Debugging fitting strategies, initial image parameter setup (96c4558f) · Commits · Elphel / imagej-elphel

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

+34 −15

Original line number	Original line	Diff line number	Diff line
	@@ -2634,6 +2634,7 @@ if (MORE_BUTTONS) {
	parFilter,		parFilter,
	""); //String defaultPath		""); //String defaultPath
	if ((pathname==null) \|\| (pathname=="")) return;		if ((pathname==null) \|\| (pathname=="")) return;
			System.out.println("*** Will not work with different size senspors !!!");
	DISTORTION_CALIBRATION_DATA.setMaskFromImageStack(pathname);		DISTORTION_CALIBRATION_DATA.setMaskFromImageStack(pathname);
	if (LENS_DISTORTIONS!=null) LENS_DISTORTIONS.updateSensorMasks();		if (LENS_DISTORTIONS!=null) LENS_DISTORTIONS.updateSensorMasks();
	return;		return;
	@@ -3642,8 +3643,8 @@ if (MORE_BUTTONS) {


	double threadPitch=0.35; // M1.6		double threadPitch=0.35; // M1.6
	double dPx0=camPars.eyesisSubCameras[stationNumber][0].px0-(camPars.sensorWidth/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaX;		double dPx0=camPars.eyesisSubCameras[stationNumber][0].px0-(camPars.getSensorWidth(0)/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaX;
	double dPy0=camPars.eyesisSubCameras[stationNumber][0].py0-(camPars.sensorHeight/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaY;		double dPy0=camPars.eyesisSubCameras[stationNumber][0].py0-(camPars.getSensorHeight(0)/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaY;
	double psi=camPars.eyesisSubCameras[stationNumber][0].psi; // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target		double psi=camPars.eyesisSubCameras[stationNumber][0].psi; // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target

	FOCUS_MEASUREMENT_PARAMETERS.result_PX0=camPars.eyesisSubCameras[stationNumber][0].px0;		FOCUS_MEASUREMENT_PARAMETERS.result_PX0=camPars.eyesisSubCameras[stationNumber][0].px0;
	@@ -5026,8 +5027,8 @@ if (MORE_BUTTONS) {
	if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"].length="+sfeParameters[numSFE].length);		if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"].length="+sfeParameters[numSFE].length);
	if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"]["+iLens+"].length="+sfeParameters[numSFE][iLens].length);		if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"]["+iLens+"].length="+sfeParameters[numSFE][iLens].length);
	sfeParameters[numSFE][iLens][iState]=FOCUS_MEASUREMENT_PARAMETERS.clone();		sfeParameters[numSFE][iLens][iState]=FOCUS_MEASUREMENT_PARAMETERS.clone();
	sensorDimensions[numSFE][0]=EYESIS_CAMERA_PARAMETERS.sensorWidth; // should be the same for all lenses/states		sensorDimensions[numSFE][0]=EYESIS_CAMERA_PARAMETERS.getSensorWidth(numSFE); // should be the same for all lenses/states
	sensorDimensions[numSFE][1]=EYESIS_CAMERA_PARAMETERS.sensorHeight;		sensorDimensions[numSFE][1]=EYESIS_CAMERA_PARAMETERS.getSensorHeight(numSFE);
	iState++;		iState++;
	}		}
	iLens++;		iLens++;
	@@ -5492,12 +5493,12 @@ if (MORE_BUTTONS) {
	String path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+		String path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+
	(modeAverage?"-summary.csv":"-tempscan.csv");		(modeAverage?"-summary.csv":"-tempscan.csv");
	if (MASTER_DEBUG_LEVEL>0) System.out.println ((modeAverage?"Saving averaged measurements to ":"Saving temperature measurement log data to ")+path);		if (MASTER_DEBUG_LEVEL>0) System.out.println ((modeAverage?"Saving averaged measurements to ":"Saving temperature measurement log data to ")+path);
	int sensorWidth=2992,sensorHeight=1936;		int sensorWidth=2592,sensorHeight=1936;
	if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)&&		if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)&&
	(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData!=null) &&		(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData!=null) &&
	(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters!=null)){		(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters!=null)){
	sensorWidth=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.sensorWidth;		sensorWidth=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(0);
	sensorHeight=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.sensorHeight;		sensorHeight=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(0);
	}		}
	if (FOCUSING_FIELD!=null){		if (FOCUSING_FIELD!=null){
	sensorWidth=FOCUSING_FIELD.sensorWidth;		sensorWidth=FOCUSING_FIELD.sensorWidth;
	@@ -5918,7 +5919,12 @@ if (MORE_BUTTONS) {
	IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set");		IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set");
	return;		return;
	}		}
	LENS_DISTORTIONS.listImageSets();		GenericDialog gd=new GenericDialog ("Select list mode");
			gd.addNumericField("Mode 0 - old, 1 - shift/Rots", 0, 0);
			gd.showDialog();
			if (gd.wasCanceled()) return;
			int listMode= (int) gd.getNextNumber();
			LENS_DISTORTIONS.listImageSets(listMode);
	return;		return;
	}		}
	/* ======================================================================== */		/* ======================================================================== */
	@@ -8986,12 +8992,20 @@ if (MORE_BUTTONS) {
	for (int nChn=0;nChn<masks.length;nChn++) if ((nChn<selectedChannels.length)&&!selectedChannels[nChn]) masks[nChn]=null;		for (int nChn=0;nChn<masks.length;nChn++) if ((nChn<selectedChannels.length)&&!selectedChannels[nChn]) masks[nChn]=null;
	}		}

