prepared elevation data, starting elevation LMA fitting (9ba553bb) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -5802,11 +5802,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	} else if (label.equals("Process Merged")) {		} else if (label.equals("Process Merged")) {
	OrangeTest.processMerged();		OrangeTest.processMerged();
	} else if (label.equals("Vegetation LMA")) {		} else if (label.equals("Vegetation LMA")) {
	VegetationModel.testVegetationLMA(		VegetationModel.processVegetationLMA(
	CLT_PARAMETERS, //CLTParameters clt_parameters,		CLT_PARAMETERS, //CLTParameters clt_parameters,
	false); //boolean combine_segments);		false); //boolean combine_segments);
	} else if (label.equals("Combine LMA Segments")) {		} else if (label.equals("Combine LMA Segments")) {
	VegetationModel.testVegetationLMA(		VegetationModel.processVegetationLMA(
	CLT_PARAMETERS, //CLTParameters clt_parameters,		CLT_PARAMETERS, //CLTParameters clt_parameters,
	true); //boolean combine_segments);		true); //boolean combine_segments);
	}		}

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

+22 −5

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

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -6368,7 +6368,7 @@ public class OpticalFlow {
	// int [] first_last = quadCLTs[ref_index].getFirstLastIndex(quadCLTs);		// int [] first_last = quadCLTs[ref_index].getFirstLastIndex(quadCLTs);
	QuadCLT [] quadCLT_tail = new QuadCLT [quadCLTs.length - earliest_scene];		QuadCLT [] quadCLT_tail = new QuadCLT [quadCLTs.length - earliest_scene];
	System.arraycopy(quadCLTs, earliest_scene, quadCLT_tail, 0, quadCLT_tail.length);		System.arraycopy(quadCLTs, earliest_scene, quadCLT_tail, 0, quadCLT_tail.length);
	VegetationModel.test_vegetation(		VegetationModel.prepareVegetationData(
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
	quadCLT_tail, // QuadCLT [] quadCLTs,		quadCLT_tail, // QuadCLT [] quadCLTs,
	ref_index-earliest_scene, // int ref_index,		ref_index-earliest_scene, // int ref_index,

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

+21 −0

Original line number	Original line	Diff line number	Diff line
	@@ -8786,6 +8786,27 @@ ImageDtt.startAndJoin(threads);
	* @return data array made of input data with replaced NaN limited by		* @return data array made of input data with replaced NaN limited by
	* optional prohibit array and amount of growth.		* optional prohibit array and amount of growth.
	*/		*/

			public static double [] fillNaNs(
			final double [] data,
			final boolean [] prohibit,
			int width,
			final int grow,
			double diagonal_weight, // relative to ortho
			int num_passes,
			final double max_rchange) // = 0.01
			{
			return fillNaNs(
			data, // final double [] data,
			null, // final double [] data_nan,
			prohibit, // final boolean [] prohibit_in,
			width, // int width,
			grow, // final int grow,
			diagonal_weight, //double diagonal_weight, // relative to ortho
			num_passes, // int num_passes,
			max_rchange, // final double max_rchange, // = 0.01
			ImageDtt.THREADS_MAX); // final int threadsMax)
			}
	public static double [] fillNaNs(		public static double [] fillNaNs(
	final double [] data,		final double [] data,
	final boolean [] prohibit,		final boolean [] prohibit,

Original line number	Original line	Diff line number	Diff line
	@@ -760,7 +760,9 @@ min_str_neib_fpn 0.35
	public double terr_difference = 100.0; // vegetation is 100 warmer (target)		public double terr_difference = 100.0; // vegetation is 100 warmer (target)
	public double terr_pull_cold = 0.001; // pull vegetations to warm, terrain to cold		public double terr_pull_cold = 0.001; // pull vegetations to warm, terrain to cold

	public double terr_alpha_dflt = 0.5;
			public double terr_alpha_contrast = 1.0; // initial alpha contrast (>=1.0)
			public double terr_alpha_dflt = 0.5; // now unused
	public double terr_alpha_loss = 100.0;		public double terr_alpha_loss = 100.0;
	public double terr_alpha_offset = 0.0;		public double terr_alpha_offset = 0.0;
	public double terr_alpha_lpf = 2.5; // pull to average of 4 neighbors		public double terr_alpha_lpf = 2.5; // pull to average of 4 neighbors
	@@ -775,6 +777,7 @@ min_str_neib_fpn 0.35
	public double terr_veget_lpf = 0.2; // pull vegetation to average of 4 neighbors (very small - maybe not needed)		public double terr_veget_lpf = 0.2; // pull vegetation to average of 4 neighbors (very small - maybe not needed)
	public double terr_terr_pull0 = 0.05; // pull terrain to zero (makes sense with UM		public double terr_terr_pull0 = 0.05; // pull terrain to zero (makes sense with UM
	public double terr_veget_pull0 = 0.05; // pull vegetation to zero (makes sense with UM		public double terr_veget_pull0 = 0.05; // pull vegetation to zero (makes sense with UM
			public double terr_scenes_pull0 = 1.0; // pull average scene offset to zero

	// LMA parameters		// LMA parameters
	public double terr_boost_parallax = 3.0; //		public double terr_boost_parallax = 3.0; //
	@@ -2013,15 +2016,19 @@ min_str_neib_fpn 0.35
	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).");

	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.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.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("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("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("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("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.");		gd.addNumericField("Pull terrain cold", terr_pull_cold, 5,7,"", "Pull vegetations to warm, terrain to cold.");
			gd.addNumericField("Alpha initial contrast",terr_alpha_contrast, 5,7,"","Initial alpha contrast (>= 1.0).");
	gd.addNumericField("Defalt alpha", terr_alpha_dflt, 5,7,"", "Default vegetation alpha.");		gd.addNumericField("Defalt alpha", terr_alpha_dflt, 5,7,"", "Default vegetation alpha.");
	gd.addNumericField("Alpha loss", terr_alpha_loss, 5,7,"", "Alpha quadratic growing loss for when out of [0,1] range");		gd.addNumericField("Alpha loss", terr_alpha_loss, 5,7,"", "Alpha quadratic growing loss for when out of [0,1] range");

	gd.addNumericField("Alpha offset", terr_alpha_offset, 5,7,"", "Start alpha losses above 0.0 and below 1.0 by this value.");		gd.addNumericField("Alpha offset", terr_alpha_offset, 5,7,"", "Start alpha losses above 0.0 and below 1.0 by this value.");
	gd.addNumericField("Alpha diffusion", terr_alpha_lpf, 5,7,"", "Alpha diffusion to 4 ortho neighbors.");		gd.addNumericField("Alpha diffusion", terr_alpha_lpf, 5,7,"", "Alpha diffusion to 4 ortho neighbors.");
	gd.addCheckbox ("Alpha piece-linear", terr_alpha_piece_linear, "Piece-linear alpha (_/\u203E, false - 0.0-cosine-1.0.");		gd.addCheckbox ("Alpha piece-linear", terr_alpha_piece_linear, "Piece-linear alpha (_/\u203E, false - 0.0-cosine-1.0.");
	@@ -2035,6 +2042,7 @@ min_str_neib_fpn 0.35
	gd.addNumericField("Vegetation diffusion", terr_veget_lpf, 5,7,"", "LPF for vegetation pixels (diffusion to 4 neighbors).");		gd.addNumericField("Vegetation diffusion", terr_veget_lpf, 5,7,"", "LPF for vegetation pixels (diffusion to 4 neighbors).");

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