updating correction (05f8b7db) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

+41 −6

Original line number	Original line	Diff line number	Diff line
	@@ -2081,7 +2081,7 @@ if (MORE_BUTTONS) {
	if (label.equals("List Eyesis4pi") \|\| label.equals("List X-cam")) {		if (label.equals("List Eyesis4pi") \|\| label.equals("List X-cam")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	DistortionCalibrationData dcd=(DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA:		DistortionCalibrationData dcd=(DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA:
	new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS);		new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS,GONIOMETER_PARAMETERS);
	dcd.listCameraParameters(label.equals("List X-cam"));		dcd.listCameraParameters(label.equals("List X-cam"));
	return;		return;
	}		}
	@@ -2137,11 +2137,27 @@ if (MORE_BUTTONS) {
	PATTERN_PARAMETERS.debugLevel=MASTER_DEBUG_LEVEL;		PATTERN_PARAMETERS.debugLevel=MASTER_DEBUG_LEVEL;
	EYESIS_CAMERA_PARAMETERS.updateNumstations (numStations);		EYESIS_CAMERA_PARAMETERS.updateNumstations (numStations);
	//if (MASTER_DEBUG_LEVEL==0) return; //TODO: Remove - just debugging		//if (MASTER_DEBUG_LEVEL==0) return; //TODO: Remove - just debugging

			if (GONIOMETER==null) {
			GONIOMETER= new Goniometer(
			CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
			DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
			PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
			EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
			LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
			SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,
			GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
			DISTORTION_PROCESS_CONFIGURATION
			);
			}


	DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(
	gridFiles,		gridFiles,
	PATTERN_PARAMETERS,		PATTERN_PARAMETERS,
	EYESIS_CAMERA_PARAMETERS,		EYESIS_CAMERA_PARAMETERS,
	LASER_POINTERS,		LASER_POINTERS,
			GONIOMETER_PARAMETERS,
	MASTER_DEBUG_LEVEL);		MASTER_DEBUG_LEVEL);
	LENS_DISTORTIONS.initImageSet(		LENS_DISTORTIONS.initImageSet(
	DISTORTION_CALIBRATION_DATA,		DISTORTION_CALIBRATION_DATA,
	@@ -2178,7 +2194,6 @@ if (MORE_BUTTONS) {
	if (label.equals("Restore Calibration")) {		if (label.equals("Restore Calibration")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	String defaultPath= (DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA.pathName:"";		String defaultPath= (DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA.pathName:"";
	// public static DistortionCalibrationData DISTORTION_CALIBRATION_DATA=null;
	DistortionCalibrationData oldDISTORTION_CALIBRATION_DATA=DISTORTION_CALIBRATION_DATA;		DistortionCalibrationData oldDISTORTION_CALIBRATION_DATA=DISTORTION_CALIBRATION_DATA;
	DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(
	false,		false,
	@@ -2187,6 +2202,7 @@ if (MORE_BUTTONS) {
	EYESIS_CAMERA_PARAMETERS,		EYESIS_CAMERA_PARAMETERS,
	ABERRATIONS_PARAMETERS,		ABERRATIONS_PARAMETERS,
	LASER_POINTERS,		LASER_POINTERS,
			GONIOMETER_PARAMETERS,
	null); // gridImages null - use specified files		null); // gridImages null - use specified files
	if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file		if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file
	DISTORTION_CALIBRATION_DATA=oldDISTORTION_CALIBRATION_DATA;		DISTORTION_CALIBRATION_DATA=oldDISTORTION_CALIBRATION_DATA;
	@@ -3563,6 +3579,7 @@ if (MORE_BUTTONS) {
	EYESIS_CAMERA_PARAMETERS, // is it null or 1?		EYESIS_CAMERA_PARAMETERS, // is it null or 1?
	ABERRATIONS_PARAMETERS,		ABERRATIONS_PARAMETERS,
	LASER_POINTERS,		LASER_POINTERS,
			GONIOMETER_PARAMETERS,
	imp_calibrated); // gridImages null - use specified files - single image		imp_calibrated); // gridImages null - use specified files - single image
	if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file		if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file
	DISTORTION_CALIBRATION_DATA=null;		DISTORTION_CALIBRATION_DATA=null;
	@@ -6262,7 +6279,8 @@ if (MORE_BUTTONS) {
	}		}
	// initialize needed classes		// initialize needed classes
	DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet
	EYESIS_CAMERA_PARAMETERS); //EyesisCameraParameters eyesisCameraParameters		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters
			GONIOMETER_PARAMETERS);
	if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)) {		if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)) {
	LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA;		LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA;
	}		}
	@@ -9861,6 +9879,7 @@ if (MORE_BUTTONS) {
	PATTERN_PARAMETERS,		PATTERN_PARAMETERS,
	EYESIS_CAMERA_PARAMETERS,		EYESIS_CAMERA_PARAMETERS,
	LASER_POINTERS, //LaserPointer laserPointers		LASER_POINTERS, //LaserPointer laserPointers
			GONIOMETER_PARAMETERS, //
	true, // boolean read_grids		true, // boolean read_grids
	MASTER_DEBUG_LEVEL);		MASTER_DEBUG_LEVEL);

