working on dual-modal calibration (9833be98) · Commits · Elphel / imagej-elphel

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

+79 −25

Original line number	Original line	Diff line number	Diff line
	@@ -6015,7 +6015,7 @@ if (MORE_BUTTONS) {
	LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointer, // LaserPointer object that specifies actual laser poiners on the target		LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointer, // LaserPointer object that specifies actual laser poiners on the target
	DISTORTION_PROCESS_CONFIGURATION.removeOutOfGridPointers, // boolean removeOutOfGridPointers,		DISTORTION_PROCESS_CONFIGURATION.removeOutOfGridPointers, // boolean removeOutOfGridPointers,
	(useHintTolerance?hintGridTolerance:0.0), //double hintGridTolerance, // alllowed mismatch (fraction of period) or 0 - orientation only		(useHintTolerance?hintGridTolerance:0.0), //double hintGridTolerance, // alllowed mismatch (fraction of period) or 0 - orientation only
	processAll, //boolean processAll, // if true - process all images, false - only disabeld		processAll, //boolean processAll, // if true - process all images, false - only disabled
	ignoreLaserPointers,		ignoreLaserPointers,
	processBlind,		processBlind,
	imageNumber,		imageNumber,
	@@ -9546,7 +9546,7 @@ if (MORE_BUTTONS) {
	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("Grid offset")) {		if (label.equals("Grid offset")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	offsetGrids(0, 0, null);		offsetGrids(0, 0, null, null);
	return;		return;
	}		}
	/* ======================================================================== */		/* ======================================================================== */
	@@ -9590,14 +9590,17 @@ if (MORE_BUTTONS) {
	boolean use_lma = true;		boolean use_lma = true;

	GenericDialog gd = new GenericDialog("Initial alignment of the secondary camera to the reference one");		GenericDialog gd = new GenericDialog("Initial alignment of the secondary camera to the reference one");
	gd.addMessage("This command used Fitting Strategy[0] that should be set with all parameters but\n"+		// gd.addMessage("This command used Fitting Strategy[last] that should be set with all parameters but\n"+
	"GXYZ0 and GXYZ1 are set to 'fixed', and GXYZ0 and GXYZ1 are set to 'individual'.\n"+		// "GXYZ0 and GXYZ1 are set to 'fixed', and GXYZ0 and GXYZ1 are set to 'individual'.\n"+
			// "Each selected set should already have GXYZ set correctly (e.g. by reference cameras)");
			gd.addMessage("This command uses Fitting Strategy[last] and set parameters but\n"+
			"GXYZ0 and GXYZ1 to 'individual', all others - to 'fixed'.\n"+
	"Each selected set should already have GXYZ set correctly (e.g. by reference cameras)");		"Each selected set should already have GXYZ set correctly (e.g. by reference cameras)");
	gd.addNumericField("Image set start", min_set, 0);		gd.addNumericField("Image set start", min_set, 0);
	gd.addNumericField("Image set last", max_set, 0);		gd.addNumericField("Image set last", max_set, 0);
	gd.addCheckbox("Adjust EO (reference) sensors", adjust_eo);		gd.addCheckbox("Adjust EO (reference) sensors", adjust_eo);
	gd.addCheckbox("Adjust LWIR (target) sensors", adjust_lwir);		gd.addCheckbox("Adjust LWIR (target) sensors", adjust_lwir);
	gd.addCheckbox("Use LMA (unchecked - initial approximate grid setum by correlation)", use_lma);		gd.addCheckbox("Use LMA (unchecked - initial approximate grid set by correlation)", use_lma);
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
	min_set = (int) gd.getNextNumber();		min_set = (int) gd.getNextNumber();
	@@ -9626,10 +9629,14 @@ if (MORE_BUTTONS) {
	continue;		continue;
	}		}
	}		}
			double [] stats = new double [3];
	int [] uvr = LENS_DISTORTIONS. findImageGridOffset(		int [] uvr = LENS_DISTORTIONS. findImageGridOffset(
	num_img,		num_img, // image num
			-1, // use last series int ser_num, // number of series to reprogram
			false, // boolean adjust_attitude, // true for eo, false for lwir (uses exact attitude from eo)
	true, // boolean even, For first time - use parameter and parity of uv_rot		true, // boolean even, For first time - use parameter and parity of uv_rot
	PATTERN_PARAMETERS);		PATTERN_PARAMETERS,
			stats); // rms, dU, dV
	if ((uvr != null) && ((uvr[0] != 0) \|\| (uvr[1] != 0))) {		if ((uvr != null) && ((uvr[0] != 0) \|\| (uvr[1] != 0))) {
	int [] uv_shift_rot = {uvr[0],uvr[1],0};		int [] uv_shift_rot = {uvr[0],uvr[1],0};
	// int [] new_uv_shift_rots =		// int [] new_uv_shift_rots =
	@@ -9639,6 +9646,8 @@ if (MORE_BUTTONS) {
	PATTERN_PARAMETERS);		PATTERN_PARAMETERS);
	if (DEBUG_LEVEL > 0) {		if (DEBUG_LEVEL > 0) {
	System.out.println(num_img+ "("+num_set+"."+nc+"): uv_shift = "+uvr[0]+":"+uvr[1]);		System.out.println(num_img+ "("+num_set+"."+nc+"): uv_shift = "+uvr[0]+":"+uvr[1]);
			System.out.println(num_img+ "("+num_set+"."+nc+"): errors: rms= "+stats[0]+", dU="+stats[1]+", dV="+stats[2]);

