Getting processed LWIR images

src/main/java/com/elphel/imagej/cameras/ThermalColor.java

@@ -26,11 +26,11 @@ public class ThermalColor {
 
 	public double [] getRGB(double v) { // Get R,G,B (0..255) triplet for input value in the range 0..1
 		double k = out_range/PALETTE_RANGE;
-		double value = (v-min)/(max-min);
-		int ivalue = (int) (value/(this.palette.length - 1));
+		double value = (v-min)/(max-min) * (this.palette.length - 1);
+		int ivalue = (int) (value);
 		if (ivalue < 0) return this.palette[0];
 		if (ivalue >= (this.palette.length -1)) return this.palette[this.palette.length -1];
-		double a = (value-ivalue)*(this.palette.length - 1); // 0..1
+		double a = (value-ivalue); // 0..1
 		double [] rslt = {
 				k*((1 - a) * this.palette[ivalue][0] + a * this.palette[ivalue+1][0]),
 				k*((1 - a) * this.palette[ivalue][1] + a * this.palette[ivalue+1][1]),
@@ -97,7 +97,8 @@ public class ThermalColor {
 				0xfff285, 0xfff28a, 0xfff38e, 0xfff492, 0xfff496, 0xfff49a, 0xfff59e, 0xfff5a2,
 				0xfff5a6, 0xfff6aa, 0xfff6af, 0xfff7b3, 0xfff7b6, 0xfff8ba, 0xfff8bd, 0xfff8c1,
 				0xfff8c4, 0xfff9c7, 0xfff9ca, 0xfff9cd, 0xfffad1, 0xfffad4, 0xfffbd8, 0xfffcdb,
-				0xfffcdf, 0xfffde2, 0xfffde5, 0xfffde8, 0xfffeeb, 0xfffeee, 0xfffef1, 0xfffef4, 0xfffff};
+				0xfffcdf, 0xfffde2, 0xfffde5, 0xfffde8, 0xfffeeb, 0xfffeee, 0xfffef1, 0xfffef4,
+				0xffffff};
 		int [][] palettes = {white_hot_palette, black_hot_palette, iron_palette};
 		if (indx <0) indx = 0;
 		else if (indx >= palettes.length) indx = palettes.length - 1;

src/main/java/com/elphel/imagej/correction/EyesisCorrections.java

@@ -1838,6 +1838,57 @@ public class EyesisCorrections {
 		return imp;
 	}
 
+	public static ImagePlus convertRGBAFloatToRGBA32(
+			ImageStack stackFloat, //r,g,b,a
+			String title,
+			double r_min,
+			double r_max,
+			double g_min,
+			double g_max,
+			double b_min,
+			double b_max,
+			double alpha_min,
+			double alpha_max){
+		double [] mins= {r_min,g_min,b_min,alpha_min};
+		double [] maxs= {r_max,g_max,b_max,alpha_max};
+		int i;
+		int length=stackFloat.getWidth()*stackFloat.getHeight();
+		int numSlices  = stackFloat.getSize();
+		if (numSlices > 4) numSlices = 4;
+		float [][] fpixels=new float[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++) {
+
+			fpixels[i]= (float[])stackFloat.getPixels(i+1);
+		}
+		for (i = 0; i < length; i++) {
+			pixels[i]=0;
+			for (int j=0; j < numSlices; j++) {
+				c = sliceSeq[j];
+				d=(int)((fpixels[c][i]-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(stackFloat.getWidth(),stackFloat.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

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -4505,6 +4505,10 @@ public class QuadCLT {
 			  }
 		  }
 		  if (isLwir()) {
+			  String [] rgb_titles =  {"red","green","blue"};
+			  String [] rgba_titles = {"red","green","blue","alpha"};
+			  String [] titles = (alpha == null) ? rgb_titles : rgba_titles;
+			  int num_slices = (alpha == null) ? 3 : 4;
 			  double offset = getLwirOffset();
 			  double mn = colorProcParameters.lwir_low - offset;
 			  double mx = colorProcParameters.lwir_high - offset;
@@ -4513,13 +4517,38 @@ public class QuadCLT {
 					  mn,
 					  mx,
 					  255.0);
-			  rbg_in = new double [3][iclt_data[green_index].length];
-			  for (int i = 0; i < rbg_in[0].length; i++) {
+			  double [][] rgba = new double [num_slices][];
+			  for (int i = 0; i < 3; i++) rgba[i] = new double [iclt_data[green_index].length];
+			  for (int i = 0; i < rbg_in[green_index].length; i++) {
+				  if (i == 700) {
+					  System.out.println("linearStackToColor(): i="+i);
+				  }
 				  double [] rgb = tc.getRGB(iclt_data[green_index][i]);
-				  rbg_in[0][i] = rgb[0]; // red
-				  rbg_in[1][i] = rgb[2]; // blue
-				  rbg_in[2][i] = rgb[1]; // green
-			  }
+				  rgba[0][i] = rgb[0]; // red
+				  rgba[1][i] = rgb[1]; // green
+				  rgba[2][i] = rgb[2]; // blue
+			  }
+			  if (alpha != null) {
+				  rgba[3] = alpha; // 0..1
+			  }
+			  ImageStack stack = sdfa_instance.makeStack(
+					  rgba,       // iclt_data,
+					  width,      // (tilesX + 0) * clt_parameters.transform_size,
+					  height,     // (tilesY + 0) * clt_parameters.transform_size,
+					  titles,     // or use null to get chn-nn slice names
+					  true);      // replace NaN with 0.0
+			  ImagePlus imp_rgba =  EyesisCorrections.convertRGBAFloatToRGBA32(
+					  stack,   // ImageStack stackFloat, //r,g,b,a
+						name+"ARGB"+suffix, // String title,
+						0.0,   // double r_min,
+						255.0, // double r_max,
+						0.0,   // double g_min,
+						255.0, // double g_max,
+						0.0,   // double b_min,
+						255.0, // double b_max,
+						0.0,   // double alpha_min,
+						1.0);  // double alpha_max)
+			  return imp_rgba;
 		  }
 
 		  ImageStack stack = sdfa_instance.makeStack(
@@ -4659,6 +4688,7 @@ public class QuadCLT {
 			  titleFull=name+"-YPrPb"+suffix;
 			  if (debugLevel > 1) System.out.println("Using full stack, including YPbPr");
 		  }
+
 		  if (alpha_pixels != null){
 			  stack.addSlice("alpha",alpha_pixels);
 		  }
@@ -8178,7 +8208,7 @@ public class QuadCLT {
 				  texture_overlap[alpha_index][i] = d;
 			  }
 		  }
-		  // for now - use just RGB. Later add oprion for RGBA
+		  // for now - use just RGB. Later add option for RGBA
 		  double [][] texture_rgb = {texture_overlap[0],texture_overlap[1],texture_overlap[2]};
 		  double [][] texture_rgba = {texture_overlap[0],texture_overlap[1],texture_overlap[2],texture_overlap[3]};
 		  double [][] texture_rgbx = ((clt_parameters.alpha1 > 0)? texture_rgba: texture_rgb);