pending commits while working on LWIR16 calibration (782eb01a) · Commits · Elphel / imagej-elphel

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

+60 −7

Original line number	Original line	Diff line number	Diff line
	@@ -1041,6 +1041,8 @@ if (MORE_BUTTONS) {
	addButton("Goniometer Move", panelLWIR,color_debug);		addButton("Goniometer Move", panelLWIR,color_debug);
	addButton("LWIR Goniometer", panelLWIR,color_conf_process);		addButton("LWIR Goniometer", panelLWIR,color_conf_process);
	addButton("LWIR grids", panelLWIR,color_process);		addButton("LWIR grids", panelLWIR,color_process);
			addButton("LWIR15 GEOM", panelLWIR,color_configure);

	addButton("Import Subsystem", panelLWIR,color_configure);		addButton("Import Subsystem", panelLWIR,color_configure);
	addButton("Select LWIR grids", panelLWIR,color_configure);		addButton("Select LWIR grids", panelLWIR,color_configure);
	addButton("Grid offset", panelLWIR,color_process);		addButton("Grid offset", panelLWIR,color_process);
	@@ -5822,7 +5824,7 @@ if (MORE_BUTTONS) {
	double patternHeight=PATTERN_PARAMETERS.patternHeight;		double patternHeight=PATTERN_PARAMETERS.patternHeight;
	double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;		double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;
	double targetAngleVertical= 360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;		double targetAngleVertical= 360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;
	if (DEBUG_LEVEL>0) System.out.println(		if (DEBUG_LEVEL>-1) System.out.println(
	"Using:\n"+		"Using:\n"+
	"Distance from target: "+IJ.d2s(distanceToTarget,1)+" mm\n"+		"Distance from target: "+IJ.d2s(distanceToTarget,1)+" mm\n"+
	" Taget width: "+IJ.d2s(patternWidth,1)+" mm\n"+		" Taget width: "+IJ.d2s(patternWidth,1)+" mm\n"+
	@@ -9387,6 +9389,7 @@ if (MORE_BUTTONS) {
	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("LWIR_ACQUIRE")) {		if (label.equals("LWIR_ACQUIRE")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			/*
	ImagePlus [][] imps;		ImagePlus [][] imps;
	if (LWIR_PARAMETERS.isLwir16()) {		if (LWIR_PARAMETERS.isLwir16()) {
	if (LWIR16_READER == null) {		if (LWIR16_READER == null) {
	@@ -9403,6 +9406,49 @@ if (MORE_BUTTONS) {
	LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save		LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
	// ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save		// ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
	}		}
			*/
			if ((GONIOMETER==null) \|\| (LWIR_PARAMETERS.isLwir16()?(GONIOMETER.lwir16Reader == null):(GONIOMETER.lwirReader == null))) {
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			GONIOMETER= new Goniometer(
			LWIR16_READER,
			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);
			LWIR16_READER.setMotorsPosition(GONIOMETER_PARAMETERS.goniometerMotors.getCurrentPositions()); // getTargetPositions()); // Used target, not current to prevent minor variations

			} else {
			if (LWIR_READER == null) {
			LWIR_READER = new LwirReader(LWIR_PARAMETERS);
			}
			GONIOMETER= new Goniometer(
			LWIR_READER,
			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);
			LWIR_READER.setMotorsPosition(GONIOMETER_PARAMETERS.goniometerMotors.getCurrentPositions()); // getTargetPositions()); // Used target, not current to prevent minor variations
			}
			if (DEBUG_LEVEL>1){
			System.out.println("Initialized Goniometer class for "+LWIR_PARAMETERS.getCameraName());
			}
			} else if (DEBUG_LEVEL>1){
			System.out.println("GONIOMETER was initialized for "+LWIR_PARAMETERS.getCameraName());
			}
			if (LWIR_PARAMETERS.isLwir16()) {
			LWIR16_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
			} else {
			LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
			}
	return;		return;
	}		}