	}		}
	}		}
	}		}
	@@ -9666,7 +9675,7 @@ if (MORE_BUTTONS) {
	return true;		return true;
	}		}

	public boolean offsetGrids(int ichoice, int inum, int [] uv_shift_rot) {		public boolean offsetGrids(int ichoice, int inum, int [] uv_shift_rot, String msg) {
	if (LENS_DISTORTIONS == null) {		if (LENS_DISTORTIONS == null) {
	System.out.println("LENS_DISTORTIONS is null");		System.out.println("LENS_DISTORTIONS is null");
	return false;		return false;
	@@ -9695,8 +9704,16 @@ if (MORE_BUTTONS) {
	String [] choices_nolwir = {"-- please select --","Image number","Image set number"};		String [] choices_nolwir = {"-- please select --","Image number","Image set number"};
	String [] choices_lwir = {"-- please select --","Image number","Image set number (all images)", "Image set (EO only)","Image set (LWIR only)"};		String [] choices_lwir = {"-- please select --","Image number","Image set number (all images)", "Image set (EO only)","Image set (LWIR only)"};
	String [] choices = has_lwir ? choices_lwir : choices_nolwir;		String [] choices = has_lwir ? choices_lwir : choices_nolwir;
			boolean readjust = true;
	GenericDialog gd = new GenericDialog("Manually offset single grid or multiple grids in a set");		GenericDialog gd = new GenericDialog("Manually offset single grid or multiple grids in a set");
			if (msg != null) {
			gd.addMessage(msg);
			}
			if (auto) {
			gd.addMessage("In 'auto' mode this command uses Fitting Strategy[last] and set parameters but\n"+
			"GXYZ0, GXYZ1, goniometerHorizontal, and goniometerAxial to 'individual', all others - to 'fixed'.\n"+
			"Each selected set should already have GXYZ set correctly (e.g. by reference cameras)");
			}
	gd. addChoice("Next number is: ",		gd. addChoice("Next number is: ",
	choices,		choices,
	choices[ichoice]);		choices[ichoice]);
	@@ -9705,6 +9722,10 @@ if (MORE_BUTTONS) {
	if (has_lwir) {		if (has_lwir) {
	gd.addCheckbox ("Auto from EO grid (calculatre from EO even if the requested image is LWIR)", false); //true		gd.addCheckbox ("Auto from EO grid (calculatre from EO even if the requested image is LWIR)", false); //true
	}		}
			if (!auto) {
			gd.addCheckbox("Run LMA to re-adjust goniometerHorizontal and goniometerAxial", readjust);
			readjust = gd.getNextBoolean();
			}
	gd.addNumericField("Grid offset U", uv_shift_rot[0], 0);		gd.addNumericField("Grid offset U", uv_shift_rot[0], 0);
	gd.addNumericField("Grid offset V", uv_shift_rot[1], 0);		gd.addNumericField("Grid offset V", uv_shift_rot[1], 0);
	gd.addNumericField("Grid offset Rot", uv_shift_rot[2], 0);		gd.addNumericField("Grid offset Rot", uv_shift_rot[2], 0);
	@@ -9712,17 +9733,24 @@ if (MORE_BUTTONS) {
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
	ichoice = gd.getNextChoiceIndex();		ichoice = gd.getNextChoiceIndex();
	inum = (int) gd.getNextNumber();		inum = (int) gd.getNextNumber();
			boolean was_auto = auto;
	auto = gd.getNextBoolean();		auto = gd.getNextBoolean();

