removing conflicts from extracted clusters (2b8dc001) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+21 −0

Original line number	Diff line number	Diff line
		@@ -2128,6 +2128,7 @@ public class EyesisCorrectionParameters {
		public int stSmplNum = 3; // Number after removing worst
		public double stSmplRms = 0.1; // Maximal RMS of the remaining tiles in a sample

		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

		public double stSmallDiff = 0.4; // Consider merging initial planes if disparity difference below
		@@ -2216,6 +2217,7 @@ public class EyesisCorrectionParameters {
		public double msScaleProj = 1.5; // Scale projection of the plane ellipsoid
		public double msFractUni = 0.3; // Spread this fraction of the ellipsoid weight among extended (double) supertile

		public boolean tsNoEdge = true; // Do not assigned tiles to thesurface edges (not having all 8 neighbors)
		public double tsMaxDiff = 0.3; // Maximal disparity difference when assigning tiles
		public double tsMinDiffOther = 0.35; // Minimal disparity difference to be considered as a competitor surface
		public double tsMinStrength = 0.05; // Minimal tile correlation strength to be assigned
		@@ -2246,6 +2248,7 @@ public class EyesisCorrectionParameters {
		public boolean tsLoopMulti = true; // Repeat multi-choice assignment while succeeding
		public boolean tsReset = false; // Reset tiles to surfaces assignment
		public boolean tsShow = false; // Show results of tiles to surfaces assignment
		public int tsNumClust = 50; // Number of clusters to keep

		public boolean replaceWeakOutlayers = true; // false;

		@@ -2473,6 +2476,7 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"stSmplNum", this.stSmplNum+"");
		properties.setProperty(prefix+"stSmplRms", this.stSmplRms +"");

		properties.setProperty(prefix+"stGrowSel", this.stGrowSel+"");
		properties.setProperty(prefix+"stMeasSel", this.stMeasSel+"");
		properties.setProperty(prefix+"stSmallDiff", this.stSmallDiff +"");
		properties.setProperty(prefix+"stHighMix", this.stHighMix +"");
		@@ -2552,6 +2556,7 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"msScaleProj", this.msScaleProj +"");
		properties.setProperty(prefix+"msFractUni", this.msFractUni +"");

		properties.setProperty(prefix+"tsNoEdge", this.tsNoEdge+"");
		properties.setProperty(prefix+"tsMaxDiff", this.tsMaxDiff +"");
		properties.setProperty(prefix+"tsMinDiffOther", this.tsMinDiffOther +"");
		properties.setProperty(prefix+"tsMinStrength", this.tsMinStrength +"");
		@@ -2577,6 +2582,7 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"tsRemoveWeak2", this.tsRemoveWeak2+"");
		properties.setProperty(prefix+"tsLoopMulti", this.tsLoopMulti+"");
		properties.setProperty(prefix+"tsShow", this.tsShow+"");
		properties.setProperty(prefix+"tsNumClust", this.tsNumClust +"");

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

		@@ -2796,6 +2802,7 @@ public class EyesisCorrectionParameters {
		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+"stGrowSel")!=null) this.stGrowSel=Integer.parseInt(properties.getProperty(prefix+"stGrowSel"));
		if (properties.getProperty(prefix+"stMeasSel")!=null) this.stMeasSel=Integer.parseInt(properties.getProperty(prefix+"stMeasSel"));
		if (properties.getProperty(prefix+"stSmallDiff")!=null) this.stSmallDiff=Double.parseDouble(properties.getProperty(prefix+"stSmallDiff"));
		if (properties.getProperty(prefix+"stHighMix")!=null) this.stHighMix=Double.parseDouble(properties.getProperty(prefix+"stHighMix"));
		@@ -2877,6 +2884,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"msFractUni")!=null) this.msFractUni=Double.parseDouble(properties.getProperty(prefix+"msFractUni"));


		if (properties.getProperty(prefix+"tsNoEdge")!=null) this.tsNoEdge=Boolean.parseBoolean(properties.getProperty(prefix+"tsNoEdge"));
		if (properties.getProperty(prefix+"tsMaxDiff")!=null) this.tsMaxDiff=Double.parseDouble(properties.getProperty(prefix+"tsMaxDiff"));
		if (properties.getProperty(prefix+"tsMinDiffOther")!=null) this.tsMinDiffOther=Double.parseDouble(properties.getProperty(prefix+"tsMinDiffOther"));
		if (properties.getProperty(prefix+"tsMinStrength")!=null) this.tsMinStrength=Double.parseDouble(properties.getProperty(prefix+"tsMinStrength"));
		@@ -2903,6 +2911,9 @@ public class EyesisCorrectionParameters {

