aberration correction with clt

src/main/java/EyesisCorrectionParameters.java

@@ -1880,13 +1880,22 @@ public class EyesisCorrectionParameters {
   		public int        ishift_x =            0; // debug feature - shift source image by this pixels left
   		public int        ishift_y =            0; // debug feature - shift source image by this pixels down
   		public double     fat_zero =          0.0; // modify phase correlation to prevent division by very small numbers
-  		public double     corr_sigma =0.8; // LPF correlarion sigma
-  		
+  		public double     corr_sigma =        0.8; // LPF correlarion sigma
   		public boolean    norm_kern =         true; // normalize kernels
   		
+  		public double     novignetting_r    = 0.2644; // reg gain in the center of sensor calibration R (instead of vignetting)
+  		public double     novignetting_g    = 0.3733; // green gain in the center of sensor calibration G
+  		public double     novignetting_b    = 0.2034; // blue gain in the center of sensor calibration B
+  		public double     scale_r =           1.0; // extra gain correction after vignetting or nonvignetting, before other processing
+  		public double     scale_g =           1.0;
+  		public double     scale_b =           1.0;
+  		public double     vignetting_max    = 0.4; // value in vignetting data to correspond to 1x in the kernel
+  		public double     vignetting_range  = 5.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
+  		public int        kernel_step =       16;  // source kernels step in pixels (have 1 kernel margin on each side)  
+  		
   		public CLTParameters(){}
   		public void setProperties(String prefix,Properties properties){
-  			properties.setProperty(prefix+"transform_size",this.transform_size+"");
+  			properties.setProperty(prefix+"transform_size",   this.transform_size+"");
   			properties.setProperty(prefix+"clt_window",       this.clt_window+"");
   			properties.setProperty(prefix+"shift_x",          this.shift_x+"");
   			properties.setProperty(prefix+"shift_y",          this.shift_y+"");
@@ -1898,6 +1907,17 @@ public class EyesisCorrectionParameters {
   			properties.setProperty(prefix+"ishift_y",         this.ishift_y+"");
   			properties.setProperty(prefix+"fat_zero",         this.fat_zero+"");
   			properties.setProperty(prefix+"corr_sigma",       this.corr_sigma+"");
+			properties.setProperty(prefix+"norm_kern",        this.norm_kern+"");
+  			properties.setProperty(prefix+"novignetting_r",   this.novignetting_r+"");
+  			properties.setProperty(prefix+"novignetting_g",   this.novignetting_g+"");
+  			properties.setProperty(prefix+"novignetting_b",   this.novignetting_b+"");
+  			properties.setProperty(prefix+"scale_r",          this.scale_r+"");
+  			properties.setProperty(prefix+"scale_g",          this.scale_g+"");
+  			properties.setProperty(prefix+"scale_b",          this.scale_b+"");
+  			properties.setProperty(prefix+"vignetting_max",   this.vignetting_max+"");
+  			properties.setProperty(prefix+"vignetting_range", this.vignetting_range+"");
+  			properties.setProperty(prefix+"kernel_step",      this.kernel_step+"");
+  			
   		}
   		public void getProperties(String prefix,Properties properties){
   			if (properties.getProperty(prefix+"transform_size")!=null) this.transform_size=Integer.parseInt(properties.getProperty(prefix+"transform_size"));
@@ -1912,10 +1932,21 @@ public class EyesisCorrectionParameters {
   			if (properties.getProperty(prefix+"ishift_y")!=null)       this.ishift_y=Integer.parseInt(properties.getProperty(prefix+"ishift_y"));
   			if (properties.getProperty(prefix+"fat_zero")!=null)       this.fat_zero=Double.parseDouble(properties.getProperty(prefix+"fat_zero"));
   			if (properties.getProperty(prefix+"corr_sigma")!=null)     this.corr_sigma=Double.parseDouble(properties.getProperty(prefix+"corr_sigma"));
+  			if (properties.getProperty(prefix+"norm_kern")!=null)      this.norm_kern=Boolean.parseBoolean(properties.getProperty(prefix+"norm_kern"));
+  			if (properties.getProperty(prefix+"novignetting_r")!=null) this.novignetting_r=Double.parseDouble(properties.getProperty(prefix+"novignetting_r"));
+  			if (properties.getProperty(prefix+"novignetting_g")!=null) this.novignetting_g=Double.parseDouble(properties.getProperty(prefix+"novignetting_g"));
+  			if (properties.getProperty(prefix+"novignetting_b")!=null) this.novignetting_b=Double.parseDouble(properties.getProperty(prefix+"novignetting_b"));
+  			if (properties.getProperty(prefix+"scale_r")!=null)        this.scale_r=Double.parseDouble(properties.getProperty(prefix+"scale_r"));
+  			if (properties.getProperty(prefix+"scale_g")!=null)        this.scale_g=Double.parseDouble(properties.getProperty(prefix+"scale_g"));
+  			if (properties.getProperty(prefix+"scale_b")!=null)        this.scale_b=Double.parseDouble(properties.getProperty(prefix+"scale_b"));
+  			if (properties.getProperty(prefix+"vignetting_max")!=null) this.vignetting_max=Double.parseDouble(properties.getProperty(prefix+"vignetting_max"));
+  			if (properties.getProperty(prefix+"vignetting_range")!=null) this.vignetting_range=Double.parseDouble(properties.getProperty(prefix+"vignetting_range"));
+  			if (properties.getProperty(prefix+"kernel_step")!=null)    this.kernel_step=Integer.parseInt(properties.getProperty(prefix+"kernel_step"));
   		}
+  		
   		public boolean showDialog() {
   			GenericDialog gd = new GenericDialog("Set DCT parameters");
-  			gd.addNumericField("DCT size",                                                       this.transform_size,            0);
+  			gd.addNumericField("Transform size (default 8)",                                              this.transform_size,            0);
   			gd.addNumericField("Lapped transform window type (0- rectangular, 1 - sinus)",                this.clt_window,                0);
    			gd.addNumericField("shift_x",                                                                 this.shift_x,                   4);
    			gd.addNumericField("shift_y",                                                                 this.shift_y,                   4);
@@ -1927,6 +1958,17 @@ public class EyesisCorrectionParameters {
   			gd.addNumericField("ishift_y: shift source image by this pixels down",                        this.ishift_y,                  0);
    			gd.addNumericField("Modify phase correlation to prevent division by very small numbers",      this.fat_zero,                  4);
    			gd.addNumericField("LPF correlarion sigma ",                                                  this.corr_sigma,                3);
+  			gd.addCheckbox    ("Normalize kernels ",                                                      this.norm_kern);
+  			gd.addNumericField("Reg gain in the center of sensor calibration R (instead of vignetting)",  this.novignetting_r,   4);
+  			gd.addNumericField("Green gain in the center of sensor calibration G (instead of vignetting)",this.novignetting_g, 4);
+  			gd.addNumericField("Blue gain in the center of sensor calibration B (instead of vignetting)", this.novignetting_b,  4);
+  			gd.addNumericField("Extra red correction to compensate for light temperature",                this.scale_r,  4);
+  			gd.addNumericField("Extra green correction to compensate for light temperature",              this.scale_g,  4);
+  			gd.addNumericField("Extra blue correction to compensate for light temperature",               this.scale_b,  4);
+  			gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel",        this.vignetting_max,      3);
+  			gd.addNumericField("Do not try to correct vignetting smaller than this fraction of max",      this.vignetting_range,  3);
+  			gd.addNumericField("Kernel step in pixels (has 1 kernel margin on each side)",                this.kernel_step,            0);
+   			
   			WindowTools.addScrollBars(gd);
   			gd.showDialog();
   			
