Next snapshot, working onpairs selection and LMA map (2f51f8e6) · Commits · Elphel / imagej-elphel

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

+3 −1

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

+2 −1

Original line number	Original line	Diff line number	Diff line
	@@ -61,6 +61,7 @@ public class ComboMatch {
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	GPUTileProcessor gpu_tile_processor, // initialized by the caller		GPUTileProcessor gpu_tile_processor, // initialized by the caller
	boolean extract_objects,		boolean extract_objects,
			boolean manual_pair,
	int debugLevel) {		int debugLevel) {
	boolean create_kernels = debugLevel>1000;		boolean create_kernels = debugLevel>1000;
	if (create_kernels) {		if (create_kernels) {
	@@ -70,7 +71,7 @@ public class ComboMatch {
	GPU_TILE_PROCESSOR = gpu_tile_processor;		GPU_TILE_PROCESSOR = gpu_tile_processor;
	PairwiseOrthoMatch pairwiseOrthoMatch = null;		PairwiseOrthoMatch pairwiseOrthoMatch = null;
	String [] pair_names = new String[2];		String [] pair_names = new String[2];
	ImagePlus imp_sel = WindowManager.getCurrentImage();		ImagePlus imp_sel = manual_pair? WindowManager.getCurrentImage() : null;
	String [] gpu_spair = null;		String [] gpu_spair = null;
	boolean use_marked_image = false; // will be set if found		boolean use_marked_image = false; // will be set if found
	String [] all_scenes = null;		String [] all_scenes = null;

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

+136 −0

Original line number	Original line	Diff line number	Diff line
	@@ -21,9 +21,11 @@ import java.time.format.DateTimeFormatter;
	import java.util.ArrayList;		import java.util.ArrayList;
	import java.util.Arrays;		import java.util.Arrays;
	import java.util.Calendar;		import java.util.Calendar;
			import java.util.Collections;
	import java.util.HashMap;		import java.util.HashMap;
	import java.util.HashSet;		import java.util.HashSet;
	import java.util.List;		import java.util.List;
			import java.util.Set;
	import java.util.concurrent.atomic.AtomicBoolean;		import java.util.concurrent.atomic.AtomicBoolean;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;

	@@ -5230,6 +5232,19 @@ public class OrthoMapsCollection implements Serializable{
	heur = (int) gd.getNextNumber();		heur = (int) gd.getNextNumber();
	use_multi = gd.getNextBoolean();		use_multi = gd.getNextBoolean();
	double max_rmse_reuse= max_rms_refine;		double max_rmse_reuse= max_rms_refine;
			int [][] pairs_defined = filterPairs(
			indices, // int [] indices_in,
			min_overlap_frac, // double min_overlap_frac,
			max_rmse_reuse, // double max_rmse,
			true, // boolean max_resolution,
			null); // int [][] remove_pairs
			int [][] pairs_undefined = filterPairs(
			indices, // int [] indices_in,
			min_overlap_frac, // double min_overlap_frac,
			0, // max_rmse_reuse, // double max_rmse,
			false, // boolean max_resolution,
			pairs_defined); // int [][] remove_pairs
			/*
	PairsGraph pairsGraph = new PairsGraph(		PairsGraph pairsGraph = new PairsGraph(
	this, // OrthoMapsCollection orthoMapsCollection,		this, // OrthoMapsCollection orthoMapsCollection,
	indices, // int [] indices,		indices, // int [] indices,
	@@ -5237,6 +5252,13 @@ public class OrthoMapsCollection implements Serializable{
	max_rmse_reuse, // double max_rmse_reuse,		max_rmse_reuse, // double max_rmse_reuse,
	use_multi, // boolean multi,		use_multi, // boolean multi,
	debugLevel); // int debugLevel);		debugLevel); // int debugLevel);
			*/
			PairsGraph pairsGraph = new PairsGraph(
			this, // OrthoMapsCollection orthoMapsCollection,
			pairs_undefined, // int [][] undefined_pairs,
			pairs_defined, // int [][] defined_pairs,
			use_multi, // boolean multi,
			debugLevel); // int debugLevel);

	if (dry_run) {		if (dry_run) {
	return pairsGraph.dryRun(		return pairsGraph.dryRun(
	@@ -6184,4 +6206,118 @@ public class OrthoMapsCollection implements Serializable{
	ImageDtt.startAndJoin(threads);		ImageDtt.startAndJoin(threads);
	return overlaps;		return overlaps;
	}		}

