Started manual pair matching by affine transform (98e487e9) · Commits · Elphel / imagej-elphel

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

+11 −0

Original line number	Original line	Diff line number	Diff line
	@@ -109,6 +109,7 @@ import com.elphel.imagej.ims.EventLogger;
	import com.elphel.imagej.ims.Imx5;		import com.elphel.imagej.ims.Imx5;
	import com.elphel.imagej.jp4.JP46_Reader_camera;		import com.elphel.imagej.jp4.JP46_Reader_camera;
	import com.elphel.imagej.lwir.LwirReader;		import com.elphel.imagej.lwir.LwirReader;
			import com.elphel.imagej.orthomosaic.ComboMatch;
	import com.elphel.imagej.readers.ChangeImageResolution;		import com.elphel.imagej.readers.ChangeImageResolution;
	import com.elphel.imagej.readers.DumpImageMetadata;		import com.elphel.imagej.readers.DumpImageMetadata;
	import com.elphel.imagej.readers.EyesisTiff;		import com.elphel.imagej.readers.EyesisTiff;
	@@ -841,6 +842,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	addButton("Build World", panelLWIRWorld, color_process);		addButton("Build World", panelLWIRWorld, color_process);
	addButton("Test IMX5", panelLWIRWorld, color_process);		addButton("Test IMX5", panelLWIRWorld, color_process);
	addButton("Show mice", panelLWIRWorld, color_process);		addButton("Show mice", panelLWIRWorld, color_process);
			addButton("Set pair", panelLWIRWorld, color_process);
			addButton("Warp pair", panelLWIRWorld, color_process);
	plugInFrame.add(panelLWIRWorld);		plugInFrame.add(panelLWIRWorld);

	}		}
	@@ -5672,6 +5675,14 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	ImagePlus imp_src = WindowManager.getCurrentImage();		ImagePlus imp_src = WindowManager.getCurrentImage();
	ImagePlus imp_mice = subtractAverage(imp_src);		ImagePlus imp_mice = subtractAverage(imp_src);
	imp_mice.show();		imp_mice.show();
			} else if (label.equals("Set pair")) {
			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
			ComboMatch.openTestPair();
			} else if (label.equals("Warp pair")) {
			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
			ComboMatch.testPair();
	}		}
	}		}

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

0 → 100644

+348 −0

Original line number	Original line	Diff line number	Diff line
			package com.elphel.imagej.orthomosaic;

			import java.util.Arrays;
			import java.util.concurrent.atomic.AtomicInteger;

			import com.elphel.imagej.common.GenericJTabbedDialog;
			import com.elphel.imagej.common.ShowDoubleFloatArrays;
			import com.elphel.imagej.tileprocessor.ImageDtt;

			import Jama.Matrix;
			import ij.ImagePlus;
			import ij.gui.PointRoi;
			import ij.process.FloatPolygon;

			public class ComboMatch {
			public static ImagePlus imp_src1 = null;
			public static ImagePlus imp_src2 = null;


			public static boolean openTestPair() {
			String [] image_paths = {
			"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_compare/02/1697877410_420287-RECT-PIX0.01-FLAT_CLN-GEO0.tiff",
			"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_compare/02/1697877412_004148-RECT-PIX0.01-FLAT_CLN-GEO0.tiff"
			};
			double [][][] image_points = {
			{ { 487.0, 637.0},
			{2237.5, 932.5},
			{2004.5, 1929.5},
			{ 320.5, 1951.500}
			},{
			{ 629.0, 179.0},
			{2376.5, 479.5},
			{2139.833, 1474.5},
			{ 461.5, 1493.5}}};
			boolean set_coords = true; // false;
			GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",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.");
			for (int n = 0; n < image_points.length; n++) {
			for (int i = 0; i < image_points[n].length; i++) {
			gd.addMessage("image["+n+"] point "+i+":");
			gd.addNumericField("x =", image_points[n][i][0], 3,7,"pix",
			"Marker "+i+ " for image "+n+" X-coordinate");
			gd.addNumericField("y =", image_points[n][i][1], 3,7,"pix",
			"Marker "+i+ " for image "+n+" Y-coordinate");
			}
			}

			gd.showDialog();
			if (gd.wasCanceled()) return false;

