Before adding BLUE_SKY to DSI_MAIN (270fcbc6) · Commits · Elphel / imagej-elphel

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

+290 −218

Original line number	Original line	Diff line number	Diff line
	@@ -3775,24 +3775,22 @@ public class OpticalFlow {
	quadCLTs[ref_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry		quadCLTs[ref_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
	*/		*/
	// public static QuadCLT buildRefDSI(		// public static QuadCLT buildRefDSI(
	public static void buildRefDSI(		public static void photoEach(
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	EyesisCorrectionParameters.DebayerParameters debayerParameters,
	ColorProcParameters colorProcParameters,		ColorProcParameters colorProcParameters,
	EyesisCorrectionParameters.RGBParameters rgbParameters,
	boolean batch_mode,
	String set_name,
	QuadCLT quadCLT_main, // tiles should be set		QuadCLT quadCLT_main, // tiles should be set
	QuadCLT quadCLT_ref, // tiles should be set		QuadCLT quadCLT_ref, // tiles should be set
	final int threadsMax, // maximal number of threads to launch		final double [][] dsi,
			final int photo_num_full, //
			final boolean batch_mode,
			final int threadsMax, // int threadsMax,
	final boolean updateStatus,		final boolean updateStatus,
	final int debugLevel) {		final int debugLevel) {
	final int debugLevelInner=clt_parameters.batch_run? -2: debugLevel; // copied from TQ		boolean [] blue_sky = quadCLT_ref.getBlueSky();
	// boolean photo_en = clt_parameters.photo_en; // false; // perform photogrammetric calibration to equalize pixel values		if (debugLevel > -3) {
	boolean photo_each = clt_parameters.photo_each; // true; // perform photogrammetric calibration to equalize pixel values		System.out.println("**** Running photometric equalization for "+quadCLT_ref.getImageName()+
	// boolean photo_to_main= clt_parameters.photo_to_main; // maybe it will not be needed, it will apply this calibration to the next scene sequence		", current was from scene "+quadCLT_ref.getPhotometricScene()+" ****");
			}
	int photo_num_full = clt_parameters.photo_num_full; // 1; // Number of full recalibrations with re-processing of the images
	int photo_num_refines = clt_parameters.photo_num_refines; // 3; // Calibrate, remove outliers, recalibrate, ...		int photo_num_refines = clt_parameters.photo_num_refines; // 3; // Calibrate, remove outliers, recalibrate, ...
	int photo_min_good = clt_parameters.photo_min_good; // 1000; // Minimal number of good pixels for photometric calibration		int photo_min_good = clt_parameters.photo_min_good; // 1000; // Minimal number of good pixels for photometric calibration
	double photo_min_strength = clt_parameters.photo_min_strength; // 0.0; // maybe add to filter out weak tiles		double photo_min_strength = clt_parameters.photo_min_strength; // 0.0; // maybe add to filter out weak tiles
	@@ -3802,77 +3800,6 @@ public class OpticalFlow {
	double photo_std_2 = clt_parameters.photo_std_2; // 200.0; // Minimal standard deviation of the filtered values for poly order 2		double photo_std_2 = clt_parameters.photo_std_2; // 200.0; // Minimal standard deviation of the filtered values for poly order 2
	int photo_offs_set = clt_parameters.photo_offs_set; // 0; // 0 - keep weighted offset average, 1 - balance result image, 2 - set weighted average to specific value		int photo_offs_set = clt_parameters.photo_offs_set; // 0; // 0 - keep weighted offset average, 1 - balance result image, 2 - set weighted average to specific value
	double photo_offs = clt_parameters.photo_offs; // 21946; // weighted average offset target value, if photo_offs_set (and not photo_offs_balance)		double photo_offs = clt_parameters.photo_offs; // 21946; // weighted average offset target value, if photo_offs_set (and not photo_offs_balance)
	// boolean photo_debug = clt_parameters.photo_debug; // false; // Generate images and text