	boolean auto_from_EO=false;		boolean auto_from_EO=false;
	if (has_lwir) {		if (has_lwir) {
	auto_from_EO = gd.getNextBoolean();		auto_from_EO = gd.getNextBoolean();
	}		}

			readjust = false;
			if (!was_auto) {
			readjust = gd.getNextBoolean();
			}

	uv_shift_rot[0] = (int) gd.getNextNumber();		uv_shift_rot[0] = (int) gd.getNextNumber();
	uv_shift_rot[1] = (int) gd.getNextNumber();		uv_shift_rot[1] = (int) gd.getNextNumber();
	uv_shift_rot[2] = (int) gd.getNextNumber();		uv_shift_rot[2] = (int) gd.getNextNumber();
	if (ichoice == 0) {		if (ichoice == 0) {
	return offsetGrids(ichoice, inum, uv_shift_rot);		return offsetGrids(ichoice, inum, uv_shift_rot, msg);
	}		}
	int ichoicemod = ichoice;		int ichoicemod = ichoice;
	if (auto && auto_from_EO) {		if (auto && auto_from_EO) {
	@@ -9766,21 +9794,24 @@ if (MORE_BUTTONS) {
	// find first enabled image		// find first enabled image
	for (int n:img_nums) {		for (int n:img_nums) {
	if (n >= 0) {		if (n >= 0) {
			double [] stats = new double[3]; // rms and 2 errors, null OK
	int [] auto_uvr = LENS_DISTORTIONS.findImageGridOffset( // null for now		int [] auto_uvr = LENS_DISTORTIONS.findImageGridOffset( // null for now
	n,		n, // image number to use for fitting (only one)
	true, // boolean even,		-1, // use last series int ser_num, // number of series to reprogram
	PATTERN_PARAMETERS); // PatternParameters patternParameters)		true, // boolean adjust_attitude, // true for eo, false for lwir (uses exact attitude from eo)
			true, // boolean even, For first time - use parameter and parity of uv_rot
	// int [] auto_uvr = dcd. suggestOffset (		PATTERN_PARAMETERS,
	// n, // int num_img,		stats);
	// true, // boolean non_estimated,		if (auto_uvr != null) {
	// true, // boolean even,		String stats_msg = String.format("Fitting errors: LMA RMS = %7.4f, dU = %6.3f, dV = %6.3f", stats[0], stats[1], stats[2]);
	// PATTERN_PARAMETERS); // PatternParameters patternParameters)		return offsetGrids(ichoice, inum, auto_uvr, stats_msg);
	return offsetGrids(ichoice, inum, auto_uvr);		} else {
			System.out.println("**** LMA FAILED - trying next image");
	}		}
	}		}
	}		}
			return offsetGrids(ichoice, inum, null, "All images failed LMA !");
			}

	int [][] new_uv_shift_rots = new int [img_nums.length][];		int [][] new_uv_shift_rots = new int [img_nums.length][];
	for (int i = 0; i < img_nums.length; i++) if (img_nums[i] >=0) {		for (int i = 0; i < img_nums.length; i++) if (img_nums[i] >=0) {
	@@ -9798,6 +9829,20 @@ if (MORE_BUTTONS) {
	System.out.println("<null>");		System.out.println("<null>");
	}		}
	}		}
			if (readjust) {
			for (int n:img_nums) {
			if (n >= 0) {
			if (LENS_DISTORTIONS.adjustAttitudeAfterOffset(
			n, // int num_img,
			-1, // int ser_num, // number of series to reprogram
			PATTERN_PARAMETERS)) {
			break; // only one image
			} else {
			System.out.println("***** LMA FAILED - trying next image");
			}
			}
			}
			}
	return true;		return true;

