working on initial z-map generation (88e3bc5d) · Commits · Elphel / imagej-elphel

src/main/java/AlignmentCorrection.java

+8 −0

Original line number	Diff line number	Diff line
		@@ -1219,6 +1219,7 @@ public class AlignmentCorrection {
		}
		return disp_strength;
		}

		public double[][] filterDisparityStrength (
		final double[][] disp_strength_in,
		final double strength_floor,
		@@ -1362,6 +1363,13 @@ public class AlignmentCorrection {
		}
		return disp_strength;
		}







		public void show_fine_corr(
		double [][][] corr,
		String prefix)

src/main/java/CLTPass3d.java

+11 −1

Original line number	Diff line number	Diff line
		@@ -74,7 +74,10 @@ public class CLTPass3d{
		{
		return texture_tiles;
		}

		public double [][] getMaxTriedDisparity()
		{
		return max_tried_disparity;
		}
		public double [][] getTileRBGA(
		int num_layers)
		{
		@@ -746,6 +749,9 @@ public class CLTPass3d{






		public SuperTiles getSuperTiles()
		{
		return this.superTiles;
		@@ -764,6 +770,7 @@ public class CLTPass3d{
		int smplSide, // = 2; // Sample size (side of a square)
		int smplNum, // = 3; // Number after removing worst
		double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
		boolean smplWnd, // use window functions for the samples
		int measSel)
		{
		this.superTiles = new SuperTiles(
		@@ -780,6 +787,7 @@ public class CLTPass3d{
		smplSide, // = 2; // Sample size (side of a square)
		smplNum, // = 3; // Number after removing worst
		smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
		smplWnd, // final boolean smplWnd, // use window functions for the samples
		measSel);
		return this.superTiles;
		}
		@@ -791,6 +799,7 @@ public class CLTPass3d{
		int smplSide, // = 2; // Sample size (side of a square)
		int smplNum, // = 3; // Number after removing worst
		double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
		boolean smplWnd, // use window functions for the samples
		int measSel)
		{
		if (this.superTiles == null){
		@@ -804,6 +813,7 @@ public class CLTPass3d{
		smplSide, // = 2; // Sample size (side of a square)
		smplNum, // = 3; // Number after removing worst
		smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
		smplWnd, // use window functions for the samples
		measSel);
		}

src/main/java/ConnectionCosts.java

+4 −2

Original line number	Diff line number	Diff line
		@@ -529,7 +529,8 @@ public class ConnectionCosts {
		conn_weight += 1.0;
		}
		}
		double [] value_weight = {merged_plane.getValue(),merged_plane.getWeight(),conn_weight};
		// double [] value_weight = {merged_plane.getValue(),merged_plane.getWeight(),conn_weight};
		double [] value_weight = {merged_plane.getNormValue(),merged_plane.getWeight(),conn_weight};
		if (starPwr != 0){
		value_weight[0] /= (Math.pow((planes[nsTile][nl].getNumNeibBest() + 1.0), starPwr));
		}
		@@ -638,7 +639,8 @@ public class ConnectionCosts {

		conn_weight += entry.getValue();
		}
		double [] value_weight = {merged_plane.getValue(),merged_plane.getWeight(),conn_weight};
		// double [] value_weight = {merged_plane.getValue(),merged_plane.getWeight(),conn_weight};
		double [] value_weight = {merged_plane.getNormValue(),merged_plane.getWeight(),conn_weight};
		if (starPwr != 0){
		value_weight[0] /= (Math.pow(tile_weights.size() + 1.0, starPwr));
		}

src/main/java/EyesisCorrectionParameters.java

+48 −5

Original line number	Diff line number	Diff line
		@@ -2070,6 +2070,11 @@ public class EyesisCorrectionParameters {
		public double ex_strength = 0.18; // minimal 4-corr strength to trust tile
		public double ex_nstrength = 0.4; // minimal 4-corr strength divided by channel diff for new (border) tiles

		public double pt_super_trust = 1.6; // If strength exceeds ex_strength * super_trust, do not apply ex_nstrength and plate_ds
		public boolean pt_keep_raw_fg = true; // Do not replace raw tiles by the plates, if raw is closer (like poles)
		public double pt_scale_pre = 1.5; // Scale plates strength before comparing to raw strength
		public double pt_scale_post = 2.5; // Scale plates strength when replacing raw (plates d/s data is more reliable if it exists)

