Updating batch mode of the 3d scene processing (24b642b0) · Commits · Elphel / imagej-elphel

src/main/java/CorrectionColorProc.java

+31 −31

Original line number	Original line	Diff line number	Diff line
	@@ -25,12 +25,12 @@
	**		**
	*/		*/

	import ij.ImageStack;
	import ij.gui.GenericDialog;

	import java.util.Properties;		import java.util.Properties;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;

			import ij.ImageStack;
			import ij.gui.GenericDialog;


	public class CorrectionColorProc {		public class CorrectionColorProc {
	showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays();		showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays();
	@@ -241,7 +241,7 @@ public class CorrectionColorProc {
	//TODO: null DENOISE_MASK if it is not calculated		//TODO: null DENOISE_MASK if it is not calculated
	if (colorProcParameters.combineWithSharpnessMask) {		if (colorProcParameters.combineWithSharpnessMask) {
	if (denoiseMask==null) {		if (denoiseMask==null) {
	System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)");		System.out.println ( "Can not combine masks as denoiseMask is null (i.e. no denoise was performed)"); // here
	} else if (denoiseMask.length!=dmask.length) {		} else if (denoiseMask.length!=dmask.length) {
	System.out.println ( "Can not combine masks as denoiseMask length is different from that of dmask");		System.out.println ( "Can not combine masks as denoiseMask length is different from that of dmask");
	} else {		} else {

src/main/java/EyesisCorrectionParameters.java

+3 −0

Original line number	Original line	Diff line number	Diff line
	@@ -3004,6 +3004,9 @@ public class EyesisCorrectionParameters {
	public HashMap<String,Double> z_corr_map = new HashMap<String,Double>();		public HashMap<String,Double> z_corr_map = new HashMap<String,Double>();
	public static String Z_CORR_PREFIX = "z_corr.";		public static String Z_CORR_PREFIX = "z_corr.";

			public boolean batch_run = false; // turned on only while running in batch mode



	public CLTParameters(){}		public CLTParameters(){}
	public void setProperties(String prefix,Properties properties){		public void setProperties(String prefix,Properties properties){

src/main/java/EyesisDCT.java

+111 −107

Original line number	Original line	Diff line number	Diff line
	@@ -25,7 +25,6 @@
	import java.util.Properties;		import java.util.Properties;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;


	import ij.CompositeImage;		import ij.CompositeImage;
	import ij.IJ;		import ij.IJ;
	import ij.ImagePlus;		import ij.ImagePlus;
	@@ -150,6 +149,7 @@ public class EyesisDCT {
	System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels);		System.out.println("calculateDCTKernel():numberOfKernels="+numberOfKernels);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	DoubleGaussianBlur gb=null;		DoubleGaussianBlur gb=null;
	if (dct_parameters.decimateSigma > 0) gb=new DoubleGaussianBlur();		if (dct_parameters.decimateSigma > 0) gb=new DoubleGaussianBlur();
	@@ -1439,7 +1439,9 @@ public class EyesisDCT {
	}		}

	if (toRGB) {		if (toRGB) {
			if (debugLevel > 0){
	System.out.println("correctionColorProc.YPrPbToRGB");		System.out.println("correctionColorProc.YPrPbToRGB");
			}
	stack = YPrPbToRGB(yPrPb,		stack = YPrPbToRGB(yPrPb,
	colorProcParameters.kr, // 0.299;		colorProcParameters.kr, // 0.299;
	colorProcParameters.kb, // 0.114;		colorProcParameters.kb, // 0.114;
	@@ -1636,6 +1638,7 @@ public class EyesisDCT {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	int tileY,tileX;		int tileY,tileX;
	double [] neibs = new double[9]; // pixels around current, first Y, then each color diff		double [] neibs = new double[9]; // pixels around current, first Y, then each color diff
	@@ -1749,6 +1752,7 @@ public class EyesisDCT {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	int tileY,tileX;		int tileY,tileX;
	double [] neibs = new double[9]; // pixels around current, first Y, then each color diff		double [] neibs = new double[9]; // pixels around current, first Y, then each color diff