	}		}
	@@ -9821,8 +9866,10 @@ if (MORE_BUTTONS) {
	gd.showDialog();		gd.showDialog();
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
	numStations= (int) gd.getNextNumber();		numStations= (int) gd.getNextNumber();
	String [] grid_extensions={".tif",".tiff"};		// String [] grid_extensions={".tif",".tiff"};
	String [] src_extensions={".tif",".tiff"};		// String [] src_extensions={".tif",".tiff"};
			String [] grid_extensions={".tiff"};
			String [] src_extensions={".tiff"};
	MultipleExtensionsFileFilter gridFilter =		MultipleExtensionsFileFilter gridFilter =
	new MultipleExtensionsFileFilter("grid",grid_extensions,"Calibrated grid files");		new MultipleExtensionsFileFilter("grid",grid_extensions,"Calibrated grid files");
	MultipleExtensionsFileFilter sourceFilter =		MultipleExtensionsFileFilter sourceFilter =
	@@ -9859,6 +9906,13 @@ if (MORE_BUTTONS) {
	int num_match = files[nFile].list(gridFilter).length;		int num_match = files[nFile].list(gridFilter).length;
	if (num_match >= min_files) {		if (num_match >= min_files) {
	filelist.add(files[nFile]);		filelist.add(files[nFile]);
			} else {
			// System.out.println("nFile="+nFile+" files[nFile]="+files[nFile]+": num_match="+num_match);
			// String[] matched=files[nFile].list(gridFilter);
			// for (String s:matched) {
			// System.out.println(s);
			// }
			// System.out.println("");
	}		}
	}		}

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

+131 −19

Original line number	Original line	Diff line number	Diff line
	@@ -1392,6 +1392,7 @@ import ij.text.TextWindow;

	// suggest set grid offset by comparing with known (by mark) set.		// suggest set grid offset by comparing with known (by mark) set.
	// Wrong Grid UV should cause parallel shift - same Z, different XY		// Wrong Grid UV should cause parallel shift - same Z, different XY
			/*
	public int [] suggestOffset (		public int [] suggestOffset (
	int num_img,		int num_img,
	boolean non_estimated,		boolean non_estimated,
	@@ -1409,14 +1410,16 @@ import ij.text.TextWindow;
	num_img,		num_img,
	diff_xyz, // z is not used, may ne just[2]		diff_xyz, // z is not used, may ne just[2]
	even,		even,
	patternParameters);		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]
	boolean even,		boolean even,
	PatternParameters patternParameters) {		PatternParameters patternParameters,
			double [] errs) { // will return errors, if not null (should be double[2]
	int num_set = this.gIP[num_img].setNumber;		int num_set = this.gIP[num_img].setNumber;
	int station = this.gIS[num_set].stationNumber;		int station = this.gIS[num_set].stationNumber;
	int [][] pixelsUV = this.gIP[num_img].pixelsUV ; // null; // for each image, each grid node - a pair of {gridU, gridV}		int [][] pixelsUV = this.gIP[num_img].pixelsUV ; // null; // for each image, each grid node - a pair of {gridU, gridV}
	@@ -1458,7 +1461,11 @@ import ij.text.TextWindow;
	UV_err[0] = dUV[0] - idUV[0];		UV_err[0] = dUV[0] - idUV[0];
	UV_err[1] = dUV[1] - idUV[1];		UV_err[1] = dUV[1] - idUV[1];
	}		}
	System.out.println(String.format("Errors U/V = %.3f:%.3f",UV_err[0],UV_err[1]));		System.out.println(String.format("idUV ="+idUV[0]+" / "+idUV[1]+", errors U/V = %.3f:%.3f",UV_err[0],UV_err[1]));
			if (errs != null) {
			errs[0] = UV_err[0];
			errs[1] = UV_err[1];
			}
	return idUV;		return idUV;
	}		}

