implemented defected pixels processing during image correction

src/main/java/Aberration_Calibration.java

@@ -9775,8 +9775,8 @@ if (MORE_BUTTONS) {
 					5.0,  // gapWidth,
 					2,    // algorithmNumber,
 					6,    // numInBase2, // number of neighbors (of 8) to use as a base if they all agree
-					3.0,  // binWidth2, // absolute
-					5.0,  // gapWidth2, // absolute
+					2.0,  // binWidth2, // absolute
+					4.0,  // gapWidth2, // absolute - will produce minimal defect of 5.0 (binWidth2/2+gapWidth2) 
 					true, // processHot,
 					true, // processCold,
 					true,  // updateSensorCalibrationFiles

src/main/java/EyesisCorrectionParameters.java

@@ -38,6 +38,8 @@ public class EyesisCorrectionParameters {
     	public boolean swapSubchannels01=      true; // false; // (false: 0-1-2, true - 1-0-2)
   		public boolean split=                  true;
   		public boolean vignetting=             true;
+  		public boolean pixelDefects=           true;
+  		public double  pixelDefectsThreshold=  8.0; // normally none with less than 5.0 are stored?
   		public boolean debayer=                true;
   		public boolean showDebayerEnergy =     false;
   		public boolean saveDebayerEnergy =     true;
@@ -103,6 +105,8 @@ public class EyesisCorrectionParameters {
     	public void setProperties(String prefix,Properties properties){
   			properties.setProperty(prefix+"split",this.split+"");
   			properties.setProperty(prefix+"vignetting",this.vignetting+"");
+  			properties.setProperty(prefix+"pixelDefects",this.pixelDefects+"");
+  			properties.setProperty(prefix+"pixelDefectsThreshold",this.pixelDefectsThreshold+"");
   			properties.setProperty(prefix+"debayer",this.debayer+"");
   			properties.setProperty(prefix+"showDebayerEnergy",this.showDebayerEnergy+"");
   			properties.setProperty(prefix+"saveDebayerEnergy",this.saveDebayerEnergy+"");
@@ -176,6 +180,8 @@ public class EyesisCorrectionParameters {
     	public void getProperties(String prefix,Properties properties){
   		    if (properties.getProperty(prefix+"split")!=null) this.split=Boolean.parseBoolean(properties.getProperty(prefix+"split"));
   		    if (properties.getProperty(prefix+"vignetting")!=null) this.vignetting=Boolean.parseBoolean(properties.getProperty(prefix+"vignetting"));
+  		    if (properties.getProperty(prefix+"pixelDefects")!=null) this.pixelDefects=Boolean.parseBoolean(properties.getProperty(prefix+"pixelDefects"));
+  		    if (properties.getProperty(prefix+"pixelDefectsThreshold")!=null) this.pixelDefectsThreshold=Double.parseDouble(properties.getProperty(prefix+"pixelDefectsThreshold"));
   		    if (properties.getProperty(prefix+"debayer")!=null) this.debayer=Boolean.parseBoolean(properties.getProperty(prefix+"debayer"));
   		    if (properties.getProperty(prefix+"showDebayerEnergy")!=null) this.showDebayerEnergy=Boolean.parseBoolean(properties.getProperty(prefix+"showDebayerEnergy"));
   		    if (properties.getProperty(prefix+"saveDebayerEnergy")!=null) this.saveDebayerEnergy=Boolean.parseBoolean(properties.getProperty(prefix+"saveDebayerEnergy"));
@@ -254,6 +260,8 @@ public class EyesisCorrectionParameters {
     		GenericDialog gd = new GenericDialog(title);
     		gd.addCheckbox ("Splt into Bayer stack (if false will exit)",       this.split);
     		gd.addCheckbox ("Apply vignetting/color correction to source files",this.vignetting);
+    		gd.addCheckbox ("Replace hot/warm/cold pixels with average of neighbors",this.pixelDefects);
+    		gd.addNumericField("Pixel difference thershold to consider it \"bad\" on 255.0 scale (0 - use all)", this.pixelDefectsThreshold, 2,6,"8.0");
 			String [] choices={"none","absolute","relative"};
 			if (this.exposureCorrectionMode<0) this.exposureCorrectionMode=0;
 			else if (this.exposureCorrectionMode>=choices.length) this.exposureCorrectionMode=choices.length-1;
@@ -340,11 +348,11 @@ public class EyesisCorrectionParameters {
     		if (gd.wasCanceled()) return false;
     		this.split=                  gd.getNextBoolean();
     		this.vignetting=             gd.getNextBoolean();
-    		
+    		this.pixelDefects=           gd.getNextBoolean();
+    		this.pixelDefectsThreshold=  gd.getNextNumber();
 			this.exposureCorrectionMode= gd.getNextChoiceIndex();
     		this.referenceExposure=0.001*gd.getNextNumber();
     		this.relativeExposure=       gd.getNextNumber();
-
     		this.debayer=           gd.getNextBoolean();
     		this.showDebayerEnergy= gd.getNextBoolean();
     		this.saveDebayerEnergy= gd.getNextBoolean();

