Cleaning up

src/main/java/com/elphel/imagej/calibration/PixelMapping.java

@@ -1221,7 +1221,7 @@ public class PixelMapping {
     		if (saveTiff){
     			String outPath=((resultDirectory.length()<1)?"":(resultDirectory+Prefs.getFileSeparator()))+impOverlap.getTitle()+".tiff";
     			try {
-    				(new EyesisTiff()).saveTiff(
+    				EyesisTiff.saveTiff(
     						impOverlap,
     						outPath,
     						3, // float32

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

@@ -2743,7 +2743,7 @@ public class EyesisCorrections {
 					try {
 						(new EyesisTiff()).saveTiffARGB32(
 								imp,
-								path, // +".tiff",
+								path+".tiff", //path, // +".tiff",
 								false, // correctionsParameters.imageJTags,
 								debugLevel);
 					} catch (IOException e) {

src/main/java/com/elphel/imagej/readers/EyesisTiff.java

@@ -295,7 +295,7 @@ the type of pixel data in this file 	getPixelType()
 
 
 
-	public void saveTiff(
+	public static void saveTiff(
 			ImagePlus imp,
 			String path,
 			int mode,     // 0 - 8-bit, 1 - 16-bit, 2 - 32-bit unsigned, 3 - 32FP (only if source image is a 4-stack of FP)
@@ -316,7 +316,7 @@ the type of pixel data in this file 	getPixelType()
 		IJ.showMessage("Not yet implemented for this image type");
 	}
 
-	public void saveTiffARGB(
+	public static void saveTiffARGB(
 			ImagePlus imp,
 			String path,
 			int mode,     // 0 - 8-bit, 1 - 16-bit, 2 - 32-bit unsigned, 3 - 32FP (only if source image is a 4-stack of FP)
@@ -428,12 +428,14 @@ the type of pixel data in this file 	getPixelType()
 			return;
 		}
 		//        System.out.println("saveTiffARGBFloat32(): mode="+mode+" pixelType="+pixelType+" bw="+bw);
+//		ExifGPSTagSet gps_set = new ExifGPSTagSet();
+//		EXIFGPSTagSet gps_set = new EXIFGPSTagSet();
 		IFD ifd=new IFD();
-		ifd.put(new Integer(IFD.LITTLE_ENDIAN), new Boolean(false));
+		ifd.put(IFD.LITTLE_ENDIAN, false);
 		//        ifd.put(new Integer(IFD.LITTLE_ENDIAN), new Boolean(true));
-		ifd.put(new Integer(IFD.IMAGE_WIDTH), imp.getWidth());
-		ifd.put(new Integer(IFD.IMAGE_LENGTH), imp.getHeight());
-		ifd.put(new Integer(IFD.SAMPLES_PER_PIXEL), 4);
+		ifd.put(IFD.IMAGE_WIDTH, imp.getWidth());
+		ifd.put(IFD.IMAGE_LENGTH, imp.getHeight());
+		ifd.put(IFD.SAMPLES_PER_PIXEL, 4);
 		ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis");
 		ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);
 		// copy some other data?
@@ -484,7 +486,7 @@ the type of pixel data in this file 	getPixelType()
 				true); // boolean last)
 	}
 
