before removing old versions (9b725244) · Commits · Elphel / imagej-elphel

src/main/java/LinkPlanes.java

+965 −281

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/SuperTiles.java

+74 −43

Original line number	Diff line number	Diff line
		@@ -1413,7 +1413,9 @@ public class SuperTiles{
		final int stilesX = (tilesX + superTileSize -1)/superTileSize;
		final int stilesY = (tilesY + superTileSize -1)/superTileSize;
		final int nStiles = stilesX * stilesY;
		final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		// final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : tileProcessor.threadsMax);

		final AtomicInteger ai = new AtomicInteger(0);
		final int debug_stile = (debugLevel > -1)? (dbg_Y * stilesX + dbg_X):-1;
		// TODO: Remove when promoting PlaneData
		@@ -1423,7 +1425,9 @@ public class SuperTiles{
		threads[ithread] = new Thread() {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		if (nsTile == debug_stile){
		// int dl = (nsTile == debug_stile) ? 3 : 0;
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
		if (dl > 1){
		System.out.println("getPlaneDispStrengths(): nsTile="+nsTile);
		}
		int stileY = nsTile / stilesX;
		@@ -1438,7 +1442,7 @@ public class SuperTiles{
		measuredLayers, // MeasuredLayers measuredLayers,
		plPreferDisparity); // boolean preferDisparity)

		int dl = (nsTile == debug_stile) ? 3 : 0;


		plane_disp_strength[nsTile] = new double[measuredLayers.getNumLayers()][][];

		@@ -1541,7 +1545,8 @@ public class SuperTiles{
		final int stilesX = (tilesX + superTileSize -1)/superTileSize;
		final int stilesY = (tilesY + superTileSize -1)/superTileSize;
		final int nStiles = stilesX * stilesY;
		final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		// final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 :tileProcessor.threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		this.planes = new TilePlanes.PlaneData[nStiles][];
		final int debug_stile = (debugLevel > -1)? (dbg_Y * stilesX + dbg_X):-1;
		@@ -1553,12 +1558,13 @@ public class SuperTiles{
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		if (disparity_strengths[nsTile] != null){
		if (nsTile == debug_stile){
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
		if (dl > 1){
		System.out.println("dispClusterize(): nsTile="+nsTile);
		}
		int stileY = nsTile / stilesX;
		int stileX = nsTile % stilesX;
		int dl = (nsTile == debug_stile) ? 3 : 0;
		// int dl = (nsTile == debug_stile) ? 3 : 0;

		double[][][] disp_strength = new double[measuredLayers.getNumLayers()][][];

		@@ -1853,7 +1859,8 @@ public class SuperTiles{
		final int stilesX = (tilesX + superTileSize -1)/superTileSize;
		final int stilesY = (tilesY + superTileSize -1)/superTileSize;
		final int nStiles = stilesX * stilesY;
		final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		// final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : tileProcessor.threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		this.planes = new TilePlanes.PlaneData[nStiles][];
		final int debug_stile = (debugLevel > -1)? (dbg_Y * stilesX + dbg_X):-1;
		@@ -1877,7 +1884,7 @@ public class SuperTiles{
		cltPass3d.getDisparity(), // double [] disparity,
		cltPass3d.getStrength(), // double [] strength,
		grown_selection); // null); // boolean [] selection) // may be null
		if (debugLevel > -1) {
		if (debugLevel > 0) {
		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][];
		@@ -1939,7 +1946,7 @@ public class SuperTiles{
		final double [][][] mmm_hor = getMaxMinMax(
		hor_disp_strength, // final double [][][][] disparity_strength, // pre-calculated disparity/strength [per super-tile][per-measurement layer][2][tiles] or null
		null); // final boolean [][] tile_sel // null or per-measurement layer, per-tile selection. For each layer null - do not use, {} - use all
		if (debugLevel > -1) {
		if (debugLevel > 0) {
		dbg_hist[1] = showDisparityHistogram();
		dbg_hist[3] = showMaxMinMax();
		}
		@@ -1960,7 +1967,7 @@ public class SuperTiles{
		sdfa_instance.showArrays(dbg_hist, hist_width0, hist_height0, true, "vert_hor_histograms_"+pass,dbg_hist_titles);
		}
		// try to independently (same selections) clusterize both ways
		if (debugLevel > -1){
		if (debugLevel > 0){
		System.out.println("initialDiscriminateTiles(): before new_planes_hor, pass =" + (pass + 1) + " ( of "+max_tries+" )");
		}