		if (properties.getProperty(prefix+"tsLoopMulti")!=null) this.tsLoopMulti=Boolean.parseBoolean(properties.getProperty(prefix+"tsLoopMulti"));
		if (properties.getProperty(prefix+"tsShow")!=null) this.tsShow=Boolean.parseBoolean(properties.getProperty(prefix+"tsShow"));
		if (properties.getProperty(prefix+"tsNumClust")!=null) this.tsNumClust=Integer.parseInt(properties.getProperty(prefix+"tsNumClust"));


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

		if (properties.getProperty(prefix+"show_ortho_combine")!=null) this.show_ortho_combine=Boolean.parseBoolean(properties.getProperty(prefix+"show_ortho_combine"));
		@@ -3144,6 +3155,7 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Number after removing worst", this.stSmplNum, 0);
		gd.addNumericField("Maximal RMS of the remaining tiles in a sample", this.stSmplRms, 6);

		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);
		gd.addNumericField("Consider merging initial planes if disparity difference below", this.stSmallDiff, 6);
		gd.addNumericField("Consider merging initial planes if jumps between ratio above", this.stHighMix, 6);
		@@ -3228,6 +3240,7 @@ public class EyesisCorrectionParameters {

		gd.addMessage ("--- Tiles assignment ---");

		gd.addCheckbox ("Do not assigned tiles to the surface edges (not having all 8 neighbors)", this.tsNoEdge);
		gd.addNumericField("Maximal disparity difference when assigning tiles", this.tsMaxDiff, 6);
		gd.addNumericField("Minimal disparity difference to be considered as a competitor surface", this.tsMinDiffOther, 6);
		gd.addNumericField("Minimal tile correlation strength to be assigned", this.tsMinStrength, 6);
		@@ -3254,6 +3267,7 @@ public class EyesisCorrectionParameters {

		gd.addCheckbox ("Repeat multi-choice assignment while succeeding", this.tsLoopMulti);
		gd.addCheckbox ("Show results of tiles to surfaces assignment", this.tsShow);
		gd.addNumericField("Number of clusters to keep", this.tsNumClust, 0);

		gd.addCheckbox ("Test new mode after migration", this.dbg_migrate);

		@@ -3479,6 +3493,7 @@ public class EyesisCorrectionParameters {
		this.stSmplNum= (int) gd.getNextNumber();
		this.stSmplRms= gd.getNextNumber();

		this.stGrowSel= (int) gd.getNextNumber();
		this.stMeasSel= (int) gd.getNextNumber();
		this.stSmallDiff= gd.getNextNumber();
		this.stHighMix= gd.getNextNumber();
		@@ -3560,6 +3575,7 @@ public class EyesisCorrectionParameters {
		this.msScaleProj= gd.getNextNumber();
		this.msFractUni= gd.getNextNumber();

		this.tsNoEdge= gd.getNextBoolean();
		this.tsMaxDiff= gd.getNextNumber();
		this.tsMinDiffOther= gd.getNextNumber();
		this.tsMinStrength= gd.getNextNumber();
		@@ -3587,6 +3603,7 @@ public class EyesisCorrectionParameters {

		this.tsLoopMulti= gd.getNextBoolean();
		this.tsShow = gd.getNextBoolean();
		this.tsNumClust = (int) gd.getNextNumber();

		this.dbg_migrate= gd.getNextBoolean();

		@@ -3609,6 +3626,7 @@ public class EyesisCorrectionParameters {

		public boolean showTsDialog() {
		GenericDialog gd = new GenericDialog("Set CLT tiles to surfaces assignment parameters");
		gd.addCheckbox ("Do not assigned tiles to the surface edges (not having all 8 neighbors)", this.tsNoEdge);
		gd.addNumericField("Maximal disparity difference when assigning tiles", this.tsMaxDiff, 6);
		gd.addNumericField("Minimal disparity difference to be considered as a competitor surface", this.tsMinDiffOther, 6);
		gd.addNumericField("Minimal tile correlation strength to be assigned", this.tsMinStrength, 6);
		@@ -3635,10 +3653,12 @@ public class EyesisCorrectionParameters {

		gd.addCheckbox ("Repeat multi-choice assignment while succeeding", this.tsLoopMulti);
		gd.addCheckbox ("Show results of tiles to surfaces assignment", this.tsShow);
		gd.addNumericField("Number of clusters to keep", this.tsNumClust, 0);