	@@ -9451,7 +9497,7 @@ if (MORE_BUTTONS) {
	double patternHeight=PATTERN_PARAMETERS.patternHeight;		double patternHeight=PATTERN_PARAMETERS.patternHeight;
	double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;		double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;
	double targetAngleVertical= 360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;		double targetAngleVertical= 360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;
	if (DEBUG_LEVEL>0) System.out.println(		if (DEBUG_LEVEL>-1) System.out.println(
	"Using:\n"+		"Using:\n"+
	"Distance from target: "+IJ.d2s(distanceToTarget,1)+" mm\n"+		"Distance from target: "+IJ.d2s(distanceToTarget,1)+" mm\n"+
	" Taget width: "+IJ.d2s(patternWidth,1)+" mm\n"+		" Taget width: "+IJ.d2s(patternWidth,1)+" mm\n"+
	@@ -9475,6 +9521,12 @@ if (MORE_BUTTONS) {
	calculateLwirGrids();		calculateLwirGrids();
	return;		return;
	}		}
			/* ======================================================================== */
			if (label.equals("LWIR15 GEOM")) {
			EYESIS_CAMERA_PARAMETERS.setLwir16Geometry();
			return;
			}

	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("Import Subsystem")) {		if (label.equals("Import Subsystem")) {
	importSystem(null, "EYESIS_CAMERA_PARAMETERS.");		importSystem(null, "EYESIS_CAMERA_PARAMETERS.");
	@@ -9978,7 +10030,8 @@ if (MORE_BUTTONS) {
	//DistortionProcessConfiguration		//DistortionProcessConfiguration
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
	int min_files = 8; // use folders that have all 8 files		// Maybe wrong ! Use folders that have at least all EO channels?
			int min_files = lwirReaderParameters.getNumChannels();// 8; // use folders that have all 8 files
	int lwir_chn0 = lwirReaderParameters.getLwirChn0();		int lwir_chn0 = lwirReaderParameters.getLwirChn0();
	int eo_chn0 = lwirReaderParameters.getEoChn0();		int eo_chn0 = lwirReaderParameters.getEoChn0();
	int numStations = 3;		int numStations = 3;
	@@ -10011,7 +10064,7 @@ if (MORE_BUTTONS) {
	for (int numStation=0;numStation<numStations;numStation++){		for (int numStation=0;numStation<numStations;numStation++){
	DirectoryChoser dc = new DirectoryChoser(		DirectoryChoser dc = new DirectoryChoser(
	gridFilter,		gridFilter,
	min_files,		min_files, // not actually used
	0,		0,
	null);		null);
	dc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);		dc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
	@@ -10215,8 +10268,8 @@ if (MORE_BUTTONS) {

	matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
	matchSimulatedPattern.invalidateFocusMask();		matchSimulatedPattern.invalidateFocusMask();
	boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel);		boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel); // Not used!
	int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // matchSimulatedPattern.PATTERN_GRID already set
	LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,		LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,
	DISTORTION, //		DISTORTION, //
	PATTERN_DETECT,		PATTERN_DETECT,
	@@ -11543,7 +11596,7 @@ if (MORE_BUTTONS) {
	} else {		} else {
	System.out.println("No pattern grid file (ground gtruth) is provided");		System.out.println("No pattern grid file (ground gtruth) is provided");
	}		}
	if ((configPaths[3] !=null) && (configPaths[3] != "")){ // load sensor		if ((configPaths[3] !=null) && !configPaths[3].equals("")){ // load sensor
	if (distortions.fittingStrategy==null) return false; // Why?		if (distortions.fittingStrategy==null) return false; // Why?
	if (DEBUG_LEVEL>0) System.out.println("Autoloading sensor calibration files "+configPaths[3]);		if (DEBUG_LEVEL>0) System.out.println("Autoloading sensor calibration files "+configPaths[3]);
	distortions.setDistortionFromImageStack(		distortions.setDistortionFromImageStack(

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

+82 −46

Original line number	Original line	Diff line number	Diff line
	@@ -45,6 +45,7 @@ import com.elphel.imagej.common.PolynomialApproximation;
	import com.elphel.imagej.common.ShowDoubleFloatArrays;		import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;
	import com.elphel.imagej.jp4.JP46_Reader_camera;		import com.elphel.imagej.jp4.JP46_Reader_camera;
			import com.elphel.imagej.lwir.LwirReaderParameters;

	import Jama.Matrix;		import Jama.Matrix;
	import ij.IJ;		import ij.IJ;
	@@ -894,6 +895,24 @@ import ij.text.TextWindow;
	}		}