		@@ -1974,11 +1981,11 @@ public class SuperTiles{
		plMinPoints, // final int plMinPoints, // = 5; // Minimal number of points for plane detection
		smallDiff, // final double smallDiff, // = 0.4; // Consider merging initial planes if disparity difference below
		highMix, // final double highMix, //stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above
		1, // debugLevel,
		debugLevel, // 1, // debugLevel,
		dbg_X,
		dbg_Y);

		if (debugLevel > -1){
		if (debugLevel > 0){
		System.out.println("initialDiscriminateTiles(): before new_planes_vert, pass =" + (pass + 1) + " ( of "+max_tries+" )");
		}
		final boolean [][][][] new_planes_vert = dispClusterize(
		@@ -1991,7 +1998,7 @@ public class SuperTiles{
		plMinPoints, // final int plMinPoints, // = 5; // Minimal number of points for plane detection
		smallDiff, // final double smallDiff, // = 0.4; // Consider merging initial planes if disparity difference below
		highMix, // final double highMix, //stHighMix = 0.4; // Consider merging initial planes if jumps between ratio above
		2, // debugLevel,
		debugLevel, // 2, // debugLevel,
		dbg_X,
		dbg_Y);

		@@ -2001,13 +2008,12 @@ public class SuperTiles{
		threads[ithread] = new Thread() {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 3 : 0;
		// int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 3 : 0;
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;

		if (dl > 0){
		System.out.println("initialDiscriminateTiles() selecting: nsTile="+nsTile);
		}
		// int stileY = nsTile / stilesX;
		// int stileX = nsTile % stilesX;
		// int [] sTiles = {stileX, stileY};
		double [][][][] ds = {vert_disp_strength[nsTile],hor_disp_strength[nsTile]};
		boolean [][][][] sels_all = {new_planes_vert[nsTile],new_planes_hor[nsTile]}; // make possible to iterate
		class SelStrength{
		@@ -2189,7 +2195,9 @@ public class SuperTiles{
		threads[ithread] = new Thread() {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 3 : 1;
		// int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 3 : 1;
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;

		if (dl > 1){
		System.out.println("refineDiscriminateTiles() selecting: nsTile="+nsTile);
		}
		@@ -2240,7 +2248,7 @@ public class SuperTiles{
		break;
		}
		// merging suggested plane pair
		if (debugLevel > -1) {
		if (debugLevel > 0) {
		System.out.println("refineDiscriminateTiles(): nsTile="+nsTile+" merging pair ["+merge_planes[0]+","+merge_planes[1]+"]");
		}
		TilePlanes.PlaneData [] new_planes = new TilePlanes.PlaneData [these_planes.length -1];
		@@ -2257,7 +2265,7 @@ public class SuperTiles{
		false, // boolean ignore_weights,
		true, // boolean sum_weights,
		these_planes[merge_planes[0]].getPreferDisparity(), // preferDisparity,
		dl-1); // int debugLevel)
		dl-2); // int debugLevel)
		// combine tile selection - if next time pd0.reDiscriminateTiles() will fail, it will
		// use old selections, we need to provide them (otherwise will use selection from the first plane)
		plane1.orMeasSelection(these_planes[merge_planes[1]].getMeasSelection());
		@@ -2352,7 +2360,9 @@ public class SuperTiles{
		threads[ithread] = new Thread() {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		if (nsTile == debug_stile){
		// int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
		if (dl > 1){
		System.out.println("createPlanesFromSelections(): nsTile="+nsTile);
		}
		if (plane_selections[nsTile] != null) {
		@@ -2362,7 +2372,8 @@ public class SuperTiles{
		int stileY = nsTile / stilesX;
		int stileX = nsTile % stilesX;
		int [] sTiles = {stileX, stileY};
		int dl = (nsTile == debug_stile) ? 3 : 0;
		// int dl = (nsTile == debug_stile) ? 3 : 0;


		result_planes[nsTile] = null;
		// first make a plane from all tiles
		@@ -2392,7 +2403,7 @@ public class SuperTiles{
		dl); // int debugLevel);

		if ((st_planes != null) && (!st_planes.isEmpty())){
		if (dl > 0){
		if (dl > 1){
		System.out.println("======= createPlanesFromSelections(): nsTile="+nsTile+" detecting bridges ==========");
		}
		boolean [][][] split_sels = pd0.filterBridges(
		@@ -2401,7 +2412,7 @@ public class SuperTiles{
		3, // int max_grow_far,
		dl); // int debugLevel)
		if (split_sels !=null){
		if (dl > -1){
		if (dl > 1){
		System.out.println("======= createPlanesFromSelections(): nsTile="+nsTile+" removing bridges ==========");
		}
		if (dl > 2) {
		@@ -2431,7 +2442,7 @@ public class SuperTiles{
		smplSide, // int smplSide, // = 2; // Sample size (side of a square)
		smplNum, // int smplNum, // = 3; // Number after removing worst
		smplRms, // double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample
		dl); // int debugLevel);
		dl - 1); // int debugLevel);
		}