	if (showSensorMasks) this.SDFA_INSTANCE.showArrays( //java.lang.ArrayIndexOutOfBoundsException: 313632		if (showSensorMasks) {
			boolean same_size = true;
			for (int i = 1; i < masks.length; i++) same_size &= (masks[i].length == masks[0].length);
			if (same_size) {
			this.SDFA_INSTANCE.showArrays( //java.lang.ArrayIndexOutOfBoundsException: 313632
	masks,		masks,
	LENS_DISTORTIONS.pixelCorrectionWidth/ LENS_DISTORTIONS.pixelCorrectionDecimation,		LENS_DISTORTIONS.getSensorWidth(0)/ LENS_DISTORTIONS.getDecimateMasks(0),
	LENS_DISTORTIONS.pixelCorrectionHeight/LENS_DISTORTIONS.pixelCorrectionDecimation,		LENS_DISTORTIONS.getSensorHeight(0)/LENS_DISTORTIONS.getDecimateMasks(0),
	true,		true,
	"nonVinetting masks");		"nonVinetting masks");
			} else {
			System.out.println("**** Can't show sesnor masks for different size sesnors as a stack! ");
			}
			}
	double [][][][] sensorGrids=LENS_DISTORTIONS.calculateGridFlatField(		double [][][][] sensorGrids=LENS_DISTORTIONS.calculateGridFlatField(
	serNumber,		serNumber,
	masks,		masks,
	@@ -9556,7 +9570,7 @@ if (MORE_BUTTONS) {
	true, // boolean read_grids		true, // boolean read_grids
	MASTER_DEBUG_LEVEL);		MASTER_DEBUG_LEVEL);

	if (MASTER_DEBUG_LEVEL <100) return true;		/// if (MASTER_DEBUG_LEVEL <100) return true;
	// patterns are not yet read here!		// patterns are not yet read here!

	/*		/*
	@@ -9639,6 +9653,11 @@ if (MORE_BUTTONS) {
	path,		path,
	PROCESS_PARAMETERS.useXML,		PROCESS_PARAMETERS.useXML,
	null); // Properties properties		null); // Properties properties
			if (LENS_DISTORTIONS==null) {
			System.out.println("Creating new LENS_DISTORTIONS");
			LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
			}
			// ABERRATIONS_PARAMETERS.selectCalibrationDirectory(true, ABERRATIONS_PARAMETERS.calibrationDirectory, true);
	return EYESIS_CAMERA_PARAMETERS.importSystem(		return EYESIS_CAMERA_PARAMETERS.importSystem(
	properties,		properties,
	prefix,		prefix,

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

+670 −102

File changed.

Preview size limit exceeded, changes collapsed.

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

+185 −400

File changed.

Preview size limit exceeded, changes collapsed.

