combining with vignetting correction

src/main/java/EyesisCorrectionParameters.java

@@ -1800,6 +1800,9 @@ public class EyesisCorrectionParameters {
   		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
+  		
+  		public double vignetting_max    = 0.4; // value in vignetting data to correspond to 1x in the kernel
+  		public double vignetting_range  = 3.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
 
   		public DCTParameters(
   				int dct_size,
@@ -1852,6 +1855,8 @@ public class EyesisCorrectionParameters {
   			properties.setProperty(prefix+"normalize",    this.normalize+"");
   			properties.setProperty(prefix+"skip_sym",    this.skip_sym+"");
   			properties.setProperty(prefix+"convolve_direct",    this.convolve_direct+"");
+  			properties.setProperty(prefix+"vignetting_max",   this.vignetting_max+"");
+  			properties.setProperty(prefix+"vignetting_range",   this.vignetting_range+"");
   			
   		}
   		public void getProperties(String prefix,Properties properties){
@@ -1887,6 +1892,8 @@ public class EyesisCorrectionParameters {
   			if (properties.getProperty(prefix+"normalize")!=null) this.normalize=Boolean.parseBoolean(properties.getProperty(prefix+"normalize"));
   			if (properties.getProperty(prefix+"skip_sym")!=null) this.skip_sym=Boolean.parseBoolean(properties.getProperty(prefix+"skip_sym"));
   			if (properties.getProperty(prefix+"convolve_direct")!=null) this.convolve_direct=Boolean.parseBoolean(properties.getProperty(prefix+"convolve_direct"));
+  			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"));
   		
   		}
   		public boolean showDialog() {
@@ -1923,7 +1930,10 @@ public class EyesisCorrectionParameters {
   			gd.addCheckbox    ("Normalize both sym and asym kernels ",                           this.normalize);
   			gd.addCheckbox    ("Do not apply symmetrical (DCT) correction ",                     this.skip_sym);
   			gd.addCheckbox    ("Convolve directly with symmetrical kernel (debug feature) ",     this.convolve_direct);
+  			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);
   			
+    		WindowTools.addScrollBars(gd);
   			gd.showDialog();
   			
   			if (gd.wasCanceled()) return false;
@@ -1958,7 +1968,9 @@ public class EyesisCorrectionParameters {
   			this.kernel_chn=      (int) gd.getNextNumber();
   			this.normalize=             gd.getNextBoolean();
   			this.skip_sym=              gd.getNextBoolean();
-  			this.convolve_direct=              gd.getNextBoolean();
+  			this.convolve_direct=       gd.getNextBoolean();
+  			this.vignetting_max=        gd.getNextNumber();
+  			this.vignetting_range=      gd.getNextNumber();
   			//  	    MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
   			return true;
   		}  

src/main/java/EyesisCorrections.java

@@ -2234,7 +2234,8 @@ public class EyesisCorrections {
 	 	  return mask;
 	   }
 	   /* ======================================================================== */
-	   private void saveAndShow(
+//	   private void saveAndShow(
+	   public void saveAndShow(
 	 		  ImagePlus             imp,
 			   EyesisCorrectionParameters.CorrectionParameters  correctionsParameters){
 	 	  saveAndShowEnable( imp,    correctionsParameters , true, true);
@@ -2254,6 +2255,7 @@ public class EyesisCorrections {
 	   }
 
 	   private void saveAndShow(
+//	   public void saveAndShow(
 			   ImagePlus             imp,
 			   EyesisCorrectionParameters.CorrectionParameters  correctionsParameters,
 			   boolean               save,

src/main/java/Eyesis_Correction.java

@@ -462,6 +462,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 			addButton("Select kernels image",      panelDct1, color_configure);
 			addButton("Create DCT kernels",        panelDct1, color_process);
 			addButton("Read DCT kernels",          panelDct1, color_process);
+			addButton("Setup DCT parameters",      panelDct1, color_configure);
+			addButton("DCT process files",         panelDct1, color_process);
 			add(panelDct1);
 		}
 		pack();
@@ -2781,8 +2783,110 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
         		true,
         		DBG_IMP.getTitle()+"-IDCTDC");  
     	return;
+/* ======================================================================== */
     	
+    } else if (label.equals("Setup DCT parameters")) {
+        DCT_PARAMETERS.showDialog();
+        return;
+
 /* ======================================================================== */
+    	
+    } else if (label.equals("DCT 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 DCT 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 (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");
+        	}
+            EYESIS_DCT.readDCTKernels(
+            		DCT_PARAMETERS,
+            		CONVOLVE_FFT_SIZE/2,
+                    THREADS_MAX,
+                    UPDATE_STATUS, // update status info
+            		DEBUG_LEVEL);
+        	if (DEBUG_LEVEL > 1){
+        		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,
+        		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;
+
+/* ======================================================================== */
+
     } else if (label.equals("DCT test 3")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	int n = 32;
@@ -3397,6 +3501,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
         
         EYESIS_DCT.createDCTKernels(
         		DCT_PARAMETERS,
+/*        		
+        		EYESIS_CORRECTIONS.pixelMapping,
+*/        		
         		CONVOLVE_FFT_SIZE/2,
                 THREADS_MAX,
                 UPDATE_STATUS, // update status info

src/main/java/ImageDtt.java

@@ -529,7 +529,7 @@ public class ImageDtt {
 						}						
 
 						
-						if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
+						if ((dct_kernels!=null) && (tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
 							double [][] dbg_tile = {
 									dct_kernels.st_direct[color][kernelTileY][kernelTileX],
 									dct_kernels.st_kernels[color][kernelTileY][kernelTileX],