extracting background

src/main/java/Aberration_Correction.java

@@ -190,7 +190,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6;
 		0.075, //  b_min;
 		1.0, //  r_max;
 		1.0, //  g_max;
-		1.0  //  b_max;
+		1.0,  //  b_max;
+		0.0, //  alpha_min;
+		1.0 //  alpha_max;
    );
    
    public static FilesParameters FILE_PARAMETERS= new FilesParameters (
@@ -802,7 +804,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
    	    		  imp_colorStack.getTitle()+"-RGB24",
 	    		  0, 65536, // r range 0->0, 65536->256
 	    		  0, 65536, // g range
-	    		  0, 65536);// b range
+	    		  0, 65536, // b range
+	    		  0, 65536);// alpha range
 	    imp_RGB24.setTitle(imp_colorStack.getTitle()+"rgb24");
 	    imp_RGB24.show();
         return;
@@ -1177,26 +1180,30 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
 		  int g_min,
 		  int g_max,
 		  int b_min,
-		  int b_max){
-	  int [] mins= {r_min,g_min,b_min};
-	  int [] maxs= {r_max,g_max,b_max};
+		  int b_max,
+		  int alpha_min,
+		  int alpha_max){
+	  int [] mins= {r_min,g_min,b_min,alpha_min};
+	  int [] maxs= {r_max,g_max,b_max,alpha_max};
       int i;
 	  int length=stack16.getWidth()*stack16.getHeight();
-	  short [][] spixels=new short[3][];
+	  int numSlices  = stack16.getSize();
+	  if (numSlices > 4) numSlices = 4;
+	  short [][] spixels=new short[numSlices][];
 	  int [] pixels=new int[length];
 	  int c,d;
-	  double [] scale=new double[3];
-	  for (c=0;c<3;c++) {
+	  double [] scale=new double[numSlices];
+	  for (c = 0; c < numSlices; c++) {
 		  scale[c]=256.0/(maxs[c]-mins[c]);
 	  }
-	  for (i=0;i<3;i++) spixels[i]= (short[])stack16.getPixels(i+1);
-	  for (i=0;i<length;i++) {
+	  for (i = 0; i < numSlices; i++) spixels[i]= (short[])stack16.getPixels(i+1);
+	  for (i = 0; i < length; i++) {
 		  pixels[i]=0;
-		  for (c=0;c<3;c++) {
+		  for (c=0;c < numSlices;c++) {
 			  d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
-			  if (d>255) d=255;
-			  else if (d<0) d=0;
-			  pixels[i]= d | (pixels[i]<<8);
+			  if (d > 255) d=255;
+			  else if (d < 0) d=0;
+			  pixels[i]= d | (pixels[i] << 8);
 		  }
 	  }
 	  ColorProcessor cp=new ColorProcessor(stack16.getWidth(),stack16.getHeight());
@@ -1976,7 +1983,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
 						  title+"-RGB24",
 						  0, 65536, // r range 0->0, 65536->256
 						  0, 65536, // g range
-						  0, 65536);// b range
+			    		  0, 65536, // b range
+			    		  0, 65536);// alpha range
 				  if (processParameters.JPEG_scale!=1.0){
 					  ImageProcessor ip=imp_RGB24.getProcessor();
 					  ip.setInterpolationMethod(ImageProcessor.BICUBIC);
@@ -3504,6 +3512,9 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
     gd.addNumericField("Red   color white level",             rgbParameters.r_max,     3);
     gd.addNumericField("Green color white level",             rgbParameters.g_max,     3);
     gd.addNumericField("Blue  color white level",             rgbParameters.b_max,     3);
+    gd.addNumericField("Alpha channel min",                   rgbParameters.alpha_min, 3);
+    gd.addNumericField("Alpha channel max",                   rgbParameters.alpha_max, 3);
+    
     gd.showDialog();
     if (gd.wasCanceled()) return false;
     rgbParameters.r_min=                gd.getNextNumber();
@@ -3512,6 +3523,8 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
     rgbParameters.r_max=                gd.getNextNumber();
     rgbParameters.g_max=                gd.getNextNumber();
     rgbParameters.b_max=                gd.getNextNumber();
+    rgbParameters.alpha_min=            gd.getNextNumber();
+    rgbParameters.alpha_max=            gd.getNextNumber();
     return true;
   }
 