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

+63 −28

Original line number	Original line	Diff line number	Diff line
	@@ -37,7 +37,6 @@ import java.util.Set;
	import org.apache.commons.configuration.ConfigurationException;		import org.apache.commons.configuration.ConfigurationException;
	import org.apache.commons.configuration.XMLConfiguration;		import org.apache.commons.configuration.XMLConfiguration;

	import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;

	import ij.IJ;		import ij.IJ;
	@@ -1627,6 +1626,16 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	"Image sets, start from empty selection", // 5		"Image sets, start from empty selection", // 5
	"Image sets, start from current selection" // 6		"Image sets, start from current selection" // 6
	};		};
			String help = "<html>"+
			"<h2>Use of buttons in this dialog:</h2>"+
			"<ul>"+
			"<li><b>More</b> will re-open dialog after performin selection modification actions,"+
			" in case of selecting individual images that may happen after multiple selection "+
			"screens</li>"+
			"<li><b>Cancel</b> - keep current selection that you do not want to modify further"+
			" (e.g. if you wrongly pressed 'More' in this dialog earlier)</li>"+
			"<li><b>OK</b> - perform selection modification once (same as 'More'...'Cancel')</li>"+
			"</ul><br/>";
	int numStations=this.distortionCalibrationData.eyesisCameraParameters.getNumStations();		int numStations=this.distortionCalibrationData.eyesisCameraParameters.getNumStations();
	int numChannels=this.distortionCalibrationData.eyesisCameraParameters.getNumChannels(0); // for station 0		int numChannels=this.distortionCalibrationData.eyesisCameraParameters.getNumChannels(0); // for station 0
	boolean [] selected= this.selectedImages[numSeries];		boolean [] selected= this.selectedImages[numSeries];
	@@ -1833,6 +1842,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	//selectionType		//selectionType
	// gd.addCheckbox("Select images with estimated orientation", selectEstimated);		// gd.addCheckbox("Select images with estimated orientation", selectEstimated);
	// gd.addCheckbox("Select new enabled images", selectNewEnabled);		// gd.addCheckbox("Select new enabled images", selectNewEnabled);
			if (this.distortionCalibrationData.hasSmallSensors()) {
			gd.addMessage("=== Filter selection by High/Low resolution sensors (such as VNIR/LWIR)");
			gd.addCheckbox("Select high-res sensors", true);
			gd.addCheckbox("Select low-res sensors", true);
			}
	gd.addMessage("=== Filter selection by the number of matched laser pointers ===");		gd.addMessage("=== Filter selection by the number of matched laser pointers ===");
	for (int i=0;i<matchedPointersIndex.length;i++){		for (int i=0;i<matchedPointersIndex.length;i++){
	gd.addCheckbox("Select images with "+matchedPointersIndex[i]+" pointers", requiredMatchedPointers[i]);		gd.addCheckbox("Select images with "+matchedPointersIndex[i]+" pointers", requiredMatchedPointers[i]);
	@@ -1850,14 +1864,21 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	gd.addCheckbox("Select channel "+i, requiredChannels[i]);		gd.addCheckbox("Select channel "+i, requiredChannels[i]);
	}		}
	gd.enableYesNoCancel("OK", "More");		gd.enableYesNoCancel("OK", "More");
			gd.addHelp(help);
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return -1;		if (gd.wasCanceled()) return -1;
	boolean more=!gd.wasOKed();		boolean more=!gd.wasOKed();
			System.out.println("manageSelection(): more=!gd.wasOKed() = "+more);
	operIndex=gd.getNextChoiceIndex();		operIndex=gd.getNextChoiceIndex();
	selectionTypeIndex=gd.getNextChoiceIndex(); // TODO:Implement!		selectionTypeIndex=gd.getNextChoiceIndex(); // TODO:Implement!
	// selectEstimated=gd.getNextBoolean();
	// selectNewEnabled=gd.getNextBoolean();		boolean [] selectHiLowRes = null;
			if (this.distortionCalibrationData.hasSmallSensors()) {
			selectHiLowRes = new boolean[2];
			selectHiLowRes[0] = gd.getNextBoolean(); // gd.addCheckbox("Select high-res sensors", true);
			selectHiLowRes[1] = gd.getNextBoolean(); // gd.addCheckbox("Select low-res sensors", true);
			}
	for (int i=0;i<matchedPointersIndex.length;i++) requiredMatchedPointers[i]=gd.getNextBoolean();		for (int i=0;i<matchedPointersIndex.length;i++) requiredMatchedPointers[i]=gd.getNextBoolean();
	for (int i=0;i<hintedMatchIndex.length;i++) requiredHintedMatch[i]= gd.getNextBoolean();		for (int i=0;i<hintedMatchIndex.length;i++) requiredHintedMatch[i]= gd.getNextBoolean();
	for (int i=0;i<requiredStations.length;i++) requiredStations[i]=gd.getNextBoolean();		for (int i=0;i<requiredStations.length;i++) requiredStations[i]=gd.getNextBoolean();
	@@ -1882,6 +1903,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	false, // allImages,		false, // allImages,
	0, // star iIndex		0, // star iIndex
	500)) return -1; //perPage))		500)) return -1; //perPage))
			break;
	case 6: // start from current selection		case 6: // start from current selection
	selection=selected.clone();		selection=selected.clone();
	break;		break;
	@@ -1899,9 +1921,19 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	for (int i=0;i<selection.length;i++) if (imageStations[i]>=0) selection[i] &= requiredStations[imageStations[i]];		for (int i=0;i<selection.length;i++) if (imageStations[i]>=0) selection[i] &= requiredStations[imageStations[i]];
	else selection[i] = false;		else selection[i] = false;