	// from data organized as image sets		// from data organized as image sets
			public static int getChannelFromPath(String path) {
			// int indexSuffix=path.length()-suffix.length();
			int indexSuffix = path.lastIndexOf(".");
			int indexLastDash=indexSuffix-1;
			while ((indexLastDash>0) &&
			(indexLastDash>(indexSuffix-3)) &&
			(path.charAt(indexLastDash)!='_') &&
			(path.charAt(indexLastDash)!='-')) indexLastDash--;
			return Integer.parseInt(path.substring(indexLastDash+1,indexSuffix));

			}

			private boolean invertColor(int chn) {
			//TODO: Add looking at the image property to find out if inversion is already contained in the grid files
			return eyesisCameraParameters.isLWIR(chn);

			}

	public void setupDirDistortionCalibrationData (		public void setupDirDistortionCalibrationData (
	String [][] stationFilenames, // per-station List of image set directories		String [][] stationFilenames, // per-station List of image set directories
	String [] source_dirs, // directories of the source files per station		String [] source_dirs, // directories of the source files per station
	@@ -927,9 +946,17 @@ import ij.text.TextWindow;
	// this.dir = dir;		// this.dir = dir;
	int dot_index = dir.lastIndexOf("_");		int dot_index = dir.lastIndexOf("_");
	String digits = "0123456789";		String digits = "0123456789";
			// allow "_<comment> after timestanp
			int end_pos =dir.length();
			while ((dot_index > 0) && (
			(digits.indexOf(dir.charAt(dot_index -1)) < 0) \|\|
			(digits.indexOf(dir.charAt(dot_index +1)) < 0))) { // not a digit before and after last "_"
			end_pos = dot_index;
			dot_index = dir.lastIndexOf("_", dot_index-1);
			}
	int ts_start = dot_index -1;		int ts_start = dot_index -1;
	while ((ts_start >=0) && (digits.indexOf(dir.charAt(ts_start)) >= 0)) ts_start--;		while ((ts_start >=0) && (digits.indexOf(dir.charAt(ts_start)) >= 0)) ts_start--;
	this.ts = Double.parseDouble(dir.substring(ts_start + 1).replace('_','.'));		this.ts = Double.parseDouble(dir.substring(ts_start + 1, end_pos).replace('_','.'));
	String [] files = (new File(dir)).list(gridFilter); // are these full files?		String [] files = (new File(dir)).list(gridFilter); // are these full files?
	paths = new String[num_chn];		paths = new String[num_chn];
	for (String path:files) {		for (String path:files) {
	@@ -1022,8 +1049,9 @@ import ij.text.TextWindow;
	String [] paths = dt.getPaths();		String [] paths = dt.getPaths();
	String [] spaths = dt.getSourcePaths();		String [] spaths = dt.getSourcePaths();
	int with_pointers = -1;		int with_pointers = -1;
	for (int nc = 0; nc < paths.length; nc++) {		for (int indx = 0; indx < paths.length; indx++) {
	String p = paths[nc];		String p = paths[indx];
			int nc = getChannelFromPath(p);
	boolean first_in_set = true;		boolean first_in_set = true;
	if (p != null) {		if (p != null) {
	this.gIP[numFile] = new GridImageParameters(numFile);		this.gIP[numFile] = new GridImageParameters(numFile);
	@@ -1031,11 +1059,13 @@ import ij.text.TextWindow;
	this.gIP[numFile].source_path = spaths[nc];		this.gIP[numFile].source_path = spaths[nc];
	this.gIP[numFile].setStationNumber(dt.getStation());		this.gIP[numFile].setStationNumber(dt.getStation());
	this.gIP[numFile].timestamp = dt.getTs();		this.gIP[numFile].timestamp = dt.getTs();
	this.gIP[numFile].channel = nc;		this.gIP[numFile].channel = nc; // **************** what if not all files present?- fixed this.gIP[numFile].setNumber = nis;
	this.gIP[numFile].setNumber = nis;
	this.gIP[numFile].gridImageSet = this.gIS[nis];		this.gIP[numFile].gridImageSet = this.gIS[nis];
			this.gIP[numFile].setNumber= nis;
	this.gIS[nis].imageSet[nc]=this.gIP[numFile];		this.gIS[nis].imageSet[nc]=this.gIP[numFile];
	boolean is_small = getImagePlusProperty(imp_grid,"WOI_WIDTH",0) <= MAX_LWIR_WIDTH;		// boolean is_small = getImagePlusProperty(imp_grid,"WOI_WIDTH",0) <= MAX_LWIR_WIDTH;
			boolean is_lwir = eyesisCameraParameters.isLWIR(nc);