	@@ -9868,7 +9887,7 @@ if (MORE_BUTTONS) {
	DISTORTION_CALIBRATION_DATA,		DISTORTION_CALIBRATION_DATA,
	EYESIS_CAMERA_PARAMETERS		EYESIS_CAMERA_PARAMETERS
	);		);
	// set initial orientation of the cameras from the sensors that see mpst of the matching pointers		// set initial orientation of the cameras from the sensors that see most of the matching pointers
	// just for the LMA to start		// just for the LMA to start
	DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);		DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
	return true;		return true;
	@@ -9899,6 +9918,7 @@ if (MORE_BUTTONS) {
	null,		null,
	LENS_DISTORTIONS,		LENS_DISTORTIONS,
	DISTORTION_CALIBRATION_DATA, // may be null, then it will not be updated, obviously (sensor masks)		DISTORTION_CALIBRATION_DATA, // may be null, then it will not be updated, obviously (sensor masks)
			GONIOMETER_PARAMETERS, // for motor sensitivity
	ABERRATIONS_PARAMETERS.calibrationDirectory);//String calibration_directory		ABERRATIONS_PARAMETERS.calibrationDirectory);//String calibration_directory
	//getProperties(String prefix,Properties properties)		//getProperties(String prefix,Properties properties)
	//EyesisCameraParameters		//EyesisCameraParameters
	@@ -9951,6 +9971,7 @@ if (MORE_BUTTONS) {
	" (of "+ sourceFilesList[nset].length+"), file "+in_file+" (of "+ numFiles+ ") success in "+saved_file+" - "+sourceFilesList[nset][nfile]);		" (of "+ sourceFilesList[nset].length+"), file "+in_file+" (of "+ numFiles+ ") success in "+saved_file+" - "+sourceFilesList[nset][nfile]);
	}		}
	String grid_path = null;		String grid_path = null;
			/*
	if (saveGrids && !overwriteGrids){ // check if result already exists		if (saveGrids && !overwriteGrids){ // check if result already exists
	i = sourceFilesList[nset][nfile].lastIndexOf('/');		i = sourceFilesList[nset][nfile].lastIndexOf('/');
	if (i>0){		if (i>0){
	@@ -9961,6 +9982,19 @@ if (MORE_BUTTONS) {
	continue;		continue;
	}		}
	}		}
			}
			*/

			if (saveGrids){ // check if result already exists
			i = sourceFilesList[nset][nfile].lastIndexOf('/');
			if (i>0){
			String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
			grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
			if (!overwriteGrids && ((new File(grid_path)).exists())){ // check if result already exists
			if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
			continue;
			}
			}
	}		}
	imp_sel=new ImagePlus(sourceFilesList[nset][nfile]); // read source file		imp_sel=new ImagePlus(sourceFilesList[nset][nfile]); // read source file
	EyesisTiff.decodeProperiesFromInfo(imp_sel);		EyesisTiff.decodeProperiesFromInfo(imp_sel);
	@@ -11260,6 +11294,7 @@ if (MORE_BUTTONS) {
	eyesisCameraParameters,		eyesisCameraParameters,
	aberrationParameters,		aberrationParameters,
	laserPointers,		laserPointers,
			GONIOMETER_PARAMETERS,
	null); // gridImages null - use specified files		null); // gridImages null - use specified files
	if (distortions.fittingStrategy!=null) {		if (distortions.fittingStrategy!=null) {
	distortions.fittingStrategy.distortionCalibrationData=dcd;		distortions.fittingStrategy.distortionCalibrationData=dcd;
	@@ -11291,7 +11326,7 @@ if (MORE_BUTTONS) {
	if (configPaths[2] !=null){ // load grid file		if (configPaths[2] !=null){ // load grid file
	patternParameters.debugLevel=debugLevel;		patternParameters.debugLevel=debugLevel;
	patternParameters.updateStatus=updateStstus;		patternParameters.updateStatus=updateStstus;
	if (DEBUG_LEVEL>0) System.out.println("Autolading grid file "+configPaths[2]);		if (DEBUG_LEVEL>0) System.out.println("Autoloading grid file "+configPaths[2]);
	patternParameters.selectAndRestore(true,configPaths[2],dcd.eyesisCameraParameters.numStations); // returns path or null on failure		patternParameters.selectAndRestore(true,configPaths[2],dcd.eyesisCameraParameters.numStations); // returns path or null on failure
	} else {		} else {
	System.out.println("No pattern grid file (ground gtruth) is provided");		System.out.println("No pattern grid file (ground gtruth) is provided");

