Added randomized ML offset, command to re-measure ml files from saved (f91340a7) · Commits · Elphel / imagej-elphel

src/main/java/BiQuadParameters.java

+11 −0

src/main/java/Eyesis_Correction.java

+192 −2

Original line number	Original line	Diff line number	Diff line
	@@ -50,6 +50,18 @@ import java.io.InputStream;
	import java.io.OutputStream;		import java.io.OutputStream;
	import java.io.PrintWriter;		import java.io.PrintWriter;
	import java.io.StringWriter;		import java.io.StringWriter;
			import java.nio.file.FileVisitOption;
			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.attribute.BasicFileAttributes;
			import java.util.ArrayList;
			import java.util.Collections;
			import java.util.Comparator;
			import java.util.EnumSet;
			import java.util.List;
	//import java.io.FileFilter;		//import java.io.FileFilter;
	//import java.io.FilenameFilter;		//import java.io.FilenameFilter;
	import java.util.Properties;		import java.util.Properties;
	@@ -615,6 +627,7 @@ private Panel panel1,
	panelClt5.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap		panelClt5.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
	addButton("LIST extrinsics", panelClt5, color_report);		addButton("LIST extrinsics", panelClt5, color_report);
	addButton("DSI histogram", panelClt5, color_report);		addButton("DSI histogram", panelClt5, color_report);
			addButton("ML recalc", panelClt5, color_process);
	add(panelClt5);		add(panelClt5);
	}		}

	@@ -4590,10 +4603,21 @@ private Panel panel1,
	return;		return;
	/* ======================================================================== */		/* ======================================================================== */
	} else if (label.equals("LIST extrinsics")) {		} else if (label.equals("LIST extrinsics")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	listExtrinsics();		listExtrinsics();
	return;		return;
			/* ======================================================================== */
			} else if (label.equals("ML recalc")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
			mlRecalc();
			return;
			//
	/* ======================================================================== */		/* ======================================================================== */
	} else if (label.equals("DSI histogram")) {		} else if (label.equals("DSI histogram")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	dsiHistogram();		dsiHistogram();
	return;		return;

	@@ -5472,6 +5496,7 @@ private Panel panel1,
	QUAD_CLT, // QuadCLT quadCLT_main,		QUAD_CLT, // QuadCLT quadCLT_main,
	QUAD_CLT_AUX, // QuadCLT quadCLT_aux,		QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
	CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
			null, //String ml_directory, // full path or null (will use config one)
	THREADS_MAX, //final int threadsMax, // maximal number of threads to launch		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
	UPDATE_STATUS, //final boolean updateStatus,		UPDATE_STATUS, //final boolean updateStatus,
	DEBUG_LEVEL);		DEBUG_LEVEL);
	@@ -5610,10 +5635,175 @@ private Panel panel1,
	if (dir!=null) {		if (dir!=null) {
	System.out.println("top directory = "+dir);		System.out.println("top directory = "+dir);
	}		}
	// return TwoQuadCLT.listExtrinsics(dir); // , mask);
	return MLStats.listExtrinsics(dir); // , mask);		return MLStats.listExtrinsics(dir); // , mask);
	//(new MLStats).
	}		}

			public boolean mlRecalc() {
			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);
			}
			// return MLStats.mlRecalc(dir); // , mask);
			return mlRecalc(dir); // , mask);
			}

			public boolean mlRecalc(String dir)
			// EyesisCorrectionParameters.CLTParameters clt_parameters,
			// EyesisCorrectionParameters.DebayerParameters debayerParameters,
			// EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
			// EyesisCorrectionParameters.RGBParameters rgbParameters,
			// final int threadsMax, // maximal number of threads to launch
			// final boolean updateStatus,
			// final int debugLevel) throws Exception

			{
			String mask = ".*EXTRINSICS\\.corr-xml";
			String full_conf_suffix = ".corr-xml";
			String dsi_suffix = "-DSI_COMBO.tiff";
			String correction_parameters_prefix = "CORRECTION_PARAMETERS.";