	//numFile		//numFile
	if (first_in_set \|\| read_grids) {		if (first_in_set \|\| read_grids) {
	if (read_grids) {		if (read_grids) {
	@@ -1068,7 +1098,8 @@ import ij.text.TextWindow;
	System.out.print("<"+(this.gIP[numFile].matchedPointers));		System.out.print("<"+(this.gIP[numFile].matchedPointers));
	// Not using LWIR pointers here!		// Not using LWIR pointers here!
	// if (!ignore_LWIR_pointers \|\| (getImagePlusProperty(imp_grid,"WOI_TOP",0) > MAX_LWIR_WIDTH)) {		// if (!ignore_LWIR_pointers \|\| (getImagePlusProperty(imp_grid,"WOI_TOP",0) > MAX_LWIR_WIDTH)) {
	if (!ignore_LWIR_pointers \|\| !is_small) {		// if (!ignore_LWIR_pointers \|\| !is_small) { // here invert_color = true;
			if (!ignore_LWIR_pointers \|\| !eyesisCameraParameters.isLWIR(nc)) { // here invert_color = true;
	with_pointers = numFile;		with_pointers = numFile;
	System.out.print("\|"+numFile);		System.out.print("\|"+numFile);
	}		}
	@@ -1113,7 +1144,8 @@ import ij.text.TextWindow;


	int [] numBadNodes = new int [2];		int [] numBadNodes = new int [2];
	double badNodeThreshold = is_small? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;		// double badNodeThreshold = is_small? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;
			double badNodeThreshold = is_lwir? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;
	if (badNodeThreshold > 0.0){		if (badNodeThreshold > 0.0){
	boolean thisDebug =false;		boolean thisDebug =false;
	// thisDebug\|= (fileNumber== 720); // chn 25		// thisDebug\|= (fileNumber== 720); // chn 25
	@@ -1134,7 +1166,7 @@ import ij.text.TextWindow;
	if (disableNoFlatfield && !this.gIP[numFile].flatFieldAvailable) this.gIP[numFile].enabled=false; // just to use old mixed data		if (disableNoFlatfield && !this.gIP[numFile].flatFieldAvailable) this.gIP[numFile].enabled=false; // just to use old mixed data

	int [][] shiftRotMatrix= MatchSimulatedPattern.getRemapMatrix(this.gIP[numFile].getUVShiftRot());		int [][] shiftRotMatrix= MatchSimulatedPattern.getRemapMatrix(this.gIP[numFile].getUVShiftRot());
	int [] sizeSizeExtra=setGridsWithRemap(		int [] sizeSizeExtra=setGridsWithRemap( // apply current remap to the grid file data
	numFile,		numFile,
	shiftRotMatrix, // int [][] reMap,		shiftRotMatrix, // int [][] reMap,
	pixels,		pixels,
	@@ -1173,13 +1205,15 @@ import ij.text.TextWindow;
	}		}
	}		}
	if (with_pointers < 0) { // no matching pointers, will try to match selected channel with the pattern		if (with_pointers < 0) { // no matching pointers, will try to match selected channel with the pattern
	int main_channel = 4; // one of the EO channels to match with the pattern		// int main_channel = 4; // one of the EO channels to match with the pattern
			int main_channel = eyesisCameraParameters.getFirstHighRes(); // one of the EO channels to match with the pattern
	// boolean [] sensor_mask = null; // later may be used to limit scope to EO-only		// boolean [] sensor_mask = null; // later may be used to limit scope to EO-only
	int extra_search = 2;		int extra_search = 2;
	// int base_channel = this.gIP[with_pointers].channel;		// int base_channel = this.gIP[with_pointers].channel;
	if (this.gIS[nis].imageSet[main_channel] != null) {		if (this.gIS[nis].imageSet[main_channel] != null) {
	int imgNum = this.gIS[nis].imageSet[main_channel].imgNumber;		int imgNum = this.gIS[nis].imageSet[main_channel].imgNumber;
	boolean invert_color = (main_channel & 4) == 0; // first 4 - LWIR		// boolean invert_color = (main_channel & 4) == 0; // first 4 - LWIR
			boolean invert_color = invertColor(main_channel); // eyesisCameraParameters.isLWIR(main_channel);

