Documenting, cleaning up

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -3172,7 +3172,7 @@ public class CLTParameters {
 		gd.addNumericField("Lazy eye cluster size",                                                             this.tileStep,                  0, 6, "tiles",
 				"Process tileStep x tileStep cluster of tiles when adjusting lazy eye parameters");
 		gd.addNumericField("Consolidate multiple clusterts around given for low-contrast infinity",             this.super_radius,              0, 6, "clusters",
-				"e.g. for clouds in tghe sky  0 - none, 1 - 3x3, 2 - 5x5");
+				"e.g. for clouds in the sky  0 - none, 1 - 3x3, 2 - 5x5");
 		gd.addNumericField("Bit mask - which of 4 transforms to combine after iclt",                            this.iclt_mask,                 0);
 		gd.addNumericField("Tile X to extract (0..163)",                                                        this.tileX,                     0);
 		gd.addNumericField("Tile Y to extract (0..122)",                                                        this.tileY,                     0);
@@ -3628,7 +3628,7 @@ public class CLTParameters {
 		gd.addNumericField("Maximal motion blur to reduce weight",this.tex_mb, 5,7,"pix",
 				"Reduce texture weight if motion blur exceeds this (as square of MB length).");
 		
-		gd.addNumericField("Max disparity for meshe generation", this.tex_max_disparity_lim, 5,7,"pix",
+		gd.addNumericField("Max disparity for mesh generation",  this.tex_max_disparity_lim, 5,7,"pix",
 				"Do not allow stray disparities above this.");
 		gd.addNumericField("Minimal disparity for FG trimming",  this.tex_min_trim_disparity, 5,7,"pix",
 				"Do not try to trim texture outlines with lower disparities.");

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

@@ -142,7 +142,7 @@ public class IntersceneMatchParameters {
 	public  double  cold_scale =                       0.2;  // <=1.0. 1.0 - disables temperature dependence
 	public  double  sky_seed =                         5.0;  // start with product of strength by diff_second below this
 	public  double  lma_seed =                         2.0;  // seed - disparity_lma limit		double sky_lim  =      15.0; // then expand to product of strength by diff_second below this
-	public  int     sky_shrink =                       3;
+	public  int     sky_shrink =                       2;
 	public  int     seed_rows =                        5; // sky should appear in this top rows 
 	public  double  sky_lim =                         15.0; // then expand to product of strength by diff_second below this
 	public  int     sky_expand_extra =                 0; // 1?

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

@@ -4878,7 +4878,7 @@ public class OpticalFlow {
 		
 		// generates 3-d modes, colors, stereos, tiffs/videos
 		
-		if (generate_mapped || reuse_video) {
+		if (generate_mapped || reuse_video) { // modifies combo_dsn_final ?
 			int tilesX =  quadCLTs[ref_index].getTileProcessor().getTilesX();
 	        int tilesY =  quadCLTs[ref_index].getTileProcessor().getTilesY();
 	        double [] disparity_fg =  null;
@@ -4895,7 +4895,7 @@ public class OpticalFlow {
 	        				0, // int         num_slices, // (0 - all)
 	        				null); // int []      wh);
 	        	}
-	        	double [][] dls = {
+	        	double [][] dls = { 
 	        			combo_dsn_final[COMBO_DSN_INDX_DISP],
 	        			combo_dsn_final[COMBO_DSN_INDX_LMA],
 	        			combo_dsn_final[COMBO_DSN_INDX_STRENGTH]
@@ -5328,7 +5328,7 @@ public class OpticalFlow {
 		
 		// debugging 3D model
 
-		if (export3d) {
+		if (export3d) { //combo_dsn_final had strength 1.0e-4 where it should not? Reset it?
 			boolean ok_3d = TexturedModel.output3d( // quadCLTs have same image name, and everything else
 					clt_parameters,      // CLTParameters                            clt_parameters,
 					colorProcParameters, // ColorProcParameters                      colorProcParameters,
@@ -10472,7 +10472,8 @@ public class OpticalFlow {
 				sigma);               // double      sigma);
 		dbg_img[11] = disp.clone();
 		double [][] ds = {disp,     dls[2]};
-		if (blue_sky != null) { // Temporary, dix - pass blue_sky to fillDisparityStrength()
+		if (blue_sky != null) { // Temporary, fix - pass blue_sky to fillDisparityStrength()
+			ds[1] = ds[1].clone();
 			for (int i = 0; i < clean_lma.length; i++) if (blue_sky[i]){
 				ds[0][i] = 0.0;
 				ds[1][i] = 0.0001;