src/main/java/EyesisCorrections.java

@@ -53,6 +53,9 @@ public class EyesisCorrections {
 	public EyesisCorrectionParameters.CorrectionParameters correctionsParameters=null;
 	public boolean [] usedChannels;
 	public float [][] channelVignettingCorrection=null;
+	public int [][][] defectsXY=null; // per each channel: pixel defects coordinates list (starting with worst)
+	public double [][] defectsDiff=null; // per each channel: pixel defects value (diff from average of neighbors), matching defectsXY
+
 	public int   [][] channelWidthHeight=null; 
 	public ImagePlus [] imageNoiseGains=null;
 	public String [] sharpKernelPaths=null;
@@ -392,9 +395,14 @@ public class EyesisCorrections {
 	public void createChannelVignetting(){
 		this.channelWidthHeight=new int [this.usedChannels.length][];
 		this.channelVignettingCorrection=new float [this.usedChannels.length][];
+		this.defectsXY=new int [this.usedChannels.length][][];
+		this.defectsDiff=new double [this.usedChannels.length][];
+		
 		for (int nChn=0;nChn< this.usedChannels.length; nChn++){
 			this.channelWidthHeight[nChn]=null;
 			this.channelVignettingCorrection[nChn]=null;
+			this.defectsXY[nChn]=null;
+			this.defectsDiff[nChn]=null;
 		}
 		int [][] bayer={{1,0},{2,1}}; // GR/BG
 		ImagePlus imp=null,imp_composite=null;
@@ -455,11 +463,29 @@ public class EyesisCorrections {
 								this.channelWidthHeight[srcChannel][1],
 								bayer);
 						if (this.debugLevel>0){
-							System.out.println("Creating vignetting info for channel "+srcChannel+
+							System.out.println("Created vignetting info for channel "+srcChannel+
 									" subchannel="+subChannel+" ("+
 									correctionsParameters.getSourcePaths()[nFile]+")");
 							System.out.println("imageWidth= "+this.channelWidthHeight[srcChannel][0]+" imageHeight="+this.channelWidthHeight[srcChannel][1]);
 						}
+						this.defectsXY[srcChannel]=this.pixelMapping.getDefectsXY(srcChannel);
+						this.defectsDiff[srcChannel]=this.pixelMapping.getDefectsDiff(srcChannel);
+						if (this.debugLevel>0){
+							if (this.defectsXY[srcChannel]==null){
+								System.out.println("No pixel defects info is availabele for channel "+srcChannel);
+							} else {
+								System.out.println("Extracted "+this.defectsXY[srcChannel].length+" pixel outlayers for channel "+srcChannel+
+										" (x:y:difference");
+								int numInLine=8;
+								for (int i=0;i<this.defectsXY[srcChannel].length;i++){
+									System.out.print(this.defectsXY[srcChannel][0]+":"+this.defectsXY[srcChannel][1]);
+									if ((this.defectsDiff[srcChannel]!=null) && (this.defectsDiff[srcChannel].length>i)){
+										System.out.print(":"+IJ.d2s(this.defectsDiff[srcChannel][i],3)+" ");
+									}
+									if (((i%numInLine)==(numInLine-1)) || (i == (this.defectsXY[srcChannel].length-1))) System.out.println();
+								}
+							}
+						}						
 					}
 				}
 			}
@@ -825,7 +851,38 @@ public class EyesisCorrections {
  		return 	imp_warped;
 	}
 