src/main/java/com/elphel/imagej/calibration/DistortionCalibrationData.java

+126 −24

Original line number	Original line	Diff line number	Diff line
	@@ -70,6 +70,7 @@ import ij.text.TextWindow;
	public static final int INDEX_B = 7;		public static final int INDEX_B = 7;
	public static final double SMALL_FRACTION = 0.8; // consider sensor to be a "small" if average grid period < this fraction of the large		public static final double SMALL_FRACTION = 0.8; // consider sensor to be a "small" if average grid period < this fraction of the large

			Goniometer.GoniometerParameters goniometerParameters = null;
	public String pathName=null;		public String pathName=null;
	public EyesisCameraParameters eyesisCameraParameters; // has "cartesian"		public EyesisCameraParameters eyesisCameraParameters; // has "cartesian"
	public int numSubCameras=1;		public int numSubCameras=1;
	@@ -631,14 +632,16 @@ import ij.text.TextWindow;
	String [] filenames,		String [] filenames,
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers		LaserPointer laserPointers,
			Goniometer.GoniometerParameters goniometerParameters
	) {		) {
	String [][] stationFilenames={filenames};		String [][] stationFilenames={filenames};
	setupDistortionCalibrationData(		setupDistortionCalibrationData(
	stationFilenames,		stationFilenames,
	patternParameters,		patternParameters,
	eyesisCameraParameters, // debugLevel		eyesisCameraParameters, // debugLevel
	laserPointers		laserPointers,
			goniometerParameters
	);		);
	}		}
	public DistortionCalibrationData (		public DistortionCalibrationData (
	@@ -646,6 +649,7 @@ import ij.text.TextWindow;
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers,		LaserPointer laserPointers,
			Goniometer.GoniometerParameters goniometerParameters,
	int debugLevel		int debugLevel
	) {		) {
	this.debugLevel=debugLevel;		this.debugLevel=debugLevel;
	@@ -654,7 +658,8 @@ import ij.text.TextWindow;
	stationFilenames,		stationFilenames,
	patternParameters,		patternParameters,
	eyesisCameraParameters, // debugLevel		eyesisCameraParameters, // debugLevel
	laserPointers		laserPointers,
			goniometerParameters
	);		);
	}		}

	@@ -663,6 +668,7 @@ import ij.text.TextWindow;
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers,		LaserPointer laserPointers,
			Goniometer.GoniometerParameters goniometerParameters,
	int debugLevel		int debugLevel
	) {		) {
	this.debugLevel=debugLevel;		this.debugLevel=debugLevel;
	@@ -670,7 +676,8 @@ import ij.text.TextWindow;
	stationFilenames,		stationFilenames,
	patternParameters,		patternParameters,
	eyesisCameraParameters, // debugLevel		eyesisCameraParameters, // debugLevel
	laserPointers		laserPointers,
			goniometerParameters
	);		);
	}		}

