Cleaning up photometric equalization (e93c08dc) · Commits · Elphel / imagej-elphel

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

+66 −5

Original line number	Original line	Diff line number	Diff line
	@@ -176,7 +176,6 @@ public class IntersceneMatchParameters {
	public double centroid_radius = 4.0; //		public double centroid_radius = 4.0; //
	public int n_recenter = 2; // when cosine window, re-center window this many times		public int n_recenter = 2; // when cosine window, re-center window this many times
	// filtering motion vectors		// filtering motion vectors
	public double min_ref_str = 0.22; // For orientations: use only tiles of the reference scene DSI_MAIN is stronger
	// TD accumulation of the inter-scene correlations demonstrated artifacts (horizontally offset by 8 pixels		// TD accumulation of the inter-scene correlations demonstrated artifacts (horizontally offset by 8 pixels
	// false maximum that is sharper than the real one. Still not understood - maybe float precision related.		// false maximum that is sharper than the real one. Still not understood - maybe float precision related.
	public double td_weight = 0.5; // mix correlations accumulated in TD with		public double td_weight = 0.5; // mix correlations accumulated in TD with
	@@ -194,7 +193,18 @@ public class IntersceneMatchParameters {
	public double half_disparity = 5.0; // Reduce weight twice for this disparity		public double half_disparity = 5.0; // Reduce weight twice for this disparity
	public double half_avg_diff = 0.2; // when L2 of x,y difference from average of neibs - reduce twice		public double half_avg_diff = 0.2; // when L2 of x,y difference from average of neibs - reduce twice

			// Photometric calibration (move elsewhere)?
			public boolean photo_en = false; // perform photogrammetric calibration to equalize pixel values
			public int photo_num_full = 1; // Number of full recalibrations with re-processing of the images
			public int photo_num_refines = 3; // Calibrate, remove outliers, recalibrate, ...
			public double photo_min_strength = 0.0; // maybe add to filter out weak tiles
			public double photo_max_diff = 40.0; // To filter mismatches. Normal (adjusted) have RMSE ~9
			public boolean photo_debug = false; // Generate images and text



	// Detect initial match		// Detect initial match
			public double min_ref_str = 0.22; // For orientations: use only tiles of the reference scene DSI_MAIN is stronger
	public int pix_step = 4; // Azimuth/tilt search step in pixels		public int pix_step = 4; // Azimuth/tilt search step in pixels
	public int search_rad = 10; // Search radius in steps		public int search_rad = 10; // Search radius in steps
	public double maybe_sum = 1.0; // minimal sum of strengths (will search for the best)		public double maybe_sum = 1.0; // minimal sum of strengths (will search for the best)
	@@ -593,9 +603,9 @@ public class IntersceneMatchParameters {
	gd.addNumericField("Refine centroids", this.n_recenter, 0,5,"",		gd.addNumericField("Refine centroids", this.n_recenter, 0,5,"",
	"Repeat centroids after moving the window center to the new centroid location this many times (0 - calculate once)");		"Repeat centroids after moving the window center to the new centroid location this many times (0 - calculate once)");

	gd.addMessage ("Filter tiles to use for scene poses");		// gd.addMessage ("Filter tiles to use for scene poses");
	gd.addNumericField("DSI_MAIN minimal strength", this.min_ref_str, 5,7,"",		// gd.addNumericField("DSI_MAIN minimal strength", this.min_ref_str, 5,7,"",
	"Match only tiles where DSI_MAIN is stronger than that (and has LMA).");		// "Match only tiles where DSI_MAIN is stronger than that (and has LMA).");


	gd.addMessage ("Mixing TD and PD accumulation of 2d correlations");		gd.addMessage ("Mixing TD and PD accumulation of 2d correlations");
	@@ -625,7 +635,25 @@ public class IntersceneMatchParameters {
	gd.addNumericField("Difference from neighbors average ", this.half_avg_diff, 5,7,"",		gd.addNumericField("Difference from neighbors average ", this.half_avg_diff, 5,7,"",
	"Reduce twice for high difference from neighbors average.");		"Reduce twice for high difference from neighbors average.");