	double sky_highest_min = clt_parameters.imp.sky_highest_min;
	double cold_frac = clt_parameters.imp.cold_frac;
	double hot_frac = clt_parameters.imp.hot_frac;
	double cold_scale = clt_parameters.imp.cold_scale;
	double sky_seed = clt_parameters.imp.sky_seed;
	double lma_seed = clt_parameters.imp.lma_seed;
	int sky_shrink = clt_parameters.imp.sky_shrink;
	int sky_bottleneck = clt_parameters.imp.sky_bottleneck;
	int seed_rows = clt_parameters.imp.seed_rows;
	double sky_lim = clt_parameters.imp.sky_lim;
	int sky_expand_extra = clt_parameters.imp.sky_expand_extra;
	double min_strength = clt_parameters.imp.min_strength;
	int lowest_sky_row = clt_parameters.imp.lowest_sky_row;
	double sky_bottom_override = clt_parameters.imp.sky_bottom_override;
	int sky_override_shrink = clt_parameters.imp.sky_override_shrink;
	double disp_boost_min = clt_parameters.imp.disp_boost_min; // 0.5;
	double disp_boost_diff = clt_parameters.imp.disp_boost_diff; // 0.35;
	int disp_boost_neibs = clt_parameters.imp.disp_boost_neibs; // 2;
	double disp_boost_amount = clt_parameters.imp.disp_boost_amount; // 2.0;
	boolean [] ref_blue_sky = null; // turn off "lma" in the ML output
	quadCLT_ref.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
	clt_parameters,
	debayerParameters,
	colorProcParameters,
	rgbParameters,
	threadsMax, // maximal number of threads to launch
	updateStatus,
	debugLevelInner);
	double [][] aux_last_scan = TileProcessor.getDSLMA(
	quadCLT_ref.tp.clt_3d_passes.get( quadCLT_ref.tp.clt_3d_passes.size() -1),
	false); // boolean force_final);
	double [][] dsi = new double [TwoQuadCLT.DSI_SLICES.length][];
	dsi[TwoQuadCLT.DSI_DISPARITY_AUX] = aux_last_scan[0];
	dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = aux_last_scan[1];
	dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA] = aux_last_scan[2];
	dsi[TwoQuadCLT.DSI_SPREAD_AUX] = aux_last_scan[3];
	dsi[TwoQuadCLT.DSI_AVGVAL_AUX] = aux_last_scan[4];

	if (quadCLT_main.correctionsParameters.clt_batch_dsi_cm_strength) {
	CLTPass3d scan = new CLTPass3d(quadCLT_ref.tp);
	scan.setTileOpDisparity(aux_last_scan[0]); // measure w/o LMA, use just strength
	quadCLT_ref.CLTMeas( // perform single pass according to prepared tiles operations and disparity
	clt_parameters, // EyesisCorrectionParameters.CLTParameters clt_parameters,
	scan, // final CLTPass3d scan,
	false, // final boolean save_textures,
	false, // final boolean need_diffs, // calculate diffs even if textures are not needed
	0, // final int clust_radius,
	true, // final boolean save_corr,
	false, // final boolean run_lma, // = true;
	0.0, // final double max_chn_diff, // filter correlation results by maximum difference between channels
	-1.0, // final double mismatch_override, // keep tile with large mismatch if there is LMA with really strong correlation
	threadsMax, // final int threadsMax, // maximal number of threads to launch
	updateStatus, // final boolean updateStatus,
	debugLevel-2); // final int debugLevel);
	dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = scan.getStrength();
	if (debugLevel > 1) {
	quadCLT_ref.tp.showScan(
	scan, // CLTPass3d scan,
	"test-strength");
	}
	} else {
	dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = aux_last_scan[1];
	}
	// perform photometric here, after first DSI
	if (photo_each && (!quadCLT_ref.isPhotometricThis() \|\| !batch_mode)) {
	if (debugLevel > -3) {
	System.out.println("**** Running photometric equalization for "+quadCLT_ref.getImageName()+
	", current was from scene "+quadCLT_ref.getPhotometricScene()+" ****");
	}