src/main/java/Eyesis_Correction.java

+2 −12

Original line number	Original line	Diff line number	Diff line
	@@ -776,7 +776,7 @@ private Panel panel1,
	Runtime runtime = Runtime.getRuntime();		Runtime runtime = Runtime.getRuntime();
	runtime.gc();		runtime.gc();
	if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");		if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
			CLT_PARAMETERS.batch_run = false;
	if (label==null) return;		if (label==null) return;
	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("Configure spilt")) {		if (label.equals("Configure spilt")) {
	@@ -5051,7 +5051,6 @@ private Panel panel1,
	RGB_PARAMETERS, // EyesisCorrectionParameters.RGBParameters rgbParameters,		RGB_PARAMETERS, // EyesisCorrectionParameters.RGBParameters rgbParameters,
	THREADS_MAX, // final int threadsMax, // maximal number of threads to launch		THREADS_MAX, // final int threadsMax, // maximal number of threads to launch
	UPDATE_STATUS, // final boolean updateStatus,		UPDATE_STATUS, // final boolean updateStatus,
	false, // final boolean batch_mode,
	DEBUG_LEVEL); //final int debugLevel);		DEBUG_LEVEL); //final int debugLevel);
	if (!OK) {		if (!OK) {
	String msg="Image data not initialized, run 'CLT 3D' command first";		String msg="Image data not initialized, run 'CLT 3D' command first";
	@@ -5059,18 +5058,9 @@ private Panel panel1,
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	}		}

	/*
	if (configPath!=null) {
	saveTimestampedProperties( // save config again
	configPath, // full path or null
	null, // use as default directory if path==null
	true,
	PROPERTIES);
	}

	*/
	} else if (label.equals("CLT batch process")) {		} else if (label.equals("CLT batch process")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			CLT_PARAMETERS.batch_run = true;
	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	if (QUAD_CLT == null){		if (QUAD_CLT == null){
	QUAD_CLT = new QuadCLT (		QUAD_CLT = new QuadCLT (

src/main/java/LinkPlanes.java

+464 −429

Original line number	Original line	Diff line number	Diff line
	@@ -188,7 +188,7 @@ public class LinkPlanes {
	plPrecision = clt_parameters.plPrecision;		plPrecision = clt_parameters.plPrecision;
	plNormPow = clt_parameters.plNormPow;		plNormPow = clt_parameters.plNormPow;

