debugging batch dsi (8c2ea7ed) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

+50 −5

Original line number	Original line	Diff line number	Diff line
	@@ -586,6 +586,15 @@ public class CLTParameters {
	public double gr_unique_tol = 0.15; // Do not re-measure correlation if target disparity differs from some previous by this		public double gr_unique_tol = 0.15; // Do not re-measure correlation if target disparity differs from some previous by this
	public double gr_unique_pretol = 0.5; // Larger tolerance for expanding (not refining)		public double gr_unique_pretol = 0.5; // Larger tolerance for expanding (not refining)

			public int gr_max_clust_radius = 4; // 7x7
			public int gr_num_refines = 4;
			public boolean gr_exp_certain = false;

			public boolean gr_reduce_sngl = true;
			public boolean gr_reduce_multi = true;
			public boolean gr_all_last = true;
			public boolean gr_nan_bg = true;


	public boolean ft_mod_strength = true; // When set, multiply each tile strength by the number of selected neighbors		public boolean ft_mod_strength = true; // When set, multiply each tile strength by the number of selected neighbors
	public boolean ft_clusterize_by_highest = true; // Clusterize using disparity horizontal maximums for fronto planes and minimums - for horizontal. False - use histograms		public boolean ft_clusterize_by_highest = true; // Clusterize using disparity horizontal maximums for fronto planes and minimums - for horizontal. False - use histograms
	@@ -1468,6 +1477,13 @@ public class CLTParameters {
	properties.setProperty(prefix+"gr_fin_diff", this.gr_fin_diff +"");		properties.setProperty(prefix+"gr_fin_diff", this.gr_fin_diff +"");
	properties.setProperty(prefix+"gr_unique_tol", this.gr_unique_tol +"");		properties.setProperty(prefix+"gr_unique_tol", this.gr_unique_tol +"");
	properties.setProperty(prefix+"gr_unique_pretol", this.gr_unique_pretol +"");		properties.setProperty(prefix+"gr_unique_pretol", this.gr_unique_pretol +"");
			properties.setProperty(prefix+"gr_max_clust_radius", this.gr_max_clust_radius +"");
			properties.setProperty(prefix+"gr_num_refines", this.gr_num_refines +"");
			properties.setProperty(prefix+"gr_exp_certain", this.gr_exp_certain +"");
			properties.setProperty(prefix+"gr_reduce_sngl", this.gr_reduce_sngl +"");
			properties.setProperty(prefix+"gr_reduce_multi", this.gr_reduce_multi +"");
			properties.setProperty(prefix+"gr_all_last", this.gr_all_last +"");
			properties.setProperty(prefix+"gr_nan_bg", this.gr_nan_bg +"");

	properties.setProperty(prefix+"ft_mod_strength", this.ft_mod_strength +"");		properties.setProperty(prefix+"ft_mod_strength", this.ft_mod_strength +"");
	properties.setProperty(prefix+"ft_clusterize_by_highest", this.ft_clusterize_by_highest +"");		properties.setProperty(prefix+"ft_clusterize_by_highest", this.ft_clusterize_by_highest +"");
	@@ -2298,7 +2314,13 @@ public class CLTParameters {
	if (properties.getProperty(prefix+"gr_fin_diff")!=null) this.gr_fin_diff=Double.parseDouble(properties.getProperty(prefix+"gr_fin_diff"));		if (properties.getProperty(prefix+"gr_fin_diff")!=null) this.gr_fin_diff=Double.parseDouble(properties.getProperty(prefix+"gr_fin_diff"));
	if (properties.getProperty(prefix+"gr_unique_tol")!=null) this.gr_unique_tol=Double.parseDouble(properties.getProperty(prefix+"gr_unique_tol"));		if (properties.getProperty(prefix+"gr_unique_tol")!=null) this.gr_unique_tol=Double.parseDouble(properties.getProperty(prefix+"gr_unique_tol"));
	if (properties.getProperty(prefix+"gr_unique_pretol")!=null) this.gr_unique_pretol=Double.parseDouble(properties.getProperty(prefix+"gr_unique_pretol"));		if (properties.getProperty(prefix+"gr_unique_pretol")!=null) this.gr_unique_pretol=Double.parseDouble(properties.getProperty(prefix+"gr_unique_pretol"));
			if (properties.getProperty(prefix+"gr_max_clust_radius")!=null) this.gr_max_clust_radius=Integer.parseInt(properties.getProperty(prefix+"gr_max_clust_radius"));
			if (properties.getProperty(prefix+"gr_num_refines")!=null) this.gr_num_refines=Integer.parseInt(properties.getProperty(prefix+"gr_num_refines"));
			if (properties.getProperty(prefix+"gr_exp_certain")!=null) this.gr_exp_certain=Boolean.parseBoolean(properties.getProperty(prefix+"gr_exp_certain"));
			if (properties.getProperty(prefix+"gr_reduce_sngl")!=null) this.gr_reduce_sngl=Boolean.parseBoolean(properties.getProperty(prefix+"gr_reduce_sngl"));
			if (properties.getProperty(prefix+"gr_reduce_multi")!=null) this.gr_reduce_multi=Boolean.parseBoolean(properties.getProperty(prefix+"gr_reduce_multi"));
			if (properties.getProperty(prefix+"gr_all_last")!=null) this.gr_all_last=Boolean.parseBoolean(properties.getProperty(prefix+"gr_all_last"));
			if (properties.getProperty(prefix+"gr_nan_bg")!=null) this.gr_nan_bg=Boolean.parseBoolean(properties.getProperty(prefix+"gr_nan_bg"));