		public double bgnd_sure = 0.18; // minimal strength to be considered definitely background
		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
		@@ -2116,6 +2121,9 @@ public class EyesisCorrectionParameters {
		public boolean poles_force_disp = true; // Set disparity to that of the bottom of existing segment (false - use hor. disparity)

		public int max_clusters = 300; // Maximal number of clusters to generate for one run
		public boolean remove_scans = true; // Remove all unneeded scans when generating x3d output to save memory


		public boolean correct_distortions = false; // Correct lens geometric distortions in a model (will need backdrop to be corrected too)
		public boolean show_triangles = true; // Show generated triangles
		public boolean avg_cluster_disp = false; // Weight-average disparity for the whole cluster
		@@ -2179,6 +2187,7 @@ public class EyesisCorrectionParameters {
		public int stSmplSide = 2; // Sample size (side of a square)
		public int stSmplNum = 3; // Number after removing worst
		public double stSmplRms = 0.1; // Maximal RMS of the remaining tiles in a sample
		public boolean stSmplWnd = false; // Use window function for the samples (TODO: change default to true after testing)

		public int stGrowSel = 2; // Grow initial selection before processing supertiles, odd - ortho. <0 - use all tiles
		public int stMeasSel = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert
		@@ -2461,6 +2470,7 @@ public class EyesisCorrectionParameters {
		public boolean show_filter_scan = false; // show 'FilterScan'
		public boolean show_combined = false; // show 'combo_scan' (combined multiple scans)
		public boolean show_unique = false; // show 'unique_scan' (removed already measured tiles with the same disparity)
		public boolean show_histograms = false; // show supertile disparity histograms
		public boolean show_init_refine = false; // show debug images during initial refinement
		public boolean show_expand = false; // show debug images during disparity expansion
		public boolean show_retry_far = false; // show debug images related to retrying far tiles near foreground
		@@ -2614,6 +2624,11 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"ex_strength", this.ex_strength +"");
		properties.setProperty(prefix+"ex_nstrength", this.ex_nstrength +"");

		properties.setProperty(prefix+"pt_super_trust", this.pt_super_trust +"");
		properties.setProperty(prefix+"pt_keep_raw_fg", this.pt_keep_raw_fg+"");
		properties.setProperty(prefix+"pt_scale_pre", this.pt_scale_pre +"");
		properties.setProperty(prefix+"pt_scale_post", this.pt_scale_post +"");

		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+"");
		@@ -2660,6 +2675,7 @@ public class EyesisCorrectionParameters {


		properties.setProperty(prefix+"max_clusters", this.max_clusters+"");
		properties.setProperty(prefix+"remove_scans", this.remove_scans+"");
		properties.setProperty(prefix+"correct_distortions",this.correct_distortions+"");
		properties.setProperty(prefix+"show_triangles", this.show_triangles+"");
		properties.setProperty(prefix+"avg_cluster_disp", this.avg_cluster_disp+"");
		@@ -2718,6 +2734,7 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"stSmplSide", this.stSmplSide+"");
		properties.setProperty(prefix+"stSmplNum", this.stSmplNum+"");
		properties.setProperty(prefix+"stSmplRms", this.stSmplRms +"");
		properties.setProperty(prefix+"stSmplWnd", this.stSmplWnd+"");

		properties.setProperty(prefix+"stGrowSel", this.stGrowSel+"");
		properties.setProperty(prefix+"stMeasSel", this.stMeasSel+"");
		@@ -2969,6 +2986,7 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"show_filter_scan", this.show_filter_scan+"");
		properties.setProperty(prefix+"show_combined", this.show_combined+"");
		properties.setProperty(prefix+"show_unique", this.show_unique+"");
		properties.setProperty(prefix+"show_histograms", this.show_histograms+"");
		properties.setProperty(prefix+"show_init_refine", this.show_init_refine+"");
		properties.setProperty(prefix+"show_expand", this.show_expand+"");
		properties.setProperty(prefix+"show_retry_far", this.show_retry_far+"");
		@@ -3123,6 +3141,11 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"ex_strength")!=null) this.ex_strength=Double.parseDouble(properties.getProperty(prefix+"ex_strength"));
		if (properties.getProperty(prefix+"ex_nstrength")!=null) this.ex_nstrength=Double.parseDouble(properties.getProperty(prefix+"ex_nstrength"));