			gd.addMessage ("Photometric calibration (move elsewhere?)");
			gd.addCheckbox ("Enable photometric calibration", this.photo_en,
			"Equalize per- sensor gains and offsets. Requires disparity map. Save to reference scene and with current scene (to .corr-zml).");
			gd.addNumericField("Full photometric (re)calibrations", this.photo_num_full, 0,3,"pix",
			"Full recalibratrions include re-importing raw images with updated offsets/gains");
			gd.addNumericField("Refines", this.photo_num_refines, 0,3,"pix",
			"Calculate calibration, remove outliers (e.g. FG/BG) and repeat");
			gd.addNumericField("Minimal DSI strength", this.photo_min_strength, 5,7,"",
			"Do not use weak tiles.");
			gd.addNumericField("Maximal channel mismatch", this.photo_max_diff, 5,7,"",
			"Detect (and remove outliers). Adjusted images have RMSE ~9 counts.");
			gd.addCheckbox ("Debug pphotometric calibration", this.photo_debug,
			"Generate debug images an text output.");


	gd.addMessage ("Initial search for the inter-scene match");		gd.addMessage ("Initial search for the inter-scene match");
			gd.addNumericField("DSI_MAIN minimal strength", this.min_ref_str, 5,7,"",
			"Match only tiles where DSI_MAIN is stronger than that (and has LMA).");

	gd.addNumericField("Azimuth/tilt step", this.pix_step, 0,3,"pix",		gd.addNumericField("Azimuth/tilt step", this.pix_step, 0,3,"pix",
	"Search in a spiral starting with no-shift with this step between probes, in approximate pixels");		"Search in a spiral starting with no-shift with this step between probes, in approximate pixels");
	gd.addNumericField("Search spiral radius", this.search_rad, 0,3,"steps",		gd.addNumericField("Search spiral radius", this.search_rad, 0,3,"steps",
	@@ -931,7 +959,7 @@ public class IntersceneMatchParameters {
	this.centroid_radius = gd.getNextNumber();		this.centroid_radius = gd.getNextNumber();
	this.n_recenter = (int) gd.getNextNumber();		this.n_recenter = (int) gd.getNextNumber();

	this.min_ref_str = gd.getNextNumber();		// this.min_ref_str = gd.getNextNumber();

	this.td_weight = gd.getNextNumber();		this.td_weight = gd.getNextNumber();
	this.pd_weight = gd.getNextNumber();		this.pd_weight = gd.getNextNumber();
	@@ -946,6 +974,15 @@ public class IntersceneMatchParameters {
	this.weight_zero_neibs = gd.getNextNumber();		this.weight_zero_neibs = gd.getNextNumber();
	this.half_disparity = gd.getNextNumber();		this.half_disparity = gd.getNextNumber();
	this.half_avg_diff = gd.getNextNumber();		this.half_avg_diff = gd.getNextNumber();

			this.photo_en = gd.getNextBoolean();
			this.photo_num_full = (int) gd.getNextNumber();
			this.photo_num_refines = (int) gd.getNextNumber();
			this.photo_min_strength = gd.getNextNumber();
			this.photo_max_diff = gd.getNextNumber();
			this.photo_debug = gd.getNextBoolean();

			this.min_ref_str = gd.getNextNumber();
	this.pix_step = (int) gd.getNextNumber();		this.pix_step = (int) gd.getNextNumber();
	this.search_rad = (int) gd.getNextNumber();		this.search_rad = (int) gd.getNextNumber();
	this.maybe_sum = gd.getNextNumber();		this.maybe_sum = gd.getNextNumber();
	@@ -1157,6 +1194,14 @@ public class IntersceneMatchParameters {
	properties.setProperty(prefix+"weight_zero_neibs", this.weight_zero_neibs+""); // double		properties.setProperty(prefix+"weight_zero_neibs", this.weight_zero_neibs+""); // double
	properties.setProperty(prefix+"half_disparity", this.half_disparity+""); // double		properties.setProperty(prefix+"half_disparity", this.half_disparity+""); // double
	properties.setProperty(prefix+"half_avg_diff", this.half_avg_diff+""); // double		properties.setProperty(prefix+"half_avg_diff", this.half_avg_diff+""); // double