	@@ -682,6 +689,7 @@ import ij.text.TextWindow;
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers, // as a backup if data is not available in the file		LaserPointer laserPointers, // as a backup if data is not available in the file
			Goniometer.GoniometerParameters goniometerParameters,
	boolean read_grids,		boolean read_grids,
	int debugLevel		int debugLevel
	) {		) {
	@@ -694,6 +702,7 @@ import ij.text.TextWindow;
	patternParameters,		patternParameters,
	eyesisCameraParameters, // debugLevel		eyesisCameraParameters, // debugLevel
	laserPointers, // as a backup if data is not available in the file		laserPointers, // as a backup if data is not available in the file
			goniometerParameters,
	read_grids		read_grids
	);		);
	}		}
	@@ -703,8 +712,10 @@ import ij.text.TextWindow;
	String [][] stationFilenames,		String [][] stationFilenames,
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers // as a backup if data is not available in the file		LaserPointer laserPointers, // as a backup if data is not available in the file
			Goniometer.GoniometerParameters goniometerParameters
	) {		) {
			this.goniometerParameters = goniometerParameters;
	setupIndices();		setupIndices();
	this.eyesisCameraParameters=eyesisCameraParameters;		this.eyesisCameraParameters=eyesisCameraParameters;
	int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;		int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;
	@@ -772,6 +783,7 @@ import ij.text.TextWindow;
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers, // as a backup if data is not available in the file		LaserPointer laserPointers, // as a backup if data is not available in the file
			Goniometer.GoniometerParameters goniometerParameters,
	boolean read_grids		boolean read_grids
	) {		) {
	class DirTs{		class DirTs{
	@@ -836,6 +848,7 @@ import ij.text.TextWindow;
	}		}
	}		}
	}		}
			this.goniometerParameters = goniometerParameters;
	boolean ignore_LWIR_pointers = true; // skip LWIR absolute marks, use them later		boolean ignore_LWIR_pointers = true; // skip LWIR absolute marks, use them later
	int max_lwir_width = 1023; // use LWIR class		int max_lwir_width = 1023; // use LWIR class
	setupIndices();		setupIndices();
	@@ -1548,9 +1561,11 @@ import ij.text.TextWindow;


	public DistortionCalibrationData (		public DistortionCalibrationData (
	EyesisCameraParameters eyesisCameraParameters		EyesisCameraParameters eyesisCameraParameters,
			Goniometer.GoniometerParameters goniometerParameters
	) {		) {
	setupIndices();		setupIndices();
			this.goniometerParameters = goniometerParameters;
	int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;		int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;

