preparing to VegetationLMA

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

@@ -331,6 +331,7 @@ public class VegetationModel {
 		}
 		/* */
 		double [][][] veg_to_terr =    new double [num_scenes][][];
+		double [][][] terr_to_terr =    new double [num_scenes][][];
 		Rectangle   window1 = new Rectangle(0,0,640,512);
 		Rectangle   window2 = out_window;
 		boolean     map_diff1 = true;
@@ -345,6 +346,14 @@ public class VegetationModel {
 					window2,                // final Rectangle   window2,
 					map_diff2,              // final boolean     map_diff2,
 					map_diff_out);          // final boolean     map_diff_out) 
+			terr_to_terr[nscene] = combineMaps(
+					terrain_pix[nscene],    // final double [][] map1,
+					window1,                // final Rectangle   window1,
+					map_diff1,              // final boolean     map_diff1,
+					terrain_inv[nscene], // final double [][] map2,
+					window2,                // final Rectangle   window2,
+					map_diff2,              // final boolean     map_diff2,
+					map_diff_out);          // final boolean     map_diff_out) 
 		}		
 		/* */
 		
@@ -397,6 +406,11 @@ public class VegetationModel {
 					tilesX*tileSize,                   // final int           width,
 					quadCLTs,                          // QuadCLT []          quadCLTs, // just for names
 					"combo_offset.tiff"); // String              title) { // with .tiff
+			showOffsetsCombo(
+					terr_to_terr,                       // final double [][][] map_combo,
+					tilesX*tileSize,                   // final int           width,
+					quadCLTs,                          // QuadCLT []          quadCLTs, // just for names
+					"combo_terr-terr.tiff"); // String              title) { // with .tiff
 			/*	*/
 		}
 
@@ -458,13 +472,17 @@ public class VegetationModel {
 		}
 		/* */
 		double [][] vegetation_mapped =    new double [num_scenes][];
+		double      scale_map = 1.0; // 0.5;
 		for (int nscene = 0; nscene < num_scenes; nscene++) {
 			vegetation_mapped[nscene] = applyMap(
-					terrain_render[nscene][0], // final double []   img,
+//					vegetation_render[nscene][0], // final double []   img,
+					terrain_vegetation_all[1][num_scenes], // final double []   img, // average vegetation
 					tilesX * tileSize,         // final int         img_width,
 					veg_to_terr[nscene],       // final double [][] map,
 					window1,                   // final Rectangle   window,
-					map_diff_out);             // final boolean     map_diff) 
+					map_diff_out,              // final boolean     map_diff)
+					scale_map);                    // final double      scale) { // debug feature, only works with differential map
+
 		}	
 
 		if (show_debug) {
@@ -477,7 +495,7 @@ public class VegetationModel {
 			ShowDoubleFloatArrays.showArraysHyperstack(
 					render3,           // double[][][] pixels, 
 					tilesX * tileSize,                // int          width, 
-					"terrain_vegetation_mapped.tiff", // String       title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
+					"terrain_vegetation_mapped-scale"+scale_map+".tiff", // String       title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
 					titles_scene,                     // String []    titles, // all slices*frames titles or just slice titles or null
 					titles_frame,                     // String []    frame_titles, // frame titles or null
 					true);                            // boolean      show)
@@ -596,6 +614,7 @@ public class VegetationModel {
 	 * @param window    Rectangle with {width, height} specifying output image size and (in
 	 *                  differential mode only) {x,y} corresponds to absolute origin
 	 * @param map_diff  true for differential mode, false - for absolute.
+	 * @param scale     debug feature, only works with differential map
 	 * @return          warped image in line-scan order, may have NaN-s.
 	 */
 	public static double [] applyMap(
@@ -603,7 +622,8 @@ public class VegetationModel {
 			final int         img_width,
 			final double [][] map,
 			final Rectangle   window,
-			final boolean     map_diff) {
+			final boolean     map_diff,
+			final double      scale) { // debug feature, only works with differential map
 		final int img_height = img.length /img_width;
 		final int num_pixels = window.width*window.height;
 		final double [] render_out = new double [num_pixels];
@@ -619,8 +639,10 @@ public class VegetationModel {
 							int iy = nPix / window.width;
 							double [] pxy = map[nPix].clone();
 							if (map_diff) {
-								pxy[0] += 0.5 + ix - window.x;
-								pxy[1] += 0.5 + iy - window.y;
+								pxy[0] *= scale;
+								pxy[1] *= scale;
+								pxy[0] += ix - window.x; //  + 0.5;
+								pxy[1] += iy - window.y; //  + 0.5;
 							}
 //							pxy[0] += window2.x;
 //							pxy[1] += window2.y;
@@ -701,8 +723,8 @@ public class VegetationModel {
 							int iy = nPix / window1.width;
 							double [] pxy = map1[nPix].clone();
 							if (map_diff1) {
-								pxy[0] += 0.5 + ix - window1.x;
-								pxy[1] += 0.5 + iy - window1.y;
+								pxy[0] += ix - window1.x; //  + 0.5;
+								pxy[1] += iy - window1.y; //  + 0.5;
 							}
 							pxy[0] += window2.x;
 							pxy[1] += window2.y;
@@ -724,8 +746,8 @@ public class VegetationModel {
 									corners[dy][dx] = corners[dy][dx].clone();
 									corner = corners[dy][dx];
 									if (map_diff2) {
-										corner[0] += x0 + dx  + 0.5 - window2.x;
-										corner[1] += y0 + dy  + 0.5 - window2.y;
+										corner[0] += x0 + dx - window2.x; //  + 0.5;
+										corner[1] += y0 + dy - window2.y; //  + 0.5;
 									}
 								}
 							}
@@ -741,8 +763,8 @@ public class VegetationModel {
 										(  fx)*(  fy)*corners[1][1][i];
 							}
 							if (map_diff_out) {
-									cxy[0] -= 0.5 + ix - window1.x;
-									cxy[1] -= 0.5 + iy - window1.y;
+									cxy[0] -= ix - window1.x; // + 0.5;
+									cxy[1] -= iy - window1.y; // + 0.5;
 							}						
 							combo_map[nPix] = cxy;
 						}
@@ -819,8 +841,8 @@ public class VegetationModel {
 										corners_cw[dir][ynx] = map_in[in_indx][ynx];
 									}
 									if (in_diff) {
-										corners_cw[dir][0] += 0.5 + ix1;
-										corners_cw[dir][1] += 0.5 + iy1;
+										corners_cw[dir][0] += ix1; //  +  0.5;
+										corners_cw[dir][1] += iy1; //  +  0.5;
 									}
 									corners_cw[dir][0] += out_window.x;
 									corners_cw[dir][1] += out_window.y;
@@ -907,8 +929,8 @@ public class VegetationModel {
 										map_out[oindx][0] = ix0 + u;
 										map_out[oindx][1] = iy0 + v;
 										if (out_diff) {
-											map_out[oindx][0] -= ox-out_window.x-0.5;
-											map_out[oindx][1] -= oy-out_window.y-0.5;
+											map_out[oindx][0] -= ox-out_window.x; // -0.5;
+											map_out[oindx][1] -= oy-out_window.y; // -0.5;
 										}
 									}									
 								}

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

@@ -176,7 +176,7 @@ public class OpticalFlow {
 	 * @param debug_level debug level
 	 */
 	
-	public void fillTilesNans(
+	public static void fillTilesNans(
 			final double [][][] nan_tiles,
 			final QuadCLT     qthis,
 			final int         num_passes,