		}
		@@ -2449,7 +2460,7 @@ public class SuperTiles{
		if (LOWEST_PLANE(2) > 0) st_planes.add(0, st_planes.get(0)); // insert dummy at pos 0;
		result_planes[nsTile] = st_planes.toArray(new TilePlanes.PlaneData[0] );
		if (LOWEST_PLANE(2) > 0) result_planes[nsTile][0] = null; // remove dummy
		if (dl >0){
		if (dl >1){
		System.out.println("createPlanesFromSelections(): nsTile="+nsTile);
		}
		if (dl > 2) {
		@@ -2575,7 +2586,7 @@ public class SuperTiles{
		smplNum, // final int smplNum, // = 3; // Number after removing worst
		smplRms, // final double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample

		debugLevel + 2, // 1, // final int debugLevel,
		debugLevel, // + 2, // 1, // final int debugLevel,
		dbg_X, // final int dbg_X,
		dbg_Y); // final int dbg_Y)
		this.planes = new_planes; // save as "measured" (as opposed to "smoothed" by neighbors) planes
		@@ -2692,7 +2703,7 @@ public class SuperTiles{

		plDiscrXMedian, //final double plDiscrXMedian, // = 1.5; // Remove outliers from the final selection that have distance more than scaled median

		2, // debugLevel, // final int debugLevel,
		debugLevel, // final int debugLevel,
		dbg_X, // final int dbg_X,
		dbg_Y); // final int dbg_Y)

		@@ -2734,7 +2745,7 @@ public class SuperTiles{
		smplNum, // final int smplNum, // = 3; // Number after removing worst
		smplRms, // final double smplRms, // = 0.1; // Maximal RMS of the remaining tiles in a sample

		debugLevel + 2, // 1, // final int debugLevel,
		debugLevel, // + 2, // 1, // final int debugLevel,
		dbg_X, // final int dbg_X,
		dbg_Y); // final int dbg_Y)
		// combine old and new planes (refineDiscriminateTiles will return null for the supertile if failed to re-disciminate)
		@@ -5844,14 +5855,14 @@ public class SuperTiles{



		public TilePlanes.PlaneData[][] copyPlanes(
		public TilePlanes.PlaneData[][] copyPlanes_old(
		TilePlanes.PlaneData[][] src_planes)
		{
		TilePlanes.PlaneData[][] dst_planes = new TilePlanes.PlaneData[src_planes.length][];
		return copyPlanes(src_planes, dst_planes);
		return copyPlanes_old(src_planes, dst_planes);
		}

		public TilePlanes.PlaneData[][] copyPlanes(
		public TilePlanes.PlaneData[][] copyPlanes_old(
		final TilePlanes.PlaneData[][] src_planes,
		final TilePlanes.PlaneData[][] dst_planes)
		{
		@@ -5881,7 +5892,7 @@ public class SuperTiles{
		return dst_planes;
		}

		public TilePlanes.PlaneData[][] planesSmooth(
		public TilePlanes.PlaneData[][] planesSmooth_old(
		final LinkPlanes lp,
		final double meas_pull,// relative pull of the original (measured) plane with respect to the average of the neighbors
		final double maxValue, // do not combine with too bad planes with primary eigenvalue above this value ( 0 any OK)
		@@ -5896,10 +5907,10 @@ public class SuperTiles{
		final int dbg_Y)
		{
		if (this.planes_mod == null){
		this.planes_mod =copyPlanes(this.planes); // make always (for now) *********************
		this.planes_mod =copyPlanes_old(this.planes); // make always (for now) *********************
		}
		for (int pass = 0; pass < num_passes; pass++){
		double diff = planesSmoothStep(
		double diff = planesSmoothStep_old(
		lp, // LinkPlanes lp,
		meas_pull, // relative pull of the original (measured) plane with respect to the average of the neighbors
		maxValue, // final double maxValue, // do not combine with too bad planes
		@@ -5926,7 +5937,7 @@ public class SuperTiles{
		return this.planes_mod;
		}

		public double planesSmoothStep(
		public double planesSmoothStep_old(
		final LinkPlanes lp,
		final double meas_pull,// relative pull of the original (measured) plane with respect to the average of the neighbors
		final double maxValue, // do not combine with too bad planes, do not merge if result is above
		@@ -5947,7 +5958,7 @@ public class SuperTiles{
		final int stilesX = (tilesX + superTileSize -1)/superTileSize;
		// final int stilesY = (tilesY + superTileSize -1)/superTileSize;
		final int debug_stile = dbg_Y * stilesX + dbg_X;
		final TilePlanes.PlaneData[][] new_planes = copyPlanes(mod_planes);
		final TilePlanes.PlaneData[][] new_planes = copyPlanes_old(mod_planes);
		final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		final int numThreads = threads.length;
		final double [] rslt_diffs = calc_diff ? new double [numThreads] : null; // all 0;
		@@ -6190,7 +6201,7 @@ public class SuperTiles{
		};
		}
		ImageDtt.startAndJoin(threads);
		copyPlanes (new_planes, mod_planes); // copy back
		copyPlanes_old (new_planes, mod_planes); // copy back
		if (rslt_diffs == null){
		return Double.NaN;
		}
		@@ -6294,9 +6305,27 @@ public class SuperTiles{
		return split_lines;
		}