	this.numSubCameras=numSubCameras;		this.numSubCameras=numSubCameras;
	@@ -1562,9 +1577,11 @@ import ij.text.TextWindow;
	ImagePlus [] images, // images in the memory		ImagePlus [] images, // images in the memory
	PatternParameters patternParameters,		PatternParameters patternParameters,
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	LaserPointer laserPointers		LaserPointer laserPointers,
			Goniometer.GoniometerParameters goniometerParameters
	) {		) {
	setupIndices();		setupIndices();
			this.goniometerParameters = goniometerParameters;
	int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;		int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;
	this.numSubCameras=numSubCameras;		this.numSubCameras=numSubCameras;
	this.eyesisCameraParameters=eyesisCameraParameters;		this.eyesisCameraParameters=eyesisCameraParameters;
	@@ -2690,9 +2707,11 @@ import ij.text.TextWindow;
	if (this.debugLevel>0) System.out.println("Failed to find any known orientation");		if (this.debugLevel>0) System.out.println("Failed to find any known orientation");
	return null;		return null;
	}		}
	if (late_set <0) iBest= early_set;		if (late_set <0) {
	else if (early_set <0) iBest= late_set;		iBest= early_set;
	else {		} else if (early_set <0) {
			iBest= late_set;
			} else {
	// interpolate		// interpolate
	double axialEarly=this.gIS[early_set].goniometerAxial;		double axialEarly=this.gIS[early_set].goniometerAxial;
	double axialLate= this.gIS[late_set].goniometerAxial;		double axialLate= this.gIS[late_set].goniometerAxial;
	@@ -2745,9 +2764,12 @@ import ij.text.TextWindow;
	}		}
	this.gIS[i].orientationEstimated=true;		this.gIS[i].orientationEstimated=true;
	double [] result = {		double [] result = {
	this.gIS[iBest].goniometerTilt,		// this.gIS[iBest].goniometerTilt,
	this.gIS[iBest].goniometerAxial,		// this.gIS[iBest].goniometerAxial,
	this.gIS[iBest].interAxisAngle		/// this.gIS[iBest].interAxisAngle
			this.gIS[i].goniometerTilt,
			this.gIS[i].goniometerAxial,
			this.gIS[i].interAxisAngle
	};		};
	return result;		return result;
	}		}
	@@ -2768,14 +2790,17 @@ import ij.text.TextWindow;
	if ( // (j!=i) && // not needed - this set does not have orientation		if ( // (j!=i) && // not needed - this set does not have orientation
	(this.gIS[j].getStationNumber()==stationNumber) &&		(this.gIS[j].getStationNumber()==stationNumber) &&
	(this.gIS[j].motors[mHorizontal]==thisMotorHorizontal) &&		(this.gIS[j].motors[mHorizontal]==thisMotorHorizontal) &&
			!this.gIS[j].orientationEstimated && // new
	!Double.isNaN(this.gIS[j].goniometerTilt) &&		!Double.isNaN(this.gIS[j].goniometerTilt) &&
	!Double.isNaN(this.gIS[j].goniometerAxial) &&		!Double.isNaN(this.gIS[j].goniometerAxial) &&
	!Double.isNaN(this.gIS[j].interAxisAngle)){		!Double.isNaN(this.gIS[j].interAxisAngle)){
			System.out.println("Found image set "+j+" with timestamp "+ timeStamp + " with known attitude to estimate this attitude");
	setList.add(new Integer(j));		setList.add(new Integer(j));
	}		}
	}		}
	if (setList.size()>=2){		if (setList.size()>=2){
	if (this.debugLevel>2) System.out.println("getImagesetTiltAxial("+timeStamp+"): estimating orientation for set # "+i+": this.debugLevel="+this.debugLevel);		// if (this.debugLevel>2) System.out.println("getImagesetTiltAxial("+timeStamp+"): estimating orientation for set # "+i+": this.debugLevel="+this.debugLevel);
			if (this.debugLevel > -1) System.out.println("getImagesetTiltAxial("+timeStamp+"): estimating orientation for set # "+i+": this.debugLevel="+this.debugLevel);
	// find the closest one		// find the closest one
	int indexClosest=setList.get(0);		int indexClosest=setList.get(0);
	double dClosest=Math.abs(this.gIS[indexClosest].motors[mAxial]-thisMotorAxial);		double dClosest=Math.abs(this.gIS[indexClosest].motors[mAxial]-thisMotorAxial);
	@@ -2849,10 +2874,22 @@ import ij.text.TextWindow;
	") is not defined, using interpolated between sets # "+indexClosest+" (timestamp "+IJ.d2s(this.gIS[indexClosest].timeStamp,6)+") "+		") is not defined, using interpolated between sets # "+indexClosest+" (timestamp "+IJ.d2s(this.gIS[indexClosest].timeStamp,6)+") "+
	"and # "+indexSecond+" (timestamp "+IJ.d2s(this.gIS[indexSecond].timeStamp,6)+")");		"and # "+indexSecond+" (timestamp "+IJ.d2s(this.gIS[indexSecond].timeStamp,6)+")");
	}		}
			// } else if (setList.size() >= 1){
			// if (this.debugLevel > -1) System.out.println("getImagesetTiltAxial("+timeStamp+
			// "): estimating orientation for set # "+i+" from a single set "+setList.get(0)+": this.debugLevel="+this.debugLevel);