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

@@ -1653,7 +1653,7 @@ public class TexturedModel {
 		final int     jpeg_quality =     clt_parameters.tex_jpeg_quality; //95;   // JPEG quality for textures
 		
 		final boolean showTri =          !batch_mode && (debugLevel > -1) && (clt_parameters.show_triangles);
-		final boolean disp_hires_tri =    clt_parameters.tex_disp_hires_tri;
+		final boolean disp_hires_tri =   !batch_mode && clt_parameters.tex_disp_hires_tri;
 		final int dbg_scale_mesh =        clt_parameters.tex_dbg_scale_mesh; //  4; // <=0 - do not show
 		
 		
@@ -1678,6 +1678,11 @@ public class TexturedModel {
 		final int width = tilesX * transform_size;
 		final int height = tp.getTilesY() * transform_size;
 		// get multi-scene disparity map for FG and BG and filter it
+		if (combo_dsn_final != null) {
+			System.out.println("output3d(): combo_dsn_final is not null - setting it to null");
+			System.out.println("As there was a problem with (wrong?) blue sky setting strength to 0.0001");
+			combo_dsn_final = null;
+		}
 		if (combo_dsn_final == null) {
 			combo_dsn_final =scenes[ref_index].readDoubleArrayFromModelDirectory(
 					"-INTER-INTRA-LMA", // String      suffix,
@@ -2000,9 +2005,8 @@ public class TexturedModel {
 								tp.getTilesY(),         // int             tilesY,
 								ref_scene.getGeometryCorrection(), // GeometryCorrection geometryCorrection,
 								clt_parameters.correct_distortions, // requires backdrop image to be corrected also
-								dbg_mesh_imgs[nslice],  //   double []       tri_img,   //
+								((dbg_mesh_imgs != null) ? dbg_mesh_imgs[nslice]:null),  //   double []       tri_img,   //
 								dbg_scaled_width,       // int             tri_img_width,
-//								showTri,                // (scanIndex < next_pass + 1) && clt_parameters.show_triangles,
 								// FIXME: make a separate parameter:
 								infinity_disparity,            //  0.25 * clt_parameters.bgnd_range,  // 0.3
 								clt_parameters.grow_disp_max,  // other_range, // 2.0 'other_range - difference from the specified (*_CM)
@@ -2010,7 +2014,6 @@ public class TexturedModel {
 							    clt_parameters.maxZtoXY,       // double          maxZtoXY,       // 10.0. <=0 - do not use
 							    clt_parameters.maxZ,
 							    clt_parameters.limitZ,
-//							    dbg_disp_tri_slice,           //   double [][]     dbg_disp_tri_slice,
 								debugLevel + 1,               //   int             debug_level) > 0
 								clt_parameters.tex_dbg_plot_center,              //   boolean         dbg_plot_center, //  = true;
 								clt_parameters.tex_dbg_line_color,               //   double          dbg_line_color, //  =  1.0;

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

@@ -392,6 +392,11 @@ public class TileNeibs{
 		return -1; // should not happen
 	}
 	
+	/**
+	 * Invert selection in a single or multithreaded environment.
+	 * @param tiles array to invert
+	 * @return inverted array
+	 */
 	public static boolean [] invertSelection(
 			final boolean [] tiles) {
 		final boolean [] itiles = new boolean [tiles.length];
@@ -399,6 +404,12 @@ public class TileNeibs{
 		return itiles;
 	}
 
+	/**
+	 * Invert selection in a single or multithreaded environment. May be in-place if tiles and itiles
+	 * are the same array.
+	 * @param tiles  input array to be inverted
+	 * @param itiles output array of the same size as the input one. May be the same as tiles
+	 */
 	public static void invertSelection(
 			final boolean [] tiles,
 			final boolean [] itiles
@@ -423,6 +434,12 @@ public class TileNeibs{
 		}
 	}
 