		if (properties.getProperty(prefix+"pt_super_trust")!=null) this.pt_super_trust=Double.parseDouble(properties.getProperty(prefix+"pt_super_trust"));
		if (properties.getProperty(prefix+"pt_keep_raw_fg")!=null) this.pt_keep_raw_fg=Boolean.parseBoolean(properties.getProperty(prefix+"pt_keep_raw_fg"));
		if (properties.getProperty(prefix+"pt_scale_pre")!=null) this.pt_scale_pre=Double.parseDouble(properties.getProperty(prefix+"pt_scale_pre"));
		if (properties.getProperty(prefix+"pt_scale_post")!=null) this.pt_scale_post=Double.parseDouble(properties.getProperty(prefix+"pt_scale_post"));

		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"));
		@@ -3167,6 +3190,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"poles_force_disp")!=null) this.poles_force_disp=Boolean.parseBoolean(properties.getProperty(prefix+"poles_force_disp"));

		if (properties.getProperty(prefix+"max_clusters")!=null) this.max_clusters=Integer.parseInt(properties.getProperty(prefix+"max_clusters"));
		if (properties.getProperty(prefix+"remove_scans")!=null) this.remove_scans=Boolean.parseBoolean(properties.getProperty(prefix+"remove_scans"));
		if (properties.getProperty(prefix+"correct_distortions")!=null) this.correct_distortions=Boolean.parseBoolean(properties.getProperty(prefix+"correct_distortions"));
		if (properties.getProperty(prefix+"show_triangles")!=null) this.show_triangles=Boolean.parseBoolean(properties.getProperty(prefix+"show_triangles"));
		if (properties.getProperty(prefix+"avg_cluster_disp")!=null) this.avg_cluster_disp=Boolean.parseBoolean(properties.getProperty(prefix+"avg_cluster_disp"));
		@@ -3225,6 +3249,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"stSmplSide")!=null) this.stSmplSide=Integer.parseInt(properties.getProperty(prefix+"stSmplSide"));
		if (properties.getProperty(prefix+"stSmplNum")!=null) this.stSmplNum=Integer.parseInt(properties.getProperty(prefix+"stSmplNum"));
		if (properties.getProperty(prefix+"stSmplRms")!=null) this.stSmplRms=Double.parseDouble(properties.getProperty(prefix+"stSmplRms"));
		if (properties.getProperty(prefix+"stSmplWnd")!=null) this.stSmplWnd=Boolean.parseBoolean(properties.getProperty(prefix+"stSmplWnd"));

		if (properties.getProperty(prefix+"stGrowSel")!=null) this.stGrowSel=Integer.parseInt(properties.getProperty(prefix+"stGrowSel"));
		if (properties.getProperty(prefix+"stMeasSel")!=null) this.stMeasSel=Integer.parseInt(properties.getProperty(prefix+"stMeasSel"));
		@@ -3478,6 +3503,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"show_filter_scan")!=null) this.show_filter_scan=Boolean.parseBoolean(properties.getProperty(prefix+"show_filter_scan"));
		if (properties.getProperty(prefix+"show_combined")!=null) this.show_combined=Boolean.parseBoolean(properties.getProperty(prefix+"show_combined"));
		if (properties.getProperty(prefix+"show_unique")!=null) this.show_unique=Boolean.parseBoolean(properties.getProperty(prefix+"show_unique"));
		if (properties.getProperty(prefix+"show_histograms")!=null) this.show_histograms=Boolean.parseBoolean(properties.getProperty(prefix+"show_histograms"));
		if (properties.getProperty(prefix+"show_init_refine")!=null) this.show_init_refine=Boolean.parseBoolean(properties.getProperty(prefix+"show_init_refine"));
		if (properties.getProperty(prefix+"show_expand")!=null) this.show_expand=Boolean.parseBoolean(properties.getProperty(prefix+"show_expand"));
		if (properties.getProperty(prefix+"show_retry_far")!=null) this.show_retry_far=Boolean.parseBoolean(properties.getProperty(prefix+"show_retry_far"));
		@@ -3654,6 +3680,12 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Minimal 4-corr strength to trust tile", this.ex_strength, 3);
		gd.addNumericField("Minimal 4-corr strength divided by channel diff for new (border) tiles", this.ex_nstrength, 3);

		gd.addMessage ("******* Plates filetering when building initial z-map *******");
		gd.addNumericField("If strength exceeds ex_strength * super_trust, do not apply ex_nstrength and plate_ds", this.pt_super_trust, 3);
		gd.addCheckbox ("Do not replace raw tiles by the plates, if raw is closer (like poles)", this.pt_keep_raw_fg);
		gd.addNumericField("Scale plates strength before comparing to raw strength", this.pt_scale_pre, 3);
		gd.addNumericField("Scale plates strength when replacing raw (plates d/s data is more reliable if it exists)", this.pt_scale_post, 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);