	} else { // old way		} else { // old way
			// first try for the same station number only:
			iBest = -1;
	double d2Min=-1;		double d2Min=-1;
	for (int j=0;j<this.gIS.length;j++) if ((j!=i) && (this.gIS[j].motors!=null) &&		int station_number = this.gIS[i].getStationNumber();
	!Double.isNaN(this.gIS[j].goniometerTilt) && !Double.isNaN(this.gIS[j].goniometerAxial ) && !Double.isNaN(this.gIS[j].interAxisAngle)) {		for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&
			(this.gIS[j].getStationNumber() == station_number) &&
			!this.gIS[j].orientationEstimated &&
			(this.gIS[j].motors!=null) &&
			!Double.isNaN(this.gIS[j].goniometerTilt) &&
			!Double.isNaN(this.gIS[j].goniometerAxial ) &&
			!Double.isNaN(this.gIS[j].interAxisAngle)) {
	double d2=0;		double d2=0;
	for (int k=0;k<this.gIS[j].motors.length;k++){		for (int k=0;k<this.gIS[j].motors.length;k++){
	d2+=1.0(this.gIS[j].motors[k]-this.gIS[i].motors[k])		d2+=1.0(this.gIS[j].motors[k]-this.gIS[i].motors[k])
	@@ -2863,21 +2900,84 @@ import ij.text.TextWindow;
	iBest=j;		iBest=j;
	}		}
	}		}
			if (iBest < 0) {
			d2Min=-1;
			for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&
			(this.gIS[j].motors!=null) &&
			!this.gIS[j].orientationEstimated &&
			!Double.isNaN(this.gIS[j].goniometerTilt) &&
			!Double.isNaN(this.gIS[j].goniometerAxial ) &&
			!Double.isNaN(this.gIS[j].interAxisAngle)) {
			double d2=0;
			for (int k=0;k<this.gIS[j].motors.length;k++){
			d2+=1.0(this.gIS[j].motors[k]-this.gIS[i].motors[k])
			(this.gIS[j].motors[k]-this.gIS[i].motors[k]);
			}
			if ((d2Min<0) \|\| (d2Min>d2)) {
			d2Min=d2;
			iBest=j;
	}		}
	}		}
	double [] result = {		if (iBest < 0) {
	this.gIS[iBest].goniometerTilt,		d2Min=-1;
	this.gIS[iBest].goniometerAxial,		for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&
	this.gIS[iBest].interAxisAngle		(this.gIS[j].motors!=null) &&
	};		!Double.isNaN(this.gIS[j].goniometerTilt) &&
			!Double.isNaN(this.gIS[j].goniometerAxial ) &&
			!Double.isNaN(this.gIS[j].interAxisAngle)) {
			double d2=0;
			for (int k=0;k<this.gIS[j].motors.length;k++){
			d2+=1.0(this.gIS[j].motors[k]-this.gIS[i].motors[k])
			(this.gIS[j].motors[k]-this.gIS[i].motors[k]);
			}
			if ((d2Min<0) \|\| (d2Min>d2)) {
			d2Min=d2;
			iBest=j;
			}
			}
			System.out.println("Used any station numer with even estimated orientation, iBest = "+iBest);
			} else {
			System.out.println("Used different station numer, iBest = "+iBest);
			}
			} else {
			System.out.println("Used the same station number, iBest = "+iBest);

			}


			}
			}
			// double [] result = {
			// this.gIS[iBest].goniometerTilt,
			// this.gIS[iBest].goniometerAxial,
			// this.gIS[iBest].interAxisAngle
			// };
	if (iBest!=i){		if (iBest!=i){
			boolean usable_tilt = (this.gIS[i].motors != null);
			boolean usable_axial = usable_tilt && (this.gIS[i].getStationNumber() == this.gIS[iBest].getStationNumber());
			double diff_axial = usable_axial? (this.gIS[i].motors[mAxial]-this.gIS[iBest].motors[mAxial])/
			goniometerParameters.goniometerMotors.stepsPerDegreeAxial : 0.0;
			double diff_horizontal = usable_tilt? (this.gIS[i].motors[mHorizontal]-this.gIS[iBest].motors[mHorizontal])/
			goniometerParameters.goniometerMotors.stepsPerDegreeTilt: 0.0;
			this.gIS[i].goniometerTilt = this.gIS[iBest].goniometerTilt + diff_horizontal;
			this.gIS[i].goniometerAxial = this.gIS[iBest].goniometerAxial + diff_axial;

			this.gIS[i].goniometerTilt-=360.0*Math.floor((this.gIS[i].goniometerTilt+180.0)/360.0);
			this.gIS[i].goniometerAxial-=360.0*Math.floor((this.gIS[i].goniometerAxial+180.0)/360.0);

	if (this.debugLevel>0) System.out.println("Orientation for set # "+i+" timestamp "+IJ.d2s(this.gIS[i].timeStamp,6)+		if (this.debugLevel>0) System.out.println("Orientation for set # "+i+" timestamp "+IJ.d2s(this.gIS[i].timeStamp,6)+
	") is not defined, using # "+iBest+" (timestamp "+IJ.d2s(this.gIS[iBest].timeStamp,6)+")" );		") is not defined, estimating from # "+iBest+" (timestamp "+IJ.d2s(this.gIS[iBest].timeStamp,6)+")" );
	this.gIS[i].orientationEstimated=true;		this.gIS[i].orientationEstimated=true;
	this.gIS[i].goniometerTilt= this.gIS[iBest].goniometerTilt;		// this.gIS[i].goniometerTilt= this.gIS[iBest].goniometerTilt;
	this.gIS[i].goniometerAxial=this.gIS[iBest].goniometerAxial;		// this.gIS[i].goniometerAxial=this.gIS[iBest].goniometerAxial;
	this.gIS[i].interAxisAngle=this.gIS[iBest].interAxisAngle;		this.gIS[i].interAxisAngle=this.gIS[iBest].interAxisAngle;
	}		}
			double [] result = {
			this.gIS[i].goniometerTilt,
			this.gIS[i].goniometerAxial,
			this.gIS[i].interAxisAngle
			};

