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

		addButton("Import Subsystem", panelLWIR,color_configure);
		addButton("Select LWIR grids", panelLWIR,color_configure);
		addButton("Grid offset", panelLWIR,color_process);
		@@ -5822,7 +5824,7 @@ if (MORE_BUTTONS) {
		double patternHeight=PATTERN_PARAMETERS.patternHeight;
		double targetAngleHorizontal=360*Math.atan(patternWidth/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"+
		"Distance from target: "+IJ.d2s(distanceToTarget,1)+" mm\n"+
		" Taget width: "+IJ.d2s(patternWidth,1)+" mm\n"+
		@@ -9387,6 +9389,7 @@ if (MORE_BUTTONS) {
		/* ======================================================================== */
		if (label.equals("LWIR_ACQUIRE")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		/*
		ImagePlus [][] imps;
		if (LWIR_PARAMETERS.isLwir16()) {
		if (LWIR16_READER == null) {
		@@ -9403,6 +9406,49 @@ if (MORE_BUTTONS) {
		LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // 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;
		}

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

		/* ======================================================================== */
		if (label.equals("Import Subsystem")) {
		importSystem(null, "EYESIS_CAMERA_PARAMETERS.");
		@@ -9978,7 +10030,8 @@ if (MORE_BUTTONS) {
		//DistortionProcessConfiguration
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		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 eo_chn0 = lwirReaderParameters.getEoChn0();
		int numStations = 3;
		@@ -10011,7 +10064,7 @@ if (MORE_BUTTONS) {
		for (int numStation=0;numStation<numStations;numStation++){
		DirectoryChoser dc = new DirectoryChoser(
		gridFilter,
		min_files,
		min_files, // not actually used
		0,
		null);
		dc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
		@@ -10215,8 +10268,8 @@ if (MORE_BUTTONS) {

		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
		matchSimulatedPattern.invalidateFocusMask();
		boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel);
		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
		boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel); // Not used!
		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // matchSimulatedPattern.PATTERN_GRID already set
		LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,
		DISTORTION, //
		PATTERN_DETECT,
		@@ -11543,7 +11596,7 @@ if (MORE_BUTTONS) {
		} else {
		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 (DEBUG_LEVEL>0) System.out.println("Autoloading sensor calibration files "+configPaths[3]);
		distortions.setDistortionFromImageStack(

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

+82 −46

Original line number	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.WindowTools;
		import com.elphel.imagej.jp4.JP46_Reader_camera;
		import com.elphel.imagej.lwir.LwirReaderParameters;

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

		// 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 (
		String [][] stationFilenames, // per-station List of image set directories
		String [] source_dirs, // directories of the source files per station
		@@ -927,9 +946,17 @@ import ij.text.TextWindow;
		// this.dir = dir;
		int dot_index = dir.lastIndexOf("_");
		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;
		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?
		paths = new String[num_chn];
		for (String path:files) {
		@@ -1022,8 +1049,9 @@ import ij.text.TextWindow;
		String [] paths = dt.getPaths();
		String [] spaths = dt.getSourcePaths();
		int with_pointers = -1;
		for (int nc = 0; nc < paths.length; nc++) {
		String p = paths[nc];
		for (int indx = 0; indx < paths.length; indx++) {
		String p = paths[indx];
		int nc = getChannelFromPath(p);
		boolean first_in_set = true;
		if (p != null) {
		this.gIP[numFile] = new GridImageParameters(numFile);
		@@ -1031,11 +1059,13 @@ import ij.text.TextWindow;
		this.gIP[numFile].source_path = spaths[nc];
		this.gIP[numFile].setStationNumber(dt.getStation());
		this.gIP[numFile].timestamp = dt.getTs();
		this.gIP[numFile].channel = nc;
		this.gIP[numFile].setNumber = nis;
		this.gIP[numFile].channel = nc; // **************** what if not all files present?- fixed this.gIP[numFile].setNumber = nis;
		this.gIP[numFile].gridImageSet = this.gIS[nis];
		this.gIP[numFile].setNumber= nis;
		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
		if (first_in_set \|\| read_grids) {
		if (read_grids) {
		@@ -1068,7 +1098,8 @@ import ij.text.TextWindow;
		System.out.print("<"+(this.gIP[numFile].matchedPointers));
		// Not using LWIR pointers here!
		// 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;
		System.out.print("\|"+numFile);
		}
		@@ -1113,7 +1144,8 @@ import ij.text.TextWindow;