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

			final List<Path> files=new ArrayList<>();
			final String fMask = mask;
			Path path= Paths.get(dir);
			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();
			return false;
			}
			int indx = 0;
			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();
			// String root = p.getRoot().toString();
			Path parent = p.getParent();
			// System.out.println(indx+": model:"+model+", version:"+version+", name: "+name);
			Path full_conf_path = p.resolveSibling(model+full_conf_suffix);
			Path dsi_combo_path = p.resolveSibling(model+dsi_suffix);
			System.out.println(indx+": model:"+model+", version:"+version+", name: "+name+ ", parent="+parent+", full_conf_path="+full_conf_path);
			// See if there is a full configuration file and DSI combo
			if (!full_conf_path.toFile().exists()) {
			System.out.println("Full configuration file for the model:"+model+", version:"+version+": "+full_conf_path+" does not exist");
			continue;
			}
			if (!dsi_combo_path.toFile().exists()) {
			System.out.println("DSI combo file (GT data) for the model:"+model+", version:"+version+": "+dsi_combo_path+" does not exist");
			continue;
			}
			// overwrite extrinsics in current properties form the model file
			MLStats.loadProperties(
			full_conf_path.toString(), // String path,
			PROPERTIES); // Properties properties)

			Properties full_properties = MLStats.loadProperties(
			full_conf_path.toString(), // String path,
			null); // Properties properties)
			// String [] sourcePaths = null;
			ArrayList<String> source_list = new ArrayList<String>();
			if (full_properties.getProperty(correction_parameters_prefix+"sourcePaths")!= null){
			int numFiles=Integer.parseInt(full_properties.getProperty(correction_parameters_prefix+"sourcePaths"));
			// sourcePaths=new String[numFiles];
			for (int i = 0; i < numFiles; i++){
			String src=full_properties.getProperty(correction_parameters_prefix+"sourcePath"+i);
			Path src_path=Paths.get(src);
			if (src_path.getName(src_path.getNameCount()-1).toString().contains(model)){
			source_list.add(src);
			}
			}
			} else {
			System.out.println("Source files are not povided for the model:"+model+", version:"+version+" in "+full_conf_path);
			continue;
			}
			Collections.sort(source_list, new Comparator<String>() {
			@Override
			public int compare(String lhs, String rhs) {
			// -1 - less than, 1 - greater than, 0 - equal, not inverted for ascending disparity
			return lhs.compareTo(rhs);
			}
			});




			// String [] sourcePaths = source_list.toArray(new String[0]);
			CORRECTION_PARAMETERS.sourcePaths= source_list.toArray(new String[0]);



			System.out.println("Got "+ source_list.size() +" source files");
			QUAD_CLT = null;
			QUAD_CLT_AUX = null; // reset images

			if (!prepareRigImages()) { // will use extrinsics properties
			return false;
			}
			// QuadCLT qcm = QUAD_CLT; // just to debug
			// QuadCLT qca = QUAD_CLT_AUX;
			String mldir=CORRECTION_PARAMETERS.mlDirectory;
			if (mldir.equals("ml")) {
			mldir = "ml"; // not to overwrite original data
			}
			try {
			TWO_QUAD_CLT.regenerateML(
			dsi_combo_path.toString(), // String path_DSI, // Combo DSI path
			parent.toString(), // String model_dir, // model/version directory
			mldir, // "ml1", // String ml_subdir, // new ML subdir (or null to use configuartion one)
			QUAD_CLT, // QuadCLT quadCLT_main,
			QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
			CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
			DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
			COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
			RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
			THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
			UPDATE_STATUS, //final boolean updateStatus,
			DEBUG_LEVEL);


			} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			} //final int debugLevel);



			if (indx > 0) { //-1) {
			return true; // temporarily
			}
			indx++;
			}
			}



			return true;
			}





	public boolean dsiHistogram() {		public boolean dsiHistogram() {
	String dir= CalibrationFileManagement.selectDirectory(		String dir= CalibrationFileManagement.selectDirectory(
	false, // true, // smart,		false, // true, // smart,

src/main/java/MLStats.java

+123 −0

Original line number	Original line	Diff line number	Diff line
	@@ -420,6 +420,129 @@ public class MLStats {
	return true;		return true;

	}		}

			public static boolean mlRecalc(String dir,
			EyesisCorrectionParameters.CLTParameters clt_parameters,
			EyesisCorrectionParameters.DebayerParameters debayerParameters,
			EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
			EyesisCorrectionParameters.RGBParameters rgbParameters,
			final int threadsMax, // maximal number of threads to launch
			final boolean updateStatus,
			final int debugLevel) throws Exception

