Commit 6b986720 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Automatic matching of multiple scene sets

parent ba9466e1

src/main/java/com/elphel/imagej/calibration/CalibrationFileManagement.java

+12 −4
Original line number Diff line number Diff line
@@ -8,6 +8,7 @@ import javax.swing.JFileChooser; 
import javax.swing.filechooser.FileFilter;



import ij.IJ;

import ij.Prefs;

import ij.io.OpenDialog;
@@ -187,6 +188,13 @@ public class CalibrationFileManagement { 
	  }

	  

	  public static void saveStringToFile (String path,String data, boolean append){

		  int dir_sep = path.lastIndexOf(Prefs.getFileSeparator());

		  if (dir_sep >=0) { // create directory if it does not exist

			  File dir = new File(path.substring(0, dir_sep));

			  if (!dir.exists()) {

				  dir.mkdirs();

			  }

		  }

		  BufferedWriter writer = null;

		  try  {

			  writer = new BufferedWriter( new FileWriter( path, append));

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

+140 −48
Original line number Diff line number Diff line
@@ -3,13 +3,18 @@ package com.elphel.imagej.orthomosaic; 
import java.awt.Point;

import java.awt.Rectangle;

import java.io.IOException;

import java.text.SimpleDateFormat;

import java.time.LocalDateTime;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Calendar;

import java.util.Collections;

import java.util.Comparator;

import java.util.Properties;

import java.util.Random;

import java.util.concurrent.atomic.AtomicInteger;



import com.elphel.imagej.calibration.CalibrationFileManagement;

import com.elphel.imagej.cameras.CLTParameters;

import com.elphel.imagej.cameras.ColorProcParameters;

import com.elphel.imagej.cameras.EyesisCorrectionParameters;
@@ -28,6 +33,7 @@ import com.elphel.imagej.tileprocessor.TDCorrTile; 
import Jama.Matrix;

import ij.ImagePlus;

import ij.ImageStack;

import ij.Prefs;

import ij.WindowManager;

import ij.gui.PointRoi;

import ij.process.FloatPolygon;
@@ -166,12 +172,16 @@ public class ComboMatch { 
		boolean bounds_to_indices =   true;

		int     temp_mode =           1;

		boolean restore_temp =        true;

		double  frac_remove  =        0.15;

		double  metric_error =        0.05; // 0.02;//  2 cm

		double  frac_remove  =        clt_parameters.imp.pmtch_frac_remove; //   0.15;

		double  metric_error =        clt_parameters.imp.pmtch_metric_err; // 0.05; // 0.02;//  2 cm

		boolean update_lla =          false; // re-read file metadata

		boolean update_kernel_patterns = false;

		boolean update_bl_bc =        false;

		String [] suffixes_bl_bc=     {"","-BL","-BC"};

		boolean log_append =           clt_parameters.imp.pwise_log_append;

		String log_path =              clt_parameters.imp.pwise_log_path;

		

		

		int  suffix_bc_bl_indx =   2;

		if (!use_marked_image) {

			process_correlation=false; // use already adjusted by default
@@ -182,7 +192,7 @@ public class ComboMatch { 
		}

		

		

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,600);

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,700);

		gd.addChoice      ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[default_list_choice]);

		gd.addCheckbox    ("Use saved maps collection", use_saved_collection, "If false - use files list.");

		gd.addCheckbox    ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
@@ -235,6 +245,8 @@ public class ComboMatch { 
				suffixes_bl_bc,

				suffixes_bl_bc[suffix_bc_bl_indx],

				"Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);

	    gd.addCheckbox    ("Write log file",         log_append, "Enable writing log file with matching results.");

	    gd.addStringField ("Log file full path",     log_path, 150, "Path of the log file to be appended.");
@@ -282,6 +294,8 @@ public class ComboMatch { 
		update_kernel_patterns=     gd.getNextBoolean();

		update_bl_bc=               gd.getNextBoolean();

		suffix_bc_bl_indx =         gd.getNextChoiceIndex();

		log_append =                gd.getNextBoolean();

		log_path =                  gd.getNextString();

		OrthoMapsCollection maps_collection=null;

		if (use_saved_collection) {

			try {
@@ -656,37 +670,6 @@ public class ComboMatch { 
					output_patt_titles); // test_titles,

			imp_inv_patt.show();

			

// select kernel and correlatde with every cut image?			