			properties.setProperty(prefix+"photo_en", this.photo_en+""); // boolean
			properties.setProperty(prefix+"photo_num_full", this.photo_num_full+""); // int
			properties.setProperty(prefix+"photo_num_refines", this.photo_num_refines+""); // int
			properties.setProperty(prefix+"photo_min_strength", this.photo_min_strength+""); // double
			properties.setProperty(prefix+"photo_max_diff", this.photo_max_diff+""); // double
			properties.setProperty(prefix+"photo_debug", this.photo_debug+""); // boolean

	properties.setProperty(prefix+"pix_step", this.pix_step+""); // int		properties.setProperty(prefix+"pix_step", this.pix_step+""); // int
	properties.setProperty(prefix+"search_rad", this.search_rad+""); // int		properties.setProperty(prefix+"search_rad", this.search_rad+""); // int
	properties.setProperty(prefix+"maybe_sum", this.maybe_sum+""); // double		properties.setProperty(prefix+"maybe_sum", this.maybe_sum+""); // double
	@@ -1394,6 +1439,14 @@ public class IntersceneMatchParameters {
	if (properties.getProperty(prefix+"weight_zero_neibs")!=null) this.weight_zero_neibs=Double.parseDouble(properties.getProperty(prefix+"weight_zero_neibs"));		if (properties.getProperty(prefix+"weight_zero_neibs")!=null) this.weight_zero_neibs=Double.parseDouble(properties.getProperty(prefix+"weight_zero_neibs"));
	if (properties.getProperty(prefix+"half_disparity")!=null) this.half_disparity=Double.parseDouble(properties.getProperty(prefix+"half_disparity"));		if (properties.getProperty(prefix+"half_disparity")!=null) this.half_disparity=Double.parseDouble(properties.getProperty(prefix+"half_disparity"));
	if (properties.getProperty(prefix+"half_avg_diff")!=null) this.half_avg_diff=Double.parseDouble(properties.getProperty(prefix+"half_avg_diff"));		if (properties.getProperty(prefix+"half_avg_diff")!=null) this.half_avg_diff=Double.parseDouble(properties.getProperty(prefix+"half_avg_diff"));

			if (properties.getProperty(prefix+"photo_en")!=null) this.photo_en=Boolean.parseBoolean(properties.getProperty(prefix+"photo_en"));
			if (properties.getProperty(prefix+"photo_num_full")!=null) this.photo_num_full=Integer.parseInt(properties.getProperty(prefix+"photo_num_full"));
			if (properties.getProperty(prefix+"photo_num_refines")!=null) this.photo_num_refines=Integer.parseInt(properties.getProperty(prefix+"photo_num_refines"));
			if (properties.getProperty(prefix+"photo_min_strength")!=null) this.photo_min_strength=Double.parseDouble(properties.getProperty(prefix+"photo_min_strength"));
			if (properties.getProperty(prefix+"photo_max_diff")!=null) this.photo_max_diff=Double.parseDouble(properties.getProperty(prefix+"photo_max_diff"));
			if (properties.getProperty(prefix+"photo_debug")!=null) this.photo_debug=Boolean.parseBoolean(properties.getProperty(prefix+"photo_debug"));

	if (properties.getProperty(prefix+"pix_step")!=null) this.pix_step=Integer.parseInt(properties.getProperty(prefix+"pix_step"));		if (properties.getProperty(prefix+"pix_step")!=null) this.pix_step=Integer.parseInt(properties.getProperty(prefix+"pix_step"));
	if (properties.getProperty(prefix+"search_rad")!=null) this.search_rad=Integer.parseInt(properties.getProperty(prefix+"search_rad"));		if (properties.getProperty(prefix+"search_rad")!=null) this.search_rad=Integer.parseInt(properties.getProperty(prefix+"search_rad"));
	if (properties.getProperty(prefix+"maybe_sum")!=null) this.maybe_sum=Double.parseDouble(properties.getProperty(prefix+"maybe_sum"));		if (properties.getProperty(prefix+"maybe_sum")!=null) this.maybe_sum=Double.parseDouble(properties.getProperty(prefix+"maybe_sum"));
	@@ -1590,6 +1643,14 @@ public class IntersceneMatchParameters {
	imp.weight_zero_neibs = this.weight_zero_neibs;		imp.weight_zero_neibs = this.weight_zero_neibs;
	imp.half_disparity = this.half_disparity;		imp.half_disparity = this.half_disparity;
	imp.half_avg_diff = this.half_avg_diff;		imp.half_avg_diff = this.half_avg_diff;

