debugging

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

@@ -529,6 +529,29 @@ import ij.process.ImageProcessor;
 	  return null;
   }
   
+  public static ImagePlus makeArrays(boolean[][] pixels, int width, int height,  String title, String [] titles) {
+	  int i,j;
+	  if (pixels==null) {
+		  System.out.println("showDoubleFloatArrays.makeArrays(): - pixel array is null");
+	  }
+	  float [] fpixels;
+	  ImageStack array_stack=new ImageStack(width,height);
+	  boolean not_empty = false;
+	  for (i=0;i<pixels.length;i++) if (pixels[i]!=null) {
+		  not_empty = true;
+		  fpixels=new float[pixels[i].length];
+		  for (j=0;j<fpixels.length;j++) fpixels[j]=pixels[i][j]?1.0f:0.0f;
+		  array_stack.addSlice(titles[i], fpixels);
+	  }
+	  if (not_empty) {
+		  ImagePlus imp_stack = new ImagePlus(title, array_stack);
+		  imp_stack.getProcessor().resetMinAndMax();
+		  return imp_stack;
+	  }
+	  return null;
+  }
+
+  
   
   public static ImagePlus makeArrays(double[][] pixels, int width, int height,  String title, String [] titles) {
 	  int i,j;

src/main/java/com/elphel/imagej/cuas/CuasMotion.java

@@ -1042,11 +1042,13 @@ public class CuasMotion {
 			final double        lambda_max,
 			final double        rms_diff,
 			final int           num_iter,
+			final float [][]    accum_debug,
 			final int           debugLevel){
 		final int tile2 = 2 * GPUTileProcessor.DTT_SIZE;
 		final int lmax_iradius = (int) Math.floor(lmax_radius);
 		final int num_seq = vector_fields.length; // same as accum_data.length
 		final int num_tiles = vector_fields[0].length;
+		final int num_pixels = accum_data[0].length;
 //		final int num_pix = accum_data[0].length;
 //		final int tilesY = num_tiles/tilesX;
 		final int width = GPUTileProcessor.DTT_SIZE * tilesX;
@@ -1077,16 +1079,21 @@ public class CuasMotion {
 							wnd_pedestal);
 					// may be faster if process only where vector_field[nseq][ntile] is not null
 					for (int nSeq = ai.getAndIncrement(); nSeq < num_seq; nSeq = ai.getAndIncrement()) {
+						if (accum_debug != null) {
+							accum_debug[nSeq] = new float [num_pixels];
+							Arrays.fill(accum_debug[nSeq], Float.NaN);
+						}
 						for (int ntile = 0; ntile < num_tiles; ntile++) {
-							if ((nSeq==dbg_seq) && (ntile == dbg_tile)) {
+							if (vector_fields[nSeq][ntile] != null) {
+								if (ntile == dbg_tile) { // if ((nSeq==dbg_seq) && (ntile == dbg_tile)) {
 									System.out.println("getAccumulatedCoordinates(): nSeq="+nSeq+", ntile="+ntile);
 								}
-							if (vector_fields[nSeq][ntile] != null) {
 								int tileX = ntile % tilesX;
 								int tileY = ntile / tilesX;
 								int px0 = tileX * GPUTileProcessor.DTT_SIZE - GPUTileProcessor.DTT_SIZE/2; // top-left of 16x16 tile 
 								int py0 = tileY * GPUTileProcessor.DTT_SIZE - GPUTileProcessor.DTT_SIZE/2; // top-left of 16x16 tile
 								// copy 16x16 tile
+								{
 									int indx_dst = 0;
 									for (int y = 0; y < tile2; y++) {
 										int indx_src = px0 + (py0 +y) * width;
@@ -1094,17 +1101,24 @@ public class CuasMotion {
 											pix_tile[indx_dst++] = accum_data[nSeq][indx_src++]; // float-> double
 										}
 									}
+								}
 								// find absolute maximum
 								int ntile_amax = TileNeibs.getAmaxTile(
 										pix_tile); //double [] data)
+								double amax_val = pix_tile[ntile_amax];
 								int use_max = -1;
-								if (!tn.isEdge(ntile_amax) && tn.isMaxIsolated(
+								if (!tn.isEdge(ntile_amax)) {
+									boolean isolated =  tn.isMaxIsolated(
 										pix_tile, // double [] data,
 										ntile_amax, // int       ntile,
 										lmax_fraction, // double    fraction,
-										lmax_iradius)) { //int       radius)) {
+										lmax_iradius); //int       radius)) {
+									if (isolated) {
 										use_max = ntile_amax;
 									}
+								}
+								boolean max_abs = (use_max >= 0); // maximum is absolute maximum
+								
 								if (use_max < 0) { // find alternative maximum
 									int [] max_indices = tn.getLocalMaxes(
 											pix_tile, //double [] data,
@@ -1113,7 +1127,7 @@ public class CuasMotion {
 									for (int indx:max_indices) {
 										boolean isolated = tn.isMaxIsolated(
 												pix_tile,      // double [] data,
-												ntile_amax, // int       ntile,
+												indx,          // int       ntile,
 												lmax_fraction, // double    fraction,
 												lmax_iradius); //int       radius)) {
 										if (isolated) {
@@ -1129,8 +1143,8 @@ public class CuasMotion {
 									// no candidate for the centroid/lma
 									continue;
 								}
-								// zero out outside the circle
-								if (lmax_zero) {
+								// zero out outside the circle if maximum is not the absolute maximum or 
+								if (lmax_zero || !max_abs) {
 									double lmax_iradius2 = (int) Math.ceil(lmax_radius * lmax_radius);
 