			if (selectHiLowRes != null) {
			boolean [] lowres_channel = this.distortionCalibrationData.getSmallSensors();
			for (int i =0; i < requiredChannels.length;i++) {
			if ((lowres_channel[i] && !selectHiLowRes[1]) \|\|(!lowres_channel[i] && !selectHiLowRes[0])) {
			requiredChannels[i] = false;
			}
			}
			}

	for (int i=0;i<selection.length;i++) if (imageChannels[i]>=0) selection[i] &= requiredChannels[imageChannels[i]];		for (int i=0;i<selection.length;i++) if (imageChannels[i]>=0) selection[i] &= requiredChannels[imageChannels[i]];
	else selection[i] = false;		else selection[i] = false;


	// now combine new/old selections		// now combine new/old selections
	switch (operIndex){		switch (operIndex){
	case 0: // keep new selection		case 0: // keep new selection
	@@ -1926,6 +1958,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	for (int i=0;i<selection.length;i++) selection[i] &= enabled[i];		for (int i=0;i<selection.length;i++) selection[i] &= enabled[i];
	// replace current selection		// replace current selection
	this.selectedImages[numSeries]=selection;		this.selectedImages[numSeries]=selection;
			System.out.println("manageSelection(): on exit more = "+more);
	return more?0:1;		return more?0:1;
	}		}
	/**		/**
	@@ -1936,21 +1969,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	* @param useParameters Select parameters for this series		* @param useParameters Select parameters for this series
	* @param askNextSeries Ask for next series number		* @param askNextSeries Ask for next series number
	* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest		* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
			* For low/high res (LWIR/VNIR) - use first /other for each class
	* @return -2 - cancel, -1, done, otherwise - number of step to edit		* @return -2 - cancel, -1, done, otherwise - number of step to edit
	public int selectStrategyStep(
	int numSeries,
	boolean useImages,
	int [] fromToImages,
	boolean allImages,
	boolean useParameters,
	boolean askLambdas,
	boolean askNextSeries,
	boolean zeroAndOther
	){
	GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+
	" number of enabled images="+this.distortionCalibrationData.getNumEnabled());
	gd.addStringField ("Comment", this.strategyComment[numSeries],80);