@@ -4233,13 +4246,15 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 
 /* ======================================================================== */
   public static class RGBParameters {
-		public double r_min;
-		public double g_min;
-		public double b_min;
-		public double r_max;
-		public double g_max;
-		public double b_max;
-
+		public double r_min = 0.075;
+		public double g_min = 0.075;
+		public double b_min = 0.075;
+		public double r_max = 1.0;
+		public double g_max = 1.0;
+		public double b_max = 1.0;
+		public double alpha_min = 0.0;
+		public double alpha_max = 1.0;
+/*
 		public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max) {
 			this.r_min = r_min;
 			this.g_min = g_min;
@@ -4248,6 +4263,18 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 			this.g_max = g_max;
 			this.b_max = b_max;
 		}
+*/		
+  		public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max, double alpha_min, double alpha_max) {
+  			this.r_min = r_min;
+  			this.g_min = g_min;
+  			this.b_min = b_min;
+  			this.r_max = r_max;
+  			this.g_max = g_max;
+  			this.b_max = b_max;
+  			this.alpha_min = alpha_min;
+  			this.alpha_max = alpha_max;
+  		}
+		
 		public void setProperties(String prefix,Properties properties){
 			properties.setProperty(prefix+"r_min",this.r_min+"");
 			properties.setProperty(prefix+"g_min",this.g_min+"");
@@ -4255,6 +4282,9 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 			properties.setProperty(prefix+"r_max",this.r_max+"");
 			properties.setProperty(prefix+"g_max",this.g_max+"");
 			properties.setProperty(prefix+"b_max",this.b_max+"");
+  			properties.setProperty(prefix+"alpha_min",this.alpha_min+"");
+  			properties.setProperty(prefix+"alpha_max",this.alpha_max+"");
+			
 		}
 		public void getProperties(String prefix,Properties properties){
 			this.r_min=Double.parseDouble(properties.getProperty(prefix+"r_min"));
@@ -4263,6 +4293,8 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 			this.r_max=Double.parseDouble(properties.getProperty(prefix+"r_max"));
 			this.g_max=Double.parseDouble(properties.getProperty(prefix+"g_max"));
 			this.b_max=Double.parseDouble(properties.getProperty(prefix+"b_max"));
+  			if (properties.getProperty(prefix+"alpha_min")!=null)  this.alpha_min=Double.parseDouble(properties.getProperty(prefix+"alpha_min"));
+  			if (properties.getProperty(prefix+"alpha_max")!=null)  this.alpha_max=Double.parseDouble(properties.getProperty(prefix+"alpha_max"));
 		}
 		
 	}

src/main/java/EyesisCorrections.java

@@ -1285,7 +1285,8 @@ public class EyesisCorrections {
 					  title+"-RGB24",
 					  0, 65536, // r range 0->0, 65536->256
 					  0, 65536, // g range
-					  0, 65536);// b range
+					  0, 65536,// b range
+					  0, 65536);// alpha range
 			  if (JPEG_scale!=1.0){
 				  ImageProcessor ip=imp_RGB.getProcessor();
 				  ip.setInterpolationMethod(ImageProcessor.BICUBIC);
@@ -1524,7 +1525,6 @@ public class EyesisCorrections {
 
 	/* ======================================================================== */
 	  public CompositeImage convertToComposite( ImagePlus imp) {
-//		  if (imp.isComposite()) return imp;
 		  if (imp.isComposite()) return null;
 		  if (imp.getNChannels()>1) {
 			  return null; // number of channels should be just 1
@@ -1532,8 +1532,6 @@ public class EyesisCorrections {
 		  int c = imp.getStackSize();
 		  imp.setDimensions(c, 1, 1);
 		  CompositeImage ci = new CompositeImage(imp, CompositeImage.COMPOSITE);
-//		  ci.show();
-//		  imp.hide();
 		  return ci;
 	  }
 