		@@ -3702,6 +3734,7 @@ public class EyesisCorrectionParameters {
		gd.addCheckbox ("Set disparity to that of the bottom of existing segment (false - use hor. disparity)",this.poles_force_disp);

		gd.addNumericField("Maximal number of clusters to generate for one run", this.max_clusters, 0);
		gd.addCheckbox ("Remove all unneeded scans when generating x3d output to save memory", this.remove_scans);
		gd.addCheckbox ("Correct lens geometric distortions in a model (will need backdrop to be corrected too)", this.correct_distortions);
		gd.addCheckbox ("Show generated triangles", this.show_triangles);
		gd.addCheckbox ("Weight-average disparity for the whole cluster ", this.avg_cluster_disp);
		@@ -3763,6 +3796,7 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Sample size (side of a square)", this.stSmplSide, 0);
		gd.addNumericField("Number after removing worst", this.stSmplNum, 0);
		gd.addNumericField("Maximal RMS of the remaining tiles in a sample", this.stSmplRms, 6);
		gd.addCheckbox ("Use window function for the samples", this.stSmplWnd);

		gd.addNumericField("Grow initial selection before processing supertiles, odd - ortho. <0 - use all tiles",this.stGrowSel, 0);
		gd.addNumericField("Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert",this.stMeasSel, 0);
		@@ -4026,6 +4060,7 @@ public class EyesisCorrectionParameters {
		gd.addCheckbox ("Show 'FilterScan'", this.show_filter_scan);
		gd.addCheckbox ("Show 'combo_scan' (combined multiple scans)", this.show_combined);
		gd.addCheckbox ("Show 'unique_scan' (removed already measured tiles with the same disparity)", this.show_unique);
		gd.addCheckbox ("Show supertile disparity histograms ", this.show_histograms);
		gd.addCheckbox ("Show debug images during initial refinement", this.show_init_refine);
		gd.addCheckbox ("Show debug images during disparity expansion", this.show_expand);
		gd.addCheckbox ("Show debug images related to retrying far tiles near foreground", this.show_retry_far);
		@@ -4187,6 +4222,11 @@ public class EyesisCorrectionParameters {
		this.ex_strength= gd.getNextNumber();
		this.ex_nstrength= gd.getNextNumber();

		this.pt_super_trust= gd.getNextNumber();
		this.pt_keep_raw_fg= gd.getNextBoolean();
		this.pt_scale_pre= gd.getNextNumber();
		this.pt_scale_post= gd.getNextNumber();

		this.bgnd_sure= gd.getNextNumber();
		this.bgnd_maybe= gd.getNextNumber();
		this.min_clstr_seed= (int) gd.getNextNumber();
		@@ -4231,6 +4271,7 @@ public class EyesisCorrectionParameters {
		this.poles_force_disp= gd.getNextBoolean();

		this.max_clusters= (int) gd.getNextNumber();
		this.remove_scans= gd.getNextBoolean();
		this.correct_distortions= gd.getNextBoolean();
		this.show_triangles= gd.getNextBoolean();
		this.avg_cluster_disp= gd.getNextBoolean();
		@@ -4289,6 +4330,7 @@ public class EyesisCorrectionParameters {
		this.stSmplSide= (int) gd.getNextNumber();
		this.stSmplNum= (int) gd.getNextNumber();
		this.stSmplRms= gd.getNextNumber();
		this.stSmplWnd= gd.getNextBoolean();

		this.stGrowSel= (int) gd.getNextNumber();
		this.stMeasSel= (int) gd.getNextNumber();
		@@ -4544,6 +4586,7 @@ public class EyesisCorrectionParameters {
		this.show_filter_scan= gd.getNextBoolean(); // first on refine
		this.show_combined= gd.getNextBoolean();
		this.show_unique= gd.getNextBoolean();
		this.show_histograms= gd.getNextBoolean();
		this.show_init_refine= gd.getNextBoolean();
		this.show_expand= gd.getNextBoolean();
		this.show_retry_far= gd.getNextBoolean();

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