			public int [][] filterPairs(
			int [] indices_in,
			double min_overlap_frac,
			double max_rmse,
			boolean max_resolution, // require defined and full resolution
			int [][] remove_pairs) {
			if (indices_in == null) {
			indices_in = new int [ortho_maps.length];
			for (int i = 0; i < indices_in.length; i++) {
			indices_in[i] = i;
			}
			}
			boolean [] used_scenes = new boolean [ortho_maps.length];
			for (int i:indices_in) {
			used_scenes[i] = true;
			}
			HashSet <Point> donotuse_set = new HashSet<Point>();
			if (remove_pairs != null) {
			for (int [] p: remove_pairs) {
			donotuse_set.add(new Point(p[0],p[1]));
			}
			}
			ArrayList<Point> pairs_list = new ArrayList<Point>();
			for (int scene0:indices_in) {
			Set<String> match_names = ortho_maps[scene0].pairwise_matches.keySet();
			ArrayList<String> names_list = new ArrayList<String>();
			names_list.addAll(match_names);
			Collections.sort(names_list);
			for (String scene1_name:names_list) {
			PairwiseOrthoMatch match = ortho_maps[scene0].getMatch(scene1_name, !max_resolution); // may be not defined only
			if (match != null) {
			int scene1 = getIndex(scene1_name);
			if ( used_scenes[scene1] && (!max_resolution \|\| match.isDefined()) &&
			(match.getOverlap() >= min_overlap_frac) &&
			((max_rmse <= 0) \|\| (match.getRMS() <= max_rmse))
			){
			if (max_resolution) {
			int min_zoom = Math.min(ortho_maps[scene0].getOriginalZoomLevel(), ortho_maps[scene1].getOriginalZoomLevel());
			if (match.getZoomLevel() < min_zoom) {
			continue;
			}
			}
			Point p = new Point(scene0, scene1);
			if (remove_pairs != null) {
			if (donotuse_set.contains(p)) {
			continue;
			}
			}
			System.out.println(String.format("%5d: %3d-%3d, %7.4f, %7.4f",
			pairs_list.size(), scene0, scene1, match.getOverlap(), match.getRMS()));
			pairs_list.add(p);
			}
			}
			}
			}
			int [][] pairs = new int [pairs_list.size()][2];
			for (int i = 0; i < pairs.length; i++) {
			Point p = pairs_list.get(i);
			pairs[i][0] = p.x;
			pairs[i][1] = p.y;
			}
			return pairs;
			}

			public int [] getScenesFromPairs(
			int [][] pairs,
			int [] indices_in) { // preselected indices or null
			boolean [] used_scenes = new boolean [ortho_maps.length];
			if (indices_in != null) {
			for (int i:indices_in) {
			used_scenes[i] = true;
			}
			}
			for (int [] p:pairs) {
			used_scenes[p[0]] = true;
			used_scenes[p[1]] = true;
			}
			int indx = 0;
			for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
			indx++;
			}
			int [] indices = new int [indx];
			indx = 0;
			for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
			indices[indx++] = i;
			}
			return indices;
			}
			/**
			* Re-index pairs to exclude scenes not present in indices[]
			* @param pairs - array of start,end absolute scene numbers
			* @param indices - ascending array of used scenes (or null - all scenes)
			* @return re-indexed pairs, indices exclude scenes that are not in indices[]
			*/
			public int [][] condensePairs(
			int [][] pairs_all,
			int [] indices) {
			if (indices == null) {
			return pairs_all;
			}
			int [] reindex = new int [ortho_maps.length];
			int [][] pairs = new int [pairs_all.length][2];
			Arrays.fill(reindex, -1);
			for (int i = 0; i < indices.length; i++) {
			reindex[indices[i]] = i;
			}
			for (int i = 0; i < pairs.length; i++) {
			pairs[i][0] = reindex[pairs_all[i][0]];
			pairs[i][1] = reindex[pairs_all[i][1]];
			}
			return pairs;
			}

	}		}

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

+62 −21

Original line number	Original line	Diff line number	Diff line
	@@ -221,6 +221,8 @@ public class OrthoMultiLMA {
	String orthoMapsCollection_path		String orthoMapsCollection_path
	) {		) {
	boolean all_pairs = true;		boolean all_pairs = true;
			double min_overlap_frac = clt_parameters.imp.pwise_overlap; // 0.25;
			double max_rms_refine = clt_parameters.imp.pwise_max_rms; // 0.35; //
	boolean move_only = clt_parameters.imp.pmap_move_only; // false;		boolean move_only = clt_parameters.imp.pmap_move_only; // false;
	boolean ignore_affines = clt_parameters.imp.pmap_ignore_affines; // false;		boolean ignore_affines = clt_parameters.imp.pmap_ignore_affines; // false;
	boolean use_inv = clt_parameters.imp.pmap_use_inv; // false;		boolean use_inv = clt_parameters.imp.pmap_use_inv; // false;
	@@ -236,6 +238,8 @@ public class OrthoMultiLMA {

