added separate hor/vert correlation results to detect vertical/horizontal features (9d378818) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+88 −10

Original line number	Diff line number	Diff line
		@@ -111,6 +111,7 @@ public class EyesisCorrectionParameters {
		public String cltKernelPrefix="clt-";
		public String cltSuffix=".clt-tiff";

		public String x3dDirectory="";

		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"split",this.split+"");
		@@ -198,6 +199,8 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"cltKernelPrefix", this.cltKernelPrefix);
		properties.setProperty(prefix+"cltSuffix", this.cltSuffix);

		properties.setProperty(prefix+"x3dDirectory", this.x3dDirectory);

		}

		public void getProperties(String prefix,Properties properties){
		@@ -289,6 +292,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"cltKernelPrefix")!= null) this.cltKernelPrefix=properties.getProperty(prefix+"cltKernelPrefix");
		if (properties.getProperty(prefix+"cltSuffix")!= null) this.cltSuffix=properties.getProperty(prefix+"cltSuffix");

		if (properties.getProperty(prefix+"x3dDirectory")!= null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");

		}

		@@ -359,6 +363,9 @@ public class EyesisCorrectionParameters {
		gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60);
		gd.addCheckbox ("Select aberration kernels for CLT directory", false);

		gd.addStringField ("x3d output directory", this.x3dDirectory, 60);
		gd.addCheckbox ("Select x3d output directory", false);

		gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 60);
		gd.addCheckbox("Select equirectangular maps directory", false);
		gd.addStringField("Results directory", this.resultsDirectory, 40);
		@@ -442,6 +449,7 @@ public class EyesisCorrectionParameters {
		this.smoothKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSmoothKernelDirectory(false, true);
		this.dctKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectDCTKernelDirectory(false, true);
		this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true);
		this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);
		this.equirectangularDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectEquirectangularDirectory(false, false);
		this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true);
		this.sourcePrefix= gd.getNextString();
		@@ -994,6 +1002,18 @@ public class EyesisCorrectionParameters {
		return dir;
		}

		public String selectX3dDirectory(boolean smart, boolean newAllowed) {
		String dir= CalibrationFileManagement.selectDirectory(
		smart,
		newAllowed, // save
		"x3d output directory", // title
		"Select x3d output directory", // button
		null, // filter
		this.x3dDirectory); //this.sourceDirectory);
		if (dir!=null) this.x3dDirectory=dir;
		return dir;
		}

		public String selectEquirectangularDirectory(boolean smart, boolean newAllowed) {
		String dir= CalibrationFileManagement.selectDirectory(
		smart,
		@@ -1931,7 +1951,12 @@ public class EyesisCorrectionParameters {
		public double min_corr_normalized = 2.0; // minimal correlation value to consider valid when normalizing correlation results
		public double max_corr_sigma = 1.5; // weights of points around global max to find fractional
		// pixel location by quadratic approximation
		public double max_corr_radius = 2.5; // maximal distance from int max to consider
		public double max_corr_radius = 3.5; // maximal distance from int max to consider

		public int enhortho_width = 2; // reduce weight of center correlation pixels from center (0 - none, 1 - center, 2 +/-1 from center)
		public double enhortho_scale = 0.2; // multiply center correlation pixels (inside enhortho_width)

		public boolean max_corr_double = false; // NOT USED double pass when masking center of mass to reduce preference for integer values
		public int corr_mode = 2; // which correlation mode to use: 0 - integer max, 1 - center of mass, 2 - polynomial

		// pixel location by quadratic approximation
		@@ -1986,12 +2011,16 @@ public class EyesisCorrectionParameters {
		public double corr_magic_scale = 0.85; // reported correlation offset vs. actual one (not yet understood)

