Cleaning up (4bdd4cd8) · Commits · Elphel / imagej-elphel

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

+17 −29

Original line number	Diff line number	Diff line
		@@ -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/IntersceneMatchParameters.java

+80 −19

Original line number	Diff line number	Diff line
		@@ -51,11 +51,19 @@ public class IntersceneMatchParameters {
		public double sfm_same_weight = 0.8; // correction weight when new SfM gain is the same as the old one
		public int sfm_shrink = 2; // shrink sfm gain area before applying sfm_fade_sigma
		public double sfm_fade_sigma = 3.0; // fade SfM gains at the edges
		public double sfm_min_str = 0.4; // update if correction strength exceeds
		public double sfm_min_str1 = 0.2; // update if correction strength exceeds
		public double sfm_min_str16 = 0.4; // update if correction strength exceeds (for >=16 pairs)
		public boolean sfm_use_neibs = true; // use neighbors if individual corr is too weak
		public double sfm_neib_too_str= 0.4; // do not count neighbors stronger than that
		public double sfm_neib_str= 0.5; // update if no-individual and neibs correction strength exceeds
		public double sfm_neib_too_str1= 0.3; // do not count neighbors stronger than that
		public double sfm_neib_too_str16= 0.4; // do not count neighbors stronger than that (for >=16 pairs)
		public double sfm_neib_str1= 0.2; // update if no-individual and neibs correction strength exceeds
		public double sfm_neib_str16= 0.5; // update if no-individual and neibs correction strength exceeds (for >=16 pairs)
		public int sfm_extrap_steps = 5; // extrapolate disparity this number over undefined by SfM area
		public int sfm_extrap_radius = 5; // find tilt for extrapolation using this radius circle around the new tile

		public boolean sfm_average_neibs = false; // Average neighbors disparity among them
		public boolean sfm_fill_weak = false; // Fill too weak tiles from nearest neighbors
		public boolean sfm_extrapolate = false; // Extrapolate tiles with no SfM data (near edges)

		public double [] getImsMountATR() {
		return new double [] {
		@@ -469,14 +477,31 @@ public class IntersceneMatchParameters {
		"Shrink sfm gain area before applying sfm_fade_sigmas.");
		gd.addNumericField("Fade SfM area sigma", this.sfm_fade_sigma, 5,8,"",
		"Fade SfM gains at the edges.");
		gd.addNumericField("Minimal correlation strength", this.sfm_min_str, 5,8,"",
		gd.addNumericField("Minimal correlation strength", this.sfm_min_str1, 5,8,"",
		"Update if correction strength of individual tiles exceeds.");
		gd.addNumericField("Minimal correlation strength >= 16 pairs", this.sfm_min_str16, 5,8,"",
		"Update if correction strength of individual tiles exceeds (for >=16 pairs).");
		gd.addCheckbox ("Use neighbors", this.sfm_use_neibs,
		"Use neighbors if individual corr is too weak.");
		gd.addNumericField("Too strong neighbors", this.sfm_neib_too_str, 5,8,"",
		gd.addNumericField("Too strong neighbors >= 16 pairs", this.sfm_neib_too_str1, 5,8,"",
		"Do not accumulate neighbors stronger than that.");
		gd.addNumericField("Minimal neighbors strength", this.sfm_neib_str, 5,8,"",
		gd.addNumericField("Too strong neighbors", this.sfm_neib_too_str16, 5,8,"",
		"Do not accumulate neighbors stronger than that (for >=16 pairs).");
		gd.addNumericField("Minimal neighbors strength", this.sfm_neib_str1, 5,8,"",
		"Update if no-individual and neighbors correction strength exceeds this.");
		gd.addNumericField("Minimal neighbors strength >=16 pairs", this.sfm_neib_str16, 5,8,"",
		"Update if no-individual and neighbors correction strength exceeds this (for >=16 pairs).");
		gd.addNumericField("Extrapolation steps", this.sfm_extrap_steps, 0,3,"",
		"Extrapolate disparity this number of times over the undefined by SfM area.");
		gd.addNumericField("Extrapolation radius", this.sfm_extrap_radius, 0,3,"",
		"Find tilt for extrapolation using this radius circle around the new tile.");
		gd.addCheckbox ("Average neighbors", this.sfm_average_neibs,
		"Average neighbors disparity among them.");
		gd.addCheckbox ("Fill too weak tiles", this.sfm_fill_weak,
		"Fill too weak tiles from nearest neighbors.");
		gd.addCheckbox ("Extrapolate no SfM data", this.sfm_extrapolate,
		"Extrapolate tiles with no SfM data (near edges).");


