aberration correction with clt

src/main/java/EyesisCorrections.java

@@ -2076,8 +2076,53 @@ public class EyesisCorrections {
 	      outStack.addSlice(chnNames[chn], outPixels[chn]);
 	    }
 	    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