@@ -1546,19 +1544,21 @@ public class EyesisCorrections {
 		  int i,j;
 		  float [] fpixels;
 		  short [] spixels;
-		  double [] mins= {rgbParameters.r_min,rgbParameters.g_min,rgbParameters.b_min};
-		  double [] maxs= {rgbParameters.r_max,rgbParameters.g_max,rgbParameters.b_max};
-		  if (stack32.getSize()<3) return null;
+		  int numSlices  = stack32.getSize();
+		  if (numSlices > 4) numSlices = 4;
+		  if (numSlices < 3) return null;
+		  double [] mins= {rgbParameters.r_min, rgbParameters.g_min, rgbParameters.b_min, rgbParameters.alpha_min};
+		  double [] maxs= {rgbParameters.r_max, rgbParameters.g_max, rgbParameters.b_max, rgbParameters.alpha_max};
 		  double value;
 		  double scale;
-		  for (i=0;i<3;i++) {
-			 fpixels= (float[])stack32.getPixels(i+1);
-			 scale=65535.0/(maxs[i]-mins[i]);
+		  for (i = 0; i < numSlices; i++) {
+			 fpixels= (float[])stack32.getPixels(i + 1);
+			 scale=65535.0 / (maxs[i] - mins[i]);
 			 spixels=new short [length];
-			 for (j=0;j<length;j++) {
+			 for (j = 0; j < length; j++) {
 				 value=(fpixels[j]-mins[i])*scale;
-				 if      (value<0.0) value=0.0;
-				 else if (value>65535.0) value=65535.0;
+				 if      (value<0.0)     value = 0.0;
+				 else if (value>65535.0) value = 65535.0;
 				 spixels[j]=(short)(value+0.5);
 			 }
 			 stack16.addSlice(stack32.getSliceLabel(i+1), spixels);
@@ -1570,37 +1570,87 @@ public class EyesisCorrections {
 	  public ImagePlus convertRGB48toRGB24(
 			  ImageStack stack16,
 			  String title,
+			  int r_min,
+			  int r_max,
+			  int g_min,
+			  int g_max,
+			  int b_min,
+			  int b_max,
+			  int alpha_min,
+			  int alpha_max){
+		  int [] mins= {r_min,g_min,b_min,alpha_min};
+		  int [] maxs= {r_max,g_max,b_max,alpha_max};
+	      int i;
+		  int length=stack16.getWidth()*stack16.getHeight();
+		  int numSlices  = stack16.getSize();
+		  if (numSlices > 4) numSlices = 4;
+		  short [][] spixels=new short[numSlices][];
+		  int [] sliceSeq = new int [numSlices];
+		  for (int j = 0; j < numSlices; j++) sliceSeq[j] = (j + ((numSlices > 3)? 3:0)) % 4; 
+		  
+		  int [] pixels=new int[length];
+		  int c,d;
+		  
+		  double [] scale=new double[numSlices];
+		  for (c = 0; c < numSlices; c++) {
+			  scale[c]=256.0/(maxs[c]-mins[c]);
+		  }
+		  for (i = 0; i < numSlices; i++) spixels[i]= (short[])stack16.getPixels(i+1);
+		  for (i = 0; i < length; i++) {
+			  pixels[i]=0;
+			  for (int j=0; j < numSlices; j++) {
+				  c = sliceSeq[j];
+				  d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
+				  if (d > 255) d=255;
+				  else if (d < 0) d=0;
+				  pixels[i]= d | (pixels[i] << 8);
+			  }
+		  }
+		  ColorProcessor cp=new ColorProcessor(stack16.getWidth(),stack16.getHeight());
+		  cp.setPixels(pixels);
+		  ImagePlus imp=new ImagePlus(title,cp);
+		  return imp;
+	  }
+
+	  public ImageStack convertRGB48toRGBA24Stack(
+			  ImageStack stack16,
+			  double [] dalpha, // alpha pixel array 0..1.0 or null 
+//			  String title,
 			  int r_min,
 			  int r_max,
 			  int g_min,
 			  int g_max,
 			  int b_min,
 			  int b_max){
+		  ImageStack stack8 = new ImageStack(stack16.getWidth(), stack16.getHeight());
 		  int [] mins= {r_min,g_min,b_min};
 		  int [] maxs= {r_max,g_max,b_max};
 	      int i;
 		  int length=stack16.getWidth()*stack16.getHeight();
 		  short [][] spixels=new short[3][];
-		  int [] pixels=new int[length];
+		  byte [][] bpixels=new byte [(dalpha != null)? 4: 3][length];
 		  int c,d;
 		  double [] scale=new double[3];
 		  for (c=0;c<3;c++) {
 			  scale[c]=256.0/(maxs[c]-mins[c]);
 		  }
-		  for (i=0;i<3;i++) spixels[i]= (short[])stack16.getPixels(i+1);
-		  for (i=0;i<length;i++) {
-			  pixels[i]=0;
-			  for (c=0;c<3;c++) {
+		  for (i = 0; i <3; i++) spixels[i]= (short[])stack16.getPixels(i+1);
+		  for (c = 0; c <3; c++) {
+			  for (i = 0; i < length; i++){
 				  d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
 				  if (d>255) d=255;
 				  else if (d<0) d=0;
-				  pixels[i]= d | (pixels[i]<<8);
+				  bpixels[c][i]= (byte) d;
 			  }
+			  stack8.addSlice(stack16.getSliceLabel(c+1), bpixels[c]);
 		  }
-		  ColorProcessor cp=new ColorProcessor(stack16.getWidth(),stack16.getHeight());
-		  cp.setPixels(pixels);
-		  ImagePlus imp=new ImagePlus(title,cp);
-		  return imp;
+		  if (dalpha != null) {
+			  for (i = 0; i < length; i++){
+				  bpixels[3][i] = (byte) (255*dalpha[i]);
+			  }
+			  stack8.addSlice("alpha", bpixels[3]);
+		  }
+		  return stack8;
 	  }
 	  
