Before starting elevations fitting (5980d194) · Commits · Elphel / imagej-elphel

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

+71 −6

Original line number	Original line	Diff line number	Diff line
	@@ -727,8 +727,12 @@ min_str_neib_fpn 0.35
	public boolean terr_um_en = true;		public boolean terr_um_en = true;
	public double terr_um_sigma = 1.0;		public double terr_um_sigma = 1.0;
	public double terr_um_weight = 0.8;		public double terr_um_weight = 0.8;
	public double terr_nan_tolerance = 0.001; // set undefined terrain (out of capture area) to nan, it is almost zero after UM		public double terr_nan_tolerance = 0.001; // set undefined terrain (out of capture area) to nan, it is almost zero after UM. if !terr_um_en will be forced ==0.0
	public int terr_nan_grow = 20; // grow undefined terrain after detection		public int terr_nan_grow = 20; // grow undefined scenes terrain after detection
			public int terr_shrink_veget = 20; // shrink accumulated vegetation for filling terrain
			public int terr_shrink_terrain= 20; // shrink accumulated terrain after cutting shrunk vegetation (added to terr_shrink_veget)
			public double terr_vegetation_over = 35; // initial vegetation over (hotter) filled terrain
			public int terr_filter_veget = 10; // shrink+grow shrunk vegetation to remove small clusters

	public boolean terr_tile_woi = true; // if false - use woi50;		public boolean terr_tile_woi = true; // if false - use woi50;
	public Rectangle terr_woi_enclos = new Rectangle(80, 210, 210, 230); // will be tiled, using width/height from woi_step;		public Rectangle terr_woi_enclos = new Rectangle(80, 210, 210, 230); // will be tiled, using width/height from woi_step;
	@@ -737,6 +741,12 @@ min_str_neib_fpn 0.35
	public boolean terr_skip_exist= true; // skip existing woi/parameters, already saved.		public boolean terr_skip_exist= true; // skip existing woi/parameters, already saved.
	public boolean terr_continue= false; // start from last/single		public boolean terr_continue= false; // start from last/single

			public boolean terr_fit_terr = true; // adjust terrain pixels
			public boolean terr_fit_veget = true; // adjust vegetation pixels
			public boolean terr_fit_alpha = true; // adjust vegetation alpha pixels
			public boolean terr_fit_scenes = true; // adjust scene offsets (start from 0 always?)
			public boolean terr_fit_elevations = false; // adjust elevation pixels (not yet implemented)

	public int terr_min_scenes = 1; // minimal number of scenes (inside woi) vegetation pixel must influence		public int terr_min_scenes = 1; // minimal number of scenes (inside woi) vegetation pixel must influence
	public int terr_min_samples_scene = 10;		public int terr_min_samples_scene = 10;
	public int terr_min_total_scenes = 2;		public int terr_min_total_scenes = 2;
	@@ -1970,11 +1980,19 @@ min_str_neib_fpn 0.35
	gd.addStringField ("Model state file", terr_model_state, 50, "Model vegetation source data (w/o extension).");		gd.addStringField ("Model state file", terr_model_state, 50, "Model vegetation source data (w/o extension).");
	gd.addStringField ("Segments subdir", terr_segments_dir, 50, "Model vegetation source data (w/o extension).");		gd.addStringField ("Segments subdir", terr_segments_dir, 50, "Model vegetation source data (w/o extension).");