	if (this.updateStatus) IJ.showStatus("Matching with the pattern, grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);		if (this.updateStatus) IJ.showStatus("Matching with the pattern, grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);
	if (this.debugLevel>-1) System.out.print(imgNum+">("+this.gIP[imgNum].getStationNumber()+		if (this.debugLevel>-1) System.out.print(imgNum+">("+this.gIP[imgNum].getStationNumber()+
	@@ -1199,7 +1233,7 @@ import ij.text.TextWindow;
	sensor_wh, // test set pixels width/height pair to reduce weight near the margins (or null)		sensor_wh, // test set pixels width/height pair to reduce weight near the margins (or null)
	false // true // boolean bdebug		false // true // boolean bdebug
	);		);
	System.out.print(" {"+uv_shift_rot[0]+":"+uv_shift_rot[1]+"]");		System.out.print(" {"+uv_shift_rot[0]+":"+uv_shift_rot[1]+"], invert_color="+invert_color);

	this.gIS[nis].imageSet[main_channel].setUVShiftRot(uv_shift_rot);		this.gIS[nis].imageSet[main_channel].setUVShiftRot(uv_shift_rot);

	@@ -1226,7 +1260,9 @@ import ij.text.TextWindow;
	int extra_search = 1;		int extra_search = 1;
	int base_channel = this.gIP[with_pointers].channel;		int base_channel = this.gIP[with_pointers].channel;
	for (int nc = 0; nc < this.gIS[nis].imageSet.length; nc++) if ((sensor_mask == null) \|\| sensor_mask[nc]) {		for (int nc = 0; nc < this.gIS[nis].imageSet.length; nc++) if ((sensor_mask == null) \|\| sensor_mask[nc]) {
	boolean invert_color = ((base_channel ^ nc) & 4) != 0;		// boolean invert_color = ((base_channel ^ nc) & 4) != 0;
			boolean invert_color = invertColor(base_channel) ^ invertColor(nc); // eyesisCameraParameters.isLWIR(main_channel);

	if ((this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions		if ((this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions
	int imgNum = this.gIS[nis].imageSet[nc].imgNumber; // with_pointers - base_channel + nc;		int imgNum = this.gIS[nis].imageSet[nc].imgNumber; // with_pointers - base_channel + nc;
	if (this.updateStatus) IJ.showStatus("Re-reading grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);		if (this.updateStatus) IJ.showStatus("Re-reading grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);
	@@ -1522,30 +1558,6 @@ import ij.text.TextWindow;
	}		}


	// suggest set grid offset by comparing with known (by mark) set.
	// Wrong Grid UV should cause parallel shift - same Z, different XY
	/*
	public int [] suggestOffset (
	int num_img,
	boolean non_estimated,
	boolean even,
	PatternParameters patternParameters) {
	int num_set = this.gIP[num_img].getSetNumber();
	double [] ref_xyz = getXYZFromMarked(num_set, non_estimated);
	if (ref_xyz == null) {
	System.out.println("Error: Could not find reference goniometer XYZ for set "+num_set);
	return null;
	}
	double [] diff_xyz = this.gIS[num_set].GXYZ.clone();
	for (int i = 0; i < diff_xyz.length; i++) diff_xyz[i]-=ref_xyz[i];
	return suggestOffset (
	num_img,
	diff_xyz, // z is not used, may ne just[2]
	even,
	patternParameters,
	null);
	}
	*/
	public int [] suggestOffset (		public int [] suggestOffset (
	int num_img,		int num_img,
	double [] diff_xyz, // This XYZ minus reference XYZ z is not used, may be just[2]		double [] diff_xyz, // This XYZ minus reference XYZ z is not used, may be just[2]
	@@ -1782,6 +1794,12 @@ import ij.text.TextWindow;
	for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);		for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
	sb.append("\n");		sb.append("\n");

			sb.append("LWIR/EO\t");
			for (int i=0;i<numSubCameras;i++) {
			sb.append("\t"+LwirReaderParameters.sensorName(eyesisCameraParameters.isLWIR(i)));
			}
			sb.append("\n");