	if (properties.getProperty(prefix+"ft_mod_strength")!=null) this.ft_mod_strength=Boolean.parseBoolean(properties.getProperty(prefix+"ft_mod_strength"));		if (properties.getProperty(prefix+"ft_mod_strength")!=null) this.ft_mod_strength=Boolean.parseBoolean(properties.getProperty(prefix+"ft_mod_strength"));
	if (properties.getProperty(prefix+"ft_clusterize_by_highest")!=null) this.ft_clusterize_by_highest=Boolean.parseBoolean(properties.getProperty(prefix+"ft_clusterize_by_highest"));		if (properties.getProperty(prefix+"ft_clusterize_by_highest")!=null) this.ft_clusterize_by_highest=Boolean.parseBoolean(properties.getProperty(prefix+"ft_clusterize_by_highest"));
	@@ -2315,8 +2337,6 @@ public class CLTParameters {
	if (properties.getProperty(prefix+"ft_used_companions")!=null) this.ft_used_companions=Integer.parseInt(properties.getProperty(prefix+"ft_used_companions"));		if (properties.getProperty(prefix+"ft_used_companions")!=null) this.ft_used_companions=Integer.parseInt(properties.getProperty(prefix+"ft_used_companions"));
	if (properties.getProperty(prefix+"ft_used_true_companions")!=null) this.ft_used_true_companions=Integer.parseInt(properties.getProperty(prefix+"ft_used_true_companions"));		if (properties.getProperty(prefix+"ft_used_true_companions")!=null) this.ft_used_true_companions=Integer.parseInt(properties.getProperty(prefix+"ft_used_true_companions"));



	if (properties.getProperty(prefix+"plPreferDisparity")!=null) this.plPreferDisparity=Boolean.parseBoolean(properties.getProperty(prefix+"plPreferDisparity"));		if (properties.getProperty(prefix+"plPreferDisparity")!=null) this.plPreferDisparity=Boolean.parseBoolean(properties.getProperty(prefix+"plPreferDisparity"));
	if (properties.getProperty(prefix+"plDispNorm")!=null) this.plDispNorm=Double.parseDouble(properties.getProperty(prefix+"plDispNorm"));		if (properties.getProperty(prefix+"plDispNorm")!=null) this.plDispNorm=Double.parseDouble(properties.getProperty(prefix+"plDispNorm"));
	if (properties.getProperty(prefix+"plFrontoTol")!=null) this.plFrontoTol=Double.parseDouble(properties.getProperty(prefix+"plFrontoTol"));		if (properties.getProperty(prefix+"plFrontoTol")!=null) this.plFrontoTol=Double.parseDouble(properties.getProperty(prefix+"plFrontoTol"));
	@@ -3290,6 +3310,24 @@ public class CLTParameters {
	gd.addNumericField("Do not re-measure correlation if target disparity differs from some previous less", this.gr_unique_tol, 6);		gd.addNumericField("Do not re-measure correlation if target disparity differs from some previous less", this.gr_unique_tol, 6);
	gd.addNumericField("Larger tolerance for expanding (not refining)", this.gr_unique_pretol, 6);		gd.addNumericField("Larger tolerance for expanding (not refining)", this.gr_unique_pretol, 6);