	*/		*/

	public void listStrategies() {		public void listStrategies() {
	@@ -2117,9 +2137,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	for (int i=0;i<constrainByStation.length;i++) constrainByStation[i]=true;		for (int i=0;i<constrainByStation.length;i++) constrainByStation[i]=true;
	if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){		if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){
	gd.addMessage("Constrain by stations");		gd.addMessage("Constrain by stations");
	// gd.addCheckbox("Remove images of unselected stations below", true);
	for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) gd.addCheckbox("Station "+i, constrainByStation[i]);		for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) gd.addCheckbox("Station "+i, constrainByStation[i]);
	}		}
			if (this.distortionCalibrationData.hasSmallSensors()) {
			gd.addMessage("Constrain by High/Low resolution sensors (such as VNIR/LWIR)");
			gd.addCheckbox("Select high-res sensors", true);
			gd.addCheckbox("Select low-res sensors", true);
			}



	if (useImages) {		if (useImages) {
	gd.addNumericField("Image selection range, from", fromToImages[0], 0);		gd.addNumericField("Image selection range, from", fromToImages[0], 0);
	@@ -2141,7 +2167,6 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit

	}		}
	if (useParameters) {		if (useParameters) {
	// choice_offsets = new int [this.parameterEnable.length];
	gd.addMessage("Select parameters to fit");		gd.addMessage("Select parameters to fit");
	for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i] &&		for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i] &&
	(!zeroAndOther \|\| (this.parameterList[i][0] <= 1) \|\| (this.parameterList[i][0] ==24))){ // in "zeroAndOther" mode do not show other subcameras		(!zeroAndOther \|\| (this.parameterList[i][0] <= 1) \|\| (this.parameterList[i][0] ==24))){ // in "zeroAndOther" mode do not show other subcameras
	@@ -2159,18 +2184,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	) { // both subcameras are "other" subcameras		) { // both subcameras are "other" subcameras
	double parValue=this.distortionCalibrationData.getParameterValue(imgNumber,parIndex);		double parValue=this.distortionCalibrationData.getParameterValue(imgNumber,parIndex);
	if (!defined) {		if (!defined) {
	// min=this.distortionCalibrationData.pars[imgNumber][parIndex];
	min=parValue;		min=parValue;
	max=min;		max=min;
	defined=true;		defined=true;
	}		}
	// if (this.distortionCalibrationData.pars[imgNumber][parIndex]<min) min=this.distortionCalibrationData.pars[imgNumber][parIndex];
	// if (this.distortionCalibrationData.pars[imgNumber][parIndex]>max) max=this.distortionCalibrationData.pars[imgNumber][parIndex];
	if (parValue<min) min=parValue;		if (parValue<min) min=parValue;
	if (parValue>max) max=parValue;		if (parValue>max) max=parValue;
	}		}
	}		}
	// System.out.println(i+": "+parIndex+":"+subCam+"defined="+defined+" min="+min+" max="+max);
	// undefined, min, max		// undefined, min, max
	String sValue=(defined)?((min==max)?(min+""):(min+"..."+max)):"undefined";		String sValue=(defined)?((min==max)?(min+""):(min+"..."+max)):"undefined";
	String sChn=(zeroAndOther && (subCam>=1)&& (subCam<24))?"-head-other":		String sChn=(zeroAndOther && (subCam>=1)&& (subCam<24))?"-head-other":
	@@ -2263,8 +2284,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	showAdvancedImageSelection=gd.getNextBoolean();		showAdvancedImageSelection=gd.getNextBoolean();
	if (showAdvancedImageSelection){		if (showAdvancedImageSelection){
	int rslt=0;		int rslt=0;
	while (rslt==0) rslt=manageSelection(numSeries);		while (rslt==0) {
	// return (rslt<0)?-2:numSeries;		rslt=manageSelection(numSeries);
			}
	return numSeries; // cancel from manageSelection will just exit that mode with no changes		return numSeries; // cancel from manageSelection will just exit that mode with no changes
	}		}
	boolean copyFromPrevious=gd.getNextBoolean();		boolean copyFromPrevious=gd.getNextBoolean();
	@@ -2276,9 +2298,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	boolean selectNewEnabled=false;		boolean selectNewEnabled=false;
	if (numNewEnabled>0) selectNewEnabled=gd.getNextBoolean();		if (numNewEnabled>0) selectNewEnabled=gd.getNextBoolean();
	if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){		if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){
	// boolean removeUnselectedStations=gd.getNextBoolean();
	for (int i=0;i<constrainByStation.length; i++) constrainByStation[i]=gd.getNextBoolean();		for (int i=0;i<constrainByStation.length; i++) constrainByStation[i]=gd.getNextBoolean();
	}		}
			boolean [] selectHiLowRes = null;
			if (this.distortionCalibrationData.hasSmallSensors()) {
			selectHiLowRes = new boolean[2];
			selectHiLowRes[0] = gd.getNextBoolean(); // gd.addCheckbox("Select high-res sensors", true);
			selectHiLowRes[1] = gd.getNextBoolean(); // gd.addCheckbox("Select low-res sensors", true);
			}