			image_paths[0] = gd.getNextString();
			image_paths[1] = gd.getNextString();
			set_coords = gd.getNextBoolean();
			for (int n = 0; n < image_points.length; n++) {
			for (int i = 0; i < image_points[n].length; i++) {
			image_points[n][i][0] = gd.getNextNumber();
			image_points[n][i][1] = gd.getNextNumber();
			}
			}
			imp_src1 = new ImagePlus(image_paths[0]);
			imp_src2 = new ImagePlus(image_paths[1]);

			if (set_coords) {
			PointRoi [] rois = new PointRoi[image_points.length];
			for (int n = 0; n < image_points.length; n++) {
			rois[n] = new PointRoi();
			rois[n].setOptions("label");
			for (int i = 0; i < image_points[n].length; i++) {
			rois[n].addPoint(image_points[n][i][0],image_points[n][i][1],i+1);
			}
			}
			imp_src1.setRoi(rois[0]);
			imp_src2.setRoi(rois[1]);
			}

			imp_src1.show();
			imp_src2.show();
			if (!(imp_src1.getRoi() instanceof PointRoi) \|\| !(imp_src2.getRoi() instanceof PointRoi)) {
			System.out.println("At least one iomage does not have PointRoi");
			return false;
			}
			FloatPolygon [] fp = {((PointRoi) imp_src1.getRoi()).getContainedFloatPoints(),
			((PointRoi) imp_src2.getRoi()).getContainedFloatPoints()};
			int expected_points = image_points[0].length;
			for (int n = 0; n < fp.length; n++) {
			if (fp[n].xpoints.length != expected_points) {
			System.out.println("openTestPair(): expecting "+expected_points+" points, image "+n+"has "+fp[n].xpoints.length);
			return false;
			}
			}
			double [][][] points_xy= new double [fp.length][fp[0].xpoints.length][2];
			for (int n = 0; n < points_xy.length; n++) {
			for (int i = 0; i < points_xy[n].length; i++) {
			points_xy[n][i][0] = fp[n].xpoints[i];
			points_xy[n][i][1] = fp[n].ypoints[i];
			}
			}
			System.out.println(String.format("%4s\t%8s\t%8s\t%8s\t%8s\t%8s\t%8s\t%8s",
			"N","X0","Y0","X1","Y1", "length1", "length2", "ratio"));
			for (int i = 0; i < points_xy[0].length; i++) {
			int ip = (i - 1 + points_xy[0].length) % points_xy[0].length;
			double [] ll = new double[2];
			for (int n = 0; n < points_xy.length; n++) {
			double dx = points_xy[n][i][0]-points_xy[n][ip][0];
			double dy = points_xy[n][i][1]-points_xy[n][ip][1];
			ll[n] = Math.sqrt(dxdx+dydy);
			}
			System.out.println(String.format("%4d\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.6f",
			i, points_xy[0][i][0], points_xy[0][i][1],points_xy[1][i][0], points_xy[1][i][1],
			ll[0], ll[1], ll[1]/ll[0]));
			}
			return true;
			}

			public static boolean testPair() {
			if (!(imp_src1.getRoi() instanceof PointRoi) \|\| !(imp_src2.getRoi() instanceof PointRoi)) {
			System.out.println("At least one iomage does not have PointRoi");
			return false;
			}
			FloatPolygon [] fp = {((PointRoi) imp_src1.getRoi()).getContainedFloatPoints(),
			((PointRoi) imp_src2.getRoi()).getContainedFloatPoints()};
			int expected_points = 4; // image_points[0].length;
			for (int n = 0; n < fp.length; n++) {
			if (fp[n].xpoints.length != expected_points) {
			System.out.println("openTestPair(): expecting "+expected_points+" points, image "+n+"has "+fp[n].xpoints.length);
			return false;
			}
			}
			double [][][] points_xy= new double [fp.length][fp[0].xpoints.length][2];
			for (int n = 0; n < points_xy.length; n++) {
			for (int i = 0; i < points_xy[n].length; i++) {
			points_xy[n][i][0] = fp[n].xpoints[i];
			points_xy[n][i][1] = fp[n].ypoints[i];
			}
			}
			System.out.println(String.format("%4s\t%8s\t%8s\t%8s\t%8s\t%8s\t%8s\t%8s",
			"N","X0","Y0","X1","Y1", "length1", "length2", "ratio"));
			for (int i = 0; i < points_xy[0].length; i++) {
			int ip = (i - 1 + points_xy[0].length) % points_xy[0].length;
			double [] ll = new double[2];
			for (int n = 0; n < points_xy.length; n++) {
			double dx = points_xy[n][i][0]-points_xy[n][ip][0];
			double dy = points_xy[n][i][1]-points_xy[n][ip][1];
			ll[n] = Math.sqrt(dxdx+dydy);
			}
			System.out.println(String.format("%4d\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.3f\t%8.6f",
			i, points_xy[0][i][0], points_xy[0][i][1],points_xy[1][i][0], points_xy[1][i][1],
			ll[0], ll[1], ll[1]/ll[0]));
			}

