Added alignment statistics (d7dab33b) · Commits · Elphel / imagej-elphel

src/main/java/Eyesis_Correction.java

+25 −1

Original line number	Diff line number	Diff line
		@@ -84,7 +84,6 @@ import loci.formats.FormatException;

		//import javax.swing.SwingUtilities;
		//import javax.swing.UIManager;

		public class Eyesis_Correction extends PlugInFrame implements ActionListener {
		/**
		*
		@@ -587,6 +586,7 @@ private Panel panel1,
		addButton("Rig offset", panelClt4, color_configure);
		addButton("Save offset", panelClt4, color_process);
		addButton("SHOW extrinsics", panelClt4, color_configure);
		addButton("LIST extrinsics", panelClt4, color_configure);
		addButton("RIG DSI", panelClt4, color_conf_process);
		addButton("MAIN extrinsics", panelClt4, color_process);
		addButton("AUX extrinsics", panelClt4, color_process);
		@@ -4579,6 +4579,11 @@ private Panel panel1,
		QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;

		return;
		/* ======================================================================== */
		} else if (label.equals("LIST extrinsics")) {
		listExtrinsics();
		return;

		/* ======================================================================== */
		} else if (label.equals("Reset GT")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		@@ -5580,6 +5585,25 @@ private Panel panel1,
		return true;
		}

		// listExtrinsics();
		public boolean listExtrinsics() {
		String dir= CalibrationFileManagement.selectDirectory(
		false, // true, // smart,
		false, // newAllowed, // save
		"Model directories to scan", // title
		"Select", // button
		null, // filter
		CORRECTION_PARAMETERS.x3dDirectory); //this.sourceDirectory);
		if (dir!=null) {
		System.out.println("top directory = "+dir);
		}
		//listExtrinsics(String dir, String mask)
		// if (TWO_QUAD_CLT == null) {
		// return false;
		// }
		return TwoQuadCLT.listExtrinsics(dir); // , mask);
		}

		public boolean showDSI() {
		if (TWO_QUAD_CLT == null) {
		System.out.println("TWO_QUAD_CLT is not initialized");

src/main/java/GeometryCorrection.java

+42 −1

Original line number	Diff line number	Diff line
		@@ -953,6 +953,22 @@ public class GeometryCorrection {
		System.out.println(" Relative zoom - difference from 1.0 in parts parts per 1/1000 "+ (par_scales[AUX_ZOOM_INDEX] * this.aux_zoom) +"pix");
		}

		public double getRigOffsetParameter(int indx, boolean inPix)
		{
		if ((indx <0.0) \|\| (indx >=par_scales.length)){
		return Double.NaN;
		}
		double k = inPix? par_scales[indx] : 1.0;
		switch (indx) {
		case AUX_AZIMUTH_INDEX: return k * this.aux_azimuth;
		case AUX_TILT_INDEX: return k * this.aux_tilt;
		case AUX_ROLL_INDEX: return k * this.aux_roll;
		case AUX_ZOOM_INDEX: return k * this.aux_zoom;
		case AUX_ANGLE_INDEX: return k * this.aux_angle;
		case AUX_BASELINE_INDEX: return k * this.baseline; // if inPix - show rig baseline/main baseline
		}
		return Double.NaN;
		}

		}

		@@ -967,6 +983,10 @@ public class GeometryCorrection {
		this.rigOffset.showRigOffsets();
		}

		public double getRigOffsetParameter(int indx, boolean inPix) {
		return this.rigOffset.getRigOffsetParameter(indx,inPix);
		}

