Cleaning up, improving results (cc9dbf30) · Commits · Elphel / imagej-elphel

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

+103 −7

Original line number	Original line	Diff line number	Diff line
	@@ -327,7 +327,29 @@ public class ComboMatch {
	"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",		"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
	"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or40.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",		"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or40.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
	"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",		"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
	"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"		"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r30.0_e15.0_ir15.0ie8.0_is-0.05_h8_w0.6_s-200.0_200x200.tiff", // morning used
			"--- 30, 28 edge 10 --",
			"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"--- 26, 32 edge 10 --",
			"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			// "patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-170.0_200x200.tif",
			"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"---- 30, 26 edge 6 ---",
			"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"---- 30, 26 edge 8 ---",
			"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
			"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif"
	};		};


	@@ -399,9 +421,39 @@ public class ComboMatch {
	for (ObjectLocation ol: object_list) {		for (ObjectLocation ol: object_list) {
	System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);		System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);
	}		}
			int [] indices = null;
			int [][] bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
			zool_lev_objects,
			indices);
			int width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
			int height = bounds[1][1] - bounds[1][0];
			if ((width != imp_sel.getWidth()) \|\| (height != imp_sel.getHeight())) {
			System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the full map size ("+
			width+"x"+height+"), will try just for a pair of the first two slices");
			String [] labels = imp_sel.getStack().getSliceLabels();
			indices = new int [2];
			for (int i = 0; i < indices.length; i++) {
			indices[i] = maps_collection.getIndex(labels[i].substring(0, 17));
			}
			bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
			zool_lev_objects,
			indices);
			width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
			height = bounds[1][1] - bounds[1][0];
			if ((width != imp_sel.getWidth()) \|\| (height != imp_sel.getHeight())) {
			System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the 2-image map size ("+
			width+"x"+height+") either.Giving up");
			return false;
			} else {
			System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does match the 2-image map size ("+
			width+"x"+height+"). Using it.");
			}
			}

	maps_collection.reverseRender(		maps_collection.reverseRender(
	object_list, // ArrayList<ObjectLocation> objects,		object_list, // ArrayList<ObjectLocation> objects,
	zool_lev_objects); // int zoom_level){		zool_lev_objects, // int zoom_level){
			indices); // int [] indices){ // null or selected image indices
	System.out.println("Object coordinates in source images: ");		System.out.println("Object coordinates in source images: ");
	for (ObjectLocation ol: object_list) {		for (ObjectLocation ol: object_list) {
	System.out.println(ol.name+": "+ol.getPixels()[0]+"/"+ol.getPixels()[1]);		System.out.println(ol.name+": "+ol.getPixels()[0]+"/"+ol.getPixels()[1]);
	@@ -416,11 +468,14 @@ public class ComboMatch {
	extr_size);		extr_size);

	}		}

	ImagePlus imp_obj = ShowDoubleFloatArrays.makeArrays(		ImagePlus imp_obj = ShowDoubleFloatArrays.makeArrays(
	object_stack,		object_stack,
	extr_size,		extr_size,
	extr_size,		extr_size,
	OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-OBJECT_"+extr_size+"x"+extr_size+".tiff",		OrthoMap.removeKnownExtension(imp_sel.getTitle())+
			OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index+
			"-OBJECT_"+extr_size+"x"+extr_size+".tiff",
	object_titles); // test_titles,		object_titles); // test_titles,
	imp_obj.show();		imp_obj.show();

	@@ -448,8 +503,10 @@ public class ComboMatch {
	}		}
	double [] kernel = OrthoMap.getConvolutionKernel(default_kernel);		double [] kernel = OrthoMap.getConvolutionKernel(default_kernel);
	double [][] centers = new double [object_stack.length][];		double [][] centers = new double [object_stack.length][];