		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		this.tsNoEdge= gd.getNextBoolean();
		this.tsMaxDiff= gd.getNextNumber();
		this.tsMinDiffOther= gd.getNextNumber();
		this.tsMinStrength= gd.getNextNumber();
		@@ -3666,6 +3686,7 @@ public class EyesisCorrectionParameters {

		this.tsLoopMulti= gd.getNextBoolean();
		this.tsShow = gd.getNextBoolean();
		this.tsNumClust= (int) gd.getNextNumber();
		return true;
		}

src/main/java/MeasuredLayers.java

+51 −0

Original line number	Diff line number	Diff line
		@@ -781,4 +781,55 @@ public class MeasuredLayers {
		}
		return ds;
		}


		public void growSelection(
		int grow, // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
		boolean [] tiles,
		boolean [] prohibit)
		{
		boolean [] src_tiles = tiles.clone(); // just in case
		// grow
		boolean hor = true;
		for (; grow > 0; grow--){
		boolean single = (grow ==1) && hor;
		src_tiles = tiles.clone();
		if (hor){
		for (int tileY = 0; tileY < tilesY; tileY++){
		for (int tileX = 0; tileX < (tilesX - 1); tileX++){
		int tindx = tileY * tilesX + tileX;
		if ((prohibit == null) \|\| (!prohibit[tindx] && !prohibit[tindx + 1])) {
		tiles[tindx + 1] \|= src_tiles[tindx];
		}

		}
		for (int tileX = 1; tileX < tilesX; tileX++){
		int tindx = tileY * tilesX + tileX;
		if ((prohibit == null) \|\| (!prohibit[tindx] && !prohibit[tindx - 1])) {
		tiles[tindx - 1] \|= src_tiles[tindx];
		}
		}
		}
		}
		if (!hor \|\| single){ // do vertically, but from previous state
		for (int tileX = 0; tileX < tilesX; tileX++){
		for (int tileY = 0; tileY < (tilesY - 1); tileY++){
		int tindx = tileY * tilesX + tileX;
		if ((prohibit == null) \|\| (!prohibit[tindx] && !prohibit[tindx + tilesX])) {
		tiles[tindx + tilesX] \|= src_tiles[tindx];
		}

		}
		for (int tileY = 1; tileY < tilesY; tileY++){
		int tindx = tileY * tilesX + tileX;
		if ((prohibit == null) \|\| (!prohibit[tindx] && !prohibit[tindx - tilesX])) {
		tiles[tindx - tilesX] \|= src_tiles[tindx];
		}
		}
		}
		}
		hor = !hor;
		}
		}

		}

src/main/java/SuperTiles.java

+30 −10

Original line number	Diff line number	Diff line
		@@ -1699,6 +1699,7 @@ public class SuperTiles{
		// find average disparity for the supertile (improve?)
		double sd = 0.0, sw = 0.0;
		for (int ml = 0; ml < plane_disp_strength[nsTile].length; ml++) if ((stMeasSel & ( 1 << ml)) != 0){
		if ((plane_disp_strength[nsTile] !=null) && (plane_disp_strength[nsTile][ml] !=null) && (plane_disp_strength[nsTile][ml][1] !=null)) {
		for (int i = 0; i < plane_disp_strength[nsTile][ml][1].length; i++){
		double w = plane_disp_strength[nsTile][ml][1][i];
		double d = plane_disp_strength[nsTile][ml][0][i];
		@@ -1706,6 +1707,7 @@ public class SuperTiles{
		sw += w;
		}
		}
		}
		if (sw > 0) {
		if (dl > 0) {
		System.out.println("Plane tilted disparity for stileX = "+stileX+" stileY="+stileY+", average disparity "+(sd/sw));
		@@ -2008,6 +2010,7 @@ public class SuperTiles{
		// Sort plane data by center (plane or supertile) disparity

		public boolean [][][][] initialDiscriminateTiles(
		final int growSelection, // grow initial selection before processing
		final int stMeasSel, // = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert
		final double plDispNorm,
		final int plMinPoints, // = 5; // Minimal number of points for plane detection
		@@ -2049,14 +2052,25 @@ public class SuperTiles{
		// final TilePlanes tpl = new TilePlanes(tileSize,superTileSize, geometryCorrection);
		final int num_layers = measuredLayers.getNumLayers();
		final int num_tiles = 4 * superTileSize * superTileSize;