			

			

			// Test invert patterns

			/*

			

			boolean test_invert = debugLevel > -1000;

			if (test_invert) {

				double invert_fz = 0;

				double [][] inverted_patterns = new double [output_patterns.length][];

				for (int i = 0; i < output_patterns.length; i++) {

					inverted_patterns[i] = output_patterns[i].clone();

					double [] dfr = new double [corr_size*corr_size];

					dfr[corr_size/2*(corr_size+1)] = corr_size*corr_size;

					double [][] data_pair = new double[][] {inverted_patterns[i],dfr};

					inverted_patterns[i]=OrthoMap.deconvolvePair(

							data_pair,

							invert_fz,

							1);





				}

				ImagePlus imp_inv_patt = ShowDoubleFloatArrays.makeArrays(

						inverted_patterns,

						corr_size,

						corr_size,

						OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-INV_PATTERN"+settings_str+"_"+corr_size+"x"+corr_size+".tiff",				

						output_patt_titles); // test_titles,

				imp_inv_patt.show();

			}

			*/

			ImagePlus imp_out_patt = ShowDoubleFloatArrays.makeArrays(

					output_patterns,

					corr_size,
@@ -765,8 +748,30 @@ public class ComboMatch { 
			maps_collection.processComboMap(debugLevel);

			return true;

		}

		

		// for all modes - needed for create_overlaps || process_correlation || render_match || pattern_match

    	if (GPU_QUAD_AFFINE == null) {

        	System.out.println("Setting up GPU");

    		try {

    			GPU_QUAD_AFFINE = new GpuQuad(//

    					GPU_TILE_PROCESSOR,   // GPUTileProcessor gpuTileProcessor,

    					gpu_max_width,        // final int        max_width,

    					gpu_max_height,       // final int        max_height,

    					1,                    // final int        num_colors, // normally 1?

    					clt_parameters.gpu_debug_level);

    		} catch (Exception e) {

    			System.out.println("Failed to initialize GpuQuad class");

    			// TODO Auto-generated catch block

    			e.printStackTrace();

    			return false;

    		} // final int debugLevel);

    	}



		

		if (create_overlaps) {

			boolean ok =maps_collection.getIntersectedPairs(debugLevel);

			boolean ok =maps_collection.getIntersectedPairs(

					clt_parameters, // CLTParameters    clt_parameters,

					orthoMapsCollection_path); // String orthoMapsCollection_path);

			if (!ok) return false;

		}

        if (process_correlation || render_match || pattern_match) {
@@ -780,6 +785,17 @@ public class ComboMatch { 
        						maps_collection.getIndex(other_name)));

        			}

        		}

        		// sort pairs_list by x then y

        		Collections.sort(pairs_list, new Comparator<Point>() {

        			@Override

        			public int compare(Point lhs, Point rhs) {

        				return (rhs.x > lhs.x) ? -1 : (rhs.x < lhs.x) ? 1 :

        					((rhs.y > lhs.y) ? -1 : (rhs.y < lhs.y) ? 1 : 0); // increasing

        			}

        		});

        		

        		

        		

        		int [][] available_pairs = new int [pairs_list.size()][2];

        		for (int i = 0; i < available_pairs.length; i++) {

        			available_pairs[i][0] = pairs_list.get(i).x;
@@ -803,7 +819,7 @@ public class ComboMatch { 
				if (pair >= choices.length) {

					int default_choice = 0;

					int num_scene_lines = 50;

					if (process_correlation) { // select a second image to match

					if (process_correlation || render_match) { // select a second image to match

						// select a second image and set gpu_spair

						int default_choice1 = 0;

						gpu_spair = maps_collection.selectTwoScenes(
@@ -843,9 +859,9 @@ public class ComboMatch { 
        	double agl_ratio = max_agl/50.0;

        	double metric_error_adj = metric_error * agl_ratio * agl_ratio; // metric_error settings is good for 50m. Increase for higher Maybe squared?

        	int initial_zoom = max_zoom_lev - 4;  // another algorithm?



