cluster texture output

src/main/java/CorrectionColorProc.java

@@ -47,7 +47,7 @@ public class CorrectionColorProc {
     void setDebug(int debugLevel){this.debugLevel=debugLevel;}
 
     
-    public void  processColorsWeights(ImageStack stack,
+    public void  processColorsWeights(ImageStack stack, // does not like NaN (in GaussianBlur
   		  double scale,     // initial maximal pixel value (16))
   		  EyesisCorrectionParameters.ColorProcParameters  colorProcParameters,
   		  CorrectionColorProc.ColorGainsParameters channelGainParameters,
@@ -107,7 +107,7 @@ public class CorrectionColorProc {
 
     	for (i=0;i<length;i++) {
     		double Y=Ar*fpixels_r[i]+Ag*fpixels_g[i]+Ab*fpixels_b[i];
-    		Y=linGamma(colorProcParameters.gamma, gamma_a, gamma_linK, colorProcParameters.minLin, Y)/Y;
+    		Y= (Y !=0.0) ? (linGamma(colorProcParameters.gamma, gamma_a, gamma_linK, colorProcParameters.minLin, Y)/Y): 0.0;
     		fpixels_r[i]*=Y*gain_red; 
     		fpixels_g[i]*=Y*gain_green; 
     		fpixels_b[i]*=Y*gain_blue; 
@@ -151,7 +151,7 @@ public class CorrectionColorProc {
     	double KPbB= -(2.0*(1-colorProcParameters.kb))/colorProcParameters.saturationBlue;
     	double KPrG=  2.0*colorProcParameters.kr*(1-colorProcParameters.kr)/Kg/colorProcParameters.saturationRed;
     	double KPbG=  2.0*colorProcParameters.kb*(1-colorProcParameters.kb)/Kg/colorProcParameters.saturationBlue;
-    	if (debugLevel>1) {
+    	if (debugLevel> 1) {
     		System.out.println ( " processColorsWeights() gain_red="+gain_red+" gain_green="+gain_green+" gain_blue="+gain_blue);
     		System.out.println ( " processColorsWeights() gamma="+colorProcParameters.gamma+      " minLin="+colorProcParameters.minLin+" gamma_a="+gamma_a+" gamma_linK="+gamma_linK);
     		System.out.println ( " processColorsWeights() Kr="+colorProcParameters.kr+" Kg="+Kg+" Kb="+colorProcParameters.kb+" Sr="+Sr+" Sb="+Sb);
@@ -221,7 +221,7 @@ public class CorrectionColorProc {
     		gb.blurDouble(dpixels_pb, width, height, colorProcParameters.chromaBrightSigma, colorProcParameters.chromaBrightSigma, 0.01);
     		gb.blurDouble(dpixels_pr_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
     		gb.blurDouble(dpixels_pb_dark, width, height, colorProcParameters.chromaDarkSigma, colorProcParameters.chromaDarkSigma, 0.01);
-    		if (debugLevel>2) {
+    		if (debugLevel> 2) {
     			SDFA_INSTANCE.showArrays(dmask, width, height,"dmask");          
     			SDFA_INSTANCE.showArrays(dpixels_pr, width, height,"dpixels_pr");          
     			SDFA_INSTANCE.showArrays(dpixels_pb, width, height,"dpixels_pb");          
@@ -340,7 +340,7 @@ public class CorrectionColorProc {
           double KPbB= -(2.0*(1-colorProcParameters.kb))/colorProcParameters.saturationBlue;
           double KPrG=  2.0*colorProcParameters.kr*(1-colorProcParameters.kr)/Kg/colorProcParameters.saturationRed;
           double KPbG=  2.0*colorProcParameters.kb*(1-colorProcParameters.kb)/Kg/colorProcParameters.saturationBlue;
-          if (debugLevel>1) {
+          if (debugLevel > 1) {
               System.out.println ( " processColorsWeights() gain_red="+gain_red+" gain_green="+gain_green+" gain_blue="+gain_blue);
               System.out.println ( " processColorsWeights() gamma="+colorProcParameters.gamma+      " minLin="+colorProcParameters.minLin+" gamma_a="+gamma_a+" gamma_linK="+gamma_linK);
               System.out.println ( " processColorsWeights() Kr="+colorProcParameters.kr+" Kg="+Kg+" Kb="+colorProcParameters.kb+" Sr="+Sr+" Sb="+Sb);