			{
			String mask = ".*EXTRINSICS\\.corr-xml";
			String full_conf_suffix = ".corr-xml";
			String dsi_suffix = "-DSI_COMBO.tiff";
			String correction_parameters_prefix = "CORRECTION_PARAMETERS.";

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

			final List<Path> files=new ArrayList<>();
			final String fMask = mask;
			Path path= Paths.get(dir);
			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();
			return false;
			}
			int indx = 0;
			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();
			// String root = p.getRoot().toString();
			Path parent = p.getParent();
			// System.out.println(indx+": model:"+model+", version:"+version+", name: "+name);
			Path full_conf_path = p.resolveSibling(model+full_conf_suffix);
			Path dsi_combo_path = p.resolveSibling(model+dsi_suffix);
			System.out.println(indx+": model:"+model+", version:"+version+", name: "+name+ ", parent="+parent+", full_conf_path="+full_conf_path);
			// See if there is a full configuration file and DSI combo
			if (!full_conf_path.toFile().exists()) {
			System.out.println("Full configuration file for model:"+model+", version:"+version+": "+full_conf_path+" does not exist");
			continue;
			}
			if (!dsi_combo_path.toFile().exists()) {
			System.out.println("DSI combo file (GT data) for model:"+model+", version:"+version+": "+dsi_combo_path+" does not exist");
			continue;
			}
			Properties full_properties = loadProperties(
			full_conf_path.toString(), // String path,
			null); // Properties properties)
			// String [] sourcePaths = null;
			ArrayList<String> source_list = new ArrayList<String>();
			if (full_properties.getProperty(correction_parameters_prefix+"sourcePaths")!= null){
			int numFiles=Integer.parseInt(full_properties.getProperty(correction_parameters_prefix+"sourcePaths"));
			// sourcePaths=new String[numFiles];
			for (int i = 0; i < numFiles; i++){
			String src=full_properties.getProperty(correction_parameters_prefix+"sourcePath"+i);
			Path src_path=Paths.get(src);
			if (src_path.getName(src_path.getNameCount()-1).toString().contains(model)){
			source_list.add(src);
			}
			}
			} else {
			System.out.println("Source files are not povided for model:"+model+", version:"+version+" in "+full_conf_path);
			continue;
			}
			System.out.println("Got "+ source_list.size() +" source files");

			if (indx > -1) {
			return true; // temporarily
			}

			/*
			*
			this.sourcePaths=new String[numFiles];
			for (int i=0;i<this.sourcePaths.length;i++){
			this.sourcePaths[i]=properties.getProperty(prefix+"sourcePath"+i);
			}

			*
			*
			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();
			*/
			indx++;
			}
			}



			return true;
			}


	public static boolean listExtrinsics(String dir) // , String mask)		public static boolean listExtrinsics(String dir) // , String mask)
	{		{
	Path path= Paths.get(dir);		Path path= Paths.get(dir);

Original line number	Original line	Diff line number	Diff line
	@@ -251,6 +251,8 @@ public class BiQuadParameters {
	public double ml_disparity_sweep = 1.0; // Disparity sweep around ground truth, each side		public double ml_disparity_sweep = 1.0; // Disparity sweep around ground truth, each side
	public int ml_sweep_steps = 21; // Number of disparity sweep steps		public int ml_sweep_steps = 21; // Number of disparity sweep steps

			public boolean ml_randomize = true; // randomize ofset within 1 step (reduces ml_sweep_steps by 1)

	public boolean ml_keep_aux = false; // true; // include auxiliary camera data in the ML output		public boolean ml_keep_aux = false; // true; // include auxiliary camera data in the ML output
	public boolean ml_keep_inter = false; // true; // include inter-camera correlation data in the ML output		public boolean ml_keep_inter = false; // true; // include inter-camera correlation data in the ML output
	public boolean ml_keep_hor_vert = true; // include combined horizontal and vertical pairs data in the ML output		public boolean ml_keep_hor_vert = true; // include combined horizontal and vertical pairs data in the ML output
	@@ -657,6 +659,10 @@ public class BiQuadParameters {
	"Sweep symmetrically target disparity around the ground truth disparity, each side");		"Sweep symmetrically target disparity around the ground truth disparity, each side");
	gd.addNumericField("Number of target disparity sweep steps", this.ml_sweep_steps, 0,3,"",		gd.addNumericField("Number of target disparity sweep steps", this.ml_sweep_steps, 0,3,"",
	"Generate this many files for each file set. Each tile results depend on the target disparity and this tile data, do not depend on other tiles target disparity");		"Generate this many files for each file set. Each tile results depend on the target disparity and this tile data, do not depend on other tiles target disparity");