        	System.out.println("Setting up GPU");

/*

        	if (GPU_QUAD_AFFINE == null) {

            	System.out.println("Setting up GPU");

        		try {

        			GPU_QUAD_AFFINE = new GpuQuad(//

        					GPU_TILE_PROCESSOR,   // GPUTileProcessor gpuTileProcessor,
@@ -860,6 +876,7 @@ public class ComboMatch { 
        			return false;

        		} // final int debugLevel);

        	}

*/        	

    		double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same

    		double [][] affine1 = null;
@@ -901,7 +918,7 @@ public class ComboMatch { 
        			affine1 = pairwiseOrthoMatch.getAffine();

        			double [][][] affines = {affine0,affine1};

        			int [] zooms = {initial_zoom, min_zoom_lev, 1000,1000}; // make automatic

        			double scale = 2.0; // scale vectors when warping;

//        			double scale = 2.0; // scale vectors when warping;

        			//				int num_tries  = 5; // make configurable

        			if (!process_correlation || !use_marked_image) { // skip low-res

        				zooms = new int[] {min_zoom_lev, 1000};
@@ -912,12 +929,17 @@ public class ComboMatch { 
        			}

 //       			debugLevel = 0;

        			boolean  batch_mode = true; // false; //  true;

        			boolean ignore_prev_rms = true;

        			

        			boolean ignore_prev_rms = clt_parameters.imp.pmtch_ignore_rms; // true;

        			Rectangle woi = new Rectangle(); // used to return actual woi from correlateOrthoPair()

        			double [][] ground_planes = null;

					double           max_std = 1.5;      // maximal standard deviation to limit center area  

					double           min_std_rad = 2.0;  // minimal radius of the central area (if less - fail)



					double      max_std =             clt_parameters.imp.pmtch_max_std;     // 1.5;      // maximal standard deviation to limit center area  

					double      min_std_rad =         clt_parameters.imp.pmtch_min_std_rad; // 2.0;  // minimal radius of the central area (if less - fail)

					double      rad_fraction =        clt_parameters.imp.pmtch_cent_rad;    // center circle radius fraction of 0.5* min(width, height) in tiles

					double      max_tile_rad =        clt_parameters.imp.pmtch_max_cent_rad;// maximal center radius in tiles (limit pmtch_cent_rad)

					double      fill_fraction =       clt_parameters.imp.pmtch_cent_fill;   // should be populated not less than this

					double      fill_fraction_final = clt_parameters.imp.pmtch_cent_final;  // should be populated not less than this during final pass

					double      ease_nosfm =          clt_parameters.imp.pmtch_ease_nosfm;  // ease metric_error when no SfM gain == 0;

        			for (int zi = 0; zi < zooms.length; zi++) {

        				zoom_lev = zooms[zi];

        				if (zoom_lev >=1000) {
@@ -947,6 +969,12 @@ public class ComboMatch { 
        						zoom_lev,        // int              zoom_lev,

        						show_vf,         // boolean show_vf,

        						ground_planes,   // double [][]      ground_planes, // null or double[2] - will return ground planes

        						rad_fraction,    // double           rad_fraction,

        						max_tile_rad,    // double           max_tile_rad, //  = 30;

        						fill_fraction,   // double           fill_fraction,

        						fill_fraction_final, // double           fill_fraction_final,

        						ease_nosfm,      // double           ease_nosfm,

        						null,            // double []        max_rms_iter, //  = {1.0, 0.6};//        						

        						debugLevel);     // final int        debugLevel)

        				if ((warp == null) || ((pmatch != null) &&  Double.isNaN(pmatch.rms))) {

        					System.out.println("Failed correlateOrthoPair()");
@@ -978,6 +1006,16 @@ public class ComboMatch { 
        						}

        						System.out.println();