			double [][] corr_ret = new double [object_stack.length][corr_size*corr_size];
	for (int i = 0; i < object_stack.length; i++) {		for (int i = 0; i < object_stack.length; i++) {
	String dbg_prefix = "corr_patt_"+i;		String dbg_prefix = "corr_patt_"+i+"-"+OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index;
	ObjectLocation ol = object_list.get(i);		ObjectLocation ol = object_list.get(i);
	centers[i] = ObjectLocation.getPatternCenter(		centers[i] = ObjectLocation.getPatternCenter(
	object_stack[i], // double [] data,		object_stack[i], // double [] data,
	@@ -460,6 +517,7 @@ public class ComboMatch {
	min_corr, // double min_corr,		min_corr, // double min_corr,
	radius_search, // int radius_search,		radius_search, // int radius_search,
	radius_centroid, // int radius_centroid,		radius_centroid, // int radius_centroid,
			corr_ret[i], //double [] corr_ret, // null or double[corr_size*corr_size]
	dbg_prefix, // String dbg_prefix,		dbg_prefix, // String dbg_prefix,
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
	System.out.println(i+": center at "+centers[i][0]+"/"+centers[i][1]+", strength="+centers[i][2]);		System.out.println(i+": center at "+centers[i][0]+"/"+centers[i][1]+", strength="+centers[i][2]);
	@@ -470,6 +528,35 @@ public class ComboMatch {
	roi.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, i+1); // ,1);		roi.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, i+1); // ,1);
	}		}
	imp_obj.setRoi(roi);		imp_obj.setRoi(roi);
			// calculate statistics for cor_ret[i]
			double [][] stats = new double [object_stack.length][];
			double search_rad = 15.0;
			double frac_max = 0.5;
			double other_rad = 25;
			for (int i = 0; i < object_stack.length; i++) {
			double [] a_cent= {corr_size/2+centers[i][0],corr_size/2+centers[i][1]};
			stats[i]=ObjectLocation.getMaxLocArea(
			corr_ret[i], // double [] data, // square data
			a_cent, // centers[i], // double [] cent_xy, // if null, use center of the square
			search_rad, // double radius, // search for maximum within this radius
			frac_max, // double frac_max,
			other_rad,
			0); // int debugLevel)
			}

			System.out.println("\nUsing pattern file: "+pattern_path+", subpattern="+sub_pattern_index);
			System.out.println(String.format("%2s (%9s): %7s %7s %7s %7s %7s %7s %17s",
			"#"," X/Y ","strengh", "radius", " elong ", " dist ", " dx "," dy ",
			"image timestamp"));
			for (int i = 0; i < object_stack.length; i++) {
			ObjectLocation ol = object_list.get(i);
			System.out.println(String.format("%2d (%4d/%4d): %7.5f %7.3f %7.3f %7.3f %7.3f %7.3f %17s",
			i, ol.getPixels()[0], ol.getPixels()[1],
			stats[i][0],stats[i][1],stats[i][2],stats[i][3],stats[i][4]+centers[i][0],stats[i][5]+centers[i][1],
			ol.getName()));
			}
			System.out.println();

	if (only_correlate) {		if (only_correlate) {
	System.out.println("testPatternCorrelate(): correlation DONE, only_correlate is set to true, exiting");		System.out.println("testPatternCorrelate(): correlation DONE, only_correlate is set to true, exiting");
	return true;		return true;
	@@ -797,7 +884,8 @@ public class ComboMatch {
	}		}
	if (render_match) {		if (render_match) {
	ImagePlus imp_img_pair = maps_collection.renderMulti (		ImagePlus imp_img_pair = maps_collection.renderMulti (
	"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+min_zoom_lev+"_"+zoom_lev, // String title,		//_zoom<integer> is needed for opening with "Extract Objects" command
			"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"_zoom"+min_zoom_lev+"_"+zoom_lev, // String title,
	false, // boolean use_alt,		false, // boolean use_alt,
	gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)		gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
	bounds_to_indices, // boolean bounds_to_indices,		bounds_to_indices, // boolean bounds_to_indices,
	@@ -824,6 +912,11 @@ public class ComboMatch {
	return true;		return true;
	}		}