		/**
		* Apply same supertile planes merge by combining tiles and re-generating ellipsoids by diagonalizing
		* covariance matrices. Some outliers may be removed after merge
		* @param planes per supertile, per plane - array of supertile instances - will be modified =by merge
		* @param merge_groups per-supertile group sets for merging. Each group set is an array of groups. Each group is an array
		* of plane indices
		* Parameters to generate planes (ellipsoids):
		* @param disp_far disparity lower limit (Double.NaN - any)
		* @param disp_near disparity upper limit (Double.NaN - any)
		* @param dispNorm disparity normalization value (when average disparity is above, difference is proportionally reduced)
		* @param min_weight minimal tile strength to be used
		* @param min_tiles minimal number of tiles to generate ellipsoid
		* Parameters for outlier removal:
		* @param targetEigen target main eigenvalue (thickness in disparity space)
		* @param fractOutliers maximal fraction of all tiles to be removed as outliers
		* @param maxOutliers maximal absolute number of outliers to be removed from each plane (ellipsoid)
		* @param debugLevel debug level
		* @param dbg_X tile x-index for detailed debug data
		* @param dbg_Y tile y-index for detailed debug data
		* @return total number of plane groups merged
		*/
		public int applyMergePlanes(
		final TilePlanes.PlaneData[][] planes,
		final int [][][] merge_groups,
		@@ -6319,14 +6348,16 @@ public class SuperTiles{
		final int superTileSize = tileProcessor.getSuperTileSize();
		final int stilesX = (tilesX + superTileSize -1)/superTileSize;
		final int debug_stile = dbg_Y * stilesX + dbg_X;
		final Thread[] threads = ImageDtt.newThreadArray(tileProcessor.threadsMax);
		final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : tileProcessor.threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);

		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < planes.length; nsTile = ai.getAndIncrement()) {
		int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 4:0;
		// int dl = ((debugLevel > -1) && (nsTile == debug_stile)) ? 4:0;
		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 4: debugLevel;

		if (merge_groups[nsTile] != null){
		// first merge all to the lowest plane (they are ordered), then re-order remaining planes
		for (int ng = 0; ng < merge_groups[nsTile].length; ng++) {

src/main/java/TilePlanes.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -4969,7 +4969,7 @@ public class TilePlanes {
		}
		}

		if (((debugLevel > -1) && ((debugLevel > 0) \|\| (max_attr_corr > attractionCorrMax)) )&& (num_planes > 1)){
		if (((debugLevel > 0) && ((debugLevel > 1) \|\| (max_attr_corr > attractionCorrMax)) )&& (num_planes > 1)){
		String dbg_s = "refineDiscriminateTiles() plane attraction correlation for "+prefix+": maximal="+max_attr_corr;
		for (int np = 0; np < num_planes; np++) {
		for (int np1 = np + 1; np1 < num_planes; np1++) {

src/main/java/TileProcessor.java

+373 −346

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/TileSurface.java

+5 −3

Original line number	Diff line number	Diff line
		@@ -416,7 +416,8 @@ public class TileSurface {
		final int nStiles = stilesX * stilesY;
		final int nTiles = nStiles * superTileSize * superTileSize;
		final double [][][][] fused_data = new double [nStiles][][][];
		final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		// final Thread[] threads = ImageDtt.newThreadArray(threadsMax);
		final Thread[] threads = ImageDtt.newThreadArray((debugLevel > 1)? 1 : threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		final int dbg_tile = dbg_Y * stilesX + dbg_X;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		@@ -424,7 +425,8 @@ public class TileSurface {
		public void run() {
		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
		if (planes[nsTile] != null) {
		int dl = ((debugLevel > -1) && (nsTile == dbg_tile)) ? 3:0;
		// int dl = ((debugLevel > -1) && (nsTile == dbg_tile)) ? 3:0;
		int dl = ((debugLevel > 1) && (nsTile == dbg_tile)) ? 3: debugLevel;
		if (dl > 0){
		System.out.println("fuseSupertilePlanes(), nsTile = "+nsTile);
		}

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