		public boolean setRigOffsetFromProperies(String parent_prefix,Properties properties) {
		RigOffset rigOffset = new RigOffset();
		boolean gotit = rigOffset.getProperties(parent_prefix, properties);
		@@ -1248,6 +1268,27 @@ public class GeometryCorrection {
		{
		return vector[6 + indx] + roll[indx] * Math.PI/180.0;
		}
		/**
		* Return parameter value for reports
		* @param indx parameter index (use CorrVector.XXX static integers)
		* @param inPix show result in pixels , false - in radians (even for zooms)
		* @return parameter value
		*/
		public double getExtrinsicParameterValue(int indx, boolean inPix) {
		if (indx <0) return Double.NaN;
		if (indx < ROLL_INDEX) return vector[indx]* (inPix? (1000.0*focalLength /pixelSize): 1.0); // tilt and azimuth
		if (indx < LENGTH_ANGLES) return vector[indx]* (inPix? (1000.0*distortionRadius/pixelSize): 1.0); // rolls
		if (indx < LENGTH) return vector[indx]* (inPix? (1000.0*distortionRadius/pixelSize): 1.0); // zooms
		return Double.NaN;
		}
		public double getExtrinsicSymParameterValue(int indx, boolean inPix) {
		double [] sym_vect = toSymArray(null);
		if (indx <0) return Double.NaN;
		if (indx < ROLL_INDEX) return sym_vect[indx]* (inPix? (1000.0*focalLength /pixelSize): 1.0); // tilt and azimuth
		if (indx < LENGTH_ANGLES) return sym_vect[indx]* (inPix? (1000.0*distortionRadius/pixelSize): 1.0); // rolls
		if (indx < LENGTH) return sym_vect[indx]* (inPix? (1000.0*distortionRadius/pixelSize): 1.0); // zooms
		return Double.NaN;
		}

		@Override
		public String toString()

src/main/java/TwoQuadCLT.java

+416 −0

Original line number	Diff line number	Diff line
		@@ -21,20 +21,32 @@
		**
		*/
		import java.io.File;
		import java.io.FileInputStream;
		import java.io.FileNotFoundException;
		import java.io.FileOutputStream;
		import java.io.IOException;
		import java.io.InputStream;
		import java.io.OutputStream;
		import java.nio.file.FileVisitResult;
		import java.nio.file.Files;
		import java.nio.file.Path;
		import java.nio.file.Paths;
		import java.nio.file.SimpleFileVisitor;
		import java.nio.file.StandardCopyOption;
		import java.nio.file.attribute.BasicFileAttributes;
		import java.util.ArrayList;
		import java.util.Collections;
		import java.util.Comparator;
		import java.util.List;
		import java.util.Properties;

		import ij.IJ;
		import ij.ImagePlus;
		import ij.ImageStack;
		import ij.Prefs;
		import ij.gui.GenericDialog;
		import ij.io.FileSaver;
		import ij.text.TextWindow;

		public class TwoQuadCLT {
		public static int DSI_DISPARITY_MAIN = 0;
		@@ -6335,5 +6347,409 @@ if (debugLevel > -100) return true; // temporarily !
		System.out.println("Configuration parameters are saved to "+path);
		}
		}
		public static boolean listExtrinsics(String dir) // , String mask)
		{
		Path path= Paths.get(dir);
		boolean inPixels = true;
		boolean inMrad = false;
		boolean showATR = true;
		boolean showZooms = true;
		boolean showSym = true;
		boolean showRigATR = true;
		boolean showRigZoom = true;
		boolean showRigAngle = true;
		boolean showRigBaseline = false;

		GenericDialog gd = new GenericDialog("Select file mask");
		gd.addStringField ("Extrinsics (or general configuration) file mask: ", ".*EXTRINSICS\\.corr-xml", 40);
		gd.addCheckbox("Show results in pixels (false in angular units)",inPixels);
		gd.addCheckbox("Show results in mrad (false in arcseconds)", inMrad);
		gd.addCheckbox("Show azimuths, tilts, rolls", showATR);
		gd.addCheckbox("Show zooms", showZooms);
		gd.addCheckbox("Show symmetric angles", showSym);
		gd.addCheckbox("Show rig azimuth, tilt, roll", showRigATR);
		gd.addCheckbox("Show rig zoom", showRigZoom);
		gd.addCheckbox("Show rig angle", showRigAngle);
		gd.addCheckbox("Show rig baseline", showRigBaseline);
		gd.showDialog ();
		if (gd.wasCanceled()) return false;
		String mask = gd.getNextString();
		inPixels = gd.getNextBoolean();
		inMrad = gd.getNextBoolean();
		showATR = gd.getNextBoolean();
		showZooms = gd.getNextBoolean();
		showSym = gd.getNextBoolean();
		showRigATR = gd.getNextBoolean();
		showRigZoom = gd.getNextBoolean();
		showRigAngle = gd.getNextBoolean();
		showRigBaseline = gd.getNextBoolean();