	// preparing same format as after combo, filling in only needed data		// preparing same format as after combo, filling in only needed data
	double [][] ds_photo = new double[TwoQuadCLT.DSI_LENGTH][];		double [][] ds_photo = new double[TwoQuadCLT.DSI_LENGTH][];
	@@ -3901,6 +3828,7 @@ public class OpticalFlow {
	photo_num_refines, // final int num_refines, // 2		photo_num_refines, // final int num_refines, // 2
	photo_min_good, // final int min_good, // minimal number of "good" pixels		photo_min_good, // final int min_good, // minimal number of "good" pixels
	ds_photo, // combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,		ds_photo, // combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,
			blue_sky, // final boolean[] blue_sky,
	threadsMax, // int threadsMax,		threadsMax, // int threadsMax,
	photo_each_debug); //final boolean debug)		photo_each_debug); //final boolean debug)
	if (!ok) {		if (!ok) {
	@@ -3923,6 +3851,7 @@ public class OpticalFlow {
	photo_num_refines, // final int num_refines, // 2		photo_num_refines, // final int num_refines, // 2
	photo_min_good, // final int min_good, // minimal number of "good" pixels		photo_min_good, // final int min_good, // minimal number of "good" pixels
	ds_photo, // combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,		ds_photo, // combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,
			blue_sky, // final boolean[] blue_sky,
	threadsMax, // int threadsMax,		threadsMax, // int threadsMax,
	photo_each_debug); //final boolean debug)		photo_each_debug); //final boolean debug)
	if (!ok) {		if (!ok) {
	@@ -3939,14 +3868,6 @@ public class OpticalFlow {

	// Re-read reference and other scenes using new offsets		// Re-read reference and other scenes using new offsets
	quadCLT_ref.setQuadClt(); // should work even when the data is new for the same scene		quadCLT_ref.setQuadClt(); // should work even when the data is new for the same scene
	/*
	quadCLT_ref = (QuadCLT) quadCLT_main.spawnQuadCLT( // restores dsi from "DSI-MAIN"
	set_name,
	clt_parameters,
	colorProcParameters, //
	threadsMax,
	debugLevel);
	*/
	quadCLT_ref.restoreFromModel(		quadCLT_ref.restoreFromModel(
	clt_parameters,		clt_parameters,
	colorProcParameters,		colorProcParameters,
	@@ -4005,23 +3926,118 @@ public class OpticalFlow {
	dsi[TwoQuadCLT.DSI_AVGVAL_AUX] = bgscan.getAvgVal(); //aux_bg_scan[4];		dsi[TwoQuadCLT.DSI_AVGVAL_AUX] = bgscan.getAvgVal(); //aux_bg_scan[4];

	quadCLT_ref.setDSI(dsi); // Restore known dsi		quadCLT_ref.setDSI(dsi); // Restore known dsi
	quadCLT_ref.setBlueSky(ref_blue_sky);		// quadCLT_ref.setBlueSky(null); //ref_blue_sky); it is null here
	quadCLT_ref.setDSRBG(		quadCLT_ref.setDSRBG(
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
	threadsMax, // int threadsMax, // maximal number of threads to launch		threadsMax, // int threadsMax, // maximal number of threads to launch
	updateStatus, // boolean updateStatus,		updateStatus, // boolean updateStatus,
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
	}		}
			}