	return result; // may have Double.NaN		return result; // may have Double.NaN
	}		}
	return null;		return null;
	@@ -2942,7 +3042,9 @@ import ij.text.TextWindow;
	EyesisCameraParameters eyesisCameraParameters,		EyesisCameraParameters eyesisCameraParameters,
	EyesisAberrations.AberrationParameters aberrationParameters,		EyesisAberrations.AberrationParameters aberrationParameters,
	LaserPointer laserPointers,		LaserPointer laserPointers,
			Goniometer.GoniometerParameters goniometerParameters,
	ImagePlus[] gridImages ){ // null - use specified files		ImagePlus[] gridImages ){ // null - use specified files
			this.goniometerParameters = goniometerParameters;
	setupIndices();		setupIndices();
	String [] extensions={".dcal-xml","-distcal.xml"};		String [] extensions={".dcal-xml","-distcal.xml"};
	MultipleExtensionsFileFilter parFilter = new MultipleExtensionsFileFilter("",extensions,"Distortion calibration *.dcal-xml files");		MultipleExtensionsFileFilter parFilter = new MultipleExtensionsFileFilter("",extensions,"Distortion calibration *.dcal-xml files");

src/main/java/com/elphel/imagej/calibration/Distortions.java

+2 −1

Original line number	Original line	Diff line number	Diff line
	@@ -3026,6 +3026,7 @@ For each point in the image
	if (imp.getRoi() instanceof PointRoi) {		if (imp.getRoi() instanceof PointRoi) {
	pointRoi = (PointRoi) imp.getRoi();		pointRoi = (PointRoi) imp.getRoi();
	} else {		} else {
			System.out.println("This image does not have point marks - please mark it in "+source_path);
	IJ.showMessage("This image does not have point marks - please mark it in "+source_path);		IJ.showMessage("This image does not have point marks - please mark it in "+source_path);
	return null;		return null;
	}		}
	@@ -3123,7 +3124,7 @@ For each point in the image
	xyuv[i][3]=0.5;		xyuv[i][3]=0.5;
	}		}
	GenericDialog gd=new GenericDialog("Specify U,V coordinates of the marker(s)");		GenericDialog gd=new GenericDialog("Specify U,V coordinates of the marker(s)");
	gd.addMessage("Center white cell U=0.5, V=0.5");		gd.addMessage("Center white (LWIR black) cell U=0.5, V=0.5");
	for (int n = 0; n < markers.length; n++) {		for (int n = 0; n < markers.length; n++) {
	String label = "Marker "+(n+1)+" (x="+markers[n][0]+", y="+markers[n][1];		String label = "Marker "+(n+1)+" (x="+markers[n][0]+", y="+markers[n][1];
	gd.addNumericField(label+" U", xyuv[n][2], 1, 5, "");		gd.addNumericField(label+" U", xyuv[n][2], 1, 5, "");

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

+33 −5

Original line number	Original line	Diff line number	Diff line
	@@ -24,6 +24,7 @@ package com.elphel.imagej.calibration;
	**		**
	*/		*/