			double [][] ab = getAffineMatrix(
			points_xy[1], // double [][] x,
			points_xy[0]); // double [][] y){
			double [][] a = {{ab[0][0],ab[0][1]},{ab[1][0],ab[1][1]}};
			double [] b = {ab[2][0],ab[2][1]};
			System.out.println("Matrix A:");
			System.out.println(String.format("%10.5f\t%10.5f", a[0][0], a[0][1]));
			System.out.println(String.format("%10.5f\t%10.5f", a[1][0], a[1][1]));
			System.out.println("Matrix B:");
			System.out.println(String.format("%10.5f", b[0]));
			System.out.println(String.format("%10.5f", b[1]));
			final int [] widths = {imp_src1.getWidth(),imp_src2.getWidth()};
			final int [] heights = {imp_src1.getHeight(),imp_src2.getHeight()};
			int [][][] corners = new int[2][4][2];
			for (int n =0; n < corners.length; n++) {
			corners[n][0][0] = 0;
			corners[n][0][1] = 0;
			corners[n][1][0] = widths[n]-1;
			corners[n][1][1] = 0;
			corners[n][2][0] = widths[n]-1;
			corners[n][2][1] = heights[n]-1;
			corners[n][3][0] = 0;
			corners[n][3][1] = heights[n]-1;
			}
			double [][] fcorners = new double[corners[1].length][2];
			int [][] xy_minmax = {{0, widths[0]-1},{0, heights[0]-1}};
			int [][] xy_minmax1 = new int[2][2];
			for (int i = 0; i < corners[1].length; i++) {
			fcorners[i][0] = corners[1][i][0] * a[0][0]+ corners[1][i][1] * a[0][1] + b[0];
			fcorners[i][1] = corners[1][i][0] * a[1][0]+ corners[1][i][1] * a[1][1] + b[1];
			xy_minmax[0][0] = Math.min(xy_minmax[0][0], (int) Math.floor(fcorners[i][0]));
			xy_minmax[0][1] = Math.max(xy_minmax[0][1], (int) Math.ceil(fcorners[i][0]));
			xy_minmax[1][0] = Math.min(xy_minmax[1][0], (int) Math.floor(fcorners[i][1]));
			xy_minmax[1][1] = Math.max(xy_minmax[1][1], (int) Math.ceil(fcorners[i][1]));
			if (i == 0) {
			xy_minmax1[0][0] = (int) Math.floor(fcorners[i][0]);
			xy_minmax1[0][1] = (int) Math.ceil(fcorners[i][0]);
			xy_minmax1[1][0] = (int) Math.floor(fcorners[i][1]);
			xy_minmax1[1][1] = (int) Math.ceil(fcorners[i][1]);
			} else {
			xy_minmax1[0][0] = Math.min(xy_minmax1[0][0], (int) Math.floor(fcorners[i][0]));
			xy_minmax1[0][1] = Math.max(xy_minmax1[0][1], (int) Math.ceil(fcorners[i][0]));
			xy_minmax1[1][0] = Math.min(xy_minmax1[1][0], (int) Math.floor(fcorners[i][1]));
			xy_minmax1[1][1] = Math.max(xy_minmax1[1][1], (int) Math.ceil(fcorners[i][1]));
			}
			}
			final int x0 = Math.max(0, -xy_minmax[0][0]);
			final int y0 = Math.max(0, -xy_minmax[1][0]);
			final int width = x0 + xy_minmax[0][1]+1;
			final int height = y0 + xy_minmax[1][1]+1;
			double [][] opix = new double [2][width*height];
			for (int n = 0; n < opix.length; n++) {
			Arrays.fill(opix[n], Double.NaN);
			}
			final Thread[] threads = ImageDtt.newThreadArray();
			final AtomicInteger ai = new AtomicInteger(0);
			final int width0= widths[0];
			final int npix0 = width0*heights[0];
			final float [] pixels0 = (float []) imp_src1.getProcessor().getPixels();
			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int ipix = ai.getAndIncrement(); ipix < npix0; ipix = ai.getAndIncrement()) {
			int y = ipix / width0;
			int x = ipix % width0;
			int p = x0 + x + (y0 + y)* width;
			opix[0][p] = pixels0[ipix];
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);