src/main/java/EyesisCorrectionParameters.java

@@ -2022,6 +2022,8 @@ public class EyesisCorrectionParameters {
   		public double     bgnd_maybe       = 0.1; // maximal strength to ignore as non-background
 //  		public double     bgnd_2diff       = 0.005; // maximal strength to ignore as non-background
   		public int        min_clstr_seed   = 2;     // number of tiles in a cluster to seed (just background?)
+  		public int        min_clstr_lone   = 4;     // number of tiles in a cluster not close to other clusters (more than 2 tiles apart)
+  		public int        fill_gaps        = 4;     // same as in grow - 1:  4 directions by 1 step, 2: 8 directions by 1 step. +2*n - alternating hor/vert
   		public int        min_clstr_block  = 3;     // number of tiles in a cluster to block (just non-background?)
   		public int        bgnd_grow        = 2;     // number of tiles to grow (1 - hor/vert, 2 - hor/vert/diagonal)
   		
@@ -2143,6 +2145,8 @@ public class EyesisCorrectionParameters {
 			properties.setProperty(prefix+"bgnd_sure",        this.bgnd_sure +"");
 			properties.setProperty(prefix+"bgnd_maybe",       this.bgnd_maybe +"");
   			properties.setProperty(prefix+"min_clstr_seed",   this.min_clstr_seed+"");
+  			properties.setProperty(prefix+"min_clstr_lone",   this.min_clstr_lone+"");
+  			properties.setProperty(prefix+"fill_gaps",        this.fill_gaps+"");
   			properties.setProperty(prefix+"min_clstr_block",  this.min_clstr_block+"");
   			properties.setProperty(prefix+"bgnd_grow",        this.bgnd_grow+"");
   			properties.setProperty(prefix+"ortho_min_hor",    this.ortho_min_hor +"");
@@ -2255,6 +2259,8 @@ public class EyesisCorrectionParameters {
   			if (properties.getProperty(prefix+"bgnd_sure")!=null)         this.bgnd_sure=Double.parseDouble(properties.getProperty(prefix+"bgnd_sure"));
   			if (properties.getProperty(prefix+"bgnd_maybe")!=null)        this.bgnd_maybe=Double.parseDouble(properties.getProperty(prefix+"bgnd_maybe"));
   			if (properties.getProperty(prefix+"min_clstr_seed")!=null)    this.min_clstr_seed=Integer.parseInt(properties.getProperty(prefix+"min_clstr_seed"));
+  			if (properties.getProperty(prefix+"min_clstr_lone")!=null)    this.min_clstr_lone=Integer.parseInt(properties.getProperty(prefix+"min_clstr_lone"));
+  			if (properties.getProperty(prefix+"fill_gaps")!=null)          this.fill_gaps=Integer.parseInt(properties.getProperty(prefix+"fill_gaps"));
   			if (properties.getProperty(prefix+"min_clstr_block")!=null)   this.min_clstr_block=Integer.parseInt(properties.getProperty(prefix+"min_clstr_block"));
   			if (properties.getProperty(prefix+"bgnd_grow")!=null)         this.bgnd_grow=Integer.parseInt(properties.getProperty(prefix+"bgnd_grow"));
   			if (properties.getProperty(prefix+"ortho_min_hor")!=null)     this.ortho_min_hor=Double.parseDouble(properties.getProperty(prefix+"ortho_min_hor"));
@@ -2382,6 +2388,8 @@ public class EyesisCorrectionParameters {
   			gd.addNumericField("Maximal strength to ignore as non-background",                                 this.bgnd_maybe,  3);
 
   			gd.addNumericField("Number of tiles in a cluster to seed (just background?)",                      this.min_clstr_seed,   0);
+  			gd.addNumericField("Number of tiles in a cluster not close to other clusters (more than 2 tiles apart)", this.min_clstr_lone,   0);
+  			gd.addNumericField("Fill gaps betsween clusters, see comments for 'grow'",                         this.fill_gaps,   0);
   			gd.addNumericField("Number of tiles in a cluster to block (just non-background?)",                 this.min_clstr_block,   0);
   			gd.addNumericField("Number of tiles to grow tile selection (1 - hor/vert, 2 - hor/vert/diagonal)", this.bgnd_grow,   0);
 
