stats: added metadata and normalization (0b346308) · Commits · Elphel / imagej-elphel

src/main/java/MLStats.java

+46 −11

Original line number	Diff line number	Diff line
		@@ -63,6 +63,7 @@ public class MLStats {
		double strength_min_clip = 0.1;
		double strength_max_drop = 1.0; //
		double strength_max_clip = 0.9; //
		boolean normalize = true;

		String mask = ".*-DSI_COMBO\\.tiff";

		@@ -78,6 +79,8 @@ public class MLStats {
		gd.addNumericField("Clip low strength with", strength_min_clip, 3);
		gd.addNumericField("Drop tiles with strength above", strength_max_drop, 3);
		gd.addNumericField("Clip high strength with", strength_max_clip, 3);
		gd.addCheckbox("Normalize histogram to average 1.0", normalize);

		gd.showDialog ();
		if (gd.wasCanceled()) return false;
		mask = gd.getNextString();
		@@ -91,6 +94,7 @@ public class MLStats {
		strength_min_clip = gd.getNextNumber();
		strength_max_drop = gd.getNextNumber();
		strength_max_clip = gd.getNextNumber();
		normalize = gd.getNextBoolean();
		// get list of all files:
		System.out.println("File mask = "+mask);

		@@ -117,16 +121,10 @@ public class MLStats {
		double strength_step = (strength_max_clip - strength_min_clip) / strength_bins;
		double disparity_offs = disparity_min_clip - disparity_step/2; // last and first bin that include clip will be 0.5 width
		double strength_offs = strength_min_clip - strength_step/2; // last and first bin that include clip will be 0.5 width
		int tnut = 0;
		int total_tiles_used = 0;
		for (Path p:files) {
		// System.out.println(p.getFileName());
		// System.out.println(p.normalize().toString());
		ImagePlus imp_dsi=new ImagePlus(p.normalize().toString());
		ImageStack dsi_stack= imp_dsi.getStack();
		// if (debugLevel>0){
		// System.out.println(" kernel_clt_stack.getWidth() = "+dsi_stack.getWidth()+
		// " kernel_clt_stack.getHeight() = "+dsi_stack.getHeight());
		// }
		float [][] dsi_float = new float [slices.length][];
		int nLayers = dsi_stack.getSize();
		for (int nl = 0; nl < nLayers; nl++){
		@@ -161,21 +159,58 @@ public class MLStats {
		}
		}
		System.out.println(p.getFileName()+": "+nut+" useful tiles counted");
		tnut += nut;
		total_tiles_used += nut;
		}
		System.out.println("Total number of useful tiles: "+tnut);
		System.out.println("Total number of useful tiles: "+total_tiles_used);
		double [] hist_double = new double [disparity_bins*strength_bins];
		double scale = 1.0;
		if (normalize) {
		scale = (1.0 disparity_bins * strength_bins) / total_tiles_used;
		}
		for (int nTile = 0; nTile < hist_double.length; nTile++) {
		int dbin = nTile % disparity_bins;
		int sbin = nTile / disparity_bins;
		hist_double[nTile] = hist[dbin][sbin];
		hist_double[nTile] = scale * hist[dbin][sbin];
		}
		(new showDoubleFloatArrays()).showArrays(
		// ImagePlus imp= makeArrays(pixels, width, height, title);
		// if (imp!=null) imp.show();

		ImagePlus imp = (new showDoubleFloatArrays()).makeArrays(
		hist_double,
		disparity_bins,
		strength_bins,
		"DSI_histogram");
		imp.setProperty("disparity_bins", disparity_bins+"");
		imp.setProperty("comment_disparity_bins", "Number of disparity bins");
		imp.setProperty("strength_bins", strength_bins+"");
		imp.setProperty("comment_strength_bins", "Number of strength (confidence) bins");

		imp.setProperty("disparity_min_drop", disparity_min_drop+"");
		imp.setProperty("comment_disparity_min_drop", "Drop tiles with disparities below");
		imp.setProperty("disparity_min_clip", disparity_min_clip+"");
		imp.setProperty("comment_disparity_min_clip", "Clip low disparities with");
		imp.setProperty("disparity_max_drop", disparity_max_drop+"");
		imp.setProperty("comment_disparity_max_drop", "Drop tiles with disparities above");
		imp.setProperty("disparity_max_clip", disparity_max_clip+"");
		imp.setProperty("comment_disparity_max_clip", "Clip high disparities with");

		imp.setProperty("strength_min_drop", strength_min_drop+"");
		imp.setProperty("comment_strength_min_drop", "Drop tiles with strength below");
		imp.setProperty("strength_min_clip", strength_min_clip+"");
		imp.setProperty("comment_strength_min_clip", "Clip low strength with");
		imp.setProperty("strength_max_drop", strength_max_drop+"");
		imp.setProperty("comment_strength_max_drop", "Drop tiles with strength above");
		imp.setProperty("strength_max_clip", strength_max_clip+"");
		imp.setProperty("comment_strength_max_clip", "Clip high strength with");

		imp.setProperty("total_tiles_used", total_tiles_used+"");
		imp.setProperty("comment_total_tiles_used", "Total number of tiles used");


		(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
		imp.show();
		return true;

		}
		public static boolean listExtrinsics(String dir) // , String mask)
		{

src/main/java/TwoQuadCLT.java

+0 −408

Original line number	Diff line number	Diff line
		@@ -6336,412 +6336,4 @@ 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";
		int num_sym = showZooms? GeometryCorrection.CorrVector.LENGTH:GeometryCorrection.CorrVector.ZOOM_INDEX;
		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_in_"+(inPixels ? "pixels":(inMrad?"mrad":"arcseconds"));
		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 < num_sym; i++) {
		header+=String.format("\tsym%02d-m", i);
		}
		num_col+=num_sym;

		}

		if (showATR) {
		header+=String.format("\taz a0 (%s)\taz a1 (%s)\taz a2 (%s)\taz a3 (%s)"+
		"\ttl a0 (%s)\ttl a1 (%s) \ttl a2 (%s)\ttl a3 (%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 < num_sym; i++) {
		header+=String.format("\tsym%02d-a", i);
		}
		num_col+=num_sym;
		}
		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, EnumSet.of(FileVisitOption.FOLLOW_LINKS), Integer.MAX_VALUE, 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 < num_sym; 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 < num_sym; 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 > 1) {
		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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