tested jt vs. jt_delta, full modification not finished (ca780c7c) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

+9 −1

Original line number	Diff line number	Diff line
		@@ -201,10 +201,18 @@ import ij.process.ImageProcessor;
		}
		}
		}
		int height = -1;
		for (int slic = 0; slic < dpixels.length; slic++) {
		if (dpixels[slic] != null) {
		height = dpixels[slic].length/width;
		break;
		}
		}

		return showArraysHyperstack(
		dpixels, // double[][] pixels,
		width, // int width,
		pixels[0][0].length/width, // int height,
		height, // int height,
		pixels[0].length, // int slices,
		title, // String title,
		combo_titles, // String [] titles);

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

+31 −6

Original line number	Diff line number	Diff line
		@@ -746,15 +746,27 @@ min_str_neib_fpn 0.35
		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 double terr_max_warp = 1.8;
		public int terr_max_elevation = 22; // maximal offset to consider when looking for vegetation influence


		@Deprecated
		public int terr_min_scenes = 1; // minimal number of scenes (inside woi) vegetation pixel must influence

		@Deprecated
		public int terr_min_samples_scene = 10;
		@Deprecated
		public int terr_min_total_scenes = 2;
		@Deprecated
		public int terr_min_pixels = 10;

		@Deprecated
		public boolean terr_warm_veget = true; // start with vegetation warmer than terrain
		@Deprecated
		public double terr_warmest = 90.0; // above - vegetation. below - terrain
		@Deprecated
		public double terr_initial_split = 0.1; // initial alpha: terrain 0.0+, vegetation 1.0-
		@Deprecated
		public double terr_min_split_frac = 0.15; // minimal modality fraction to use split by temperature

		public double terr_difference = 100.0; // vegetation is 100 warmer (target)
		@@ -2014,15 +2026,18 @@ min_str_neib_fpn 0.35
		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("Maximal warp", terr_max_warp, 5,7,"pix", "(1.8) Do not use scenes where distance between vegetation projection exceeds this.");
		gd.addNumericField("Min elevation/offset", terr_max_elevation, 0,3,"pix","Maximal offset to consider when looking for vegetation influence.");

		gd.addNumericField("(Min influenced scenes)",terr_min_scenes, 0,3, "", "Deprecated: 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("Minimum scenes used", terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");

		gd.addNumericField("Minimal pixels fitted",terr_min_pixels, 0,3,"", "Minimal number of terrain and vegetation pixels used for fitting in this segment(skip segment if less).");
		gd.addCheckbox ("Start by temperature", terr_warm_veget, "Start with vegetation warmer than terrain.");
		gd.addNumericField("Warmest terrain", terr_warmest, 5,7,"", "Above - vegetation. below - terrain.");
		gd.addNumericField("Initial split", terr_initial_split, 5,7,"", "Initial alpha: terrain 0.0+, vegetation 1.0-.");
		gd.addNumericField("Min. split fraction", terr_min_split_frac, 5,7,"", "minimal modality fraction to use split by temperature (otherwise use default alpha).");
		gd.addCheckbox ("(Start by temperature)", terr_warm_veget, "Start with vegetation warmer than terrain.");
		gd.addNumericField("(Warmest terrain)", terr_warmest, 5,7,"", "Above - vegetation. below - terrain.");
		gd.addNumericField("(Initial split)", terr_initial_split, 5,7,"", "Initial alpha: terrain 0.0+, vegetation 1.0-.");
		gd.addNumericField("(Min. split fraction)", terr_min_split_frac, 5,7,"", "minimal modality fraction to use split by temperature (otherwise use default alpha).");
		gd.addNumericField("Vegetation warmer", terr_difference, 5,7,"", "Pull vegetation to be this warmer.");

		gd.addNumericField("Pull terrain cold", terr_pull_cold, 5,7,"", "Pull vegetations to warm, terrain to cold.");
		@@ -2721,6 +2736,9 @@ min_str_neib_fpn 0.35
		terr_fit_scenes = gd.getNextBoolean();// boolean
		terr_fit_elevations = gd.getNextBoolean();// boolean

		terr_max_warp = gd.getNextNumber();// double
		terr_max_elevation = (int) gd.getNextNumber();// int

		terr_min_scenes = (int) gd.getNextNumber();// int
		terr_min_samples_scene=(int) gd.getNextNumber();// int
		terr_min_total_scenes=(int) gd.getNextNumber();// int
		@@ -3393,6 +3411,8 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_fit_scenes", terr_fit_scenes+""); // boolean
		properties.setProperty(prefix+"terr_fit_elevations", terr_fit_elevations+""); // boolean

		properties.setProperty(prefix+"terr_max_warp", terr_max_warp+""); // double
		properties.setProperty(prefix+"terr_max_elevation", terr_max_elevation+""); // 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_total_scenes", terr_min_total_scenes+""); // int
		@@ -4087,6 +4107,9 @@ min_str_neib_fpn 0.35
		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_max_warp")!= null) terr_max_warp=Double.parseDouble(properties.getProperty(prefix+"terr_max_warp"));
		if (properties.getProperty(prefix+"terr_max_elevation")!= null) terr_max_elevation=Integer.parseInt(properties.getProperty(prefix+"terr_max_elevation"));
		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_total_scenes")!= null) terr_min_total_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_total_scenes"));
		@@ -4751,6 +4774,8 @@ min_str_neib_fpn 0.35
		imp.terr_fit_scenes = this.terr_fit_scenes;
		imp.terr_fit_elevations = this.terr_fit_elevations;