			public void printSceneStats() {

			}


	/*		/*
	double [][] affine1 = {		double [][] affine1 = {
	{1,0,0},		{1,0,0},
	@@ -1056,7 +1149,10 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
	int nSlices = stack_scenes.getSize();		int nSlices = stack_scenes.getSize();
	String [] scene_names = new String [nSlices];		String [] scene_names = new String [nSlices];
	for (int n = 0; n < scene_names.length; n++) {		for (int n = 0; n < scene_names.length; n++) {
	scene_names[n] = stack_scenes.getSliceLabel(n+1).substring(0,17);		scene_names[n] = stack_scenes.getSliceLabel(n+1);
			if (scene_names[n].length() >= 17) {
			scene_names[n] = scene_names[n].substring(0,17);
			}
	}		}
	PointRoi pRoi = (PointRoi) imp.getRoi();		PointRoi pRoi = (PointRoi) imp.getRoi();
	FloatPolygon fp = pRoi.getContainedFloatPoints();		FloatPolygon fp = pRoi.getContainedFloatPoints();

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

+45 −5

Original line number	Original line	Diff line number	Diff line
	@@ -125,6 +125,7 @@ public class ObjectLocation {
	* @param cent_xy offset from the square center to search		* @param cent_xy offset from the square center to search
	* @param radius search for maximum within this radius		* @param radius search for maximum within this radius
	* @param frac_max fraction of maximum to measure area		* @param frac_max fraction of maximum to measure area
			* @param other_radius measure maximal disconnected pixel fraction of the maximum within this radius
	* @return {maximum, area, dist, x, y}. No interpolation yet, each returned value is integer.		* @return {maximum, area, dist, x, y}. No interpolation yet, each returned value is integer.
	* Returns null if no local maximum within area. x,y are offsets from the (provided) center		* Returns null if no local maximum within area. x,y are offsets from the (provided) center
	*/		*/
	@@ -133,12 +134,14 @@ public class ObjectLocation {
	double [] cent_xy, // if null, use center of the square		double [] cent_xy, // if null, use center of the square
	double radius, // search for maximum within this radius		double radius, // search for maximum within this radius
	double frac_max,		double frac_max,
			double other_radius,
	int debugLevel) {		int debugLevel) {
	double [] rslt = getMaxLocArea(		double [] rslt = getMaxLocArea(
	data, // square data		data, // square data
	cent_xy, // if null, use center of the square		cent_xy, // if null, use center of the square
	radius, // search for maximum within this radius		radius, // search for maximum within this radius
	frac_max,		frac_max,
			other_radius,
	debugLevel);		debugLevel);
	if (rslt != null) {		if (rslt != null) {
	return rslt;		return rslt;
	@@ -152,6 +155,7 @@ public class ObjectLocation {
	double [] cent_xy, // if null, use center of the square		double [] cent_xy, // if null, use center of the square
	double radius, // search for maximum within this radius		double radius, // search for maximum within this radius
	double frac_max,		double frac_max,
			double other_radius,
	int debugLevel) {		int debugLevel) {
	boolean debug = debugLevel > 1;		boolean debug = debugLevel > 1;
	int size = (int) Math.sqrt(data.length);		int size = (int) Math.sqrt(data.length);
	@@ -201,8 +205,11 @@ public class ObjectLocation {
	false); // boolean ordered)		false); // boolean ordered)
	int center_cluster = clusters[best_indx];		int center_cluster = clusters[best_indx];

	double xc = best_indx % size - cent_xy[0];		int best_x = best_indx % size;
	double yc = best_indx / size - cent_xy[1];		int best_y = best_indx / size;
			double xc = best_x - cent_xy[0];
			double yc = best_y - cent_xy[1];