			public static void buildRefDSI(
			CLTParameters clt_parameters,
			EyesisCorrectionParameters.DebayerParameters debayerParameters,
			ColorProcParameters colorProcParameters,
			EyesisCorrectionParameters.RGBParameters rgbParameters,
			boolean batch_mode,
			String set_name,
			QuadCLT quadCLT_main, // tiles should be set
			QuadCLT quadCLT_ref, // tiles should be set
			final int threadsMax, // maximal number of threads to launch
			final boolean updateStatus,
			final int debugLevel) {
			final int debugLevelInner=clt_parameters.batch_run? -2: debugLevel; // copied from TQ
			boolean photo_each = clt_parameters.photo_each; // true; // perform photogrammetric calibration to equalize pixel values

			double sky_highest_min = clt_parameters.imp.sky_highest_min;
			double cold_frac = clt_parameters.imp.cold_frac;
			double hot_frac = clt_parameters.imp.hot_frac;
			double cold_scale = clt_parameters.imp.cold_scale;
			double sky_seed = clt_parameters.imp.sky_seed;
			double lma_seed = clt_parameters.imp.lma_seed;
			int sky_shrink = clt_parameters.imp.sky_shrink;
			int sky_bottleneck = clt_parameters.imp.sky_bottleneck;
			int seed_rows = clt_parameters.imp.seed_rows;
			double sky_lim = clt_parameters.imp.sky_lim;
			int sky_expand_extra = clt_parameters.imp.sky_expand_extra;
			double min_strength = clt_parameters.imp.min_strength;
			int lowest_sky_row = clt_parameters.imp.lowest_sky_row;
			double sky_bottom_override = clt_parameters.imp.sky_bottom_override;
			int sky_override_shrink = clt_parameters.imp.sky_override_shrink;
			double disp_boost_min = clt_parameters.imp.disp_boost_min; // 0.5;
			double disp_boost_diff = clt_parameters.imp.disp_boost_diff; // 0.35;
			int disp_boost_neibs = clt_parameters.imp.disp_boost_neibs; // 2;
			double disp_boost_amount = clt_parameters.imp.disp_boost_amount; // 2.0;
			boolean [] ref_blue_sky = null; // turn off "lma" in the ML output
			quadCLT_ref.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
			clt_parameters,
			debayerParameters,
			colorProcParameters,
			rgbParameters,
			threadsMax, // maximal number of threads to launch
			updateStatus,
			debugLevelInner);
			double [][] aux_last_scan = TileProcessor.getDSLMA(
			quadCLT_ref.tp.clt_3d_passes.get( quadCLT_ref.tp.clt_3d_passes.size() -1),
			false); // boolean force_final);
			double [][] dsi = new double [TwoQuadCLT.DSI_SLICES.length][];
			dsi[TwoQuadCLT.DSI_DISPARITY_AUX] = aux_last_scan[0];
			dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = aux_last_scan[1];
			dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA] = aux_last_scan[2];
			dsi[TwoQuadCLT.DSI_SPREAD_AUX] = aux_last_scan[3];
			dsi[TwoQuadCLT.DSI_AVGVAL_AUX] = aux_last_scan[4];