		// 3d reconstruction
		public double min_smth = 0.25; // minimal noise-normalized pixel difference in a channel to suspect something
		public boolean show_textures = true; // show generated textures
		public boolean debug_filters = false;// show intermediate results of filtering
		public double min_smth = 0.5; // 0.25 minimal noise-normalized pixel difference in a channel to suspect something
		public double sure_smth = 2.0; // reliable noise-normalized pixel difference in a channel to have something
		public double bgnd_range = 0.3; // disparity range to be considered background
		public double other_range = 2.0; // disparity difference from center (provided) disparity to trust

		public double bgnd_sure = 0.02; // minimal strength to be considered definitely background
		public double bgnd_maybe = 0.005; // maximal strength to ignore as non-background
		public double bgnd_2diff = 0.005; // maximal strength to ignore as non-background
		public double bgnd_maybe = 0.004; // 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 = 3; // number of tiles in a cluster to seed (just background?)
		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)
		@@ -2041,6 +2070,12 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"min_corr_normalized",this.min_corr_normalized +"");
		properties.setProperty(prefix+"max_corr_sigma", this.max_corr_sigma +"");
		properties.setProperty(prefix+"max_corr_radius", this.max_corr_radius +"");

		properties.setProperty(prefix+"enhortho_width", this.enhortho_width +"");
		properties.setProperty(prefix+"enhortho_scale", this.enhortho_scale +"");


		properties.setProperty(prefix+"max_corr_double", this.max_corr_double+"");
		properties.setProperty(prefix+"corr_mode", this.corr_mode+"");
		properties.setProperty(prefix+"corr_border_contrast", this.corr_border_contrast +"");
		properties.setProperty(prefix+"tile_task_op", this.tile_task_op+"");
		@@ -2087,10 +2122,13 @@ public class EyesisCorrectionParameters {

		properties.setProperty(prefix+"corr_magic_scale", this.corr_magic_scale +"");

		properties.setProperty(prefix+"show_textures", this.show_textures+"");
		properties.setProperty(prefix+"debug_filters", this.debug_filters+"");

		properties.setProperty(prefix+"min_smth", this.min_smth +"");
		properties.setProperty(prefix+"sure_smth", this.sure_smth +"");
		properties.setProperty(prefix+"bgnd_range", this.bgnd_range +"");
		properties.setProperty(prefix+"other_range", this.other_range +"");
		properties.setProperty(prefix+"bgnd_sure", this.bgnd_sure +"");
		properties.setProperty(prefix+"bgnd_maybe", this.bgnd_maybe +"");

		@@ -2138,6 +2176,11 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"min_corr_normalized")!=null)this.min_corr_normalized=Double.parseDouble(properties.getProperty(prefix+"min_corr_normalized"));
		if (properties.getProperty(prefix+"max_corr_sigma")!=null) this.max_corr_sigma=Double.parseDouble(properties.getProperty(prefix+"max_corr_sigma"));
		if (properties.getProperty(prefix+"max_corr_radius")!=null)this.max_corr_radius=Double.parseDouble(properties.getProperty(prefix+"max_corr_radius"));

		if (properties.getProperty(prefix+"enhortho_width")!=null) this.enhortho_width=Integer.parseInt(properties.getProperty(prefix+"enhortho_width"));
		if (properties.getProperty(prefix+"enhortho_scale")!=null) this.enhortho_scale=Double.parseDouble(properties.getProperty(prefix+"enhortho_scale"));

		if (properties.getProperty(prefix+"max_corr_double")!=null)this.max_corr_double=Boolean.parseBoolean(properties.getProperty(prefix+"max_corr_double"));
		if (properties.getProperty(prefix+"corr_mode")!=null) this.corr_mode=Integer.parseInt(properties.getProperty(prefix+"corr_mode"));
		if (properties.getProperty(prefix+"corr_border_contrast")!=null) this.corr_border_contrast=Double.parseDouble(properties.getProperty(prefix+"corr_border_contrast"));
		if (properties.getProperty(prefix+"tile_task_op")!=null) this.tile_task_op=Integer.parseInt(properties.getProperty(prefix+"tile_task_op"));
		@@ -2181,9 +2224,13 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"fcorr_ignore")!=null) this.fcorr_ignore=Boolean.parseBoolean(properties.getProperty(prefix+"fcorr_ignore"));
		if (properties.getProperty(prefix+"corr_magic_scale")!=null) this.corr_magic_scale=Double.parseDouble(properties.getProperty(prefix+"corr_magic_scale"));

		if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
		if (properties.getProperty(prefix+"debug_filters")!=null) this.debug_filters=Boolean.parseBoolean(properties.getProperty(prefix+"debug_filters"));

		if (properties.getProperty(prefix+"min_smth")!=null) this.min_smth=Double.parseDouble(properties.getProperty(prefix+"min_smth"));
		if (properties.getProperty(prefix+"sure_smth")!=null) this.sure_smth=Double.parseDouble(properties.getProperty(prefix+"sure_smth"));
		if (properties.getProperty(prefix+"bgnd_range")!=null) this.bgnd_range=Double.parseDouble(properties.getProperty(prefix+"bgnd_range"));
		if (properties.getProperty(prefix+"other_range")!=null) this.other_range=Double.parseDouble(properties.getProperty(prefix+"other_range"));
		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"));