	GenericJTabbedDialog gd = new GenericJTabbedDialog("Pairwise Match Parameters",1200,400);		GenericJTabbedDialog gd = new GenericJTabbedDialog("Pairwise Match Parameters",1200,400);
	gd.addCheckbox ("Use all available pairs", all_pairs, "Use all available pairs.");		gd.addCheckbox ("Use all available pairs", all_pairs, "Use all available pairs.");
			gd.addNumericField("Minimal overlap fraction", min_overlap_frac, 3,7,"", "Minimal overlap fraction.");
			gd.addNumericField("Satisfactory RMSE, final", max_rms_refine,3,7,"scaled pix", "Maximal RMSE to consider match, in scaled pixels, during refine.");
	gd.addCheckbox ("Moves only", move_only, "Moves only, no affine transform.");		gd.addCheckbox ("Moves only", move_only, "Moves only, no affine transform.");
	gd.addCheckbox ("Ignore existing affines", ignore_affines, "Start from unity matrices, ignore saved affines.");		gd.addCheckbox ("Ignore existing affines", ignore_affines, "Start from unity matrices, ignore saved affines.");
	gd.addCheckbox ("Use reversed pairs", use_inv, "Use reversed (late-early timestamps) pairs.");		gd.addCheckbox ("Use reversed pairs", use_inv, "Use reversed (late-early timestamps) pairs.");
	@@ -252,6 +256,8 @@ public class OrthoMultiLMA {
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return -1;		if (gd.wasCanceled()) return -1;
	all_pairs = gd.getNextBoolean();		all_pairs = gd.getNextBoolean();
			min_overlap_frac = gd.getNextNumber();
			max_rms_refine = gd.getNextNumber();
	move_only = gd.getNextBoolean();		move_only = gd.getNextBoolean();
	ignore_affines = gd.getNextBoolean();		ignore_affines = gd.getNextBoolean();
	use_inv = gd.getNextBoolean();		use_inv = gd.getNextBoolean();
	@@ -270,6 +276,10 @@ public class OrthoMultiLMA {
	maps_collection, // OrthoMapsCollection maps_collection,		maps_collection, // OrthoMapsCollection maps_collection,
	orthoMapsCollection_path, // String orthoMapsCollection_path,		orthoMapsCollection_path, // String orthoMapsCollection_path,
	all_pairs, // boolean all_pairs,		all_pairs, // boolean all_pairs,
			// filtering of the pairs
			min_overlap_frac, // double min_overlap_frac,
			max_rms_refine, // double max_rms,

	move_only, // boolean move_only,		move_only, // boolean move_only,
	ignore_affines, // boolean ignore_affines,		ignore_affines, // boolean ignore_affines,
	use_inv, // boolean use_inv,		use_inv, // boolean use_inv,
	@@ -288,6 +298,9 @@ public class OrthoMultiLMA {
	OrthoMapsCollection maps_collection,		OrthoMapsCollection maps_collection,
	String orthoMapsCollection_path,		String orthoMapsCollection_path,
	boolean all_pairs,		boolean all_pairs,
			double min_overlap_frac,
			double max_rms,

	boolean move_only,		boolean move_only,
	boolean ignore_affines,		boolean ignore_affines,
	boolean use_inv,		boolean use_inv,
	@@ -304,6 +317,7 @@ public class OrthoMultiLMA {
	boolean corr_avg= (skew_pull > 0) \|\| (tilt_pull > 0) \|\| (scale_pull > 0);		boolean corr_avg= (skew_pull > 0) \|\| (tilt_pull > 0) \|\| (scale_pull > 0);
	int [] indices = null;		int [] indices = null;
	if (all_pairs) {		if (all_pairs) {
			/*
	boolean [] used_scenes = new boolean [maps_collection.ortho_maps.length];		boolean [] used_scenes = new boolean [maps_collection.ortho_maps.length];
	for (int scene0 = 0; scene0 < (used_scenes.length-1); scene0++) {		for (int scene0 = 0; scene0 < (used_scenes.length-1); scene0++) {
	Set<String> match_names = maps_collection.ortho_maps[scene0].pairwise_matches.keySet();		Set<String> match_names = maps_collection.ortho_maps[scene0].pairwise_matches.keySet();
	@@ -328,11 +342,25 @@ public class OrthoMultiLMA {
	if (debugLevel > -1) {		if (debugLevel > -1) {
	System.out.println("buildOrthoMap(): got "+indices.length+" scenes with pairs");		System.out.println("buildOrthoMap(): got "+indices.length+" scenes with pairs");
	}		}
			*/
	} else {		} else {
	indices = maps_collection.getScenesSelection(		indices = maps_collection.getScenesSelection(
	null, // boolean select_all,		null, // boolean select_all,
	" to build a map with LMA from pair-wise matches"); // String purpose)		" to build a map with LMA from pair-wise matches"); // String purpose)
	}		}