			gd.addMessage ("--- Mukti-tile DSI expansion ---");
			gd.addNumericField("Maximal cluster radius", this.gr_max_clust_radius, 0,6,"",
			"2 - 3x3, 3 - 5x5, 4 - 7x7 tiles");
			gd.addNumericField("Number of refines for each cluster radius", this.gr_num_refines, 0,6,"",
			"Each tile will be processed until change fallls below gr_unique_tol ('Do not re-measure...' above), buit hard-limited by this value");
			gd.addCheckbox ("Expand DSI over weak tiles", this.gr_exp_certain,
			"Has problems (produces dips), disable");
			gd.addCheckbox ("Reduce number of pairs when refining single-tile DSI", this.gr_reduce_sngl,
			"Currently to 40 pairs: neigbors, squares, diameters");
			gd.addCheckbox ("Reduce number of pairs when refining single-tile DSI", this.gr_reduce_multi,
			"Currently to 40 pairs: neigbors, squares, diameters");
			gd.addCheckbox ("Restore to all configured pairs for the last refine cycles", this.gr_all_last,
			"Use configured (ImageDtt tab) pairs for the last refine cycles (both single and multi-tile");
			gd.addCheckbox ("Undefine disparity for the background tiles", this.gr_nan_bg,
			"Set DSI disparity to NaN for the BG tiles");



	gd.addTab ("Alt CLusterize", "Alternative initial tiles clusterization");		gd.addTab ("Alt CLusterize", "Alternative initial tiles clusterization");

	gd.addCheckbox ("Modify cluster strengths", this.ft_mod_strength,		gd.addCheckbox ("Modify cluster strengths", this.ft_mod_strength,
	@@ -4170,6 +4208,13 @@ public class CLTParameters {
	this.gr_fin_diff= gd.getNextNumber();		this.gr_fin_diff= gd.getNextNumber();
	this.gr_unique_tol= gd.getNextNumber();		this.gr_unique_tol= gd.getNextNumber();
	this.gr_unique_pretol= gd.getNextNumber();		this.gr_unique_pretol= gd.getNextNumber();
			this.gr_max_clust_radius= (int) gd.getNextNumber();
			this.gr_num_refines= (int) gd.getNextNumber();
			this.gr_exp_certain= gd.getNextBoolean();
			this.gr_reduce_sngl= gd.getNextBoolean();
			this.gr_reduce_multi= gd.getNextBoolean();
			this.gr_all_last= gd.getNextBoolean();
			this.gr_nan_bg= gd.getNextBoolean();

	this.ft_mod_strength= gd.getNextBoolean();		this.ft_mod_strength= gd.getNextBoolean();
	this.ft_clusterize_by_highest= gd.getNextBoolean();		this.ft_clusterize_by_highest= gd.getNextBoolean();

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -1019,7 +1019,7 @@ public class EyesisCorrectionParameters {
	gd.addCheckbox ("Include/genarate separate aux camera DSI data in the combo DSI", this.clt_batch_dsi_aux,		gd.addCheckbox ("Include/genarate separate aux camera DSI data in the combo DSI", this.clt_batch_dsi_aux,
	"8-rig: DSI for the AUX camera is offset (by the rig baseline) from the main and rig DSI. Aux DSI requires extra processing time."+		"8-rig: DSI for the AUX camera is offset (by the rig baseline) from the main and rig DSI. Aux DSI requires extra processing time."+
	" EO+LWIR - generate a separate GT+AUX file");		" EO+LWIR - generate a separate GT+AUX file");
	gd.addCheckbox ("Additional steps to calculate Auf DSI (more than for LY adjustment)", this.clt_batch_dsi_aux_full,		gd.addCheckbox ("Additional steps to calculate Aux DSI (more than for LY adjustment)", this.clt_batch_dsi_aux_full,
	"(Not yet tested)");		"(Not yet tested)");