			imp.photo_en = this.photo_en;
			imp.photo_num_full = this.photo_num_full;
			imp.photo_num_refines = this.photo_num_refines;
			imp.photo_min_strength = this.photo_min_strength;
			imp.photo_max_diff = this.photo_max_diff;
			imp.photo_debug = this.photo_debug;

	imp.pix_step = this.pix_step;		imp.pix_step = this.pix_step;
	imp.search_rad = this.search_rad;		imp.search_rad = this.search_rad;
	imp.maybe_sum = this.maybe_sum;		imp.maybe_sum = this.maybe_sum;

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

+49 −41

Original line number	Original line	Diff line number	Diff line
	@@ -4045,7 +4045,14 @@ public class OpticalFlow {
	boolean export_images = clt_parameters.imp.export_images;		boolean export_images = clt_parameters.imp.export_images;
	boolean export_dsi_image = clt_parameters.imp.export_ranges;		boolean export_dsi_image = clt_parameters.imp.export_ranges;
	boolean export_ml_files = clt_parameters.imp.export_ml_files;		boolean export_ml_files = clt_parameters.imp.export_ml_files;
	boolean calibrate_photometric = true;
			//boolean calibrate_photometric = true;
			boolean photo_en = clt_parameters.imp.photo_en; // false; // perform photogrammetric calibration to equalize pixel values
			int photo_num_full = clt_parameters.imp.photo_num_full; // 1; // Number of full recalibrations with re-processing of the images
			int photo_num_refines = clt_parameters.imp.photo_num_refines; // 3; // Calibrate, remove outliers, recalibrate, ...
			double photo_min_strength = clt_parameters.imp.photo_min_strength; // 0.0; // maybe add to filter out weak tiles
			double photo_max_diff = clt_parameters.imp.photo_max_diff; // 40.0; // To filter mismatches. Normal (adjusted) have RMSE ~9
			boolean photo_debug = clt_parameters.imp.photo_debug; // false; // Generate images and text

	boolean show_dsi_image = clt_parameters.imp.show_ranges && !batch_mode;		boolean show_dsi_image = clt_parameters.imp.show_ranges && !batch_mode;
	boolean show_images = clt_parameters.imp.show_images && !batch_mode;		boolean show_images = clt_parameters.imp.show_images && !batch_mode;
	@@ -4507,7 +4514,7 @@ public class OpticalFlow {
	}		}
	}		}

	if (calibrate_photometric) {		if (photo_en && !reuse_video) {
	if (combo_dsn_final == null) { // always re-read?		if (combo_dsn_final == null) { // always re-read?
	combo_dsn_final =quadCLTs[ref_index].readDoubleArrayFromModelDirectory( // always re-read?		combo_dsn_final =quadCLTs[ref_index].readDoubleArrayFromModelDirectory( // always re-read?
	"-INTER-INTRA-LMA", // String suffix,		"-INTER-INTRA-LMA", // String suffix,
	@@ -4521,15 +4528,16 @@ public class OpticalFlow {
	combo_dsn_final, // double [][] combo_dsn_final, // dls,		combo_dsn_final, // double [][] combo_dsn_final, // dls,
	quadCLTs[ref_index], // QuadCLT scene,		quadCLTs[ref_index], // QuadCLT scene,
	debugLevel); // int debugLevel);// > 0		debugLevel); // int debugLevel);// > 0
			for (int nrecalib = 0; nrecalib < photo_num_full; nrecalib++) {
	QuadCLT.calibratePhotometric(		QuadCLT.calibratePhotometric(
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
	quadCLTs[ref_index], // final QuadCLT ref_scene, // now - may be null - for testing if scene is rotated ref		quadCLTs[ref_index], // final QuadCLT ref_scene, // now - may be null - for testing if scene is rotated ref
	0.0, // final double min_strength,		photo_min_strength, // final double min_strength,
	100.0, // final double max_diff, // 30.0		photo_max_diff, // final double max_diff, // 30.0
	2, // final int num_refines, // 2		photo_num_refines, // final int num_refines, // 2
	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,
	threadsMax, // int threadsMax,		threadsMax, // int threadsMax,
	true); //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?
	quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)		quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
	null, // String path, // full name with extension or w/o path to use x3d directory		null, // String path, // full name with extension or w/o path to use x3d directory
	@@ -4549,7 +4557,8 @@ public class OpticalFlow {
	updateStatus, // boolean updateStatus,		updateStatus, // boolean updateStatus,
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
	ers_reference = quadCLTs[ref_index].getErsCorrection();		ers_reference = quadCLTs[ref_index].getErsCorrection();
	if (!reuse_video) { // reuse_video only uses reference scene		}
			// propagate to other scenes in this sequence
	for (int scene_index = ref_index - 1; scene_index >= earliest_scene ; scene_index--) {		for (int scene_index = ref_index - 1; scene_index >= earliest_scene ; scene_index--) {
	// quadCLTs[scene_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // restores image data		// quadCLTs[scene_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // restores image data
	// to include ref scene photometric calibration		// to include ref scene photometric calibration
	@@ -4561,7 +4570,6 @@ public class OpticalFlow {
	debugLevel-2);		debugLevel-2);
	}		}
	}		}
	}