 	/* ======================================================================== */
@@ -2312,16 +2362,77 @@ public class EyesisCorrections {
 
 		   if (path!=null) {
 			   path+=Prefs.getFileSeparator()+imp.getTitle();
-	 		  if (((imp.getStackSize()==1)) && (jpegQuality!=0) && ((imp.getFileInfo().fileType== FileInfo.RGB) || (jpegQuality>0))) {
+			   boolean hasAlphaHighByte = false;
+			   if ((imp.getStackSize()==1) && (imp.getFileInfo().fileType== FileInfo.RGB)) {
+				   int [] pixels = (int []) imp.getProcessor().getPixels();
+				   for (int i = 0; i < pixels.length; i++){
+					   if ((pixels[i] & 0xff000000) != 0){
+						   hasAlphaHighByte = true;
+						   break;
+					   }
+				   }
+			   }
+			   
+			   if (hasAlphaHighByte){
+				   if (correctionsParameters.png){
+					   if (this.debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
+					   (new EyesisTiff()).savePNG_ARGB32(
+							   imp,
+							   path+".png"
+							   );
+
+				   } else {
+					   if (this.debugLevel > 0) System.out.println("Saving RGBA result to "+path+".tiff");
+					   try {
+						   (new EyesisTiff()).saveTiffARGB32(
+								   imp,
+								   path+".tiff",
+								   false, // correctionsParameters.imageJTags,	
+								   debugLevel);
+					   } catch (IOException e) {
+						   e.printStackTrace();
+					   } catch (FormatException e) {
+						   e.printStackTrace();
+					   } catch (ServiceException e) {
+						   e.printStackTrace();
+					   } catch (DependencyException e) {
+						   e.printStackTrace();
+					   }
+				   }
+				   
+			   } else if (((imp.getStackSize()==1)) && (jpegQuality!=0) && ((imp.getFileInfo().fileType== FileInfo.RGB) || (jpegQuality>0))) {
 				   if (this.debugLevel>0) System.out.println("Saving result to "+path+".jpeg");
 				   FileSaver fs=new FileSaver(imp);
 				   if (jpegQuality>0) FileSaver.setJpegQuality(jpegQuality);
 				   fs.saveAsJpeg(path+".jpeg");
-	 		  }
-	 		  else {
+			   } else {
 				   if (this.debugLevel>0) System.out.println("Saving result to "+path+".tiff");
 				   FileSaver fs=new FileSaver(imp);
-	 			  if (imp.getStackSize()>1)  fs.saveAsTiffStack(path+".tiff");
+				   // Save as RGBA if it is RGBA
+				   int bytesPerPixel = imp.getBytesPerPixel();
+				   int mode = 0;
+				   if (bytesPerPixel > 1) mode = 1;
+				   if (bytesPerPixel > 3) mode = 3;// float, mode 2 not supported
+
+				   if ((imp.getStackSize() == 4) && imp.getStack().getSliceLabel(4).equals("alpha")){
+					   try {
+						   (new EyesisTiff()).saveTiff(
+								   imp,
+								   path+".tiff",
+								   mode, //
+								   1.0, // full scale, absolute
+								   false, // correctionsParameters.imageJTags,	
+								   debugLevel);
+					   } catch (IOException e) {
+						   e.printStackTrace();
+					   } catch (FormatException e) {
+						   e.printStackTrace();
+					   } catch (ServiceException e) {
+						   e.printStackTrace();
+					   } catch (DependencyException e) {
+						   e.printStackTrace();
+					   }
+				   } else if (imp.getStackSize()>1)  fs.saveAsTiffStack(path+".tiff");
 				   else fs.saveAsTiff(path+".tiff");
 			   }
 		   }