		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){
		boolean thisDebug =false;
		// 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

		int [][] shiftRotMatrix= MatchSimulatedPattern.getRemapMatrix(this.gIP[numFile].getUVShiftRot());
		int [] sizeSizeExtra=setGridsWithRemap(
		int [] sizeSizeExtra=setGridsWithRemap( // apply current remap to the grid file data
		numFile,
		shiftRotMatrix, // int [][] reMap,
		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
		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
		int extra_search = 2;
		// int base_channel = this.gIP[with_pointers].channel;
		if (this.gIS[nis].imageSet[main_channel] != null) {
		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.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)
		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);

		@@ -1226,7 +1260,9 @@ import ij.text.TextWindow;
		int extra_search = 1;
		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]) {
		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
		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);
		@@ -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 (
		int num_img,
		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]);
		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");
		for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
		sb.append("\n");
		@@ -1796,8 +1814,14 @@ import ij.text.TextWindow;
		for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
		// parameters same order as in this
		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));
		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("---"); 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]);
		// 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");
		for (int i=0;i<numSubCameras;i++) sb.append("\t"+eyesisCameraParameters.getSensorWidth(i));
		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");
		int flindex =getParameterIndexByName("subcamFocalLength");
		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("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].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
		} else {
		if (
		@@ -2572,7 +2605,7 @@ import ij.text.TextWindow;
		}
		if (bestRating>0){
		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(
		esp.px0, // final double px,
		esp.py0, // final double py,
		@@ -2587,11 +2620,11 @@ import ij.text.TextWindow;
		if (this.debugLevel>0) {
		System.out.println("Center UV = "+uv_center[0]+","+uv_center[1]);
		}
		// Now will try bilinear interpolate first, then extrapolate
		double [] patt_xyz = patternParameters.getXYZ(
		uv_center, // double [] uv,
		false, // boolean verbose,
		this.gIS[i].getStationNumber()); // int station); // u=0,v=0 - center!

		if (patt_xyz == null) {
		if (this.debugLevel>0) {
		System.out.println("Center UV = NULL");
		@@ -3886,7 +3919,8 @@ import ij.text.TextWindow;
		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(
		getImagePlusProperty(imp_grid,"WOI_LEFT",0),
		getImagePlusProperty(imp_grid,"WOI_TOP",0),
		@@ -3929,7 +3963,8 @@ import ij.text.TextWindow;
		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?

		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);
		}
		// 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;
		}

		// TODO: Cleanup below to use isLWIR form EyesisCameraParameters

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

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

+3 −0

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

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

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

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

+40 −2

File changed.

Preview size limit exceeded, changes collapsed.

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

+6 −2

Original line number	Diff line number	Diff line
		@@ -2016,6 +2016,9 @@ public class MatchSimulatedPattern {
		ix = (interpolateXY[maxIndex][0] + j) % size;
		for (int i = 0; i < 2; i++) {
		iy = interpolateXY[maxIndex][1] + i; // next: OOB 2147483647
		if (iy >= fft_complex.length) {
		iy = fft_complex.length - 1; // was Index 17 out of bounds for length 17
		}
		interpolateAmplitudes[maxIndex][i][j] = Math.sqrt(fft_complex[iy][ix][0] * fft_complex[iy][ix][0]
		+ fft_complex[iy][ix][1] * fft_complex[iy][ix][1]);
		interpolatePhases[maxIndex][i][j] = Math.atan2(
		@@ -7688,7 +7691,7 @@ public class MatchSimulatedPattern {
		int shiftSelect = (((shifts[0][0] - coeff[0][2]) * (shifts[0][0] - coeff[0][2]) + (shifts[0][1] - coeff[1][2])
		* (shifts[0][1] - coeff[1][2])) > ((shifts[1][0] - coeff[0][2]) * (shifts[1][0] - coeff[0][2])
		+ (shifts[1][1] - coeff[1][2]) * (shifts[1][1] - coeff[1][2]))) ? 1 : 0;
		if (this.debugLevel > 1) {
		if (this.debugLevel > 0) {
		double d1 = Math.sqrt((shifts[0][0] - coeff[0][2]) * (shifts[0][0] - coeff[0][2])
		+ (shifts[0][1] - coeff[1][2]) * (shifts[0][1] - coeff[1][2]));
		double d2 = Math.sqrt((shifts[1][0] - coeff[0][2]) * (shifts[1][0] - coeff[0][2])
		@@ -8068,7 +8071,8 @@ public class MatchSimulatedPattern {
		numCells++;
		}
		if (numCells > 0) {
		setPatternGridArray(maxU - minU + 1, maxV - minV + 1);
		// setPatternGridArray(maxU - minU + 1, maxV - minV + 1); // FIXME: Does nothing
		this.PATTERN_GRID = setPatternGridArray(maxU - minU + 1, maxV - minV + 1); // FIXME: Does nothing
		double[] xy = new double[2];
		int[] uv = new int[2];
		for (int i = 0; i < pixels[0].length; i++)

Admin message