src/main/java/com/elphel/imagej/tileprocessor/ImageDtt.java

+4 −2

Original line number	Original line	Diff line number	Diff line
	@@ -2468,7 +2468,7 @@ public class ImageDtt extends ImageDttCPU {
	}		}
	nTile = tileY * tilesX + tileX;		nTile = tileY * tilesX + tileX;
	if (tp_tasks[iTile].getTask() == 0) continue; // nothing to do for this tile		if (tp_tasks[iTile].getTask() == 0) continue; // nothing to do for this tile
	boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > -6);		boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > 0);
	if (debugTile0) {		if (debugTile0) {
	System.out.println("clt_process_tl_correlations(): tileX="+tileX+", tileY="+tileY+", iTile="+iTile+", nTile="+nTile);		System.out.println("clt_process_tl_correlations(): tileX="+tileX+", tileY="+tileY+", iTile="+iTile+", nTile="+nTile);
	}		}
	@@ -2517,7 +2517,9 @@ public class ImageDtt extends ImageDttCPU {
	corrs[npair] , //double [] corr_tile,		corrs[npair] , //double [] corr_tile,
	npair); // int num_pair)		npair); // int num_pair)
	if (pair_width < 0.1) {		if (pair_width < 0.1) {
			if (globalDebugLevel > 0) {
	System.out.println("pair_width["+npair+"]="+pair_width);		System.out.println("pair_width["+npair+"]="+pair_width);
			}
	} else {		} else {
	weights[npair] /= Math.pow(pair_width, imgdtt_params.mcorr_weights_power);		weights[npair] /= Math.pow(pair_width, imgdtt_params.mcorr_weights_power);
	}		}

src/main/java/com/elphel/imagej/tileprocessor/ImageDttCPU.java

+8 −6

Original line number	Original line	Diff line number	Diff line
	@@ -15970,7 +15970,7 @@ public class ImageDttCPU {
	}		}
	}		}
	}		}
	boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > -6);		boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > 0);
	if (debugTile0) {		if (debugTile0) {
	System.out.println("clt_process_tl_correlations(): tileX="+tileX+", tileY="+tileY);		System.out.println("clt_process_tl_correlations(): tileX="+tileX+", tileY="+tileY);
	}		}
	@@ -16027,7 +16027,9 @@ public class ImageDttCPU {
	corrs[npair] , //double [] corr_tile,		corrs[npair] , //double [] corr_tile,
	npair); // int num_pair)		npair); // int num_pair)
	if (pair_width < 0.1) {		if (pair_width < 0.1) {
			if (globalDebugLevel > 0) {
	System.out.println("pair_width["+npair+"]="+pair_width);		System.out.println("pair_width["+npair+"]="+pair_width);
			}
	} else {		} else {
	weights[npair] /= Math.pow(pair_width, imgdtt_params.mcorr_weights_power);		weights[npair] /= Math.pow(pair_width, imgdtt_params.mcorr_weights_power);
	}		}
	@@ -16884,7 +16886,7 @@ public class ImageDttCPU {
	tileYC = tp_tasks[iTileC].getTileY(); // /tilesX;		tileYC = tp_tasks[iTileC].getTileY(); // /tilesX;
	tileXC = tp_tasks[iTileC].getTileX(); //nTile % tilesX;		tileXC = tp_tasks[iTileC].getTileX(); //nTile % tilesX;
	nTileC = tileYC * tilesX + tileXC;		nTileC = tileYC * tilesX + tileXC;
	if ((tileXC == debug_tileX) && (tileYC == debug_tileY)) {		if ((globalDebugLevel > -2) && (tileXC == debug_tileX) && (tileYC == debug_tileY)) {
	System.out.println("quadCorrTD_tilted(): tileXC="+tileXC+", tileYC="+tileYC+", iTileC="+iTileC);		System.out.println("quadCorrTD_tilted(): tileXC="+tileXC+", tileYC="+tileYC+", iTileC="+iTileC);
	}		}
	//quadCorrTD_tilted		//quadCorrTD_tilted
	@@ -16963,7 +16965,7 @@ public class ImageDttCPU {
	} else {		} else {
	tp_index_multi[offset_index][cindex] = iTileC;		tp_index_multi[offset_index][cindex] = iTileC;
	}		}
	if ((globalDebugLevel > 0) && (tileXC == debug_tileX) && (tileYC == debug_tileY)) {		if ((globalDebugLevel > -2) && (tileXC == debug_tileX) && (tileYC == debug_tileY)) {
	System.out.println("mindx="+mindx+", cindex="+cindex+", disparity_target="+disparity_target+		System.out.println("mindx="+mindx+", cindex="+cindex+", disparity_target="+disparity_target+
	", offset_index="+offset_index+", cindex="+cindex+", tileX="+tileX+", tileY="+tileY );		", offset_index="+offset_index+", cindex="+cindex+", tileX="+tileX+", tileY="+tileY );
	}		}
	@@ -17037,7 +17039,7 @@ public class ImageDttCPU {
	globalDebugLevel);		globalDebugLevel);
	if (globalDebugLevel > 0) {		if (globalDebugLevel > 0) {
	for (TpTask tt: tp_tasks_pass) {		for (TpTask tt: tp_tasks_pass) {
	if ((globalDebugLevel > 0) && ((tt.getTileY() - idy) == debug_tileY) && ((tt.getTileX()-idx) == debug_tileX)) {		if ((globalDebugLevel > -2) && ((tt.getTileY() - idy) == debug_tileY) && ((tt.getTileX()-idx) == debug_tileX)) {
	System.out.println(" +++ neib_index="+neib_index+" tX="+tt.getTileX()+" tY="+tt.getTileY()		System.out.println(" +++ neib_index="+neib_index+" tX="+tt.getTileX()+" tY="+tt.getTileY()
	+ " target_disparity="+tt.getTargetDisparity()+" idx="+idx+" idy="+idy);		+ " target_disparity="+tt.getTargetDisparity()+" idx="+idx+" idy="+idy);
	}		}
	@@ -17064,7 +17066,7 @@ public class ImageDttCPU {
	float [][] src_corrs = fcorr_td_part[tY_src][tX_src];		float [][] src_corrs = fcorr_td_part[tY_src][tX_src];
	if (src_corrs != null) {		if (src_corrs != null) {
	// TODO: finish checking correct fcorr_td_part		// TODO: finish checking correct fcorr_td_part
	if ((globalDebugLevel > 0) && (tX_dst == debug_tileX) && (tY_dst == debug_tileY)) {		if ((globalDebugLevel > -2) && (tX_dst == debug_tileX) && (tY_dst == debug_tileY)) {
	System.out.println("*** quadCorrTD_tilted_sum(): neib_index="+fneib_index+", tX_dst="+tX_dst+", tY_dst="+tY_dst+		System.out.println("*** quadCorrTD_tilted_sum(): neib_index="+fneib_index+", tX_dst="+tX_dst+", tY_dst="+tY_dst+
	", iTileC="+iTileC+", tX_src="+tX_src+", tY_src="+tY_src+", w="+w);		", iTileC="+iTileC+", tX_src="+tX_src+", tY_src="+tY_src+", w="+w);
	}		}