			if (quadCLT_main.correctionsParameters.clt_batch_dsi_cm_strength) {
			CLTPass3d scan = new CLTPass3d(quadCLT_ref.tp);
			scan.setTileOpDisparity(aux_last_scan[0]); // measure w/o LMA, use just strength
			quadCLT_ref.CLTMeas( // perform single pass according to prepared tiles operations and disparity
			clt_parameters, // EyesisCorrectionParameters.CLTParameters clt_parameters,
			scan, // final CLTPass3d scan,
			false, // final boolean save_textures,
			false, // final boolean need_diffs, // calculate diffs even if textures are not needed
			0, // final int clust_radius,
			true, // final boolean save_corr,
			false, // final boolean run_lma, // = true;
			0.0, // final double max_chn_diff, // filter correlation results by maximum difference between channels
			-1.0, // final double mismatch_override, // keep tile with large mismatch if there is LMA with really strong correlation
			threadsMax, // final int threadsMax, // maximal number of threads to launch
			updateStatus, // final boolean updateStatus,
			debugLevel-2); // final int debugLevel);
			dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = scan.getStrength();
			if (debugLevel > 1) {
			quadCLT_ref.tp.showScan(
			scan, // CLTPass3d scan,
			"test-strength");
			}
			} else {
			dsi[TwoQuadCLT.DSI_STRENGTH_AUX] = aux_last_scan[1];
			}
			boolean ran_photo_each = false;
			// perform photometric here, after first DSI
			if (photo_each && (!quadCLT_ref.isPhotometricThis() \|\| !batch_mode)) {
			// if (debugLevel > -3) {
			// System.out.println("**** Running photometric equalization for "+quadCLT_ref.getImageName()+
			// ", current was from scene "+quadCLT_ref.getPhotometricScene()+" ****");
			// }
			photoEach(
			clt_parameters, // CLTParameters clt_parameters,
			colorProcParameters, // ColorProcParameters colorProcParameters,
			quadCLT_main, // QuadCLT quadCLT_main, // tiles should be set
			quadCLT_ref, // QuadCLT quadCLT_ref, // tiles should be set
			dsi, // final double [][] dsi,
			clt_parameters.photo_num_full, // int photo_num_full =
			batch_mode, // final boolean batch_mode,
			threadsMax, // final int threadsMax, // int threadsMax,
			updateStatus, // final boolean updateStatus,
			debugLevel); // final int debugLevel)
			ran_photo_each = true; // will need to re-run after blue sky detection

	} else {		} else {
	System.out.println("(Re)using photometric calibration from this sequence reference "+quadCLT_ref.getPhotometricScene());		System.out.println("(Re)using photometric calibration from this sequence reference "+quadCLT_ref.getPhotometricScene());
	quadCLT_ref.setQuadClt(); // just in case ?		quadCLT_ref.setQuadClt(); // just in case ?
	}		}

	boolean retry=false;
	while (true) {
	quadCLT_ref.setBlueSky (		quadCLT_ref.setBlueSky (
	sky_seed, // double sky_seed, // = 7.0; // start with product of strength by diff_second below this		sky_seed, // double sky_seed, // = 7.0; // start with product of strength by diff_second below this
	lma_seed,		lma_seed,
	@@ -4047,10 +4063,36 @@ public class OpticalFlow {
	dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], // double [] spread,		dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], // double [] spread,
	dsi[TwoQuadCLT.DSI_AVGVAL_AUX],// double [] avg_val,		dsi[TwoQuadCLT.DSI_AVGVAL_AUX],// double [] avg_val,
	batch_mode? -1: 1); /// debugLevel); // int debugLevel)		batch_mode? -1: 1); /// debugLevel); // int debugLevel)
	if (!retry) {		if (ran_photo_each) {
			// quadCLT_ref.setBlueSky(null); // Reset blue sky - is it needed?
			// see if blue sky was detected - rerun photoEach
			boolean [] blue_sky = quadCLT_ref.getBlueSky();
			boolean has_blue_sky = false;
			for (int i = 0; i < blue_sky.length; i++) if (blue_sky[i]) {
			has_blue_sky = true;
	break;		break;
	}		}
			if (has_blue_sky) {
			if (debugLevel > -3) {
			System.out.println("Detected non-empty Blue Sky after initial DSI in "+quadCLT_ref.getImageName()+
			", re-running photoEach()");
	}		}
			photoEach(
			clt_parameters, // CLTParameters clt_parameters,
			colorProcParameters, // ColorProcParameters colorProcParameters,
			quadCLT_main, // QuadCLT quadCLT_main, // tiles should be set
			quadCLT_ref, // QuadCLT quadCLT_ref, // tiles should be set
			dsi, // final double [][] dsi,
			// just once?
			clt_parameters.photo_num_full, // int photo_num_full =
			batch_mode, // final boolean batch_mode,
			threadsMax, // final int threadsMax, // int threadsMax,
			updateStatus, // final boolean updateStatus,
			debugLevel); // final int debugLevel)