		measuredLayers.setLayer (
		boolean [] grown_selection = null;
		if (growSelection >= 0) {
		grown_selection = cltPass3d.getSelected();
		if (growSelection > 0) {
		grown_selection = grown_selection.clone();
		measuredLayers.growSelection(
		growSelection, // grow,
		grown_selection, // tiles,
		null); // prohibit);
		}
		}
		measuredLayers.setLayer ( // overwrite?
		0, // int num_layer,
		cltPass3d.getDisparity(), // double [] disparity,
		cltPass3d.getStrength(), // double [] strength,
		null); // boolean [] selection) // may be null
		grown_selection); // null); // boolean [] selection) // may be null
		if (debugLevel > -1) {
		String [] titles = {"d0","s0","d1","s1","d2","s2","d3","s3","s","d"};
		String [] titles = {"d0","s0","d1","s1","d2","s2","d3","s3","s","d","selection"};
		boolean [] dbg_sel= grown_selection; // cltPass3d.getSelected();
		double [][] dbg_img = new double [titles.length][];
		for (int i = 0; i < measuredLayers.getNumLayers(); i++){
		dbg_img[2 * i] = measuredLayers.getDisparity(i);
		@@ -2064,6 +2078,10 @@ public class SuperTiles{
		}
		dbg_img[8] = cltPass3d.getDisparity();
		dbg_img[9] = cltPass3d.getStrength();
		dbg_img[10]= new double [dbg_sel.length];
		for (int i = 0; i < dbg_sel.length; i++){
		dbg_img[10][i] = ((dbg_sel == null) \|\| dbg_sel[i])? 1.0:0.0;
		}
		showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays();
		sdfa_instance.showArrays(dbg_img, tileProcessor.getTilesX(), tileProcessor.getTilesY(), true, "measuredLayers",titles);
		}
		@@ -2442,6 +2460,7 @@ public class SuperTiles{


		public void processPlanes5(
		final int growSelection, // grow initial selection before processing
		final int stMeasSel, // = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert
		final double plDispNorm,
		final int plMinPoints, // = 5; // Minimal number of points for plane detection
		@@ -2461,7 +2480,7 @@ public class SuperTiles{
		final double bin_blur_vert, // Blur disparity histograms for constant disparity clusters by this sigma (in bins)
		final double max_diff_hor, // maximal disparity difference (to assign to a cluster (of Double.NaN) at first run for horizontal planes
		final double max_diff_vert, // maximal disparity difference (to assign to a cluster (of Double.NaN) at first run for vertical plane
		final int max_tries, // on last run - assign all rfemaining pixels to some cluster (disregard max_diff)
		final int max_tries, // on last run - assign all remaining pixels to some cluster (disregard max_diff)

		final boolean msUseSel, // final boolean use_sel,
		final boolean msDivideByArea, // final boolean divide_by_area,
		@@ -2482,6 +2501,7 @@ public class SuperTiles{
		// Sort plane data by center (plane or supertile) disparity

		boolean [][][][] plane_selections = initialDiscriminateTiles(
		growSelection, // final int growSelection, // grow initial selection before processing
		stMeasSel, // final int stMeasSel, // = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert
		plDispNorm, // final double plDispNorm,
		plMinPoints, // final int plMinPoints, // = 5; // Minimal number of points for plane detection