@@ -1943,6 +1985,17 @@ public class EyesisCorrectionParameters {
   			this.ishift_y=        (int) gd.getNextNumber();
   			this.fat_zero =             gd.getNextNumber();
   			this.corr_sigma =           gd.getNextNumber();
+  			this.norm_kern=             gd.getNextBoolean();
+  			this.novignetting_r=        gd.getNextNumber();
+  			this.novignetting_g=        gd.getNextNumber();
+  			this.novignetting_b=        gd.getNextNumber();
+  			this.scale_r=               gd.getNextNumber();
+  			this.scale_g=               gd.getNextNumber();
+  			this.scale_b=               gd.getNextNumber();
+  			this.vignetting_max=        gd.getNextNumber();
+  			this.vignetting_range=      gd.getNextNumber();
+  			this.kernel_step=     (int) gd.getNextNumber();
+  			
   			return true;
   		}
     }
@@ -2272,17 +2325,16 @@ public class EyesisCorrectionParameters {
   			this.antiwindow=            gd.getNextBoolean();
   			this.skip_sym=              gd.getNextBoolean();
   			this.convolve_direct=       gd.getNextBoolean();
+
   			this.novignetting_r=        gd.getNextNumber();
   			this.novignetting_g=        gd.getNextNumber();
   			this.novignetting_b=        gd.getNextNumber();
-
   			this.scale_r=               gd.getNextNumber();
   			this.scale_g=               gd.getNextNumber();
   			this.scale_b=               gd.getNextNumber();
-  			
-  			
   			this.vignetting_max=        gd.getNextNumber();
   			this.vignetting_range=      gd.getNextNumber();
+
   			this.post_debayer=          gd.getNextBoolean();
   			this.color_DCT=             gd.getNextBoolean();
   			this.sigma_rb=              gd.getNextNumber();