			}
			}

	quadCLT_ref.saveDSIAll (		quadCLT_ref.saveDSIAll (
	"-DSI_MAIN", // String suffix, // "-DSI_MAIN"		"-DSI_MAIN", // String suffix, // "-DSI_MAIN"
	dsi);		dsi);
	@@ -4081,8 +4123,12 @@ public class OpticalFlow {

	public static void reuseRefDSI(		public static void reuseRefDSI(
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
			ColorProcParameters colorProcParameters,
	QuadCLT quadCLT_main, // tiles should be set		QuadCLT quadCLT_main, // tiles should be set
	QuadCLT quadCLT_ref, // tiles should be set		QuadCLT quadCLT_ref, // tiles should be set
			final boolean batch_mode,
			final int threadsMax, // int threadsMax,
			final boolean updateStatus,
	final int debugLevel) {		final int debugLevel) {
	boolean photo_each = clt_parameters.photo_each; // true; // perform photogrammetric calibration to equalize pixel values		boolean photo_each = clt_parameters.photo_each; // true; // perform photogrammetric calibration to equalize pixel values
	boolean photo_to_main= clt_parameters.photo_to_main; // maybe it will not be needed, it will apply this calibration to the next scene sequence		boolean photo_to_main= clt_parameters.photo_to_main; // maybe it will not be needed, it will apply this calibration to the next scene sequence
	@@ -4129,6 +4175,8 @@ public class OpticalFlow {
	if (dsi[TwoQuadCLT.DSI_SPREAD_AUX] == null) {		if (dsi[TwoQuadCLT.DSI_SPREAD_AUX] == null) {
	System.out.println("DSI_MAIN file has old format and does not have spread data, will recalculate.");		System.out.println("DSI_MAIN file has old format and does not have spread data, will recalculate.");
	} else {		} else {
			boolean [] ref_blue_sky = quadCLT_ref.getBlueSky();
			if (ref_blue_sky == null) {
	quadCLT_ref.setBlueSky (		quadCLT_ref.setBlueSky (
	sky_seed, // double sky_seed, // = 7.0; // start with product of strength by diff_second below this		sky_seed, // double sky_seed, // = 7.0; // start with product of strength by diff_second below this
	lma_seed, // 2.0; // seed - disparity_lma limit		lma_seed, // 2.0; // seed - disparity_lma limit
	@@ -4154,6 +4202,24 @@ public class OpticalFlow {
	dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], //double [] disp_lma,		dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], //double [] disp_lma,
	dsi[TwoQuadCLT.DSI_AVGVAL_AUX],// double [] avg_val,		dsi[TwoQuadCLT.DSI_AVGVAL_AUX],// double [] avg_val,
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
			if (debugLevel > -3) {
			System.out.println("Calculated missing Blue Sky in "+quadCLT_ref.getImageName()+
			", re-running photoEach()");
			}
			photoEach(
			clt_parameters, // CLTParameters clt_parameters,
			colorProcParameters, // ColorProcParameters colorProcParameters,
			quadCLT_main, // QuadCLT quadCLT_main, // tiles should be set
			quadCLT_ref, // QuadCLT quadCLT_ref, // tiles should be set
			dsi, // final double [][] dsi,
			// just once?
			clt_parameters.photo_num_full, // int photo_num_full =
			batch_mode, // final boolean batch_mode,
			threadsMax, // final int threadsMax, // int threadsMax,
			updateStatus, // final boolean updateStatus,
			debugLevel); // final int debugLevel)