			final int x10 = x0+ xy_minmax1[0][0]; // output image coordiantes
			final int y10 = y0+ xy_minmax1[1][0]; // output image coordiantes
			final int width1 = x0 + xy_minmax1[0][1] + 1;
			final int height1 = y0 + xy_minmax1[0][1] + 1;
			final int npix1 = width1 * height1;
			double [][] ab1 = getAffineMatrix(
			points_xy[0], // double [][] x,
			points_xy[1]); // double [][] y){
			final double [][] a1 = {{ab1[0][0],ab1[0][1]},{ab1[1][0],ab1[1][1]}};
			final double [] b1 = {ab1[2][0]-x0,ab1[2][1]-y0}; // from output coordinates to image2 coordinates
			System.out.println("Matrix A1:");
			System.out.println(String.format("%10.5f\t%10.5f", a1[0][0], a1[0][1]));
			System.out.println(String.format("%10.5f\t%10.5f", a1[1][0], a1[1][1]));
			System.out.println("Matrix B1:");
			System.out.println(String.format("%10.5f", b1[0]));
			System.out.println(String.format("%10.5f", b1[1]));
			ai.set(0);
			final int img2_width = widths[1];
			final int img2_height = heights[1];
			final float [] pixels1 = (float []) imp_src2.getProcessor().getPixels();
			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int ipix = ai.getAndIncrement(); ipix < npix1; ipix = ai.getAndIncrement()) {
			int y = ipix / width1 + x10; // output image coordinates
			int x = ipix % width1 + y10; // output image coordinates
			int p = x + y * width;
			double fx = a1[0][0] * x + a1[0][1] * y + b1[0];
			double fy = a1[1][0] * x + a1[1][1] * y + b1[1];
			int ix = (int) Math.floor(fx);
			int iy = (int) Math.floor(fy);
			double dx = fx - ix;
			double dy = fy - iy;
			if ((ix >= 0) && (iy >= 0) && (ix < (img2_width -1)) && (iy < (img2_height -1))) {
			int indx0 = ix + iy * img2_width;
			double d00 = pixels1[indx0];
			double d01 = pixels1[indx0+1];
			double d10 = pixels1[indx0+img2_width];
			double d11 = pixels1[indx0+img2_width+1];
			opix[1][p] = d00(1-dx)(1-dy)+d01dx(1-dy)+d10(1-dx)dy+d11dxdy;
			}
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);

			ShowDoubleFloatArrays.showArrays(
			opix,
			width,
			height,
			true,
			"overlap");


			return true;
			}

			public static double [][] getAffineMatrix(
			double [][] x,
			double [][] y){
			if (x.length != y.length) {
			System.out.println("getAffineMatrix(): x.length != y.length ("+x.length+" != "+y.length+")");
			return null;
			}
			/*
			Ui = A00 * Xi + A01* Yi + B0
			Vi = A10 * Xi + A11* Yi + B1

			A00^2Xi^2 + A01^2Yi^2 +B0^2 +Ui^2 + 2A00XiA01Yi + 2A00XiB0 - 2A00XiUi + 2A01YiB0 -2A01YiUi - 2B0Ui
			d/2dA00 = A00Xi^2 + A01XiYi + B0 Xi - XiUi = 0
			d/2dA01 = A01Yi^2 + A00XiYi + B0 Yi - YiUi = 0
			d/2dB0 = B0 + A00Xi + A01Yi - Ui = 0

			d/2dA10 = A10Xi^2 + A11XiYi + B1 Xi - XiVi = 0
			d/2dA11 = A11Yi^2 + A10XiYi + B1 Yi - YiVi = 0
			d/2dB1 = B1 + A10Xi + A11Yi - Vi = 0

