Added alignment statistics

src/main/java/Eyesis_Correction.java

@@ -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

@@ -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

@@ -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.PI*60*60)); //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);
+	}
 
 }