			}
	}		}
	}		}

	@@ -4179,7 +4245,8 @@ public class OpticalFlow {
	int photo_offs_set = clt_parameters.photo_offs_set; // 0; // 0 - keep weighted offset average, 1 - balance result image, 2 - set weighted average to specific value		int photo_offs_set = clt_parameters.photo_offs_set; // 0; // 0 - keep weighted offset average, 1 - balance result image, 2 - set weighted average to specific value
	double photo_offs = clt_parameters.photo_offs; // 21946; // weighted average offset target value, if photo_offs_set (and not photo_offs_balance)		double photo_offs = clt_parameters.photo_offs; // 21946; // weighted average offset target value, if photo_offs_set (and not photo_offs_balance)
	boolean photo_debug = clt_parameters.photo_debug; // false; // Generate images and text		boolean photo_debug = clt_parameters.photo_debug; // false; // Generate images and text
	boolean [] ref_blue_sky = null; // turn off "lma" in the ML output		boolean [] ref_blue_sky = quadCLTs[ref_index].getBlueSky(); // null; // turn off "lma" in the ML output

	for (int nrecalib = 0; nrecalib < photo_num_full; nrecalib++) {		for (int nrecalib = 0; nrecalib < photo_num_full; nrecalib++) {
	int poly_order = photo_order;		int poly_order = photo_order;
	if ((poly_order > 1) && (nrecalib == 0)) {		if ((poly_order > 1) && (nrecalib == 0)) {
	@@ -4198,6 +4265,7 @@ public class OpticalFlow {
	photo_num_refines, // final int num_refines, // 2		photo_num_refines, // final int num_refines, // 2
	photo_min_good, // final int min_good, // minimal number of "good" pixels		photo_min_good, // final int min_good, // minimal number of "good" pixels
	combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,		combo_dsn_final_filtered, // final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,
			ref_blue_sky, // final boolean[] blue_sky,
	threadsMax, // int threadsMax,		threadsMax, // int threadsMax,
	photo_debug); //final boolean debug)		photo_debug); //final boolean debug)
	// copy offsets to the current to be saved with other properties. Is it correct/needed?		// copy offsets to the current to be saved with other properties. Is it correct/needed?
	@@ -4475,8 +4543,12 @@ public class OpticalFlow {
	// need to read photometric from reference scene -INTERFRAME.corr-xml, and if it exists - set and propagate to main?		// need to read photometric from reference scene -INTERFRAME.corr-xml, and if it exists - set and propagate to main?
	reuseRefDSI(		reuseRefDSI(
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
			colorProcParameters, // ColorProcParameters colorProcParameters,
	quadCLT_main, // QuadCLT quadCLT_main, // tiles should be set		quadCLT_main, // QuadCLT quadCLT_main, // tiles should be set
	quadCLTs[ref_index], // QuadCLT quadCLT_ref, // tiles should be set		quadCLTs[ref_index], // QuadCLT quadCLT_ref, // tiles should be set
			batch_mode, // final boolean batch_mode,
			threadsMax, // final int threadsMax,
			updateStatus, // final boolean updateStatus,
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
	}		}

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

+7 −1

Original line number	Original line	Diff line number	Diff line
	@@ -847,6 +847,7 @@ public class QuadCLT extends QuadCLTCPU {
	final int num_refines, // 2		final int num_refines, // 2
	final int min_good, // minimal number of "good" pixels		final int min_good, // minimal number of "good" pixels
	final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,		final double [][] combo_dsn_final, // double [][] combo_dsn_final, // dls,
			final boolean[] blue_sky,
	int threadsMax,		int threadsMax,
	final boolean debug)		final boolean debug)
	{		{
	@@ -861,6 +862,11 @@ public class QuadCLT extends QuadCLTCPU {
	disparity_ref[i] = Double.NaN;		disparity_ref[i] = Double.NaN;
	}		}
	}		}
			if (blue_sky != null) {
			for (int i = 0; i < blue_sky.length; i++) if (blue_sky[i]) {
			disparity_ref[i] = 0.0;
			}
			}

	ImagePlus img_ref = renderGPUFromDSI(		ImagePlus img_ref = renderGPUFromDSI(
	-1, // final int sensor_mask,		-1, // final int sensor_mask,

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