		gd.addTab ("Scene Series", "Processing series of scenes and multi-series sets");
		gd.addMessage ("Build series options");
		@@ -1156,10 +1181,19 @@ public class IntersceneMatchParameters {
		this.sfm_same_weight = gd.getNextNumber();
		this.sfm_shrink = (int) gd.getNextNumber();
		this.sfm_fade_sigma = gd.getNextNumber();
		this.sfm_min_str = gd.getNextNumber();
		this.sfm_min_str1 = gd.getNextNumber();
		this.sfm_min_str16 = gd.getNextNumber();
		this.sfm_use_neibs = gd.getNextBoolean();
		this.sfm_neib_too_str = gd.getNextNumber();
		this.sfm_neib_str = gd.getNextNumber();
		this.sfm_neib_too_str1 = gd.getNextNumber();
		this.sfm_neib_too_str16 = gd.getNextNumber();
		this.sfm_neib_str1 = gd.getNextNumber();
		this.sfm_neib_str16 = gd.getNextNumber();
		this.sfm_extrap_steps = (int) gd.getNextNumber();
		this.sfm_extrap_radius = (int) gd.getNextNumber();
		this.sfm_average_neibs = gd.getNextBoolean();
		this.sfm_fill_weak = gd.getNextBoolean();
		this.sfm_extrapolate = gd.getNextBoolean();

		this.center_reference = gd.getNextBoolean();
		this.force_ref_dsi = gd.getNextBoolean();
		this.force_orientations = gd.getNextBoolean();
		@@ -1522,10 +1556,19 @@ public class IntersceneMatchParameters {
		properties.setProperty(prefix+"sfm_same_weight", this.sfm_same_weight+""); // double
		properties.setProperty(prefix+"sfm_shrink", this.sfm_shrink+""); // int
		properties.setProperty(prefix+"sfm_fade_sigma", this.sfm_fade_sigma+""); // double
		properties.setProperty(prefix+"sfm_min_str", this.sfm_min_str+""); // double
		properties.setProperty(prefix+"sfm_min_str1", this.sfm_min_str1+""); // double
		properties.setProperty(prefix+"sfm_min_str16", this.sfm_min_str16+""); // double
		properties.setProperty(prefix+"sfm_use_neibs", this.sfm_use_neibs+""); // boolean
		properties.setProperty(prefix+"sfm_neib_too_str", this.sfm_neib_too_str+""); // double
		properties.setProperty(prefix+"sfm_neib_str", this.sfm_neib_str +""); // double
		properties.setProperty(prefix+"sfm_neib_too_str1", this.sfm_neib_too_str1+""); // double
		properties.setProperty(prefix+"sfm_neib_too_str16", this.sfm_neib_too_str16+""); // double
		properties.setProperty(prefix+"sfm_neib_str1", this.sfm_neib_str1 +""); // double
		properties.setProperty(prefix+"sfm_neib_str16", this.sfm_neib_str16 +""); // double
		properties.setProperty(prefix+"sfm_extrap_steps", this.sfm_extrap_steps+""); // int
		properties.setProperty(prefix+"sfm_extrap_radius", this.sfm_extrap_radius+""); // int
		properties.setProperty(prefix+"sfm_average_neibs", this.sfm_average_neibs + ""); // boolean
		properties.setProperty(prefix+"sfm_fill_weak", this.sfm_fill_weak + ""); // boolean
		properties.setProperty(prefix+"sfm_extrapolate", this.sfm_extrapolate + ""); // boolean