	sb.append("Sensor width\t");		sb.append("Sensor width\t");
	for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));		for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
	sb.append("\n");		sb.append("\n");
	@@ -1796,8 +1814,14 @@ import ij.text.TextWindow;
	for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);		for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
	// parameters same order as in this		// parameters same order as in this
	for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){		for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){
			int digits = 3;
			if (getParameterName(n).startsWith("subcamP")) {
			digits = 2;
			} else if (getParameterName(n).startsWith("subcamDistortion")) {
			digits = 4;
			}
	sb.append(getParameterName(n)+"\t"+getParameterUnits(n));		sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
	for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));		for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],digits));
	sb.append("\n");		sb.append("\n");
	}		}
	sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");		sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
	@@ -1863,6 +1887,12 @@ import ij.text.TextWindow;
	// for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);		// for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
	// sb.append("\n");		// sb.append("\n");

			sb.append("LWIR/EO\t");
			for (int i=0;i<numSubCameras;i++) {
			sb.append("\t"+LwirReaderParameters.sensorName(eyesisCameraParameters.isLWIR(i)));
			}
			sb.append("\n");

	sb.append("Sensor width\t");		sb.append("Sensor width\t");
	for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));		for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
	sb.append("\n");		sb.append("\n");
	@@ -1941,7 +1971,9 @@ import ij.text.TextWindow;
	// sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");		// sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
	int flindex =getParameterIndexByName("subcamFocalLength");		int flindex =getParameterIndexByName("subcamFocalLength");
	sb.append(getParameterName(flindex)+"\t"+getParameterUnits(flindex));		sb.append(getParameterName(flindex)+"\t"+getParameterUnits(flindex));
	for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][flindex],3));		for (int i=0;i<numSubCameras;i++) {
			sb.append("\t"+IJ.d2s(cameraPars[i][flindex],3));
			}
	sb.append("\n");		sb.append("\n");

	sb.append("Camera roll"+"\t"+"degrees"+"\t"+IJ.d2s(commonRot,3));		sb.append("Camera roll"+"\t"+"degrees"+"\t"+IJ.d2s(commonRot,3));
	@@ -2394,7 +2426,8 @@ import ij.text.TextWindow;
	this.gIP[i].hintedMatch=0; // is it needed?		this.gIP[i].hintedMatch=0; // is it needed?
	this.gIP[i].enabled=false; // failed against minimal grid period (too far) - probably double reflection in the windows		this.gIP[i].enabled=false; // failed against minimal grid period (too far) - probably double reflection in the windows
	}		}
	if (this.gIP[i].hintedMatch==0) {		// if (this.gIP[i].hintedMatch==0) {
			if ((this.gIP[i].hintedMatch==0) && (this.gIP[i].matchedPointers < minPointers)) { // added
	this.gIP[i].enabled=false; // failed against predicted grid		this.gIP[i].enabled=false; // failed against predicted grid
	} else {		} else {
	if (		if (
	@@ -2572,7 +2605,7 @@ import ij.text.TextWindow;
	}		}
	if (bestRating>0){		if (bestRating>0){
	EyesisSubCameraParameters esp = this.eyesisCameraParameters.eyesisSubCameras[stationNumber][bestChannel];		EyesisSubCameraParameters esp = this.eyesisCameraParameters.eyesisSubCameras[stationNumber][bestChannel];
	System.out.println("Image number: "+this.gIS[i].imageSet[bestChannel].getImageNumber());		System.out.println("setInitialOrientation(): Image number: "+this.gIS[i].imageSet[bestChannel].getImageNumber());
	double [] uv_center = getGridUVfromXY(		double [] uv_center = getGridUVfromXY(
	esp.px0, // final double px,		esp.px0, // final double px,
	esp.py0, // final double py,		esp.py0, // final double py,
	@@ -2587,11 +2620,11 @@ import ij.text.TextWindow;
	if (this.debugLevel>0) {		if (this.debugLevel>0) {
	System.out.println("Center UV = "+uv_center[0]+","+uv_center[1]);		System.out.println("Center UV = "+uv_center[0]+","+uv_center[1]);
	}		}
			// Now will try bilinear interpolate first, then extrapolate
	double [] patt_xyz = patternParameters.getXYZ(		double [] patt_xyz = patternParameters.getXYZ(
	uv_center, // double [] uv,		uv_center, // double [] uv,
	false, // boolean verbose,		false, // boolean verbose,
	this.gIS[i].getStationNumber()); // int station); // u=0,v=0 - center!		this.gIS[i].getStationNumber()); // int station); // u=0,v=0 - center!