			SX2A00 + SXYA01 + 0A10 + 0A11 + SXB0 + 0B1 = SXU
			SXYA00 + SY2A01 + 0A10 + 0A11 + SYB0 + 0B1 = SYU
			SX A00 + SY A01 + 0A10 + 0A11 + 1B0 + 0B1 = SU
			0 A00 + 0 A01 + SX2A10 + SXYA11 + 0B0 + SXB1 = SXV
			0 A00 + 0 A01 + SXYA10 + SY2A11 + 0B0 + SYB1 = SYV
			0 A00 + 0 A01 + SX A10 + SY A11 + 0B0 + 1B1 = SV
			*/
			double sx=0, sy=0, sx2=0, sy2=0, sxy=0,sxu=0,syu=0,sxv=0,syv=0,su=0,sv=0;
			for (int n = 0; n < x.length; n++) {
			sx += x[n][0];
			sy += x[n][1];
			sx2+= x[n][0]*x[n][0];
			sy2+= x[n][1]*x[n][1];
			sxy+= x[n][0]*x[n][1];

			sxu+= x[n][0]*y[n][0];
			syu+= x[n][1]*y[n][0];
			su+= y[n][0];

			sxv+= x[n][0]*y[n][1];
			syv+= x[n][1]*y[n][1];
			sv+= y[n][1];
			}
			double s0 = x.length;
			double [][] a = {
			{sx2, sxy, 0, 0, sx, 0},
			{sxy, sy2, 0, 0, sy, 0},
			{ sx, sy, 0, 0, s0, 0},
			{ 0, 0, sx2, sxy, 0, sx},
			{ 0, 0, sxy, sy2, 0, sy},
			{ 0, 0, sx, sy, 0, s0}};
			Matrix A = new Matrix(a);
			A.print(15,4);
			double [][] b = {{sxu,syu,su,sxv,syv,sv}};
			Matrix B = new Matrix(b).transpose();
			B.print(15,4);
			double [] v = A.solve(B).getRowPackedCopy();
			double [][] ab = {
			{v[0], v[1]}, // \|a00, a01\|,
			{v[2], v[3]}, // \|a10, a11\|,
			{v[4], v[5]}}; // \| b0, b1\|,
			return ab;
			}

			}

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

+4 −0

Original line number	Original line	Diff line number	Diff line
	@@ -11624,6 +11624,10 @@ public class ImageDttCPU {
	* From Stephan Preibisch's Multithreading.java class. See:		* From Stephan Preibisch's Multithreading.java class. See:
	* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD		* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
	*/		*/
			public static Thread[] newThreadArray() {
			return newThreadArray(THREADS_MAX);
			}

	public static Thread[] newThreadArray(int maxCPUs) { // USED in lwir		public static Thread[] newThreadArray(int maxCPUs) { // USED in lwir
	int n_cpus = Runtime.getRuntime().availableProcessors();		int n_cpus = Runtime.getRuntime().availableProcessors();
	if (n_cpus>maxCPUs)n_cpus=maxCPUs;		if (n_cpus>maxCPUs)n_cpus=maxCPUs;

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

+3 −1

Original line number	Original line	Diff line number	Diff line
	@@ -2673,12 +2673,14 @@ public class TexturedModel {
	}		}
	}		}
	// -------		// -------
			boolean mixed_flat = false;
	if (gsmth_enable && (!has_sfm \|\| gsmth_sfm_gnd)) {		if (gsmth_enable && (!has_sfm \|\| gsmth_sfm_gnd)) {
	double [] smooth_ground = scenes[ref_index].getSmoothGround(		double [] smooth_ground = scenes[ref_index].getSmoothGround(
	clt_parameters,		clt_parameters,
	has_sfm, // boolean sfm_mode,		has_sfm, // boolean sfm_mode,
	debugLevel);		debugLevel);
	if (has_sfm && gsmth_sfm_deviate) {		if (has_sfm && gsmth_sfm_deviate) {
			mixed_flat = true;
	// Change!		// Change!
	// Use FG for FG, and ground plane as BG?		// Use FG for FG, and ground plane as BG?
	TileNeibs tn = new TileNeibs(tilesX, smooth_ground.length/tilesX);		TileNeibs tn = new TileNeibs(tilesX, smooth_ground.length/tilesX);
	@@ -3189,7 +3191,7 @@ public class TexturedModel {
	String suffix ="-RECT";		String suffix ="-RECT";
	suffix +="-PIX"+pix_size * hdr_whs[2];		suffix +="-PIX"+pix_size * hdr_whs[2];
	if (gsmth_enable) {		if (gsmth_enable) {
	suffix +="-FLAT"; // flattened ground		suffix +=mixed_flat ? "-FLAT_MIX":"-FLAT_CLN"; // flattened ground - mixed or clean
	}		}
	scenes[ref_index].saveDoubleArrayInModelDirectory(		scenes[ref_index].saveDoubleArrayInModelDirectory(
	suffix+"-FULL", // String suffix,		suffix+"-FULL", // String suffix,

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