	@@ -2244,7 +2251,9 @@ import ij.text.TextWindow;
	int stationNumber=this.gIP[i].getStationNumber();		int stationNumber=this.gIP[i].getStationNumber();
	boolean enableNoLaser=this.eyesisCameraParameters.getEnableNoLaser(stationNumber,this.gIP[i].channel);		boolean enableNoLaser=this.eyesisCameraParameters.getEnableNoLaser(stationNumber,this.gIP[i].channel);
	boolean wasEnabled=this.gIP[i].enabled;		boolean wasEnabled=this.gIP[i].enabled;
	if (resetHinted) this.gIP[i].hintedMatch=-1; // undefined		if (resetHinted) {
			this.gIP[i].hintedMatch=-1; // undefined
			}
	/// if (Double.isNaN(this.gIP[i].getGridPeriod()) \|\|		/// if (Double.isNaN(this.gIP[i].getGridPeriod()) \|\|
	/// ((minGridPeriodFraction>0) && ((this.gIP[i].getGridPeriod()<minGridPeriod[stationNumber]) \|\| (this.gIP[i].getGridPeriod()>maxGridPeriod[stationNumber])))){		/// ((minGridPeriodFraction>0) && ((this.gIP[i].getGridPeriod()<minGridPeriod[stationNumber]) \|\| (this.gIP[i].getGridPeriod()>maxGridPeriod[stationNumber])))){
	if (Double.isNaN(getEffectivePeriod(i)) \|\|		if (Double.isNaN(getEffectivePeriod(i)) \|\|
	@@ -2431,6 +2440,7 @@ 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());
	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,
	@@ -2486,18 +2496,40 @@ import ij.text.TextWindow;
	Matrix mview_tilt = mtilt.times(mview_gon); // view point on the target from the tilted goniometer		Matrix mview_tilt = mtilt.times(mview_gon); // view point on the target from the tilted goniometer
	double az = Math.atan2(mview_tilt.get(0, 0), mview_tilt.get(2, 0)); // x pointed right		double az = Math.atan2(mview_tilt.get(0, 0), mview_tilt.get(2, 0)); // x pointed right

	double tilt_deg = tilt/Math.PI*180;		double tilt_deg = -tilt/Math.PI*180; // why "-" (experimentally)
	double az_deg = az/Math.PI*180;		double az_deg = az/Math.PI*180;
	if (this.debugLevel>0) {		if (this.debugLevel>0) {
	System.out.println("Tilt = "+tilt_deg+", az = "+az_deg);		System.out.println("Tilt = "+tilt_deg+", az = "+az_deg);
	System.out.print("");		System.out.print("");
	}		}

			if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerAxial)){
			this.gIS[i].goniometerAxial=az_deg;
			for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial);
			this.gIS[i].orientationEstimated=true;
			if (this.debugLevel>1) {
			System.out.print(String.format("Setting goniometerAxial for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));
			System.out.println(""+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
			// System.out.println("Setting goniometerAxial for the image set #"+i+" ("+this.gIS[i].timeStamp+") to "+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
			}
			}
			if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerTilt )){
			this.gIS[i].goniometerTilt= tilt_deg;
			for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt);
			this.gIS[i].orientationEstimated=true;
			if (this.debugLevel>1) {
			System.out.print(String.format("Setting goniometerTilt for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));
			System.out.println(""+this.gIS[i].goniometerTilt+" ===== orientationEstimated==true =====");
	}		}
	}		}

	if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerAxial)){
	// System.out.println("setInitialOrientation("+overwriteAll+"), Double.isNaN(this.gIS["+i+"].goniometerAxial)="+Double.isNaN(this.gIS[i].goniometerAxial));