src/main/java/EyesisCorrections.java

@@ -2078,6 +2078,51 @@ public class EyesisCorrections {
 	    return outStack;
 	  }
 
+	  // return 2-d double array instead of the stack
+	  public double [][]bayerToDoubleStack(ImagePlus imp, // source bayer image, linearized, 32-bit (float))
+			  EyesisCorrectionParameters.SplitParameters splitParameters){ // if null - no margins, no oversample
+		  if (imp==null) return null;
+		  boolean adv = splitParameters != null;
+		  int oversample = adv? splitParameters.oversample : 1;
+		  int addTop=      adv?splitParameters.addTop:       0;  
+		  int addLeft=     adv?splitParameters.addLeft:      0;  
+		  int addBottom=   adv?splitParameters.addBottom:    0;  
+		  int addRight=    adv?splitParameters.addRight:     0;  
+		  String [] chnNames={"Red","Blue","Green"}; //Different sequence than RGB!!
+		  int nChn=chnNames.length;
+		  ImageProcessor ip=imp.getProcessor();
+		  int inWidth=imp.getWidth();
+		  int inHeight=imp.getHeight();
+		  int outHeight=inHeight*oversample + addTop +  addBottom;
+		  int outWidth= inWidth* oversample + addLeft + addRight;
+		  int outLength=outWidth*outHeight;
+
+		  double [][] outPixels=new double[nChn][outLength];
+		  float [] pixels = (float[]) ip.getPixels();
+		  int chn,y,x,i,index;
+		  int bayerPeriod=2*oversample;
+		  int ovrWidth=   inWidth * oversample;
+		  int ovrHeight= inHeight *  oversample;
+		  for (chn=0;chn<nChn;chn++) for (i=0;i<outPixels[chn].length;i++) outPixels[chn][i]=0.0f;
+		  /* Can be optimized - now it calculate input address for all those 0-es */
+		  for (index=0; index<outLength; index++) {
+			  y=(index / outWidth) - addTop;
+			  x=(index % outWidth) - addLeft;
+			  if (y<0) y= (bayerPeriod-((-y) % bayerPeriod))%bayerPeriod;
+			  else if (y>=ovrHeight) y= ovrHeight-bayerPeriod +((y-ovrHeight) % bayerPeriod);
+			  if (x<0) x= (bayerPeriod-((-x) % bayerPeriod))%bayerPeriod;
+			  else  if (x>=ovrWidth) x= ovrWidth-bayerPeriod +((x-ovrWidth) % bayerPeriod);
+			  if (((y% oversample)==0) && ((x% oversample)==0)) {
+				  x/=oversample;
+				  y/=oversample;
+				  chn=((x&1)==(y&1))?2:(((x&1)!=0)?0:1);
+				  outPixels[chn][index]=pixels[y*inWidth+x];
+			  }
+		  }
+		  return outPixels;
+	  }
+	  
+	  
 	