		properties.setProperty(prefix+"center_reference", this.center_reference + ""); // boolean
		properties.setProperty(prefix+"force_ref_dsi", this.force_ref_dsi + ""); // boolean
		properties.setProperty(prefix+"force_orientations", this.force_orientations + ""); // boolean
		@@ -1848,10 +1891,19 @@ public class IntersceneMatchParameters {
		if (properties.getProperty(prefix+"sfm_same_weight")!=null) this.sfm_same_weight=Double.parseDouble(properties.getProperty(prefix+"sfm_same_weight"));
		if (properties.getProperty(prefix+"sfm_shrink")!=null) this.sfm_shrink=Integer.parseInt(properties.getProperty(prefix+"sfm_shrink"));
		if (properties.getProperty(prefix+"sfm_fade_sigma")!=null) this.sfm_fade_sigma=Double.parseDouble(properties.getProperty(prefix+"sfm_fade_sigma"));
		if (properties.getProperty(prefix+"sfm_min_str")!=null) this.sfm_min_str=Double.parseDouble(properties.getProperty(prefix+"sfm_min_str"));
		if (properties.getProperty(prefix+"sfm_min_str1")!=null) this.sfm_min_str1=Double.parseDouble(properties.getProperty(prefix+"sfm_min_str1"));
		if (properties.getProperty(prefix+"sfm_min_str16")!=null) this.sfm_min_str16=Double.parseDouble(properties.getProperty(prefix+"sfm_min_str16"));
		if (properties.getProperty(prefix+"sfm_use_neibs")!=null) this.sfm_use_neibs=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_use_neibs"));
		if (properties.getProperty(prefix+"sfm_neib_too_str")!=null) this.sfm_neib_too_str=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_too_str"));
		if (properties.getProperty(prefix+"sfm_neib_str")!=null) this.sfm_neib_str=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_str"));
		if (properties.getProperty(prefix+"sfm_neib_too_str1")!=null) this.sfm_neib_too_str1=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_too_str1"));
		if (properties.getProperty(prefix+"sfm_neib_too_str16")!=null) this.sfm_neib_too_str16=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_too_str16"));
		if (properties.getProperty(prefix+"sfm_neib_str1")!=null) this.sfm_neib_str1=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_str1"));
		if (properties.getProperty(prefix+"sfm_neib_str16")!=null) this.sfm_neib_str16=Double.parseDouble(properties.getProperty(prefix+"sfm_neib_str16"));
		if (properties.getProperty(prefix+"sfm_extrap_steps")!=null) this.sfm_extrap_steps=Integer.parseInt(properties.getProperty(prefix+"sfm_extrap_steps"));
		if (properties.getProperty(prefix+"sfm_extrap_radius")!=null) this.sfm_extrap_radius=Integer.parseInt(properties.getProperty(prefix+"sfm_extrap_radius"));
		if (properties.getProperty(prefix+"sfm_average_neibs")!=null) this.sfm_average_neibs=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_average_neibs"));
		if (properties.getProperty(prefix+"sfm_fill_weak")!=null) this.sfm_fill_weak=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_fill_weak"));
		if (properties.getProperty(prefix+"sfm_extrapolate")!=null) this.sfm_extrapolate=Boolean.parseBoolean(properties.getProperty(prefix+"sfm_extrapolate"));

		if (properties.getProperty(prefix+"center_reference")!=null) this.center_reference=Boolean.parseBoolean(properties.getProperty(prefix+"center_reference"));
		if (properties.getProperty(prefix+"force_ref_dsi")!=null) this.force_ref_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"force_ref_dsi"));
		if (properties.getProperty(prefix+"force_orientations")!=null) this.force_orientations=Boolean.parseBoolean(properties.getProperty(prefix+"force_orientations"));
		@@ -2201,10 +2253,19 @@ public class IntersceneMatchParameters {
		imp.sfm_same_weight = this.sfm_same_weight;
		imp.sfm_shrink = this.sfm_shrink;
		imp.sfm_fade_sigma = this.sfm_fade_sigma;
		imp.sfm_min_str = this.sfm_min_str;
		imp.sfm_min_str1 = this.sfm_min_str1;
		imp.sfm_min_str16 = this.sfm_min_str16;
		imp.sfm_use_neibs = this.sfm_use_neibs;
		imp.sfm_neib_too_str = this.sfm_neib_too_str;
		imp.sfm_neib_str = this.sfm_neib_str;
		imp.sfm_neib_too_str1 = this.sfm_neib_too_str1;
		imp.sfm_neib_too_str16 = this.sfm_neib_too_str16;
		imp.sfm_neib_str1 = this.sfm_neib_str1;
		imp.sfm_neib_str16 = this.sfm_neib_str16;
		imp.sfm_extrap_steps = this.sfm_extrap_steps;
		imp.sfm_extrap_radius = this.sfm_extrap_radius;
		imp.sfm_average_neibs = this.sfm_average_neibs;
		imp.sfm_fill_weak = this.sfm_fill_weak;
		imp.sfm_extrapolate = this.sfm_extrapolate;

		imp.center_reference = this.center_reference;
		imp.force_ref_dsi = this.force_ref_dsi;
		imp.force_orientations = this.force_orientations;

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

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