@@ -2503,6 +2511,8 @@ public class EyesisCorrectionParameters {
   			this.bgnd_sure=             gd.getNextNumber();
   			this.bgnd_maybe=            gd.getNextNumber();
   			this.min_clstr_seed=  (int) gd.getNextNumber();
+  			this.min_clstr_lone=  (int) gd.getNextNumber();
+  			this.fill_gaps=       (int) gd.getNextNumber();
   			this.min_clstr_block= (int) gd.getNextNumber();
   			this.bgnd_grow=       (int) gd.getNextNumber();
   			this.ortho_min_hor=         gd.getNextNumber();

src/main/java/EyesisCorrections.java

@@ -1398,7 +1398,7 @@ public class EyesisCorrections {
 				  break;
 			  }
 		  }
-		  if (debugLevel>2) {
+		  if (debugLevel > 2) {
 			  System.out.println ( "Input file color slice numbers:");
 			  System.out.println ( "  Red -   slice "+((rgbNumbers[0]>0)?rgbNumbers[0]:"missing"));
 			  System.out.println ( "  Green - slice "+((rgbNumbers[1]>0)?rgbNumbers[1]:"missing"));

src/main/java/EyesisTiff.java

@@ -70,7 +70,7 @@ public class EyesisTiff {
 		int width = imp.getWidth();
 		int height = imp.getHeight();
 		int [] pixels = (int []) imp.getProcessor().getPixels();
-		System.out.println("width="+width+", height="+height+" length="+pixels.length);
+		System.out.println("savePNG_ARGB32("+path+"): width="+width+", height="+height+" length="+pixels.length);
 		
 		DataBufferInt buffer = new DataBufferInt(pixels, pixels.length);
 

src/main/java/ImageDtt.java

@@ -1044,7 +1044,7 @@ public class ImageDtt {
 			if (i == (transform_size-1)) enh_ortho_scale[i] = 0.0 ; // hardwired 0 in the center
 			enh_ortho_scale[i] *= Math.sin(Math.PI*(i+1.0)/(2*transform_size));
 		}
-		if (globalDebugLevel > -1){
+		if (globalDebugLevel > 0){
 			System.out.println("enhortho_width="+ enhortho_width+" enhortho_scale="+ enhortho_scale);
 			for (int i = 0; i < corr_size; i++){
 				System.out.println(" enh_ortho_scale["+i+"]="+ enh_ortho_scale[i]);

src/main/java/X3dOutput.java

@@ -137,3 +137,24 @@ public class X3dOutput {
 		return bbox;
 	}
 }
+/*
+An IndexedFaceSet geometry node creates geometry out of faces
+
+    texCoord and texCoordIndex - specify texture pieces 
+
+Shape {
+    appearance Appearance { . . . }
+    geometry IndexedFaceSet {
+        coord Coordinate { . . . }
+        coordIndex [ . . . ]
+        texCoord TextureCoordinate { . . . }
+        texCoordIndex [ . . . ]
+    }
+}
+<IndexedFaceSet coordIndex="0 1 2 -1 0 2 3 -1 ..." texCoordIndex="0 1 2 -1 0 2 3 -1 ...">
+ <Coordinate point="-37.500000 4.000000 -46.450000 .../>
+ <TextureCoordinate point="-37.500000 4.000000 -46.450000 .../>
+ </IndexedFaceSet>
+ 
+ */
+*/
\ No newline at end of file

src/main/java/showDoubleFloatArrays.java

@@ -180,6 +180,9 @@ import ij.process.*;
   }
 
   public ImageStack makeStack(double[][] pixels, int width, int height, String [] titles) {
+	  return makeStack( pixels, width, height, titles, false);
+  }
+  public ImageStack makeStack(double[][] pixels, int width, int height, String [] titles, boolean noNaN) {
       float [] fpixels;
       ImageStack array_stack=new ImageStack(width,height);
       for (int i=0;i<pixels.length;i++) if (pixels[i]!=null) {
@@ -188,7 +191,11 @@ import ij.process.*;
         	  return null;
           }
         fpixels=new float[pixels[i].length];
+        if (noNaN){
+        	for (int j=0;j<fpixels.length;j++) fpixels[j]= Double.isNaN(pixels[i][j])? 0.0F: ((float)pixels[i][j]);
+        } else {
         	for (int j=0;j<fpixels.length;j++) fpixels[j]=(float)pixels[i][j];
+        }
         if (titles!=null){
             array_stack.addSlice(titles[i],    fpixels);
         } else {