	if (patt_xyz == null) {		if (patt_xyz == null) {
	if (this.debugLevel>0) {		if (this.debugLevel>0) {
	System.out.println("Center UV = NULL");		System.out.println("Center UV = NULL");
	@@ -3886,7 +3919,8 @@ import ij.text.TextWindow;
	this.gIP[fileNumber].gridImage = imp_grid;		this.gIP[fileNumber].gridImage = imp_grid;
	}		}
	}		}
	boolean is_small = getImagePlusProperty(imp_grid,"WOI_WIDTH",0) <= MAX_LWIR_WIDTH;		// boolean is_small = getImagePlusProperty(imp_grid,"WOI_WIDTH",0) <= MAX_LWIR_WIDTH;
			boolean is_lwir = eyesisCameraParameters.isLWIR(this.gIP[fileNumber].channel);
	this.gIP[fileNumber].woi = new Rectangle(		this.gIP[fileNumber].woi = new Rectangle(
	getImagePlusProperty(imp_grid,"WOI_LEFT",0),		getImagePlusProperty(imp_grid,"WOI_LEFT",0),
	getImagePlusProperty(imp_grid,"WOI_TOP",0),		getImagePlusProperty(imp_grid,"WOI_TOP",0),
	@@ -3929,7 +3963,8 @@ import ij.text.TextWindow;
	woi_compensated = true;		woi_compensated = true;

	}		}
	double badNodeThreshold = is_small? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;		// double badNodeThreshold = is_small? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;
			double badNodeThreshold = is_lwir? this.eyesisCameraParameters.badNodeThresholdLWIR : this.eyesisCameraParameters.badNodeThreshold;
	// TODO: maybe adjust threshold to grid period, not the sensor type?		// TODO: maybe adjust threshold to grid period, not the sensor type?

	if (badNodeThreshold>0.0){		if (badNodeThreshold>0.0){
	@@ -3994,7 +4029,7 @@ import ij.text.TextWindow;
	}		}
	}		}
	}		}
	if (this.debugLevel>0) {		if (this.debugLevel>-1) {
	System.out.println("readAllGrids(), numImages="+numImages+", total number of grid nodes="+numOfGridNodes+", unused nodes "+numOfGridNodes_extra);		System.out.println("readAllGrids(), numImages="+numImages+", total number of grid nodes="+numOfGridNodes+", unused nodes "+numOfGridNodes_extra);
	}		}
	// probably - do not need to verify that this.gIS is null - should do that anyway. UPDATE: no, now reading config file creates gIS		// probably - do not need to verify that this.gIS is null - should do that anyway. UPDATE: no, now reading config file creates gIS
	@@ -4371,6 +4406,7 @@ import ij.text.TextWindow;
	return 0;		return 0;
	}		}

			// TODO: Cleanup below to use isLWIR form EyesisCameraParameters

	// get "effective" grid period scaled for low-res (as LWIR) sensors		// get "effective" grid period scaled for low-res (as LWIR) sensors
	public double getEffectivePeriod(int numImg) {		public double getEffectivePeriod(int numImg) {

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

+3 −0

Original line number	Original line	Diff line number	Diff line
	@@ -25,6 +25,7 @@ package com.elphel.imagej.calibration;

	import java.io.File;		import java.io.File;
	import java.io.FilenameFilter;		import java.io.FilenameFilter;
			import java.util.Arrays;
	import java.util.Properties;		import java.util.Properties;

	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;
	@@ -223,8 +224,10 @@ import ij.gui.GenericDialog;
	return new File(current, name).isDirectory();		return new File(current, name).isDirectory();
	}		}
	});		});
			// TODO:Sort set list
	String [] sourceSets = new String[sourceFileSets.length];		String [] sourceSets = new String[sourceFileSets.length];
	for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();		for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
			Arrays.sort(sourceSets);
	return sourceSets;		return sourceSets;
	}		}

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