+	/**
+	 * And boolean array to another boolean array in a single or multithreaded environment.
+	 * dst_tiles &= src_tiles
+	 * @param src_tiles array to AND to another one
+	 * @param dst_tiles array to be modified by AND-ing with the first one
+	 */
 	public static void andSelection(
 			final boolean [] src_tiles,
 			final boolean [] dst_tiles
@@ -448,10 +465,16 @@ public class TileNeibs{
 	}
 	
 	
-	
+	/**
+	 * Shrink boolean array (single or multithreaded depending on is
+	 * it called from the main thread or not) 
+	 * @param shrink    see definitons for growSelection()
+	 * @param tiles     selection array (should be [sizeX * sizeY])
+	 * @param prohibit  optional (may be null) array of prohibited tiles (for both originating and destination)
+	 */
 	public void shrinkSelection(
-			int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
-			final boolean [] tiles,
+			final int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
+			final boolean [] tiles,  
 			final boolean [] prohibit)
 	{
 		final boolean [] itiles = invertSelection(tiles);
@@ -463,6 +486,14 @@ public class TileNeibs{
 	}
 
 	
+	/**
+	 * Select outmost pixels of the selection (single or multithreaded depending on is
+	 * it called from the main thread or not)
+	 * @param shrink    see definitons for growSelection()
+	 * @param tiles     selection array (should be [sizeX * sizeY])
+	 * @param prohibit  optional (may be null) array of prohibited tiles
+	 * @return tile selection of the outmost tiles of the input tiles
+	 */
 	public boolean [] getEdgeSelection(
 			int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
 			boolean [] tiles,
@@ -807,6 +838,14 @@ public class TileNeibs{
 		}
 	}
 
+	/**
+	 * Grow pixel selection in multiple threads.
+	 * @param grow     amount of growth: 1 - 1 pixel in ortho (up/down, right/left) directions,
+	 *                 2 - ortho+diagonal, 3 - 2 steps in ortho, etc.
+	 * @param tiles    boolean array to grow (should be [sizeX * sizeY])
+	 * @param prohibit optional array (may be null) that prohibits growth (for both originating and
+	 *                 destination tiles). 
+	 */
 	public void growSelectionMulti( // multithreaded version
 			int        grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
 			final boolean [] tiles,
@@ -925,12 +964,26 @@ public class TileNeibs{
 	
 	
 	
-	
+	/**
+	 * Find out if the current thread is main.
+	 * @return true for the main thread, false - for others
+	 */
 	public static boolean isMainThread() {
 		return Thread.currentThread().getName().equals("main");
 	}
 	
 
+	
+	/**
+	 * Grow pixel selection in either a single thread (if the method is called from one of
+	 * concurrent threads (already used by multiple callers) or in multiple threads if the
+	 * current thread is "main"
+	 * @param grow     amount of growth: 1 - 1 pixel in ortho (up/down, right/left) directions,
+	 *                 2 - ortho+diagonal, 3 - 2 steps in ortho, etc.
+	 * @param tiles    boolean array to grow (should be [sizeX * sizeY])
+	 * @param prohibit optional array (may be null) that prohibits growth (for both originating and
+	 *                 destination tiles). 
+	 */
 	public void growSelection(
 			int              grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
 			final boolean [] tiles,

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

@@ -8591,10 +8591,6 @@ ImageDtt.startAndJoin(threads);
 	}
 
 
-
-
-
-
 	public double [] convolveTiles(
 			double [] tiles,
 			double [][] kernel_in) // should be odd * odd, with non-zero sum (result will be normalized
@@ -8639,7 +8635,23 @@ ImageDtt.startAndJoin(threads);
 		return -1;
 	}
 