		String units = inPixels ? "pix":(inMrad?"mil":"\"");
		String zunits = inPixels ? "pix":(inMrad?"mil":"\"");
		double scale = inPixels ? 1.0 : (inMrad?1000.0:(180.0/Math.PI6060)); //leave pixels as is, convert radians to arc-sec
		String fmt = "\t"+(inPixels ? "%8.4f":(inMrad?"%8.4f":"%8.2f"));
		String fmt_angle = "\t%8.3f";
		String fmt_len = "\t%8.3f";
		class ModVerString{
		String model;
		String version;
		String txt;
		ModVerString (String model, String version, String txt){
		this.model = model;
		this.version = version;
		this.txt = txt;
		}
		@Override
		public String toString() {
		return model+"\t"+version+txt;
		}

		}

		ArrayList<ModVerString> line_list = new ArrayList<ModVerString>();
		String title = "Extrinsic parameters variations";
		String header="#\tModel\tVersion";
		int num_col = 0;
		if (showATR) {
		header+=String.format("\taz m0 (%s)\taz m1 (%s) \taz m2 (%s)\taz m3 (%s)"+
		"\ttl m0 (%s)\ttl m1 (%s) \ttl m2 (%s)\ttl m3 (%s)"+
		"\trl m0 (%s)\trl m1 (%s) \trl m2 (%s)\trl m3 (%s)",
		units,units,units,units,units,units,units,units,units,units,units,units);
		num_col+=12;
		}
		if (showZooms) {
		header+=String.format("\tzm m0 (%s)\tzm m1 (%s)\tzm m2 (%s)\tzm m3 (%s)", zunits, zunits, zunits, zunits);
		num_col+=4;
		}

		if (showSym) {
		for (int i = 0; i < GeometryCorrection.CorrVector.LENGTH; i++) {
		header+=String.format("\tsym%02d-m", i);
		}
		num_col+=GeometryCorrection.CorrVector.LENGTH;

		}

		if (showATR) {
		header+=String.format("\taz a0 (%s)\taz a1 (%s) \taz a2 (%s)\taz a3 (%s)"+
		"\ttl a0 (%s)\ttl m1 (%s) \ttl m2 (%s)\ttl m3 (%s)"+
		"\trl a0 (%s)\trl a1 (%s) \trl a2 (%s)\trl a3 (%s)",
		units,units,units,units,units,units,units,units,units,units,units,units);
		num_col+=12;
		}
		if (showZooms) {
		header+=String.format("\tzm a0 (%s)\tzm a1 (%s)\tzm a2 (%s)\tzm a3 (%s)", zunits, zunits, zunits, zunits);
		num_col+=4;
		}
		if (showSym) {
		for (int i = 0; i < GeometryCorrection.CorrVector.LENGTH; i++) {
		header+=String.format("\tsym%02d-a", i);
		}
		num_col+=GeometryCorrection.CorrVector.LENGTH;
		}
		if (showRigATR) {
		header+=String.format("\trig azmth (%s)\trig tilt(%s)\trig roll (%s)", units, units, units);
		num_col+=3;
		}
		if (showRigZoom) {
		header+=String.format("\trig zoom (%s)", zunits);
		num_col+=1;
		}
		//
		if (showRigAngle) {
		header+="\trig angle (°)";
		num_col+=1;
		}
		if (showRigBaseline) {
		header+="\trig baseline (mm)";
		num_col+=1;
		}