	if (test_ers) { // only debug feature		if (test_ers) { // only debug feature
	test_ers0 = quadCLTs.length -1; // make it always == reference !		test_ers0 = quadCLTs.length -1; // make it always == reference !

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

+11 −1

Original line number	Original line	Diff line number	Diff line
	@@ -152,6 +152,7 @@ public class QuadCLTCPU {
	boolean is_aux = false;		boolean is_aux = false;
	double [] lwir_offsets = null; // per image subtracted values		double [] lwir_offsets = null; // per image subtracted values
	double [] lwir_scales = null; // per image scales		double [] lwir_scales = null; // per image scales
			@Deprecated
	double lwir_offset = Double.NaN; // average of lwir_offsets[]		double lwir_offset = Double.NaN; // average of lwir_offsets[]
	// hot and cold are calculated during autoranging (when generating 4 images for restored (added lwir_offset)		// hot and cold are calculated during autoranging (when generating 4 images for restored (added lwir_offset)
	// absolute temperatures to be used instead of colorProcParameters lwir_low and lwir_high if autoranging		// absolute temperatures to be used instead of colorProcParameters lwir_low and lwir_high if autoranging
	@@ -1478,7 +1479,15 @@ public class QuadCLTCPU {
	public boolean isLwir() {return geometryCorrection.isLwir();} // clt_kernels // USED in lwir		public boolean isLwir() {return geometryCorrection.isLwir();} // clt_kernels // USED in lwir
	public boolean isMonochrome() {return geometryCorrection.isMonochrome();} // clt_kernels // USED in lwir		public boolean isMonochrome() {return geometryCorrection.isMonochrome();} // clt_kernels // USED in lwir

	public double getLwirOffset() {return lwir_offset;} // USED in lwir		public double getLwirOffset() {
			double s = 0;
			if (lwir_offsets == null) {
			throw new IllegalArgumentException ("Trying to use non-existing lwir_offsets!");
			}
			for (double offset:lwir_offsets) s+=offset;
			lwir_offset = s/lwir_offsets.length;
			return lwir_offset;
			}

	public boolean isLwirCalibrated() {		public boolean isLwirCalibrated() {
	return lwir_offsets != null;		return lwir_offsets != null;
	@@ -5256,6 +5265,7 @@ public class QuadCLTCPU {
	set_name, // just for debug messages == setNames.get(nSet)		set_name, // just for debug messages == setNames.get(nSet)
	threadsMax,		threadsMax,
	debugLevel));		debugLevel));
			// will actually is now calculated by setLwirOffsets()
	int num_avg = 0;		int num_avg = 0;
	this.lwir_offset = 0.0;		this.lwir_offset = 0.0;
	for (int srcChannel=0; srcChannel < channelFiles.length; srcChannel++){		for (int srcChannel=0; srcChannel < channelFiles.length; srcChannel++){

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