			gd.addMessage ("Unsharp mask filter of the input data (currently not used as both DC and HF fitting are implemented simultaneously).");
	gd.addCheckbox ("Enable UM", terr_um_en, "Enable unsharp mask filter.");		gd.addCheckbox ("Enable UM", terr_um_en, "Enable unsharp mask filter.");
	gd.addNumericField("UM sigma", terr_um_sigma, 5,7, "pix", "Unsharp mask sigma.");		gd.addNumericField("UM sigma", terr_um_sigma, 5,7, "pix", "Unsharp mask sigma.");
	gd.addNumericField("UM weight", terr_um_weight, 5,7, "", "Unsharp mask weight.");		gd.addNumericField("UM weight", terr_um_weight, 5,7, "", "Unsharp mask weight.");
	gd.addNumericField("NaN tolerance", terr_nan_tolerance, 5,7,"", "Replace continuous almost zeros with NaN-s.");
	gd.addNumericField("NaN grow", terr_nan_grow, 0,3,"pix", "Grow \"almost\" zero areas after detection (+2 - 8 directions, +1 - only ortho).");		gd.addMessage ("Preparaion of the initial LMA approximation");
			gd.addNumericField("NaN tolerance", terr_nan_tolerance, 5,7,"", "Replace continuous almost zeros with NaN-s (ignored and forced to 0 if no UM filter).");
			gd.addNumericField("NaN grow", terr_nan_grow, 0,3,"pix", "Grow zero/\"almost\" zero rendered scene areas (+2 - 8 directions, +1 - only ortho), replace with NaNs.");
			gd.addNumericField("Shrink vegetation", terr_shrink_veget, 0,3,"pix", "Shrink detected vegetation areas for terrain separation.");
			gd.addNumericField("Shrink terrain", terr_shrink_terrain, 0,3,"pix", "Shrink remaining detected terrain areas before filling with laplacian (terr_shrink_veget is added to start from the original size).");
			gd.addNumericField("Vegetation hotter", terr_vegetation_over, 5,7,"", "Initially consider to be vegetation if it is this hotter than filled in terrain holes.");
			gd.addNumericField("Vegetation shrink+grow", terr_filter_veget, 0,3,"pix", "Shrink + grow hot enough vegetation to filter from small clusters - needed for initial alpha.");


	gd.addMessage ("Scan WOI parameters");		gd.addMessage ("Scan WOI parameters");
	gd.addCheckbox ("Tiled WOI", terr_tile_woi, "Process tiled WOI (False - a single one).");		gd.addCheckbox ("Tiled WOI", terr_tile_woi, "Process tiled WOI (False - a single one).");
	@@ -1985,6 +2003,13 @@ min_str_neib_fpn 0.35
	gd.addCheckbox ("Skip existing WOI", terr_skip_exist, "Skip already esisting WOIs during scanning.");		gd.addCheckbox ("Skip existing WOI", terr_skip_exist, "Skip already esisting WOIs during scanning.");

	gd.addMessage ("LMA losses and goals for alpha, terrain and vegetation pixels");		gd.addMessage ("LMA losses and goals for alpha, terrain and vegetation pixels");

			gd.addCheckbox ("Adjust terrain", terr_fit_terr, "Adjust terrain pixels.");
			gd.addCheckbox ("Adjust vegetation", terr_fit_veget, "Adjust vegetation pixels.");
			gd.addCheckbox ("Adjust alpha", terr_fit_alpha, "Adjust vegetation alpha pixels.");
			gd.addCheckbox ("Adjust scene offsets", terr_fit_scenes, "Adjust scene offsets (start from 0 always?).");
			gd.addCheckbox ("Adjust elevation", terr_fit_elevations,"Adjust elevation pixels (not yet implemented).");

	gd.addNumericField("Min influenced scenes",terr_min_scenes, 0,3, "", "Minimal number of scenes (inside woi) vegetation pixel must influence.");		gd.addNumericField("Min influenced scenes",terr_min_scenes, 0,3, "", "Minimal number of scenes (inside woi) vegetation pixel must influence.");
	gd.addNumericField("Minimal samples/scene",terr_min_samples_scene, 0,3,"","Minimal samples per scene used for fitting (skip scene if less).");		gd.addNumericField("Minimal samples/scene",terr_min_samples_scene, 0,3,"","Minimal samples per scene used for fitting (skip scene if less).");
	gd.addNumericField("Minimum scenes used", terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");		gd.addNumericField("Minimum scenes used", terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");
	@@ -2668,6 +2693,10 @@ min_str_neib_fpn 0.35
	terr_nan_tolerance = gd.getNextNumber();// double		terr_nan_tolerance = gd.getNextNumber();// double
	terr_nan_grow = (int) gd.getNextNumber();// int		terr_nan_grow = (int) gd.getNextNumber();// int

