Commit d3389b58 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

More on quaternions - affines

parent 0abd52b8

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

+63 −8
Original line number Diff line number Diff line
@@ -177,7 +177,7 @@ public class ComboMatch { 
		

		

		boolean use_saved_collection = true; // false;

		boolean save_collection =     true;

		boolean save_collection =     false; // true;

		boolean process_correlation = true; // use false to save new version of data

		int     num_tries_fit =       10;

		boolean update_match =        true; // use false to save new version of data
@@ -210,7 +210,7 @@ public class ComboMatch { 
			pattern_match = false;

		}

		

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);

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

		gd.addChoice      ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, omtch_img_set);

		gd.addCheckbox    ("Use saved maps collection ", use_saved_collection, " (if available). If false - use files list.");
@@ -433,7 +433,7 @@ public class ComboMatch { 
					};

			

			

			GenericJTabbedDialog gdo = new GenericJTabbedDialog("Set image pair",1200,900);

			GenericJTabbedDialog gdo = new GenericJTabbedDialog("Set image pair",1200,1000);

			gdo.addNumericField("Correlation size",          corr_size,       0,4,"",

					"Correlation size, power of 2");

			gdo.addNumericField("Extracted size",            extr_size,  0,4,"",
@@ -858,6 +858,12 @@ public class ComboMatch { 
		}

        if (process_correlation || render_match || pattern_match || test_multi_lma) {

//        	int [] gpu_pair;

			boolean removeTilt =   false;

			boolean removeRot =    false;

			boolean removeScale =  false;

			boolean removeOffset = false;

			boolean max_is_scale = false;



        	if (gpu_spair == null) {

        		ArrayList<Point> pairs_list = new ArrayList<Point>(); 

        		for (OrthoMap map : maps_collection.ortho_maps) {
@@ -905,7 +911,7 @@ public class ComboMatch { 
        		boolean flt_show_alt =       clt_parameters.imp.flt_show_alt;      //  true;

        		boolean flt_update_config = false;

        		String  flt_extra_line =    "--- select a single image ---";

				GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,500);

				GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,600);

				gdf.addCheckbox    ("Filter pairs",                flt_list, "Filter available pairs.");

				gdf.addCheckbox    ("Keep undefined pairs only",   flt_undef_only, "Keep only undefined pairs (affines== null).");

				gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap,  3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
@@ -999,15 +1005,27 @@ public class ComboMatch { 
						false,             // boolean          use_tab,

						flt_extra_line);   // String           extra_line)

				

				GenericJTabbedDialog gdc = new GenericJTabbedDialog("Select image pair",1200,100);

				GenericJTabbedDialog gdc = new GenericJTabbedDialog("Select image pair",1200,300);

				int num_choice_lines = 50;

				gdc.addChoice("Image pair:",

						choices_all,

						choices_all[choices_all.length - 1], // -1],

						"Select processed image pair or request a single image selection", num_choice_lines);

				gdc.addCheckbox    ("Remove tilt",             removeTilt,   "Remove tilts from the pairwise affine transform.");

				gdc.addCheckbox    ("Remove Rotation",         removeRot,    "Remove rotation from the pairwise affine transform.");

				gdc.addCheckbox    ("Remove Scale",            removeScale,  "Remove scale from the pairwise affine transform.");

				gdc.addCheckbox    ("Remove Translation",      removeOffset, "Remove translation from the pairwise affine transform.");

				gdc.addCheckbox    ("Max eigenvalue is scale", max_is_scale, "Maximal eigenvalue is scale (false - minimal is).");

				//        			boolean max_is_scale = false;



				gdc.showDialog();

				if (gdc.wasCanceled()) return false;

				int pair=      gdc.getNextChoiceIndex();

				removeTilt =   gdc.getNextBoolean();

				removeRot =    gdc.getNextBoolean();

				removeScale =  gdc.getNextBoolean();

				removeOffset = gdc.getNextBoolean();

				max_is_scale = gdc.getNextBoolean();

				if (pair >= (choices_all.length -1)) {

					int default_choice = 0;

					int num_scene_lines = 50;
@@ -1118,7 +1136,36 @@ public class ComboMatch { 
        			

        			

        		} else {

        			affine1 = pairwiseOrthoMatch.getAffine();

        			affine1 = pairwiseOrthoMatch.getAffine().clone();

        			if (debugLevel > -4) {

            			System.out.println("removeTilt="+  removeTilt);

            			System.out.println("removeRot="+   removeRot);

            			System.out.println("removeScale="+ removeScale);

            			System.out.println("removeOffset="+removeOffset);

            			System.out.println("max_is_scale="+max_is_scale);

            			if (removeTilt || removeRot || removeScale || removeOffset) {

                			SingularValueDecomposition svd_affine_pair =  SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine1, true); // y_down_ccw); // boolean y_down_ccw)