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

+82 −49

Original line number	Original line	Diff line number	Diff line
	@@ -8243,7 +8243,7 @@ public class QuadCLTCPU {
	tp.clt_3d_passes.add(bgnd_data);		tp.clt_3d_passes.add(bgnd_data);
	// if (show_init_refine)		// if (show_init_refine)
	// if ((debugLevel > -2) && clt_parameters.show_first_bg) {		// if ((debugLevel > -2) && clt_parameters.show_first_bg) {
	if ((debugLevel > -3) && clt_parameters.show_first_bg) {		if ((debugLevel > -2) && clt_parameters.show_first_bg) {
	tp.showScan(		tp.showScan(
	tp.clt_3d_passes.get(0), // CLTPass3d scan,		tp.clt_3d_passes.get(0), // CLTPass3d scan,
	"bgnd_data-"+tp.clt_3d_passes.size());		"bgnd_data-"+tp.clt_3d_passes.size());
	@@ -8269,7 +8269,7 @@ public class QuadCLTCPU {
	updateStatus,		updateStatus,
	debugLevel);		debugLevel);

	if (debugLevel > -3) {		if (debugLevel > -2) {
	imp_bgnd_int.show(); /// OK		imp_bgnd_int.show(); /// OK
	}		}

	@@ -8448,8 +8448,9 @@ public class QuadCLTCPU {

	}		}
	}		}
			// boolean reduce_pairs_multi = true;
	// Save pair selection and minimaize them for scanning, then restore;		// boolean last_iter_all = true;
			// Save pair selection and minimize them for scanning, then restore;
	int save_pairs_selection = clt_parameters.img_dtt.getMcorr(getNumSensors());		int save_pairs_selection = clt_parameters.img_dtt.getMcorr(getNumSensors());
	clt_parameters.img_dtt.setMcorr(getNumSensors(), 0 ); // remove all		clt_parameters.img_dtt.setMcorr(getNumSensors(), 0 ); // remove all
	clt_parameters.img_dtt.setMcorrNeib(getNumSensors(),true);		clt_parameters.img_dtt.setMcorrNeib(getNumSensors(),true);
	@@ -8458,14 +8459,14 @@ public class QuadCLTCPU {
	boolean save_run_lma = clt_parameters.correlate_lma;		boolean save_run_lma = clt_parameters.correlate_lma;
	clt_parameters.correlate_lma = false;		clt_parameters.correlate_lma = false;