			}
			}
			/*
			* Remove old method completely
			if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerAxial)){
	double subcam_heading = (esp.heading + (esp.cartesian? 0: esp.azimuth));		double subcam_heading = (esp.heading + (esp.cartesian? 0: esp.azimuth));
	this.gIS[i].goniometerAxial=-subcam_heading;		this.gIS[i].goniometerAxial=-subcam_heading;
	for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial);		for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial);
	@@ -2505,11 +2537,9 @@ import ij.text.TextWindow;
	if (this.debugLevel>1) {		if (this.debugLevel>1) {
	System.out.print(String.format("Setting goniometerAxial for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));		System.out.print(String.format("Setting goniometerAxial for the image set #%4d (%18.6f) to ", i, this.gIS[i].timeStamp));
	System.out.println(""+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");		System.out.println(""+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
	// System.out.println("Setting goniometerAxial for the image set #"+i+" ("+this.gIS[i].timeStamp+") to "+this.gIS[i].goniometerAxial+" +++++ orientationEstimated==true +++++");
	}		}
	}		}
	if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerTilt )){		if (overwriteAll \|\| Double.isNaN(this.gIS[i].goniometerTilt )){
	// System.out.println("setInitialOrientation("+overwriteAll+"), Double.isNaN(this.gIS["+i+"].goniometerTilt)="+Double.isNaN(this.gIS[i].goniometerTilt));
	this.gIS[i].goniometerTilt= -esp.theta;		this.gIS[i].goniometerTilt= -esp.theta;
	for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt);		for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt);
	this.gIS[i].orientationEstimated=true;		this.gIS[i].orientationEstimated=true;
	@@ -2518,6 +2548,9 @@ import ij.text.TextWindow;
	System.out.println(""+this.gIS[i].goniometerTilt+" ===== orientationEstimated==true =====");		System.out.println(""+this.gIS[i].goniometerTilt+" ===== orientationEstimated==true =====");
	}		}
	}		}
			*/


	}		}
	}		}
	}		}
	@@ -2531,6 +2564,9 @@ import ij.text.TextWindow;
	* Updated version - only flag as orientationEstimated if no enabled images exist in the set or any of the angles is NaN		* Updated version - only flag as orientationEstimated if no enabled images exist in the set or any of the angles is NaN
	* Temporarily duplicate image parameters from those of the set (should not be needed)		* Temporarily duplicate image parameters from those of the set (should not be needed)
	* selectedImages will not be used		* selectedImages will not be used
			* Modified (selectedImages was not used) 2020: do not touch set if nothing is selected there
			* was: if selectedImages[] is not null will set orientationEstimated for unselected images
			* restored to how it was
	*/		*/
	public void updateSetOrientation(boolean [] selectedImages){ // if selectedImages[] is not null will set orientationEstimated for unselected images		public void updateSetOrientation(boolean [] selectedImages){ // if selectedImages[] is not null will set orientationEstimated for unselected images
	if (this.gIS==null){		if (this.gIS==null){
	@@ -2564,6 +2600,50 @@ import ij.text.TextWindow;
	}		}
	}		}


			public void updateSetOrientation1(boolean [] selectedImages){
			if (this.gIS==null){
			String msg="Image set is not initilaized";
			System.out.println(msg);
			IJ.showMessage(msg);
			}

			for (int i=0; i<this.gIS.length;i++){
			if (!Double.isNaN(this.gIS[i].goniometerAxial) && !Double.isNaN(this.gIS[i].goniometerTilt)) {
			boolean has_selected = false;
			boolean has_enabled = false;
			for (int j=0;j<this.gIS[i].imageSet.length;j++) {
			if ((this.gIS[i].imageSet[j]!=null) && this.gIS[i].imageSet[j].enabled){
			has_enabled = true;
			break;
			}
			has_selected \|= (selectedImages == null) \|\| selectedImages[this.gIS[i].imageSet[j].imgNumber];
			}
			if (has_enabled) {
			this.gIS[i].orientationEstimated=false;
			this.gIS[i].goniometerAxial-=360.0*Math.floor((this.gIS[i].goniometerAxial+180.0)/360.0);
			} else if (has_selected) { // nut none enabled!
			this.gIS[i].orientationEstimated=true;
			}