 									int x0 = use_max % tile2;
@@ -1144,10 +1158,24 @@ public class CuasMotion {
 											int r2 = dy2+dx*dx;
 											if (r2 > lmax_iradius2) {
 												pix_tile[x + tile2 * y] = 0.0;
+											} else {
+												double rratio = Math.sqrt(r2)/lmax_iradius;
+												pix_tile[x + tile2 * y] *= Math.cos(0.5*Math.PI*rratio);
+											}
+										}
 									}
 								}
+								if (accum_debug != null) {
+									int indx_src = 0;
+									for (int y = 0; y < tile2; y++) {
+										int indx_dst = px0 + (py0 +y) * width;
+										for (int x = 0; x < tile2; x++) {
+											accum_debug[nSeq][indx_dst++] = (float) pix_tile[indx_src++]; // double -> float
 										}
 									}
+								}
+								
+								
 								double [] mv = Correlation2d.getMaxXYCm( // last, average (Will be relative to the center of the tile)
 										pix_tile,        // corrs.length-1], // double [] data,
 										tile2,           // int       data_width,      //  = 2 * transform_size - 1; // negative - will return center fraction
@@ -3587,6 +3615,23 @@ public class CuasMotion {
 					speed_pref,        // double              speed_pref,		
 					speed_boost);      // double              speed_boost);
 			if (debugLevel > -4) printRemain(remain, "filter5", true);
+			if (save_filtered_low) {
+ 				ImagePlus imp_filter5 = ShowDoubleFloatArrays.makeArrays(
+ 						filter5, // double[][] pixels,
+						cuasMotion.gpu_max_width,
+						cuasMotion.gpu_max_height, 
+						model_prefix+"-FILTER5-n"+niter,   // String title,
+						slice_titles);
+				if (!batch_mode) {
+					imp_filter5.show();
+				}
+				parentCLT.saveImagePlusInModelDirectory(imp_filter5);  // ImagePlus   imp)
+
+			}
+			
+			
+			
+			
 			double [][][] motion_scan_filtered = applyFilter( // motion vectors
 					motion_scan,          // double [][][] motion_scan,
 					filter5);             // boolean [][] filter5)
@@ -3759,6 +3804,7 @@ public class CuasMotion {
 				    lambda_max,           // final double        lambda_max,
 				    rms_diff,             // final double        rms_diff,
 				    num_iter,             // final int           num_iter,
+				    null,                 // final float [][]    accum_debug,
 				    debugLevel);          // final int           debugLevel);
 			double [][][] coord_centroid = 	coord_data2[0];	// centroid
 			double [][][] coord_lma =    	coord_data2[1];	// lma
@@ -3835,6 +3881,7 @@ public class CuasMotion {
 						!batch_mode,          // boolean       show,
 						cuasMotion.tilesX);   //  int           tilesX) {
 				parentCLT.saveImagePlusInModelDirectory(imp_good);  // ImagePlus   imp)
+				
 			}
 			// remove all good (by the LMA) 
 			double [][][] targets_bad_last  = subtractMotionScans( // centroids
@@ -3851,6 +3898,21 @@ public class CuasMotion {
 					remain); //
 			if (debugLevel > -4) printRemain(remain, "targets_bad", true);
 			