	int num_macro_refine = 3;		// int num_macro_refine = 3;
	int dbg_num_new = 0;		int dbg_num_new = 0;
	for (CLTPass3d from_macro_pass: new_meas) {		for (CLTPass3d from_macro_pass: new_meas) {
	if (debugLevel > -2) {		if (debugLevel > -2) {
	System.out.println("Next from new_meas: "+dbg_num_new);		System.out.println("Next from new_meas: "+dbg_num_new);
	}		}
	dbg_num_new++;		dbg_num_new++;
	for (int nnn = 0; nnn < num_macro_refine; nnn ++){ //		for (int nnn = 0; nnn < clt_parameters.gr_num_refines; nnn ++){ //
	refine_pass = tp.clt_3d_passes.size(); // 1		refine_pass = tp.clt_3d_passes.size(); // 1
	CLTPass3d refined = tp.refinePassSetup( // prepare tile tasks for the refine pass (re-measure disparities)		CLTPass3d refined = tp.refinePassSetup( // prepare tile tasks for the refine pass (re-measure disparities)
	// final double [][][] image_data, // first index - number of image in a quad		// final double [][][] image_data, // first index - number of image in a quad
	@@ -8516,6 +8517,7 @@ public class QuadCLTCPU {
	"after_refinePassSetup-"+tp.clt_3d_passes.size());		"after_refinePassSetup-"+tp.clt_3d_passes.size());

	// Just debugging		// Just debugging
			/*
	if (clt_parameters.gpu_debug_accum) { //		if (clt_parameters.gpu_debug_accum) { //
	CLTMeasureCorrTesting( // perform single pass according to prepared tiles operations and disparity		CLTMeasureCorrTesting( // perform single pass according to prepared tiles operations and disparity
	clt_parameters,		clt_parameters,
	@@ -8533,9 +8535,11 @@ public class QuadCLTCPU {
	updateStatus,		updateStatus,
	debugLevel);		debugLevel);
	}		}
			*/
	// End of just debugging		// End of just debugging
	// will split old/new		// will split old/new
	CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity		// CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity
			CLTMeasCorr( // perform single pass according to prepared tiles operations and disparity
	// CLTMeasCorr(		// CLTMeasCorr(
	clt_parameters,		clt_parameters,
	refine_pass,		refine_pass,
	@@ -8551,7 +8555,7 @@ public class QuadCLTCPU {
	if (show_init_refine) tp.showScan(		if (show_init_refine) tp.showScan(
	tp.clt_3d_passes.get(refine_pass), // CLTPass3d scan,		tp.clt_3d_passes.get(refine_pass), // CLTPass3d scan,
	"after_measure-"+tp.clt_3d_passes.size());		"after_measure-"+tp.clt_3d_passes.size());
	if (nnn < (num_macro_refine-1)) { // all but last		if (nnn < (clt_parameters.gr_num_refines-1)) { // all but last
	// if (clt_parameters.combine_refine){		// if (clt_parameters.combine_refine){
	CLTPass3d combo_pass = tp.compositeScan(		CLTPass3d combo_pass = tp.compositeScan(
	tp.clt_3d_passes, // final ArrayList <CLTPass3d> passes,		tp.clt_3d_passes, // final ArrayList <CLTPass3d> passes,
	@@ -8583,7 +8587,8 @@ public class QuadCLTCPU {
	}		}
	// add new scan from macro		// add new scan from macro
	tp.clt_3d_passes.add(from_macro_pass);		tp.clt_3d_passes.add(from_macro_pass);
	CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity		// CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity
			CLTMeasCorr( // perform single pass according to prepared tiles operations and disparity
	// image_data, // first index - number of image in a quad		// image_data, // first index - number of image in a quad
	// saturation_imp, //final boolean [][] saturation_imp, // (near) saturated pixels or null		// saturation_imp, //final boolean [][] saturation_imp, // (near) saturated pixels or null
	clt_parameters,		clt_parameters,
	@@ -8602,17 +8607,22 @@ public class QuadCLTCPU {
	}		}

	// Restore pair selection and minimize them for scanning, then restore;		// Restore pair selection and minimize them for scanning, then restore;
			if (!clt_parameters.gr_reduce_sngl) {
	clt_parameters.img_dtt.setMcorr(getNumSensors(), save_pairs_selection); // restore		clt_parameters.img_dtt.setMcorr(getNumSensors(), save_pairs_selection); // restore
			}
	clt_parameters.correlate_lma = save_run_lma; // restore		clt_parameters.correlate_lma = save_run_lma; // restore