	double s0=0, sx=0, sy=0, sx2 = 0, sy2=0, sxy = 0;		double s0=0, sx=0, sy=0, sx2 = 0, sy2=0, sxy = 0;
	for (int i = 0; i < clusters.length; i++) {		for (int i = 0; i < clusters.length; i++) {
	@@ -233,6 +240,35 @@ public class ObjectLocation {
	double elong = Math.sqrt(eigval[1]/eigval[0]);		double elong = Math.sqrt(eigval[1]/eigval[0]);
	double eff_rad = Math.sqrt(Math.sqrt(eigval[1]*eigval[0]));		double eff_rad = Math.sqrt(Math.sqrt(eigval[1]*eigval[0]));
	double dist = Math.sqrt(cent_offs[0]cent_offs[0] + cent_offs[1]cent_offs[1]);		double dist = Math.sqrt(cent_offs[0]cent_offs[0] + cent_offs[1]cent_offs[1]);
			double max_other = 0.0;
			if (other_radius > 0) { // only calculate if asked for
			double or2 = other_radius*other_radius;
			min_x = Math.max(1, (int) Math.floor(best_x-other_radius));
			min_y = Math.max(1, (int) Math.floor(best_y-other_radius));
			max_x = Math.min(size-2, (int) Math.ceil(best_x+other_radius));
			max_y = Math.min(size-2, (int) Math.ceil(best_y+other_radius));
			for (int y = min_y; y <= max_y; y++) { // do not search on very edges
			double dy = (y-best_y);
			double y2 = dy*dy;
			if (y2 < or2) {
			for (int x = min_x; x <= max_x; x++) {
			double dx = x - best_x;
			double r2 = y2 + dx*dx;
			if (r2 < or2) {
			int indx = y * size + x;
			if (clusters[indx] != center_cluster) { // only disconnected from the central area
			double d = data[indx];
			if (d > max_other) {
			max_other = d;
			}
			}
			}
			}
			}
			}
			max_other /= best_d;
			}

	if (debug) {		if (debug) {
	System.out.println("\ncenter offset ["+(sx/s0)+","+(sy/s0)+"] , from center: ["+cent_offs[0]+","+cent_offs[1]+"]");		System.out.println("\ncenter offset ["+(sx/s0)+","+(sy/s0)+"] , from center: ["+cent_offs[0]+","+cent_offs[1]+"]");
	System.out.println("Covariance matrix:");		System.out.println("Covariance matrix:");
	@@ -241,11 +277,11 @@ public class ObjectLocation {
	eig.getV().print(8, 6);		eig.getV().print(8, 6);
	System.out.println("eig.getD()");		System.out.println("eig.getD()");
	eig.getD().print(8, 6);		eig.getD().print(8, 6);
	System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f",		System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f, mo=%5.3f",
	best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]));		best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1], max_other));
	}		}

	return new double [] {best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]} ;		return new double [] {best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1], max_other} ;
	}		}


	@@ -326,6 +362,7 @@ public class ObjectLocation {
	double min_corr,		double min_corr,
	int radius_search,		int radius_search,
	int radius_centroid,		int radius_centroid,
			double [] corr_ret, // null or double[corr_size*corr_size]
	String dbg_prefix,		String dbg_prefix,
	int debugLevel){		int debugLevel){
	int refine = 1;		int refine = 1;
	@@ -393,6 +430,9 @@ public class ObjectLocation {
	false, // final boolean convolve, // convolve, not correlate		false, // final boolean convolve, // convolve, not correlate
	phaseCoeff, // final double phaseCoeff,		phaseCoeff, // final double phaseCoeff,
	debugLevel); // final int debugLevel)		debugLevel); // final int debugLevel)
			if (corr_ret != null) {
			System.arraycopy(corr_out, 0, corr_ret, 0, corr_out.length);
			}
	int data_width = 2 *radius_search + 1;		int data_width = 2 *radius_search + 1;
	int offs = corr_size/2 - radius_search;		int offs = corr_size/2 - radius_search;

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

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -3841,7 +3841,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	if (ipix1 >= 0) {		if (ipix1 >= 0) {
	bestcorr[ipix1] = corrs[patt][ipix1];		bestcorr[ipix1] = corrs[patt][ipix1];
	if (combine_full) {		if (combine_full) {
	bestcorr[ipix1] *= corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix];		bestcorr[ipix1] *= Math.max(0, corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix]);
	}		}
	bestpatt[ipix1] = patt;		bestpatt[ipix1] = patt;
	}		}

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