			int [][] pairs_defined_abs = maps_collection.filterPairs( // absolute indices
			indices, // int [] indices_in,
			min_overlap_frac, // double min_overlap_frac,
			max_rms, // double max_rmse,
			true, // boolean max_resolution,
			null); // int [][] remove_pairs
			indices= maps_collection.getScenesFromPairs(
			pairs_defined_abs,// int [][] pairs,
			null); // int [] indices_in) // preselected indices or null
			int [][] defined_pairs = maps_collection.condensePairs (pairs_defined_abs,indices);


	OrthoMultiLMA oml = new OrthoMultiLMA(		OrthoMultiLMA oml = new OrthoMultiLMA(
	corr_avg,		corr_avg,
	move_only);		move_only);
	@@ -345,6 +373,7 @@ public class OrthoMultiLMA {
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
	maps_collection, // OrthoMapsCollection maps_collection,		maps_collection, // OrthoMapsCollection maps_collection,
	indices, // int [] indices,		indices, // int [] indices,
			defined_pairs, // int [][] pairs, // or null? condensed
	ignore_affines, // boolean ignore_affines,		ignore_affines, // boolean ignore_affines,
	val_coord, // double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors		val_coord, // double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
	position_pull, // double position_pull,		position_pull, // double position_pull,
	@@ -442,6 +471,7 @@ public class OrthoMultiLMA {
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	OrthoMapsCollection maps_collection,		OrthoMapsCollection maps_collection,
	int [] indices,		int [] indices,
			int [][] pairs_pre, // or null?
	boolean ignore_affines,		boolean ignore_affines,
	double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors		double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
	double position_pull,		double position_pull,
	@@ -456,6 +486,16 @@ public class OrthoMultiLMA {
	matches = new PairwiseOrthoMatch[indices.length][indices.length];		matches = new PairwiseOrthoMatch[indices.length][indices.length];
	ArrayList<Point> pairs_list = new ArrayList<Point>();		ArrayList<Point> pairs_list = new ArrayList<Point>();
	// ArrayList<Double> offset_list = new ArrayList<Double>();		// ArrayList<Double> offset_list = new ArrayList<Double>();
			if (pairs_pre != null) {
			for (int [] pair:pairs_pre) {
			int i = pair[0], j = pair[1];
			int scene0=indices[i],scene1=indices[j];
			PairwiseOrthoMatch match = maps_collection.ortho_maps[scene0].getMatch(maps_collection.ortho_maps[scene1].getName());
			matches[i][j] = match;
			// matches[j][i] = inv_match;
			pairs_list.add(new Point(i,j)); // only once?
			}
			} else {
	for (int i = 0; i < num_scenes-1; i++) {		for (int i = 0; i < num_scenes-1; i++) {
	int scene0 = indices[i];		int scene0 = indices[i];
	for (int j = i+1; j < num_scenes; j++){		for (int j = i+1; j < num_scenes; j++){
	@@ -482,6 +522,7 @@ public class OrthoMultiLMA {
	}		}
	}		}
	}		}
			}
	num_pairs = pairs_list.size();		num_pairs = pairs_list.size();
	offsets = new double [num_pairs][2];		offsets = new double [num_pairs][2];
	pairs = new int[num_pairs][2];		pairs = new int[num_pairs][2];

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

+45 −0

Original line number	Original line	Diff line number	Diff line
	@@ -54,6 +54,7 @@ public class PairsGraph {
	private final int debugLevel;		private final int debugLevel;
	private boolean multi; // use single-threaded in debug mode?		private boolean multi; // use single-threaded in debug mode?