	if (selectNewEnabled) {		if (selectNewEnabled) {
	this.selectedImages[numSeries]=this.distortionCalibrationData.selectNewEnabled();		this.selectedImages[numSeries]=this.distortionCalibrationData.selectNewEnabled();
	for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){		for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
	@@ -2308,9 +2336,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	return numSeries; // caller will repeat with the same series		return numSeries; // caller will repeat with the same series
	}		}
	if (removeAllImages \|\| selectAllImages) {		if (removeAllImages \|\| selectAllImages) {
	//
	for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){		for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
	// this.selectedImages[numSeries][i]=false; // invalidate - all, regardless of .enabled
	this.selectedImages[numSeries][i]=selectAllImages \|\| ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled		this.selectedImages[numSeries][i]=selectAllImages \|\| ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled
	this.selectedImages[numSeries][i]&=constrainByStation[this.distortionCalibrationData.gIP[i].getStationNumber()];		this.selectedImages[numSeries][i]&=constrainByStation[this.distortionCalibrationData.gIP[i].getStationNumber()];
	}		}
	@@ -2329,6 +2355,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	if (this.masterImages[numSeries]<0)this.masterImages[numSeries]=0;		if (this.masterImages[numSeries]<0)this.masterImages[numSeries]=0;
	if (this.masterImages[numSeries]>=this.selectedImages[numSeries].length)this.masterImages[numSeries]=this.selectedImages[numSeries].length;		if (this.masterImages[numSeries]>=this.selectedImages[numSeries].length)this.masterImages[numSeries]=this.selectedImages[numSeries].length;
	}		}
			if (selectHiLowRes != null) {
			for (int i =0; i<this.distortionCalibrationData.getNumImages();i++) {
			boolean low_res = this.distortionCalibrationData.isSmallSensor(i);
			if ((low_res && !selectHiLowRes[1]) && (!low_res && !selectHiLowRes[0])){
			this.selectedImages[numSeries][i]= false;
			}
			}
			}

	if (useParameters) {		if (useParameters) {
	int [] lastGroups=null;		int [] lastGroups=null;
	for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i] &&		for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i] &&

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

+74 −51

Original line number	Original line	Diff line number	Diff line
	package com.elphel.imagej.calibration;		package com.elphel.imagej.calibration;
			import java.awt.Rectangle;
			import java.util.Properties;

			import com.elphel.imagej.jp4.JP46_Reader_camera;

	/*		/*
	**		**
	** PatternParameters.java		** PatternParameters.java
	@@ -28,12 +33,6 @@ import ij.ImageStack;
	import ij.gui.GenericDialog;		import ij.gui.GenericDialog;
	import ij.io.FileSaver;		import ij.io.FileSaver;
	import ij.io.Opener;		import ij.io.Opener;

	import java.awt.Rectangle;
	import java.util.Properties;