			} else {
			this.gIS[i].orientationEstimated=true;
			}

			if (!this.gIS[i].orientationEstimated){
			// now fill that data to all disabled images of the same set (just for listing RMS errors and debugging)
			for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { // fill even those that are enabled
			setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial );
			setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt );
			}
			} else {
			this.gIS[i].goniometerAxial=Double.NaN;
			this.gIS[i].goniometerTilt= Double.NaN;
			System.out.println("updateSetOrientation(): imageSet "+i+" orientationEstimated == true");
			}
			}
			}

	public void updateSetOrientationOld(boolean [] selectedImages){		public void updateSetOrientationOld(boolean [] selectedImages){
	if (this.gIS==null){		if (this.gIS==null){
	String msg="Image set is not initilaized";		String msg="Image set is not initilaized";
	@@ -2751,6 +2831,11 @@ import ij.text.TextWindow;
	public double [] getImagesetTiltAxial(double timeStamp){		public double [] getImagesetTiltAxial(double timeStamp){
	int mAxial=1; // m2		int mAxial=1; // m2
	int mHorizontal=2;// m3		int mHorizontal=2;// m3
			double [] degree_per_step = new double[3];
			degree_per_step[mAxial] = 1.0/goniometerParameters.goniometerMotors.stepsPerDegreeAxial;
			degree_per_step[mHorizontal] = 1.0/goniometerParameters.goniometerMotors.stepsPerDegreeTilt;


	// this is probably already set		// this is probably already set
	for (int i=0;i<this.gIS.length;i++){		for (int i=0;i<this.gIS.length;i++){
	if ((this.gIS[i].imageSet!=null) && (this.gIS[i].imageSet.length>0) && (this.gIS[i].imageSet[0]!=null)) this.gIS[i].setStationNumber(this.gIS[i].imageSet[0].getStationNumber());		if ((this.gIS[i].imageSet!=null) && (this.gIS[i].imageSet.length>0) && (this.gIS[i].imageSet[0]!=null)) this.gIS[i].setStationNumber(this.gIS[i].imageSet[0].getStationNumber());
	@@ -2941,7 +3026,7 @@ import ij.text.TextWindow;
	(this.gIS[indexSecond].motors[mAxial]-this.gIS[indexClosest].motors[mAxial]);		(this.gIS[indexSecond].motors[mAxial]-this.gIS[indexClosest].motors[mAxial]);
	// 06/06/2015 Andrey: Was missing setting estimated orientation. Was it a bug?		// 06/06/2015 Andrey: Was missing setting estimated orientation. Was it a bug?
	this.gIS[i].orientationEstimated=true;		this.gIS[i].orientationEstimated=true;
	if (this.debugLevel>0) System.out.println("Orientation for set # "+i+" timestamp "+IJ.d2s(this.gIS[i].timeStamp,6)+		if (this.debugLevel>-1) System.out.println("Orientation for set # "+i+" timestamp "+IJ.d2s(this.gIS[i].timeStamp,6)+
	") 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)+")");
	}		}
	@@ -2963,14 +3048,36 @@ import ij.text.TextWindow;
	!Double.isNaN(this.gIS[j].interAxisAngle)) {		!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])		double da = (this.gIS[j].motors[k]-this.gIS[i].motors[k]) * degree_per_step[k];
	(this.gIS[j].motors[k]-this.gIS[i].motors[k]);		d2+=da * da;
			}
			if ((d2Min<0) \|\| (d2Min>d2)) {
			d2Min=d2;
			iBest=j;
			}
			}
			if (iBest < 0) {
			// next try for the same station number only (any tilt):
			d2Min=-1;
			for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&
			(this.gIS[j].getStationNumber() == station_number) &&
			(this.gIS[j].motors[mHorizontal] == this.gIS[i].motors[mHorizontal]) &&
			!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;
			for (int k=0;k<this.gIS[j].motors.length;k++){
			double da = (this.gIS[j].motors[k]-this.gIS[i].motors[k]) * degree_per_step[k];
			d2+=da * da;
	}		}
	if ((d2Min<0) \|\| (d2Min>d2)) {		if ((d2Min<0) \|\| (d2Min>d2)) {
	d2Min=d2;		d2Min=d2;
	iBest=j;		iBest=j;
	}		}
	}		}
			}
	if (iBest < 0) {		if (iBest < 0) {
	d2Min=-1;		d2Min=-1;
	for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&		for (int j=0;j<this.gIS.length;j++) if ((j!=i) &&
	@@ -2980,9 +3087,12 @@ import ij.text.TextWindow;
	!Double.isNaN(this.gIS[j].goniometerAxial ) &&		!Double.isNaN(this.gIS[j].goniometerAxial ) &&
	!Double.isNaN(this.gIS[j].interAxisAngle)) {		!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])		double da = (this.gIS[j].motors[k]-this.gIS[i].motors[k]) * degree_per_step[k];
	(this.gIS[j].motors[k]-this.gIS[i].motors[k]);		d2 += da* da;
	}		}
	if ((d2Min<0) \|\| (d2Min>d2)) {		if ((d2Min<0) \|\| (d2Min>d2)) {
	d2Min=d2;		d2Min=d2;
	@@ -2998,8 +3108,8 @@ import ij.text.TextWindow;
	!Double.isNaN(this.gIS[j].interAxisAngle)) {		!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])		double da = (this.gIS[j].motors[k]-this.gIS[i].motors[k]) * degree_per_step[k];
	(this.gIS[j].motors[k]-this.gIS[i].motors[k]);		d2 += da* da;
	}		}
	if ((d2Min<0) \|\| (d2Min>d2)) {		if ((d2Min<0) \|\| (d2Min>d2)) {
	d2Min=d2;		d2Min=d2;
	@@ -3024,6 +3134,7 @@ import ij.text.TextWindow;
	// this.gIS[iBest].interAxisAngle		// this.gIS[iBest].interAxisAngle
	// };		// };
	if (iBest!=i){		if (iBest!=i){