-	public void saveTiffARGB32(
+	public static void saveTiffARGB32(
 			ImagePlus imp,
 			String path,
 			boolean imageJTags,
@@ -511,18 +513,19 @@ the type of pixel data in this file 	getPixelType()
 			bytes[pIndex++]=(byte) ((iPixels[i]>>24)& 0xff); // alpha
 		}
 		IFD ifd=new IFD();
-		ifd.put(new Integer(IFD.LITTLE_ENDIAN), new Boolean(false));
+		ifd.put(IFD.LITTLE_ENDIAN, false);
 		//        ifd.put(new Integer(IFD.LITTLE_ENDIAN), new Boolean(true));
-		ifd.put(new Integer(IFD.IMAGE_WIDTH), imp.getWidth());
-		ifd.put(new Integer(IFD.IMAGE_LENGTH), imp.getHeight());
-		ifd.put(new Integer(IFD.SAMPLES_PER_PIXEL), 4);
+		ifd.put(IFD.IMAGE_WIDTH, imp.getWidth());
+		ifd.put(IFD.IMAGE_LENGTH, imp.getHeight());
+		ifd.put(IFD.SAMPLES_PER_PIXEL, 4);
 		ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis");
 		ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);
 		// copy some other data?
 		ifd.putIFDValue(IFD.COMPRESSION, 1); //TiffCompression.UNCOMPRESSED);
 		ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB
-		ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra bytes (over 3) meaning Unassociated alpha data
-
+//		ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra bytes (over 3) meaning Unassociated alpha data
+		ifd.putIFDValue(IFD.EXTRA_SAMPLES,1); // extra bytes (over 3) meaning Unassociated alpha data
+		ifd.putIFDValue(IFD.SAMPLE_FORMAT,1); // 
 		//        int [] bpsArray={8,8,8,8};
 		//        ifd.putIFDValue(IFD.BITS_PER_SAMPLE, bpsArray); // will be done automatically
 		if (imp.getProperty("XPosition")!=null) {
@@ -548,24 +551,9 @@ the type of pixel data in this file 	getPixelType()
 			int index=0;
 			for (int i=0;i<ImageJInfoMagic.length;i++) bInfo[index++]=ImageJInfoMagic[i];
 			for (int i=skipFirstBytes;i<bInfoBody.length;      i++) bInfo[index++]=bInfoBody[i]; // first 2 bytes {-2, -1} ???
-			/*
-        	StringBuffer sb=new StringBuffer("bInfo: ");
-        	for (int i=0;i<bInfo.length;i++) sb.append(bInfo[i]+" ");
-        	System.out.println(sb.toString());
-        	sb=new StringBuffer("ImageJInfoMagic: ");
-        	for (int i=0;i<ImageJInfoMagic.length;i++) sb.append(ImageJInfoMagic[i]+" ");
-        	System.out.println(sb.toString());
-        	sb=new StringBuffer("bInfoBody: ");
-        	for (int i=0;i<bInfoBody.length;i++) sb.append(bInfoBody[i]+" ");
-        	System.out.println(sb.toString());
-        	System.out.println("info[0]="+info.charAt(0));
-        	System.out.println("info[1]="+info.charAt(1));
-        	System.out.println("info[2]="+info.charAt(2));
-			 */
 			long [] imageJcounts={12, bInfoBody.length-skipFirstBytes};
 			ifd.putIFDValue(IFDImageJByteCounts, imageJcounts);
 			ifd.putIFDValue(IFDImageJInfo, bInfo);
-
 		}
 		(new File(path)).delete(); // Otherwise TiffSaver appends!
 		TiffSaver tiffSaver = new TiffSaver(path);
@@ -584,7 +572,7 @@ the type of pixel data in this file 	getPixelType()
 
 
 
-	public void propertiesTiff(ImagePlus imp){
+	public static void propertiesTiff(ImagePlus imp){
 		FileInfo fi = imp.getOriginalFileInfo();
 		if ((fi==null) ||(fi.directory==null) ||  (fi.fileFormat!=FileInfo.TIFF)) {
 			IJ.error("TIFF Dumper", "File path not available or not TIFF file");

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

@@ -3070,7 +3070,7 @@ public class TexturedModel {
 							hdr_whs[0],    // int     width,
 							wh,            // int []  wh, // should be initialized to int [2]
 							full_render);  // double [][] img_src) 
-					if (img_cropped != null) {
+					if (img_cropped != null) { // has NaN and alpha 0-1
 						scenes[ref_index].saveDoubleArrayInModelDirectory(
 								suffix+"-CROP", // String      suffix,
 								null,           // String []   labels, // or null

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

@@ -131,7 +131,7 @@ public class TileNeibs{
 	 * @param dy offset in y direction
 	 * @return new index or -1 if leaving
 	 */
-	int getNeibIndex(int indx, int dx, int dy) {
+	public int getNeibIndex(int indx, int dx, int dy) {
 		int y = indx / sizeX + dy;
 		int x = indx % sizeX + dx;
 		if ((x < 0) || (y < 0 ) || (x >= sizeX) || (y >= sizeY)) return -1;