                			System.out.println("Full (original) affine transform:");

            	        	System.out.println(QuatUtils.affinesToString(affine1, "full_affine"));

            	        	System.out.println("full_affine_svd" + svd_affine_pair.toString(true)); // use_degrees));

            			}

        			}

        			affine1 = SingularValueDecomposition.removeTiltRotScale(

        					affine1,       // double [][] A,

        					removeTilt,    // boolean removeTilt,

        					removeRot,     // boolean removeRot,

        					removeScale,   // boolean removeScale,

        					removeOffset,  // boolean removeOffset)

        					max_is_scale); //boolean max_is_scale)

        			if (debugLevel > -4) {

            			if (removeTilt || removeRot || removeScale || removeOffset) {

                			SingularValueDecomposition svd_affine_pair =  SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine1, true); // y_down_ccw); // boolean y_down_ccw)

                			System.out.println("Final differential affine transform:");

            	        	System.out.println(QuatUtils.affinesToString(affine1, "affine1    "));

            	        	System.out.println("affine1_svd    " + svd_affine_pair.toString(true)); // use_degrees));

            			}

        			}

        			

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

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

//        			double scale = 2.0; // scale vectors when warping;
@@ -1239,6 +1286,14 @@ public class ComboMatch { 
        				}

        				if (render_match) {

        					String title=String.format("multi_%03d-%03d_%s-%s_zoom%d_%d",gpu_pair[0],gpu_pair[1],gpu_spair[0],gpu_spair[1],min_zoom_lev,zoom_lev);

        					if (removeTilt || removeRot || removeScale || removeOffset) {

        						title += "_no-";

        						if (removeTilt)   title += "T";

        						if (removeRot)    title += "R";

        						if (removeScale)  title += "S";

        						if (removeOffset) title += "O";

        						if (max_is_scale) title += "X"; 

        					}

        					// Avoid renderMulti() - it duplicates code renderMultiDouble()

        					int eq_mode = 2; // calculate

        					ImagePlus imp_img_pair = 	maps_collection.renderMulti (
@@ -2077,7 +2132,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341 
					{2139.833, 1474.5},

					{ 461.5,   1493.5}}};

		boolean set_coords = true; // false;

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1090,900);

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Select processing moder",1090,900);

		gd.addStringField ("First image path",  image_paths[0], 120, "First image full path");		

		gd.addStringField ("Second image path", image_paths[1], 120, "Second image full path");		

		gd.addCheckbox    ("Set image markers to following coordinates", set_coords, "Delete markers and set them according to data.");

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

+241 −88

File changed.

Preview size limit exceeded, changes collapsed.

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

+17 −3
Original line number Diff line number Diff line
@@ -3732,7 +3732,21 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{ 
			final double []  weight,

			final int        width,

			final double []  xy0) {

		int debug = -1;

		return getPlane(

				   data, // final double []   data,

				mask,  // final boolean [] mask,

				weight, //final double []  weight,

				width, // final int        width,

				xy0, // final double []  xy0,

				null); // String dbg_title)

	}

	public static double [] getPlane(

			final double []   data,

			final boolean [] mask,

			final double []  weight,

			final int        width,

			final double []  xy0,

			String dbg_title) {

		final double [][][] mdatai = new double [data.length][][];

		AtomicInteger anum_good = new AtomicInteger(0);

		final Thread[] threads = ImageDtt.newThreadArray();
@@ -3770,7 +3784,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{ 
				null,       // damping,    // double [] damping, null OK

				-1);        // debug level

		if (approx2d != null) {

			if (debug > 0) {

			if (dbg_title != null) {

				double [] plane=new double[data.length];

				double [] diff=new double[data.length];

				double [] dweight = (weight != null) ? weight: new double[data.length];
@@ -3794,7 +3808,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{ 
						width,

						data.length/width,

						true,

						"plane_approximation",

						dbg_title,

						new String[] {"data","approx","diff","masked","weight","mask"});

			}

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

+3 −3
Original line number Diff line number Diff line
@@ -5204,7 +5204,7 @@ public class OrthoMapsCollection implements Serializable{ 
		

		boolean flt_update_config =  false;

		

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);

		gdf.addMessage("Filter pairs parameters");

		gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap,  3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");

		gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap,  3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
@@ -6342,7 +6342,7 @@ public class OrthoMapsCollection implements Serializable{ 
		boolean flt_update_config =  false;

		boolean select_pairs =       false;

		

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);

		gdf.addMessage("Filter pairs parameters");

		gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap,  3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");

		gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap,  3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");
@@ -6581,7 +6581,7 @@ public class OrthoMapsCollection implements Serializable{ 
		boolean flt_update_config =  false;