	/// Refining after all added		/// Refining after all added
	if (debugLevel > -1){		if (debugLevel > -3){
	System.out.println("---- Refining after all added ----");		System.out.println("---- Refining after all added ----");
	}		}
	// find out - why first pass corresponds to last scan step?		// find out - why first pass corresponds to last scan step?
	// first ("before_makeUnique-41-" was empty)		// first ("before_makeUnique-41-" was empty)
	for (int nnn = 0; nnn < num_macro_refine; nnn ++){ //		for (int nnn = 0; nnn < clt_parameters.gr_num_refines; nnn ++){ //
			if ((nnn == (clt_parameters.gr_num_refines - 1)) && clt_parameters.gr_all_last) {
			clt_parameters.img_dtt.setMcorr(getNumSensors(), save_pairs_selection); // restore
			}
	refine_pass = tp.clt_3d_passes.size(); // 1		refine_pass = tp.clt_3d_passes.size(); // 1
	CLTPass3d refined = tp.refinePassSetup( // prepare tile tasks for the refine pass (re-measure disparities)		CLTPass3d refined = tp.refinePassSetup( // prepare tile tasks for the refine pass (re-measure disparities)
	// final double [][][] image_data, // first index - number of image in a quad		// final double [][][] image_data, // first index - number of image in a quad
	@@ -8666,7 +8676,8 @@ public class QuadCLTCPU {


	// first time - last scan step????		// first time - last scan step????
	CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity		// CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity
			CLTMeasCorr( // perform single pass according to prepared tiles operations and disparity
	// image_data, // first index - number of image in a quad		// image_data, // first index - number of image in a quad
	// saturation_imp, //final boolean [][] saturation_imp, // (near) saturated pixels or null		// saturation_imp, //final boolean [][] saturation_imp, // (near) saturated pixels or null
	clt_parameters,		clt_parameters,
	@@ -8704,16 +8715,23 @@ public class QuadCLTCPU {
	tp.clt_3d_passes.add(combo_pass);		tp.clt_3d_passes.add(combo_pass);
	}		}



	// create and measure several variable-cluster scans from the same single-tile combo_pass		// create and measure several variable-cluster scans from the same single-tile combo_pass
	CLTPass3d combo_pass = tp.clt_3d_passes.get(tp.clt_3d_passes.size() - 1); // last pass created by tp.compositeScan		CLTPass3d combo_pass = tp.clt_3d_passes.get(tp.clt_3d_passes.size() - 1); // last pass created by tp.compositeScan
	int max_clust_radius = 4; // 7x7		// int max_clust_radius = 4; // 7x7
	CLTPass3d [] combo_multi = new CLTPass3d[max_clust_radius+1];		CLTPass3d [] combo_multi = new CLTPass3d[clt_parameters.gr_max_clust_radius+1];
	combo_multi[0] = combo_pass;		combo_multi[0] = combo_pass;
	int max_expand_radius = 0; // max_clust_radius;		int max_expand_radius = 0; // max_clust_radius;
	for (int clust_radius = 2; clust_radius <= max_clust_radius; clust_radius++) {		for (int clust_radius = 2; clust_radius <= clt_parameters.gr_max_clust_radius; clust_radius++) {
	// for (int clust_radius = 4; clust_radius <= max_clust_radius; clust_radius++) { // just for faster testing		// for (int clust_radius = 4; clust_radius <= max_clust_radius; clust_radius++) { // just for faster testing

			if (clt_parameters.gr_reduce_multi) {
			clt_parameters.img_dtt.setMcorr(getNumSensors(), 0 ); // remove all
			clt_parameters.img_dtt.setMcorrNeib(getNumSensors(),true);
			clt_parameters.img_dtt.setMcorrSq (getNumSensors(),true); // remove even more?
			clt_parameters.img_dtt.setMcorrDia (getNumSensors(),true); // remove even more?
			}