        					}

        					if (log_append && (log_path != null)) { // assuming directory exists

        						StringBuffer sb = new StringBuffer();

        						sb.append(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+"\n");

        						sb.append(String.format("%d\t%d", gpu_pair[0], gpu_pair[1]));

        						sb.append(String.format("\t%6.4f\t%d\n", pairwiseOrthoMatch.rms, pairwiseOrthoMatch.zoom_lev));

        						CalibrationFileManagement.saveStringToFile (

        								log_path,          //String path,

        								sb.toString(), // data,

        								true); // boolean append)

        					}

        				}



        				if (pattern_match) {
@@ -1053,8 +1091,19 @@ public class ComboMatch { 
		int    min_overlap =           clt_parameters.imp.ospir_overlap;  // 3000; // do not try to match if there is too small overlap (scaled pixels)

		int    num_iter_lma =          clt_parameters.imp.ospir_num_iter; // 5;

		boolean ignore_rms =           clt_parameters.imp.ospir_ignore_rms; // false

		int    spiral_debug =          clt_parameters.imp.ospir_debug;    // -3;

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Setup SpiralMatch",1200,300);

		int    spiral_debug =          clt_parameters.imp.ospir_debug;    // 0;

		boolean log_append =           clt_parameters.imp.pwise_log_append;

		String log_path =              clt_parameters.imp.pwise_log_path;

		

		double      max_std =             clt_parameters.imp.pmtch_max_std;    // 1.5;      // maximal standard deviation to limit center area  

		double      min_std_rad =         clt_parameters.imp.pmtch_min_std_rad;// 2.0;  // minimal radius of the central area (if less - fail)

		double      rad_fraction =        clt_parameters.imp.pmtch_cent_rad; // center circle radius fraction of 0.5* min(width, height) in tiles

		double      max_tile_rad =        clt_parameters.imp.pmtch_max_cent_rad;// maximal center radius in tiles (limit pmtch_cent_rad)

		double      fill_fraction =       clt_parameters.imp.pmtch_cent_fill; // should be populated not less than this

		double      fill_fraction_final = clt_parameters.imp.pmtch_cent_final; // should be populated not less than this during final pass

		double      ease_nosfm =          clt_parameters.imp.pmtch_ease_nosfm; // ease metric_error when no SfM gain == 0;

		

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Setup Spiral Match",1200,350);

		if (pairwiseOrthoMatch != null) {

			gd.addCheckbox    ("Use existing image pair",  use_existing_pair, "Use existing affine settings for this pair, do not use spiral search.");

		} else {
@@ -1072,8 +1121,20 @@ public class ComboMatch { 
		gd.addNumericField("Minimal overlap",        min_overlap,  0,4,"scaled pix ^ 2","Minimal overlap area in square scaled pixels.");

		gd.addNumericField("LMA iterations",         num_iter_lma, 0,2,"",              "Number of LMA iterations.");

		gd.addCheckbox    ("Ignore worsening RMSE",  ignore_rms, "Ignore worsening/not improving RMSE during spiral search.");

	    gd.addCheckbox    ("Write log file",         log_append, "Enable writing log file with matching results.");

	    gd.addStringField ("Log file full path",     log_path, 150, "Path of the log file to be appended.");	

		gd.addNumericField("Spiral search debug level",spiral_debug, 0,3,"","Debug level during Spiral search.");

		

		gd.addMessage("Parameters, common to all matching, not only spiral");

		gd.addNumericField("Central area standard deviation",  max_std,  3,7,"",	"Central area limit by the standard deviation.");

		gd.addNumericField("Central area minimal radius",      min_std_rad,  3,7,"tile",	"Minimal radius of the central area after all LMA passes.");

		gd.addNumericField("Central area radius as fraction",  rad_fraction,   3,7,"",	"Central area radius as fraction of half minimal WOI dimension.");

		gd.addNumericField("Maximal central area radius",      max_tile_rad,   3,7,"tiles",	"Absolute limit to the center area radius (eases bad peripheral matching).");

		gd.addNumericField("Central area minimal fill",        fill_fraction,  3,7,"",	"Central area minimal fill for all but the last iteration.");

		gd.addNumericField("Central area minimal fill final",  fill_fraction_final, 3,7,"",	"Central area minimal fill for the last iteration.");

		gd.addNumericField("Relax metric error for no-SfM",    ease_nosfm, 3,7,"",	"Relax metric error for no-SfM scenes (sfm_gain==0).");