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

src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java

+2318 −1302

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/com/elphel/imagej/vegetation/VegetationModel.java

+25 −23

Original line number	Diff line number	Diff line
		@@ -59,8 +59,8 @@ public class VegetationModel {
		public double [] vegetation_full = null; // ~same as vegetation_average_render
		public double [] vegetation_filtered = null; // more NaNs than in vegetation_average_render
		public double [] vegetation_pull = null; // filled around actual vegetation to use as LMA pull
		public double initial_transparent= 0.0;
		public double initial_opaque= 1.0;
		// public double initial_transparent= 0.0;
		// public double initial_opaque= 1.0;


		public double [][][] vegetation_warp = null;
		@@ -1380,16 +1380,18 @@ public class VegetationModel {
		Rectangle woi_last = clt_parameters.imp.terr_woi_last; // new Rectangle(160,310,20,20); // 170
		boolean skip_existing_woi = clt_parameters.imp.terr_skip_exist; // skip existing woi/parameters, already saved.
		boolean continue_woi = clt_parameters.imp.terr_continue; // false;

		int min_scenes = clt_parameters.imp.terr_min_scenes; // 1;
		int min_samples_scene = clt_parameters.imp.terr_min_samples_scene; //10;
		int min_total_scenes = clt_parameters.imp.terr_min_total_scenes; // 2;
		int min_pixels = clt_parameters.imp.terr_min_pixels; //10;

		boolean start_warm_veget = clt_parameters.imp.terr_warm_veget; // start with vegetation warmer than terrain
		double terrain_warmest = clt_parameters.imp.terr_warmest; // pull vegetations to warm, terrain to cold
		double initial_split = clt_parameters.imp.terr_initial_split; // pull vegetations to warm, terrain to cold
		double min_split_frac = clt_parameters.imp.terr_min_split_frac;// 0.15;
		double max_warp = clt_parameters.imp.terr_max_warp; // 1.8 - do not use scenes where distance between vegetation projection exceeds this
		int max_offset = clt_parameters.imp.terr_max_elevation; // maximal "elevation" to consider

		// int min_scenes = clt_parameters.imp.terr_min_scenes; // 1;
		// int min_samples_scene = clt_parameters.imp.terr_min_samples_scene; //10;
		// int min_total_scenes = clt_parameters.imp.terr_min_total_scenes; // 2;
		// int min_pixels = clt_parameters.imp.terr_min_pixels; //10;

		// boolean start_warm_veget = clt_parameters.imp.terr_warm_veget; // start with vegetation warmer than terrain
		// double terrain_warmest = clt_parameters.imp.terr_warmest; // pull vegetations to warm, terrain to cold
		// double initial_split = clt_parameters.imp.terr_initial_split; // pull vegetations to warm, terrain to cold
		// double min_split_frac = clt_parameters.imp.terr_min_split_frac;// 0.15;
		double terr_difference = clt_parameters.imp.terr_difference; // Pull vegetation to be this warmer
		double terr_pull_cold = clt_parameters.imp.terr_pull_cold; // pull vegetations to warm, terrain to cold

		@@ -1859,8 +1861,8 @@ public class VegetationModel {
		// }


		initial_transparent = initial_split;
		initial_opaque = 1.0 - initial_split;
		// initial_transparent = initial_split;
		// initial_opaque = 1.0 - initial_split;

		VegetationLMA vegetationLMA = new VegetationLMA (
		this,
		@@ -1915,19 +1917,19 @@ public class VegetationModel {
		} else {
		System.out.println("===== Will process a single WOI ("+woi.x+", "+woi.y+", "+woi.width+", "+woi.height+").");
		}
		final int max_offset = 22; // maximal "elevation" to consider
		int num_samples = vegetationLMA.prepareLMA(
		false, // final boolean keep_parameters,
		woi, // final Rectangle woi,
		min_scenes, // final int min_dependent_scenes, // minimal number of scenes (inside woi) vegetation pixel must influence
		max_warp, // final double max_warp, // 1.8 - do not use scenes where distance between vegetation projection exceeds this
		// min_scenes, // final int min_dependent_scenes, // minimal number of scenes (inside woi) vegetation pixel must influence
		max_offset, // final int max_offset, // maximal "elevation" to consider
		min_total_scenes, // final int min_total_scenes,
		min_samples_scene, //final int min_samples_scene, // 10
		min_pixels, // final int min_pixels,
		start_warm_veget, // final boolean start_warm_veget, // start with vegetation warmer than terrain
		terrain_warmest, // final double terrain_warmest, // warmest terrain (above is initially vegetation)
		initial_split, // final double initial_split, // initial alpha: terrain 0.0+, vegetation 1.0-.
		min_split_frac, // final double min_frac, // minimal modality fraction to use split by temperature
		// min_total_scenes, // final int min_total_scenes,
		// min_samples_scene, //final int min_samples_scene, // 10
		// min_pixels, // final int min_pixels,
		// start_warm_veget, // final boolean start_warm_veget, // start with vegetation warmer than terrain
		// terrain_warmest, // final double terrain_warmest, // warmest terrain (above is initially vegetation)
		// initial_split, // final double initial_split, // initial alpha: terrain 0.0+, vegetation 1.0-.
		// min_split_frac, // final double min_frac, // minimal modality fraction to use split by temperature
		terr_difference, // final double terr_difference, // pull vegetation to be this warmer
		terr_pull_cold, // final double terr_pull_cold, // pull vegetations to warm, terrain to cold
		default_alpha, // final double default_alpha,

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