	// using combo_pass (latest)		// using combo_pass (latest)
	int num_added = 0;		int num_added = 0;
	if (clust_radius < max_expand_radius) {		if (clust_radius < max_expand_radius) {
	@@ -8734,8 +8752,10 @@ public class QuadCLTCPU {
	System.out.println("Added "+num_added+" tiles before cluster radius "+clust_radius);		System.out.println("Added "+num_added+" tiles before cluster radius "+clust_radius);
	boolean [] has_lma = combo_pass.getLMA();		boolean [] has_lma = combo_pass.getLMA();
	double [] disparity = combo_pass.getDisparity(1); // calc_disparity (skip NaN!)		double [] disparity = combo_pass.getDisparity(1); // calc_disparity (skip NaN!)
	for (int nnn = 0; nnn < num_macro_refine; nnn ++){ //		for (int nnn = 0; nnn < clt_parameters.gr_num_refines; nnn ++){ //
			if ((nnn == (clt_parameters.gr_num_refines - 1)) && clt_parameters.gr_all_last) {
			clt_parameters.img_dtt.setMcorr(getNumSensors(), save_pairs_selection); // restore
			}
	refine_pass = tp.clt_3d_passes.size();		refine_pass = tp.clt_3d_passes.size();
	CLTPass3d refined_multi = tp.refinePassSetupMulti( // prepare tile tasks for the second pass based on the previous one(s)		CLTPass3d refined_multi = tp.refinePassSetupMulti( // prepare tile tasks for the second pass based on the previous one(s)
	combo_pass, // CLTPass3d combo_pass,		combo_pass, // CLTPass3d combo_pass,
	@@ -8776,8 +8796,8 @@ public class QuadCLTCPU {
	// double [] saved_target_disparity = tp.clt_3d_passes.get(refine_pass).getDA(); // TODO: remove when done		// double [] saved_target_disparity = tp.clt_3d_passes.get(refine_pass).getDA(); // TODO: remove when done
	// for (int ii = 0; ii < rpt; ii++) { // TODO: remove when done		// for (int ii = 0; ii < rpt; ii++) { // TODO: remove when done
	// tp.clt_3d_passes.get(refine_pass).setDA(saved_target_disparity); // TODO: remove when done		// tp.clt_3d_passes.get(refine_pass).setDA(saved_target_disparity); // TODO: remove when done
	boolean alt_clt = true;		/// boolean alt_clt = true;
	if (alt_clt) {		/// if (alt_clt) {
	CLTMeasCorr( // perform single pass according to prepared tiles operations and disparity		CLTMeasCorr( // perform single pass according to prepared tiles operations and disparity
	clt_parameters,		clt_parameters,
	refine_pass,		refine_pass,
	@@ -8786,16 +8806,16 @@ public class QuadCLTCPU {
	threadsMax,		threadsMax,
	updateStatus,		updateStatus,
	debugLevel);		debugLevel);
	} else {		/// } else {
	CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity		/// CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity
	clt_parameters,		/// clt_parameters,
	refine_pass,		/// refine_pass,
	false, // true, // final boolean save_textures,		/// false, // true, // final boolean save_textures,
	clust_radius, // final int clust_radius,		/// clust_radius, // final int clust_radius,
	threadsMax,		/// threadsMax,
	updateStatus,		/// updateStatus,
	debugLevel);		/// debugLevel);
	}		/// }


	if (show_init_refine) tp.showScan(		if (show_init_refine) tp.showScan(
	@@ -8839,6 +8859,18 @@ public class QuadCLTCPU {

	}		}
	}		}
			// Restore pairs selection
			clt_parameters.img_dtt.setMcorr(getNumSensors(), save_pairs_selection); // restore
			if (clt_parameters.gr_nan_bg) {
			if (debugLevel > -3) {
			tp.showScan(
			tp.clt_3d_passes.get(bg_pass), // CLTPass3d scan,
			"bg_passs-"+tp.clt_3d_passes.size());
			}
			}


			if (clt_parameters.gr_exp_certain) {
	int num_added = tp.expandCertainMulti (		int num_added = tp.expandCertainMulti (
	combo_pass, // CLTPass3d combo_pass, // modify		combo_pass, // CLTPass3d combo_pass, // modify
	tp.clt_3d_passes, //ArrayList <CLTPass3d> passes,		tp.clt_3d_passes, //ArrayList <CLTPass3d> passes,
	@@ -8856,7 +8888,7 @@ public class QuadCLTCPU {
	if (debugLevel > -2) tp.showScan(		if (debugLevel > -2) tp.showScan(
	combo_pass, // CLTPass3d scan,		combo_pass, // CLTPass3d scan,
	"after_multi-tile_disparity_extension");		"after_multi-tile_disparity_extension");
			}

	///// Refining after all added - end		///// Refining after all added - end
	Runtime.getRuntime().gc();		Runtime.getRuntime().gc();
	@@ -12175,6 +12207,7 @@ public class QuadCLTCPU {
	}		}

	}		}
			@Deprecated
	public CLTPass3d CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity // not used in lwir		public CLTPass3d CLTMeasureCorr( // perform single pass according to prepared tiles operations and disparity // not used in lwir
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	final int scanIndex,		final int scanIndex,

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