			import java.awt.Point;
	import java.awt.Rectangle;		import java.awt.Rectangle;
	import java.util.ArrayList;		import java.util.ArrayList;
	import java.util.Arrays;		import java.util.Arrays;
	@@ -49,6 +50,7 @@ import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
	import ij.IJ;		import ij.IJ;
	import ij.ImagePlus;		import ij.ImagePlus;
	import ij.ImageStack;		import ij.ImageStack;
			import ij.gui.PointRoi;
	import ij.gui.Roi;		import ij.gui.Roi;
	import ij.process.FHT; // get rid, change to double		import ij.process.FHT; // get rid, change to double
	import ij.process.FloatProcessor;		import ij.process.FloatProcessor;
	@@ -3133,7 +3135,7 @@ public class MatchSimulatedPattern {
	if (roi==null){		if (roi==null){
	selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());		selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
	} else {		} else {
	selection=roi.getBounds();		selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
	}		}
	MatchSimulatedPattern matchSimulatedPattern=new MatchSimulatedPattern(distortionParameters.FFTSize);		MatchSimulatedPattern matchSimulatedPattern=new MatchSimulatedPattern(distortionParameters.FFTSize);
	matchSimulatedPattern.debugLevel=debugLevel;		matchSimulatedPattern.debugLevel=debugLevel;
	@@ -3299,7 +3301,7 @@ public class MatchSimulatedPattern {
	if (roi==null){		if (roi==null){
	selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());		selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
	} else {		} else {
	selection=roi.getBounds();		selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
	}		}
	Rectangle initialPatternCell=new Rectangle(xc-fft_size,		Rectangle initialPatternCell=new Rectangle(xc-fft_size,
	yc-fft_size,		yc-fft_size,
	@@ -3626,7 +3628,7 @@ public class MatchSimulatedPattern {
	if (roi==null){		if (roi==null){
	selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());		selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
	} else {		} else {
	selection=roi.getBounds();		selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
	}		}
	} else {		} else {
	if ((getImageHeight()!=imp.getHeight()) \|\| (getImageWidth()!=imp.getWidth())){		if ((getImageHeight()!=imp.getHeight()) \|\| (getImageWidth()!=imp.getWidth())){
	@@ -6190,12 +6192,36 @@ public class MatchSimulatedPattern {
	Roi roi= imp.getRoi();		Roi roi= imp.getRoi();
	Rectangle selection;		Rectangle selection;
	if (roi==null){		if (roi==null){
			setWOI(0, 0, imp.getWidth(), imp.getHeight());
			selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
			} else {
			if (roi instanceof PointRoi) {
			PointRoi pointRoi = (PointRoi) roi;
			Point [] points = pointRoi.getContainedPoints();
			int [][] ipoints = new int [points.length][2];
			for (int n = 0; n < ipoints.length; n++) {
			ipoints[n][0] = points[n].x;
			ipoints[n][1] = points[n].y;
			}
			// as if they a laser pointers
			double [][] xyuv = new double [points.length][4];
			for (int i =0; i < ipoints.length; i++) {
			xyuv[i][0]=ipoints[i][0];
			xyuv[i][1]=ipoints[i][1];
			xyuv[i][2]=0.5;
			xyuv[i][3]=0.5;
			}
			System.out.println("Setting first marker (of "+ipoints.length+") as pointer 0.5/0.5 - use use multiple?");
			System.out.println("** Not yet implemented, use 'Manual hint' command for each of the annotated files **");
			// setPointersXYUV(imp, xyuv);

	setWOI(0, 0, imp.getWidth(), imp.getHeight());		setWOI(0, 0, imp.getWidth(), imp.getHeight());
	selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());		selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
	} else {		} else {
	setWOI(roi.getBounds());		setWOI(roi.getBounds());
	selection=roi.getBounds();		selection=roi.getBounds();
	}		}
			}
	this.debugLevel=global_debug_level;		this.debugLevel=global_debug_level;
	int patternCells=0;		int patternCells=0;
	// save initial distortionParameters.correlationMinInitialContrast		// save initial distortionParameters.correlationMinInitialContrast
	@@ -6377,6 +6403,8 @@ public class MatchSimulatedPattern {

	int numPointers=(laserPointer!=null)?laserPointer.laserUVMap.length:0;		int numPointers=(laserPointer!=null)?laserPointer.laserUVMap.length:0;
	double [][] pointersXY=(numPointers>0)?getPointersXYUV(imp, laserPointer):null;		double [][] pointersXY=(numPointers>0)?getPointersXYUV(imp, laserPointer):null;


	if (global_debug_level > (debugThreshold+1)){		if (global_debug_level > (debugThreshold+1)){
	if (pointersXY!=null){		if (pointersXY!=null){
	System.out.println("calculateDistortions() numPointers="+numPointers+" pointersXY.length="+pointersXY.length);		System.out.println("calculateDistortions() numPointers="+numPointers+" pointersXY.length="+pointersXY.length);

src/main/java/com/elphel/imagej/cameras/EyesisCameraParameters.java

+5 −2

File changed.

Preview size limit exceeded, changes collapsed.

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