 //double []  DENOISE_MASK=null; 	
 	

src/main/java/Eyesis_Correction.java

@@ -2890,16 +2890,7 @@ private Panel panel1,
         int numChannels=EYESIS_CORRECTIONS.getNumChannels();
         NONLIN_PARAMETERS.modifyNumChannels(numChannels);
         CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
-/*        
-        if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
-        EYESIS_CORRECTIONS.updateImageNoiseGains(
-        		NONLIN_PARAMETERS,     //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
-        		CONVOLVE_FFT_SIZE,     //int          fftSize, // 128 - fft size, kernel size should be size/2
-    			THREADS_MAX,           // int          threadsMax,  // maximal number of threads to launch                         
-    			UPDATE_STATUS,         // boolean    updateStatus,
-    			DEBUG_LEVEL);           //int        globalDebugLevel){
-        }
-*/
+
         if (!EYESIS_DCT.DCTKernelsAvailable()){
         	if (DEBUG_LEVEL > 0){
         		System.out.println("Reading/converting DCT kernels");
@@ -2914,11 +2905,7 @@ private Panel panel1,
         		EYESIS_DCT.showKernels(); // show restored kernels
         	}
         }
-        
-        
-//        EYESIS_CORRECTIONS.processChannelImages(
         EYESIS_DCT.processDCTChannelImages(
-//        		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters         splitParameters,
         		DCT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
         		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
         		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
@@ -4096,6 +4083,7 @@ private Panel panel1,
         if (EYESIS_DCT != null){
         	EYESIS_DCT.resetCLTKernels();
         }
+        
     } else if (label.equals("Read CLT kernels")) {
         if (!CLT_PARAMETERS.showDialog()) return;
         if (EYESIS_DCT == null){
@@ -4145,6 +4133,92 @@ private Panel panel1,
         			DEBUG_LEVEL);
         }
 
+        return;
+    } else if (label.equals("CLT process files")) {
+    	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+        if (EYESIS_DCT == null){
+        	EYESIS_DCT = new  EyesisDCT (
+        			EYESIS_CORRECTIONS,
+        			CORRECTION_PARAMETERS,
+        			DCT_PARAMETERS);
+        	if (DEBUG_LEVEL > 0){
+        		System.out.println("Created new EyesisDCT instance, will need to read CLT kernels");
+        	}
+        }
+    	String configPath=null;
+    	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
+    		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
+    				true,
+    				true);
+    		if (configPath==null){
+    			String msg="No results directory selected, command aborted";
+    			System.out.println("Warning: "+msg);
+    			IJ.showMessage("Warning",msg);
+    			return;
+    		}
+    		configPath+=Prefs.getFileSeparator()+"autoconfig";
+    		try {
+    			saveTimestampedProperties(
+    					configPath,      // full path or null
+    					null, // use as default directory if path==null 
+    					true,
+    					PROPERTIES);
+
+    		} catch (Exception e){
+    			String msg="Failed to save configuration to "+configPath+", command aborted";
+    			System.out.println("Error: "+msg);
+    			IJ.showMessage("Error",msg);
+    			return;
+    		}
+    	}      
+        
+        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
+        int numChannels=EYESIS_CORRECTIONS.getNumChannels();
+        NONLIN_PARAMETERS.modifyNumChannels(numChannels);
+        CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
+
+        if (!EYESIS_DCT.CLTKernelsAvailable()){
+        	if (DEBUG_LEVEL > 0){
+        		System.out.println("Reading CLT kernels");
+        	}
+            EYESIS_DCT.readCLTKernels(
+            		CLT_PARAMETERS,
+                    THREADS_MAX,
+                    UPDATE_STATUS, // update status info
+            		DEBUG_LEVEL);
+
+            if (DEBUG_LEVEL > 1){
+            	EYESIS_DCT.showCLTKernels(
+            			THREADS_MAX,
+            			UPDATE_STATUS, // update status info
+            			DEBUG_LEVEL);
+        	}
+        }
+        
+///========================================        
+        
+        EYESIS_DCT.processCLTChannelImages(
+        		CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
+        		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
+        		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
+        		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
+        		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters     channelGainParameters,
+        		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters             rgbParameters,
+        		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
+        		CONVOLVE_FFT_SIZE, //int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
+        		THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch                         
+        		UPDATE_STATUS, //final boolean    updateStatus,
+        		DEBUG_LEVEL); //final int        debugLevel);
+        
+        if (configPath!=null) {
+        	saveTimestampedProperties( // save config again
+        			configPath,      // full path or null
+        			null, // use as default directory if path==null 
+        			true,
+        			PROPERTIES);
+        }
+
         return;
     	
 // End of buttons code