		

		

		gd.showDialog();

		if (gd.wasCanceled()) return null;

		if (pairwiseOrthoMatch != null) {
@@ -1089,7 +1150,18 @@ public class ComboMatch { 
		min_overlap =        (int) gd.getNextNumber();

		num_iter_lma =       (int) gd.getNextNumber();

		ignore_rms =               gd.getNextBoolean();

		log_append =               gd.getNextBoolean();

		log_path =                 gd.getNextString();

		spiral_debug =       (int) gd.getNextNumber();

		search_step=               gd.getNextNumber();

		max_std=                   gd.getNextNumber();

		min_std_rad=               gd.getNextNumber();

		rad_fraction=              gd.getNextNumber();

		max_tile_rad   =           gd.getNextNumber();

		fill_fraction=             gd.getNextNumber();

		fill_fraction_final=       gd.getNextNumber();

		ease_nosfm=                gd.getNextNumber();

		

		if (use_existing_pair) {

			if (invert_exixting_pair) {

				System.out.println("Both direct and inverted matches are selected, using direct match");
@@ -1104,11 +1176,17 @@ public class ComboMatch { 
		double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same

		double [][] affine1 = {{1,0,0},{0,1,0}}; // here (manual mode) start from the center, may use prediction in auto

		double [][][] affines = new double[][][] {affine0,affine1};



		pairwiseOrthoMatch = maps_collection.SpiralMatch (

				clt_parameters,  // CLTParameters    clt_parameters,

				frac_remove,     // double           frac_remove, //  =        0.25

				metric_error,    // double           metric_error,

				max_std,         // double           max_std,     // maximal standard deviation to limit center area  

				min_std_rad,     // double           min_std_rad, // minimal radius of the central area (if less - fail)

				rad_fraction,    // double           rad_fraction,

				max_tile_rad,    //double           max_tile_rad, //  = 30;			

				fill_fraction,   // double           fill_fraction,

				fill_fraction_final, // double           fill_fraction_final,

				ease_nosfm,      // double           ease_nosfm,

				gpu_pair,        // int []           gpu_pair,

				affines,         // double [][][]    affines_init,  // here in meters, relative to vertical points

				initial_zoom,    // int              zoom_lev,
@@ -1119,12 +1197,26 @@ public class ComboMatch { 
				num_iter_lma,    // int              num_tries, //  = 5

				min_overlap,     // int              min_overlap, // 3000

				ignore_rms,      // boolean          ignore_rms,

				null,//double []        max_rms_iter, //  = {1.0, 0.6};//

				spiral_debug);     // int              debugLevel){

		if (log_append && (log_path != null)) { // assuming directory exists

			StringBuffer sb = new StringBuffer();

			sb.append(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+"\n");

			sb.append(String.format("%d\t%d", gpu_pair[0], gpu_pair[1]));

			if ((pairwiseOrthoMatch != null) && !Double.isNaN(pairwiseOrthoMatch.rms)) {

				sb.append(String.format("\t%d\t%d\t%6.4f\t%d\n",

						pairwiseOrthoMatch.nxy[0], pairwiseOrthoMatch.nxy[1], pairwiseOrthoMatch.rms, pairwiseOrthoMatch.zoom_lev));

			} else {

				sb.append("\tFAILED");

			}

			CalibrationFileManagement.saveStringToFile (

					log_path,          //String path,

					sb.toString(), // data,

					true); // boolean append)

		}

		return pairwiseOrthoMatch;

	}

	

	

	

	public static boolean updateBlBcFileNames(

			String suffix,

			String before,

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

+7 −0
Original line number Diff line number Diff line
@@ -191,6 +191,13 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{ 
			PairwiseOrthoMatch match) {

		pairwise_matches.put(name, match);

	}



	public void unsetMatch(

			String name) {

		pairwise_matches.remove(name);

	}



	

	public PairwiseOrthoMatch getMatch(String name) {

		return pairwise_matches.get(name);

	}