		System.out.println("File mask = "+mask);

		final List<Path> files=new ArrayList<>();
		final String fMask = mask;
		try {
		Files.walkFileTree(path, new SimpleFileVisitor<Path>(){
		@Override
		public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
		if(!attrs.isDirectory()){
		if (file.toString().matches(fMask)) {
		files.add(file);
		}
		}
		return FileVisitResult.CONTINUE;
		}
		});
		} catch (IOException e) {
		e.printStackTrace();
		}
		int indx=1;
		double [][] stats = new double [num_col][2];
		String [] fmts = new String[num_col];
		for (Path p:files) {

		int count = p.getNameCount();
		if (count >=3) {
		String model = p.getName(count-3).toString();
		String version = p.getName(count-2).toString();
		String name = p.getName(count-1).toString();
		System.out.println(indx+": model:"+model+", version:"+version+", name: "+name);
		Properties properties = loadProperties(
		p.toString(), // String path,
		null); // Properties properties)
		QuadCLT qcm = new QuadCLT(
		QuadCLT.PREFIX, // String prefix,
		properties, // Properties properties,
		null, // EyesisCorrections eyesisCorrections,
		null // EyesisCorrectionParameters.CorrectionParameters correctionsParameters
		);
		QuadCLT qca = new QuadCLT(
		QuadCLT.PREFIX_AUX, // String prefix,
		properties, // Properties properties,
		null, // EyesisCorrections eyesisCorrections,
		null // EyesisCorrectionParameters.CorrectionParameters correctionsParameters
		);
		System.out.println(indx+": model:"+model+", version:"+version+", name: "+name);
		GeometryCorrection.CorrVector cvm = qcm.geometryCorrection.getCorrVector();
		GeometryCorrection.CorrVector cva = qca.geometryCorrection.getCorrVector();
		// double [] vect_main = qcm.geometryCorrection.getCorrVector().toArray();
		StringBuffer sb = new StringBuffer();
		int ncol = 0;
		// sb.append(indx+"\t"+model+"\t"+version);
		if (showATR) { // main camera
		double [] v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cvm.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.AZIMUTH_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // azimuths
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cvm.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.TILT_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // tilts
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cvm.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.ROLL_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // rolls
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		}
		if (showZooms) { // main camera
		double [] v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cvm.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.ZOOM_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // zooms
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		}

		if (showSym) {
		for (int i = 0; i < GeometryCorrection.CorrVector.LENGTH; i++) {
		double v = scale * cvm.getExtrinsicSymParameterValue(i, inPixels);
		sb.append(String.format(fmt,v)); // sym parameters
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;
		}
		}


		if (showATR) { // aux camera
		double [] v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cva.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.AZIMUTH_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // azimuths
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cva.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.TILT_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // tilts
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cva.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.ROLL_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // rolls
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		}
		if (showZooms) { // aux camera
		double [] v = new double[4];
		for (int i = 0; i <4; i++) {
		if (i < 3) {
		v[i] = scale * cva.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.ZOOM_INDEX, inPixels);
		v[3] -= v[i];
		}
		sb.append(String.format(fmt,v[i])); // zooms
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v[i];
		stats[ncol++][1]+=v[i]*v[i];
		}
		}
		if (showSym) {
		for (int i = 0; i < GeometryCorrection.CorrVector.LENGTH; i++) {
		double v = scale * cva.getExtrinsicSymParameterValue(i, inPixels);
		sb.append(String.format(fmt,v)); // sym parameters
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;
		}
		}
		if (showRigATR) {
		int [] indices = {
		GeometryCorrection.RigOffset.AUX_AZIMUTH_INDEX,
		GeometryCorrection.RigOffset.AUX_TILT_INDEX,
		GeometryCorrection.RigOffset.AUX_ROLL_INDEX};
		for (int i = 0; i < indices.length; i++) {
		double v = scale * qca.geometryCorrection.getRigOffsetParameter(indices[i], inPixels);
		sb.append(String.format(fmt,v)); // tig atz parameters
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;
		}
		}
		if (showRigZoom) {
		double v = scale * qca.geometryCorrection.getRigOffsetParameter(GeometryCorrection.RigOffset.AUX_ZOOM_INDEX, inPixels);
		sb.append(String.format(fmt,v)); // tig atz parameters
		fmts [ncol] = fmt;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;
		}