src/main/java/TileProcessor.java

+109 −0

Original line number	Diff line number	Diff line
		@@ -2972,6 +2972,7 @@ public class TileProcessor {
		// assign tiles that do not depend on other assigned tiles - single pass
		if (clt_parameters.tsEnSingle) {
		int [] stats= tileSurface.assignTilesToSurfaces(
		clt_parameters.tsNoEdge , // final boolean noEdge,
		clt_parameters.tsMaxDiff, //final double maxDiff,
		clt_parameters.tsMinDiffOther, //final double minDiffOther, // should be >= maxDiff
		clt_parameters.tsMinStrength, //final double minStrength,
		@@ -2999,6 +3000,7 @@ public class TileProcessor {
		if (clt_parameters.tsEnMulti) {
		for (int nTry = 0; nTry < 100; nTry++) {
		int [] stats= tileSurface.assignTilesToSurfaces(
		clt_parameters.tsNoEdge , // final boolean noEdge,
		clt_parameters.tsMaxDiff, //final double maxDiff,
		clt_parameters.tsMinDiffOther, //final double minDiffOther, // should be >= maxDiff
		clt_parameters.tsMinStrength, //final double minStrength,
		@@ -3044,6 +3046,7 @@ public class TileProcessor {
		if (clt_parameters.tsGrowSurround) {
		for (int nTry = 0; nTry < 100; nTry++) {
		int [] stats= tileSurface.assignFromFarthest(
		clt_parameters.tsNoEdge , // final boolean noEdge,
		clt_parameters.tsMinNeib , // final int minNeib, // **
		clt_parameters.tsMaxSurStrength , // final double maxStrength, // **
		clt_parameters.tsCountDis, // final boolean includeImpossible, // ** // count prohibited neighbors as assigned
		@@ -3086,6 +3089,111 @@ public class TileProcessor {
		"assignments", // String title,
		dispStrength); // final double [][][] dispStrength)
		}
		boolean [][] assigned_sel = tileSurface.extractSelection(
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);


		int [][] clusters1 = tileSurface.enumerateClusters(
		assigned_sel, //final boolean [][] selection,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		int [][] cluster_stats1 = tileSurface.clusterStats(
		clusters1, // int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		tileSurface.showClusterStats(
		cluster_stats1, // int [][] cluster_stats,
		clt_parameters.tsNumClust); // int max_clusters){

		if (clt_parameters.tsShow){
		tileSurface.showClusters(
		"clusters_individual", // String title,
		cluster_stats1, // int [][] cluster_stats,
		clt_parameters.tsNumClust, // int max_clusters
		clusters1); // int [][] clusters); // final double [][][] dispStrength)
		}

		// Try splitting (currently no initial conflicts):
		int [][] clusters1a = tileSurface.spitConflictClusters(
		clusters1, // final int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);
		int [][] cluster_stats1a = tileSurface.clusterStats(
		clusters1a, // int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		tileSurface.showClusterStats(
		cluster_stats1a, // int [][] cluster_stats,
		clt_parameters.tsNumClust); // int max_clusters){




		boolean [][] grown_sel = tileSurface.growSelection(
		2, // int grow,
		assigned_sel, // final boolean [][] sel_in,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		int [][] clusters2 = tileSurface.enumerateClusters(
		grown_sel, // final boolean [][] selection,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		int [][] cluster_stats2 = tileSurface.clusterStats(
		clusters2, // int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		tileSurface.showClusterStats(
		cluster_stats2, // int [][] cluster_stats,
		clt_parameters.tsNumClust); // int max_clusters){

		if (clt_parameters.tsShow){
		tileSurface.showClusters(
		"clusters_merged", // String title,
		cluster_stats2, // int [][] cluster_stats,
		clt_parameters.tsNumClust, // int max_clusters
		clusters2); // int [][] clusters); // final double [][][] dispStrength)
		}

		// Just for testing: splitting combined clusters
		int [][] clusters2a = tileSurface.spitConflictClusters(
		clusters2, // final int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		int [][] cluster_stats2a = tileSurface.clusterStats(
		clusters2a, // int [][] clusters,
		0, // final int debugLevel,
		clt_parameters.tileX,
		clt_parameters.tileY);

		tileSurface.showClusterStats(
		cluster_stats2a, // int [][] cluster_stats,
		clt_parameters.tsNumClust); // int max_clusters){

		if (clt_parameters.tsShow){
		tileSurface.showClusters(
		"clusters_merged_split", // String title,
		cluster_stats2a, // int [][] cluster_stats,
		clt_parameters.tsNumClust, // int max_clusters
		clusters2a); // int [][] clusters); // final double [][][] dispStrength)
		}

		return true;
		}

		@@ -3192,6 +3300,7 @@ public class TileProcessor {
		// separate each supertile data into clusters, trying both horizontal and perpendicular to view planes
		double [] world_hor = {0.0, 1.0, 0.0};
		st.processPlanes5(
		clt_parameters.stGrowSel, // = 2; // = -1; //Grow initial selection before processing supertiles, odd - ortho. <0 - use all tiles
		clt_parameters.stMeasSel, // = 1 //Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert
		clt_parameters.plDispNorm, // = 2.0; // Normalize disparities to the average if above
		clt_parameters.plMinPoints, // = 5; // Minimal number of points for plane detection

src/main/java/TileSurface.java

+756 −51

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