		@@ -2194,7 +2241,7 @@ public class EyesisCorrectionParameters {
		}

		public boolean showDialog() {
		GenericDialog gd = new GenericDialog("Set DCT parameters");
		GenericDialog gd = new GenericDialog("Set CLT parameters");
		gd.addNumericField("Transform size (default 8)", this.transform_size, 0);
		gd.addNumericField("Lapped transform window type (0- rectangular, 1 - sinus)", this.clt_window, 0);
		gd.addNumericField("shift_x", this.shift_x, 4);
		@@ -2234,10 +2281,22 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Minimal correlation value to consider valid when normalizing results", this.min_corr_normalized, 6);
		gd.addNumericField("Sigma for weights of points around global max to find fractional", this.max_corr_sigma, 3);
		gd.addNumericField("Maximal distance from int max to consider", this.max_corr_radius, 3);


		gd.addMessage("--- Enhance detection of horizontal/vertical features (when enh_ortho is enabled for tile ---");
		gd.addNumericField("Reduce weight of center correlation pixels from center (0 - none, 1 - center, 2 +/-1 from center)", this.enhortho_width, 0);
		gd.addNumericField("Multiply center correlation pixels (inside enhortho_width) (1.0 - disables enh_orttho)", this.enhortho_scale, 3);


		gd.addCheckbox ("Double pass when masking center of mass to reduce preference for integer values", this.max_corr_double);
		gd.addNumericField("Correlation mode: 0 - integer max, 1 - center of mass, 2 - polynomial", this.corr_mode, 0);
		gd.addNumericField("Contrast of dotted border on correlation results", this.corr_border_contrast, 6);
		gd.addMessage("--- tiles tasks ---");
		gd.addNumericField("Tile operations bits: +(0..f) - images, +(00.f0) - process pairs +256, ... ", this.tile_task_op, 0);
		gd.addMessage("--- tiles tasks (current tile_task_op = "+this.tile_task_op+") ---");
		gd.addCheckbox ("Enhace ortho lines detection (enh_ortho)", ImageDtt.getOrthoLines(this.tile_task_op));
		gd.addCheckbox ("Force disparity for image rendering (false - use folund by tile correlation)", ImageDtt.getForcedDisparity(this.tile_task_op));
		gd.addNumericField("Bitmask of used images (1 - top left, 2 - top right, 4 - bottom left, 8 bottom right)", ImageDtt.getImgMask(this.tile_task_op), 0);
		gd.addNumericField("Bitmask of used pairs (1 - top, 2 - bottom, 4 - left, 8 - right)", ImageDtt.getPairMask(this.tile_task_op), 0);
		// gd.addNumericField("Tile operations bits: +(0..f) - images, +(00.f0) - process pairs +256, ... ", this.tile_task_op, 0);
		gd.addNumericField("Tile operations window left (in 8x8 tiles)", this.tile_task_wl, 0);
		gd.addNumericField("Tile operations window top", this.tile_task_wt, 0);
		gd.addNumericField("Tile operations window width", this.tile_task_ww, 0);
		@@ -2281,9 +2340,14 @@ public class EyesisCorrectionParameters {
		gd.addCheckbox ("Ignore current calculated fine correction (use manual only)", this.fcorr_ignore);
		gd.addNumericField("Calculated from correlation offset vs. actual one (not yet understood)", this.corr_magic_scale, 3);

		gd.addMessage ("--- 3D reconstruction ---");
		gd.addCheckbox ("Show generated textures", this.show_textures);
		gd.addCheckbox ("show intermediate results of filtering", this.debug_filters);

		gd.addNumericField("Minimal noise-normalized pixel difference in a channel to suspect something", this.min_smth, 3);
		gd.addNumericField("Reliable noise-normalized pixel difference in a channel to have something ", this.sure_smth, 3);
		gd.addNumericField("Disparity range to be considered background", this.bgnd_range, 3);
		gd.addNumericField("Disparity difference from the center (provided) disparity to trust", this.other_range, 3);
		gd.addNumericField("Minimal strength to be considered definitely background", this.bgnd_sure, 3);
		gd.addNumericField("Maximal strength to ignore as non-background", this.bgnd_maybe, 3);