	public PairsGraph (		public PairsGraph (
	OrthoMapsCollection orthoMapsCollection,		OrthoMapsCollection orthoMapsCollection,
	int [] indices,		int [] indices,
	@@ -121,6 +122,50 @@ public class PairsGraph {
	}		}
	}		}


			public PairsGraph (
			OrthoMapsCollection orthoMapsCollection,
			int [][] undefined_pairs_all, // indices in orthoMapsCollection.ortho_maps[] (all scenes, not just selected)
			int [][] defined_pairs_all, // indices in orthoMapsCollection.ortho_maps[] (all scenes, not just selected)
			boolean multi,
			int debugLevel) {
			this.orthoMapsCollection = orthoMapsCollection;
			int [] indices0 = orthoMapsCollection.getScenesFromPairs(undefined_pairs_all, null);
			this.indices = orthoMapsCollection.getScenesFromPairs(defined_pairs_all, indices0);
			int [][] undefined_pairs = orthoMapsCollection.condensePairs (undefined_pairs_all,indices);
			int [][] defined_pairs = orthoMapsCollection.condensePairs (defined_pairs_all,indices);
			this.debugLevel = debugLevel;
			this.multi = multi;
			pair_state = new int [indices.length][indices.length];
			overlaps = new double [indices.length][indices.length];
			timestamps = new double [indices.length];
			groups = new int [indices.length];
			dist = new int [indices.length][indices.length];
			OrthoMap [] ortho_maps=orthoMapsCollection.getMaps();
			for (int i = 0; i < indices.length; i++) {
			groups[i] = i;
			timestamps[i] = ortho_maps[indices[i]].getTimeStamp();
			}

			for (int [] u_pair: undefined_pairs) {
			pair_state[u_pair[0]][u_pair[0]] = PAIR_UNDEFINED;
			}
			for (int [] d_pair: defined_pairs) {
			pair_state[d_pair[0]][d_pair[0]] = PAIR_DEFINED;
			recordPair(
			d_pair, // int [] pair,
			true, // boolean success,
			multi);
			}
			pairs = multi? getPairsIndicesMulti():getPairsIndicesSingle();
			if (debugLevel > -1) {
			System.out.println("Number of scenes - "+indices.length);
			System.out.println("Number of defined pairs - "+defined_pairs.length);
			System.out.println("Number of undefined pairs - "+undefined_pairs.length);
			System.out.println("Number of disconnected groups - "+getNumberOfGroups());
			}
			}

	public int getNumberOfGroups() {		public int getNumberOfGroups() {
	HashSet<Integer> hs = new HashSet<Integer>();		HashSet<Integer> hs = new HashSet<Integer>();
	for (int i:groups) {		for (int i:groups) {

Original line number	Original line	Diff line number	Diff line
	@@ -849,6 +849,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	addButton("Read Tiff", panelLWIRWorld, color_process);		addButton("Read Tiff", panelLWIRWorld, color_process);
	addButton("Test video", panelLWIRWorld, color_process);		addButton("Test video", panelLWIRWorld, color_process);
	addButton("Ortho Pairs", panelLWIRWorld, color_process);		addButton("Ortho Pairs", panelLWIRWorld, color_process);
			addButton("Manual pair", panelLWIRWorld, color_process);
	addButton("Extract Objects", panelLWIRWorld, color_process);		addButton("Extract Objects", panelLWIRWorld, color_process);
	addButton("Mismatched resolutions", panelLWIRWorld, color_process);		addButton("Mismatched resolutions", panelLWIRWorld, color_process);
	addButton("Generate DATI", panelLWIRWorld, color_process);		addButton("Generate DATI", panelLWIRWorld, color_process);
	@@ -5709,7 +5710,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	e.printStackTrace();		e.printStackTrace();
	}		}
	// ComboMatch.testReadTiff();		// ComboMatch.testReadTiff();
	} else if (label.equals("Ortho Pairs") \|\| label.equals("Extract Objects")) {		} else if (label.equals("Ortho Pairs") \|\| label.equals("Extract Objects") \|\| label.equals("Manual pair")) {
	DEBUG_LEVEL = MASTER_DEBUG_LEVEL;		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	if (GPU_TILE_PROCESSOR == null) {		if (GPU_TILE_PROCESSOR == null) {
	@@ -5731,6 +5732,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	CLT_PARAMETERS, // CLTParameters clt_parameters,		CLT_PARAMETERS, // CLTParameters clt_parameters,
	GPU_TILE_PROCESSOR,		GPU_TILE_PROCESSOR,
	label.equals("Extract Objects"), // boolean extract_mines,		label.equals("Extract Objects"), // boolean extract_mines,
			label.equals("Manual pair"), // boolean manual_pair,
	DEBUG_LEVEL);		DEBUG_LEVEL);
	} else if (label.equals("Test video")) {		} else if (label.equals("Test video")) {
	ImagePlus imp_sel = WindowManager.getCurrentImage();		ImagePlus imp_sel = WindowManager.getCurrentImage();

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