
 				if (imp_kernel_sharp.getStackSize()<3) {
 					System.out.println("Need a 3-layer stack with kernels");
@@ -145,22 +125,60 @@ public class EyesisDCT {
 						kernel_sharp_stack,            // final ImageStack kernelStack,  // first stack with 3 colors/slices convolution kernels
 						srcKernelSize,                 // final int          kernelSize, // 64
 						dct_parameters,                // final double       blurSigma,
-/*						
-						vignetting,
-						vign_width,
-						vign_height,
-						vign_decimation,
-*/						
 						threadsMax,  // maximal number of threads to launch                         
 						updateStatus,
 						debugLevel); // update status info
 				int sym_width =  kernels.numHor * kernels.dct_size;
 				int sym_height = kernels.sym_kernels[0].length /sym_width;
-				sdfa_instance.showArrays(kernels.sym_kernels,  sym_width, sym_height, true, imp_kernel_sharp.getTitle()+"-sym");
+// save files
+				String [] symNames = {"red_sym","blue_sym","green_sym"};
+				String [] asymNames = {"red_asym","blue_asym","green_asym"};
+				ImageStack symStack = sdfa_instance.makeStack(
+						kernels.sym_kernels,
+						sym_width,
+						sym_height,
+						symNames);
+	    		String symPath=correctionsParameters.dctKernelDirectory+
+	    				           Prefs.getFileSeparator()+
+	    				           correctionsParameters.dctKernelPrefix+
+	    				           String.format("%02d",chn)+
+	    				           correctionsParameters.dctSymSuffix;
+	    		String msg="Saving symmetrical convolution kernels to "+symPath;
+	    		IJ.showStatus(msg);
+	    		if (debugLevel>0) System.out.println(msg);
+				ImagePlus imp_sym=new ImagePlus(imp_kernel_sharp.getTitle()+"-sym",symStack);
+	    		if (debugLevel > 1) {
+	    			imp_sym.getProcessor().resetMinAndMax();
+	    			imp_sym.show();
+	    		}
+        		FileSaver fs=new FileSaver(imp_sym);
+        		fs.saveAsTiffStack(symPath);
+				
+//				sdfa_instance.showArrays(kernels.sym_kernels,  sym_width, sym_height, true, imp_kernel_sharp.getTitle()+"-sym");
 
 				int asym_width =  kernels.numHor * kernels.asym_size;
 				int asym_height = kernels.asym_kernels[0].length /asym_width;
-				sdfa_instance.showArrays(kernels.asym_kernels,  asym_width, asym_height, true, imp_kernel_sharp.getTitle()+"-asym");
+				ImageStack asymStack = sdfa_instance.makeStack(
+						kernels.asym_kernels,
+						asym_width,
+						asym_height,
+						asymNames);
+	    		String asymPath=correctionsParameters.dctKernelDirectory+
+	    				           Prefs.getFileSeparator()+
+	    				           correctionsParameters.dctKernelPrefix+
+	    				           String.format("%02d",chn)+
+	    				           correctionsParameters.dctAsymSuffix;
+	    		msg="Saving asymmetrical convolution kernels "+asymPath;
+	    		IJ.showStatus(msg);
+	    		if (debugLevel>0) System.out.println(msg);
+				ImagePlus imp_asym=new ImagePlus(imp_kernel_sharp.getTitle()+"-asym",asymStack);
+	    		if (debugLevel > 1) {
+	    			imp_asym.getProcessor().resetMinAndMax();
+	    			imp_asym.show();
+	    		}
+        		fs=new FileSaver(imp_asym);
+        		fs.saveAsTiffStack(asymPath);
+//				sdfa_instance.showArrays(kernels.asym_kernels,  asym_width, asym_height, true, imp_kernel_sharp.getTitle()+"-asym");
 			}
 		}
 		return true;