		

		

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1100);

		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,1200);

		gdf.addMessage("Filter pairs parameters");

		gdf.addNumericField("Minimal scene overlap (0..1)",flt_min_overlap,  3,7,"", "Minimal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");

		gdf.addNumericField("Maximal scene overlap (0..1)",flt_max_overlap,  3,7,"", "Maximal overlap of the scenes to keep (0-no overlap, 1.0 - smaller scene is inside the parger one.");

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

+65 −3
Original line number Diff line number Diff line
@@ -45,7 +45,8 @@ public final class QuatUtils { // static class 
		String fmt_deg = "[%12.9f, %12.9f,%12.9f, %12.9f], tilt=%12.7f\u00B0, dir=%12.7f\u00B0, scale=%12.10f";

		double s = degrees ? (180/Math.PI):1;

		String fmt=degrees ? fmt_deg : fmt_rad;

		return String.format(fmt, quat[0], quat[1],quat[2],quat[3], s*2*Math.acos(quat[0]), s*Math.atan2(quat[2],quat[1]), scale);

		String rslt=String.format(fmt, quat[0], quat[1],quat[2],quat[3], s*2*Math.acos(quat[0]), s*Math.atan2(quat[2],quat[1]), scale);

		return rslt;

	}

	

	/**
@@ -300,7 +301,10 @@ public final class QuatUtils { // static class 
		if (t == 0) {

			return UNIT_QUAT;

		}

		double [] axis = {ty/t,-tx/t,0}; // pi/2 CW

		tx/=t;

		ty/=t;

		

		double [] axis = {ty,-tx,0}; // pi/2 CW

		

		/* sin (A/2) = +-sqrt((1 - cos(A))/2)

		 * cos (A/2) = +-sqrt((1 + cos(A))/2)
@@ -313,6 +317,64 @@ public final class QuatUtils { // static class 
		return quat;

	}

	

	public static String tiltToString (

			double [] txy,

			boolean	y_down_ccw,

			boolean degrees) {

		String fmt_rad = " tilt= %10.7f, dir=%10.7f";

		String fmt_deg = " tilt= %10.5f\u00B0, dir=%10.5f\u00B0";

		double k = degrees ? (180/Math.PI):1;

		String fmt=degrees ? fmt_deg : fmt_rad;



		String s = String.format(" = [%12.9f, %12.9f, %15.9f]", txy[0], txy[1], txy[2]);

		double tx = txy[0], ty = y_down_ccw?-txy[1]:txy[1]; // invert y

		double t2 = tx*tx + ty*ty;

		double t = Math.sqrt(t2);

		if (t == 0) {

			return s;

		}

		tx/=t;

		ty/=t;

		

		double [] axis = {ty,-tx,0}; // pi/2 CW

		double dir = Math.atan2(axis[1],axis[0]);

		double tilt = Math.atan(t);

		

		s+= String.format(fmt, k*tilt, k*dir);

		return s;

	}

	

	

	public static double [] sceneRelLocalGround(

			double []   txy,

			double [][] affine, // used for rot and scale Now can be null

			boolean	    y_down_ccw) { // boolean y_down_ccw) for tilts and affine

		double [] qtilts = tiltToQuaternion(txy,y_down_ccw);

		boolean inv_aff = true; // invert affine

		double scale = 1.0;

		double rot = 0;

		if (affine != null) {

			if (inv_aff) {

				affine = matInverse2x2(affine);

			}

			SingularValueDecomposition svd= SingularValueDecomposition.singularValueDecomposeScaleTiltBeta(

					affine,

					y_down_ccw);

			scale = svd.getMaxScale();

			rot = svd.getRotAngle(); // TODO: check sign !

		}		

		

		// Now beta,rot correspond to Y - up

		double chalfrot = Math.cos(rot/2); 

		double shalfrot = Math.sin(rot/2); 

		double [] qrot = {chalfrot,0,0,shalfrot}; // rotation around vertical axis

		double [] qinv_tilts = invert(qtilts); //scene to ground

		double [] qrt=  multiply(qrot,qinv_tilts);

//		double [] quat= scale(multiply(qrot,qinv_tilts),scale);

		double [] quat= scale(multiply(qinv_tilts,qrot),scale);

		return    quat;

	}	

	

	/**

	 * Remove rotation around Z-axis, keep only tilt around axis in XY plane

	 * @param quat_in input rotation that may include rotation around Z (vertical) axis
@@ -563,7 +625,7 @@ q11 - q22 = c3 
	 */

	public static double [][] affineToQuatScaled (

			double [][] affine,

			boolean     stretch,

			boolean     stretch,// false

			boolean     y_down_ccw) {

		affine = matInverse2x2(affine);