		@@ -2334,9 +2398,20 @@ public class EyesisCorrectionParameters {
		this.min_corr_normalized= gd.getNextNumber();
		this.max_corr_sigma= gd.getNextNumber();
		this.max_corr_radius= gd.getNextNumber();

		this.enhortho_width= (int) gd.getNextNumber();
		this.enhortho_scale= gd.getNextNumber();

		this.max_corr_double= gd.getNextBoolean();
		this.corr_mode= (int) gd.getNextNumber();
		this.corr_border_contrast= gd.getNextNumber();
		this.tile_task_op= (int) gd.getNextNumber();

		// this.tile_task_op= (int) gd.getNextNumber();
		this.tile_task_op = ImageDtt.setOrthoLines (this.tile_task_op, gd.getNextBoolean());
		this.tile_task_op = ImageDtt.setForcedDisparity (this.tile_task_op, gd.getNextBoolean());
		this.tile_task_op = ImageDtt.setImgMask (this.tile_task_op, (int) gd.getNextNumber());
		this.tile_task_op = ImageDtt.setPairMask (this.tile_task_op, (int) gd.getNextNumber());

		this.tile_task_wl= (int) gd.getNextNumber();
		this.tile_task_wt= (int) gd.getNextNumber();
		this.tile_task_ww= (int) gd.getNextNumber();
		@@ -2377,9 +2452,12 @@ public class EyesisCorrectionParameters {
		this.fcorr_ignore= gd.getNextBoolean();
		this.corr_magic_scale= gd.getNextNumber();

		this.show_textures= gd.getNextBoolean();
		this.debug_filters= gd.getNextBoolean();
		this.min_smth= gd.getNextNumber();
		this.sure_smth= gd.getNextNumber();
		this.bgnd_range= gd.getNextNumber();
		this.other_range= gd.getNextNumber();
		this.bgnd_sure= gd.getNextNumber();
		this.bgnd_maybe= gd.getNextNumber();
		this.min_clstr_seed= (int) gd.getNextNumber();

src/main/java/EyesisCorrections.java

+17 −23

Original line number	Diff line number	Diff line
		@@ -2360,6 +2360,20 @@ public class EyesisCorrections {
		true, // smart,
		true); //newAllowed, // save

		saveAndShow(
		imp,
		path,
		correctionsParameters.png,
		show,
		jpegQuality);
		}

		void saveAndShow(
		ImagePlus imp,
		String path,
		boolean png,
		boolean show,
		int jpegQuality){// <0 - keep current, 0 - force Tiff, >0 use for JPEG
		if (path!=null) {
		path+=Prefs.getFileSeparator()+imp.getTitle();
		boolean hasAlphaHighByte = false;
		@@ -2374,7 +2388,7 @@ public class EyesisCorrections {
		}

		if (hasAlphaHighByte){
		if (correctionsParameters.png){
		if (png){
		if (this.debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
		(new EyesisTiff()).savePNG_ARGB32(
		imp,
		@@ -2441,27 +2455,7 @@ public class EyesisCorrections {
		imp.show();
		}
		}
		/*
		private void saveAndShow(
		CompositeImage compositeImage,
		EyesisCorrectionParameters.ProcessParameters processParameters,
		EyesisCorrectionParameters.CorrectionParameters correctionsParameters){
		saveAndShow(compositeImage, processParameters, correctionsParameters , true, true);
		}

		private void saveAndShow(
		CompositeImage compositeImage,
		EyesisCorrectionParameters.ProcessParameters processParameters,
		EyesisCorrectionParameters.CorrectionParameters correctionsParameters,
		boolean enableSave,
		boolean enableShow){
		saveAndShow(
		compositeImage,
		correctionsParameters,
		processParameters.save && enableSave,
		processParameters.show && enableShow);
		}
		*/
		private void saveAndShow(
		CompositeImage compositeImage,
		EyesisCorrectionParameters.CorrectionParameters correctionsParameters,

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