	dbg_tileX = clt_parameters.tileX;		dbg_tileX = clt_parameters.batch_run?-1:clt_parameters.tileX;
	dbg_tileY = clt_parameters.tileY;		dbg_tileY = clt_parameters.tileY;
	this.st = st;		this.st = st;
	}		}
	@@ -862,6 +862,7 @@ public class LinkPlanes {
	// Select best symmetrical match, consider only N, NE, E, SE - later opposite ones will be copied		// Select best symmetrical match, consider only N, NE, E, SE - later opposite ones will be copied
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	// TilePlanes.PlaneData [] dbg_planes = null;		// TilePlanes.PlaneData [] dbg_planes = null;
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	@@ -960,6 +961,7 @@ public class LinkPlanes {
	ai.set(0);		ai.set(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	// TilePlanes.PlaneData [][] dbg_planes = planes;		// TilePlanes.PlaneData [][] dbg_planes = planes;
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	@@ -1056,6 +1058,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	// int dl = ((debugLevel > -1) && (nsTile0 == debug_stile)) ? 1:0;		// int dl = ((debugLevel > -1) && (nsTile0 == debug_stile)) ? 1:0;
	@@ -1159,6 +1162,7 @@ public class LinkPlanes {
	// Reset neighbors		// Reset neighbors
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	if ( planes[nsTile0] != null) {		if ( planes[nsTile0] != null) {
	@@ -1187,6 +1191,7 @@ public class LinkPlanes {
	boolean hasConflict(LinkPair lp){		boolean hasConflict(LinkPair lp){
	return (src == lp.src) \|\| (dst == lp.dst);		return (src == lp.src) \|\| (dst == lp.dst);
	}		}
			@Override
	public String toString(){		public String toString(){
	return String.format("%d-(%6.3f)->%d", src,cost,dst);		return String.format("%d-(%6.3f)->%d", src,cost,dst);
	}		}
	@@ -1194,6 +1199,7 @@ public class LinkPlanes {
	}		}
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	// int dl = ((debugLevel > -1) && (nsTile0 == debug_stile)) ? 1:0;		// int dl = ((debugLevel > -1) && (nsTile0 == debug_stile)) ? 1:0;
	@@ -1298,6 +1304,7 @@ public class LinkPlanes {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	// TilePlanes.PlaneData [][] dbg_planes = planes;		// TilePlanes.PlaneData [][] dbg_planes = planes;
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	@@ -1412,6 +1419,7 @@ public class LinkPlanes {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	// TilePlanes.PlaneData [][] dbg_planes = planes;		// TilePlanes.PlaneData [][] dbg_planes = planes;
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	@@ -1666,6 +1674,7 @@ public class LinkPlanes {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) {
	if ( planes[nsTile0] != null) {		if ( planes[nsTile0] != null) {
	@@ -1684,6 +1693,7 @@ public class LinkPlanes {
	ai.set(0);		ai.set(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]		int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]
	double [][] quality_stats = all_quality_stats[numThread];		double [][] quality_stats = all_quality_stats[numThread];
	@@ -1911,6 +1921,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( planes[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( planes[nsTile] != null) {
	ArrayList<LayersLinks> links_list = new ArrayList<LayersLinks>();		ArrayList<LayersLinks> links_list = new ArrayList<LayersLinks>();
	@@ -2002,6 +2013,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {
	// merge_pairs[nsTile] = new boolean [merge_candidates[nsTile].length];		// merge_pairs[nsTile] = new boolean [merge_candidates[nsTile].length];
	@@ -2130,6 +2142,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {
	int dl = ((debugLevel > 0) && (nsTile == debug_stile)) ? 2: ((debugLevel > 1) ? 1:0);		int dl = ((debugLevel > 0) && (nsTile == debug_stile)) ? 2: ((debugLevel > 1) ? 1:0);
	@@ -2305,6 +2318,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {
	int sty0 = nsTile0 / stilesX;		int sty0 = nsTile0 / stilesX;
	@@ -2461,6 +2475,7 @@ public class LinkPlanes {
	final boolean [][] weak_fgnd = new boolean [valid_candidates.length][];		final boolean [][] weak_fgnd = new boolean [valid_candidates.length][];
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {
	int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;		int dl = ((debugLevel > 1) && (nsTile == debug_stile)) ? 3: debugLevel;
	@@ -2528,6 +2543,9 @@ public class LinkPlanes {
	final int dbg_X,		final int dbg_X,
	final int dbg_Y)		final int dbg_Y)
	{		{
			if (debugLevel > 0) {
			System.out.println("Debug debugLevel");
			}
	final int tilesX = st.tileProcessor.getTilesX();		final int tilesX = st.tileProcessor.getTilesX();
	final int tilesY = st.tileProcessor.getTilesY();		final int tilesY = st.tileProcessor.getTilesY();
	final int superTileSize = st.tileProcessor.getSuperTileSize();		final int superTileSize = st.tileProcessor.getSuperTileSize();
	@@ -2541,6 +2559,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {
	// int dl = ((debugLevel > 0) && (nsTile0 == debug_stile)) ? 3: ((debugLevel > 1) ? 2:0);		// int dl = ((debugLevel > 0) && (nsTile0 == debug_stile)) ? 3: ((debugLevel > 1) ? 2:0);
	@@ -2731,6 +2750,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) {
	if ((merge_candidates[nsTile] != null) && (conflicts[nsTile] != null)) {		if ((merge_candidates[nsTile] != null) && (conflicts[nsTile] != null)) {
	@@ -2829,6 +2849,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {
	// int dl = ((debugLevel > 0) && (nsTile0 == debug_stile)) ? 3: ((debugLevel > 1) ? 2:0);		// int dl = ((debugLevel > 0) && (nsTile0 == debug_stile)) ? 3: ((debugLevel > 1) ? 2:0);
	@@ -3055,6 +3076,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {		for (int nsTile0 = ai.getAndIncrement(); nsTile0 < nStiles; nsTile0 = ai.getAndIncrement()) if ( merge_candidates[nsTile0] != null) {
	int sty0 = nsTile0 / stilesX;		int sty0 = nsTile0 / stilesX;
	@@ -3271,6 +3293,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {
	merge_pairs[nsTile] = new boolean [merge_candidates[nsTile].length];		merge_pairs[nsTile] = new boolean [merge_candidates[nsTile].length];
	@@ -3350,6 +3373,7 @@ public class LinkPlanes {
	// TODO Make nooverlaps be overriden if ne of the planes is very weak and they are close by disparity		// TODO Make nooverlaps be overriden if ne of the planes is very weak and they are close by disparity
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {		for (int nsTile = ai.getAndIncrement(); nsTile < nStiles; nsTile = ai.getAndIncrement()) if ( merge_candidates[nsTile] != null) {
	if (planes[nsTile] == null){		if (planes[nsTile] == null){
	@@ -3680,6 +3704,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	ConnectionCosts connectionCosts = new ConnectionCosts(		ConnectionCosts connectionCosts = new ConnectionCosts(
	orthoWeight, // double orthoWeight,		orthoWeight, // double orthoWeight,
	@@ -3738,6 +3763,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	ConnectionCosts connectionCosts = new ConnectionCosts(		ConnectionCosts connectionCosts = new ConnectionCosts(
	orthoWeight, // double orthoWeight,		orthoWeight, // double orthoWeight,
	@@ -3970,6 +3996,7 @@ public class LinkPlanes {
	final AtomicInteger ai = new AtomicInteger(0);		final AtomicInteger ai = new AtomicInteger(0);
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	for (int nsTile = ai.getAndIncrement(); nsTile < src_planes.length; nsTile = ai.getAndIncrement()) {		for (int nsTile = ai.getAndIncrement(); nsTile < src_planes.length; nsTile = ai.getAndIncrement()) {
	if (src_planes[nsTile] != null){		if (src_planes[nsTile] != null){
	@@ -4059,6 +4086,7 @@ public class LinkPlanes {