		if (showRigAngle) {
		// sb.append(String.format(fmt_angle, 180/Math.PI * qca.geometryCorrection.getRigOffsetParameter(GeometryCorrection.RigOffset.AUX_ANGLE_INDEX, false)));
		double v = 180/Math.PI * qca.geometryCorrection.getRigOffsetParameter(GeometryCorrection.RigOffset.AUX_ANGLE_INDEX, inPixels);
		sb.append(String.format(fmt_angle,v)); // tig atz parameters
		fmts [ncol] = fmt_angle;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;

		}
		if (showRigBaseline) {
		// sb.append(String.format(fmt_len, qca.geometryCorrection.getRigOffsetParameter(GeometryCorrection.RigOffset.AUX_BASELINE_INDEX, false)));
		double v = qca.geometryCorrection.getRigOffsetParameter(GeometryCorrection.RigOffset.AUX_ANGLE_INDEX, inPixels);
		sb.append(String.format(fmt_len,v)); // tig atz parameters
		fmts [ncol] = fmt_len;
		stats[ncol ][0]+=v;
		stats[ncol++][1]+=v*v;
		}
		sb.append("\n");
		line_list.add( new ModVerString(model,version,sb.toString()));
		indx++;
		}
		}
		Collections.sort(line_list, new Comparator<ModVerString>() {
		@Override
		public int compare(ModVerString lhs, ModVerString rhs) {
		// -1 - less than, 1 - greater than, 0 - equal, not inverted for ascending disparity
		int rslt = lhs.model.compareTo(rhs.model);
		if (rslt == 0) rslt = lhs.version.compareTo(rhs.version);
		return rslt;
		}
		});

		StringBuffer sb_avg = new StringBuffer();
		StringBuffer sb_rms = new StringBuffer();
		sb_avg.append("--\tAverage\t");
		sb_rms.append("--\tStandard deviation\t");
		int nrows = indx -1;
		if (indx > 0) {
		for (int ncol = 0; ncol < num_col; ncol++) {
		stats[ncol][0] /= nrows;
		stats[ncol][1] /= nrows;
		stats[ncol][1] = Math.sqrt(stats[ncol][1] - stats[ncol][0]*stats[ncol][0]);
		if (Double.isNaN(stats[ncol][1])) { // small negative by rounding error?
		stats[ncol][1] = 0.0;
		}
		sb_avg.append(String.format(fmts[ncol],stats[ncol][0]));
		sb_rms.append(String.format(fmts[ncol],stats[ncol][1]));
		}
		}
		// ~1280

		// int a = GeometryCorrection.RigOffset.VECTOR_LENGTH;
		StringBuffer sb = new StringBuffer();
		indx = 1;
		for (ModVerString mvs:line_list) {
		sb.append((indx++)+"\t"+mvs.toString());
		}
		sb.append(sb_avg.toString()+"\n");
		sb.append(sb_rms.toString()+"\n");
		new TextWindow (title, header, sb.toString(), 1200,800);
		return true;
		}



		public static Properties loadProperties(
		String path,
		Properties properties){
		if (properties == null) {
		properties = new Properties();
		}
		InputStream is;
		try {
		is = new FileInputStream(path);
		} catch (FileNotFoundException e) {
		IJ.showMessage("Error","Failed to open configuration file: "+path);
		return null;
		}
		try {
		properties.loadFromXML(is);

		} catch (IOException e) {
		IJ.showMessage("Error","Failed to read XML configuration file: "+path);
		return null;
		}
		try {
		is.close();
		} catch (IOException e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		}
		return properties;
		// getAllProperties(properties);
		// if (DEBUG_LEVEL>0) System.out.println("Configuration parameters are restored from "+path);
		}

		}

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