+			if (save_filtered_low) { // targets_good now has
+				ImagePlus imp_bad = showVectorFieldsSequence(
+						targets_bad,          // double [][][] vector_fields_sequence,
+						0.0,                  // double        speed_min,	// 	
+						0.0,                  // double        speed_pref,		
+						1.0,                  // double        speed_boost, 
+						slice_titles,         // String []     titles, // all slices*frames titles or just slice titles or null
+						model_prefix+"-BAD-n"+niter,    // String        title,
+						false,                // boolean       nan_effective_strength,
+						!batch_mode,          // boolean       show,
+						cuasMotion.tilesX);   //  int           tilesX) {
+				parentCLT.saveImagePlusInModelDirectory(imp_bad);  // ImagePlus   imp)
+				
+			}			
+			
 			// TODO See if they are needed here at all 
 			/*
 			fpixels_accumulated_filtered = getTargetImages(
@@ -4032,7 +4094,7 @@ public class CuasMotion {
 		}
 		
 		
-		
+		float [][] accum_debug = intermed_high ? (new float [accum.length][]) : null;
         double [][][][] coord_data2 = 	getAccumulatedCoordinates(
         		vf_sequence,          // final double [][][] vector_fields, // centers
 				accum,                // final double [][]   accum_data,    // should be around 0, no low-freq
@@ -4061,7 +4123,24 @@ public class CuasMotion {
 			    lambda_max,           // final double        lambda_max,
 			    rms_diff,             // final double        rms_diff,
 			    num_iter,             // final int           num_iter,
+			    accum_debug,          // final float [][]    accum_debug,
 			    debugLevel);          // final int           debugLevel);
+		if (accum_debug != null) {
+			ImagePlus imp_accumulated_filtered = ShowDoubleFloatArrays.makeArrays(
+					accum_debug, // float[][] pixels,
+					cuasMotion.gpu_max_width, // int width,
+					cuasMotion.gpu_max_height, // int height,
+					model_prefix+"-ACCUMULATED-FILT", //String title,
+					slice_titles); //String [] titles)
+			imp_accumulated_filtered.getProcessor().setMinAndMax(-input_range/2, input_range/2);
+			if (!batch_mode) {
+				imp_accumulated_filtered.show();
+			}		
+			parentCLT.saveImagePlusInModelDirectory(imp_accumulated_filtered);            // ImagePlus   imp)
+		}
+
+        
+        
 		double [][][] coord_data = 	coord_data2[0];	
 		double [][][] coord_lma = 	coord_data2[1];	
 		if (intermed_low) {

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

@@ -724,9 +724,9 @@ min_str_neib_fpn	0.35
     public double   cuas_speed_boost =   1.0;     // speed boost limit
 	// target filtering after constant velocity accumulation
     
-    public double   cuas_lmax_fraction = 0.7;     // Check if local maximum is separated from tye surrounding by this fraction of the maximum value 
-    public double   cuas_lmax_radius =   3.5;     // look inside ((int)cuas_lmax_radius) * 2 + 1 square for the local maximum isolation 
-	public boolean  cuas_lmax_zero =     true;    // zero all data outside this radius from the maximum
+    public double   cuas_lmax_fraction = 0.6;     // Check if local maximum is separated from tye surrounding by this fraction of the maximum value 
+    public double   cuas_lmax_radius =   4.5;     // look inside ((int)cuas_lmax_radius) * 2 + 1 square for the local maximum isolation 
+	public boolean  cuas_lmax_zero =     false;   // true;    // zero all data outside this radius from the maximum
      
     
 	public double   cuas_target_radius = 3.0;     // target centroids center radius

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

@@ -1546,7 +1546,8 @@ public class TileNeibs{
 	 * @return
 	 */
 	public boolean isEdge(int indx) {
-		return !getFullRectangle().contains(getPoint(indx));
+		boolean isedge = !getInnerRectangle().contains(getPoint(indx));
+		return isedge;
 	}