	boolean usable_tilt = (this.gIS[i].motors != null);		boolean usable_tilt = (this.gIS[i].motors != null);
	boolean usable_axial = usable_tilt && (this.gIS[i].getStationNumber() == this.gIS[iBest].getStationNumber());		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])/		double diff_axial = usable_axial? (this.gIS[i].motors[mAxial]-this.gIS[iBest].motors[mAxial])/
	@@ -3037,7 +3148,8 @@ import ij.text.TextWindow;
	this.gIS[i].goniometerAxial-=360.0*Math.floor((this.gIS[i].goniometerAxial+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, estimating from # "+iBest+" (timestamp "+IJ.d2s(this.gIS[iBest].timeStamp,6)+")" );		") is not defined, estimating from # "+iBest+" (timestamp "+IJ.d2s(this.gIS[iBest].timeStamp,6)+"): "+
			"tilt="+this.gIS[i].goniometerTilt+", axial = " + this.gIS[i].goniometerAxial);
	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;

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

+212 −79

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

+16 −3

Original line number	Original line	Diff line number	Diff line
	@@ -2470,9 +2470,22 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	if (useImages) {		if (useImages) {
	fromToImages[0]= (int) gd.getNextNumber();		fromToImages[0]= (int) gd.getNextNumber();
	fromToImages[1]= (int) gd.getNextNumber();		fromToImages[1]= (int) gd.getNextNumber();
	for (int i =0; i<this.distortionCalibrationData.getNumImages();i++)		for (int i =0; i<this.distortionCalibrationData.getNumImages();i++) {
	if ((allImages \|\| this.distortionCalibrationData.gIP[i].enabled) && (i>=fromToImages[0]) && (i<=fromToImages[1])){		// if ((allImages \|\| this.distortionCalibrationData.gIP[i].enabled) && (i>=fromToImages[0]) && (i<=fromToImages[1])){
			// this.selectedImages[numSeries][i]=gd.getNextBoolean();
			// }
			if ((i>=fromToImages[0]) && (i<=fromToImages[1])){
			if (allImages \|\| this.distortionCalibrationData.gIP[i].enabled) {
	this.selectedImages[numSeries][i]=gd.getNextBoolean();		this.selectedImages[numSeries][i]=gd.getNextBoolean();
			} else {
			this.selectedImages[numSeries][i]=false; // unselect stray non-shown images
			}



			}


	}		}
	if (allImages) enableDisableSelected=gd.getNextBoolean();		if (allImages) enableDisableSelected=gd.getNextBoolean();
	this.masterImages[numSeries]=(int) gd.getNextNumber();		this.masterImages[numSeries]=(int) gd.getNextNumber();

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

+11 −6

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