			terr_shrink_veget = (int) gd.getNextNumber();// int
			terr_shrink_terrain =(int) gd.getNextNumber();// int
			terr_vegetation_over = gd.getNextNumber();// double
			terr_filter_veget = (int) gd.getNextNumber();// int

	terr_tile_woi = gd.getNextBoolean();// boolean		terr_tile_woi = gd.getNextBoolean();// boolean
	terr_continue = gd.getNextBoolean();// boolean		terr_continue = gd.getNextBoolean();// boolean
	@@ -2676,6 +2705,12 @@ min_str_neib_fpn 0.35
	terr_woi_last = stringToRectangle(gd.getNextString());// Rectangle		terr_woi_last = stringToRectangle(gd.getNextString());// Rectangle
	terr_skip_exist = gd.getNextBoolean();// boolean		terr_skip_exist = gd.getNextBoolean();// boolean

			terr_fit_terr = gd.getNextBoolean();// boolean
			terr_fit_veget = gd.getNextBoolean();// boolean
			terr_fit_alpha = gd.getNextBoolean();// boolean
			terr_fit_scenes = gd.getNextBoolean();// boolean
			terr_fit_elevations = gd.getNextBoolean();// boolean

	terr_min_scenes = (int) gd.getNextNumber();// int		terr_min_scenes = (int) gd.getNextNumber();// int
	terr_min_samples_scene=(int) gd.getNextNumber();// int		terr_min_samples_scene=(int) gd.getNextNumber();// int
	terr_min_total_scenes=(int) gd.getNextNumber();// int		terr_min_total_scenes=(int) gd.getNextNumber();// int
	@@ -3328,6 +3363,11 @@ min_str_neib_fpn 0.35
	properties.setProperty(prefix+"terr_nan_tolerance", terr_nan_tolerance+""); // double		properties.setProperty(prefix+"terr_nan_tolerance", terr_nan_tolerance+""); // double
	properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int		properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int

			properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int
			properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int
			properties.setProperty(prefix+"terr_nan_tolerance", terr_nan_tolerance+""); // double
			properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int

	properties.setProperty(prefix+"terr_tile_woi", terr_tile_woi+""); // boolean		properties.setProperty(prefix+"terr_tile_woi", terr_tile_woi+""); // boolean
	properties.setProperty(prefix+"terr_continue", terr_continue+""); // boolean		properties.setProperty(prefix+"terr_continue", terr_continue+""); // boolean
	properties.setProperty(prefix+"terr_woi_enclos", rectangleToString(terr_woi_enclos)+""); // Rectangle		properties.setProperty(prefix+"terr_woi_enclos", rectangleToString(terr_woi_enclos)+""); // Rectangle
	@@ -3335,6 +3375,12 @@ min_str_neib_fpn 0.35
	properties.setProperty(prefix+"terr_woi_last", rectangleToString(terr_woi_last)+""); // Rectangle		properties.setProperty(prefix+"terr_woi_last", rectangleToString(terr_woi_last)+""); // Rectangle
	properties.setProperty(prefix+"terr_skip_exist", terr_skip_exist+""); // boolean		properties.setProperty(prefix+"terr_skip_exist", terr_skip_exist+""); // boolean