+	
 
+	/**
+	 * Fill NaN values in 2D array from neighbors using Laplassian==0
+	 * @param data            data array (in line-scan order) with NaN values to be filled,
+	 *                        non-NaN values will not be modified. 
+	 * @param prohibit        optional (may be null) boolean array of the same size specifying
+	 *                        prohibited pixels.
+	 * @param width           data width (height = data.length/width) 
+	 * @param grow            limit area to process by expanding defined pixel area.
+	 * @param diagonal_weight weight of 4 diagonal neighbors relative to 4 ortho ones.
+	 * @param num_passes      maximal number of iterations.
+	 * @param max_rchange     max relative (to data RMS) step change to exit iterations.
+	 * @param threadsMax      maximal number of concurrent threads to launch. 
+	 * @return                data array made of input data with replaced NaN limited by
+	 *                        optional prohibit array and amount of growth. 
+	 */
 	public static double [] fillNaNs(
 			final double []  data,
 			final boolean [] prohibit,
@@ -8657,8 +8669,8 @@ ImageDtt.startAndJoin(threads);
 		final int tiles = width * height;
 		final boolean [] fixed = new boolean [tiles]; // Original non-NaN, will not be modified
 		int num_fixed = 0;
-		double davg = 0.0; // average of all fixed samples
-		double davg2 = 0.0; // average of all fixed samples
+		double davg =   0.0; // average of all fixed samples
+		double davg2 =  0.0; // average of all fixed samples
 		for (int i = 0; i < tiles; i++)	{
 			if (!Double.isNaN(data[i])) {
 				fixed[i] = true;
@@ -8687,14 +8699,6 @@ ImageDtt.startAndJoin(threads);
 		int last_grown = tn.getLastGrown(); // actual grown (0 <= last_grown <= grow)
 		final int scan0 = last_grown/2 + 2; //  ( 3* grow) / 2;
 
-		/*
-		growTiles(
-				grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
-				grown,
-				null,
-				width,
-				height);
-		*/
 		int num_active = 0;
 		for (int i = 0; i < tiles; i++) {
 			if (grown[i] && !fixed[i]) num_active++;
@@ -8709,7 +8713,6 @@ ImageDtt.startAndJoin(threads);
 		for (int i = 0; i < tiles; i++) {
 			if (grown[i] && !fixed[i]) {
 				active [num_active++] = i;
-//				data_io[0][i] = davg; // initial value - needed?
 			}
 		}
 		final Thread[] threads = ImageDtt.newThreadArray(threadsMax);

src/main/java/com/elphel/imagej/x3d/export/TriMesh.java

@@ -2094,12 +2094,10 @@ public class TriMesh {
 		}
 		return -1;
 	}
-
+// used in old code - change to the new one?
 	  public static void generateClusterX3d( 
 			  boolean         full_texture, // true - full size image, false - bounds only
 			  int             subdivide_mesh, // 0,1 - full tiles only, 2 - 2x2 pixels, 4 - 2x2 pixels
-//			  boolean []      alpha,     // boolean alpha - true - opaque, false - transparent. Full/bounds
-			                             // matching selection
 			  X3dOutput       x3dOutput, // output x3d if not null
 			  WavefrontExport wfOutput,  // output WSavefront if not null
 			  ArrayList<TriMesh> tri_meshes,
@@ -2125,7 +2123,6 @@ public class TriMesh {
 			  int             debug_level
 			  ) throws IOException
 	  {
-//		  int debug_level = 1;
 		  if (bounds == null) {
 			  return; // not used in lwir
 		  }
@@ -2314,14 +2311,12 @@ public class TriMesh {
 			  double          maxZtoXY,           // 10.0. <=0 - do not use
 			  double          maxZ,               // far clip (0 - do not clip). Negative - limit by max
 			  boolean         limitZ,
-//			  double [][]     dbg_disp_tri_slice,
 			  int             debug_level,
 			  boolean         dbg_plot_center, //  = true;
 			  double          dbg_line_color, //  =  1.0;
 			  double          dbg_center_color// = 3.0;
 			  ) throws IOException
 	  {
-//		  boolean         show_triangles = tri_img != null; 
 		  if (bounds == null) {
 			  return; // not used in lwir
 		  }
@@ -2329,8 +2324,6 @@ public class TriMesh {
 		  boolean display_src = debug_level > 1;
 		  boolean display_for_mesh = debug_level > 1;
 		  
-		  
-		  
 		  if (display_src) {
 			  double [][] dbg_img = new double [3][selected.length];
 			  for (int i = 0; i < dbg_img[0].length; i++) {
@@ -2378,12 +2371,6 @@ public class TriMesh {
 			  }
 		  }
 		  
-		  /*
-		  int [][] indices =  getCoordIndices( // starting with 0, -1 - not selected // updated 09.18.2022
-				  bounds, 
-				  selected,
-				  tilesX); 
-		  */
 		  int [] pnum_indices = new int[1];
 		  /*
 		   * Enumerate "large" and "small" tiles, where "large" are actual tiles and "small" are