	import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
	import com.elphel.imagej.jp4.JP46_Reader_camera;
	/* gridGeometry:		/* gridGeometry:
	* [v][u][0] - x(mm) of the node(u,v), right (looking to the wall) - positive		* [v][u][0] - x(mm) of the node(u,v), right (looking to the wall) - positive
	* [v][u][1] - y(mm) of the node(u,v), down - positive		* [v][u][1] - y(mm) of the node(u,v), down - positive
	@@ -260,6 +259,7 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
	setPhotometric(viewMap);		setPhotometric(viewMap);
	calculateGridGeometryAndPhotometric(true);		calculateGridGeometryAndPhotometric(true);
	}		}
			@Override
	public PatternParameters clone() {		public PatternParameters clone() {
	PatternParameters patternParameters= new PatternParameters(		PatternParameters patternParameters= new PatternParameters(
	this.viewMap,		this.viewMap,
	@@ -609,13 +609,15 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
	GenericDialog gd = new GenericDialog("Initial Wall pattern parameters");		GenericDialog gd = new GenericDialog("Initial Wall pattern parameters");
	gd.addNumericField("Pattern full width", this.patternWidth, 1,6,"mm"); // pattern full width in mm		gd.addNumericField("Pattern full width", this.patternWidth, 1,6,"mm"); // pattern full width in mm
	gd.addNumericField("Pattern full height", this.patternHeight, 1,6,"mm"); // pattern full width in mm		gd.addNumericField("Pattern full height", this.patternHeight, 1,6,"mm"); // pattern full width in mm
	gd.addNumericField("Distance between opposite sign nodes",this.patternHalfPeriod, 4,8,"mm"); // istance between opposite sign nodes in mm		gd.addNumericField("Distance between opposite sign nodes",this.patternHalfPeriod, 4,8,"mm"); // distance between opposite sign nodes in mm
	gd.addNumericField("Pattern tilt (clockwise)", this.patternTilt, 1,5,"degrees"); // pattern tilt (degrees) - U clockwise from X-right (V clockwise from Y-down)		gd.addNumericField("Pattern tilt (clockwise)", this.patternTilt, 3,8,"degrees"); // pattern tilt (degrees) - U clockwise from X-right (V clockwise from Y-down)
	gd.addNumericField("Average grid RED (1.0 for white)", this.averageRGB[0], 3,5,"x"); //		gd.addNumericField("Average grid RED (1.0 for white)", this.averageRGB[0], 3,5,"x"); //
	gd.addNumericField("Average grid GREEN (1.0 for white)", this.averageRGB[1], 3,5,"x"); //		gd.addNumericField("Average grid GREEN (1.0 for white)", this.averageRGB[1], 3,5,"x"); //
	gd.addNumericField("Average grid BLUE (1.0 for white)", this.averageRGB[2], 3,5,"x"); //		gd.addNumericField("Average grid BLUE (1.0 for white)", this.averageRGB[2], 3,5,"x"); //

	gd.addNumericField("Number of sensors (>24 - two groups, 0 - do not change)",this.defaultNumberOfChannels,0); //		gd.addNumericField("Number of sensors (>24 - two groups, 0 - do not change)",this.defaultNumberOfChannels,0); //
			gd.addCheckbox("Reset to standard fine pitch pattern" , false);
			gd.addCheckbox("Reset to standard LWIR pattern" , false);

	gd.addMessage("Pressing OK will recalculate grid and clear current grid calibration");		gd.addMessage("Pressing OK will recalculate grid and clear current grid calibration");
	gd.showDialog();		gd.showDialog();
	@@ -628,6 +630,27 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
	this.averageRGB[1]= gd.getNextNumber();		this.averageRGB[1]= gd.getNextNumber();
	this.averageRGB[2]= gd.getNextNumber();		this.averageRGB[2]= gd.getNextNumber();
	int numberOfChannels= (int)gd.getNextNumber();		int numberOfChannels= (int)gd.getNextNumber();
			boolean use_fine_pattern = gd.getNextBoolean();
			boolean use_lwir_pattern = gd.getNextBoolean();

			if (use_fine_pattern) {
			this.patternWidth= 7010.0;
			this.patternHeight= 3073.0;
			this.patternHalfPeriod= 41.57;
			this.patternTilt= 5.0;
			this.averageRGB[0]= 1.0;
			this.averageRGB[1]= 1.0;
			this.averageRGB[2]= 1.0;

			} else if (use_lwir_pattern) {
			this.patternWidth= 7010.0; // 7192.0
			this.patternHeight= 2997.2;
			this.patternHalfPeriod= 178.65;
			this.patternTilt= 14.036;
			this.averageRGB[0]= 1.0;
			this.averageRGB[1]= 1.0;
			this.averageRGB[2]= 1.0;
			}

	if (numberOfChannels>0){		if (numberOfChannels>0){
	initDefaultChannels(numberOfChannels);		initDefaultChannels(numberOfChannels);

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