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	double [][] dbg_img=null;		double [][] dbg_img=null;
	int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]		int numThread = ai_numThread.getAndIncrement(); // unique number of thread to write to rslt_diffs[numThread]
	@@ -4660,6 +4688,9 @@ public class LinkPlanes {
	final TileNeibs tnSurface = new TileNeibs(stilesX, stilesY);		final TileNeibs tnSurface = new TileNeibs(stilesX, stilesY);
	final int debug_stile = dbg_Y * stilesX + dbg_X;		final int debug_stile = dbg_Y * stilesX + dbg_X;
	// final int nStiles = stilesX * stilesY;		// final int nStiles = stilesX * stilesY;
			if (debugLevel >-1) {
			System.out.println("fillSquares(): Debug debugLevel");
			}
	int num_added = 0;		int num_added = 0;
	for (int stY = 0; stY < (stilesY - 1); stY++ ) {		for (int stY = 0; stY < (stilesY - 1); stY++ ) {
	for (int stX = 0; stX < (stilesX - 1); stX++ ) {		for (int stX = 0; stX < (stilesX - 1); stX++ ) {
	@@ -4732,6 +4763,10 @@ public class LinkPlanes {
	final int stilesY = (tilesY + superTileSize -1)/superTileSize;		final int stilesY = (tilesY + superTileSize -1)/superTileSize;
	final TileNeibs tnSurface = new TileNeibs(stilesX, stilesY);		final TileNeibs tnSurface = new TileNeibs(stilesX, stilesY);
	final int debug_stile = dbg_Y * stilesX + dbg_X;		final int debug_stile = dbg_Y * stilesX + dbg_X;
			if (debugLevel >-1) {
			System.out.println("fillHypotenuse(): Debug debugLevel");
			}

	// final int nStiles = stilesX * stilesY;		// final int nStiles = stilesX * stilesY;
	int num_added = 0;		int num_added = 0;
	for (int stY = 0; stY < (stilesY - 1); stY++ ) {		for (int stY = 0; stY < (stilesY - 1); stY++ ) {

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