			properties.setProperty(prefix+"terr_fit_terr", terr_fit_terr+""); // boolean
			properties.setProperty(prefix+"terr_fit_veget", terr_fit_veget+""); // boolean
			properties.setProperty(prefix+"terr_fit_alpha", terr_fit_alpha+""); // boolean
			properties.setProperty(prefix+"terr_fit_scenes", terr_fit_scenes+""); // boolean
			properties.setProperty(prefix+"terr_fit_elevations", terr_fit_elevations+""); // boolean

	properties.setProperty(prefix+"terr_min_scenes", terr_min_scenes+""); // int		properties.setProperty(prefix+"terr_min_scenes", terr_min_scenes+""); // int
	properties.setProperty(prefix+"terr_min_samples_scene", terr_min_samples_scene+""); // int		properties.setProperty(prefix+"terr_min_samples_scene", terr_min_samples_scene+""); // int
	properties.setProperty(prefix+"terr_min_total_scenes", terr_min_total_scenes+""); // int		properties.setProperty(prefix+"terr_min_total_scenes", terr_min_total_scenes+""); // int
	@@ -4008,6 +4054,10 @@ min_str_neib_fpn 0.35
	if (properties.getProperty(prefix+"terr_um_weight")!= null) terr_um_weight=Double.parseDouble(properties.getProperty(prefix+"terr_um_weight"));		if (properties.getProperty(prefix+"terr_um_weight")!= null) terr_um_weight=Double.parseDouble(properties.getProperty(prefix+"terr_um_weight"));
	if (properties.getProperty(prefix+"terr_nan_tolerance")!= null) terr_nan_tolerance=Double.parseDouble(properties.getProperty(prefix+"terr_nan_tolerance"));		if (properties.getProperty(prefix+"terr_nan_tolerance")!= null) terr_nan_tolerance=Double.parseDouble(properties.getProperty(prefix+"terr_nan_tolerance"));
	if (properties.getProperty(prefix+"terr_nan_grow")!= null) terr_nan_grow=Integer.parseInt(properties.getProperty(prefix+"terr_nan_grow"));		if (properties.getProperty(prefix+"terr_nan_grow")!= null) terr_nan_grow=Integer.parseInt(properties.getProperty(prefix+"terr_nan_grow"));
			if (properties.getProperty(prefix+"terr_shrink_veget")!= null) terr_shrink_veget=Integer.parseInt(properties.getProperty(prefix+"terr_shrink_veget"));
			if (properties.getProperty(prefix+"terr_shrink_terrain")!= null) terr_shrink_terrain=Integer.parseInt(properties.getProperty(prefix+"terr_shrink_terrain"));
			if (properties.getProperty(prefix+"terr_vegetation_over")!= null) terr_vegetation_over=Double.parseDouble(properties.getProperty(prefix+"terr_vegetation_over"));
			if (properties.getProperty(prefix+"terr_filter_veget")!= null) terr_filter_veget=Integer.parseInt(properties.getProperty(prefix+"terr_filter_veget"));

	if (properties.getProperty(prefix+"terr_tile_woi")!= null) terr_tile_woi=Boolean.parseBoolean(properties.getProperty(prefix+"terr_tile_woi"));		if (properties.getProperty(prefix+"terr_tile_woi")!= null) terr_tile_woi=Boolean.parseBoolean(properties.getProperty(prefix+"terr_tile_woi"));
	if (properties.getProperty(prefix+"terr_continue")!= null) terr_continue=Boolean.parseBoolean(properties.getProperty(prefix+"terr_continue"));		if (properties.getProperty(prefix+"terr_continue")!= null) terr_continue=Boolean.parseBoolean(properties.getProperty(prefix+"terr_continue"));
	@@ -4016,6 +4066,11 @@ min_str_neib_fpn 0.35
	if (properties.getProperty(prefix+"terr_woi_last")!= null) terr_woi_last=stringToRectangle((String) properties.getProperty(prefix+"terr_woi_last"));		if (properties.getProperty(prefix+"terr_woi_last")!= null) terr_woi_last=stringToRectangle((String) properties.getProperty(prefix+"terr_woi_last"));
	if (properties.getProperty(prefix+"terr_skip_exist")!= null) terr_skip_exist=Boolean.parseBoolean(properties.getProperty(prefix+"terr_skip_exist"));		if (properties.getProperty(prefix+"terr_skip_exist")!= null) terr_skip_exist=Boolean.parseBoolean(properties.getProperty(prefix+"terr_skip_exist"));