-	
+	public int correctDefects(
+			ImagePlus imp,
+			int channel,
+			int debugLevel){
+		int numApplied=0;
+		if (this.correctionsParameters.pixelDefects && (this.defectsXY!=null)&& (this.defectsXY[channel]!=null)){
+			// apply pixel correction
+			float [] pixels=(float []) imp.getProcessor().getPixels();
+			int width=imp.getWidth();
+			int height=pixels.length/width;
+			int [] dirsRB={2,2*width,-2,-2*width};
+			int [] dirsG={width+1,width-1,-width-1,-width+1};
+			for (int i=0;i<this.defectsXY[channel].length;i++){
+				if ( // difference provided and is smaller than threshold
+						(this.defectsDiff != null) &&
+						(this.defectsDiff[channel]!=null) &&
+						(this.defectsDiff[channel].length>i) &&
+						(Math.abs(this.defectsDiff[channel][i])<this.correctionsParameters.pixelDefectsThreshold)) break;
+				int x=this.defectsXY[channel][i][0];
+				int y=this.defectsXY[channel][i][1];
+				int index=x+y*width;
+				int [] dirs=(((x^y)&1)==0)?dirsG:dirsRB;
+				// do not bother to correct border pixels
+				if ((x<2) || (y<2) || (x>(width-3)) || (y>height-3)) continue;
+				double s=0.0;
+				for (int dir=0;dir<dirs.length;dir++) s+=pixels[index+dirs[dir]];
+				pixels[index]=(float) (s/dirs.length);
+				numApplied++;
+			}
+		}
+		return numApplied;
+	}
 	
 	
 	public ImagePlus processChannelImage(
@@ -852,6 +909,16 @@ public class EyesisCorrections {
 		//		int channel= Integer.parseInt((String) imp_src.getProperty("channel"));
 		int channel= (Integer) imp_src.getProperty("channel");
 		String path= (String) imp_src.getProperty("path");
+		if (this.correctionsParameters.pixelDefects && (this.defectsXY!=null)&& (this.defectsXY[channel]!=null)){
+			// apply pixel correction
+			int numApplied=	correctDefects(
+					imp_src,
+					channel,
+					debugLevel);
+			if ((debugLevel>0) && (numApplied>0)) { // reduce verbosity after verified defect correction works
+				System.out.println("Corrected "+numApplied+" pixels in "+path);
+			}
+		}
 		if (this.correctionsParameters.vignetting){
 			if ((this.channelVignettingCorrection==null) || (channel<0) || (channel>=this.channelVignettingCorrection.length) || (this.channelVignettingCorrection[channel]==null)){
 				System.out.println("No vignetting data for channel "+channel);

src/main/java/PixelMapping.java

@@ -178,6 +178,18 @@ public class PixelMapping {
 				bayer);
 	}
 	
+	public int [][] getDefectsXY(
+			int channel){
+		if ((this.sensors == null) || (channel<0)  && (channel>=this.sensors.length))return null;
+		return this.sensors[channel].getDefectsXY();
+	}
+
+	public double[] getDefectsDiff(
+			int channel){
+		if ((this.sensors == null) || (channel<0)  && (channel>=this.sensors.length))return null;
+		return this.sensors[channel].getDefectsDiff();
+	}
+
 ///SensorData
        	/*
 		public float [] getBayerFlatFieldFloat(
@@ -15550,6 +15562,10 @@ public class PixelMapping {
 	    public int    debugLevel=1;
 	    public DirectMap directMap=null;
 	    public EquirectangularMap equirectangularMap=null;
+
+	    public int [][] defectsXY=null; // pixel defects coordinates list (starting with worst)
+		public double [] defectsDiff=null; // pixel defects value (diff from average of neighbors), matching defectsXY
+	    
 	    // TODO - add option to generate individual flat projections
 		public InterSensor interSensor=null; // multiple sensors may have the same instance of the interSensor
 
@@ -15715,6 +15731,12 @@ public class PixelMapping {
 			}
 			return corrScale;
 		}
+		public int [][] getDefectsXY(){
+			return this.defectsXY;
+		}
+		public double [] getDefectsDiff(){
+			return this.defectsDiff;
+		}
 	    
 	    public class  DirectMap{
 	    	public int width;
@@ -16048,6 +16070,23 @@ public class PixelMapping {
 	        for (int n=0;n<pixels.length;n++) for (int i= 0;i<this.pixelCorrection[0].length;i++){
 	        	this.pixelCorrection[n][i]=pixels[n][i];
 	        }
+
+	        if (imp.getProperty("defects")!=null) {
+        		String sDefects=(String) imp.getProperty("defects");
+        		String [] asDefects=sDefects.trim().split(" ");
+        		this.defectsXY=new int [asDefects.length][2];
+        		this.defectsDiff=new double [asDefects.length];
+        		for (int i=0;i<asDefects.length;i++) {
+        			String [] stDefect=asDefects[i].split(":");
+        			this.defectsXY[i][0]=Integer.parseInt(stDefect[0]);
+        			this.defectsXY[i][1]=Integer.parseInt(stDefect[1]);
+        			this.defectsDiff[i]=Double.parseDouble(stDefect[2]);
+        		}
+        	} else {
+        		this.defectsXY=null;
+        		this.defectsDiff=null;
+        	}
+	        
 	        // now mask    
 	    }
 	    /**