			gd.addCheckbox ("Randomize offset", this.ml_randomize,
			"Each tile will have individual offset, but it the range between the filename and next higher. Reduces sweep steps by 1");

	gd.addCheckbox ("Include auxiliary camera data in the ML output", this.ml_keep_aux,		gd.addCheckbox ("Include auxiliary camera data in the ML output", this.ml_keep_aux,
	"ML output will have the second set of the layers for the auxiliary camera. Disparity values should be scaled for the camera baseline");		"ML output will have the second set of the layers for the auxiliary camera. Disparity values should be scaled for the camera baseline");
	gd.addCheckbox ("Keep inter-camera correlation data", this.ml_keep_inter,		gd.addCheckbox ("Keep inter-camera correlation data", this.ml_keep_inter,
	@@ -875,6 +881,7 @@ public class BiQuadParameters {
	this.ml_hwidth= (int) gd.getNextNumber();		this.ml_hwidth= (int) gd.getNextNumber();
	this.ml_disparity_sweep= gd.getNextNumber();		this.ml_disparity_sweep= gd.getNextNumber();
	this.ml_sweep_steps= (int) gd.getNextNumber();		this.ml_sweep_steps= (int) gd.getNextNumber();
			this.ml_randomize= gd.getNextBoolean();
	this.ml_keep_aux= gd.getNextBoolean();		this.ml_keep_aux= gd.getNextBoolean();
	this.ml_keep_inter= gd.getNextBoolean();		this.ml_keep_inter= gd.getNextBoolean();
	this.ml_keep_tbrl= gd.getNextBoolean();		this.ml_keep_tbrl= gd.getNextBoolean();
	@@ -1085,6 +1092,7 @@ public class BiQuadParameters {
	properties.setProperty(prefix+"ml_hwidth", this.ml_hwidth+"");		properties.setProperty(prefix+"ml_hwidth", this.ml_hwidth+"");
	properties.setProperty(prefix+"ml_disparity_sweep", this.ml_disparity_sweep+"");		properties.setProperty(prefix+"ml_disparity_sweep", this.ml_disparity_sweep+"");
	properties.setProperty(prefix+"ml_sweep_steps", this.ml_sweep_steps+"");		properties.setProperty(prefix+"ml_sweep_steps", this.ml_sweep_steps+"");
			properties.setProperty(prefix+"ml_randomize", this.ml_randomize+"");
	properties.setProperty(prefix+"ml_keep_aux", this.ml_keep_aux+"");		properties.setProperty(prefix+"ml_keep_aux", this.ml_keep_aux+"");
	properties.setProperty(prefix+"ml_keep_inter", this.ml_keep_inter+"");		properties.setProperty(prefix+"ml_keep_inter", this.ml_keep_inter+"");
	properties.setProperty(prefix+"ml_keep_tbrl", this.ml_keep_tbrl+"");		properties.setProperty(prefix+"ml_keep_tbrl", this.ml_keep_tbrl+"");
	@@ -1292,6 +1300,8 @@ public class BiQuadParameters {
	if (properties.getProperty(prefix+"ml_hwidth")!=null) this.ml_hwidth=Integer.parseInt(properties.getProperty(prefix+"ml_hwidth"));		if (properties.getProperty(prefix+"ml_hwidth")!=null) this.ml_hwidth=Integer.parseInt(properties.getProperty(prefix+"ml_hwidth"));
	if (properties.getProperty(prefix+"ml_disparity_sweep")!=null) this.ml_disparity_sweep=Double.parseDouble(properties.getProperty(prefix+"ml_disparity_sweep"));		if (properties.getProperty(prefix+"ml_disparity_sweep")!=null) this.ml_disparity_sweep=Double.parseDouble(properties.getProperty(prefix+"ml_disparity_sweep"));
	if (properties.getProperty(prefix+"ml_sweep_steps")!=null) this.ml_sweep_steps=Integer.parseInt(properties.getProperty(prefix+"ml_sweep_steps"));		if (properties.getProperty(prefix+"ml_sweep_steps")!=null) this.ml_sweep_steps=Integer.parseInt(properties.getProperty(prefix+"ml_sweep_steps"));

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