			if (properties.getProperty(prefix+"terr_fit_terr")!= null) terr_fit_terr=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_terr"));
			if (properties.getProperty(prefix+"terr_fit_veget")!= null) terr_fit_veget=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_veget"));
			if (properties.getProperty(prefix+"terr_fit_alpha")!= null) terr_fit_alpha=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_alpha"));
			if (properties.getProperty(prefix+"terr_fit_scenes")!= null) terr_fit_scenes=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_scenes"));
			if (properties.getProperty(prefix+"terr_fit_elevations")!= null) terr_fit_elevations=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_elevations"));
	if (properties.getProperty(prefix+"terr_min_scenes")!= null) terr_min_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_scenes"));		if (properties.getProperty(prefix+"terr_min_scenes")!= null) terr_min_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_scenes"));
	if (properties.getProperty(prefix+"terr_min_samples_scene")!= null) terr_min_samples_scene=Integer.parseInt(properties.getProperty(prefix+"terr_min_samples_scene"));		if (properties.getProperty(prefix+"terr_min_samples_scene")!= null) terr_min_samples_scene=Integer.parseInt(properties.getProperty(prefix+"terr_min_samples_scene"));
	if (properties.getProperty(prefix+"terr_min_total_scenes")!= null) terr_min_total_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_total_scenes"));		if (properties.getProperty(prefix+"terr_min_total_scenes")!= null) terr_min_total_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_total_scenes"));
	@@ -4658,6 +4713,10 @@ min_str_neib_fpn 0.35
	imp.terr_um_weight = this.terr_um_weight;		imp.terr_um_weight = this.terr_um_weight;
	imp.terr_nan_tolerance = this.terr_nan_tolerance;		imp.terr_nan_tolerance = this.terr_nan_tolerance;
	imp.terr_nan_grow = this.terr_nan_grow;		imp.terr_nan_grow = this.terr_nan_grow;
			imp.terr_shrink_veget = this.terr_shrink_veget;
			imp.terr_shrink_terrain = this.terr_shrink_terrain;
			imp.terr_vegetation_over = this.terr_vegetation_over;
			imp.terr_filter_veget = this.terr_filter_veget;

	imp.terr_tile_woi = this.terr_tile_woi;		imp.terr_tile_woi = this.terr_tile_woi;
	imp.terr_continue = this.terr_continue;		imp.terr_continue = this.terr_continue;
	@@ -4666,6 +4725,12 @@ min_str_neib_fpn 0.35
	imp.terr_woi_last = new Rectangle(this.terr_woi_last);		imp.terr_woi_last = new Rectangle(this.terr_woi_last);
	imp.terr_skip_exist = this.terr_skip_exist;		imp.terr_skip_exist = this.terr_skip_exist;

			imp.terr_fit_terr = this.terr_fit_terr;
			imp.terr_fit_veget = this.terr_fit_veget;
			imp.terr_fit_alpha = this.terr_fit_alpha;
			imp.terr_fit_scenes = this.terr_fit_scenes;
			imp.terr_fit_elevations = this.terr_fit_elevations;

	imp.terr_min_scenes = this.terr_min_scenes;		imp.terr_min_scenes = this.terr_min_scenes;
	imp.terr_min_samples_scene = this.terr_min_samples_scene;		imp.terr_min_samples_scene = this.terr_min_samples_scene;
	imp.terr_min_total_scenes = this.terr_min_total_scenes;		imp.terr_min_total_scenes = this.terr_min_total_scenes;

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